Merge pull request #288 from Clinical-Genomics/more_coverage_threshol…

…ds_on_report

Custom coverage thresholds on report

.env

@@ -3,4 +3,5 @@
 # MYSQL_DATABASE_NAME=chanjo2_test
 # MYSQL_HOST_NAME=localhost
 # MYSQL_PORT=3306
+# REPORT_COVERAGE_LEVELS=[100,150,200,300,500]
 DEMO=Y

CHANGELOG.md

@@ -1,6 +1,7 @@
 ## [unreleased]
 ### Added
 - Coverage report and genes coverage overview endpoints now accept also requests with application/x-www-form-urlencoded data
+- Allow system admin to customise coverage levels to be used in reports' metrics by editing the REPORT_COVERAGE_LEVELS in .env file
 ### Changed
 - Templates form submit data as application/x-www-form-urlencoded without having to transform it into json
 ### Fixed

src/chanjo2/models/pydantic_models.py

@@ -1,5 +1,6 @@
 import json
 import logging
+import os
 from datetime import datetime
 from enum import Enum
 from pathlib import Path
@@ -20,6 +21,13 @@
 LOG = logging.getLogger("uvicorn.access")
 
 
+def default_report_coverage_levels() -> List[int]:
+    """Sets the coverage thresholds to be used for report metrics whenever a request doesn't contain 'completeness_thresholds' values."""
+    if os.getenv("REPORT_COVERAGE_LEVELS"):
+        return json.loads(os.getenv("REPORT_COVERAGE_LEVELS"))
+    return DEFAULT_COMPLETENESS_LEVELS
+
+
 class Builds(str, Enum):
     build_37 = "GRCh37"
     build_38 = "GRCh38"
@@ -223,7 +231,7 @@ class ReportQuerySample(BaseModel):
 
 class ReportQuery(BaseModel):
     build: Builds
-    completeness_thresholds: Optional[List[int]] = DEFAULT_COMPLETENESS_LEVELS
+    completeness_thresholds: Optional[List[int]] = default_report_coverage_levels()
     ensembl_gene_ids: Optional[List[str]] = None
     hgnc_gene_ids: Optional[List[int]] = None
     hgnc_gene_symbols: Optional[List[str]] = None
@@ -253,7 +261,7 @@ def as_form(cls, form_data: FormData) -> "ReportQuery":
                 comma_sep_values=form_data.get("completeness_thresholds"),
                 items_format=int,
             )
-            or DEFAULT_COMPLETENESS_LEVELS,
+            or default_report_coverage_levels(),
             ensembl_gene_ids=cls.comma_sep_values_to_list(
                 comma_sep_values=form_data.get("ensembl_gene_ids"), items_format=str
             ),
@@ -294,7 +302,7 @@ def check_genes_lists(cls, values: dict):
 
 class GeneReportForm(BaseModel):
     build: Builds
-    completeness_thresholds: Optional[List[int]] = DEFAULT_COMPLETENESS_LEVELS
+    completeness_thresholds: Optional[List[int]] = default_report_coverage_levels()
     hgnc_gene_id: int
     default_level: int = 10
     samples: List[ReportQuerySample]