From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 22 Mar 2006 14:12:12 +0000 (+0000)
Subject: added new method for writing an AppData jar entry directly from an InputStream.
X-Git-Tag: Release_0.2~323
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=3e8b089a7838da522348f8601ef261deeb2ec5fc;p=vamsas.git

added new method for writing an AppData jar entry directly from an InputStream.
Also reprioritised some TODOs and made comments

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@197 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
index 93c775c..d510d51 100644
--- a/src/org/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchive.java
@@ -149,7 +149,7 @@ public class VamsasArchive {
   
   /**
    * name of backup of existing archive that has been updated/overwritten.
-   * onlu one backup will be made - and this is it.
+   * only one backup will be made - and this is it.
    */
   File originalBackup = null;
   
@@ -157,9 +157,10 @@ public class VamsasArchive {
   private final int _TRANSFER_BUFFER=4096*4;
   protected SimpleDocument vorba = null;
   /**
+   * LATER: ? CUT'n'Paste error ?
    * Access and return current vamsas Document, if it exists, or create a new one 
    * (without affecting VamsasArchive object state - so is NOT THREAD SAFE)
-   * TODO: possibly modify internal state to lock low-level files 
+   * _TODO: possibly modify internal state to lock low-level files 
    * (like the IClientDocument interface instance constructer would do) 
    * @see org.vamsas.simpleclient.VamsasArchive.getOriginalVamsasDocument for additional caveats
    * 
@@ -167,6 +168,7 @@ public class VamsasArchive {
    * @throws IOException
    * @throws org.exolab.castor.xml.MarshalException
    * @throws org.exolab.castor.xml.ValidationException
+   * ????? where does this live JBPNote ?
    */
   private VamsasDocument _doc=null;
   
@@ -502,7 +504,7 @@ public class VamsasArchive {
    * opens the new archive ready for writing. If the new archive is replacing an existing one, 
    * then the existing archive will be locked, and the new archive written to a temporary file. 
    * The new archive will be put in place once close() is called.
-   * @param doclock TODO
+   * @param doclock LATER - pass existing lock on document, if it exists.... no need yet?
    * @throws IOException
    */
   private void openArchive() throws IOException {
@@ -598,7 +600,23 @@ public class VamsasArchive {
   public boolean transferAppDataEntry(String AppDataReference) throws IOException {
     return transferAppDataEntry(AppDataReference, AppDataReference);
   }
-  
+  /**
+   * Validates the AppDataReference: not null and not already written to archive.
+   * @param AppDataReference
+   * @return true if valid. false if not
+   * @throws IOException for really broken references!
+   */
+  protected boolean _validNewAppDataReference(String newAppDataReference) throws IOException {
+    // LATER: Specify valid AppDataReference form in all VamsasArchive handlers
+    if (newAppDataReference==null)
+      throw new IOException("null newAppDataReference!");
+    if (entries.containsKey(newAppDataReference)) {
+      log.warn("Attempt to write '"+newAppDataReference+"' twice! - IGNORED");
+      // LATER: fix me? warning message should raise an exception here.
+      return false;
+    }
+    return true;
+  }
   /**
    * Transfers an AppDataReference from old to new vamsas archive, with a name change.
    * @see transferAppDataEntry(String AppDataReference)
@@ -608,17 +626,15 @@ public class VamsasArchive {
    * @throws IOException
    */
   public boolean transferAppDataEntry(String AppDataReference, String NewAppDataReference) throws IOException {
-    // TODO: Specify valid AppDataReference form in all VamsasArchive handlers
-    if (AppDataReference==null)
-      throw new IOException("null AppDataReference!");
     if (original==null || !original.exists()) {
       log.warn("No backup archive exists.");
       return false;
     }
-    if (entries.containsKey(NewAppDataReference)) {
-      log.warn("Attempt to write '"+NewAppDataReference+"' twice! - IGNORED");
-      return true;
-    }
+    if (AppDataReference==null)
+      throw new IOException("null AppDataReference!");
+
+    if (!_validNewAppDataReference(NewAppDataReference))
+      return false;
     
     accessOriginal();
     
@@ -645,11 +661,42 @@ public class VamsasArchive {
         +AppDataReference+"' as '"+NewAppDataReference+"' ("+count+" bytes)");
     return true;
   }
-  
+  /**
+   * write data from a stream into an appData reference.
+   * @param AppDataReference - New AppDataReference not already written to archive
+   * @param adstream Source of data for appData reference - read until .read(buffer) returns -1
+   * @return true on success.
+   * @throws IOException for file IO or invalid AppDataReference string
+   */
+  public boolean writeAppdataFromStream(String AppDataReference, java.io.InputStream adstream) throws IOException {
+    if (!_validNewAppDataReference(AppDataReference)) {
+      log.warn("Invalid AppDataReference passed to writeAppdataFromStream");
+      throw new IOException("Invalid AppDataReference! (null, or maybe non-unique)!");
+    }
+      
+    if (AppDataReference==null) {
+      log.warn("null appdata passed.");
+      throw new IOException("Null AppDataReference");
+    }
+    
+    java.io.OutputStream adout = getAppDataStream(AppDataReference);
+    // copy over the bytes
+    int written=-1;
+    long count=0;
+    byte[] buffer = new byte[_TRANSFER_BUFFER]; // conservative estimate of a sensible buffer
+    do {
+      if ((written = adstream.read(buffer))>-1) {
+        adout.write(buffer, 0, written);
+        log.debug("Transferring "+written+".");
+        count+=written;
+      }
+    } while (written>-1);
+    return true;
+  }
   /**
    * transfers any AppDataReferences existing in the old document 
    * that haven't already been transferred to the new one
-   * TODO: LATER: do the same for transfers requiring a namechange - more document dependent.
+   * LATER: do the same for transfers requiring a namechange - more document dependent.
    *  @return true if data was transferred.
    */
   public boolean transferRemainingAppDatas() throws IOException {
@@ -698,7 +745,7 @@ public class VamsasArchive {
         odoclock.updateFrom(null, rchive);
       }
       catch (IOException e) {
-        // TODO: LATER: decide if leaving nastily named backup files around is necessary. 
+        // LATER: decide if leaving nastily named backup files around is necessary. 
         log.error("Problem updating archive from temporary file! - backup left in '"
             +backupFile().getAbsolutePath()+"'",e);
       }