merge problems resolved

DEIB-GECO · Sep 11, 2018 · 9b37ccd · 9b37ccd
1 parent 857434a
commit 9b37ccd
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Showing 3 changed files with 16 additions and 33 deletions.
diff --git a/...cala/it/polimi/genomics/metadata/downloader_transformer/cistrome/CistromeDownloader.scala b/...cala/it/polimi/genomics/metadata/downloader_transformer/cistrome/CistromeDownloader.scala
@@ -1,39 +1,21 @@
 package it.polimi.genomics.importer.CistromeImporter
 
-import it.polimi.genomics.importer.GMQLImporter.{GMQLDownloader, GMQLSource}
 import java.io.File
 import java.net.URL
 
-import it.polimi.genomics.importer.FileDatabase.{FileDatabase, STAGE}
-import it.polimi.genomics.importer.GMQLImporter.{GMQLDownloader, GMQLSource}
-import org.joda.time.DateTime
+import it.polimi.genomics.metadata.database.{FileDatabase, Stage}
+import it.polimi.genomics.metadata.downloader_transformer.Downloader
+import it.polimi.genomics.metadata.step.xml.Source
 import org.slf4j.LoggerFactory
 
-import scala.util.Try
-
-
-
-
-import java.io.File
-import java.net.URL
-import java.nio.file.Paths
-
-import it.polimi.genomics.importer.DefaultImporter.utils.{OAuth, csvDownload}
-import it.polimi.genomics.importer.FileDatabase.{FileDatabase, STAGE}
-import it.polimi.genomics.importer.GMQLImporter.{GMQLDownloader, GMQLSource}
-import org.jsoup.Jsoup
-import org.jsoup.nodes.Document
-import org.slf4j.{Logger, LoggerFactory}
-
 import scala.language.postfixOps
 import scala.sys.process._
-import scala.util.{Failure, Success, Try}
-import scala.collection.JavaConverters._
+import scala.util.Try
 
 /**
   * Created by nachon on 7/28/17.
   */
-class CistromeDownloader extends GMQLDownloader{
+class CistromeDownloader extends Downloader{
   val logger = LoggerFactory.getLogger( this.getClass )
 
   /**
@@ -62,7 +44,7 @@ class CistromeDownloader extends GMQLDownloader{
     */
 
 
-  override def download(source: GMQLSource, parallelExecution: Boolean): Unit = {
+  override def download(source: Source, parallelExecution: Boolean): Unit = {
     val sourceId = FileDatabase.sourceId(source.name)
 
 
@@ -85,7 +67,7 @@ class CistromeDownloader extends GMQLDownloader{
         val urlSource = scala.io.Source.fromURL(path)
         totalFiles += 1
 
-        val fileId = FileDatabase.fileId(datasetId, path, STAGE.DOWNLOAD, name)
+        val fileId = FileDatabase.fileId(datasetId, path, Stage.DOWNLOAD, name)
 
         val outputPath = source.outputFolder + File.separator + dataset.outputFolder + File.separator + "Downloads"
         if (!new java.io.File(outputPath).exists) {
@@ -131,7 +113,7 @@ class CistromeDownloader extends GMQLDownloader{
     * @param source            contains specific download and sorting info.
     * @param parallelExecution defines parallel or sequential execution
     */
-  override def downloadFailedFiles(source: GMQLSource, parallelExecution: Boolean): Unit = {
+  override def downloadFailedFiles(source: Source, parallelExecution: Boolean): Unit = {
 
   }
 }

diff --git a/...ala/it/polimi/genomics/metadata/downloader_transformer/cistrome/CistromeTransformer.scala b/...ala/it/polimi/genomics/metadata/downloader_transformer/cistrome/CistromeTransformer.scala
@@ -2,7 +2,8 @@ package it.polimi.genomics.importer.CistromeImporter
 
 import java.io._
 
-import it.polimi.genomics.importer.GMQLImporter.{GMQLDataset, GMQLSource, GMQLTransformer}
+import it.polimi.genomics.metadata.downloader_transformer.Transformer
+import it.polimi.genomics.metadata.step.xml.{Dataset, Source}
 import org.apache.commons.compress.archivers.tar.{TarArchiveEntry, TarArchiveInputStream}
 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream
 import org.apache.commons.io.IOUtils
@@ -13,7 +14,7 @@ import scala.io.BufferedSource
 /**
   * Created by nachon on 7/28/17.
   */
-class CistromeTransformer extends GMQLTransformer {
+class CistromeTransformer extends Transformer {
   val logger = LoggerFactory.getLogger(this.getClass)
 
   var metadataFileLines: Map[String, Array[String]] = _
@@ -28,7 +29,7 @@ class CistromeTransformer extends GMQLTransformer {
     * @param filename         name of the new file .meta/.bed
     * @return List(fileId, filename) for the transformed files.
     */
-  override def transform(source: GMQLSource, originPath: String, destinationPath: String, originalFilename: String, filename: String): Boolean = {
+  override def transform(source: Source, originPath: String, destinationPath: String, originalFilename: String, filename: String): Boolean = {
     val fileTransformationPath = destinationPath + File.separator + filename
     val fileDownloadPath = originPath + File.separator + originalFilename
 
@@ -62,7 +63,7 @@ class CistromeTransformer extends GMQLTransformer {
     * @param source   source where the files belong to.
     * @return candidate names for the files derived from the original filename.
     */
-  override def getCandidateNames(filename: String, dataset: GMQLDataset, source: GMQLSource): List[String] = {
+  override def getCandidateNames(filename: String, dataset: Dataset, source: Source): List[String] = {
     val path = source.outputFolder + File.separator + dataset.outputFolder + File.separator + "Downloads" + File.separator + filename
     //    println("path:", path)
 

diff --git a/src/main/scala/it/polimi/genomics/metadata/step/TransformerStep.scala b/src/main/scala/it/polimi/genomics/metadata/step/TransformerStep.scala
@@ -1,4 +1,4 @@
-package it.polimi.genomics.importer.GMQLImporter
+package it.polimi.genomics.metadata.step
 
 import java.io._
 
@@ -65,7 +65,7 @@ object TransformerStep extends Step {
 
               val transformationClass = Class
                 .forName(source.transformer)
-                .newInstance.asInstanceOf[GMQLTransformer]
+                .newInstance.asInstanceOf[Transformer]
 
               val t0Dataset: Long = System.nanoTime()
               var modifiedRegionFilesDataset = 0
@@ -138,7 +138,7 @@ object TransformerStep extends Step {
                 FileDatabase.checkIfUpdateFile(fileId, originDetails._1, originDetails._2, originDetails._3)
                 val transformed = Class
                   .forName(source.transformer)
-                  .newInstance.asInstanceOf[GMQLTransformer]
+                  .newInstance.asInstanceOf[Transformer]
                   .transform(source, downloadsFolder, transformationsFolder, originalFileName, name)
                 val fileTransformationPath = transformationsFolder + File.separator + name
                 //add copy numbers if needed.