Merge pull request #670 from kids-first/fix-biobank-contact

♻️ Refactor biobank_contact to be two columns
kids-first · Jun 6, 2024 · ef9eb9e · ef9eb9e
2 parents a470710 + 2859cc2
commit ef9eb9e
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Showing 5 changed files with 51 additions and 5 deletions.
diff --git a/dataservice/api/study/models.py b/dataservice/api/study/models.py
@@ -56,7 +56,11 @@ class Study(db.Model, Base):
                             doc='Link to attribution prose provided by dbGaP')
     release_status = db.Column(db.Text(),
                                doc='Release status of the study')
-    biobank_contact = db.Column(
+    biobank_name = db.Column(
+        db.Text(),
+        doc='Name of study biobank or source of specimens'
+    )
+    biobank_email = db.Column(
         db.Text(),
         doc='Email for study biobank or source of specimens'
     )

diff --git a/migrations/versions/f07d043290d0_fix_biobank_contact.py b/migrations/versions/f07d043290d0_fix_biobank_contact.py
@@ -0,0 +1,38 @@
+"""
+1.23.0
+
+Rename biobank_contact to biobank_email
+Add biobank_name column
+
+Revision ID: f07d043290d0
+Revises: 1f14248ec4cf
+Create Date: 2024-06-06 14:54:46.201004
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'f07d043290d0'
+down_revision = '1f14248ec4cf'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column(
+        'biobank_email', sa.Text(), nullable=True))
+    op.add_column('study', sa.Column('biobank_name', sa.Text(), nullable=True))
+    op.drop_column('study', 'biobank_contact')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column('biobank_contact',
+                  sa.TEXT(), autoincrement=False, nullable=True))
+    op.drop_column('study', 'biobank_name')
+    op.drop_column('study', 'biobank_email')
+    # ### end Alembic commands ###
diff --git a/tests/data.json b/tests/data.json
@@ -6,7 +6,8 @@
       "release_status": "Pending",
       "program": "Kids First",
       "domain": "Cancer",
-      "biobank_contact": "research@cbtn.org"
+      "biobank_name": "CBTN Biobank",
+      "biobank_email": "research@cbtn.org"
     },
     "/investigators": { "name": "Investigator_0", "external_id": "inv001" },
     "/study-files": {
@@ -153,7 +154,8 @@
         "short_code": "KF-ST0",
         "program": "Kids First",
         "domain": "Cancer",
-        "biobank_contact": "research@cbtn.org"
+        "biobank_name": "CBTN Biobank",
+        "biobank_email": "research@cbtn.org"
       },
       "invalid": []
     },

diff --git a/tests/study/test_study_models.py b/tests/study/test_study_models.py
@@ -165,7 +165,8 @@ def create_study(self):
             'short_name': 'S1',
             'version': 'v1',
             'release_status': 'Pending',
-            'biobank_contact': 'research@cbtn.org',
+            'biobank_name': 'CBTN Biobank',
+            'biobank_email': 'research@cbtn.org',
         }
         study = Study(**kwargs)
 

diff --git a/tests/study/test_study_resources.py b/tests/study/test_study_resources.py
@@ -216,7 +216,8 @@ def _make_study(self, include_nullables=True, **kwargs):
             'short_code': 'KF-ST0',
             'program': 'Kids First',
             'domain': 'Cancer',
-            'biobank_contact': 'research@cbtn.org',
+            'biobank_name': 'CBTN Biobank',
+            'biobank_email': 'research@cbtn.org',
         }
         body.update(kwargs)
         if include_nullables: