Merge pull request #5 from genepattern/develop

v1.2.4 release
genepattern · Apr 13, 2017 · 7163f29 · 7163f29
2 parents 6d9a7fc + 49f3fcd
commit 7163f29
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diff --git a/.classpath b/.classpath
@@ -1,7 +1,31 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
@@ -0,0 +1,106 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=disabled
+org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
+org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
+org.eclipse.jdt.core.compiler.annotation.nonnull.secondary=
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault.secondary=
+org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
+org.eclipse.jdt.core.compiler.annotation.nullable.secondary=
+org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
+org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning
+org.eclipse.jdt.core.compiler.problem.deadCode=warning
+org.eclipse.jdt.core.compiler.problem.deprecation=warning
+org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
+org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
+org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
+org.eclipse.jdt.core.compiler.problem.emptyStatement=ignore
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=ignore
+org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore
+org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
+org.eclipse.jdt.core.compiler.problem.fieldHiding=ignore
+org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning
+org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning
+org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
+org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning
+org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=ignore
+org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=ignore
+org.eclipse.jdt.core.compiler.problem.localVariableHiding=ignore
+org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning
+org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
+org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
+org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
+org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=ignore
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=ignore
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=enabled
+org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
+org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=ignore
+org.eclipse.jdt.core.compiler.problem.noEffectAssignment=warning
+org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=warning
+org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
+org.eclipse.jdt.core.compiler.problem.nonnullParameterAnnotationDropped=warning
+org.eclipse.jdt.core.compiler.problem.nonnullTypeVariableFromLegacyInvocation=warning
+org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error
+org.eclipse.jdt.core.compiler.problem.nullReference=warning
+org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
+org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
+org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
+org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
+org.eclipse.jdt.core.compiler.problem.pessimisticNullAnalysisForFreeTypeVariables=warning
+org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=ignore
+org.eclipse.jdt.core.compiler.problem.potentialNullReference=ignore
+org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=ignore
+org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullCheck=ignore
+org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=ignore
+org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=ignore
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=ignore
+org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
+org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
+org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
+org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
+org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=disabled
+org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=ignore
+org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
+org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
+org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
+org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
+org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=ignore
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
+org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=ignore
+org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=ignore
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
+org.eclipse.jdt.core.compiler.problem.unusedExceptionParameter=ignore
+org.eclipse.jdt.core.compiler.problem.unusedImport=warning
+org.eclipse.jdt.core.compiler.problem.unusedLabel=warning
+org.eclipse.jdt.core.compiler.problem.unusedLocal=warning
+org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=ignore
+org.eclipse.jdt.core.compiler.problem.unusedParameter=ignore
+org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
+org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
+org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore
+org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
+org.eclipse.jdt.core.compiler.source=1.8
diff --git a/.settings/org.eclipse.ltk.core.refactoring.prefs b/.settings/org.eclipse.ltk.core.refactoring.prefs
@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.eclipse.ltk.core.refactoring.enable.project.refactoring.history=false
diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1
diff --git a/pom.xml b/pom.xml
@@ -7,28 +7,33 @@
         GenePattern Visualizer Launcher Maven Project 
     ==================================================
     Usage:
+      # build ...
+      #   ... creates single jar executable (signed)
+      #   ... creates Mac OS X application bundle (unsigned)
+      mvn package
+    
       # run visualizer launcher (for debugging, testing)
       mvn -q clean package exec:java
-      # create single jar application
-      mvn clean compile assembly:single 
-      # create Mac OS X application bundle
-      mvn package appbundle:bundle
-      
+
       # run visualizer launcher with the java command
       java -jar launcher/${jarName}-full.jar
       
-      
       # use a different certificate ...
       mvn -Dsignjar.keystore=${HOME}/.gp_build/genepattern-codesign.jks
         -Dsignjar.alias=codesign
         -Dsignjar.storepass=....
         
+      # ===== additional commands =====
+      # check for newer versions of dependencies
+      mvn versions:display-dependency-updates
+      
+      mvn dependency:help
   -->
 
   <modelVersion>4.0.0</modelVersion>
   <groupId>genepattern.org</groupId>
   <artifactId>visualizerLauncher</artifactId>
-  <version>1.2.3</version>
+  <version>1.2.4</version>
   <name>VisualizerLauncher</name>
   <url>http://maven.apache.org</url>
 
@@ -153,42 +158,6 @@
           </execution>
         </executions>
       </plugin>
-
-    <!-- 
-      ==================================================
-          maven-assembly-plugin 
-      ==================================================
-      Usage:
-          mvn clean compile assembly:single 
-
-      Create executable jar file including all library dependencies.
-      See: http://stackoverflow.com/questions/574594/how-can-i-create-an-executable-jar-with-dependencies-using-maven  
-    -->
-    <!--
-      <plugin>
-        <artifactId>maven-assembly-plugin</artifactId>
-        <configuration>
-          <archive>
-            <manifest>
-              <mainClass>${mainClass}</mainClass>
-            </manifest>
-          </archive>
-          <descriptorRefs>
-            <descriptorRef>jar-with-dependencies</descriptorRef>
-          </descriptorRefs>
-          <appendAssemblyId>true</appendAssemblyId>
-        </configuration>
-        <executions>
-          <execution>
-            <id>make-assembly</id> --><!-- this is used for inheritance merges --><!--
-            <phase>prepare-package</phase> --><!-- bind to the prepare-package phase --><!--
-            <goals>
-              <goal>single</goal>
-            </goals>
-          </execution>
-        </executions>
-      </plugin>
--->
 
     <!-- 
       ==================================================
@@ -305,45 +274,59 @@
         <version>1.6.0</version>
       </plugin>
 
+    <!-- 
+      ==================================================
+          maven-clean-plugin
+      ==================================================
+      Cleanup additional files which are created when you run the application
+        ./logs
+        ./visualizerLauncher 
+      By default only the target directory is deleted.
+      See: 
+        https://maven.apache.org/plugins/maven-clean-plugin/
+    -->
+      <plugin>
+        <artifactId>maven-clean-plugin</artifactId>
+        <version>3.0.0</version>
+        <configuration>
+          <filesets>
+            <fileset>
+              <followSymlinks>false</followSymlinks>
+              <directory>visualizerLauncher</directory>
+            </fileset>
+            <fileset>
+              <followSymlinks>false</followSymlinks>
+              <directory>logs</directory>
+            </fileset>
+          </filesets>
+        </configuration>
+      </plugin>
+
     </plugins>
 
   </build>
 
   <dependencies>
 
-    <!-- https://mvnrepository.com/artifact/commons-codec/commons-codec -->
-    <dependency>
-      <groupId>commons-codec</groupId>
-      <artifactId>commons-codec</artifactId>
-      <version>1.10</version>
-    </dependency>
-
     <!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpclient -->
     <dependency>
       <groupId>org.apache.httpcomponents</groupId>
       <artifactId>httpclient</artifactId>
-      <version>4.5.2</version>
-    </dependency>
-
-    <!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpcore -->
-    <dependency>
-      <groupId>org.apache.httpcomponents</groupId>
-      <artifactId>httpcore</artifactId>
-      <version>4.4.4</version>
+      <version>4.5.3</version>
     </dependency>
 
     <!-- https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-api -->
     <dependency>
       <groupId>org.apache.logging.log4j</groupId>
       <artifactId>log4j-api</artifactId>
-      <version>2.8.1</version>
+      <version>2.8.2</version>
     </dependency>
 
     <!-- https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-core -->
     <dependency>
       <groupId>org.apache.logging.log4j</groupId>
       <artifactId>log4j-core</artifactId>
-      <version>2.8.1</version>
+      <version>2.8.2</version>
     </dependency>
 
     <!-- https://mvnrepository.com/artifact/org.json/json -->

diff --git a/src/main/java/org/genepattern/desktop/Util.java b/src/main/java/org/genepattern/desktop/Util.java
@@ -21,12 +21,14 @@
 import org.apache.http.util.EntityUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.json.JSONException;
+import org.json.JSONObject;
 
 /**
  * Created by nazaire on 4/6/16.
  */
 public class Util {
-    final static private Logger log = LogManager.getLogger(Util.class);
+    private static final Logger log = LogManager.getLogger(Util.class);
 
     public static boolean isNullOrEmpty(final String str) {
         return (str==null || str.length()==0);
@@ -86,6 +88,19 @@ public String handleResponse(final HttpResponse response) throws ClientProtocolE
         }
     }
 
+    protected static String retrieveJobDetails(final String basicAuthHeader, final String gpServer, final String jobId) 
+    throws Exception, JSONException {
+        final String response = Util.doGetRequest(basicAuthHeader, 
+            gpServer + VisualizerLauncher.REST_API_JOB_PATH + "/" + jobId);
+        log.trace(response);
+        final JSONObject root = new JSONObject(response);
+        final String taskLsid = root.getString("taskLsid");
+        if(taskLsid == null || taskLsid.length() == 0) {
+            throw new Exception("taskLsid not found");
+        }
+        return taskLsid;
+    }
+
     /**
      * Download a URL to a local file and return a File object for it.
      *
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		eclipse.preferences.version=1
		org.eclipse.ltk.core.refactoring.enable.project.refactoring.history=false