cg 83.14.0__py3-none-any.whl → 83.15.1__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.14.0"
+__version__ = "83.15.1"

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/services/sequencing_qc_service/quality_checks/checks.py

@@ -7,6 +7,7 @@ from cg.services.sequencing_qc_service.quality_checks.utils import (
     any_sample_in_case_has_reads,
     case_pass_sequencing_qc_on_hifi_yield,
     case_pass_sequencing_qc_on_reads,
+    raw_data_case_pass_qc,
     sample_pass_sequencing_qc_on_reads,
 )
 from cg.store.models import Case
@@ -24,6 +25,7 @@ class SequencingQCCheck(QualityCheck):
     SAMPLE_PASSES: Callable = sample_pass_sequencing_qc_on_reads
     ALL_SAMPLES_IN_CASE_HAVE_READS: Callable = all_samples_in_case_have_reads
     ANY_SAMPLE_IN_CASE_HAS_READS: Callable = any_sample_in_case_has_reads
+    RAW_DATA_CASE_QC: Callable = raw_data_case_pass_qc
 
 
 def get_sequencing_quality_check_for_case(case: Case) -> Callable:
@@ -41,7 +43,7 @@ def get_sequencing_quality_check_for_case(case: Case) -> Callable:
         Workflow.MUTANT: SequencingQCCheck.ANY_SAMPLE_IN_CASE_HAS_READS,
         Workflow.NALLO: SequencingQCCheck.CASE_PASSES_ON_YIELD,
         Workflow.RAREDISEASE: SequencingQCCheck.CASE_PASSES_ON_READS,
-        Workflow.RAW_DATA: SequencingQCCheck.ANY_SAMPLE_IN_CASE_HAS_READS,
+        Workflow.RAW_DATA: SequencingQCCheck.RAW_DATA_CASE_QC,
         Workflow.RNAFUSION: SequencingQCCheck.CASE_PASSES_ON_READS,
         Workflow.TAXPROFILER: SequencingQCCheck.ALL_SAMPLES_IN_CASE_HAVE_READS,
         Workflow.TOMTE: SequencingQCCheck.CASE_PASSES_ON_READS,

cg/services/sequencing_qc_service/quality_checks/utils.py

@@ -1,5 +1,6 @@
 import logging
 
+from cg.constants.devices import DeviceType
 from cg.constants.priority import Priority
 from cg.constants.sequencing import SeqLibraryPrepCategory
 from cg.exc import ApplicationDoesNotHaveHiFiYieldError
@@ -132,6 +133,31 @@ def any_sample_in_case_has_reads(case: Case) -> bool:
     return passed_quality_check
 
 
+def raw_data_case_pass_qc(case: Case) -> bool:
+    if is_case_ready_made_library(case):
+        return ready_made_library_case_pass_sequencing_qc(case)
+    if is_first_sample_yield_based_and_processed(case):
+        return all(sample_has_enough_hifi_yield(sample) for sample in case.samples)
+    elif is_first_sample_reads_based_and_processed(case):
+        return all(sample_has_enough_reads(sample) for sample in case.samples)
+    LOG.warning(f"Not all samples for case {case.internal_id} have been post-processed.")
+    return False
+
+
+def is_first_sample_yield_based_and_processed(case: Case) -> bool:
+    sample: Sample = case.samples[0]
+    if metrics := sample.sample_run_metrics:
+        return metrics[0].type == DeviceType.PACBIO
+    return False
+
+
+def is_first_sample_reads_based_and_processed(case: Case) -> bool:
+    sample: Sample = case.samples[0]
+    if metrics := sample.sample_run_metrics:
+        return metrics[0].type == DeviceType.ILLUMINA
+    return False
+
+
 def is_case_express_priority(case: Case) -> bool:
     """
     Check if a case is express priority.

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-83.14.0.dist-info → cg-83.15.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.14.0
+Version: 83.15.1
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.14.0.dist-info → cg-83.15.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=RgHAoKbllDMi7ckyAB45aoTMtNGv5zZDVucQHnz9MkM,41
+cg/__init__.py,sha256=8ACeYoaEs1BYFgYUmNeRwB0QUDpYryqJO79lU4ZH59A,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
@@ -853,9 +853,9 @@ cg/services/sample_run_metrics_service/dtos.py,sha256=bJ0BL-QkqXIAAIg3F9edIdzAa_
 cg/services/sample_run_metrics_service/sample_run_metrics_service.py,sha256=aQvOuorTG97lUbw7OREO8nsPhO3ouQ38RwksstGwguQ,1795
 cg/services/sample_run_metrics_service/utils.py,sha256=BwICxptnhGg8oBghCLhzHaMNu0LuEV40cSYz1e8mB0A,829
 cg/services/sequencing_qc_service/__init__.py,sha256=OaL9dyyI6B8uRjopTIoD1zcX_H-SbGj46ZM-V-aoq6w,88
-cg/services/sequencing_qc_service/quality_checks/checks.py,sha256=Dew1xNjUBShAgv-kZtHNIL4HK6sMicu-cgACeeDjy20,2523
-cg/services/sequencing_qc_service/quality_checks/utils.py,sha256=JCP__el8dflPuSE0QUea4NdRz_9XWu5l254VizNAy-U,7945
-cg/services/sequencing_qc_service/sequencing_qc_service.py,sha256=2QIJ9IDZeMtO74ZHJ9bfzyK3-RhDK-m9xaoKsi9RHt8,1969
+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=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-83.14.0.dist-info/METADATA,sha256=NfSMZZpwQzFwb2vRaPhpKv6sY5l3gfuNbeDIL81JQyk,4940
-cg-83.14.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-cg-83.14.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.14.0.dist-info/RECORD,,
+cg-83.15.1.dist-info/METADATA,sha256=tIIqVq7JGccOTUpRusR2vHoN8WBQJWunoqbXS4IWrZQ,4940
+cg-83.15.1.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+cg-83.15.1.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.15.1.dist-info/RECORD,,

{cg-83.14.0.dist-info → cg-83.15.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.2.1
+Generator: poetry-core 2.3.0
 Root-Is-Purelib: true
 Tag: py3-none-any