Test call to config case fails

cg/cli/workflow/balsamic/base.py

@@ -2,6 +2,8 @@
 
 import logging
 import traceback
+from typing import cast
+
 
 import rich_click as click
 from pydantic.v1 import ValidationError
@@ -20,12 +22,16 @@
 )
 from cg.cli.workflow.commands import ARGUMENT_CASE_ID, link, resolve_compression
 from cg.cli.workflow.utils import validate_force_store_option
-from cg.constants import EXIT_FAIL, EXIT_SUCCESS
+from cg.constants import EXIT_FAIL, EXIT_SUCCESS, Workflow
 from cg.constants.cli_options import COMMENT, DRY_RUN, FORCE, LIMIT
 from cg.exc import AnalysisNotReadyError, CgError
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI
 from cg.models.cg_config import CGConfig
+from cg.services.analysis_starter.configurator.implementations.balsamic import BalsamicConfigurator
+from cg.services.analysis_starter.factories.configurator_factory import ConfiguratorFactory
+from cg.services.analysis_starter.factories.starter_factory import AnalysisStarterFactory
+from cg.services.analysis_starter.service import AnalysisStarter
 from cg.store.models import Case
 from cg.store.store import Store
 
@@ -299,3 +305,54 @@ def store_available(context: click.Context, dry_run: bool) -> None:
             was_successful = False
     if not was_successful:
         raise click.Abort()
+
+
+@balsamic.command()
+@OPTION_PANEL_BED
+@ARGUMENT_CASE_ID
+@click.pass_obj
+def dev_config_case(cg_config: CGConfig, case_id: str, panel_bed: str | None):
+    """Configure a Balsamic case so that it is ready to be run."""
+    factory = ConfiguratorFactory(cg_config)
+    configurator = cast(BalsamicConfigurator, factory.get_configurator(Workflow.BALSAMIC))
+    configurator.configure(case_id=case_id, panel_bed=panel_bed)
+
+
+@balsamic.command("dev-run")
+@OPTION_WORKFLOW_PROFILE
+@ARGUMENT_CASE_ID
+@click.pass_obj
+def dev_run(cg_config: CGConfig, case_id: str, workflow_profile: click.Path | None):
+    """Run a preconfigured Balsamic case."""
+    factory = AnalysisStarterFactory(cg_config)
+    analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(Workflow.BALSAMIC)
+    analysis_starter.run(case_id=case_id, workflow_profile=workflow_profile)
+
+
+@balsamic.command("dev-start")
+@OPTION_PANEL_BED
+@OPTION_WORKFLOW_PROFILE
+@ARGUMENT_CASE_ID
+@click.pass_obj
+def dev_start(
+    cg_config: CGConfig,
+    case_id: str,
+    panel_bed: str | None,
+    workflow_profile: click.Path | None,
+):
+    """Start a Balsamic case. Configures the case if needed."""
+    factory = AnalysisStarterFactory(cg_config)
+    analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(Workflow.BALSAMIC)
+    analysis_starter.start(case_id=case_id, workflow_profile=workflow_profile, panel_bed=panel_bed)
+
+
+@balsamic.command("dev-start-available")
+@click.pass_obj
+def dev_start_available(cg_config: CGConfig):
+    """Starts all available raredisease cases."""
+    LOG.info("Starting Balsamic workflow for all available cases.")
+    factory = AnalysisStarterFactory(cg_config)
+    analysis_starter = factory.get_analysis_starter_for_workflow(Workflow.BALSAMIC)
+    succeeded: bool = analysis_starter.start_available()
+    if not succeeded:
+        raise click.Abort

cg/constants/constants.py

@@ -156,12 +156,12 @@ class FileFormat(StrEnum):
 
 
 class GenomeVersion(StrEnum):
-    GRCh37: str = "GRCh37"
-    GRCh38: str = "GRCh38"
-    T2T_CHM13: str = "T2T-CHM13v2.0"
+    GRCh37 = "GRCh37"
+    GRCh38 = "GRCh38"
+    T2T_CHM13 = "T2T-CHM13v2.0"
     CANFAM3 = auto()
-    HG19: str = "hg19"
-    HG38: str = "hg38"
+    HG19 = "hg19"
+    HG38 = "hg38"
 
 
 class SampleType(StrEnum):

cg/exc.py

@@ -334,5 +334,9 @@ class Chanjo2ResponseError(Chanjo2APIClientError):
     """Exception raised when the response from Chanjo2 API client fails validation."""
 
 
+class CaseNotConfiguredError(CgError):
+    """Exception raised when a case is being run without a configuration."""
+
+
 class MissingConfigFilesError(CgError):
     """Exception raised when a case is being run with missing configuration files."""

cg/meta/workflow/balsamic.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 
 from housekeeper.store.models import File, Version
+from pydantic import EmailStr
 from pydantic.v1 import ValidationError
 
 from cg.constants import Workflow
@@ -55,23 +56,24 @@ def __init__(
     ):
         super().__init__(workflow=workflow, config=config)
         self.account: str = config.balsamic.slurm.account
-        self.balsamic_cache: str = config.balsamic.balsamic_cache
-        self.bed_path: str = config.balsamic.bed_path
-        self.binary_path: str = config.balsamic.binary_path
-        self.cadd_path: str = config.balsamic.cadd_path
-        self.conda_binary: str = config.balsamic.conda_binary
+        self.balsamic_cache: str = str(config.balsamic.balsamic_cache)
+        self.bed_path: str = str(config.balsamic.bed_path)
+        self.binary_path: str = str(config.balsamic.binary_path)
+        self.cadd_path: str = str(config.balsamic.cadd_path)
+        self.conda_binary: str = str(config.balsamic.conda_binary)
         self.conda_env: str = config.balsamic.conda_env
-        self.genome_interval_path: str = config.balsamic.genome_interval_path
-        self.gens_coverage_female_path: str = config.balsamic.gens_coverage_female_path
-        self.gens_coverage_male_path: str = config.balsamic.gens_coverage_male_path
-        self.gnomad_af5_path: str = config.balsamic.gnomad_af5_path
+        self.email: EmailStr = config.balsamic.slurm.mail_user
+        self.genome_interval_path: str = str(config.balsamic.genome_interval_path)
+        self.gens_coverage_female_path: str = str(config.balsamic.gens_coverage_female_path)
+        self.gens_coverage_male_path: str = str(config.balsamic.gens_coverage_male_path)
+        self.gnomad_af5_path: str = str(config.balsamic.gnomad_af5_path)
         self.head_job_partition: str = config.balsamic.head_job_partition
-        self.loqusdb_path: str = config.balsamic.loqusdb_path
-        self.pon_path: str = config.balsamic.pon_path
+        self.loqusdb_path: str = str(config.balsamic.loqusdb_path)
+        self.pon_path: str = str(config.balsamic.pon_path)
         self.qos: SlurmQos = config.balsamic.slurm.qos
-        self.root_dir: str = config.balsamic.root
-        self.sentieon_licence_path: str = config.balsamic.sentieon_licence_path
-        self.sentieon_licence_server: str = config.sentieon_licence_server
+        self.root_dir: str = str(config.balsamic.root)
+        self.sentieon_licence_path: str = str(config.balsamic.sentieon_licence_path)
+        self.sentieon_licence_server: str = config.balsamic.sentieon_licence_server
         self.swegen_path: str = config.balsamic.swegen_path
 
     @property
@@ -589,11 +591,11 @@ def config_case(
             {
                 "--analysis-dir": self.root_dir,
                 "--analysis-workflow": arguments.get("analysis_workflow"),
+                "--artefact-snv-observations": arguments.get("artefact_somatic_snv"),
+                "--artefact-sv-observations": arguments.get("loqusdb_wgs_dump_file"),
                 "--balsamic-cache": self.balsamic_cache,
                 "--cache-version": cache_version,
                 "--cadd-annotations": self.cadd_path,
-                "--artefact-snv-observations": arguments.get("artefact_somatic_snv"),
-                "--artefact-sv-observations": arguments.get("loqusdb_wgs_dump_file"),
                 "--cancer-germline-snv-observations": arguments.get("cancer_germline_snv"),
                 "--cancer-germline-sv-observations": arguments.get("cancer_germline_sv"),
                 "--cancer-somatic-snv-observations": arguments.get("cancer_somatic_snv"),
@@ -612,8 +614,8 @@ def config_case(
                 "--gnomad-min-af5": arguments.get("gnomad_min_af5"),
                 "--normal-sample-name": arguments.get("normal_sample_name"),
                 "--panel-bed": arguments.get("panel_bed"),
+                "--exome": arguments.get("exome"),  # MUST be after panel bed
                 "--pon-cnn": arguments.get("pon_cnn"),
-                "--exome": arguments.get("exome"),
                 "--sentieon-install-dir": self.sentieon_licence_path,
                 "--sentieon-license": self.sentieon_licence_server,
                 "--soft-filter-normal": arguments.get("soft_filter_normal"),

cg/meta/workflow/fastq.py

@@ -212,6 +212,14 @@ def create_fastq_name(
         date: str = date if isinstance(date, str) else date.strftime("%y%m%d")
         return f"{lane}_{date}_{flow_cell}_{sample}_{index}_R_{read_direction}{FileExtensions.FASTQ}{FileExtensions.GZIP}"
 
+    def get_sample_fastq_destination_dir(self, case: Case, sample: Sample) -> Path:
+        """Get fastq paths for a Balsamic case (sample-independent)."""
+        return self.get_fastq_dir(case_id=case.internal_id)
+
+    def get_fastq_dir(self, case_id: str) -> Path:
+        """Get fastq directory for a Balsamic case."""
+        return Path(self.root_dir, case_id, "fastq")
+
 
 class MipFastqHandler(FastqHandler):
     @staticmethod

cg/models/cg_config.py

@@ -22,7 +22,7 @@
 from cg.clients.arnold.api import ArnoldAPIClient
 from cg.clients.chanjo2.client import Chanjo2APIClient
 from cg.clients.janus.api import JanusAPIClient
-from cg.constants.observations import LoqusdbInstance
+from cg.constants.observations import BalsamicObservationPanel, LoqusdbInstance
 from cg.constants.priority import SlurmQos
 from cg.meta.delivery.delivery import DeliveryAPI
 from cg.services.analysis_service.analysis_service import AnalysisService
@@ -178,24 +178,40 @@ class MutaccAutoConfig(CommonAppConfig):
     padding: int = 300
 
 
+class LoqusDBDumpFiles(BaseModel):
+    artefact_sv: Path  # WGS
+    artefact_snv: Path
+    cancer_germline_snv: Path
+    cancer_somatic_snv: Path
+    cancer_somatic_sv: Path
+    clinical_snv: Path
+    clinical_sv: Path
+    cancer_somatic_snv_panels: dict[BalsamicObservationPanel, Path]  # Panel
+
+
 class BalsamicConfig(CommonAppConfig):
-    balsamic_cache: str
-    bed_path: str
-    binary_path: str
-    cadd_path: str
-    conda_binary: str
+    balsamic_cache: Path
+    bed_path: Path
+    binary_path: Path
+    cadd_path: Path
+    conda_binary: Path
     conda_env: str
-    genome_interval_path: str
-    gens_coverage_female_path: str
-    gens_coverage_male_path: str
-    gnomad_af5_path: str
+    genome_interval_path: Path
+    gens_coverage_female_path: Path
+    gens_coverage_male_path: Path
+    gnomad_af5_path: Path
     head_job_partition: str
-    loqusdb_path: str
-    pon_path: str
-    root: str
-    sentieon_licence_path: str
+    loqusdb_path: Path
+    loqusdb_dump_files: LoqusDBDumpFiles
+    panel_of_normals: dict[str, Path]  # For TGS and Exome
+    pon_path: Path
+    root: Path
+    sentieon_licence_path: Path
+    sentieon_licence_server: str
     slurm: SlurmConfig
-    swegen_path: str
+    swegen_path: Path
+    swegen_snv: Path
+    swegen_sv: Path
 
 
 class MutantConfig(BaseModel):
@@ -416,7 +432,6 @@ class CGConfig(BaseModel):
     max_flowcells: int | None = None
     nanopore_data_directory: str
     run_instruments: RunInstruments
-    sentieon_licence_server: str
     tower_binary_path: str
 
     # Base APIs that always should exist