Rm is uploaded to vogue (#2810) (major)

### Changed

- Remove uploaded to vogue from the database and models

alembic/versions/2023_12_27_584840c706a0_remove_uploaded_to_vogue_at.py

@@ -0,0 +1,24 @@
+"""remove_uploaded_to_vogue_at
+
+Revision ID: 584840c706a0
+Revises: 27ec5c4c0380
+Create Date: 2023-12-27 11:50:22.278213
+
+"""
+import sqlalchemy as sa
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "584840c706a0"
+down_revision = "27ec5c4c0380"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.drop_column("analysis", "uploaded_to_vogue_at")
+
+
+def downgrade():
+    op.add_column("analysis", sa.Column("uploaded_to_vogue_at", sa.DateTime(), nullable=True))

cg/store/models.py

@@ -218,7 +218,6 @@ class Analysis(Model):
 
     created_at = Column(types.DateTime, default=dt.datetime.now, 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")
 

tests/store/api/conftest.py

@@ -465,7 +465,6 @@ def store_with_analyses_for_cases(
             started_at=timestamp_yesterday,
             uploaded_at=timestamp_yesterday,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=timestamp_yesterday,
             completed_at=timestamp_yesterday,
         )
         helpers.add_analysis(
@@ -474,7 +473,6 @@ def store_with_analyses_for_cases(
             started_at=timestamp_now,
             uploaded_at=timestamp_now,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=None,
             completed_at=timestamp_now,
         )
         sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
@@ -505,7 +503,6 @@ def store_with_analyses_for_cases_not_uploaded_fluffy(
             started_at=timestamp_yesterday,
             uploaded_at=timestamp_yesterday,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=timestamp_yesterday,
             pipeline=Pipeline.FLUFFY,
         )
         helpers.add_analysis(
@@ -514,7 +511,6 @@ def store_with_analyses_for_cases_not_uploaded_fluffy(
             started_at=timestamp_now,
             uploaded_at=None,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=timestamp_now,
             pipeline=Pipeline.FLUFFY,
         )
         sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
@@ -545,7 +541,6 @@ def store_with_analyses_for_cases_not_uploaded_microsalt(
             started_at=timestamp_yesterday,
             uploaded_at=timestamp_yesterday,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=timestamp_yesterday,
             pipeline=Pipeline.MICROSALT,
         )
         helpers.add_analysis(
@@ -554,7 +549,6 @@ def store_with_analyses_for_cases_not_uploaded_microsalt(
             started_at=timestamp_now,
             uploaded_at=None,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=timestamp_now,
             pipeline=Pipeline.MICROSALT,
         )
         sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
@@ -584,7 +578,6 @@ def store_with_analyses_for_cases_to_deliver(
             started_at=timestamp_yesterday,
             uploaded_at=None,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=timestamp_yesterday,
             completed_at=timestamp_yesterday,
             pipeline=Pipeline.FLUFFY,
         )
@@ -594,7 +587,6 @@ def store_with_analyses_for_cases_to_deliver(
             started_at=timestamp_now,
             uploaded_at=None,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=None,
             completed_at=timestamp_now,
             pipeline=Pipeline.MIP_DNA,
         )

tests/store/conftest.py

@@ -401,7 +401,6 @@ def store_with_older_and_newer_analyses(
     """Return a store with  older and newer analyses."""
     analysis = base_store._get_query(table=Analysis).first()
     analysis.uploaded_at = timestamp_now
-    analysis.uploaded_to_vogue_at = timestamp_now
     analysis.cleaned_at = timestamp_now
     analysis.started_at = timestamp_now
     analysis.completed_at = timestamp_now
@@ -416,7 +415,6 @@ def store_with_older_and_newer_analyses(
             started_at=time,
             completed_at=time,
             uploaded_at=time,
-            uploaded_to_vogue_at=time,
             cleaned_at=time,
         )
 
@@ -442,15 +440,13 @@ def store_with_analyses_for_cases(
             started_at=timestamp_yesterday,
             uploaded_at=timestamp_yesterday,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=timestamp_yesterday,
         )
         helpers.add_analysis(
             analysis_store,
             case=case,
             started_at=timestamp_now,
             uploaded_at=timestamp_now,
             delivery_reported_at=None,
-            uploaded_to_vogue_at=timestamp_now,
         )
         sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
         link: CaseSample = analysis_store.relate_sample(

tests/store_helpers.py

@@ -322,7 +322,6 @@ def add_analysis(
         data_delivery: DataDelivery = DataDelivery.FASTQ_QC,
         uploading: bool = False,
         config_path: str = None,
-        uploaded_to_vogue_at: datetime = None,
     ) -> Analysis:
         """Utility function to add an analysis for tests."""
 
@@ -346,8 +345,6 @@ def add_analysis(
             analysis.config_path = config_path
         if pipeline:
             analysis.pipeline = str(pipeline)
-        if uploaded_to_vogue_at:
-            analysis.uploaded_to_vogue_at = uploaded_to_vogue_at
 
         analysis.limitations = "A limitation"
         analysis.case = case