Added executables

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

@@ -129,8 +129,6 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
         Await.result(createFile(db, qscript.summaryRunId, pipelineId, Some(moduleId), sampleId, libId, key, file, outputDir), Duration.Inf)
     }
 
-    //TODO: Add executables
-
     qscript match {
       case tag: SampleLibraryTag =>
         val sampleId = tag.sampleId.flatMap(name => Await.result(db.getSampleId(qscript.summaryRunId, name), Duration.Inf))
@@ -165,6 +163,21 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
         db.createOrUpdateSetting(qscript.summaryRunId, pipelineId, None, None, None, ConfigUtils.mapToJson(q.summarySettings).nospaces)
     }
 
+    for ((name, f) <- qscript.functions.flatMap(_ match {
+      case c:Configurable with Version => Some(c)
+      case _ => None
+    }).groupBy(_.configNamespace)) yield {
+      f match {
+        case f: BiopetJavaCommandLineFunction with Version =>
+          db.createOrUpdateExecutable(qscript.summaryRunId, name, f.getVersion, f.getJavaVersion, javaMd5 = BiopetCommandLineFunction.executableMd5Cache.get(f.executable), jarPath = Some(f.jarFile.getAbsolutePath))
+        case f: BiopetCommandLineFunction with Version =>
+          db.createOrUpdateExecutable(qscript.summaryRunId, name, f.getVersion, Option(f.executable))
+        case f: Configurable with Version =>
+          db.createOrUpdateExecutable(qscript.summaryRunId, name, f.getVersion)
+        case _ => None
+      }
+
+    }
 
     db.close()
 

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

@@ -272,6 +272,31 @@ class SummaryDb(db: Database) extends Closeable {
     if (r == 0) createFile(runId, pipelineId, moduleId, sampleId, libId, key, path, md5, link, size)
     else db.run(filter.update(File(runId, pipelineId, moduleId, sampleId, libId, key, path, md5, link, size)))
   }
+
+  def executablesFilter(runId: Option[Int], toolName: Option[String]) = {
+    val l: List[Option[Query[Executables, Executables#TableElementType, Seq] => Query[Executables, Executables#TableElementType, Seq]]] = List(
+      runId.map(x => y => y.filter(_.runId === x)),
+      toolName.map(x => y => y.filter(_.toolName === x))
+    )
+    l.flatten.foldLeft(executables.subquery)((a, b) => b(a))
+  }
+
+  def getFiles(runId: Option[Int], toolName: Option[String]) = {
+    db.run(executablesFilter(runId, toolName).result)
+  }
+
+  def createExecutable(runId: Int, toolName: String, version: Option[String] = None, path: Option[String] = None,
+                       javaVersion: Option[String] = None, exeMd5: Option[String] = None, javaMd5: Option[String] = None, jarPath: Option[String] = None) = {
+    db.run(executables.forceInsert(Executable(runId, toolName, version, path, javaVersion, exeMd5, javaMd5, jarPath)))
+  }
+
+  def createOrUpdateExecutable(runId: Int, toolName: String, version: Option[String] = None, path: Option[String] = None,
+                               javaVersion: Option[String] = None, exeMd5: Option[String] = None, javaMd5: Option[String] = None, jarPath: Option[String] = None) = {
+    val filter = executablesFilter(Some(runId), Some(toolName))
+    val r = Await.result(db.run(filter.size.result), Duration.Inf)
+    if (r == 0) createExecutable(runId, toolName, version, javaVersion, exeMd5, javaMd5)
+    else db.run(filter.update(Executable(runId, toolName, version, path, javaVersion, exeMd5, javaMd5, jarPath)))
+  }
 }
 
 object SummaryDb {

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

@@ -118,16 +118,18 @@ object Schema {
   }
   val files = TableQuery[Files]
 
-  case class Executable(runId: Int, toolName: String, version: Option[String], javaVersion: Option[String], exeMd5: Option[String], javaMd5: Option[String])
+  case class Executable(runId: Int, toolName: String, version: Option[String], path = Option[String], javaVersion: Option[String], exeMd5: Option[String], javaMd5: Option[String], jarPath: Option[String])
   class Executables(tag: Tag) extends Table[Executable](tag, "Executables") {
     def runId = column[Int]("runId")
     def toolName = column[String]("toolName")
     def version = column[Option[String]]("version")
+    def path = column[Option[String]]("path")
     def javaVersion = column[Option[String]]("javaVersion")
     def exeMd5 = column[Option[String]]("exeMd5")
     def javaMd5 = column[Option[String]]("javaMd5")
+    def jarPath = column[Option[String]]("jarPath")
 
-    def * = (runId, toolName, version, javaVersion, exeMd5, javaMd5) <> (Executable.tupled, Executable.unapply)
+    def * = (runId, toolName, version, path, javaVersion, exeMd5, javaMd5, jarPath) <> (Executable.tupled, Executable.unapply)
 
     def idx = index("idx_executables", (runId, toolName), unique = true)
   }