♻️ Rename GenomicFile.release_status

dataservice/api/genomic_file/models.py

@@ -52,7 +52,7 @@ class GenomicFile(db.Model, Base, IndexdFile):
     to generate the file. For source files, this field should be NULL
     :param workflow_version:  Indicates the major version of the workflow. For
     source files, this field should be NULL
-    :param release_status: Indicates the release status
+    :param file_version_descriptor: Indicates the release status
     :param data_category: Type of data
     """
     __tablename__ = 'genomic_file'
@@ -87,7 +87,7 @@ class GenomicFile(db.Model, Base, IndexdFile):
         doc='Indicates the major version of the workflow. For source files, '
         ' this field should be NULL'
     )
-    release_status = db.Column(
+    file_version_descriptor = db.Column(
         db.Text(),
         doc='Inidicates release status'
     )

dataservice/api/genomic_file/schemas.py

@@ -162,7 +162,7 @@
     "Somatic-Mutation",
 }
 
-RELEASE_STATUS_ENUM = {
+FILE_VERSION_DESCRIPTOR_ENUM = {
     "latest",
     "previous",
     "unharmonized",
@@ -201,9 +201,9 @@ 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)
+    file_version_descriptor = field_for(
+        GenomicFile, 'file_version_descriptor',
+        validate=enum_validation_generator(FILE_VERSION_DESCRIPTOR_ENUM)
     )
 
     _links = ma.Hyperlinks({

migrations/versions/7cab6c9d8a24_rename_release_status.py

@@ -0,0 +1,31 @@
+"""
+1.19.0 Rename release_status to file_version_descriptor
+
+Revision ID: 7cab6c9d8a24
+Revises: 1dd6c503d77f
+Create Date: 2024-04-15 16:07:44.081102
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '7cab6c9d8a24'
+down_revision = '1dd6c503d77f'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('genomic_file', sa.Column('file_version_descriptor', sa.Text(), nullable=True))
+    op.drop_column('genomic_file', 'release_status')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('genomic_file', sa.Column('release_status', sa.TEXT(), autoincrement=False, nullable=True))
+    op.drop_column('genomic_file', 'file_version_descriptor')
+    # ### end Alembic commands ###

tests/data.json

@@ -114,7 +114,7 @@
       "workflow_type": "Alignment",
       "workflow_tool": "tool",
       "workflow_version": "v1",
-      "release_status": "latest",
+      "file_version_descriptor": "latest",
       "data_category": "foo",
       "visible": true
     },
@@ -282,7 +282,7 @@
         "paired_end": 1,
         "data_type": "Expression",
         "workflow_type": "Alignment",
-        "release_status": "latest"
+        "file_version_descriptor": "latest"
       },
       "invalid": [
         { "paired_end": -1 },
@@ -291,7 +291,7 @@
         { "availability": "availble for download" },
         { "data_type": "read" },
         { "workflow_type": "foo" },
-        { "release_status": "foo" }
+        { "file_version_descriptor": "foo" }
       ]
     },
     "/biospecimen-genomic-files": {

tests/genomic_file/test_genomic_file_models.py

@@ -52,7 +52,7 @@ def test_create_and_find(self):
                 'workflow_type': 'Alignment',
                 'workflow_tool': 'tool',
                 'workflow_version': 'v1',
-                'release_status': 'released',
+                'file_version_descriptor': 'released',
                 'data_category': 'foo',
             }
             # Add genomic file to db session

tests/genomic_file/test_genomic_file_resources.py

@@ -111,7 +111,7 @@ def test_new_validation_error(client, entities):
         'workflow_type': "Alignment",
         'workflow_tool': "tool",
         'workflow_version': "v1",
-        'release_status': "released",
+        'file_version_descriptor': "released",
         'data_category': "foo",
     }
     init_count = GenomicFile.query.count()