Merge branch 'master' into release-1.2.5-Beta

i2b2-tranSMART · May 25, 2016 · 7d096c7 · 7d096c7
2 parents c0d5c49 + c275749
commit 7d096c7
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Showing 12 changed files with 50 additions and 25 deletions.
diff --git a/config/Config-template.groovy b/config/Config-template.groovy
@@ -442,11 +442,11 @@ grails { plugin { springsecurity {
         grails.exceptionresolver.params.exclude = ['password', 'client_secret']
 
         def glowingBearRedirectUris = [
-                transmartURL - ~/transmart\/?$/ + '#/login',
+                transmartURL - ~/transmart\/?$/ + 'connections',
         ]
         if (transmartURL.startsWith('http://localhost:')) {
             // for dev, node reverse proxy runs on 8001
-            glowingBearRedirectUris << 'http://localhost:8001/#/login'
+            glowingBearRedirectUris << 'http://localhost:8001/connections'
         }
 
         oauthProvider {

diff --git a/ddl/oracle/deapp/de_qpcr_mirna_annotation.sql b/ddl/oracle/deapp/de_qpcr_mirna_annotation.sql
@@ -1,14 +1,17 @@
 --
 -- Type: TABLE; Owner: DEAPP; Name: DE_QPCR_MIRNA_ANNOTATION
 --
- CREATE TABLE "DEAPP"."DE_QPCR_MIRNA_ANNOTATION" 
-  (	"ID_REF" VARCHAR2(100 BYTE), 
-"PROBE_ID" VARCHAR2(100 BYTE), 
-"MIRNA_SYMBOL" VARCHAR2(100 BYTE), 
-"MIRNA_ID" VARCHAR2(100 BYTE), 
-"PROBESET_ID" NUMBER(38,0), 
-"ORGANISM" VARCHAR2(200 BYTE), 
-"GPL_ID" VARCHAR2(20 BYTE)
+ CREATE TABLE "DEAPP"."DE_QPCR_MIRNA_ANNOTATION"
+  (	"ID_REF" VARCHAR2(100 BYTE),
+"PROBE_ID" VARCHAR2(100 BYTE),
+"MIRNA_SYMBOL" VARCHAR2(100 BYTE),
+"MIRNA_ID" VARCHAR2(100 BYTE),
+"PROBESET_ID" NUMBER(38,0),
+"ORGANISM" VARCHAR2(200 BYTE),
+"GPL_ID" VARCHAR2(20 BYTE),
+ PRIMARY KEY ("PROBESET_ID")
+ USING INDEX
+ TABLESPACE "TRANSMART"  ENABLE
   ) SEGMENT CREATION IMMEDIATE
+NOCOMPRESS LOGGING
  TABLESPACE "TRANSMART" ;
-
diff --git a/ddl/oracle/deapp/de_subject_acgh_data.sql b/ddl/oracle/deapp/de_subject_acgh_data.sql
@@ -9,6 +9,7 @@
 "CHIP" FLOAT(126), 
 "SEGMENTED" FLOAT(126), 
 "FLAG" NUMBER(*,0), 
+"PROBHOMLOSS" FLOAT(126), 
 "PROBLOSS" FLOAT(126), 
 "PROBNORM" FLOAT(126), 
 "PROBGAIN" FLOAT(126), 

diff --git a/ddl/oracle/deapp/de_subject_mirna_data.sql b/ddl/oracle/deapp/de_subject_mirna_data.sql
@@ -1,15 +1,18 @@
 --
 -- Type: TABLE; Owner: DEAPP; Name: DE_SUBJECT_MIRNA_DATA
 --
- CREATE TABLE "DEAPP"."DE_SUBJECT_MIRNA_DATA" 
-  (	"TRIAL_SOURCE" VARCHAR2(200 BYTE), 
-"TRIAL_NAME" VARCHAR2(50 BYTE), 
-"ASSAY_ID" NUMBER(18,0), 
-"PATIENT_ID" NUMBER(18,0), 
-"RAW_INTENSITY" NUMBER, 
-"LOG_INTENSITY" NUMBER, 
-"PROBESET_ID" NUMBER(38,0), 
-"ZSCORE" NUMBER(18,9)
+ CREATE TABLE "DEAPP"."DE_SUBJECT_MIRNA_DATA"
+  (	"TRIAL_SOURCE" VARCHAR2(200 BYTE),
+"TRIAL_NAME" VARCHAR2(50 BYTE),
+"ASSAY_ID" NUMBER(18,0),
+"PATIENT_ID" NUMBER(18,0),
+"RAW_INTENSITY" NUMBER,
+"LOG_INTENSITY" NUMBER,
+"PROBESET_ID" NUMBER(38,0),
+"ZSCORE" NUMBER(18,9),
+ PRIMARY KEY ("ASSAY_ID", "PROBESET_ID")
+ USING INDEX
+ TABLESPACE "TRANSMART"  ENABLE
   ) SEGMENT CREATION IMMEDIATE
+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
@@ -8,6 +8,7 @@
 "CHIP" VARCHAR2(50 BYTE), 
 "SEGMENTED" VARCHAR2(50 BYTE), 
 "FLAG" VARCHAR2(50 BYTE), 
+"PROBHOMLOSS" VARCHAR2(50 BYTE), 
 "PROBLOSS" VARCHAR2(50 BYTE), 
 "PROBNORM" VARCHAR2(50 BYTE), 
 "PROBGAIN" VARCHAR2(50 BYTE), 

diff --git a/ddl/oracle/tm_wz/wt_subject_acgh_region.sql b/ddl/oracle/tm_wz/wt_subject_acgh_region.sql
@@ -7,6 +7,7 @@
 "CHIP" FLOAT(126), 
 "SEGMENTED" FLOAT(126), 
 "FLAG" NUMBER(*,0), 
+"PROBHOMLOSS" FLOAT(126), 
 "PROBLOSS" FLOAT(126), 
 "PROBNORM" FLOAT(126), 
 "PROBGAIN" FLOAT(126), 

diff --git a/ddl/postgres/deapp/de_qpcr_mirna_annotation.sql b/ddl/postgres/deapp/de_qpcr_mirna_annotation.sql
@@ -6,8 +6,14 @@ CREATE TABLE de_qpcr_mirna_annotation (
     probe_id character varying(100),
     mirna_symbol character varying(100),
     mirna_id character varying(100),
-    probeset_id numeric(38,0),
+    probeset_id numeric(38,0) NOT NULL,
     organism character varying(200),
     gpl_id character varying(20)
 );
 
+--
+-- Name: de_qpcr_mirna_annotation_pkey; Type: CONSTRAINT; Schema: deapp; Owner: -
+--
+ALTER TABLE ONLY de_qpcr_mirna_annotation
+    ADD CONSTRAINT de_qpcr_mirna_annotation_pkey PRIMARY KEY (probeset_id);
+
diff --git a/ddl/postgres/deapp/de_subject_acgh_data.sql b/ddl/postgres/deapp/de_subject_acgh_data.sql
@@ -9,6 +9,7 @@ CREATE TABLE de_subject_acgh_data (
     chip double precision,
     segmented double precision,
     flag smallint,
+    probhomloss double precision,
     probloss double precision,
     probnorm double precision,
     probgain double precision,
@@ -29,7 +30,7 @@ COMMENT ON COLUMN de_subject_acgh_data.segmented IS 'segmented log2ratio';
 --
 -- Name: COLUMN de_subject_acgh_data.flag; Type: COMMENT; Schema: deapp; Owner: -
 --
-COMMENT ON COLUMN de_subject_acgh_data.flag IS 'call  -1:loss, 0:normal, 1:gain, 2:amplification';
+COMMENT ON COLUMN de_subject_acgh_data.flag IS 'call  -2:homloss, -1:loss, 0:normal, 1:gain, 2:amp';
 
 --
 -- Name: de_subject_acgh_data_pkey; Type: CONSTRAINT; Schema: deapp; Owner: -

diff --git a/ddl/postgres/deapp/de_subject_mirna_data.sql b/ddl/postgres/deapp/de_subject_mirna_data.sql
@@ -4,12 +4,18 @@
 CREATE TABLE de_subject_mirna_data (
     trial_source character varying(200),
     trial_name character varying(50),
-    assay_id numeric(18,0),
+    assay_id numeric(18,0) NOT NULL,
     patient_id numeric(18,0),
     raw_intensity numeric,
     log_intensity numeric,
-    probeset_id numeric(38,0),
+    probeset_id numeric(38,0) NOT NULL,
     zscore numeric(18,9),
     partition_id numeric
 );
 
+--
+-- Name: de_subject_mirna_data_pkey; Type: CONSTRAINT; Schema: deapp; Owner: -
+--
+ALTER TABLE ONLY de_subject_mirna_data
+    ADD CONSTRAINT de_subject_mirna_data_pkey PRIMARY KEY (assay_id, probeset_id);
+
diff --git a/ddl/postgres/tm_lz/lt_src_acgh_data.sql b/ddl/postgres/tm_lz/lt_src_acgh_data.sql
@@ -8,6 +8,7 @@ CREATE TABLE lt_src_acgh_data (
     chip character varying(50),
     segmented character varying(50),
     flag character varying(50),
+    probhomloss character varying(50),
     probloss character varying(50),
     probnorm character varying(50),
     probgain character varying(50),

diff --git a/ddl/postgres/tm_wz/wt_subject_acgh_region.sql b/ddl/postgres/tm_wz/wt_subject_acgh_region.sql
@@ -7,6 +7,7 @@ CREATE TABLE wt_subject_acgh_region (
     chip double precision,
     segmented double precision,
     flag smallint,
+    probhomloss double precision,
     probloss double precision,
     probnorm double precision,
     probgain double precision,

diff --git a/samples/common/makefile.inc b/samples/common/makefile.inc
@@ -217,6 +217,7 @@ define TSBATCH_TEMPLATE
 	../../env/transmart-batch-capsule.jar \
 		-p '$$(realpath ../studies)/$$*/$(1).params' \
 		-c '$$(realpath ../../env)/$$(BATCH_PROPS)' \
+		-d 'STUDY_ID=$$*' \
 		$$(EXTRA_TSBATCH_ARGS)
 endef