add(yield parsing to bclconvert metrics parser)

cg/services/bcl_convert_metrics_service/bcl_convert_metrics_service.py

@@ -6,7 +6,11 @@
 from cg.constants.devices import DeviceType
 from cg.models.flow_cell.flow_cell import FlowCellDirectoryData
 from cg.services.bcl_convert_metrics_service.parser import MetricsParser
-from cg.store.models import SampleLaneSequencingMetrics, IlluminaSampleSequencingMetrics
+from cg.store.models import (
+    SampleLaneSequencingMetrics,
+    IlluminaSampleSequencingMetrics,
+    IlluminaSequencingRun,
+)
 from cg.store.store import Store
 from cg.utils.flow_cell import get_flow_cell_id
 
@@ -84,7 +88,6 @@ def _create_bcl_convert_sequencing_metrics(
     def create_sample_run_metrics(
         sample_internal_id: str,
         lane: int,
-        run_metrics_id: int,
         metrics_parser: MetricsParser,
         store: Store,
     ) -> IlluminaSampleSequencingMetrics:
@@ -101,21 +104,29 @@ def create_sample_run_metrics(
         )
         sample_id: int = store.get_sample_by_internal_id(sample_internal_id).id
 
+        yield_: float = metrics_parser.get_yield_for_sample_in_lane(
+            sample_internal_id=sample_internal_id, lane=lane
+        )
+        yield_q30: float = metrics_parser.get_yield_q30_for_sample_in_lane(
+            sample_internal_id=sample_internal_id, lane=lane
+        )
+
         return IlluminaSampleSequencingMetrics(
-            run_metrics_id=run_metrics_id,
             sample_id=sample_id,
             type=DeviceType.ILLUMINA,
             flow_cell_lane=lane,
             total_reads_in_lane=total_reads,
             base_percentage_passing_q30=q30_bases_percent,
             base_mean_quality_score=mean_quality_score,
+            _yield=yield_,
+            yield_q30=yield_q30,
             created_at=datetime.now(),
         )
 
     def create_sample_sequencing_metrics_for_flow_cell(
         self,
         flow_cell_directory: Path,
-        run_metrics_id: int,
+        sequencing_run: IlluminaSequencingRun,
         store: Store,
     ) -> list[IlluminaSampleSequencingMetrics]:
         """Parse the demultiplexing metrics data into the sequencing statistics model."""
@@ -129,8 +140,8 @@ def create_sample_sequencing_metrics_for_flow_cell(
                     sample_internal_id=sample_internal_id,
                     lane=lane,
                     metrics_parser=metrics_parser,
-                    run_metrics_id=run_metrics_id,
                     store=store,
                 )
+                sample_lane_sequencing_metrics.instrument_run = sequencing_run
                 sample_lane_sequencing_metrics.append(metrics)
         return sample_lane_sequencing_metrics

cg/services/bcl_convert_metrics_service/models.py

@@ -12,6 +12,8 @@ class SequencingQualityMetrics(BaseModel):
         ..., alias=QualityMetricsColumnNames.MEAN_QUALITY_SCORE_Q30
     )
     q30_bases_percent: float = Field(..., alias=QualityMetricsColumnNames.Q30_BASES_PERCENT)
+    yield_: int = Field(..., alias=QualityMetricsColumnNames.YIELD)
+    yield_q30: float = Field(..., alias=QualityMetricsColumnNames.YIELD_Q30)
 
 
 class DemuxMetrics(BaseModel):

cg/services/bcl_convert_metrics_service/parser.py

@@ -112,6 +112,20 @@ def get_q30_bases_percent_for_sample_in_lane(self, sample_internal_id: str, lane
         )
         return self.calculate_mean_read_pair_q30_bases_percent(metrics=metrics)
 
+    def get_yield_for_sample_in_lane(self, sample_internal_id: str, lane: int) -> float:
+        """Return the yield for a sample and lane."""
+        metrics: list[SequencingQualityMetrics] = self.get_read_pair_metrics_for_sample_and_lane(
+            sample_internal_id=sample_internal_id, lane=lane
+        )
+        return self.calculate_mean_yield(metrics=metrics)
+
+    def get_yield_q30_for_sample_in_lane(self, sample_internal_id: str, lane: int) -> float:
+        """Return the yield Q30 for a sample and lane."""
+        metrics: list[SequencingQualityMetrics] = self.get_read_pair_metrics_for_sample_and_lane(
+            sample_internal_id=sample_internal_id, lane=lane
+        )
+        return self.calculate_mean_yield_q30(metrics=metrics)
+
     @classmethod
     def calculate_mean_read_pair_q30_bases_percent(
         cls, metrics: list[SequencingQualityMetrics]
@@ -130,6 +144,22 @@ def calculate_mean_quality_score(cls, metrics: list[SequencingQualityMetrics]) -
             total_q_score += metric.mean_quality_score_q30
         return round(total_q_score / SCALE_TO_READ_PAIRS, 2)
 
+    @classmethod
+    def calculate_mean_yield(cls, metrics: list[SequencingQualityMetrics]) -> float:
+        """Calculate the mean yield for a list of metrics."""
+        total_yield: float = 0
+        for metric in metrics:
+            total_yield += metric.yield_
+        return round(total_yield / SCALE_TO_READ_PAIRS, 2)
+
+    @classmethod
+    def calculate_mean_yield_q30(cls, metrics: list[SequencingQualityMetrics]) -> float:
+        """Calculate the mean yield Q30 for a list of metrics."""
+        total_yield_q30: float = 0
+        for metric in metrics:
+            total_yield_q30 += metric.yield_q30
+        return round(total_yield_q30 / SCALE_TO_READ_PAIRS, 2)
+
     def get_mean_quality_score_for_sample_in_lane(
         self, sample_internal_id: str, lane: int
     ) -> float:

cg/services/illumina_post_processing_service/illumina_post_processing_service.py

@@ -7,10 +7,8 @@
 from cg.constants.devices import DeviceType
 from cg.exc import MissingFilesError, FlowCellError
 from cg.models.flow_cell.flow_cell import FlowCellDirectoryData
-from cg.services.illumina_post_processing_service.database_utils import store_illumina_flow_cell
 from cg.services.illumina_post_processing_service.utils import (
     create_delivery_file_in_flow_cell_directory,
-    get_flow_cell_model_from_run_parameters,
 )
 from cg.services.illumina_post_processing_service.validation import (
     is_flow_cell_ready_for_postprocessing,
@@ -45,7 +43,6 @@ def store_illumina_flow_cell(
     @staticmethod
     def store_illumina_sequencing_metrics(flow_cell: IlluminaFlowCell) -> None:
         """Store illumina run metrics in the status database."""
-        pass
 
     @staticmethod
     def store_illumina_sample_sequencing_metrics():

tests/services/bcl_convert_metrics_service/conftest.py

@@ -81,6 +81,8 @@ def bcl_convert_quality_metric_model_with_data(
             QualityMetricsColumnNames.SAMPLE_INTERNAL_ID.value: test_sample_internal_id,
             QualityMetricsColumnNames.MEAN_QUALITY_SCORE_Q30.value: 36.15,
             QualityMetricsColumnNames.Q30_BASES_PERCENT.value: 0.95,
+            QualityMetricsColumnNames.YIELD.value: 415032696,
+            QualityMetricsColumnNames.YIELD_Q30.value: 393745856,
         }
     )