Merge remote-tracking branch 'origin/archiving-retrieve-ddn-files' in…

…to archiving-retrieve-ddn-files

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 52.1.2
+current_version = 52.1.3
 commit = True
 tag = True
 tag_name = v{new_version}

alembic/versions/2023_11_08_b105b426af99_rename_family_in_db.py

@@ -0,0 +1,67 @@
+"""Rename family in db
+
+Revision ID: b105b426af99
+Revises: 70e641d723b3
+Create Date: 2023-11-08 15:13:25.197537
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision = "b105b426af99"
+down_revision = "70e641d723b3"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # Drop foreign key constraints that reference the unique constraint to be dropped
+    op.drop_constraint("analysis_ibfk_1", "analysis", type_="foreignkey")
+    op.drop_constraint("family_sample_ibfk_1", "family_sample", type_="foreignkey")
+
+    # Rename tables
+    op.rename_table("family", "case")
+    op.rename_table("family_sample", "case_sample")
+
+    # Rename foreign keys
+    op.alter_column("analysis", "family_id", new_column_name="case_id", existing_type=sa.Integer())
+    op.alter_column(
+        "case_sample", "family_id", new_column_name="case_id", existing_type=sa.Integer()
+    )
+
+    # Drop the unique constraint
+    op.drop_constraint("_family_sample_uc", "case_sample", type_="unique")
+
+    # Create the new unique constraint
+    op.create_unique_constraint("_case_sample_uc", "case_sample", ["case_id", "sample_id"])
+
+    # Recreate foreign key constraints referencing the new unique constraint
+    op.create_foreign_key("analysis_ibfk_1", "analysis", "case", ["case_id"], ["id"])
+    op.create_foreign_key("case_sample_ibfk_1", "case_sample", "case", ["case_id"], ["id"])
+
+
+def downgrade():
+    # Drop foreign key constraints before renaming them back
+    op.drop_constraint("analysis_ibfk_1", "analysis", type_="foreignkey")
+    op.drop_constraint("case_sample_ibfk_1", "case_sample", type_="foreignkey")
+
+    # Drop the unique constraint
+    op.drop_constraint("_case_sample_uc", "case_sample", type_="unique")
+
+    # Rename foreign keys back to original before renaming tables
+    op.alter_column("analysis", "case_id", new_column_name="family_id", existing_type=sa.Integer())
+    op.alter_column(
+        "case_sample", "case_id", new_column_name="family_id", existing_type=sa.Integer()
+    )
+
+    # Rename tables back to original
+    op.rename_table("case", "family")
+    op.rename_table("case_sample", "family_sample")
+
+    # Recreate the original unique constraint
+    op.create_unique_constraint("_family_sample_uc", "family_sample", ["family_id", "sample_id"])
+
+    # Recreate foreign key constraints referencing the original unique constraint
+    op.create_foreign_key("analysis_ibfk_1", "analysis", "family", ["family_id"], ["id"])
+    op.create_foreign_key("family_sample_ibfk_1", "family_sample", "family", ["family_id"], ["id"])

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "52.1.2"
+__version__ = "52.1.3"

cg/cli/workflow/fastq/base.py

@@ -33,7 +33,7 @@ def store_fastq_analysis(context: click.Context, case_id: str, dry_run: bool = F
         completed_at=dt.datetime.now(),
         primary=True,
         started_at=dt.datetime.now(),
-        family_id=case_obj.id,
+        case_id=case_obj.id,
     )
     if dry_run:
         return

cg/server/admin.py

@@ -33,8 +33,8 @@ def view_priority(unused1, unused2, model, unused3):
     return Markup("%s" % model.priority.name) if model else ""
 
 
-def view_family_sample_link(unused1, unused2, model, unused3):
-    """column formatter to open the family-sample view"""
+def view_case_sample_link(unused1, unused2, model, unused3):
+    """column formatter to open the case-sample view"""
 
     del unused1, unused2, unused3
 
@@ -258,7 +258,7 @@ class CaseView(BaseView):
         "tickets",
     ]
     column_formatters = {
-        "internal_id": view_family_sample_link,
+        "internal_id": view_case_sample_link,
         "priority": view_priority,
     }
     column_searchable_list = [
@@ -279,7 +279,7 @@ class CaseView(BaseView):
     }
 
     @staticmethod
-    def view_family_link(unused1, unused2, model, unused3):
+    def view_case_link(unused1, unused2, model, unused3):
         """column formatter to open this view"""
         del unused1, unused2, unused3
         markup = ""
@@ -310,9 +310,9 @@ def action_set_empty(self, ids: list[str]):
     def set_action_for_cases(self, action: Union[CaseActions, None], case_entry_ids: list[str]):
         try:
             for entry_id in case_entry_ids:
-                family = db.get_case_by_entry_id(entry_id=entry_id)
-                if family:
-                    family.action = action
+                case = db.get_case_by_entry_id(entry_id=entry_id)
+                if case:
+                    case.action = action
 
             db.session.commit()
 
@@ -328,7 +328,7 @@ def set_action_for_cases(self, action: Union[CaseActions, None], case_entry_ids:
             if not self.handle_view_exception(ex):
                 raise
 
-            flash(gettext(f"Failed to set family action. {str(ex)}"))
+            flash(gettext(f"Failed to set case action. {str(ex)}"))
 
 
 class FlowcellView(BaseView):
@@ -392,7 +392,7 @@ class AnalysisView(BaseView):
     column_default_sort = ("created_at", True)
     column_editable_list = ["is_primary"]
     column_filters = ["pipeline", "pipeline_version", "is_primary"]
-    column_formatters = {"case": CaseView.view_family_link}
+    column_formatters = {"case": CaseView.view_case_link}
     column_searchable_list = [
         "case.internal_id",
         "case.name",
@@ -448,7 +448,7 @@ class SampleView(BaseView):
     column_filters = ["customer.internal_id", "priority", "sex", "application_version.application"]
     column_formatters = {
         "is_external": is_external_application,
-        "internal_id": view_family_sample_link,
+        "internal_id": view_case_sample_link,
         "invoice": InvoiceView.view_invoice_link,
         "priority": view_priority,
     }
@@ -570,7 +570,7 @@ class CaseSampleView(BaseView):
     column_editable_list = ["status"]
     column_filters = ["status"]
     column_formatters = {
-        "case": CaseView.view_family_link,
+        "case": CaseView.view_case_link,
         "sample": SampleView.view_sample_link,
     }
     column_searchable_list = ["case.internal_id", "case.name", "sample.internal_id"]

cg/store/api/base.py

@@ -92,7 +92,7 @@ def _get_subquery_with_latest_case_analysis_date(self) -> Query:
         case_and_date: Query = (
             self._get_join_analysis_case_query()
             .group_by(Case.id)
-            .with_entities(Analysis.family_id, func.max(Analysis.started_at).label("started_at"))
+            .with_entities(Analysis.case_id, func.max(Analysis.started_at).label("started_at"))
             .subquery()
         )
         return case_and_date
@@ -104,7 +104,7 @@ def _get_latest_analyses_for_cases_query(self) -> Query:
         return analyses.join(
             case_and_date_subquery,
             and_(
-                Analysis.family_id == case_and_date_subquery.c.family_id,
+                Analysis.case_id == case_and_date_subquery.c.case_id,
                 Analysis.started_at == case_and_date_subquery.c.started_at,
             ),
         )

cg/store/api/find_business_data.py

@@ -59,7 +59,7 @@ def has_active_cases_for_sample(self, internal_id: str) -> bool:
         active_actions = ["analyze", "running"]
 
         for family_sample in sample.links:
-            case: Case = self.get_case_by_entry_id(entry_id=family_sample.family_id)
+            case: Case = self.get_case_by_entry_id(entry_id=family_sample.case_id)
             if case.action in active_actions:
                 return True
 

cg/store/filters/status_analysis_filters.py

@@ -67,7 +67,7 @@ def order_analyses_by_uploaded_at_asc(analyses: Query, **kwargs) -> Query:
 
 def filter_analyses_by_case_entry_id(analyses: Query, case_entry_id: int, **kwargs) -> Query:
     """Return a query of analysis filtered by case entry id."""
-    return analyses.filter(Analysis.family_id == case_entry_id)
+    return analyses.filter(Analysis.case_id == case_entry_id)
 
 
 def filter_analyses_started_before(analyses: Query, started_at_date: datetime, **kwargs) -> Query:

cg/store/models.py

@@ -216,7 +216,7 @@ class Analysis(Model):
     is_primary = Column(types.Boolean, default=False)
 
     created_at = Column(types.DateTime, default=dt.datetime.now, nullable=False)
-    family_id = Column(ForeignKey("family.id", ondelete="CASCADE"), nullable=False)
+    case_id = Column(ForeignKey("case.id", ondelete="CASCADE"), nullable=False)
     uploaded_to_vogue_at = Column(types.DateTime, nullable=True)
 
     case = orm.relationship("Case", back_populates="analyses")
@@ -377,7 +377,7 @@ def to_dict(self):
 
 
 class Case(Model, PriorityMixin):
-    __tablename__ = "family"
+    __tablename__ = "case"
     __table_args__ = (UniqueConstraint("customer_id", "name", name="_customer_name_uc"),)
 
     action = Column(types.Enum(*CASE_ACTIONS))
@@ -516,11 +516,11 @@ def to_dict(self, links: bool = False, analyses: bool = False) -> dict:
 
 
 class CaseSample(Model):
-    __tablename__ = "family_sample"
-    __table_args__ = (UniqueConstraint("family_id", "sample_id", name="_family_sample_uc"),)
+    __tablename__ = "case_sample"
+    __table_args__ = (UniqueConstraint("case_id", "sample_id", name="_case_sample_uc"),)
 
     id = Column(types.Integer, primary_key=True)
-    family_id = Column(ForeignKey("family.id", ondelete="CASCADE"), nullable=False)
+    case_id = Column(ForeignKey("case.id", ondelete="CASCADE"), nullable=False)
     sample_id = Column(ForeignKey("sample.id", ondelete="CASCADE"), nullable=False)
     status = Column(types.Enum(*STATUS_OPTIONS), default="unknown", nullable=False)
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "52.1.2"
+version = "52.1.3"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"

tests/cli/workflow/fastq/test_fastq_base.py

@@ -23,7 +23,7 @@ def test_store_fastq_analysis(caplog, another_case_id: str, cli_runner, fastq_co
     assert (
         len(
             fastq_context.status_db._get_query(table=Analysis)
-            .filter(Analysis.family_id == case_obj.id)
+            .filter(Analysis.case_id == case_obj.id)
             .all()
         )
         > 0

tests/store_helpers.py

@@ -292,9 +292,7 @@ def add_analysis(
         if not case:
             case = StoreHelpers.add_case(store, data_analysis=pipeline, data_delivery=data_delivery)
 
-        analysis = store.add_analysis(
-            pipeline=pipeline, version=pipeline_version, family_id=case.id
-        )
+        analysis = store.add_analysis(pipeline=pipeline, version=pipeline_version, case_id=case.id)
 
         analysis.started_at = started_at or datetime.now()
         if completed_at: