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DSuvegesireneisdoomed
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fix: removing reference to missing chembl column
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src/main/scala/io/opentargets/etl/backend/drug/Molecule.scala

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@ object Molecule extends LazyLogging {
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val hierarchy: DataFrame = processMoleculeHierarchy(mols)
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// combine molecule components
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val molCombined = mols
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.drop("cross_references", "syns", "chebi_par_id")
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.drop("cross_references", "syns")
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.join(synonyms, Seq("id"), "left_outer")
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.join(crossReferences, Seq("id"), "left_outer")
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.join(hierarchy, Seq("id"), "left_outer")
@@ -72,7 +72,6 @@ object Molecule extends LazyLogging {
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col("molecule_structures.canonical_smiles").as("canonicalSmiles"),
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col("molecule_structures.standard_inchi_key").as("inchiKey"),
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coalesce(col("molecule_type"), lit("Unknown")).as("drugType"),
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col("chebi_par_id"),
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col("black_box_warning").as("blackBoxWarning"),
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col("pref_name").as("name"),
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col("cross_references"),
@@ -156,8 +155,7 @@ object Molecule extends LazyLogging {
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val chemblCrossReferences = processChemblCrossReferences(preProcessedMolecules)
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val singletonRefs: List[(String, String)] = List(
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("drugbank_id", "drugbank"),
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("chebi_par_id", "chEBI")
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("drugbank_id", "drugbank")
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)
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val references = singletonRefs

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