Finalize changes

nf-osi · Nov 26, 2024 · dfcf96f · dfcf96f
1 parent e429341
commit dfcf96f
Show file tree

Hide file tree

Showing 8 changed files with 1,323 additions and 1,305 deletions.
diff --git a/.github/workflows/propagate.yml b/.github/workflows/propagate.yml
@@ -39,20 +39,4 @@ jobs:
       - name: Push to Synapse schema registry only JSON schemas that changed
         run: |
           CHANGED=$(git diff --name-only HEAD HEAD~1 registered-json-schemas)
-          for FILE in $CHANGED
-          do
-            REQUEST_BODY=$(jq '. + { concreteType: "org.sagebionetworks.repo.model.schema.CreateSchemaRequest", dryRun: false }' $FILE)
-            RESPONSE=$(curl -X POST https://repo-prod.prod.sagebase.org/repo/v1/schema/type/create/async/start \
-            -H "Authorization: Bearer $SYNAPSE_AUTH_TOKEN" \
-            -H "Content-Type: application/json" \
-            -d "$REQUEST_BODY")
-            
-            # Will error if token not within response
-            TOKEN=$( echo $RESPONSE | jq -e -r '.token')
-            sleep 1
-            STATUS=$(curl "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/create/async/get/$TOKEN" \
-            -H "Authorization: Bearer $SYNAPSE_AUTH_TOKEN")
-
-            echo $STATUS | jq -e '.newVersionInfo'
-          done
-
+          .github/workflows/register-schema.sh $CHANGED
diff --git a/Makefile b/Makefile
@@ -13,19 +13,10 @@ PortalDataset:
 	yq '.slots |= with_entries(select(.value.in_subset[] == "portal"))' modules/props.yaml > relevant_props.yaml
 	yq ea '. as $$item ireduce ({}; . * $$item )' modules/Data/Data.yaml modules/Assay/Assay.yaml modules/Sample/Species.yaml modules/DCC/Portal.yaml > relevant_enums.yaml
 	cat header.yaml relevant_props.yaml relevant_enums.yaml modules/Template/PortalDataset.yaml > temp.yaml
-	gen-json-schema --inline --no-metadata --not-closed temp.yaml > tmp.json
-	rm relevant_props.yaml relevant_enums.yaml temp.yaml
+	gen-json-schema --inline --no-metadata --title-from=title --not-closed temp.yaml > tmp.json
 	json-dereference -s tmp.json -o tmp.json
-	jq '{ schema: { "$$schema": "http://json-schema.org/draft-07/schema#", "$$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portaldataset", properties: ."$$defs".PortalDataset.properties, required: ."$$defs".PortalDataset.required }}' tmp.json > registered-json-schemas/PortalDataset.json
-	rm tmp.json
-# There is a LinkML bug that needs some titles to be adjusted manually
-	yq -iP '.schema.properties.accessType.title="accessType"' registered-json-schemas/PortalDataset.json -o json
-	yq -iP '.schema.properties.assay.title="assay"' registered-json-schemas/PortalDataset.json -o json
-	yq -iP '.schema.properties.dataType.title="dataType"' registered-json-schemas/PortalDataset.json -o json
-	yq -iP '.schema.properties.fundingAgency.title="fundingAgency"' registered-json-schemas/PortalDataset.json -o json
-	yq -iP '.schema.properties.license.title="license"' registered-json-schemas/PortalDataset.json -o json
-	yq -iP '.schema.properties.manifestation.title="manifestation"' registered-json-schemas/PortalDataset.json -o json
-	yq -iP '.schema.properties.species.title="species"' registered-json-schemas/PortalDataset.json -o json
+	jq '."$$defs".PortalDataset | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portaldataset"' tmp.json > registered-json-schemas/PortalDataset.json
+	rm -f relevant_props.yaml relevant_enums.yaml temp.yaml tmp.json
 	@echo "--- Saved registered-json-schemas/PortalDataset.json ---"
 
 
@@ -34,10 +25,9 @@ PortalStudy:
 	yq eval-all '. as $$item ireduce ({}; . * $$item )' modules/Data/Data.yaml modules/DCC/Portal.yaml modules/Other/Organization.yaml > relevant_enums.yaml
 	cat header.yaml relevant_enums.yaml modules/Template/PortalStudy.yaml > temp.yaml
 	gen-json-schema --inline --no-metadata --not-closed temp.yaml > tmp.json
-	rm relevant_enums.yaml temp.yaml
 	json-dereference -s tmp.json -o tmp.json
-	jq '{ schema: { "$$schema": "http://json-schema.org/draft-07/schema#", "$$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portalstudy", properties: ."$$defs".PortalStudy.properties, required: ."$$defs".PortalStudy.required }}' tmp.json > registered-json-schemas/PortalStudy.json
-	rm tmp.json
+	jq '."$$defs".PortalStudy | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portalstudy"' tmp.json > registered-json-schemas/PortalStudy.json
+	rm -f relevant_enums.yaml temp.yaml tmp.json
 	@echo "--- Saved registered-json-schemas/PortalStudy.json ---"
 
 Protocol:
@@ -46,12 +36,13 @@ Protocol:
 	cat header.yaml relevant_props.yaml relevant_enums.yaml modules/Template/Protocol.yaml > temp.yaml
 	gen-json-schema --inline --no-metadata --not-closed temp.yaml > tmp.json
 	json-dereference -s tmp.json -o tmp.json
-	jq '.["$$defs"].ProtocolTemplate' tmp.json > registered-json-schemas/Protocol.json
+	jq '."$$defs".Protocol | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-protocol"' tmp.json > registered-json-schemas/Protocol.json
 	rm -f relevant_props.yaml relevant_enums.yaml temp.yaml tmp.json 
 	@echo "--- Saved registered-json-schemas/Protocol.json ---"
 
 Superdataset:
-	jq '.schema += input | del('.schema.required') | .schema["$$id"] = "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-superdataset"' registered-json-schemas/PortalDataset.json registered-json-schemas/super_rules.json > registered-json-schemas/Superdataset.json
+	jq '. += input | del(.required) | ."$$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
+	@echo "--- Saved registered-json-schemas/Superdataset.json ---"
 
 PortalPublication:
 	yq ea '. as $$item ireduce ({}; . * $$item )' modules/DCC/Portal.yaml modules/Other/PublicationEnum.yaml > relevant_enums.yaml
@@ -61,3 +52,4 @@ PortalPublication:
 	jq '."$$defs".PortalPublication | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portalpublication"' tmp.json > registered-json-schemas/PortalPublication.json
 	rm -f tmp.json temp.yaml relevant_enums.yaml
 	@echo "--- Saved registered-json-schemas/PortalPublication.json ---"
+
diff --git a/modules/Template/PortalDataset.yaml b/modules/Template/PortalDataset.yaml
@@ -23,66 +23,82 @@ classes:
     # - datasetSizeInBytes 
     # - publisher # should be autoset
       title:
+        title: Title
         range: string
         required: true
       creator:
+        title: Creator
         range: string
         required: true
       contributor:
+        title: Contributor(s)
         range: string
         multivalued: true
         required: false
       description:
+        title: Description
         range: string
         required: false
       accessType:
-        title: accessType
+        title: Access Type
         range: AccessTypeEnum
         required: true
       license:
+        title: License
         range: License
         required: true
       assay:
-        title: assay
+        title: Assay
         range: AssayEnum
         required: false # not applicable for curated data, e.g. dataset of compounds from a database and then enhanced for machine learning or other exploration  
       dataType:
+        title: Data Type
         range: Data
         multivalued: true
         required: true
       species:
+        title: Species
         range: SpeciesEnum
         multivalued: true
         required: false # not all datasets from assays that use biological samples
       studyId:
+        title: Study ID
         range: string
         required: true
       manifestation:
+        title: Manifestation(s)
         range: ManifestationEnum
         multivalued: true
         required: false
       diseaseFocus:
+        title: Disease Focus
         range: DiseaseFocusEnum
         multivalued: true
         required: true
       fundingAgency:
+        title: Funding Agency
         range: FundingAgencyEnum
         multivalued: true
         required: true
       series:
+        title: Catalog Series
         range: string
         required: false
       visualizeDataOn:
+        title: Visualize Data On
         range: string
         multivalued: true
         required: false
       yearProcessed:
+        title: Year Processed
         range: integer
         required: false
       yearPublished:
+        title: Year Published
         range: integer
         required: false
       includedInDataCatalog:
+        title: Included In Data Catalog
         range: string
         required: false
 
diff --git a/modules/Template/Protocol.yaml b/modules/Template/Protocol.yaml
@@ -4,7 +4,7 @@ classes:
 # Protocols and other documents   
 #######################################
 
-  ProtocolTemplate:
+  Protocol:
     description: Template for describing a protocol document. 
     source: https://bioschemas.org/profiles/LabProtocol/0.7-DRAFT
     slots: