Created prelim yaml file for PortalPublication (#542)

* Created prelim yaml file for PortalPublication * Rebuild NF.jsonld, json * Add compilation step * Created a parent publication model and an nf specific model. Anh nyuget edits were also incorporated * Rebuild NF.jsonld, json * Updated PortalPublication with new Enum for StudyUse * Rebuild NF.jsonld, json * fixed string vs int for pmid * Fixed string vs int for pmid * Rebuild NF.jsonld, json * Update make step * Rebuild NF.jsonld, json * Made requested changes to PortalPublication model, along with fixed typos * Rebuild NF.jsonld, json * Update Makefile, make final revisions, recompile * Rebuild NF.jsonld, json --------- Co-authored-by: nf-osi[bot] <[email protected]> Co-authored-by: Anh Nguyet Vu <[email protected]> Co-authored-by: Anh Nguyet Vu <[email protected]>
nf-osi · Nov 25, 2024 · 4c2a051 · 4c2a051
1 parent 15a0c13
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diff --git a/Makefile b/Makefile
@@ -43,3 +43,11 @@ PortalStudy:
 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:
+	yq ea '. as $$item ireduce ({}; . * $$item )' modules/DCC/Portal.yaml modules/Other/PublicationEnum.yaml > relevant_enums.yaml
+	cat header.yaml modules/Template/PortalPublication.yaml relevant_enums.yaml > temp.yaml
+	gen-json-schema --top-class=PortalPublication --no-metadata --not-closed --title-from=title temp.yaml > tmp.json
+	json-dereference -s tmp.json -o tmp.json
+	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/NF.jsonld b/NF.jsonld
@@ -755,6 +755,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:PublicationAccessibilityEnum",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "PublicationAccessibilityEnum",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "PublicationAccessibilityEnum",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Metadata",
             "@type": "rdfs:Class",
@@ -1095,6 +1112,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:PublicationTypeEnum",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "PublicationTypeEnum",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "PublicationTypeEnum",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Resource",
             "@type": "rdfs:Class",
@@ -34800,6 +34834,154 @@
             "sms:required": "sms:true",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:PublicationTemplate",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "A generalized data model template for Publications to be hopefully used across dccs",
+            "rdfs:label": "PublicationTemplate",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "PublicationTemplate",
+            "sms:required": "sms:false",
+            "sms:requiresDependency": [
+                {
+                    "@id": "bts:GrantNumber"
+                },
+                {
+                    "@id": "bts:Doi"
+                },
+                {
+                    "@id": "bts:Journal"
+                },
+                {
+                    "@id": "bts:Pmid"
+                },
+                {
+                    "@id": "bts:Title"
+                },
+                {
+                    "@id": "bts:Year"
+                },
+                {
+                    "@id": "bts:Author"
+                },
+                {
+                    "@id": "bts:Abstract"
+                },
+                {
+                    "@id": "bts:Accessibility"
+                }
+            ],
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:GrantNumber",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "GrantNumber",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "grantNumber",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Journal",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Journal",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "journal",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Pmid",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Pmid",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "pmid",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Year",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Year",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "year",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Abstract",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Abstract",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "abstract",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Accessibility",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Accessibility",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "accessibility",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:MassSpecAssayTemplate",
             "@type": "rdfs:Class",
@@ -36227,6 +36409,80 @@
             ],
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:PortalPublication",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "A slightly more specialized publication concept intended for the specific scope of the NF Portal.",
+            "rdfs:label": "PortalPublication",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:PublicationTemplate"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "PortalPublication",
+            "sms:required": "sms:false",
+            "sms:requiresDependency": [
+                {
+                    "@id": "bts:PublicationType"
+                },
+                {
+                    "@id": "bts:DiseaseFocus"
+                },
+                {
+                    "@id": "bts:Dataset"
+                },
+                {
+                    "@id": "bts:Manifestation"
+                },
+                {
+                    "@id": "bts:FundingAgency"
+                },
+                {
+                    "@id": "bts:StudyId"
+                },
+                {
+                    "@id": "bts:StudyName"
+                }
+            ],
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:PublicationType",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "PublicationType",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "publicationType",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Dataset",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Dataset",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "dataset",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:GenomicsAssayTemplateExtended",
             "@type": "rdfs:Class",
@@ -39699,6 +39955,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Secondary",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Secondary",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Secondary",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Braindevelopment",
             "@type": "rdfs:Class",
@@ -39835,6 +40108,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:RestrictedAccess",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "RestrictedAccess",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Restricted Access",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:ODC-ODbL",
             "@type": "rdfs:Class",
@@ -39971,6 +40261,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Primary",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Primary",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Primary",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:CC-BY",
             "@type": "rdfs:Class",

diff --git a/modules/Other/PublicationEnum.yaml b/modules/Other/PublicationEnum.yaml
@@ -0,0 +1,18 @@
+enums:
+  PublicationTypeEnum:
+    permissible_values:
+      Primary:
+        description: This publication is used as a primary publication for the dataset
+        meaning: 
+      Secondary:
+        description: This publication is used as a secondary publication for the dataset
+        meaning: 
+
+  PublicationAccessibilityEnum:
+    permissible_values:
+      Open Access:
+        description: This publication is open access
+        meaning: 
+      Restricted Access:
+        description: This publication is restricted access
+        meaning: