Validate mapped rate

cg/constants/constants.py

@@ -213,6 +213,7 @@ class APIMethods(StrEnum):
 class MicrosaltQC:
     QC_PERCENT_THRESHOLD_MWX: float = 0.1
     COVERAGE_10X_THRESHOLD: float = 0.75
+    MAPPED_RATE_THRESHOLD: float = 0.3
     NEGATIVE_CONTROL_READS_THRESHOLD: float = 0.2
     TARGET_READS: int = 6000000
     TARGET_READS_FAIL_THRESHOLD: float = 0.7

cg/meta/workflow/microsalt/models.py

@@ -29,7 +29,7 @@ class MicrosaltSamtoolsStats(BaseModel):
     coverage_100x: float
 
 
-class Sample(BaseModel):
+class SampleMetrics(BaseModel):
     blast_pubmlst: BlastPubmlst
     quast_assembly: QuastAssembly
     blast_resfinder_resistence: List[str]
@@ -38,4 +38,10 @@ class Sample(BaseModel):
 
 
 class QualityMetrics(BaseModel):
-    samples: Dict[str, Sample]
+    samples: Dict[str, SampleMetrics]
+
+
+class QualityResult(BaseModel):
+    sample_id: str
+    passed: bool
+    fail_message: str | None = None

cg/meta/workflow/microsalt/quality_checker.py

@@ -4,7 +4,13 @@
 from cg.io.json import read_json, write_json
 
 from cg.constants.constants import MicrosaltAppTags, MicrosaltQC
-from cg.meta.workflow.microsalt.utils import is_valid_total_reads, is_valid_total_reads_for_control
+from cg.meta.workflow.microsalt.models import QualityMetrics, QualityResult, SampleMetrics
+from cg.meta.workflow.microsalt.utils import (
+    is_valid_mapped_rate,
+    is_valid_total_reads,
+    is_valid_total_reads_for_control,
+    parse_quality_metrics,
+)
 from cg.models.orders.sample_base import ControlEnum
 from cg.store.api.core import Store
 from cg.store.models import Sample
@@ -16,6 +22,27 @@ class QualityChecker:
     def __init__(self, status_db: Store):
         self.status_db = status_db
 
+    def quality_control(self, run_dir_path: Path, lims_project: str):
+        metrics_file_path: Path = Path(run_dir_path, f"{lims_project}.json")
+        quality_metrics: QualityMetrics = parse_quality_metrics(metrics_file_path)
+
+        sample_results: list[QualityResult] = []
+
+        for sample_metrics in quality_metrics:
+            result = self.quality_control_sample(sample_metrics)
+            sample_results.append(result)
+
+        self.quality_control_case(sample_results)
+
+    def quality_control_sample(
+        self, sample_id: str, sample_metrics: SampleMetrics
+    ) -> QualityResult:
+        reads_passes_qc: bool = self.is_valid_total_reads(sample_id)
+        mapped_rate_passes_qc: bool = self.is_valid_mapped_rate(sample_metrics)
+
+    def quality_control_case(self, sample_results: list[QualityResult]) -> bool:
+        pass
+
     def microsalt_qc(self, case_id: str, run_dir_path: Path, lims_project: str) -> bool:
         """Check if given microSALT case passes QC check."""
         failed_samples: dict = {}
@@ -131,3 +158,7 @@ def is_valid_total_reads(self, sample_id: str) -> bool:
                 sample_reads=sample_reads, target_reads=target_reads
             )
         return is_valid_total_reads(sample_reads=sample_reads, target_reads=target_reads)
+
+    def is_valid_mapped_rate(self, metrics: SampleMetrics) -> bool:
+        mapped_rate: float = metrics.microsalt_samtools_stats.mapped_rate
+        return is_valid_mapped_rate(mapped_rate)

cg/meta/workflow/microsalt/utils.py

@@ -1,4 +1,8 @@
+from pathlib import Path
+
 from cg.constants.constants import MicrosaltQC
+from cg.io.json import read_json
+from cg.meta.workflow.microsalt.models import QualityMetrics
 
 
 def is_valid_total_reads(sample_reads: int, target_reads: int) -> bool:
@@ -7,3 +11,12 @@ def is_valid_total_reads(sample_reads: int, target_reads: int) -> bool:
 
 def is_valid_total_reads_for_control(sample_reads: int, target_reads: int) -> bool:
     return sample_reads < target_reads * MicrosaltQC.NEGATIVE_CONTROL_READS_THRESHOLD
+
+
+def is_valid_mapped_rate(sample_mapped_rate: float) -> bool:
+    return sample_mapped_rate > MicrosaltQC.MAPPED_RATE_THRESHOLD
+
+
+def parse_quality_metrics(file_path: Path) -> QualityMetrics:
+    data = read_json(file_path)
+    return QualityMetrics.model_validate_json(data)