fix config

pom.xml

@@ -85,6 +85,11 @@
   <build>
     <sourceDirectory>src/main/scala</sourceDirectory>
     <testSourceDirectory>src/test/scala</testSourceDirectory>
+    <resources>
+      <resource>
+        <directory>src/main/resources</directory>
+      </resource>
+    </resources>
     <plugins>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
@@ -116,6 +121,7 @@
         <configuration>
           <archive>
             <manifest>
+              <addClasspath>true</addClasspath>
               <mainClass>org.racerdfix.Hippodrome</mainClass>
             </manifest>
           </archive>
@@ -128,6 +134,9 @@
             <manifest>
               <mainClass>org.racerdfix.Hippodrome</mainClass>
             </manifest>
+        <!--    <manifestEntries>
+              <Class-Path>config/</Class-Path>
+            </manifestEntries> -->
           </archive>
           <descriptorRefs>
             <descriptorRef>jar-with-dependencies</descriptorRef>
@@ -157,6 +166,7 @@
         <version>3.2.2</version>
         <executions>
           <execution>
+            <phase>process-resources</phase>
             <goals>
               <goal>compile</goal>
               <goal>testCompile</goal>

src/main/scala/inferAPI/InterpretJson.scala

@@ -470,7 +470,7 @@ class InterpretJson(val config: FixConfig) {
   def getJsonToolConfig() = {
     import ToolConfigProtocol._
     val fm  = new FileManipulation
-    val src = fm.fileToString(config.tools_config_file)
+    val src = fm.resourceFileToString(config.tools_config_file)
     val jsonAst = src.parseJson
     val toolsConfigObj = jsonAst.convertTo[ToolConfig]
     toolsConfigObj

src/main/scala/utils/BugsStore.scala

@@ -47,7 +47,7 @@ class BugsStore {
           key
         }
 
-      val key   = contains_key(true)
+      val key  = contains_key(true)
       val key2 = contains_key(false)
 
       key match {

src/main/scala/utils/FileManipulation.scala

@@ -1,9 +1,10 @@
 package org.racerdfix.utils
 
-import java.io.{BufferedWriter, File, FileWriter}
+import java.io.{BufferedWriter, File, FileNotFoundException, FileWriter, InputStream}
 import java.nio.file.{Files, Paths, StandardCopyOption}
 
 import scala.io.Source
+import scala.util.Try
 
 class FileManipulation {
 
@@ -49,6 +50,25 @@ class FileManipulation {
     Source.fromFile(filename).getLines.foldLeft("") { (str, line) => str + " \n " + line.toString }
   }
 
+  def resourceFileToString(filename: String) = {
+    /*
+     def main(args: Array[String]): Unit = {
+
+    val ipfileStream = getClass.getResourceAsStream("/folder/a-words.txt")
+    val readlines = Source.fromInputStream(ipfileStream).getLines
+    readlines.foreach(readlines => println(readlines))
+
+  }
+    * */
+    //val stream: InputStream = getClass.getResourceAsStream("/" + filename)
+    println(getClass.getResource(filename))
+    println(filename)
+    /*Try(*/
+      Source.fromResource(filename).getLines.foldLeft("") { (str, line) => str + " \n " + line.toString }
+    /*).recover(throw new FileNotFoundException(filename))
+    ""*/
+  }
+
   def getFile(path: String, filename: String) = {
      /* TODO strip the last / from path*/
      val path_processes = if(path.length > 0 && path.last == '/') path.dropRight(1) else path