Merge pull request #465 from bento-platform/patch/phenopacket-version…

…-validation patch: validate phenopacket version string to be 2.0 only
bento-platform · Dec 22, 2023 · c4785df · c4785df
2 parents 4d153a5 + 5e81fcf
commit c4785df
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Showing 7 changed files with 849 additions and 849 deletions.
diff --git a/chord_metadata_service/chord/tests/example_multiple_phenopackets.json b/chord_metadata_service/chord/tests/example_multiple_phenopackets.json
@@ -53,7 +53,7 @@
           "iri_prefix": "https://ncit.nci.nih.gov"
         }
       ],
-      "phenopacket_schema_version": "2.0.0"
+      "phenopacket_schema_version": "2.0"
     }
   },
   {
@@ -84,7 +84,7 @@
     "meta_data": {
       "created_by": "Admin",
       "submitted_by": "Admin",
-      "phenopacket_schema_version": "2.0.0",
+      "phenopacket_schema_version": "2.0",
       "resources": [
         {
           "id": "NCBITaxon:2018-07-27",
@@ -141,7 +141,7 @@
     "meta_data": {
       "created_by": "Admin",
       "submitted_by": "Admin",
-      "phenopacket_schema_version": "2.0.0",
+      "phenopacket_schema_version": "2.0",
       "resources": [
         {
           "id": "NCBITaxon:2018-07-27",
@@ -194,7 +194,7 @@
     "meta_data": {
       "created_by": "Admin",
       "submitted_by": "Admin",
-      "phenopacket_schema_version": "2.0.0",
+      "phenopacket_schema_version": "2.0",
       "resources": [
         {
           "id": "NCBITaxon:2018-07-27",
@@ -253,7 +253,7 @@
     "meta_data": {
       "created_by": "Admin",
       "submitted_by": "Admin",
-      "phenopacket_schema_version": "2.0.0",
+      "phenopacket_schema_version": "2.0",
       "resources": [
         {
           "id": "NCBITaxon:2018-07-27",
@@ -303,7 +303,7 @@
     "meta_data": {
       "created_by": "Admin",
       "submitted_by": "Admin",
-      "phenopacket_schema_version": "2.0.0",
+      "phenopacket_schema_version": "2.0",
       "resources": [
         {
           "id": "NCBITaxon:2018-07-27",
@@ -351,7 +351,7 @@
     "meta_data": {
       "created_by": "Admin",
       "submitted_by": "Admin",
-      "phenopacket_schema_version": "2.0.0",
+      "phenopacket_schema_version": "2.0",
       "resources": [
         {
           "id": "NCBITaxon:2018-07-27",

diff --git a/chord_metadata_service/chord/tests/example_phenopacket_2_v2.json b/chord_metadata_service/chord/tests/example_phenopacket_2_v2.json
@@ -227,7 +227,7 @@
         "iri_prefix": "http://purl.obolibrary.org/obo/NCIT_"
       }
     ],
-    "phenopacket_schema_version": "2.0.0",
+    "phenopacket_schema_version": "2.0",
     "external_references": [
       {
         "id": "PMID:29221636",

diff --git a/chord_metadata_service/chord/tests/example_phenopacket_v2.json b/chord_metadata_service/chord/tests/example_phenopacket_v2.json
@@ -501,7 +501,7 @@
         "iri_prefix": "http://purl.obolibrary.org/obo/NCIT_"
       }
     ],
-    "phenopacket_schema_version": "2.0.0",
+    "phenopacket_schema_version": "2.0",
     "external_references": [
       {
         "id": "PMID:29221636",

diff --git a/chord_metadata_service/experiments/tests/example_phenopackets.json b/chord_metadata_service/experiments/tests/example_phenopackets.json
@@ -48,7 +48,7 @@
           "iri_prefix": "https://ncit.nci.nih.gov"
         }
       ],
-      "phenopacket_schema_version": "2.0.0"
+      "phenopacket_schema_version": "2.0"
     },
     "biosamples": [
         {
@@ -217,7 +217,7 @@
           "iri_prefix": "https://ncit.nci.nih.gov"
         }
       ],
-      "phenopacket_schema_version": "2.0.0"
+      "phenopacket_schema_version": "2.0"
     },
     "biosamples": [
         {
@@ -360,7 +360,7 @@
           "iri_prefix": "https://ncit.nci.nih.gov"
         }
       ],
-      "phenopacket_schema_version": "2.0.0"
+      "phenopacket_schema_version": "2.0"
     },
     "biosamples": [
         {

diff --git a/chord_metadata_service/phenopackets/schemas.py b/chord_metadata_service/phenopackets/schemas.py
@@ -100,7 +100,7 @@
         "submitted_by": base_type(SCHEMA_TYPES.STRING),
         "resources": array_of(RESOURCE_SCHEMA),
         "updates": array_of(PHENOPACKET_UPDATE_SCHEMA),
-        "phenopacket_schema_version": enum_of(["2.0", "2.0.0"]),
+        "phenopacket_schema_version": enum_of(["2.0"]),
         "external_references": array_of(PHENOPACKET_EXTERNAL_REFERENCE_SCHEMA),
         "extra_properties": EXTRA_PROPERTIES_SCHEMA
     },

diff --git a/chord_metadata_service/phenopackets/tests/examples/covid.json b/chord_metadata_service/phenopackets/tests/examples/covid.json
@@ -357,7 +357,7 @@
       "namespacePrefix": "UCUM",
       "iriPrefix": "https://units-of-measurement.org/"
     }],
-    "phenopacketSchemaVersion": "2.0.0",
+    "phenopacketSchemaVersion": "2.0",
     "externalReferences": [{
       "id": "DOI:10.1016/j.jaccas.2020.04.001",
       "reference": "PMID:32292915",