Merge pull request #655 from kids-first/bix-enums

✨ Modify GenomicFile release_status, data_type enums
kids-first · Apr 12, 2024 · 8462709 · 8462709
2 parents 40a4a7a + 3d4d8c0
commit 8462709
Show file tree

Hide file tree

Showing 2 changed files with 33 additions and 4 deletions.
diff --git a/dataservice/api/genomic_file/schemas.py b/dataservice/api/genomic_file/schemas.py
@@ -130,7 +130,24 @@
     "Variant Calling Metrics",
     "Variant Summary",
     "WGS Metric",
-    "WXS Metric"}
+    "WXS Metric",
+    "Adapter Stats",
+    "Alignment Metrics",
+    "Alignment Stats",
+    "Artifact Metrics",
+    "Chimeric Aligned Reads",
+    "Cutadapter Metrics",
+    "GC Metrics",
+    "Gender Metrics",
+    "Gender QC Metrics",
+    "Genome Aligned Reads",
+    "Genome Aligned Reads Index",
+    "Het Call QC Metrics",
+    "Insert Size Metrics",
+    "QC Metrics",
+    "WGS Metrics",
+    "WXS Metrics",
+}
 
 PAIRED_END_ENUM = {1, 2}
 
@@ -145,6 +162,12 @@
     "Somatic-Mutation",
 }
 
+RELEASE_STATUS_ENUM = {
+    "latest",
+    "previous",
+    "unharmonized",
+}
+
 
 class GenomicFileSchema(BaseSchema, IndexdFileSchema):
     class Meta(BaseSchema.Meta, IndexdFileSchema.Meta):
@@ -178,6 +201,10 @@ class Meta(BaseSchema.Meta, IndexdFileSchema.Meta):
         GenomicFile, 'workflow_type',
         validate=enum_validation_generator(WORKFLOW_TYPE_ENUM)
     )
+    release_status = field_for(
+        GenomicFile, 'release_status',
+        validate=enum_validation_generator(RELEASE_STATUS_ENUM)
+    )
 
     _links = ma.Hyperlinks({
         'self': ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),

diff --git a/tests/data.json b/tests/data.json
@@ -114,7 +114,7 @@
       "workflow_type": "Alignment",
       "workflow_tool": "tool",
       "workflow_version": "v1",
-      "release_status": "released",
+      "release_status": "latest",
       "data_category": "foo",
       "visible": true
     },
@@ -281,15 +281,17 @@
         "controlled_access": true,
         "paired_end": 1,
         "data_type": "Expression",
-        "workflow_type": "Alignment"
+        "workflow_type": "Alignment",
+        "release_status": "latest"
       },
       "invalid": [
         { "paired_end": -1 },
         { "paired_end": "one" },
         { "controlled_access": "hello", "size": "hello" },
         { "availability": "availble for download" },
         { "data_type": "read" },
-        { "workflow_type": "foo" }
+        { "workflow_type": "foo" },
+        { "release_status": "foo" }
       ]
     },
     "/biospecimen-genomic-files": {