Refactor pipeline to workflow (#2885)

### Changed

- Refactor Pipeline to workflow for enum
- Remove casting to str

alembic/versions/2024_01_25_d241d8c493fb_add_pipeline_to_order.py

@@ -9,7 +9,7 @@
 import sqlalchemy as sa
 
 from alembic import op
-from cg.constants import Pipeline
+from cg.constants import Workflow
 
 # revision identifiers, used by Alembic.
 revision = "d241d8c493fb"
@@ -21,7 +21,7 @@
 def upgrade():
     op.add_column(
         table_name="order",
-        column=sa.Column("workflow", sa.Enum(*tuple(Pipeline)), nullable=False),
+        column=sa.Column("workflow", sa.Enum(*tuple(Workflow)), nullable=False),
     )
 
 

alembic/versions/2024_01_25_de0f5b78dca4_rename_pipeline_sars_cov2.py

@@ -10,7 +10,7 @@
 from sqlalchemy.dialects import mysql
 
 from alembic import op
-from cg.constants import Pipeline
+from cg.constants import Workflow
 from cg.store.models import Analysis, Case
 
 # revision identifiers, used by Alembic.
@@ -58,12 +58,12 @@ def upgrade():
 
     for case in session.query(Case).filter(Case.data_analysis == "sars-cov-2"):
         print(f"Altering case: {str(case)}")
-        case.data_analysis = str(Pipeline.MUTANT)
+        case.data_analysis = str(Workflow.MUTANT)
         print(f"Altered case: {str(case)}")
 
     for analysis in session.query(Analysis).filter(Analysis.pipeline == "sars-cov-2"):
         print(f"Altering analysis: {str(analysis)}")
-        analysis.pipeline = str(Pipeline.MUTANT)
+        analysis.pipeline = str(Workflow.MUTANT)
         print(f"Altered analysis: {str(analysis)}")
 
     session.commit()

alembic/versions/432379a1adfa_fix_sars_cov_2_data_analysis_to_database.py

@@ -12,7 +12,7 @@
 from sqlalchemy.orm import declarative_base
 
 from alembic import op
-from cg.constants import DataDelivery, Pipeline
+from cg.constants import DataDelivery, Workflow
 
 Base = declarative_base()
 
@@ -29,7 +29,7 @@ class Case(Base):
     id = sa.Column(sa.types.Integer, primary_key=True)
     internal_id = sa.Column(sa.types.String(32), unique=True, nullable=False)
     name = sa.Column(sa.types.String(128), nullable=False)
-    data_analysis = Column(types.Enum(*list(Pipeline)))
+    data_analysis = Column(types.Enum(*list(Workflow)))
     data_delivery = Column(types.Enum(*list(DataDelivery)))
 
     def __str__(self) -> str:
@@ -58,7 +58,7 @@ def upgrade():
         .filter(Case.data_analysis == "")
     ):
         print(f"Altering family: {str(family)}")
-        family.data_analysis = str(Pipeline.SARS_COV_2)
+        family.data_analysis = str(Workflow.SARS_COV_2)
         print(f"Altered family: {str(family)}")
 
     session.commit()

alembic/versions/9008aa5065b4_add_taxprofiler_analysis_option.py

@@ -11,7 +11,7 @@
 from sqlalchemy.orm import declarative_base
 
 from alembic import op
-from cg.constants import Pipeline
+from cg.constants import Workflow
 
 # revision identifiers, used by Alembic.
 revision = "9008aa5065b4"
@@ -46,13 +46,13 @@
 class Analysis(Base):
     __tablename__ = "analysis"
     id = sa.Column(sa.types.Integer, primary_key=True)
-    pipeline = sa.Column(sa.types.Enum(*list(Pipeline)))
+    pipeline = sa.Column(sa.types.Enum(*list(Workflow)))
 
 
 class Case(Base):
     __tablename__ = "family"
     id = sa.Column(sa.types.Integer, primary_key=True)
-    data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
+    data_analysis = sa.Column(sa.types.Enum(*list(Workflow)))
 
 
 def upgrade():

alembic/versions/9073c61bc72b_add_raredisease_to_analysis_options.py

@@ -11,7 +11,7 @@
 from sqlalchemy.orm import declarative_base
 
 from alembic import op
-from cg.constants import Pipeline
+from cg.constants import Workflow
 
 # revision identifiers, used by Alembic.
 revision = "9073c61bc72b"
@@ -47,13 +47,13 @@
 class Analysis(Base):
     __tablename__ = "analysis"
     id = sa.Column(sa.types.Integer, primary_key=True)
-    pipeline = sa.Column(sa.types.Enum(*list(Pipeline)))
+    pipeline = sa.Column(sa.types.Enum(*list(Workflow)))
 
 
 class Case(Base):
     __tablename__ = "family"
     id = sa.Column(sa.types.Integer, primary_key=True)
-    data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
+    data_analysis = sa.Column(sa.types.Enum(*list(Workflow)))
 
 
 def upgrade():

alembic/versions/998be2e367cf_fix_mip_on_fastq_wgs_cases.py

@@ -13,7 +13,7 @@
 from sqlalchemy.orm import declarative_base
 
 from alembic import op
-from cg.constants import PREP_CATEGORIES, DataDelivery, Pipeline
+from cg.constants import PREP_CATEGORIES, DataDelivery, Workflow
 
 Base = declarative_base()
 
@@ -38,7 +38,7 @@ class Case(Base):
     name = sa.Column(sa.types.String(128), nullable=False)
     customer_id = sa.Column(sa.ForeignKey("customer.id", ondelete="CASCADE"), nullable=False)
     customer = orm.relationship(Customer, foreign_keys=[customer_id])
-    data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
+    data_analysis = sa.Column(sa.types.Enum(*list(Workflow)))
     data_delivery = sa.Column(sa.types.Enum(*list(DataDelivery)))
     priority = sa.Column(sa.types.Integer, default=1, nullable=False)
     _panels = sa.Column(sa.types.Text)
@@ -111,7 +111,7 @@ def upgrade():
         session.query(Case)
         .filter(Case.customer_id == 1)
         .filter(Case.data_delivery == DataDelivery.FASTQ)
-        .filter(Case.data_analysis == Pipeline.FASTQ)
+        .filter(Case.data_analysis == Workflow.FASTQ)
         .filter(Case.priority == "research")
         .filter(Case.ordered_at >= datetime(year=2021, month=2, day=2))
     ):
@@ -126,7 +126,7 @@ def upgrade():
                 and sample.name == family.name
             ):
                 print(f"changing data analysis from FASTQ to MIP for: {family}")
-                family.data_analysis = Pipeline.MIP_DNA
+                family.data_analysis = Workflow.MIP_DNA
                 count += 1
 
     session.commit()
@@ -143,7 +143,7 @@ def downgrade():
         session.query(Case)
         .filter(Case.customer_id == 1)
         .filter(Case.data_delivery == DataDelivery.FASTQ)
-        .filter(Case.data_analysis == Pipeline.MIP_DNA)
+        .filter(Case.data_analysis == Workflow.MIP_DNA)
         .filter(Case.priority == "research")
         .filter(Case.ordered_at >= datetime(year=2021, month=2, day=2))
     ):
@@ -158,7 +158,7 @@ def downgrade():
                 and sample.name == family.name
             ):
                 print(f"changing data analysis from MIP to FASTQ for: {family}")
-                family.data_analysis = Pipeline.FASTQ
+                family.data_analysis = Workflow.FASTQ
                 count += 1
 
     session.commit()

alembic/versions/e853d21feaa0_add_pipeline_limitations_table.py

@@ -9,7 +9,7 @@
 import sqlalchemy as sa
 
 from alembic import op
-from cg.constants.constants import Pipeline
+from cg.constants.constants import Workflow
 
 # revision identifiers, used by Alembic.
 revision = "e853d21feaa0"
@@ -30,7 +30,7 @@ def upgrade():
             sa.ForeignKey("application.id", ondelete="CASCADE"),
             nullable=False,
         ),
-        sa.Column("pipeline", sa.Enum(*list(Pipeline)), nullable=False),
+        sa.Column("pipeline", sa.Enum(*list(Workflow)), nullable=False),
         sa.Column("limitations", sa.Text()),
         sa.Column("comment", sa.Text()),
         sa.Column("created_at", sa.DateTime(), server_default=sa.func.now()),

alembic/versions/e9df15a35de4_fix_tumour_not_to_maf.py

@@ -13,7 +13,7 @@
 from sqlalchemy.orm import declarative_base
 
 from alembic import op
-from cg.constants import PREP_CATEGORIES, DataDelivery, Pipeline
+from cg.constants import PREP_CATEGORIES, DataDelivery, Workflow
 
 # revision identifiers, used by Alembic.
 revision = "e9df15a35de4"
@@ -38,7 +38,7 @@ class Case(Base):
     name = sa.Column(sa.types.String(128), nullable=False)
     customer_id = sa.Column(sa.ForeignKey("customer.id", ondelete="CASCADE"), nullable=False)
     customer = orm.relationship(Customer, foreign_keys=[customer_id])
-    data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
+    data_analysis = sa.Column(sa.types.Enum(*list(Workflow)))
     data_delivery = sa.Column(sa.types.Enum(*list(DataDelivery)))
     priority = sa.Column(sa.types.Integer, default=1, nullable=False)
     _panels = sa.Column(sa.types.Text)
@@ -112,7 +112,7 @@ def upgrade():
         session.query(Case)
         .filter(Case.customer_id == 1)
         .filter(Case.data_delivery == DataDelivery.FASTQ)
-        .filter(Case.data_analysis == Pipeline.MIP_DNA)
+        .filter(Case.data_analysis == Workflow.MIP_DNA)
         .filter(Case.priority == "research")
     ):
         if len(family.links) > 1:
@@ -130,7 +130,7 @@ def upgrade():
                 and sample.name == family.name
             ):
                 print(f"changing data analysis from MIP to FASTQ for: {family}")
-                family.data_analysis = Pipeline.FASTQ
+                family.data_analysis = Workflow.FASTQ
                 count += 1
 
     session.commit()
@@ -146,7 +146,7 @@ def downgrade():
         session.query(Case)
         .filter(Case.customer_id == 1)
         .filter(Case.data_delivery == DataDelivery.FASTQ)
-        .filter(Case.data_analysis == Pipeline.FASTQ)
+        .filter(Case.data_analysis == Workflow.FASTQ)
         .filter(Case.priority == "research")
     ):
         if len(family.links) > 1:
@@ -164,7 +164,7 @@ def downgrade():
                 and sample.name == family.name
             ):
                 print(f"changing data analysis from FASTQ to MIP-DNA for: {family}")
-                family.data_analysis = Pipeline.MIP_DNA
+                family.data_analysis = Workflow.MIP_DNA
                 count += 1
 
     session.commit()

cg/apps/demultiplex/demultiplex_api.py

@@ -10,7 +10,7 @@
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.apps.slurm.slurm_api import SlurmAPI
 from cg.apps.tb import TrailblazerAPI
-from cg.constants.constants import FileFormat, Pipeline
+from cg.constants.constants import FileFormat, Workflow
 from cg.constants.demultiplexing import BclConverter, DemultiplexingDirsAndFiles
 from cg.constants.priority import SlurmQos
 from cg.constants.tb import AnalysisTypes
@@ -207,7 +207,7 @@ 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=str(Pipeline.DEMULTIPLEX),
+            data_analysis=Workflow.DEMULTIPLEX,
         )
 
     def start_demultiplexing(self, flow_cell: FlowCellDirectoryData):

cg/apps/orderform/json_orderform_parser.py

@@ -1,15 +1,15 @@
 from cg.apps.orderform.orderform_parser import OrderformParser
-from cg.constants import DataDelivery, Pipeline
+from cg.constants import DataDelivery, Workflow
 from cg.exc import OrderFormError
 from cg.models.orders.json_sample import JsonSample
 from cg.models.orders.order import OrderType
 
 
 class JsonOrderformParser(OrderformParser):
     ACCEPTED_DATA_ANALYSES: list[str] = [
-        str(Pipeline.MIP_DNA),
-        str(Pipeline.FLUFFY),
-        str(Pipeline.BALSAMIC),
+        Workflow.MIP_DNA,
+        Workflow.FLUFFY,
+        Workflow.BALSAMIC,
     ]
     NO_VALUE: str = "no_value"
     samples: list[JsonSample] = []

cg/apps/tb/api.py

@@ -6,10 +6,10 @@
 
 from google.auth import jwt
 from google.auth.crypt import RSASigner
-from cg.apps.tb.dto.create_job_request import CreateJobRequest
 
+from cg.apps.tb.dto.create_job_request import CreateJobRequest
 from cg.apps.tb.models import TrailblazerAnalysis
-from cg.constants import Pipeline
+from cg.constants import Workflow
 from cg.constants.constants import APIMethods, FileFormat, JobType, WorkflowManager
 from cg.constants.priority import SlurmQos
 from cg.constants.tb import AnalysisStatus
@@ -101,7 +101,7 @@ def add_pending_analysis(
         out_dir: str,
         slurm_quality_of_service: SlurmQos,
         email: str = None,
-        data_analysis: Pipeline = None,
+        data_analysis: Workflow = None,
         ticket: str = None,
         workflow_manager: str = WorkflowManager.Slurm,
     ) -> TrailblazerAnalysis:

cg/cli/add.py

@@ -2,7 +2,7 @@
 
 import click
 
-from cg.constants import STATUS_OPTIONS, DataDelivery, Pipeline, Priority
+from cg.constants import STATUS_OPTIONS, DataDelivery, Priority, Workflow
 from cg.constants.archiving import PDC_ARCHIVE_LOCATION
 from cg.constants.subject import Sex
 from cg.meta.transfer.external_data import ExternalDataAPI
@@ -225,7 +225,7 @@ def add_sample(
     "data_analysis",
     help="Analysis workflow",
     required=True,
-    type=EnumChoice(Pipeline),
+    type=EnumChoice(Workflow),
 )
 @click.option(
     "-dd",
@@ -243,7 +243,7 @@ def add_case(
     context: CGConfig,
     priority: Priority,
     panel_abbreviations: tuple[str],
-    data_analysis: Pipeline,
+    data_analysis: Workflow,
     data_delivery: DataDelivery,
     customer_id: str,
     name: str,

cg/cli/clean.py

@@ -23,7 +23,7 @@
     rnafusion_past_run_dirs,
     rsync_past_run_dirs,
 )
-from cg.constants.constants import DRY_RUN, SKIP_CONFIRMATION, Pipeline
+from cg.constants.constants import DRY_RUN, SKIP_CONFIRMATION, Workflow
 from cg.constants.housekeeper_tags import AlignmentFileTag, ScoutTag
 from cg.exc import CleanFlowCellFailedError, FlowCellError
 from cg.meta.clean.api import CleanAPI
@@ -172,7 +172,7 @@ def hk_case_bundle_files(context: CGConfig, days_old: int, dry_run: bool = False
 
 @clean.command("hk-bundle-files")
 @click.option("-c", "--case-id", type=str, required=False)
-@click.option("-p", "--pipeline", type=Pipeline, required=False)
+@click.option("-p", "--pipeline", type=Workflow, required=False)
 @click.option("-t", "--tags", multiple=True, required=True)
 @click.option("-o", "--days-old", type=int, default=30)
 @DRY_RUN
@@ -182,7 +182,7 @@ def hk_bundle_files(
     case_id: str | None,
     tags: list,
     days_old: int | None,
-    pipeline: Pipeline | None,
+    pipeline: Workflow | None,
     dry_run: bool,
 ):
     """Remove files found in Housekeeper bundles."""

cg/cli/delete/observations.py

@@ -10,7 +10,7 @@
     ARGUMENT_CASE_ID,
     OPTION_LOQUSDB_SUPPORTED_PIPELINES,
 )
-from cg.constants.constants import DRY_RUN, SKIP_CONFIRMATION, Pipeline
+from cg.constants.constants import DRY_RUN, SKIP_CONFIRMATION, Workflow
 from cg.exc import CaseNotFoundError, LoqusdbError
 from cg.meta.observations.balsamic_observations_api import BalsamicObservationsAPI
 from cg.meta.observations.mip_dna_observations_api import MipDNAObservationsAPI
@@ -49,7 +49,7 @@ def delete_observations(context: CGConfig, case_id: str, dry_run: bool, yes: boo
 @DRY_RUN
 @click.pass_context
 def delete_available_observations(
-    context: click.Context, pipeline: Pipeline | None, dry_run: bool, yes: bool
+    context: click.Context, pipeline: Workflow | None, dry_run: bool, yes: bool
 ):
     """Delete available observation from Loqusdb."""
 

cg/cli/generate/report/base.py

@@ -21,7 +21,7 @@
     get_report_api_pipeline,
     get_report_case,
 )
-from cg.constants import EXIT_FAIL, EXIT_SUCCESS, Pipeline
+from cg.constants import EXIT_FAIL, EXIT_SUCCESS, Workflow
 from cg.exc import CgError
 from cg.meta.report.report_api import ReportAPI
 from cg.store.models import Case
@@ -90,7 +90,7 @@ def generate_delivery_report(
 @OPTION_DRY_RUN
 @click.pass_context
 def generate_available_delivery_reports(
-    context: click.Context, pipeline: Pipeline, force_report: bool, dry_run: bool
+    context: click.Context, pipeline: Workflow, force_report: bool, dry_run: bool
 ) -> None:
     """Generates delivery reports for all cases that need one and stores them in housekeeper."""