cg 83.20.2__py3-none-any.whl → 84.0.0__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.20.2"
+__version__ = "84.0.0"

cg/server/endpoints/sequencing_run/dtos.py

@@ -19,20 +19,22 @@ class PacbioSmrtCellMetricsDTO(BaseModel):
     p2_percent: float
     percent_reads_passing_q30: float
     plate: int
-    run_name: str
+    run_id: str
     started_at: datetime
     well: str
 
 
 class PacbioSmrtCellMetricsResponse(BaseModel):
-    runs: list[PacbioSmrtCellMetricsDTO]
+    metrics: list[PacbioSmrtCellMetricsDTO]
 
 
 class PacbioSequencingRunDTO(BaseModel):
     id: int
-    run_name: str
     comment: str
     processed: bool
+    run_id: str
+    run_name: str | None
+    unique_id: str | None
 
 
 class PacbioSequencingRunResponse(BaseModel):

cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py

@@ -11,10 +11,10 @@ PACBIO_SMRT_CELL_METRICS_BLUEPRINT = Blueprint(
 PACBIO_SMRT_CELL_METRICS_BLUEPRINT.before_request(before_request)
 
 
-@PACBIO_SMRT_CELL_METRICS_BLUEPRINT.route("/<run_name>", methods=["GET"])
+@PACBIO_SMRT_CELL_METRICS_BLUEPRINT.route("/<run_id>", methods=["GET"])
 @handle_missing_entries
-def get_smrt_cell_metrics(run_name: str):
+def get_smrt_cell_metrics(run_id: str):
     response: PacbioSmrtCellMetricsResponse = (
-        pacbio_sequencing_runs_service.get_sequencing_runs_by_name(run_name)
+        pacbio_sequencing_runs_service.get_sequencing_runs_by_run_id(run_id)
     )
     return jsonify(response.model_dump())

cg/services/run_devices/pacbio/sequencing_runs_service.py

@@ -13,17 +13,17 @@ class PacbioSequencingRunsService:
     def __init__(self, store: Store):
         self.store = store
 
-    def get_sequencing_runs_by_name(self, run_name: str) -> PacbioSmrtCellMetricsResponse:
+    def get_sequencing_runs_by_run_id(self, run_id: str) -> PacbioSmrtCellMetricsResponse:
         metrics: list[PacbioSmrtCellMetricsDTO] = []
         db_smrt_cell_metrics: list[PacbioSMRTCellMetrics] = (
-            self.store.get_pacbio_smrt_cell_metrics_by_run_id(run_name)
+            self.store.get_pacbio_smrt_cell_metrics_by_run_id(run_id)
         )
         for metric in db_smrt_cell_metrics:
             metric_dict = metric.to_dict()
             metric_dict["internal_id"] = metric.device.internal_id
-            metric_dict["run_name"] = metric.run_id
+            metric_dict["run_id"] = metric.run_id
             metrics.append(PacbioSmrtCellMetricsDTO.model_validate(metric_dict))
-        return PacbioSmrtCellMetricsResponse(runs=metrics)
+        return PacbioSmrtCellMetricsResponse(metrics=metrics)
 
     def get_sequencing_runs(self, page: int = 0, page_size: int = 0) -> PacbioSequencingRunResponse:
         db_runs, total_count = self.store.get_pacbio_sequencing_runs(page=page, page_size=page_size)
@@ -31,9 +31,11 @@ class PacbioSequencingRunsService:
         for db_run in db_runs:
             run = PacbioSequencingRunDTO(
                 id=db_run.id,
-                run_name=db_run.run_id,
+                run_id=db_run.run_id,
+                run_name=db_run.run_name,
                 comment=db_run.comment,
                 processed=db_run.processed,
+                unique_id=db_run.unique_id,
             )
             runs.append(run)
         return PacbioSequencingRunResponse(pacbio_sequencing_runs=runs, total_count=total_count)

cg/services/sequencing_qc_service/quality_checks/utils.py

@@ -63,9 +63,6 @@ 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:
@@ -74,9 +71,6 @@ 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
@@ -142,34 +136,26 @@ 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_any_processed_sample_yield_based(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_any_processed_sample_read_based(case):
+    elif is_first_sample_reads_based_and_processed(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_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_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 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 are_all_samples_external(case: Case) -> bool:
-    return all(sample.is_external 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_case_express_priority(case: Case) -> bool:
@@ -219,9 +205,6 @@ 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.")
@@ -235,12 +218,7 @@ def sample_has_enough_hifi_yield(sample: Sample) -> bool:
     Raises:
         ApplicationDoesNotHaveHiFiYieldError if the sample doesn't have 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:
+    if not sample.expected_hifi_yield:
         raise ApplicationDoesNotHaveHiFiYieldError(
             f"Application for sample {sample.internal_id} does not have target HiFi yield."
         )

{cg-83.20.2.dist-info → cg-84.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.20.2
+Version: 84.0.0
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.20.2.dist-info → cg-84.0.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=BeY80I67U51q6aLgK7vrT1Z-paSugKRtXMtbF02Y5OY,41
+cg/__init__.py,sha256=-0zb_Vkke33twQaAco0uQC7O2Ll3XJ-mQnXVj4OaNnc,40
 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
@@ -497,9 +497,9 @@ cg/server/endpoints/sequencing_metrics/dtos.py,sha256=DXh9xFLrS0RQIxHrkAZa71AkcL
 cg/server/endpoints/sequencing_metrics/error_handler.py,sha256=rVASP7uk1qSA5qu__-JcSZ6vXpBy3s7n4GdBVg0zAUA,758
 cg/server/endpoints/sequencing_metrics/illumina_sequencing_metrics.py,sha256=IvXMH2KIeOH98lJkaFLPFIRj7j6uW3oBaJZozQ5Tva0,810
 cg/server/endpoints/sequencing_metrics/pacbio_sequencing_metrics.py,sha256=iglo2cOYSPuK4HAWH4XPGLgbZOst2spdB7A6mQ8th8g,1218
-cg/server/endpoints/sequencing_run/dtos.py,sha256=ezs1TW0XyKO8gYyRreq6iQsFwLtgV8tzO96fzXT6kWg,1023
+cg/server/endpoints/sequencing_run/dtos.py,sha256=o2al0uUnGbZdMRvOZ5z9zb67peJmBM7EyBSA7xizv3Y,1073
 cg/server/endpoints/sequencing_run/pacbio_sequencing_run.py,sha256=HvV7EPwrh_xe5ZjerQYoBK-bIdKLBZ1nk16whGSDAmw,1524
-cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py,sha256=FVETf-KUghGbb7KGO2sDYWISp3Z9gnublo-9ekQHUuk,819
+cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py,sha256=0cV6wybrsLmYMuW3noM6RHy8Sb7RunavMEpWMSJtiAo,815
 cg/server/endpoints/users.py,sha256=48z9Si2EuJ6wcN8jBIr0yvmtgygozYgUIytyFuTzFao,696
 cg/server/endpoints/utils.py,sha256=RjhrcBqY3Mfg_hZIeXr6SfmCTu4FMpan-n5UNDjOeMg,2251
 cg/server/ext.py,sha256=rQIv4qKS_N5whB158SGa2FZp-JuGDaUydCBjGhAxaOE,3923
@@ -842,7 +842,7 @@ cg/services/run_devices/pacbio/run_data_generator/run_data.py,sha256=h0TfMtHwyXl
 cg/services/run_devices/pacbio/run_file_manager/models.py,sha256=C6kycBPx6YKNq2oFJOIhdrcPloi3QIBOrlbaAgeYzgs,192
 cg/services/run_devices/pacbio/run_file_manager/run_file_manager.py,sha256=QDJKvMTwHNlP9ovU5wgqA8FbTx6xI0zdc26A1RY4W1M,5440
 cg/services/run_devices/pacbio/run_validator/pacbio_run_validator.py,sha256=d8fvmJcByEFPMnwqOe6mQsXXIO87WkXwfK9L_Bx7whg,3037
-cg/services/run_devices/pacbio/sequencing_runs_service.py,sha256=n_noNrPfOAUGizgTpE5n1ezZA0O92XAB9o_FYIzcus8,2145
+cg/services/run_devices/pacbio/sequencing_runs_service.py,sha256=VLc5EicDpD2fb-fz_x7G5j3qcHRl75N5cCaky5DriNQ,2228
 cg/services/run_devices/run_names/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/services/run_devices/run_names/pacbio.py,sha256=4l-fCejTMMgAnVQ2RqIyQaqMtVbs_SeDEm6JJ4Dg36U,678
 cg/services/run_devices/run_names/service.py,sha256=d6-paeXsENHlU59eo4FcSXBAhoz50oL6bSglscRo2rQ,293
@@ -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=MkFUyQQz1RFHbgD9cyqEuOkYe0NYQlbkJkyy9BkOWQw,9844
+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
@@ -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-83.20.2.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,,
+cg-84.0.0.dist-info/METADATA,sha256=CBtOiLTIEUPklgHRGi26_vu_dZqtde_Iq8sj4FiPcEE,4939
+cg-84.0.0.dist-info/WHEEL,sha256=kJCRJT_g0adfAJzTx2GUMmS80rTJIVHRCfG0DQgLq3o,88
+cg-84.0.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-84.0.0.dist-info/RECORD,,