Change sample and libraries to createOrUpdate

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -264,12 +264,12 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     for ((sampleName, sample) <- samples) {
       val sampleTags = if (sample.sampleTags.nonEmpty) Some(ConfigUtils.mapToJson(sample.sampleTags).nospaces) else None
       val sampleId: Int = if (!namesOld.contains(sampleName))
-        Await.result(db.createSample(sampleName, summaryRunId, sampleTags), Duration.Inf)
+        Await.result(db.createOrUpdateSample(sampleName, summaryRunId, sampleTags), Duration.Inf)
       else Await.result(db.getSamples(runId = Some(summaryRunId), name = Some(sampleName)).map(_.head.id), Duration.Inf)
       val libNamesOld = Await.result(db.getLibraries(runId = summaryRunId, sampleId = sampleId).map(_.map(_.name)), Duration.Inf)
       for ((libName, lib) <- sample.libraries) {
         val libraryTags = if (lib.libTags.nonEmpty) Some(ConfigUtils.mapToJson(sample.sampleTags).nospaces) else None
-        if (!libNamesOld.contains(libName)) Await.result(db.createLibrary(libName, summaryRunId, sampleId, libraryTags), Duration.Inf)
+        if (!libNamesOld.contains(libName)) Await.result(db.createOrUpdateLibrary(libName, summaryRunId, sampleId, libraryTags), Duration.Inf)
       }
     }
   }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -67,11 +67,11 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
         case t: SampleLibraryTag => t.sampleId.foreach {
           case sampleName =>
             val sampleId = Await.result(db.getSamples(name = Some(sampleName), runId = Some(qscript.summaryRunId)).map(_.headOption.map(_.id)), Duration.Inf).getOrElse {
-              Await.result(db.createSample(sampleName, qscript.summaryRunId), Duration.Inf)
+              Await.result(db.createOrUpdateSample(sampleName, qscript.summaryRunId), Duration.Inf)
             }
             t.libId.foreach { libName =>
               val libId = Await.result(db.getSamples(name = Some(libName), runId = Some(qscript.summaryRunId), sampleId = Some(sampleId)).map(_.headOption.map(_.id)), Duration.Inf).getOrElse {
-                Await.result(db.createLibrary(libName, qscript.summaryRunId, sampleId), Duration.Inf)
+                Await.result(db.createOrUpdateLibrary(libName, qscript.summaryRunId, sampleId), Duration.Inf)
               }
             }
         }

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala

@@ -62,6 +62,16 @@ class SummaryDb(val db: Database) extends Closeable {
     db.run(samples.forceInsert(Sample(id, name, runId, tags))).map(_ => id)
   }
 
+  def createOrUpdateSample(name: String, runId: Int, tags: Option[String] = None): Future[Int] = {
+    getSampleId(runId, name).flatMap(_ match {
+      case Some(id: Int) =>
+        db.run(samples.filter(_.name === name).filter(_.id === id).map(_.tags).update(tags))
+          .map(_ => id)
+      case _ => createSample(name, runId, tags)
+    })
+  }
+
+
   /** This will return all samples that match given criteria */
   def getSamples(sampleId: Option[Int] = None, runId: Option[Int] = None, name: Option[String] = None): Future[Seq[Sample]] = {
     val q = samples.filter { sample =>
@@ -96,6 +106,15 @@ class SummaryDb(val db: Database) extends Closeable {
     db.run(libraries.forceInsert(Library(id, name, runId, sampleId, tags))).map(_ => id)
   }
 
+  def createOrUpdateLibrary(name: String, runId: Int, sampleId: Int, tags: Option[String] = None): Future[Int] = {
+    getLibraryId(runId, sampleId, name).flatMap(_ match {
+      case Some(id: Int) =>
+        db.run(libraries.filter(_.name === name).filter(_.id === id).filter(_.sampleId === sampleId).map(_.tags).update(tags))
+          .map(_ => id)
+      case _ => createLibrary(name, runId, sampleId, tags)
+    })
+  }
+
   /** This returns all libraries that match the given criteria */
   def getLibraries(libId: Option[Int] = None, name: Option[String] = None, runId: Option[Int] = None, sampleId: Option[Int] = None): Future[Seq[Library]] = {
     val q = libraries.filter { lib =>

biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala

@@ -49,14 +49,17 @@ class SummaryDbTest extends TestNGSuite with Matchers {
     val runId = Await.result(db.createRun("name", "dir", "version", "hash", date), Duration.Inf)
     Await.result(db.getSamples(), Duration.Inf) shouldBe empty
     val sampleId = Await.result(db.createSample("test_sample", runId), Duration.Inf)
+    Await.result(db.createOrUpdateSample("test_sample", runId), Duration.Inf) shouldBe sampleId
     Await.result(db.getSamples(), Duration.Inf) shouldBe Seq(Schema.Sample(sampleId, "test_sample", runId, None))
     Await.result(db.getSampleName(sampleId), Duration.Inf) shouldBe Some("test_sample")
     Await.result(db.getSampleId(runId, "test_sample"), Duration.Inf) shouldBe Some(sampleId)
     Await.result(db.getSampleTags(sampleId), Duration.Inf) shouldBe None
+    Await.result(db.createOrUpdateSample("test_sample", runId, Some("""{"test": "test"}""")), Duration.Inf) shouldBe sampleId
+    Await.result(db.getSampleTags(sampleId), Duration.Inf) shouldBe Some(Map("test" -> "test"))
 
     val sampleId2 = Await.result(db.createSample("test_sample2", runId, Some("""{"test": "test"}""")), Duration.Inf)
     Await.result(db.getSampleTags(sampleId2), Duration.Inf) shouldBe Some(Map("test" -> "test"))
-    Await.result(db.getSamples(), Duration.Inf) shouldBe Seq(Schema.Sample(sampleId, "test_sample", runId, None), Schema.Sample(sampleId2, "test_sample2", runId, Some("""{"test": "test"}""")))
+    Await.result(db.getSamples(), Duration.Inf) shouldBe Seq(Schema.Sample(sampleId, "test_sample", runId, Some("""{"test": "test"}""")), Schema.Sample(sampleId2, "test_sample2", runId, Some("""{"test": "test"}""")))
 
     db.close()
   }
@@ -74,6 +77,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
     val sampleId = Await.result(db.createSample("test_sample", runId), Duration.Inf)
     Await.result(db.getLibraries(), Duration.Inf) shouldBe empty
     val libraryId = Await.result(db.createLibrary("test_lib", runId, sampleId), Duration.Inf)
+    Await.result(db.createOrUpdateLibrary("test_lib", runId, sampleId), Duration.Inf) shouldBe libraryId
 
     Await.result(db.getLibraries(), Duration.Inf) shouldBe Seq(Schema.Library(libraryId, "test_lib", runId, sampleId, None))
     Await.result(db.getLibraryName(libraryId), Duration.Inf) shouldBe Some("test_lib")