Merge branch 'refs/heads/improve-order-flow-storing-main' into minima…

…l-implementation

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 64.5.12
+current_version = 64.5.22
 commit = True
 tag = True
 tag_name = v{new_version}

alembic/versions/2024_12_02_5552c02a4966_add_nallo_to_analysis_options.py

@@ -0,0 +1,105 @@
+"""add-nallo-to-analysis-options
+
+Revision ID: 5552c02a4966
+Revises: 05ffb5e13d7b
+Create Date: 2024-12-02 11:35:31.725343
+
+"""
+
+from enum import StrEnum
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import mysql
+from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column
+
+# revision identifiers, used by Alembic.
+revision = "5552c02a4966"
+down_revision = "05ffb5e13d7b"
+branch_labels = None
+depends_on = None
+
+base_options = (
+    "balsamic",
+    "balsamic-pon",
+    "balsamic-qc",
+    "balsamic-umi",
+    "demultiplex",
+    "raw-data",
+    "fluffy",
+    "microsalt",
+    "mip-dna",
+    "mip-rna",
+    "mutant",
+    "raredisease",
+    "rnafusion",
+    "rsync",
+    "spring",
+    "taxprofiler",
+    "tomte",
+    "jasen",
+)
+
+old_options = sorted(base_options)
+new_options = sorted(base_options + ("nallo",))
+
+old_analysis_enum = mysql.ENUM(*old_options)
+new_analysis_enum = mysql.ENUM(*new_options)
+
+
+class Pipeline(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"
+    NALLO: str = "nallo"
+    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 Analysis(Base):
+    __tablename__ = "analysis"
+    id = sa.Column(sa.types.Integer, primary_key=True)
+    workflow = sa.Column(sa.types.Enum(*list(Pipeline)))
+
+
+class Case(Base):
+    __tablename__ = "case"
+    id = sa.Column(sa.types.Integer, primary_key=True)
+    data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
+    internal_id = sa.Column(sa.types.String)
+
+
+def upgrade():
+    op.alter_column("case", "data_analysis", type_=new_analysis_enum)
+    op.alter_column("analysis", "workflow", type_=new_analysis_enum)
+
+
+def downgrade():
+    bind = op.get_bind()
+    session = sa.orm.Session(bind=bind)
+    for analysis in session.query(Analysis).filter(Analysis.workflow == "nallo"):
+        print(f"Changing pipeline for Case {Case.internal_id} to raw-data")
+        analysis.workflow = "raw-data"
+    for case in session.query(Case).filter(Case.data_analysis == "nallo"):
+        print(f"Changing data_analysis for Case {case.internal_id} to raw-data")
+        case.data_analysis = "raw-data"
+    op.alter_column("case", "data_analysis", type_=old_analysis_enum)
+    op.alter_column("analysis", "workflow", type_=old_analysis_enum)
+    session.commit()

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "64.5.12"
+__version__ = "64.5.22"

cg/apps/demultiplex/demultiplex_api.py

@@ -13,7 +13,7 @@
 from cg.constants.constants import FileFormat, Workflow
 from cg.constants.demultiplexing import DemultiplexingDirsAndFiles
 from cg.constants.priority import SlurmQos
-from cg.constants.tb import AnalysisTypes
+from cg.constants.tb import AnalysisType
 from cg.exc import HousekeeperFileMissingError
 from cg.io.controller import WriteFile
 from cg.models.demultiplex.sbatch import SbatchCommand, SbatchError
@@ -210,7 +210,7 @@ def add_to_trailblazer(
         )
         tb_api.add_pending_analysis(
             case_id=sequencing_run.id,
-            analysis_type=AnalysisTypes.OTHER,
+            analysis_type=AnalysisType.OTHER,
             config_path=sequencing_run.trailblazer_config_path.as_posix(),
             out_dir=sequencing_run.trailblazer_config_path.parent.as_posix(),
             slurm_quality_of_service=self.slurm_quality_of_service,

cg/apps/demultiplex/sample_sheet/api.py

@@ -1,7 +1,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 
 from cg.apps.demultiplex.sample_sheet.read_sample_sheet import get_samples_from_content
 from cg.apps.demultiplex.sample_sheet.sample_models import IlluminaSampleIndexSetting

cg/apps/orderform/orderform_parser.py

@@ -4,6 +4,7 @@
 
 from pydantic import BaseModel, ConfigDict, constr
 
+from cg.apps.orderform.utils import ORDER_TYPES_WITH_CASES
 from cg.constants import DataDelivery
 from cg.exc import OrderFormError
 from cg.models.orders.order import OrderType
@@ -142,10 +143,11 @@ def expand_case(case_id: str, case_samples: list[OrderSample]) -> OrderCase:
 
     def generate_orderform(self) -> Orderform:
         """Generate an orderform"""
-        cases_map: dict[str, list[OrderSample]] = self.group_cases()
         case_objs: list[OrderCase] = []
-        for case_id in cases_map:
-            case_objs.append(self.expand_case(case_id=case_id, case_samples=cases_map[case_id]))
+        if self.project_type in ORDER_TYPES_WITH_CASES:
+            cases_map: dict[str, list[OrderSample]] = self.group_cases()
+            for case_id in cases_map:
+                case_objs.append(self.expand_case(case_id=case_id, case_samples=cases_map[case_id]))
         return Orderform(
             comment=self.order_comment,
             samples=self.samples,

cg/apps/orderform/utils.py

@@ -1,5 +1,16 @@
+from cg.models.orders.constants import OrderType
 from cg.models.orders.excel_sample import ExcelSample
 
+ORDER_TYPES_WITH_CASES = [
+    OrderType.BALSAMIC,
+    OrderType.BALSAMIC_QC,
+    OrderType.BALSAMIC_UMI,
+    OrderType.MIP_DNA,
+    OrderType.MIP_RNA,
+    OrderType.RNAFUSION,
+    OrderType.TOMTE,
+]
+
 
 def are_all_samples_metagenome(samples: list[ExcelSample]) -> bool:
     """Check if all samples are metagenome samples"""

cg/cli/add.py

@@ -1,6 +1,6 @@
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS, is_case_name_allowed
 from cg.constants import DataDelivery, Priority, Workflow

cg/cli/archive.py

@@ -1,4 +1,4 @@
-import click
+import rich_click as click
 from click.core import ParameterSource
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS

cg/cli/backup.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Iterable
 
-import click
+import rich_click as click
 import housekeeper.store.models as hk_models
 
 from cg.apps.housekeeper.hk import HousekeeperAPI

cg/cli/base.py

@@ -4,7 +4,7 @@
 import sys
 from pathlib import Path
 
-import click
+import rich_click as click
 import coloredlogs
 from sqlalchemy.orm import scoped_session
 

cg/cli/clean.py

@@ -4,7 +4,7 @@
 from datetime import datetime, timedelta
 from pathlib import Path
 
-import click
+import rich_click as click
 from housekeeper.store.models import File, Version
 
 from cg.apps.housekeeper.hk import HousekeeperAPI

cg/cli/compress/base.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.compress.fastq import (
     clean_fastq,

cg/cli/compress/fastq.py

@@ -3,7 +3,7 @@
 import logging
 from typing import Iterable
 
-import click
+import rich_click as click
 
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.cli.compress.helpers import (

cg/cli/delete/base.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.delete.case import delete_case
 from cg.cli.delete.cases import delete_cases

cg/cli/delete/case.py

@@ -3,7 +3,7 @@
 import datetime
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.get import get_case as print_case
 from cg.constants.cli_options import DRY_RUN, SKIP_CONFIRMATION

cg/cli/delete/cases.py

@@ -1,6 +1,6 @@
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.delete.case import delete_case
 from cg.constants.cli_options import DRY_RUN

cg/cli/delete/illumina_sequencing_run.py

@@ -1,4 +1,4 @@
-import click
+import rich_click as click
 
 from cg.constants.cli_options import DRY_RUN
 from cg.services.illumina.post_processing.housekeeper_storage import (

cg/cli/delete/observations.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 from sqlalchemy.orm import Query
 
 from cg.cli.upload.observations.utils import get_observations_api

cg/cli/deliver/base.py

@@ -3,7 +3,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 
 from cg.apps.tb import TrailblazerAPI
 from cg.cli.deliver.utils import deliver_raw_data_for_analyses

cg/cli/demultiplex/base.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.cli.demultiplex.demux import (

cg/cli/demultiplex/demux.py

@@ -2,7 +2,7 @@
 from glob import glob
 from pathlib import Path
 
-import click
+import rich_click as click
 from pydantic import ValidationError
 
 from cg.apps.demultiplex.demultiplex_api import DemultiplexingAPI

cg/cli/demultiplex/finish.py

@@ -3,7 +3,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.constants.cli_options import DRY_RUN, FORCE

cg/cli/demultiplex/sample_sheet.py

@@ -1,7 +1,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 from pydantic import ValidationError
 
 from cg.apps.demultiplex.sample_sheet.api import IlluminaSampleSheetService

cg/cli/downsample.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Tuple
 
-import click
+import rich_click as click
 
 from cg.apps.downsample.downsample import DownsampleAPI
 from cg.apps.downsample.utils import store_downsampled_sample_bundle

cg/cli/generate/base.py

@@ -1,6 +1,6 @@
 """Common CLI file generation functions"""
 
-import click
+import rich_click as click
 
 from cg.cli.generate.delivery_report.base import (
     generate_available_delivery_reports,

cg/cli/generate/delivery_report/base.py

@@ -5,7 +5,7 @@
 from datetime import datetime
 from pathlib import Path
 
-import click
+import rich_click as click
 from housekeeper.store.models import Version
 
 from cg.cli.generate.delivery_report.options import (

cg/cli/generate/delivery_report/options.py

@@ -1,6 +1,6 @@
 """Delivery report specific command options."""
 
-import click
+import rich_click as click
 
 from cg.constants import REPORT_SUPPORTED_WORKFLOW
 

cg/cli/generate/delivery_report/utils.py

@@ -3,7 +3,7 @@
 import logging
 from datetime import datetime
 
-import click
+import rich_click as click
 
 from cg.constants import REPORT_SUPPORTED_DATA_DELIVERY, REPORT_SUPPORTED_WORKFLOW, Workflow
 from cg.meta.delivery_report.balsamic import BalsamicDeliveryReportAPI

cg/cli/get.py

@@ -2,7 +2,7 @@
 import re
 from typing import Iterable
 
-import click
+import rich_click as click
 from tabulate import tabulate
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS

cg/cli/post_process/post_process.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.post_process.utils import (
     UnprocessedRunInfo,

cg/cli/sequencing_qc/sequencing_qc.py

@@ -1,5 +1,5 @@
 import logging
-import click
+import rich_click as click
 
 from cg.models.cg_config import CGConfig
 from cg.services.sequencing_qc_service.sequencing_qc_service import SequencingQCService