From 618a9d57eb0ac4641c6aab0def638974720f36dc Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Thu, 7 Aug 2014 12:47:28 +0200
Subject: [PATCH 01/31] Configurable DB user passwords

---
 config/DataSource.groovy.php                  |  4 +--
 data/postgres/Makefile                        | 12 +++----
 ddl/oracle/GLOBAL/passwords.sql.php           | 18 +++++++++++
 ddl/oracle/Makefile                           |  5 +++
 ddl/postgres/GLOBAL/Makefile                  |  7 ++++-
 ddl/postgres/GLOBAL/passwords.sql.php         | 31 +++++++++++++++++++
 .../php/env_helper.inc.php                    |  3 ++
 samples/oracle/gen_kettle_properties.php      | 15 ++++++---
 samples/postgres/gen_kettle_properties.php    | 16 ++++++----
 .../oracle/data-config_sanofi.xml.php         |  3 +-
 .../postgres/data-config_rwg.xml.php          |  4 +--
 .../postgres/data-config_sample.xml.php       |  4 +--
 vars.sample                                   | 20 ++++++++++++
 13 files changed, 117 insertions(+), 25 deletions(-)
 create mode 100644 ddl/oracle/GLOBAL/passwords.sql.php
 create mode 100644 ddl/postgres/GLOBAL/passwords.sql.php
 rename inc/host_fixup.php => lib/php/env_helper.inc.php (74%)

diff --git a/config/DataSource.groovy.php b/config/DataSource.groovy.php
index 0905bad8..77139434 100644
--- a/config/DataSource.groovy.php
+++ b/config/DataSource.groovy.php
@@ -1,9 +1,9 @@
-<?php require __DIR__ . '/../inc/host_fixup.php'; ?>
+<?php require __DIR__ . '/../lib/php/env_helper.inc.php'; ?>
 dataSource {
     driverClassName = 'org.postgresql.Driver'
     url             = 'jdbc:postgresql://<?= $host ?>:<?= $_ENV['PGPORT'] ?>/<?= $_ENV['PGDATABASE'] ?>'
     username        = 'biomart_user'
-    password        = 'biomart_user'
+    password        = '<?= $biomart_user_pwd ?>'
     dialect         = 'org.hibernate.dialect.PostgreSQLDialect'
     dbCreate        = 'none'
 }
diff --git a/data/postgres/Makefile b/data/postgres/Makefile
index 4a454127..b438fb71 100644
--- a/data/postgres/Makefile
+++ b/data/postgres/Makefile
@@ -11,18 +11,18 @@ row_counts:
 analyze:
 	$(PSQL_COMMAND) -c 'ANALYZE VERBOSE'
 
-BIOMART_PSW ?= biomart
-DEAPP_PSW ?= deapp
-SEARCHAPP_PSW ?= searchapp
+BIOMART_PWD ?= biomart
+DEAPP_PWD ?= deapp
+SEARCHAPP_PWD ?= searchapp
 $(ENV_DIR)/$(TRANSMART_LOADER)/conf/Common.properties:
 	echo "driver_class=org.postgresql.Driver" > $@ \
 	&& echo "url=jdbc:postgresql://localhost:$(PGPORT)/$(PGDATABASE)" >> $@ \
 	&& echo "biomart_username=biomart" >> $@ \
-	&& echo "biomart_password=$(BIOMART_PSW)" >> $@ \
+	&& echo "biomart_password=$(BIOMART_PWD)" >> $@ \
 	&& echo "deapp_username=deapp" >> $@ \
-	&& echo "deapp_password=$(DEAPP_PSW)" >> $@ \
+	&& echo "deapp_password=$(DEAPP_PWD)" >> $@ \
 	&& echo "searchapp_username=searchapp" >> $@ \
-	&& echo "searchapp_password=$(SEARCHAPP_PSW)" >> $@
+	&& echo "searchapp_password=$(SEARCHAPP_PWD)" >> $@
 
 .PHONY: row_counts analyze $(ENV_DIR)/$(TRANSMART_LOADER)/conf/Common.properties
 
diff --git a/ddl/oracle/GLOBAL/passwords.sql.php b/ddl/oracle/GLOBAL/passwords.sql.php
new file mode 100644
index 00000000..aef2424b
--- /dev/null
+++ b/ddl/oracle/GLOBAL/passwords.sql.php
@@ -0,0 +1,18 @@
+<?php
+array_shift($argv);
+$roles = $argv;
+$unspec = [];
+foreach ($roles as $r) {
+	$env_var = strtoupper($r) . '_PWD';
+	if (isset($_ENV[$env_var])) {
+		$password = $_ENV[$env_var];
+	} else {
+		continue;
+	}
+	$escaped_password = str_replace('"', '""', $password);
+	echo "ALTER USER $r IDENTIFIED BY \"$escaped_password\"\n";
+}
+if ($unspec) {
+	$roles_j = implode(', ', $unspec);
+	fprintf(STDERR, "No password specified for $roles_j; defaults will be kept\n");
+}
diff --git a/ddl/oracle/Makefile b/ddl/oracle/Makefile
index 9be4856d..c7719329 100644
--- a/ddl/oracle/Makefile
+++ b/ddl/oracle/Makefile
@@ -33,6 +33,11 @@ $(LOAD_USER_TARGETS):
 
 load_users:
 	$(RUN_SQL) $(foreach u,$(SCHEMAS),-f GLOBAL/$(u).sql)
+	$(MAKE) load_passwords
+
+load_passwords:
+	php -d variables_order=E GLOBAL/passwords.sql.php $(SCHEMAS) | \
+		$(RUN_SQL) --sequential
 
 load_user_objects: $(WRITE_SYNONYM_TARGETS) $(WRITE_GRANT_TARGETS)
 	$(LOAD_DDL) $(foreach s,$(SCHEMAS),-u $(s)) -j 10
diff --git a/ddl/postgres/GLOBAL/Makefile b/ddl/postgres/GLOBAL/Makefile
index 140f16c8..43d5a268 100644
--- a/ddl/postgres/GLOBAL/Makefile
+++ b/ddl/postgres/GLOBAL/Makefile
@@ -46,6 +46,10 @@ load_%:
 	$(PSQL_COMMAND) -f $*.sql
 
 load: load_cast_varchar_numeric load_roles load_extensions tablespaces
+	$(MAKE) load_passwords
+
+load_passwords:
+	php -d variables_order=E passwords.sql.php | $(PSQL_COMMAND)
 
 drop_roles:
 	$(PSQL_COMMAND) -d template1 -f drop_roles.sql
@@ -67,4 +71,5 @@ clean_generated: clean
 	rm -f roles.sql
 
 .PHONY: $(TBDROP_TARGETS)
-.PHONY: createdb clean_generated clean tablespaces load drop_roles drop_database drop_tablespaces drop
+.PHONY: createdb clean_generated clean tablespaces load drop_roles \
+	drop_database drop_tablespaces drop load_passwords
diff --git a/ddl/postgres/GLOBAL/passwords.sql.php b/ddl/postgres/GLOBAL/passwords.sql.php
new file mode 100644
index 00000000..cbb204ac
--- /dev/null
+++ b/ddl/postgres/GLOBAL/passwords.sql.php
@@ -0,0 +1,31 @@
+<?php
+
+$relevant_lines = array_filter(
+	file(__DIR__ . '/roles.sql'),
+	function ($line) {
+		return preg_match('/^CREATE ROLE/', $line);
+	});
+
+$roles = array_map(function($line) {
+	if (!preg_match('/^CREATE ROLE ([^;]+);$/', $line, $m)) {
+		throw new Exception("Expected a match");
+	}
+	return $m[1];
+}, $relevant_lines);
+
+$unspec = [];
+foreach ($roles as $r) {
+	$env_var = strtoupper($r) . '_PWD';
+	if (isset($_ENV[$env_var])) {
+		$password = $_ENV[$env_var];
+	} else {
+		$unspec[] = $r;
+		continue;
+	}
+	$hash = md5($password . $r);
+	echo "ALTER ROLE $r WITH ENCRYPTED PASSWORD 'md5$hash'\n";
+}
+if ($unspec) {
+	$roles_j = implode(', ', $unspec);
+	fprintf(STDERR, "No password specified for $roles_j; defaults will be kept\n");
+}
diff --git a/inc/host_fixup.php b/lib/php/env_helper.inc.php
similarity index 74%
rename from inc/host_fixup.php
rename to lib/php/env_helper.inc.php
index aaf0aa33..b3d513c4 100644
--- a/inc/host_fixup.php
+++ b/lib/php/env_helper.inc.php
@@ -5,3 +5,6 @@
 $host = (empty($_ENV['PGHOST']) || $_ENV['PGHOST'][0] == '/')
 		? 'localhost'
 		: $_ENV['PGHOST'];
+
+$biomart_user_pwd = isset($_ENV['BIOMART_USER_PWD']) ?
+	$_ENV['BIOMART_USER_PWD'] : 'biomart_user';
diff --git a/samples/oracle/gen_kettle_properties.php b/samples/oracle/gen_kettle_properties.php
index f0411c04..4a44288d 100644
--- a/samples/oracle/gen_kettle_properties.php
+++ b/samples/oracle/gen_kettle_properties.php
@@ -1,25 +1,30 @@
+<?php
+function get($key, $default) {
+	return isset($_ENV[$key]) ? $_ENV[$key] : $default;
+}
+?>
 TM_CZ_DB_NAME=<?= $_ENV['ORASID'], "\n" ?>
 TM_CZ_DB_PORT=<?= $_ENV['ORAPORT'], "\n" ?>
-TM_CZ_DB_PWD=tm_cz
+TM_CZ_DB_PWD=<?= get('TM_CZ_PWD', 'tm_cz') ?>
 TM_CZ_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
 TM_CZ_DB_USER=tm_cz
 TM_LZ_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 TM_LZ_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
-TM_LZ_DB_PWD=tm_lz
+TM_LZ_DB_PWD=<?= get('TM_LZ_PWD', 'tm_lz') ?>
 TM_LZ_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
 TM_LZ_DB_USER=tm_lz
 TM_WZ_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 TM_WZ_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
-TM_WZ_DB_PWD=tm_wz
+TM_WZ_DB_PWD=<?= get('TM_WZ_PWD', 'tm_wz') ?>
 TM_WZ_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
 TM_WZ_DB_USER=tm_wz
 DEAPP_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 DEAPP_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
 DEAPP_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
-DEAPP_PWD=deapp
+DEAPP_PWD=<?= get('DEAPP_PWD', 'deapp') ?>
 DEAPP_USER=deapp
 BIOMART_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 BIOMART_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
 BIOMART_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
-BIOMART_PWD=biomart
+BIOMART_PWD=<?= get('BIOMART_PWD', 'biomart') ?>
 BIOMART_USER=biomart
diff --git a/samples/postgres/gen_kettle_properties.php b/samples/postgres/gen_kettle_properties.php
index 122eaa60..38531ad9 100644
--- a/samples/postgres/gen_kettle_properties.php
+++ b/samples/postgres/gen_kettle_properties.php
@@ -1,26 +1,30 @@
-<?php require __DIR__ . '/../../inc/host_fixup.php' ?>
+<?php require __DIR__ . '/../../lib/php/env_helper.inc.php'
+function get($key, $default) {
+	return isset($_ENV[$key]) ? $_ENV[$key] : $default;
+}
+?>
 TM_CZ_DB_NAME=<?= $_ENV['PGDATABASE'], "\n" ?>
 TM_CZ_DB_PORT=<?= $_ENV['PGPORT'], "\n" ?>
-TM_CZ_DB_PWD=tm_cz
+TM_CZ_DB_PWD=<?= get('TM_CZ_PWD', 'tm_cz') ?>
 TM_CZ_DB_SERVER=<?= $host, "\n" ?>
 TM_CZ_DB_USER=tm_cz
 TM_LZ_DB_NAME=<?= $_ENV['PGDATABASE'] , "\n" ?>
 TM_LZ_DB_PORT=<?= $_ENV['PGPORT'] , "\n" ?>
-TM_LZ_DB_PWD=tm_lz
+TM_LZ_DB_PWD=<?= get('TM_LZ_PWD', 'tm_lz') ?>
 TM_LZ_DB_SERVER=<?= $host, "\n" ?>
 TM_LZ_DB_USER=tm_lz
 TM_WZ_DB_NAME=<?= $_ENV['PGDATABASE'] , "\n" ?>
 TM_WZ_DB_PORT=<?= $_ENV['PGPORT'] , "\n" ?>
-TM_WZ_DB_PWD=tm_wz
+TM_WZ_DB_PWD=<?= get('TM_WZ_PWD', 'tm_wz') ?>
 TM_WZ_DB_SERVER=<?= $host, "\n" ?>
 TM_WZ_DB_USER=tm_wz
 DEAPP_DB_NAME=<?= $_ENV['PGDATABASE'] , "\n" ?>
 DEAPP_DB_PORT=<?= $_ENV['PGPORT'] , "\n" ?>
 DEAPP_DB_SERVER=<?= $host, "\n" ?>
-DEAPP_PWD=deapp
+DEAPP_PWD=<?= get('DEAPP_PWD', 'deapp') ?>
 DEAPP_USER=deapp
 BIOMART_DB_NAME=<?= $_ENV['PGDATABASE'] , "\n" ?>
 BIOMART_DB_PORT=<?= $_ENV['PGPORT'] , "\n" ?>
 BIOMART_DB_SERVER=<?= $host, "\n" ?>
-BIOMART_PWD=biomart
+BIOMART_PWD=<?= get('BIOMART_PWD', 'biomart') ?>
 BIOMART_USER=biomart
diff --git a/solr/data-config/oracle/data-config_sanofi.xml.php b/solr/data-config/oracle/data-config_sanofi.xml.php
index fdceeaf0..59feee0c 100644
--- a/solr/data-config/oracle/data-config_sanofi.xml.php
+++ b/solr/data-config/oracle/data-config_sanofi.xml.php
@@ -1,5 +1,6 @@
+<?php require __DIR__ . '/../../../lib/php/env_helper.inc.php'; ?>
 <dataConfig>
-<dataSource driver="oracle.jdbc.driver.OracleDriver" url="jdbc:oracle:thin:@<?= $_ENV['ORAHOST'] ?>:<?= $_ENV['ORAPORT'] ?>:<?= $_ENV['ORASID'] ?>" user="biomart_user" password="biomart_user" />
+<dataSource driver="oracle.jdbc.driver.OracleDriver" url="jdbc:oracle:thin:@<?= $_ENV['ORAHOST'] ?>:<?= $_ENV['ORAPORT'] ?>:<?= $_ENV['ORASID'] ?>" user="biomart_user" password="<?= htmlspecialchars($biomart_user_pwd) ?>" />
     <document>
         <entity name="I2B2" query="select SAMPLE_ID,TRIAL_NAME,DISEASE,TISSUE_TYPE,DATA_TYPES,BIOBANK,SOURCE_ORGANISM,SAMPLE_TREATMENT,SUBJECT_TREATMENT from i2b2DemoData.sample_categories">
             <field name="id" column="SAMPLE_ID" />
diff --git a/solr/data-config/postgres/data-config_rwg.xml.php b/solr/data-config/postgres/data-config_rwg.xml.php
index e6e60a9a..dd11b875 100644
--- a/solr/data-config/postgres/data-config_rwg.xml.php
+++ b/solr/data-config/postgres/data-config_rwg.xml.php
@@ -1,8 +1,8 @@
-<?php require __DIR__ . '/../../../inc/host_fixup.php'; ?>
+<?php require __DIR__ . '/../../../lib/php/env_helper.inc.php'; ?>
 <dataConfig>
 <dataSource name="ds1" driver="org.postgresql.Driver"
 			url="jdbc:postgresql://<?= $host ?>:<?= $_ENV['PGPORT'] ?>/<?= $_ENV['PGDATABASE'] ?>"
-			user="biomart_user" password="biomart_user" readOnly="true"
+			user="biomart_user" password="<?= htmlspecialchars($biomart_user_pwd) ?>" readOnly="true"
  autoCommit="false" />
 
     <document name="terms">
diff --git a/solr/data-config/postgres/data-config_sample.xml.php b/solr/data-config/postgres/data-config_sample.xml.php
index 826e4e58..aeddfb37 100644
--- a/solr/data-config/postgres/data-config_sample.xml.php
+++ b/solr/data-config/postgres/data-config_sample.xml.php
@@ -1,8 +1,8 @@
-<?php require __DIR__ . '/../../../inc/host_fixup.php'; ?>
+<?php require __DIR__ . '/../../../lib/php/env_helper.inc.php'; ?>
 <dataConfig>
   <dataSource name="ds1" driver="org.postgresql.Driver"
               url="jdbc:postgresql://<?= $host ?>:<?= $_ENV['PGPORT'] ?>/<?= $_ENV['PGDATABASE'] ?>"
-              user="biomart_user" password="biomart_user" readOnly="true" />
+              user="biomart_user" password="<?= htmlspecialchars($biomart_user_pwd) ?>" readOnly="true" />
   <document>
     <entity name="id" query="select sample_id,trial_name,disease,tissue_type,data_types,biobank,source_organism,sample_treatment,subject_treatment from i2b2DemoData.sample_categories">
       <field name="id" column="sample_id"/>
diff --git a/vars.sample b/vars.sample
index ce20560c..425bae6b 100755
--- a/vars.sample
+++ b/vars.sample
@@ -58,6 +58,26 @@ KITCHEN=/path/to/data-integration/kitchen.sh
 #end with /
 TSUSER_HOME=$HOME/
 
+# {{{ DB user passwords
+#     They default to the same as the username.
+#     These are set when the database is created and they are used when
+#     connecting to the database (e.g. for ETL).
+#     You can reset passwords to the values specified here with:
+#       make -C ddl/postgres/GLOBAL load_passwords
+#       make -C ddl/oracle load_passwords
+#     Depending on whether you're using oracle or postgres.
+#
+#BIOMART_USER_PWD=biomart_user
+#BIOMART_PWD=biomart
+#DEAPP_PWD=deapp
+#I2B2METADATA_PWD=i2b2metadata
+#I2B2DEMODATA_PWD=i2b2demodata
+#SEARCHAPP_PWD=searchapp
+#TM_CZ_PWD=tm_cz
+#TM_LZ_PWD=tm_lz
+#TM_WZ_PWD=tm_wz
+# }}}
+
 # If your distro uses an old version of groovy, do make -C env groovy,
 # and uncomment this. Version 2.1.9 is known to work, versions before 2
 # are known not to work

From 2a1afe3503b7ebf4dd7e3a29ec216a424e921b64 Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Thu, 7 Aug 2014 12:57:22 +0200
Subject: [PATCH 02/31] Rename vars-ubuntu to standard vars

---
 README.md    | 4 ++--
 env/Makefile | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 01b57ac1..887a2123 100644
--- a/README.md
+++ b/README.md
@@ -65,10 +65,10 @@ Start with copying the `vars.sample` file, editing it and sourcing it in:
     # edit file and save...
 	. ./vars
 
-If you ran `make -C env ubuntu_deps_regular`, you will have a `vars-ubuntu` file
+If you ran `make -C env ubuntu_deps_regular`, you will have a `vars` file
 created for you. You can skip the previous step and do only:
 
-    . ./vars-ubuntu
+    . ./vars
 
 The several options are fairly self-explanatory.
 
diff --git a/env/Makefile b/env/Makefile
index c5952ef1..03957b7a 100644
--- a/env/Makefile
+++ b/env/Makefile
@@ -92,7 +92,7 @@ data-integration: $(KETTLE_ARCHIVE)
 	/bin/bash -c 'mkdir -p $@/{biomart,deapp,indx,search_app,transmart}'
 	chown -R postgres:postgres $@
 
-../vars-ubuntu: vars-ubuntu.php
+../vars: vars-ubuntu.php
 	php -d variables_order=E $< > $@
 
 ubuntu_deps_root: install_ubuntu_packages /var/lib/postgresql/tablespaces

From 650a90f44b30a84a6271196ed2296c16c2b79e1b Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Thu, 7 Aug 2014 15:53:00 +0200
Subject: [PATCH 03/31] Add dependencies on vars file

when a generated file depends on the values of environment variables.
---
 .gitignore                          |  2 +-
 config/Makefile                     |  2 +-
 data/oracle/Common.properties.php   |  9 +++++++++
 data/oracle/Makefile                | 16 ++--------------
 data/postgres/Common.properties.php |  9 +++++++++
 data/postgres/Makefile              | 16 +++-------------
 lib/php/env_helper.inc.php          |  4 ++++
 samples/common/makefile.inc         |  8 ++++----
 solr/Makefile                       |  2 +-
 9 files changed, 34 insertions(+), 34 deletions(-)
 create mode 100644 data/oracle/Common.properties.php
 create mode 100644 data/postgres/Common.properties.php

diff --git a/.gitignore b/.gitignore
index cad24eb9..b8f0c608 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,5 +2,5 @@
 *.iml
 /.idea
 /vars
-/vars-ubuntu
+/vars-*
 /private-feeds
diff --git a/config/Makefile b/config/Makefile
index 64c8904e..86e4ad3a 100644
--- a/config/Makefile
+++ b/config/Makefile
@@ -14,7 +14,7 @@ Config-extra.php BuildConfig.groovy:
 Config.groovy: Config-template.groovy Config-extra.php build-config.php
 	php build-config.php > $@
 
-DataSource.groovy: DataSource.groovy.php
+DataSource.groovy: DataSource.groovy.php ../vars
 	php -d 'variables_order=E' $< > $@
 
 TSCONFIG = $(TSUSER_HOME).grails/transmartConfig/
diff --git a/data/oracle/Common.properties.php b/data/oracle/Common.properties.php
new file mode 100644
index 00000000..a2c1daa5
--- /dev/null
+++ b/data/oracle/Common.properties.php
@@ -0,0 +1,9 @@
+<?php require __DIR__ . '/../../lib/php/env_helper.inc.php' ?>
+driver_class=oracle.jdbc.driver.OracleDriver
+url=jdbc:oracle:thin:@<?= $_ENV['ORAHOST'] ?>:<?= $_ENV['ORAPORT'] ?>:<?= $_ENV['ORASID'] ?>"
+biomart_username=biomart
+biomart_password=<?= get_env('BIOMART_PWD', 'biomart') ?>
+deapp_username=deapp
+deapp_password=<?= get_env('DEAPP_PWD', 'deapp') ?>
+searchapp_username=searchapp
+searchapp_password=<?= get_env('SEARCHAPP_PWD', 'searchapp') ?>
diff --git a/data/oracle/Makefile b/data/oracle/Makefile
index 19218d29..8d02466d 100644
--- a/data/oracle/Makefile
+++ b/data/oracle/Makefile
@@ -1,20 +1,8 @@
 include ../common/makefile.inc
 include ../../lib/makefile.inc
 
-BIOMART_PSW ?= biomart
-DEAPP_PSW ?= deapp
-SEARCHAPP_PSW ?= searchapp
-$(ENV_DIR)/$(TRANSMART_LOADER)/conf/Common.properties:
-	echo "driver_class=oracle.jdbc.driver.OracleDriver" > $@ \
-	&& echo "url=jdbc:oracle:thin:@$(ORAHOST):$(ORAPORT):$(ORASID)" >> $@ \
-	&& echo "biomart_username=biomart" >> $@ \
-	&& echo "biomart_password=$(BIOMART_PSW)" >> $@ \
-	&& echo "deapp_username=deapp" >> $@ \
-	&& echo "deapp_password=$(DEAPP_PSW)" >> $@ \
-	&& echo "searchapp_username=searchapp" >> $@ \
-	&& echo "searchapp_password=$(SEARCHAPP_PSW)" >> $@
-
-.PHONY: $(ENV_DIR)/$(TRANSMART_LOADER)/conf/Common.properties
+$(ENV_DIR)/$(TRANSMART_LOADER)/conf/Common.properties: Common.properties.php ../../vars
+	php -d variables_order=E $< > $@
 
 start_pool: $(NETTY_JAR_PATH) $(JDBC_DRIVER_ORA_PATH)
 	NLS_DATE_FORMAT='yyyy-mm-dd hh24:mi:ss' \
diff --git a/data/postgres/Common.properties.php b/data/postgres/Common.properties.php
new file mode 100644
index 00000000..c5ca06ae
--- /dev/null
+++ b/data/postgres/Common.properties.php
@@ -0,0 +1,9 @@
+<?php require __DIR__ . '/../../lib/php/env_helper.inc.php' ?>
+driver_class=org.postgresql.Driver
+url=jdbc:postgresql://<?= $host ?>:<?= $_ENV['PGPORT'] ?>/<?= $_ENV['PGDATABASE'] ?>
+biomart_username=biomart
+biomart_password=<?= get_env('BIOMART_PWD', 'biomart') ?>
+deapp_username=deapp
+deapp_password=<?= get_env('DEAPP_PWD', 'deapp') ?>
+searchapp_username=searchapp
+searchapp_password=<?= get_env('SEARCHAPP_PWD', 'searchapp') ?>
diff --git a/data/postgres/Makefile b/data/postgres/Makefile
index b438fb71..d599ec07 100644
--- a/data/postgres/Makefile
+++ b/data/postgres/Makefile
@@ -11,19 +11,9 @@ row_counts:
 analyze:
 	$(PSQL_COMMAND) -c 'ANALYZE VERBOSE'
 
-BIOMART_PWD ?= biomart
-DEAPP_PWD ?= deapp
-SEARCHAPP_PWD ?= searchapp
-$(ENV_DIR)/$(TRANSMART_LOADER)/conf/Common.properties:
-	echo "driver_class=org.postgresql.Driver" > $@ \
-	&& echo "url=jdbc:postgresql://localhost:$(PGPORT)/$(PGDATABASE)" >> $@ \
-	&& echo "biomart_username=biomart" >> $@ \
-	&& echo "biomart_password=$(BIOMART_PWD)" >> $@ \
-	&& echo "deapp_username=deapp" >> $@ \
-	&& echo "deapp_password=$(DEAPP_PWD)" >> $@ \
-	&& echo "searchapp_username=searchapp" >> $@ \
-	&& echo "searchapp_password=$(SEARCHAPP_PWD)" >> $@
+$(ENV_DIR)/$(TRANSMART_LOADER)/conf/Common.properties: Common.properties.php ../../vars
+	php -d variables_order=E $< > $@
 
-.PHONY: row_counts analyze $(ENV_DIR)/$(TRANSMART_LOADER)/conf/Common.properties
+.PHONY: row_counts analyze
 
 # vim: set filetype=make:
diff --git a/lib/php/env_helper.inc.php b/lib/php/env_helper.inc.php
index b3d513c4..3c4722bb 100644
--- a/lib/php/env_helper.inc.php
+++ b/lib/php/env_helper.inc.php
@@ -8,3 +8,7 @@
 
 $biomart_user_pwd = isset($_ENV['BIOMART_USER_PWD']) ?
 	$_ENV['BIOMART_USER_PWD'] : 'biomart_user';
+
+function get_env($key, $default) {
+	return isset($_ENV[$key]) ? $_ENV[$key] : $default;
+}
diff --git a/samples/common/makefile.inc b/samples/common/makefile.inc
index 7f487297..e25d3546 100644
--- a/samples/common/makefile.inc
+++ b/samples/common/makefile.inc
@@ -39,13 +39,13 @@ LOAD_MIRNA_PARAMS_TARGETS := $(shell php ../studies/enumerate.php load_targets m
 
 KETTLE_TARGETS := $(LOAD_CLINICAL_TARGETS) $(LOAD_EXPRESSION_PARAMS_TARGETS) $(LOAD_ANALYSIS_PARAMS_TARGETS) $(LOAD_ACGH_PARAMS_TARGETS) $(LOAD_PROTEOMICS_PARAMS_TARGETS) $(LOAD_MIRNA_PARAMS_TARGETS)
 
-$(KETTLE_TARGETS): write_kettle_properties
+$(KETTLE_TARGETS): kettle-home/kettle.properties
 #these ones are here just for autocompletion:
 $(LOAD_ANNOTATION_TARGETS):
 $(LOAD_REF_ANNOTATION_TARGETS):
 
-write_kettle_properties: gen_kettle_properties.php
-	php -d variables_order=E $< > kettle-home/kettle.properties
+kettle-home/kettle.properties: gen_kettle_properties.php ../../vars
+	php -d variables_order=E $< > $@
 
 ../studies/%:
 	$(MAKE) -C ../studies $*
@@ -152,6 +152,6 @@ load_mirna_%: ../studies/%/mirna.params ../studies/%/mirna load_mirna_annotation
 clean:
 	rm -f logs/*.log kettle-home/kettle.properties
 
-.PHONY: write_kettle_properties clean
+.PHONY: clean
 
 # vim: ft=make :
diff --git a/solr/Makefile b/solr/Makefile
index 89fce8d6..21907ca4 100644
--- a/solr/Makefile
+++ b/solr/Makefile
@@ -64,7 +64,7 @@ solr/%/conf/schema.xml: solr/% schemas/schema_%.xml
 	test -d solr/$* || $(MAKE) solr/$* #solr/$* is touched on each solr run
 	cp schemas/schema_$*.xml $@
 
-solr/%/conf/data-config.xml: data-config/$(DBSUBDIR)/data-config_%.xml.php
+solr/%/conf/data-config.xml: data-config/$(DBSUBDIR)/data-config_%.xml.php ../../vars
 	test -d solr/$* || $(MAKE) solr/$* #solr/$* is touched on each solr run
 	php -d variables_order=E $< > $@
 

From 4ff7ae52039f5603252de070490e0d327f2be80a Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Thu, 7 Aug 2014 17:25:39 +0200
Subject: [PATCH 04/31] vars.sample: add export to passwords

---
 vars.sample | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/vars.sample b/vars.sample
index 425bae6b..74a58898 100755
--- a/vars.sample
+++ b/vars.sample
@@ -67,15 +67,15 @@ TSUSER_HOME=$HOME/
 #       make -C ddl/oracle load_passwords
 #     Depending on whether you're using oracle or postgres.
 #
-#BIOMART_USER_PWD=biomart_user
-#BIOMART_PWD=biomart
-#DEAPP_PWD=deapp
-#I2B2METADATA_PWD=i2b2metadata
-#I2B2DEMODATA_PWD=i2b2demodata
-#SEARCHAPP_PWD=searchapp
-#TM_CZ_PWD=tm_cz
-#TM_LZ_PWD=tm_lz
-#TM_WZ_PWD=tm_wz
+#export BIOMART_USER_PWD=biomart_user
+#export BIOMART_PWD=biomart
+#export DEAPP_PWD=deapp
+#export I2B2METADATA_PWD=i2b2metadata
+#export I2B2DEMODATA_PWD=i2b2demodata
+#export SEARCHAPP_PWD=searchapp
+#export TM_CZ_PWD=tm_cz
+#export TM_LZ_PWD=tm_lz
+#export TM_WZ_PWD=tm_wz
 # }}}
 
 # If your distro uses an old version of groovy, do make -C env groovy,

From ea5537f05c0296c99633ee0f7a90a1b1629c849b Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Fri, 8 Aug 2014 15:18:12 +0200
Subject: [PATCH 05/31] Fix wrong R rpath when LIBnn=lib64

Done this by forcing LIBnn=lib
---
 R/Makefile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/Makefile b/R/Makefile
index 72c0dec3..b0efd999 100644
--- a/R/Makefile
+++ b/R/Makefile
@@ -15,6 +15,7 @@ build/Makefile: $(R_SOURCE)
 		CFLAGS="$(R_FLAGS)" \
 		CXXFLAGS="$(R_FLAGS)" \
 		FFLAGS="$(R_FLAGS)" \
+		LIBnn=lib \
 		LDFLAGS="-Wl,-rpath=$(R_PREFIX)/lib/R/lib,--enable-new-dtags" \
 		../$(R_SOURCE)/configure --prefix=$(R_PREFIX) \
 		--enable-R-shlib --with-readline \

From ddd7410821a70954ed79a47d988169222bb72519 Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Fri, 8 Aug 2014 16:08:22 +0200
Subject: [PATCH 06/31] Support diff biomart_user password in solr/rwg

---
 solr/data-config/oracle/data-config_rwg.xml.php | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/solr/data-config/oracle/data-config_rwg.xml.php b/solr/data-config/oracle/data-config_rwg.xml.php
index becf4256..fa84a875 100644
--- a/solr/data-config/oracle/data-config_rwg.xml.php
+++ b/solr/data-config/oracle/data-config_rwg.xml.php
@@ -1,5 +1,9 @@
+<?php require __DIR__ . '/../../../lib/php/env_helper.inc.php'; ?>
 <dataConfig>
-<dataSource driver="oracle.jdbc.driver.OracleDriver" url="jdbc:oracle:thin:@<?= $_ENV['ORAHOST'] ?>:<?= $_ENV['ORAPORT'] ?>:<?= $_ENV['ORASID'] ?>" user="biomart_user" password="biomart_user" />
+  <dataSource driver="oracle.jdbc.driver.OracleDriver"
+              url="jdbc:oracle:thin:@<?= $_ENV['ORAHOST'] ?>:<?= $_ENV['ORAPORT'] ?>:<?= $_ENV['ORASID'] ?>"
+              user="biomart_user"
+              password="<?= htmlspecialchars($biomart_user_pwd) ?>" />
          <document>
         <entity transformer="RegexTransformer" name="analysis" query="
 select FACET_ID, fs.ANALYSIS_ID, STUDY, STUDY_ID, coalesce(SOLR_HIERARCHY,'') as SOLR_HIERARCHY, ANALYSES, DATA_TYPE, PLATFORM, PLATFORM_DESCRIPTION, PLATFORM_VENDOR, OBSERVATION, STUDY_TITLE,STUDY_DESCRIPTION,STUDY_DESIGN,STUDY_PRIMARY_INV,STUDY_CONTACT_FIELD,STUDY_OVERALL_DESIGN,STUDY_INSTITUTION,STUDY_ACCESSION,STUDY_COUNTRY,STUDY_BIOMARKER_TYPE,STUDY_TARGET,STUDY_ACCESS_TYPE,ANALYSIS_NAME,ANALYSIS_DESCRIPTION_S,ANALYSIS_DESCRIPTION_L,ANALYSIS_TYPE,ANALYSIS_ANALYST_NAME,ANALYSIS_METHOD,ANALYSIS_DATA_TYPE,ANALYSIS_QA_CRITERIA,MODEL_NAME,MODEL_DESCRIPTION,RESEARCH_UNIT from biomart.vw_faceted_search fs
@@ -44,3 +48,6 @@
         </entity>
     </document>
 </dataConfig>
+
+<!-- vim: et tw=80 ts=2 sw=2
+-->

From bb4e8de679b69082e86c86731f51b9cc03eef8cc Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Fri, 8 Aug 2014 16:08:34 +0200
Subject: [PATCH 07/31] ws

---
 .../oracle/data-config_rwg.xml.php            | 80 ++++++++--------
 .../postgres/data-config_rwg.xml.php          | 94 ++++++++++---------
 2 files changed, 88 insertions(+), 86 deletions(-)

diff --git a/solr/data-config/oracle/data-config_rwg.xml.php b/solr/data-config/oracle/data-config_rwg.xml.php
index fa84a875..39319ad1 100644
--- a/solr/data-config/oracle/data-config_rwg.xml.php
+++ b/solr/data-config/oracle/data-config_rwg.xml.php
@@ -4,49 +4,49 @@
               url="jdbc:oracle:thin:@<?= $_ENV['ORAHOST'] ?>:<?= $_ENV['ORAPORT'] ?>:<?= $_ENV['ORASID'] ?>"
               user="biomart_user"
               password="<?= htmlspecialchars($biomart_user_pwd) ?>" />
-         <document>
-        <entity transformer="RegexTransformer" name="analysis" query="
+  <document>
+    <entity transformer="RegexTransformer" name="analysis" query="
 select FACET_ID, fs.ANALYSIS_ID, STUDY, STUDY_ID, coalesce(SOLR_HIERARCHY,'') as SOLR_HIERARCHY, ANALYSES, DATA_TYPE, PLATFORM, PLATFORM_DESCRIPTION, PLATFORM_VENDOR, OBSERVATION, STUDY_TITLE,STUDY_DESCRIPTION,STUDY_DESIGN,STUDY_PRIMARY_INV,STUDY_CONTACT_FIELD,STUDY_OVERALL_DESIGN,STUDY_INSTITUTION,STUDY_ACCESSION,STUDY_COUNTRY,STUDY_BIOMARKER_TYPE,STUDY_TARGET,STUDY_ACCESS_TYPE,ANALYSIS_NAME,ANALYSIS_DESCRIPTION_S,ANALYSIS_DESCRIPTION_L,ANALYSIS_TYPE,ANALYSIS_ANALYST_NAME,ANALYSIS_METHOD,ANALYSIS_DATA_TYPE,ANALYSIS_QA_CRITERIA,MODEL_NAME,MODEL_DESCRIPTION,RESEARCH_UNIT from biomart.vw_faceted_search fs
 LEFT JOIN biomart.vw_faceted_search_disease fsd ON fs.analysis_id = fsd.bio_assay_analysis_id
-" >
-            <field name="FACET_ID" column="FACET_ID" />
-            <field name="ANALYSIS_ID" column="ANALYSIS_ID" />
-            <field name="STUDY" column="STUDY" />
-            <field name="STUDY_ID" column="STUDY_ID" />
-            <field name="ANALYSES" column="ANALYSES" />
-            <field name="DATA_TYPE" column="DATA_TYPE" />
-            <field name="PLATFORM" column="PLATFORM" />
-        <field name="PLATFORM_DESCRIPTION" column="PLATFORM_VENDOR" />
-        <field name="PLATFORM_VENDOR" column="PLATFORM_DESCRIPTION" />
-        <field name="PLATFORM_NAME" column="PLATFORM_NAME" />
-            <field name="OBSERVATION" column="OBSERVATION" />
-            <field column="DISEASE" splitBy="/" sourceColName="SOLR_HIERARCHY" />
+">
+      <field name="FACET_ID" column="FACET_ID" />
+      <field name="ANALYSIS_ID" column="ANALYSIS_ID" />
+      <field name="STUDY" column="STUDY" />
+      <field name="STUDY_ID" column="STUDY_ID" />
+      <field name="ANALYSES" column="ANALYSES" />
+      <field name="DATA_TYPE" column="DATA_TYPE" />
+      <field name="PLATFORM" column="PLATFORM" />
+      <field name="PLATFORM_DESCRIPTION" column="PLATFORM_VENDOR" />
+      <field name="PLATFORM_VENDOR" column="PLATFORM_DESCRIPTION" />
+      <field name="PLATFORM_NAME" column="PLATFORM_NAME" />
+      <field name="OBSERVATION" column="OBSERVATION" />
+      <field column="DISEASE" splitBy="/" sourceColName="SOLR_HIERARCHY" />
 
-        <field name="STUDY_TITLE" column="STUDY_TITLE" />
-        <field name="STUDY_DESCRIPTION" column="STUDY_DESCRIPTION" />
-        <field name="STUDY_DESIGN" column="STUDY_DESIGN" />
-        <field name="STUDY_PRIMARY_INV" column="STUDY_PRIMARY_INV" />
-        <field name="STUDY_CONTACT_FIELD" column="STUDY_CONTACT_FIELD" />
-        <field name="STUDY_OVERALL_DESIGN" column="STUDY_OVERALL_DESIGN" />
-        <field name="STUDY_INSTITUTION" column="STUDY_INSTITUTION" />
-        <field name="STUDY_ACCESSION" column="STUDY_ACCESSION" />
-        <field name="STUDY_COUNTRY" column="STUDY_COUNTRY" />
-        <field name="STUDY_BIOMARKER_TYPE" column="STUDY_BIOMARKER_TYPE" />
-        <field name="STUDY_TARGET" column="STUDY_TARGET" />
-        <field name="STUDY_ACCESS_TYPE" column="STUDY_ACCESS_TYPE" />
-        <field name="ANALYSIS_NAME" column="ANALYSIS_NAME" />
-        <field name="ANALYSIS_DESCRIPTION_S" column="ANALYSIS_DESCRIPTION_S" />
-        <field name="ANALYSIS_DESCRIPTION_L" column="ANALYSIS_DESCRIPTION_L" />
-        <field name="ANALYSIS_TYPE" column="ANALYSIS_TYPE" />
-        <field name="ANALYSIS_ANALYST_NAME" column="ANALYSIS_ANALYST_NAME" />
-        <field name="ANALYSIS_METHOD" column="ANALYSIS_METHOD" />
-        <field name="ANALYSIS_DATA_TYPE" column="ANALYSIS_DATA_TYPE" />
-        <field name="ANALYSIS_QA_CRITERIA" column="ANALYSIS_QA_CRITERIA" />
-        <field name="MODEL_NAME" column="MODEL_NAME" />
-        <field name="MODEL_DESCRIPTION" column="MODEL_DESCRIPTION" />
-        <field name="RESEARCH_UNIT" column="RESEARCH_UNIT" splitBy="\|" />              
-        </entity>
-    </document>
+      <field name="STUDY_TITLE" column="STUDY_TITLE" />
+      <field name="STUDY_DESCRIPTION" column="STUDY_DESCRIPTION" />
+      <field name="STUDY_DESIGN" column="STUDY_DESIGN" />
+      <field name="STUDY_PRIMARY_INV" column="STUDY_PRIMARY_INV" />
+      <field name="STUDY_CONTACT_FIELD" column="STUDY_CONTACT_FIELD" />
+      <field name="STUDY_OVERALL_DESIGN" column="STUDY_OVERALL_DESIGN" />
+      <field name="STUDY_INSTITUTION" column="STUDY_INSTITUTION" />
+      <field name="STUDY_ACCESSION" column="STUDY_ACCESSION" />
+      <field name="STUDY_COUNTRY" column="STUDY_COUNTRY" />
+      <field name="STUDY_BIOMARKER_TYPE" column="STUDY_BIOMARKER_TYPE" />
+      <field name="STUDY_TARGET" column="STUDY_TARGET" />
+      <field name="STUDY_ACCESS_TYPE" column="STUDY_ACCESS_TYPE" />
+      <field name="ANALYSIS_NAME" column="ANALYSIS_NAME" />
+      <field name="ANALYSIS_DESCRIPTION_S" column="ANALYSIS_DESCRIPTION_S" />
+      <field name="ANALYSIS_DESCRIPTION_L" column="ANALYSIS_DESCRIPTION_L" />
+      <field name="ANALYSIS_TYPE" column="ANALYSIS_TYPE" />
+      <field name="ANALYSIS_ANALYST_NAME" column="ANALYSIS_ANALYST_NAME" />
+      <field name="ANALYSIS_METHOD" column="ANALYSIS_METHOD" />
+      <field name="ANALYSIS_DATA_TYPE" column="ANALYSIS_DATA_TYPE" />
+      <field name="ANALYSIS_QA_CRITERIA" column="ANALYSIS_QA_CRITERIA" />
+      <field name="MODEL_NAME" column="MODEL_NAME" />
+      <field name="MODEL_DESCRIPTION" column="MODEL_DESCRIPTION" />
+      <field name="RESEARCH_UNIT" column="RESEARCH_UNIT" splitBy="\|" />
+    </entity>
+  </document>
 </dataConfig>
 
 <!-- vim: et tw=80 ts=2 sw=2
diff --git a/solr/data-config/postgres/data-config_rwg.xml.php b/solr/data-config/postgres/data-config_rwg.xml.php
index f600e0d8..0d2acc52 100644
--- a/solr/data-config/postgres/data-config_rwg.xml.php
+++ b/solr/data-config/postgres/data-config_rwg.xml.php
@@ -1,50 +1,52 @@
 <?php require __DIR__ . '/../../../lib/php/env_helper.inc.php'; ?>
 <dataConfig>
-<dataSource name="ds1" driver="org.postgresql.Driver"
-			url="jdbc:postgresql://<?= $host ?>:<?= $_ENV['PGPORT'] ?>/<?= $_ENV['PGDATABASE'] ?>"
-			user="biomart_user" password="<?= htmlspecialchars($biomart_user_pwd) ?>" readOnly="true"
- autoCommit="false" />
-     <document>
-        <entity transformer="RegexTransformer" name="analysis" query="
-select FACET_ID, fs.ANALYSIS_ID, STUDY, STUDY_ID, ANALYSES, DATA_TYPE, PLATFORM, PLATFORM_DESCRIPTION, PLATFORM_VENDOR, OBSERVATION, STUDY_TITLE,STUDY_DESCRIPTION,STUDY_DESIGN,STUDY_PRIMARY_INV,STUDY_CONTACT_FIELD,STUDY_OVERALL_DESIGN,STUDY_INSTITUTION,STUDY_ACCESSION,STUDY_COUNTRY,STUDY_BIOMARKER_TYPE,STUDY_TARGET,STUDY_ACCESS_TYPE,ANALYSIS_NAME,ANALYSIS_DESCRIPTION_S,ANALYSIS_DESCRIPTION_L,ANALYSIS_TYPE,ANALYSIS_ANALYST_NAME,ANALYSIS_METHOD,ANALYSIS_DATA_TYPE,ANALYSIS_QA_CRITERIA,MODEL_NAME,MODEL_DESCRIPTION,RESEARCH_UNIT from biomart.vw_faceted_search fs
-LEFT JOIN biomart.vw_faceted_search_disease fsd ON fs.analysis_id = fsd.bio_assay_analysis_id
-" >
-        <field name="FACET_ID" column="FACET_ID" />
-        <field name="ANALYSIS_ID" column="ANALYSIS_ID" />
-        <field name="STUDY" column="STUDY" />
-        <field name="STUDY_ID" column="STUDY_ID" />
-        <field name="ANALYSES" column="ANALYSES" />
-        <field name="DATA_TYPE" column="DATA_TYPE" />
-        <field name="PLATFORM" column="PLATFORM" />
-        <field name="PLATFORM_DESCRIPTION" column="PLATFORM_VENDOR" />
-        <field name="PLATFORM_VENDOR" column="PLATFORM_DESCRIPTION" />
-        <field name="PLATFORM_NAME" column="PLATFORM_NAME" />
-        <field name="OBSERVATION" column="OBSERVATION" />
-        <field column="DISEASE" splitBy="/" sourceColName="SOLR_HIERARCHY" />
+  <dataSource name="ds1" driver="org.postgresql.Driver"
+        url="jdbc:postgresql://<?= $host ?>:<?= $_ENV['PGPORT'] ?>/<?= $_ENV['PGDATABASE'] ?>"
+        user="biomart_user" password="<?= htmlspecialchars($biomart_user_pwd) ?>"
+        readOnly="true" autoCommit="false" />
+  <document>
+    <entity transformer="RegexTransformer" name="analysis" query="
+    select FACET_ID, fs.ANALYSIS_ID, STUDY, STUDY_ID, ANALYSES, DATA_TYPE, PLATFORM, PLATFORM_DESCRIPTION, PLATFORM_VENDOR, OBSERVATION, STUDY_TITLE,STUDY_DESCRIPTION,STUDY_DESIGN,STUDY_PRIMARY_INV,STUDY_CONTACT_FIELD,STUDY_OVERALL_DESIGN,STUDY_INSTITUTION,STUDY_ACCESSION,STUDY_COUNTRY,STUDY_BIOMARKER_TYPE,STUDY_TARGET,STUDY_ACCESS_TYPE,ANALYSIS_NAME,ANALYSIS_DESCRIPTION_S,ANALYSIS_DESCRIPTION_L,ANALYSIS_TYPE,ANALYSIS_ANALYST_NAME,ANALYSIS_METHOD,ANALYSIS_DATA_TYPE,ANALYSIS_QA_CRITERIA,MODEL_NAME,MODEL_DESCRIPTION,RESEARCH_UNIT from biomart.vw_faceted_search fs
+    LEFT JOIN biomart.vw_faceted_search_disease fsd ON fs.analysis_id = fsd.bio_assay_analysis_id
+    ">
+      <field name="FACET_ID" column="FACET_ID" />
+      <field name="ANALYSIS_ID" column="ANALYSIS_ID" />
+      <field name="STUDY" column="STUDY" />
+      <field name="STUDY_ID" column="STUDY_ID" />
+      <field name="ANALYSES" column="ANALYSES" />
+      <field name="DATA_TYPE" column="DATA_TYPE" />
+      <field name="PLATFORM" column="PLATFORM" />
+      <field name="PLATFORM_DESCRIPTION" column="PLATFORM_VENDOR" />
+      <field name="PLATFORM_VENDOR" column="PLATFORM_DESCRIPTION" />
+      <field name="PLATFORM_NAME" column="PLATFORM_NAME" />
+      <field name="OBSERVATION" column="OBSERVATION" />
+      <field column="DISEASE" splitBy="/" sourceColName="SOLR_HIERARCHY" />
 
-        <field name="STUDY_TITLE" column="STUDY_TITLE" />
-        <field name="STUDY_DESCRIPTION" column="STUDY_DESCRIPTION" />
-        <field name="STUDY_DESIGN" column="STUDY_DESIGN" />
-        <field name="STUDY_PRIMARY_INV" column="STUDY_PRIMARY_INV" />
-        <field name="STUDY_CONTACT_FIELD" column="STUDY_CONTACT_FIELD" />
-        <field name="STUDY_OVERALL_DESIGN" column="STUDY_OVERALL_DESIGN" />
-        <field name="STUDY_INSTITUTION" column="STUDY_INSTITUTION" />
-        <field name="STUDY_ACCESSION" column="STUDY_ACCESSION" />
-        <field name="STUDY_COUNTRY" column="STUDY_COUNTRY" />
-        <field name="STUDY_BIOMARKER_TYPE" column="STUDY_BIOMARKER_TYPE" />
-        <field name="STUDY_TARGET" column="STUDY_TARGET" />
-        <field name="STUDY_ACCESS_TYPE" column="STUDY_ACCESS_TYPE" />
-        <field name="ANALYSIS_NAME" column="ANALYSIS_NAME" />
-        <field name="ANALYSIS_DESCRIPTION_S" column="ANALYSIS_DESCRIPTION_S" />
-        <field name="ANALYSIS_DESCRIPTION_L" column="ANALYSIS_DESCRIPTION_L" />
-        <field name="ANALYSIS_TYPE" column="ANALYSIS_TYPE" />
-        <field name="ANALYSIS_ANALYST_NAME" column="ANALYSIS_ANALYST_NAME" />
-        <field name="ANALYSIS_METHOD" column="ANALYSIS_METHOD" />
-        <field name="ANALYSIS_DATA_TYPE" column="ANALYSIS_DATA_TYPE" />
-        <field name="ANALYSIS_QA_CRITERIA" column="ANALYSIS_QA_CRITERIA" />
-        <field name="MODEL_NAME" column="MODEL_NAME" />
-        <field name="MODEL_DESCRIPTION" column="MODEL_DESCRIPTION" />
-        <field name="RESEARCH_UNIT" column="RESEARCH_UNIT" splitBy="\|" />
-            </entity>
-    </document>
+      <field name="STUDY_TITLE" column="STUDY_TITLE" />
+      <field name="STUDY_DESCRIPTION" column="STUDY_DESCRIPTION" />
+      <field name="STUDY_DESIGN" column="STUDY_DESIGN" />
+      <field name="STUDY_PRIMARY_INV" column="STUDY_PRIMARY_INV" />
+      <field name="STUDY_CONTACT_FIELD" column="STUDY_CONTACT_FIELD" />
+      <field name="STUDY_OVERALL_DESIGN" column="STUDY_OVERALL_DESIGN" />
+      <field name="STUDY_INSTITUTION" column="STUDY_INSTITUTION" />
+      <field name="STUDY_ACCESSION" column="STUDY_ACCESSION" />
+      <field name="STUDY_COUNTRY" column="STUDY_COUNTRY" />
+      <field name="STUDY_BIOMARKER_TYPE" column="STUDY_BIOMARKER_TYPE" />
+      <field name="STUDY_TARGET" column="STUDY_TARGET" />
+      <field name="STUDY_ACCESS_TYPE" column="STUDY_ACCESS_TYPE" />
+      <field name="ANALYSIS_NAME" column="ANALYSIS_NAME" />
+      <field name="ANALYSIS_DESCRIPTION_S" column="ANALYSIS_DESCRIPTION_S" />
+      <field name="ANALYSIS_DESCRIPTION_L" column="ANALYSIS_DESCRIPTION_L" />
+      <field name="ANALYSIS_TYPE" column="ANALYSIS_TYPE" />
+      <field name="ANALYSIS_ANALYST_NAME" column="ANALYSIS_ANALYST_NAME" />
+      <field name="ANALYSIS_METHOD" column="ANALYSIS_METHOD" />
+      <field name="ANALYSIS_DATA_TYPE" column="ANALYSIS_DATA_TYPE" />
+      <field name="ANALYSIS_QA_CRITERIA" column="ANALYSIS_QA_CRITERIA" />
+      <field name="MODEL_NAME" column="MODEL_NAME" />
+      <field name="MODEL_DESCRIPTION" column="MODEL_DESCRIPTION" />
+      <field name="RESEARCH_UNIT" column="RESEARCH_UNIT" splitBy="\|" />
+    </entity>
+  </document>
 </dataConfig>
+<!-- vim: et tw=80 ts=2 sw=2
+-->

From 8da1b88d2f87134c2298bfc6667083db808d2fe8 Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Mon, 11 Aug 2014 12:24:18 +0100
Subject: [PATCH 08/31] Missing newline for all passwords

---
 samples/oracle/gen_kettle_properties.php | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/samples/oracle/gen_kettle_properties.php b/samples/oracle/gen_kettle_properties.php
index 4a44288d..e006a381 100644
--- a/samples/oracle/gen_kettle_properties.php
+++ b/samples/oracle/gen_kettle_properties.php
@@ -5,26 +5,26 @@ function get($key, $default) {
 ?>
 TM_CZ_DB_NAME=<?= $_ENV['ORASID'], "\n" ?>
 TM_CZ_DB_PORT=<?= $_ENV['ORAPORT'], "\n" ?>
-TM_CZ_DB_PWD=<?= get('TM_CZ_PWD', 'tm_cz') ?>
+TM_CZ_DB_PWD=<?= get('TM_CZ_PWD', 'tm_cz'), "\n" ?>
 TM_CZ_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
 TM_CZ_DB_USER=tm_cz
 TM_LZ_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 TM_LZ_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
-TM_LZ_DB_PWD=<?= get('TM_LZ_PWD', 'tm_lz') ?>
+TM_LZ_DB_PWD=<?= get('TM_LZ_PWD', 'tm_lz'), "\n" ?>
 TM_LZ_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
 TM_LZ_DB_USER=tm_lz
 TM_WZ_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 TM_WZ_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
-TM_WZ_DB_PWD=<?= get('TM_WZ_PWD', 'tm_wz') ?>
+TM_WZ_DB_PWD=<?= get('TM_WZ_PWD', 'tm_wz'), "\n" ?>
 TM_WZ_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
 TM_WZ_DB_USER=tm_wz
 DEAPP_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 DEAPP_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
 DEAPP_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
-DEAPP_PWD=<?= get('DEAPP_PWD', 'deapp') ?>
+DEAPP_PWD=<?= get('DEAPP_PWD', 'deapp'), "\n" ?>
 DEAPP_USER=deapp
 BIOMART_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 BIOMART_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
 BIOMART_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
-BIOMART_PWD=<?= get('BIOMART_PWD', 'biomart') ?>
+BIOMART_PWD=<?= get('BIOMART_PWD', 'biomart'), "\n" ?>
 BIOMART_USER=biomart

From eabdd6297c01588006e55ee7db6f3b889b79b01d Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Mon, 11 Aug 2014 12:24:18 +0100
Subject: [PATCH 09/31] Missing newline for all passwords (cherry-pick)

Cherry-pick from london_hackathon branch.
---
 samples/oracle/gen_kettle_properties.php | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/samples/oracle/gen_kettle_properties.php b/samples/oracle/gen_kettle_properties.php
index 4a44288d..e006a381 100644
--- a/samples/oracle/gen_kettle_properties.php
+++ b/samples/oracle/gen_kettle_properties.php
@@ -5,26 +5,26 @@ function get($key, $default) {
 ?>
 TM_CZ_DB_NAME=<?= $_ENV['ORASID'], "\n" ?>
 TM_CZ_DB_PORT=<?= $_ENV['ORAPORT'], "\n" ?>
-TM_CZ_DB_PWD=<?= get('TM_CZ_PWD', 'tm_cz') ?>
+TM_CZ_DB_PWD=<?= get('TM_CZ_PWD', 'tm_cz'), "\n" ?>
 TM_CZ_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
 TM_CZ_DB_USER=tm_cz
 TM_LZ_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 TM_LZ_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
-TM_LZ_DB_PWD=<?= get('TM_LZ_PWD', 'tm_lz') ?>
+TM_LZ_DB_PWD=<?= get('TM_LZ_PWD', 'tm_lz'), "\n" ?>
 TM_LZ_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
 TM_LZ_DB_USER=tm_lz
 TM_WZ_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 TM_WZ_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
-TM_WZ_DB_PWD=<?= get('TM_WZ_PWD', 'tm_wz') ?>
+TM_WZ_DB_PWD=<?= get('TM_WZ_PWD', 'tm_wz'), "\n" ?>
 TM_WZ_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
 TM_WZ_DB_USER=tm_wz
 DEAPP_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 DEAPP_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
 DEAPP_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
-DEAPP_PWD=<?= get('DEAPP_PWD', 'deapp') ?>
+DEAPP_PWD=<?= get('DEAPP_PWD', 'deapp'), "\n" ?>
 DEAPP_USER=deapp
 BIOMART_DB_NAME=<?= $_ENV['ORASID'] , "\n" ?>
 BIOMART_DB_PORT=<?= $_ENV['ORAPORT'] , "\n" ?>
 BIOMART_DB_SERVER=<?= $_ENV['ORAHOST'], "\n" ?>
-BIOMART_PWD=<?= get('BIOMART_PWD', 'biomart') ?>
+BIOMART_PWD=<?= get('BIOMART_PWD', 'biomart'), "\n" ?>
 BIOMART_USER=biomart

From b92b45eff4d2091b410c0c31e8a4dcf195e84b1d Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Mon, 11 Aug 2014 15:46:59 +0200
Subject: [PATCH 10/31] Fix missing LF chars in pg/gen_kettle_properties

---
 samples/postgres/gen_kettle_properties.php | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/samples/postgres/gen_kettle_properties.php b/samples/postgres/gen_kettle_properties.php
index 38531ad9..c6dc8d45 100644
--- a/samples/postgres/gen_kettle_properties.php
+++ b/samples/postgres/gen_kettle_properties.php
@@ -5,26 +5,26 @@ function get($key, $default) {
 ?>
 TM_CZ_DB_NAME=<?= $_ENV['PGDATABASE'], "\n" ?>
 TM_CZ_DB_PORT=<?= $_ENV['PGPORT'], "\n" ?>
-TM_CZ_DB_PWD=<?= get('TM_CZ_PWD', 'tm_cz') ?>
+TM_CZ_DB_PWD=<?= get('TM_CZ_PWD', 'tm_cz'), "\n" ?>
 TM_CZ_DB_SERVER=<?= $host, "\n" ?>
 TM_CZ_DB_USER=tm_cz
 TM_LZ_DB_NAME=<?= $_ENV['PGDATABASE'] , "\n" ?>
 TM_LZ_DB_PORT=<?= $_ENV['PGPORT'] , "\n" ?>
-TM_LZ_DB_PWD=<?= get('TM_LZ_PWD', 'tm_lz') ?>
+TM_LZ_DB_PWD=<?= get('TM_LZ_PWD', 'tm_lz'), "\n" ?>
 TM_LZ_DB_SERVER=<?= $host, "\n" ?>
 TM_LZ_DB_USER=tm_lz
 TM_WZ_DB_NAME=<?= $_ENV['PGDATABASE'] , "\n" ?>
 TM_WZ_DB_PORT=<?= $_ENV['PGPORT'] , "\n" ?>
-TM_WZ_DB_PWD=<?= get('TM_WZ_PWD', 'tm_wz') ?>
+TM_WZ_DB_PWD=<?= get('TM_WZ_PWD', 'tm_wz'), "\n" ?>
 TM_WZ_DB_SERVER=<?= $host, "\n" ?>
 TM_WZ_DB_USER=tm_wz
 DEAPP_DB_NAME=<?= $_ENV['PGDATABASE'] , "\n" ?>
 DEAPP_DB_PORT=<?= $_ENV['PGPORT'] , "\n" ?>
 DEAPP_DB_SERVER=<?= $host, "\n" ?>
-DEAPP_PWD=<?= get('DEAPP_PWD', 'deapp') ?>
+DEAPP_PWD=<?= get('DEAPP_PWD', 'deapp'), "\n" ?>
 DEAPP_USER=deapp
 BIOMART_DB_NAME=<?= $_ENV['PGDATABASE'] , "\n" ?>
 BIOMART_DB_PORT=<?= $_ENV['PGPORT'] , "\n" ?>
 BIOMART_DB_SERVER=<?= $host, "\n" ?>
-BIOMART_PWD=<?= get('BIOMART_PWD', 'biomart') ?>
+BIOMART_PWD=<?= get('BIOMART_PWD', 'biomart'), "\n" ?>
 BIOMART_USER=biomart

From 870f1bf0f6f5d2cd8587ec919a25cec8bd7fa2da Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Mon, 11 Aug 2014 16:39:19 +0200
Subject: [PATCH 11/31] Fix ubuntu_deps_regular target

---
 env/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/env/Makefile b/env/Makefile
index 03957b7a..d94393cc 100644
--- a/env/Makefile
+++ b/env/Makefile
@@ -96,7 +96,7 @@ data-integration: $(KETTLE_ARCHIVE)
 	php -d variables_order=E $< > $@
 
 ubuntu_deps_root: install_ubuntu_packages /var/lib/postgresql/tablespaces
-ubuntu_deps_regular: update_etl data-integration ../vars-ubuntu groovy
+ubuntu_deps_regular: update_etl data-integration ../vars groovy
 
 .DELETE_ON_ERROR:
 

From 9ee4999769d7bd2c59f863903c671ea8959e09f8 Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Mon, 11 Aug 2014 17:08:18 +0100
Subject: [PATCH 12/31] use varchar2 to avoid size limit

---
 ddl/oracle/biomart/bio_experiment.sql | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/ddl/oracle/biomart/bio_experiment.sql b/ddl/oracle/biomart/bio_experiment.sql
index d1bdccd1..68a5808d 100644
--- a/ddl/oracle/biomart/bio_experiment.sql
+++ b/ddl/oracle/biomart/bio_experiment.sql
@@ -3,18 +3,18 @@
 --
  CREATE TABLE "BIOMART"."BIO_EXPERIMENT" 
   (	"BIO_EXPERIMENT_ID" NUMBER(18,0) NOT NULL ENABLE, 
-"BIO_EXPERIMENT_TYPE" NVARCHAR2(200), 
-"TITLE" NVARCHAR2(1000), 
-"DESCRIPTION" NVARCHAR2(4000), 
-"DESIGN" NVARCHAR2(2000), 
+"BIO_EXPERIMENT_TYPE" VARCHAR2(200), 
+"TITLE" VARCHAR2(1000), 
+"DESCRIPTION" VARCHAR2(4000), 
+"DESIGN" VARCHAR2(2000), 
 "START_DATE" DATE, 
 "COMPLETION_DATE" DATE, 
-"PRIMARY_INVESTIGATOR" NVARCHAR2(400), 
-"CONTACT_FIELD" NVARCHAR2(400), 
-"ETL_ID" NVARCHAR2(100), 
+"PRIMARY_INVESTIGATOR" VARCHAR2(400), 
+"CONTACT_FIELD" VARCHAR2(400), 
+"ETL_ID" VARCHAR2(100), 
 "STATUS" VARCHAR2(100 BYTE), 
-"OVERALL_DESIGN" NVARCHAR2(2000), 
-"ACCESSION" NVARCHAR2(100), 
+"OVERALL_DESIGN" VARCHAR2(2000), 
+"ACCESSION" VARCHAR2(100), 
 "ENTRYDT" DATE, 
 "UPDATED" DATE, 
 "INSTITUTION" VARCHAR2(400 BYTE), 

From 3311c9b5a2e302af6aa21044ae853d35fb2d581b Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Mon, 11 Aug 2014 17:09:09 +0100
Subject: [PATCH 13/31] biomart missing table

---
 ddl/oracle/biomart/items.json   | 7 +++++++
 ddl/oracle/biomart/mesh_all.sql | 4 ++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/ddl/oracle/biomart/items.json b/ddl/oracle/biomart/items.json
index 25b8e5e2..ca5f8a92 100644
--- a/ddl/oracle/biomart/items.json
+++ b/ddl/oracle/biomart/items.json
@@ -5242,6 +5242,13 @@
       "name" : "MESH"
     },
     "file" : "biomart/mesh.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "MESH_ALL"
+    },
+    "file" : "biomart/mesh_all.sql"
   }, {
     "item" : {
       "type" : "TABLE",
diff --git a/ddl/oracle/biomart/mesh_all.sql b/ddl/oracle/biomart/mesh_all.sql
index fac7a800..631a9daa 100644
--- a/ddl/oracle/biomart/mesh_all.sql
+++ b/ddl/oracle/biomart/mesh_all.sql
@@ -6,7 +6,7 @@
 "MH" VARCHAR2(200 BYTE), 
  PRIMARY KEY ("UI")
  USING INDEX
- TABLESPACE "BIOMART"  ENABLE
+ TABLESPACE "TRANSMART"  ENABLE
   ) SEGMENT CREATION IMMEDIATE
 NOCOMPRESS NOLOGGING
- TABLESPACE "BIOMART" ;
+ TABLESPACE "TRANSMART" ;

From fb909983f4db0ea3cd7ea743078052a60cd7daff Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Mon, 11 Aug 2014 17:09:30 +0100
Subject: [PATCH 14/31] biomart_user missing tables

---
 ddl/oracle/biomart_user/gene_ontology.sql     |  2 +-
 .../biomart_user/gene_ontology_data.sql       |  6 +-
 ddl/oracle/biomart_user/items.json            | 71 +++++++++++++++++++
 3 files changed, 75 insertions(+), 4 deletions(-)

diff --git a/ddl/oracle/biomart_user/gene_ontology.sql b/ddl/oracle/biomart_user/gene_ontology.sql
index 4b112b54..272e8b5e 100644
--- a/ddl/oracle/biomart_user/gene_ontology.sql
+++ b/ddl/oracle/biomart_user/gene_ontology.sql
@@ -6,4 +6,4 @@
 "DESCR" VARCHAR2(500 BYTE)
   ) SEGMENT CREATION IMMEDIATE
 NOCOMPRESS LOGGING
- TABLESPACE "BIOMART" ;
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/biomart_user/gene_ontology_data.sql b/ddl/oracle/biomart_user/gene_ontology_data.sql
index de18416e..f9d944bf 100644
--- a/ddl/oracle/biomart_user/gene_ontology_data.sql
+++ b/ddl/oracle/biomart_user/gene_ontology_data.sql
@@ -8,14 +8,14 @@
 "ORGANISM" VARCHAR2(100 BYTE)
   ) SEGMENT CREATION IMMEDIATE
 NOCOMPRESS LOGGING
- TABLESPACE "BIOMART" ;
+ TABLESPACE "TRANSMART" ;
 --
 -- Type: INDEX; Owner: BIOMART_USER; Name: IDX_GOD_SYMBOL
 --
 CREATE INDEX "BIOMART_USER"."IDX_GOD_SYMBOL" ON "BIOMART_USER"."GENE_ONTOLOGY_DATA" (UPPER("GENE_SYMBOL"))
-TABLESPACE "BIOMART" ;
+TABLESPACE "TRANSMART" ;
 --
 -- Type: INDEX; Owner: BIOMART_USER; Name: IDX_GOD_ORGANISM
 --
 CREATE BITMAP INDEX "BIOMART_USER"."IDX_GOD_ORGANISM" ON "BIOMART_USER"."GENE_ONTOLOGY_DATA" (UPPER("ORGANISM"))
-TABLESPACE "BIOMART" ;
+TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/biomart_user/items.json b/ddl/oracle/biomart_user/items.json
index 431d409f..3e60e502 100644
--- a/ddl/oracle/biomart_user/items.json
+++ b/ddl/oracle/biomart_user/items.json
@@ -2944,6 +2944,28 @@
       "owner" : "I2B2METADATA",
       "name" : "I2B2_TRIAL_NODES"
     } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART_USER",
+      "name" : "IDX_GOD_ORGANISM"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART_USER",
+      "name" : "GENE_ONTOLOGY_DATA"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART_USER",
+      "name" : "IDX_GOD_SYMBOL"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART_USER",
+      "name" : "GENE_ONTOLOGY_DATA"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -4603,6 +4625,27 @@
     } ]
   } ],
   "fileAssignments" : [ {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART_USER",
+      "name" : "GENE_ONTOLOGY"
+    },
+    "file" : "biomart_user/gene_ontology.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART_USER",
+      "name" : "GENE_ONTOLOGY"
+    },
+    "file" : "biomart_user/gene_ontology.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART_USER",
+      "name" : "GENE_ONTOLOGY_DATA"
+    },
+    "file" : "biomart_user/gene_ontology_data.sql"
+  }, {
     "item" : {
       "type" : "VIEW",
       "owner" : "BIOMART_USER",
@@ -4644,6 +4687,34 @@
       "name" : "CONCEPT_CD_TAB"
     },
     "file" : "biomart_user/_misc.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART_USER",
+      "name" : "GENE_ONTOLOGY"
+    },
+    "file" : "biomart_user/gene_ontology.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART_USER",
+      "name" : "GENE_ONTOLOGY_DATA"
+    },
+    "file" : "biomart_user/gene_ontology_data.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART_USER",
+      "name" : "IDX_GOD_ORGANISM"
+    },
+    "file" : "biomart_user/gene_ontology_data.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART_USER",
+      "name" : "IDX_GOD_SYMBOL"
+    },
+    "file" : "biomart_user/gene_ontology_data.sql"
   }, {
     "item" : {
       "type" : "TYPE",

From 5ebc7b01ed8530e204a136ecc62b81161fa228af Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Mon, 11 Aug 2014 17:10:18 +0100
Subject: [PATCH 15/31] merge test server update

---
 ddl/oracle/deapp/de_variant_population_data.sql | 7 +------
 ddl/oracle/deapp/de_variant_population_info.sql | 7 +------
 2 files changed, 2 insertions(+), 12 deletions(-)

diff --git a/ddl/oracle/deapp/de_variant_population_data.sql b/ddl/oracle/deapp/de_variant_population_data.sql
index 78023cf8..be3676e0 100644
--- a/ddl/oracle/deapp/de_variant_population_data.sql
+++ b/ddl/oracle/deapp/de_variant_population_data.sql
@@ -42,9 +42,4 @@ for each row begin
 end;
 /
 ALTER TRIGGER "DEAPP"."TRG_DE_VARIANT_PD_ID" ENABLE;
- 
---
--- Type: REF_CONSTRAINT; Owner: DEAPP; Name: DE_VARIANT_POPULATION_DATA_FK
---
-ALTER TABLE "DEAPP"."DE_VARIANT_POPULATION_DATA" ADD CONSTRAINT "DE_VARIANT_POPULATION_DATA_FK" FOREIGN KEY ("DATASET_ID")
- REFERENCES "DEAPP"."DE_VARIANT_DATASET" ("DATASET_ID") ENABLE;
+
diff --git a/ddl/oracle/deapp/de_variant_population_info.sql b/ddl/oracle/deapp/de_variant_population_info.sql
index 0e953db4..8284530a 100644
--- a/ddl/oracle/deapp/de_variant_population_info.sql
+++ b/ddl/oracle/deapp/de_variant_population_info.sql
@@ -43,9 +43,4 @@ end;
 /
 ALTER TRIGGER "DEAPP"."TRG_DE_VP_INFO_ID" ENABLE;
  
- 
---
--- Type: REF_CONSTRAINT; Owner: DEAPP; Name: DE_VARIANT_POPULATION_INFO_FK
---
-ALTER TABLE "DEAPP"."DE_VARIANT_POPULATION_INFO" ADD CONSTRAINT "DE_VARIANT_POPULATION_INFO_FK" FOREIGN KEY ("DATASET_ID")
- REFERENCES "DEAPP"."DE_VARIANT_DATASET" ("DATASET_ID") ENABLE;
+

From 39412a9dbf9c6efbc75b293f1ea2d2c59ff94637 Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Mon, 11 Aug 2014 17:10:39 +0100
Subject: [PATCH 16/31] deapp missing table

---
 ddl/oracle/deapp/items.json    | 7 +++++++
 ddl/oracle/deapp/kegg_data.sql | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/ddl/oracle/deapp/items.json b/ddl/oracle/deapp/items.json
index c1544883..990dd6aa 100644
--- a/ddl/oracle/deapp/items.json
+++ b/ddl/oracle/deapp/items.json
@@ -2744,6 +2744,13 @@
       "name" : "KEGG"
     },
     "file" : "deapp/kegg.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "KEGG_DATA"
+    },
+    "file" : "deapp/kegg_data.sql"
   }, {
     "item" : {
       "type" : "TABLE",
diff --git a/ddl/oracle/deapp/kegg_data.sql b/ddl/oracle/deapp/kegg_data.sql
index d24d9207..f48dca7e 100644
--- a/ddl/oracle/deapp/kegg_data.sql
+++ b/ddl/oracle/deapp/kegg_data.sql
@@ -7,4 +7,4 @@
 "GENE" VARCHAR2(200 BYTE)
   ) SEGMENT CREATION IMMEDIATE
 NOCOMPRESS LOGGING
- TABLESPACE "DEAPP" ;
+ TABLESPACE "TRANSMART" ;

From 1f6b311781219c613e9a0598fd955d60497179fc Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Mon, 11 Aug 2014 17:11:12 +0100
Subject: [PATCH 17/31] use transmart tablespace

---
 ddl/oracle/searchapp/report.sql      | 2 +-
 ddl/oracle/searchapp/report_item.sql | 2 +-
 ddl/oracle/searchapp/subset.sql      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/ddl/oracle/searchapp/report.sql b/ddl/oracle/searchapp/report.sql
index 00c5490b..7f340d0b 100644
--- a/ddl/oracle/searchapp/report.sql
+++ b/ddl/oracle/searchapp/report.sql
@@ -10,5 +10,5 @@
 "CREATE_DATE" TIMESTAMP (6), 
 "STUDY" VARCHAR2(200 BYTE)
   ) SEGMENT CREATION DEFERRED
- TABLESPACE "SEARCH_APP" ;
+ TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/searchapp/report_item.sql b/ddl/oracle/searchapp/report_item.sql
index 2d35db2e..aa7366cf 100644
--- a/ddl/oracle/searchapp/report_item.sql
+++ b/ddl/oracle/searchapp/report_item.sql
@@ -6,5 +6,5 @@
 "REPORT_ID" NUMBER(18,0), 
 "CODE" VARCHAR2(200 BYTE)
   ) SEGMENT CREATION DEFERRED
- TABLESPACE "SEARCH_APP" ;
+ TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/searchapp/subset.sql b/ddl/oracle/searchapp/subset.sql
index 4c41753b..90583e82 100644
--- a/ddl/oracle/searchapp/subset.sql
+++ b/ddl/oracle/searchapp/subset.sql
@@ -12,5 +12,5 @@
 "QUERY_MASTER_ID_2" NUMBER, 
 "STUDY" VARCHAR2(200 BYTE)
   ) SEGMENT CREATION IMMEDIATE
- TABLESPACE "SEARCH_APP" ;
+ TABLESPACE "TRANSMART" ;
 

From 07d5c57f55e74e423df3b4e6c4b10e378d4f7472 Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 10:42:34 +0100
Subject: [PATCH 18/31] tm_wz updates from test server

---
 ddl/oracle/tm_wz/de_subject_rbm_data.sql      |  27 ++++
 ddl/oracle/tm_wz/i2b2_load_path.sql           |  10 ++
 .../tm_wz/i2b2_load_path_with_count.sql       |  10 ++
 ddl/oracle/tm_wz/items.json                   | 152 ++++++++++++++++++
 ddl/oracle/tm_wz/tmp_subject_rbm_calcs.sql    |  13 ++
 ddl/oracle/tm_wz/tmp_subject_rbm_logs.sql     |  19 +++
 ddl/oracle/tm_wz/tmp_subject_rbm_med.sql      |  23 +++
 ddl/oracle/tm_wz/wrk_clinical_data.sql        |   9 +-
 ddl/oracle/tm_wz/wt_subject_acgh_region.sql   |   2 +-
 ddl/oracle/tm_wz/wt_subject_rnaseq_region.sql |   2 +-
 ddl/oracle/tm_wz/wt_trial_nodes.sql           |  12 ++
 11 files changed, 276 insertions(+), 3 deletions(-)
 create mode 100644 ddl/oracle/tm_wz/de_subject_rbm_data.sql
 create mode 100644 ddl/oracle/tm_wz/i2b2_load_path.sql
 create mode 100644 ddl/oracle/tm_wz/i2b2_load_path_with_count.sql
 create mode 100644 ddl/oracle/tm_wz/tmp_subject_rbm_calcs.sql
 create mode 100644 ddl/oracle/tm_wz/tmp_subject_rbm_logs.sql
 create mode 100644 ddl/oracle/tm_wz/tmp_subject_rbm_med.sql

diff --git a/ddl/oracle/tm_wz/de_subject_rbm_data.sql b/ddl/oracle/tm_wz/de_subject_rbm_data.sql
new file mode 100644
index 00000000..46a07c1d
--- /dev/null
+++ b/ddl/oracle/tm_wz/de_subject_rbm_data.sql
@@ -0,0 +1,27 @@
+--
+-- Type: TABLE; Owner: TM_WZ; Name: DE_SUBJECT_RBM_DATA
+--
+ CREATE TABLE "TM_WZ"."DE_SUBJECT_RBM_DATA" 
+  (	"TRIAL_NAME" VARCHAR2(100 BYTE), 
+"ANTIGEN_NAME" VARCHAR2(100 BYTE), 
+"N_VALUE" NUMBER, 
+"PATIENT_ID" NUMBER(38,0), 
+"GENE_SYMBOL" VARCHAR2(100 BYTE), 
+"GENE_ID" NUMBER(10,0), 
+"ASSAY_ID" NUMBER, 
+"NORMALIZED_VALUE" NUMBER(18,5), 
+"CONCEPT_CD" NVARCHAR2(100), 
+"TIMEPOINT" VARCHAR2(100 BYTE), 
+"DATA_UID" VARCHAR2(100 BYTE), 
+"VALUE" NUMBER(18,4), 
+"LOG_INTENSITY" NUMBER, 
+"MEAN_INTENSITY" NUMBER, 
+"STDDEV_INTENSITY" NUMBER, 
+"MEDIAN_INTENSITY" NUMBER, 
+"ZSCORE" NUMBER(18,4), 
+"RBM_PANEL" VARCHAR2(50 BYTE), 
+"UNIT" VARCHAR2(50 CHAR), 
+"ID" NUMBER(38,0) NOT NULL ENABLE
+  ) SEGMENT CREATION IMMEDIATE
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_wz/i2b2_load_path.sql b/ddl/oracle/tm_wz/i2b2_load_path.sql
new file mode 100644
index 00000000..002a8fc9
--- /dev/null
+++ b/ddl/oracle/tm_wz/i2b2_load_path.sql
@@ -0,0 +1,10 @@
+--
+-- Type: TABLE; Owner: TM_WZ; Name: I2B2_LOAD_PATH
+--
+ CREATE TABLE "TM_WZ"."I2B2_LOAD_PATH" 
+  (	"PATH" VARCHAR2(700 BYTE), 
+"RECORD_ID" ROWID, 
+ PRIMARY KEY ("PATH", "RECORD_ID") ENABLE
+  ) ORGANIZATION INDEX NOCOMPRESS
+ TABLESPACE "TRANSMART" 
+PCTTHRESHOLD 50;
diff --git a/ddl/oracle/tm_wz/i2b2_load_path_with_count.sql b/ddl/oracle/tm_wz/i2b2_load_path_with_count.sql
new file mode 100644
index 00000000..dacf37f8
--- /dev/null
+++ b/ddl/oracle/tm_wz/i2b2_load_path_with_count.sql
@@ -0,0 +1,10 @@
+--
+-- Type: TABLE; Owner: TM_WZ; Name: I2B2_LOAD_PATH_WITH_COUNT
+--
+ CREATE TABLE "TM_WZ"."I2B2_LOAD_PATH_WITH_COUNT" 
+  (	"C_FULLNAME" VARCHAR2(700 BYTE), 
+"NBR_CHILDREN" NUMBER, 
+ PRIMARY KEY ("C_FULLNAME") ENABLE
+  ) ORGANIZATION INDEX NOCOMPRESS
+ TABLESPACE "TRANSMART" 
+PCTTHRESHOLD 50;
diff --git a/ddl/oracle/tm_wz/items.json b/ddl/oracle/tm_wz/items.json
index 1367cbb8..ec3cba0f 100644
--- a/ddl/oracle/tm_wz/items.json
+++ b/ddl/oracle/tm_wz/items.json
@@ -6,6 +6,60 @@
       "name" : "BIO_ASSAY_ANALYSIS_DATA_NEW"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "DE_SUBJECT_RBM_DATA"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "I2B2_LOAD_PATH"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "I2B2_LOAD_PATH_WITH_COUNT"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "TM_WZ",
+      "name" : "IDX_WRK_CD"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "WRK_CLINICAL_DATA"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "TM_WZ",
+      "name" : "IDX_WTN_LOAD_CLINICAL"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "WT_TRIAL_NODES"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "TM_WZ",
+      "name" : "IDX_WT_TRIALNODES"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "WT_TRIAL_NODES"
+    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -13,6 +67,34 @@
       "name" : "TMP_ASSAY_ANALYSIS_METRICS"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "TMP_SUBJECT_RBM_CALCS"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "TMP_SUBJECT_RBM_LOGS"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "TMP_SUBJECT_RBM_MED"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_WZ",
+      "name" : "UTIL_GRANT_ALL"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -487,6 +569,48 @@
       "name" : "BIO_ASSAY_ANALYSIS_DATA_NEW"
     },
     "file" : "tm_wz/bio_assay_analysis_data_new.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "DE_SUBJECT_RBM_DATA"
+    },
+    "file" : "tm_wz/de_subject_rbm_data.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "I2B2_LOAD_PATH"
+    },
+    "file" : "tm_wz/i2b2_load_path.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "I2B2_LOAD_PATH_WITH_COUNT"
+    },
+    "file" : "tm_wz/i2b2_load_path_with_count.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "TM_WZ",
+      "name" : "IDX_WRK_CD"
+    },
+    "file" : "tm_wz/wrk_clinical_data.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "TM_WZ",
+      "name" : "IDX_WTN_LOAD_CLINICAL"
+    },
+    "file" : "tm_wz/wt_trial_nodes.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "TM_WZ",
+      "name" : "IDX_WT_TRIALNODES"
+    },
+    "file" : "tm_wz/wt_trial_nodes.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -494,6 +618,34 @@
       "name" : "TMP_ASSAY_ANALYSIS_METRICS"
     },
     "file" : "tm_wz/tmp_assay_analysis_metrics.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "TMP_SUBJECT_RBM_CALCS"
+    },
+    "file" : "tm_wz/tmp_subject_rbm_calcs.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "TMP_SUBJECT_RBM_LOGS"
+    },
+    "file" : "tm_wz/tmp_subject_rbm_logs.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "TMP_SUBJECT_RBM_MED"
+    },
+    "file" : "tm_wz/tmp_subject_rbm_med.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_WZ",
+      "name" : "UTIL_GRANT_ALL"
+    },
+    "file" : "tm_wz/procedures/util_grant_all.sql"
   }, {
     "item" : {
       "type" : "TABLE",
diff --git a/ddl/oracle/tm_wz/tmp_subject_rbm_calcs.sql b/ddl/oracle/tm_wz/tmp_subject_rbm_calcs.sql
new file mode 100644
index 00000000..ec2bcea7
--- /dev/null
+++ b/ddl/oracle/tm_wz/tmp_subject_rbm_calcs.sql
@@ -0,0 +1,13 @@
+--
+-- Type: TABLE; Owner: TM_WZ; Name: TMP_SUBJECT_RBM_CALCS
+--
+ CREATE TABLE "TM_WZ"."TMP_SUBJECT_RBM_CALCS" 
+  (	"TRIAL_NAME" VARCHAR2(100 BYTE), 
+"GENE_SYMBOL" VARCHAR2(100 BYTE), 
+"ANTIGEN_NAME" VARCHAR2(100 BYTE), 
+"MEAN_INTENSITY" NUMBER, 
+"MEDIAN_INTENSITY" NUMBER, 
+"STDDEV_INTENSITY" NUMBER
+  ) SEGMENT CREATION DEFERRED
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_wz/tmp_subject_rbm_logs.sql b/ddl/oracle/tm_wz/tmp_subject_rbm_logs.sql
new file mode 100644
index 00000000..8029528a
--- /dev/null
+++ b/ddl/oracle/tm_wz/tmp_subject_rbm_logs.sql
@@ -0,0 +1,19 @@
+--
+-- Type: TABLE; Owner: TM_WZ; Name: TMP_SUBJECT_RBM_LOGS
+--
+ CREATE TABLE "TM_WZ"."TMP_SUBJECT_RBM_LOGS" 
+  (	"TRIAL_NAME" VARCHAR2(100 BYTE), 
+"ANTIGEN_NAME" VARCHAR2(100 BYTE), 
+"N_VALUE" NUMBER, 
+"PATIENT_ID" NUMBER(38,0), 
+"GENE_SYMBOL" VARCHAR2(100 BYTE), 
+"GENE_ID" NUMBER(10,0), 
+"ASSAY_ID" NUMBER, 
+"NORMALIZED_VALUE" NUMBER(18,5), 
+"CONCEPT_CD" NVARCHAR2(100), 
+"TIMEPOINT" VARCHAR2(100 BYTE), 
+"VALUE" NUMBER(18,4), 
+"LOG_INTENSITY" NUMBER
+  ) SEGMENT CREATION DEFERRED
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_wz/tmp_subject_rbm_med.sql b/ddl/oracle/tm_wz/tmp_subject_rbm_med.sql
new file mode 100644
index 00000000..ce2b096d
--- /dev/null
+++ b/ddl/oracle/tm_wz/tmp_subject_rbm_med.sql
@@ -0,0 +1,23 @@
+--
+-- Type: TABLE; Owner: TM_WZ; Name: TMP_SUBJECT_RBM_MED
+--
+ CREATE TABLE "TM_WZ"."TMP_SUBJECT_RBM_MED" 
+  (	"TRIAL_NAME" VARCHAR2(100 BYTE), 
+"ANTIGEN_NAME" VARCHAR2(100 BYTE), 
+"N_VALUE" NUMBER, 
+"PATIENT_ID" NUMBER(38,0), 
+"GENE_SYMBOL" VARCHAR2(100 BYTE), 
+"GENE_ID" NUMBER(10,0), 
+"ASSAY_ID" NUMBER, 
+"NORMALIZED_VALUE" NUMBER(18,5), 
+"CONCEPT_CD" NVARCHAR2(100), 
+"TIMEPOINT" VARCHAR2(100 BYTE), 
+"LOG_INTENSITY" NUMBER, 
+"VALUE" NUMBER(18,4), 
+"MEAN_INTENSITY" NUMBER, 
+"STDDEV_INTENSITY" NUMBER, 
+"MEDIAN_INTENSITY" NUMBER, 
+"ZSCORE" NUMBER
+  ) SEGMENT CREATION DEFERRED
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_wz/wrk_clinical_data.sql b/ddl/oracle/tm_wz/wrk_clinical_data.sql
index 4cf871a5..d60f4d17 100644
--- a/ddl/oracle/tm_wz/wrk_clinical_data.sql
+++ b/ddl/oracle/tm_wz/wrk_clinical_data.sql
@@ -34,5 +34,12 @@
 "DATE_TIMESTAMP" DATE, 
 "SAMPLE_CD" VARCHAR2(200 BYTE)
   ) SEGMENT CREATION IMMEDIATE
- TABLESPACE "TRANSMART" ;
+NOCOMPRESS NOLOGGING
+ TABLESPACE "TRANSMART" 
+  CACHE ;
+--
+-- Type: INDEX; Owner: TM_WZ; Name: IDX_WRK_CD
+--
+CREATE INDEX "TM_WZ"."IDX_WRK_CD" ON "TM_WZ"."WRK_CLINICAL_DATA" ("DATA_TYPE", "DATA_VALUE", "VISIT_NAME", "DATA_LABEL", "CATEGORY_CD", "USUBJID")
+TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_wz/wt_subject_acgh_region.sql b/ddl/oracle/tm_wz/wt_subject_acgh_region.sql
index 480fa620..381c5e80 100644
--- a/ddl/oracle/tm_wz/wt_subject_acgh_region.sql
+++ b/ddl/oracle/tm_wz/wt_subject_acgh_region.sql
@@ -22,6 +22,6 @@
 "SAMPLE_TYPE" VARCHAR2(200 BYTE), 
 "PLATFORM" VARCHAR2(200 BYTE), 
 "TISSUE_TYPE" VARCHAR2(200 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_wz/wt_subject_rnaseq_region.sql b/ddl/oracle/tm_wz/wt_subject_rnaseq_region.sql
index f3f93371..0a195b16 100644
--- a/ddl/oracle/tm_wz/wt_subject_rnaseq_region.sql
+++ b/ddl/oracle/tm_wz/wt_subject_rnaseq_region.sql
@@ -14,6 +14,6 @@
 "SAMPLE_TYPE" VARCHAR2(200 BYTE), 
 "PLATFORM" VARCHAR2(200 BYTE), 
 "TISSUE_TYPE" VARCHAR2(200 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_wz/wt_trial_nodes.sql b/ddl/oracle/tm_wz/wt_trial_nodes.sql
index 47ae993e..70bf17c3 100644
--- a/ddl/oracle/tm_wz/wt_trial_nodes.sql
+++ b/ddl/oracle/tm_wz/wt_trial_nodes.sql
@@ -20,3 +20,15 @@
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: INDEX; Owner: TM_WZ; Name: IDX_WT_TRIALNODES
+--
+CREATE INDEX "TM_WZ"."IDX_WT_TRIALNODES" ON "TM_WZ"."WT_TRIAL_NODES" ("LEAF_NODE", "NODE_NAME")
+TABLESPACE "TRANSMART" ;
+
+--
+-- Type: INDEX; Owner: TM_WZ; Name: IDX_WTN_LOAD_CLINICAL
+--
+CREATE INDEX "TM_WZ"."IDX_WTN_LOAD_CLINICAL" ON "TM_WZ"."WT_TRIAL_NODES" ("LEAF_NODE", "CATEGORY_CD", "DATA_LABEL")
+TABLESPACE "TRANSMART" ;
+

From dbc11f3df62702b49c177e5c23d5030014b0dc8b Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 10:43:33 +0100
Subject: [PATCH 19/31] biomart_stage update from test server

---
 ddl/oracle/biomart_stage/bio_assay_analysis_gwas.sql | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ddl/oracle/biomart_stage/bio_assay_analysis_gwas.sql b/ddl/oracle/biomart_stage/bio_assay_analysis_gwas.sql
index 5fac9666..527d2449 100644
--- a/ddl/oracle/biomart_stage/bio_assay_analysis_gwas.sql
+++ b/ddl/oracle/biomart_stage/bio_assay_analysis_gwas.sql
@@ -7,7 +7,8 @@
 "RS_ID" NVARCHAR2(50), 
 "P_VALUE_CHAR" VARCHAR2(100 BYTE), 
 "ETL_ID" NUMBER(18,0), 
-"EXT_DATA" VARCHAR2(4000 BYTE)
+"EXT_DATA" VARCHAR2(4000 BYTE), 
+"LOG10_PVAL_CHAR" VARCHAR2(100 BYTE)
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 

From ebdab7082c6516999aff327f4f968afd88613b6b Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 10:44:01 +0100
Subject: [PATCH 20/31] biomart_user update from test server

---
 ddl/oracle/biomart_user/_cross.sql |   20 +-
 ddl/oracle/biomart_user/_misc.sql  |    6 +-
 ddl/oracle/biomart_user/items.json | 1101 ++++++++++++++++++++++++----
 3 files changed, 957 insertions(+), 170 deletions(-)

diff --git a/ddl/oracle/biomart_user/_cross.sql b/ddl/oracle/biomart_user/_cross.sql
index 11bab54c..0943fad6 100644
--- a/ddl/oracle/biomart_user/_cross.sql
+++ b/ddl/oracle/biomart_user/_cross.sql
@@ -1,7 +1,7 @@
 --
 -- Type: VIEW; Owner: BIOMART_USER; Name: BROWSE_ANALYSES_VIEW
 --
-  CREATE OR REPLACE FORCE VIEW "BIOMART_USER"."BROWSE_ANALYSES_VIEW" ("ID", "TITLE", "DESCRIPTION", "MEASUREMENT_TYPE", "PLATFORM_NAME", "VENDOR", "TECHNOLOGY") AS 
+  CREATE OR REPLACE FORCE EDITIONABLE VIEW "BIOMART_USER"."BROWSE_ANALYSES_VIEW" ("ID", "TITLE", "DESCRIPTION", "MEASUREMENT_TYPE", "PLATFORM_NAME", "VENDOR", "TECHNOLOGY") AS 
   select
 fd.unique_id
 , baa.analysis_name as title
@@ -22,11 +22,15 @@ where
     ata.object_type in ('BIO_ASSAY_PLATFORM')
     and ff.active_ind = 1
 group by  fd.unique_id, baa.analysis_name, baa.long_description;
- 
+--
+-- Type: INDEX; Owner: BIOMART_USER; Name: OBSERVATION_FACT_PD
+--
+CREATE INDEX "BIOMART_USER"."OBSERVATION_FACT_PD" ON "I2B2DEMODATA"."OBSERVATION_FACT" ("PATIENT_NUM")
+TABLESPACE "BIOMART" ;
 --
 -- Type: VIEW; Owner: BIOMART_USER; Name: BROWSE_STUDIES_VIEW
 --
-  CREATE OR REPLACE FORCE VIEW "BIOMART_USER"."BROWSE_STUDIES_VIEW" ("ID", "TITLE", "DESCRIPTION", "DESIGN", "BIOMARKER_TYPE", "ACCESS_TYPE", "ACCESSION", "INSTITUTION", "COUNTRY", "DISEASE", "COMPOUND", "STUDY_OBJECTIVE", "ORGANISM", "STUDY_PHASE") AS 
+  CREATE OR REPLACE FORCE EDITIONABLE VIEW "BIOMART_USER"."BROWSE_STUDIES_VIEW" ("ID", "TITLE", "DESCRIPTION", "DESIGN", "BIOMARKER_TYPE", "ACCESS_TYPE", "ACCESSION", "INSTITUTION", "COUNTRY", "DISEASE", "COMPOUND", "STUDY_OBJECTIVE", "ORGANISM", "STUDY_PHASE") AS 
   SELECT
   fd.unique_id
 , exp.title
@@ -75,11 +79,10 @@ left outer join (select id, disease, compound, study_objective, species, phase f
 )
 )x on  x.id = fd.unique_id
 where ff.active_ind = 1;
- 
 --
 -- Type: VIEW; Owner: BIOMART_USER; Name: BROWSE_PROGRAMS_VIEW
 --
-  CREATE OR REPLACE FORCE VIEW "BIOMART_USER"."BROWSE_PROGRAMS_VIEW" ("ID", "TITLE", "DESCRIPTION", "DISEASE", "OBSERVATION", "PATHWAY", "GENE", "THERAPEUTIC_DOMAIN", "INSTITUTION", "TARGET") AS 
+  CREATE OR REPLACE FORCE EDITIONABLE VIEW "BIOMART_USER"."BROWSE_PROGRAMS_VIEW" ("ID", "TITLE", "DESCRIPTION", "DISEASE", "OBSERVATION", "PATHWAY", "GENE", "THERAPEUTIC_DOMAIN", "INSTITUTION", "TARGET") AS 
   select fd.unique_id
 , f.folder_name as title
 , f.description
@@ -176,11 +179,10 @@ left outer join
   )
   ) x on x.id = fd.unique_id
 where f.folder_type = 'PROGRAM' and f.active_ind = 1;
- 
 --
 -- Type: VIEW; Owner: BIOMART_USER; Name: BROWSE_FOLDERS_VIEW
 --
-  CREATE OR REPLACE FORCE VIEW "BIOMART_USER"."BROWSE_FOLDERS_VIEW" ("ID", "TITLE", "DESCRIPTION", "FILE_TYPE") AS 
+  CREATE OR REPLACE FORCE EDITIONABLE VIEW "BIOMART_USER"."BROWSE_FOLDERS_VIEW" ("ID", "TITLE", "DESCRIPTION", "FILE_TYPE") AS 
   select fd.unique_id
 , f.folder_name as title
 , f.description
@@ -192,11 +194,10 @@ where f.folder_type = 'FOLDER' and f.active_ind = 1
 and ata.object_type='BIO_CONCEPT_CODE'
 and ata.object_uid like 'FILE_TYPE%'
 group by fd.unique_id, f.folder_name, f.description;
- 
 --
 -- Type: VIEW; Owner: BIOMART_USER; Name: BROWSE_ASSAYS_VIEW
 --
-  CREATE OR REPLACE FORCE VIEW "BIOMART_USER"."BROWSE_ASSAYS_VIEW" ("ID", "TITLE", "DESCRIPTION", "MEASUREMENT_TYPE", "PLATFORM_NAME", "VENDOR", "TECHNOLOGY", "GENE", "MIRNA", "BIOMARKER_TYPE") AS 
+  CREATE OR REPLACE FORCE EDITIONABLE VIEW "BIOMART_USER"."BROWSE_ASSAYS_VIEW" ("ID", "TITLE", "DESCRIPTION", "MEASUREMENT_TYPE", "PLATFORM_NAME", "VENDOR", "TECHNOLOGY", "GENE", "MIRNA", "BIOMARKER_TYPE") AS 
   select DISTINCT fd.unique_id
   , f.folder_name as title
   , f.description
@@ -244,4 +245,3 @@ group by fd.unique_id, f.folder_name, f.description;
     ) x on x.id = fd.unique_id
   where f.folder_type = 'ASSAY' and f.active_ind = 1
 group by fd.unique_id, f.folder_name, f.description, x.gene, x.mirna, x.biomarker_type;
- 
diff --git a/ddl/oracle/biomart_user/_misc.sql b/ddl/oracle/biomart_user/_misc.sql
index a90efc38..e9f45370 100644
--- a/ddl/oracle/biomart_user/_misc.sql
+++ b/ddl/oracle/biomart_user/_misc.sql
@@ -1,14 +1,12 @@
 --
 -- Type: TYPE; Owner: BIOMART_USER; Name: CONCEPT_CD_TAB
 --
-  CREATE OR REPLACE TYPE "BIOMART_USER"."CONCEPT_CD_TAB" IS TABLE OF VARCHAR2(50)
+  CREATE OR REPLACE EDITIONABLE TYPE "BIOMART_USER"."CONCEPT_CD_TAB" IS TABLE OF VARCHAR2(50)
 /
 
- 
 --
 -- Type: TYPE; Owner: BIOMART_USER; Name: PATIENTS_TAB
 --
-  CREATE OR REPLACE TYPE "BIOMART_USER"."PATIENTS_TAB" IS TABLE OF NUMBER(10,0)
+  CREATE OR REPLACE EDITIONABLE TYPE "BIOMART_USER"."PATIENTS_TAB" IS TABLE OF NUMBER(10,0)
 /
 
- 
diff --git a/ddl/oracle/biomart_user/items.json b/ddl/oracle/biomart_user/items.json
index 3e60e502..f9afa9d5 100644
--- a/ddl/oracle/biomart_user/items.json
+++ b/ddl/oracle/biomart_user/items.json
@@ -1,5 +1,16 @@
 {
   "dependencies" : [ {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "ADD_ONTOLOGY_NODE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2METADATA",
+      "name" : "ADD_ONTOLOGY_NODE"
+    } ]
+  }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
@@ -21,6 +32,17 @@
       "owner" : "AMAPP",
       "name" : "AM_TAG_ASSOCIATION"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "AM_TAG_DISPLAY_VW"
+    },
+    "parents" : [ {
+      "type" : "VIEW",
+      "owner" : "AMAPP",
+      "name" : "AM_TAG_DISPLAY_VW"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -76,6 +98,17 @@
       "owner" : "BIOMART",
       "name" : "ANNOTATION"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "ANNOTATION_DEAPP"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "ANNOTATION_DEAPP"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -241,17 +274,6 @@
       "owner" : "BIOMART",
       "name" : "BIO_ASSAY_ANALYSIS_EXT"
     } ]
-  }, {
-    "child" : {
-      "type" : "SYNONYM",
-      "owner" : "BIOMART_USER",
-      "name" : "BIO_ASSAY_ANALYSIS_GWAS"
-    },
-    "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "BIOMART",
-      "name" : "BIO_ASSAY_ANALYSIS_GWAS"
-    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -494,6 +516,17 @@
       "owner" : "BIOMART",
       "name" : "BIO_CLINICAL_TRIAL_DESIGN"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "BIO_CLINICAL_TRIAL_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "BIO_CLINICAL_TRIAL_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -527,6 +560,13 @@
       "owner" : "BIOMART",
       "name" : "BIO_CONCEPT_CODE"
     } ]
+  }, {
+    "child" : {
+      "type" : "FUNCTION",
+      "owner" : "BIOMART_USER",
+      "name" : "BIO_CONCEPT_CODE_UID"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -604,6 +644,17 @@
       "owner" : "BIOMART",
       "name" : "BIO_DATA_COMPOUND"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "BIO_DATA_COMPOUND_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "BIO_DATA_COMPOUND_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -714,6 +765,17 @@
       "owner" : "BIOMART",
       "name" : "BIO_DATA_UID"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "BIO_DATA_UID_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "BIO_DATA_UID_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -736,6 +798,17 @@
       "owner" : "BIOMART",
       "name" : "BIO_EXPERIMENT"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "BIO_EXPERIMENT_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "BIO_EXPERIMENT_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -857,6 +930,17 @@
       "owner" : "BIOMART",
       "name" : "BIO_MARKER_CORREL_MV"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "BIO_MARKER_EXP_ANALYSIS_MV"
+    },
+    "parents" : [ {
+      "type" : "VIEW",
+      "owner" : "BIOMART",
+      "name" : "BIO_MARKER_EXP_ANALYSIS_MV"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -956,6 +1040,17 @@
       "owner" : "BIOMART",
       "name" : "BIO_TAXONOMY"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "BIRN"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2METADATA",
+      "name" : "BIRN"
+    } ]
   }, {
     "child" : {
       "type" : "VIEW",
@@ -1119,6 +1214,17 @@
       "owner" : "FMAPP",
       "name" : "FM_FOLDER_ASSOCIATION"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "CATEGORY_PATH_EXCLUDED_WORDS"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "CATEGORY_PATH_EXCLUDED_WORDS"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -1192,6 +1298,17 @@
       "owner" : "I2B2DEMODATA",
       "name" : "CONCEPT_DIMENSION_BK"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "CONCEPT_DIMENSION_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "CONCEPT_DIMENSION_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -1225,6 +1342,83 @@
       "owner" : "I2B2DEMODATA",
       "name" : "CRC_DB_LOOKUP"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "CREATE_TEMP_CONCEPT_TABLE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "CREATE_TEMP_CONCEPT_TABLE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "CREATE_TEMP_EID_TABLE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "CREATE_TEMP_EID_TABLE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "CREATE_TEMP_PATIENT_TABLE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "CREATE_TEMP_PATIENT_TABLE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "CREATE_TEMP_PID_TABLE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "CREATE_TEMP_PID_TABLE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "CREATE_TEMP_PROVIDER_TABLE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "CREATE_TEMP_PROVIDER_TABLE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "CREATE_TEMP_TABLE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "CREATE_TEMP_TABLE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "CREATE_TEMP_VISIT_TABLE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "CREATE_TEMP_VISIT_TABLE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -1735,271 +1929,414 @@
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DATAMART_REPORT"
+      "name" : "CZ_FORM_LAYOUT"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "I2B2DEMODATA",
-      "name" : "DATAMART_REPORT"
+      "owner" : "TM_CZ",
+      "name" : "CZ_FORM_LAYOUT"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DD"
+      "name" : "CZ_JOB_AUDIT"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "BIOMART",
-      "name" : "DD"
+      "owner" : "TM_CZ",
+      "name" : "CZ_JOB_AUDIT"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DEAPP_ANNOTATION"
+      "name" : "CZ_JOB_ERROR"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DEAPP_ANNOTATION"
+      "owner" : "TM_CZ",
+      "name" : "CZ_JOB_ERROR"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_CHROMOSOMAL_REGION"
+      "name" : "CZ_JOB_MASTER"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_CHROMOSOMAL_REGION"
+      "owner" : "TM_CZ",
+      "name" : "CZ_JOB_MASTER"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_CHROMO_REGION_ID_SEQ"
+      "name" : "CZ_JOB_MESSAGE"
     },
     "parents" : [ {
-      "type" : "SEQUENCE",
-      "owner" : "DEAPP",
-      "name" : "DE_CHROMO_REGION_ID_SEQ"
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_JOB_MESSAGE"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_CONCEPT_VISIT"
+      "name" : "CZ_PERSON"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_CONCEPT_VISIT"
+      "owner" : "TM_CZ",
+      "name" : "CZ_PERSON"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_ENCOUNTER_LEVEL"
+      "name" : "CZ_TEST"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_ENCOUNTER_LEVEL"
+      "owner" : "TM_CZ",
+      "name" : "CZ_TEST"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_ENCOUNTER_TYPE"
+      "name" : "CZ_TEST_CATEGORY"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_ENCOUNTER_TYPE"
+      "owner" : "TM_CZ",
+      "name" : "CZ_TEST_CATEGORY"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_GPL_INFO"
+      "name" : "CZ_TEST_RESULT"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_GPL_INFO"
+      "owner" : "TM_CZ",
+      "name" : "CZ_TEST_RESULT"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_METABOLITE_ANNOTATION"
+      "name" : "CZ_XTRIAL_CTRL_VOCAB"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_METABOLITE_ANNOTATION"
+      "owner" : "TM_CZ",
+      "name" : "CZ_XTRIAL_CTRL_VOCAB"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_METABOLITE_SUB_PATHWAYS"
+      "name" : "CZ_XTRIAL_EXCLUSION"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_METABOLITE_SUB_PATHWAYS"
+      "owner" : "TM_CZ",
+      "name" : "CZ_XTRIAL_EXCLUSION"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_METABOLITE_SUB_PWAY_METAB"
+      "name" : "DATAMART_REPORT"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_METABOLITE_SUB_PWAY_METAB"
+      "owner" : "I2B2DEMODATA",
+      "name" : "DATAMART_REPORT"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_METABOLITE_SUPER_PATHWAYS"
+      "name" : "DD"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_METABOLITE_SUPER_PATHWAYS"
+      "owner" : "BIOMART",
+      "name" : "DD"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_MRNA_ANNOTATION"
+      "name" : "DEAPP_ANNOTATION"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "DEAPP",
-      "name" : "DE_MRNA_ANNOTATION"
+      "name" : "DEAPP_ANNOTATION"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_MRNA_ANNOTATION_BKP"
+      "name" : "DE_CHROMOSOMAL_REGION"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "DEAPP",
-      "name" : "DE_MRNA_ANNOTATION_BKP"
+      "name" : "DE_CHROMOSOMAL_REGION"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_OBS_ENROLL_DAYS"
+      "name" : "DE_CHROMO_REGION_ID_SEQ"
     },
     "parents" : [ {
-      "type" : "TABLE",
+      "type" : "SEQUENCE",
       "owner" : "DEAPP",
-      "name" : "DE_OBS_ENROLL_DAYS"
+      "name" : "DE_CHROMO_REGION_ID_SEQ"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_PARENT_CD_SEQ"
+      "name" : "DE_CONCEPT_VISIT"
     },
     "parents" : [ {
-      "type" : "SEQUENCE",
+      "type" : "TABLE",
       "owner" : "DEAPP",
-      "name" : "DE_PARENT_CD_SEQ"
+      "name" : "DE_CONCEPT_VISIT"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_PATHWAY"
+      "name" : "DE_ENCOUNTER_LEVEL"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "DEAPP",
-      "name" : "DE_PATHWAY"
+      "name" : "DE_ENCOUNTER_LEVEL"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_PATHWAY_GENE"
+      "name" : "DE_ENCOUNTER_TYPE"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "DEAPP",
-      "name" : "DE_PATHWAY_GENE"
+      "name" : "DE_ENCOUNTER_TYPE"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_PROTEIN_ANNOTATION"
+      "name" : "DE_GPL_INFO"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "DEAPP",
-      "name" : "DE_PROTEIN_ANNOTATION"
+      "name" : "DE_GPL_INFO"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_QPCR_MIRNA_ANNOTATION"
+      "name" : "DE_GPL_INFO_RELEASE"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "DE_QPCR_MIRNA_ANNOTATION"
+      "owner" : "TM_CZ",
+      "name" : "DE_GPL_INFO_RELEASE"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_RBM_ANNOTATION"
+      "name" : "DE_METABOLITE_ANNOTATION"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "DEAPP",
-      "name" : "DE_RBM_ANNOTATION"
+      "name" : "DE_METABOLITE_ANNOTATION"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_RBM_DATA_ANNOTATION_JOIN"
+      "name" : "DE_METABOLITE_SUB_PATHWAYS"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "DEAPP",
-      "name" : "DE_RBM_DATA_ANNOTATION_JOIN"
+      "name" : "DE_METABOLITE_SUB_PATHWAYS"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_RC_SNP_INFO"
+      "name" : "DE_METABOLITE_SUB_PWAY_METAB"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "DEAPP",
-      "name" : "DE_RC_SNP_INFO"
+      "name" : "DE_METABOLITE_SUB_PWAY_METAB"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "DE_RC_SNP_INFO_SEQ"
+      "name" : "DE_METABOLITE_SUPER_PATHWAYS"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_METABOLITE_SUPER_PATHWAYS"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_MRNA_ANNOTATION"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_MRNA_ANNOTATION"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_MRNA_ANNOTATION_BKP"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_MRNA_ANNOTATION_BKP"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_MRNA_ANNOTATION_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_MRNA_ANNOTATION_RELEASE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_OBS_ENROLL_DAYS"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_OBS_ENROLL_DAYS"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_PARENT_CD_SEQ"
+    },
+    "parents" : [ {
+      "type" : "SEQUENCE",
+      "owner" : "DEAPP",
+      "name" : "DE_PARENT_CD_SEQ"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_PATHWAY"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_PATHWAY"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_PATHWAY_GENE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_PATHWAY_GENE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_PROTEIN_ANNOTATION"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_PROTEIN_ANNOTATION"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_QPCR_MIRNA_ANNOTATION"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_QPCR_MIRNA_ANNOTATION"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_RBM_ANNOTATION"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_RBM_ANNOTATION"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_RBM_DATA_ANNOTATION_JOIN"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_RBM_DATA_ANNOTATION_JOIN"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_RC_SNP_INFO"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_RC_SNP_INFO"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_RC_SNP_INFO_SEQ"
     },
     "parents" : [ {
       "type" : "SEQUENCE",
@@ -2072,6 +2409,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SNP_DATA_BY_PATIENT"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SNP_DATA_BY_PATIENT_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SNP_DATA_BY_PATIENT_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2083,6 +2431,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SNP_DATA_BY_PROBE"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SNP_DATA_BY_PROBE_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SNP_DATA_BY_PROBE_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2105,6 +2464,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SNP_DATA_DATASET_LOC_BK"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SNP_DATA_DS_LOC_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SNP_DATA_DS_LOC_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2116,6 +2486,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SNP_GENE_MAP"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SNP_GENE_MAP_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SNP_GENE_MAP_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2127,6 +2508,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SNP_INFO"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SNP_INFO_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SNP_INFO_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2138,6 +2530,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SNP_PROBE"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SNP_PROBE_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SNP_PROBE_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2160,6 +2563,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SNP_PROBE_SORTED_DEF_BK"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SNP_PROBE_SORT_DEF_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SNP_PROBE_SORT_DEF_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2259,6 +2673,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SUBJECT_MIRNA_DATA"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SUBJECT_MRNA_DATA_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_MRNA_DATA_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2292,6 +2717,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SUBJECT_RBM_DATA"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SUBJECT_RBM_DATA_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_RBM_DATA_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2380,6 +2816,28 @@
       "owner" : "DEAPP",
       "name" : "DE_SUBJECT_SNP_DATASET_GSK"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SUBJ_PROTEIN_DATA_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJ_PROTEIN_DATA_RELEASE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DE_SUBJ_SAMPLE_MAP_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJ_SAMPLE_MAP_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2600,6 +3058,17 @@
       "owner" : "I2B2DEMODATA",
       "name" : "DR$OF_CTX_BLOB$R"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "DUMP_TABLE_TO_CSV"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "DEAPP",
+      "name" : "DUMP_TABLE_TO_CSV"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2622,6 +3091,17 @@
       "owner" : "I2B2DEMODATA",
       "name" : "ENCOUNTER_MAPPING"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "FACETED_SEARCH"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "FACETED_SEARCH"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2823,6 +3303,17 @@
       "owner" : "DEAPP",
       "name" : "HAPLOVIEW_DATA"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "HAPLOVIEW_DATA_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "HAPLOVIEW_DATA_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -2891,80 +3382,191 @@
     } ]
   }, {
     "child" : {
-      "type" : "SYNONYM",
+      "type" : "PROCEDURE",
+      "owner" : "BIOMART_USER",
+      "name" : "I2B2_LOAD_EQTL_TOP50"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASY_ANALYSIS_EQTL_TOP50"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_RC_SNP_INFO"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "I2B2_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_RELEASE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "I2B2_SECURE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2METADATA",
+      "name" : "I2B2_SECURE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "I2B2_SECURE_BK"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2METADATA",
+      "name" : "I2B2_SECURE_BK"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "I2B2_SECURE_BK1"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2METADATA",
+      "name" : "I2B2_SECURE_BK1"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "I2B2_TAGS"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2METADATA",
+      "name" : "I2B2_TAGS"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "I2B2_TAGS_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_TAGS_RELEASE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "I2B2_TRIAL_NODES"
+    },
+    "parents" : [ {
+      "type" : "VIEW",
+      "owner" : "I2B2METADATA",
+      "name" : "I2B2_TRIAL_NODES"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART_USER",
+      "name" : "IDX_GOD_ORGANISM"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART_USER",
+      "name" : "GENE_ONTOLOGY_DATA"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
       "owner" : "BIOMART_USER",
-      "name" : "I2B2_SECURE"
+      "name" : "IDX_GOD_SYMBOL"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "I2B2METADATA",
-      "name" : "I2B2_SECURE"
+      "owner" : "BIOMART_USER",
+      "name" : "GENE_ONTOLOGY_DATA"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "I2B2_SECURE_BK"
+      "name" : "INSERT_CONCEPT_FROMTEMP"
     },
     "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "I2B2METADATA",
-      "name" : "I2B2_SECURE_BK"
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "INSERT_CONCEPT_FROMTEMP"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "I2B2_SECURE_BK1"
+      "name" : "INSERT_EID_MAP_FROMTEMP"
     },
     "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "I2B2METADATA",
-      "name" : "I2B2_SECURE_BK1"
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "INSERT_EID_MAP_FROMTEMP"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "I2B2_TAGS"
+      "name" : "INSERT_ENCOUNTERVISIT_FROMTEMP"
     },
     "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "I2B2METADATA",
-      "name" : "I2B2_TAGS"
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "INSERT_ENCOUNTERVISIT_FROMTEMP"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "I2B2_TRIAL_NODES"
+      "name" : "INSERT_PATIENT_MAP_FROMTEMP"
     },
     "parents" : [ {
-      "type" : "VIEW",
-      "owner" : "I2B2METADATA",
-      "name" : "I2B2_TRIAL_NODES"
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "INSERT_PATIENT_MAP_FROMTEMP"
     } ]
   }, {
     "child" : {
-      "type" : "INDEX",
+      "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "IDX_GOD_ORGANISM"
+      "name" : "INSERT_PID_MAP_FROMTEMP"
     },
     "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "BIOMART_USER",
-      "name" : "GENE_ONTOLOGY_DATA"
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "INSERT_PID_MAP_FROMTEMP"
     } ]
   }, {
     "child" : {
-      "type" : "INDEX",
+      "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "IDX_GOD_SYMBOL"
+      "name" : "INSERT_PROVIDER_FROMTEMP"
     },
     "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "BIOMART_USER",
-      "name" : "GENE_ONTOLOGY_DATA"
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "INSERT_PROVIDER_FROMTEMP"
     } ]
   }, {
     "child" : {
@@ -3036,78 +3638,78 @@
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "KEGG_DEF"
+      "name" : "LISTSIG_GENES"
     },
     "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "KEGG_DEF"
+      "type" : "VIEW",
+      "owner" : "SEARCHAPP",
+      "name" : "LISTSIG_GENES"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "LISTSIG_GENES"
+      "name" : "LZ_SRC_ANALYSIS_METADATA"
     },
     "parents" : [ {
-      "type" : "VIEW",
-      "owner" : "SEARCHAPP",
-      "name" : "LISTSIG_GENES"
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LZ_SRC_ANALYSIS_METADATA"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "MAP"
+      "name" : "LZ_SRC_STUDY_METADATA"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "I2B2DEMODATA",
-      "name" : "MAP"
+      "owner" : "TM_LZ",
+      "name" : "LZ_SRC_STUDY_METADATA"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "MASTER_QUERY_GLOBAL_TEMP"
+      "name" : "MAP"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "I2B2DEMODATA",
-      "name" : "MASTER_QUERY_GLOBAL_TEMP"
+      "name" : "MAP"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "MESH"
+      "name" : "MASTER_QUERY_GLOBAL_TEMP"
     },
     "parents" : [ {
       "type" : "TABLE",
-      "owner" : "BIOMART",
-      "name" : "MESH"
+      "owner" : "I2B2DEMODATA",
+      "name" : "MASTER_QUERY_GLOBAL_TEMP"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "MESH_DESCRIPTOR"
+      "name" : "MESH_ALL"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "BIOMART",
-      "name" : "MESH_DESCRIPTOR"
+      "name" : "MESH_ALL"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "MESH_ENTRY"
+      "name" : "MESH_DESCRIPTOR"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "BIOMART",
-      "name" : "MESH_ENTRY"
+      "name" : "MESH_DESCRIPTOR"
     } ]
   }, {
     "child" : {
@@ -3230,6 +3832,17 @@
       "owner" : "I2B2DEMODATA",
       "name" : "NEWS_UPDATES"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "NODE_CURATION"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "NODE_CURATION"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -3252,6 +3865,28 @@
       "owner" : "I2B2DEMODATA",
       "name" : "OBSERVATION_FACT_BK"
     } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART_USER",
+      "name" : "OBSERVATION_FACT_PD"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "OBSERVATION_FACT"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "OBSERVATION_FACT_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "OBSERVATION_FACT_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -3303,6 +3938,17 @@
       "owner" : "I2B2DEMODATA",
       "name" : "PATIENT_DIMENSION"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "PATIENT_DIMENSION_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "PATIENT_DIMENSION_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -3380,6 +4026,28 @@
       "owner" : "SEARCHAPP",
       "name" : "PLUGIN_SEQ"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "PROBESET_DEAPP"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "PROBESET_DEAPP"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "PROBESET_DEAPP_20120206"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "PROBESET_DEAPP_20120206"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -3699,6 +4367,17 @@
       "owner" : "DEAPP",
       "name" : "RBM_ANNOTATION_ID"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "REMOVE_TEMP_TABLE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "REMOVE_TEMP_TABLE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -3743,6 +4422,17 @@
       "owner" : "I2B2DEMODATA",
       "name" : "SAMPLE_CATEGORIES"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "SAMPLE_CATEGORIES_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "SAMPLE_CATEGORIES_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -3886,6 +4576,17 @@
       "owner" : "SEARCHAPP",
       "name" : "SEARCH_BIO_MKR_CORREL_FST_VIEW"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "SEARCH_BIO_MKR_CORREL_VIEW"
+    },
+    "parents" : [ {
+      "type" : "VIEW",
+      "owner" : "SEARCHAPP",
+      "name" : "SEARCH_BIO_MKR_CORREL_VIEW"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -4029,6 +4730,17 @@
       "owner" : "SEARCHAPP",
       "name" : "SEARCH_SECURE_OBJECT_PATH"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "SEARCH_SECURE_OBJECT_RELEASE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "SEARCH_SECURE_OBJECT_RELEASE"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -4260,6 +4972,17 @@
       "owner" : "I2B2DEMODATA",
       "name" : "SEQ_ENCOUNTER_NUM"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "SEQ_ETL_ID"
+    },
+    "parents" : [ {
+      "type" : "SEQUENCE",
+      "owner" : "TM_LZ",
+      "name" : "SEQ_ETL_ID"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -4381,6 +5104,17 @@
       "owner" : "I2B2DEMODATA",
       "name" : "SOURCE_MASTER"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "SP_XTAB"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "SP_XTAB"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -4491,6 +5225,17 @@
       "owner" : "I2B2DEMODATA",
       "name" : "TIMERS"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "TJEA_JUNK"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "TJEA_JUNK"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -4502,6 +5247,17 @@
       "owner" : "BIOMART",
       "name" : "TMP_BIO_MARKER"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "TMP_NUM_DATA_TYPES"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "TMP_NUM_DATA_TYPES"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -4568,6 +5324,39 @@
       "owner" : "I2B2METADATA",
       "name" : "TMP_SECURE_TOKEN"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "TMP_SUBJECT_INFO"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "TMP_SUBJECT_INFO"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "TMP_TRIAL_DATA"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "TMP_TRIAL_DATA"
+    } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "BIOMART_USER",
+      "name" : "TMP_TRIAL_NODES"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "TMP_TRIAL_NODES"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -4583,68 +5372,54 @@
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "UPLOAD_STATUS"
+      "name" : "UPDATE_OBSERVATION_FACT"
     },
     "parents" : [ {
-      "type" : "TABLE",
+      "type" : "PROCEDURE",
       "owner" : "I2B2DEMODATA",
-      "name" : "UPLOAD_STATUS"
+      "name" : "UPDATE_OBSERVATION_FACT"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "VISIT_DIMENSION"
+      "name" : "UPLOAD_STATUS"
     },
     "parents" : [ {
       "type" : "TABLE",
       "owner" : "I2B2DEMODATA",
-      "name" : "VISIT_DIMENSION"
+      "name" : "UPLOAD_STATUS"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "VW_FACETED_SEARCH"
+      "name" : "VISIT_DIMENSION"
     },
     "parents" : [ {
-      "type" : "VIEW",
-      "owner" : "BIOMART",
-      "name" : "VW_FACETED_SEARCH"
+      "type" : "TABLE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "VISIT_DIMENSION"
     } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
       "owner" : "BIOMART_USER",
-      "name" : "VW_FACETED_SEARCH_DISEASE"
+      "name" : "VW_FACETED_SEARCH"
     },
     "parents" : [ {
       "type" : "VIEW",
       "owner" : "BIOMART",
-      "name" : "VW_FACETED_SEARCH_DISEASE"
+      "name" : "VW_FACETED_SEARCH"
     } ]
   } ],
   "fileAssignments" : [ {
     "item" : {
-      "type" : "TABLE",
-      "owner" : "BIOMART_USER",
-      "name" : "GENE_ONTOLOGY"
-    },
-    "file" : "biomart_user/gene_ontology.sql"
-  }, {
-    "item" : {
-      "type" : "TABLE",
-      "owner" : "BIOMART_USER",
-      "name" : "GENE_ONTOLOGY"
-    },
-    "file" : "biomart_user/gene_ontology.sql"
-  }, {
-    "item" : {
-      "type" : "TABLE",
+      "type" : "FUNCTION",
       "owner" : "BIOMART_USER",
-      "name" : "GENE_ONTOLOGY_DATA"
+      "name" : "BIO_CONCEPT_CODE_UID"
     },
-    "file" : "biomart_user/gene_ontology_data.sql"
+    "file" : "biomart_user/functions/bio_concept_code_uid.sql"
   }, {
     "item" : {
       "type" : "VIEW",
@@ -4701,6 +5476,13 @@
       "name" : "GENE_ONTOLOGY_DATA"
     },
     "file" : "biomart_user/gene_ontology_data.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "BIOMART_USER",
+      "name" : "I2B2_LOAD_EQTL_TOP50"
+    },
+    "file" : "biomart_user/procedures/i2b2_load_eqtl_top50.sql"
   }, {
     "item" : {
       "type" : "INDEX",
@@ -4715,6 +5497,13 @@
       "name" : "IDX_GOD_SYMBOL"
     },
     "file" : "biomart_user/gene_ontology_data.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART_USER",
+      "name" : "OBSERVATION_FACT_PD"
+    },
+    "file" : "biomart_user/_cross.sql"
   }, {
     "item" : {
       "type" : "TYPE",
@@ -4723,4 +5512,4 @@
     },
     "file" : "biomart_user/_misc.sql"
   } ]
-}
+}
\ No newline at end of file

From b0aae0e7e02b83a56648bf192fc1caef2091369b Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 10:45:25 +0100
Subject: [PATCH 21/31] biomart_user functions and procedures from test server

---
 .../functions/bio_concept_code_uid.sql        |  14 ++
 .../procedures/i2b2_load_eqtl_top50.sql       | 156 ++++++++++++++++++
 2 files changed, 170 insertions(+)
 create mode 100644 ddl/oracle/biomart_user/functions/bio_concept_code_uid.sql
 create mode 100644 ddl/oracle/biomart_user/procedures/i2b2_load_eqtl_top50.sql

diff --git a/ddl/oracle/biomart_user/functions/bio_concept_code_uid.sql b/ddl/oracle/biomart_user/functions/bio_concept_code_uid.sql
new file mode 100644
index 00000000..e3789290
--- /dev/null
+++ b/ddl/oracle/biomart_user/functions/bio_concept_code_uid.sql
@@ -0,0 +1,14 @@
+--
+-- Type: FUNCTION; Owner: BIOMART_USER; Name: BIO_CONCEPT_CODE_UID
+--
+  CREATE OR REPLACE EDITIONABLE FUNCTION "BIOMART_USER"."BIO_CONCEPT_CODE_UID" (
+  CODE_TYPE_NAME VARCHAR2,
+  BIO_CONCEPT_CODE VARCHAR2
+) RETURN VARCHAR2 AS
+BEGIN
+  -- $Id$
+  -- Creates uid for bio_concept_code.
+
+  RETURN nvl(CODE_TYPE_NAME,'ERROR') || ':' || nvl(BIO_CONCEPT_CODE, 'ERROR');
+END bio_concept_code_uid;
+/
diff --git a/ddl/oracle/biomart_user/procedures/i2b2_load_eqtl_top50.sql b/ddl/oracle/biomart_user/procedures/i2b2_load_eqtl_top50.sql
new file mode 100644
index 00000000..6e201814
--- /dev/null
+++ b/ddl/oracle/biomart_user/procedures/i2b2_load_eqtl_top50.sql
@@ -0,0 +1,156 @@
+--
+-- Type: PROCEDURE; Owner: BIOMART_USER; Name: I2B2_LOAD_EQTL_TOP50
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "BIOMART_USER"."I2B2_LOAD_EQTL_TOP50" 
+(i_bio_assay_analysis_id number
+,i_job_id        number := null
+)
+ AS
+        --Audit variables
+    newJobFlag     INTEGER(1);
+    databaseName     VARCHAR(100);
+    procedureName VARCHAR(100);
+    jobID         number(18,0);
+    stepCt         number(18,0);
+
+        v_sqlText                varchar2(2000);
+
+BEGIN
+    --Set Audit Parameters
+    newJobFlag := 0; -- False (Default)
+    jobID := i_job_id;
+
+    SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+    procedureName := $$PLSQL_UNIT;
+
+    --Audit JOB Initialization
+    --If Job ID does not exist, then this is a single procedure run and we need to create it
+    IF(jobID IS NULL or jobID < 1)
+    THEN
+        newJobFlag := 1; -- True
+        cz_start_audit (procedureName, databaseName, jobID);
+    END IF;
+
+    stepCt := 1;
+    cz_write_audit(jobID,databaseName,procedureName,'Starting ' || procedureName,0,stepCt,'Done');
+
+        --        delete existing data from bio_asy_analysis_eqtl_top50
+
+        delete from biomart.bio_asy_analysis_eqtl_top50
+        where bio_assay_analysis_id = i_bio_assay_analysis_id;
+    stepCt := stepCt + 1;
+        cz_write_audit(jobID,databaseName,procedureName,'Delete data for analysis from biomart.bio_asy_analysis_eqtls_top50',SQL%ROWCOUNT,stepCt,'Done');
+        commit;
+
+/*
+        --        disable indexes
+
+        for eqtl_idx in (select index_name
+                                                        ,table_name
+                                         from all_indexes
+                                         where owner = 'BIOMART'
+                                           and table_name = 'BIO_ASY_ANALYSIS_EQTL_TOP50')
+        loop
+                v_sqlText := 'alter index ' || eqtl_idx.index_name || ' unusable';
+                stepCt := stepCt + 1;
+                cz_write_audit(jobId,databaseName,procedureName,'Disabling index ' || eqtl_idx.index_name || ' on ' || eqtl_idx.table_name,0,stepCt,'Done');
+                execute immediate(v_sqlText);
+                stepCt := stepCt + 1;
+                cz_write_audit(jobId,databaseName,procedureName,'Disabling complete',0,stepCt,'Done');
+        end loop;
+*/
+
+        --        insert analysis into bio_asy_analysis_eqtl_top50
+
+        insert into biomart.bio_asy_analysis_eqtl_top50
+        (bio_assay_analysis_id
+        ,analysis
+        ,chrom
+        ,pos
+        ,rsgene
+        ,rsid
+        ,pvalue
+        ,logpvalue
+        ,extdata
+        ,rnum
+        ,intronexon
+        ,recombinationrate
+        ,regulome
+        )
+        select a.bio_assay_analysis_id
+                  ,a.analysis
+                  ,info.chrom
+                  ,info.pos
+                  ,a.gene
+                  ,a.rsid
+                  ,a.pvalue
+                  ,a.logpvalue
+                  ,a.extdata
+                  ,a.rnum
+                  ,info.exon_intron as intronexon
+                  ,info.recombination_rate as recombinationrate
+                  ,info.regulome_score as regulome
+        from (select b.bio_assay_analysis_id
+                                ,b.analysis
+                                ,b.rsid
+                                ,b.pvalue
+                                ,b.logpvalue
+                                ,b.extdata
+                                ,b.gene
+                                ,b.cis_trans
+                                ,b.distance_from_gene
+                                ,b.rnum
+                 from (select eqtl.bio_assay_analysis_id
+                                         ,baa.analysis_name as analysis
+                                         ,eqtl.rs_id as rsid
+                                         ,eqtl.p_value as pvalue
+                                         ,eqtl.log_p_value as logpvalue
+                                         ,eqtl.ext_data as extdata
+                                         ,eqtl.gene
+                                         ,eqtl.cis_trans
+                                         ,eqtl.distance_from_gene
+                                         ,row_number () over (order by eqtl.p_value asc, eqtl.rs_id asc) as rnum
+                          from biomart.bio_assay_analysis_eqtl eqtl
+                          inner join biomart.bio_assay_analysis baa
+                                        on  baa.bio_assay_analysis_id = eqtl.bio_assay_analysis_id
+                          where eqtl.bio_assay_analysis_id = i_bio_assay_analysis_id) b
+                 where b.rnum < 500) a
+        inner join deapp.de_rc_snp_info info
+                  on  a.rsid = info.rs_id
+                  and hg_version='19';
+    stepCt := stepCt + 1;
+        cz_write_audit(jobID,databaseName,procedureName,'Insert data for analysis from biomart.bio_asy_analysis_eaqtl_top50',SQL%ROWCOUNT,stepCt,'Done');
+        commit;
+
+/*
+        --        rebuild indexes
+
+        for eqtl_idx in (select index_name
+                                                           ,table_name
+                                                 from all_indexes
+                                                 where owner = 'BIOMART'
+                                                   and table_name = 'BIO_ASY_ANALYSIS_EQTL_TOP50')
+                loop
+                        v_sqlText := 'alter index ' || eqtl_idx.index_name || ' rebuild';
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobId,databaseName,procedureName,'Rebuilding index ' || eqtl_idx.index_name || ' on ' || eqtl_idx.table_name,0,stepCt,'Done');
+                        execute immediate(v_sqlText);
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobId,databaseName,procedureName,'Rebuilding complete',SQL%ROWCOUNT,stepCt,'Done');
+                end loop;
+*/
+
+        cz_write_audit(jobID,databaseName,procedureName,'End ' || procedureName,0,stepCt,'Done');
+    stepCt := stepCt + 1;
+
+    cz_end_audit(jobID, 'Success');
+
+    exception
+    when others then
+    --Handle errors.
+        cz_error_handler (jobID, procedureName);
+    --End Proc
+        cz_end_audit (jobID, 'FAIL');
+
+END I2B2_LOAD_eqtl_TOP50;
+/

From 07ac6c8486e8452247afcf2f7029bd6bd871e8e6 Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 10:50:28 +0100
Subject: [PATCH 22/31] i2b2demodata updates from test server

---
 ddl/oracle/i2b2metadata/i2b2.sql              |  7 ++++++-
 ddl/oracle/i2b2metadata/items.json            | 20 ++++++++++++++++++-
 .../procedures/add_ontology_node.sql          | 11 ++++++++--
 3 files changed, 34 insertions(+), 4 deletions(-)

diff --git a/ddl/oracle/i2b2metadata/i2b2.sql b/ddl/oracle/i2b2metadata/i2b2.sql
index 882d20c0..224c2343 100644
--- a/ddl/oracle/i2b2metadata/i2b2.sql
+++ b/ddl/oracle/i2b2metadata/i2b2.sql
@@ -36,7 +36,6 @@ LOB ("C_METADATAXML") STORE AS BASICFILE (
 LOB ("C_COMMENT") STORE AS BASICFILE (
  TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 PCTVERSION 10
  NOCACHE NOLOGGING ) ;
-
 --
 -- Type: INDEX; Owner: I2B2METADATA; Name: I2B2_INDX1
 --
@@ -70,6 +69,12 @@ end;
 /
 ALTER TRIGGER "I2B2METADATA"."TRG_I2B2_ID" ENABLE;
  
+--
+-- Type: INDEX; Owner: I2B2METADATA; Name: IDX_I2B2_FULLNAME_BASECODE
+--
+CREATE INDEX "I2B2METADATA"."IDX_I2B2_FULLNAME_BASECODE" ON "I2B2METADATA"."I2B2" ("C_FULLNAME", "C_BASECODE")
+TABLESPACE "TRANSMART" ;
+
 --
 -- Type: INDEX; Owner: I2B2METADATA; Name: META_APPLIED_PATH_I2B2_IDX
 --
diff --git a/ddl/oracle/i2b2metadata/items.json b/ddl/oracle/i2b2metadata/items.json
index 450a170c..288732be 100644
--- a/ddl/oracle/i2b2metadata/items.json
+++ b/ddl/oracle/i2b2metadata/items.json
@@ -103,6 +103,17 @@
       "owner" : "I2B2METADATA",
       "name" : "I2B2"
     } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "I2B2METADATA",
+      "name" : "IDX_I2B2_FULLNAME_BASECODE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2METADATA",
+      "name" : "I2B2"
+    } ]
   }, {
     "child" : {
       "type" : "INDEX",
@@ -350,6 +361,13 @@
       "name" : "I2B2_TRIAL_NODES"
     },
     "file" : "i2b2metadata/views/i2b2_trial_nodes.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "I2B2METADATA",
+      "name" : "IDX_I2B2_FULLNAME_BASECODE"
+    },
+    "file" : "i2b2metadata/i2b2.sql"
   }, {
     "item" : {
       "type" : "INDEX",
@@ -477,4 +495,4 @@
     },
     "file" : "i2b2metadata/ont_process_status.sql"
   } ]
-}
+}
\ No newline at end of file
diff --git a/ddl/oracle/i2b2metadata/procedures/add_ontology_node.sql b/ddl/oracle/i2b2metadata/procedures/add_ontology_node.sql
index 6eaf5e3e..e20fc4b5 100644
--- a/ddl/oracle/i2b2metadata/procedures/add_ontology_node.sql
+++ b/ddl/oracle/i2b2metadata/procedures/add_ontology_node.sql
@@ -95,7 +95,7 @@ begin
 ------------------------------------------------------------
 -- add the new node into the i2b2 table
 ------------------------------------------------------------
-    insert into i2b2metadata.i2b2(
+    insert into i2b2demodata.i2b2(
     C_HLEVEL, C_FULLNAME, C_NAME
     , C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOTALNUM
     , C_BASECODE, C_METADATAXML, C_FACTTABLECOLUMN
@@ -114,5 +114,12 @@ begin
     commit;
   end;
 end;
-/
  
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+/

From e9c3b1cc210ad85a4ab577abf7420c0d0b5390b5 Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 10:57:54 +0100
Subject: [PATCH 23/31] update i2b2demodata from test server

---
 ddl/oracle/i2b2demodata/items.json            | 54 ++++++++++++-------
 ddl/oracle/i2b2demodata/jms_transactions.sql  |  8 +--
 .../i2b2demodata/modifier_dimension.sql       |  2 +-
 ddl/oracle/i2b2demodata/modifier_metadata.sql |  2 +-
 ddl/oracle/i2b2demodata/observation_fact.sql  |  5 +-
 ddl/oracle/i2b2demodata/patient_dimension.sql |  7 ++-
 ddl/oracle/i2b2demodata/sample_dimension.sql  | 14 ++---
 ddl/oracle/i2b2demodata/upload_status.sql     |  9 ++--
 8 files changed, 61 insertions(+), 40 deletions(-)

diff --git a/ddl/oracle/i2b2demodata/items.json b/ddl/oracle/i2b2demodata/items.json
index bc1563ec..14362891 100644
--- a/ddl/oracle/i2b2demodata/items.json
+++ b/ddl/oracle/i2b2demodata/items.json
@@ -337,6 +337,28 @@
       "owner" : "I2B2DEMODATA",
       "name" : "OBSERVATION_FACT"
     } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "I2B2DEMODATA",
+      "name" : "IDX_OB_FACT_PATIENT_NUMBER"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "OBSERVATION_FACT"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "I2B2DEMODATA",
+      "name" : "IDX_PD_SOURCESYSTEMCD_PNUM"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "PATIENT_DIMENSION"
+    } ]
   }, {
     "child" : {
       "type" : "PROCEDURE",
@@ -522,17 +544,6 @@
       "name" : "OBSERVATION_FACT_BK"
     },
     "parents" : [ ]
-  }, {
-    "child" : {
-      "type" : "INDEX",
-      "owner" : "I2B2DEMODATA",
-      "name" : "OBSERVATION_FACT_PD"
-    },
-    "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "I2B2DEMODATA",
-      "name" : "OBSERVATION_FACT"
-    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -1688,6 +1699,20 @@
       "name" : "IDX_OB_FACT_2"
     },
     "file" : "i2b2demodata/observation_fact.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "I2B2DEMODATA",
+      "name" : "IDX_OB_FACT_PATIENT_NUMBER"
+    },
+    "file" : "i2b2demodata/observation_fact.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "I2B2DEMODATA",
+      "name" : "IDX_PD_SOURCESYSTEMCD_PNUM"
+    },
+    "file" : "i2b2demodata/patient_dimension.sql"
   }, {
     "item" : {
       "type" : "PROCEDURE",
@@ -1849,13 +1874,6 @@
       "name" : "OBSERVATION_FACT_BK"
     },
     "file" : "i2b2demodata/observation_fact_bk.sql"
-  }, {
-    "item" : {
-      "type" : "INDEX",
-      "owner" : "I2B2DEMODATA",
-      "name" : "OBSERVATION_FACT_PD"
-    },
-    "file" : "i2b2demodata/observation_fact.sql"
   }, {
     "item" : {
       "type" : "TABLE",
diff --git a/ddl/oracle/i2b2demodata/jms_transactions.sql b/ddl/oracle/i2b2demodata/jms_transactions.sql
index 8dbda32a..2ca3bec9 100644
--- a/ddl/oracle/i2b2demodata/jms_transactions.sql
+++ b/ddl/oracle/i2b2demodata/jms_transactions.sql
@@ -1,8 +1,8 @@
 --
 -- Type: TABLE; Owner: I2B2DEMODATA; Name: JMS_TRANSACTIONS
 --
-CREATE TABLE "I2B2DEMODATA"."JMS_TRANSACTIONS" 
- (	"TXID" NUMBER(*,0)
- ) SEGMENT CREATION IMMEDIATE
-TABLESPACE "TRANSMART" ;
+ CREATE TABLE "I2B2DEMODATA"."JMS_TRANSACTIONS" 
+  (	"TXID" NUMBER(*,0)
+  ) SEGMENT CREATION IMMEDIATE
+ TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/i2b2demodata/modifier_dimension.sql b/ddl/oracle/i2b2demodata/modifier_dimension.sql
index e94a2a91..ad33e40c 100644
--- a/ddl/oracle/i2b2demodata/modifier_dimension.sql
+++ b/ddl/oracle/i2b2demodata/modifier_dimension.sql
@@ -16,7 +16,7 @@
  CONSTRAINT "MODIFIER_DIMENSION_PK" PRIMARY KEY ("MODIFIER_PATH")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" 
 LOB ("MODIFIER_BLOB") STORE AS BASICFILE (
  TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 RETENTION 
diff --git a/ddl/oracle/i2b2demodata/modifier_metadata.sql b/ddl/oracle/i2b2demodata/modifier_metadata.sql
index c61bb4b3..a1cb7f7b 100644
--- a/ddl/oracle/i2b2demodata/modifier_metadata.sql
+++ b/ddl/oracle/i2b2demodata/modifier_metadata.sql
@@ -6,6 +6,6 @@
 "VALTYPE_CD" VARCHAR2(10 BYTE), 
 "STD_UNITS" VARCHAR2(50 BYTE), 
 "VISIT_IND" CHAR(1 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/i2b2demodata/observation_fact.sql b/ddl/oracle/i2b2demodata/observation_fact.sql
index 6e2f2530..33e8c11a 100644
--- a/ddl/oracle/i2b2demodata/observation_fact.sql
+++ b/ddl/oracle/i2b2demodata/observation_fact.sql
@@ -33,7 +33,6 @@
 LOB ("OBSERVATION_BLOB") STORE AS BASICFILE (
  TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 PCTVERSION 10
  NOCACHE NOLOGGING ) ;
-
 --
 -- Type: INDEX; Owner: I2B2DEMODATA; Name: IDX_OB_FACT_2
 --
@@ -67,8 +66,8 @@ CREATE SEQUENCE  "I2B2DEMODATA"."SEQ_ENCOUNTER_NUM"  MINVALUE 1 MAXVALUE 9999999
 ALTER TRIGGER "I2B2DEMODATA"."TRG_ENCOUNTER_NUM" ENABLE;
  
 --
--- Type: INDEX; Owner: I2B2DEMODATA; Name: OBSERVATION_FACT_PD
+-- Type: INDEX; Owner: I2B2DEMODATA; Name: IDX_OB_FACT_PATIENT_NUMBER
 --
-CREATE INDEX "I2B2DEMODATA"."OBSERVATION_FACT_PD" ON "I2B2DEMODATA"."OBSERVATION_FACT" ("PATIENT_NUM")
+CREATE INDEX "I2B2DEMODATA"."IDX_OB_FACT_PATIENT_NUMBER" ON "I2B2DEMODATA"."OBSERVATION_FACT" ("PATIENT_NUM", "CONCEPT_CD")
 TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/i2b2demodata/patient_dimension.sql b/ddl/oracle/i2b2demodata/patient_dimension.sql
index f21aa910..3a48599c 100644
--- a/ddl/oracle/i2b2demodata/patient_dimension.sql
+++ b/ddl/oracle/i2b2demodata/patient_dimension.sql
@@ -34,7 +34,6 @@ CREATE SEQUENCE  "I2B2DEMODATA"."SEQ_PATIENT_NUM"  MINVALUE 1 MAXVALUE 999999999
 LOB ("PATIENT_BLOB") STORE AS BASICFILE (
  TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 PCTVERSION 10
  NOCACHE NOLOGGING ) ;
-
 --
 -- Type: INDEX; Owner: I2B2DEMODATA; Name: PD_IDX_ALLPATIENTDIM
 --
@@ -57,3 +56,9 @@ select SEQ_PATIENT_NUM.nextval into :NEW."PATIENT_NUM" from dual;       end if;
 /
 ALTER TRIGGER "I2B2DEMODATA"."TRG_PATIENT_DIMENSION" ENABLE;
  
+--
+-- Type: INDEX; Owner: I2B2DEMODATA; Name: IDX_PD_SOURCESYSTEMCD_PNUM
+--
+CREATE INDEX "I2B2DEMODATA"."IDX_PD_SOURCESYSTEMCD_PNUM" ON "I2B2DEMODATA"."PATIENT_DIMENSION" ("SOURCESYSTEM_CD", "PATIENT_NUM")
+TABLESPACE "TRANSMART" ;
+
diff --git a/ddl/oracle/i2b2demodata/sample_dimension.sql b/ddl/oracle/i2b2demodata/sample_dimension.sql
index e7266d14..78502239 100644
--- a/ddl/oracle/i2b2demodata/sample_dimension.sql
+++ b/ddl/oracle/i2b2demodata/sample_dimension.sql
@@ -1,11 +1,11 @@
 --
 -- Type: TABLE; Owner: I2B2DEMODATA; Name: SAMPLE_DIMENSION
 --
-CREATE TABLE "I2B2DEMODATA"."SAMPLE_DIMENSION" 
- (	"SAMPLE_CD" VARCHAR2(200 BYTE) NOT NULL ENABLE, 
-CONSTRAINT "SAMPLE_DIMENSION_PK" PRIMARY KEY ("SAMPLE_CD")
-USING INDEX
-TABLESPACE "TRANSMART"  ENABLE
- ) SEGMENT CREATION IMMEDIATE
-TABLESPACE "TRANSMART" ;
+ CREATE TABLE "I2B2DEMODATA"."SAMPLE_DIMENSION" 
+  (	"SAMPLE_CD" VARCHAR2(200 BYTE) NOT NULL ENABLE, 
+ CONSTRAINT "SAMPLE_DIMENSION_PK" PRIMARY KEY ("SAMPLE_CD")
+ USING INDEX
+ TABLESPACE "TRANSMART"  ENABLE
+  ) SEGMENT CREATION IMMEDIATE
+ TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/i2b2demodata/upload_status.sql b/ddl/oracle/i2b2demodata/upload_status.sql
index 5a9d91c2..cb325ee6 100644
--- a/ddl/oracle/i2b2demodata/upload_status.sql
+++ b/ddl/oracle/i2b2demodata/upload_status.sql
@@ -1,8 +1,3 @@
---
--- Type: SEQUENCE; Owner: I2B2DEMODATA; Name: SQ_UPLOADSTATUS_UPLOADID
---
-CREATE SEQUENCE  "I2B2DEMODATA"."SQ_UPLOADSTATUS_UPLOADID"  MINVALUE 1 MAXVALUE 9999999999999 INCREMENT BY 1 START WITH 1 NOCACHE  ORDER  NOCYCLE ;
-
 --
 -- Type: TABLE; Owner: I2B2DEMODATA; Name: UPLOAD_STATUS
 --
@@ -35,6 +30,10 @@ LOB ("INPUT_FILE_NAME") STORE AS BASICFILE (
 LOB ("LOG_FILE_NAME") STORE AS BASICFILE (
  TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 RETENTION 
  NOCACHE LOGGING ) ;
+--
+-- Type: SEQUENCE; Owner: I2B2DEMODATA; Name: SQ_UPLOADSTATUS_UPLOADID
+--
+CREATE SEQUENCE  "I2B2DEMODATA"."SQ_UPLOADSTATUS_UPLOADID"  MINVALUE 1 MAXVALUE 9999999999999 INCREMENT BY 1 START WITH 1 NOCACHE  ORDER  NOCYCLE ;
 
 --
 -- Type: TRIGGER; Owner: I2B2DEMODATA; Name: TRG_UPLOAD_STATUS_UPLOAD_ID

From c95c970faf557f219a949eed234a4fe31c9e9f54 Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 11:08:35 +0100
Subject: [PATCH 24/31] searchapp updates from oracle test server

---
 ddl/oracle/searchapp/_cross.sql               | 13 ------
 ddl/oracle/searchapp/_misc.sql                | 12 +++---
 ddl/oracle/searchapp/items.json               | 42 ++++++++++++++++---
 ddl/oracle/searchapp/saved_faceted_search.sql | 36 ++++++++--------
 .../searchapp/search_auth_principal.sql       | 21 +++++++++-
 .../search_auth_sec_object_access.sql         | 24 +++++------
 .../searchapp/search_auth_user_sec_access.sql | 12 +++---
 ddl/oracle/searchapp/search_keyword.sql       | 12 ++++++
 ddl/oracle/searchapp/search_keyword_term.sql  | 12 +++---
 ddl/oracle/searchapp/search_taxonomy.sql      |  4 +-
 ddl/oracle/searchapp/search_taxonomy_rels.sql | 26 ++++++------
 ddl/oracle/searchapp/views/pathway_genes.sql  | 11 +++++
 .../views/search_bio_mkr_correl_fast_mv.sql   |  3 +-
 13 files changed, 146 insertions(+), 82 deletions(-)
 create mode 100644 ddl/oracle/searchapp/views/pathway_genes.sql

diff --git a/ddl/oracle/searchapp/_cross.sql b/ddl/oracle/searchapp/_cross.sql
index 0b1b4eb0..d976392a 100644
--- a/ddl/oracle/searchapp/_cross.sql
+++ b/ddl/oracle/searchapp/_cross.sql
@@ -40,16 +40,3 @@ FROM
   AND bada.bio_assay_feature_group_id = i.bio_assay_feature_group_id
   AND i.bio_assay_feature_group_id   IS NOT NULL
 );
- 
---
--- Type: VIEW; Owner: SEARCHAPP; Name: PATHWAY_GENES
---
-  CREATE OR REPLACE FORCE VIEW "SEARCHAPP"."PATHWAY_GENES" ("GENE_KEYWORD_ID", "PATHWAY_KEYWORD_ID", "GENE_BIOMARKER_ID") AS 
-  SELECT k_gene.search_keyword_id AS gene_keyword_id,
-  k_pathway.search_keyword_id AS pathway_keyword_id,
-  b.asso_bio_marker_id AS gene_biomarker_id
- FROM searchapp.search_keyword k_pathway,
-  biomart.bio_marker_correl_mv b,
-  searchapp.search_keyword k_gene
-WHERE ((((((b.correl_type) = 'PATHWAY_GENE') AND (b.bio_marker_id = k_pathway.bio_data_id)) AND ((k_pathway.data_category) = 'PATHWAY')) AND (b.asso_bio_marker_id = k_gene.bio_data_id)) AND ((k_gene.data_category) = 'GENE'));
- 
diff --git a/ddl/oracle/searchapp/_misc.sql b/ddl/oracle/searchapp/_misc.sql
index a9a0011b..69daa5b0 100644
--- a/ddl/oracle/searchapp/_misc.sql
+++ b/ddl/oracle/searchapp/_misc.sql
@@ -1,7 +1,7 @@
 --
--- Type: SEQUENCE; Owner: SEARCHAPP; Name: PLUGIN_SEQ
+-- Type: SEQUENCE; Owner: SEARCHAPP; Name: PLUGIN_MODULE_SEQ
 --
-CREATE SEQUENCE  "SEARCHAPP"."PLUGIN_SEQ"  MINVALUE 1 MAXVALUE 9999999999999999999999999999 INCREMENT BY 1 START WITH 1 CACHE 20 NOORDER  NOCYCLE ;
+CREATE SEQUENCE  "SEARCHAPP"."PLUGIN_MODULE_SEQ"  MINVALUE 1 MAXVALUE 9999999999999999999999999999 INCREMENT BY 1 START WITH 1 CACHE 20 NOORDER  NOCYCLE ;
 
 --
 -- Type: SEQUENCE; Owner: SEARCHAPP; Name: SEQ_SEARCH_DATA_ID
@@ -9,12 +9,12 @@ CREATE SEQUENCE  "SEARCHAPP"."PLUGIN_SEQ"  MINVALUE 1 MAXVALUE 99999999999999999
 CREATE SEQUENCE  "SEARCHAPP"."SEQ_SEARCH_DATA_ID"  MINVALUE 1 MAXVALUE 999999999999999999999999999 INCREMENT BY 1 START WITH 3017276 CACHE 20 NOORDER  NOCYCLE ;
 
 --
--- Type: SEQUENCE; Owner: SEARCHAPP; Name: PLUGIN_MODULE_SEQ
+-- Type: SEQUENCE; Owner: SEARCHAPP; Name: HIBERNATE_SEQUENCE
 --
-CREATE SEQUENCE  "SEARCHAPP"."PLUGIN_MODULE_SEQ"  MINVALUE 1 MAXVALUE 9999999999999999999999999999 INCREMENT BY 1 START WITH 1 CACHE 20 NOORDER  NOCYCLE ;
+CREATE SEQUENCE  "SEARCHAPP"."HIBERNATE_SEQUENCE"  MINVALUE 1 MAXVALUE 999999999999999999999999999 INCREMENT BY 1 START WITH 100442 CACHE 20 NOORDER  NOCYCLE ;
 
 --
--- Type: SEQUENCE; Owner: SEARCHAPP; Name: HIBERNATE_SEQUENCE
+-- Type: SEQUENCE; Owner: SEARCHAPP; Name: PLUGIN_SEQ
 --
-CREATE SEQUENCE  "SEARCHAPP"."HIBERNATE_SEQUENCE"  MINVALUE 1 MAXVALUE 999999999999999999999999999 INCREMENT BY 1 START WITH 100042 CACHE 20 NOORDER  NOCYCLE ;
+CREATE SEQUENCE  "SEARCHAPP"."PLUGIN_SEQ"  MINVALUE 1 MAXVALUE 9999999999999999999999999999 INCREMENT BY 1 START WITH 1 CACHE 20 NOORDER  NOCYCLE ;
 
diff --git a/ddl/oracle/searchapp/items.json b/ddl/oracle/searchapp/items.json
index 7f103372..482f8d1a 100644
--- a/ddl/oracle/searchapp/items.json
+++ b/ddl/oracle/searchapp/items.json
@@ -119,6 +119,17 @@
       "name" : "HIBERNATE_SEQUENCE"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "SEARCHAPP",
+      "name" : "IDX_SK_DISPLAY_CATEGORY1"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "SEARCHAPP",
+      "name" : "SEARCH_KEYWORD"
+    } ]
   }, {
     "child" : {
       "type" : "VIEW",
@@ -152,10 +163,6 @@
       "name" : "PATHWAY_GENES"
     },
     "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "BIOMART",
-      "name" : "BIO_MARKER_CORREL_MV"
-    }, {
       "type" : "TABLE",
       "owner" : "SEARCHAPP",
       "name" : "SEARCH_KEYWORD"
@@ -246,6 +253,17 @@
       "owner" : "SEARCHAPP",
       "name" : "SAVED_FACETED_SEARCH"
     } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "SEARCHAPP",
+      "name" : "SCH_KWD_DT_CAT_IDX"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "SEARCHAPP",
+      "name" : "SEARCH_KEYWORD"
+    } ]
   }, {
     "child" : {
       "type" : "REF_CONSTRAINT",
@@ -1194,6 +1212,13 @@
       "name" : "HIBERNATE_SEQUENCE"
     },
     "file" : "searchapp/_misc.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "SEARCHAPP",
+      "name" : "IDX_SK_DISPLAY_CATEGORY1"
+    },
+    "file" : "searchapp/search_keyword.sql"
   }, {
     "item" : {
       "type" : "VIEW",
@@ -1214,7 +1239,7 @@
       "owner" : "SEARCHAPP",
       "name" : "PATHWAY_GENES"
     },
-    "file" : "searchapp/_cross.sql"
+    "file" : "searchapp/views/pathway_genes.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -1285,6 +1310,13 @@
       "name" : "SAVED_FACETED_SEARCH_USER_ID"
     },
     "file" : "searchapp/saved_faceted_search.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "SEARCHAPP",
+      "name" : "SCH_KWD_DT_CAT_IDX"
+    },
+    "file" : "searchapp/search_keyword.sql"
   }, {
     "item" : {
       "type" : "REF_CONSTRAINT",
diff --git a/ddl/oracle/searchapp/saved_faceted_search.sql b/ddl/oracle/searchapp/saved_faceted_search.sql
index 4cddba44..1fed4cc1 100644
--- a/ddl/oracle/searchapp/saved_faceted_search.sql
+++ b/ddl/oracle/searchapp/saved_faceted_search.sql
@@ -1,8 +1,3 @@
---
--- Type: SEQUENCE; Owner: SEARCHAPP; Name: SEQ_SAVED_FACETED_SEARCH_ID
---
-CREATE SEQUENCE  "SEARCHAPP"."SEQ_SAVED_FACETED_SEARCH_ID"  MINVALUE 1 MAXVALUE 9999999999999999999999999999 INCREMENT BY 1 START WITH 278 CACHE 20 NOORDER  NOCYCLE ;
-
 --
 -- Type: TABLE; Owner: SEARCHAPP; Name: SAVED_FACETED_SEARCH
 --
@@ -25,20 +20,10 @@ CREATE SEQUENCE  "SEARCHAPP"."SEQ_SAVED_FACETED_SEARCH_ID"  MINVALUE 1 MAXVALUE
  TABLESPACE "TRANSMART" ;
 
 --
--- Type: TRIGGER; Owner: SEARCHAPP; Name: TRG_UPD_SAVED_FACETED_SEARCH
+-- Type: SEQUENCE; Owner: SEARCHAPP; Name: SEQ_SAVED_FACETED_SEARCH_ID
 --
-  CREATE OR REPLACE TRIGGER "SEARCHAPP"."TRG_UPD_SAVED_FACETED_SEARCH" 
-before insert on searchapp.saved_faceted_search
-for each row begin
-       	if inserting then
-               	if :NEW.modified_dt is null then
-                       	:NEW.modified_dt := sysdate;
-               	end if;
-       	end if;
-end;
-/
-ALTER TRIGGER "SEARCHAPP"."TRG_UPD_SAVED_FACETED_SEARCH" ENABLE;
- 
+CREATE SEQUENCE  "SEARCHAPP"."SEQ_SAVED_FACETED_SEARCH_ID"  MINVALUE 1 MAXVALUE 9999999999999999999999999999 INCREMENT BY 1 START WITH 278 CACHE 20 NOORDER  NOCYCLE ;
+
 --
 -- Type: TRIGGER; Owner: SEARCHAPP; Name: TRG_SAVED_FACETED_SEARCH_ID
 --
@@ -60,3 +45,18 @@ ALTER TRIGGER "SEARCHAPP"."TRG_SAVED_FACETED_SEARCH_ID" ENABLE;
 ALTER TABLE "SEARCHAPP"."SAVED_FACETED_SEARCH" ADD CONSTRAINT "SAVED_FACETED_SEARCH_USER_ID" FOREIGN KEY ("USER_ID")
  REFERENCES "SEARCHAPP"."SEARCH_AUTH_USER" ("ID") ENABLE;
 
+--
+-- Type: TRIGGER; Owner: SEARCHAPP; Name: TRG_UPD_SAVED_FACETED_SEARCH
+--
+  CREATE OR REPLACE TRIGGER "SEARCHAPP"."TRG_UPD_SAVED_FACETED_SEARCH" 
+before insert on searchapp.saved_faceted_search
+for each row begin
+       	if inserting then
+               	if :NEW.modified_dt is null then
+                       	NEW.modified_dt = sysdate;
+               	end if;
+       	end if;
+end;
+/
+ALTER TRIGGER "SEARCHAPP"."TRG_UPD_SAVED_FACETED_SEARCH" ENABLE;
+ 
diff --git a/ddl/oracle/searchapp/search_auth_principal.sql b/ddl/oracle/searchapp/search_auth_principal.sql
index f90ecad7..7886b69a 100644
--- a/ddl/oracle/searchapp/search_auth_principal.sql
+++ b/ddl/oracle/searchapp/search_auth_principal.sql
@@ -14,5 +14,24 @@
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
   ) SEGMENT CREATION IMMEDIATE
- TABLESPACE "TRANSMART" ; 
+ TABLESPACE "TRANSMART" ;
 
+--
+-- Type: TRIGGER; Owner: SEARCHAPP; Name: TRG_SEARCH_AU_PRCPL_ID
+--
+  CREATE OR REPLACE TRIGGER "SEARCHAPP"."TRG_SEARCH_AU_PRCPL_ID" 
+ before insert on SEARCH_AUTH_PRINCIPAL   
+ for each row begin     
+ if inserting then      
+ if(:NEW.ID is null or :NEW.ID = -2000) then       
+ select SEQ_SEARCH_DATA_ID.nextval into :NEW.ID from dual;      
+ end if;    end if; end;
+
+
+
+
+
+
+/
+ALTER TRIGGER "SEARCHAPP"."TRG_SEARCH_AU_PRCPL_ID" ENABLE;
+ 
diff --git a/ddl/oracle/searchapp/search_auth_sec_object_access.sql b/ddl/oracle/searchapp/search_auth_sec_object_access.sql
index 31759d86..8f86e156 100644
--- a/ddl/oracle/searchapp/search_auth_sec_object_access.sql
+++ b/ddl/oracle/searchapp/search_auth_sec_object_access.sql
@@ -12,18 +12,24 @@
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
---
--- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: SCH_SEC_S_A_L_FK
---
-ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_SEC_OBJECT_ACCESS" ADD CONSTRAINT "SCH_SEC_S_A_L_FK" FOREIGN KEY ("SECURE_ACCESS_LEVEL_ID")
- REFERENCES "SEARCHAPP"."SEARCH_SEC_ACCESS_LEVEL" ("SEARCH_SEC_ACCESS_LEVEL_ID") ENABLE;
-
 --
 -- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: SCH_SEC_S_O_FK
 --
 ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_SEC_OBJECT_ACCESS" ADD CONSTRAINT "SCH_SEC_S_O_FK" FOREIGN KEY ("SECURE_OBJECT_ID")
  REFERENCES "SEARCHAPP"."SEARCH_SECURE_OBJECT" ("SEARCH_SECURE_OBJECT_ID") ENABLE;
 
+--
+-- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: SCH_SEC_A_U_FK
+--
+ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_SEC_OBJECT_ACCESS" ADD CONSTRAINT "SCH_SEC_A_U_FK" FOREIGN KEY ("AUTH_PRINCIPAL_ID")
+ REFERENCES "SEARCHAPP"."SEARCH_AUTH_PRINCIPAL" ("ID") ENABLE;
+
+--
+-- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: SCH_SEC_S_A_L_FK
+--
+ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_SEC_OBJECT_ACCESS" ADD CONSTRAINT "SCH_SEC_S_A_L_FK" FOREIGN KEY ("SECURE_ACCESS_LEVEL_ID")
+ REFERENCES "SEARCHAPP"."SEARCH_SEC_ACCESS_LEVEL" ("SEARCH_SEC_ACCESS_LEVEL_ID") ENABLE;
+
 --
 -- Type: TRIGGER; Owner: SEARCHAPP; Name: TRG_SEARCH_AU_OBJ_ACCESS_ID
 --
@@ -37,9 +43,3 @@ ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_SEC_OBJECT_ACCESS" ADD CONSTRAINT "SCH_SEC_
 /
 ALTER TRIGGER "SEARCHAPP"."TRG_SEARCH_AU_OBJ_ACCESS_ID" ENABLE;
  
---
--- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: SCH_SEC_A_U_FK
---
-ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_SEC_OBJECT_ACCESS" ADD CONSTRAINT "SCH_SEC_A_U_FK" FOREIGN KEY ("AUTH_PRINCIPAL_ID")
- REFERENCES "SEARCHAPP"."SEARCH_AUTH_PRINCIPAL" ("ID") ENABLE;
-
diff --git a/ddl/oracle/searchapp/search_auth_user_sec_access.sql b/ddl/oracle/searchapp/search_auth_user_sec_access.sql
index 7c4249a2..3b4c7372 100644
--- a/ddl/oracle/searchapp/search_auth_user_sec_access.sql
+++ b/ddl/oracle/searchapp/search_auth_user_sec_access.sql
@@ -18,6 +18,12 @@
 ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_USER_SEC_ACCESS" ADD CONSTRAINT "SEARCH_SEC_S_A_L_FK" FOREIGN KEY ("SEARCH_SEC_ACCESS_LEVEL_ID")
  REFERENCES "SEARCHAPP"."SEARCH_SEC_ACCESS_LEVEL" ("SEARCH_SEC_ACCESS_LEVEL_ID") ENABLE;
 
+--
+-- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: SEARCH_SEC_S_O_FK
+--
+ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_USER_SEC_ACCESS" ADD CONSTRAINT "SEARCH_SEC_S_O_FK" FOREIGN KEY ("SEARCH_SECURE_OBJECT_ID")
+ REFERENCES "SEARCHAPP"."SEARCH_SECURE_OBJECT" ("SEARCH_SECURE_OBJECT_ID") ENABLE;
+
 --
 -- Type: TRIGGER; Owner: SEARCHAPP; Name: TRG_SEARCH_A_U_SEC_ACCESS_ID
 --
@@ -35,12 +41,6 @@ ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_USER_SEC_ACCESS" ADD CONSTRAINT "SEARCH_SEC
 /
 ALTER TRIGGER "SEARCHAPP"."TRG_SEARCH_A_U_SEC_ACCESS_ID" ENABLE;
  
---
--- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: SEARCH_SEC_S_O_FK
---
-ALTER TABLE "SEARCHAPP"."SEARCH_AUTH_USER_SEC_ACCESS" ADD CONSTRAINT "SEARCH_SEC_S_O_FK" FOREIGN KEY ("SEARCH_SECURE_OBJECT_ID")
- REFERENCES "SEARCHAPP"."SEARCH_SECURE_OBJECT" ("SEARCH_SECURE_OBJECT_ID") ENABLE;
-
 --
 -- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: SEARCH_SEC_A_U_FK
 --
diff --git a/ddl/oracle/searchapp/search_keyword.sql b/ddl/oracle/searchapp/search_keyword.sql
index c6f52058..a0b1cd35 100644
--- a/ddl/oracle/searchapp/search_keyword.sql
+++ b/ddl/oracle/searchapp/search_keyword.sql
@@ -19,6 +19,18 @@
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: INDEX; Owner: SEARCHAPP; Name: SCH_KWD_DT_CAT_IDX
+--
+CREATE INDEX "SEARCHAPP"."SCH_KWD_DT_CAT_IDX" ON "SEARCHAPP"."SEARCH_KEYWORD" ("DATA_CATEGORY")
+TABLESPACE "INDX" ;
+
+--
+-- Type: INDEX; Owner: SEARCHAPP; Name: IDX_SK_DISPLAY_CATEGORY1
+--
+CREATE BITMAP INDEX "SEARCHAPP"."IDX_SK_DISPLAY_CATEGORY1" ON "SEARCHAPP"."SEARCH_KEYWORD" ("DATA_CATEGORY", "DISPLAY_DATA_CATEGORY")
+TABLESPACE "INDX" 
+PARALLEL ;
 --
 -- Type: INDEX; Owner: SEARCHAPP; Name: SEARCH_KEYWORD_INDEX3
 --
diff --git a/ddl/oracle/searchapp/search_keyword_term.sql b/ddl/oracle/searchapp/search_keyword_term.sql
index 940c1d80..a4f5c9fd 100644
--- a/ddl/oracle/searchapp/search_keyword_term.sql
+++ b/ddl/oracle/searchapp/search_keyword_term.sql
@@ -14,6 +14,12 @@
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: INDEX; Owner: SEARCHAPP; Name: SEARCH_KW_TERM_SKID_IDX
+--
+CREATE INDEX "SEARCHAPP"."SEARCH_KW_TERM_SKID_IDX" ON "SEARCHAPP"."SEARCH_KEYWORD_TERM" ("SEARCH_KEYWORD_ID")
+TABLESPACE "TRANSMART" ;
+
 --
 -- Type: TRIGGER; Owner: SEARCHAPP; Name: TRG_SEARCH_KEYWORD_TERM_ID
 --
@@ -29,12 +35,6 @@
 /
 ALTER TRIGGER "SEARCHAPP"."TRG_SEARCH_KEYWORD_TERM_ID" ENABLE;
  
---
--- Type: INDEX; Owner: SEARCHAPP; Name: SEARCH_KW_TERM_SKID_IDX
---
-CREATE INDEX "SEARCHAPP"."SEARCH_KW_TERM_SKID_IDX" ON "SEARCHAPP"."SEARCH_KEYWORD_TERM" ("SEARCH_KEYWORD_ID")
-TABLESPACE "TRANSMART" ;
-
 --
 -- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: SEARCH_KW_FK
 --
diff --git a/ddl/oracle/searchapp/search_taxonomy.sql b/ddl/oracle/searchapp/search_taxonomy.sql
index ca3591cd..05448a2e 100644
--- a/ddl/oracle/searchapp/search_taxonomy.sql
+++ b/ddl/oracle/searchapp/search_taxonomy.sql
@@ -10,15 +10,17 @@
  CONSTRAINT "SEARCH_TAXONOMY_PK" PRIMARY KEY ("TERM_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+
 --
 -- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: FK_SEARCH_TAX_SEARCH_KEYWORD
 --
 ALTER TABLE "SEARCHAPP"."SEARCH_TAXONOMY" ADD CONSTRAINT "FK_SEARCH_TAX_SEARCH_KEYWORD" FOREIGN KEY ("SEARCH_KEYWORD_ID")
  REFERENCES "SEARCHAPP"."SEARCH_KEYWORD" ("SEARCH_KEYWORD_ID") ENABLE;
 
+
 --
 -- Type: TRIGGER; Owner: SEARCHAPP; Name: TRG_SEARCH_TAXONOMY_TERM_ID
 --
diff --git a/ddl/oracle/searchapp/search_taxonomy_rels.sql b/ddl/oracle/searchapp/search_taxonomy_rels.sql
index 5621819f..c75b8800 100644
--- a/ddl/oracle/searchapp/search_taxonomy_rels.sql
+++ b/ddl/oracle/searchapp/search_taxonomy_rels.sql
@@ -11,9 +11,21 @@
  CONSTRAINT "U_CHILD_ID_PARENT_ID" UNIQUE ("CHILD_ID", "PARENT_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: FK_SEARCH_TAX_RELS_PARENT
+--
+ALTER TABLE "SEARCHAPP"."SEARCH_TAXONOMY_RELS" ADD CONSTRAINT "FK_SEARCH_TAX_RELS_PARENT" FOREIGN KEY ("PARENT_ID")
+ REFERENCES "SEARCHAPP"."SEARCH_TAXONOMY" ("TERM_ID") ENABLE;
+
+--
+-- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: FK_SEARCH_TAX_RELS_CHILD
+--
+ALTER TABLE "SEARCHAPP"."SEARCH_TAXONOMY_RELS" ADD CONSTRAINT "FK_SEARCH_TAX_RELS_CHILD" FOREIGN KEY ("CHILD_ID")
+ REFERENCES "SEARCHAPP"."SEARCH_TAXONOMY" ("TERM_ID") ENABLE;
+
 --
 -- Type: TRIGGER; Owner: SEARCHAPP; Name: TRG_SEARCH_TAXONOMY_RELS_ID
 --
@@ -29,15 +41,3 @@ end;
 /
 ALTER TRIGGER "SEARCHAPP"."TRG_SEARCH_TAXONOMY_RELS_ID" ENABLE;
  
---
--- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: FK_SEARCH_TAX_RELS_PARENT
---
-ALTER TABLE "SEARCHAPP"."SEARCH_TAXONOMY_RELS" ADD CONSTRAINT "FK_SEARCH_TAX_RELS_PARENT" FOREIGN KEY ("PARENT_ID")
- REFERENCES "SEARCHAPP"."SEARCH_TAXONOMY" ("TERM_ID") ENABLE;
-
---
--- Type: REF_CONSTRAINT; Owner: SEARCHAPP; Name: FK_SEARCH_TAX_RELS_CHILD
---
-ALTER TABLE "SEARCHAPP"."SEARCH_TAXONOMY_RELS" ADD CONSTRAINT "FK_SEARCH_TAX_RELS_CHILD" FOREIGN KEY ("CHILD_ID")
- REFERENCES "SEARCHAPP"."SEARCH_TAXONOMY" ("TERM_ID") ENABLE;
-
diff --git a/ddl/oracle/searchapp/views/pathway_genes.sql b/ddl/oracle/searchapp/views/pathway_genes.sql
new file mode 100644
index 00000000..a28693eb
--- /dev/null
+++ b/ddl/oracle/searchapp/views/pathway_genes.sql
@@ -0,0 +1,11 @@
+--
+-- Type: VIEW; Owner: SEARCHAPP; Name: PATHWAY_GENES
+--
+  CREATE OR REPLACE FORCE EDITIONABLE VIEW "SEARCHAPP"."PATHWAY_GENES" ("GENE_KEYWORD_ID", "PATHWAY_KEYWORD_ID", "GENE_BIOMARKER_ID") AS 
+  SELECT k_gene.search_keyword_id AS gene_keyword_id,
+  k_pathway.search_keyword_id AS pathway_keyword_id,
+  b.asso_bio_marker_id AS gene_biomarker_id
+ FROM searchapp.search_keyword k_pathway,
+  biomart.bio_marker_correl_mv b,
+  searchapp.search_keyword k_gene
+WHERE ((((((b.correl_type) = 'PATHWAY_GENE') AND (b.bio_marker_id = k_pathway.bio_data_id)) AND ((k_pathway.data_category) = 'PATHWAY')) AND (b.asso_bio_marker_id = k_gene.bio_data_id)) AND ((k_gene.data_category) = 'GENE'));
diff --git a/ddl/oracle/searchapp/views/search_bio_mkr_correl_fast_mv.sql b/ddl/oracle/searchapp/views/search_bio_mkr_correl_fast_mv.sql
index f13d4132..35d8c16c 100644
--- a/ddl/oracle/searchapp/views/search_bio_mkr_correl_fast_mv.sql
+++ b/ddl/oracle/searchapp/views/search_bio_mkr_correl_fast_mv.sql
@@ -2,7 +2,8 @@
 -- Type: MATERIALIZED_VIEW; Owner: SEARCHAPP; Name: SEARCH_BIO_MKR_CORREL_FAST_MV
 --
   CREATE MATERIALIZED VIEW "SEARCHAPP"."SEARCH_BIO_MKR_CORREL_FAST_MV" ("DOMAIN_OBJECT_ID", "ASSO_BIO_MARKER_ID", "CORREL_TYPE", "VALUE_METRIC", "MV_ID")
-  ORGANIZATION HEAP PCTFREE 10 PCTUSED 40 INITRANS 1 MAXTRANS 255 NOCOMPRESS NOLOGGING
+  ORGANIZATION HEAP PCTFREE 10 PCTUSED 40 INITRANS 1 MAXTRANS 255 
+ NOCOMPRESS NOLOGGING
   TABLESPACE "TRANSMART" 
   BUILD IMMEDIATE
   USING INDEX 

From 2dd60474c3f062bf3c05f33df038906b86c49e0a Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 11:11:00 +0100
Subject: [PATCH 25/31] deapp updates from oracle test server

---
 ddl/oracle/deapp/de_chromosomal_region.sql    |   2 +-
 ddl/oracle/deapp/de_encounter_level.sql       |   2 +-
 ddl/oracle/deapp/de_encounter_type.sql        |   2 +-
 ddl/oracle/deapp/de_gene_info.sql             |  46 ++++
 ddl/oracle/deapp/de_gene_source.sql           |  36 ++++
 ddl/oracle/deapp/de_rc_snp_info.sql           |   5 +-
 ddl/oracle/deapp/de_snp_calls_by_gsm.sql      |  11 +-
 ddl/oracle/deapp/de_snp_copy_number.sql       |  11 +-
 ddl/oracle/deapp/de_snp_gene_map.sql          |  12 ++
 ddl/oracle/deapp/de_subject_acgh_data.sql     |   4 +-
 .../deapp/de_subject_microarray_data.sql      |  37 ++--
 .../deapp/de_subject_microarray_data_new.sql  |   7 +-
 .../deapp/de_subject_microarray_logs.sql      |   4 +-
 ddl/oracle/deapp/de_subject_rnaseq_data.sql   |   4 +-
 .../deapp/de_subject_sample_mapping.sql       |   6 +
 ddl/oracle/deapp/de_variant_dataset.sql       |   3 +-
 ddl/oracle/deapp/de_variant_metadata.sql      |   3 +-
 .../deapp/de_variant_population_data.sql      |   4 +-
 .../deapp/de_variant_population_info.sql      |   4 +-
 .../deapp/de_variant_subject_detail.sql       |   9 +-
 ddl/oracle/deapp/de_variant_subject_idx.sql   |   2 +-
 .../deapp/de_variant_subject_summary.sql      |   2 +-
 ddl/oracle/deapp/items.json                   | 196 +++++++++++++++++-
 ddl/oracle/deapp/kegg_def.sql                 |   4 +-
 24 files changed, 356 insertions(+), 60 deletions(-)
 create mode 100644 ddl/oracle/deapp/de_gene_info.sql
 create mode 100644 ddl/oracle/deapp/de_gene_source.sql

diff --git a/ddl/oracle/deapp/de_chromosomal_region.sql b/ddl/oracle/deapp/de_chromosomal_region.sql
index 8803ee33..2903edff 100644
--- a/ddl/oracle/deapp/de_chromosomal_region.sql
+++ b/ddl/oracle/deapp/de_chromosomal_region.sql
@@ -16,7 +16,7 @@
  CONSTRAINT "DE_CHROMOSOMAL_REGION_PKEY" PRIMARY KEY ("REGION_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
diff --git a/ddl/oracle/deapp/de_encounter_level.sql b/ddl/oracle/deapp/de_encounter_level.sql
index 4b7fa431..fd84d35f 100644
--- a/ddl/oracle/deapp/de_encounter_level.sql
+++ b/ddl/oracle/deapp/de_encounter_level.sql
@@ -5,6 +5,6 @@
   (	"STUDY_ID" VARCHAR2(50 BYTE), 
 "CONCEPT_ID" VARCHAR2(500 BYTE), 
 "LINK_TYPE" VARCHAR2(50 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/deapp/de_encounter_type.sql b/ddl/oracle/deapp/de_encounter_type.sql
index 3704d88a..886248c5 100644
--- a/ddl/oracle/deapp/de_encounter_type.sql
+++ b/ddl/oracle/deapp/de_encounter_type.sql
@@ -6,6 +6,6 @@
 "LINK_TYPE" VARCHAR2(50 BYTE), 
 "LINK_VALUE" VARCHAR2(200 BYTE), 
 "ENCOUNTER_NUM" NUMBER(38,0)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/deapp/de_gene_info.sql b/ddl/oracle/deapp/de_gene_info.sql
new file mode 100644
index 00000000..59269241
--- /dev/null
+++ b/ddl/oracle/deapp/de_gene_info.sql
@@ -0,0 +1,46 @@
+--
+-- Type: TABLE; Owner: DEAPP; Name: DE_GENE_INFO
+--
+ CREATE TABLE "DEAPP"."DE_GENE_INFO" 
+  (	"GENE_INFO_ID" NUMBER(22,0), 
+"GENE_SOURCE_ID" NUMBER(5,0) NOT NULL ENABLE, 
+"ENTREZ_ID" NUMBER(10,0), 
+"GENE_SYMBOL" VARCHAR2(255 BYTE) NOT NULL ENABLE, 
+"GENE_NAME" VARCHAR2(255 BYTE), 
+"CHROM" VARCHAR2(16 BYTE) NOT NULL ENABLE, 
+"CHROM_START" NUMBER, 
+"CHROM_STOP" NUMBER, 
+"STRAND" NUMBER(2,0), 
+ UNIQUE ("GENE_SOURCE_ID", "GENE_SYMBOL")
+ USING INDEX
+ TABLESPACE "TRANSMART"  ENABLE, 
+ PRIMARY KEY ("GENE_INFO_ID")
+ USING INDEX
+ TABLESPACE "TRANSMART"  ENABLE
+  ) SEGMENT CREATION IMMEDIATE
+NOCOMPRESS NOLOGGING
+ TABLESPACE "TRANSMART" ;
+
+--
+-- Type: REF_CONSTRAINT; Owner: DEAPP; Name: SYS_C0029766
+--
+ALTER TABLE "DEAPP"."DE_GENE_INFO" ADD FOREIGN KEY ("GENE_SOURCE_ID")
+ REFERENCES "DEAPP"."DE_GENE_SOURCE" ("GENE_SOURCE_ID") ON DELETE CASCADE ENABLE;
+
+--
+-- Type: TRIGGER; Owner: DEAPP; Name: TRG_DE_GENE_INFO_ID
+--
+  CREATE OR REPLACE TRIGGER "DEAPP"."TRG_DE_GENE_INFO_ID" 
+BEFORE
+  INSERT ON DEAPP.DE_GENE_INFO FOR EACH ROW
+BEGIN
+  IF inserting THEN
+    IF :NEW.GENE_INFO_ID IS NULL THEN
+        SELECT DEAPP.SEQ_GENE_INFO_ID.nextval INTO :NEW.GENE_INFO_ID FROM dual;
+    END IF;
+  END IF;
+END;
+
+/
+ALTER TRIGGER "DEAPP"."TRG_DE_GENE_INFO_ID" ENABLE;
+ 
diff --git a/ddl/oracle/deapp/de_gene_source.sql b/ddl/oracle/deapp/de_gene_source.sql
new file mode 100644
index 00000000..68b01ad6
--- /dev/null
+++ b/ddl/oracle/deapp/de_gene_source.sql
@@ -0,0 +1,36 @@
+--
+-- Type: TABLE; Owner: DEAPP; Name: DE_GENE_SOURCE
+--
+ CREATE TABLE "DEAPP"."DE_GENE_SOURCE" 
+  (	"GENE_SOURCE_ID" NUMBER(5,0), 
+"GENE_SOURCE_NAME" VARCHAR2(255 BYTE) NOT NULL ENABLE, 
+"VERSION" VARCHAR2(32 BYTE), 
+"RELEASE_DATE" DATE, 
+"URL" VARCHAR2(255 BYTE), 
+ UNIQUE ("GENE_SOURCE_NAME")
+ USING INDEX
+ TABLESPACE "TRANSMART"  ENABLE, 
+ PRIMARY KEY ("GENE_SOURCE_ID")
+ USING INDEX
+ TABLESPACE "TRANSMART"  ENABLE
+  ) SEGMENT CREATION IMMEDIATE
+NOCOMPRESS NOLOGGING
+ TABLESPACE "TRANSMART" ;
+
+--
+-- Type: TRIGGER; Owner: DEAPP; Name: TRG_DE_GENE_SOURCE_ID
+--
+  CREATE OR REPLACE TRIGGER "DEAPP"."TRG_DE_GENE_SOURCE_ID" 
+BEFORE
+  INSERT ON DEAPP.DE_GENE_SOURCE FOR EACH ROW
+BEGIN
+  IF inserting THEN
+    IF :NEW.GENE_SOURCE_ID IS NULL THEN
+        SELECT DEAPP.SEQ_GENE_SOURCE_ID.nextval INTO :NEW.GENE_SOURCE_ID FROM dual;
+    END IF;
+  END IF;
+END;
+
+/
+ALTER TRIGGER "DEAPP"."TRG_DE_GENE_SOURCE_ID" ENABLE;
+ 
diff --git a/ddl/oracle/deapp/de_rc_snp_info.sql b/ddl/oracle/deapp/de_rc_snp_info.sql
index 7b824371..7e24d62c 100644
--- a/ddl/oracle/deapp/de_rc_snp_info.sql
+++ b/ddl/oracle/deapp/de_rc_snp_info.sql
@@ -32,8 +32,9 @@ CREATE SEQUENCE  "DEAPP"."DE_RC_SNP_INFO_SEQ"  MINVALUE 1 MAXVALUE 9999999999999
 "ENTREZ_ID" VARCHAR2(50 BYTE), 
 "RECOMBINATION_RATE" NUMBER(18,6), 
 "RECOMBINATION_MAP" NUMBER(18,6), 
-"REGULOME_SCORE" VARCHAR2(10 BYTE)
-  ) SEGMENT CREATION DEFERRED
+"REGULOME_SCORE" VARCHAR2(10 BYTE), 
+"EXON_INTRON" VARCHAR2(10 BYTE)
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
diff --git a/ddl/oracle/deapp/de_snp_calls_by_gsm.sql b/ddl/oracle/deapp/de_snp_calls_by_gsm.sql
index a2eb6419..b93298cd 100644
--- a/ddl/oracle/deapp/de_snp_calls_by_gsm.sql
+++ b/ddl/oracle/deapp/de_snp_calls_by_gsm.sql
@@ -9,15 +9,14 @@
 "SNP_CALLS" VARCHAR2(4 BYTE)
   )
  TABLESPACE "TRANSMART" 
- PARTITION BY LIST ("PATIENT_NUM") 
-(PARTITION "NULL_PARTITION"  VALUES (NULL)
- TABLESPACE "TRANSMART" NOCOMPRESS ) ;
-
+ PARTITION BY HASH ("PATIENT_NUM") 
+(PARTITION "SYS_P387" SEGMENT CREATION DEFERRED 
+ TABLESPACE "TRANSMART" 
+NOCOMPRESS ) ;
 --
 -- Type: INDEX; Owner: DEAPP; Name: IDX_SNP_CALLS_BY_GSM_PG
 --
  CREATE BITMAP INDEX "DEAPP"."IDX_SNP_CALLS_BY_GSM_PG" ON "DEAPP"."DE_SNP_CALLS_BY_GSM" ("PATIENT_NUM", "GSM_NUM") 
  LOCAL
-(PARTITION "NULL_PARTITION"
+(PARTITION "SYS_P388" 
  TABLESPACE "TRANSMART" ) ;
-
diff --git a/ddl/oracle/deapp/de_snp_copy_number.sql b/ddl/oracle/deapp/de_snp_copy_number.sql
index 75a8ece5..c41475b8 100644
--- a/ddl/oracle/deapp/de_snp_copy_number.sql
+++ b/ddl/oracle/deapp/de_snp_copy_number.sql
@@ -10,15 +10,14 @@
 "COPY_NUMBER" NUMBER(2,0)
   )
  TABLESPACE "TRANSMART" 
- PARTITION BY LIST ("PATIENT_NUM") 
-(PARTITION "NULL_PARTITION"  VALUES (NULL)
- TABLESPACE "TRANSMART" NOCOMPRESS ) ;
-
+ PARTITION BY HASH ("PATIENT_NUM") 
+(PARTITION "SYS_P389" SEGMENT CREATION DEFERRED 
+ TABLESPACE "TRANSMART" 
+NOCOMPRESS ) ;
 --
 -- Type: INDEX; Owner: DEAPP; Name: IDX_SNP_COPY_NUMBER_PS
 --
  CREATE BITMAP INDEX "DEAPP"."IDX_SNP_COPY_NUMBER_PS" ON "DEAPP"."DE_SNP_COPY_NUMBER" ("PATIENT_NUM", "SNP_NAME") 
  LOCAL
-(PARTITION "NULL_PARTITION"
+(PARTITION "SYS_P390" 
  TABLESPACE "TRANSMART" ) ;
-
diff --git a/ddl/oracle/deapp/de_snp_gene_map.sql b/ddl/oracle/deapp/de_snp_gene_map.sql
index 35486282..93dfa165 100644
--- a/ddl/oracle/deapp/de_snp_gene_map.sql
+++ b/ddl/oracle/deapp/de_snp_gene_map.sql
@@ -8,6 +8,18 @@
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: INDEX; Owner: DEAPP; Name: SNP_NAME_IDX1
+--
+CREATE INDEX "DEAPP"."SNP_NAME_IDX1" ON "DEAPP"."DE_SNP_GENE_MAP" ("SNP_NAME")
+TABLESPACE "INDX" ;
+
+--
+-- Type: INDEX; Owner: DEAPP; Name: ENTREZ_IDX1
+--
+CREATE INDEX "DEAPP"."ENTREZ_IDX1" ON "DEAPP"."DE_SNP_GENE_MAP" ("ENTREZ_GENE_ID")
+TABLESPACE "INDX" ;
+
 --
 -- Type: REF_CONSTRAINT; Owner: DEAPP; Name: FK_SNP_GENE_MAP_SNP_ID
 --
diff --git a/ddl/oracle/deapp/de_subject_acgh_data.sql b/ddl/oracle/deapp/de_subject_acgh_data.sql
index 718403b1..4191eb8c 100644
--- a/ddl/oracle/deapp/de_subject_acgh_data.sql
+++ b/ddl/oracle/deapp/de_subject_acgh_data.sql
@@ -13,11 +13,11 @@
 "PROBNORM" FLOAT(126), 
 "PROBGAIN" FLOAT(126), 
 "PROBAMP" FLOAT(126), 
-"PARTITION_ID" NUMBER(*,0), 
+"TRIAL_SOURCE" VARCHAR2(200 BYTE), 
  CONSTRAINT "DE_SUBJECT_ACGH_DATA_PKEY" PRIMARY KEY ("ASSAY_ID", "REGION_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
diff --git a/ddl/oracle/deapp/de_subject_microarray_data.sql b/ddl/oracle/deapp/de_subject_microarray_data.sql
index f83e25bb..69670298 100644
--- a/ddl/oracle/deapp/de_subject_microarray_data.sql
+++ b/ddl/oracle/deapp/de_subject_microarray_data.sql
@@ -15,25 +15,36 @@
 "NEW_LOG" NUMBER(18,4), 
 "NEW_ZSCORE" NUMBER(18,4), 
 "TRIAL_SOURCE" VARCHAR2(200 BYTE)
-  )
- TABLESPACE "TRANSMART" 
- PARTITION BY LIST ("TRIAL_NAME") 
-(PARTITION "NULL_PARTITION"  VALUES (NULL)
- TABLESPACE "TRANSMART" NOCOMPRESS ) ;
+  ) SEGMENT CREATION IMMEDIATE
+ TABLESPACE "TRANSMART" ;
+
+--
+-- Type: INDEX; Owner: DEAPP; Name: DE_MICROARRAY_DATA_IDX5
+--
+CREATE INDEX "DEAPP"."DE_MICROARRAY_DATA_IDX5" ON "DEAPP"."DE_SUBJECT_MICROARRAY_DATA" ("TRIAL_SOURCE")
+TABLESPACE "INDX" ;
 
 --
 -- Type: INDEX; Owner: DEAPP; Name: DE_MICROARRAY_DATA_IDX1
 --
- CREATE INDEX "DEAPP"."DE_MICROARRAY_DATA_IDX1" ON "DEAPP"."DE_SUBJECT_MICROARRAY_DATA" ("PROBESET_ID")
- TABLESPACE "INDX"  LOCAL
-(PARTITION "NULL_PARTITION"
- TABLESPACE "INDX" ) COMPRESS 1 ;
+CREATE INDEX "DEAPP"."DE_MICROARRAY_DATA_IDX1" ON "DEAPP"."DE_SUBJECT_MICROARRAY_DATA" ("TRIAL_NAME", "ASSAY_ID", "PROBESET_ID")
+TABLESPACE "INDX" ;
 
 --
 -- Type: INDEX; Owner: DEAPP; Name: DE_MICROARRAY_DATA_IDX2
 --
- CREATE INDEX "DEAPP"."DE_MICROARRAY_DATA_IDX2" ON "DEAPP"."DE_SUBJECT_MICROARRAY_DATA" ("ASSAY_ID")
- TABLESPACE "INDX"  LOCAL
-(PARTITION "NULL_PARTITION"
- TABLESPACE "INDX" ) COMPRESS 1 ;
+CREATE INDEX "DEAPP"."DE_MICROARRAY_DATA_IDX2" ON "DEAPP"."DE_SUBJECT_MICROARRAY_DATA" ("ASSAY_ID", "PROBESET_ID")
+TABLESPACE "INDX" ;
+
+--
+-- Type: INDEX; Owner: DEAPP; Name: DE_MICROARRAY_DATA_IDX3
+--
+CREATE BITMAP INDEX "DEAPP"."DE_MICROARRAY_DATA_IDX3" ON "DEAPP"."DE_SUBJECT_MICROARRAY_DATA" ("ASSAY_ID")
+TABLESPACE "INDX" ;
+
+--
+-- Type: INDEX; Owner: DEAPP; Name: DE_MICROARRAY_DATA_IDX4
+--
+CREATE BITMAP INDEX "DEAPP"."DE_MICROARRAY_DATA_IDX4" ON "DEAPP"."DE_SUBJECT_MICROARRAY_DATA" ("PROBESET_ID")
+TABLESPACE "INDX" ;
 
diff --git a/ddl/oracle/deapp/de_subject_microarray_data_new.sql b/ddl/oracle/deapp/de_subject_microarray_data_new.sql
index 51715954..207c31a1 100644
--- a/ddl/oracle/deapp/de_subject_microarray_data_new.sql
+++ b/ddl/oracle/deapp/de_subject_microarray_data_new.sql
@@ -10,9 +10,6 @@
 "RAW_INTENSITY" NUMBER(18,4), 
 "LOG_INTENSITY" NUMBER(18,4), 
 "ZSCORE" NUMBER(18,4)
-  )
- TABLESPACE "TRANSMART" 
- PARTITION BY LIST ("TRIAL_SOURCE") 
-(PARTITION "NULL_PARTITION"  VALUES (NULL)
- TABLESPACE "TRANSMART" NOCOMPRESS ) ;
+  ) SEGMENT CREATION DEFERRED
+ TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/deapp/de_subject_microarray_logs.sql b/ddl/oracle/deapp/de_subject_microarray_logs.sql
index 70588ff7..50364204 100644
--- a/ddl/oracle/deapp/de_subject_microarray_logs.sql
+++ b/ddl/oracle/deapp/de_subject_microarray_logs.sql
@@ -14,5 +14,5 @@
 "TIMEPOINT" VARCHAR2(30 BYTE), 
 "LOG_INTENSITY" NUMBER
   ) SEGMENT CREATION IMMEDIATE
- TABLESPACE "TRANSMART" ;
-
+NOCOMPRESS LOGGING
+ TABLESPACE "DEAPP" ;
diff --git a/ddl/oracle/deapp/de_subject_rnaseq_data.sql b/ddl/oracle/deapp/de_subject_rnaseq_data.sql
index 73510b97..2cec5296 100644
--- a/ddl/oracle/deapp/de_subject_rnaseq_data.sql
+++ b/ddl/oracle/deapp/de_subject_rnaseq_data.sql
@@ -7,11 +7,11 @@
 "ASSAY_ID" NUMBER NOT NULL ENABLE, 
 "PATIENT_ID" NUMBER, 
 "READCOUNT" NUMBER, 
-"PARTITION_ID" NUMBER, 
+"TRIAL_SOURCE" VARCHAR2(200 BYTE), 
  CONSTRAINT "DE_SUBJECT_RNASEQ_DATA_PKEY" PRIMARY KEY ("ASSAY_ID", "REGION_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
diff --git a/ddl/oracle/deapp/de_subject_sample_mapping.sql b/ddl/oracle/deapp/de_subject_sample_mapping.sql
index bac4719e..45b7c75b 100644
--- a/ddl/oracle/deapp/de_subject_sample_mapping.sql
+++ b/ddl/oracle/deapp/de_subject_sample_mapping.sql
@@ -32,6 +32,12 @@
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: INDEX; Owner: DEAPP; Name: IDX_DE_SUBJ_SMPL_TRIAL_CCODE
+--
+CREATE INDEX "DEAPP"."IDX_DE_SUBJ_SMPL_TRIAL_CCODE" ON "DEAPP"."DE_SUBJECT_SAMPLE_MAPPING" ("TRIAL_NAME", "CONCEPT_CODE")
+TABLESPACE "TRANSMART" ;
+
 --
 -- Type: INDEX; Owner: DEAPP; Name: DE_SUBJECT_SMPL_MPNG_IDX3
 --
diff --git a/ddl/oracle/deapp/de_variant_dataset.sql b/ddl/oracle/deapp/de_variant_dataset.sql
index c0d73fc1..6b39481d 100644
--- a/ddl/oracle/deapp/de_variant_dataset.sql
+++ b/ddl/oracle/deapp/de_variant_dataset.sql
@@ -13,12 +13,11 @@
  CONSTRAINT "DATASET_ID" PRIMARY KEY ("DATASET_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" 
 LOB ("METADATA_COMMENT") STORE AS BASICFILE (
  TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 RETENTION 
  NOCACHE LOGGING ) ;
-
 --
 -- Type: REF_CONSTRAINT; Owner: DEAPP; Name: GPL_ID
 --
diff --git a/ddl/oracle/deapp/de_variant_metadata.sql b/ddl/oracle/deapp/de_variant_metadata.sql
index 97d50ba2..181b0212 100644
--- a/ddl/oracle/deapp/de_variant_metadata.sql
+++ b/ddl/oracle/deapp/de_variant_metadata.sql
@@ -9,12 +9,11 @@
  CONSTRAINT "DE_VARIANT_METADATA_PK" PRIMARY KEY ("DE_VARIANT_METADATA_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" 
 LOB ("VALUE") STORE AS BASICFILE (
  TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 RETENTION 
  NOCACHE LOGGING ) ;
-
 --
 -- Type: REF_CONSTRAINT; Owner: DEAPP; Name: VAR_MET_DATASET_ID
 --
diff --git a/ddl/oracle/deapp/de_variant_population_data.sql b/ddl/oracle/deapp/de_variant_population_data.sql
index be3676e0..4ce00392 100644
--- a/ddl/oracle/deapp/de_variant_population_data.sql
+++ b/ddl/oracle/deapp/de_variant_population_data.sql
@@ -14,7 +14,7 @@
  CONSTRAINT "DE_VAR_POPULAT_DATA_ID_IDX" PRIMARY KEY ("VARIANT_POPULATION_DATA_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
@@ -42,4 +42,4 @@ for each row begin
 end;
 /
 ALTER TRIGGER "DEAPP"."TRG_DE_VARIANT_PD_ID" ENABLE;
-
+ 
diff --git a/ddl/oracle/deapp/de_variant_population_info.sql b/ddl/oracle/deapp/de_variant_population_info.sql
index 8284530a..1e2c4f02 100644
--- a/ddl/oracle/deapp/de_variant_population_info.sql
+++ b/ddl/oracle/deapp/de_variant_population_info.sql
@@ -16,12 +16,11 @@ CREATE SEQUENCE  "DEAPP"."DE_VARIANT_POPULATION_INFO_SEQ"  MINVALUE 1 MAXVALUE 9
  CONSTRAINT "DE_VAR_POPULAT_INFO_ID_IDX" PRIMARY KEY ("VARIANT_POPULATION_INFO_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" 
 LOB ("DESCRIPTION") STORE AS BASICFILE (
  TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 RETENTION 
  NOCACHE LOGGING ) ;
-
 --
 -- Type: INDEX; Owner: DEAPP; Name: VAR_POPULAT_INFO_DATASET_NAME
 --
@@ -43,4 +42,3 @@ end;
 /
 ALTER TRIGGER "DEAPP"."TRG_DE_VP_INFO_ID" ENABLE;
  
-
diff --git a/ddl/oracle/deapp/de_variant_subject_detail.sql b/ddl/oracle/deapp/de_variant_subject_detail.sql
index 6be632c8..52c3b0bf 100644
--- a/ddl/oracle/deapp/de_variant_subject_detail.sql
+++ b/ddl/oracle/deapp/de_variant_subject_detail.sql
@@ -17,15 +17,14 @@
  CONSTRAINT "VARIANT_SUBJECT_DETAIL_ID" PRIMARY KEY ("VARIANT_SUBJECT_DETAIL_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" 
-LOB ("INFO") STORE AS BASICFILE (
- TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 RETENTION 
- NOCACHE LOGGING ) 
+LOB ("INFO") STORE AS SECUREFILE (
+ TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192
+ NOCACHE LOGGING  NOCOMPRESS  KEEP_DUPLICATES ) 
 LOB ("VARIANT_VALUE") STORE AS BASICFILE (
  TABLESPACE "TRANSMART" ENABLE STORAGE IN ROW CHUNK 8192 RETENTION 
  NOCACHE LOGGING ) ;
-
 --
 -- Type: REF_CONSTRAINT; Owner: DEAPP; Name: VARIANT_SUBJECT_DETAIL_FK
 --
diff --git a/ddl/oracle/deapp/de_variant_subject_idx.sql b/ddl/oracle/deapp/de_variant_subject_idx.sql
index 12eea20a..1d9fb2cb 100644
--- a/ddl/oracle/deapp/de_variant_subject_idx.sql
+++ b/ddl/oracle/deapp/de_variant_subject_idx.sql
@@ -6,7 +6,7 @@
 "SUBJECT_ID" VARCHAR2(50 BYTE), 
 "POSITION" NUMBER, 
 "VARIANT_SUBJECT_IDX_ID" NUMBER NOT NULL ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
diff --git a/ddl/oracle/deapp/de_variant_subject_summary.sql b/ddl/oracle/deapp/de_variant_subject_summary.sql
index 3cdb5f50..6b63d7fb 100644
--- a/ddl/oracle/deapp/de_variant_subject_summary.sql
+++ b/ddl/oracle/deapp/de_variant_subject_summary.sql
@@ -23,7 +23,7 @@ CREATE SEQUENCE  "DEAPP"."DE_VARIANT_SUBJECT_SUMMARY_SEQ"  MINVALUE 1 MAXVALUE 9
  CONSTRAINT "VARIANT_SUBJECT_SUMMARY_ID" PRIMARY KEY ("VARIANT_SUBJECT_SUMMARY_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
diff --git a/ddl/oracle/deapp/items.json b/ddl/oracle/deapp/items.json
index 990dd6aa..5fd51396 100644
--- a/ddl/oracle/deapp/items.json
+++ b/ddl/oracle/deapp/items.json
@@ -67,6 +67,24 @@
       "name" : "DE_ENCOUNTER_TYPE"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_GENE_INFO"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_GENE_SOURCE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_GENE_SOURCE"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -169,6 +187,39 @@
       "owner" : "DEAPP",
       "name" : "DE_SUBJECT_MICROARRAY_DATA"
     } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "DE_MICROARRAY_DATA_IDX3"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_MICROARRAY_DATA"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "DE_MICROARRAY_DATA_IDX4"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_MICROARRAY_DATA"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "DE_MICROARRAY_DATA_IDX5"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_MICROARRAY_DATA"
+    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -987,6 +1038,17 @@
       "name" : "DUMP_TABLE_TO_CSV"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "ENTREZ_IDX1"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SNP_GENE_MAP"
+    } ]
   }, {
     "child" : {
       "type" : "REF_CONSTRAINT",
@@ -1154,6 +1216,17 @@
       "owner" : "DEAPP",
       "name" : "DE_SAMPLE_SNP_DATA"
     } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "IDX_DE_SUBJ_SMPL_TRIAL_CCODE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_SAMPLE_MAPPING"
+    } ]
   }, {
     "child" : {
       "type" : "INDEX",
@@ -1434,6 +1507,28 @@
       "name" : "SEQ_MRNA_PARTITION_ID"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "SNP_NAME_IDX1"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SNP_GENE_MAP"
+    } ]
+  }, {
+    "child" : {
+      "type" : "REF_CONSTRAINT",
+      "owner" : "DEAPP",
+      "name" : "SYS_C0029766"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_GENE_INFO"
+    } ]
   }, {
     "child" : {
       "type" : "FUNCTION",
@@ -1460,6 +1555,28 @@
       "owner" : "DEAPP",
       "name" : "DE_CHROMO_REGION_ID_SEQ"
     } ]
+  }, {
+    "child" : {
+      "type" : "TRIGGER",
+      "owner" : "DEAPP",
+      "name" : "TRG_DE_GENE_INFO_ID"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_GENE_INFO"
+    } ]
+  }, {
+    "child" : {
+      "type" : "TRIGGER",
+      "owner" : "DEAPP",
+      "name" : "TRG_DE_GENE_SOURCE_ID"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_GENE_SOURCE"
+    } ]
   }, {
     "child" : {
       "type" : "TRIGGER",
@@ -1897,6 +2014,20 @@
       "name" : "DE_ENCOUNTER_TYPE"
     },
     "file" : "deapp/de_encounter_type.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_GENE_INFO"
+    },
+    "file" : "deapp/de_gene_info.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_GENE_SOURCE"
+    },
+    "file" : "deapp/de_gene_source.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -1967,6 +2098,27 @@
       "name" : "DE_MICROARRAY_DATA_IDX2"
     },
     "file" : "deapp/de_subject_microarray_data.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "DE_MICROARRAY_DATA_IDX3"
+    },
+    "file" : "deapp/de_subject_microarray_data.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "DE_MICROARRAY_DATA_IDX4"
+    },
+    "file" : "deapp/de_subject_microarray_data.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "DE_MICROARRAY_DATA_IDX5"
+    },
+    "file" : "deapp/de_subject_microarray_data.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -2597,6 +2749,13 @@
       "name" : "DUMP_TABLE_TO_CSV"
     },
     "file" : "deapp/procedures/dump_table_to_csv.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "ENTREZ_IDX1"
+    },
+    "file" : "deapp/de_snp_gene_map.sql"
   }, {
     "item" : {
       "type" : "REF_CONSTRAINT",
@@ -2716,6 +2875,13 @@
       "name" : "IDX_DE_SAMPLE_SNP_DATA_SNP"
     },
     "file" : "deapp/de_sample_snp_data.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "IDX_DE_SUBJ_SMPL_TRIAL_CCODE"
+    },
+    "file" : "deapp/de_subject_sample_mapping.sql"
   }, {
     "item" : {
       "type" : "INDEX",
@@ -2884,6 +3050,20 @@
       "name" : "SEQ_MRNA_PARTITION_ID"
     },
     "file" : "deapp/_misc.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "DEAPP",
+      "name" : "SNP_NAME_IDX1"
+    },
+    "file" : "deapp/de_snp_gene_map.sql"
+  }, {
+    "item" : {
+      "type" : "REF_CONSTRAINT",
+      "owner" : "DEAPP",
+      "name" : "SYS_C0029766"
+    },
+    "file" : "deapp/de_gene_info.sql"
   }, {
     "item" : {
       "type" : "FUNCTION",
@@ -2898,6 +3078,20 @@
       "name" : "TRG_DE_CHROMOSOMAL_REGION_ID"
     },
     "file" : "deapp/de_chromosomal_region.sql"
+  }, {
+    "item" : {
+      "type" : "TRIGGER",
+      "owner" : "DEAPP",
+      "name" : "TRG_DE_GENE_INFO_ID"
+    },
+    "file" : "deapp/de_gene_info.sql"
+  }, {
+    "item" : {
+      "type" : "TRIGGER",
+      "owner" : "DEAPP",
+      "name" : "TRG_DE_GENE_SOURCE_ID"
+    },
+    "file" : "deapp/de_gene_source.sql"
   }, {
     "item" : {
       "type" : "TRIGGER",
@@ -3095,4 +3289,4 @@
     },
     "file" : "deapp/de_variant_population_info.sql"
   } ]
-}
+}
\ No newline at end of file
diff --git a/ddl/oracle/deapp/kegg_def.sql b/ddl/oracle/deapp/kegg_def.sql
index 447d7a2d..5bd7363d 100644
--- a/ddl/oracle/deapp/kegg_def.sql
+++ b/ddl/oracle/deapp/kegg_def.sql
@@ -2,8 +2,8 @@
 -- Type: TABLE; Owner: DEAPP; Name: KEGG_DEF
 --
  CREATE TABLE "DEAPP"."KEGG_DEF" 
-  (	"PATHWAY" VARCHAR2(80 BYTE), 
-"DESCR" VARCHAR2(200 BYTE)
+  (	"PATHWAY" VARCHAR2(100 BYTE), 
+"DESCR" VARCHAR2(500 BYTE)
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 

From 32b15eb44ecf89464d2a3ba86ef2de413044708c Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 12:26:24 +0100
Subject: [PATCH 26/31] biomart update from oracle test server

---
 ddl/oracle/biomart/_cross.sql                 |  84 +++---
 ddl/oracle/biomart/assay_analysis_data.sql    |   8 +-
 ddl/oracle/biomart/bio_ad_hoc_property.sql    |   2 +-
 .../bio_analysis_attribute_lineage.sql        |  20 ++
 .../biomart/bio_assay_analysis_eqtl.sql       |  26 +-
 ddl/oracle/biomart/bio_assay_analysis_ext.sql |   8 +-
 .../biomart/bio_assay_analysis_gwas.sql       |  39 ++-
 .../biomart/bio_asy_analysis_data_idx.sql     |   2 +-
 .../biomart/bio_asy_analysis_eqtl_top50.sql   |   5 +-
 .../biomart/bio_asy_analysis_gwas_top50.sql   |   7 +-
 ddl/oracle/biomart/bio_concept_code.sql       |   8 +
 ddl/oracle/biomart/bio_experiment.sql         |  20 +-
 ddl/oracle/biomart/faceted_search.sql         |  19 ++
 ddl/oracle/biomart/gwas_partition.sql         |  24 ++
 ddl/oracle/biomart/items.json                 | 254 +++++++++++++++++-
 ddl/oracle/biomart/mesh.sql                   |   2 +-
 .../biomart/tmp_analysis_eqtl_top500.sql      |  29 ++
 .../biomart/tmp_analysis_gwas_top500.sql      |  16 ++
 .../biomart/views/bio_marker_correl_mv.sql    | 211 +++++++--------
 ddl/oracle/biomart/views/gwas_anlysis.sql     |   5 +
 .../biomart/views/vw_faceted_search.sql       |   6 +-
 21 files changed, 610 insertions(+), 185 deletions(-)
 create mode 100644 ddl/oracle/biomart/faceted_search.sql
 create mode 100644 ddl/oracle/biomart/gwas_partition.sql
 create mode 100644 ddl/oracle/biomart/tmp_analysis_eqtl_top500.sql
 create mode 100644 ddl/oracle/biomart/tmp_analysis_gwas_top500.sql
 create mode 100644 ddl/oracle/biomart/views/gwas_anlysis.sql

diff --git a/ddl/oracle/biomart/_cross.sql b/ddl/oracle/biomart/_cross.sql
index 56b0217d..4225cc72 100644
--- a/ddl/oracle/biomart/_cross.sql
+++ b/ddl/oracle/biomart/_cross.sql
@@ -1,24 +1,47 @@
 --
 -- Type: VIEW; Owner: BIOMART; Name: BIO_METAB_SUBPATHWAY_VIEW
 --
-  CREATE OR REPLACE FORCE VIEW "BIOMART"."BIO_METAB_SUBPATHWAY_VIEW" ("SUBPATHWAY_ID", "ASSO_BIO_MARKER_ID", "CORREL_TYPE") AS 
-  SELECT
-              SP.id,
-              B.bio_marker_id,
-              'SUBPATHWAY TO METABOLITE'
-          FROM
-              deapp.de_metabolite_sub_pathways SP
-              INNER JOIN deapp.de_metabolite_sub_pway_metab J ON (SP.id = J.sub_pathway_id)
-              INNER JOIN deapp.de_metabolite_annotation M ON (M.id = J.metabolite_id)
-              INNER JOIN biomart.bio_marker B ON (
-                  B.bio_marker_type = 'METABOLITE' AND
-B.primary_external_id = M.hmdb_id);
+CREATE OR REPLACE FORCE VIEW "BIOMART"."BIO_METAB_SUBPATHWAY_VIEW" ("SUBPATHWAY_ID", "ASSO_BIO_MARKER_ID", "CORREL_TYPE") AS 
+SELECT SP.id,
+  B.bio_marker_id,
+  'SUBPATHWAY TO METABOLITE'
+FROM deapp.de_metabolite_sub_pathways SP
+INNER JOIN deapp.de_metabolite_sub_pway_metab J
+ON (SP.id = J.sub_pathway_id)
+INNER JOIN deapp.de_metabolite_annotation M
+ON (M.id = J.metabolite_id)
+INNER JOIN biomart.bio_marker B
+ON ( B.bio_marker_type    = 'METABOLITE'
+AND B.primary_external_id = M.hmdb_id);
  
+--
+-- Type: TRIGGER; Owner: BIOMART; Name: TRG_BIO_ANALYSIS_ATT_BAAL
+--
+  CREATE OR REPLACE TRIGGER "BIOMART"."TRG_BIO_ANALYSIS_ATT_BAAL" 
+  after insert on "BIOMART"."BIO_ANALYSIS_ATTRIBUTE"
+  for each row
+declare
+  -- local variables here
+begin
+  if inserting then
+    -- create a new record in the lineage table for each ancestor of this term (including self)
+    insert into BIO_ANALYSIS_ATTRIBUTE_LINEAGE
+    (BIO_ANALYSIS_ATTRIBUTE_ID, ANCESTOR_TERM_ID, ANCESTOR_SEARCH_KEYWORD_ID)
+    SELECT :NEW.BIO_ANALYSIS_ATTRIBUTE_ID, skl.ancestor_id, skl.search_keyword_id
+    FROM searchapp.solr_keywords_lineage skl
+    WHERE skl.term_id = :NEW.TERM_ID;
+  end if;
+
+end TRG_BIO_ANALYSIS_ATT_BAAL;
+
+
+/
+ALTER TRIGGER "BIOMART"."TRG_BIO_ANALYSIS_ATT_BAAL" DISABLE;
 --
 -- Type: VIEW; Owner: BIOMART; Name: BIO_MARKER_EXP_ANALYSIS_MV
 --
-  CREATE OR REPLACE FORCE VIEW "BIOMART"."BIO_MARKER_EXP_ANALYSIS_MV" ("BIO_MARKER_ID", "BIO_EXPERIMENT_ID", "BIO_ASSAY_ANALYSIS_ID", "MV_ID") AS 
-  SELECT DISTINCT t4.bio_marker_id,
+CREATE OR REPLACE FORCE VIEW "BIOMART"."BIO_MARKER_EXP_ANALYSIS_MV" ("BIO_MARKER_ID", "BIO_EXPERIMENT_ID", "BIO_ASSAY_ANALYSIS_ID", "MV_ID") AS 
+SELECT DISTINCT t4.bio_marker_id,
   t1.bio_experiment_id,
   t1.bio_assay_analysis_id,
   t1.bio_assay_analysis_id*100+t4.bio_marker_id
@@ -26,25 +49,26 @@ FROM BIO_ASSAY_ANALYSIS_DATA t1,
   BIO_EXPERIMENT t2,
   DEAPP.DE_MRNA_ANNOTATION t3,
   BIO_MARKER t4
-WHERE t1.bio_experiment_id       = t2.bio_experiment_id
-AND t2.bio_experiment_type       ='Experiment'
-AND t3.probeset_id= t1.probeset_id
+WHERE t1.bio_experiment_id = t2.bio_experiment_id
+AND t2.bio_experiment_type ='Experiment'
+AND t3.probeset_id         = t1.probeset_id
 AND t4.primary_external_id = CAST(t3.gene_id AS VARCHAR(200));
  
 --
 -- Type: VIEW; Owner: BIOMART; Name: BIO_METAB_SUPERPATHWAY_VIEW
 --
-  CREATE OR REPLACE FORCE VIEW "BIOMART"."BIO_METAB_SUPERPATHWAY_VIEW" ("SUPERPATHWAY_ID", "ASSO_BIO_MARKER_ID", "CORREL_TYPE") AS 
-  SELECT
-              SUPP.id,
-              B.bio_marker_id,
-              'SUPERPATHWAY TO METABOLITE'
-          FROM
-              deapp.de_metabolite_super_pathways SUPP
-              INNER JOIN deapp.de_metabolite_sub_pathways SUBP ON (SUPP.id = SUBP.super_pathway_id)
-              INNER JOIN deapp.de_metabolite_sub_pway_metab J ON (SUBP.id = J.sub_pathway_id)
-              INNER JOIN deapp.de_metabolite_annotation M ON (M.id = J.metabolite_id)
-              INNER JOIN biomart.bio_marker B ON (
-                  B.bio_marker_type = 'METABOLITE' AND
-B.primary_external_id = M.hmdb_id);
+CREATE OR REPLACE FORCE VIEW "BIOMART"."BIO_METAB_SUPERPATHWAY_VIEW" ("SUPERPATHWAY_ID", "ASSO_BIO_MARKER_ID", "CORREL_TYPE") AS 
+SELECT SUPP.id,
+  B.bio_marker_id,
+  'SUPERPATHWAY TO METABOLITE'
+FROM deapp.de_metabolite_super_pathways SUPP
+INNER JOIN deapp.de_metabolite_sub_pathways SUBP
+ON (SUPP.id = SUBP.super_pathway_id)
+INNER JOIN deapp.de_metabolite_sub_pway_metab J
+ON (SUBP.id = J.sub_pathway_id)
+INNER JOIN deapp.de_metabolite_annotation M
+ON (M.id = J.metabolite_id)
+INNER JOIN biomart.bio_marker B
+ON ( B.bio_marker_type    = 'METABOLITE'
+AND B.primary_external_id = M.hmdb_id);
  
diff --git a/ddl/oracle/biomart/assay_analysis_data.sql b/ddl/oracle/biomart/assay_analysis_data.sql
index 6a3de90a..2060b68c 100644
--- a/ddl/oracle/biomart/assay_analysis_data.sql
+++ b/ddl/oracle/biomart/assay_analysis_data.sql
@@ -15,7 +15,7 @@
 "PREFERRED_PVALUE" NUMBER(18,5)
   )
  TABLESPACE "TRANSMART" 
- PARTITION BY LIST ("BIO_EXPERIMENT_ID") 
-(PARTITION "NULL_PARTITION"  VALUES (NULL)
- TABLESPACE "TRANSMART" NOCOMPRESS ) ;
-
+ PARTITION BY HASH ("BIO_EXPERIMENT_ID") 
+(PARTITION "SYS_P391" SEGMENT CREATION DEFERRED 
+ TABLESPACE "TRANSMART" 
+NOCOMPRESS ) ;
diff --git a/ddl/oracle/biomart/bio_ad_hoc_property.sql b/ddl/oracle/biomart/bio_ad_hoc_property.sql
index f3dcebe4..55f598a7 100644
--- a/ddl/oracle/biomart/bio_ad_hoc_property.sql
+++ b/ddl/oracle/biomart/bio_ad_hoc_property.sql
@@ -3,7 +3,7 @@
 --
  CREATE TABLE "BIOMART"."BIO_AD_HOC_PROPERTY" 
   (	"AD_HOC_PROPERTY_ID" NUMBER(22,0) NOT NULL ENABLE, 
-"BIO_DATA_ID" NUMBER(22,0), 
+"BIO_DATA_ID" NUMBER(22,0) NOT NULL ENABLE, 
 "PROPERTY_KEY" NVARCHAR2(50), 
 "PROPERTY_VALUE" NVARCHAR2(2000), 
  CONSTRAINT "BIO_AD_HOC_PROPERTY_PK" PRIMARY KEY ("AD_HOC_PROPERTY_ID")
diff --git a/ddl/oracle/biomart/bio_analysis_attribute_lineage.sql b/ddl/oracle/biomart/bio_analysis_attribute_lineage.sql
index a4ab3719..e9eeeb58 100644
--- a/ddl/oracle/biomart/bio_analysis_attribute_lineage.sql
+++ b/ddl/oracle/biomart/bio_analysis_attribute_lineage.sql
@@ -12,6 +12,26 @@
   ) SEGMENT CREATION DEFERRED
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: TRIGGER; Owner: BIOMART; Name: TRG_BIO_ANALYSIS_ATT_LINEAGE
+--
+  CREATE OR REPLACE TRIGGER "BIOMART"."TRG_BIO_ANALYSIS_ATT_LINEAGE" 
+  before insert on "BIOMART"."BIO_ANALYSIS_ATTRIBUTE_LINEAGE"
+  for each row
+declare
+  -- local variables here
+begin
+  if inserting then
+    if :NEW.BIO_ANALYSIS_ATT_LINEAGE_ID is null then
+      select SEQ_BIO_ANALYSIS_ATT_LIN_ID.nextval into :NEW.BIO_ANALYSIS_ATT_LINEAGE_ID from dual;
+    end if;
+  end if;
+end TRG_BIO_ANALYSIS_ATT_LINEAGE;
+
+
+/
+ALTER TRIGGER "BIOMART"."TRG_BIO_ANALYSIS_ATT_LINEAGE" ENABLE;
+ 
 --
 -- Type: TRIGGER; Owner: BIOMART; Name: TRG_BIO_ANALYSIS_AL_ID
 --
diff --git a/ddl/oracle/biomart/bio_assay_analysis_eqtl.sql b/ddl/oracle/biomart/bio_assay_analysis_eqtl.sql
index a56204d4..aa4f55f3 100644
--- a/ddl/oracle/biomart/bio_assay_analysis_eqtl.sql
+++ b/ddl/oracle/biomart/bio_assay_analysis_eqtl.sql
@@ -2,8 +2,8 @@
 -- Type: TABLE; Owner: BIOMART; Name: BIO_ASSAY_ANALYSIS_EQTL
 --
  CREATE TABLE "BIOMART"."BIO_ASSAY_ANALYSIS_EQTL" 
-  (	"BIO_ASY_ANALYSIS_EQTL_ID" NUMBER, 
-"BIO_ASSAY_ANALYSIS_ID" NUMBER, 
+  (	"BIO_ASY_ANALYSIS_EQTL_ID" NUMBER NOT NULL ENABLE, 
+"BIO_ASSAY_ANALYSIS_ID" NUMBER NOT NULL ENABLE, 
 "RS_ID" VARCHAR2(50 BYTE), 
 "GENE" VARCHAR2(50 BYTE), 
 "P_VALUE_CHAR" VARCHAR2(100 BYTE), 
@@ -16,3 +16,25 @@
   ) SEGMENT CREATION DEFERRED
  TABLESPACE "TRANSMART" ;
 
+
+--
+-- Type: TRIGGER; Owner: BIOMART; Name: TRG_BIO_ASY_ANALYSIS_EQTL_ID
+--
+  CREATE OR REPLACE TRIGGER "BIOMART"."TRG_BIO_ASY_ANALYSIS_EQTL_ID" before insert on BIOMART.BIO_ASSAY_ANALYSIS_EQTL for each row
+begin
+  if inserting then
+    if :NEW."BIO_ASY_ANALYSIS_EQTL_ID" is null then
+      select SEQ_BIO_DATA_ID.nextval into :NEW."BIO_ASY_ANALYSIS_EQTL_ID" from dual;
+    end if;
+  end if;
+end;
+
+/
+ALTER TRIGGER "BIOMART"."TRG_BIO_ASY_ANALYSIS_EQTL_ID" ENABLE;
+ 
+--
+-- Type: INDEX; Owner: BIOMART; Name: BIO_ASSAY_ANALYSIS_EQTL_IDX1
+--
+CREATE INDEX "BIOMART"."BIO_ASSAY_ANALYSIS_EQTL_IDX1" ON "BIOMART"."BIO_ASSAY_ANALYSIS_EQTL" ("BIO_ASSAY_ANALYSIS_ID")
+TABLESPACE "INDX" ;
+
diff --git a/ddl/oracle/biomart/bio_assay_analysis_ext.sql b/ddl/oracle/biomart/bio_assay_analysis_ext.sql
index 1dd7d776..48d83b7b 100644
--- a/ddl/oracle/biomart/bio_assay_analysis_ext.sql
+++ b/ddl/oracle/biomart/bio_assay_analysis_ext.sql
@@ -16,6 +16,12 @@
 "MODEL_DESC" VARCHAR2(500 BYTE), 
 "SENSITIVE_FLAG" NUMBER(*,0), 
 "SENSITIVE_DESC" VARCHAR2(500 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: INDEX; Owner: BIOMART; Name: BIO_ASSAY_ANALYSIS_EXT_IDX1
+--
+CREATE INDEX "BIOMART"."BIO_ASSAY_ANALYSIS_EXT_IDX1" ON "BIOMART"."BIO_ASSAY_ANALYSIS_EXT" ("BIO_ASSAY_ANALYSIS_ID")
+TABLESPACE "INDX" ;
+
diff --git a/ddl/oracle/biomart/bio_assay_analysis_gwas.sql b/ddl/oracle/biomart/bio_assay_analysis_gwas.sql
index 6b123113..22ab826f 100644
--- a/ddl/oracle/biomart/bio_assay_analysis_gwas.sql
+++ b/ddl/oracle/biomart/bio_assay_analysis_gwas.sql
@@ -2,14 +2,33 @@
 -- Type: TABLE; Owner: BIOMART; Name: BIO_ASSAY_ANALYSIS_GWAS
 --
  CREATE TABLE "BIOMART"."BIO_ASSAY_ANALYSIS_GWAS" 
-  (	"BIO_ASY_ANALYSIS_GWAS_ID" NUMBER, 
-"BIO_ASSAY_ANALYSIS_ID" NUMBER, 
-"RS_ID" VARCHAR2(50 BYTE), 
+  (	"BIO_ASY_ANALYSIS_GWAS_ID" NUMBER(18,0) NOT NULL ENABLE, 
+"BIO_ASSAY_ANALYSIS_ID" NUMBER(18,0) NOT NULL ENABLE, 
+"RS_ID" NVARCHAR2(50), 
 "P_VALUE_CHAR" VARCHAR2(100 BYTE), 
-"ETL_ID" NUMBER, 
-"EXT_DATA" VARCHAR2(4000 BYTE), 
-"P_VALUE" FLOAT(126), 
-"LOG_P_VALUE" FLOAT(126)
-  ) SEGMENT CREATION DEFERRED
- TABLESPACE "TRANSMART" ;
-
+"P_VALUE" BINARY_DOUBLE, 
+"LOG_P_VALUE" BINARY_DOUBLE, 
+"ETL_ID" NUMBER(18,0), 
+"EXT_DATA" VARCHAR2(4000 BYTE)
+  )
+COMPRESS BASIC  NOLOGGING 
+ TABLESPACE "TRANSMART" 
+ PARTITION BY LIST ("BIO_ASSAY_ANALYSIS_ID") 
+(PARTITION "1"  VALUES (1) SEGMENT CREATION DEFERRED
+COMPRESS BASIC NOLOGGING 
+ TABLESPACE "TRANSMART" , 
+PARTITION "393525752"  VALUES (393525752) SEGMENT CREATION IMMEDIATE
+COMPRESS BASIC NOLOGGING 
+ TABLESPACE "TRANSMART" , 
+PARTITION "393525754"  VALUES (393525754) SEGMENT CREATION IMMEDIATE
+COMPRESS BASIC NOLOGGING 
+ TABLESPACE "TRANSMART" , 
+PARTITION "393525758"  VALUES (393525758) SEGMENT CREATION IMMEDIATE
+COMPRESS BASIC NOLOGGING 
+ TABLESPACE "TRANSMART" , 
+PARTITION "393525756"  VALUES (393525756) SEGMENT CREATION IMMEDIATE
+COMPRESS BASIC NOLOGGING 
+ TABLESPACE "TRANSMART" , 
+PARTITION "393525760"  VALUES (393525760) SEGMENT CREATION IMMEDIATE
+COMPRESS BASIC NOLOGGING 
+ TABLESPACE "TRANSMART" ) ;
diff --git a/ddl/oracle/biomart/bio_asy_analysis_data_idx.sql b/ddl/oracle/biomart/bio_asy_analysis_data_idx.sql
index 2594dc2c..f19cf677 100644
--- a/ddl/oracle/biomart/bio_asy_analysis_data_idx.sql
+++ b/ddl/oracle/biomart/bio_asy_analysis_data_idx.sql
@@ -8,7 +8,7 @@
 "FIELD_NAME" VARCHAR2(255 BYTE) NOT NULL ENABLE, 
 "DISPLAY_IDX" NUMBER(10,0) NOT NULL ENABLE, 
 "DISPLAY_NAME" VARCHAR2(255 BYTE) NOT NULL ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
diff --git a/ddl/oracle/biomart/bio_asy_analysis_eqtl_top50.sql b/ddl/oracle/biomart/bio_asy_analysis_eqtl_top50.sql
index d712dc46..8f8e567b 100644
--- a/ddl/oracle/biomart/bio_asy_analysis_eqtl_top50.sql
+++ b/ddl/oracle/biomart/bio_asy_analysis_eqtl_top50.sql
@@ -11,7 +11,10 @@
 "PVALUE" FLOAT(126), 
 "LOGPVALUE" FLOAT(126), 
 "EXTDATA" VARCHAR2(4000 BYTE), 
-"RNUM" NUMBER
+"RNUM" NUMBER, 
+"INTRONEXON" VARCHAR2(10 BYTE), 
+"REGULOME" VARCHAR2(10 BYTE), 
+"RECOMBINATIONRATE" NUMBER(18,6)
   ) SEGMENT CREATION DEFERRED
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/biomart/bio_asy_analysis_gwas_top50.sql b/ddl/oracle/biomart/bio_asy_analysis_gwas_top50.sql
index 7941b681..bd393e8c 100644
--- a/ddl/oracle/biomart/bio_asy_analysis_gwas_top50.sql
+++ b/ddl/oracle/biomart/bio_asy_analysis_gwas_top50.sql
@@ -11,7 +11,10 @@
 "PVALUE" FLOAT(126), 
 "LOGPVALUE" FLOAT(126), 
 "EXTDATA" VARCHAR2(4000 BYTE), 
-"RNUM" NUMBER
-  ) SEGMENT CREATION DEFERRED
+"RNUM" NUMBER, 
+"INTRONEXON" VARCHAR2(10 BYTE), 
+"REGULOME" VARCHAR2(10 BYTE), 
+"RECOMBINATIONRATE" NUMBER(18,6)
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/biomart/bio_concept_code.sql b/ddl/oracle/biomart/bio_concept_code.sql
index 85633dfc..a3bb434e 100644
--- a/ddl/oracle/biomart/bio_concept_code.sql
+++ b/ddl/oracle/biomart/bio_concept_code.sql
@@ -17,6 +17,14 @@
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: TRIGGER; Owner: BIOMART; Name: TMP_TRG_BIO_CONCEPT_CODE_ID
+--
+  CREATE OR REPLACE TRIGGER "BIOMART"."TMP_TRG_BIO_CONCEPT_CODE_ID" before insert on "BIOMART"."BIO_CONCEPT_CODE"    for each row begin     if inserting then       if :NEW."BIO_CONCEPT_CODE_ID" is null then          select SEQ_BIO_DATA_ID.nextval into :NEW."BIO_CONCEPT_CODE_ID" from dual;       end if;    end if; end;
+
+/
+ALTER TRIGGER "BIOMART"."TMP_TRG_BIO_CONCEPT_CODE_ID" ENABLE;
+ 
 --
 -- Type: TRIGGER; Owner: BIOMART; Name: TRG_BIO_CONCEPT_CODE_ID
 --
diff --git a/ddl/oracle/biomart/bio_experiment.sql b/ddl/oracle/biomart/bio_experiment.sql
index 68a5808d..84a10357 100644
--- a/ddl/oracle/biomart/bio_experiment.sql
+++ b/ddl/oracle/biomart/bio_experiment.sql
@@ -3,18 +3,18 @@
 --
  CREATE TABLE "BIOMART"."BIO_EXPERIMENT" 
   (	"BIO_EXPERIMENT_ID" NUMBER(18,0) NOT NULL ENABLE, 
-"BIO_EXPERIMENT_TYPE" VARCHAR2(200), 
-"TITLE" VARCHAR2(1000), 
-"DESCRIPTION" VARCHAR2(4000), 
-"DESIGN" VARCHAR2(2000), 
+"BIO_EXPERIMENT_TYPE" VARCHAR2(200 BYTE), 
+"TITLE" VARCHAR2(1000 BYTE), 
+"DESCRIPTION" VARCHAR2(4000 BYTE), 
+"DESIGN" VARCHAR2(2000 BYTE), 
 "START_DATE" DATE, 
 "COMPLETION_DATE" DATE, 
-"PRIMARY_INVESTIGATOR" VARCHAR2(400), 
-"CONTACT_FIELD" VARCHAR2(400), 
-"ETL_ID" VARCHAR2(100), 
+"PRIMARY_INVESTIGATOR" VARCHAR2(400 BYTE), 
+"CONTACT_FIELD" VARCHAR2(400 BYTE), 
+"ETL_ID" VARCHAR2(100 BYTE), 
 "STATUS" VARCHAR2(100 BYTE), 
-"OVERALL_DESIGN" VARCHAR2(2000), 
-"ACCESSION" VARCHAR2(100), 
+"OVERALL_DESIGN" VARCHAR2(2000 BYTE), 
+"ACCESSION" VARCHAR2(100 BYTE), 
 "ENTRYDT" DATE, 
 "UPDATED" DATE, 
 "INSTITUTION" VARCHAR2(400 BYTE), 
@@ -34,14 +34,12 @@
 CREATE INDEX "BIOMART"."BIO_EXP_ACEN_IDX" ON "BIOMART"."BIO_EXPERIMENT" ("ACCESSION")
 TABLESPACE "INDX" 
 PARALLEL 4 ;
-
 --
 -- Type: INDEX; Owner: BIOMART; Name: BIO_EXP_TYPE_IDX
 --
 CREATE INDEX "BIOMART"."BIO_EXP_TYPE_IDX" ON "BIOMART"."BIO_EXPERIMENT" ("BIO_EXPERIMENT_TYPE")
 TABLESPACE "INDX" 
 PARALLEL 4 ;
-
 --
 -- Type: TRIGGER; Owner: BIOMART; Name: TRG_BIO_EXPERIMENT_ID
 --
diff --git a/ddl/oracle/biomart/faceted_search.sql b/ddl/oracle/biomart/faceted_search.sql
new file mode 100644
index 00000000..fdaabbd9
--- /dev/null
+++ b/ddl/oracle/biomart/faceted_search.sql
@@ -0,0 +1,19 @@
+--
+-- Type: TABLE; Owner: BIOMART; Name: FACETED_SEARCH
+--
+ CREATE TABLE "BIOMART"."FACETED_SEARCH" 
+  (	"ANALYSIS_ID" NUMBER(18,0), 
+"STUDY" NUMBER(18,0), 
+"STUDY_ID" NUMBER(18,0), 
+"DISEASE" NVARCHAR2(510), 
+"ANALYSES" NVARCHAR2(200), 
+"DATA_TYPE" VARCHAR2(50 BYTE), 
+"PLATFORM" VARCHAR2(20 BYTE), 
+"OBSERVATION" NVARCHAR2(200), 
+"FACET_ID" NUMBER(10,0), 
+ PRIMARY KEY ("FACET_ID")
+ USING INDEX
+ TABLESPACE "BIOMART"  ENABLE
+  ) SEGMENT CREATION IMMEDIATE
+NOCOMPRESS NOLOGGING
+ TABLESPACE "BIOMART" ;
diff --git a/ddl/oracle/biomart/gwas_partition.sql b/ddl/oracle/biomart/gwas_partition.sql
new file mode 100644
index 00000000..bad1ba74
--- /dev/null
+++ b/ddl/oracle/biomart/gwas_partition.sql
@@ -0,0 +1,24 @@
+--
+-- Type: TABLE; Owner: BIOMART; Name: GWAS_PARTITION
+--
+ CREATE TABLE "BIOMART"."GWAS_PARTITION" 
+  (	"BIO_ASY_ANALYSIS_GWAS_ID" NUMBER(18,0) NOT NULL ENABLE, 
+"BIO_ASSAY_ANALYSIS_ID" NUMBER(18,0) NOT NULL ENABLE, 
+"RS_ID" NVARCHAR2(50), 
+"P_VALUE_CHAR" VARCHAR2(100 BYTE), 
+"P_VALUE" BINARY_DOUBLE, 
+"LOG_P_VALUE" BINARY_DOUBLE, 
+"ETL_ID" NUMBER(18,0), 
+"EXT_DATA" VARCHAR2(4000 BYTE)
+  )
+COMPRESS BASIC  NOLOGGING 
+ TABLESPACE "BIOMART" 
+ PARTITION BY LIST ("BIO_ASSAY_ANALYSIS_ID") 
+(PARTITION "1"  VALUES (1) SEGMENT CREATION DEFERRED
+COMPRESS BASIC NOLOGGING 
+ TABLESPACE "BIOMART" ) ;
+--
+-- Type: REF_CONSTRAINT; Owner: BIOMART; Name: BIO_AA_GWAS_FK
+--
+ALTER TABLE "BIOMART"."GWAS_PARTITION" ADD CONSTRAINT "BIO_AA_GWAS_FK" FOREIGN KEY ("BIO_ASSAY_ANALYSIS_ID")
+ REFERENCES "BIOMART"."BIO_ASSAY_ANALYSIS" ("BIO_ASSAY_ANALYSIS_ID") ENABLE;
diff --git a/ddl/oracle/biomart/items.json b/ddl/oracle/biomart/items.json
index ca5f8a92..82d8280d 100644
--- a/ddl/oracle/biomart/items.json
+++ b/ddl/oracle/biomart/items.json
@@ -232,6 +232,17 @@
       "name" : "BIOMARKER_PATHWAY_UID"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "REF_CONSTRAINT",
+      "owner" : "BIOMART",
+      "name" : "BIO_AA_GWAS_FK"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "GWAS_PARTITION"
+    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -405,6 +416,17 @@
       "name" : "BIO_ASSAY_ANALYSIS_EQTL"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL_IDX1"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL"
+    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -412,6 +434,17 @@
       "name" : "BIO_ASSAY_ANALYSIS_EXT"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EXT_IDX1"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EXT"
+    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -2428,6 +2461,13 @@
       "owner" : "BIOMART",
       "name" : "BIO_CONTENT"
     } ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "FACETED_SEARCH"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "FUNCTION",
@@ -2470,6 +2510,28 @@
       "name" : "GSE_PROBESET"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "VIEW",
+      "owner" : "BIOMART",
+      "name" : "GWAS_ANLYSIS"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS"
+    } ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "GWAS_PARTITION"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS"
+    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -2593,6 +2655,20 @@
       "name" : "TESTS"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "TMP_ANALYSIS_EQTL_TOP500"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "TMP_ANALYSIS_GWAS_TOP500"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -2635,6 +2711,21 @@
       "name" : "TMP_PROJECT_DISEASE"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TRIGGER",
+      "owner" : "BIOMART",
+      "name" : "TMP_TRG_BIO_CONCEPT_CODE_ID"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_CONCEPT_CODE"
+    }, {
+      "type" : "SEQUENCE",
+      "owner" : "BIOMART",
+      "name" : "SEQ_BIO_DATA_ID"
+    } ]
   }, {
     "child" : {
       "type" : "TRIGGER",
@@ -2680,6 +2771,32 @@
       "owner" : "BIOMART",
       "name" : "SEQ_BIO_DATA_ID"
     } ]
+  }, {
+    "child" : {
+      "type" : "TRIGGER",
+      "owner" : "BIOMART",
+      "name" : "TRG_BIO_ANALYSIS_ATT_BAAL"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ANALYSIS_ATTRIBUTE"
+    }, {
+      "type" : "VIEW",
+      "owner" : "SEARCHAPP",
+      "name" : "SOLR_KEYWORDS_LINEAGE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "TRIGGER",
+      "owner" : "BIOMART",
+      "name" : "TRG_BIO_ANALYSIS_ATT_LINEAGE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ANALYSIS_ATTRIBUTE_LINEAGE"
+    } ]
   }, {
     "child" : {
       "type" : "TRIGGER",
@@ -2834,6 +2951,21 @@
       "owner" : "BIOMART",
       "name" : "SEQ_BIO_DATA_ID"
     } ]
+  }, {
+    "child" : {
+      "type" : "TRIGGER",
+      "owner" : "BIOMART",
+      "name" : "TRG_BIO_ASY_ANALYSIS_EQTL_ID"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL"
+    }, {
+      "type" : "SEQUENCE",
+      "owner" : "BIOMART",
+      "name" : "SEQ_BIO_DATA_ID"
+    } ]
   }, {
     "child" : {
       "type" : "TRIGGER",
@@ -3468,6 +3600,28 @@
       "owner" : "BIOMART",
       "name" : "SEQ_CLINICAL_TRIAL_DESIGN_ID"
     } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART",
+      "name" : "T_A_GAE_T500_IDX"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "TMP_ANALYSIS_EQTL_TOP500"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART",
+      "name" : "T_A_GE_T500_IDX"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "TMP_ANALYSIS_EQTL_TOP500"
+    } ]
   }, {
     "child" : {
       "type" : "VIEW",
@@ -3688,6 +3842,13 @@
       "name" : "BIOMARKER_PATHWAY_UID"
     },
     "file" : "biomart/functions/biomarker_pathway_uid.sql"
+  }, {
+    "item" : {
+      "type" : "REF_CONSTRAINT",
+      "owner" : "BIOMART",
+      "name" : "BIO_AA_GWAS_FK"
+    },
+    "file" : "biomart/gwas_partition.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -3793,6 +3954,13 @@
       "name" : "BIO_ASSAY_ANALYSIS_EQTL"
     },
     "file" : "biomart/bio_assay_analysis_eqtl.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL_IDX1"
+    },
+    "file" : "biomart/bio_assay_analysis_eqtl.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -3800,6 +3968,13 @@
       "name" : "BIO_ASSAY_ANALYSIS_EXT"
     },
     "file" : "biomart/bio_assay_analysis_ext.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EXT_IDX1"
+    },
+    "file" : "biomart/bio_assay_analysis_ext.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -5172,6 +5347,13 @@
       "name" : "EXT_FILE_CNT_CNT_REPO_FK"
     },
     "file" : "biomart/bio_content.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "FACETED_SEARCH"
+    },
+    "file" : "biomart/faceted_search.sql"
   }, {
     "item" : {
       "type" : "FUNCTION",
@@ -5214,6 +5396,20 @@
       "name" : "GSE_PROBESET"
     },
     "file" : "biomart/gse_probeset.sql"
+  }, {
+    "item" : {
+      "type" : "VIEW",
+      "owner" : "BIOMART",
+      "name" : "GWAS_ANLYSIS"
+    },
+    "file" : "biomart/views/gwas_anlysis.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "GWAS_PARTITION"
+    },
+    "file" : "biomart/gwas_partition.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -5333,6 +5529,20 @@
       "name" : "TESTS"
     },
     "file" : "biomart/tests.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "TMP_ANALYSIS_EQTL_TOP500"
+    },
+    "file" : "biomart/tmp_analysis_eqtl_top500.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "TMP_ANALYSIS_GWAS_TOP500"
+    },
+    "file" : "biomart/tmp_analysis_gwas_top500.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -5375,6 +5585,13 @@
       "name" : "TMP_PROJECT_DISEASE"
     },
     "file" : "biomart/tmp_project_disease.sql"
+  }, {
+    "item" : {
+      "type" : "TRIGGER",
+      "owner" : "BIOMART",
+      "name" : "TMP_TRG_BIO_CONCEPT_CODE_ID"
+    },
+    "file" : "biomart/bio_concept_code.sql"
   }, {
     "item" : {
       "type" : "TRIGGER",
@@ -5396,6 +5613,20 @@
       "name" : "TRG_BIO_ANALYSIS_ATTRIBUTE_ID"
     },
     "file" : "biomart/bio_analysis_attribute.sql"
+  }, {
+    "item" : {
+      "type" : "TRIGGER",
+      "owner" : "BIOMART",
+      "name" : "TRG_BIO_ANALYSIS_ATT_BAAL"
+    },
+    "file" : "biomart/_cross.sql"
+  }, {
+    "item" : {
+      "type" : "TRIGGER",
+      "owner" : "BIOMART",
+      "name" : "TRG_BIO_ANALYSIS_ATT_LINEAGE"
+    },
+    "file" : "biomart/bio_analysis_attribute_lineage.sql"
   }, {
     "item" : {
       "type" : "TRIGGER",
@@ -5466,6 +5697,13 @@
       "name" : "TRG_BIO_ASY_ANALYSIS_DATA_ID"
     },
     "file" : "biomart/bio_assay_analysis_data.sql"
+  }, {
+    "item" : {
+      "type" : "TRIGGER",
+      "owner" : "BIOMART",
+      "name" : "TRG_BIO_ASY_ANALYSIS_EQTL_ID"
+    },
+    "file" : "biomart/bio_assay_analysis_eqtl.sql"
   }, {
     "item" : {
       "type" : "TRIGGER",
@@ -5760,6 +5998,20 @@
       "name" : "TRIG_CLINICAL_TRIAL_DESIGN_ID "
     },
     "file" : "biomart/ctd_full.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART",
+      "name" : "T_A_GAE_T500_IDX"
+    },
+    "file" : "biomart/tmp_analysis_eqtl_top500.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "BIOMART",
+      "name" : "T_A_GE_T500_IDX"
+    },
+    "file" : "biomart/tmp_analysis_eqtl_top500.sql"
   }, {
     "item" : {
       "type" : "VIEW",
@@ -5775,4 +6027,4 @@
     },
     "file" : "biomart/views/vw_faceted_search_disease.sql"
   } ]
-}
+}
\ No newline at end of file
diff --git a/ddl/oracle/biomart/mesh.sql b/ddl/oracle/biomart/mesh.sql
index 00a91333..fed003ae 100644
--- a/ddl/oracle/biomart/mesh.sql
+++ b/ddl/oracle/biomart/mesh.sql
@@ -2,7 +2,7 @@
 -- Type: TABLE; Owner: BIOMART; Name: MESH
 --
  CREATE TABLE "BIOMART"."MESH" 
-  (	"UI" VARCHAR2(20 BYTE) NOT NULL ENABLE, 
+  (	"UI" VARCHAR2(20 BYTE), 
 "MH" VARCHAR2(200 BYTE), 
 "MN" VARCHAR2(200 BYTE), 
  PRIMARY KEY ("UI")
diff --git a/ddl/oracle/biomart/tmp_analysis_eqtl_top500.sql b/ddl/oracle/biomart/tmp_analysis_eqtl_top500.sql
new file mode 100644
index 00000000..9f2918ee
--- /dev/null
+++ b/ddl/oracle/biomart/tmp_analysis_eqtl_top500.sql
@@ -0,0 +1,29 @@
+--
+-- Type: TABLE; Owner: BIOMART; Name: TMP_ANALYSIS_EQTL_TOP500
+--
+ CREATE TABLE "BIOMART"."TMP_ANALYSIS_EQTL_TOP500" 
+  (	"BIO_ASY_ANALYSIS_EQTL_ID" NUMBER(22,0) NOT NULL ENABLE, 
+"BIO_ASSAY_ANALYSIS_ID" NUMBER(22,0) NOT NULL ENABLE, 
+"RS_ID" NVARCHAR2(50), 
+"P_VALUE" BINARY_DOUBLE, 
+"LOG_P_VALUE" BINARY_DOUBLE, 
+"ETL_ID" NUMBER(18,0), 
+"EXT_DATA" VARCHAR2(4000 BYTE), 
+"P_VALUE_CHAR" VARCHAR2(100 BYTE), 
+"GENE" VARCHAR2(50 BYTE), 
+"CIS_TRANS" VARCHAR2(10 BYTE), 
+"DISTANCE_FROM_GENE" VARCHAR2(10 BYTE), 
+"RNUM" NUMBER
+  ) SEGMENT CREATION IMMEDIATE
+NOCOMPRESS NOLOGGING
+ TABLESPACE "BIOMART" ;
+--
+-- Type: INDEX; Owner: BIOMART; Name: T_A_GAE_T500_IDX
+--
+CREATE INDEX "BIOMART"."T_A_GAE_T500_IDX" ON "BIOMART"."TMP_ANALYSIS_EQTL_TOP500" ("BIO_ASSAY_ANALYSIS_ID")
+TABLESPACE "INDX" ;
+--
+-- Type: INDEX; Owner: BIOMART; Name: T_A_GE_T500_IDX
+--
+CREATE INDEX "BIOMART"."T_A_GE_T500_IDX" ON "BIOMART"."TMP_ANALYSIS_EQTL_TOP500" ("RS_ID")
+TABLESPACE "INDX" ;
diff --git a/ddl/oracle/biomart/tmp_analysis_gwas_top500.sql b/ddl/oracle/biomart/tmp_analysis_gwas_top500.sql
new file mode 100644
index 00000000..f385e2f3
--- /dev/null
+++ b/ddl/oracle/biomart/tmp_analysis_gwas_top500.sql
@@ -0,0 +1,16 @@
+--
+-- Type: TABLE; Owner: BIOMART; Name: TMP_ANALYSIS_GWAS_TOP500
+--
+ CREATE TABLE "BIOMART"."TMP_ANALYSIS_GWAS_TOP500" 
+  (	"BIO_ASY_ANALYSIS_GWAS_ID" NUMBER(18,0) NOT NULL ENABLE, 
+"BIO_ASSAY_ANALYSIS_ID" NUMBER(18,0) NOT NULL ENABLE, 
+"RS_ID" NVARCHAR2(50), 
+"P_VALUE" BINARY_DOUBLE, 
+"LOG_P_VALUE" BINARY_DOUBLE, 
+"ETL_ID" NUMBER(18,0), 
+"EXT_DATA" VARCHAR2(4000 BYTE), 
+"P_VALUE_CHAR" VARCHAR2(100 BYTE), 
+"RNUM" NUMBER
+  ) SEGMENT CREATION IMMEDIATE
+NOCOMPRESS NOLOGGING
+ TABLESPACE "BIOMART" ;
diff --git a/ddl/oracle/biomart/views/bio_marker_correl_mv.sql b/ddl/oracle/biomart/views/bio_marker_correl_mv.sql
index 4e29f34e..9590a2a3 100644
--- a/ddl/oracle/biomart/views/bio_marker_correl_mv.sql
+++ b/ddl/oracle/biomart/views/bio_marker_correl_mv.sql
@@ -1,121 +1,98 @@
 --
 -- Type: MATERIALIZED_VIEW; Owner: BIOMART; Name: BIO_MARKER_CORREL_MV
 --
-  CREATE MATERIALIZED VIEW "BIOMART"."BIO_MARKER_CORREL_MV" ("BIO_MARKER_ID", "ASSO_BIO_MARKER_ID", "CORREL_TYPE", "MV_ID")
-  ORGANIZATION HEAP PCTFREE 10 PCTUSED 40 INITRANS 1 MAXTRANS 255 NOCOMPRESS LOGGING
-  TABLESPACE "TRANSMART" 
-  BUILD IMMEDIATE
-  USING INDEX 
-  REFRESH FORCE ON DEMAND
-  USING DEFAULT LOCAL ROLLBACK SEGMENT
-  USING ENFORCED CONSTRAINTS DISABLE QUERY REWRITE
-  AS SELECT DISTINCT
-              b.bio_marker_id,
-              b.bio_marker_id AS asso_bio_marker_id,
-              'GENE' AS correl_type,
-              1 AS mv_id
-          FROM
-                  biomart.bio_marker b
-          WHERE
-                  b.bio_marker_type = 'GENE'
-          UNION
-          SELECT DISTINCT
-              b.bio_marker_id,
-              b.bio_marker_id AS asso_bio_marker_id,
-              'PROTEIN' AS correl_type,
-              4 AS mv_id
-          FROM
-              biomart.bio_marker b
-          WHERE
-             b.bio_marker_type = 'PROTEIN'
-          UNION
-          SELECT DISTINCT
-              b.bio_marker_id,
-              b.bio_marker_id AS asso_bio_marker_id,
-              'MIRNA' AS correl_type,
-              7 AS mv_id
-          FROM
-              biomart.bio_marker b
-          WHERE
-             b.bio_marker_type = 'MIRNA'
-          UNION
-          SELECT DISTINCT
-              c.bio_data_id AS bio_marker_id,
-              c.asso_bio_data_id AS asso_bio_marker_id,
-              'PATHWAY GENE' AS correl_type,
-              2 AS mv_id
-          FROM
-              biomart.bio_marker b,
-              biomart.bio_data_correlation c,
-              biomart.bio_data_correl_descr d
-          WHERE
-              b.bio_marker_id = c.bio_data_id
-              AND c.bio_data_correl_descr_id = d.bio_data_correl_descr_id
-              AND b.primary_source_code <> 'ARIADNE'
-              AND d.correlation = 'PATHWAY GENE'
-          UNION
-          SELECT DISTINCT
-              c.bio_data_id AS bio_marker_id,
-              c.asso_bio_data_id AS asso_bio_marker_id,
-              'HOMOLOGENE_GENE' AS correl_type,
-              3 AS mv_id
-          FROM
-              biomart.bio_marker b,
-              biomart.bio_data_correlation c,
-              biomart.bio_data_correl_descr d
-          WHERE
-              b.bio_marker_id = c.bio_data_id
-              AND c.bio_data_correl_descr_id = d.bio_data_correl_descr_id
-              AND d.correlation = 'HOMOLOGENE GENE'
-          UNION
-          SELECT DISTINCT
-              c.bio_data_id AS bio_marker_id,
-              c.asso_bio_data_id AS asso_bio_marker_id,
-              'PROTEIN TO GENE' AS correl_type,
-              5 AS mv_id
-          FROM
-              biomart.bio_marker b,
-              biomart.bio_data_correlation c,
-              biomart.bio_data_correl_descr d
-          WHERE
-              b.bio_marker_id = c.bio_data_id
-              AND c.bio_data_correl_descr_id = d.bio_data_correl_descr_id
-              AND d.correlation = 'PROTEIN TO GENE'
-          UNION
-          SELECT DISTINCT
-              c.bio_data_id AS bio_marker_id,
-              c.asso_bio_data_id AS asso_bio_marker_id,
-              'GENE TO PROTEIN' AS correl_type,
-              6 AS mv_id
-          FROM
-              biomart.bio_marker b,
-              biomart.bio_data_correlation c,
-              biomart.bio_data_correl_descr d
-          WHERE
-              b.bio_marker_id = c.bio_data_id
-              AND c.bio_data_correl_descr_id = d.bio_data_correl_descr_id
-              AND d.correlation = 'GENE TO PROTEIN'
-          UNION
-          SELECT
-              c1.bio_data_id,
-              c2.asso_bio_data_id,
-              'PATHWAY TO PROTEIN' as correl_type,
-              8 AS mv_id
-          FROM
-              bio_data_correlation c1
-              INNER JOIN bio_data_correlation c2 ON c1.asso_bio_data_id = c2.bio_data_id
-              INNER JOIN bio_data_correl_descr d1 ON c1.bio_data_correl_descr_id = d1.bio_data_correl_descr_id
-              INNER JOIN bio_data_correl_descr d2 ON c2.bio_data_correl_descr_id = d2.bio_data_correl_descr_id
-              WHERE d1.correlation = 'PATHWAY GENE'
-              AND d2.correlation = 'GENE TO PROTEIN'
-          UNION
-          SELECT DISTINCT
-              b.bio_marker_id,
-              b.bio_marker_id AS asso_bio_marker_id,
-              'METABOLITE' AS correl_type,
-              9 AS mv_id
-          FROM
-              biomart.bio_marker b
-          WHERE
-b.bio_marker_type = 'METABOLITE';
+ CREATE MATERIALIZED VIEW "BIOMART"."BIO_MARKER_CORREL_MV" ("BIO_MARKER_ID", "ASSO_BIO_MARKER_ID", "CORREL_TYPE", "MV_ID")
+ ORGANIZATION HEAP PCTFREE 10 PCTUSED 40 INITRANS 1 MAXTRANS 255 
+ TABLESPACE "TRANSMART" 
+ BUILD IMMEDIATE
+ USING INDEX 
+ REFRESH FORCE ON DEMAND
+ USING DEFAULT LOCAL ROLLBACK SEGMENT
+ USING ENFORCED CONSTRAINTS DISABLE QUERY REWRITE
+ AS SELECT DISTINCT b.bio_marker_id,
+   b.bio_marker_id AS asso_bio_marker_id,
+   'GENE'          AS correl_type,
+   1               AS mv_id
+ FROM biomart.bio_marker b
+ WHERE b.bio_marker_type = 'GENE'
+ UNION
+ SELECT DISTINCT b.bio_marker_id,
+   b.bio_marker_id AS asso_bio_marker_id,
+   'PROTEIN'       AS correl_type,
+   4               AS mv_id
+ FROM biomart.bio_marker b
+ WHERE b.bio_marker_type = 'PROTEIN'
+ UNION
+ SELECT DISTINCT b.bio_marker_id,
+   b.bio_marker_id AS asso_bio_marker_id,
+   'MIRNA'         AS correl_type,
+   7               AS mv_id
+ FROM biomart.bio_marker b
+ WHERE b.bio_marker_type = 'MIRNA'
+ UNION
+ SELECT DISTINCT c.bio_data_id AS bio_marker_id,
+   c.asso_bio_data_id          AS asso_bio_marker_id,
+   'PATHWAY GENE'              AS correl_type,
+   2                           AS mv_id
+ FROM biomart.bio_marker b,
+   biomart.bio_data_correlation c,
+   biomart.bio_data_correl_descr d
+ WHERE b.bio_marker_id          = c.bio_data_id
+ AND c.bio_data_correl_descr_id = d.bio_data_correl_descr_id
+ AND b.primary_source_code     <> 'ARIADNE'
+ AND d.correlation              = 'PATHWAY GENE'
+ UNION
+ SELECT DISTINCT c.bio_data_id AS bio_marker_id,
+   c.asso_bio_data_id          AS asso_bio_marker_id,
+   'HOMOLOGENE_GENE'           AS correl_type,
+   3                           AS mv_id
+ FROM biomart.bio_marker b,
+   biomart.bio_data_correlation c,
+   biomart.bio_data_correl_descr d
+ WHERE b.bio_marker_id          = c.bio_data_id
+ AND c.bio_data_correl_descr_id = d.bio_data_correl_descr_id
+ AND d.correlation              = 'HOMOLOGENE GENE'
+ UNION
+ SELECT DISTINCT c.bio_data_id AS bio_marker_id,
+   c.asso_bio_data_id          AS asso_bio_marker_id,
+   'PROTEIN TO GENE'           AS correl_type,
+   5                           AS mv_id
+ FROM biomart.bio_marker b,
+   biomart.bio_data_correlation c,
+   biomart.bio_data_correl_descr d
+ WHERE b.bio_marker_id          = c.bio_data_id
+ AND c.bio_data_correl_descr_id = d.bio_data_correl_descr_id
+ AND d.correlation              = 'PROTEIN TO GENE'
+ UNION
+ SELECT DISTINCT c.bio_data_id AS bio_marker_id,
+   c.asso_bio_data_id          AS asso_bio_marker_id,
+   'GENE TO PROTEIN'           AS correl_type,
+   6                           AS mv_id
+ FROM biomart.bio_marker b,
+   biomart.bio_data_correlation c,
+   biomart.bio_data_correl_descr d
+ WHERE b.bio_marker_id          = c.bio_data_id
+ AND c.bio_data_correl_descr_id = d.bio_data_correl_descr_id
+ AND d.correlation              = 'GENE TO PROTEIN'
+ UNION
+ SELECT c1.bio_data_id,
+   c2.asso_bio_data_id,
+   'PATHWAY TO PROTEIN' AS correl_type,
+   8                    AS mv_id
+ FROM bio_data_correlation c1
+ INNER JOIN bio_data_correlation c2
+ ON c1.asso_bio_data_id = c2.bio_data_id
+ INNER JOIN bio_data_correl_descr d1
+ ON c1.bio_data_correl_descr_id = d1.bio_data_correl_descr_id
+ INNER JOIN bio_data_correl_descr d2
+ ON c2.bio_data_correl_descr_id = d2.bio_data_correl_descr_id
+ WHERE d1.correlation           = 'PATHWAY GENE'
+ AND d2.correlation             = 'GENE TO PROTEIN'
+ UNION
+ SELECT DISTINCT b.bio_marker_id,
+   b.bio_marker_id AS asso_bio_marker_id,
+   'METABOLITE'    AS correl_type,
+   9               AS mv_id
+ FROM biomart.bio_marker b
+ WHERE b.bio_marker_type = 'METABOLITE';
  
diff --git a/ddl/oracle/biomart/views/gwas_anlysis.sql b/ddl/oracle/biomart/views/gwas_anlysis.sql
new file mode 100644
index 00000000..742fc6f8
--- /dev/null
+++ b/ddl/oracle/biomart/views/gwas_anlysis.sql
@@ -0,0 +1,5 @@
+--
+-- Type: VIEW; Owner: BIOMART; Name: GWAS_ANLYSIS
+--
+CREATE OR REPLACE FORCE EDITIONABLE VIEW "BIOMART"."GWAS_ANLYSIS" ("BIO_ASSAY_ANALYSIS_ID", "ETL_ID", "ANALYSIS_NAME", "BIO_ASSAY_DATA_TYPE") AS 
+SELECT  to_char(bio_assay_analysis_id) bio_assay_analysis_id, etl_id, analysis_name, bio_assay_data_type from biomart.bio_assay_analysis where bio_assay_data_type not in ('Gene Expression');
diff --git a/ddl/oracle/biomart/views/vw_faceted_search.sql b/ddl/oracle/biomart/views/vw_faceted_search.sql
index a80463ab..24feb530 100644
--- a/ddl/oracle/biomart/views/vw_faceted_search.sql
+++ b/ddl/oracle/biomart/views/vw_faceted_search.sql
@@ -6,7 +6,7 @@
 ,be.bio_experiment_id as STUDY
 ,be.bio_experiment_id as STUDY_ID
 ,ba.analysis_type as ANALYSES
-,ba.bio_assay_data_type as DATA_TYPE 
+,ba.bio_assay_data_type as DATA_TYPE
 ,bplat.platform_accession as PLATFORM
 ,bplat.platform_description as PLATFORM_DESCRIPTION
 ,bplat.platform_vendor as PLATFORM_VENDOR
@@ -37,7 +37,7 @@
 ,bae.research_unit as RESEARCH_UNIT
 ,row_number() over (order by ba.bio_assay_analysis_id) as FACET_ID
 from bio_assay_analysis ba
-Join bio_experiment be 
+Join bio_experiment be
 on ba.etl_id = be.accession
 left outer join bio_assay_analysis_ext bae
 on bae.bio_assay_analysis_id = ba.bio_assay_analysis_id
@@ -51,5 +51,5 @@ left outer join bio_observation bpobs
 on bdpobs.bio_observation_id = bpobs.bio_observation_id
 left outer join bio_asy_analysis_pltfm baap
 on baap.bio_asy_analysis_pltfm_id = ba.bio_asy_analysis_pltfm_id
-WHERE lower(be.bio_experiment_type) = 'experiment';
+where lower(be.bio_experiment_type) = 'experiment';
  

From e544d34be93317e129d00cfe7186442375e02f0d Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 12:47:23 +0100
Subject: [PATCH 27/31] tm_lz updates from oracle test server

---
 ddl/oracle/tm_lz/items.json                   | 116 ++++++++++++++++++
 ddl/oracle/tm_lz/lt_chromosomal_region.sql    |   2 +-
 ddl/oracle/tm_lz/lt_snp_calls_by_gsm.sql      |  10 ++
 ddl/oracle/tm_lz/lt_snp_copy_number.sql       |  12 ++
 ddl/oracle/tm_lz/lt_snp_gene_map.sql          |   9 ++
 ddl/oracle/tm_lz/lt_src_acgh_data.sql         |   2 +-
 ddl/oracle/tm_lz/lt_src_cel_files.sql         |   8 +-
 ddl/oracle/tm_lz/lt_src_clinical_data.sql     |  10 +-
 ddl/oracle/tm_lz/lt_src_rnaseq_data.sql       |   2 +-
 ddl/oracle/tm_lz/lt_src_study_metadata.sql    |   2 +-
 ddl/oracle/tm_lz/lz_src_analysis_metadata.sql |   4 +-
 ddl/oracle/tm_lz/rwg_analysis_data_ext.sql    |   2 +-
 ddl/oracle/tm_lz/rwg_analysis_ext.sql         |   4 +-
 ddl/oracle/tm_lz/rwg_cohorts_ext.sql          |   2 +-
 ddl/oracle/tm_lz/rwg_samples_ext.sql          |   2 +-
 15 files changed, 171 insertions(+), 16 deletions(-)
 create mode 100644 ddl/oracle/tm_lz/lt_snp_calls_by_gsm.sql
 create mode 100644 ddl/oracle/tm_lz/lt_snp_copy_number.sql
 create mode 100644 ddl/oracle/tm_lz/lt_snp_gene_map.sql

diff --git a/ddl/oracle/tm_lz/items.json b/ddl/oracle/tm_lz/items.json
index 57a44cf2..52fb2fcb 100644
--- a/ddl/oracle/tm_lz/items.json
+++ b/ddl/oracle/tm_lz/items.json
@@ -6,6 +6,52 @@
       "name" : "CLINICAL_TRIAL_METADATA_EXT"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_LZ",
+      "name" : "I2B2_LOAD_CLINICAL_DATA_BACKUP"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_OBS_ENROLL_DAYS"
+    }, {
+      "type" : "TABLE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "OBSERVATION_FACT"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SRC_CLINICAL_DATA"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SRC_SUBJ_ENROLL_DATE"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LZ_SRC_CLINICAL_DATA"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "WRK_CLINICAL_DATA"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "WT_TRIAL_NODES"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "TM_LZ",
+      "name" : "IDX_SCD_STUDY"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SRC_CLINICAL_DATA"
+    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -55,6 +101,27 @@
       "name" : "LT_RNASEQ_ANNOTATION"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SNP_CALLS_BY_GSM"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SNP_COPY_NUMBER"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SNP_GENE_MAP"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -463,6 +530,13 @@
       "owner" : "TM_LZ",
       "name" : "SEQ_ETL_ID"
     } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_LZ",
+      "name" : "UTIL_GRANT_ALL"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -485,6 +559,20 @@
       "name" : "CLINICAL_TRIAL_METADATA_EXT"
     },
     "file" : "tm_lz/clinical_trial_metadata_ext.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_LZ",
+      "name" : "I2B2_LOAD_CLINICAL_DATA_BACKUP"
+    },
+    "file" : "tm_lz/procedures/i2b2_load_clinical_data_backup.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "TM_LZ",
+      "name" : "IDX_SCD_STUDY"
+    },
+    "file" : "tm_lz/lt_src_clinical_data.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -534,6 +622,27 @@
       "name" : "LT_RNASEQ_ANNOTATION"
     },
     "file" : "tm_lz/lt_rnaseq_annotation.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SNP_CALLS_BY_GSM"
+    },
+    "file" : "tm_lz/lt_snp_calls_by_gsm.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SNP_COPY_NUMBER"
+    },
+    "file" : "tm_lz/lt_snp_copy_number.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SNP_GENE_MAP"
+    },
+    "file" : "tm_lz/lt_snp_gene_map.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -926,6 +1035,13 @@
       "name" : "TRG_LZ_SRC_ANALYSIS_META_ID"
     },
     "file" : "tm_lz/lz_src_analysis_metadata.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_LZ",
+      "name" : "UTIL_GRANT_ALL"
+    },
+    "file" : "tm_lz/procedures/util_grant_all.sql"
   }, {
     "item" : {
       "type" : "TABLE",
diff --git a/ddl/oracle/tm_lz/lt_chromosomal_region.sql b/ddl/oracle/tm_lz/lt_chromosomal_region.sql
index 741e986c..f2e0e85e 100644
--- a/ddl/oracle/tm_lz/lt_chromosomal_region.sql
+++ b/ddl/oracle/tm_lz/lt_chromosomal_region.sql
@@ -21,7 +21,7 @@ CREATE SEQUENCE  "TM_LZ"."LT_CHROMO_REGION_ID_SEQ"  MINVALUE 1 MAXVALUE 99999999
  CONSTRAINT "LT_CHROMOSOMAL_REGION_PKEY" PRIMARY KEY ("REGION_ID")
  USING INDEX
  TABLESPACE "TRANSMART"  ENABLE
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
diff --git a/ddl/oracle/tm_lz/lt_snp_calls_by_gsm.sql b/ddl/oracle/tm_lz/lt_snp_calls_by_gsm.sql
new file mode 100644
index 00000000..b87d9e70
--- /dev/null
+++ b/ddl/oracle/tm_lz/lt_snp_calls_by_gsm.sql
@@ -0,0 +1,10 @@
+--
+-- Type: TABLE; Owner: TM_LZ; Name: LT_SNP_CALLS_BY_GSM
+--
+ CREATE TABLE "TM_LZ"."LT_SNP_CALLS_BY_GSM" 
+  (	"GSM_NUM" VARCHAR2(10 BYTE), 
+"SNP_NAME" VARCHAR2(100 BYTE), 
+"SNP_CALLS" VARCHAR2(4 BYTE)
+  ) SEGMENT CREATION DEFERRED
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_lz/lt_snp_copy_number.sql b/ddl/oracle/tm_lz/lt_snp_copy_number.sql
new file mode 100644
index 00000000..7d53d0e2
--- /dev/null
+++ b/ddl/oracle/tm_lz/lt_snp_copy_number.sql
@@ -0,0 +1,12 @@
+--
+-- Type: TABLE; Owner: TM_LZ; Name: LT_SNP_COPY_NUMBER
+--
+ CREATE TABLE "TM_LZ"."LT_SNP_COPY_NUMBER" 
+  (	"SNP_NAME" VARCHAR2(50 BYTE), 
+"CHROM" VARCHAR2(2 BYTE), 
+"CHROM_POS" NUMBER(20,0), 
+"COPY_NUMBER" FLOAT(53), 
+"GSM_NUM" VARCHAR2(10 BYTE)
+  ) SEGMENT CREATION DEFERRED
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_lz/lt_snp_gene_map.sql b/ddl/oracle/tm_lz/lt_snp_gene_map.sql
new file mode 100644
index 00000000..0b9a1a3b
--- /dev/null
+++ b/ddl/oracle/tm_lz/lt_snp_gene_map.sql
@@ -0,0 +1,9 @@
+--
+-- Type: TABLE; Owner: TM_LZ; Name: LT_SNP_GENE_MAP
+--
+ CREATE TABLE "TM_LZ"."LT_SNP_GENE_MAP" 
+  (	"SNP_NAME" VARCHAR2(256 BYTE), 
+"ENTREZ_GENE_ID" NUMBER
+  ) SEGMENT CREATION DEFERRED
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_lz/lt_src_acgh_data.sql b/ddl/oracle/tm_lz/lt_src_acgh_data.sql
index b1421bdc..be41c32e 100644
--- a/ddl/oracle/tm_lz/lt_src_acgh_data.sql
+++ b/ddl/oracle/tm_lz/lt_src_acgh_data.sql
@@ -12,6 +12,6 @@
 "PROBNORM" VARCHAR2(50 BYTE), 
 "PROBGAIN" VARCHAR2(50 BYTE), 
 "PROBAMP" VARCHAR2(50 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_lz/lt_src_cel_files.sql b/ddl/oracle/tm_lz/lt_src_cel_files.sql
index 5a8e806b..39e16d71 100644
--- a/ddl/oracle/tm_lz/lt_src_cel_files.sql
+++ b/ddl/oracle/tm_lz/lt_src_cel_files.sql
@@ -1,8 +1,8 @@
 --
 -- Type: TABLE; Owner: TM_LZ; Name: LT_SRC_CEL_FILES
 --
-CREATE TABLE "TM_LZ"."LT_SRC_CEL_FILES" 
- (	"CEL_FILE_NAME" VARCHAR2(500 BYTE)
- ) SEGMENT CREATION IMMEDIATE
-TABLESPACE "TRANSMART" ;
+ CREATE TABLE "TM_LZ"."LT_SRC_CEL_FILES" 
+  (	"CEL_FILE_NAME" VARCHAR2(500 BYTE)
+  ) SEGMENT CREATION IMMEDIATE
+ TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_lz/lt_src_clinical_data.sql b/ddl/oracle/tm_lz/lt_src_clinical_data.sql
index d27329a8..f357e9dc 100644
--- a/ddl/oracle/tm_lz/lt_src_clinical_data.sql
+++ b/ddl/oracle/tm_lz/lt_src_clinical_data.sql
@@ -27,5 +27,13 @@
 "MODIFIER_CD" VARCHAR2(100 BYTE), 
 "SAMPLE_CD" VARCHAR2(200 BYTE)
   ) SEGMENT CREATION IMMEDIATE
- TABLESPACE "TRANSMART" ;
+NOCOMPRESS NOLOGGING
+ TABLESPACE "TRANSMART" 
+  CACHE ;
+--
+-- Type: INDEX; Owner: TM_LZ; Name: IDX_SCD_STUDY
+--
+CREATE INDEX "TM_LZ"."IDX_SCD_STUDY" ON "TM_LZ"."LT_SRC_CLINICAL_DATA" ("STUDY_ID")
+TABLESPACE "TRANSMART" ;
+
 
diff --git a/ddl/oracle/tm_lz/lt_src_rnaseq_data.sql b/ddl/oracle/tm_lz/lt_src_rnaseq_data.sql
index 4c8a361e..5c53737e 100644
--- a/ddl/oracle/tm_lz/lt_src_rnaseq_data.sql
+++ b/ddl/oracle/tm_lz/lt_src_rnaseq_data.sql
@@ -6,6 +6,6 @@
 "REGION_NAME" VARCHAR2(100 BYTE), 
 "EXPR_ID" VARCHAR2(100 BYTE), 
 "READCOUNT" VARCHAR2(50 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_lz/lt_src_study_metadata.sql b/ddl/oracle/tm_lz/lt_src_study_metadata.sql
index c5f22780..c06bbff8 100644
--- a/ddl/oracle/tm_lz/lt_src_study_metadata.sql
+++ b/ddl/oracle/tm_lz/lt_src_study_metadata.sql
@@ -58,6 +58,6 @@
 "STUDY_DESIGN_FACTORS" VARCHAR2(2000 BYTE), 
 "STUDY_NBR_SUBJECTS" VARCHAR2(20 BYTE), 
 "STUDY_ORGANISM" VARCHAR2(500 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_lz/lz_src_analysis_metadata.sql b/ddl/oracle/tm_lz/lz_src_analysis_metadata.sql
index 8c5139b1..7351491e 100644
--- a/ddl/oracle/tm_lz/lz_src_analysis_metadata.sql
+++ b/ddl/oracle/tm_lz/lz_src_analysis_metadata.sql
@@ -5,7 +5,7 @@
   (	"STUDY_ID" VARCHAR2(50 BYTE), 
 "DATA_TYPE" VARCHAR2(50 BYTE), 
 "ANALYSIS_NAME" VARCHAR2(500 BYTE), 
-"DESCRIPTION" VARCHAR2(500 BYTE), 
+"DESCRIPTION" VARCHAR2(2048 BYTE), 
 "PHENOTYPE_IDS" VARCHAR2(250 BYTE), 
 "POPULATION" VARCHAR2(500 BYTE), 
 "TISSUE" VARCHAR2(500 BYTE), 
@@ -27,7 +27,7 @@
 "MODEL_DESC" VARCHAR2(500 BYTE), 
 "SENSITIVE_FLAG" NUMBER(18,0), 
 "SENSITIVE_DESC" VARCHAR2(500 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
 --
diff --git a/ddl/oracle/tm_lz/rwg_analysis_data_ext.sql b/ddl/oracle/tm_lz/rwg_analysis_data_ext.sql
index fb33bf1b..94af7a64 100644
--- a/ddl/oracle/tm_lz/rwg_analysis_data_ext.sql
+++ b/ddl/oracle/tm_lz/rwg_analysis_data_ext.sql
@@ -10,6 +10,6 @@
 "FOLD_CHANGE" VARCHAR2(100 BYTE), 
 "LSMEAN_1" VARCHAR2(100 BYTE), 
 "LSMEAN_2" VARCHAR2(100 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_lz/rwg_analysis_ext.sql b/ddl/oracle/tm_lz/rwg_analysis_ext.sql
index 523e7632..649770e1 100644
--- a/ddl/oracle/tm_lz/rwg_analysis_ext.sql
+++ b/ddl/oracle/tm_lz/rwg_analysis_ext.sql
@@ -13,6 +13,6 @@
 "PLATFORM" VARCHAR2(500 BYTE), 
 "LONG_DESC" VARCHAR2(500 BYTE), 
 "SHORT_DESC" VARCHAR2(500 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
+NOCOMPRESS LOGGING
  TABLESPACE "TRANSMART" ;
-
diff --git a/ddl/oracle/tm_lz/rwg_cohorts_ext.sql b/ddl/oracle/tm_lz/rwg_cohorts_ext.sql
index 6636f143..d5cf4d9f 100644
--- a/ddl/oracle/tm_lz/rwg_cohorts_ext.sql
+++ b/ddl/oracle/tm_lz/rwg_cohorts_ext.sql
@@ -12,6 +12,6 @@
 "COHORT_TITLE" VARCHAR2(500 BYTE), 
 "SHORT_DESC" VARCHAR2(500 BYTE), 
 "LONG_DESC" VARCHAR2(500 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_lz/rwg_samples_ext.sql b/ddl/oracle/tm_lz/rwg_samples_ext.sql
index 8f5cbd79..3eaefd59 100644
--- a/ddl/oracle/tm_lz/rwg_samples_ext.sql
+++ b/ddl/oracle/tm_lz/rwg_samples_ext.sql
@@ -5,6 +5,6 @@
   (	"STUDY_ID" VARCHAR2(500 BYTE), 
 "EXPR_ID" VARCHAR2(500 BYTE), 
 "COHORTS" VARCHAR2(500 BYTE)
-  ) SEGMENT CREATION DEFERRED
+  ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 

From ad7aa3c61eaaaaff6f4a8cfd73f88de364173f84 Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 13:27:24 +0100
Subject: [PATCH 28/31] tm_cz updates from oracle test server

---
 ddl/oracle/tm_cz/_cross.sql                   |   18 +
 ddl/oracle/tm_cz/az_test_comparison_info.sql  |    2 +-
 .../tm_cz/category_path_excluded_words.sql    |    8 +-
 ddl/oracle/tm_cz/cz_job_audit.sql             |    6 +
 ddl/oracle/tm_cz/cz_xtrial_exclusion.sql      |    8 +-
 .../tm_cz/de_snp__data_by_probe_release.sql   |    0
 ddl/oracle/tm_cz/dk1.sql                      |    8 +-
 ddl/oracle/tm_cz/functions/repeat_char.sql    |   30 +
 ddl/oracle/tm_cz/items.json                   | 1286 +++++++++++--
 .../tm_cz/procedures/cz_error_handler.sql     |    6 +-
 .../tm_cz/procedures/czx_error_handler.sql    |    8 +-
 .../procedures/i2b2_load_chrom_region.sql     |  150 ++
 .../tm_cz/procedures/i2b2_load_eqtl_top50.sql |  156 ++
 .../tm_cz/procedures/i2b2_load_gwas_top50.sql |  146 ++
 .../procedures/i2b2_load_proteomics_annot.sql |   90 +-
 ddl/oracle/tm_cz/procedures/i2b2_load_rbm_    |    0
 .../procedures/i2b2_move_analysis_to_prod.sql |  353 ++++
 .../i2b2_move_analysis_to_prod_new.sql        |  353 ++++
 .../procedures/i2b2_mrna_index_maint.sql      |   97 +-
 .../procedures/i2b2_process_acgh_data.sql     |  980 ++++++++++
 .../procedures/i2b2_process_rnaseq_data.sql   |  956 ++++++++++
 .../procedures/i2b2_process_snp_data.sql      | 1621 +++++++++++++++++
 .../tm_cz/procedures/partition_gwas_data.sql  |  112 ++
 ddl/oracle/tm_cz/stg_rbm_antigen_gene.sql     |   10 +
 ddl/oracle/tm_cz/stg_subject_rbm_data.sql     |   16 +
 ddl/oracle/tm_cz/stg_subject_rbm_data_raw.sql |   16 +
 ddl/oracle/tm_cz/tmp_subject_info.sql         |    6 +
 ddl/oracle/tm_cz/views/patient_info.sql       |    6 +
 28 files changed, 6203 insertions(+), 245 deletions(-)
 create mode 100644 ddl/oracle/tm_cz/de_snp__data_by_probe_release.sql
 create mode 100644 ddl/oracle/tm_cz/functions/repeat_char.sql
 create mode 100644 ddl/oracle/tm_cz/procedures/i2b2_load_chrom_region.sql
 create mode 100644 ddl/oracle/tm_cz/procedures/i2b2_load_eqtl_top50.sql
 create mode 100644 ddl/oracle/tm_cz/procedures/i2b2_load_gwas_top50.sql
 create mode 100644 ddl/oracle/tm_cz/procedures/i2b2_load_rbm_
 create mode 100644 ddl/oracle/tm_cz/procedures/i2b2_move_analysis_to_prod.sql
 create mode 100644 ddl/oracle/tm_cz/procedures/i2b2_move_analysis_to_prod_new.sql
 create mode 100644 ddl/oracle/tm_cz/procedures/i2b2_process_acgh_data.sql
 create mode 100644 ddl/oracle/tm_cz/procedures/i2b2_process_rnaseq_data.sql
 create mode 100644 ddl/oracle/tm_cz/procedures/i2b2_process_snp_data.sql
 create mode 100644 ddl/oracle/tm_cz/procedures/partition_gwas_data.sql
 create mode 100644 ddl/oracle/tm_cz/stg_rbm_antigen_gene.sql
 create mode 100644 ddl/oracle/tm_cz/stg_subject_rbm_data.sql
 create mode 100644 ddl/oracle/tm_cz/stg_subject_rbm_data_raw.sql
 create mode 100644 ddl/oracle/tm_cz/views/patient_info.sql

diff --git a/ddl/oracle/tm_cz/_cross.sql b/ddl/oracle/tm_cz/_cross.sql
index 24f78dcf..b09a22c9 100644
--- a/ddl/oracle/tm_cz/_cross.sql
+++ b/ddl/oracle/tm_cz/_cross.sql
@@ -53,3 +53,21 @@ from
 			,f.c_name 
 ) x;
  
+--
+-- Type: INDEX; Owner: TM_CZ; Name: IDX_I2B2_SECURE_FULLNAME
+--
+CREATE INDEX "TM_CZ"."IDX_I2B2_SECURE_FULLNAME" ON "I2B2METADATA"."I2B2_SECURE" ("C_FULLNAME")
+TABLESPACE "TRANSMART" ;
+
+--
+-- Type: INDEX; Owner: TM_CZ; Name: IX_I2B2_SOURCE_SYSTEM_CD
+--
+CREATE INDEX "TM_CZ"."IX_I2B2_SOURCE_SYSTEM_CD" ON "I2B2METADATA"."I2B2" ("SOURCESYSTEM_CD")
+TABLESPACE "TRANSMART" ;
+
+--
+-- Type: INDEX; Owner: TM_CZ; Name: IX_DE_SUBJECT_SMPL_MPNG_MRNA
+--
+CREATE INDEX "TM_CZ"."IX_DE_SUBJECT_SMPL_MPNG_MRNA" ON "DEAPP"."DE_SUBJECT_SAMPLE_MAPPING" ("TRIAL_NAME", "PLATFORM", "SOURCE_CD", "CONCEPT_CODE")
+TABLESPACE "TRANSMART" ;
+
diff --git a/ddl/oracle/tm_cz/az_test_comparison_info.sql b/ddl/oracle/tm_cz/az_test_comparison_info.sql
index e30069e8..26442215 100644
--- a/ddl/oracle/tm_cz/az_test_comparison_info.sql
+++ b/ddl/oracle/tm_cz/az_test_comparison_info.sql
@@ -13,5 +13,5 @@
 "CURR_RUN_DATE" DATE, 
 "PREV_RUN_DATE" DATE
   ) SEGMENT CREATION IMMEDIATE
+NOCOMPRESS LOGGING
  TABLESPACE "TRANSMART" ;
-
diff --git a/ddl/oracle/tm_cz/category_path_excluded_words.sql b/ddl/oracle/tm_cz/category_path_excluded_words.sql
index 89d924ec..afe45c94 100644
--- a/ddl/oracle/tm_cz/category_path_excluded_words.sql
+++ b/ddl/oracle/tm_cz/category_path_excluded_words.sql
@@ -1,8 +1,8 @@
 --
 -- Type: TABLE; Owner: TM_CZ; Name: CATEGORY_PATH_EXCLUDED_WORDS
 --
-CREATE TABLE "TM_CZ"."CATEGORY_PATH_EXCLUDED_WORDS" 
- (	"EXCLUDED_TEXT" VARCHAR2(100 BYTE)
- ) SEGMENT CREATION IMMEDIATE
-TABLESPACE "TRANSMART" ;
+ CREATE TABLE "TM_CZ"."CATEGORY_PATH_EXCLUDED_WORDS" 
+  (	"EXCLUDED_TEXT" VARCHAR2(100 BYTE)
+  ) SEGMENT CREATION IMMEDIATE
+ TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_cz/cz_job_audit.sql b/ddl/oracle/tm_cz/cz_job_audit.sql
index c5aa824e..7d702606 100644
--- a/ddl/oracle/tm_cz/cz_job_audit.sql
+++ b/ddl/oracle/tm_cz/cz_job_audit.sql
@@ -43,3 +43,9 @@ CREATE SEQUENCE  "TM_CZ"."SEQ_CZ_JOB_AUDIT"  MINVALUE 1 MAXVALUE 999999999999999
 /
 ALTER TRIGGER "TM_CZ"."TRG_CZ_SEQ_ID" ENABLE;
  
+--
+-- Type: INDEX; Owner: TM_CZ; Name: CZ_JOB_AUDIT_JOBID_DATE
+--
+CREATE INDEX "TM_CZ"."CZ_JOB_AUDIT_JOBID_DATE" ON "TM_CZ"."CZ_JOB_AUDIT" ("JOB_ID", "JOB_DATE")
+TABLESPACE "TRANSMART" ;
+
diff --git a/ddl/oracle/tm_cz/cz_xtrial_exclusion.sql b/ddl/oracle/tm_cz/cz_xtrial_exclusion.sql
index 9ca6eba9..3991d473 100644
--- a/ddl/oracle/tm_cz/cz_xtrial_exclusion.sql
+++ b/ddl/oracle/tm_cz/cz_xtrial_exclusion.sql
@@ -1,8 +1,8 @@
 --
 -- Type: TABLE; Owner: TM_CZ; Name: CZ_XTRIAL_EXCLUSION
 --
-CREATE TABLE "TM_CZ"."CZ_XTRIAL_EXCLUSION" 
- (	"TRIAL_ID" VARCHAR2(200 BYTE)
- ) SEGMENT CREATION DEFERRED
-TABLESPACE "TRANSMART" ;
+ CREATE TABLE "TM_CZ"."CZ_XTRIAL_EXCLUSION" 
+  (	"TRIAL_ID" VARCHAR2(200 BYTE)
+  ) SEGMENT CREATION DEFERRED
+ TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_cz/de_snp__data_by_probe_release.sql b/ddl/oracle/tm_cz/de_snp__data_by_probe_release.sql
new file mode 100644
index 00000000..e69de29b
diff --git a/ddl/oracle/tm_cz/dk1.sql b/ddl/oracle/tm_cz/dk1.sql
index ef16f9cd..85652a06 100644
--- a/ddl/oracle/tm_cz/dk1.sql
+++ b/ddl/oracle/tm_cz/dk1.sql
@@ -1,8 +1,8 @@
 --
 -- Type: TABLE; Owner: TM_CZ; Name: DK1
 --
-CREATE TABLE "TM_CZ"."DK1" 
- (	"C1" VARCHAR2(10 BYTE)
- ) SEGMENT CREATION IMMEDIATE
-TABLESPACE "TRANSMART" ;
+ CREATE TABLE "TM_CZ"."DK1" 
+  (	"C1" VARCHAR2(10 BYTE)
+  ) SEGMENT CREATION IMMEDIATE
+ TABLESPACE "TRANSMART" ;
 
diff --git a/ddl/oracle/tm_cz/functions/repeat_char.sql b/ddl/oracle/tm_cz/functions/repeat_char.sql
new file mode 100644
index 00000000..60c88d48
--- /dev/null
+++ b/ddl/oracle/tm_cz/functions/repeat_char.sql
@@ -0,0 +1,30 @@
+--
+-- Type: FUNCTION; Owner: TM_CZ; Name: REPEAT_CHAR
+--
+  CREATE OR REPLACE EDITIONABLE FUNCTION "TM_CZ"."REPEAT_CHAR" (i_value varchar2, i_count integer, i_char VARCHAR2)
+   return varchar2
+is
+
+--	use this function if version of Oracle does not support REPEAT string function
+	v_loop_ct	integer;
+	v_value		varchar2(4000);
+
+begin
+
+	if i_count < 1 then
+		return i_value;
+	end if;
+
+	v_loop_ct := 1;
+	v_value := i_value;
+
+	while v_loop_ct <= i_count
+	loop
+		v_value := v_value || i_char;
+		v_loop_ct := v_loop_ct + 1;
+	end loop;
+
+	return v_value;
+
+end repeat_char;
+/
diff --git a/ddl/oracle/tm_cz/items.json b/ddl/oracle/tm_cz/items.json
index e36d6aa6..9423a23a 100644
--- a/ddl/oracle/tm_cz/items.json
+++ b/ddl/oracle/tm_cz/items.json
@@ -433,17 +433,6 @@
       "owner" : "BIOMART",
       "name" : "BIO_ASSAY_ANALYSIS_EXT"
     } ]
-  }, {
-    "child" : {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "BIO_ASSAY_ANALYSIS_GWAS"
-    },
-    "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "BIOMART",
-      "name" : "BIO_ASSAY_ANALYSIS_GWAS"
-    } ]
   }, {
     "child" : {
       "type" : "FUNCTION",
@@ -1118,17 +1107,6 @@
       "owner" : "BIOMART",
       "name" : "BIO_MARKER"
     } ]
-  }, {
-    "child" : {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "BIO_MARKER_CORREL_MV"
-    },
-    "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "BIOMART",
-      "name" : "BIO_MARKER_CORREL_MV"
-    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -1228,6 +1206,17 @@
       "owner" : "BIOMART",
       "name" : "BIO_TAXONOMY"
     } ]
+  }, {
+    "child" : {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "BIRN"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2METADATA",
+      "name" : "BIRN"
+    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -2125,6 +2114,17 @@
       "name" : "CZ_JOB_AUDIT"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "CZ_JOB_AUDIT_JOBID_DATE"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_JOB_AUDIT"
+    } ]
   }, {
     "child" : {
       "type" : "TABLE",
@@ -4087,6 +4087,53 @@
       "owner" : "TM_LZ",
       "name" : "LT_SRC_DEAPP_ANNOT"
     } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_CHROM_REGION"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_MARKER"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_CHROMOSOMAL_REGION"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_GPL_INFO"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_CHROMOSOMAL_REGION"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "LT_CHROMOSOMAL_REGION"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_CHROMOSOMAL_REGION"
+    } ]
   }, {
     "child" : {
       "type" : "PROCEDURE",
@@ -4699,6 +4746,84 @@
       "owner" : "TM_WZ",
       "name" : "WRK_CLINICAL_DATA"
     } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_EQTL_TOP50"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASY_ANALYSIS_EQTL_TOP50"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_RC_SNP_INFO"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_GWAS_TOP50"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_GWAS"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASY_ANALYSIS_GWAS_TOP50"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_RC_SNP_INFO"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    } ]
   }, {
     "child" : {
       "type" : "PROCEDURE",
@@ -5782,12 +5907,32 @@
     "child" : {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
-      "name" : "I2B2_MOVE_NODE"
+      "name" : "I2B2_MOVE_ANALYSIS_TO_PROD"
     },
     "parents" : [ {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "CONCEPT_DIMENSION"
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_GWAS"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASY_ANALYSIS_DATA_IDX"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART_STAGE",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART_STAGE",
+      "name" : "BIO_ASSAY_ANALYSIS_GWAS"
     }, {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
@@ -5805,32 +5950,48 @@
       "owner" : "TM_CZ",
       "name" : "CZ_WRITE_AUDIT"
     }, {
-      "type" : "SYNONYM",
+      "type" : "PROCEDURE",
       "owner" : "TM_CZ",
-      "name" : "I2B2"
+      "name" : "I2B2_LOAD_EQTL_TOP50"
     }, {
-      "type" : "FUNCTION",
+      "type" : "PROCEDURE",
       "owner" : "TM_CZ",
-      "name" : "PARSE_NTH_VALUE"
+      "name" : "I2B2_LOAD_GWAS_TOP50"
     }, {
-      "type" : "SYNONYM",
+      "type" : "FUNCTION",
       "owner" : "TM_CZ",
-      "name" : "TABLE_ACCESS"
+      "name" : "REPEAT_CHAR"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LZ_SRC_ANALYSIS_METADATA"
     } ]
   }, {
     "child" : {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
-      "name" : "I2B2_MOVE_STUDY"
+      "name" : "I2B2_MOVE_ANALYSIS_TO_PROD_NEW"
     },
     "parents" : [ {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "CONCEPT_COUNTS"
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS"
     }, {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "CONCEPT_DIMENSION"
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "BIO_ASY_ANALYSIS_DATA_IDX"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART_STAGE",
+      "name" : "BIO_ASSAY_ANALYSIS_EQTL"
+    }, {
+      "type" : "TABLE",
+      "owner" : "BIOMART_STAGE",
+      "name" : "BIO_ASSAY_ANALYSIS_GWAS"
     }, {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
@@ -5847,38 +6008,42 @@
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
       "name" : "CZ_WRITE_AUDIT"
-    }, {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "I2B2"
-    }, {
-      "type" : "PROCEDURE",
-      "owner" : "TM_CZ",
-      "name" : "I2B2_ADD_ROOT_NODE"
     }, {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
-      "name" : "I2B2_FILL_IN_TREE"
+      "name" : "I2B2_LOAD_EQTL_TOP50"
     }, {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
-      "name" : "I2B2_LOAD_SECURITY_DATA"
+      "name" : "I2B2_LOAD_GWAS_TOP50"
     }, {
       "type" : "FUNCTION",
       "owner" : "TM_CZ",
-      "name" : "PARSE_NTH_VALUE"
+      "name" : "REPEAT_CHAR"
     }, {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "TABLE_ACCESS"
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LZ_SRC_ANALYSIS_METADATA"
     } ]
   }, {
     "child" : {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
-      "name" : "I2B2_MRNA_INC_SUB_ZSCORE"
+      "name" : "I2B2_MOVE_NODE"
     },
     "parents" : [ {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "CONCEPT_DIMENSION"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
       "name" : "CZ_START_AUDIT"
@@ -5889,9 +6054,91 @@
     }, {
       "type" : "SYNONYM",
       "owner" : "TM_CZ",
-      "name" : "DE_SUBJECT_MICROARRAY_DATA"
-    } ]
-  }, {
+      "name" : "I2B2"
+    }, {
+      "type" : "FUNCTION",
+      "owner" : "TM_CZ",
+      "name" : "PARSE_NTH_VALUE"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "TABLE_ACCESS"
+    } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_MOVE_STUDY"
+    },
+    "parents" : [ {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "CONCEPT_COUNTS"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "CONCEPT_DIMENSION"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "I2B2"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_ADD_ROOT_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_FILL_IN_TREE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_SECURITY_DATA"
+    }, {
+      "type" : "FUNCTION",
+      "owner" : "TM_CZ",
+      "name" : "PARSE_NTH_VALUE"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "TABLE_ACCESS"
+    } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_MRNA_INC_SUB_ZSCORE"
+    },
+    "parents" : [ {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_MICROARRAY_DATA"
+    } ]
+  }, {
     "child" : {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
@@ -6008,6 +6255,145 @@
       "owner" : "TM_CZ",
       "name" : "WT_SUBJECT_MRNA_PROBESET"
     } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROCESS_ACGH_DATA"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_CHROMOSOMAL_REGION"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_ACGH_DATA"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_SAMPLE_MAPPING"
+    }, {
+      "type" : "SEQUENCE",
+      "owner" : "DEAPP",
+      "name" : "SEQ_ASSAY_ID"
+    }, {
+      "type" : "TABLE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "SAMPLE_DIMENSION"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "CONCEPT_DIMENSION"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_CHROMOSOMAL_REGION"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_GPL_INFO"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_ACGH_DATA"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_SAMPLE_MAPPING"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "I2B2"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_ADD_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_ADD_ROOT_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_CREATE_CONCEPT_COUNTS"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_CREATE_SECURITY_FOR_TRIAL"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_DELETE_1_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_FILL_IN_TREE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_SECURITY_DATA"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "LT_SRC_MRNA_SUBJ_SAMP_MAP"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "OBSERVATION_FACT"
+    }, {
+      "type" : "FUNCTION",
+      "owner" : "TM_CZ",
+      "name" : "PARSE_NTH_VALUE"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "PATIENT_DIMENSION"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "SEQ_PATIENT_NUM"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "TABLE_ACCESS"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_MRNA_NODES"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_MRNA_NODE_VALUES"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SRC_ACGH_DATA"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SRC_DISPLAY_MAPPING"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "WT_SUBJECT_ACGH_REGION"
+    } ]
   }, {
     "child" : {
       "type" : "PROCEDURE",
@@ -7251,9 +7637,17 @@
     "child" : {
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
-      "name" : "I2B2_PROCESS_RNA_SEQ_DATA"
+      "name" : "I2B2_PROCESS_RNASEQ_DATA"
     },
     "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_CHROMOSOMAL_REGION"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_RNASEQ_DATA"
+    }, {
       "type" : "TABLE",
       "owner" : "DEAPP",
       "name" : "DE_SUBJECT_SAMPLE_MAPPING"
@@ -7288,7 +7682,15 @@
     }, {
       "type" : "SYNONYM",
       "owner" : "TM_CZ",
-      "name" : "DE_SUBJECT_RNA_DATA"
+      "name" : "DE_CHROMOSOMAL_REGION"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_GPL_INFO"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_RNASEQ_DATA"
     }, {
       "type" : "SYNONYM",
       "owner" : "TM_CZ",
@@ -7325,18 +7727,10 @@
       "type" : "PROCEDURE",
       "owner" : "TM_CZ",
       "name" : "I2B2_LOAD_SECURITY_DATA"
-    }, {
-      "type" : "PROCEDURE",
-      "owner" : "TM_CZ",
-      "name" : "I2B2_RNA_SEQ_ZSCORE_CALC"
-    }, {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "LT_SRC_RNA_SEQ_DATA"
     }, {
       "type" : "SYNONYM",
       "owner" : "TM_CZ",
-      "name" : "LT_SRC_RNA_SEQ_SUBJ_SAMP_MAP"
+      "name" : "LT_SRC_MRNA_SUBJ_SAMP_MAP"
     }, {
       "type" : "SYNONYM",
       "owner" : "TM_CZ",
@@ -7349,10 +7743,141 @@
       "type" : "SYNONYM",
       "owner" : "TM_CZ",
       "name" : "PATIENT_DIMENSION"
-    }, {
-      "type" : "TABLE",
-      "owner" : "TM_CZ",
-      "name" : "PROBESET_DEAPP"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "SEQ_PATIENT_NUM"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "TABLE_ACCESS"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_MRNA_NODES"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_MRNA_NODE_VALUES"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SRC_DISPLAY_MAPPING"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SRC_RNASEQ_DATA"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_WZ",
+      "name" : "WT_SUBJECT_RNASEQ_REGION"
+    } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROCESS_RNA_SEQ_DATA"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_SAMPLE_MAPPING"
+    }, {
+      "type" : "SEQUENCE",
+      "owner" : "DEAPP",
+      "name" : "SEQ_ASSAY_ID"
+    }, {
+      "type" : "TABLE",
+      "owner" : "I2B2DEMODATA",
+      "name" : "SAMPLE_DIMENSION"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "CONCEPT_DIMENSION"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_RNA_DATA"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_SAMPLE_MAPPING"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "I2B2"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_ADD_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_ADD_ROOT_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_CREATE_CONCEPT_COUNTS"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_CREATE_SECURITY_FOR_TRIAL"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_DELETE_1_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_FILL_IN_TREE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_SECURITY_DATA"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_RNA_SEQ_ZSCORE_CALC"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "LT_SRC_RNA_SEQ_DATA"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "LT_SRC_RNA_SEQ_SUBJ_SAMP_MAP"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "OBSERVATION_FACT"
+    }, {
+      "type" : "FUNCTION",
+      "owner" : "TM_CZ",
+      "name" : "PARSE_NTH_VALUE"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "PATIENT_DIMENSION"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "PROBESET_DEAPP"
     }, {
       "type" : "SYNONYM",
       "owner" : "TM_CZ",
@@ -7624,6 +8149,149 @@
       "owner" : "TM_LZ",
       "name" : "LT_SRC_RNA_DISPLAY_MAPPING"
     } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROCESS_SNP_DATA"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SNP_CALLS_BY_GSM"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SNP_COPY_NUMBER"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_SAMPLE_MAPPING"
+    }, {
+      "type" : "SEQUENCE",
+      "owner" : "DEAPP",
+      "name" : "SEQ_ASSAY_ID"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "CONCEPT_DIMENSION"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_GPL_INFO"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_MRNA_ANNOTATION"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_MICROARRAY_DATA"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_SAMPLE_MAPPING"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "I2B2"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_ADD_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_ADD_ROOT_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_CREATE_CONCEPT_COUNTS"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_CREATE_SECURITY_FOR_TRIAL"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_DELETE_1_NODE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_FILL_IN_TREE"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_SECURITY_DATA"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_MRNA_ZSCORE_CALC"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "LT_SRC_MRNA_DATA"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "LT_SRC_MRNA_SUBJ_SAMP_MAP"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "OBSERVATION_FACT"
+    }, {
+      "type" : "FUNCTION",
+      "owner" : "TM_CZ",
+      "name" : "PARSE_NTH_VALUE"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "PATIENT_DIMENSION"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "PROBESET_DEAPP"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "SEQ_PATIENT_NUM"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "TABLE_ACCESS"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_MRNA_NODES"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_MRNA_NODE_VALUES"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_SUBJECT_MRNA_PROBESET"
+    }, {
+      "type" : "TABLE",
+      "owner" : "TM_LZ",
+      "name" : "LT_SRC_MRNA_SUBJ_SAMP_MAP"
+    } ]
   }, {
     "child" : {
       "type" : "PROCEDURE",
@@ -7767,6 +8435,24 @@
       "owner" : "TM_LZ",
       "name" : "LT_SRC_METABOLOMIC_MAP"
     } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEIN_INC_SUB_ZSCORE"
+    },
+    "parents" : [ {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_PROTEIN_DATA"
+    } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEIN_INC_SUB_ZSCORE2"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "PROCEDURE",
@@ -7818,6 +8504,115 @@
       "owner" : "TM_CZ",
       "name" : "WT_SUBJECT_PROTEOMICS_PROBESET"
     } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEIN_INC_ZSCORE_CALC2"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_PROTEIN_ANNOTATION"
+    }, {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_PROTEIN_DATA"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_PROTEIN_DATA"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_SUBJECT_PROTEOMICS_CALCS"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_SUBJECT_PROTEOMICS_LOGS"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_SUBJECT_PROTEOMICS_MED"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_SUBJECT_PROTEOMICS_PROBESET"
+    } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEIN_INC_ZSCORE_CALC3"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_PROTEIN_ANNOTATION"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "DE_SUBJECT_PROTEIN_DATA"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEIN_INC_SUB_ZSCORE"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_SUBJECT_PROTEOMICS_CALCS"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_SUBJECT_PROTEOMICS_LOGS"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_SUBJECT_PROTEOMICS_MED"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "WT_SUBJECT_PROTEOMICS_PROBESET"
+    } ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEOMICS_INC_SUB_ZSCORE"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "PROCEDURE",
@@ -8589,13 +9384,35 @@
       "name" : "I2B2_UI_LABEL_CHANGE_BK"
     },
     "parents" : [ {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "CONCEPT_DIMENSION"
-    }, {
-      "type" : "SYNONYM",
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "CONCEPT_DIMENSION"
+    }, {
+      "type" : "SYNONYM",
+      "owner" : "TM_CZ",
+      "name" : "I2B2"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "IDX_I2B2_SECURE_FULLNAME"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2METADATA",
+      "name" : "I2B2_SECURE"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "IDX_TMP_SUBJ_USUBJID"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
       "owner" : "TM_CZ",
-      "name" : "I2B2"
+      "name" : "TMP_SUBJECT_INFO"
     } ]
   }, {
     "child" : {
@@ -8618,6 +9435,28 @@
       "name" : "IS_NUMBER_V2"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "IX_DE_SUBJECT_SMPL_MPNG_MRNA"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "DEAPP",
+      "name" : "DE_SUBJECT_SAMPLE_MAPPING"
+    } ]
+  }, {
+    "child" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "IX_I2B2_SOURCE_SYSTEM_CD"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "I2B2METADATA",
+      "name" : "I2B2"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -8695,17 +9534,6 @@
       "owner" : "DEAPP",
       "name" : "KEGG"
     } ]
-  }, {
-    "child" : {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "KEGG_DEF"
-    },
-    "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "DEAPP",
-      "name" : "KEGG_DEF"
-    } ]
   }, {
     "child" : {
       "type" : "VIEW",
@@ -9373,17 +10201,6 @@
       "owner" : "I2B2DEMODATA",
       "name" : "MASTER_QUERY_GLOBAL_TEMP"
     } ]
-  }, {
-    "child" : {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "MESH"
-    },
-    "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "BIOMART",
-      "name" : "MESH"
-    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -9395,17 +10212,6 @@
       "owner" : "BIOMART",
       "name" : "MESH_DESCRIPTOR"
     } ]
-  }, {
-    "child" : {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "MESH_ENTRY"
-    },
-    "parents" : [ {
-      "type" : "TABLE",
-      "owner" : "BIOMART",
-      "name" : "MESH_ENTRY"
-    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -9598,6 +10404,33 @@
       "name" : "PARSE_NTH_VALUE"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "PARTITION_GWAS_DATA"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "BIOMART",
+      "name" : "GWAS_PARTITION"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_END_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_ERROR_HANDLER"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_START_AUDIT"
+    }, {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "CZ_WRITE_AUDIT"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -9616,6 +10449,17 @@
       "name" : "PATIENT_DIMENSION_RELEASE"
     },
     "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "VIEW",
+      "owner" : "TM_CZ",
+      "name" : "PATIENT_INFO"
+    },
+    "parents" : [ {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "STG_SUBJECT_RBM_DATA"
+    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -10123,6 +10967,13 @@
       "owner" : "I2B2METADATA",
       "name" : "I2B2_SECURE"
     } ]
+  }, {
+    "child" : {
+      "type" : "FUNCTION",
+      "owner" : "TM_CZ",
+      "name" : "REPEAT_CHAR"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -11003,6 +11854,27 @@
       "owner" : "I2B2DEMODATA",
       "name" : "SQ_UP_PATDIM_PATIENTNUM"
     } ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "STG_RBM_ANTIGEN_GENE"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "STG_SUBJECT_RBM_DATA"
+    },
+    "parents" : [ ]
+  }, {
+    "child" : {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "STG_SUBJECT_RBM_DATA_RAW"
+    },
+    "parents" : [ ]
   }, {
     "child" : {
       "type" : "FUNCTION",
@@ -11639,28 +12511,6 @@
       "owner" : "I2B2DEMODATA",
       "name" : "VISIT_DIMENSION"
     } ]
-  }, {
-    "child" : {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "VW_FACETED_SEARCH"
-    },
-    "parents" : [ {
-      "type" : "VIEW",
-      "owner" : "BIOMART",
-      "name" : "VW_FACETED_SEARCH"
-    } ]
-  }, {
-    "child" : {
-      "type" : "SYNONYM",
-      "owner" : "TM_CZ",
-      "name" : "VW_FACETED_SEARCH_DISEASE"
-    },
-    "parents" : [ {
-      "type" : "VIEW",
-      "owner" : "BIOMART",
-      "name" : "VW_FACETED_SEARCH_DISEASE"
-    } ]
   }, {
     "child" : {
       "type" : "SYNONYM",
@@ -12635,6 +13485,13 @@
       "name" : "CZ_JOB_AUDIT"
     },
     "file" : "tm_cz/cz_job_audit.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "CZ_JOB_AUDIT_JOBID_DATE"
+    },
+    "file" : "tm_cz/cz_job_audit.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -12978,6 +13835,13 @@
       "name" : "I2B2_LOAD_ANNOTATION_DEAPP"
     },
     "file" : "tm_cz/procedures/i2b2_load_annotation_deapp.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_CHROM_REGION"
+    },
+    "file" : "tm_cz/procedures/i2b2_load_chrom_region.sql"
   }, {
     "item" : {
       "type" : "PROCEDURE",
@@ -13006,6 +13870,20 @@
       "name" : "I2B2_LOAD_CLINICAL_INC_DATA"
     },
     "file" : "tm_cz/procedures/i2b2_load_clinical_inc_data.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_EQTL_TOP50"
+    },
+    "file" : "tm_cz/procedures/i2b2_load_eqtl_top50.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_LOAD_GWAS_TOP50"
+    },
+    "file" : "tm_cz/procedures/i2b2_load_gwas_top50.sql"
   }, {
     "item" : {
       "type" : "PROCEDURE",
@@ -13125,6 +14003,20 @@
       "name" : "I2B2_MIRNA_ZSCORE_CALC"
     },
     "file" : "tm_cz/procedures/i2b2_mirna_zscore_calc.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_MOVE_ANALYSIS_TO_PROD"
+    },
+    "file" : "tm_cz/procedures/i2b2_move_analysis_to_prod.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_MOVE_ANALYSIS_TO_PROD_NEW"
+    },
+    "file" : "tm_cz/procedures/i2b2_move_analysis_to_prod_new.sql"
   }, {
     "item" : {
       "type" : "PROCEDURE",
@@ -13167,6 +14059,13 @@
       "name" : "I2B2_MRNA_ZSCORE_CALC"
     },
     "file" : "tm_cz/procedures/i2b2_mrna_zscore_calc.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROCESS_ACGH_DATA"
+    },
+    "file" : "tm_cz/procedures/i2b2_process_acgh_data.sql"
   }, {
     "item" : {
       "type" : "PROCEDURE",
@@ -13230,6 +14129,13 @@
       "name" : "I2B2_PROCESS_QPCR_MIRNA_DATA"
     },
     "file" : "tm_cz/procedures/i2b2_process_qpcr_mirna_data.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROCESS_RNASEQ_DATA"
+    },
+    "file" : "tm_cz/procedures/i2b2_process_rnaseq_data.sql"
   }, {
     "item" : {
       "type" : "PROCEDURE",
@@ -13251,6 +14157,13 @@
       "name" : "I2B2_PROCESS_RNA_SEQ_INC_DATA"
     },
     "file" : "tm_cz/procedures/i2b2_process_rna_seq_inc_data.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROCESS_SNP_DATA"
+    },
+    "file" : "tm_cz/procedures/i2b2_process_snp_data.sql"
   }, {
     "item" : {
       "type" : "PROCEDURE",
@@ -13258,6 +14171,20 @@
       "name" : "I2B2_PROC_METABOLOMIC_INC_DATA"
     },
     "file" : "tm_cz/procedures/i2b2_proc_metabolomic_inc_data.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEIN_INC_SUB_ZSCORE"
+    },
+    "file" : "tm_cz/procedures/i2b2_protein_inc_sub_zscore.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEIN_INC_SUB_ZSCORE2"
+    },
+    "file" : "tm_cz/procedures/i2b2_protein_inc_sub_zscore2.sql"
   }, {
     "item" : {
       "type" : "PROCEDURE",
@@ -13265,6 +14192,27 @@
       "name" : "I2B2_PROTEIN_INC_ZSCORE_CALC"
     },
     "file" : "tm_cz/procedures/i2b2_protein_inc_zscore_calc.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEIN_INC_ZSCORE_CALC2"
+    },
+    "file" : "tm_cz/procedures/i2b2_protein_inc_zscore_calc2.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEIN_INC_ZSCORE_CALC3"
+    },
+    "file" : "tm_cz/procedures/i2b2_protein_inc_zscore_calc3.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "I2B2_PROTEOMICS_INC_SUB_ZSCORE"
+    },
+    "file" : "tm_cz/procedures/i2b2_proteomics_inc_sub_zscore.sql"
   }, {
     "item" : {
       "type" : "PROCEDURE",
@@ -13412,6 +14360,20 @@
       "name" : "I2B2_UI_LABEL_CHANGE_BK"
     },
     "file" : "tm_cz/procedures/i2b2_ui_label_change_bk.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "IDX_I2B2_SECURE_FULLNAME"
+    },
+    "file" : "tm_cz/_cross.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "IDX_TMP_SUBJ_USUBJID"
+    },
+    "file" : "tm_cz/tmp_subject_info.sql"
   }, {
     "item" : {
       "type" : "FUNCTION",
@@ -13433,6 +14395,20 @@
       "name" : "IS_NUMBER_V2"
     },
     "file" : "tm_cz/functions/is_number_v2.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "IX_DE_SUBJECT_SMPL_MPNG_MRNA"
+    },
+    "file" : "tm_cz/_cross.sql"
+  }, {
+    "item" : {
+      "type" : "INDEX",
+      "owner" : "TM_CZ",
+      "name" : "IX_I2B2_SOURCE_SYSTEM_CD"
+    },
+    "file" : "tm_cz/_cross.sql"
   }, {
     "item" : {
       "type" : "FUNCTION",
@@ -13510,6 +14486,13 @@
       "name" : "PARSE_NTH_VALUE"
     },
     "file" : "tm_cz/functions/parse_nth_value.sql"
+  }, {
+    "item" : {
+      "type" : "PROCEDURE",
+      "owner" : "TM_CZ",
+      "name" : "PARTITION_GWAS_DATA"
+    },
+    "file" : "tm_cz/procedures/partition_gwas_data.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -13517,6 +14500,13 @@
       "name" : "PATIENT_DIMENSION_RELEASE"
     },
     "file" : "tm_cz/patient_dimension_release.sql"
+  }, {
+    "item" : {
+      "type" : "VIEW",
+      "owner" : "TM_CZ",
+      "name" : "PATIENT_INFO"
+    },
+    "file" : "tm_cz/views/patient_info.sql"
   }, {
     "item" : {
       "type" : "TABLE",
@@ -13580,6 +14570,13 @@
       "name" : "RENAME_STUDY"
     },
     "file" : "tm_cz/procedures/rename_study.sql"
+  }, {
+    "item" : {
+      "type" : "FUNCTION",
+      "owner" : "TM_CZ",
+      "name" : "REPEAT_CHAR"
+    },
+    "file" : "tm_cz/functions/repeat_char.sql"
   }, {
     "item" : {
       "type" : "SEQUENCE",
@@ -13734,6 +14731,27 @@
       "name" : "SET_BIO_DATA_UID_PATH"
     },
     "file" : "tm_cz/procedures/set_bio_data_uid_path.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "STG_RBM_ANTIGEN_GENE"
+    },
+    "file" : "tm_cz/stg_rbm_antigen_gene.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "STG_SUBJECT_RBM_DATA"
+    },
+    "file" : "tm_cz/stg_subject_rbm_data.sql"
+  }, {
+    "item" : {
+      "type" : "TABLE",
+      "owner" : "TM_CZ",
+      "name" : "STG_SUBJECT_RBM_DATA_RAW"
+    },
+    "file" : "tm_cz/stg_subject_rbm_data_raw.sql"
   }, {
     "item" : {
       "type" : "FUNCTION",
@@ -14022,4 +15040,4 @@
     },
     "file" : "tm_cz/_misc.sql"
   } ]
-}
+}
\ No newline at end of file
diff --git a/ddl/oracle/tm_cz/procedures/cz_error_handler.sql b/ddl/oracle/tm_cz/procedures/cz_error_handler.sql
index c3e842d2..30f6fe5f 100644
--- a/ddl/oracle/tm_cz/procedures/cz_error_handler.sql
+++ b/ddl/oracle/tm_cz/procedures/cz_error_handler.sql
@@ -25,9 +25,9 @@ AS
 
   databaseName NVARCHAR2(100);
 	errorNumber NUMBER(18,0);
-	errorMessage NVARCHAR2(1000);
-  errorStack NVARCHAR2(4000);
-  errorBackTrace NVARCHAR2(4000);
+	errorMessage VARCHAR2(1000);
+  errorStack VARCHAR2(4000);
+  errorBackTrace VARCHAR2(4000);
 	stepNo NUMBER(18,0);
 
 BEGIN
diff --git a/ddl/oracle/tm_cz/procedures/czx_error_handler.sql b/ddl/oracle/tm_cz/procedures/czx_error_handler.sql
index 64465342..d6c3914a 100644
--- a/ddl/oracle/tm_cz/procedures/czx_error_handler.sql
+++ b/ddl/oracle/tm_cz/procedures/czx_error_handler.sql
@@ -23,11 +23,11 @@ AS
 * limitations under the License.
 ******************************************************************/
 
-  databaseName NVARCHAR2(100);
+  databaseName VARCHAR2(100);
 	errorNumber NUMBER(18,0);
-	errorMessage NVARCHAR2(1000);
-  errorStack NVARCHAR2(4000);
-  errorBackTrace NVARCHAR2(4000);
+	errorMessage VARCHAR2(1000);
+  errorStack VARCHAR2(4000);
+  errorBackTrace VARCHAR2(4000);
 	stepNo NUMBER(18,0);
 
 BEGIN
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_load_chrom_region.sql b/ddl/oracle/tm_cz/procedures/i2b2_load_chrom_region.sql
new file mode 100644
index 00000000..599f9c29
--- /dev/null
+++ b/ddl/oracle/tm_cz/procedures/i2b2_load_chrom_region.sql
@@ -0,0 +1,150 @@
+--
+-- Type: PROCEDURE; Owner: TM_CZ; Name: I2B2_LOAD_CHROM_REGION
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "TM_CZ"."I2B2_LOAD_CHROM_REGION" 
+(
+  platform_t in varchar2 := ''
+, genome_release in varchar2 := ''
+, currentjobid in number := NULL
+) as
+ --Audit variables
+  newJobFlag     INTEGER;
+  databaseName   VARCHAR(100);
+  procedureName  VARCHAR(100);
+  jobID          NUMBER(18,0);
+  stepCt         NUMBER(18,0);
+  gplId          VARCHAR2(100);
+  organismId     VARCHAR2(100);
+  platform_title VARCHAR(500);
+
+begin
+    stepCt := 0;
+
+  --Set Audit Parameters
+  newJobFlag := 0; -- False (Default)
+  jobID      := currentJobID;
+
+  SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+  procedureName := $$PLSQL_UNIT;
+
+  --Audit JOB Initialization
+  --If Job ID does not exist, then this is a single procedure run and we need to create it
+  IF(jobID IS NULL OR jobID < 1) THEN
+    newJobFlag := 1; -- True
+    cz_start_audit (procedureName, databaseName, jobID);
+  END IF;
+
+  stepCt := stepCt + 1;
+  tm_cz.cz_write_audit(jobId,databaseName,procedureName,'Starting i2b2_load_chrom_region',0,stepCt,'Done');
+
+
+  -- The data should already be in the landing zone (tm_lz.lt_chromosomal_region)
+  -- We now do some basic check's:
+  -- + is chromosomal_region already in deapp.de_chromosomal_region (gpl_id/region_name)
+  --   if true then remove these lines?
+  -- + ...
+
+  -- insert region definitions into deapp-schema
+  -- First remove previous definitions for gpl_id
+  SELECT DISTINCT gpl_id INTO gplId FROM lt_chromosomal_region;
+
+  DELETE FROM deapp.de_chromosomal_region WHERE gpl_id = gplId;
+  stepCt                := stepCt + 1;
+  tm_cz.cz_write_audit(jobId,databaseName,procedureName,'Delete existing data from deapp.de_chromosomal_region for plaform: ' || gplId,SQL%ROWCOUNT,stepCt,'Done');
+
+  DELETE FROM deapp.de_gpl_info WHERE platform = gplId;
+  stepCt                := stepCt + 1;
+  tm_cz.cz_write_audit(jobId,databaseName,procedureName,'Delete existing data from deapp.de_gpl_info for platform: ' || gplID,SQL%ROWCOUNT,stepCt,'Done');
+
+  -- Insert platform into deapp.de_gpl_info
+  platform_title := platform_t;
+  IF (LENGTH(platform_title) = 0) THEN
+      platform_title := gplId;
+  END IF;
+  SELECT DISTINCT organism INTO organismId FROM tm_lz.lt_chromosomal_region;
+
+  INSERT INTO deapp.de_gpl_info
+          (
+            platform ,
+            title ,
+            organism ,
+            annotation_date ,
+            marker_type ,
+            release_nbr
+          )
+          VALUES
+          (
+            gplId,
+            platform_title,
+            organismId,
+            CURRENT_TIMESTAMP,
+            'Chromosomal',
+            genome_release
+          );
+  stepCt := stepCt + 1;
+  tm_cz.cz_write_audit(jobId,databaseName,procedureName,'Load platform info into deapp.de_gpl_info for platform: ' || gplID,SQL%ROWCOUNT,stepCt,'Done');
+
+  -- Next insert the new definitions
+  INSERT INTO deapp.de_chromosomal_region
+            (
+              GPL_ID ,
+              REGION_NAME ,
+              CHROMOSOME ,
+              START_BP ,
+              END_BP ,
+              NUM_PROBES ,
+              CYTOBAND ,
+              GENE_SYMBOL ,
+              GENE_ID ,
+              ORGANISM
+            )
+          SELECT lz.GPL_ID ,
+            lz.REGION_NAME ,
+            lz.CHROMOSOME ,
+            lz.START_BP ,
+            lz.END_BP ,
+            lz.NUM_PROBES ,
+            lz.CYTOBAND ,
+            lz.GENE_SYMBOL ,
+            lz.GENE_ID ,
+            lz.ORGANISM
+          FROM tm_lz.lt_chromosomal_region lz;
+          stepCt                := stepCt + 1;
+          tm_cz.cz_write_audit(jobId,databaseName,procedureName,'Load chromosomal region data into deapp.de_chromosomal_region for platform: ' || gplId,SQL%ROWCOUNT,stepCt,'Done');
+
+  -- update gene_id if null
+  update de_chromosomal_region t
+	set gene_id=(select to_number(min(b.primary_external_id)) as gene_id
+				 from biomart.bio_marker b
+				 where t.gene_symbol = b.bio_marker_name
+				   and upper(b.organism) = upper(t.organism)
+				   and upper(b.bio_marker_type) = 'GENE')
+	where t.gpl_id = gplId
+	  and t.gene_id is null
+	  and t.gene_symbol is not null
+	  and exists
+		 (select 1 from biomart.bio_marker x
+		  where t.gene_symbol = x.bio_marker_name
+			and upper(x.organism) = upper(t.organism)
+			and upper(x.bio_marker_type) = 'GENE');
+  stepCt                := stepCt + 1;
+  tm_cz.cz_write_audit(jobId,databaseName,procedureName,'Updated missing gene_id in de_chromosomal_region',SQL%ROWCOUNT,stepCt,'Done');
+
+  -- wrapping up
+  stepCt := stepCt + 1;
+  tm_cz.cz_write_audit(jobId,databaseName,procedureName,'End i2b2_load_chrom_region',0,stepCt,'Done');
+
+  ---Cleanup OVERALL JOB if this proc is being run standalone
+  IF newJobFlag = 1 THEN
+    tm_cz.cz_end_audit (jobID, 'SUCCESS');
+  END IF;
+
+  EXCEPTION
+  WHEN OTHERS THEN
+    --Handle errors.
+    cz_error_handler (jobID, procedureName);
+    --End Proc
+    cz_end_audit (jobID, 'FAIL');
+
+end i2b2_load_chrom_region;
+/
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_load_eqtl_top50.sql b/ddl/oracle/tm_cz/procedures/i2b2_load_eqtl_top50.sql
new file mode 100644
index 00000000..705a681b
--- /dev/null
+++ b/ddl/oracle/tm_cz/procedures/i2b2_load_eqtl_top50.sql
@@ -0,0 +1,156 @@
+--
+-- Type: PROCEDURE; Owner: TM_CZ; Name: I2B2_LOAD_EQTL_TOP50
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "TM_CZ"."I2B2_LOAD_EQTL_TOP50" 
+(i_bio_assay_analysis_id number
+,i_job_id        number := null
+)
+ AS
+        --Audit variables
+    newJobFlag     INTEGER(1);
+    databaseName     VARCHAR(100);
+    procedureName VARCHAR(100);
+    jobID         number(18,0);
+    stepCt         number(18,0);
+
+        v_sqlText                varchar2(2000);
+
+BEGIN
+    --Set Audit Parameters
+    newJobFlag := 0; -- False (Default)
+    jobID := i_job_id;
+
+    SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+    procedureName := $$PLSQL_UNIT;
+
+    --Audit JOB Initialization
+    --If Job ID does not exist, then this is a single procedure run and we need to create it
+    IF(jobID IS NULL or jobID < 1)
+    THEN
+        newJobFlag := 1; -- True
+        cz_start_audit (procedureName, databaseName, jobID);
+    END IF;
+
+    stepCt := 1;
+    cz_write_audit(jobID,databaseName,procedureName,'Starting ' || procedureName,0,stepCt,'Done');
+
+        --        delete existing data from bio_asy_analysis_eqtl_top50
+
+        delete from biomart.bio_asy_analysis_eqtl_top50
+        where bio_assay_analysis_id = i_bio_assay_analysis_id;
+    stepCt := stepCt + 1;
+        cz_write_audit(jobID,databaseName,procedureName,'Delete data for analysis from biomart.bio_asy_analysis_eqtls_top50',SQL%ROWCOUNT,stepCt,'Done');
+        commit;
+
+/*
+        --        disable indexes
+
+        for eqtl_idx in (select index_name
+                                                        ,table_name
+                                         from all_indexes
+                                         where owner = 'BIOMART'
+                                           and table_name = 'BIO_ASY_ANALYSIS_EQTL_TOP50')
+        loop
+                v_sqlText := 'alter index ' || eqtl_idx.index_name || ' unusable';
+                stepCt := stepCt + 1;
+                cz_write_audit(jobId,databaseName,procedureName,'Disabling index ' || eqtl_idx.index_name || ' on ' || eqtl_idx.table_name,0,stepCt,'Done');
+                execute immediate(v_sqlText);
+                stepCt := stepCt + 1;
+                cz_write_audit(jobId,databaseName,procedureName,'Disabling complete',0,stepCt,'Done');
+        end loop;
+*/
+
+        --        insert analysis into bio_asy_analysis_eqtl_top50
+
+        insert into biomart.bio_asy_analysis_eqtl_top50
+        (bio_assay_analysis_id
+        ,analysis
+        ,chrom
+        ,pos
+        ,rsgene
+        ,rsid
+        ,pvalue
+        ,logpvalue
+        ,extdata
+        ,rnum
+        ,intronexon
+        ,recombinationrate
+        ,regulome
+        )
+        select a.bio_assay_analysis_id
+                  ,a.analysis
+                  ,info.chrom
+                  ,info.pos
+                  ,a.gene
+                  ,a.rsid
+                  ,a.pvalue
+                  ,a.logpvalue
+                  ,a.extdata
+                  ,a.rnum
+                  ,info.exon_intron as intronexon
+                  ,info.recombination_rate as recombinationrate
+                  ,info.regulome_score as regulome
+        from (select b.bio_assay_analysis_id
+                                ,b.analysis
+                                ,b.rsid
+                                ,b.pvalue
+                                ,b.logpvalue
+                                ,b.extdata
+                                ,b.gene
+                                ,b.cis_trans
+                                ,b.distance_from_gene
+                                ,b.rnum
+                 from (select eqtl.bio_assay_analysis_id
+                                         ,baa.analysis_name as analysis
+                                         ,eqtl.rs_id as rsid
+                                         ,eqtl.p_value as pvalue
+                                         ,eqtl.log_p_value as logpvalue
+                                         ,eqtl.ext_data as extdata
+                                         ,eqtl.gene
+                                         ,eqtl.cis_trans
+                                         ,eqtl.distance_from_gene
+                                         ,row_number () over (order by eqtl.p_value asc, eqtl.rs_id asc) as rnum
+                          from biomart.bio_assay_analysis_eqtl eqtl
+                          inner join biomart.bio_assay_analysis baa
+                                        on  baa.bio_assay_analysis_id = eqtl.bio_assay_analysis_id
+                          where eqtl.bio_assay_analysis_id = i_bio_assay_analysis_id) b
+                 where b.rnum < 500) a
+        inner join deapp.de_rc_snp_info info
+                  on  a.rsid = info.rs_id
+                  and hg_version='19';
+    stepCt := stepCt + 1;
+        cz_write_audit(jobID,databaseName,procedureName,'Insert data for analysis from biomart.bio_asy_analysis_eaqtl_top50',SQL%ROWCOUNT,stepCt,'Done');
+        commit;
+
+/*
+        --        rebuild indexes
+
+        for eqtl_idx in (select index_name
+                                                           ,table_name
+                                                 from all_indexes
+                                                 where owner = 'BIOMART'
+                                                   and table_name = 'BIO_ASY_ANALYSIS_EQTL_TOP50')
+                loop
+                        v_sqlText := 'alter index ' || eqtl_idx.index_name || ' rebuild';
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobId,databaseName,procedureName,'Rebuilding index ' || eqtl_idx.index_name || ' on ' || eqtl_idx.table_name,0,stepCt,'Done');
+                        execute immediate(v_sqlText);
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobId,databaseName,procedureName,'Rebuilding complete',SQL%ROWCOUNT,stepCt,'Done');
+                end loop;
+*/
+
+        cz_write_audit(jobID,databaseName,procedureName,'End ' || procedureName,0,stepCt,'Done');
+    stepCt := stepCt + 1;
+
+    cz_end_audit(jobID, 'Success');
+
+    exception
+    when others then
+    --Handle errors.
+        cz_error_handler (jobID, procedureName);
+    --End Proc
+        cz_end_audit (jobID, 'FAIL');
+
+END I2B2_LOAD_eqtl_TOP50;
+/
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_load_gwas_top50.sql b/ddl/oracle/tm_cz/procedures/i2b2_load_gwas_top50.sql
new file mode 100644
index 00000000..6705af0d
--- /dev/null
+++ b/ddl/oracle/tm_cz/procedures/i2b2_load_gwas_top50.sql
@@ -0,0 +1,146 @@
+--
+-- Type: PROCEDURE; Owner: TM_CZ; Name: I2B2_LOAD_GWAS_TOP50
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "TM_CZ"."I2B2_LOAD_GWAS_TOP50" 
+(i_bio_assay_analysis_id number
+,i_job_id        number := null
+)
+ AS
+        --Audit variables
+    newJobFlag     INTEGER(1);
+    databaseName     VARCHAR(100);
+    procedureName VARCHAR(100);
+    jobID         number(18,0);
+    stepCt         number(18,0);
+
+    v_sqlText                varchar2(2000);
+
+BEGIN
+    --Set Audit Parameters
+    newJobFlag := 0; -- False (Default)
+    jobID := i_job_id;
+
+    SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+    procedureName := $$PLSQL_UNIT;
+
+    --Audit JOB Initialization
+    --If Job ID does not exist, then this is a single procedure run and we need to create it
+    IF(jobID IS NULL or jobID < 1)
+    THEN
+        newJobFlag := 1; -- True
+        cz_start_audit (procedureName, databaseName, jobID);
+    END IF;
+
+    stepCt := 1;
+    cz_write_audit(jobID,databaseName,procedureName,'Starting ' || procedureName,0,stepCt,'Done');
+
+        --        delete existing data from bio_asy_analysis_gwas_top50
+
+        delete from biomart.bio_asy_analysis_gwas_top50
+        where bio_assay_analysis_id = i_bio_assay_analysis_id;
+    stepCt := stepCt + 1;
+        cz_write_audit(jobID,databaseName,procedureName,'Delete data for analysis from biomart.bio_asy_analysis_gwas_top50',SQL%ROWCOUNT,stepCt,'Done');
+        commit;
+
+/*
+        --        disable indexes
+
+        for gwas_idx in (select index_name
+                                                        ,table_name
+                                         from all_indexes
+                                         where owner = 'BIOMART'
+                                           and table_name = 'BIO_ASY_ANALYSIS_gwas_TOP50')
+        loop
+                v_sqlText := 'alter index ' || gwas_idx.index_name || ' unusable';
+                stepCt := stepCt + 1;
+                cz_write_audit(jobId,databaseName,procedureName,'Disabling index ' || gwas_idx.index_name || ' on ' || gwas_idx.table_name,0,stepCt,'Done');
+                execute immediate(v_sqlText);
+                stepCt := stepCt + 1;
+                cz_write_audit(jobId,databaseName,procedureName,'Disabling complete',0,stepCt,'Done');
+        end loop;
+*/
+
+        --        insert analysis into bio_asy_analysis_gwas_top50
+
+        insert into biomart.bio_asy_analysis_gwas_top50
+        (bio_assay_analysis_id
+        ,analysis
+        ,chrom
+        ,pos
+        ,rsgene
+        ,rsid
+        ,pvalue
+        ,logpvalue
+        ,extdata
+        ,rnum
+        ,intronexon
+        ,recombinationrate
+        ,regulome
+        )
+        select a.bio_assay_analysis_id
+                  ,a.analysis
+                  ,info.chrom
+                  ,info.pos
+                  ,info.gene_name AS rsgene
+                  ,a.rsid
+                  ,a.pvalue
+                  ,a.logpvalue
+                  ,a.extdata
+                  ,a.rnum
+                  ,info.exon_intron as intronexon
+                  ,info.recombination_rate as recombinationrate
+                  ,info.regulome_score as regulome
+        from (select b.bio_assay_analysis_id
+                                ,b.analysis
+                                ,b.rsid
+                                ,b.pvalue
+                                ,b.logpvalue
+                                ,b.extdata
+                                ,b.rnum
+                 from (select gwas.bio_assay_analysis_id
+                                         ,baa.analysis_name as analysis
+                                         ,gwas.rs_id as rsid
+                                         ,gwas.p_value as pvalue
+                                         ,gwas.log_p_value as logpvalue
+                                         ,gwas.ext_data as extdata
+                                         ,row_number () over (order by gwas.p_value asc, gwas.rs_id asc) as rnum
+                          from biomart.bio_assay_analysis_gwas gwas
+                          left join biomart.bio_assay_analysis baa
+                                        on  baa.bio_assay_analysis_id = gwas.bio_assay_analysis_id
+                          where gwas.bio_assay_analysis_id = i_bio_assay_analysis_id) b
+                 where b.rnum < 500) a
+        left join deapp.de_rc_snp_info info
+                  on  a.rsid = info.rs_id
+                  and hg_version='19';
+    stepCt := stepCt + 1;
+        cz_write_audit(jobID,databaseName,procedureName,'Insert data for analysis from biomart.bio_asy_analysis_gwas_top50',SQL%ROWCOUNT,stepCt,'Done');
+        commit;
+
+     /*   for gwas_idx in (select index_name
+                                                           ,table_name
+                                                 from all_indexes
+                                                 where owner = 'BIOMART'
+                                                   and table_name = 'BIO_ASY_ANALYSIS_GWAS_TOP50')
+                loop
+                        v_sqlText := 'alter index ' || gwas_idx.index_name || ' rebuild';
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobId,databaseName,procedureName,'Rebuilding index ' || gwas_idx.index_name || ' on ' || gwas_idx.table_name,0,stepCt,'Done');
+                        execute immediate(v_sqlText);
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobId,databaseName,procedureName,'Rebuilding complete',SQL%ROWCOUNT,stepCt,'Done');
+                end loop;
+        */
+        cz_write_audit(jobID,databaseName,procedureName,'End ' || procedureName,0,stepCt,'Done');
+    stepCt := stepCt + 1;
+
+    cz_end_audit(jobID, 'Success');
+
+    exception
+    when others then
+    --Handle errors.
+        cz_error_handler (jobID, procedureName);
+    --End Proc
+        cz_end_audit (jobID, 'FAIL');
+
+END I2B2_LOAD_GWAS_TOP50;
+/
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_load_proteomics_annot.sql b/ddl/oracle/tm_cz/procedures/i2b2_load_proteomics_annot.sql
index 52457aaa..0a297c5d 100644
--- a/ddl/oracle/tm_cz/procedures/i2b2_load_proteomics_annot.sql
+++ b/ddl/oracle/tm_cz/procedures/i2b2_load_proteomics_annot.sql
@@ -46,31 +46,6 @@ BEGIN
       select distinct gpl_id into gplId from lt_protein_annotation ;
 
 	
-/*	
-	--	delete any existing data from probeset_deapp
-	
-	delete from peptide_deapp
-	where platform = idREF;
-
-	stepCt := stepCt + 1;
-	cz_write_audit(jobId,databaseName,procedureName,'Delete existing data from REFERENCE peptide_probeset_deapp',SQL%ROWCOUNT,stepCt,'Done');
-*/
-		
-	--	delete any existing data from peptide_annotation_deapp
-	
-	/*delete from mirna_annotation_deapp
-	where id_ref in ( select distinct id_ref from lt_qpcr_mirna_annotation);
-
-	stepCt := stepCt + 1;
-	cz_write_audit(jobId,databaseName,procedureName,'Delete existing data from mirna_annotation_deapp',SQL%ROWCOUNT,stepCt,'Done');*/
-        
-      /*  delete from peptide_deapp
-	where peptide in ( select distinct peptide from lt_protein_annotation);
-
-	stepCt := stepCt + 1;
-	cz_write_audit(jobId,databaseName,procedureName,'Delete existing data from peptide_deapp',SQL%ROWCOUNT,stepCt,'Done');
-        
-        */
         --	delete any existing data from deapp.de_protien_annotation
         delete from deapp.de_protein_annotation
 	where gpl_id =gplId;
@@ -78,48 +53,7 @@ BEGIN
 
 	stepCt := stepCt + 1;
 	cz_write_audit(jobId,databaseName,procedureName,'Delete existing data from de_protein_annotation',SQL%ROWCOUNT,stepCt,'Done');
-
-	
-
-	--	update organism for existing probesets in peptide_deapp
-	/*
-	update peptide_deapp p
-	set organism=(select distinct t.organism from lt_protein_annotation t
-				  where p.platform = t.gpl_id  
-				    and p.peptide = t.peptide
-                                    )
-	where exists
-		 (select 1 from lt_protein_annotation x
-		  where p.platform =x.gpl_id
-		    and p.peptide = x.peptide);
-	
-	stepCt := stepCt + 1;
-	cz_write_audit(jobId,databaseName,procedureName,'Update organism in peptide_deapp',SQL%ROWCOUNT,stepCt,'Done');
-		*/	 
-	--	insert any new probesets into peptide_deapp
-	
-	/*insert into peptide_deapp
-	(peptide
-	,organism
-	,platform)
-	select distinct peptide
-		  ,coalesce(organism,'Homo sapiens')
-	      ,gpl_id
-	from lt_protein_annotation t
-	where not exists
-		 (select 1 from peptide_deapp x
-		  where t.gpl_id = x.platform
-                      and   t.peptide = x.peptide
-			and coalesce(t.organism,'Homo sapiens') = coalesce(x.organism,'Homo sapiens'))
-	;
-        commit;
-     
-	--where id_ref is not null 
-	--   or gene_symbol is not null;
-	
-	stepCt := stepCt + 1;
-	cz_write_audit(jobId,databaseName,procedureName,'Insert new probesets into peptide_deapp',SQL%ROWCOUNT,stepCt,'Done'); */
-
+	 	
 	insert into  deapp.de_protein_annotation
 	(gpl_id
 	,peptide 
@@ -135,33 +69,11 @@ BEGIN
 	,biomart.bio_marker p
 	where d.gpl_id = gplId
         and p.primary_external_id = d.uniprot_id 
-	--  and coalesce(d.organism,'Homo sapiens') = coalesce(p.organism,'Homo sapiens')
-	 -- and (d.gpl_id is not null or d.gene_symbol is not null)
 	  ;
 	
 	stepCt := stepCt + 1;
 	cz_write_audit(jobId,databaseName,procedureName,'Load annotation data into DEAPP de_protien_annotation',SQL%ROWCOUNT,stepCt,'Done');
 		
-	--	update id_ref if null
-	
-/*	update deapp.de_peptide_annotation t
-	set id_ref=(select to_number(min(b.primary_external_id)) as mirna_id
-				 from biomart.mirna_bio_marker b
-				 where t.mirna_symbol = b.bio_marker_name
-				   and upper(b.organism) = upper(t.organism)
-				   and upper(b.bio_marker_type) = 'PROTIEN')
-	where t.id_ref = idREF
-	  and t.gene_id is null 
-	  and t.gene_symbol is not null
-	  and exists
-		 (select 1 from biomart.mirna_bio_marker x
-		  where t.mirna_symbol = x.bio_marker_name
-			and upper(x.organism) = upper(t.organism)
-			and upper(x.bio_marker_type) = 'PROTEIN');
-			
-	stepCt := stepCt + 1;
-	cz_write_audit(jobId,databaseName,procedureName,'Updated missing id_ref in de_protien_annotation',SQL%ROWCOUNT,stepCt,'Done');
-	*/
 	--	update gene_symbol if null
 	
 	update deapp.de_protein_annotation t
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_load_rbm_ b/ddl/oracle/tm_cz/procedures/i2b2_load_rbm_
new file mode 100644
index 00000000..e69de29b
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_move_analysis_to_prod.sql b/ddl/oracle/tm_cz/procedures/i2b2_move_analysis_to_prod.sql
new file mode 100644
index 00000000..9d42c8e1
--- /dev/null
+++ b/ddl/oracle/tm_cz/procedures/i2b2_move_analysis_to_prod.sql
@@ -0,0 +1,353 @@
+--
+-- Type: PROCEDURE; Owner: TM_CZ; Name: I2B2_MOVE_ANALYSIS_TO_PROD
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "TM_CZ"."I2B2_MOVE_ANALYSIS_TO_PROD" 
+(i_etl_id        number    := -1
+,i_job_id        number    := null
+)
+AS
+    -- For partitioned table  2/4/2014
+    --Audit variables
+    newJobFlag     INTEGER(1);
+    databaseName     VARCHAR(100);
+    procedureName VARCHAR(100);
+    jobID         number(18,0);
+    stepCt         number(18,0);
+
+    v_etl_id                                        number(18,0);
+    v_bio_assay_analysis_id                number(18,0);
+    v_data_type                                        varchar2(50);
+    v_sqlText                                        varchar2(2000);
+    v_exists                    int;
+    v_GWAS_staged                                int;
+    v_EQTL_staged                                int;
+        v_gwas_indx                                        int;
+        v_eqtl_indx                                        int;
+        v_max_ext_flds                                int;
+
+    BEGIN
+
+    --Set Audit Parameters
+    newJobFlag := 0; -- False (Default)
+    jobID := -1;
+
+    SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+    procedureName := $$PLSQL_UNIT;
+
+    --Audit JOB Initialization
+    --If Job ID does not exist, then this is a single procedure run and we need to create it
+    IF(jobID IS NULL or jobID < 1)
+    THEN
+        newJobFlag := 1; -- True
+        cz_start_audit (procedureName, databaseName, jobID);
+    END IF;
+
+    stepCt := 1;
+    cz_write_audit(jobID,databaseName,procedureName,'Starting i2b2_move_analysis_to_prod',0,stepCt,'Done');
+
+        v_GWAS_staged := 0;
+        v_EQTL_staged := 0;
+        v_gwas_indx := 0;
+
+    --    load staged analysis to array
+
+        for stage_rec in
+                (select baa.bio_assay_analysis_id
+                          ,lz.etl_id
+                          ,lz.study_id
+                          ,case when lz.data_type = 'Metabolic GWAS' then 'GWAS' else lz.data_type end as data_type
+                          ,lz.data_type as orig_data_type
+                          ,lz.analysis_name
+                from tm_lz.lz_src_analysis_metadata lz
+                        ,biomart.bio_assay_analysis baa
+                where lz.status = 'STAGED'
+                  and lz.study_id = baa.etl_id
+                  and lz.etl_id = baa.etl_id_source
+                  and case when i_etl_id = -1 then 1
+               when lz.etl_id = i_etl_id then 1
+               else 0 end = 1)
+        loop
+                stepCt := stepCt + 1;
+        cz_write_audit(jobId,databaseName,procedureName,'Loading ' || stage_rec.study_id || ' ' || stage_rec.orig_data_type || ' ' ||
+                       stage_rec.analysis_name,0,stepCt,'Done');
+
+                v_bio_assay_analysis_id := stage_rec.bio_assay_analysis_id;
+                v_etl_id := stage_rec.etl_id;
+                v_data_type := stage_rec.data_type;
+
+                --        get max nbr fields in ext_data for original data type
+
+                select max(field_idx) into v_max_ext_flds
+                from biomart.bio_asy_analysis_data_idx
+                where ext_type = stage_rec.orig_data_type;
+
+        if stage_rec.data_type = 'GWAS' then
+                        --        GWAS data
+            v_GWAS_staged := 1;
+                /* comment out for not disabling the indexes   by HZ 1/15/2014
+                        if v_gwas_indx = 0 then
+                                --        disable indexes if loading GWAS data
+                                for gwas_idx in (select index_name
+                                                                           ,table_name
+                                                                 from all_indexes
+                                                             where owner = 'BIOMART'
+                                                                   and table_name in ('BIO_ASSAY_ANALYSIS_GWAS','BIO_ASY_ANALYSIS_GWAS_TOP50')
+                                                                   and partitioned = 'NO' and compression!='DISABLED' )
+                                loop
+                                        v_sqlText := 'alter index biomart.' || gwas_idx.index_name || ' unusable';
+                                        stepCt := stepCt + 1;
+                                        cz_write_audit(jobID,databaseName,procedureName,'Disabling index ' || gwas_idx.index_name || ' on ' || gwas_idx.table_name,SQL%ROWCOUNT,stepCt,'Done');
+                                        execute immediate(v_sqlText);
+                                        stepCt := stepCt + 1;
+                                        cz_write_audit(jobID,databaseName,procedureName,'Disabling complete',SQL%ROWCOUNT,stepCt,'Done');
+                                end loop;
+                                v_gwas_indx := 1;
+                        end if;
+              */
+                        --        check if partition exists for bio_assay_analysis_id, if not, add, if yes, truncate
+                        select count(*) into v_exists
+                        from all_tab_partitions
+                        where table_name = 'BIO_ASSAY_ANALYSIS_GWAS'
+                          and partition_name = to_char(v_bio_assay_analysis_id);
+
+                        if v_exists = 0 then
+                                --        add partition to bio_assay_analysis_gwas
+                                v_sqlText := 'alter table biomart.bio_assay_analysis_gwas add PARTITION "' || to_char(v_bio_assay_analysis_id) || '"  VALUES (' ||
+                                                    to_char(v_bio_assay_analysis_id) || ') ' ||
+                                                   'NOLOGGING TABLESPACE "BIOMART" ';
+                                execute immediate(v_sqlText);
+                                stepCt := stepCt + 1;
+                                cz_write_audit(jobID,databaseName,procedureName,'Adding partition to bio_assay_analysis_gwas '|| to_char(v_bio_assay_analysis_id),0,stepCt,'Done');
+                        else
+                                --        truncate existing partition
+                                v_sqlText := 'alter table biomart.bio_assay_analysis_gwas truncate partition "' || to_char(v_bio_assay_analysis_id) || '"';
+                                execute immediate(v_sqlText);
+                                stepCt := stepCt + 1;
+                                cz_write_audit(jobID,databaseName,procedureName,'Truncating partition in bio_assay_analysis_gwas '|| to_char(v_bio_assay_analysis_id),0,stepCt,'Done');
+                        end if;
+
+            insert into biomart.bio_assay_analysis_gwas
+            (bio_asy_analysis_gwas_id
+            ,bio_assay_analysis_id
+            ,rs_id
+            ,p_value
+            ,p_value_char
+            ,etl_id
+            ,ext_data
+            ,log_p_value)
+            select bio_asy_analysis_gwas_id
+                  ,bio_assay_analysis_id
+                  ,rs_id
+                  ,to_binary_double(p_value_char)
+                  ,p_value_char
+                  ,etl_id
+                  ,case when length(ext_data)-length(replace(ext_data,';','')) < v_max_ext_flds
+                                                then tm_cz.repeat_char(ext_data,v_max_ext_flds-(length(ext_data)-length(replace(ext_data,';',''))),';')
+                                                else ext_data
+                                   end
+                  ,case when log10_pval_char is null then log(10,to_binary_double(p_value_char))*-1
+                  else
+                  to_binary_double(log10_pval_char)
+                  end
+            from biomart_stage.bio_assay_analysis_gwas
+            where bio_assay_analysis_id = v_bio_assay_analysis_id;
+            stepCt := stepCt + 1;
+            cz_write_audit(jobID,databaseName,procedureName,'Insert data for analysis from biomart.bio_assay_analysis_gwas',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        update data_count in bio_assay_analysis
+
+            update biomart.bio_assay_analysis baa
+                        set data_count=(select count(*) from biomart.bio_assay_analysis_gwas x
+                                                        where x.bio_assay_analysis_id=v_bio_assay_analysis_id)
+            where baa.bio_assay_analysis_id=v_bio_assay_analysis_id;
+            stepCt := stepCt +1;
+            cz_write_audit(jobID,databaseName,procedureName,'Update data_count for analysis',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        update status in lz_src_analysis_metadata
+
+                        update tm_lz.lz_src_analysis_metadata
+                        set status='PRODUCTION'
+                        where etl_id = v_etl_id;
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Set status to PRODUCTION in tm_lz.lz_src_analysis_metadata',SQL%ROWCOUNT,stepCt,'Done');
+                        commit;
+
+                        --        delete data from biomart_stage
+
+                        delete from biomart_stage.bio_assay_analysis_gwas
+                        where bio_assay_analysis_id = v_bio_assay_analysis_id;
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Delete data for analysis from biomart_stage.bio_assay_analysis_gwas',SQL%ROWCOUNT,stepCt,'Done');
+                        commit;
+
+                        --        load top50 table
+                        i2b2_load_gwas_top50(v_bio_assay_analysis_id, jobID);
+
+                else
+                        --        EQTL data
+                        v_EQTL_staged := 1;
+                      /*
+                        if v_eqtl_indx = 0 then
+                                --        disable indexes if loading eqtl data
+                                for eqtl_idx in (select index_name
+                                                                           ,table_name
+                                                                 from all_indexes
+                                                             where owner = 'BIOMART'
+                                                                   and table_name = 'BIO_ASY_ANALYSIS_EQTL_TOP50' )
+                                loop
+                                        v_sqlText := 'alter index ' || eqtl_idx.index_name || ' unusable';
+                                        stepCt := stepCt + 1;
+                                        cz_write_audit(jobID,databaseName,procedureName,'Disabling index ' || eqtl_idx.index_name || ' on ' || eqtl_idx.table_name,SQL%ROWCOUNT,stepCt,'Done');
+                                        execute immediate(v_sqlText);
+                                        stepCt := stepCt + 1;
+                                        cz_write_audit(jobID,databaseName,procedureName,'Disabling complete',SQL%ROWCOUNT,stepCt,'Done');
+                                end loop;
+                                v_eqtl_indx := 1;
+                        end if;
+                        */
+                        --        delete existing data from bio_assay_analysis_eqtl
+                        delete from biomart.bio_assay_analysis_eqtl g
+                        where g.bio_assay_analysis_id = v_bio_assay_analysis_id;
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Delete exising data for staged analyses from biomart.bio_assay_analysis_eqtl',SQL%ROWCOUNT,stepCt,'Done');
+                        commit;
+
+            insert into biomart.bio_assay_analysis_eqtl
+            (bio_asy_analysis_eqtl_id
+            ,bio_assay_analysis_id
+            ,rs_id
+            ,gene
+            ,p_value
+            ,p_value_char
+            ,cis_trans
+            ,distance_from_gene
+            ,etl_id
+            ,ext_data
+            ,log_p_value)
+            select bio_asy_analysis_eqtl_id
+                  ,bio_assay_analysis_id
+                  ,rs_id
+                  ,gene
+                  ,to_binary_double(p_value_char)
+                  ,p_value_char
+                  ,cis_trans
+                  ,distance_from_gene
+                  ,etl_id
+                  ,case when length(ext_data)-length(replace(ext_data,';','')) < v_max_ext_flds
+                                                then tm_cz.repeat_char(ext_data,v_max_ext_flds-(length(ext_data)-length(replace(ext_data,';',''))),';')
+                                                else ext_data
+                                   end
+                  ,log(10,to_binary_double(p_value_char))*-1
+            from biomart_stage.bio_assay_analysis_eqtl
+            where bio_assay_analysis_id = v_bio_assay_analysis_id;
+            stepCt := stepCt + 1;
+            cz_write_audit(jobID,databaseName,procedureName,'Insert data for analysis into biomart.bio_assay_analysis_eqtl',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        update data_count in bio_assay_analysis
+
+            update biomart.bio_assay_analysis baa
+                        set data_count=(select count(*) from biomart.bio_assay_analysis_eqtl x
+                                                        where x.bio_assay_analysis_id=v_bio_assay_analysis_id)
+            where baa.bio_assay_analysis_id=v_bio_assay_analysis_id;
+            stepCt := stepCt +1;
+            cz_write_audit(jobID,databaseName,procedureName,'Update data_count for analysis',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        update status in lz_src_analysis_metadata
+
+                        update tm_lz.lz_src_analysis_metadata
+                        set status='PRODUCTION'
+                        where etl_id = v_etl_id;
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Set status to PRODUCTION in tm_lz.lz_src_analysis_metadata',SQL%ROWCOUNT,stepCt,'Done');
+                        commit;
+
+                        --        delete data from biomart_stage
+
+                        delete from biomart_stage.bio_assay_analysis_eqtl
+            where bio_assay_analysis_id = v_bio_assay_analysis_id;
+            stepCt := stepCt + 1;
+            cz_write_audit(jobID,databaseName,procedureName,'Delete data for analysis from biomart_stage.bio_assay_analysis_eqtl',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        load top50 table
+                        i2b2_load_eqtl_top50(v_bio_assay_analysis_id, jobID);
+
+                end if;
+        end loop;
+
+    --    rebuild indexes if loading GWAS data
+    /*
+    if v_GWAS_staged = 1 then
+                for gwas_idx in (select index_name
+                                                           ,table_name
+                                                 from all_indexes
+                                                 where owner = 'BIOMART'
+                                                   and table_name In ('BIO_ASSAY_ANALYSIS_GWAS','BIO_ASY_ANALYSIS_GWAS_TOP50') )
+                loop
+                        v_sqlText := 'alter index ' || gwas_idx.index_name || ' rebuild';
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Rebuilding index ' || gwas_idx.index_name || ' on ' || gwas_idx.table_name,SQL%ROWCOUNT,stepCt,'Done');
+                        execute immediate(v_sqlText);
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Rebuilding complete',SQL%ROWCOUNT,stepCt,'Done');
+                end loop;
+        end if;
+        */
+        if v_gwas_staged = 0 and v_eqtl_staged = 0 then
+        cz_write_audit(jobID, databaseName, procedureName, 'No staged data - run terminating normally',0,stepCt,'Done');
+        cz_end_audit(jobID, 'Success');
+        end if;
+
+    --    rebuild indexes if loading EQTL data
+    /*
+    if v_eqtl_staged = 1 then
+                for eqtl_idx in (select index_name
+                                                           ,table_name
+                                                 from all_indexes
+                                                 where owner = 'BIOMART'
+                                                   and table_name = 'BIO_ASY_ANALYSIS_EQTL_TOP50')
+                loop
+                        v_sqlText := 'alter index ' || eqtl_idx.index_name || ' rebuild';
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Rebuilding index ' || eqtl_idx.index_name || ' on ' || eqtl_idx.table_name,SQL%ROWCOUNT,stepCt,'Done');
+                        execute immediate(v_sqlText);
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Rebuilding complete',SQL%ROWCOUNT,stepCt,'Done');
+                end loop;
+        end if;
+        */
+     /*   if v_eqtl_staged = 0 and v_eqtl_staged = 0 then
+        cz_write_audit(jobID, databaseName, procedureName, 'No staged data - run terminating normally',0,stepCt,'Done');
+        cz_end_audit(jobID, 'Success');
+        end if;
+        */
+        --        check if any data left in staging tables, ususally indicated no bio_assay_analysis record in biomart
+
+        select count(*) into v_exists
+        from (select distinct bio_assay_analysis_id from biomart_stage.bio_assay_analysis_gwas
+                  union
+                  select distinct bio_assay_analysis_id from biomart_stage.bio_assay_analysis_eqtl);
+
+        if v_exists > 0 then
+        cz_write_audit(jobID, databaseName, procedureName, '**WARNING ** data remains in stage tables',0,stepCt,'Done');
+      --  cz_end_audit(jobID, 'Success');
+        end if;
+
+    cz_write_audit(jobID,databaseName,procedureName,'End ' || procedureName,0,stepCt,'Done');
+    stepCt := stepCt + 1;
+
+    cz_end_audit(jobID, 'Success');
+
+    exception
+    when others then
+    --Handle errors.
+        cz_error_handler (jobID, procedureName);
+    --End Proc
+        cz_end_audit (jobID, 'FAIL');
+
+END;
+/
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_move_analysis_to_prod_new.sql b/ddl/oracle/tm_cz/procedures/i2b2_move_analysis_to_prod_new.sql
new file mode 100644
index 00000000..776977ed
--- /dev/null
+++ b/ddl/oracle/tm_cz/procedures/i2b2_move_analysis_to_prod_new.sql
@@ -0,0 +1,353 @@
+--
+-- Type: PROCEDURE; Owner: TM_CZ; Name: I2B2_MOVE_ANALYSIS_TO_PROD_NEW
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "TM_CZ"."I2B2_MOVE_ANALYSIS_TO_PROD_NEW" 
+(i_etl_id        number    := -1
+,i_job_id        number    := null
+)
+AS
+    -- For partitioned table  2/4/2014
+    --Audit variables
+    newJobFlag     INTEGER(1);
+    databaseName     VARCHAR(100);
+    procedureName VARCHAR(100);
+    jobID         number(18,0);
+    stepCt         number(18,0);
+
+    v_etl_id                                        number(18,0);
+    v_bio_assay_analysis_id                number(18,0);
+    v_data_type                                        varchar2(50);
+    v_sqlText                                        varchar2(2000);
+    v_exists                    int;
+    v_GWAS_staged                                int;
+    v_EQTL_staged                                int;
+        v_gwas_indx                                        int;
+        v_eqtl_indx                                        int;
+        v_max_ext_flds                                int;
+
+    BEGIN
+
+    --Set Audit Parameters
+    newJobFlag := 0; -- False (Default)
+    jobID := -1;
+
+    SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+    procedureName := $$PLSQL_UNIT;
+
+    --Audit JOB Initialization
+    --If Job ID does not exist, then this is a single procedure run and we need to create it
+    IF(jobID IS NULL or jobID < 1)
+    THEN
+        newJobFlag := 1; -- True
+        cz_start_audit (procedureName, databaseName, jobID);
+    END IF;
+
+    stepCt := 1;
+    cz_write_audit(jobID,databaseName,procedureName,'Starting i2b2_move_analysis_to_prod',0,stepCt,'Done');
+
+        v_GWAS_staged := 0;
+        v_EQTL_staged := 0;
+        v_gwas_indx := 0;
+
+    --    load staged analysis to array
+
+        for stage_rec in
+                (select baa.bio_assay_analysis_id
+                          ,lz.etl_id
+                          ,lz.study_id
+                          ,case when lz.data_type = 'Metabolic GWAS' then 'GWAS' else lz.data_type end as data_type
+                          ,lz.data_type as orig_data_type
+                          ,lz.analysis_name
+                from tm_lz.lz_src_analysis_metadata lz
+                        ,biomart.bio_assay_analysis baa
+                where lz.status = 'STAGED'
+                  and lz.study_id = baa.etl_id
+                  and lz.etl_id = baa.etl_id_source
+                  and case when i_etl_id = -1 then 1
+               when lz.etl_id = i_etl_id then 1
+               else 0 end = 1)
+        loop
+                stepCt := stepCt + 1;
+        cz_write_audit(jobId,databaseName,procedureName,'Loading ' || stage_rec.study_id || ' ' || stage_rec.orig_data_type || ' ' ||
+                       stage_rec.analysis_name,0,stepCt,'Done');
+
+                v_bio_assay_analysis_id := stage_rec.bio_assay_analysis_id;
+                v_etl_id := stage_rec.etl_id;
+                v_data_type := stage_rec.data_type;
+
+                --        get max nbr fields in ext_data for original data type
+
+                select max(field_idx) into v_max_ext_flds
+                from biomart.bio_asy_analysis_data_idx
+                where ext_type = stage_rec.orig_data_type;
+
+        if stage_rec.data_type = 'GWAS' then
+                        --        GWAS data
+            v_GWAS_staged := 1;
+                /* comment out for not disabling the indexes   by HZ 1/15/2014
+                        if v_gwas_indx = 0 then
+                                --        disable indexes if loading GWAS data
+                                for gwas_idx in (select index_name
+                                                                           ,table_name
+                                                                 from all_indexes
+                                                             where owner = 'BIOMART'
+                                                                   and table_name in ('BIO_ASSAY_ANALYSIS_GWAS','BIO_ASY_ANALYSIS_GWAS_TOP50')
+                                                                   and partitioned = 'NO' and compression!='DISABLED' )
+                                loop
+                                        v_sqlText := 'alter index biomart.' || gwas_idx.index_name || ' unusable';
+                                        stepCt := stepCt + 1;
+                                        cz_write_audit(jobID,databaseName,procedureName,'Disabling index ' || gwas_idx.index_name || ' on ' || gwas_idx.table_name,SQL%ROWCOUNT,stepCt,'Done');
+                                        execute immediate(v_sqlText);
+                                        stepCt := stepCt + 1;
+                                        cz_write_audit(jobID,databaseName,procedureName,'Disabling complete',SQL%ROWCOUNT,stepCt,'Done');
+                                end loop;
+                                v_gwas_indx := 1;
+                        end if;
+              */
+                        --        check if partition exists for bio_assay_analysis_id, if not, add, if yes, truncate
+                        select count(*) into v_exists
+                        from all_tab_partitions
+                        where table_name = 'BIO_ASSAY_ANALYSIS_GWAS'
+                          and partition_name = to_char(v_bio_assay_analysis_id);
+
+                        if v_exists = 0 then
+                                --        add partition to bio_assay_analysis_gwas
+                                v_sqlText := 'alter table biomart.bio_assay_analysis_gwas add PARTITION "' || to_char(v_bio_assay_analysis_id) || '"  VALUES (' ||
+                                                    to_char(v_bio_assay_analysis_id) || ') ' ||
+                                                   'NOLOGGING TABLESPACE "BIOMART" ';
+                                execute immediate(v_sqlText);
+                                stepCt := stepCt + 1;
+                                cz_write_audit(jobID,databaseName,procedureName,'Adding partition to bio_assay_analysis_gwas '|| to_char(v_bio_assay_analysis_id),0,stepCt,'Done');
+                        else
+                                --        truncate existing partition
+                                v_sqlText := 'alter table biomart.bio_assay_analysis_gwas truncate partition "' || to_char(v_bio_assay_analysis_id) || '"';
+                                execute immediate(v_sqlText);
+                                stepCt := stepCt + 1;
+                                cz_write_audit(jobID,databaseName,procedureName,'Truncating partition in bio_assay_analysis_gwas '|| to_char(v_bio_assay_analysis_id),0,stepCt,'Done');
+                        end if;
+
+            insert into biomart.bio_assay_analysis_gwas
+            (bio_asy_analysis_gwas_id
+            ,bio_assay_analysis_id
+            ,rs_id
+            ,p_value
+            ,p_value_char
+            ,etl_id
+            ,ext_data
+            ,log_p_value)
+            select bio_asy_analysis_gwas_id
+                  ,bio_assay_analysis_id
+                  ,rs_id
+                  ,to_binary_double(p_value_char)
+                  ,p_value_char
+                  ,etl_id
+                  ,case when length(ext_data)-length(replace(ext_data,';','')) < v_max_ext_flds
+                                                then tm_cz.repeat_char(ext_data,v_max_ext_flds-(length(ext_data)-length(replace(ext_data,';',''))),';')
+                                                else ext_data
+                                   end
+                  ,case when log10_pval_char is null then log(10,to_binary_double(p_value_char))*-1
+                  else
+                  to_binary_double(log10_pval_char)
+                  end
+            from biomart_stage.bio_assay_analysis_gwas
+            where bio_assay_analysis_id = v_bio_assay_analysis_id;
+            stepCt := stepCt + 1;
+            cz_write_audit(jobID,databaseName,procedureName,'Insert data for analysis from biomart.bio_assay_analysis_gwas',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        update data_count in bio_assay_analysis
+
+            update biomart.bio_assay_analysis baa
+                        set data_count=(select count(*) from biomart.bio_assay_analysis_gwas x
+                                                        where x.bio_assay_analysis_id=v_bio_assay_analysis_id)
+            where baa.bio_assay_analysis_id=v_bio_assay_analysis_id;
+            stepCt := stepCt +1;
+            cz_write_audit(jobID,databaseName,procedureName,'Update data_count for analysis',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        update status in lz_src_analysis_metadata
+
+                        update tm_lz.lz_src_analysis_metadata
+                        set status='PRODUCTION'
+                        where etl_id = v_etl_id;
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Set status to PRODUCTION in tm_lz.lz_src_analysis_metadata',SQL%ROWCOUNT,stepCt,'Done');
+                        commit;
+
+                        --        delete data from biomart_stage
+
+                        delete from biomart_stage.bio_assay_analysis_gwas
+                        where bio_assay_analysis_id = v_bio_assay_analysis_id;
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Delete data for analysis from biomart_stage.bio_assay_analysis_gwas',SQL%ROWCOUNT,stepCt,'Done');
+                        commit;
+
+                        --        load top50 table
+                        i2b2_load_gwas_top50(v_bio_assay_analysis_id, jobID);
+
+                else
+                        --        EQTL data
+                        v_EQTL_staged := 1;
+                      /*
+                        if v_eqtl_indx = 0 then
+                                --        disable indexes if loading eqtl data
+                                for eqtl_idx in (select index_name
+                                                                           ,table_name
+                                                                 from all_indexes
+                                                             where owner = 'BIOMART'
+                                                                   and table_name = 'BIO_ASY_ANALYSIS_EQTL_TOP50' )
+                                loop
+                                        v_sqlText := 'alter index ' || eqtl_idx.index_name || ' unusable';
+                                        stepCt := stepCt + 1;
+                                        cz_write_audit(jobID,databaseName,procedureName,'Disabling index ' || eqtl_idx.index_name || ' on ' || eqtl_idx.table_name,SQL%ROWCOUNT,stepCt,'Done');
+                                        execute immediate(v_sqlText);
+                                        stepCt := stepCt + 1;
+                                        cz_write_audit(jobID,databaseName,procedureName,'Disabling complete',SQL%ROWCOUNT,stepCt,'Done');
+                                end loop;
+                                v_eqtl_indx := 1;
+                        end if;
+                        */
+                        --        delete existing data from bio_assay_analysis_eqtl
+                        delete from biomart.bio_assay_analysis_eqtl g
+                        where g.bio_assay_analysis_id = v_bio_assay_analysis_id;
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Delete exising data for staged analyses from biomart.bio_assay_analysis_eqtl',SQL%ROWCOUNT,stepCt,'Done');
+                        commit;
+
+            insert into biomart.bio_assay_analysis_eqtl
+            (bio_asy_analysis_eqtl_id
+            ,bio_assay_analysis_id
+            ,rs_id
+            ,gene
+            ,p_value
+            ,p_value_char
+            ,cis_trans
+            ,distance_from_gene
+            ,etl_id
+            ,ext_data
+            ,log_p_value)
+            select bio_asy_analysis_eqtl_id
+                  ,bio_assay_analysis_id
+                  ,rs_id
+                  ,gene
+                  ,to_binary_double(p_value_char)
+                  ,p_value_char
+                  ,cis_trans
+                  ,distance_from_gene
+                  ,etl_id
+                  ,case when length(ext_data)-length(replace(ext_data,';','')) < v_max_ext_flds
+                                                then tm_cz.repeat_char(ext_data,v_max_ext_flds-(length(ext_data)-length(replace(ext_data,';',''))),';')
+                                                else ext_data
+                                   end
+                  ,log(10,to_binary_double(p_value_char))*-1
+            from biomart_stage.bio_assay_analysis_eqtl
+            where bio_assay_analysis_id = v_bio_assay_analysis_id;
+            stepCt := stepCt + 1;
+            cz_write_audit(jobID,databaseName,procedureName,'Insert data for analysis into biomart.bio_assay_analysis_eqtl',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        update data_count in bio_assay_analysis
+
+            update biomart.bio_assay_analysis baa
+                        set data_count=(select count(*) from biomart.bio_assay_analysis_eqtl x
+                                                        where x.bio_assay_analysis_id=v_bio_assay_analysis_id)
+            where baa.bio_assay_analysis_id=v_bio_assay_analysis_id;
+            stepCt := stepCt +1;
+            cz_write_audit(jobID,databaseName,procedureName,'Update data_count for analysis',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        update status in lz_src_analysis_metadata
+
+                        update tm_lz.lz_src_analysis_metadata
+                        set status='PRODUCTION'
+                        where etl_id = v_etl_id;
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Set status to PRODUCTION in tm_lz.lz_src_analysis_metadata',SQL%ROWCOUNT,stepCt,'Done');
+                        commit;
+
+                        --        delete data from biomart_stage
+
+                        delete from biomart_stage.bio_assay_analysis_eqtl
+            where bio_assay_analysis_id = v_bio_assay_analysis_id;
+            stepCt := stepCt + 1;
+            cz_write_audit(jobID,databaseName,procedureName,'Delete data for analysis from biomart_stage.bio_assay_analysis_eqtl',SQL%ROWCOUNT,stepCt,'Done');
+            commit;
+
+                        --        load top50 table
+                        i2b2_load_eqtl_top50(v_bio_assay_analysis_id, jobID);
+
+                end if;
+        end loop;
+
+    --    rebuild indexes if loading GWAS data
+    /*
+    if v_GWAS_staged = 1 then
+                for gwas_idx in (select index_name
+                                                           ,table_name
+                                                 from all_indexes
+                                                 where owner = 'BIOMART'
+                                                   and table_name In ('BIO_ASSAY_ANALYSIS_GWAS','BIO_ASY_ANALYSIS_GWAS_TOP50') )
+                loop
+                        v_sqlText := 'alter index ' || gwas_idx.index_name || ' rebuild';
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Rebuilding index ' || gwas_idx.index_name || ' on ' || gwas_idx.table_name,SQL%ROWCOUNT,stepCt,'Done');
+                        execute immediate(v_sqlText);
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Rebuilding complete',SQL%ROWCOUNT,stepCt,'Done');
+                end loop;
+        end if;
+        */
+        if v_gwas_staged = 0 and v_eqtl_staged = 0 then
+        cz_write_audit(jobID, databaseName, procedureName, 'No staged data - run terminating normally',0,stepCt,'Done');
+        cz_end_audit(jobID, 'Success');
+        end if;
+
+    --    rebuild indexes if loading EQTL data
+    /*
+    if v_eqtl_staged = 1 then
+                for eqtl_idx in (select index_name
+                                                           ,table_name
+                                                 from all_indexes
+                                                 where owner = 'BIOMART'
+                                                   and table_name = 'BIO_ASY_ANALYSIS_EQTL_TOP50')
+                loop
+                        v_sqlText := 'alter index ' || eqtl_idx.index_name || ' rebuild';
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Rebuilding index ' || eqtl_idx.index_name || ' on ' || eqtl_idx.table_name,SQL%ROWCOUNT,stepCt,'Done');
+                        execute immediate(v_sqlText);
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobID,databaseName,procedureName,'Rebuilding complete',SQL%ROWCOUNT,stepCt,'Done');
+                end loop;
+        end if;
+        */
+     /*   if v_eqtl_staged = 0 and v_eqtl_staged = 0 then
+        cz_write_audit(jobID, databaseName, procedureName, 'No staged data - run terminating normally',0,stepCt,'Done');
+        cz_end_audit(jobID, 'Success');
+        end if;
+        */
+        --        check if any data left in staging tables, ususally indicated no bio_assay_analysis record in biomart
+
+        select count(*) into v_exists
+        from (select distinct bio_assay_analysis_id from biomart_stage.bio_assay_analysis_gwas
+                  union
+                  select distinct bio_assay_analysis_id from biomart_stage.bio_assay_analysis_eqtl);
+
+        if v_exists > 0 then
+        cz_write_audit(jobID, databaseName, procedureName, '**WARNING ** data remains in stage tables',0,stepCt,'Done');
+      --  cz_end_audit(jobID, 'Success');
+        end if;
+
+    cz_write_audit(jobID,databaseName,procedureName,'End ' || procedureName,0,stepCt,'Done');
+    stepCt := stepCt + 1;
+
+    cz_end_audit(jobID, 'Success');
+
+    exception
+    when others then
+    --Handle errors.
+        cz_error_handler (jobID, procedureName);
+    --End Proc
+        cz_end_audit (jobID, 'FAIL');
+
+END;
+/
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_mrna_index_maint.sql b/ddl/oracle/tm_cz/procedures/i2b2_mrna_index_maint.sql
index 68aba0d5..29222252 100644
--- a/ddl/oracle/tm_cz/procedures/i2b2_mrna_index_maint.sql
+++ b/ddl/oracle/tm_cz/procedures/i2b2_mrna_index_maint.sql
@@ -107,6 +107,58 @@ BEGIN
 			stepCt := stepCt + 1;
 			cz_write_audit(jobId,databaseName,procedureName,'Drop de_microarray_data_idx2',0,stepCt,'Done');
 		end if;
+				
+		select count(*) 
+		into idxExists
+		from all_indexes
+		where table_name = 'DE_SUBJECT_MICROARRAY_DATA'
+		  and index_name = 'DE_MICROARRAY_DATA_IDX3'
+		  and owner = 'DEAPP';
+		
+		if idxExists = 1 then
+			execute immediate('drop index deapp.de_microarray_data_idx3');
+			stepCt := stepCt + 1;
+			cz_write_audit(jobId,databaseName,procedureName,'Drop de_microarray_data_idx3',0,stepCt,'Done');
+		end if;
+				
+		select count(*) 
+		into idxExists
+		from all_indexes
+		where table_name = 'DE_SUBJECT_MICROARRAY_DATA'
+		  and index_name = 'DE_MICROARRAY_DATA_IDX4'
+		  and owner = 'DEAPP';
+		
+		if idxExists = 1 then
+			execute immediate('drop index deapp.de_microarray_data_idx4');
+			stepCt := stepCt + 1;
+			cz_write_audit(jobId,databaseName,procedureName,'Drop de_microarray_data_idx4',0,stepCt,'Done');
+		end if;
+				
+		select count(*) 
+		into idxExists
+		from all_indexes
+		where table_name = 'DE_SUBJECT_MICROARRAY_DATA'
+		  and index_name = 'DE_MICROARRAY_DATA_IDX5'
+		  and owner = 'DEAPP';
+		
+		if idxExists = 1 then
+			execute immediate('drop index deapp.de_microarray_data_idx5');
+			stepCt := stepCt + 1;
+			cz_write_audit(jobId,databaseName,procedureName,'Drop de_microarray_data_idx5',0,stepCt,'Done');
+		end if;
+				
+		select count(*) 
+		into idxExists
+		from all_indexes
+		where table_name = 'DE_SUBJECT_MICROARRAY_DATA'
+		  and index_name = 'DE_MICROARRAY_DATA_IDX10'
+		  and owner = 'DEAPP';
+		
+		if idxExists = 1 then
+			execute immediate('drop index deapp.de_microarray_data_idx10');
+			stepCt := stepCt + 1;
+			cz_write_audit(jobId,databaseName,procedureName,'Drop de_microarray_data_idx10',0,stepCt,'Done');
+		end if;
 						
 	else
 		--	add indexes
@@ -121,7 +173,7 @@ BEGIN
 		  and owner = 'DEAPP';
                   
 		if idxExists = 0 then                      
-                        execute immediate('create index deapp.de_microarray_data_idx1 on deapp.de_subject_microarray_data(probeset_id) ' || localVar || ' nologging compress tablespace "' || tableSpace || '"');
+                        execute immediate('create index deapp.de_microarray_data_idx1 on deapp.de_subject_microarray_data(trial_name, assay_id, probeset_id) ' || localVar || ' nologging compress tablespace "' || tableSpace || '"');
 			stepCt := stepCt + 1;
 			cz_write_audit(jobId,databaseName,procedureName,'Create de_microarray_data_idx1',0,stepCt,'Done');
 		end if;
@@ -134,10 +186,36 @@ BEGIN
 		  and owner = 'DEAPP';
 		  
 		if idxExists = 0 then		
-			execute immediate('create index deapp.de_microarray_data_idx2 on deapp.de_subject_microarray_data(assay_id) ' || localVar || ' nologging compress tablespace "' || tableSpace || '"');
+			execute immediate('create index deapp.de_microarray_data_idx2 on deapp.de_subject_microarray_data(assay_id, probeset_id) ' || localVar || ' nologging compress tablespace "' || tableSpace || '"');
 			stepCt := stepCt + 1;
 			cz_write_audit(jobId,databaseName,procedureName,'Create de_microarray_data_idx2',0,stepCt,'Done');
 		end if;
+				
+		select count(*) 
+		into idxExists
+		from all_indexes
+		where table_name = 'DE_SUBJECT_MICROARRAY_DATA'
+		  and index_name = 'DE_MICROARRAY_DATA_IDX3'
+		  and owner = 'DEAPP';
+		  
+		if idxExists = 0 then		
+			execute immediate('create ' || bitmapVar || ' index deapp.de_microarray_data_idx3 on deapp.de_subject_microarray_data(assay_id) ' || localVar || ' nologging ' || bitmapCompress || ' tablespace "' || tableSpace || '"');
+			stepCt := stepCt + 1;
+			cz_write_audit(jobId,databaseName,procedureName,'Create de_microarray_data_idx3',0,stepCt,'Done');
+		end if;
+				
+		select count(*) 
+		into idxExists
+		from all_indexes
+		where table_name = 'DE_SUBJECT_MICROARRAY_DATA'
+		  and index_name = 'DE_MICROARRAY_DATA_IDX4'
+		  and owner = 'DEAPP';
+		  
+		if idxExists = 0 then
+			execute immediate('create ' || bitmapVar || ' index deapp.de_microarray_data_idx4 on deapp.de_subject_microarray_data(probeset_id) ' || localVar || ' nologging ' || bitmapCompress || ' tablespace "' || tableSpace || '"');
+			stepCt := stepCt + 1;
+			cz_write_audit(jobId,databaseName,procedureName,'Create de_microarray_data_idx4',0,stepCt,'Done');
+		end if;
 
 		if pExists = 0 then
 			--	only create this index if the table is not partitioned.  This is the column that the table would be partitioned on
@@ -156,6 +234,21 @@ BEGIN
 			end if;
 		end if;
 
+/*		not used
+	
+		select count(*) 
+		into idxExists
+		from all_indexes
+		where table_name = 'DE_SUBJECT_MICROARRAY_DATA'
+		  and index_name = 'DE_MICROARRAY_DATA_IDX10'
+		  and owner = 'DEAPP';
+		  
+		if idxExists = 0 then
+			execute immediate('create index deapp.de_microarray_data_idx10 on deapp.de_subject_microarray_data(assay_id, subject_id, probeset_id, zscore) ' || localVar || ' nologging compress tablespace "' || tableSpace || '"');
+			stepCt := stepCt + 1;
+			cz_write_audit(jobId,databaseName,procedureName,'Create de_microarray_data_idx10',0,stepCt,'Done');
+		end if;
+*/							
 	end if;
 	
 	stepCt := stepCt + 1;
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_process_acgh_data.sql b/ddl/oracle/tm_cz/procedures/i2b2_process_acgh_data.sql
new file mode 100644
index 00000000..3efb6e0f
--- /dev/null
+++ b/ddl/oracle/tm_cz/procedures/i2b2_process_acgh_data.sql
@@ -0,0 +1,980 @@
+--
+-- Type: PROCEDURE; Owner: TM_CZ; Name: I2B2_PROCESS_ACGH_DATA
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "TM_CZ"."I2B2_PROCESS_ACGH_DATA" 
+(
+  trial_id 	VARCHAR2
+ ,top_node	varchar2
+ ,source_cd	varchar2 := 'STD'	--	default source_cd = 'STD'
+ ,secure_study	varchar2			--	security setting if new patients added to patient_dimension
+ ,currentJobID 	NUMBER := null
+ ,rtn_code	OUT	NUMBER
+)
+AS
+/*************************************************************************
+* Copyright 2008-2012 Janssen Research BIOMART_USER, LLC.
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+******************************************************************/
+--	***  NOTE ***
+--	The input file columns are mapped to the following table columns.  This is done so that the javascript for the advanced workflows
+--	selects the correct data for the dropdowns.
+
+--		tissue_type	=>	sample_type
+--		attribute_1	=>	tissue_type
+--		atrribute_2	=>	timepoint
+
+  TrialID	varchar2(100);
+  RootNode	VARCHAR2(2000);
+  root_level	integer;
+  topNode	varchar2(2000);
+  topLevel	integer;
+  tPath		varchar2(2000);
+  study_name	varchar2(100);
+  sourceCd	varchar2(50);
+  secureStudy	varchar2(1);
+
+  dataType		varchar2(10);
+  sqlText		varchar2(1000);
+  tText			varchar2(1000);
+  gplTitle		varchar2(1000);
+  pExists		number;
+  partTbl   		number;
+  partExists 		number;
+  sampleCt		number;
+  idxExists 		number;
+  logBase		number;
+  pCount		integer;
+  sCount		integer;
+  tablespaceName	varchar2(200);
+  v_bio_experiment_id	number(18,0);
+
+    --Audit variables
+  newJobFlag 	INTEGER(1);
+  databaseName 	VARCHAR(100);
+  procedureName VARCHAR(100);
+  jobID 	number(18,0);
+  stepCt 	number(18,0);
+
+  --unmapped_patients exception;
+  missing_platform	exception;
+  missing_tissue	EXCEPTION;
+  unmapped_platform 	exception;
+  multiple_platform	exception;
+  no_probeset_recs	exception;
+
+
+
+  CURSOR addNodes is
+    select distinct t.leaf_node,t.node_name
+      from  wt_mrna_nodes t
+	where not exists (select 1 from i2b2 x where t.leaf_node = x.c_fullname);
+
+  -- cursor to define the path for delete_one_node  this will delete any nodes that are hidden after i2b2_create_concept_counts
+  CURSOR delNodes is
+    select distinct c_fullname
+      from  i2b2 where c_fullname like topNode || '%'  and
+                       substr(c_visualattributes,2,1) = 'H';
+
+  CURSOR uploadI2b2 is
+    select category_cd,display_value,display_label,display_unit
+      from tm_lz.lt_src_display_mapping
+        group by category_cd,display_value,display_label,display_unit;
+
+
+BEGIN
+
+  EXECUTE IMMEDIATE 'alter session set NLS_NUMERIC_CHARACTERS=".,"';
+
+  TrialID := upper(trial_id);
+  secureStudy := upper(secure_study);
+
+  if (secureStudy not in ('Y','N') ) then
+	secureStudy := 'Y';
+  end if;
+
+  topNode := REGEXP_REPLACE('\' || top_node || '\','(\\){2,}', '\');
+  select length(topNode)-length(replace(topNode,'\','')) into topLevel from dual;
+
+  sourceCd := upper(nvl(source_cd,'STD'));
+
+  --Set Audit Parameters
+  newJobFlag := 0;             -- False (Default)
+  jobID      := currentJobID;
+
+  SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+  procedureName := $$PLSQL_UNIT;
+
+  --Audit JOB Initialization
+  --If Job ID does not exist, then this is a single procedure run and we need to create it
+  IF(jobID IS NULL or jobID < 1)
+  THEN
+    newJobFlag := 1; -- True
+    cz_start_audit (procedureName, databaseName, jobID);
+  END IF;
+
+  stepCt := 0;
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Starting i2b2_process_acgh_data',0,stepCt,'Done');
+
+  -- Get count of records in lt_src_mrna_subj_samp_map
+
+  select count(*) into sCount from lt_src_mrna_subj_samp_map;
+
+  -- check if all subject_sample map records have a platform, If not, abort run
+
+  select count(*) into pCount
+    from lt_src_mrna_subj_samp_map where platform is null;
+
+ if pCount > 0 then
+	raise missing_platform;
+  end if;
+
+ -- check if platform exists in de_chromosomal_region .  If not, abort run.
+
+  select count(*) into pCount
+    from DE_CHROMOSOMAL_REGION
+      where GPL_ID in (select distinct m.platform from lt_src_mrna_subj_samp_map m);
+
+  if PCOUNT = 0 then
+ 	RAISE UNMAPPED_platform;
+  end if;
+
+  select count(*) into pCount
+    from DE_gpl_info
+      where platform in (select distinct m.platform from lt_src_mrna_subj_samp_map m);
+
+  if PCOUNT = 0 then
+	RAISE UNMAPPED_platform;
+  end if;
+
+  -- check if all subject_sample map records have a tissue_type, If not, abort run
+
+  select count(*) into pCount
+    from lt_src_mrna_subj_samp_map
+      where tissue_type is null;
+
+  if pCount > 0 then
+	raise missing_tissue;
+  end if;
+
+  -- check if there are multiple platforms, if yes, then platform must be supplied in lt_src_mrna_data
+  select count(*) into pCount
+    from (select sample_cd
+      from lt_src_mrna_subj_samp_map
+        group by sample_cd having count(distinct platform) > 1);
+
+  if pCount > 0 then
+	raise multiple_platform;
+  end if;
+
+  -- Get root_node from topNode
+
+  select parse_nth_value(topNode, 2, '\') into RootNode from dual;
+
+  select count(*) into pExists
+    from table_access where c_name = rootNode;
+
+  if pExists = 0 then
+	i2b2_add_root_node(rootNode, jobId);
+  end if;
+
+  select c_hlevel into root_level
+    from i2b2 where c_name = RootNode;
+
+  -- Get study name from topNode
+
+  select parse_nth_value(topNode, topLevel, '\') into study_name from dual;
+
+  --	Add any upper level nodes as needed
+
+  tPath := REGEXP_REPLACE(replace(top_node,study_name,null),'(\\){2,}', '\');
+  select length(tPath) - length(replace(tPath,'\',null)) into pCount from dual;
+
+  if pCount > 2 then
+ 	i2b2_fill_in_tree(null, tPath, jobId);
+  end if;
+
+  --	uppercase study_id in lt_src_mrna_subj_samp_map in case curator forgot
+
+  update lt_src_mrna_subj_samp_map
+  set trial_name=upper(trial_name);
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Uppercase trial_name in lt_src_mrna_subj_samp_map',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	create records in patient_dimension for subject_ids if they do not exist
+  --	format of sourcesystem_cd:  trial:[site:]subject_cd
+
+  insert into patient_dimension
+    ( patient_num,
+      sex_cd,
+      age_in_years_num,
+      race_cd,
+      update_date,
+      download_date,
+      import_date,
+      sourcesystem_cd
+    )
+    select seq_patient_num.nextval
+		  ,x.sex_cd
+		  ,x.age_in_years_num
+		  ,x.race_cd
+		  ,sysdate
+		  ,sysdate
+		  ,sysdate
+		  ,x.sourcesystem_cd
+	from (select distinct 'Unknown' as sex_cd,
+				 0 as age_in_years_num,
+				 null as race_cd,
+				 regexp_replace(TrialID || ':' || s.site_id || ':' || s.subject_id,'(::){1,}', ':') as sourcesystem_cd
+		 from lt_src_mrna_subj_samp_map s
+		     ,de_gpl_info g
+		 where s.subject_id is not null
+		   and s.trial_name = TrialID
+		   and s.source_cd = sourceCD
+		   and s.platform = g.platform
+		   and upper(g.marker_type) = 'CHROMOSOMAL'
+		   and not exists
+			  (select 1 from patient_dimension x
+			   where x.sourcesystem_cd =
+				 regexp_replace(TrialID || ':' || s.site_id || ':' || s.subject_id,'(::){1,}', ':'))
+		) x;
+
+  pCount := SQL%ROWCOUNT;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert subjects to patient_dimension',pCount,stepCt,'Done');
+  commit;
+
+  i2b2_create_security_for_trial(TrialId, secureStudy, jobID);
+
+  --	Delete existing observation_fact data, will be repopulated
+
+  delete from observation_fact obf
+    where obf.concept_cd in
+		 (select distinct x.concept_code
+		  from de_subject_sample_mapping x
+		  where x.trial_name = TrialId
+		    and nvl(x.source_cd,'STD') = sourceCD
+		    and x.platform = 'ACGH');
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Delete data from observation_fact',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  select count(*) into pExists
+    from all_tables
+      where table_name  = 'DE_SUBJECT_MICROARRAY_DATA' and
+	    partitioned = 'YES';
+
+  if pExists = 0 then
+	--	dataset is not partitioned so must delete
+	delete from de_subject_acgh_data
+	where trial_source = TrialId || ':' || sourceCd;
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Delete data from de_subject_acgh_data',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+  else
+	--	Create partition in de_subject_acgh_data if it doesn't exist else truncate partition
+	select count(*)	into pExists
+	  from all_tab_partitions
+	    where table_name     = 'DE_SUBJECT_MICROARRAY_DATA' and
+		  partition_name = TrialId;
+
+	if pExists = 0 then
+		--	needed to add partition to de_subject_acgh_data
+		sqlText := 'alter table deapp.de_subject_acgh_data add PARTITION "' ||
+			   TrialID                                                        ||
+                           '"  VALUES ('                                                  ||
+                           ''''                                                           ||
+                           TrialID                                                        ||
+                           ''''                                                           ||
+                           ') '                                                           ||
+			   'NOLOGGING COMPRESS TABLESPACE "TRANSMART" ';
+		execute immediate(sqlText);
+		stepCt := stepCt + 1;
+		cz_write_audit(jobId,databaseName,procedureName,'Adding partition to de_subject_acgh_data',0,stepCt,'Done');
+	else
+		sqlText := 'alter table deapp.de_subject_acgh_data truncate partition "' || TrialID || '"';
+		execute immediate(sqlText);
+		stepCt := stepCt + 1;
+		cz_write_audit(jobId,databaseName,procedureName,'Truncating partition in de_subject_acgh_data',0,stepCt,'Done');
+	end if;
+
+  end if;
+
+  --	Cleanup any existing data in de_subject_sample_mapping.
+
+  delete from DE_SUBJECT_SAMPLE_MAPPING
+    where trial_name           = TrialID     and
+          nvl(source_cd,'STD') = sourceCd    and
+	  platform             = 'ACGH'; --Making sure only mRNA data is deleted
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Delete trial from DEAPP de_subject_sample_mapping',SQL%ROWCOUNT,stepCt,'Done');
+
+  commit;
+
+  --	truncate tmp node table
+
+  execute immediate('truncate table tm_wz.wt_mrna_nodes');
+
+  --	load temp table with leaf node path, use temp table with distinct sample_type, ATTR2, platform, and title   this was faster than doing subselect
+  --	from wt_subject_mrna_data
+
+  execute immediate('truncate table tm_wz.wt_mrna_node_values');
+
+  insert into wt_mrna_node_values
+	(category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+	,attribute_2
+	,title
+	)
+	select distinct a.category_cd
+				   ,nvl(a.platform,'GPL570')
+				   ,nvl(a.tissue_type,'Unspecified Tissue Type')
+	               ,a.attribute_1
+				   ,a.attribute_2
+				   ,g.title
+    from lt_src_mrna_subj_samp_map a
+	    ,de_gpl_info g
+	where a.trial_name = TrialID
+	  and nvl(a.platform,'GPL570') = g.platform
+	  and a.source_cd = sourceCD
+	  and a.platform = g.platform
+	  and upper(g.marker_type) = 'CHROMOSOMAL'
+	  and g.title = (select min(x.title) from de_gpl_info x where nvl(a.platform,'GPL570') = x.platform)
+      -- and upper(g.organism) = 'HOMO SAPIENS'
+	  ;
+	--  and decode(dataType,'R',sign(a.intensity_value),1) = 1;	--	take all values when dataType T, only >0 for dataType R
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert node values into DEAPP wt_mrna_node_values',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+    ,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       category_cd,'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\','(\\){2,}', '\')
+		  ,category_cd
+		  ,platform as platform
+		  ,tissue_type
+		  ,attribute_1 as attribute_1
+          ,attribute_2 as attribute_2
+		  ,'LEAF'
+	from  wt_mrna_node_values;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Create leaf nodes in DEAPP tmp_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	insert for platform node so platform concept can be populated
+
+  insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+    ,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'PLATFORM')+8)
+		  ,platform as platform
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'TISSUETYPE') > 1 then tissue_type else null end as tissue_type
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'ATTR1') > 1 then attribute_1 else null end as attribute_1
+          ,case when instr(substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'ATTR2') > 1 then attribute_2 else null end as attribute_2
+		  ,'PLATFORM'
+	from  wt_mrna_node_values;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Create platform nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	insert for ATTR1 node so ATTR1 concept can be populated in tissue_type_cd
+
+  insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+    ,attribute_1
+	,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'ATTR1')+5),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'ATTR1')+5)
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'PLATFORM') > 1 then platform else null end as platform
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'TISSUETYPE') > 1 then tissue_type else null end as tissue_type
+		  ,attribute_1 as attribute_1
+          ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'ATTR2') > 1 then attribute_2 else null end as attribute_2
+		  ,'ATTR1'
+	from  wt_mrna_node_values
+	where category_cd like '%ATTR1%'
+	  and attribute_1 is not null;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Create ATTR1 nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	insert for ATTR2 node so ATTR2 concept can be populated in timepoint_cd
+
+  insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+    ,attribute_1
+	,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'ATTR2')+5),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'ATTR2')+5)
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR2')+5),'PLATFORM') > 1 then platform else null end as platform
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'TISSUETYPE') > 1 then tissue_type else null end as tissue_type
+          ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR2')+5),'ATTR1') > 1 then attribute_1 else null end as attribute_1
+		  ,attribute_2 as attribute_2
+		  ,'ATTR2'
+	from  wt_mrna_node_values
+	where category_cd like '%ATTR2%'
+	  and attribute_2 is not null;
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create ATTR2 nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+	--	insert for tissue_type node so sample_type_cd can be populated
+
+	insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+    ,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10)
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'PLATFORM') > 1 then platform else null end as platform
+		  ,tissue_type as tissue_type
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'ATTR1') > 1 then attribute_1 else null end as attribute_1
+          ,case when instr(substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'ATTR2') > 1 then attribute_2 else null end as attribute_2
+		  ,'TISSUETYPE'
+	from  wt_mrna_node_values
+	where category_cd like '%TISSUETYPE%';
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Create ATTR2 nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  update wt_mrna_nodes
+    set node_name=parse_nth_value(leaf_node,length(leaf_node)-length(replace(leaf_node,'\',null)),'\');
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Updated node_name in DEAPP tmp_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	add leaf nodes for mRNA data  The cursor will only add nodes that do not already exist.
+
+  FOR r_addNodes in addNodes Loop
+       --Add nodes for all types (ALSO DELETES EXISTING NODE)
+	i2b2_add_node(TrialID, r_addNodes.leaf_node, r_addNodes.node_name, jobId);
+	stepCt := stepCt + 1;
+	tText := 'Added Leaf Node: ' || r_addNodes.leaf_node || '  Name: ' || r_addNodes.node_name;
+	cz_write_audit(jobId,databaseName,procedureName,tText,SQL%ROWCOUNT,stepCt,'Done');
+	i2b2_fill_in_tree(TrialId, r_addNodes.leaf_node, jobID);
+  END LOOP;
+
+  --	set sourcesystem_cd, c_comment to null if any added upper-level nodes
+
+  update i2b2 b
+	set sourcesystem_cd=null,c_comment=null
+	where b.sourcesystem_cd = TrialId
+	  and length(b.c_fullname) < length(topNode);
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Set sourcesystem_cd to null for added upper level nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	update concept_cd for nodes, this is done to make the next insert easier
+
+  update wt_mrna_nodes t
+	set concept_cd=(select c.concept_cd from concept_dimension c
+	                where c.concept_path = t.leaf_node
+				   )
+    where exists
+         (select 1 from concept_dimension x
+	                where x.concept_path = t.leaf_node
+				   )
+	  and t.concept_cd is null;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Update wt_mrna_nodes with newly created concept_cds',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+
+  --Load the DE_SUBJECT_SAMPLE_MAPPING from wt_subject_mrna_data
+
+  --PATIENT_ID      = PATIENT_ID (SAME AS ID ON THE PATIENT_DIMENSION)
+  --SITE_ID         = site_id
+  --SUBJECT_ID      = subject_id
+  --SUBJECT_TYPE    = NULL
+  --CONCEPT_CODE    = from LEAF records in wt_mrna_nodes
+  --SAMPLE_TYPE    	= TISSUE_TYPE
+  --SAMPLE_TYPE_CD  = concept_cd from TISSUETYPE records in wt_mrna_nodes
+  --TRIAL_NAME      = TRIAL_NAME
+  --TIMEPOINT		= attribute_2
+  --TIMEPOINT_CD	= concept_cd from ATTR2 records in wt_mrna_nodes
+  --TISSUE_TYPE     = attribute_1
+  --TISSUE_TYPE_CD  = concept_cd from ATTR1 records in wt_mrna_nodes
+  --PLATFORM        = MRNA_AFFYMETRIX - this is required by ui code
+  --PLATFORM_CD     = concept_cd from PLATFORM records in wt_mrna_nodes
+  --DATA_UID		= concatenation of concept_cd-patient_num
+  --GPL_ID			= platform from wt_subject_mrna_data
+  --CATEGORY_CD		= category_cd that generated ontology
+  --SAMPLE_ID		= id of sample (trial:S:[site_id]:subject_id:sample_cd) from patient_dimension, may be the same as patient_num
+  --SAMPLE_CD		= sample_cd
+  --SOURCE_CD		= sourceCd
+
+  --ASSAY_ID        = generated by trigger
+
+  insert into de_subject_sample_mapping
+	(patient_id
+	,site_id
+	,subject_id
+	,subject_type
+	,concept_code
+	,assay_id
+	,sample_type
+	,sample_type_cd
+	,trial_name
+	,timepoint
+	,timepoint_cd
+	,tissue_type
+	,tissue_type_cd
+	,platform
+	,platform_cd
+	,data_uid
+	,gpl_id
+	,sample_id
+	,sample_cd
+	,category_cd
+	,source_cd
+	,omic_source_study
+	,omic_patient_id
+    )
+	select t.patient_id
+		  ,t.site_id
+		  ,t.subject_id
+		  ,t.subject_type
+		  ,t.concept_code
+		  ,deapp.seq_assay_id.nextval
+		  ,t.sample_type
+		  ,t.sample_type_cd
+		  ,t.trial_name
+		  ,t.timepoint
+		  ,t.timepoint_cd
+		  ,t.tissue_type
+		  ,t.tissue_type_cd
+		  ,t.platform
+		  ,t.platform_cd
+		  ,t.data_uid
+		  ,t.gpl_id
+		  ,t.sample_id
+		  ,t.sample_cd
+		  ,t.category_cd
+		  ,t.source_cd
+		  ,t.omic_source_study
+		  ,t.omic_patient_id
+	from (select distinct b.patient_num as patient_id
+			  ,a.site_id
+			  ,a.subject_id
+			  ,null as subject_type
+			  ,ln.concept_cd as concept_code
+			  ,a.tissue_type as sample_type
+			  ,ttp.concept_cd as sample_type_cd
+			  ,a.trial_name
+			  ,a.attribute_2 as timepoint
+			  ,a2.concept_cd as timepoint_cd
+			  ,a.attribute_1 as tissue_type
+			  ,a1.concept_cd as tissue_type_cd
+			  ,'ACGH' as platform
+			  ,pn.concept_cd as platform_cd
+			  ,ln.concept_cd || '-' || to_char(b.patient_num) as data_uid
+			  ,a.platform as gpl_id
+			  ,coalesce(sid.patient_num,b.patient_num) as sample_id
+			  ,a.sample_cd
+			  ,nvl(a.category_cd,'Biomarker_Data+Gene_Expression+PLATFORM+TISSUETYPE+ATTR1+ATTR2') as category_cd
+			  ,a.source_cd
+			  ,TrialId as omic_source_study
+			  ,b.patient_num as omic_patient_id
+		from lt_src_mrna_subj_samp_map a
+		--Joining to Pat_dim to ensure the ID's match. If not I2B2 won't work.
+		inner join patient_dimension b
+		  on regexp_replace(TrialID || ':' || a.site_id || ':' || a.subject_id,'(::){1,}', ':') = b.sourcesystem_cd
+		inner join wt_mrna_nodes ln
+			on a.platform = ln.platform
+			and a.tissue_type = ln.tissue_type
+                        and a.category_cd=ln.category_cd  --modified
+			and nvl(a.attribute_1,'@') = nvl(ln.attribute_1,'@')
+			and nvl(a.attribute_2,'@') = nvl(ln.attribute_2,'@')
+			and ln.node_type = 'LEAF'
+		inner join wt_mrna_nodes pn
+			on a.platform = pn.platform
+                        and pn.category_cd=substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8)
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8),'TISSUETYPE') > 1 then a.tissue_type else '@' end = nvl(pn.tissue_type,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8),'ATTR1') > 1 then a.attribute_1 else '@' end = nvl(pn.attribute_1,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8),'ATTR2') > 1 then a.attribute_2 else '@' end = nvl(pn.attribute_2,'@')
+			and pn.node_type = 'PLATFORM'
+		left outer join wt_mrna_nodes ttp
+			on a.tissue_type = ttp.tissue_type
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10),'PLATFORM') > 1 then a.platform else '@' end = nvl(ttp.platform,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10),'ATTR1') > 1 then a.attribute_1 else '@' end = nvl(ttp.attribute_1,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10),'ATTR2') > 1 then a.attribute_2 else '@' end = nvl(ttp.attribute_2,'@')
+			and ttp.node_type = 'TISSUETYPE'
+                        and ttp.category_cd=substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10)
+		left outer join wt_mrna_nodes a1
+			on a.attribute_1 = a1.attribute_1
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5),'PLATFORM') > 1 then a.platform else '@' end = nvl(a1.platform,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5),'TISSUETYPE') > 1 then a.tissue_type else '@' end = nvl(a1.tissue_type,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5),'ATTR2') > 1 then a.attribute_2 else '@' end = nvl(a1.attribute_2,'@')
+			and a1.node_type = 'ATTR1'
+                        and a1.category_cd=substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5)
+		left outer join wt_mrna_nodes a2
+			on a.attribute_2 = a1.attribute_2
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5),'PLATFORM') > 1 then a.platform else '@' end = nvl(a2.platform,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5),'TISSUETYPE') > 1 then a.tissue_type else '@' end = nvl(a2.tissue_type,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5),'ATTR1') > 1 then a.attribute_1 else '@' end = nvl(a2.attribute_1,'@')
+			and a2.node_type = 'ATTR2'
+                        and a2.category_cd=substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5)
+		left outer join patient_dimension sid
+			on  regexp_replace(TrialId || ':S:' || a.site_id || ':' || a.subject_id || ':' || a.sample_cd,
+							  '(::){1,}', ':') = sid.sourcesystem_cd
+		where a.trial_name = TrialID
+		  and a.source_cd = sourceCD
+		  and  ln.concept_cd is not null) t;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert trial into DEAPP de_subject_sample_mapping',SQL%ROWCOUNT,stepCt,'Done');
+
+  commit;
+
+  insert into observation_fact
+    (patient_num
+	,concept_cd
+	,modifier_cd
+	,valtype_cd
+	,tval_char
+	,nval_num
+	,sourcesystem_cd
+	,import_date
+	,valueflag_cd
+	,provider_id
+	,location_cd
+	,units_cd
+        ,sample_cd
+        ,instance_num
+    )
+    select distinct m.patient_id
+		  ,m.concept_code
+		  ,'@'
+		  ,'T' -- Text data type
+		  ,'E'  --Stands for Equals for Text Types
+		  ,null	--	not numeric for mRNA
+		  ,m.trial_name
+		  ,sysdate
+		  ,'@'
+		  ,'@'
+		  ,'@'
+		  ,'' -- no units available
+                  ,m.sample_cd
+                  ,1
+    from  de_subject_sample_mapping m
+    where m.trial_name = TrialID
+	  and m.source_cd = sourceCD
+      and m.platform = 'ACGH';
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert patient facts into I2B2DEMODATA observation_fact',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	Insert sample facts
+
+  insert into observation_fact
+    (patient_num
+	,concept_cd
+	,modifier_cd
+	,valtype_cd
+	,tval_char
+	,nval_num
+	,sourcesystem_cd
+	,import_date
+	,valueflag_cd
+	,provider_id
+	,location_cd
+	,units_cd
+  ,sample_cd
+  ,instance_num
+    )
+    select distinct m.sample_id
+		  ,m.concept_code
+		  ,m.trial_name
+		  ,'T' -- Text data type
+		  ,'E'  --Stands for Equals for Text Types
+		  ,null	--	not numeric for mRNA
+		  ,m.trial_name
+		  ,sysdate
+		  ,'@'
+		  ,'@'
+		  ,'@'
+		  ,'' -- no units available
+      ,m.sample_cd
+      ,1
+    from  de_subject_sample_mapping m
+    where m.trial_name = TrialID
+	  and m.source_cd = sourceCd
+      and m.platform = 'ACGH'
+	  and m.patient_id != m.sample_id;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert sample facts into I2B2DEMODATA observation_fact',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  ---INSERT sample_dimension
+  INSERT INTO I2B2DEMODATA.SAMPLE_DIMENSION(SAMPLE_CD)
+         SELECT DISTINCT SAMPLE_CD FROM
+           DEAPP.DE_SUBJECT_SAMPLE_MAPPING WHERE SAMPLE_CD NOT IN (SELECT SAMPLE_CD FROM I2B2DEMODATA.SAMPLE_DIMENSION) ;
+
+  --Update I2b2 for correct data type
+  update i2b2 t
+	set c_columndatatype = 'T', c_metadataxml = null, c_visualattributes='FA'
+	where t.c_basecode in (select distinct x.concept_cd from wt_mrna_nodes x);
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Initialize data_type and xml in i2b2',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  for ul in uploadI2b2
+  loop
+	update i2b2 n
+	SET n.c_columndatatype = 'T',
+      --Static XML String
+		n.c_metadataxml =  ('<?xml version="1.0"?><ValueMetadata><Version>3.02</Version><CreationDateTime>08/14/2008 01:22:59</CreationDateTime><TestID></TestID><TestName></TestName><DataType>PosFloat</DataType><CodeType></CodeType><Loinc></Loinc><Flagstouse></Flagstouse><Oktousevalues>Y</Oktousevalues><MaxStringLength></MaxStringLength><LowofLowValue>0</LowofLowValue>
+                <HighofLowValue>0</HighofLowValue><LowofHighValue>100</LowofHighValue>100<HighofHighValue>100</HighofHighValue>
+                <LowofToxicValue></LowofToxicValue><HighofToxicValue></HighofToxicValue>
+                <EnumValues></EnumValues><CommentsDeterminingExclusion><Com></Com></CommentsDeterminingExclusion>
+                <UnitValues><NormalUnits>ratio</NormalUnits><EqualUnits></EqualUnits>
+                <ExcludingUnits></ExcludingUnits><ConvertingUnits><Units></Units><MultiplyingFactor></MultiplyingFactor>
+                </ConvertingUnits></UnitValues><Analysis><Enums /><Counts />
+                <New /></Analysis>'||(select xmlelement(name "SeriesMeta",xmlforest(m.display_value as "Value",m.display_unit as "Unit",m.display_label as "DisplayName")) as hi
+      from tm_lz.lt_src_display_mapping m where m.category_cd=ul.category_cd)||
+                '</ValueMetadata>') where n.c_fullname=(select leaf_node from wt_mrna_nodes where category_cd=ul.category_cd and leaf_node=n.c_fullname);
+
+                end loop;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Update c_columndatatype and c_metadataxml for numeric data types in I2B2METADATA i2b2',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --UPDATE VISUAL ATTRIBUTES for Leaf Active (Default is folder)
+  update i2b2 a
+    set c_visualattributes = 'LAH'
+	where a.c_basecode in (select distinct x.concept_code from de_subject_sample_mapping x
+						   where x.trial_name = TrialId
+						     and x.platform = 'ACGH'
+							 and x.concept_code is not null);
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Update visual attributes for leaf nodes in I2B2METADATA i2b2',SQL%ROWCOUNT,stepCt,'Done');
+  COMMIT;
+
+  update i2b2 a
+ 	set c_visualattributes='FAS'
+        where a.c_fullname = substr(topNode,1,instr(topNode,'\',1,3));
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Update visual attributes for study nodes in I2B2METADATA i2b2',SQL%ROWCOUNT,stepCt,'Done');
+  COMMIT;
+
+  --Build concept Counts
+  --Also marks any i2B2 records with no underlying data as Hidden, need to do at Trial level because there may be multiple platform and there is no longer
+  -- a unique top-level node for mRNA data
+
+  i2b2_create_concept_counts(topNode ,jobID );
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create concept counts',0,stepCt,'Done');
+
+	--	delete each node that is hidden
+
+  FOR r_delNodes in delNodes Loop
+	--	deletes hidden nodes for a trial one at a time
+	i2b2_delete_1_node(r_delNodes.c_fullname);
+	stepCt := stepCt + 1;
+	tText := 'Deleted node: ' || r_delNodes.c_fullname;
+	cz_write_audit(jobId,databaseName,procedureName,tText,SQL%ROWCOUNT,stepCt,'Done');
+  END LOOP;
+
+
+  --Reload Security: Inserts one record for every I2B2 record into the security table
+
+  i2b2_load_security_data(jobId);
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Load security data',0,stepCt,'Done');
+
+  --	tag data with probeset_id from reference.probeset_deapp
+
+  execute immediate ('truncate table tm_wz.wt_subject_mrna_probeset');
+
+  --	note: assay_id represents a unique subject/site/sample
+
+  insert into tm_wz.wt_subject_acgh_region
+       (region_id
+       ,chip
+       ,segmented
+       ,flag
+       ,probloss
+       ,probnorm
+       ,probgain
+       ,probamp
+       ,patient_id
+       ,trial_name
+       ,assay_id
+       )
+  select gs.region_id
+                 ,cast(md.chip as double precision)
+                 ,cast(md.segmented as double precision)
+                 ,cast(md.flag as smallint)
+                 ,cast(md.probloss as double precision)
+                 ,cast(md.probnorm as double precision)
+                 ,cast(md.probgain as double precision)
+                 ,cast(md.probamp as double precision)
+                 ,sd.patient_id
+                 ,TrialId
+                 ,sd.assay_id
+       from deapp.de_subject_sample_mapping sd
+               ,tm_lz.lt_src_acgh_data md
+               ,deapp.de_chromosomal_region gs
+       where sd.sample_cd = md.expr_id
+         and sd.platform = 'ACGH'
+         and sd.trial_name = TrialId
+         and sd.source_cd = sourceCd
+         and sd.gpl_id = gs.gpl_id
+         and md.region_name = gs.region_name
+       group by gs.region_id, md.chip, md.segmented, md.flag, md.probloss, md.probnorm, md.probgain, md.probamp
+                 ,sd.patient_id,sd.assay_id;
+
+  insert into deapp.de_subject_acgh_data
+	(   region_id
+          , assay_id
+          , patient_id
+          , trial_name
+          , chip
+          , segmented
+          , flag
+          , probloss
+          , probnorm
+          , probgain
+          , probamp
+        )
+        select  region_id
+              , assay_id
+              , patient_id
+              , trial_name
+              , chip
+              , segmented
+              , flag
+              , probloss
+              , probnorm
+              , probgain
+              , probamp
+        from tm_wz.wt_subject_acgh_region;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert into DEAPP wt_subject_mrna_probeset',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  if pExists = 0 then
+	raise no_probeset_recs;
+  end if;
+
+
+  ---Cleanup OVERALL JOB if this proc is being run standalone
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'End i2b2_process_acgh_data',0,stepCt,'Done');
+
+  IF newJobFlag = 1
+  THEN
+	cz_end_audit (jobID, 'SUCCESS');
+  END IF;
+
+ select 0 into rtn_code from dual;
+
+  EXCEPTION
+	--when unmapped_patients then
+	--	cz_write_audit(jobId,databasename,procedurename,'No site_id/subject_id mapped to patient_dimension',1,stepCt,'ERROR');
+	--	cz_error_handler(jobid,procedurename);
+	--	cz_end_audit (jobId,'FAIL');
+	when missing_platform then
+		cz_write_audit(jobId,databasename,procedurename,'Platform data missing from one or more subject_sample mapping records',1,stepCt,'ERROR');
+		cz_error_handler(jobid,procedurename);
+		cz_end_audit (jobId,'FAIL');
+		select 161 into rtn_code from dual;
+	when missing_tissue then
+		cz_write_audit(jobId,databasename,procedurename,'Tissue Type data missing from one or more subject_sample mapping records',1,stepCt,'ERROR');
+		cz_error_handler(jobid,procedurename);
+		CZ_END_AUDIT (JOBID,'FAIL');
+		select 162 into rtn_code from dual;
+	when unmapped_platform then
+		cz_write_audit(jobId,databasename,procedurename,'Platform not found in de_chromosomal_region',1,stepCt,'ERROR');
+		CZ_ERROR_HANDLER(JOBID,PROCEDURENAME);
+		cz_end_audit (jobId,'FAIL');
+		select 169 into rtn_code from dual;
+	when multiple_platform then
+		cz_write_audit(jobId,databasename,procedurename,'Multiple platforms for sample_cd in lt_src_mrna_subj_samp_map',1,stepCt,'ERROR');
+		CZ_ERROR_HANDLER(JOBID,PROCEDURENAME);
+		cz_end_audit (jobId,'FAIL');
+		select 163 into rtn_code from dual;
+	when no_probeset_recs then
+		cz_write_audit(jobId,databasename,procedurename,'Unable to match probesets to platform in probeset_deapp',1,stepCt,'ERROR');
+		CZ_ERROR_HANDLER(JOBID,PROCEDURENAME);
+		cz_end_audit (jobId,'FAIL');
+		select 165 into rtn_code from dual;
+	WHEN OTHERS THEN
+		--Handle errors.
+		cz_error_handler (jobID, procedureName);
+		--End Proc
+		cz_end_audit (jobID, 'FAIL');
+		select 166 into rtn_code from dual;
+END;
+/
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_process_rnaseq_data.sql b/ddl/oracle/tm_cz/procedures/i2b2_process_rnaseq_data.sql
new file mode 100644
index 00000000..b9615ae9
--- /dev/null
+++ b/ddl/oracle/tm_cz/procedures/i2b2_process_rnaseq_data.sql
@@ -0,0 +1,956 @@
+--
+-- Type: PROCEDURE; Owner: TM_CZ; Name: I2B2_PROCESS_RNASEQ_DATA
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "TM_CZ"."I2B2_PROCESS_RNASEQ_DATA" 
+(
+  trial_id 	VARCHAR2
+ ,top_node	varchar2
+ ,source_cd	varchar2 := 'STD'	--	default source_cd = 'STD'
+ ,secure_study	varchar2			--	security setting if new patients added to patient_dimension
+ ,currentJobID 	NUMBER := null
+ ,rtn_code	OUT	NUMBER
+)
+AS
+/*************************************************************************
+* Copyright 2008-2012 Janssen Research BIOMART_USER, LLC.
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+******************************************************************/
+--	***  NOTE ***
+--	The input file columns are mapped to the following table columns.  This is done so that the javascript for the advanced workflows
+--	selects the correct data for the dropdowns.
+
+--		tissue_type	=>	sample_type
+--		attribute_1	=>	tissue_type
+--		atrribute_2	=>	timepoint
+
+  TrialID	varchar2(100);
+  RootNode	VARCHAR2(2000);
+  root_level	integer;
+  topNode	varchar2(2000);
+  topLevel	integer;
+  tPath		varchar2(2000);
+  study_name	varchar2(100);
+  sourceCd	varchar2(50);
+  secureStudy	varchar2(1);
+
+  dataType		varchar2(10);
+  sqlText		varchar2(1000);
+  tText			varchar2(1000);
+  gplTitle		varchar2(1000);
+  pExists		number;
+  partTbl   		number;
+  partExists 		number;
+  sampleCt		number;
+  idxExists 		number;
+  logBase		number;
+  pCount		integer;
+  sCount		integer;
+  tablespaceName	varchar2(200);
+  v_bio_experiment_id	number(18,0);
+
+    --Audit variables
+  newJobFlag 	INTEGER(1);
+  databaseName 	VARCHAR(100);
+  procedureName VARCHAR(100);
+  jobID 	number(18,0);
+  stepCt 	number(18,0);
+
+  --unmapped_patients exception;
+  missing_platform	exception;
+  missing_tissue	EXCEPTION;
+  unmapped_platform 	exception;
+  multiple_platform	exception;
+  no_probeset_recs	exception;
+
+
+
+  CURSOR addNodes is
+    select distinct t.leaf_node,t.node_name
+      from  wt_mrna_nodes t
+	where not exists (select 1 from i2b2 x where t.leaf_node = x.c_fullname);
+
+  -- cursor to define the path for delete_one_node  this will delete any nodes that are hidden after i2b2_create_concept_counts
+  CURSOR delNodes is
+    select distinct c_fullname
+      from  i2b2 where c_fullname like topNode || '%'  and
+                       substr(c_visualattributes,2,1) = 'H';
+
+  CURSOR uploadI2b2 is
+    select category_cd,display_value,display_label,display_unit
+      from tm_lz.lt_src_display_mapping
+        group by category_cd,display_value,display_label,display_unit;
+
+
+BEGIN
+
+  EXECUTE IMMEDIATE 'alter session set NLS_NUMERIC_CHARACTERS=".,"';
+
+  TrialID := upper(trial_id);
+  secureStudy := upper(secure_study);
+
+  if (secureStudy not in ('Y','N') ) then
+	secureStudy := 'Y';
+  end if;
+
+  topNode := REGEXP_REPLACE('\' || top_node || '\','(\\){2,}', '\');
+  select length(topNode)-length(replace(topNode,'\','')) into topLevel from dual;
+
+  sourceCd := upper(nvl(source_cd,'STD'));
+
+  --Set Audit Parameters
+  newJobFlag := 0;             -- False (Default)
+  jobID      := currentJobID;
+
+  SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+  procedureName := $$PLSQL_UNIT;
+
+  --Audit JOB Initialization
+  --If Job ID does not exist, then this is a single procedure run and we need to create it
+  IF(jobID IS NULL or jobID < 1)
+  THEN
+    newJobFlag := 1; -- True
+    cz_start_audit (procedureName, databaseName, jobID);
+  END IF;
+
+  stepCt := 0;
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Starting i2b2_process_rnaseq_data',0,stepCt,'Done');
+
+  -- Get count of records in lt_src_mrna_subj_samp_map
+
+  select count(*) into sCount from lt_src_mrna_subj_samp_map;
+
+  -- check if all subject_sample map records have a platform, If not, abort run
+
+  select count(*) into pCount
+    from lt_src_mrna_subj_samp_map where platform is null;
+
+ if pCount > 0 then
+	raise missing_platform;
+  end if;
+
+ -- check if platform exists in de_chromosomal_region .  If not, abort run.
+
+  select count(*) into pCount
+    from DE_CHROMOSOMAL_REGION
+      where GPL_ID in (select distinct m.platform from lt_src_mrna_subj_samp_map m);
+
+  if PCOUNT = 0 then
+ 	RAISE UNMAPPED_platform;
+  end if;
+
+  select count(*) into pCount
+    from DE_gpl_info
+      where platform in (select distinct m.platform from lt_src_mrna_subj_samp_map m);
+
+  if PCOUNT = 0 then
+	RAISE UNMAPPED_platform;
+  end if;
+
+  -- check if all subject_sample map records have a tissue_type, If not, abort run
+
+  select count(*) into pCount
+    from lt_src_mrna_subj_samp_map
+      where tissue_type is null;
+
+  if pCount > 0 then
+	raise missing_tissue;
+  end if;
+
+  -- check if there are multiple platforms, if yes, then platform must be supplied in lt_src_mrna_data
+  select count(*) into pCount
+    from (select sample_cd
+      from lt_src_mrna_subj_samp_map
+        group by sample_cd having count(distinct platform) > 1);
+
+  if pCount > 0 then
+	raise multiple_platform;
+  end if;
+
+  -- Get root_node from topNode
+
+  select parse_nth_value(topNode, 2, '\') into RootNode from dual;
+
+  select count(*) into pExists
+    from table_access where c_name = rootNode;
+
+  if pExists = 0 then
+	i2b2_add_root_node(rootNode, jobId);
+  end if;
+
+  select c_hlevel into root_level
+    from i2b2 where c_name = RootNode;
+
+  -- Get study name from topNode
+
+  select parse_nth_value(topNode, topLevel, '\') into study_name from dual;
+
+  --	Add any upper level nodes as needed
+
+  tPath := REGEXP_REPLACE(replace(top_node,study_name,null),'(\\){2,}', '\');
+  select length(tPath) - length(replace(tPath,'\',null)) into pCount from dual;
+
+  if pCount > 2 then
+ 	i2b2_fill_in_tree(null, tPath, jobId);
+  end if;
+
+  --	uppercase study_id in lt_src_mrna_subj_samp_map in case curator forgot
+
+  update lt_src_mrna_subj_samp_map
+  set trial_name=upper(trial_name);
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Uppercase trial_name in lt_src_mrna_subj_samp_map',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	create records in patient_dimension for subject_ids if they do not exist
+  --	format of sourcesystem_cd:  trial:[site:]subject_cd
+
+  insert into patient_dimension
+    ( patient_num,
+      sex_cd,
+      age_in_years_num,
+      race_cd,
+      update_date,
+      download_date,
+      import_date,
+      sourcesystem_cd
+    )
+    select seq_patient_num.nextval
+		  ,x.sex_cd
+		  ,x.age_in_years_num
+		  ,x.race_cd
+		  ,sysdate
+		  ,sysdate
+		  ,sysdate
+		  ,x.sourcesystem_cd
+	from (select distinct 'Unknown' as sex_cd,
+				 0 as age_in_years_num,
+				 null as race_cd,
+				 regexp_replace(TrialID || ':' || s.site_id || ':' || s.subject_id,'(::){1,}', ':') as sourcesystem_cd
+		 from lt_src_mrna_subj_samp_map s
+		     ,de_gpl_info g
+		 where s.subject_id is not null
+		   and s.trial_name = TrialID
+		   and s.source_cd = sourceCD
+		   and s.platform = g.platform
+		   and upper(g.marker_type) = 'CHROMOSOMAL'
+		   and not exists
+			  (select 1 from patient_dimension x
+			   where x.sourcesystem_cd =
+				 regexp_replace(TrialID || ':' || s.site_id || ':' || s.subject_id,'(::){1,}', ':'))
+		) x;
+
+  pCount := SQL%ROWCOUNT;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert subjects to patient_dimension',pCount,stepCt,'Done');
+  commit;
+
+  i2b2_create_security_for_trial(TrialId, secureStudy, jobID);
+
+  --	Delete existing observation_fact data, will be repopulated
+
+  delete from observation_fact obf
+    where obf.concept_cd in
+		 (select distinct x.concept_code
+		  from de_subject_sample_mapping x
+		  where x.trial_name = TrialId
+		    and nvl(x.source_cd,'STD') = sourceCD
+		    and x.platform = 'RNASEQ');
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Delete data from observation_fact',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  select count(*) into pExists
+    from all_tables
+      where table_name  = 'DE_SUBJECT_MICROARRAY_DATA' and
+	    partitioned = 'YES';
+
+  if pExists = 0 then
+	--	dataset is not partitioned so must delete
+	delete from de_subject_rnaseq_data
+	where trial_source = TrialId || ':' || sourceCd;
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Delete data from de_subject_rnaseq_data',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+  else
+	--	Create partition in de_subject_rnaseq_data if it doesn't exist else truncate partition
+	select count(*)	into pExists
+	  from all_tab_partitions
+	    where table_name     = 'DE_SUBJECT_MICROARRAY_DATA' and
+		  partition_name = TrialId;
+
+	if pExists = 0 then
+		--	needed to add partition to de_subject_rnaseq_data
+		sqlText := 'alter table deapp.de_subject_rnaseq_data add PARTITION "' ||
+			   TrialID                                                        ||
+                           '"  VALUES ('                                                  ||
+                           ''''                                                           ||
+                           TrialID                                                        ||
+                           ''''                                                           ||
+                           ') '                                                           ||
+			   'NOLOGGING COMPRESS TABLESPACE "TRANSMART" ';
+		execute immediate(sqlText);
+		stepCt := stepCt + 1;
+		cz_write_audit(jobId,databaseName,procedureName,'Adding partition to de_subject_rnaseq_data',0,stepCt,'Done');
+	else
+		sqlText := 'alter table deapp.de_subject_rnaseq_data truncate partition "' || TrialID || '"';
+		execute immediate(sqlText);
+		stepCt := stepCt + 1;
+		cz_write_audit(jobId,databaseName,procedureName,'Truncating partition in de_subject_rnaseq_data',0,stepCt,'Done');
+	end if;
+
+  end if;
+
+  --	Cleanup any existing data in de_subject_sample_mapping.
+
+  delete from DE_SUBJECT_SAMPLE_MAPPING
+    where trial_name           = TrialID     and
+          nvl(source_cd,'STD') = sourceCd    and
+	  platform             = 'RNASEQ'; --Making sure only mRNA data is deleted
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Delete trial from DEAPP de_subject_sample_mapping',SQL%ROWCOUNT,stepCt,'Done');
+
+  commit;
+
+  --	truncate tmp node table
+
+  execute immediate('truncate table tm_wz.wt_mrna_nodes');
+
+  --	load temp table with leaf node path, use temp table with distinct sample_type, ATTR2, platform, and title   this was faster than doing subselect
+  --	from wt_subject_mrna_data
+
+  execute immediate('truncate table tm_wz.wt_mrna_node_values');
+
+  insert into wt_mrna_node_values
+	(category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+	,attribute_2
+	,title
+	)
+	select distinct a.category_cd
+				   ,nvl(a.platform,'GPL570')
+				   ,nvl(a.tissue_type,'Unspecified Tissue Type')
+	               ,a.attribute_1
+				   ,a.attribute_2
+				   ,g.title
+    from lt_src_mrna_subj_samp_map a
+	    ,de_gpl_info g
+	where a.trial_name = TrialID
+	  and nvl(a.platform,'GPL570') = g.platform
+	  and a.source_cd = sourceCD
+	  and a.platform = g.platform
+	  and upper(g.marker_type) = 'CHROMOSOMAL'
+	  and g.title = (select min(x.title) from de_gpl_info x where nvl(a.platform,'GPL570') = x.platform)
+      -- and upper(g.organism) = 'HOMO SAPIENS'
+	  ;
+	--  and decode(dataType,'R',sign(a.intensity_value),1) = 1;	--	take all values when dataType T, only >0 for dataType R
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert node values into DEAPP wt_mrna_node_values',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+    ,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       category_cd,'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\','(\\){2,}', '\')
+		  ,category_cd
+		  ,platform as platform
+		  ,tissue_type
+		  ,attribute_1 as attribute_1
+          ,attribute_2 as attribute_2
+		  ,'LEAF'
+	from  wt_mrna_node_values;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Create leaf nodes in DEAPP tmp_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	insert for platform node so platform concept can be populated
+
+  insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+    ,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'PLATFORM')+8)
+		  ,platform as platform
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'TISSUETYPE') > 1 then tissue_type else null end as tissue_type
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'ATTR1') > 1 then attribute_1 else null end as attribute_1
+          ,case when instr(substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'ATTR2') > 1 then attribute_2 else null end as attribute_2
+		  ,'PLATFORM'
+	from  wt_mrna_node_values;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Create platform nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	insert for ATTR1 node so ATTR1 concept can be populated in tissue_type_cd
+
+  insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+    ,attribute_1
+	,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'ATTR1')+5),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'ATTR1')+5)
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'PLATFORM') > 1 then platform else null end as platform
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'TISSUETYPE') > 1 then tissue_type else null end as tissue_type
+		  ,attribute_1 as attribute_1
+          ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'ATTR2') > 1 then attribute_2 else null end as attribute_2
+		  ,'ATTR1'
+	from  wt_mrna_node_values
+	where category_cd like '%ATTR1%'
+	  and attribute_1 is not null;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Create ATTR1 nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	insert for ATTR2 node so ATTR2 concept can be populated in timepoint_cd
+
+  insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+    ,attribute_1
+	,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'ATTR2')+5),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'ATTR2')+5)
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR2')+5),'PLATFORM') > 1 then platform else null end as platform
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'TISSUETYPE') > 1 then tissue_type else null end as tissue_type
+          ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR2')+5),'ATTR1') > 1 then attribute_1 else null end as attribute_1
+		  ,attribute_2 as attribute_2
+		  ,'ATTR2'
+	from  wt_mrna_node_values
+	where category_cd like '%ATTR2%'
+	  and attribute_2 is not null;
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create ATTR2 nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+	--	insert for tissue_type node so sample_type_cd can be populated
+
+	insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+    ,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10)
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'PLATFORM') > 1 then platform else null end as platform
+		  ,tissue_type as tissue_type
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'ATTR1') > 1 then attribute_1 else null end as attribute_1
+          ,case when instr(substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'ATTR2') > 1 then attribute_2 else null end as attribute_2
+		  ,'TISSUETYPE'
+	from  wt_mrna_node_values
+	where category_cd like '%TISSUETYPE%';
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Create ATTR2 nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  update wt_mrna_nodes
+    set node_name=parse_nth_value(leaf_node,length(leaf_node)-length(replace(leaf_node,'\',null)),'\');
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Updated node_name in DEAPP tmp_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	add leaf nodes for mRNA data  The cursor will only add nodes that do not already exist.
+
+  FOR r_addNodes in addNodes Loop
+       --Add nodes for all types (ALSO DELETES EXISTING NODE)
+	i2b2_add_node(TrialID, r_addNodes.leaf_node, r_addNodes.node_name, jobId);
+	stepCt := stepCt + 1;
+	tText := 'Added Leaf Node: ' || r_addNodes.leaf_node || '  Name: ' || r_addNodes.node_name;
+	cz_write_audit(jobId,databaseName,procedureName,tText,SQL%ROWCOUNT,stepCt,'Done');
+	i2b2_fill_in_tree(TrialId, r_addNodes.leaf_node, jobID);
+  END LOOP;
+
+  --	set sourcesystem_cd, c_comment to null if any added upper-level nodes
+
+  update i2b2 b
+	set sourcesystem_cd=null,c_comment=null
+	where b.sourcesystem_cd = TrialId
+	  and length(b.c_fullname) < length(topNode);
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Set sourcesystem_cd to null for added upper level nodes',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	update concept_cd for nodes, this is done to make the next insert easier
+
+  update wt_mrna_nodes t
+	set concept_cd=(select c.concept_cd from concept_dimension c
+	                where c.concept_path = t.leaf_node
+				   )
+    where exists
+         (select 1 from concept_dimension x
+	                where x.concept_path = t.leaf_node
+				   )
+	  and t.concept_cd is null;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Update wt_mrna_nodes with newly created concept_cds',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+
+  --Load the DE_SUBJECT_SAMPLE_MAPPING from wt_subject_mrna_data
+
+  --PATIENT_ID      = PATIENT_ID (SAME AS ID ON THE PATIENT_DIMENSION)
+  --SITE_ID         = site_id
+  --SUBJECT_ID      = subject_id
+  --SUBJECT_TYPE    = NULL
+  --CONCEPT_CODE    = from LEAF records in wt_mrna_nodes
+  --SAMPLE_TYPE    	= TISSUE_TYPE
+  --SAMPLE_TYPE_CD  = concept_cd from TISSUETYPE records in wt_mrna_nodes
+  --TRIAL_NAME      = TRIAL_NAME
+  --TIMEPOINT		= attribute_2
+  --TIMEPOINT_CD	= concept_cd from ATTR2 records in wt_mrna_nodes
+  --TISSUE_TYPE     = attribute_1
+  --TISSUE_TYPE_CD  = concept_cd from ATTR1 records in wt_mrna_nodes
+  --PLATFORM        = MRNA_AFFYMETRIX - this is required by ui code
+  --PLATFORM_CD     = concept_cd from PLATFORM records in wt_mrna_nodes
+  --DATA_UID		= concatenation of concept_cd-patient_num
+  --GPL_ID			= platform from wt_subject_mrna_data
+  --CATEGORY_CD		= category_cd that generated ontology
+  --SAMPLE_ID		= id of sample (trial:S:[site_id]:subject_id:sample_cd) from patient_dimension, may be the same as patient_num
+  --SAMPLE_CD		= sample_cd
+  --SOURCE_CD		= sourceCd
+
+  --ASSAY_ID        = generated by trigger
+
+  insert into de_subject_sample_mapping
+	(patient_id
+	,site_id
+	,subject_id
+	,subject_type
+	,concept_code
+	,assay_id
+	,sample_type
+	,sample_type_cd
+	,trial_name
+	,timepoint
+	,timepoint_cd
+	,tissue_type
+	,tissue_type_cd
+	,platform
+	,platform_cd
+	,data_uid
+	,gpl_id
+	,sample_id
+	,sample_cd
+	,category_cd
+	,source_cd
+	,omic_source_study
+	,omic_patient_id
+    )
+	select t.patient_id
+		  ,t.site_id
+		  ,t.subject_id
+		  ,t.subject_type
+		  ,t.concept_code
+		  ,deapp.seq_assay_id.nextval
+		  ,t.sample_type
+		  ,t.sample_type_cd
+		  ,t.trial_name
+		  ,t.timepoint
+		  ,t.timepoint_cd
+		  ,t.tissue_type
+		  ,t.tissue_type_cd
+		  ,t.platform
+		  ,t.platform_cd
+		  ,t.data_uid
+		  ,t.gpl_id
+		  ,t.sample_id
+		  ,t.sample_cd
+		  ,t.category_cd
+		  ,t.source_cd
+		  ,t.omic_source_study
+		  ,t.omic_patient_id
+	from (select distinct b.patient_num as patient_id
+			  ,a.site_id
+			  ,a.subject_id
+			  ,null as subject_type
+			  ,ln.concept_cd as concept_code
+			  ,a.tissue_type as sample_type
+			  ,ttp.concept_cd as sample_type_cd
+			  ,a.trial_name
+			  ,a.attribute_2 as timepoint
+			  ,a2.concept_cd as timepoint_cd
+			  ,a.attribute_1 as tissue_type
+			  ,a1.concept_cd as tissue_type_cd
+			  ,'RNASEQ' as platform
+			  ,pn.concept_cd as platform_cd
+			  ,ln.concept_cd || '-' || to_char(b.patient_num) as data_uid
+			  ,a.platform as gpl_id
+			  ,coalesce(sid.patient_num,b.patient_num) as sample_id
+			  ,a.sample_cd
+			  ,nvl(a.category_cd,'Biomarker_Data+Gene_Expression+PLATFORM+TISSUETYPE+ATTR1+ATTR2') as category_cd
+			  ,a.source_cd
+			  ,TrialId as omic_source_study
+			  ,b.patient_num as omic_patient_id
+		from lt_src_mrna_subj_samp_map a
+		--Joining to Pat_dim to ensure the ID's match. If not I2B2 won't work.
+		inner join patient_dimension b
+		  on regexp_replace(TrialID || ':' || a.site_id || ':' || a.subject_id,'(::){1,}', ':') = b.sourcesystem_cd
+		inner join wt_mrna_nodes ln
+			on a.platform = ln.platform
+			and a.tissue_type = ln.tissue_type
+                        and a.category_cd=ln.category_cd  --modified
+			and nvl(a.attribute_1,'@') = nvl(ln.attribute_1,'@')
+			and nvl(a.attribute_2,'@') = nvl(ln.attribute_2,'@')
+			and ln.node_type = 'LEAF'
+		inner join wt_mrna_nodes pn
+			on a.platform = pn.platform
+                        and pn.category_cd=substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8)
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8),'TISSUETYPE') > 1 then a.tissue_type else '@' end = nvl(pn.tissue_type,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8),'ATTR1') > 1 then a.attribute_1 else '@' end = nvl(pn.attribute_1,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8),'ATTR2') > 1 then a.attribute_2 else '@' end = nvl(pn.attribute_2,'@')
+			and pn.node_type = 'PLATFORM'
+		left outer join wt_mrna_nodes ttp
+			on a.tissue_type = ttp.tissue_type
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10),'PLATFORM') > 1 then a.platform else '@' end = nvl(ttp.platform,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10),'ATTR1') > 1 then a.attribute_1 else '@' end = nvl(ttp.attribute_1,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10),'ATTR2') > 1 then a.attribute_2 else '@' end = nvl(ttp.attribute_2,'@')
+			and ttp.node_type = 'TISSUETYPE'
+                        and ttp.category_cd=substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10)
+		left outer join wt_mrna_nodes a1
+			on a.attribute_1 = a1.attribute_1
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5),'PLATFORM') > 1 then a.platform else '@' end = nvl(a1.platform,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5),'TISSUETYPE') > 1 then a.tissue_type else '@' end = nvl(a1.tissue_type,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5),'ATTR2') > 1 then a.attribute_2 else '@' end = nvl(a1.attribute_2,'@')
+			and a1.node_type = 'ATTR1'
+                        and a1.category_cd=substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5)
+		left outer join wt_mrna_nodes a2
+			on a.attribute_2 = a1.attribute_2
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5),'PLATFORM') > 1 then a.platform else '@' end = nvl(a2.platform,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5),'TISSUETYPE') > 1 then a.tissue_type else '@' end = nvl(a2.tissue_type,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5),'ATTR1') > 1 then a.attribute_1 else '@' end = nvl(a2.attribute_1,'@')
+			and a2.node_type = 'ATTR2'
+                        and a2.category_cd=substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5)
+		left outer join patient_dimension sid
+			on  regexp_replace(TrialId || ':S:' || a.site_id || ':' || a.subject_id || ':' || a.sample_cd,
+							  '(::){1,}', ':') = sid.sourcesystem_cd
+		where a.trial_name = TrialID
+		  and a.source_cd = sourceCD
+		  and  ln.concept_cd is not null) t;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert trial into DEAPP de_subject_sample_mapping',SQL%ROWCOUNT,stepCt,'Done');
+
+  commit;
+
+  insert into observation_fact
+    (patient_num
+	,concept_cd
+	,modifier_cd
+	,valtype_cd
+	,tval_char
+	,nval_num
+	,sourcesystem_cd
+	,import_date
+	,valueflag_cd
+	,provider_id
+	,location_cd
+	,units_cd
+        ,sample_cd
+        ,instance_num
+    )
+    select distinct m.patient_id
+		  ,m.concept_code
+		  ,'@'
+		  ,'T' -- Text data type
+		  ,'E'  --Stands for Equals for Text Types
+		  ,null	--	not numeric for mRNA
+		  ,m.trial_name
+		  ,sysdate
+		  ,'@'
+		  ,'@'
+		  ,'@'
+		  ,'' -- no units available
+                  ,m.sample_cd
+                  ,1
+    from  de_subject_sample_mapping m
+    where m.trial_name = TrialID
+	  and m.source_cd = sourceCD
+      and m.platform = 'RNASEQ';
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert patient facts into I2B2DEMODATA observation_fact',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --	Insert sample facts
+
+  insert into observation_fact
+    (patient_num
+	,concept_cd
+	,modifier_cd
+	,valtype_cd
+	,tval_char
+	,nval_num
+	,sourcesystem_cd
+	,import_date
+	,valueflag_cd
+	,provider_id
+	,location_cd
+	,units_cd
+  ,sample_cd
+  ,instance_num
+    )
+    select distinct m.sample_id
+		  ,m.concept_code
+		  ,m.trial_name
+		  ,'T' -- Text data type
+		  ,'E'  --Stands for Equals for Text Types
+		  ,null	--	not numeric for mRNA
+		  ,m.trial_name
+		  ,sysdate
+		  ,'@'
+		  ,'@'
+		  ,'@'
+		  ,'' -- no units available
+      ,m.sample_cd
+      ,1
+    from  de_subject_sample_mapping m
+    where m.trial_name = TrialID
+	  and m.source_cd = sourceCd
+      and m.platform = 'RNASEQ'
+	  and m.patient_id != m.sample_id;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert sample facts into I2B2DEMODATA observation_fact',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  ---INSERT sample_dimension
+  INSERT INTO I2B2DEMODATA.SAMPLE_DIMENSION(SAMPLE_CD)
+         SELECT DISTINCT SAMPLE_CD FROM
+           DEAPP.DE_SUBJECT_SAMPLE_MAPPING WHERE SAMPLE_CD NOT IN (SELECT SAMPLE_CD FROM I2B2DEMODATA.SAMPLE_DIMENSION) ;
+
+  --Update I2b2 for correct data type
+  update i2b2 t
+	set c_columndatatype = 'T', c_metadataxml = null, c_visualattributes='FA'
+	where t.c_basecode in (select distinct x.concept_cd from wt_mrna_nodes x);
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Initialize data_type and xml in i2b2',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  for ul in uploadI2b2
+  loop
+	update i2b2 n
+	SET n.c_columndatatype = 'T',
+      --Static XML String
+		n.c_metadataxml =  ('<?xml version="1.0"?><ValueMetadata><Version>3.02</Version><CreationDateTime>08/14/2008 01:22:59</CreationDateTime><TestID></TestID><TestName></TestName><DataType>PosFloat</DataType><CodeType></CodeType><Loinc></Loinc><Flagstouse></Flagstouse><Oktousevalues>Y</Oktousevalues><MaxStringLength></MaxStringLength><LowofLowValue>0</LowofLowValue>
+                <HighofLowValue>0</HighofLowValue><LowofHighValue>100</LowofHighValue>100<HighofHighValue>100</HighofHighValue>
+                <LowofToxicValue></LowofToxicValue><HighofToxicValue></HighofToxicValue>
+                <EnumValues></EnumValues><CommentsDeterminingExclusion><Com></Com></CommentsDeterminingExclusion>
+                <UnitValues><NormalUnits>ratio</NormalUnits><EqualUnits></EqualUnits>
+                <ExcludingUnits></ExcludingUnits><ConvertingUnits><Units></Units><MultiplyingFactor></MultiplyingFactor>
+                </ConvertingUnits></UnitValues><Analysis><Enums /><Counts />
+                <New /></Analysis>'||(select xmlelement(name "SeriesMeta",xmlforest(m.display_value as "Value",m.display_unit as "Unit",m.display_label as "DisplayName")) as hi
+      from tm_lz.lt_src_display_mapping m where m.category_cd=ul.category_cd)||
+                '</ValueMetadata>') where n.c_fullname=(select leaf_node from wt_mrna_nodes where category_cd=ul.category_cd and leaf_node=n.c_fullname);
+
+                end loop;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Update c_columndatatype and c_metadataxml for numeric data types in I2B2METADATA i2b2',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  --UPDATE VISUAL ATTRIBUTES for Leaf Active (Default is folder)
+  update i2b2 a
+    set c_visualattributes = 'LAH'
+	where a.c_basecode in (select distinct x.concept_code from de_subject_sample_mapping x
+						   where x.trial_name = TrialId
+						     and x.platform = 'RNASEQ'
+							 and x.concept_code is not null);
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Update visual attributes for leaf nodes in I2B2METADATA i2b2',SQL%ROWCOUNT,stepCt,'Done');
+  COMMIT;
+
+  update i2b2 a
+ 	set c_visualattributes='FAS'
+        where a.c_fullname = substr(topNode,1,instr(topNode,'\',1,3));
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Update visual attributes for study nodes in I2B2METADATA i2b2',SQL%ROWCOUNT,stepCt,'Done');
+  COMMIT;
+
+  --Build concept Counts
+  --Also marks any i2B2 records with no underlying data as Hidden, need to do at Trial level because there may be multiple platform and there is no longer
+  -- a unique top-level node for mRNA data
+
+  i2b2_create_concept_counts(topNode ,jobID );
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create concept counts',0,stepCt,'Done');
+
+	--	delete each node that is hidden
+
+  FOR r_delNodes in delNodes Loop
+	--	deletes hidden nodes for a trial one at a time
+	i2b2_delete_1_node(r_delNodes.c_fullname);
+	stepCt := stepCt + 1;
+	tText := 'Deleted node: ' || r_delNodes.c_fullname;
+	cz_write_audit(jobId,databaseName,procedureName,tText,SQL%ROWCOUNT,stepCt,'Done');
+  END LOOP;
+
+
+  --Reload Security: Inserts one record for every I2B2 record into the security table
+
+  i2b2_load_security_data(jobId);
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Load security data',0,stepCt,'Done');
+
+  --	tag data with probeset_id from reference.probeset_deapp
+
+  execute immediate ('truncate table tm_wz.wt_subject_mrna_probeset');
+
+  --	note: assay_id represents a unique subject/site/sample
+
+  insert into tm_wz.wt_subject_rnaseq_region
+       (region_id
+       ,readcount
+       ,patient_id
+       ,trial_name
+       ,assay_id
+       )
+  select gs.region_id
+                 ,cast(md.readcount as number)
+                 ,sd.patient_id
+                 ,TrialId
+                 ,sd.assay_id
+       from deapp.de_subject_sample_mapping sd
+               ,tm_lz.lt_src_rnaseq_data md
+               ,deapp.de_chromosomal_region gs
+       where sd.sample_cd = md.expr_id
+         and sd.platform = 'RNASEQ'
+         and sd.trial_name = TrialId
+         and sd.source_cd = sourceCd
+         and sd.gpl_id = gs.gpl_id
+         and md.region_name = gs.region_name
+       group by gs.region_id, md.readcount, sd.patient_id, sd.assay_id;
+
+  insert into deapp.de_subject_rnaseq_data
+	(   region_id
+          , assay_id
+          , patient_id
+          , trial_name
+          , readcount
+        )
+        select  region_id
+              , assay_id
+              , patient_id
+              , trial_name
+              , readcount
+        from tm_wz.wt_subject_rnaseq_region;
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'Insert into DEAPP wt_subject_mrna_probeset',SQL%ROWCOUNT,stepCt,'Done');
+  commit;
+
+  if pExists = 0 then
+	raise no_probeset_recs;
+  end if;
+
+
+  ---Cleanup OVERALL JOB if this proc is being run standalone
+
+  stepCt := stepCt + 1;
+  cz_write_audit(jobId,databaseName,procedureName,'End i2b2_process_rnaseq_data',0,stepCt,'Done');
+
+  IF newJobFlag = 1
+  THEN
+	cz_end_audit (jobID, 'SUCCESS');
+  END IF;
+
+ select 0 into rtn_code from dual;
+
+  EXCEPTION
+	--when unmapped_patients then
+	--	cz_write_audit(jobId,databasename,procedurename,'No site_id/subject_id mapped to patient_dimension',1,stepCt,'ERROR');
+	--	cz_error_handler(jobid,procedurename);
+	--	cz_end_audit (jobId,'FAIL');
+	when missing_platform then
+		cz_write_audit(jobId,databasename,procedurename,'Platform data missing from one or more subject_sample mapping records',1,stepCt,'ERROR');
+		cz_error_handler(jobid,procedurename);
+		cz_end_audit (jobId,'FAIL');
+		select 161 into rtn_code from dual;
+	when missing_tissue then
+		cz_write_audit(jobId,databasename,procedurename,'Tissue Type data missing from one or more subject_sample mapping records',1,stepCt,'ERROR');
+		cz_error_handler(jobid,procedurename);
+		CZ_END_AUDIT (JOBID,'FAIL');
+		select 162 into rtn_code from dual;
+	when unmapped_platform then
+		cz_write_audit(jobId,databasename,procedurename,'Platform not found in de_chromosomal_region',1,stepCt,'ERROR');
+		CZ_ERROR_HANDLER(JOBID,PROCEDURENAME);
+		cz_end_audit (jobId,'FAIL');
+		select 169 into rtn_code from dual;
+	when multiple_platform then
+		cz_write_audit(jobId,databasename,procedurename,'Multiple platforms for sample_cd in lt_src_mrna_subj_samp_map',1,stepCt,'ERROR');
+		CZ_ERROR_HANDLER(JOBID,PROCEDURENAME);
+		cz_end_audit (jobId,'FAIL');
+		select 163 into rtn_code from dual;
+	when no_probeset_recs then
+		cz_write_audit(jobId,databasename,procedurename,'Unable to match probesets to platform in probeset_deapp',1,stepCt,'ERROR');
+		CZ_ERROR_HANDLER(JOBID,PROCEDURENAME);
+		cz_end_audit (jobId,'FAIL');
+		select 165 into rtn_code from dual;
+	WHEN OTHERS THEN
+		--Handle errors.
+		cz_error_handler (jobID, procedureName);
+		--End Proc
+		cz_end_audit (jobID, 'FAIL');
+		select 166 into rtn_code from dual;
+END;
+
+/
diff --git a/ddl/oracle/tm_cz/procedures/i2b2_process_snp_data.sql b/ddl/oracle/tm_cz/procedures/i2b2_process_snp_data.sql
new file mode 100644
index 00000000..f859a773
--- /dev/null
+++ b/ddl/oracle/tm_cz/procedures/i2b2_process_snp_data.sql
@@ -0,0 +1,1621 @@
+--
+-- Type: PROCEDURE; Owner: TM_CZ; Name: I2B2_PROCESS_SNP_DATA
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "TM_CZ"."I2B2_PROCESS_SNP_DATA" 
+(
+  trial_id 		VARCHAR2
+ ,top_node		varchar2
+ ,data_type		varchar2 := 'R'		--	R = raw data, do zscore calc, T = transformed data, load raw values as zscore,
+									--	L = log intensity data, skip log step in zscore calc
+ ,source_cd		varchar2 := 'STD'	--	default source_cd = 'STD'
+ ,log_base		number := 2			--	log base value for conversion back to raw
+ ,secure_study	varchar2			--	security setting if new patients added to patient_dimension
+ ,currentJobID 	NUMBER := null
+ ,rtn_code		OUT	NUMBER
+)
+AS
+
+
+
+
+
+
+
+
+
+
+--	Procedure to load the DE_SUBJECT_MICROARRAY_DATA and DE_SUBJECT_SAMPLE_MAPPING tables, compute the Z-Score, and create the I2B2 data for mRNA (gene expression) data
+--	wt_subject_mrna_data must be pre-loaded with gene expression data.  Because the format/content of gene expression data varies,
+--	the loading of wt_subject_mrna_data is not done within this procedure
+
+
+
+
+
+
+
+
+
+
+--	***  NOTE ***
+--	The input file columns are mapped to the following table columns.  This is done so that the javascript for the advanced workflows
+--	selects the correct data for the dropdowns.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+--		tissue_type	=>	sample_type
+--		attribute_1	=>	tissue_type
+--		atrribute_2	=>	timepoint
+
+
+
+
+
+
+
+--	JEA@90090904	New, modified version from JnJ
+--	JEA@20111017	Remove JnJ-specific ontology, use path derived from category_cd
+--	JEA@20111028	Use lt_ tables instead of extrnl to accomodate clients without external tables
+--	JEA@20111116	Insert subject_id to patient_dimension if not exists (no clinical data)
+--	JEA@20111116	Added source_cd handling to account for multiple transformations for same study
+--	JEA@@0111117	Removed code to insert sample into patient_dimension
+--	JEA@20111201	Added i2b2 attribute update code
+--	JEA@20111207	Added distinct to patient insert
+--	JEA@21001209	Added platform to lt_src_mrna_data, lz_src_mrna_data, use probeset_deapp for probe_id
+--	JEA@20112121	Remove platform stuff, add exception if sample_cd has multiple platforms
+--	JEA@20111214	Throw exception if no rows inserted into wt_subject_mrna_probeset
+--	JEA@20120113	Added H to c_visualattributes for high-density biomarker
+--	JEA@20120131	Remove check for organism in de_gpl_info.
+--	JEA@20120301	Custom for Millennium to support multiple gene expression analysis per study,
+--	JEA@20120314	Pass sourceCD to i2b2_mrna_zscore_calc so correct trial_source set
+--	JEA@20120416	Add omic_source_study, omic_patient_id to de_subject_sample_mapping and populate
+--	JEA@@0120510	Add root_node using i2b2_add_root_node if missing
+--	JEA@20120526	Set sourcesystem_cd, c_comment to null if any upper-level nodes added, set sex_cd to Unknown if adding subjects
+--  ER @20121203   Added "Z" datatype as a temporary workaround for "T" data processing bug
+
+
+  TrialID		varchar2(100);
+  RootNode		VARCHAR2(2000);
+  root_level	integer;
+  topNode		varchar2(2000);
+  topLevel		integer;
+  tPath			varchar2(2000);
+  study_name	varchar2(100);
+  sourceCd		varchar2(50);
+  secureStudy	varchar2(1);
+
+  dataType		varchar2(10);
+  sqlText		varchar2(1000);
+  tText			varchar2(1000);
+  gplTitle		varchar2(1000);
+  pExists		number;
+  dataParitioned number;
+  partTbl   	number;
+  partExists 	number;
+  sampleCt		number;
+  idxExists 	number;
+  logBase		number;
+  pCount		integer;
+  sCount		integer;
+  tablespaceName	varchar2(200);
+
+    --Audit variables
+  newJobFlag INTEGER(1);
+  databaseName VARCHAR(100);
+  procedureName VARCHAR(100);
+  jobID number(18,0);
+  stepCt number(18,0);
+
+  --unmapped_patients exception;
+  missing_platform	exception;
+  missing_tissue	EXCEPTION;
+  unmapped_platform exception;
+  multiple_platform	exception;
+  no_probeset_recs	exception;
+
+
+
+	CURSOR addNodes is
+	select distinct t.leaf_node
+          ,t.node_name
+	from  wt_mrna_nodes t
+	where not exists
+		 (select 1 from i2b2 x
+		  where t.leaf_node = x.c_fullname);
+
+
+--	cursor to define the path for delete_one_node  this will delete any nodes that are hidden after i2b2_create_concept_counts
+
+  CURSOR delNodes is
+  select distinct c_fullname
+
+  from  i2b2
+  where c_fullname like topNode || '%'
+    and substr(c_visualattributes,2,1) = 'H';
+    --and c_visualattributes like '_H_';
+
+
+BEGIN
+	TrialID := upper(trial_id);
+	secureStudy := upper(secure_study);
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+	if (secureStudy not in ('Y','N') ) then
+		secureStudy := 'Y';
+	end if;
+
+
+
+	topNode := REGEXP_REPLACE('\' || top_node || '\','(\\){2,}', '\');
+	select length(topNode)-length(replace(topNode,'\','')) into topLevel from dual;
+
+	if data_type is null then
+		dataType := 'R';
+	else
+		if data_type in ('R','T','L','Z') then
+			dataType := data_type;
+		else
+			dataType := 'R';
+		end if;
+	end if;
+
+
+
+
+
+	logBase := log_base;
+	sourceCd := upper(nvl(source_cd,'STD'));
+
+  --Set Audit Parameters
+  newJobFlag := 0; -- False (Default)
+  jobID := currentJobID;
+
+  SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+  procedureName := $$PLSQL_UNIT;
+
+  --Audit JOB Initialization
+  --If Job ID does not exist, then this is a single procedure run and we need to create it
+  IF(jobID IS NULL or jobID < 1)
+  THEN
+    newJobFlag := 1; -- True
+    cz_start_audit (procedureName, databaseName, jobID);
+  END IF;
+
+	stepCt := 0;
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Starting i2b2_process_mrna_data',0,stepCt,'Done');
+
+	--	Get count of records in lt_src_mrna_subj_samp_map
+
+	select count(*) into sCount
+	from lt_src_mrna_subj_samp_map;
+
+	--	check if all subject_sample map records have a platform, If not, abort run
+
+	select count(*) into pCount
+	from lt_src_mrna_subj_samp_map
+	where platform is null;
+
+	if pCount > 0 then
+
+
+
+
+		raise missing_platform;
+	end if;
+
+
+  	--	check if platform exists in de_mrna_annotation .  If not, abort run.
+
+	select count(*) into pCount
+
+	from DE_MRNA_ANNOTATION
+	where GPL_ID in (select distinct m.platform from lt_src_mrna_subj_samp_map m);
+
+	if PCOUNT = 0 then
+
+
+
+		RAISE UNMAPPED_platform;
+	end if;
+
+
+
+	select count(*) into pCount
+
+
+
+
+
+
+	from DE_gpl_info
+	where platform in (select distinct m.platform from lt_src_mrna_subj_samp_map m);
+
+	if PCOUNT = 0 then
+
+
+
+		RAISE UNMAPPED_platform;
+	end if;
+
+	--	check if all subject_sample map records have a tissue_type, If not, abort run
+
+	select count(*) into pCount
+	from lt_src_mrna_subj_samp_map
+	where tissue_type is null;
+
+	if pCount > 0 then
+
+
+
+		raise missing_tissue;
+	end if;
+
+	--	check if there are multiple platforms, if yes, then platform must be supplied in lt_src_mrna_data
+
+	select count(*) into pCount
+	from (select sample_cd
+		  from lt_src_mrna_subj_samp_map
+		  group by sample_cd
+		  having count(distinct platform) > 1);
+
+	if pCount > 0 then
+
+
+
+		raise multiple_platform;
+	end if;
+
+	-- Get root_node from topNode
+
+
+	select parse_nth_value(topNode, 2, '\') into RootNode from dual;
+
+	select count(*) into pExists
+
+	from table_access
+	where c_name = rootNode;
+
+	if pExists = 0 then
+		i2b2_add_root_node(rootNode, jobId);
+	end if;
+
+	select c_hlevel into root_level
+	from table_access /* from i2b2 */
+	where c_name = RootNode;
+
+	-- Get study name from topNode
+
+
+	select parse_nth_value(topNode, topLevel, '\') into study_name from dual;
+
+	--	Add any upper level nodes as needed
+
+	tPath := REGEXP_REPLACE(replace(top_node,study_name,null),'(\\){2,}', '\');
+	select length(tPath) - length(replace(tPath,'\',null)) into pCount from dual;
+
+	if pCount > 2 then
+		i2b2_fill_in_tree(null, tPath, jobId);
+	end if;
+
+
+
+
+	--	uppercase study_id in lt_src_mrna_subj_samp_map in case curator forgot
+
+
+
+
+
+
+
+
+
+
+
+
+	update lt_src_mrna_subj_samp_map
+	set trial_name=upper(trial_name);
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Uppercase trial_name in lt_src_mrna_subj_samp_map',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+	--	create records in patient_dimension for subject_ids if they do not exist
+	--	format of sourcesystem_cd:  trial:[site:]subject_cd
+
+
+	insert into patient_dimension
+    ( patient_num,
+      sex_cd,
+      age_in_years_num,
+      race_cd,
+      update_date,
+      download_date,
+      import_date,
+      sourcesystem_cd
+
+    )
+    select seq_patient_num.nextval
+		  ,x.sex_cd
+		  ,x.age_in_years_num
+		  ,x.race_cd
+
+
+
+		  ,sysdate
+		  ,sysdate
+		  ,sysdate
+		  ,x.sourcesystem_cd
+	from (select distinct 'Unknown' as sex_cd,
+				 0 as age_in_years_num,
+				 null as race_cd,
+				 regexp_replace(TrialID || ':' || s.site_id || ':' || s.subject_id,'(::){1,}', ':') as sourcesystem_cd
+		 from lt_src_mrna_subj_samp_map s
+		     ,de_gpl_info g
+		 where s.subject_id is not null
+		   and s.trial_name = TrialID
+		   and s.source_cd = sourceCD
+		   and s.platform = g.platform
+		   and upper(g.marker_type) = 'GENE EXPRESSION'
+		   and not exists
+			  (select 1 from patient_dimension x
+			   where x.sourcesystem_cd =
+				 regexp_replace(TrialID || ':' || s.site_id || ':' || s.subject_id,'(::){1,}', ':'))
+		) x;
+
+
+
+
+
+
+
+
+
+
+
+	pCount := SQL%ROWCOUNT;
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Insert subjects to patient_dimension',pCount,stepCt,'Done');
+	commit;
+
+	--	add security for trial if new subjects added to patient_dimension
+
+	if pCount > 0 then
+		i2b2_create_security_for_trial(TrialId, secureStudy, jobID);
+	end if;
+
+	--	Delete existing observation_fact data, will be repopulated
+
+
+	delete from observation_fact obf
+	where obf.concept_cd in
+		 (select distinct x.concept_code
+		  from de_subject_sample_mapping x
+		  where x.trial_name = TrialId
+		    and nvl(x.source_cd,'STD') = sourceCD
+		    and x.platform = 'SNP');
+
+
+
+
+
+
+
+
+
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Delete data from observation_fact',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+  select count(*) into dataParitioned
+    from all_tables
+    where table_name = 'DE_SUBJECT_MICROARRAY_DATA'
+    and partitioned = 'YES';
+
+  select count(*)
+		into pExists
+		from all_tab_partitions
+		where table_name = 'DE_SUBJECT_MICROARRAY_DATA'
+		and partition_name = TrialId || ':' || sourceCd;
+
+
+	if dataParitioned = 0 or pExists <> 0  then
+		--	dataset is not partitioned so must delete
+		delete from de_subject_microarray_data
+		where trial_source = TrialId || ':' || sourceCd
+		and assay_id in (
+			select dssm.assay_id from
+				TM_LZ.lt_src_mrna_subj_samp_map ltssm
+				left join
+				deapp.de_subject_sample_mapping dssm
+				on
+				dssm.trial_name = ltssm.trial_name
+				and dssm.gpl_id = ltssm.platform
+				and dssm.subject_id = ltssm.subject_id
+				and dssm.sample_cd  = ltssm.sample_cd
+			where
+				dssm.trial_name = TrialId
+				and nvl(dssm.source_cd,'STD') = sourceCd
+				and dssm.platform = 'SNP'
+		);
+
+		stepCt := stepCt + 1;
+    cz_write_audit(jobId,databaseName,procedureName,'Delete data from de_subject_microarray_data',SQL%ROWCOUNT,stepCt,'Done');
+    commit;
+
+  end if;
+
+  if dataParitioned <> 0 and pExists = 0 then
+		  --	Create partition in de_subject_microarray_data if it doesn't exist else truncate partition
+			--	needed to add partition to de_subject_microarray_data
+			sqlText := 'alter table deapp.de_subject_microarray_data add PARTITION "' || TrialID || ':' || sourceCd || '"  VALUES (' || '''' || TrialID || ':' || sourceCd || '''' || ') ' ||
+						   'NOLOGGING COMPRESS ';
+			execute immediate(sqlText);
+			stepCt := stepCt + 1;
+			cz_write_audit(jobId,databaseName,procedureName,'Adding partition to de_subject_microarray_data',0,stepCt,'Done');
+
+	end if;
+
+	--	Cleanup any existing data in de_subject_sample_mapping.
+  delete from de_subject_sample_mapping where
+  assay_id in (
+    select dssm.assay_id from
+      TM_LZ.lt_src_mrna_subj_samp_map ltssm
+      left join
+      deapp.de_subject_sample_mapping dssm
+      on
+      dssm.trial_name     = ltssm.trial_name
+      and dssm.gpl_id     = ltssm.platform
+      and dssm.subject_id = ltssm.subject_id
+      and dssm.sample_cd  = ltssm.sample_cd
+    where
+      dssm.trial_name = TrialID
+      and nvl(dssm.source_cd,'STD') = sourceCd
+      and dssm.platform = 'SNP'
+  );
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Delete trial from DEAPP de_subject_sample_mapping',SQL%ROWCOUNT,stepCt,'Done');
+
+	commit;
+
+--	truncate tmp node table
+
+	execute immediate('truncate table tm_wz.wt_mrna_nodes');
+
+
+
+--	load temp table with leaf node path, use temp table with distinct sample_type, ATTR2, platform, and title   this was faster than doing subselect
+--	from wt_subject_mrna_data
+
+	execute immediate('truncate table tm_wz.wt_mrna_node_values');
+
+	insert into wt_mrna_node_values
+	(category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+	,attribute_2
+	,title
+	)
+	select distinct a.category_cd
+				   ,nvl(a.platform,'GPL570')
+				   ,nvl(a.tissue_type,'Unspecified Tissue Type')
+	               ,a.attribute_1
+				   ,a.attribute_2
+				   ,g.title
+    from lt_src_mrna_subj_samp_map a
+	    ,de_gpl_info g
+	where a.trial_name = TrialID
+	  and nvl(a.platform,'GPL570') = g.platform
+	  and a.source_cd = sourceCD
+	  and a.platform = g.platform
+	  and upper(g.marker_type) = 'GENE EXPRESSION'
+
+
+
+
+
+
+
+
+
+      -- and upper(g.organism) = 'HOMO SAPIENS'
+	  ;
+	--  and decode(dataType,'R',sign(a.intensity_value),1) = 1;	--	take all values when dataType T, only >0 for dataType R
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Insert node values into DEAPP wt_mrna_node_values',SQL%ROWCOUNT,stepCt,'Done');
+
+
+	commit;
+
+
+	insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+    ,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       category_cd,'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\','(\\){2,}', '\')
+		  ,category_cd
+		  ,platform as platform
+		  ,tissue_type
+		  ,attribute_1 as attribute_1
+          ,attribute_2 as attribute_2
+		  ,'LEAF'
+	from  wt_mrna_node_values;
+
+
+
+
+
+
+
+
+
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create leaf nodes in DEAPP tmp_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+	--	insert for platform node so platform concept can be populated
+
+
+	insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+    ,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'PLATFORM')+8)
+		  ,platform as platform
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'TISSUETYPE') > 1 then tissue_type else null end as tissue_type
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'ATTR1') > 1 then attribute_1 else null end as attribute_1
+          ,case when instr(substr(category_cd,1,instr(category_cd,'PLATFORM')+8),'ATTR2') > 1 then attribute_2 else null end as attribute_2
+		  ,'PLATFORM'
+	from  wt_mrna_node_values;
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create platform nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+
+
+
+
+
+
+
+
+
+
+	--	insert for ATTR1 node so ATTR1 concept can be populated in tissue_type_cd
+
+
+	insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+    ,attribute_1
+	,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'ATTR1')+5),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'ATTR1')+5)
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'PLATFORM') > 1 then platform else null end as platform
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'TISSUETYPE') > 1 then tissue_type else null end as tissue_type
+		  ,attribute_1 as attribute_1
+          ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'ATTR2') > 1 then attribute_2 else null end as attribute_2
+		  ,'ATTR1'
+	from  wt_mrna_node_values
+	where category_cd like '%ATTR1%'
+	  and attribute_1 is not null;
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create ATTR1 nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+
+
+
+
+
+
+
+
+
+
+	--	insert for ATTR2 node so ATTR2 concept can be populated in timepoint_cd
+
+
+	insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+    ,attribute_1
+	,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'ATTR2')+5),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'ATTR2')+5)
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR2')+5),'PLATFORM') > 1 then platform else null end as platform
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR1')+5),'TISSUETYPE') > 1 then tissue_type else null end as tissue_type
+          ,case when instr(substr(category_cd,1,instr(category_cd,'ATTR2')+5),'ATTR1') > 1 then attribute_1 else null end as attribute_1
+		  ,attribute_2 as attribute_2
+		  ,'ATTR2'
+	from  wt_mrna_node_values
+	where category_cd like '%ATTR2%'
+	  and attribute_2 is not null;
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create ATTR2 nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+
+
+
+
+
+
+
+
+
+
+	--	insert for tissue_type node so sample_type_cd can be populated
+
+
+	insert into wt_mrna_nodes
+	(leaf_node
+	,category_cd
+	,platform
+	,tissue_type
+	,attribute_1
+    ,attribute_2
+	,node_type
+	)
+	select distinct topNode || regexp_replace(replace(replace(replace(replace(replace(replace(
+	       substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'PLATFORM',title),'ATTR1',attribute_1),'ATTR2',attribute_2),'TISSUETYPE',tissue_type),'+','\'),'_',' ') || '\',
+		   '(\\){2,}', '\')
+		  ,substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10)
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'PLATFORM') > 1 then platform else null end as platform
+		  ,tissue_type as tissue_type
+		  ,case when instr(substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'ATTR1') > 1 then attribute_1 else null end as attribute_1
+          ,case when instr(substr(category_cd,1,instr(category_cd,'TISSUETYPE')+10),'ATTR2') > 1 then attribute_2 else null end as attribute_2
+		  ,'TISSUETYPE'
+	from  wt_mrna_node_values
+	where category_cd like '%TISSUETYPE%';
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create ATTR2 nodes in wt_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+
+
+
+
+
+
+
+
+
+
+	update wt_mrna_nodes
+	set node_name=parse_nth_value(leaf_node,length(leaf_node)-length(replace(leaf_node,'\',null)),'\');
+
+
+
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Updated node_name in DEAPP tmp_mrna_nodes',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+
+
+
+
+
+
+
+
+
+
+--	add leaf nodes for mRNA data  The cursor will only add nodes that do not already exist.
+
+	 FOR r_addNodes in addNodes Loop
+
+    --Add nodes for all types (ALSO DELETES EXISTING NODE)
+
+		i2b2_add_node(TrialID, r_addNodes.leaf_node, r_addNodes.node_name, jobId);
+		stepCt := stepCt + 1;
+		tText := 'Added Leaf Node: ' || r_addNodes.leaf_node || '  Name: ' || r_addNodes.node_name;
+
+		cz_write_audit(jobId,databaseName,procedureName,tText,SQL%ROWCOUNT,stepCt,'Done');
+
+		i2b2_fill_in_tree(TrialId, r_addNodes.leaf_node, jobID);
+
+	END LOOP;
+
+	--	set sourcesystem_cd, c_comment to null if any added upper-level nodes
+
+
+	update i2b2 b
+	set sourcesystem_cd=null,c_comment=null
+	where b.sourcesystem_cd = TrialId
+	  and length(b.c_fullname) < length(topNode);
+
+
+
+
+
+
+
+
+
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Set sourcesystem_cd to null for added upper level nodes',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+--	update concept_cd for nodes, this is done to make the next insert easier
+
+
+	update wt_mrna_nodes t
+	set concept_cd=(select c.concept_cd from concept_dimension c
+	                where c.concept_path = t.leaf_node
+				   )
+    where exists
+         (select 1 from concept_dimension x
+	                where x.concept_path = t.leaf_node
+				   )
+	  and t.concept_cd is null;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Update wt_mrna_nodes with newly created concept_cds',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  --Load the DE_SUBJECT_SAMPLE_MAPPING from wt_subject_mrna_data
+
+
+
+
+
+
+  --PATIENT_ID      = PATIENT_ID (SAME AS ID ON THE PATIENT_DIMENSION)
+  --SITE_ID         = site_id
+  --SUBJECT_ID      = subject_id
+  --SUBJECT_TYPE    = NULL
+  --CONCEPT_CODE    = from LEAF records in wt_mrna_nodes
+  --SAMPLE_TYPE    	= TISSUE_TYPE
+  --SAMPLE_TYPE_CD  = concept_cd from TISSUETYPE records in wt_mrna_nodes
+  --TRIAL_NAME      = TRIAL_NAME
+  --TIMEPOINT		= attribute_2
+  --TIMEPOINT_CD	= concept_cd from ATTR2 records in wt_mrna_nodes
+  --TISSUE_TYPE     = attribute_1
+  --TISSUE_TYPE_CD  = concept_cd from ATTR1 records in wt_mrna_nodes
+  --PLATFORM        = MRNA_AFFYMETRIX - this is required by ui code
+  --PLATFORM_CD     = concept_cd from PLATFORM records in wt_mrna_nodes
+  --DATA_UID		= concatenation of concept_cd-patient_num
+  --GPL_ID			= platform from wt_subject_mrna_data
+  --CATEGORY_CD		= category_cd that generated ontology
+  --SAMPLE_ID		= id of sample (trial:S:[site_id]:subject_id:sample_cd) from patient_dimension, may be the same as patient_num
+  --SAMPLE_CD		= sample_cd
+  --SOURCE_CD		= sourceCd
+
+  --ASSAY_ID        = generated by trigger
+
+
+	insert into de_subject_sample_mapping
+	(patient_id
+	,site_id
+	,subject_id
+	,subject_type
+	,concept_code
+	,assay_id
+	,sample_type
+	,sample_type_cd
+	,trial_name
+	,timepoint
+	,timepoint_cd
+	,tissue_type
+	,tissue_type_cd
+	,platform
+	,platform_cd
+	,data_uid
+	,gpl_id
+	,sample_id
+	,sample_cd
+	,category_cd
+	,source_cd
+	,omic_source_study
+	,omic_patient_id
+
+    )
+	select t.patient_id
+		  ,t.site_id
+		  ,t.subject_id
+		  ,t.subject_type
+		  ,t.concept_code
+		  ,deapp.seq_assay_id.nextval
+		  ,t.sample_type
+		  ,t.sample_type_cd
+		  ,t.trial_name
+		  ,t.timepoint
+		  ,t.timepoint_cd
+		  ,t.tissue_type
+		  ,t.tissue_type_cd
+		  ,t.platform
+		  ,t.platform_cd
+		  ,t.data_uid
+		  ,t.gpl_id
+		  ,t.sample_id
+		  ,t.sample_cd
+		  ,t.category_cd
+		  ,t.source_cd
+		  ,t.omic_source_study
+		  ,t.omic_patient_id
+	from (select distinct b.patient_num as patient_id
+			  ,a.site_id
+			  ,a.subject_id
+			  ,null as subject_type
+			  ,ln.concept_cd as concept_code
+			  ,a.tissue_type as sample_type
+			  ,ttp.concept_cd as sample_type_cd
+			  ,a.trial_name
+			  ,a.attribute_2 as timepoint
+			  ,a2.concept_cd as timepoint_cd
+			  ,a.attribute_1 as tissue_type
+			  ,a1.concept_cd as tissue_type_cd
+
+			  ,'SNP' as platform
+			  ,pn.concept_cd as platform_cd
+			  ,ln.concept_cd || '-' || to_char(b.patient_num) as data_uid
+			  ,a.platform as gpl_id
+			  ,coalesce(sid.patient_num,b.patient_num) as sample_id
+			  ,a.sample_cd
+			  ,nvl(a.category_cd,'Biomarker_Data+Gene_Expression+PLATFORM+TISSUETYPE+ATTR1+ATTR2') as category_cd
+			  ,a.source_cd
+			  ,TrialId as omic_source_study
+			  ,b.patient_num as omic_patient_id
+		from lt_src_mrna_subj_samp_map a
+		--Joining to Pat_dim to ensure the ID's match. If not I2B2 won't work.
+		inner join patient_dimension b
+		  on regexp_replace(TrialID || ':' || a.site_id || ':' || a.subject_id,'(::){1,}', ':') = b.sourcesystem_cd
+		inner join wt_mrna_nodes ln
+			on a.platform = ln.platform
+			and a.tissue_type = ln.tissue_type
+			and nvl(a.attribute_1,'@') = nvl(ln.attribute_1,'@')
+			and nvl(a.attribute_2,'@') = nvl(ln.attribute_2,'@')
+			and ln.node_type = 'LEAF'
+		inner join wt_mrna_nodes pn
+			on a.platform = pn.platform
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8),'TISSUETYPE') > 1 then a.tissue_type else '@' end = nvl(pn.tissue_type,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8),'ATTR1') > 1 then a.attribute_1 else '@' end = nvl(pn.attribute_1,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'PLATFORM')+8),'ATTR2') > 1 then a.attribute_2 else '@' end = nvl(pn.attribute_2,'@')
+			and pn.node_type = 'PLATFORM'
+		left outer join wt_mrna_nodes ttp
+			on a.tissue_type = ttp.tissue_type
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10),'PLATFORM') > 1 then a.platform else '@' end = nvl(ttp.platform,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10),'ATTR1') > 1 then a.attribute_1 else '@' end = nvl(ttp.attribute_1,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'TISSUETYPE')+10),'ATTR2') > 1 then a.attribute_2 else '@' end = nvl(ttp.attribute_2,'@')
+			and ttp.node_type = 'TISSUETYPE'
+		left outer join wt_mrna_nodes a1
+			on a.attribute_1 = a1.attribute_1
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5),'PLATFORM') > 1 then a.platform else '@' end = nvl(a1.platform,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5),'TISSUETYPE') > 1 then a.tissue_type else '@' end = nvl(a1.tissue_type,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR1')+5),'ATTR2') > 1 then a.attribute_2 else '@' end = nvl(a1.attribute_2,'@')
+			and a1.node_type = 'ATTR1'
+		left outer join wt_mrna_nodes a2
+			on a.attribute_2 = a1.attribute_2
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5),'PLATFORM') > 1 then a.platform else '@' end = nvl(a2.platform,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5),'TISSUETYPE') > 1 then a.tissue_type else '@' end = nvl(a2.tissue_type,'@')
+			and case when instr(substr(a.category_cd,1,instr(a.category_cd,'ATTR2')+5),'ATTR1') > 1 then a.attribute_1 else '@' end = nvl(a2.attribute_1,'@')
+			and a2.node_type = 'ATTR2'
+		left outer join patient_dimension sid
+			on  regexp_replace(TrialId || ':S:' || a.site_id || ':' || a.subject_id || ':' || a.sample_cd,
+							  '(::){1,}', ':') = sid.sourcesystem_cd
+		where a.trial_name = TrialID
+		  and a.source_cd = sourceCD
+		  and  ln.concept_cd is not null) t;
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Insert trial into DEAPP de_subject_sample_mapping',SQL%ROWCOUNT,stepCt,'Done');
+
+  commit;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+--	recreate de_subject_sample_mapping indexes
+
+
+	--execute immediate('create index de_subject_smpl_mpng_idx1 on de_subject_sample_mapping(timepoint, patient_id, trial_name) parallel nologging');
+	--execute immediate('create index de_subject_smpl_mpng_idx2 on de_subject_sample_mapping(patient_id, timepoint_cd, platform_cd, assay_id, trial_name) parallel nologging');
+	--execute immediate('create bitmap index de_subject_smpl_mpng_idx3 on de_subject_sample_mapping(sample_type_cd) parallel nologging');
+	--execute immediate('create index de_subject_smpl_mpng_idx4 on de_subject_sample_mapping(gpl_id) parallel nologging');
+	--execute immediate('create index de_subject_smpl_mpng_idx4 on de_subject_sample_mapping(platform, gpl_id) parallel nologging');
+    --stepCt := stepCt + 1;
+	--cz_write_audit(jobId,databaseName,procedureName,'Recreate indexes on DEAPP de_subject_sample_mapping',0,stepCt,'Done');
+
+--	Insert records for patients and samples into observation_fact
+
+	insert into observation_fact
+    (patient_num
+	,concept_cd
+	,modifier_cd
+	,valtype_cd
+	,tval_char
+	,nval_num
+	,sourcesystem_cd
+	,import_date
+	,valueflag_cd
+	,provider_id
+	,location_cd
+
+
+	,UNITS_CD
+  ,instance_num
+    )
+    select distinct m.patient_id
+		  ,m.concept_code
+		  ,m.trial_name
+		  ,'T' -- Text data type
+		  ,'E'  --Stands for Equals for Text Types
+		  ,null	--	not numeric for mRNA
+		  ,m.trial_name
+
+		  ,sysdate
+		  ,'@'
+		  ,'@'
+		  ,'@'
+		  ,'' -- no units available
+      ,1
+    from  de_subject_sample_mapping m
+    where m.trial_name = TrialID
+	  and m.source_cd = sourceCD
+      and m.platform = 'SNP';
+
+
+
+
+
+
+
+
+
+
+
+
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Insert patient facts into I2B2DEMODATA observation_fact',SQL%ROWCOUNT,stepCt,'Done');
+
+
+    commit;
+
+	--	Insert sample facts
+
+	insert into observation_fact
+    (patient_num
+	,concept_cd
+	,modifier_cd
+	,valtype_cd
+	,tval_char
+	,nval_num
+	,sourcesystem_cd
+	,import_date
+	,valueflag_cd
+	,provider_id
+	,location_cd
+	,UNITS_CD
+  ,instance_num
+    )
+    select distinct m.sample_id
+		  ,m.concept_code
+		  ,m.trial_name
+		  ,'T' -- Text data type
+		  ,'E'  --Stands for Equals for Text Types
+		  ,null	--	not numeric for mRNA
+		  ,m.trial_name
+		  ,sysdate
+		  ,'@'
+		  ,'@'
+		  ,'@'
+		  ,'' -- no units available
+      ,1
+    from  de_subject_sample_mapping m
+    where m.trial_name = TrialID
+	  and m.source_cd = sourceCd
+      and m.platform = 'SNP'
+	  and m.patient_id != m.sample_id;
+
+    stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Insert sample facts into I2B2DEMODATA observation_fact',SQL%ROWCOUNT,stepCt,'Done');
+
+    commit;
+
+	--Update I2b2 for correct data type
+
+	update i2b2 t
+	set c_columndatatype = 'T', c_metadataxml = null, c_visualattributes='FA'
+	where t.c_basecode in (select distinct x.concept_cd from wt_mrna_nodes x);
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Initialize data_type and xml in i2b2',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+
+
+
+
+
+
+
+
+	update i2b2
+	SET c_columndatatype = 'N',
+      --Static XML String
+		c_metadataxml = '<?xml version="1.0"?><ValueMetadata><Version>3.02</Version><CreationDateTime>08/14/2008 01:22:59</CreationDateTime><TestID></TestID><TestName></TestName><DataType>PosFloat</DataType><CodeType></CodeType><Loinc></Loinc><Flagstouse></Flagstouse><Oktousevalues>Y</Oktousevalues><MaxStringLength></MaxStringLength><LowofLowValue>0</LowofLowValue><HighofLowValue>0</HighofLowValue><LowofHighValue>100</LowofHighValue>100<HighofHighValue>100</HighofHighValue><LowofToxicValue></LowofToxicValue><HighofToxicValue></HighofToxicValue><EnumValues></EnumValues><CommentsDeterminingExclusion><Com></Com></CommentsDeterminingExclusion><UnitValues><NormalUnits>ratio</NormalUnits><EqualUnits></EqualUnits><ExcludingUnits></ExcludingUnits><ConvertingUnits><Units></Units><MultiplyingFactor></MultiplyingFactor></ConvertingUnits></UnitValues><Analysis><Enums /><Counts /><New /></Analysis></ValueMetadata>'
+	where c_basecode IN (
+		  select xd.concept_cd
+		  from wt_mrna_nodes xd
+			  ,observation_fact xf
+		  where xf.concept_cd = xd.concept_cd
+		  group by xd.concept_Cd
+		  having Max(xf.valtype_cd) = 'N');
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Update c_columndatatype and c_metadataxml for numeric data types in I2B2METADATA i2b2',SQL%ROWCOUNT,stepCt,'Done');
+	commit;
+
+/*
+	--UPDATE VISUAL ATTRIBUTES for Leaf Active (Default is folder)
+	update i2b2 a
+    set c_visualattributes = 'LA'
+    where 1 = (
+      select count(*)
+      from i2b2 b
+      where b.c_fullname like (a.c_fullname || '%'))
+      and c_fullname like '%' || topNode || '%';
+*/
+
+
+
+
+	--UPDATE VISUAL ATTRIBUTES for Leaf Active (Default is folder)
+	update i2b2 a
+    set c_visualattributes = 'LAH'
+	where a.c_basecode in (select distinct x.concept_code from de_subject_sample_mapping x
+						   where x.trial_name = TrialId
+						     and x.platform = 'SNP'
+							 and x.concept_code is not null);
+
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Update visual attributes for leaf nodes in I2B2METADATA i2b2',SQL%ROWCOUNT,stepCt,'Done');
+
+	COMMIT;
+
+  --Build concept Counts
+  --Also marks any i2B2 records with no underlying data as Hidden, need to do at Trial level because there may be multiple platform and there is no longer
+  -- a unique top-level node for mRNA data
+
+    i2b2_create_concept_counts(topNode ,jobID );
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Create concept counts',0,stepCt,'Done');
+
+	--	delete each node that is hidden
+
+	 FOR r_delNodes in delNodes Loop
+
+    --	deletes hidden nodes for a trial one at a time
+
+		i2b2_delete_1_node(r_delNodes.c_fullname);
+		stepCt := stepCt + 1;
+		tText := 'Deleted node: ' || r_delNodes.c_fullname;
+
+		cz_write_audit(jobId,databaseName,procedureName,tText,SQL%ROWCOUNT,stepCt,'Done');
+
+	END LOOP;
+
+  --Reload Security: Inserts one record for every I2B2 record into the security table
+
+
+    i2b2_load_security_data(jobId);
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Load security data',0,stepCt,'Done');
+
+	delete from deapp.de_snp_calls_by_gsm
+	where patient_num in (
+	  select omic_patient_id
+	  from deapp.de_subject_sample_mapping
+	  where trial_name = TrialID
+	);
+
+	commit;
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Truncated de_snp_calls_by_gsm',0,stepCt,'Done');
+
+	delete from deapp.de_snp_copy_number
+	where patient_num in (
+	  select omic_patient_id
+	  from deapp.de_subject_sample_mapping
+	  where trial_name = TrialID
+	);
+
+	commit;
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Truncated de_snp_copy_number',0,stepCt,'Done');
+
+	insert into deapp.DE_SNP_CALLS_BY_GSM
+	(gsm_num, snp_name, snp_calls, patient_num)
+	select ltscbg.gsm_num, ltscbg.snp_name, ltscbg.snp_calls, sm.omic_patient_id from
+		tm_lz.lt_snp_calls_by_gsm ltscbg
+		inner join deapp.de_subject_sample_mapping sm
+		on sm.sample_cd = ltscbg.gsm_num
+		where sm.trial_name = TrialID;
+	commit;
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Inserting into DE_SNP_CALLS_BY_GSM',0,stepCt,'Done');
+
+  	insert into deapp.DE_SNP_COPY_NUMBER
+	(snp_name, chrom, chrom_pos, copy_number, patient_num)
+	select lscn.snp_name, lscn.chrom, lscn.chrom_pos, power(2, lscn.copy_number) as copy_number, sm.omic_patient_id as patient_num from
+		tm_lz.LT_SNP_COPY_NUMBER lscn
+		inner join deapp.de_subject_sample_mapping sm
+		on sm.sample_cd = lscn.gsm_num
+		where sm.trial_name = TrialID;
+	commit;
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Inserting into de_snp_copy_number',0,stepCt,'Done');
+
+	execute immediate ('truncate table tm_lz.lt_src_mrna_data');
+	commit;
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'trancated lt_src_mrna_data',0,stepCt,'Done');
+
+	insert into tm_lz.lt_src_mrna_data
+	(expr_id, probeset, intensity_value)
+	select gsm_num, snp_name, copy_number
+	from tm_lz.lt_snp_copy_number;
+	commit;
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Inserting into lt_src_mrna_data',0,stepCt,'Done');
+
+
+
+
+--	tag data with probeset_id from reference.probeset_deapp
+
+	execute immediate ('truncate table tm_wz.wt_subject_mrna_probeset');
+
+	--	note: assay_id represents a unique subject/site/sample
+
+
+
+	insert into wt_subject_mrna_probeset
+	(probeset_id
+--	,expr_id
+	,intensity_value
+
+	,patient_id
+--	,sample_cd
+--	,subject_id
+	,trial_name
+	,assay_id
+	)
+	select gs.probeset_id
+--		  ,sd.sample_cd
+		  ,cast(avg(cast (md.intensity_value as number(30,20))) as number) as aiv -- temporary fix to avoid overflow in some cases, need to address this properly by changing staging tables
+
+		  ,sd.patient_id
+--		  ,sd.sample_cd
+--		  ,sd.subject_id
+		  ,TrialId
+		  ,sd.assay_id
+	from de_subject_sample_mapping sd
+		,lt_src_mrna_data md
+		,probeset_deapp gs
+
+	where sd.sample_cd = md.expr_id
+	  and sd.platform = 'SNP'
+	  and sd.trial_name = TrialId
+	  and sd.source_cd = sourceCd
+
+
+	  and sd.gpl_id = gs.platform
+	  and md.probeset = gs.probeset
+	  and decode(dataType,'R',sign(md.intensity_value),1) = 1  --	take only >0 for dataType R
+	group by gs.probeset_id
+		--  ,sd.sample_cd
+		  ,sd.patient_id
+		--  ,sd.sample_cd
+		--  ,sd.subject_id
+		  ,sd.assay_id;
+
+	pExists := SQL%ROWCOUNT;
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'Insert into DEAPP wt_subject_mrna_probeset',SQL%ROWCOUNT,stepCt,'Done');
+
+	commit;
+
+
+	if pExists = 0 then
+		raise no_probeset_recs;
+	end if;
+
+	--	insert into de_subject_microarray_data when dataType is T (transformed)
+
+	if dataType = 'T' then
+		insert into de_subject_microarray_data
+		(trial_source
+		,probeset_id
+		,assay_id
+		,patient_id
+		--,sample_id
+		--,subject_id
+		,trial_name
+		,zscore
+		)
+		select TrialId || ':' || sourceCd
+			  ,probeset_id
+			  ,assay_id
+			  ,patient_id
+			  --,sample_id
+			  --,subject_id
+			  ,trial_name
+			  ,case when intensity_value < -2.5
+			        then -2.5
+					when intensity_value > 2.5
+					then 2.5
+					else intensity_value
+			   end as zscore
+		from wt_subject_mrna_probeset
+		where trial_name = TrialID;
+		stepCt := stepCt + 1;
+		cz_write_audit(jobId,databaseName,procedureName,'Insert transformed into DEAPP de_subject_microarray_data',SQL%ROWCOUNT,stepCt,'Done');
+
+		commit;
+	else
+    --	insert into de_subject_microarray_data when dataType is T (transformed)
+
+
+    if dataType = 'Z' then
+      insert into de_subject_microarray_data
+      (trial_source
+      ,probeset_id
+      ,assay_id
+      ,patient_id
+      --,sample_id
+      --,subject_id
+      ,TRIAL_NAME
+      ,log_intensity
+      ,zscore
+
+      )
+      select TrialId || ':' || sourceCd
+          ,probeset_id
+          ,assay_id
+          ,patient_id
+          --,sample_id
+          --,subject_id
+          ,TRIAL_NAME
+          ,intensity_value
+          ,case when intensity_value < -2.5
+
+                then -2.5
+            when intensity_value > 2.5
+            then 2.5
+            else intensity_value
+           end as zscore
+      from wt_subject_mrna_probeset
+      where trial_name = TrialID;
+      STEPCT := STEPCT + 1;
+      cz_write_audit(jobId,databaseName,procedureName,'Insert transformed (workaround) into DEAPP de_subject_microarray_data',SQL%ROWCOUNT,stepCt,'Done');
+
+
+      commit;
+    else
+    --	Calculate ZScores and insert data into de_subject_microarray_data.  The 'L' parameter indicates that the gene expression data will be selected from
+    --	wt_subject_mrna_probeset as part of a Load.
+
+
+      if dataType = 'R' or dataType = 'L' then
+        i2b2_mrna_zscore_calc(TrialID,'L',jobId,dataType,logBase,sourceCD);
+        stepCt := stepCt + 1;
+        cz_write_audit(jobId,databaseName,procedureName,'Calculate Z-Score',0,stepCt,'Done');
+        commit;
+
+      end if;
+
+    end if;
+end if;
+
+
+	stepCt := stepCt + 1;
+	cz_write_audit(jobId,databaseName,procedureName,'End i2b2_process_snp_data',0,stepCt,'Done');
+
+	IF newJobFlag = 1
+	THEN
+		cz_end_audit (jobID, 'SUCCESS');
+	END IF;
+
+
+	select 0 into rtn_code from dual;
+
+
+	EXCEPTION
+	--when unmapped_patients then
+	--	cz_write_audit(jobId,databasename,procedurename,'No site_id/subject_id mapped to patient_dimension',1,stepCt,'ERROR');
+	--	cz_error_handler(jobid,procedurename);
+	--	cz_end_audit (jobId,'FAIL');
+	when missing_platform then
+		cz_write_audit(jobId,databasename,procedurename,'Platform data missing from one or more subject_sample mapping records',1,stepCt,'ERROR');
+		cz_error_handler(jobid,procedurename);
+		cz_end_audit (jobId,'FAIL');
+		select 16 into rtn_code from dual;
+	when missing_tissue then
+		cz_write_audit(jobId,databasename,procedurename,'Tissue Type data missing from one or more subject_sample mapping records',1,stepCt,'ERROR');
+		cz_error_handler(jobid,procedurename);
+		CZ_END_AUDIT (JOBID,'FAIL');
+		select 16 into rtn_code from dual;
+	when unmapped_platform then
+		cz_write_audit(jobId,databasename,procedurename,'Platform not found in de_mrna_annotation',1,stepCt,'ERROR');
+		CZ_ERROR_HANDLER(JOBID,PROCEDURENAME);
+		cz_end_audit (jobId,'FAIL');
+		select 16 into rtn_code from dual;
+	when multiple_platform then
+		cz_write_audit(jobId,databasename,procedurename,'Multiple platforms for sample_cd in lt_src_mrna_subj_samp_map',1,stepCt,'ERROR');
+		CZ_ERROR_HANDLER(JOBID,PROCEDURENAME);
+		cz_end_audit (jobId,'FAIL');
+		select 16 into rtn_code from dual;
+	when no_probeset_recs then
+		cz_write_audit(jobId,databasename,procedurename,'Unable to match probesets to platform in probeset_deapp',1,stepCt,'ERROR');
+		CZ_ERROR_HANDLER(JOBID,PROCEDURENAME);
+		cz_end_audit (jobId,'FAIL');
+		select 16 into rtn_code from dual;
+	WHEN OTHERS THEN
+		--Handle errors.
+		cz_error_handler (jobID, procedureName);
+		--End Proc
+		cz_end_audit (jobID, 'FAIL');
+		select 16 into rtn_code from dual;
+END;
+/
diff --git a/ddl/oracle/tm_cz/procedures/partition_gwas_data.sql b/ddl/oracle/tm_cz/procedures/partition_gwas_data.sql
new file mode 100644
index 00000000..21e74282
--- /dev/null
+++ b/ddl/oracle/tm_cz/procedures/partition_gwas_data.sql
@@ -0,0 +1,112 @@
+--
+-- Type: PROCEDURE; Owner: TM_CZ; Name: PARTITION_GWAS_DATA
+--
+  CREATE OR REPLACE EDITIONABLE PROCEDURE "TM_CZ"."PARTITION_GWAS_DATA" 
+AS
+
+  sqlText                varchar2(1000);
+  tText                        varchar2(1000);
+  pExists                number;
+
+    --Audit variables
+  newJobFlag INTEGER(1);
+  databaseName VARCHAR(100);
+  procedureName VARCHAR(100);
+  jobID number(18,0);
+  stepCt number(18,0);
+
+BEGIN
+
+  --Set Audit Parameters
+  newJobFlag := 0; -- False (Default)
+  jobID := -1;
+
+  SELECT sys_context('USERENV', 'CURRENT_SCHEMA') INTO databaseName FROM dual;
+  procedureName := $$PLSQL_UNIT;
+
+  --Audit JOB Initialization
+  --If Job ID does not exist, then this is a single procedure run and we need to create it
+  IF(jobID IS NULL or jobID < 1)
+  THEN
+    newJobFlag := 1; -- True
+    cz_start_audit (procedureName, databaseName, jobID);
+  END IF;
+
+        for gwas_data in (select distinct bio_assay_analysis_id from biomart.bio_assay_analysis_gwas )
+        loop
+
+                stepCt := 0;
+                stepCt := stepCt + 1;
+                tText := 'Starting load for ' || to_char(gwas_data.bio_assay_analysis_id);
+                cz_write_audit(jobId,databaseName,procedureName,tText,0,stepCt,'Done');
+
+                --        Create partition in gwas_partition if it doesn't exist else truncate partition
+
+                select count(*)
+                        into pExists
+                        from all_tab_partitions
+                        where table_name = 'GWAS_PARTITION'
+                          and partition_name = to_char(gwas_data.bio_assay_analysis_id);
+
+                if pExists = 0 then
+                        --        needed to add partition to GWAS_PARTITION
+
+                        sqlText := 'alter table biomart.GWAS_PARTITION add PARTITION "' || to_char(gwas_data.bio_assay_analysis_id) || '"  VALUES (' ||
+                                           to_char(gwas_data.bio_assay_analysis_id) || ') ' ||
+                                                   'NOLOGGING TABLESPACE "BIOMART" ';
+                        execute immediate(sqlText);
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobId,databaseName,procedureName,'Adding partition to GWAS_PARTITION',0,stepCt,'Done');
+
+                else
+                        sqlText := 'alter table biomart.GWAS_PARTITION truncate partition "' || to_char(gwas_data.bio_assay_analysis_id) || '"';
+                        execute immediate(sqlText);
+                        stepCt := stepCt + 1;
+                        cz_write_audit(jobId,databaseName,procedureName,'Truncating partition in GWAS_PARTITION',0,stepCt,'Done');
+                end if;
+
+                insert into biomart.GWAS_PARTITION
+                (bio_asy_analysis_gwas_id
+                ,bio_assay_analysis_id
+                ,rs_id
+                ,p_value_char
+                ,p_value
+                ,log_p_value
+                ,etl_id
+                ,ext_data
+                )
+                select g.bio_asy_analysis_gwas_id
+                          ,g.bio_assay_analysis_id
+                          ,g.rs_id
+                          ,g.p_value_char
+                          ,g.p_value
+                          ,g.log_p_value
+                          ,g.etl_id
+                          ,g.ext_data
+                from biomart.bio_assay_analysis_gwas g
+                where g.bio_assay_analysis_id = gwas_data.bio_assay_analysis_id;
+                stepCt := stepCt + 1;
+                cz_write_audit(jobId,databaseName,procedureName,'Insert data for analysis into GWAS_PARTITION',SQL%ROWCOUNT,stepCt,'Done');
+                commit;
+
+        end loop;
+
+           ---Cleanup OVERALL JOB if this proc is being run standalone
+
+        stepCt := stepCt + 1;
+        cz_write_audit(jobId,databaseName,procedureName,procedureName,0,stepCt,'Done');
+
+        IF newJobFlag = 1
+        THEN
+                cz_end_audit (jobID, 'SUCCESS');
+        END IF;
+
+        EXCEPTION
+        WHEN OTHERS THEN
+                --Handle errors.
+                cz_error_handler (jobID, procedureName);
+                --End Proc
+                cz_end_audit (jobID, 'FAIL');
+                --select 16 into rtn_code from dual;
+END;
+/
diff --git a/ddl/oracle/tm_cz/stg_rbm_antigen_gene.sql b/ddl/oracle/tm_cz/stg_rbm_antigen_gene.sql
new file mode 100644
index 00000000..e1a5a25d
--- /dev/null
+++ b/ddl/oracle/tm_cz/stg_rbm_antigen_gene.sql
@@ -0,0 +1,10 @@
+--
+-- Type: TABLE; Owner: TM_CZ; Name: STG_RBM_ANTIGEN_GENE
+--
+ CREATE TABLE "TM_CZ"."STG_RBM_ANTIGEN_GENE" 
+  (	"ANTIGEN_NAME" VARCHAR2(255 BYTE), 
+"GENE_SYMBOL" VARCHAR2(100 BYTE), 
+"GENE_ID" VARCHAR2(100 BYTE)
+  ) SEGMENT CREATION DEFERRED
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_cz/stg_subject_rbm_data.sql b/ddl/oracle/tm_cz/stg_subject_rbm_data.sql
new file mode 100644
index 00000000..01c51056
--- /dev/null
+++ b/ddl/oracle/tm_cz/stg_subject_rbm_data.sql
@@ -0,0 +1,16 @@
+--
+-- Type: TABLE; Owner: TM_CZ; Name: STG_SUBJECT_RBM_DATA
+--
+ CREATE TABLE "TM_CZ"."STG_SUBJECT_RBM_DATA" 
+  (	"TRIAL_NAME" VARCHAR2(100 BYTE), 
+"ANTIGEN_NAME" VARCHAR2(100 BYTE), 
+"VALUE_TEXT" VARCHAR2(100 BYTE), 
+"VALUE_NUMBER" NUMBER, 
+"TIMEPOINT" VARCHAR2(100 BYTE), 
+"ASSAY_ID" VARCHAR2(100 BYTE), 
+"SAMPLE_ID" VARCHAR2(100 BYTE), 
+"SUBJECT_ID" VARCHAR2(100 BYTE), 
+"SITE_ID" VARCHAR2(100 BYTE)
+  ) SEGMENT CREATION DEFERRED
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_cz/stg_subject_rbm_data_raw.sql b/ddl/oracle/tm_cz/stg_subject_rbm_data_raw.sql
new file mode 100644
index 00000000..94cd1f8c
--- /dev/null
+++ b/ddl/oracle/tm_cz/stg_subject_rbm_data_raw.sql
@@ -0,0 +1,16 @@
+--
+-- Type: TABLE; Owner: TM_CZ; Name: STG_SUBJECT_RBM_DATA_RAW
+--
+ CREATE TABLE "TM_CZ"."STG_SUBJECT_RBM_DATA_RAW" 
+  (	"TRIAL_NAME" VARCHAR2(100 BYTE), 
+"ANTIGEN_NAME" VARCHAR2(100 BYTE), 
+"VALUE_TEXT" VARCHAR2(100 BYTE), 
+"VALUE_NUMBER" NUMBER, 
+"TIMEPOINT" VARCHAR2(100 BYTE), 
+"ASSAY_ID" VARCHAR2(100 BYTE), 
+"SAMPLE_ID" VARCHAR2(100 BYTE), 
+"SUBJECT_ID" VARCHAR2(100 BYTE), 
+"SITE_ID" VARCHAR2(100 BYTE)
+  ) SEGMENT CREATION DEFERRED
+NOCOMPRESS LOGGING
+ TABLESPACE "TRANSMART" ;
diff --git a/ddl/oracle/tm_cz/tmp_subject_info.sql b/ddl/oracle/tm_cz/tmp_subject_info.sql
index 7dae0263..b1cb450c 100644
--- a/ddl/oracle/tm_cz/tmp_subject_info.sql
+++ b/ddl/oracle/tm_cz/tmp_subject_info.sql
@@ -9,3 +9,9 @@
   ) SEGMENT CREATION IMMEDIATE
  TABLESPACE "TRANSMART" ;
 
+--
+-- Type: INDEX; Owner: TM_CZ; Name: IDX_TMP_SUBJ_USUBJID
+--
+CREATE INDEX "TM_CZ"."IDX_TMP_SUBJ_USUBJID" ON "TM_CZ"."TMP_SUBJECT_INFO" ("USUBJID")
+TABLESPACE "TRANSMART" ;
+
diff --git a/ddl/oracle/tm_cz/views/patient_info.sql b/ddl/oracle/tm_cz/views/patient_info.sql
new file mode 100644
index 00000000..6167edf2
--- /dev/null
+++ b/ddl/oracle/tm_cz/views/patient_info.sql
@@ -0,0 +1,6 @@
+--
+-- Type: VIEW; Owner: TM_CZ; Name: PATIENT_INFO
+--
+CREATE OR REPLACE FORCE EDITIONABLE VIEW "TM_CZ"."PATIENT_INFO" ("STUDY_ID", "SUBJECT_ID", "SITE_ID", "USUBJID") AS 
+select TRIAL_NAME as STUDY_ID, SUBJECT_ID, SITE_ID, REGEXP_REPLACE(TRIAL_NAME || ':' || SITE_ID || ':' || SUBJECT_ID,
+                 '(::){1,}', ':') as usubjid from tm_cz.stg_subject_rbm_data;

From 93a739a10ff21efb65fcfa780ee9ae9eb74dd92b Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 13:37:07 +0100
Subject: [PATCH 29/31] user roles updated from oracle test server

---
 ddl/oracle/GLOBAL/amapp.sql         |  55 ++------
 ddl/oracle/GLOBAL/biomart.sql       |  25 +---
 ddl/oracle/GLOBAL/biomart_stage.sql |  25 +---
 ddl/oracle/GLOBAL/biomart_user.sql  |  44 +-----
 ddl/oracle/GLOBAL/deapp.sql         | 210 ++++++++++++++++++++++++----
 ddl/oracle/GLOBAL/fmapp.sql         |  48 +------
 ddl/oracle/GLOBAL/i2b2demodata.sql  |  48 +------
 ddl/oracle/GLOBAL/i2b2metadata.sql  |  48 +------
 ddl/oracle/GLOBAL/searchapp.sql     |  48 +------
 ddl/oracle/GLOBAL/tm_cz.sql         | 204 +++++++++++++++++++++++----
 ddl/oracle/GLOBAL/tm_lz.sql         |  47 +------
 ddl/oracle/GLOBAL/tm_wz.sql         |  47 +------
 12 files changed, 396 insertions(+), 453 deletions(-)

diff --git a/ddl/oracle/GLOBAL/amapp.sql b/ddl/oracle/GLOBAL/amapp.sql
index 9bf64634..b8eb019c 100644
--- a/ddl/oracle/GLOBAL/amapp.sql
+++ b/ddl/oracle/GLOBAL/amapp.sql
@@ -4,55 +4,24 @@
 CREATE USER "AMAPP" IDENTIFIED BY VALUES 'S:9571FFB20AE27E19978ABB02101BD2F2057143B93D977AC576CC50197513;02955D58870FE54F'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: ROLE_GRANT; Name: AMAPP
 --
 --
 -- Type: TABLESPACE_QUOTA; Name: AMAPP
 --
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "AMAPP" QUOTA UNLIMITED ON "TRANSMART"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''TRANSMART'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "AMAPP" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
 --
 -- Type: SYSTEM_GRANT; Name: AMAPP
 --
+GRANT GLOBAL QUERY REWRITE TO "AMAPP" WITH ADMIN OPTION;
+GRANT QUERY REWRITE TO "AMAPP" WITH ADMIN OPTION;
+GRANT DROP ANY MATERIALIZED VIEW TO "AMAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY MATERIALIZED VIEW TO "AMAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY MATERIALIZED VIEW TO "AMAPP" WITH ADMIN OPTION;
+GRANT CREATE TRIGGER TO "AMAPP";
+GRANT CREATE PROCEDURE TO "AMAPP";
+GRANT CREATE VIEW TO "AMAPP";
+GRANT SELECT ANY TABLE TO "AMAPP";
+GRANT CREATE TABLE TO "AMAPP";
+GRANT UNLIMITED TABLESPACE TO "AMAPP";
+GRANT CREATE SESSION TO "AMAPP";
diff --git a/ddl/oracle/GLOBAL/biomart.sql b/ddl/oracle/GLOBAL/biomart.sql
index 50d9bd54..f4b9d511 100644
--- a/ddl/oracle/GLOBAL/biomart.sql
+++ b/ddl/oracle/GLOBAL/biomart.sql
@@ -4,31 +4,9 @@
 CREATE USER "BIOMART" IDENTIFIED BY VALUES 'S:AC6B55347D02816D681B481FB130C75B6334E91A6B9AC3EE02B5D80AB4B0;EE8EC2CF8301F8AE'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: TABLESPACE_QUOTA; Name: BIOMART
 --
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "BIOMART" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
   DECLARE 
   TEMP_COUNT NUMBER; 
   SQLSTR VARCHAR2(200); 
@@ -50,15 +28,18 @@ EXCEPTION
 END;
 /
  
+ 
 --
 -- Type: ROLE_GRANT; Name: BIOMART
 --
 GRANT "CONNECT" TO "BIOMART";
 
 GRANT "RESOURCE" TO "BIOMART";
+GRANT "DBA" TO "BIOMART";
 
 --
 -- Type: SYSTEM_GRANT; Name: BIOMART
 --
 GRANT CREATE TABLE TO "BIOMART";
+GRANT UNLIMITED TABLESPACE TO "BIOMART";
 
diff --git a/ddl/oracle/GLOBAL/biomart_stage.sql b/ddl/oracle/GLOBAL/biomart_stage.sql
index baa41c68..b4a0b021 100644
--- a/ddl/oracle/GLOBAL/biomart_stage.sql
+++ b/ddl/oracle/GLOBAL/biomart_stage.sql
@@ -4,7 +4,6 @@
 CREATE USER "BIOMART_STAGE" IDENTIFIED BY VALUES 'S:FA2819401185E87BB34E022CB387A6B2D56735660A55BF2E96FF9621D7C8;0AF103800E386834'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: TABLESPACE_QUOTA; Name: BIOMART_STAGE
 --
@@ -29,36 +28,16 @@ EXCEPTION
 END;
 /
  
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "BIOMART_STAGE" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
  
 --
 -- Type: SYSTEM_GRANT; Name: BIOMART_STAGE
 --
+GRANT UNLIMITED TABLESPACE TO "BIOMART_STAGE";
+
 --
 -- Type: ROLE_GRANT; Name: BIOMART_STAGE
 --
 GRANT "CONNECT" TO "BIOMART_STAGE";
 
 GRANT "RESOURCE" TO "BIOMART_STAGE";
-
 GRANT "DBA" TO "BIOMART_STAGE";
-
diff --git a/ddl/oracle/GLOBAL/biomart_user.sql b/ddl/oracle/GLOBAL/biomart_user.sql
index d2aa0da7..98b6c63b 100644
--- a/ddl/oracle/GLOBAL/biomart_user.sql
+++ b/ddl/oracle/GLOBAL/biomart_user.sql
@@ -12,51 +12,11 @@ GRANT "CONNECT" TO "BIOMART_USER";
 
 GRANT "RESOURCE" TO "BIOMART_USER";
 
+GRANT "DBA" TO "BIOMART_USER";
 --
 -- Type: TABLESPACE_QUOTA; Name: BIOMART_USER
 --
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "BIOMART_USER" QUOTA UNLIMITED ON "TRANSMART"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''TRANSMART'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "BIOMART_USER" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
 --
 -- Type: SYSTEM_GRANT; Name: BIOMART_USER
 --
+GRANT UNLIMITED TABLESPACE TO "BIOMART_USER";
diff --git a/ddl/oracle/GLOBAL/deapp.sql b/ddl/oracle/GLOBAL/deapp.sql
index 2567fc11..df2237d1 100644
--- a/ddl/oracle/GLOBAL/deapp.sql
+++ b/ddl/oracle/GLOBAL/deapp.sql
@@ -4,17 +4,200 @@
 CREATE USER "DEAPP" IDENTIFIED BY VALUES 'S:499EBB6329A6A236B428E5AEB991C06E27856F29A3480065D019B36F570E;9F7EF5372B0017FD'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: SYSTEM_GRANT; Name: DEAPP
 --
+GRANT FLASHBACK ARCHIVE ADMINISTER TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER DATABASE LINK TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER PUBLIC DATABASE LINK TO "DEAPP" WITH ADMIN OPTION;
+GRANT ADMINISTER SQL MANAGEMENT OBJECT TO "DEAPP" WITH ADMIN OPTION;
+GRANT UPDATE ANY CUBE DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT UPDATE ANY CUBE BUILD PROCESS TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY CUBE BUILD PROCESS TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY CUBE BUILD PROCESS TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE CUBE BUILD PROCESS TO "DEAPP" WITH ADMIN OPTION;
+GRANT INSERT ANY MEASURE FOLDER TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY MEASURE FOLDER TO "DEAPP" WITH ADMIN OPTION;
+GRANT DELETE ANY MEASURE FOLDER TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY MEASURE FOLDER TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE MEASURE FOLDER TO "DEAPP" WITH ADMIN OPTION;
+GRANT UPDATE ANY CUBE TO "DEAPP" WITH ADMIN OPTION;
+GRANT SELECT ANY CUBE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY CUBE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY CUBE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY CUBE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE CUBE TO "DEAPP" WITH ADMIN OPTION;
+GRANT SELECT ANY CUBE DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT INSERT ANY CUBE DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY CUBE DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT DELETE ANY CUBE DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY CUBE DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY CUBE DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE CUBE DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT COMMENT ANY MINING MODEL TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY MINING MODEL TO "DEAPP" WITH ADMIN OPTION;
+GRANT SELECT ANY MINING MODEL TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY MINING MODEL TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY MINING MODEL TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE MINING MODEL TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXECUTE ASSEMBLY TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXECUTE ANY ASSEMBLY TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY ASSEMBLY TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY ASSEMBLY TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY ASSEMBLY TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ASSEMBLY TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY EDITION TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY EDITION TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY EDITION TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE EXTERNAL JOB TO "DEAPP" WITH ADMIN OPTION;
+GRANT CHANGE NOTIFICATION TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXEMPT IDENTITY POLICY TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY SQL PROFILE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ADMINISTER ANY SQL TUNING SET TO "DEAPP" WITH ADMIN OPTION;
+GRANT ADMINISTER SQL TUNING SET TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY SQL PROFILE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY SQL PROFILE TO "DEAPP" WITH ADMIN OPTION;
+GRANT SELECT ANY TRANSACTION TO "DEAPP" WITH ADMIN OPTION;
+GRANT MANAGE SCHEDULER TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXECUTE ANY CLASS TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXECUTE ANY PROGRAM TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY JOB TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE JOB TO "DEAPP" WITH ADMIN OPTION;
+GRANT ADVISOR TO "DEAPP" WITH ADMIN OPTION;
+GRANT ANALYZE ANY DICTIONARY TO "DEAPP" WITH ADMIN OPTION;
+GRANT IMPORT FULL DATABASE TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXPORT FULL DATABASE TO "DEAPP" WITH ADMIN OPTION;
+GRANT GRANT ANY OBJECT PRIVILEGE TO "DEAPP" WITH ADMIN OPTION;
+GRANT FLASHBACK ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DEBUG ANY PROCEDURE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DEBUG CONNECT SESSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT SELECT ANY DICTIONARY TO "DEAPP" WITH ADMIN OPTION;
+GRANT RESUMABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXEMPT ACCESS POLICY TO "DEAPP" WITH ADMIN OPTION;
+GRANT ON COMMIT REFRESH TO "DEAPP" WITH ADMIN OPTION;
+GRANT MERGE ANY VIEW TO "DEAPP" WITH ADMIN OPTION;
+GRANT ADMINISTER DATABASE TRIGGER TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY OUTLINE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY OUTLINE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY OUTLINE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY CONTEXT TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY CONTEXT TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE DIMENSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT UNDER ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXECUTE ANY INDEXTYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT GLOBAL QUERY REWRITE TO "DEAPP" WITH ADMIN OPTION;
+GRANT QUERY REWRITE TO "DEAPP" WITH ADMIN OPTION;
+GRANT UNDER ANY VIEW TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY INDEXTYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY INDEXTYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY INDEXTYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE INDEXTYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXECUTE ANY OPERATOR TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY OPERATOR TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY OPERATOR TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY OPERATOR TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE OPERATOR TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXECUTE ANY LIBRARY TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY LIBRARY TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY LIBRARY TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY LIBRARY TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE LIBRARY TO "DEAPP" WITH ADMIN OPTION;
+GRANT UNDER ANY TYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXECUTE ANY TYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY TYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY TYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY TYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE TYPE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY DIRECTORY TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY DIRECTORY TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY MATERIALIZED VIEW TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY MATERIALIZED VIEW TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY MATERIALIZED VIEW TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE MATERIALIZED VIEW TO "DEAPP" WITH ADMIN OPTION;
+ 
+GRANT GRANT ANY PRIVILEGE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ANALYZE ANY TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER RESOURCE COST TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP PROFILE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER PROFILE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE PROFILE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY TRIGGER TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY TRIGGER TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY TRIGGER TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE TRIGGER TO "DEAPP" WITH ADMIN OPTION;
+GRANT EXECUTE ANY PROCEDURE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY PROCEDURE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY PROCEDURE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY PROCEDURE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE PROCEDURE TO "DEAPP" WITH ADMIN OPTION;
+GRANT FORCE ANY TRANSACTION TO "DEAPP" WITH ADMIN OPTION;
+GRANT FORCE TRANSACTION TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER DATABASE TO "DEAPP" WITH ADMIN OPTION;
+GRANT AUDIT ANY TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY ROLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT GRANT ANY ROLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY ROLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ROLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP PUBLIC DATABASE LINK TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE PUBLIC DATABASE LINK TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE DATABASE LINK TO "DEAPP" WITH ADMIN OPTION;
+GRANT SELECT ANY SEQUENCE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY SEQUENCE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY SEQUENCE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY SEQUENCE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE SEQUENCE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY VIEW TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY VIEW TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE VIEW TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP PUBLIC SYNONYM TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE PUBLIC SYNONYM TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY SYNONYM TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY SYNONYM TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE SYNONYM TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY INDEX TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY INDEX TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY INDEX TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY CLUSTER TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY CLUSTER TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY CLUSTER TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE CLUSTER TO "DEAPP" WITH ADMIN OPTION;
+GRANT DELETE ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT UPDATE ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT INSERT ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT SELECT ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT COMMENT ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT LOCK ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT BACKUP ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ANY TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE TABLE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP ROLLBACK SEGMENT TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER ROLLBACK SEGMENT TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE ROLLBACK SEGMENT TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP USER TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER USER TO "DEAPP" WITH ADMIN OPTION;
+GRANT BECOME USER TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE USER TO "DEAPP" WITH ADMIN OPTION;
+GRANT UNLIMITED TABLESPACE TO "DEAPP" WITH ADMIN OPTION;
+GRANT DROP TABLESPACE TO "DEAPP" WITH ADMIN OPTION;
+GRANT MANAGE TABLESPACE TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER TABLESPACE TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE TABLESPACE TO "DEAPP" WITH ADMIN OPTION;
+GRANT RESTRICTED SESSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER SESSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT CREATE SESSION TO "DEAPP" WITH ADMIN OPTION;
+GRANT AUDIT SYSTEM TO "DEAPP" WITH ADMIN OPTION;
+GRANT ALTER SYSTEM TO "DEAPP" WITH ADMIN OPTION;
 --
 -- Type: ROLE_GRANT; Name: DEAPP
 --
 GRANT "CONNECT" TO "DEAPP";
-
 GRANT "RESOURCE" TO "DEAPP";
-
+GRANT "DBA" TO "DEAPP";
 --
 -- Type: TABLESPACE_QUOTA; Name: DEAPP
 --
@@ -37,26 +220,5 @@ EXCEPTION
       RAISE;
     END IF;
 END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "DEAPP" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
 /
  
diff --git a/ddl/oracle/GLOBAL/fmapp.sql b/ddl/oracle/GLOBAL/fmapp.sql
index 7a55335b..16d86c35 100644
--- a/ddl/oracle/GLOBAL/fmapp.sql
+++ b/ddl/oracle/GLOBAL/fmapp.sql
@@ -4,7 +4,6 @@
 CREATE USER "FMAPP" IDENTIFIED BY VALUES 'S:2AFD1E3EB1A960DE3051FCAEEF5E3AEB06302157ADD0D3240063327453F3;D684DB54467F1F56'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: ROLE_GRANT; Name: FMAPP
 --
@@ -12,55 +11,10 @@ CREATE USER "FMAPP" IDENTIFIED BY VALUES 'S:2AFD1E3EB1A960DE3051FCAEEF5E3AEB0630
 -- Type: SYSTEM_GRANT; Name: FMAPP
 --
 GRANT CREATE TRIGGER TO "FMAPP";
-
 GRANT CREATE PROCEDURE TO "FMAPP";
-
 GRANT CREATE TABLE TO "FMAPP";
-
+GRANT UNLIMITED TABLESPACE TO "FMAPP";
 GRANT CREATE SESSION TO "FMAPP";
-
 --
 -- Type: TABLESPACE_QUOTA; Name: FMAPP
 --
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "FMAPP" QUOTA UNLIMITED ON "TRANSMART"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''TRANSMART'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "FMAPP" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
diff --git a/ddl/oracle/GLOBAL/i2b2demodata.sql b/ddl/oracle/GLOBAL/i2b2demodata.sql
index d1d950b8..7318da42 100644
--- a/ddl/oracle/GLOBAL/i2b2demodata.sql
+++ b/ddl/oracle/GLOBAL/i2b2demodata.sql
@@ -4,61 +4,17 @@
 CREATE USER "I2B2DEMODATA" IDENTIFIED BY VALUES 'S:00C945EB67B2A497CD615FA4D750635389749696075B29F80E2E3E474C71;4EE49A6D1DE00414'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: SYSTEM_GRANT; Name: I2B2DEMODATA
 --
+GRANT UNLIMITED TABLESPACE TO "I2B2DEMODATA";
 GRANT CREATE SESSION TO "I2B2DEMODATA";
-
 --
 -- Type: TABLESPACE_QUOTA; Name: I2B2DEMODATA
 --
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "I2B2DEMODATA" QUOTA UNLIMITED ON "TRANSMART"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''TRANSMART'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "I2B2DEMODATA" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
 --
 -- Type: ROLE_GRANT; Name: I2B2DEMODATA
 --
 GRANT "CONNECT" TO "I2B2DEMODATA";
-
 GRANT "RESOURCE" TO "I2B2DEMODATA";
-
+GRANT "DBA" TO "I2B2DEMODATA";
diff --git a/ddl/oracle/GLOBAL/i2b2metadata.sql b/ddl/oracle/GLOBAL/i2b2metadata.sql
index 5bf7667c..8b34e91f 100644
--- a/ddl/oracle/GLOBAL/i2b2metadata.sql
+++ b/ddl/oracle/GLOBAL/i2b2metadata.sql
@@ -4,61 +4,17 @@
 CREATE USER "I2B2METADATA" IDENTIFIED BY VALUES 'S:C73A8B4E8B2A62D16A9AB6BA9B9C5980E37D87D05BB946D1C222BEF89011;61AA7B443983457E'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: ROLE_GRANT; Name: I2B2METADATA
 --
 GRANT "CONNECT" TO "I2B2METADATA";
-
 GRANT "RESOURCE" TO "I2B2METADATA";
-
+GRANT "DBA" TO "I2B2METADATA";
 --
 -- Type: TABLESPACE_QUOTA; Name: I2B2METADATA
 --
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "I2B2METADATA" QUOTA UNLIMITED ON "TRANSMART"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''TRANSMART'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "I2B2METADATA" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
 --
 -- Type: SYSTEM_GRANT; Name: I2B2METADATA
 --
+GRANT UNLIMITED TABLESPACE TO "I2B2METADATA";
 GRANT CREATE SESSION TO "I2B2METADATA";
-
diff --git a/ddl/oracle/GLOBAL/searchapp.sql b/ddl/oracle/GLOBAL/searchapp.sql
index b870560c..3148af49 100644
--- a/ddl/oracle/GLOBAL/searchapp.sql
+++ b/ddl/oracle/GLOBAL/searchapp.sql
@@ -10,8 +10,11 @@ CREATE USER "SEARCHAPP" IDENTIFIED BY VALUES 'S:57DA75ABEE5261239772396129231919
 --
 GRANT ON COMMIT REFRESH TO "SEARCHAPP";
 
-GRANT CREATE TABLE TO "SEARCHAPP";
+GRANT CREATE MATERIALIZED VIEW TO "SEARCHAPP";
+ 
 
+GRANT CREATE TABLE TO "SEARCHAPP";
+GRANT UNLIMITED TABLESPACE TO "SEARCHAPP";
 --
 -- Type: ROLE_GRANT; Name: SEARCHAPP
 --
@@ -19,48 +22,7 @@ GRANT "CONNECT" TO "SEARCHAPP";
 
 GRANT "RESOURCE" TO "SEARCHAPP";
 
+GRANT "DBA" TO "SEARCHAPP";
 --
 -- Type: TABLESPACE_QUOTA; Name: SEARCHAPP
 --
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "SEARCHAPP" QUOTA UNLIMITED ON "TRANSMART"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''TRANSMART'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "SEARCHAPP" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
diff --git a/ddl/oracle/GLOBAL/tm_cz.sql b/ddl/oracle/GLOBAL/tm_cz.sql
index 9aabe669..549c4649 100644
--- a/ddl/oracle/GLOBAL/tm_cz.sql
+++ b/ddl/oracle/GLOBAL/tm_cz.sql
@@ -4,7 +4,6 @@
 CREATE USER "TM_CZ" IDENTIFIED BY VALUES 'S:75081C84B645CEC6972544D98598A31EC0FC0EE20AD66BBF6A8C71430CA5;5DFF82A621539D10'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: TABLESPACE_QUOTA; Name: TM_CZ
 --
@@ -27,42 +26,193 @@ EXCEPTION
       RAISE;
     END IF;
 END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "TM_CZ" QUOTA UNLIMITED ON "TRANSMART"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''TRANSMART'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
 /
  
 --
 -- Type: SYSTEM_GRANT; Name: TM_CZ
 --
+GRANT FLASHBACK ARCHIVE ADMINISTER TO "TM_CZ";
+GRANT ADMINISTER SQL MANAGEMENT OBJECT TO "TM_CZ";
+GRANT UPDATE ANY CUBE DIMENSION TO "TM_CZ";
+GRANT UPDATE ANY CUBE BUILD PROCESS TO "TM_CZ";
+GRANT DROP ANY CUBE BUILD PROCESS TO "TM_CZ";
+GRANT CREATE ANY CUBE BUILD PROCESS TO "TM_CZ";
+GRANT CREATE CUBE BUILD PROCESS TO "TM_CZ";
+GRANT INSERT ANY MEASURE FOLDER TO "TM_CZ";
+GRANT DROP ANY MEASURE FOLDER TO "TM_CZ";
+GRANT DELETE ANY MEASURE FOLDER TO "TM_CZ";
+GRANT CREATE ANY MEASURE FOLDER TO "TM_CZ";
+GRANT CREATE MEASURE FOLDER TO "TM_CZ";
+GRANT UPDATE ANY CUBE TO "TM_CZ";
+GRANT SELECT ANY CUBE TO "TM_CZ";
+GRANT DROP ANY CUBE TO "TM_CZ";
+GRANT CREATE ANY CUBE TO "TM_CZ";
+GRANT ALTER ANY CUBE TO "TM_CZ";
+GRANT CREATE CUBE TO "TM_CZ";
+GRANT SELECT ANY CUBE DIMENSION TO "TM_CZ";
+GRANT INSERT ANY CUBE DIMENSION TO "TM_CZ";
+GRANT DROP ANY CUBE DIMENSION TO "TM_CZ";
+GRANT DELETE ANY CUBE DIMENSION TO "TM_CZ";
+GRANT CREATE ANY CUBE DIMENSION TO "TM_CZ";
+GRANT ALTER ANY CUBE DIMENSION TO "TM_CZ";
+GRANT CREATE CUBE DIMENSION TO "TM_CZ";
+GRANT COMMENT ANY MINING MODEL TO "TM_CZ";
+GRANT ALTER ANY MINING MODEL TO "TM_CZ";
+GRANT SELECT ANY MINING MODEL TO "TM_CZ";
+GRANT DROP ANY MINING MODEL TO "TM_CZ";
+GRANT CREATE ANY MINING MODEL TO "TM_CZ";
+GRANT CREATE MINING MODEL TO "TM_CZ";
+GRANT EXECUTE ASSEMBLY TO "TM_CZ";
+GRANT EXECUTE ANY ASSEMBLY TO "TM_CZ";
+GRANT DROP ANY ASSEMBLY TO "TM_CZ";
+GRANT ALTER ANY ASSEMBLY TO "TM_CZ";
+GRANT CREATE ANY ASSEMBLY TO "TM_CZ";
+GRANT CREATE ASSEMBLY TO "TM_CZ";
+GRANT ALTER ANY EDITION TO "TM_CZ";
+GRANT DROP ANY EDITION TO "TM_CZ";
+GRANT CREATE ANY EDITION TO "TM_CZ";
+GRANT CREATE EXTERNAL JOB TO "TM_CZ";
+GRANT CHANGE NOTIFICATION TO "TM_CZ";
+GRANT CREATE ANY SQL PROFILE TO "TM_CZ";
+GRANT ADMINISTER ANY SQL TUNING SET TO "TM_CZ";
+GRANT ADMINISTER SQL TUNING SET TO "TM_CZ";
+GRANT ALTER ANY SQL PROFILE TO "TM_CZ";
+GRANT DROP ANY SQL PROFILE TO "TM_CZ";
+GRANT SELECT ANY TRANSACTION TO "TM_CZ";
+GRANT MANAGE SCHEDULER TO "TM_CZ";
+GRANT EXECUTE ANY CLASS TO "TM_CZ";
+GRANT EXECUTE ANY PROGRAM TO "TM_CZ";
+GRANT CREATE ANY JOB TO "TM_CZ";
+GRANT CREATE JOB TO "TM_CZ";
+GRANT ADVISOR TO "TM_CZ";
+GRANT IMPORT FULL DATABASE TO "TM_CZ";
+GRANT EXPORT FULL DATABASE TO "TM_CZ";
+GRANT GRANT ANY OBJECT PRIVILEGE TO "TM_CZ";
+GRANT FLASHBACK ANY TABLE TO "TM_CZ";
+GRANT DEBUG ANY PROCEDURE TO "TM_CZ";
+GRANT DEBUG CONNECT SESSION TO "TM_CZ";
+GRANT RESUMABLE TO "TM_CZ";
+GRANT ON COMMIT REFRESH TO "TM_CZ";
+GRANT MERGE ANY VIEW TO "TM_CZ";
+GRANT ADMINISTER DATABASE TRIGGER TO "TM_CZ";
+GRANT DROP ANY OUTLINE TO "TM_CZ";
+GRANT ALTER ANY OUTLINE TO "TM_CZ";
+GRANT CREATE ANY OUTLINE TO "TM_CZ";
+GRANT DROP ANY CONTEXT TO "TM_CZ";
+GRANT CREATE ANY CONTEXT TO "TM_CZ";
+GRANT DROP ANY DIMENSION TO "TM_CZ";
+GRANT ALTER ANY DIMENSION TO "TM_CZ";
+GRANT CREATE ANY DIMENSION TO "TM_CZ";
+GRANT CREATE DIMENSION TO "TM_CZ";
+GRANT UNDER ANY TABLE TO "TM_CZ";
+GRANT EXECUTE ANY INDEXTYPE TO "TM_CZ";
+GRANT GLOBAL QUERY REWRITE TO "TM_CZ";
+GRANT QUERY REWRITE TO "TM_CZ";
+GRANT UNDER ANY VIEW TO "TM_CZ";
+GRANT DROP ANY INDEXTYPE TO "TM_CZ";
+GRANT ALTER ANY INDEXTYPE TO "TM_CZ";
+GRANT CREATE ANY INDEXTYPE TO "TM_CZ";
+GRANT CREATE INDEXTYPE TO "TM_CZ";
+GRANT EXECUTE ANY OPERATOR TO "TM_CZ";
+GRANT DROP ANY OPERATOR TO "TM_CZ";
+GRANT ALTER ANY OPERATOR TO "TM_CZ";
+GRANT CREATE ANY OPERATOR TO "TM_CZ";
+GRANT CREATE OPERATOR TO "TM_CZ";
+GRANT EXECUTE ANY LIBRARY TO "TM_CZ";
+GRANT DROP ANY LIBRARY TO "TM_CZ";
+GRANT ALTER ANY LIBRARY TO "TM_CZ";
+GRANT CREATE ANY LIBRARY TO "TM_CZ";
+GRANT CREATE LIBRARY TO "TM_CZ";
+GRANT UNDER ANY TYPE TO "TM_CZ";
+GRANT EXECUTE ANY TYPE TO "TM_CZ";
+GRANT DROP ANY TYPE TO "TM_CZ";
+GRANT ALTER ANY TYPE TO "TM_CZ";
+GRANT CREATE ANY TYPE TO "TM_CZ";
+GRANT CREATE TYPE TO "TM_CZ";
+GRANT DROP ANY DIRECTORY TO "TM_CZ";
+GRANT CREATE ANY DIRECTORY TO "TM_CZ";
+GRANT DROP ANY MATERIALIZED VIEW TO "TM_CZ";
+GRANT ALTER ANY MATERIALIZED VIEW TO "TM_CZ";
+GRANT CREATE ANY MATERIALIZED VIEW TO "TM_CZ";
+GRANT CREATE MATERIALIZED VIEW TO "TM_CZ";
+ 
+GRANT GRANT ANY PRIVILEGE TO "TM_CZ";
+GRANT ANALYZE ANY TO "TM_CZ";
+GRANT ALTER RESOURCE COST TO "TM_CZ";
+GRANT DROP PROFILE TO "TM_CZ";
+GRANT ALTER PROFILE TO "TM_CZ";
+GRANT CREATE PROFILE TO "TM_CZ";
+GRANT DROP ANY TRIGGER TO "TM_CZ";
+GRANT ALTER ANY TRIGGER TO "TM_CZ";
+GRANT CREATE ANY TRIGGER TO "TM_CZ";
+GRANT CREATE TRIGGER TO "TM_CZ";
+GRANT EXECUTE ANY PROCEDURE TO "TM_CZ";
+GRANT DROP ANY PROCEDURE TO "TM_CZ";
+GRANT ALTER ANY PROCEDURE TO "TM_CZ";
+GRANT CREATE ANY PROCEDURE TO "TM_CZ";
+GRANT CREATE PROCEDURE TO "TM_CZ";
+GRANT FORCE ANY TRANSACTION TO "TM_CZ";
+GRANT FORCE TRANSACTION TO "TM_CZ";
+GRANT ALTER DATABASE TO "TM_CZ";
+GRANT AUDIT ANY TO "TM_CZ";
+GRANT ALTER ANY ROLE TO "TM_CZ";
+GRANT GRANT ANY ROLE TO "TM_CZ";
+GRANT DROP ANY ROLE TO "TM_CZ";
+GRANT CREATE ROLE TO "TM_CZ";
+GRANT DROP PUBLIC DATABASE LINK TO "TM_CZ";
+GRANT CREATE PUBLIC DATABASE LINK TO "TM_CZ";
+GRANT CREATE DATABASE LINK TO "TM_CZ";
+GRANT SELECT ANY SEQUENCE TO "TM_CZ";
+GRANT DROP ANY SEQUENCE TO "TM_CZ";
+GRANT ALTER ANY SEQUENCE TO "TM_CZ";
+GRANT CREATE ANY SEQUENCE TO "TM_CZ";
+GRANT CREATE SEQUENCE TO "TM_CZ";
+GRANT DROP ANY VIEW TO "TM_CZ";
+GRANT CREATE ANY VIEW TO "TM_CZ";
+GRANT CREATE VIEW TO "TM_CZ";
+GRANT DROP PUBLIC SYNONYM TO "TM_CZ";
+GRANT CREATE PUBLIC SYNONYM TO "TM_CZ";
+GRANT DROP ANY SYNONYM TO "TM_CZ";
+GRANT CREATE ANY SYNONYM TO "TM_CZ";
+GRANT CREATE SYNONYM TO "TM_CZ";
 GRANT DROP ANY INDEX TO "TM_CZ";
-
+GRANT ALTER ANY INDEX TO "TM_CZ";
 GRANT CREATE ANY INDEX TO "TM_CZ";
-
+GRANT DROP ANY CLUSTER TO "TM_CZ";
+GRANT ALTER ANY CLUSTER TO "TM_CZ";
+GRANT CREATE ANY CLUSTER TO "TM_CZ";
+GRANT CREATE CLUSTER TO "TM_CZ";
+GRANT DELETE ANY TABLE TO "TM_CZ";
+GRANT UPDATE ANY TABLE TO "TM_CZ";
+GRANT INSERT ANY TABLE TO "TM_CZ";
+GRANT SELECT ANY TABLE TO "TM_CZ";
+GRANT COMMENT ANY TABLE TO "TM_CZ";
+GRANT LOCK ANY TABLE TO "TM_CZ";
 GRANT DROP ANY TABLE TO "TM_CZ";
-
+GRANT BACKUP ANY TABLE TO "TM_CZ";
+GRANT ALTER ANY TABLE TO "TM_CZ";
+GRANT CREATE ANY TABLE TO "TM_CZ";
+GRANT CREATE TABLE TO "TM_CZ";
+GRANT DROP ROLLBACK SEGMENT TO "TM_CZ";
+GRANT ALTER ROLLBACK SEGMENT TO "TM_CZ";
+GRANT CREATE ROLLBACK SEGMENT TO "TM_CZ";
+GRANT DROP USER TO "TM_CZ";
+GRANT ALTER USER TO "TM_CZ";
+GRANT BECOME USER TO "TM_CZ";
+GRANT CREATE USER TO "TM_CZ";
+GRANT UNLIMITED TABLESPACE TO "TM_CZ";
+GRANT DROP TABLESPACE TO "TM_CZ";
+GRANT MANAGE TABLESPACE TO "TM_CZ";
+GRANT ALTER TABLESPACE TO "TM_CZ";
+GRANT CREATE TABLESPACE TO "TM_CZ";
+GRANT RESTRICTED SESSION TO "TM_CZ";
+GRANT ALTER SESSION TO "TM_CZ";
+GRANT CREATE SESSION TO "TM_CZ";
+GRANT AUDIT SYSTEM TO "TM_CZ";
+GRANT ALTER SYSTEM TO "TM_CZ";
 --
 -- Type: ROLE_GRANT; Name: TM_CZ
 --
 GRANT "CONNECT" TO "TM_CZ";
-
 GRANT "RESOURCE" TO "TM_CZ";
-
+GRANT "DBA" TO "TM_CZ";
diff --git a/ddl/oracle/GLOBAL/tm_lz.sql b/ddl/oracle/GLOBAL/tm_lz.sql
index 3a5b2580..a652fa18 100644
--- a/ddl/oracle/GLOBAL/tm_lz.sql
+++ b/ddl/oracle/GLOBAL/tm_lz.sql
@@ -4,59 +4,16 @@
 CREATE USER "TM_LZ" IDENTIFIED BY VALUES 'S:6F9B91291DD92132F98582AF777B6FE0AC75037237D6F3905CA5DE935E3E;61EBD96BB8F1822E'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: SYSTEM_GRANT; Name: TM_LZ
 --
+GRANT UNLIMITED TABLESPACE TO "TM_LZ";
 --
 -- Type: TABLESPACE_QUOTA; Name: TM_LZ
 --
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "TM_LZ" QUOTA UNLIMITED ON "TRANSMART"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''TRANSMART'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "TM_LZ" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
 --
 -- Type: ROLE_GRANT; Name: TM_LZ
 --
 GRANT "CONNECT" TO "TM_LZ";
-
 GRANT "RESOURCE" TO "TM_LZ";
-
+GRANT "DBA" TO "TM_LZ";
diff --git a/ddl/oracle/GLOBAL/tm_wz.sql b/ddl/oracle/GLOBAL/tm_wz.sql
index 2d453748..9474ea0e 100644
--- a/ddl/oracle/GLOBAL/tm_wz.sql
+++ b/ddl/oracle/GLOBAL/tm_wz.sql
@@ -4,59 +4,16 @@
 CREATE USER "TM_WZ" IDENTIFIED BY VALUES 'S:DA4EDB9C0E0DCCADB7B62185D4D3BFC6000ED28FA8A99F1AAD6BB5770299;4F6EDC12B7127966'
    DEFAULT TABLESPACE "TRANSMART"
    TEMPORARY TABLESPACE "TEMP";
-
 --
 -- Type: TABLESPACE_QUOTA; Name: TM_WZ
 --
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "TM_WZ" QUOTA UNLIMITED ON "TRANSMART"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''TRANSMART'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
-  DECLARE 
-  TEMP_COUNT NUMBER; 
-  SQLSTR VARCHAR2(200); 
-BEGIN 
-  SQLSTR := 'ALTER USER "TM_WZ" QUOTA UNLIMITED ON "INDX"';
-  EXECUTE IMMEDIATE SQLSTR;
-EXCEPTION 
-  WHEN OTHERS THEN
-    IF SQLCODE = -30041 THEN 
-      SQLSTR := 'SELECT COUNT(*) FROM USER_TABLESPACES 
-              WHERE TABLESPACE_NAME = ''INDX'' AND CONTENTS = ''TEMPORARY''';
-      EXECUTE IMMEDIATE SQLSTR INTO TEMP_COUNT;
-      IF TEMP_COUNT = 1 THEN RETURN; 
-      ELSE RAISE; 
-      END IF;
-    ELSE
-      RAISE;
-    END IF;
-END;
-/
- 
 --
 -- Type: SYSTEM_GRANT; Name: TM_WZ
 --
+GRANT UNLIMITED TABLESPACE TO "TM_WZ";
 --
 -- Type: ROLE_GRANT; Name: TM_WZ
 --
 GRANT "CONNECT" TO "TM_WZ";
-
 GRANT "RESOURCE" TO "TM_WZ";
-
+GRANT "DBA" TO "TM_WZ";

From 30554f53a716e0e01903a9b258489953bbff1f42 Mon Sep 17 00:00:00 2001
From: Peter Rice <p.rice@imperial.ac.uk>
Date: Tue, 12 Aug 2014 13:38:38 +0100
Subject: [PATCH 30/31] load_analysis was only on postgres

---
 samples/oracle/load_analysis.sh | 44 +++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100755 samples/oracle/load_analysis.sh

diff --git a/samples/oracle/load_analysis.sh b/samples/oracle/load_analysis.sh
new file mode 100755
index 00000000..80f89706
--- /dev/null
+++ b/samples/oracle/load_analysis.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+
+set -x
+set -e
+
+if [ -z "$KETTLE_HOME" ]; then
+	echo "KETTLE_HOME is not set"
+	exit 1
+fi
+if [ -z "$DATA_LOCATION" ]; then
+	echo "DATA_LOCATION is not set"
+	exit 1
+fi
+
+# $KETTLE_HOME should have been set by the caller
+export KETTLE_HOME
+
+# Should define ANALYSIS_DATA_FILENAME, ANALYSIS_FILENAME, COHORTS_FILENAME,
+# SAMPLES_FILENAME, STUDY_DATA_CATEGORY AND STUDY_DISPLAY_CATEGORY
+source $1
+
+# the ETL script insist on interpreting LOG_FILENAME as a relative path...
+if [ -h $DATA_LOCATION/logs ]; then
+	rm $DATA_LOCATION/logs
+fi
+ln -s `pwd`/logs $DATA_LOCATION/logs
+
+$KITCHEN -norep=Y                                                \
+-file=$KETTLE_JOBS/ETL.search.process_analysis_data.kjb          \
+-log=logs/search.process_analysis_data_$(date +"%Y%m%d%H%M").log \
+-param:DATA_LOCATION="$DATA_LOCATION"                            \
+-param:ANALYSIS_DATA_FILENAME="$ANALYSIS_DATA_FILENAME"          \
+-param:ANALYSIS_FILENAME="$ANALYSIS_FILENAME"                    \
+-param:COHORTS_FILENAME="$COHORTS_FILENAME"                      \
+-param:LOG_FILENAME=logs/search.process_analysis_data_e          \
+-param:SAMPLES_FILENAME="$SAMPLES_FILENAME"                      \
+-param:STUDY_ID="$STUDY_ID"                                      \
+-param:SORT_DIR=/tmp                                             \
+-param:STUDY_DATA_CATEGORY="$STUDY_DATA_CATEGORY"                \
+-param:STUDY_DISPLAY_CATEGORY="$STUDY_DISPLAY_CATEGORY"
+
+echo -e '\e[32mDONE\e[m Do not forget to reindex Solr'
+
+rm $DATA_LOCATION/logs

From 2fc5276d10b231e56d9acbc9711925b93c345ba1 Mon Sep 17 00:00:00 2001
From: Gustavo Lopes <glopes@nebm.ist.utl.pt>
Date: Wed, 13 Aug 2014 09:56:59 +0200
Subject: [PATCH 31/31] Fix syntax error in pg/gen_kettle_properties.php

---
 samples/postgres/gen_kettle_properties.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/samples/postgres/gen_kettle_properties.php b/samples/postgres/gen_kettle_properties.php
index c6dc8d45..d1f170a4 100644
--- a/samples/postgres/gen_kettle_properties.php
+++ b/samples/postgres/gen_kettle_properties.php
@@ -1,4 +1,4 @@
-<?php require __DIR__ . '/../../lib/php/env_helper.inc.php'
+<?php require __DIR__ . '/../../lib/php/env_helper.inc.php';
 function get($key, $default) {
 	return isset($_ENV[$key]) ? $_ENV[$key] : $default;
 }