X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Ftest%2Fsimpleclient%2FVamsasArchive.java;h=3d78cb8f44148a0a221bfbdab0cdf5d8531e80aa;hb=1eea4b639911330e7cd65e17c5421cc584f0d22e;hp=d682f10ad3277bdfb2f9be7d64f985dd74bad60e;hpb=3b92275c26c14a678519f1d7d2ffaa477eb76cdb;p=vamsas.git

diff --git a/src/uk/ac/vamsas/test/simpleclient/VamsasArchive.java b/src/uk/ac/vamsas/test/simpleclient/VamsasArchive.java
index d682f10..3d78cb8 100644
--- a/src/uk/ac/vamsas/test/simpleclient/VamsasArchive.java
+++ b/src/uk/ac/vamsas/test/simpleclient/VamsasArchive.java
@@ -1,206 +1,273 @@
-package uk.ac.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.io.ObjectOutputStream;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.test.objects.Core;
-
-import uk.ac.vamsas.client.simpleclient.Lock;
-import uk.ac.vamsas.client.simpleclient.SessionFile;
-import uk.ac.vamsas.client.simpleclient.SimpleDocument;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.User;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-public class VamsasArchive {
-  /**
-   * test the org.vamsas.simpleclient.vamsasArchive class
-   */
-  static Log log = LogFactory.getLog(VamsasArchive.class);
-  public static ApplicationData makeDemoAppdata(uk.ac.vamsas.client.simpleclient.VamsasArchive va, String apname, String userName, String userOrg) {
-    if (va==null)
-      return null;
-    VamsasArchiveReader vread=null;
-    try {
-      vread = va.getOriginalArchiveReader();
-    }
-    catch (Exception e) {
-      log.error("Failed to get original archive reader!",e);
-      return null;
-    }
-    ApplicationData appdata = new ApplicationData();
-    appdata.setName("uk.ac.vamsas.test.simpleclient.VamsasArchive");
-    appdata.setData(new String("this is some test data.").getBytes());
-    User apuser = new User();
-    apuser.setFullname(userName);
-    apuser.setOrganization(userOrg);
-    String appdata_ref = "vamsas:"+apname+"/"+apuser.getOrganization()+"/"+apuser.getFullname();
-    SimpleDocument sdoc = new SimpleDocument("test.simpleclient.VamsasArchive");
-    if (vread!=null) {
-      VamsasDocument orignalnew;
-      try {
-        orignalnew = sdoc.getVamsasDocument(vread);
-        log.info("*** Dump follows ***");
-        
-        ArchiveReports.reportDocument(orignalnew, vread, false, System.out);
-        log.info("*** Dump precedes ***");
-      } catch (Exception e) {
-        log.info("makeDemoAppdata: Problems accessing original document");
-      }
-      
-      log.info("Reading (and avoiding references to) original data");
-      if (vread.getAppdataStream(appdata_ref)!=null) {
-        // transfer over
-        try {
-          va.transferAppDataEntry(appdata_ref);
-        } catch (Exception e) {
-          log.warn("Exception when transferring appdata reference : "+appdata_ref, e);
-        }
-        int i=0;
-        while (vread.getAppdataStream(appdata_ref+"/"+Integer.toString(++i))!=null) {
-          try {
-            // copy over another duplicate.
-            va.transferAppDataEntry(appdata_ref+"/"+Integer.toString(i));
-          } catch (Exception e) {
-            log.warn("Exception when transferring appdata reference : "+appdata_ref, e);
-          }
-        }
-        // this one must be unique!
-        appdata_ref+="/"+Integer.toString(i);
-      }
-    }
-    
-    log.info("Adding new data stuff.");
-    log.info("Writing an apdata reference using AppDataStream interface.");
-    apuser.setDataReference(appdata_ref);
-    appdata.addUser(apuser);
-    appdata.setVersion("noggin");
-    //TODO: write instance appdata  appdata.setUrn("program:/the.nog/");
-    try {
-      ObjectOutputStream ost = new ObjectOutputStream(va.getAppDataStream(appdata_ref));
-      ost.writeObject(appdata);
-      ost.close();
-    } catch (Exception e) {
-      log.warn("Couldn't write appdata reference "+appdata_ref);
-    }
-    return appdata;
-  }
-  public static void main(String args[]) {
-    
-    try {
-      File av;
-      if (args.length>0)
-        av = new File(args[0]);
-      else
-        av = new File("test/vamsas.zip");
-      log.info("Opening archive "+av);
-      uk.ac.vamsas.client.simpleclient.VamsasArchive varchive = new uk.ac.vamsas.client.simpleclient.VamsasArchive(av, true);
-      
-      VAMSAS[] roots = (VAMSAS[]) varchive.getOriginalRoots();
-      
-      if (roots!=null) {
-        log.info("Report on Original roots in archive:");
-        ArchiveReports.rootReport(roots, true, System.out);
-      }
-      log.info("Getting current vamsas document.");
-      VamsasDocument doc = varchive.getVamsasDocument();
-      ArchiveReports.reportDocument(doc, varchive.getOriginalArchiveReader(), true, System.out); // not modified document so references will still be valid
-      // do some stuff
-      log.info("Retrieving backup");
-      File backup = varchive.backupFile();
-      if (backup==null)
-        log.info(av+" is a New Archive.");
-      else 
-        log.info(av+" has been backed up as "+backup);
-      File newf=new File(av.getAbsolutePath()+"_new.zip");
-      VamsasFile sfile = new VamsasFile(newf);
-      /* if (newf.exists()) {
-        int q=1;
-        do {
-          newf=new File(av.getAbsolutePath()+"_"+q+++"_new.zip");
-        }
-        while (newf.exists()); 
-      } */
-      if (newf.exists()) {
-        log.info("Removing existing "+newf);
-        newf.delete();
-      }
-        
-      log.info("Now writing new Archive into "+newf.getAbsolutePath());
-      uk.ac.vamsas.client.simpleclient.VamsasArchive va=null;
-      { // hold lock over deletion and write of new archive.
-        //Lock wlock = sfile.getLock();
-        //newf.delete(); // clear out old file.
-        sfile.getLock();
-        va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, true, true, sfile);
-        // open another and...
-        ApplicationData appdata = makeDemoAppdata(va, 
-            "uk.ac.vamsas.test.simpleclient.VamsasArchive", "arnold Bugger esq", "disOrganised");
-        log.info("Preparing to write new document.");
-        doc.addApplicationData(appdata);
-        doc.addVAMSAS(Core.getDemoVamsas());
-        va.putVamsasDocument(doc); // gets stream and puts it.
-        va.closeArchive();
-        sfile.unLock();
-      }
-      log.info("Dump of new vamsas document :");
-      log.info("Testing update: ");
-      {
-        Lock lock=sfile.getLock();
-        if (lock==null)
-          while ((lock=sfile.getLock())==null) {
-            log.info("Waiting for lock.");
-            Thread.sleep(100);
-          }
-        VamsasArchiveReader vreader = new VamsasArchiveReader(sfile.getVamsasFile());// lock); // cannot do new JarFile on a locked file. // newf);
-        SimpleDocument sdoc = new SimpleDocument("testing new vamsas write");
-        ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true, System.out);
-        sfile.unLock();
-      }
-      // backup.delete(); // tidy up
-      
-      log.info("Now Cancelling write to original archive "+av);
-      if (varchive.cancelArchive())
-        log.info("Successfully cancelled.");
-      else
-        log.info("Didn't cancel.");
-      long t=System.currentTimeMillis()+200; while (t>System.currentTimeMillis());
-      log.info("Now testing archive update.");
-      va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, false, true, sfile);
-      doc = va.getVamsasDocument();
-      doc.addVAMSAS(Core.getDemoVamsas());
-      doc.addApplicationData(makeDemoAppdata(va, 
-          "uk.ac.vamsas.test.simpleclient.VamsasArchive", "another old Bugger esq", "rescinded"));
-      if (va.transferRemainingAppDatas())
-        log.info("Remain appdatas were transferred.");
-      else
-        log.warn("No appdatas were transferred. This is wrong.");
-      va.putVamsasDocument(doc);
-      va.closeArchive();
-      sfile.unLock();
-      log.info("Testing update: ");
-      {
-        Lock lock=sfile.getLock();
-        if (lock==null)
-          while ((lock=sfile.getLock())==null)
-            log.info("Waiting for lock.");
-        // VamsasArchiveReader vreader = new VamsasArchiveReader(lock);
-        VamsasArchiveReader vreader = new VamsasArchiveReader(newf);
-        
-        SimpleDocument sdoc = new SimpleDocument("testing vamsas update");
-        VamsasDocument finaldoc = sdoc.getVamsasDocument(vreader);
-        if (finaldoc!=null)
-          ArchiveReports.reportDocument(finaldoc, vreader, true, System.out);
-        else 
-          log.error("Null Document Read from "+newf);
-      }
-    } catch (Exception e) {
-      e.printStackTrace(System.err);
-    }
-  }
-}
+/*
+ * This file is part of the Vamsas Client version 0.2. 
+ * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package uk.ac.vamsas.test.simpleclient;
+
+import java.io.File;
+import java.io.ObjectOutputStream;
+import java.io.RandomAccessFile;
+import java.util.jar.JarFile;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import uk.ac.vamsas.client.simpleclient.Lock;
+import uk.ac.vamsas.client.simpleclient.SessionFile;
+import uk.ac.vamsas.client.simpleclient.SimpleDocument;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+import uk.ac.vamsas.client.simpleclient.VamsasFile;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.User;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
+import uk.ac.vamsas.test.objects.Core;
+
+public class VamsasArchive {
+  /**
+   * test the org.vamsas.simpleclient.vamsasArchive class
+   */
+  static Log log = LogFactory.getLog(VamsasArchive.class);
+
+  public static ApplicationData makeDemoAppdata(
+      uk.ac.vamsas.client.simpleclient.VamsasArchive va, String apname,
+      String userName, String userOrg) {
+    if (va == null)
+      return null;
+    VamsasArchiveReader vread = null;
+    try {
+      vread = va.getOriginalArchiveReader();
+    } catch (Exception e) {
+      log.error("Failed to get original archive reader!", e);
+      return null;
+    }
+    ApplicationData appdata = new ApplicationData();
+    appdata.setName("uk.ac.vamsas.test.simpleclient.VamsasArchive");
+    appdata.setData(new String("this is some test data.").getBytes());
+    User apuser = new User();
+    apuser.setFullname(userName);
+    apuser.setOrganization(userOrg);
+    String appdata_ref = "vamsas:" + apname + "/" + apuser.getOrganization()
+        + "/" + apuser.getFullname();
+    SimpleDocument sdoc = new SimpleDocument("test.simpleclient.VamsasArchive");
+    if (vread != null) {
+      VamsasDocument orignalnew;
+      try {
+        orignalnew = sdoc.getVamsasDocument(vread);
+        log.info("*** Dump follows ***");
+
+        ArchiveReports.reportDocument(orignalnew, vread, false, System.out);
+        log.info("*** Dump precedes ***");
+      } catch (Exception e) {
+        log.info("makeDemoAppdata: Problems accessing original document");
+      }
+
+      log.info("Reading (and avoiding references to) original data");
+      if (vread.getAppdataStream(appdata_ref) != null) {
+        // transfer over
+        try {
+          va.transferAppDataEntry(appdata_ref);
+        } catch (Exception e) {
+          log.warn("Exception when transferring appdata reference : "
+              + appdata_ref, e);
+        }
+        int i = 0;
+        while (vread
+            .getAppdataStream(appdata_ref + "/" + Integer.toString(++i)) != null) {
+          try {
+            // copy over another duplicate.
+            va.transferAppDataEntry(appdata_ref + "/" + Integer.toString(i));
+          } catch (Exception e) {
+            log.warn("Exception when transferring appdata reference : "
+                + appdata_ref, e);
+          }
+        }
+        // this one must be unique!
+        appdata_ref += "/" + Integer.toString(i);
+      }
+    }
+
+    log.info("Adding new data stuff.");
+    log.info("Writing an apdata reference using AppDataStream interface.");
+    apuser.setDataReference(appdata_ref);
+    appdata.addUser(apuser);
+    appdata.setVersion("noggin");
+    // TODO: write instance appdata appdata.setUrn("program:/the.nog/");
+    try {
+      ObjectOutputStream ost = new ObjectOutputStream(va
+          .getAppDataStream(appdata_ref));
+      ost.writeObject(appdata);
+      ost.close();
+    } catch (Exception e) {
+      log.warn("Couldn't write appdata reference " + appdata_ref);
+    }
+    return appdata;
+  }
+
+  public static void main(String args[]) {
+
+    try {
+      File av;
+      if (args.length > 0)
+        av = new File(args[0]);
+      else
+        av = new File("test/vamsas.zip");
+      try {
+        RandomAccessFile raf = new RandomAccessFile(av, "r");
+        raf.readByte();
+        raf.close();
+      } catch (Exception f) {
+        log.info("Couldn't random access file archive " + av, f);
+      }
+      try {
+        JarFile jf = new JarFile(av, true, JarFile.OPEN_READ);
+        if (jf.getEntry("vamsasDocument.xml") != null) {
+          log.info("Valid archive (sun) " + av);
+        }
+        jf.close();
+      } catch (Exception f) {
+        log.warn("Couldn't access jar archive with sun jartools: " + av, f);
+      }
+      try {
+        org.apache.tools.zip.ZipFile jf = new org.apache.tools.zip.ZipFile(av);
+        if (jf.getEntry("vamsasDocument.xml") != null) {
+          log.info("Valid archive (apache) " + av);
+        }
+        jf.close();
+      } catch (Exception f) {
+        log.warn("Couldn't access jar archive with apache ziptool: " + av, f);
+      }
+
+      log.info("Opening archive " + av);
+      uk.ac.vamsas.client.simpleclient.VamsasArchive varchive = new uk.ac.vamsas.client.simpleclient.VamsasArchive(
+          av, true);
+
+      VAMSAS[] roots = (VAMSAS[]) varchive.getOriginalRoots();
+
+      if (roots != null) {
+        log.info("Report on Original roots in archive:");
+        ArchiveReports.rootReport(roots, true, System.out);
+      }
+      log.info("Getting current vamsas document.");
+      VamsasDocument doc = varchive.getVamsasDocument();
+      ArchiveReports.reportDocument(doc, varchive.getOriginalArchiveReader(),
+          true, System.out); // not modified document so references will still
+                             // be valid
+      // do some stuff
+      log.info("Retrieving backup");
+      File backup = varchive.backupFile();
+      if (backup == null)
+        log.info(av + " is a New Archive.");
+      else
+        log.info(av + " has been backed up as " + backup);
+      File newf = new File(av.getAbsolutePath() + "_new.zip");
+      VamsasFile sfile = new VamsasFile(newf);
+      /*
+       * if (newf.exists()) { int q=1; do { newf=new
+       * File(av.getAbsolutePath()+"_"+q+++"_new.zip"); } while (newf.exists());
+       * }
+       */
+      if (newf.exists()) {
+        log.info("Removing existing " + newf);
+        newf.delete();
+      }
+
+      log.info("Now writing new Archive into " + newf.getAbsolutePath());
+      uk.ac.vamsas.client.simpleclient.VamsasArchive va = null;
+      { // hold lock over deletion and write of new archive.
+        // Lock wlock = sfile.getLock();
+        // newf.delete(); // clear out old file.
+        sfile.getLock();
+        va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, true,
+            true, sfile);
+        // open another and...
+        ApplicationData appdata = makeDemoAppdata(va,
+            "uk.ac.vamsas.test.simpleclient.VamsasArchive",
+            "arnold Bugger esq", "disOrganised");
+        log.info("Preparing to write new document.");
+        doc.addApplicationData(appdata);
+        doc.addVAMSAS(Core.getDemoVamsas());
+        va.putVamsasDocument(doc); // gets stream and puts it.
+        va.closeArchive();
+        sfile.unLock();
+      }
+      log.info("Dump of new vamsas document :");
+      log.info("Testing update: ");
+      {
+        Lock lock = sfile.getLock();
+        if (lock == null)
+          while ((lock = sfile.getLock()) == null) {
+            log.info("Waiting for lock.");
+            Thread.sleep(100);
+          }
+        VamsasArchiveReader vreader = new VamsasArchiveReader(sfile
+            .getVamsasFile());// lock); // cannot do new JarFile on a locked
+                              // file. // newf);
+        SimpleDocument sdoc = new SimpleDocument("testing new vamsas write");
+        ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader,
+            true, System.out);
+        sfile.unLock();
+      }
+      // backup.delete(); // tidy up
+
+      log.info("Now Cancelling write to original archive " + av);
+      if (varchive.cancelArchive())
+        log.info("Successfully cancelled.");
+      else
+        log.info("Didn't cancel.");
+      long t = System.currentTimeMillis() + 200;
+      while (t > System.currentTimeMillis())
+        ;
+      log.info("Now testing archive update.");
+      va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, false,
+          true, sfile);
+      doc = va.getVamsasDocument();
+      doc.addVAMSAS(Core.getDemoVamsas());
+      doc.addApplicationData(makeDemoAppdata(va,
+          "uk.ac.vamsas.test.simpleclient.VamsasArchive",
+          "another old Bugger esq", "rescinded"));
+      if (va.transferRemainingAppDatas())
+        log.info("Remain appdatas were transferred.");
+      else
+        log.warn("No appdatas were transferred. This is wrong.");
+      va.putVamsasDocument(doc);
+      va.closeArchive();
+      sfile.unLock();
+      log.info("Testing update: ");
+      {
+        Lock lock = sfile.getLock();
+        if (lock == null)
+          while ((lock = sfile.getLock()) == null)
+            log.info("Waiting for lock.");
+        // VamsasArchiveReader vreader = new VamsasArchiveReader(lock);
+        VamsasArchiveReader vreader = new VamsasArchiveReader(newf);
+
+        SimpleDocument sdoc = new SimpleDocument("testing vamsas update");
+        VamsasDocument finaldoc = sdoc.getVamsasDocument(vreader);
+        if (finaldoc != null)
+          ArchiveReports.reportDocument(finaldoc, vreader, true, System.out);
+        else
+          log.error("Null Document Read from " + newf);
+      }
+    } catch (Exception e) {
+      e.printStackTrace(System.err);
+    }
+  }
+}