Try setup with sqlite

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/JsonToHdf5.scala → biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala

@@ -2,14 +2,16 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import ncsa.hdf.`object`.h5.H5File
-import nl.lumc.sasc.biopet.tools.GvcfToBed.Args
+import slick.driver.H2Driver.api._
+
+import scala.concurrent.ExecutionContext.Implicits.global
+
 import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand}
 
 /**
   * Created by pjvanthof on 26/01/2017.
   */
-object JsonToHdf5 extends ToolCommand {
+object SummaryToSqlite extends ToolCommand {
 
   case class Args(inputJson: File = null,
                   outputHdf5: File = null) extends AbstractArgs
@@ -29,8 +31,12 @@ object JsonToHdf5 extends ToolCommand {
 
     val jsonMap = ConfigUtils.fileToConfigMap(cmdArgs.inputJson)
 
-    val hdf5 = new H5File(cmdArgs.outputHdf5.getAbsolutePath)
+    val db = Database.forURL(s"jdbc:sqlite:${cmdArgs.outputHdf5.getAbsolutePath}", driver = "org.sqlite.JDBC")
 
+    try {
+
+    } finally db.close
   }
 
+
 }

biopet-utils/pom.xml

@@ -31,9 +31,14 @@
 
     <dependencies>
         <dependency>
-            <groupId>org.hdfgroup</groupId>
-            <artifactId>hdf-java</artifactId>
-            <version>2.6.1</version>
+            <groupId>com.typesafe.slick</groupId>
+            <artifactId>slick_2.10</artifactId>
+            <version>3.1.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-nop</artifactId>
+            <version>1.6.4</version>
         </dependency>
         <dependency>
             <groupId>colt</groupId>

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

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