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Fix: issues with pipeline run #411

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Merged
DSuveges merged 2 commits into from
Feb 20, 2026
Merged

Fix: issues with pipeline run #411

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a8e9aaf
fix(EBISearch): following up association score column name change
DSuveges Feb 20, 2026
0e2f69a
fix(search): association score change
DSuveges Feb 20, 2026
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3 changes: 2 additions & 1 deletion src/main/scala/io/opentargets/etl/backend/Search.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -782,9 +782,10 @@ object Search extends LazyLogging {

// TODO check the overall score column name
logger.info("subselect indirect LLR associations just id and score and persist")

val associationScores = inputDataFrame("association").data
.withColumn("associationId", concat_ws("-", col("diseaseId"), col("targetId")))
.withColumnRenamed("overallDatasourceHarmonicScore", "score")
.withColumnRenamed("associationScore", "score")
.select(associationColumns.head, associationColumns.tail: _*)
.persist(StorageLevel.DISK_ONLY)

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18 changes: 15 additions & 3 deletions src/main/scala/io/opentargets/etl/backend/SearchEBI.scala
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Expand Up @@ -4,6 +4,7 @@ import com.typesafe.scalalogging.LazyLogging
import org.apache.spark.sql._
import io.opentargets.etl.backend.spark.{IOResource, IoHelpers}
import org.apache.spark.sql.SparkSession
import org.apache.spark.sql.functions.col

object SearchEBI extends LazyLogging {

Expand All @@ -17,13 +18,24 @@ object SearchEBI extends LazyLogging {
val datasetAssociations = associationsDirectOverall
.join(targets, Seq("targetId"), "inner")
.join(diseases, Seq("diseaseId"), "inner")
.select("targetId", "diseaseId", "approvedSymbol", "name", "score")
.select(
col("targetId"),
col("diseaseId"),
col("approvedSymbol"),
col("name"),
col("associationScore").alias("score")
)

val datasetEvidence = evidence
.join(targets, Seq("targetId"), "inner")
.join(diseases, Seq("diseaseId"), "inner")
.select("targetId", "diseaseId", "approvedSymbol", "name", "score")

.select(
col("targetId"),
col("diseaseId"),
col("approvedSymbol"),
col("name"),
col("associationScore").alias("score")
)
Map(
"ebisearchAssociations" -> datasetAssociations,
"ebisearchEvidence" -> datasetEvidence
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