Merge pull request #225 from VariantEffect/jstone-uw/ucsc-genome-browser-links

Data model for external links

Author: jstone-dev

alembic/versions/ec5d2787bec9_external_links.py

@@ -0,0 +1,24 @@
+"""External links
+
+Revision ID: ec5d2787bec9
+Revises: 7a345f1bf9c3
+Create Date: 2024-05-29 06:39:17.930675
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = 'ec5d2787bec9'
+down_revision = '7a345f1bf9c3'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.add_column("scoresets", sa.Column("external_links", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default='{}'))
+
+
+def downgrade():
+    op.drop_column("scoresets", "external_links")

src/mavedb/models/score_set.py

@@ -72,6 +72,7 @@ class ScoreSet(Base):
     short_description = Column(String, nullable=False)
     extra_metadata = Column(JSONB, nullable=False)
     dataset_columns = Column(JSONB, nullable=False, default={})
+    external_links = Column(JSONB, nullable=False, default={})
 
     normalised = Column(Boolean, nullable=False, default=False)
     private = Column(Boolean, nullable=False, default=True)

src/mavedb/view_models/score_set.py

@@ -34,6 +34,10 @@
 from mavedb.view_models.variant import VariantInDbBase
 
 
+class ExternalLink(BaseModel):
+    url: Optional[str]
+
+
 class ScoreSetGetter(PublicationIdentifiersGetter):
     def get(self, key: Any, default: Any = ...) -> Any:
         if key == "meta_analyzes_score_set_urns":
@@ -229,6 +233,7 @@ class SavedScoreSet(ScoreSetBase):
     modified_by: Optional[SavedUser]
     target_genes: Sequence[SavedTargetGene]
     dataset_columns: Dict
+    external_links: Dict[str, ExternalLink]
     keywords: list[str]
 
     class Config:
@@ -290,4 +295,4 @@ class ScoreSetPublicDump(SavedScoreSet):
     target_genes: Sequence[TargetGene]
     private: bool
     processing_state: Optional[ProcessingState]
-    processing_errors: Optional[dict]
+    processing_errors: Optional[Dict]

tests/helpers/constants.py

@@ -210,6 +210,7 @@
     "primaryPublicationIdentifiers": [],
     "secondaryPublicationIdentifiers": [],
     "datasetColumns": {},
+    "externalLinks": {},
     "private": True,
     "experiment": TEST_MINIMAL_EXPERIMENT_RESPONSE,
     # keys to be set after receiving response