Merge branch 'dev' of https://github.com/opentargets/genetics_etl_python

into il-group-overlaps
opentargets · Jan 4, 2024 · e119770 · e119770
2 parents 8a93e11 + ee79424
commit e119770
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Showing 2 changed files with 1 addition and 25 deletions.
diff --git a/src/otg/assets/schemas/study_locus.json b/src/otg/assets/schemas/study_locus.json
@@ -164,18 +164,6 @@
               "nullable": true,
               "type": "integer"
             },
-            {
-              "metadata": {},
-              "name": "pValueMantissaConditioned",
-              "nullable": true,
-              "type": "float"
-            },
-            {
-              "metadata": {},
-              "name": "pValueExponentConditioned",
-              "nullable": true,
-              "type": "integer"
-            },
             {
               "metadata": {},
               "name": "beta",
@@ -188,18 +176,6 @@
               "nullable": true,
               "type": "double"
             },
-            {
-              "metadata": {},
-              "name": "betaConditioned",
-              "nullable": true,
-              "type": "double"
-            },
-            {
-              "metadata": {},
-              "name": "standardErrorConditioned",
-              "nullable": true,
-              "type": "double"
-            },
             {
               "metadata": {},
               "name": "r2Overall",

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -192,7 +192,7 @@ def mock_study_locus_data(spark: SparkSession) -> DataFrame:
         .withColumnSpec("finemappingMethod", percentNulls=0.1)
         .withColumnSpec(
             "locus",
-            expr='array(named_struct("is95CredibleSet", cast(rand() > 0.5 as boolean), "is99CredibleSet", cast(rand() > 0.5 as boolean), "logABF", rand(), "posteriorProbability", rand(), "variantId", cast(rand() as string), "beta", rand(), "standardError", rand(), "betaConditioned", rand(), "standardErrorConditioned", rand(), "r2Overall", rand(), "pValueMantissaConditioned", rand(), "pValueExponentConditioned", rand(), "pValueMantissa", rand(), "pValueExponent", rand()))',
+            expr='array(named_struct("is95CredibleSet", cast(rand() > 0.5 as boolean), "is99CredibleSet", cast(rand() > 0.5 as boolean), "logABF", rand(), "posteriorProbability", rand(), "variantId", cast(rand() as string), "beta", rand(), "standardError", rand(), "r2Overall", rand(), "pValueMantissa", rand(), "pValueExponent", rand()))',
             percentNulls=0.1,
         )
     )