Ailibs/refactor/namespacing (#130)

* Update README.md

* Updated Javadoc references

* Mlplan/bugfix/twophasehasco/wrongassert optimal solution (#128)

* Modified logging behavior of MCCV, commented out incorrect assert

* Removed .travis_push_javadoc.sh

* Updated dependency specification examples in readme

* Updated ML-Plan readme

* removed unnessary files from ML-Plan top level

* Update README.md

* Update readme.md

* Update readme.md

* Update readme.md

* Update readme.md

* Update readme.md

* Update readme.md

* Update readme.md

* Update readme.md

* Update readme.md

* Configured the projects correctly for mvn repository. (#129)

* Configured the projects correctly for mvn repository.

Moved resources to resource folder.
Relaxed python version check.
Included searchgraph stylesheet via resources.

* Added empty default values for ossrhUsername and ossrhPassword

* Removed signs from travis builds

* Added intteruptible meka and weka via maven central.

* Fixed typos in build.gradle files.

* Configured the projects correctly for mvn repository.

Moved resources to resource folder.
Relaxed python version check.
Included searchgraph stylesheet via resources.

* Added empty default values for ossrhUsername and ossrhPassword

* Removed signs from travis builds

* Added intteruptible meka and weka via maven central.

* Fixed typos in build.gradle files.

* Renaming search packages.

Fix for some resource loading issues.

Fix for some logging issues.

Fix for some search space configurations.

* Update readme.md

* Update README.md

* modified travis.yml and removed settings.gradle from ML-Plan

.travis.yml

@@ -24,7 +24,7 @@ jobs:
   include:
   - stage: compile
     script:
-    - "./gradlew build -x test"
+    - "./gradlew build -x test -x signArchives"
   - stage: analysis
     addons:
       sonarcloud:
@@ -33,9 +33,9 @@ jobs:
     - ./gradlew compileJava
     - ./gradlew testClasses
     - ./gradlew sonarqube -x test
-  - stage: deploy
-    script: 
-    - "./gradlew publish -PnexusBaseUrl=$nexusBaseUrl -PnexusUpRepo=$nexusUpRepo -PnexusUser=$nexusUser -PnexusPassword=$nexusPassword"
+  #- stage: deploy
+    #script: 
+    #- "./gradlew publish -PnexusBaseUrl=$nexusBaseUrl -PnexusUpRepo=$nexusUpRepo -PnexusUser=$nexusUser -PnexusPassword=$nexusPassword"
 env:
   global:
   - secure: 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

JAICore/jaicore-basic/build.gradle

@@ -8,12 +8,15 @@ dependencies {
 uploadArchives {
 	repositories {
 		mavenDeployer {
+			def ossrhUsername =  project.hasProperty('ossrhUsername') ? project.property('ossrhUsername') : ""
+			def ossrhPassword = project.hasProperty('ossrhPassword') ? project.property('ossrhPassword') : ""
+
 			beforeDeployment { MavenDeployment deployment -> signing.signPom(deployment) }
 			repository(url: "https://oss.sonatype.org/service/local/staging/deploy/maven2/") {
-        		authentication(userName: "${ossrhUsername}", password: "${ossrhPassword}")
+        		authentication(userName: ossrhUsername, password: ossrhPassword)
       		}	
       		snapshotRepository(url: "https://oss.sonatype.org/content/repositories/snapshots/") {
-        		authentication(userName: "${ossrhUsername}", password: "${ossrhPassword}")
+        		authentication(userName: ossrhUsername, password: ossrhPassword)
       		}
 
       		pom.project {
@@ -49,8 +52,8 @@ uploadArchives {
           			}
           			developer {
           			    id 'ahetzer'
-          			    name 'Alexander Hetzer'
-          			    email 'alexander.hetzer@upb.de'
+          			    name 'Alexander Tornede'
+          			    email 'alexander.tornede@upb.de'
           			}
         		}
       		}

JAICore/jaicore-basic/conf/log4j.xml

@@ -46,7 +46,7 @@
     </layout>
   </appender>
 
-  <logger name="jaicore">
+  <logger name="ai.libs.jaicore">
     <level value="warn" />
     <appender-ref ref="console" />
     <appender-ref ref="infoFileAppender" />
@@ -55,19 +55,19 @@
     <appender-ref ref="traceFileAppender" />
   </logger>
 
-  <logger name="jaicore.basic.algorithm.GeneralAlgorithmTester">
+  <logger name="ai.libs.jaicore.basic.algorithm.GeneralAlgorithmTester">
    <level value="trace" />
   </logger>
 
-  <logger name="jaicore.graphvisualizer">
+  <logger name="ai.libs.jaicore.graphvisualizer">
     <level value="warn" />
   </logger>
 
-  <logger name="jaicore.interrupt">
+  <logger name="ai.libs.jaicore.interrupt">
     <level value="debug" />
   </logger>
 
-  <logger name="jaicore.timing">
+  <logger name="ai.libs.jaicore.timing">
     <level value="debug" />
   </logger>
 

JAICore/jaicore-basic/resources/ai/libs/jaicore/basic/testrsc/dummy2.resource

@@ -0,0 +1 @@
+Lorem ipsum dolor sit amet.

JAICore/jaicore-basic/src/main/java/ai/libs/jaicore/basic/FileUtil.java

@@ -43,7 +43,11 @@ private FileUtil() {
 	}
 
 	public static List<String> readFileAsList(final File file) throws IOException {
-		return readFileAsList(file.getAbsolutePath());
+		if (file instanceof ResourceFile) {
+			return ResourceUtil.readResourceFileToStringList((ResourceFile) file);
+		} else {
+			return readFileAsList(file.getAbsolutePath());
+		}
 	}
 
 	public static List<String> readFileAsList(final String filename) throws IOException {
@@ -180,6 +184,10 @@ public static Properties readPropertiesFile(final File propertiesFile) throws IO
 	 */
 	public static void requireFileExists(final File file) throws FileIsDirectoryException, FileNotFoundException {
 		Objects.requireNonNull(file);
+		if (file instanceof ResourceFile) {
+			return;
+		}
+
 		if (!file.exists()) {
 			throw new FileNotFoundException("File " + file.getAbsolutePath() + " does not exist");
 		}
@@ -207,6 +215,7 @@ public static File getExistingFileWithHighestPriority(final String resourcePath,
 				}
 			}
 		}
+
 		return ResourceUtil.getResourceAsFile(resourcePath);
 	}
 }

JAICore/jaicore-basic/src/main/java/ai/libs/jaicore/basic/LoadResourceAsFileFailedException.java

@@ -0,0 +1,13 @@
+package ai.libs.jaicore.basic;
+
+public class LoadResourceAsFileFailedException extends RuntimeException {
+
+	public LoadResourceAsFileFailedException(final String msg) {
+		super(msg);
+	}
+
+	public LoadResourceAsFileFailedException(final String msg, final Throwable cause) {
+		super(msg, cause);
+	}
+
+}

JAICore/jaicore-basic/src/main/java/ai/libs/jaicore/basic/ResourceFile.java

@@ -0,0 +1,76 @@
+package ai.libs.jaicore.basic;
+
+import java.io.File;
+import java.io.InputStream;
+import java.util.LinkedList;
+import java.util.List;
+
+import ai.libs.jaicore.basic.sets.SetUtil;
+
+public class ResourceFile extends File {
+
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -404232145050366072L;
+	private final String pathName;
+
+	public ResourceFile(final String pathname) {
+		super(pathname);
+		this.pathName = pathname;
+	}
+
+	public ResourceFile(final ResourceFile baseFile, final String pathname) {
+		super(getPathName(baseFile, pathname));
+		this.pathName = getPathName(baseFile, pathname);
+	}
+
+	private static String getPathName(final ResourceFile baseFile, final String pathName) {
+		List<String> pathConstruct = new LinkedList<>();
+		List<String> concatPaths = new LinkedList<>();
+
+		concatPaths.addAll(SetUtil.explode(baseFile.getPathName(), "/"));
+		concatPaths.addAll(SetUtil.explode(pathName, "/"));
+
+		for (String pathElement : concatPaths) {
+			if (pathElement.equals(".")) {
+				continue;
+			} else if (pathElement.equals("..")) {
+				if (pathConstruct.isEmpty()) {
+					throw new IllegalArgumentException("Cannot construct path from " + baseFile.getPathName() + " and " + pathName);
+				} else {
+					pathConstruct.remove(pathConstruct.size() - 1);
+				}
+			} else {
+				pathConstruct.add(pathElement);
+			}
+		}
+
+		return SetUtil.implode(pathConstruct, "/");
+	}
+
+	public InputStream getInputStream() {
+		return this.getClass().getClassLoader().getResourceAsStream(this.pathName);
+	}
+
+	public final String getPathName() {
+		return this.pathName;
+	}
+
+	@Override
+	public final ResourceFile getParentFile() {
+		List<String> stringList = SetUtil.explode(this.pathName, "/");
+		if (stringList.size() >= 1) {
+			stringList.remove(stringList.size() - 1);
+			return new ResourceFile(SetUtil.implode(stringList, "/"));
+		} else {
+			return null;
+		}
+	}
+
+	@Override
+	public boolean exists() {
+		return true;
+	}
+
+}

JAICore/jaicore-basic/src/main/java/ai/libs/jaicore/basic/ResourceUtil.java

@@ -1,13 +1,17 @@
 package ai.libs.jaicore.basic;
 
 import java.io.BufferedReader;
+import java.io.BufferedWriter;
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
+import java.io.FileWriter;
 import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
 import java.util.LinkedList;
 import java.util.List;
 
+import ai.libs.jaicore.basic.sets.SetUtil;
+
 /**
  * Utils for handling resource access in a more convenient way.
  *
@@ -27,14 +31,7 @@ private ResourceUtil() {
 	 * @throws IOException Throws an IOException if the file could not be read.
 	 */
 	public static String readResourceFileToString(final String path) throws IOException {
-		StringBuilder sb = new StringBuilder();
-		try (BufferedReader br = new BufferedReader(new FileReader(getResourceAsFile(path)))) {
-			String line;
-			while ((line = br.readLine()) != null) {
-				sb.append(line + "\n");
-			}
-		}
-		return sb.toString();
+		return SetUtil.implode(readResourceFileToStringList(path), "\n");
 	}
 
 	/**
@@ -43,11 +40,10 @@ public static String readResourceFileToString(final String path) throws IOExcept
 	 * @param path The path of the resource that shall be read.
 	 * @return The contents of the resource parsed to a string.
 	 * @throws IOException Throws an IOException if the file could not be read.
-	 * @throws FileNotFoundException Thrown if the file could not be found.
 	 */
 	public static List<String> readResourceFileToStringList(final String path) throws IOException {
 		List<String> list = new LinkedList<>();
-		try (BufferedReader br = new BufferedReader(new FileReader(getResourceAsFile(path)))) {
+		try (BufferedReader br = new BufferedReader(new InputStreamReader(ResourceUtil.class.getClassLoader().getResourceAsStream(path)))) {
 			String line;
 			while ((line = br.readLine()) != null) {
 				list.add(line);
@@ -56,14 +52,55 @@ public static List<String> readResourceFileToStringList(final String path) throw
 		return list;
 	}
 
+	/**
+	 * Reads the contents of a resource to a list of strings.
+	 *
+	 * @param resourceFile The resource file to read.
+	 * @return The contents of the resource parsed to a string.
+	 * @throws IOException Throws an IOException if the file could not be read.
+	 */
+	public static List<String> readResourceFileToStringList(final ResourceFile resourceFile) throws IOException {
+		return readResourceFileToStringList(resourceFile.getPathName());
+	}
+
 	/**
 	 * Returns the file corresponding to the given path.
 	 *
 	 * @param path The path for which a resource shall be retrieved.
 	 * @return The resource file corresponding to the given path.
+	 * @throws IOException
 	 */
-	public static File getResourceAsFile(final String path) {
-		return new File(ResourceUtil.class.getClassLoader().getResource(path).getFile());
+	public static ResourceFile getResourceAsFile(final String path) {
+		return new ResourceFile(path);
+	}
+
+	/**
+	 * Returns the file corresponding to the given path.
+	 *
+	 * @param path The path for which a resource shall be retrieved.
+	 * @return The resource file corresponding to the given path.
+	 * @throws IOException
+	 */
+	public static URL getResourceAsURL(final String path) {
+		return ResourceUtil.class.getClassLoader().getResource(path);
+	}
+
+	/**
+	 * Creates a temporary file from the resource to load.
+	 * @param resourcePath The path to the resource.
+	 * @return The canonical path to the temporary file reflecting the contents of the resource.
+	 */
+	public static String getResourceAsTempFile(final String resourcePath) {
+		try {
+			File tempFile = File.createTempFile("ai.libs-", ".res");
+			tempFile.deleteOnExit();
+			try (BufferedWriter bw = new BufferedWriter(new FileWriter(tempFile))) {
+				bw.write(ResourceUtil.readResourceFileToString(resourcePath));
+			}
+			return tempFile.getCanonicalPath();
+		} catch (IOException e) {
+			throw new LoadResourceAsFileFailedException("Could not load resource as a temporary file", e);
+		}
 	}
 
 }