moved database/viw creation of mapper outside the source/dataset code

tomalf2 · Jul 25, 2019 · b8eec00 · b8eec00
1 parent 6dd2cf0
commit b8eec00
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Showing 2 changed files with 25 additions and 8 deletions.
diff --git a/src/main/scala/it/polimi/genomics/metadata/Program.scala b/src/main/scala/it/polimi/genomics/metadata/Program.scala
@@ -4,6 +4,8 @@ import java.io.File
 
 import it.polimi.genomics.metadata.database.FileDatabase
 import it.polimi.genomics.metadata.downloader_transformer.Downloader
+import it.polimi.genomics.metadata.mapper.RemoteDatabase.DbHandler
+import it.polimi.genomics.metadata.step.MapperStep.logger
 import it.polimi.genomics.metadata.step._
 import it.polimi.genomics.metadata.step.utils.ExecutionLevel.{ExecutionLevel, _}
 import it.polimi.genomics.metadata.step.utils.{ParameterUtil, SchemaLocation, SchemaValidator}
@@ -417,6 +419,15 @@ object Program extends App {
   }
 
   def executeLevel(sources: Seq[Source], level: ExecutionLevel, parallelExecution: Boolean): Unit = {
+
+    //new lines to test
+    if(level == Map) {
+      DbHandler.setDatabase
+      DbHandler.setDWViews
+      DbHandler.setFlattenMaterialized
+      logger.info("Database has been set")
+    }
+
     val integrateThreads = sources.filter(_.isEnabled(level)).map(source => {
       new Thread {
         override def run(): Unit = {
@@ -446,6 +457,13 @@ object Program extends App {
     else
       integrateThreads.foreach(_.go())
 
+    //new lines to test
+    if(level == Map) {
+      DbHandler.refreshFlattenMaterialized
+      DbHandler.setUnifiedPair
+      DbHandler.closeDatabase()
+    }
+
     val t3 = System.nanoTime()
     logger.info(s"Total time for transformations: ${getTotalTimeFormatted(t2, t3)}")
   }

diff --git a/src/main/scala/it/polimi/genomics/metadata/step/MapperStep.scala b/src/main/scala/it/polimi/genomics/metadata/step/MapperStep.scala
@@ -54,10 +54,10 @@ object MapperStep extends Step {
   override def execute(source: Source, parallelExecution: Boolean): Unit = {
     if (source.mapperEnabled) {
 
-      DbHandler.setDatabase
-      DbHandler.setDWViews
-      DbHandler.setFlattenMaterialized
-      logger.info("Database has been set")
+      //DbHandler.setDatabase
+      //DbHandler.setDWViews
+      //DbHandler.setFlattenMaterialized
+      //logger.info("Database has been set")
 
       logger.info("Starting mapper for on folder: " + source.outputFolder)
 
@@ -112,10 +112,9 @@ object MapperStep extends Step {
         }
       }
 
-      DbHandler.refreshFlattenMaterialized
-      DbHandler.setUnifiedPair
-
-      DbHandler.closeDatabase()
+      //DbHandler.refreshFlattenMaterialized
+      //DbHandler.setUnifiedPair
+      //DbHandler.closeDatabase()
 
 
       logger.info(s"Source ${source.name} mapping finished")