Merge branch 'master' into balsamic_v16

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 63.0.1
+current_version = 63.2.11
 commit = True
 tag = True
 tag_name = v{new_version}

.github/ISSUE_TEMPLATE/user-story.md

@@ -15,6 +15,22 @@ As a [type of user],
 I want [an action or feature],
 So that [benefit or reason].
 
+# Work impact
+<!--
+Filled in by the Product Owner or the Stakeholders.
+-->
+
+Answer the following questions:
+- Is there currently a workaround for this issue? If so, what is it?
+    - 
+- How much time would be saved by implementing this feature on a weekly basis?
+    - 
+- How many users are affected by this issue?
+    - 
+- Are customers affected by this issue?
+    - 
+
+
 # Acceptance Criteria
 <!--
 Filled in by the Product Owner or the Stakeholders.
@@ -32,12 +48,4 @@ Filled in by the Product Owner or the Stakeholders.
 
 - Additional information.
 - Dependencies.
-- Related user stories.
-
-# Implementation plan
-<!--
-This section will be populated by the developers during their technical refinements.
--->
-
-- [ ] Work item 1
-- [ ] Work item 2
+- Related user stories.

alembic/versions/2024_08_09_7770dcad8bde_rename_order_status.py

@@ -0,0 +1,50 @@
+"""Rename order status
+Revision ID: 7770dcad8bde
+Revises: bb4c6dbad991
+Create Date: 2024-08-09 09:47:47.814700
+"""
+
+import sqlalchemy as sa
+from sqlalchemy import orm
+from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "7770dcad8bde"
+down_revision = "bb4c6dbad991"
+branch_labels = None
+depends_on = None
+
+
+class Base(DeclarativeBase):
+    pass
+
+
+class Order(Base):
+    __tablename__ = "order"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    is_open: Mapped[str]
+
+
+def upgrade():
+    op.alter_column(
+        table_name="order", column_name="is_delivered", type_=sa.Boolean, new_column_name="is_open"
+    )
+    bind = op.get_bind()
+    session = orm.Session(bind=bind)
+    for order in session.query(Order).all():
+        order.is_open = not order.is_open
+    session.commit()
+
+
+def downgrade():
+    bind = op.get_bind()
+    session = orm.Session(bind=bind)
+    for order in session.query(Order).all():
+        order.is_open = not order.is_open
+    session.commit()
+    op.alter_column(
+        table_name="order", new_column_name="is_delivered", type_=sa.Boolean, column_name="is_open"
+    )

alembic/versions/2024_09_11_18dbadd8c436_rename_fastq_to_raw_data.py

@@ -0,0 +1,169 @@
+"""rename_fastq_to_raw_data
+Revision ID: 18dbadd8c436
+Revises: bb4c6dbad991
+Create Date: 2024-09-11 13:15:11.876822
+"""
+
+from enum import StrEnum
+
+from sqlalchemy import orm
+from sqlalchemy.dialects import mysql
+from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "18dbadd8c436"
+down_revision = "7770dcad8bde"
+branch_labels = None
+depends_on = None
+
+
+base_options = (
+    "balsamic",
+    "balsamic-pon",
+    "balsamic-qc",
+    "balsamic-umi",
+    "demultiplex",
+    "fluffy",
+    "jasen",
+    "microsalt",
+    "mip-dna",
+    "mip-rna",
+    "mutant",
+    "raredisease",
+    "rnafusion",
+    "rsync",
+    "spring",
+    "taxprofiler",
+    "tomte",
+)
+old_options = sorted(base_options + ("fastq",))
+new_options = sorted(base_options + ("raw-data",))
+
+old_enum = mysql.ENUM(*old_options)
+new_enum = mysql.ENUM(*new_options)
+
+
+class Workflow(StrEnum):
+    BALSAMIC: str = "balsamic"
+    BALSAMIC_PON: str = "balsamic-pon"
+    BALSAMIC_QC: str = "balsamic-qc"
+    BALSAMIC_UMI: str = "balsamic-umi"
+    DEMULTIPLEX: str = "demultiplex"
+    FLUFFY: str = "fluffy"
+    JASEN: str = "jasen"
+    MICROSALT: str = "microsalt"
+    MIP_DNA: str = "mip-dna"
+    MIP_RNA: str = "mip-rna"
+    MUTANT: str = "mutant"
+    RAREDISEASE: str = "raredisease"
+    RAW_DATA: str = "raw-data"
+    RNAFUSION: str = "rnafusion"
+    RSYNC: str = "rsync"
+    SPRING: str = "spring"
+    TAXPROFILER: str = "taxprofiler"
+    TOMTE: str = "tomte"
+
+
+class Base(DeclarativeBase):
+    pass
+
+
+class Case(Base):
+    __tablename__ = "case"
+    id: Mapped[int] = mapped_column(primary_key=True)
+    data_analysis: Mapped[str | None]
+
+
+class Analysis(Base):
+    __tablename__ = "analysis"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    workflow: Mapped[str | None]
+
+
+class Order(Base):
+    __tablename__ = "order"
+    id: Mapped[int] = mapped_column(primary_key=True)
+    workflow: Mapped[str | None]
+
+
+class ApplicationLimitations(Base):
+    __tablename__ = "application_limitations"
+    id: Mapped[int] = mapped_column(primary_key=True)
+    workflow: Mapped[str | None]
+
+
+def upgrade():
+    bind = op.get_bind()
+    session = orm.Session(bind=bind)
+    try:
+        # Case
+        op.alter_column("case", "data_analysis", type_=mysql.VARCHAR(64), existing_nullable=True)
+        session.query(Case).filter(Case.data_analysis == "fastq").update(
+            {"data_analysis": Workflow.RAW_DATA}, synchronize_session="evaluate"
+        )
+        op.alter_column("case", "data_analysis", type_=new_enum, existing_nullable=True)
+        # Analysis
+        op.alter_column("analysis", "workflow", type_=mysql.VARCHAR(64), existing_nullable=True)
+        session.query(Analysis).filter(Analysis.workflow == "fastq").update(
+            {"workflow": Workflow.RAW_DATA}, synchronize_session="evaluate"
+        )
+        op.alter_column("analysis", "workflow", type_=new_enum, existing_nullable=True)
+        # Order
+        op.alter_column("order", "workflow", type_=mysql.VARCHAR(64), existing_nullable=True)
+        session.query(Order).filter(Order.workflow == "fastq").update(
+            {"workflow": Workflow.RAW_DATA}, synchronize_session="evaluate"
+        )
+        op.alter_column("order", "workflow", type_=new_enum, existing_nullable=True)
+        # Application Limitation
+        op.alter_column(
+            "application_limitations", "workflow", type_=mysql.VARCHAR(64), existing_nullable=True
+        )
+        session.query(ApplicationLimitations).filter(
+            ApplicationLimitations.workflow == "fastq"
+        ).update({"workflow": Workflow.RAW_DATA}, synchronize_session="evaluate")
+        op.alter_column(
+            "application_limitations", "workflow", type_=new_enum, existing_nullable=True
+        )
+        session.commit()
+    finally:
+        session.close()
+
+
+def downgrade():
+    bind = op.get_bind()
+    session = orm.Session(bind=bind)
+    try:
+        # Case
+        op.alter_column("case", "data_analysis", type_=mysql.VARCHAR(64), existing_nullable=True)
+        session.query(Case).filter(Case.data_analysis == Workflow.RAW_DATA).update(
+            {"data_analysis": "fastq"}, synchronize_session="evaluate"
+        )
+        op.alter_column("case", "data_analysis", type_=old_enum, existing_nullable=True)
+        # Analysis
+        op.alter_column("analysis", "workflow", type_=mysql.VARCHAR(64), existing_nullable=True)
+        session.query(Analysis).filter(Analysis.workflow == Workflow.RAW_DATA).update(
+            {"workflow": "fastq"}, synchronize_session="evaluate"
+        )
+        op.alter_column("analysis", "workflow", type_=old_enum, existing_nullable=True)
+        # Order
+        op.alter_column("order", "workflow", type_=mysql.VARCHAR(64), existing_nullable=True)
+        session.query(Order).filter(Order.workflow == Workflow.RAW_DATA).update(
+            {"workflow": "fastq"}, synchronize_session="evaluate"
+        )
+        op.alter_column("order", "workflow", type_=old_enum, existing_nullable=True)
+        # Application Limitation
+        op.alter_column(
+            "application_limitations", "workflow", type_=mysql.VARCHAR(64), existing_nullable=True
+        )
+        session.query(ApplicationLimitations).filter(
+            ApplicationLimitations.workflow == Workflow.RAW_DATA
+        ).update({"workflow": "fastq"}, synchronize_session="evaluate")
+        op.alter_column(
+            "application_limitations", "workflow", type_=old_enum, existing_nullable=True
+        )
+        session.commit()
+    finally:
+        session.close()

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "63.0.1"
+__version__ = "63.2.11"

cg/cli/base.py

@@ -27,7 +27,6 @@
 from cg.cli.transfer import transfer_group
 from cg.cli.upload.base import upload
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
-from cg.cli.validate import validate
 from cg.cli.workflow.base import workflow as workflow_cmd
 from cg.constants.cli_options import FORCE
 from cg.constants.constants import FileFormat
@@ -121,5 +120,4 @@ def init(context: CGConfig, reset: bool, force: bool):
 base.add_command(generate_cmd)
 base.add_command(downsample)
 base.add_command(post_processing)
-base.add_command(validate)
 base.add_command(sequencing_qc)

cg/cli/deliver/base.py

@@ -11,17 +11,17 @@
 from cg.constants import Workflow
 from cg.constants.cli_options import DRY_RUN
 from cg.constants.delivery import FileDeliveryOption
-from cg.services.deliver_files.delivery_rsync_service.delivery_rsync_service import (
-    DeliveryRsyncService,
-)
 from cg.models.cg_config import CGConfig
 from cg.services.deliver_files.deliver_files_service.deliver_files_service import (
     DeliverFilesService,
 )
 from cg.services.deliver_files.deliver_files_service.deliver_files_service_factory import (
     DeliveryServiceFactory,
 )
-from cg.store.models import Case, Analysis
+from cg.services.deliver_files.delivery_rsync_service.delivery_rsync_service import (
+    DeliveryRsyncService,
+)
+from cg.store.models import Analysis, Case
 
 LOG = logging.getLogger(__name__)
 
@@ -148,7 +148,7 @@ def deliver_auto_raw_data(context: CGConfig, dry_run: bool):
        clinical-delivery."""
     service_builder: DeliveryServiceFactory = context.delivery_service_factory
     analyses: list[Analysis] = context.analysis_service.get_analyses_to_upload_for_workflow(
-        workflow=Workflow.FASTQ
+        workflow=Workflow.RAW_DATA
     )
     deliver_raw_data_for_analyses(
         analyses=analyses,

cg/cli/deliver/utils.py

@@ -9,10 +9,9 @@
 from cg.services.deliver_files.deliver_files_service.deliver_files_service_factory import (
     DeliveryServiceFactory,
 )
-from cg.store.models import Case, Analysis
+from cg.store.models import Analysis, Case
 from cg.store.store import Store
 
-
 LOG = logging.getLogger(__name__)
 
 
@@ -29,7 +28,7 @@ def deliver_raw_data_for_analyses(
             case: Case = analysis.case
             delivery_service: DeliverFilesService = service_builder.build_delivery_service(
                 delivery_type=case.data_delivery,
-                workflow=Workflow.FASTQ,
+                workflow=Workflow.RAW_DATA,
             )
 
             delivery_service.deliver_files_for_case(

cg/cli/workflow/fastq/base.py

@@ -44,6 +44,6 @@ def store_fastq_analysis(context: click.Context, case_id: str, dry_run: bool = F
 def store_available_fastq_analysis(context: click.Context, dry_run: bool = False):
     """Creates an analysis object in status-db for all fastq cases to be delivered."""
     status_db: Store = context.obj.status_db
-    for case in status_db.cases_to_analyse(workflow=Workflow.FASTQ):
+    for case in status_db.cases_to_analyse(workflow=Workflow.RAW_DATA):
         if SequencingQCService.case_pass_sequencing_qc(case):
             context.invoke(store_fastq_analysis, case_id=case.internal_id, dry_run=dry_run)

cg/cli/workflow/fastq/fastq_service.py

@@ -25,7 +25,7 @@ def _get_case(self, case_id: str) -> Case:
 
     def _add_analysis_to_store(self, case: Case) -> None:
         new_analysis: Analysis = self.store.add_analysis(
-            workflow=Workflow.FASTQ,
+            workflow=Workflow.RAW_DATA,
             completed_at=dt.datetime.now(),
             primary=True,
             started_at=dt.datetime.now(),
@@ -42,7 +42,7 @@ def _add_analysis_to_trailblazer(self, case: Case) -> None:
             order_id=case.latest_order.id,
             out_dir="",
             slurm_quality_of_service=case.slurm_priority,
-            workflow=Workflow.FASTQ,
+            workflow=Workflow.RAW_DATA,
             ticket=case.latest_ticket,
         )
         self.trailblazer_api.set_analysis_status(

cg/cli/workflow/nf_analysis.py

@@ -12,6 +12,7 @@
 from cg.constants.constants import MetaApis
 from cg.exc import AnalysisNotReadyError, CgError, HousekeeperStoreError
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
+
 from cg.models.cg_config import CGConfig
 
 LOG = logging.getLogger(__name__)