cg 83.15.0__tar.gz → 83.15.2__tar.gz

{cg-83.15.0 → cg-83.15.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.15.0
+Version: 83.15.2
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

cg-83.15.2/cg/__init__.py

@@ -0,0 +1,2 @@
+__title__ = "cg"
+__version__ = "83.15.2"

{cg-83.15.0 → cg-83.15.2}/cg/cli/sequencing_qc/sequencing_qc.py

@@ -1,4 +1,5 @@
 import logging
+
 import rich_click as click
 
 from cg.models.cg_config import CGConfig
@@ -11,4 +12,6 @@ LOG = logging.getLogger(__name__)
 @click.pass_obj
 def sequencing_qc(context: CGConfig):
     service: SequencingQCService = context.sequencing_qc_service
-    service.run_sequencing_qc()
+    succeeded: bool = service.run_sequencing_qc()
+    if not succeeded:
+        raise click.Abort

{cg-83.15.0 → cg-83.15.2}/cg/exc.py

@@ -356,5 +356,9 @@ class SeqeraError(CgError):
     """Exception raised when receiving an unexpected response from Seqera platform"""
 
 
+class MultipleCaptureKitsError(CgError):
+    """Exception raised when multiple capture kits are found where only one is expected."""
+
+
 class ApplicationDoesNotHaveHiFiYieldError(CgError):
     """Exception raised when application does not have HiFi yield set."""

{cg-83.15.0 → cg-83.15.2}/cg/services/analysis_starter/configurator/implementations/balsamic.py

@@ -2,8 +2,9 @@ import logging
 from pathlib import Path
 from typing import cast
 
+from cg.apps.lims.api import LimsAPI
 from cg.constants.priority import SlurmQos
-from cg.exc import CaseNotConfiguredError
+from cg.exc import CaseNotConfiguredError, MultipleCaptureKitsError
 from cg.meta.workflow.fastq import BalsamicFastqHandler
 from cg.models.cg_config import BalsamicConfig
 from cg.services.analysis_starter.configurator.configurator import Configurator
@@ -11,6 +12,7 @@ from cg.services.analysis_starter.configurator.file_creators.balsamic_config imp
     BalsamicConfigFileCreator,
 )
 from cg.services.analysis_starter.configurator.models.balsamic import BalsamicCaseConfig
+from cg.store.models import Case
 from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
@@ -22,6 +24,7 @@ class BalsamicConfigurator(Configurator):
         config: BalsamicConfig,
         config_file_creator: BalsamicConfigFileCreator,
         fastq_handler: BalsamicFastqHandler,
+        lims_api: LimsAPI,
         store: Store,
     ):
         self.store: Store = store
@@ -35,9 +38,11 @@ class BalsamicConfigurator(Configurator):
 
         self.fastq_handler: BalsamicFastqHandler = fastq_handler
         self.config_file_creator: BalsamicConfigFileCreator = config_file_creator
+        self.lims_api = lims_api
 
     def configure(self, case_id: str, **flags) -> BalsamicCaseConfig:
         LOG.info(f"Configuring case {case_id}")
+        self._ensure_consistent_capture_kits(case_id)
         self.fastq_handler.link_fastq_files(case_id)
         fastq_path: Path = self.fastq_handler.get_fastq_dir(case_id)
         self.config_file_creator.create(case_id=case_id, fastq_path=fastq_path, **flags)
@@ -61,6 +66,16 @@ class BalsamicConfigurator(Configurator):
     def _get_sample_config_path(self, case_id: str) -> Path:
         return Path(self.root_dir, case_id, f"{case_id}.json")
 
+    def _ensure_consistent_capture_kits(self, case_id):
+        case: Case = self.store.get_case_by_internal_id_strict(case_id)
+        capture_kits: set[str | None] = {
+            self.lims_api.capture_kit(sample.internal_id) for sample in case.samples
+        }
+        if len(capture_kits) > 1:
+            raise MultipleCaptureKitsError(
+                f"Multiple capture kits found for {case_id}: {capture_kits}"
+            )
+
     def _ensure_required_config_files_exist(self, config: BalsamicCaseConfig) -> None:
         if not config.sample_config.exists():
             raise CaseNotConfiguredError(

{cg-83.15.0 → cg-83.15.2}/cg/services/analysis_starter/factories/configurator_factory.py

@@ -228,6 +228,7 @@ class ConfiguratorFactory:
                 status_db=self.store,
             ),
             config=self.cg_config.balsamic,
+            lims_api=self.lims_api,
             store=self.store,
         )
 

{cg-83.15.0 → cg-83.15.2}/cg/services/sequencing_qc_service/sequencing_qc_service.py

@@ -18,9 +18,15 @@ class SequencingQCService:
     def __init__(self, store: Store):
         self.store = store
 
-    def run_sequencing_qc(self) -> None:
-        """Run QC for samples in pending or failed cases and store the aggregated score on each case."""
+    def run_sequencing_qc(self) -> bool:
+        """
+        Run QC for samples in pending or failed cases and store the aggregated score on each case.
+        Return True if all checks could run succesfully
+        Return False if at least one of the checks raised an exception
+        """
         cases: list[Case] = self.store.get_cases_for_sequencing_qc()
+        all_checks_ran_succesfully: bool = True
+
         for case in cases:
             LOG.debug(f"Performing sequencing QC for case: {case.internal_id}")
             try:
@@ -30,6 +36,9 @@ class SequencingQCService:
                 LOG.info(f"Sequencing QC status for case {case.internal_id}: {qc_status}")
             except Exception as e:
                 LOG.error(f"Error found during sequencing QC of case: {case.internal_id}: {e}")
+                all_checks_ran_succesfully = False
+
+        return all_checks_ran_succesfully
 
     @staticmethod
     def case_pass_sequencing_qc(case: Case) -> bool:

{cg-83.15.0 → cg-83.15.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "cg"
-version = "83.15.0"
+version = "83.15.2"
 description = "Clinical Genomics command center"
 readme = {file = "README.md", content-type = "text/markdown"}
 homepage = "https://github.com/Clinical-Genomics/cg"

cg-83.15.0/cg/__init__.py

@@ -1,2 +0,0 @@
-__title__ = "cg"
-__version__ = "83.15.0"