Merge pull request thehyve#29 from transmart/london_hackathon

Merge london_hackathon branch into master branch

.gitignore

@@ -2,5 +2,5 @@
 *.iml
 /.idea
 /vars
-/vars-ubuntu
+/vars-*
 /private-feeds

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 \

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.
 

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'
 }

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/

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') ?>

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' \

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') ?>

data/postgres/Makefile

@@ -11,19 +11,9 @@ row_counts:
 analyze:
 	$(PSQL_COMMAND) -c 'ANALYZE VERBOSE'
 
-BIOMART_PSW ?= biomart
-DEAPP_PSW ?= deapp
-SEARCHAPP_PSW ?= 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 "deapp_username=deapp" >> $@ \
-	&& echo "deapp_password=$(DEAPP_PSW)" >> $@ \
-	&& echo "searchapp_username=searchapp" >> $@ \
-	&& echo "searchapp_password=$(SEARCHAPP_PSW)" >> $@
+$(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:

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";

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";
 

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";
-

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";