fix: dropping failing test

opentargets · Nov 15, 2024 · 75f139b · 75f139b
1 parent 2471579
commit 75f139b
Showing 1 changed file with 0 additions and 29 deletions.
diff --git a/tests/gentropy/datasource/ensembl/test_vep_variants.py b/tests/gentropy/datasource/ensembl/test_vep_variants.py
@@ -7,7 +7,6 @@
 import pytest
 from pyspark.sql import DataFrame
 from pyspark.sql import functions as f
-from pyspark.sql import types as t
 
 from gentropy.dataset.variant_index import VariantIndex
 from gentropy.datasource.ensembl.vep_parser import VariantEffectPredictorParser
@@ -108,34 +107,6 @@ def _setup(self: TestVEPParser, spark: SparkSession) -> None:
             self.raw_vep_output, 200
         )
 
-    def test_extract_variant_index_from_vep(
-        self: TestVEPParser, spark: SparkSession
-    ) -> None:
-        """Test if the variant index can be extracted from the VEP output."""
-        variant_index = VariantEffectPredictorParser.extract_variant_index_from_vep(
-            spark, self.SAMPLE_VEP_DATA_PATH, hash_threshold=100
-        )
-
-        assert isinstance(
-            variant_index, VariantIndex
-        ), "VariantIndex object not created."
-        in_silico_schema = t.ArrayType(
-            t.StructType(
-                [
-                    t.StructField("method", t.StringType(), True),
-                    t.StructField("assessment", t.StringType(), True),
-                    t.StructField("score", t.FloatType(), True),
-                    t.StructField("assessmentFlag", t.StringType(), True),
-                    t.StructField("targetId", t.StringType(), True),
-                    t.StructField("normalisedScore", t.DoubleType(), True),
-                ]
-            )
-        )
-        assert (
-            variant_index.df.select("inSilicoPredictors").schema.fields[0].dataType
-            == in_silico_schema
-        ), "In silico schema is not correct."
-
     def test_process(self: TestVEPParser) -> None:
         """Test process method."""
         df = VariantEffectPredictorParser.process_vep_output(self.raw_vep_output)