Merge pull request #556 from nf-osi/portal-pub-model-update-make-comp…

…ilation Update make step
nf-osi · Nov 25, 2024 · 91dc7db · 91dc7db
2 parents 430fe5a + 0389ac2
commit 91dc7db
Show file tree

Hide file tree

Showing 3 changed files with 26 additions and 46 deletions.
diff --git a/Makefile b/Makefile
@@ -44,7 +44,8 @@ Superdataset:
 	jq '.schema += input | del('.schema.required') | .schema["$$id"] = "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-superdataset"' registered-json-schemas/PortalDataset.json registered-json-schemas/super_rules.json > registered-json-schemas/Superdataset.json
 
 PortalPublication:
-	cat header.yaml modules/Template/PortalPublication.yaml > temp.yaml
+	cat header.yaml modules/Template/PortalPublication.yaml modules/Other/PublicationEnum.yaml > temp.yaml
 	gen-json-schema --top-class=PortalPublication --no-metadata --not-closed temp.yaml > tmp.json
 	jq '{ "$$schema": "http://json-schema.org/draft-07/schema#", "$$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portalpublication", PortalPublication: ."$$defs".PortalPublication }' tmp.json > registered-json-schemas/PortalPublication.json
 	rm tmp.json temp.yaml
+	@echo "--- Saved registered-json-schemas/PortalPublication.json ---"
diff --git a/modules/Template/PortalPublication.yaml b/modules/Template/PortalPublication.yaml
@@ -6,7 +6,6 @@
 
 classes:
   PublicationTemplate:
-    is_a: Template
     description: A generalized data model template for Publications to be hopefully used across dccs
     notes:
     - This structure is based on a CSV file from MC2 annotations with customized fields as attributes.
@@ -58,4 +57,4 @@ classes:
       dataset:
         range: string
         multivalued: true
-        required: false
+        required: false
diff --git a/registered-json-schemas/PortalPublication.json b/registered-json-schemas/PortalPublication.json
@@ -5,86 +5,66 @@
     "additionalProperties": false,
     "description": "A slightly more specialized publication concept intended for the specific scope of the NF Portal.",
     "properties": {
-      "component": {
+      "abstract": {
         "type": "string"
       },
-      "publicationAbstract": {
+      "accessibility": {
         "type": "string"
       },
-      "publicationAccessibility": {
-        "type": "string"
-      },
-      "publicationAssay": {
+      "assay": {
         "items": {
           "type": "string"
         },
         "type": "array"
       },
-      "publicationAuthors": {
+      "author": {
         "items": {
           "type": "string"
         },
         "type": "array"
       },
-      "publicationConsortiumName": {
-        "type": "string"
-      },
-      "publicationDatasetAlias": {
+      "dataset": {
         "items": {
           "type": "string"
         },
         "type": "array"
       },
-      "publicationDoi": {
-        "type": "string"
-      },
-      "publicationGrantNumber": {
-        "type": "string"
-      },
-      "publicationJournal": {
-        "type": "string"
-      },
-      "publicationKeywords": {
+      "diseaseFocus": {
         "items": {
           "type": "string"
         },
         "type": "array"
       },
-      "publicationThemeName": {
+      "doi": {
         "type": "string"
       },
-      "publicationTissue": {
+      "grantNumber": {
         "type": "string"
       },
-      "publicationTitle": {
+      "journal": {
         "type": "string"
       },
-      "publicationTumorType": {
+      "pmid": {
         "type": "string"
       },
-      "publicationYear": {
-        "type": "integer"
+      "studyUse": {},
+      "title": {
+        "type": "string"
       },
-      "pubmedId": {
+      "year": {
         "type": "integer"
-      },
-      "pubmedUrl": {
-        "type": "string"
       }
     },
     "required": [
-      "component",
-      "publicationGrantNumber",
-      "publicationConsortiumName",
-      "publicationThemeName",
-      "publicationDoi",
-      "publicationJournal",
-      "pubmedId",
-      "pubmedUrl",
-      "publicationTitle",
-      "publicationYear",
-      "publicationAbstract",
-      "publicationAccessibility"
+      "studyUse",
+      "grantNumber",
+      "doi",
+      "journal",
+      "pmid",
+      "title",
+      "year",
+      "abstract",
+      "accessibility"
     ],
     "title": "PortalPublication",
     "type": "object"