deprecate evidence and mousePhenotype steps (#402)

* deprecate evidence step and all dependencies

* deprecate mousephenotype step and all dependencies

Author: ireneisdoomed

src/main/scala/io/opentargets/etl/Main.scala

@@ -6,7 +6,7 @@ import scala.util._
 import io.opentargets.etl.backend._
 import io.opentargets.etl.backend.target.Target
 import io.opentargets.etl.backend.drug.Drug
-import io.opentargets.etl.backend.evidence.Evidence
+
 import io.opentargets.etl.backend.literature.Literature
 import io.opentargets.etl.backend.searchFacet.FacetSearch
 import io.opentargets.etl.backend.pharmacogenomics.Pharmacogenomics
@@ -19,7 +19,6 @@ object ETL extends LazyLogging {
       case "association"      => Association()
       case "association_otf"  => AssociationOTF()
       case "drug"             => Drug()
-      case "evidence"         => Evidence()
       case "expression"       => Expression()
       case "openfda"          => OpenFda()
       case "go"               => Go()
@@ -34,7 +33,7 @@ object ETL extends LazyLogging {
       case "search_facet"     => FacetSearch()
       case "target"           => Target()
       case "target_engine"    => TargetEngine()
-      case "mouse_phenotype"  => MousePhenotype()
+      
       case _                  => throw new IllegalArgumentException(s"step $step is unknown")
     }
     logger.info(s"finished running step $step")

src/main/scala/io/opentargets/etl/backend/Configuration.scala

@@ -58,35 +58,7 @@ object Configuration extends LazyLogging {
       output: IOResourceConfigurations
   )
 
-  // evidence
-  case class EvidenceEntry(
-      id: String,
-      uniqueFields: List[String],
-      datatypeId: Option[String],
-      scoreExpr: String,
-      excludedBiotypes: Option[List[String]]
-  )
-
-  case class DirectionOfEffectSection(
-      varFilterLof: List[String],
-      gof: List[String],
-      lof: List[String],
-      oncotsgList: List[String],
-      inhibitors: List[String],
-      activators: List[String],
-      sources: List[String]
-  )
-
-  case class EvidenceSection(
-      input: IOResourceConfigurations,
-      uniqueFields: List[String],
-      scoreExpr: String,
-      datatypeId: String,
-      dataSourcesExclude: List[String],
-      dataSources: List[EvidenceEntry],
-      directionOfEffect: DirectionOfEffectSection,
-      output: IOResourceConfigurations
-  )
+  
 
   // expression
   case class ExpressionSection(
@@ -164,11 +136,7 @@ object Configuration extends LazyLogging {
       epmc: Epmc
   )
 
-  // mouse_phenotype
-  case class MousePhenotypeSection(
-      input: IOResourceConfigurations,
-      output: IOResourceConfigurations
-  )
+  
 
   // openfda
   case class OpenfdaMontecarloSection(
@@ -262,13 +230,11 @@ object Configuration extends LazyLogging {
       association: AssociationSection,
       associationOtf: AssociationOTFSection,
       drug: DrugSection,
-      evidence: EvidenceSection,
       expression: ExpressionSection,
       go: GOSection,
       interaction: InteractionSection,
       knownDrug: KnownDrugSection,
       literature: LiteratureSection,
-      mousePhenotype: MousePhenotypeSection,
       openfda: OpenfdaSection,
       otar: OtarSection,
       pharmacogenomics: PharmacogenomicsSection,

src/main/scala/io/opentargets/etl/backend/ETLSessionContext.scala

@@ -19,18 +19,11 @@ object ETLSessionContext extends LazyLogging {
       config <- Configuration.config
     } yield {
       logger.info("Generating ETL Session Context")
-      val filteredEvidence = if (config.steps.evidence.dataSourcesExclude.nonEmpty) {
-        logger.info(s"Excluding evidence datasources: ${config.steps.evidence.dataSourcesExclude}")
-        val ds = config.steps.evidence.dataSources.filter(d =>
-          !config.steps.evidence.dataSourcesExclude.contains(d.id)
-        )
-        config.steps.evidence.copy(dataSources = ds)
-      } else config.steps.evidence
 
       val configurations = config.sparkSettings.defaultSparkSessionConfig
 
       ETLSessionContext(
-        config.copy(steps = config.steps.copy(evidence = filteredEvidence)),
+        config,
         getOrCreateSparkSession(progName, configurations, config.sparkUri)
       )
     }