cg 83.20.0__py3-none-any.whl → 83.20.2__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.20.0"
+__version__ = "83.20.2"

cg/server/admin.py

@@ -911,6 +911,7 @@ class PacbioSmrtCellMetricsView(BaseView):
 
     column_list = (
         "internal_id",
+        "sequencing_run.run_name",
         "sequencing_run.run_id",
         "movie_name",
         "well",
@@ -935,9 +936,14 @@ class PacbioSmrtCellMetricsView(BaseView):
         "internal_id": view_pacbio_sample_sequencing_metrics_link,
         "model": view_smrt_cell_model,
     }
-    column_labels = {"sequencing_run.run_id": "Run ID"}
+    column_labels = {"sequencing_run.run_name": "Run Name", "sequencing_run.run_id": "Run ID"}
     column_default_sort = ("completed_at", True)
-    column_searchable_list = ["device.internal_id", "movie_name", "sequencing_run.run_id"]
+    column_searchable_list = [
+        "device.internal_id",
+        "movie_name",
+        "sequencing_run.run_id",
+        "sequencing_run.run_name",
+    ]
     column_sortable_list = [
         ("internal_id", "device.internal_id"),
         "started_at",

cg/services/sequencing_qc_service/quality_checks/utils.py

@@ -63,6 +63,9 @@ def express_sample_has_enough_reads(sample: Sample) -> bool:
     Checks if given express sample has enough reads. Gets the threshold from the sample's
     application version.
     """
+    if sample.is_external:
+        LOG.info(f"Sample {sample.internal_id} is external, skipping check.")
+        return True
     express_reads_threshold: int = get_express_reads_threshold_for_sample(sample)
     enough_reads: bool = sample.reads >= express_reads_threshold
     if not enough_reads:
@@ -71,6 +74,9 @@ def express_sample_has_enough_reads(sample: Sample) -> bool:
 
 
 def express_sample_has_enough_yield(sample: Sample) -> bool:
+    if sample.is_external:
+        LOG.info(f"Sample {sample.internal_id} is external, skipping check.")
+        return True
     if not sample.hifi_yield:
         LOG.debug(f"Sample {sample.internal_id} has no hifi yield.")
         return False
@@ -136,26 +142,34 @@ def any_sample_in_case_has_reads(case: Case) -> bool:
 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):
+    if is_any_processed_sample_yield_based(case):
         return all(sample_has_enough_hifi_yield(sample) for sample in case.samples)
-    elif is_first_sample_reads_based_and_processed(case):
+    elif is_any_processed_sample_read_based(case):
         return all(sample_has_enough_reads(sample) for sample in case.samples)
+    elif are_all_samples_external(case):
+        LOG.info(f"All samples in case {case.internal_id} are external, QC passes.")
+        return True
     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_any_processed_sample_yield_based(case: Case) -> bool:
+    """Returns True if any sample has any sample sequencing metrics of Pacbio type."""
+    return any(
+        any(metric.type == DeviceType.PACBIO for metric in sample.sample_run_metrics)
+        for sample in case.samples
+    )
 
 
-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_any_processed_sample_read_based(case: Case) -> bool:
+    return any(
+        any(metric.type == DeviceType.ILLUMINA for metric in sample.sample_run_metrics)
+        for sample in case.samples
+    )
+
+
+def are_all_samples_external(case: Case) -> bool:
+    return all(sample.is_external for sample in case.samples)
 
 
 def is_case_express_priority(case: Case) -> bool:
@@ -205,6 +219,9 @@ def sample_has_enough_reads(sample: Sample) -> bool:
     """
     Check if the sample has more or equal reads than the expected reads for the sample.
     """
+    if sample.is_external:
+        LOG.info(f"Sample {sample.internal_id} is external, skipping check.")
+        return True
     enough_reads: bool = sample.reads >= sample.expected_reads_for_sample
     if not enough_reads:
         LOG.warning(f"Sample {sample.internal_id} has too few reads.")
@@ -218,7 +235,12 @@ def sample_has_enough_hifi_yield(sample: Sample) -> bool:
     Raises:
         ApplicationDoesNotHaveHiFiYieldError if the sample doesn't have expected HiFi yield.
     """
-    if not sample.expected_hifi_yield:
+    if sample.is_external:
+        # An external sample will have None as yield in StatusDB
+        LOG.info(f"Sample {sample.internal_id} is external, skipping check.")
+        return True
+
+    if sample.expected_hifi_yield is None:
         raise ApplicationDoesNotHaveHiFiYieldError(
             f"Application for sample {sample.internal_id} does not have target HiFi yield."
         )

{cg-83.20.0.dist-info → cg-83.20.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.20.0
+Version: 83.20.2
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.20.0.dist-info → cg-83.20.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=U84EL-vxvV632Z0nBmzc8wQ5kA2gkFRMbFq-OAJWA20,41
+cg/__init__.py,sha256=BeY80I67U51q6aLgK7vrT1Z-paSugKRtXMtbF02Y5OY,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
@@ -466,7 +466,7 @@ cg/resources/rnafusion_bundle_filenames.yaml,sha256=hoXuTobKbjH7W7dld87rSF7X0r4K
 cg/resources/taxprofiler_bundle_filenames.yaml,sha256=AULMEAYkMzADYUtVtuSmBj7UaAIlLGRDyBMEOO0xWz8,2871
 cg/resources/tomte_bundle_filenames.yaml,sha256=lFxk9GssmCyKBUn5lbRBtBS9FS9cABaoVzb-e2zrJac,4144
 cg/server/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cg/server/admin.py,sha256=cvVOR9eMtSbLn7zIGVYjRz8sQ5WnD0x4Hc34yTZVaMk,30123
+cg/server/admin.py,sha256=65jyelYOwJXoltuTNM8NJXdZbam2ROMIq5m9qBN5T7c,30263
 cg/server/app.py,sha256=WEULzx5JeC0aJHag3Vltzopd8r7tgHPr_1nbytS-AI8,6975
 cg/server/app_config.py,sha256=8DaNtYtdp6A29FAuTFX-Lk7SLv7Zx-_f57ZU0-T_3ZI,1403
 cg/server/auto.py,sha256=5DqokNScv483imZTvOYrJo6wV9-P7ZGnJaaHnfnNJLs,57
@@ -853,7 +853,7 @@ cg/services/sample_run_metrics_service/sample_run_metrics_service.py,sha256=aQvO
 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=qdcHRwZD7uxrOmacyiAG4-EN6nG5z-r4rLxcReU5kSI,2593
-cg/services/sequencing_qc_service/quality_checks/utils.py,sha256=2WN7S4kYsN_9iYPx7d4coAYcWHeueQWrPP2pJ8ztMMc,8969
+cg/services/sequencing_qc_service/quality_checks/utils.py,sha256=MkFUyQQz1RFHbgD9cyqEuOkYe0NYQlbkJkyy9BkOWQw,9844
 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
@@ -922,7 +922,7 @@ 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-83.20.0.dist-info/METADATA,sha256=pyTGhg9xcSSz96tYt1RQZGZDd5jcWC6KZkBm1RJtK8Q,4940
-cg-83.20.0.dist-info/WHEEL,sha256=kJCRJT_g0adfAJzTx2GUMmS80rTJIVHRCfG0DQgLq3o,88
-cg-83.20.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.20.0.dist-info/RECORD,,
+cg-83.20.2.dist-info/METADATA,sha256=UdpEj8WSTQ1TsybITznTSh8ak0oewz9hSw1rF31ijEA,4940
+cg-83.20.2.dist-info/WHEEL,sha256=kJCRJT_g0adfAJzTx2GUMmS80rTJIVHRCfG0DQgLq3o,88
+cg-83.20.2.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.20.2.dist-info/RECORD,,