JAL-3384 Redirect stdout and stderr to output.log file

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 02e53ec..45bb8d1 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -47,6 +47,7 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
+import java.io.PrintStream;
 import java.io.PrintWriter;
 import java.net.MalformedURLException;
 import java.net.URI;
@@ -197,6 +198,37 @@ public class Jalview
   void doMain(String[] args)
   {
     System.setSecurityManager(null);
+
+    // set stdout and stderr to file if launched by getdown
+    String appdirString = System.getProperty("getdownappdir");
+    if (appdirString != null)
+    {
+      String logFilename = "output.log";
+      File logFile = new File(appdirString, logFilename);
+      if (logFile.exists())
+      {
+        logFile.delete();
+      }
+      try
+      {
+        PrintStream logOut = new PrintStream(new FileOutputStream(logFile),
+                true);
+        System.setOut(logOut);
+        System.setErr(logOut);
+
+      } catch (IOException ioe)
+      {
+        System.err.println("Failed to open debug log [path="
+                + logFile.getAbsolutePath() + ", exception=" + ioe + "]");
+      }
+      // if we've redirected our log output, note where to
+      if (logFile != null)
+      {
+        System.out.println("Logging to '" + logFile + "'.");
+      }
+
+    }
+
     System.out
             .println("Java version: " + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "
@@ -408,7 +440,7 @@ public class Jalview
 
     // Move any new getdown-launcher-new.jar into place over old
     // getdown-launcher.jar
-    String appdirString = System.getProperty("getdownappdir");
+    // String appdirString = System.getProperty("getdownappdir");
     if (appdirString != null && appdirString.length() > 0)
     {
       final File appdir = new File(appdirString);
@@ -441,91 +473,6 @@ public class Jalview
       System.out.println("No files to open!");
       System.exit(1);
     }
-    String vamsasImport = aparser.getValue("vdoc");
-    String vamsasSession = aparser.getValue("vsess");
-    if (vamsasImport != null || vamsasSession != null)
-    {
-      if (desktop == null || headless)
-      {
-        System.out.println(
-                "Headless vamsas sessions not yet supported. Sorry.");
-        System.exit(1);
-      }
-      // if we have a file, start a new session and import it.
-      boolean inSession = false;
-      if (vamsasImport != null)
-      {
-        try
-        {
-          DataSourceType viprotocol = AppletFormatAdapter
-                  .checkProtocol(vamsasImport);
-          if (viprotocol == DataSourceType.FILE)
-          {
-            inSession = desktop.vamsasImport(new File(vamsasImport));
-          }
-          else if (viprotocol == DataSourceType.URL)
-          {
-            inSession = desktop.vamsasImport(new URL(vamsasImport));
-          }
-
-        } catch (Exception e)
-        {
-          System.err.println("Exeption when importing " + vamsasImport
-                  + " as a vamsas document.");
-          e.printStackTrace();
-        }
-        if (!inSession)
-        {
-          System.err.println("Failed to import " + vamsasImport
-                  + " as a vamsas document.");
-        }
-        else
-        {
-          System.out.println("Imported Successfully into new session "
-                  + desktop.getVamsasApplication().getCurrentSession());
-        }
-      }
-      if (vamsasSession != null)
-      {
-        if (vamsasImport != null)
-        {
-          // close the newly imported session and import the Jalview specific
-          // remnants into the new session later on.
-          desktop.vamsasStop_actionPerformed(null);
-        }
-        // now join the new session
-        try
-        {
-          if (desktop.joinVamsasSession(vamsasSession))
-          {
-            System.out.println(
-                    "Successfully joined vamsas session " + vamsasSession);
-          }
-          else
-          {
-            System.err.println("WARNING: Failed to join vamsas session "
-                    + vamsasSession);
-          }
-        } catch (Exception e)
-        {
-          System.err.println(
-                  "ERROR: Failed to join vamsas session " + vamsasSession);
-          e.printStackTrace();
-        }
-        if (vamsasImport != null)
-        {
-          // the Jalview specific remnants can now be imported into the new
-          // session at the user's leisure.
-          Cache.log.info(
-                  "Skipping Push for import of data into existing vamsas session."); // TODO:
-          // enable
-          // this
-          // when
-          // debugged
-          // desktop.getVamsasApplication().push_update();
-        }
-      }
-    }
     long progress = -1;
     // Finally, deal with the remaining input data.
     if (file != null)
@@ -761,7 +708,7 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (!headless && file == null && vamsasImport == null
+    if (!headless && file == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",
@@ -867,10 +814,6 @@ public class Jalview
                     // passed in correctly)"
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
-                    // +
-                    // "-vdoc vamsas-document\tImport vamsas document into new
-                    // session or join existing session with same URN\n"
-                    // + "-vses vamsas-session\tJoin session with given URN\n"
                     + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
                     + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
   }