cg 83.15.0__py3-none-any.whl → 83.15.2__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.15.0"
+__version__ = "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/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/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/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/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.dist-info → cg-83.15.2.dist-info}/METADATA

@@ -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-83.15.0.dist-info → cg-83.15.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=LzHKmL8dVmAmq-6AHs2IvH5WkbB5nsiiArjFCiCZoEA,41
+cg/__init__.py,sha256=h1_DpaXm14buebvsKjVmxOLYjMT2n5LWfEifGHaVN3I,41
 cg/apps/__init__.py,sha256=pYf0vxo4iYQqURzFRYzqpOCdV8Cm9MWx0GHvJOz0EMg,315
 cg/apps/coverage/__init__.py,sha256=dJtsmNf8tODE2-VEomMIoYA7ugLYZAk_upsfOQCZeF8,27
 cg/apps/coverage/api.py,sha256=e_ozC3QeNKoEfpjjMaL-XjeBLtz-JySWccrtw0E9mLM,2940
@@ -104,7 +104,7 @@ cg/cli/get.py,sha256=sqKX2tDWnCE6zTwcMBCOb796Bc9rvu1AYLkONQ3Sq0w,8852
 cg/cli/post_process/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/cli/post_process/post_process.py,sha256=f6bCOsNLIHYHJdbKBVcjRO684MS258CptsmAVknoYI0,2367
 cg/cli/post_process/utils.py,sha256=XrzBhVDybFa4sBGDz5Dbwah0YrYD1IS_j3WzPjWjUfs,3193
-cg/cli/sequencing_qc/sequencing_qc.py,sha256=UxdfUBryKq5Pj82-8Ihjmqb9EClNzcuJtZKrB7YAB_A,427
+cg/cli/sequencing_qc/sequencing_qc.py,sha256=anMscRw9Ulp3t2tQuLNuPE1HDtWTISgh_4yJourvAyA,494
 cg/cli/set/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/cli/set/base.py,sha256=gqdDpKS32rM29sQxPyK6fLf0Of6G1Un7htkAxZHkvKo,10453
 cg/cli/set/case.py,sha256=5QFZdnp7XdyaPFl6KDtM31TkX5XFjgOtRjQM2umb3Qk,4613
@@ -225,7 +225,7 @@ cg/constants/slurm.py,sha256=_Y_InISKpGKT-oVMnES7k7Csz2G1l52MNtJwBZm0prI,313
 cg/constants/subject.py,sha256=EE26Emu6T3_HWvsWeuI5GRGGIvB0BwCjN53KHrsr18U,577
 cg/constants/symbols.py,sha256=c06D1mYFWstZbVEgiby2lUNriswUPVRU5TnSSy889tY,71
 cg/constants/tb.py,sha256=UJHdsu109oR_zxvQrko9SqFANiSUn_UJTw5BFebWcds,621
-cg/exc.py,sha256=IYYRa6saq17OT8pA_PBdiorf2XyXTaxNV20JBkdx8QE,8418
+cg/exc.py,sha256=lGr9DFUkOyXzK9y1bF2qxRZT_Tp2Falb5fmAa8fdM94,8553
 cg/io/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/io/api.py,sha256=WaiompYmK4bkl94fZkGzP2CTsQPmHaTSvy0oD0SKw4s,1037
 cg/io/controller.py,sha256=4TTHm9fNY7Ti3S0r-uhxB3oycJ-Ni5Y44lFj5Yvl3_I,2978
@@ -544,7 +544,7 @@ cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/rn
 cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/taxprofiler_sample_sheet_creator.py,sha256=dBbgE0TtZG3xNRrOkLbiGQdY2ZVfCKUsSL4jUOotNuo,1757
 cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/tomte_sample_sheet_creator.py,sha256=8OsMI7ZbcEHsPZAwbG1YRklINBISxsiyli5iaRspKYY,1488
 cg/services/analysis_starter/configurator/file_creators/nextflow/utils.py,sha256=Fr7s-_lo6UHwmmWt4peeW0eZBxB7KZcE_S2CykdIr1M,559
-cg/services/analysis_starter/configurator/implementations/balsamic.py,sha256=-5Omv61f20lQsVf5G_5NCwNPXn-BrRBdgu6XjfrrNUo,2894
+cg/services/analysis_starter/configurator/implementations/balsamic.py,sha256=YUvWwLZlNonqzFUxDKnMwIbtHcGMX1bekiVBR0manCk,3539
 cg/services/analysis_starter/configurator/implementations/microsalt.py,sha256=4bqeDS2LjV5Dl2cQkAb3FOTQ3uEoOXkSMyHP1lhkUKQ,3350
 cg/services/analysis_starter/configurator/implementations/mip_dna.py,sha256=dhzXUGNvFDpgHL-o2Fh24WlDHpJpVrk0bKRrIbm4Ik8,5073
 cg/services/analysis_starter/configurator/implementations/nextflow.py,sha256=hNbFybR1PdpZyasNMMWmVfSRQuLR1NT26dEo8lYldD4,6947
@@ -553,7 +553,7 @@ cg/services/analysis_starter/configurator/models/microsalt.py,sha256=PvwYS9sL1hh
 cg/services/analysis_starter/configurator/models/mip_dna.py,sha256=-9wiSIPeqp7McCnS_MWYS7DqkAoB0BEXVVYGnov1QUg,1156
 cg/services/analysis_starter/configurator/models/nextflow.py,sha256=Ug-Kj179TW5hnaCBPJFu9rigbBnmFYSfv02kkItmn2o,610
 cg/services/analysis_starter/constants.py,sha256=69R7TyZWXQlDMowpV87faHcY7zpH5KTTjHLViYadeo8,268
-cg/services/analysis_starter/factories/configurator_factory.py,sha256=2K3vTqNd-6eZCeajTZ3PsOuik9CUSfrksKulQ7es_jE,12259
+cg/services/analysis_starter/factories/configurator_factory.py,sha256=CB9iyjaH43cEMQb9_Q9JdHGbLvodEwhhXKZatZhkcEI,12295
 cg/services/analysis_starter/factories/starter_factory.py,sha256=hhM-5pRgklJiQ-vZYEyD0bwZ_v1IcybMfVCeKC_ySR8,6138
 cg/services/analysis_starter/input_fetcher/implementations/bam_fetcher.py,sha256=ttpexbRji6VjlxYi_ayevfjNAtgkV25OQbAV7fagKYA,2530
 cg/services/analysis_starter/input_fetcher/implementations/fastq_fetcher.py,sha256=P2NVYgjLNwnmRsebuVVMUA4_ks-1wx2ALfHBxoucmUg,9676
@@ -855,7 +855,7 @@ cg/services/sample_run_metrics_service/utils.py,sha256=BwICxptnhGg8oBghCLhzHaMNu
 cg/services/sequencing_qc_service/__init__.py,sha256=OaL9dyyI6B8uRjopTIoD1zcX_H-SbGj46ZM-V-aoq6w,88
 cg/services/sequencing_qc_service/quality_checks/checks.py,sha256=qdcHRwZD7uxrOmacyiAG4-EN6nG5z-r4rLxcReU5kSI,2593
 cg/services/sequencing_qc_service/quality_checks/utils.py,sha256=2WN7S4kYsN_9iYPx7d4coAYcWHeueQWrPP2pJ8ztMMc,8969
-cg/services/sequencing_qc_service/sequencing_qc_service.py,sha256=2QIJ9IDZeMtO74ZHJ9bfzyK3-RhDK-m9xaoKsi9RHt8,1969
+cg/services/sequencing_qc_service/sequencing_qc_service.py,sha256=QQHShCiq-OAobzHnTKQ1buQVyDIqGbVEPyPM4WEV9B0,2257
 cg/services/sequencing_qc_service/utils.py,sha256=5WHJltBICfRODEzFVPFTdCbGNaMKCaVeOswHgIOGgFc,199
 cg/services/slurm_service/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/services/slurm_service/slurm_cli_service.py,sha256=t-XZoAOPgL-eufwK0A6H8WJvGtfWnlIYxnvKZJIX5-Y,702
@@ -923,7 +923,7 @@ cg/utils/flask/enum.py,sha256=xwNVtFPkSzoloJctLHu7obRyxcng1GJrhkeYkqwf9tw,1052
 cg/utils/mapping.py,sha256=oZpZW2kgsbtAP2FZ7RtRPELiEE1zZk_nAGisHGtCOUo,491
 cg/utils/time.py,sha256=_VOglhrFEZ5cwHK1U1g36SdwzB7UvV-Nvlt4ymuZUho,1501
 cg/utils/utils.py,sha256=RciI_UhWcnG_pMZrmQZ1ZYb-O1N0DweTYMmhE0SIRgQ,1410
-cg-83.15.0.dist-info/METADATA,sha256=wj51NyMN6wmwfhFYzc6eCNr6yc2UzVNWHh5V_r30Vgs,4940
-cg-83.15.0.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-cg-83.15.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.15.0.dist-info/RECORD,,
+cg-83.15.2.dist-info/METADATA,sha256=auXlXIG1QVGKCp6xq7jKsHnieLTQ406wudFiN1HSVww,4940
+cg-83.15.2.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+cg-83.15.2.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.15.2.dist-info/RECORD,,