feat(gold_standard): add traitFromSourceMappedId to schema (opentarge…

…ts#924) * feat(gold_standard): add traitFromSourceMappedId to schema * chore: adapt tests * feat(feature_matrix): consider `traitFromSourceMappedId` a static column * feat(feature_matrix): consider `traitFromSourceMappedId` an optional column
thehyve · Nov 27, 2024 · 4837a4b · 4837a4b
1 parent 008aa38
commit 4837a4b
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diff --git a/src/gentropy/assets/schemas/l2g_gold_standard.json b/src/gentropy/assets/schemas/l2g_gold_standard.json
@@ -25,6 +25,12 @@
       "nullable": false,
       "metadata": {}
     },
+    {
+      "name": "traitFromSourceMappedId",
+      "type": "string",
+      "nullable": true,
+      "metadata": {}
+    },
     {
       "name": "goldStandardSet",
       "type": "string",

diff --git a/src/gentropy/dataset/l2g_feature_matrix.py b/src/gentropy/dataset/l2g_feature_matrix.py
@@ -39,6 +39,8 @@ def __init__(
         self.fixed_cols = ["studyLocusId", "geneId"]
         if self.with_gold_standard:
             self.fixed_cols.append("goldStandardSet")
+        if "traitFromSourceMappedId" in _df.columns:
+            self.fixed_cols.append("traitFromSourceMappedId")
 
         self.features_list = features_list or [
             col for col in _df.columns if col not in self.fixed_cols

diff --git a/tests/gentropy/dataset/test_l2g_feature_matrix.py b/tests/gentropy/dataset/test_l2g_feature_matrix.py
@@ -87,7 +87,7 @@ def _setup(self: TestFromFeaturesList, spark: SparkSession) -> None:
         """Setup fixture."""
         self.sample_gold_standard = L2GGoldStandard(
             _df=spark.createDataFrame(
-                [(1, "var1", "gwas1", "g1", "positive", ["a_source"])],
+                [(1, "var1", "gwas1", "g1", "efo1", "positive", ["a_source"])],
                 L2GGoldStandard.get_schema(),
             ),
             _schema=L2GGoldStandard.get_schema(),