Merge branch 'master' into add_order_to_new_cases

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 58.1.9
+current_version = 59.2.1
 commit = True
 tag = True
 tag_name = v{new_version}

alembic/versions/2024_02_19_43eb680d6181_add_order_case_table.py

@@ -0,0 +1,32 @@
+"""Add order case table
+
+Revision ID: 43eb680d6181
+Revises: d241d8c493fb
+Create Date: 2024-02-19 10:13:21.075891
+
+"""
+
+import sqlalchemy as sa
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "43eb680d6181"
+down_revision = "d241d8c493fb"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.create_table(
+        "order_case",
+        sa.Column("order_id", sa.Integer, nullable=False, index=True),
+        sa.Column("case_id", sa.Integer, nullable=False, index=True),
+        sa.ForeignKeyConstraint(["order_id"], ["order.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["case_id"], ["case.id"], ondelete="CASCADE"),
+        sa.UniqueConstraint("order_id", "case_id", name="_order_case_uc"),
+    )
+
+
+def downgrade():
+    op.drop_table(table_name="order_case")

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "58.1.9"
+__version__ = "59.2.1"

cg/apps/demultiplex/demultiplex_api.py

@@ -209,7 +209,7 @@ def add_to_trailblazer(
             out_dir=flow_cell.trailblazer_config_path.parent.as_posix(),
             slurm_quality_of_service=self.slurm_quality_of_service,
             email=self.mail,
-            data_analysis=Workflow.DEMULTIPLEX,
+            workflow=Workflow.DEMULTIPLEX,
         )
 
     def start_demultiplexing(self, flow_cell: FlowCellDirectoryData):

cg/apps/tb/api.py

@@ -13,7 +13,7 @@
 from cg.constants.constants import APIMethods, FileFormat, JobType, WorkflowManager
 from cg.constants.priority import SlurmQos
 from cg.constants.tb import AnalysisStatus
-from cg.exc import TrailblazerAPIHTTPError, TrailblazerAnalysisNotFound
+from cg.exc import TrailblazerAnalysisNotFound, TrailblazerAPIHTTPError
 from cg.io.controller import APIRequest, ReadStream
 
 LOG = logging.getLogger(__name__)
@@ -109,7 +109,7 @@ def add_pending_analysis(
         out_dir: str,
         slurm_quality_of_service: SlurmQos,
         email: str = None,
-        data_analysis: Workflow = None,
+        workflow: Workflow = None,
         ticket: str = None,
         workflow_manager: str = WorkflowManager.Slurm,
     ) -> TrailblazerAnalysis:
@@ -120,13 +120,14 @@ def add_pending_analysis(
             "config_path": config_path,
             "out_dir": out_dir,
             "priority": slurm_quality_of_service,
-            "data_analysis": str(data_analysis).upper(),
+            "workflow": workflow.upper(),
             "ticket": ticket,
             "workflow_manager": workflow_manager,
         }
         LOG.debug(f"Submitting job to Trailblazer: {request_body}")
-        response = self.query_trailblazer(command="add-pending-analysis", request_body=request_body)
-        if response:
+        if response := self.query_trailblazer(
+            command="add-pending-analysis", request_body=request_body
+        ):
             return TrailblazerAnalysis.model_validate(response)
 
     def set_analysis_uploaded(self, case_id: str, uploaded_at: datetime) -> None:

cg/apps/tb/models.py

@@ -24,7 +24,7 @@ class TrailblazerAnalysis(BaseModel):
     type: str | None = None
     user_id: int | None = None
     progress: float | None = 0.0
-    data_analysis: str | None = None
+    workflow: str | None = None
     ticket: str | None = None
     uploaded_at: str | None = None
 

cg/cli/backup.py

@@ -169,7 +169,7 @@ def archive_spring_files(config: CGConfig, context: click.Context, dry_run: bool
     LOG.info("Getting all spring files from Housekeeper.")
     spring_files: Iterable[hk_models.File] = housekeeper_api.files(
         tags=[SequencingFileTag.SPRING]
-    ).filter(hk_models.File.path.like(f"%{config.environment}/{config.demultiplex.out_dir}%"))
+    ).filter(hk_models.File.path.contains(f"{config.environment}/{config.demultiplex.out_dir}"))
     for spring_file in spring_files:
         LOG.info(f"Attempting encryption and PDC archiving for file {spring_file.path}")
         if Path(spring_file.path).exists():

cg/cli/upload/clinical_delivery.py

@@ -73,7 +73,7 @@ def upload_clinical_delivery(context: click.Context, case_id: str, dry_run: bool
             config_path=rsync_api.trailblazer_config_path.as_posix(),
             out_dir=rsync_api.log_dir.as_posix(),
             slurm_quality_of_service=Priority.priority_to_slurm_qos().get(case.priority),
-            data_analysis=Workflow.RSYNC,
+            workflow=Workflow.RSYNC,
             ticket=case.latest_ticket,
         )
         trailblazer_api.add_upload_job_to_analysis(analysis_id=analysis.id, slurm_id=job_id)

cg/cli/workflow/fastq/fastq_service.py

@@ -38,10 +38,10 @@ def _add_analysis_to_trailblazer(self, case: Case) -> None:
         self.trailblazer_api.add_pending_analysis(
             case_id=case.internal_id,
             analysis_type=AnalysisType.OTHER,
-            data_analysis=Workflow.FASTQ,
             config_path="",
             out_dir="",
             slurm_quality_of_service=case.slurm_priority,
+            workflow=Workflow.FASTQ,
             ticket=case.latest_ticket,
         )
         self.trailblazer_api.set_analysis_status(

cg/constants/delivery.py

@@ -138,13 +138,14 @@
     {"fastq"},
 ]
 
-SARSCOV2_ANALYSIS_CASE_TAGS: list[set[str]] = [
+MUTANT_ANALYSIS_CASE_TAGS: list[set[str]] = [
     {"pangolin"},
     {"ks-delivery"},
 ]
 
-SARSCOV2_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
+MUTANT_ANALYSIS_SAMPLE_TAGS: list[set[str]] = [
     {"fastq"},
+    {"vcf", "vcf-report", "fohm-delivery"},
 ]
 
 RNAFUSION_ANALYSIS_CASE_TAGS: list[set[str]] = [
@@ -198,8 +199,8 @@
         "sample_tags": FASTQ_ANALYSIS_SAMPLE_TAGS,
     },
     Workflow.MUTANT: {
-        "case_tags": SARSCOV2_ANALYSIS_CASE_TAGS,
-        "sample_tags": SARSCOV2_ANALYSIS_SAMPLE_TAGS,
+        "case_tags": MUTANT_ANALYSIS_CASE_TAGS,
+        "sample_tags": MUTANT_ANALYSIS_SAMPLE_TAGS,
     },
     Workflow.RNAFUSION: {
         "case_tags": RNAFUSION_ANALYSIS_CASE_TAGS,

cg/meta/rsync/rsync_api.py

@@ -136,7 +136,7 @@ def add_to_trailblazer_api(
             out_dir=self.log_dir.as_posix(),
             slurm_quality_of_service=self.slurm_quality_of_service,
             email=self.mail_user,
-            data_analysis=Workflow.RSYNC,
+            workflow=Workflow.RSYNC,
             ticket=ticket,
         )
 

cg/meta/workflow/analysis.py

@@ -209,14 +209,14 @@ def add_pending_trailblazer_analysis(self, case_id: str) -> None:
         self.check_analysis_ongoing(case_id)
         self.trailblazer_api.add_pending_analysis(
             case_id=case_id,
-            email=environ_email(),
             analysis_type=self.get_application_type(
                 self.status_db.get_case_by_internal_id(case_id).links[0].sample
             ),
-            out_dir=self.get_job_ids_path(case_id).parent.as_posix(),
             config_path=self.get_job_ids_path(case_id).as_posix(),
+            out_dir=self.get_job_ids_path(case_id).parent.as_posix(),
             slurm_quality_of_service=self.get_slurm_qos_for_case(case_id),
-            data_analysis=str(self.workflow),
+            email=environ_email(),
+            workflow=self.workflow,
             ticket=self.status_db.get_latest_ticket_from_case(case_id),
             workflow_manager=self.get_workflow_manager(),
         )

cg/meta/workflow/microsalt/microsalt.py

@@ -89,13 +89,21 @@ def get_config_path(self, filename: str) -> Path:
 
     def get_job_ids_path(self, case_id: str) -> Path:
         project_id: str = self.get_project_id(case_id)
-        return Path(
+        job_ids_path = Path(
             self.root_dir,
             "results",
             "reports",
             "trailblazer",
             f"{project_id}_slurm_ids{FileExtensions.YAML}",
         )
+        # Necessary due to how microsalt structures its output
+        self._ensure_old_job_ids_are_removed(job_ids_path)
+        return job_ids_path
+
+    def _ensure_old_job_ids_are_removed(self, job_ids_path: Path) -> None:
+        is_yaml_file: bool = job_ids_path.suffix == FileExtensions.YAML
+        if job_ids_path.exists() and is_yaml_file:
+            job_ids_path.unlink()
 
     def get_deliverables_file_path(self, case_id: str) -> Path:
         """Returns a path where the microSALT deliverables file for the order_id should be

cg/store/filters/status_case_filters.py

@@ -25,8 +25,8 @@ def filter_cases_by_case_search(cases: Query, case_search: str, **kwargs) -> Que
     return (
         cases.filter(
             or_(
-                Case.internal_id.like(f"%{case_search}%"),
-                Case.name.like(f"%{case_search}%"),
+                Case.internal_id.contains(case_search),
+                Case.name.contains(case_search),
             )
         )
         if case_search
@@ -58,7 +58,7 @@ def filter_case_by_internal_id(cases: Query, internal_id: str, **kwargs) -> Quer
 
 def filter_cases_by_internal_id_search(cases: Query, internal_id_search: str, **kwargs) -> Query:
     """Filter cases with internal ids matching the search pattern."""
-    return cases.filter(Case.internal_id.like(f"%{internal_id_search}%"))
+    return cases.filter(Case.internal_id.contains(internal_id_search))
 
 
 def filter_cases_by_name(cases: Query, name: str, **kwargs) -> Query:
@@ -68,12 +68,12 @@ def filter_cases_by_name(cases: Query, name: str, **kwargs) -> Query:
 
 def filter_cases_by_name_search(cases: Query, name_search: str, **kwargs) -> Query:
     """Filter cases with names matching the search pattern."""
-    return cases.filter(Case.name.like(f"%{name_search}%"))
+    return cases.filter(Case.name.contains(name_search))
 
 
 def filter_cases_by_workflow_search(cases: Query, workflow_search: str, **kwargs) -> Query:
     """Filter cases with a workflow search pattern."""
-    return cases.filter(Case.data_analysis.ilike(f"%{workflow_search}%"))
+    return cases.filter(Case.data_analysis.contains(workflow_search))
 
 
 def filter_cases_by_priority(cases: Query, priority: str, **kwargs) -> Query:

cg/store/filters/status_flow_cell_filters.py

@@ -18,7 +18,7 @@ def filter_flow_cell_by_name(flow_cells: Query, flow_cell_name: str, **kwargs) -
 
 def filter_flow_cell_by_name_search(flow_cells: Query, name_search: str, **kwargs) -> Query:
     """Return flow cell by flow cell id enquiry."""
-    return flow_cells.filter(Flowcell.name.like(f"%{name_search}%"))
+    return flow_cells.filter(Flowcell.name.contains(name_search))
 
 
 def filter_flow_cells_with_statuses(

cg/store/filters/status_pool_filters.py

@@ -13,12 +13,12 @@ def filter_pools_by_customer_id(pools: Query, customer_ids: list[int], **kwargs)
 
 def filter_pools_by_name_enquiry(pools: Query, name_enquiry: str, **kwargs) -> Query:
     """Return pools by name enquiry."""
-    return pools.filter(Pool.name.like(f"%{name_enquiry}%"))
+    return pools.filter(Pool.name.contains(name_enquiry))
 
 
 def filter_pools_by_order_enquiry(pools: Query, order_enquiry: str, **kwargs) -> Query:
     """Return pools by order enquiry."""
-    return pools.filter(Pool.order.like(f"%{order_enquiry}%"))
+    return pools.filter(Pool.order.contains(order_enquiry))
 
 
 def filter_pools_by_entry_id(pools: Query, entry_id: int, **kwargs) -> Query:

cg/store/filters/status_sample_filters.py

@@ -125,7 +125,7 @@ def filter_samples_by_internal_id_pattern(
     samples: Query, internal_id_pattern: str, **kwargs
 ) -> Query:
     """Return samples matching the internal id pattern."""
-    return samples.filter(Sample.internal_id.like(f"%{internal_id_pattern}%"))
+    return samples.filter(Sample.internal_id.contains(internal_id_pattern))
 
 
 def filter_samples_by_internal_id_or_name_search(
@@ -134,8 +134,8 @@ def filter_samples_by_internal_id_or_name_search(
     """Return samples matching the internal id or name search."""
     return samples.filter(
         or_(
-            Sample.name.like(f"%{search_pattern}%"),
-            Sample.internal_id.like(f"%{search_pattern}%"),
+            Sample.name.contains(search_pattern),
+            Sample.internal_id.contains(search_pattern),
         )
     )
 

cg/store/models.py

@@ -55,6 +55,14 @@ def to_dict(model_instance):
     UniqueConstraint("customer_id", "collaboration_id", name="_customer_collaboration_uc"),
 )
 
+order_case = Table(
+    "order_case",
+    Model.metadata,
+    Column("order_id", ForeignKey("order.id", ondelete="CASCADE"), nullable=False),
+    Column("case_id", ForeignKey("case.id", ondelete="CASCADE"), nullable=False),
+    UniqueConstraint("order_id", "case_id", name="_order_case_uc"),
+)
+
 
 class PriorityMixin:
     @property
@@ -403,6 +411,7 @@ class Case(Model, PriorityMixin):
 
     analyses = orm.relationship(Analysis, back_populates="case", order_by="-Analysis.completed_at")
     links = orm.relationship("CaseSample", back_populates="case")
+    orders = orm.relationship("Order", secondary=order_case, back_populates="cases")
 
     @property
     def cohorts(self) -> list[str]:
@@ -882,6 +891,7 @@ class Order(Model):
     __tablename__ = "order"
 
     id = Column(types.Integer, primary_key=True, unique=True)
+    cases = orm.relationship("Case", secondary=order_case, back_populates="orders")
     customer_id = Column(ForeignKey("customer.id"), nullable=False)
     customer = orm.relationship(Customer, foreign_keys=[customer_id])
     order_date = Column(types.DateTime, nullable=False, default=dt.datetime.now())

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "58.1.9"
+version = "59.2.1"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"

tests/meta/upload/scout/test_meta_upload_scoutapi_rna.py

@@ -580,7 +580,7 @@ def test_add_rna_sample(
     # GIVEN an RNA case and the associated RNA samples
     rna_case: Case = rna_store.get_case_by_internal_id(internal_id=rna_case_id)
     rna_sample_list: list[Sample] = (
-        rna_store._get_query(table=Sample).filter(Sample.internal_id.like("rna")).all()
+        rna_store._get_query(table=Sample).filter(Sample.internal_id.contains("rna")).all()
     )
 
     # WHEN running the method to create a list of RNADNACollections
@@ -590,9 +590,10 @@ def test_add_rna_sample(
     )
 
     # THEN the resulting RNADNACollections should contain all RNA samples in the case
+    assert rna_sample_list
     for sample in rna_sample_list:
         assert sample.internal_id in [
-            rna_dna_collection.rna_sample_id for rna_dna_collection in rna_dna_collections
+            rna_dna_collection.rna_sample_internal_id for rna_dna_collection in rna_dna_collections
         ]