Merge remote-tracking branch 'origin/develop'

NOTICE

@@ -43,6 +43,7 @@ This project includes:
   CDI APIs under Apache License, Version 2.0
   Common Eclipse Runtime under Eclipse Public License - v 1.0
   Commons Codec under The Apache Software License, Version 2.0
+  Commons Compiler under New BSD License
   Commons IO under The Apache Software License, Version 2.0
   Commons Logging under The Apache Software License, Version 2.0
   Core Runtime under Eclipse Public License - v 1.0
@@ -57,7 +58,7 @@ This project includes:
   Fluent API for Apache HttpClient under Apache License
   Guava: Google Core Libraries for Java under The Apache Software License, Version 2.0
   Hamcrest Core under New BSD License
-  janino.wso2:janino under Apache License, Version 2.0
+  Janino under New BSD License
   javax.inject under The Apache Software License, Version 2.0
   JCL 1.1.1 implemented over SLF4J under MIT License
   JSR-250 Common Annotations for the JavaTM Platform under COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0

pepper-doc/src/main/docbkx/pepper_modulesDevelopersGuide/codeIt.xml

@@ -438,7 +438,7 @@ public PepperMapper createPepperMapper(SElementId sElementId){
                     <para>In case you are wondering, yes this sounds a bit strange, since each file
                         ending which is not contained in the second list won't be imported by
                         default. But there is an option to set this to import each file, no matter
-                        wjat's the ending.</para>
+                        what's the ending.</para>
                 </footnote> Now let's show some code for adapting. The following snippet is placed
                 into the method 'isReadyToStart()', but even could be located inside the
                 constructor:
@@ -454,7 +454,7 @@ public PepperMapper createPepperMapper(SElementId sElementId){
     getSDocumentEndings().add(ENDING_LEAF_FOLDER);
     ...
 }</programlisting></para>
-            <para>In general the paramter of the method '<emphasis role="italic"
+            <para>In general the parameter of the method '<emphasis role="italic"
                     >getSDocumentEndings()</emphasis>' is just a String, but there are some
                 predefined endings you can use. The two lines marked as option 1, will add the
                 endings 'xml' and 'tab' to the list of file endings to be imported. That means, that

pepper-doc/src/main/docbkx/pepper_modulesDevelopersGuide/quickStart.xml

@@ -18,7 +18,7 @@
                 <listitem>
                     <para>Download Eclipse <footnote>
                             <para>Eclipse is available in several flavors e.g. for web developers,
-                                mobile developers, C++ developers etc.. We recommend the Eclipse
+                                mobile developers, C++ developers etc. We recommend the Eclipse
                                 Modeling Tools, since you might want to create or use a model for
                                 the format you want to support. In this documentation, we used
                                 Eclipse kepler, version 4.3.1 (see: <link
@@ -196,7 +196,8 @@
                             GraphViz tool (see: <link xlink:href="http://www.graphviz.org/"
                                 >http://www.graphviz.org/</link>) into a svg, png or another
                             graphical format.</para>
-                    </footnote>. </para>
+                    </footnote>
+                </para>
                 <para>Replace the entry with an absolute path to that file.</para>
             </listitem>
             <listitem>
@@ -373,8 +374,8 @@ public class MyImporter extends PepperImporterImpl
                 <para>Sometimes it is necessary to include libraries, which are not accessible via a
                     Maven repository and therefore can not be resolved by Maven. In that case we
                     recommend, to create a 'lib' folder in the project directory and to copy all the
-                    libraries you need into it. Unfortunately, you have register them twice, first
-                    for Maven and second for OSGi.</para>
+                    libraries you need into it. Unfortunately, you have to register them twice,
+                    first for Maven and second for OSGi.</para>
                 <para>To register such a library to Maven, you need to install them to your local
                     Maven repository. You can do that with:
                     <programlisting>

pepper-doc/src/main/docbkx/pepper_modulesDevelopersGuide/testing.xml

@@ -77,8 +77,8 @@ protected void setUp() throws Exception {
     //X SCorpus objects
     assertEquals(X, getFixture().getSaltProject()
         .getSCorpusGraphs().getSCorpora().size());
-}</programlisting>More
-            samples for tests can be found in the sample project in the classes
+}</programlisting></para>
+        <para>More samples for tests can be found in the sample project in the classes
                 <classname>SampleImporterTest</classname>,
                 <classname>SampleManipulatorTest</classname> and
                 <classname>SampleExporterTest</classname>. </para>
@@ -88,5 +88,16 @@ protected void setUp() throws Exception {
             the layers, you want to use. For more information, take a look into the Salt quick
             user's guide (see <link xlink:href="u.hu-berlin.de/saltnpepper"
             />).</para>
+        <para>The class de.hu_berlin.german.korpling.saltnpepper.pepper.testFramework.PepperTestUtil
+            provides some very helpful methods like getSrcResources() to get a reference to the
+            resources folder (.../src/main/resources) or the method getTestResources to get a
+            reference to the test resource folder (.../src/test/resources). </para>
+        <para>When you are implementing an importer and an exporter you may want to make sure that
+            no data is lost, you can orchestrate the im- and the exporter and compare the input
+            files with the output files. In that case implementing the classes PepperImporterTest
+            and PepperExporterTest want do the job, because they assume that you are testing a
+            single module. To load multiple modules in the Pepper test environment, use the method
+            PepperUtil.start(Collection&lt;PepperModule> fixtures) instead and pass your im- and
+            your exporter.</para>
     </sect1>
 </chapter>

pepper-framework/NOTICE

@@ -21,6 +21,7 @@ This project includes:
   Apache Commons Lang under The Apache Software License, Version 2.0
   carrot-osgi-anno-scr-core under The BSD License
   carrot-osgi-anno-scr-make under The BSD License
+  Commons IO under The Apache Software License, Version 2.0
   Guava: Google Core Libraries for Java under The Apache Software License, Version 2.0
   Hamcrest Core under New BSD License
   JUnit under Common Public License Version 1.0

pepper-framework/pepper-testEnvironment.launch

@@ -15,12 +15,8 @@
 <stringAttribute key="featurePluginResolution" value="workspace"/>
 <booleanAttribute key="includeOptional" value="true"/>
 <mapAttribute key="org.eclipse.debug.core.environmentVariables">
-<<<<<<< .mine
-<mapEntry key="PEPPER_TEST_WORKFLOW_FILE" value="/home/florian/Test/Druskat/paula2relANNIS.pepperParams"/>
-=======
 <mapEntry key="PEPPER_TEST" value="d:\projects_work\SaltNPepper\PEPPER_TEST\"/>
 <mapEntry key="PEPPER_TEST_WORKFLOW_FILE" value="d:\Test\tigerProblem\tiger2EXMARaLDA.pepperparams"/>
->>>>>>> .r8615
 </mapAttribute>
 <stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
 <stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="-os ${target.os} -ws ${target.ws} -arch ${target.arch} -nl ${target.nl} -consoleLog -console"/>
@@ -238,11 +234,7 @@
 <setEntry value="org.sonatype.tycho.m2e.feature:default"/>
 </setAttribute>
 <booleanAttribute key="show_selected_only" value="false"/>
-<<<<<<< .mine
-<stringAttribute key="target_bundles" value="com.google.guava*14.0.1@default:default,com.ibm.icu@default:default,javax.inject@default:default,javax.servlet@default:default,javax.xml@default:default,org.apache.commons.lang@default:default,org.apache.felix.gogo.command@default:default,org.apache.felix.gogo.runtime@default:default,org.apache.felix.gogo.shell@default:default,org.apache.log4j@1:default,org.eclipse.ant.core@default:default,org.eclipse.compare.core@default:default,org.eclipse.core.contenttype@default:default,org.eclipse.core.expressions@default:default,org.eclipse.core.filesystem.linux.x86_64@default:false,org.eclipse.core.filesystem@default:default,org.eclipse.core.jobs@default:default,org.eclipse.core.resources@default:default,org.eclipse.core.runtime.compatibility.auth@default:default,org.eclipse.core.runtime.compatibility.registry@default:false,org.eclipse.core.runtime@default:true,org.eclipse.core.variables@default:default,org.eclipse.emf.cdo.ecore.retrofit@default:false,org.eclipse.emf.common@default:default,org.eclipse.emf.ecore.xmi@default:default,org.eclipse.emf.ecore@default:default,org.eclipse.equinox.app@default:default,org.eclipse.equinox.common@2:true,org.eclipse.equinox.console@default:default,org.eclipse.equinox.ds@1:true,org.eclipse.equinox.preferences@default:default,org.eclipse.equinox.registry@default:default,org.eclipse.equinox.util@default:default,org.eclipse.osgi.services@default:default,org.eclipse.osgi@-1:true,org.eclipse.team.core@default:default,org.hamcrest.core@default:default,org.junit@default:default,org.slf4j.api*1.6.4.v20120130-2120@default:default,org.slf4j.api*1.7.2.v20121108-1250@default:default"/>
-=======
 <stringAttribute key="target_bundles" value="com.google.guava*14.0.1@default:default,javax.servlet@default:default,org.apache.commons.lang@default:default,org.apache.felix.gogo.command@default:default,org.apache.felix.gogo.runtime@default:default,org.apache.felix.gogo.shell@default:default,org.apache.log4j@1:default,org.eclipse.ant.core@default:default,org.eclipse.core.contenttype@default:default,org.eclipse.core.expressions@default:default,org.eclipse.core.filesystem@default:default,org.eclipse.core.jobs@default:default,org.eclipse.core.resources@default:default,org.eclipse.core.runtime.compatibility.auth@default:default,org.eclipse.core.runtime.compatibility.registry@default:false,org.eclipse.core.runtime@default:true,org.eclipse.core.variables@default:default,org.eclipse.emf.common@default:default,org.eclipse.emf.ecore.xmi@default:default,org.eclipse.emf.ecore@default:default,org.eclipse.equinox.app@default:default,org.eclipse.equinox.common@2:true,org.eclipse.equinox.console@default:default,org.eclipse.equinox.ds@1:true,org.eclipse.equinox.preferences@default:default,org.eclipse.equinox.registry@default:default,org.eclipse.equinox.util@default:default,org.eclipse.osgi.services@default:default,org.eclipse.osgi@-1:true,org.eclipse.team.core@default:default,org.hamcrest.core@default:default,org.junit@default:default,org.slf4j.api*1.6.4.v20120130-2120@default:default,org.slf4j.api*1.7.2.v20121108-1250@default:default"/>
->>>>>>> .r8615
 <booleanAttribute key="tracing" value="true"/>
 <booleanAttribute key="useCustomFeatures" value="false"/>
 <booleanAttribute key="useDefaultConfigArea" value="true"/>

pepper-framework/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>de.hu_berlin.german.korpling.saltnpepper</groupId>
 		<artifactId>pepper</artifactId>
-		<version>2.1.0</version>
+		<version>2.1.1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 	<scm>

pepper-framework/src/main/java/de/hu_berlin/german/korpling/saltnpepper/pepper/common/CorpusDesc.java

@@ -20,9 +20,10 @@
 import org.eclipse.emf.common.util.URI;
 
 /**
- * This class realizes a description of a corpus to be imported or exported. The description consists of a 
- * path addressing the location of the corpus and a format description, in which the corpus currently is or 
- * is supposed to be persist in.  
+ * This class realizes a description of a corpus to be imported or exported. The
+ * description consists of a path addressing the location of the corpus and a
+ * format description, in which the corpus currently is or is supposed to be
+ * persist in.
  * 
  * @author Florian Zipser
  */
@@ -33,64 +34,77 @@ public class CorpusDesc {
 	public CorpusDesc() {
 		super();
 	}
+
 	/** format description belonging to this corpus */
-	protected FormatDesc formatDesc= null;
+	protected FormatDesc formatDesc = null;
+
 	/**
-	 * Returns a set format description.
-	 * If no {@link FormatDesc} object was set, a new one is created.
+	 * Returns a set format description. If no {@link FormatDesc} object was
+	 * set, a new one is created.
+	 * 
 	 * @return a format description
 	 */
 	public FormatDesc getFormatDesc() {
-		if (formatDesc== null){
+		if (formatDesc == null) {
 			synchronized (this) {
-				formatDesc= new FormatDesc();
+				formatDesc = new FormatDesc();
 			}
 		}
 		return formatDesc;
 	}
+
 	/**
 	 * Sets the format description for this corpus description.
-	 * @param formatDesc format description object
+	 * 
+	 * @param formatDesc
+	 *            format description object
 	 * @return this
 	 */
 	public CorpusDesc setFormatDesc(FormatDesc formatDesc) {
 		this.formatDesc = formatDesc;
-		return(this);
+		return (this);
 	}
-
-	/** location of corpus**/
-	protected URI corpusPath= null;
+
+	/** location of corpus **/
+	protected URI corpusPath = null;
+
 	/**
 	 * Returns the path of where to store or from where to load this corpus.
+	 * 
 	 * @return location of corpus
 	 */
 	public URI getCorpusPath() {
 		return corpusPath;
 	}
+
 	/**
 	 * Sets the path of where to store or from where to load this corpus.
-	 * @param corpusPath location of corpus
+	 * 
+	 * @param corpusPath
+	 *            location of corpus
 	 * @param this object
 	 */
 	public CorpusDesc setCorpusPath(URI corpusPath) {
 		this.corpusPath = corpusPath;
-		return(this);
+		return (this);
 	}
+
 	/**
-	 * Returns a string representation of this object. 
-	 * <strong>Note: This representation cannot be used for serialization/deserialization purposes.</strong>
+	 * Returns a string representation of this object. <strong>Note: This
+	 * representation cannot be used for serialization/deserialization
+	 * purposes.</strong>
 	 */
 	@Override
-	public String toString(){
-		StringBuilder str= new StringBuilder();
+	public String toString() {
+		StringBuilder str = new StringBuilder();
 		str.append(getCorpusPath());
-		if (getFormatDesc()!= null){
+		if (getFormatDesc() != null) {
 			str.append("(");
 			str.append(getFormatDesc().getFormatName());
 			str.append(", ");
 			str.append(getFormatDesc().getFormatVersion());
 			str.append(")");
 		}
-		return(str.toString());
+		return (str.toString());
 	}
 }

pepper-framework/src/main/java/de/hu_berlin/german/korpling/saltnpepper/pepper/common/FormatDesc.java

@@ -106,11 +106,8 @@ public FormatDesc setFormatReference(URI formatReference) {
 	}
 
 	/**
-	 * Two objects are equal: 
-	 * <ul>
-	 *  <li>if they are the same object</li>
-	 *  <li>if the passed object is of type {@link FormatDesc} and both {@link FormatDesc#formatName} and both {@link FormatDesc#formatName} are the same</li>
-	 * </ul>
+	 * Compares a {@link CorpusDesc} object with this object. Both objects are equal, if and only if
+	 * the have the same format name and format version. The comparison is case insensitive.
 	 */
 	@Override
 	public boolean equals(Object obj){
@@ -120,9 +117,9 @@ public boolean equals(Object obj){
 		if (obj!= null){
 			if (obj instanceof FormatDesc){
 				if (	(getFormatName()!= null)&&
-						(getFormatName().equals(((FormatDesc) obj).getFormatName()))&&
+						(getFormatName().equalsIgnoreCase(((FormatDesc) obj).getFormatName()))&&
 						(getFormatVersion()!= null)&&
-						(getFormatVersion().equals(((FormatDesc) obj).getFormatVersion()))){
+						(getFormatVersion().equalsIgnoreCase(((FormatDesc) obj).getFormatVersion()))){
 					return(true);
 				}else{
 					return(false);

pepper-framework/src/main/java/de/hu_berlin/german/korpling/saltnpepper/pepper/common/PepperConfiguration.java

@@ -107,6 +107,11 @@ public class PepperConfiguration extends Properties {
 	 * terminates.
 	 */
 	public static final String PROP_KEEP_TEMP_DOCS = PROP_PREFIX + ".keepTempDocs";
+	/**
+	 * Name of the property to determine Property to determine whether the status report should contain a progress for each module 
+	 * or just the global progress. 
+	 */
+	public static final String PROP_DETAILED_STATUS_REPORT = PROP_PREFIX + ".detailedStatusReport";
 	/**
 	 * name of the flag to determine a workspace for pepper, where all jobs are
 	 * stored by default.
@@ -148,6 +153,7 @@ public PepperConfiguration() {
 		put(PROP_CALL_GC_AFTER_DOCUMENT, Boolean.TRUE);
 		put(PROP_MEMORY_POLICY, MEMORY_POLICY.MODERATE);
 		put(PROP_MAX_AMOUNT_OF_SDOCUMENTS, 10);
+		put(PROP_DETAILED_STATUS_REPORT, true);
 	}
 
 	/**
@@ -362,4 +368,12 @@ public Integer getReportInterval() {
 		String interval = getProperty(PROP_REPORT_INTERVAL, new Integer(1000).toString());
 		return (Integer.valueOf(interval));
 	}
+	/**
+	 * Property to determine whether the status report should contain a progress for each module or just the global progress.
+	 * @return
+	 */
+	public Boolean getDetaialedStatReport() {
+		String callGC = getProperty(PROP_DETAILED_STATUS_REPORT);
+		return (Boolean.valueOf(callGC));
+	}
 }

pepper-framework/src/main/java/de/hu_berlin/german/korpling/saltnpepper/pepper/common/PepperJob.java

@@ -17,12 +17,15 @@
  */
 package de.hu_berlin.german.korpling.saltnpepper.pepper.common;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.List;
 import java.util.Vector;
 
 import org.eclipse.emf.common.util.URI;
 
 import de.hu_berlin.german.korpling.saltnpepper.pepper.exceptions.WorkflowException;
+import de.hu_berlin.german.korpling.saltnpepper.pepper.modules.ModuleController;
 import de.hu_berlin.german.korpling.saltnpepper.salt.saltCommon.SaltProject;
 
 public abstract class PepperJob {
@@ -35,6 +38,38 @@ public abstract class PepperJob {
 	public String getId() {
 		return id;
 	}
+
+	/** The base directory is either the directory from which the Pepper workflow description was loaded or the directory from 
+	 * which Pepper was started. **/
+	private URI baseDir= null;
+
+	/**
+	 * Sets the base directory for this {@link ModuleController}. The base directory is either 
+	 * the directory from which the Pepper workflow description was loaded or the directory from 
+	 * which Pepper was started.
+	 * @param baseDir base directory
+	 */
+	public void setBaseDir(URI baseDir){
+		this.baseDir= baseDir;
+	}
+
+	/**
+	 * Returns the base directory for this {@link ModuleController}. The base directory is either 
+	 * the directory from which the Pepper workflow description was loaded or the directory from 
+	 * which Pepper was started.
+	 * @return base directory
+	 */
+	public URI getBaseDir(){
+		if (baseDir== null){
+			try {
+				baseDir= URI.createFileURI(new File("./").getCanonicalPath());
+			} catch (IOException e) {
+				baseDir= URI.createFileURI(new File("./").getAbsolutePath());
+			}
+		}
+		return(baseDir);
+	}
+
 	/** status of job **/
 	protected JOB_STATUS status= JOB_STATUS.NOT_STARTED;
 	/**
@@ -89,21 +124,6 @@ public void addStepDesc(StepDesc stepDesc){
 	public StepDesc createStepDesc(){
 		return(new StepDesc());
 	}
-//	/**
-//	 * Creates a {@link StepDesc} object an returns it. Further the {@link StepDesc} type {@link StepDesc}s
-//	 * module type is set to the passed one.
-//	 * @param moduleType 
-//	 * @return
-//	 */
-//	public StepDesc createStepDesc(MODULE_TYPE moduleType){
-//		if (moduleType== null){
-//			throw new PepperException("Cannot create a step desc object when passed module type is empty.");
-//		}
-//		StepDesc stepDesc= createStepDesc();
-//		stepDesc.setModuleType(moduleType);
-//		addStepDesc(stepDesc);
-//		return(stepDesc);
-//	}
 
 	/**
 	 * Starts the conversion of this job.

pepper-framework/src/main/java/de/hu_berlin/german/korpling/saltnpepper/pepper/common/PepperUtil.java

@@ -534,9 +534,11 @@ public static class PepperJobReporter extends Thread {
 		 *            the interval in which the status is printed
 		 */
 		public PepperJobReporter(PepperJob pepperJob, int interval) {
-			if (pepperJob == null)
+			if (pepperJob == null){
 				throw new PepperException("Cannot observe Pepper job, because it was null.");
+			}
 			this.pepperJob = pepperJob;
+			this.interval= interval;
 		}
 
 		/**