IP-3074 - Documentation discrepancies (#449)

* catalog referral model after changes * * Fixes describe in IP-3074 * Catalog Variable Set created * * typos * * version changed * * IndividualId changed to ParticipantId * TumourPresentation/PrimaryOrMetastatic moved to Tumour * * Fixes describe in IP-3074 * Catalog Variable Set created * * IndividualId changed to ParticipantId * TumourPresentation/PrimaryOrMetastatic moved to Tumour * removed unneeded spaces
genomicsengland · Mar 1, 2019 · ef067b9 · ef067b9
1 parent 3131301
commit ef067b9
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Showing 6 changed files with 45 additions and 43 deletions.
diff --git a/pom.xml b/pom.xml
@@ -7,7 +7,7 @@
 
     <groupId>org.gel.models</groupId>
     <artifactId>gel-models</artifactId>
-    <version>7.3.1b1</version>
+    <version>7.3.1b2</version>
     <packaging>${p.type}</packaging>
 
     <properties>

diff --git a/protocols/catalog_variable_set/v7.3/Referral.catalog_vs.json b/protocols/catalog_variable_set/v7.3/Referral.catalog_vs.json
@@ -379,8 +379,8 @@
       "multiValue": false, 
       "required": false, 
       "type": "TEXT", 
-      "name": "individualUid", 
-      "description": "In GMS, this is the individualUid of the sample"
+      "name": "participantId", 
+      "description": "Participant Id of the sample"
      }, 
      {
       "multiValue": false, 
@@ -2401,8 +2401,8 @@
       "multiValue": false, 
       "required": false, 
       "type": "TEXT", 
-      "name": "individualUid", 
-      "description": "In GMS, this is the individualUid of the sample"
+      "name": "participantId", 
+      "description": "Participant Id of the sample"
      }, 
      {
       "multiValue": false, 
@@ -2843,6 +2843,31 @@
       "type": "TEXT", 
       "name": "tumourPrognosticScore", 
       "description": "Prognostic Score of the Tumour"
+     }, 
+     {
+      "name": "tumourPresentation", 
+      "required": false, 
+      "allowedValues": [
+       "FIRST_PRESENTATION", 
+       "RECURRENCE", 
+       "UNKNOWN"
+      ], 
+      "multiValue": false, 
+      "type": "CATEGORICAL", 
+      "description": "In GMS, tumour presentation"
+     }, 
+     {
+      "name": "primaryOrMetastatic", 
+      "required": false, 
+      "allowedValues": [
+       "PRIMARY", 
+       "METASTATIC", 
+       "UNKNOWN", 
+       "NOT_APPLICABLE"
+      ], 
+      "multiValue": false, 
+      "type": "CATEGORICAL", 
+      "description": "In GMS, primary or metastatic"
      }
     ], 
     "type": "OBJECT", 
@@ -2900,31 +2925,6 @@
     ], 
     "type": "OBJECT", 
     "description": "In GMS, any previous treatment recorded in TOMs"
-   }, 
-   {
-    "name": "tumourPresentation", 
-    "required": false, 
-    "allowedValues": [
-     "FIRST_PRESENTATION", 
-     "RECURRENCE", 
-     "UNKNOWN"
-    ], 
-    "multiValue": false, 
-    "type": "CATEGORICAL", 
-    "description": "In GMS, tumour presentation"
-   }, 
-   {
-    "name": "primaryOrMetastatic", 
-    "required": false, 
-    "allowedValues": [
-     "PRIMARY", 
-     "METASTATIC", 
-     "UNKNOWN", 
-     "NOT_APPLICABLE"
-    ], 
-    "multiValue": false, 
-    "type": "CATEGORICAL", 
-    "description": "In GMS, primary or metastatic"
    }
   ], 
   "type": "OBJECT", 

diff --git a/protocols/catalog_variable_set/v7.3/TumourSample.catalog_vs.json b/protocols/catalog_variable_set/v7.3/TumourSample.catalog_vs.json
@@ -258,8 +258,8 @@
   "multiValue": false, 
   "required": false, 
   "type": "TEXT", 
-  "name": "individualUid", 
-  "description": "In GMS, this is the individualUid of the sample"
+  "name": "participantId", 
+  "description": "Participant Id of the sample"
  }, 
  {
   "multiValue": false, 

diff --git a/schemas/IDLs/org.gel.models.participant.avro/1.2.0/CancerParticipant.avdl b/schemas/IDLs/org.gel.models.participant.avro/1.2.0/CancerParticipant.avdl
@@ -87,6 +87,16 @@ protocol CancerParticipants {
         */
         union {null, string} tumourPrognosticScore;
 
+        /**
+        In GMS, tumour presentation
+        */
+        union {null, TumourPresentation} tumourPresentation;
+
+        /**
+        In GMS, primary or metastatic
+        */
+        union {null, PrimaryOrMetastatic} primaryOrMetastatic;
+
     }
 
 
@@ -193,14 +203,6 @@ protocol CancerParticipants {
         */
         union {null, array<PreviousTreatment>} previousTreatment;
 
-        /**
-        In GMS, tumour presentation
-        */
-        union {null, TumourPresentation} tumourPresentation;
 
-        /**
-        In GMS, primary or metastatic
-        */
-        union {null, PrimaryOrMetastatic} primaryOrMetastatic;
     }
 }
diff --git a/schemas/IDLs/org.gel.models.participant.avro/1.2.0/CommonParticipant.avdl b/schemas/IDLs/org.gel.models.participant.avro/1.2.0/CommonParticipant.avdl
@@ -643,9 +643,9 @@ protocol CommonParticipant {
         union {null, string} sampleUid;
 
     /**
-        In GMS, this is the individualUid of the sample
+        Participant Id of the sample
         */
-        union {null, string} individualUid;
+        union {null, string} participantId;
 
     /**
         In GMS, this is the maskedPID

diff --git a/setup.py b/setup.py
@@ -25,7 +25,7 @@
 else:
     raise ValueError("Not supported python version {}".format(target_version))
 
-VERSION = "7.3.1b1"
+VERSION = "7.3.1b2"
 setup(
     name='GelReportModels',
     version=VERSION,