small old fixes for errors in mapper

tomalf2 · Jan 22, 2019 · 037b41e · 037b41e
1 parent 74ad3a3
commit 037b41e
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Showing 3 changed files with 20 additions and 14 deletions.
diff --git a/src/main/scala/it/polimi/genomics/metadata/cleaner/Rule.scala b/src/main/scala/it/polimi/genomics/metadata/cleaner/Rule.scala
@@ -17,11 +17,11 @@ case class Rule(antecedent: String, consequent: String) extends PartiallyOrdered
     if (that.isInstanceOf[Rule]) {
       val thatIns = that.asInstanceOf[Rule]
 
-      val autoThis = new RegExp(this.antecedent).toAutomaton()
+      val autoThis = new RegExp(this.antecedent).toAutomaton() //autoThis = existing
       autoThis.expandSingleton()
       //autoThis.determinize()
 
-      val autoThat = new RegExp(thatIns.antecedent).toAutomaton()
+      val autoThat = new RegExp(thatIns.antecedent).toAutomaton() //autoThat = newRule
       autoThat.expandSingleton()
       //autoThat.determinize()
 
@@ -31,10 +31,10 @@ case class Rule(antecedent: String, consequent: String) extends PartiallyOrdered
         //val inter = BasicOperations.intersection(autoThis, autoThat)
         //inter.determinize()
         //if (inter.equals(autoThat)) //L(a') is contained in L(a) (new is contained in existing)
-        if (autoThat.subsetOf(autoThis))
+        if (autoThat.subsetOf(autoThis)) //existing contains newRule = 1
           Some(1)
         //else if (inter.equals(autoThis)) //L(a) is contained in L(a') (existing is contained in new)
-        else if (autoThis.subsetOf(autoThat))
+        else if (autoThis.subsetOf(autoThat)) // existing is contained in newRule = -1
           Some(-1)
         else {
           val inter = BasicOperations.intersection(autoThis, autoThat)

diff --git a/src/main/scala/it/polimi/genomics/metadata/mapper/Main.scala b/src/main/scala/it/polimi/genomics/metadata/mapper/Main.scala
@@ -323,7 +323,7 @@ object main {
       val bioSampleList = new REP.Utils.BioSampleList(old_lines.toArray, repTableId)
 
       //in files with simple epi__donor_id, it adds the keys epi__donor_id__X for each biosample present (same for other attributes)
-      val lines = enrichLinesREP(old_lines.toArray, bioSampleList)
+      val lines = enrichLinesREP(old_lines.toArray, bioSampleList,path)
 
       //prepares ficticious replicate tuples (id=biosample_id, bio/tech replicate number = 1)
       val replicateList = new REP.Utils.ReplicateList(lines, bioSampleList)
@@ -479,7 +479,7 @@ object main {
     states
   }
 
-  def enrichLinesREP(lines: Array[String], bioSampleList: REP.Utils.BioSampleList): Array[String] = {
+  def enrichLinesREP(lines: Array[String], bioSampleList: REP.Utils.BioSampleList,path:String): Array[String] = {
     val bioNumbers = 1 to bioSampleList.BiosampleList.length toList
     var linesFromSet = scala.collection.mutable.Set(lines: _*) //transform array into set
     for (l <- linesFromSet.toList) {
@@ -532,7 +532,7 @@ object main {
           None
       else
         None
-    }.flatten.head
+    }.flatten.headOption.getOrElse("Error during EnrichLinesREP method")
 
     val hasDonorId = linesFromSet.toList.map{l=>
       val pair = l.split("\t", 2)
@@ -564,6 +564,12 @@ object main {
       linesFromSet += "epi__sample_alias__1" +  "\t" + manCurId
 
 
+    //useful for tads which do not have a file name
+    val str : Array[String] = path.split("/")
+    val file_name: String = str.last.split("\\.").head
+    linesFromSet += "file_name" +  "\t" + file_name
+
+
     linesFromSet.toArray
   }
 

diff --git a/src/main/scala/it/polimi/genomics/metadata/mapper/REP/Table/BioSampleREP.scala b/src/main/scala/it/polimi/genomics/metadata/mapper/REP/Table/BioSampleREP.scala
@@ -54,7 +54,7 @@ class BioSampleREP(repTableId: REPTableId, quantity: Int) extends REPTable(repTa
         this.insertPosition = resetPosition(this.insertPosition, quantity)
       }
       case "TYPES" => {
-        param match{
+        param match {
           case "PrimaryCell" => this.typesArray(typesInsertPosition) = insertMethod(this.typesArray(typesInsertPosition), "Primary cell")
           case "PrimaryTissue" => this.typesArray(typesInsertPosition) = insertMethod(this.typesArray(typesInsertPosition), "Primary tissue")
           case "ESCDerived" => this.typesArray(typesInsertPosition) = insertMethod(this.typesArray(typesInsertPosition), "ESC derived cell line")
@@ -66,14 +66,14 @@ class BioSampleREP(repTableId: REPTableId, quantity: Int) extends REPTable(repTa
       }
 
       case "TISSUE" => {
-        if (typesArray(tissueInsertPosition) == null  || typesArray(tissueInsertPosition).toLowerCase.contains("tissue"))
-          this.tissueArray(tissueInsertPosition) = insertMethod(this.tissueArray(tissueInsertPosition), param)
-        else
-          this.tissueArray(tissueInsertPosition) = null
+        // if (typesArray(tissueInsertPosition) == null  || typesArray(tissueInsertPosition).toLowerCase.contains("tissue"))
+        this.tissueArray(tissueInsertPosition) = insertMethod(this.tissueArray(tissueInsertPosition), param)
+        // else
+        //   this.tissueArray(tissueInsertPosition) = null
         this.tissueInsertPosition = resetPosition(this.tissueInsertPosition, quantity)
       }
       case "CELLLINE" => {
-        if (typesArray(tissueInsertPosition) == null  || typesArray(tissueInsertPosition).toLowerCase.contains("tissue"))
+        if (typesArray(tissueInsertPosition) == null || typesArray(tissueInsertPosition).toLowerCase.contains("tissue"))
           this.cellLineArray(cellLineInsertPosition) = null
         else
           this.cellLineArray(cellLineInsertPosition) = insertMethod(this.cellLineArray(cellLineInsertPosition), param)
@@ -85,7 +85,7 @@ class BioSampleREP(repTableId: REPTableId, quantity: Int) extends REPTable(repTa
       }
       case "DISEASE" => {
         val a: String = this.disease.getOrElse(null)
-        val b: String = insertMethod(a,param)
+        val b: String = insertMethod(a, param)
         this.diseaseArray(diseaseInsertPosition) = Some(b)
         this.diseaseInsertPosition = resetPosition(diseaseInsertPosition, quantity)
       }