From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 31 Aug 2007 16:11:15 +0000 (+0000)
Subject: refactoring to enable initialisation of session from an existing vamsas archive and... 
X-Git-Tag: Release_0.2~67
X-Git-Url: http://source.jalview.org/gitweb/?p=vamsas.git;a=commitdiff_plain;h=6fd63fba9b32d6c8da1862e76f2407a08d246c95

refactoring to enable initialisation of session from an existing vamsas archive and bug fix to store session document in an external file.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@453 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/uk/ac/vamsas/client/simpleclient/VamsasSession.java b/src/uk/ac/vamsas/client/simpleclient/VamsasSession.java
index 45766d4..477cec5 100644
--- a/src/uk/ac/vamsas/client/simpleclient/VamsasSession.java
+++ b/src/uk/ac/vamsas/client/simpleclient/VamsasSession.java
@@ -196,13 +196,25 @@ public class VamsasSession {
   public static final String VAMSAS_OBJ = "VamDoc.jar";
 
   /**
-   * sets up the vamsas session files and watchers in sessionDir
+   * sets up the vamsas session files and watchers in sessionDir1
    * @param sessionDir1
    */
   protected VamsasSession(File sessionDir1) throws IOException {
+    this(sessionDir1, null);
+  }
+  /**
+   * sets up the vamsas session files and watchers in sessionDir1
+   * @param sessionDir1 
+   * @param extVamDoc null or an existing archive to initialise the session with
+   * @throws any IOExceptions from creating session directory and files.
+   * @throws error if both extVamDoc and sessionDir1 already exist (cannot import new data into session in this way)
+   */
+  protected VamsasSession(File sessionDir1, File extVamDoc) throws IOException {
     if (sessionDir1 == null)
       throw new Error("Null directory for VamsasSession.");
     if (sessionDir1.exists()) {
+      if (extVamDoc!=null && extVamDoc.exists())
+        throw new Error("Client Initialisation Error: Cannot join an existing session directory with an  existing vamsas document to import.");
       if (!sessionDir1.isDirectory() || !sessionDir1.canWrite()
           || !sessionDir1.canRead())
         throw new IOException("Cannot access '" + sessionDir1
@@ -220,7 +232,7 @@ public class VamsasSession {
       if (!sessionDir1.mkdir())
         throw new IOException("Failed to make VamsasSession directory in "
             + sessionDir1);
-      createSessionFiles();
+      createSessionFiles(extVamDoc);
       initSessionObjects();
       slog.debug("Session directory created.");
       log.debug("Initialised VamsasSession in " + sessionDir1);
@@ -245,6 +257,14 @@ public class VamsasSession {
    *
    */
   private void createSessionFiles() throws IOException {
+    createSessionFiles(null);
+  }
+  /**
+   * 
+   * @param extVamDoc null or an existing vamsas document to initialise session with
+   * @throws IOException
+   */
+  private void createSessionFiles(File extVamDoc) throws IOException {
     if (sessionDir == null)
       throw new IOException(
           "Invalid call to createSessionFiles() with null sessionDir");
@@ -252,8 +272,32 @@ public class VamsasSession {
     File v_doc = new File(sessionDir, VAMSAS_OBJ);
     if (!c_file.exists() && c_file.createNewFile())
       log.debug("Created new ClientFile " + c_file); // don't care if this works or not
-    if (!v_doc.exists() && v_doc.createNewFile())
-      log.debug("Created new Vamsas Session Document File " + v_doc);
+    if (!v_doc.exists())
+      {
+      if (extVamDoc==null)
+        {
+          if (v_doc.createNewFile())
+          {
+            log.debug("Created new Vamsas Session Document File " + v_doc);
+          } else {
+            log.warn("Didn't create Vamsas Session Document file in "+v_doc);
+          }
+        } else {
+          log.debug("Creating new session document from "+extVamDoc);
+          try {
+            SessionFile sesdoc = new SessionFile(new File(sessionDir, VAMSAS_OBJ));
+            SessionFile extdoc = new SessionFile(extVamDoc);
+            sesdoc.updateFrom(null, extdoc);
+          } catch (Exception e)
+          {
+            v_doc.delete();
+            v_doc.createNewFile();
+            log.warn("Problem initialising new session ("+v_doc+") from existing vamsas document ("+extVamDoc+")",e);
+            throw new IOException("Couldn't initialise session from existing vamsas document");
+          }
+          log.debug("Session document initialised from "+extVamDoc);
+        }
+      }
   }
 
   /**
@@ -353,7 +397,7 @@ public class VamsasSession {
       while (!vamArchive.lockFile())
         log.info("Trying to get lock for " + vamArchive.sessionFile);
     // TODO: LATER: decide if a provenance entry should be written in the exported document recording the export from the session
-    newdoc.updateFrom(extlock, vamArchive);
+    newdoc.updateFrom(null, vamArchive);
     // LATER: LATER: fix use of updateFrom for file systems where locks cannot be made (because they don't have a lockManager, ie NFS/Unix, etc).
     vamArchive.unLock();
     newdoc.unlockFile();