Merge branch 'main' into version_4.88

Clinical-Genomics · Sep 5, 2024 · ae5b172 · ae5b172
2 parents 5277cc0 + 642ecc0
commit ae5b172
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Showing 4 changed files with 6 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Broken upload to Codecov step in Tests & Coverage GitHub action
 - Tomte DROP column names have been updated (backwards compatibility preserved for main fields)
 - WTS outlierS view to display correct individual IDs for cases with multiple individuals
+- WTS outlierS not displayed on WTS outlierS view
 
 ## [4.87.1]
 ### Fixed

diff --git a/scout/adapter/mongo/omics_variant.py b/scout/adapter/mongo/omics_variant.py
@@ -82,7 +82,7 @@ def set_samples(self, case_obj: dict, omics_model: dict):
         )
 
         sample = {
-            "sample_id": match.get("omics_sample_id", match["individual_id"]),
+            "sample_id": match["individual_id"],
             "display_name": match["display_name"],
             "genotype_call": "./1",
         }

diff --git a/scout/build/individual.py b/scout/build/individual.py
@@ -107,7 +107,6 @@ def build_individual(ind: dict) -> dict:
     ind_obj["predicted_ancestry"] = ind.get("predicted_ancestry")
     ind_obj["chromograph_images"] = ind.get("chromograph_images")
     ind_obj["reviewer"] = ind.get("reviewer")
-    ind_obj["omics_sample_id"] = ind.get("omics_sample_id")
     ind_obj["mitodel"] = ind.get("mitodel")
     ind_obj["mitodel_file"] = ind.get("mitodel_file")
 
@@ -143,4 +142,8 @@ def build_individual(ind: dict) -> dict:
     ind_obj["bionano_access"] = ind.get("bionano_access", None)
     ind_obj["fshd_loci"] = ind.get("fshd_loci", None)
 
+    # omics variants
+    if "omics_sample_id" in ind:
+        ind_obj["omics_sample_id"] = ind["omics_sample_id"]
+
     return ind_obj
diff --git a/scout/models/omics_variant.py b/scout/models/omics_variant.py
@@ -231,14 +231,6 @@ def set_omics_variant_id(cls, values) -> "OmicsVariantLoader":
         )
         return values
 
-    @model_validator(mode="before")
-    def set_sample_display_name(cls, values) -> "OmicsVariantLoader":
-        """Set a display name."""
-        values["display_name"] = values.get(
-            "display_name", values.get("sample_name", values.get("individual_id"))
-        )
-        return values
-
 
 def get_qualification(values: dict) -> str:
     """Get qualification string for ID and display name.