Merge pull request #5 from Ferlab-Ste-Justine/fix/CQDG-498

fix: CQDG-498 remove unwanted parents form term ancerstors

Author: adipaul1981

src/main/scala/bio/ferlab/HPOMain.scala

@@ -55,17 +55,19 @@ def generateTermsWithAncestors(fileBuffer: BufferedSource, topNode: Option[Strin
 
   val ontologyWithParents = DownloadTransformer.transformOntologyData(dTwAncestorsParents)
 
-  val ontologyWithParentsFiltered = topNode match {
-    case Some(topNode) => filterOntologiesForTopNode(ontologyWithParents, topNode)
-    case None => ontologyWithParents
+  val excludedParentsIds = topNode.flatMap(node => ontologyWithParents
+    .find{ case(term, _) => term.id == node }
+    .map{ case(_, parents) => parents.map(_.id) })
+
+  val ontologyWithParentsFiltered = (excludedParentsIds, topNode) match {
+    case (Some(parentsIds), Some(node)) => filterOntologiesForTopNode(ontologyWithParents, node, parentsIds)
+
+    case _ => ontologyWithParents
   }
 
   ontologyWithParentsFiltered.map {
     case (k, v) if allParents.contains(k.id) => k -> (v, false)
     case (k, v) => k -> (v, true)
   }
 }
-
-
-
 }

src/main/scala/bio/ferlab/transform/DownloadTransformer.scala

@@ -69,8 +69,11 @@ object DownloadTransformer {
     })
   }
 
-  def filterOntologiesForTopNode(ontologyWithParents: Map[OntologyTerm, Set[OntologyTerm]], desiredTopNode: String): Map[OntologyTerm, Set[OntologyTerm]] = {
-    ontologyWithParents.filter(t => t._2.map(_.id).contains(desiredTopNode) || t._1.id == desiredTopNode)
+  def filterOntologiesForTopNode(ontologyWithParents: Map[OntologyTerm, Set[OntologyTerm]], desiredTopNode: String, unwantedParentsIds: Set[String]):
+  Map[OntologyTerm, Set[OntologyTerm]] = {
+    ontologyWithParents
+      .filter { case(term, parents) => parents.map(_.id).contains(desiredTopNode) || term.id == desiredTopNode }
+      .map{ case(term, parents) => (term, parents.filter( r => !unwantedParentsIds.contains(r.id))) }
   }
 
   def getAllParentPath(term: OntologyTerm, originalTerm: OntologyTerm, data: Map[String, OntologyTerm], list: Set[OntologyTerm], cumulativeList: mutable.Map[OntologyTerm, Set[OntologyTerm]], allParents: Set[String]): mutable.Map[OntologyTerm, Set[OntologyTerm]] = {

src/test/scala/HPOMainSpec.scala

@@ -34,8 +34,13 @@ class HPOMainSpec extends AnyFlatSpec with Matchers {
     val file = Source.fromFile("src/test/scala/resources/hp.obo")
     val result = HPOMain.generateTermsWithAncestors(file, Some("HP:22"))
 
-    result.filter(t => t._1.id.startsWith("HP:2")).keySet.map(_.id) shouldEqual Set("HP:22")
-    result.filter(t => t._1.id.startsWith("HP:3")).keySet.map(_.id) shouldEqual Set("HP:33","HP:34")
-    result.filter(t => t._1.id.startsWith("HP:4")).keySet.map(_.id) shouldEqual Set("HP:43","HP:44")
+    result.filter(t => t._1.id.startsWith("HP:2")).keySet.map(_.id) should contain theSameElementsAs Set("HP:22")
+    result.filter(t => t._1.id.startsWith("HP:3")).keySet.map(_.id) should contain theSameElementsAs Set("HP:33","HP:34")
+    result.filter(t => t._1.id.startsWith("HP:4")).keySet.map(_.id) should contain theSameElementsAs Set("HP:43","HP:44")
+
+    val  testLeaf = result.find(t => t._1.id.equals("HP:44")).get._2._1
+    val testLeafParentsIds = testLeaf.map(_.id)
+    // Should not have HP:1 as one of its parents
+    testLeafParentsIds.toList should contain theSameElementsAs Seq("HP:22", "HP:34")
   }
 }