-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);
- }
- }
-}
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package uk.ac.vamsas.test.simpleclient;\r
+\r
+import java.io.File;\r
+import java.io.ObjectOutputStream;\r
+import java.io.RandomAccessFile;\r
+import java.util.jar.JarFile;\r
+\r
+import org.apache.commons.logging.Log;\r
+import org.apache.commons.logging.LogFactory;\r
+\r
+import uk.ac.vamsas.client.simpleclient.Lock;\r
+import uk.ac.vamsas.client.simpleclient.SessionFile;\r
+import uk.ac.vamsas.client.simpleclient.SimpleDocument;\r
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;\r
+import uk.ac.vamsas.client.simpleclient.VamsasFile;\r
+import uk.ac.vamsas.objects.core.ApplicationData;\r
+import uk.ac.vamsas.objects.core.User;\r
+import uk.ac.vamsas.objects.core.VAMSAS;\r
+import uk.ac.vamsas.objects.core.VamsasDocument;\r
+import uk.ac.vamsas.test.objects.Core;\r
+\r
+public class VamsasArchive {\r
+ /**\r
+ * test the org.vamsas.simpleclient.vamsasArchive class\r
+ */\r
+ static Log log = LogFactory.getLog(VamsasArchive.class);\r
+\r
+ public static ApplicationData makeDemoAppdata(\r
+ uk.ac.vamsas.client.simpleclient.VamsasArchive va, String apname,\r
+ String userName, String userOrg) {\r
+ if (va == null)\r
+ return null;\r
+ VamsasArchiveReader vread = null;\r
+ try {\r
+ vread = va.getOriginalArchiveReader();\r
+ } catch (Exception e) {\r
+ log.error("Failed to get original archive reader!", e);\r
+ return null;\r
+ }\r
+ ApplicationData appdata = new ApplicationData();\r
+ appdata.setName("uk.ac.vamsas.test.simpleclient.VamsasArchive");\r
+ appdata.setData(new String("this is some test data.").getBytes());\r
+ User apuser = new User();\r
+ apuser.setFullname(userName);\r
+ apuser.setOrganization(userOrg);\r
+ String appdata_ref = "vamsas:" + apname + "/" + apuser.getOrganization()\r
+ + "/" + apuser.getFullname();\r
+ SimpleDocument sdoc = new SimpleDocument("test.simpleclient.VamsasArchive");\r
+ if (vread != null) {\r
+ VamsasDocument orignalnew;\r
+ try {\r
+ orignalnew = sdoc.getVamsasDocument(vread);\r
+ log.info("*** Dump follows ***");\r
+\r
+ ArchiveReports.reportDocument(orignalnew, vread, false, System.out);\r
+ log.info("*** Dump precedes ***");\r
+ } catch (Exception e) {\r
+ log.info("makeDemoAppdata: Problems accessing original document");\r
+ }\r
+\r
+ log.info("Reading (and avoiding references to) original data");\r
+ if (vread.getAppdataStream(appdata_ref) != null) {\r
+ // transfer over\r
+ try {\r
+ va.transferAppDataEntry(appdata_ref);\r
+ } catch (Exception e) {\r
+ log.warn("Exception when transferring appdata reference : "\r
+ + appdata_ref, e);\r
+ }\r
+ int i = 0;\r
+ while (vread\r
+ .getAppdataStream(appdata_ref + "/" + Integer.toString(++i)) != null) {\r
+ try {\r
+ // copy over another duplicate.\r
+ va.transferAppDataEntry(appdata_ref + "/" + Integer.toString(i));\r
+ } catch (Exception e) {\r
+ log.warn("Exception when transferring appdata reference : "\r
+ + appdata_ref, e);\r
+ }\r
+ }\r
+ // this one must be unique!\r
+ appdata_ref += "/" + Integer.toString(i);\r
+ }\r
+ }\r
+\r
+ log.info("Adding new data stuff.");\r
+ log.info("Writing an apdata reference using AppDataStream interface.");\r
+ apuser.setDataReference(appdata_ref);\r
+ appdata.addUser(apuser);\r
+ appdata.setVersion("noggin");\r
+ // TODO: write instance appdata appdata.setUrn("program:/the.nog/");\r
+ try {\r
+ ObjectOutputStream ost = new ObjectOutputStream(va\r
+ .getAppDataStream(appdata_ref));\r
+ ost.writeObject(appdata);\r
+ ost.close();\r
+ } catch (Exception e) {\r
+ log.warn("Couldn't write appdata reference " + appdata_ref);\r
+ }\r
+ return appdata;\r
+ }\r
+\r
+ public static void main(String args[]) {\r
+\r
+ try {\r
+ File av;\r
+ if (args.length > 0)\r
+ av = new File(args[0]);\r
+ else\r
+ av = new File("test/vamsas.zip");\r
+ try {\r
+ RandomAccessFile raf = new RandomAccessFile(av, "r");\r
+ raf.readByte();\r
+ raf.close();\r
+ } catch (Exception f) {\r
+ log.info("Couldn't random access file archive " + av, f);\r
+ }\r
+ try {\r
+ JarFile jf = new JarFile(av, true, JarFile.OPEN_READ);\r
+ if (jf.getEntry("vamsasDocument.xml") != null) {\r
+ log.info("Valid archive (sun) " + av);\r
+ }\r
+ jf.close();\r
+ } catch (Exception f) {\r
+ log.warn("Couldn't access jar archive with sun jartools: " + av, f);\r
+ }\r
+ try {\r
+ org.apache.tools.zip.ZipFile jf = new org.apache.tools.zip.ZipFile(av);\r
+ if (jf.getEntry("vamsasDocument.xml") != null) {\r
+ log.info("Valid archive (apache) " + av);\r
+ }\r
+ jf.close();\r
+ } catch (Exception f) {\r
+ log.warn("Couldn't access jar archive with apache ziptool: " + av, f);\r
+ }\r
+\r
+ log.info("Opening archive " + av);\r
+ uk.ac.vamsas.client.simpleclient.VamsasArchive varchive = new uk.ac.vamsas.client.simpleclient.VamsasArchive(\r
+ av, true);\r
+\r
+ VAMSAS[] roots = (VAMSAS[]) varchive.getOriginalRoots();\r
+\r
+ if (roots != null) {\r
+ log.info("Report on Original roots in archive:");\r
+ ArchiveReports.rootReport(roots, true, System.out);\r
+ }\r
+ log.info("Getting current vamsas document.");\r
+ VamsasDocument doc = varchive.getVamsasDocument();\r
+ ArchiveReports.reportDocument(doc, varchive.getOriginalArchiveReader(),\r
+ true, System.out); // not modified document so references will still\r
+ // be valid\r
+ // do some stuff\r
+ log.info("Retrieving backup");\r
+ File backup = varchive.backupFile();\r
+ if (backup == null)\r
+ log.info(av + " is a New Archive.");\r
+ else\r
+ log.info(av + " has been backed up as " + backup);\r
+ File newf = new File(av.getAbsolutePath() + "_new.zip");\r
+ VamsasFile sfile = new VamsasFile(newf);\r
+ /*\r
+ * if (newf.exists()) { int q=1; do { newf=new\r
+ * File(av.getAbsolutePath()+"_"+q+++"_new.zip"); } while (newf.exists());\r
+ * }\r
+ */\r
+ if (newf.exists()) {\r
+ log.info("Removing existing " + newf);\r
+ newf.delete();\r
+ }\r
+\r
+ log.info("Now writing new Archive into " + newf.getAbsolutePath());\r
+ uk.ac.vamsas.client.simpleclient.VamsasArchive va = null;\r
+ { // hold lock over deletion and write of new archive.\r
+ // Lock wlock = sfile.getLock();\r
+ // newf.delete(); // clear out old file.\r
+ sfile.getLock();\r
+ va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, true,\r
+ true, sfile);\r
+ // open another and...\r
+ ApplicationData appdata = makeDemoAppdata(va,\r
+ "uk.ac.vamsas.test.simpleclient.VamsasArchive",\r
+ "arnold Bugger esq", "disOrganised");\r
+ log.info("Preparing to write new document.");\r
+ doc.addApplicationData(appdata);\r
+ doc.addVAMSAS(Core.getDemoVamsas());\r
+ va.putVamsasDocument(doc); // gets stream and puts it.\r
+ va.closeArchive();\r
+ sfile.unLock();\r
+ }\r
+ log.info("Dump of new vamsas document :");\r
+ log.info("Testing update: ");\r
+ {\r
+ Lock lock = sfile.getLock();\r
+ if (lock == null)\r
+ while ((lock = sfile.getLock()) == null) {\r
+ log.info("Waiting for lock.");\r
+ Thread.sleep(100);\r
+ }\r
+ VamsasArchiveReader vreader = new VamsasArchiveReader(sfile\r
+ .getVamsasFile());// lock); // cannot do new JarFile on a locked\r
+ // file. // newf);\r
+ SimpleDocument sdoc = new SimpleDocument("testing new vamsas write");\r
+ ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader,\r
+ true, System.out);\r
+ sfile.unLock();\r
+ }\r
+ // backup.delete(); // tidy up\r
+\r
+ log.info("Now Cancelling write to original archive " + av);\r
+ if (varchive.cancelArchive())\r
+ log.info("Successfully cancelled.");\r
+ else\r
+ log.info("Didn't cancel.");\r
+ long t = System.currentTimeMillis() + 200;\r
+ while (t > System.currentTimeMillis())\r
+ ;\r
+ log.info("Now testing archive update.");\r
+ va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, false,\r
+ true, sfile);\r
+ doc = va.getVamsasDocument();\r
+ doc.addVAMSAS(Core.getDemoVamsas());\r
+ doc.addApplicationData(makeDemoAppdata(va,\r
+ "uk.ac.vamsas.test.simpleclient.VamsasArchive",\r
+ "another old Bugger esq", "rescinded"));\r
+ if (va.transferRemainingAppDatas())\r
+ log.info("Remain appdatas were transferred.");\r
+ else\r
+ log.warn("No appdatas were transferred. This is wrong.");\r
+ va.putVamsasDocument(doc);\r
+ va.closeArchive();\r
+ sfile.unLock();\r
+ log.info("Testing update: ");\r
+ {\r
+ Lock lock = sfile.getLock();\r
+ if (lock == null)\r
+ while ((lock = sfile.getLock()) == null)\r
+ log.info("Waiting for lock.");\r
+ // VamsasArchiveReader vreader = new VamsasArchiveReader(lock);\r
+ VamsasArchiveReader vreader = new VamsasArchiveReader(newf);\r
+\r
+ SimpleDocument sdoc = new SimpleDocument("testing vamsas update");\r
+ VamsasDocument finaldoc = sdoc.getVamsasDocument(vreader);\r
+ if (finaldoc != null)\r
+ ArchiveReports.reportDocument(finaldoc, vreader, true, System.out);\r
+ else\r
+ log.error("Null Document Read from " + newf);\r
+ }\r
+ } catch (Exception e) {\r
+ e.printStackTrace(System.err);\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff