Merge pull request #6 from genepattern/develop

release 1.2.5 fix for '/gp/jobResults'
genepattern · May 8, 2017 · 82999ff · 82999ff
2 parents 7163f29 + 8aa610f
commit 82999ff
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Showing 6 changed files with 42 additions and 22 deletions.
diff --git a/INSTALL.md → BUILD.md b/INSTALL.md → BUILD.md
diff --git a/README.md b/README.md
@@ -1,6 +1,13 @@
 ## VisualizerLauncher
-Launches a GenePattern visualizer from the desktop. Use this as a replacement for the 'Open Visualizer' link embedded in the web page. The application is available for download directly from the [releases](https://github.com/genepattern/VisualizerLauncher/releases/latest) page. 
 
-See the [INSTALL page](INSTALL.md) for instructions on building the application.
+Launch a GenePattern visualizer from the desktop. Use this as a replacement for the 'Open Visualizer' link on the Job Status page. 
 
-See the [home page](https://genepattern.github.io/VisualizerLauncher/) for more usage instructions.
+See the [home page](https://genepattern.github.io/VisualizerLauncher/) for usage instructions.
+
+### Developer documentation
+
+See the [BUILD page](BUILD.md) for instructions on building the application from source code.
+
+### Release archive
+
+See the [releases page](https://github.com/genepattern/VisualizerLauncher/releases/latest) for release notes and older versions.
diff --git a/pom.xml b/pom.xml
@@ -33,7 +33,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>genepattern.org</groupId>
   <artifactId>visualizerLauncher</artifactId>
-  <version>1.2.4</version>
+  <version>1.2.5</version>
   <name>VisualizerLauncher</name>
   <url>http://maven.apache.org</url>
 

diff --git a/src/main/java/org/genepattern/desktop/JobInfo.java b/src/main/java/org/genepattern/desktop/JobInfo.java
@@ -10,7 +10,7 @@ public class JobInfo
     private String jobNumber;
     private GPTask gpTask;
     private String[] commandLine;
-    private Map inputURLToFilePathMap;
+    private Map<String,String> inputURLToFilePathMap;
 
     public String getJobNumber() {
         return jobNumber;
@@ -40,7 +40,7 @@ public Map<String, String> getInputURLToFilePathMap() {
         return inputURLToFilePathMap;
     }
 
-    public void setInputURLToFilePathMap(Map inputURLToFilePathMap) {
+    public void setInputURLToFilePathMap(Map<String,String> inputURLToFilePathMap) {
         this.inputURLToFilePathMap = inputURLToFilePathMap;
     }
 }
diff --git a/src/main/java/org/genepattern/desktop/Util.java b/src/main/java/org/genepattern/desktop/Util.java
@@ -108,18 +108,18 @@ protected static String retrieveJobDetails(final String basicAuthHeader, final S
      * @param dir, The directory to download the URL to.
      * @param filename, The filename to download the URL to.
      */
-    public static File downloadFile(String authString, URL fromUrl, File toDir, String filename) throws IOException {
+    public static File downloadFile(final String authString, final URL fromUrl, final File toDir, final String filename) throws IOException {
         InputStream is = null;
         FileOutputStream fos = null;
-        File file = null;
+        File toFile = null;
         try {
             URLConnection conn = fromUrl.openConnection();
             conn.setRequestProperty("Authorization", authString);
 
             is = conn.getInputStream();
             toDir.mkdirs();
-            file = new File(toDir, filename);
-            fos = new FileOutputStream(file);
+            toFile = new File(toDir, filename);
+            fos = new FileOutputStream(toFile);
             byte[] buf = new byte[100000];
             int j;
             while ((j = is.read(buf, 0, buf.length)) != -1) {
@@ -136,17 +136,19 @@ public static File downloadFile(String authString, URL fromUrl, File toDir, Stri
                     is.close();
                 }
                 catch (IOException e) {
+                    log.error("Unexpected error closing input stream, fromUrl="+fromUrl, e);
                 }
             }
             if (fos != null) {
                 try {
                     fos.close();
                 }
                 catch (IOException e) {
+                    log.error("Unexpected error closing output stream, toFile="+toFile, e);
                 }
             }
         }
-        return file;
+        return toFile;
     }
 
     /** create thread to read from a process output or error stream */

diff --git a/src/main/java/org/genepattern/desktop/VisualizerLauncher.java b/src/main/java/org/genepattern/desktop/VisualizerLauncher.java
@@ -64,7 +64,7 @@ public class VisualizerLauncher {
         this.jobInfo = new JobInfo();
     }
 
-    private void login() {
+    private void run() {
         JPanel panel = new JPanel(new GridLayout(4, 1));
         panel.setBorder(BorderFactory.createEmptyBorder(20, 20, 20, 20));
 
@@ -182,10 +182,6 @@ public void actionPerformed(ActionEvent e) {
         frame.setVisible(true);
     }
 
-    public void run() {
-        login();
-    }
-
     private void downloadSupportFiles(final GPTask task) throws Exception {
         for(final String supportFileURL : task.getSupportFileUrls()) {
             final int slashIndex = supportFileURL.lastIndexOf('=');
@@ -317,6 +313,10 @@ private void prepareCommandLineStep() throws IOException {
         final String[] cmdLineList = new String[cmdLineArr.length()];
         for(int i=0;i< cmdLineArr.length(); i++) {
             String argValue = cmdLineArr.getString(i);
+            if (argValue.startsWith("/gp/")) {
+                // e.g. gpServer=http://127.0.0.1:8080/gp
+                argValue=argValue.replaceFirst("/gp", gpServer);
+            }
             if(inputURLMap.containsKey(argValue)) {
                 argValue = downloadLocation.getAbsolutePath() + "/" + inputURLMap.get(argValue);
             }
@@ -355,17 +355,28 @@ protected void downloadInputFiles() throws Exception {
         final JSONArray inputFiles=inputFilesJsonObj.getJSONArray("inputFiles");
         final Map<String, String> map = new HashMap<String, String>();
         for(int i=0;i<inputFiles.length();i++) {
-            String inputFile = inputFiles.getString(i);
-            if (inputFile.startsWith("<GenePatternURL>")) {
-                inputFile=inputFile.replaceFirst("<GenePatternURL>", gpServer+"/");
-            }
-            final String filenameWithExtension=filenameWithExt(inputFile);
-            final URL fileURL = downloadInputFile(inputFile);
+            final String inputFile = inputFiles.getString(i);
+            final String inputFileUrlStr=initInputFileUrlStr(inputFile);
+            final String filenameWithExtension=filenameWithExt(inputFileUrlStr);
+            final URL fileURL = downloadInputFile(inputFileUrlStr);
             map.put(fileURL.toString(), filenameWithExtension);
         }
         jobInfo.setInputURLToFilePathMap(map);
     }
 
+    protected String initInputFileUrlStr(final String inputFile) {
+        if (inputFile.startsWith("<GenePatternURL>")) {
+            return inputFile.replaceFirst("<GenePatternURL>", gpServer+"/");
+        }
+        else if (inputFile.startsWith("/gp/")) {
+            // e.g. gpServer=http://127.0.0.1:8080/gp
+            return inputFile.replaceFirst("/gp", gpServer);
+        }
+        else {
+            return inputFile;
+        }
+    }
+
     protected String filenameWithExt(final String inputFile) {
         final int slashIndex = inputFile.lastIndexOf('/');
         final String filenameWithExtension =  inputFile.substring(slashIndex + 1);