Adding more tables

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala

@@ -2,41 +2,61 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.utils.summary.db.{Libraries, Samples}
 import slick.driver.H2Driver.api._
 
 import scala.concurrent.ExecutionContext.Implicits.global
-
 import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand}
 
+import scala.concurrent.Await
+import scala.concurrent.duration.Duration
+
 /**
   * Created by pjvanthof on 26/01/2017.
   */
 object SummaryToSqlite extends ToolCommand {
 
   case class Args(inputJson: File = null,
-                  outputHdf5: File = null) extends AbstractArgs
+                  outputSqlite: File = null,
+                  force: Boolean = false) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('I', "inputJson") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(inputJson = x)
     } text "Input json file"
     opt[File]('o', "outputHdf5") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
-      c.copy(outputHdf5 = x)
+      c.copy(outputSqlite = x)
     } text "Output hdf5 file"
+    opt[Unit]('f', "force") action { (x, c) =>
+      c.copy(force = true)
+    } text "If database already exist it will be moved"
   }
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
     val cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+    logger.info("Start")
 
     val jsonMap = ConfigUtils.fileToConfigMap(cmdArgs.inputJson)
 
-    val db = Database.forURL(s"jdbc:sqlite:${cmdArgs.outputHdf5.getAbsolutePath}", driver = "org.sqlite.JDBC")
+    if (cmdArgs.outputSqlite.exists()) {
+      if (cmdArgs.force) cmdArgs.outputSqlite.delete()
+      else throw new IllegalArgumentException(s"Db already exist: ${cmdArgs.outputSqlite}")
+    }
 
-    try {
+    val db = Database.forURL(s"jdbc:sqlite:${cmdArgs.outputSqlite.getAbsolutePath}", driver = "org.sqlite.JDBC")
 
+    try {
+      val samples = TableQuery[Samples]
+      val libraries = TableQuery[Libraries]
+
+      val setup = DBIO.seq(
+        (samples.schema ++ libraries.schema).create
+      )
+      val setupFuture = db.run(setup)
+      Await.result(setupFuture, Duration.Inf)
     } finally db.close
+    logger.info("Done")
   }
 
-
 }

biopet-utils/pom.xml

@@ -36,9 +36,9 @@
             <version>3.1.1</version>
         </dependency>
         <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-nop</artifactId>
-            <version>1.6.4</version>
+            <groupId>org.xerial</groupId>
+            <artifactId>sqlite-jdbc</artifactId>
+            <version>3.16.1</version>
         </dependency>
         <dependency>
             <groupId>colt</groupId>

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

+package nl.lumc.sasc.biopet.utils.summary.db
+
+import java.sql.Blob
+
+import slick.driver.H2Driver.api._
+
+/**
+  * Created by pjvan_thof on 26-1-17.
+  */
+class Libraries(tag: Tag) extends Table[(Int, String, Int, Blob)](tag, "Libraries") {
+  def libraryId = column[Int]("libraryId", O.PrimaryKey) // This is the primary key column
+  def libraryName = column[String]("libraryName")
+  def sampleId = column[Int]("sampleId")
+  def tags = column[Blob]("tags")
+  // Every table needs a * projection with the same type as the table's type parameter
+  def * = (libraryId, libraryName, sampleId, tags)
+}
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Pipelines.scala

+package nl.lumc.sasc.biopet.utils.summary.db
+
+import slick.driver.H2Driver.api._
+
+/**
+  * Created by pjvanthof on 27/01/2017.
+  */
+class Pipelines(tag: Tag) extends Table[(Int, String)](tag, "Pipelines") {
+  def pipelineId = column[Int]("runId", O.PrimaryKey) // This is the primary key column
+  def pipelineName = column[String]("sampleName")
+  // Every table needs a * projection with the same type as the table's type parameter
+  def * = (pipelineId, pipelineName)
+}
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Runs.scala

+package nl.lumc.sasc.biopet.utils.summary.db
+
+import slick.driver.H2Driver.api._
+
+/**
+  * Created by pjvanthof on 27/01/2017.
+  */
+class Runs(tag: Tag) extends Table[(Int, String)](tag, "Runs") {
+  def runId = column[Int]("runId", O.PrimaryKey) // This is the primary key column
+  def runName = column[String]("sampleName")
+  // Every table needs a * projection with the same type as the table's type parameter
+  def * = (runId, runName)
+}
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Samples.scala

 package nl.lumc.sasc.biopet.utils.summary.db
 
+import java.sql.Blob
+
 import slick.driver.H2Driver.api._
 
 /**
   * Created by pjvan_thof on 26-1-17.
   */
-class Samples(tag: Tag) extends Table[(Int, String)](tag, "SUPPLIERS") {
+class Samples(tag: Tag) extends Table[(Int, String, Blob)](tag, "Samples") {
   def sampleId = column[Int]("sampleId", O.PrimaryKey) // This is the primary key column
   def sampleName = column[String]("sampleName")
+  def tags = column[Blob]("tags")
   // Every table needs a * projection with the same type as the table's type parameter
-  def * = (sampleId, sampleName)
+  def * = (sampleId, sampleName, tags)
 }
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