+++ /dev/null
-/**
- *
- */
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Date;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.ValidationException;
-import org.vamsas.test.objects.Core;
-
-import uk.ac.vamsas.client.ClientHandle;
-import uk.ac.vamsas.client.IVorbaIdFactory;
-import uk.ac.vamsas.client.SessionHandle;
-import uk.ac.vamsas.client.UserHandle;
-import uk.ac.vamsas.client.Vobject;
-import uk.ac.vamsas.client.VorbaId;
-import uk.ac.vamsas.client.simpleclient.AppDataOutputStream;
-import uk.ac.vamsas.client.simpleclient.FileWatcher;
-import uk.ac.vamsas.client.simpleclient.IdFactory;
-import uk.ac.vamsas.client.simpleclient.SessionFile;
-import uk.ac.vamsas.client.simpleclient.SimpleDocBinding;
-import uk.ac.vamsas.client.simpleclient.SimpleDocument;
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.AppData;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.User;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-import uk.ac.vamsas.objects.utils.AppDataReference;
-import uk.ac.vamsas.objects.utils.DocumentStuff;
-import uk.ac.vamsas.objects.utils.ProvenanceStuff;
-import uk.ac.vamsas.objects.utils.SeqSet;
-import uk.ac.vamsas.objects.utils.document.VersionEntries;
-
-/**
- * @author jimp
- * test the VamsasFile routines for watching, reading and updating a vamsas document jar file.
- * simple document access base class.
- */
-public class ArchiveClient extends IdFactory {
-
- private Log log = LogFactory.getLog(ArchiveClient.class);
- // protected UserHandle user=null;
- // protected ClientHandle me = new ClientHandle("ArchiveClient","0.01");
- VamsasFile vsess;
-
- /**
- * @param user
- * @param vsess
- */
- public ArchiveClient(UserHandle user, VamsasFile vsess) {
- super(new SessionHandle("vamsasfile://"+vsess.getVamsasFile()), new ClientHandle("ArchiveClient","0.01"), user);
- this.vsess = vsess;
- valid();
- }
- private void _openVsess(File vsess) {
- try {
- this.vsess = new VamsasFile(vsess);
- }
- catch (Exception e) {
- log.error("Couldn't open session for file "+vsess,e);
- this.vsess = null;
- }
- }
- public ArchiveClient(String username, String organization, File vsess) {
- super(new SessionHandle("vamsasfile://"+vsess), new ClientHandle("ArchiveClient","0.01"), new UserHandle(username, organization));
- _openVsess(vsess);
- valid();
- }
- public ArchiveClient(String username, String organization, String clientName, String clientVersion, File vsess) {
- super(new SessionHandle("vamsasfile://"+vsess), new ClientHandle(clientName, clientVersion), new UserHandle(username, organization));
- _openVsess(vsess);
- valid();
- }
- public void valid() {
- if (vsess==null)
- throw new Error("ArchiveClient instance is invalid!.");
- }
- /**
- * set this to false if watch loop should end immediately
- */
- protected boolean watchForChange=true;
- public static int WATCH_SLEEP=300;
- /**
- * watch the document file for updates.
- * @param time - length of time to watch for.
- * @return read only IO interface for session document.
- */
- public ClientDoc watch(long time) {
- valid();
- vsess.unLock(); // doh.
- FileWatcher watcher = new FileWatcher(vsess.getVamsasFile());
- // watcher.setState();
- watchForChange=true;
- long endtime=System.currentTimeMillis()+time;
- try {
- uk.ac.vamsas.client.simpleclient.Lock doclock;
- do {
- doclock=watcher.getChangedState();
- if (doclock==null)
- Thread.sleep(WATCH_SLEEP);
- } while (watchForChange && doclock==null && (time==0 || endtime>System.currentTimeMillis())); // tuning.
- if (doclock==null)
- return null;
- else {
- return getUpdateable(vsess.getLock(doclock));
- /*VamsasArchiveReader varc = new VamsasArchiveReader(vsess.getVamsasFile());
- return _getReadonly(varc);*/
- }
- } catch (Exception e) {
- log.error("Whilst watching file "+vsess.getVamsasFile(), e);
- }
- return null;
- }
-
- // from ClientDocument.getClientAppdata
- private AppData[] getAppData(VamsasDocument doc) {
- if (doc==null) {
- log.debug("extractAppData called for null document object");
- return null;
- }
- AppData appsGlobal=null, usersData=null;
- Vector apldataset = AppDataReference.getUserandApplicationsData(
- doc, this.getUserHandle(), this.getClientHandle());
- if (apldataset!=null) {
- if (apldataset.size()>0) {
- AppData clientdat = (AppData) apldataset.get(0);
- if (clientdat instanceof ApplicationData) {
- appsGlobal = (ApplicationData) clientdat;
- if (apldataset.size()>1) {
- clientdat = (AppData) apldataset.get(1);
- if (clientdat instanceof User) {
- usersData = (User) clientdat;
- }
- if (apldataset.size()>2)
- log.info("Ignoring additional ("+(apldataset.size()-2)+") AppDatas returned by document appdata query.");
- }
- } else {
- log.warn("Unexpected entry in AppDataReference query: id="+clientdat.getVorbaId()+" type="+clientdat.getClass().getName());
- }
- apldataset.removeAllElements(); // destroy references.
- }
- }
- return new AppData[] { appsGlobal, usersData};
- }
-
- protected ClientDoc _getReadonly(VamsasArchiveReader vreader) throws IOException, ValidationException, MarshalException {
- valid();
- if (vreader!=null) {
- SimpleDocBinding docb = new SimpleDocBinding();
- docb.setVorba(this);
- VamsasDocument d;
- d = docb.getVamsasDocument(vreader);
-
- if (d!=null) {
- ClientDoc creader = new ClientDoc(d, null, vreader, getClientHandle().getClientUrn(), getProvenanceUser(), getVorbaIdHash());
- return creader;
- }
- }
- return null;
- }
- /**
- * from SimpleClient
- * @return user field for a provenance entry
- */
- protected String getProvenanceUser() {
- return new String(getUserHandle().getFullName()+" ["+getClientHandle().getClientUrn()+"]");
- }
-
- public ClientDoc getUpdateable() {
- return getUpdateable(null);
- }
- public ClientDoc getUpdateable(uk.ac.vamsas.client.simpleclient.Lock lock) {
- getVorbaIdHash().clear();
- valid();
- try {
- // patiently wait for a lock on the document.
- long tries=5000;
- while (lock==null && ((lock=vsess.getLock())==null || !lock.isLocked()) && --tries>0) {
-// Thread.sleep(1);
- log.debug("Trying to get a document lock for the "+tries+"'th time.");
- }
- VamsasArchive varc = new VamsasArchive(vsess, true, false); // read archive, write as vamsasDocument, don't erase original contents.
- varc.setVorba(this);
- VamsasDocument d = varc.getVamsasDocument(getProvenanceUser(), "Created new document.", VersionEntries.latestVersion()); // VAMSAS: provenance user and client combined
-
- if (d==null) {
- log.warn("Backing out from opening a VamsasArchive writable IO session");
- varc.cancelArchive();
- return null;
- }
- ClientDoc cdoc = new ClientDoc(d, varc, varc.getOriginalArchiveReader(), getClientHandle().getClientUrn(), getProvenanceUser(), getVorbaIdHash());
- return cdoc;
- // do appHandle?
- } catch (Exception e) {
- log.error("Failed to get Updateable version of "+vsess.getVamsasFile(), e);
- }
- return null;
- }
- /**
- * trust client to not do anything stupid to the document roots which will now be written to the archive.
- * @param cdoc
- * @return true if write was a success.
- */
- public boolean doUpdate(ClientDoc cdoc) {
- valid();
- if (cdoc==null) {
- log.warn("Invalid ClientDoc passed to org.vamsas.test.simpleclient.doUpdate()");
- return false;
- }
- if (cdoc.iohandler==null) {
- log.warn("Read only ClientDoc object passed to org.vamsas.test.simpleclient.doUpdate()");
- return false;
- }
- if (cdoc.iohandler.getVorba()!=this) {
- log.error("Mismatch between ClientDoc instances and ArchiveClient instances!");
- return false;
- }
- try {
- // do any appDatas first.
- if (cdoc.iohandler.transferRemainingAppDatas())
- log.debug("Remaining appdatas were transfered.");
- cdoc.updateDocumentRoots();
- cdoc.iohandler.putVamsasDocument(cdoc.doc);
- cdoc.iohandler.closeArchive();
- this.extantids.clear();// we forget our ids after we close the document.
- cdoc.iohandler=null;
- cdoc = null;
- vsess.unLock();
- } catch (Exception e) {
- log.warn("While updating archive in "+vsess.getVamsasFile(),e);
- return false;
- }
- return true;
- }
- /**
- * @param args
- */
- public static void usage() {
- throw new Error("Usage: Username Organization VamsasFile [command,args]*");
- }
- public static void main(String[] args) {
- // really simple.
- if (args.length<3)
- usage();
-
- ArchiveClient client = new ArchiveClient(args[0],args[1], new File(args[2]));
- ClientDoc cdoc=null;
- // sanity test.
- try {
- cdoc = client.getUpdateable();
- // ArchiveReports.reportDocument(cdoc.doc, cdoc.getReader(), true, System.out);
- System.out.println("Report Roots :");
- ArchiveReports.rootReport(cdoc.getVamsasRoots(), true, System.out);
- cdoc.addVamsasRoot(Core.getDemoVamsas());
- System.out.println("Doing update.");
- client.doUpdate(cdoc);
- cdoc.closeDoc();
- cdoc = null;
- int u=5;
- while (--u>0) {
- System.out.println("Watch for more... ("+u+" left)");
- ClientDoc ucdoc = client.watch(0000);
- if (ucdoc!=null) {
- System.out.println("****\nUpdate detected at "+new Date());
- ArchiveReports.reportDocument(ucdoc.doc, ucdoc.getReader(), true, System.out);
- ucdoc.closeDoc();
- ucdoc=null;
- } else {
- System.out.println("!!!! Null document update detected at "+new Date());
- }
- }
- }
- catch (Exception e) {
- client.log.error("Broken!", e);
- }
- System.out.println("Finished at "+new Date());
- }
- public uk.ac.vamsas.client.Vobject getObject(VorbaId id) {
- Hashtable idhash = this.getVorbaIdHash();
- if (idhash!=null && idhash.containsKey(id))
- return (Vobject) idhash.get(id);
- return null;
- }
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-
-
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-public class ArchiveReader {
- /**
- * tests VamsasArchiveReader archive reader on a vamsas jar file
- * @param args
- */
- public static void main(String args[]) {
-
- try {
- File av = new File(args[0]);
- VamsasArchiveReader var = new VamsasArchiveReader(av);
- VAMSAS roots[]=null;
- if (var.isValid()) {
- InputStreamReader vdoc = new InputStreamReader(var.getVamsasDocumentStream());
- VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
- if (ArchiveReports.reportDocument(doc, var, true, System.out)) {
- roots = doc.getVAMSAS();
- }
- } else {
- InputStream vxmlis = var.getVamsasXmlStream();
-
- if (vxmlis!=null) { // Might be an old vamsas file.
- BufferedInputStream ixml = new BufferedInputStream(var.getVamsasXmlStream());
- InputStreamReader vxml = new InputStreamReader(ixml);
- VAMSAS root;
- // unmarshal seems to always close the stream (should check this)
- if ((root = VAMSAS.unmarshal(vxml))!=null) {
- System.out.println("Read a root.");
- roots = new VAMSAS[1];
- roots[0] = root;
- }
- }
- }
- if (!ArchiveReports.rootReport(roots, true, System.out))
- System.err.print(args[0]+" is not a valid vamsas archive.");
- } catch (Exception e) {
- e.printStackTrace(System.err);
- }
- }
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.io.InputStream;
-import java.io.PrintStream;
-import java.io.PrintWriter;
-
-
-import uk.ac.vamsas.client.ClientDocument;
-import uk.ac.vamsas.client.Vobject;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.Alignment;
-import uk.ac.vamsas.objects.core.AppData;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.DataSet;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.Instance;
-import uk.ac.vamsas.objects.core.Provenance;
-import uk.ac.vamsas.objects.core.Tree;
-import uk.ac.vamsas.objects.core.User;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-/**
- * this class contains static methods for writing info to stdout about a vamsas document
- * Methods have a 'cascade' switch to indicate if sub-objects should have info printed on them.
- * Methods return true or false - indicating if the Vobject was valid or not
- * TODO: LATER: propagate true/false return so that an invalid vamsas Vobject invalidates the whole document
- * @author jimp
- *
- */
-public class ArchiveReports {
- /**
- * print an informative summary on a VamsasDocument
- * @param outstr TODO
- * @param document - the document itself
- * @param archive - document source archive for resolving any appData refs
- * @return
- */
- public static boolean reportProvenance(Provenance p, PrintStream outstr) {
- if (p==null) {
- outstr.println("No Provenance");
- return false;
- }
- Entry[] pe = p.getEntry();
- for (int i=0; i<pe.length; i++)
- outstr.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getApp()+"\t'"+pe[i].getAction()+"'");
- return true;
- }
- public static boolean appDataEntryReport(AppData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
- if (appD!=null) {
- boolean nulldata=false;
- if (appD.getDataReference()!=null) {
- String appData=appD.getDataReference();
- if (appData==null) { outstr.println("Empty DataReference - not valid ?"); }
- else
- if (appData.length()>1) {
- outstr.print("a reference ("+appData+")");
- InputStream jstrm;
- if ((jstrm=archive.getAppdataStream(appData))!=null)
- outstr.println(" which resolves to a JarEntry.");
- else {
- outstr.println(" which does not resolve to a JarEntry.");
- outstr.println("Unresolved appdata reference '"+appData+"'");
- }
- } else {
- nulldata=true;
- }
- } else {
- if (appD.getData()==null)
- nulldata &= true;
- else
- outstr.println("an embedded chunk of "+appD.getData().length+" bytes.");
- }
- if (nulldata)
- outstr.println("Null AppData reference/data chunk.");
- }
- return true;
- }
-
- public static boolean appDataReport(ApplicationData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
- if (appD!=null) {
- // Report on root appData
- appDataEntryReport(appD, archive, cascade, outstr);
- if (appD.getInstanceCount()>0) {
- Instance inst[] = appD.getInstance();
- for (int i=0,j=inst.hashCode(); i<j; i++) {
- outstr.println("Data for App Instance URN: '"+inst[i].getUrn());
- appDataEntryReport(inst[i],archive,cascade,outstr);
- }
- }
- if (appD.getUserCount()>0) {
- User users[] = appD.getUser();
- for (int i=0,j=users.length; i<j; i++) {
- outstr.println("Data for User '"+users[i].getFullname()+"' of '"+users[i].getOrganization()+"'");
- appDataEntryReport(users[i], archive, cascade, outstr);
- }
- }
- }
-
- return true;
- }
- public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
- if (document!=null) {
- outstr.println("Vamsas Document version '"+document.getVersion()+"'");
- reportProvenance(document.getProvenance(), outstr);
- outstr.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" Application data elements.\n");
- if (document.getVAMSASCount()>0 && cascade)
- rootReport(document.getVAMSAS(), true, outstr);
- if (document.getApplicationDataCount()>0) {
- outstr.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n");
- ApplicationData appd[] = document.getApplicationData();
- for (int i=0,j=appd.length; i<j; i++) {
- outstr.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\n");
- outstr.print("AppData is :");
- appDataReport(appd[i], archive, cascade, outstr);
- }
-
- }
- return true;
- } else {
- outstr.println("Document Object is null");
- }
- return false;
- }
-
- /**
- * summarises all the datasets in a vamsas document.
- * @param roots
- * @param cascade TODO
- * @param outstr TODO
- * @return
- */
- public static boolean rootReport(VAMSAS[] roots, boolean cascade, PrintStream outstr) {
- if (roots!=null) {
- for (int i=0; i<roots.length; i++) {
- VAMSAS r = roots[i];
- int ds, tr;
- outstr.print("Vamsas Root "+i+" (id="
- +((r.getId()!=null) ? r.getId():"<none>")
- +") contains "+(ds=r.getDataSetCount())+" DataSets, "
- + (tr=r.getTreeCount())+" Global trees\n");
- if (cascade) {
- for (int j=0; j<ds; j++) {
- outstr.println("Dataset "+j);
- cascade = datasetReport(r.getDataSet(j), true, outstr) && cascade ;
- }
- for (int j=0; j<tr; j++) {
- outstr.println("Global tree "+j);
- cascade = treeReport(r.getTree(j), true, outstr) && cascade;
- }
- }
- }
- return true;
- }
- return false;
- }
- public static boolean datasetReport(DataSet ds, boolean cascade, PrintStream outstr) {
- if (cascade)
- reportProvenance(ds.getProvenance(), outstr);
- outstr.println("Dataset contains : "+ds.getSequenceCount()
- +" sequences, "+ds.getAlignmentCount()+" alignments and "+ds.getTreeCount()+" trees.");
- if (cascade)
- alignmentReport(ds.getAlignment(), true, outstr);
- return true;
- }
- public static boolean alignmentReport(Alignment[] al, boolean cascade, PrintStream outstr) {
- boolean val=true;
- if (al!=null && al.length>0) {
- for (int i=0; i<al.length; i++) {
- outstr.println("Alignment "+i+(al[i].isRegistered() ? " ("+al[i].getVorbaId()+")" : " (unregistered)"));
- if (cascade)
- reportProvenance(al[i].getProvenance(), outstr);
- outstr.println("Involves "+al[i].getAlignmentSequenceCount()+" sequences, has "
- +al[i].getAlignmentAnnotationCount()+" annotations and "+al[i].getTreeCount()+" trees.");
- if (cascade) {
- for (int t=0; t<al[i].getTreeCount(); t++)
- treeReport(al[i].getTree(t), true, outstr);
- }
- }
- }
- return val;
- }
- public static boolean treeReport(Tree t, boolean cascade, PrintStream outstr) {
- outstr.println("Tree: '"+t.getTitle()+"'");
- return !cascade || reportProvenance(t.getProvenance(), outstr);
- }
-
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-
-
-import uk.ac.vamsas.client.simpleclient.SessionFile;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-public class ArchiveStreamReader {
- /**
- * tests VamsasArchiveReader archive reader on a vamsas jar file opened as a stream
- * @param args
- */
- public static void main(String args[]) {
-
- try {
- VamsasFile av = new VamsasFile(new File(args[0]));
- VamsasArchiveReader var = new VamsasArchiveReader(av.getLock());
- VAMSAS roots[]=null;
- if (var.isValid()) {
- InputStreamReader vdoc = new InputStreamReader(var.getVamsasDocumentStream());
- VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
- if (ArchiveReports.reportDocument(doc, var, true, System.out)) {
- roots = doc.getVAMSAS();
- }
- } else {
- InputStream vxmlis = var.getVamsasXmlStream();
-
- if (vxmlis!=null) { // Might be an old vamsas file.
- BufferedInputStream ixml = new BufferedInputStream(var.getVamsasXmlStream());
- InputStreamReader vxml = new InputStreamReader(ixml);
- VAMSAS root;
- // unmarshal seems to always close the stream (should check this)
- if ((root = VAMSAS.unmarshal(vxml))!=null) {
- System.out.println("Read a root.");
- roots = new VAMSAS[1];
- roots[0] = root;
- }
- }
- }
- if (!ArchiveReports.rootReport(roots, true, System.out))
- System.err.print(args[0]+" is not a valid vamsas archive.");
- } catch (Exception e) {
- e.printStackTrace(System.err);
- }
- }
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import uk.ac.vamsas.client.ClientHandle;
-import uk.ac.vamsas.client.simpleclient.FileWatcher;
-import uk.ac.vamsas.client.simpleclient.Lock;
-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.VamsasDocument;
-/**
- * demo of archive watching process - should mimic the clientsfileTest watcher/monitor process.
- * @author jimp
- *
- */
-public class ArchiveWatcher {
- private static Log log = LogFactory.getLog(ArchiveWatcher.class);
- private static CommandProcessor cproc=new CommandProcessor();
- static {
- cproc.addCommand("new", 0, "no args");
- cproc.addCommand("delete", 0, "no args");
- cproc.addCommand("watch", 0, "no args");
- cproc.addCommand("file", 1, "Need vamsas archive as argument.");
- }
-
- public static void main(String[] args) {
- try {
-
- if (args!=null && args.length>0) {
- File archive = new File(args[0]);
- log.info("Watching file "+args[0]);
- int argc=1;
- while (argc < args.length) {
- // vars needed for operations
- ClientHandle ch;
- int com = cproc.getCommand(args, argc);
- argc++;
- switch (com) {
- case 0:
- // new
- log.info("Doing locked deletion and new-file creation.");
- {
- if (!archive.exists())
- archive.createNewFile();
- VamsasFile sf = new VamsasFile(archive);
- Lock l = sf.getLock();
- archive.delete();
- archive.createNewFile();
- sf.unLock();
- }
- break;
- case 1:
- // delete
- log.info("Deleting "+archive+" without locking it first.");
- archive.delete();
- break;
- case 2:
- // watch
- log.info("Endlessly Watching file "+archive);
- /* if (!archive.exists())
- archive.createNewFile();
- */ // watch the new file... - taken straight from ClientsFileTest
- FileWatcher w = new FileWatcher(archive);
- while (true) {
- // get watcher's lock to ensure state change is fixed for retrieval
- Lock chlock = w.getChangedState();
- if (chlock != null) {
- log.info("Got lock on "+archive+(archive.exists() ? " exists l="+archive.length() : "(non existant)"));
- if (archive.length()>0) {
- VamsasArchiveReader vreader = new VamsasArchiveReader(archive);
- SimpleDocument sdoc = new SimpleDocument("testing vamsas watcher");
- try {
- VamsasDocument d = sdoc.getVamsasDocument(vreader);
- if (d!=null) {
- ArchiveReports.reportDocument(d, vreader, false, System.out);
- }
- System.out.println("Update at "+System.currentTimeMillis()+"\n\n********************************************************\n");
- } catch (Exception e) {
- log.error("Unmarshalling failed.",e);
- }
- vreader.close();
- w.setState();
- }
- }
- }
- // break;
- case 3: // set file
- archive = new File(args[argc++]);
- break;
- case 4:
- break;
- default:
- log.warn("Unknown command + "+args[argc++]);
- }
- }
- }
- } catch (Exception e) {
- log.error(e);
- }
-
- }
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
-import java.text.DateFormat;
-import java.util.Date;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-der;
-import uk.ac.vamsas.objects.core.Alignment;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.Instance;
-import uk.ac.vamsas.objects.core.Provenance;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-import uk.ac.vamsas.objects.ut
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-ils.ProvenanceStuff;
-
-public class ArchiveWriter {
-
- /**
- * Test program for writing archive files.
- * form is ArchiveWriter new/modified argive command list
- */
-
- static Log log = LogFactory.getLog(ArchiveWriter.class);
-
- private static void mergeVecs(Object[] destvec, Object[] svec1, Object[] svec2) {
- int i;
- for (i=0; i<svec1.length; i++)
- destvec[i] = svec1[i];
- for (int j=0; j<svec2.length; i++, j++)
- destvec[i] = svec2[j];
- }
- // Merge appDataReferences require transfer of jar entries, perhaps with a renaming of the entry.
- // Merge appDatas require eventually unique URNS
- // TODO: merging global appdata from different documents where same app has written them causes conflict
-
- public static Hashtable hashOfAppDatas(Hashtable ht, Instance[] appdatas) {
- if (ht==null)
- ht = new Hashtable();
- for (int i=0, j=appdatas.length; i<j; i++) {
- if (!ht.containsKey(appdatas[i].getUrn())) {
- Hashtable aphash = new Hashtable();
- ht.put(appdatas[i].getUrn(), aphash);
- aphash.put(appdatas[i], appdatas[i].getDataReference());
- } else {
- // ensure urns and references are unique
-
-
- }
-
- }
- return ht;
- }
- /**
- * safely copies an appData from one archive to another.
- * @param darc destination archive
- * @param dest destination document Vobject
- * @param sarc source archive reader
- * @param entry application data to be copied from source archive
- */
- public static void addAppDataEntry(VamsasArchive darc, VamsasDocument dest, VamsasArchiveReader sarc, ApplicationData entry) {
- // TODO: fix instances
- // check uniqueness of instance's[] entry.urn amongst dest.ApplicationData[].getInstances[].urn
- // check uniqueness of entry.user[].urn amongst dest.ApplicationData[].user[].urn
- // check uniqueness of entry.user
- // entry.getAppDataChoice().getData() or getDataReference is unique
- ApplicationData newo = new ApplicationData();
- for (int i=0, j=dest.getApplicationDataCount(); i<j; i++) {
- ApplicationData o = dest.getApplicationData()[i];
- // ensure new urn is really unique
- //String urn = entry.getUrn();
- int v = 1;
- //while (o.getUrn().equals(urn)) {
- // urn = entry.getUrn()+v++;
- // }
- // uniqueness of urn
- // check each user ApplicationData
- // uniqueness (again)
- // copy over valid objects
- //
- }
- }
- /**
- * Copy new datasets and appdatas from one vamsas document to another.
- * @param darc
- * @param dest
- * @param sarc
- * @param source
- * @return true if merge was successful.
- */
- public static boolean mergeDocs(VamsasArchive darc, VamsasDocument dest, VamsasArchiveReader sarc, VamsasDocument source) {
- log.debug("mergeDocs entered.");
- // search for appDatas in cdoc
- VAMSAS[] newr = new VAMSAS[dest.getVAMSASCount()+source.getVAMSASCount()];
- mergeVecs(newr, dest.getVAMSAS(), source.getVAMSAS());
- dest.setVAMSAS(newr);
- /** TODO: LATER: should verify that all ids really are unique in newly merged document. If not then what ?
- * investigate possibility of having an id translation between appDatas and the core document -
- * the mapping is stored when an external application performs a merge, but when the owning
- * Application accesses the Vobject, the vorba_id is updated to the new one when it writes its
- * references in to its appdata again
- */
- if (source.getApplicationDataCount()>0) {
- ApplicationData[] newdat = new ApplicationData[source.getApplicationDataCount()+dest.getApplicationDataCount()];
- ApplicationData[] sappd = source.getApplicationData();
- // check refs and update/modify if necessary
- for (int i=0; i<sappd.length; i++) {
- addAppDataEntry(darc, dest, sarc, sappd[i]);
- }
-
- }
-
- return true; // success
- }
-
- private static CommandProcessor cproc;
- static {
- cproc.addCommand("new", 0, "no args");
- cproc.addCommand("add", 1, "Need another vamsas document archive filename as argument.");
- cproc.addCommand("repair", 0, "no args");
- cproc.addCommand("list", 0, "no args");
- cproc.addCommand("monitor", 0, "no args");
- }
-
- public static void main(String argv[]) {
- /**
- * TODO: switches for setting user identities for writing to vamsas document
- */
- if (argv.length<1) {
- log.fatal("Usage : <archive to create> [(commands)]");
- return;
- }
- File newarch = new File(argv[0]);
- int argpos = 0;
- try {
- // test fully fledged doc construction
- VamsasArchive varc = new VamsasArchive(newarch, true);
- VamsasDocument docroot;
- docroot = new VamsasDocument();
- docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter", "user", "Created new Vamsas Document"));
- while (++argpos<argv.length) {
- File archive = new File(argv[argpos]);
- InputStream istream;
- if (archive.exists()) {
- VamsasArchiveReader vdoc = new VamsasArchiveReader(archive);
- if (vdoc.isValid()) {
- istream = vdoc.getVamsasDocumentStream();
- if (istream!=null) {
- VamsasDocument cdocroot = VamsasDocument.unmarshal(new InputStreamReader(istream));
- if (cdocroot!=null)
- mergeDocs(varc, docroot, vdoc, cdocroot);
- } else
- log.warn("Unexpectedly null document stream from existing document "+archive);
- } else {
- // updating an oldformat stream ?
- if ((istream = vdoc.getVamsasXmlStream())!=null) {
- // make a new vamsas document from the vamsas.xml entry
- VAMSAS root = VAMSAS.unmarshal(new InputStreamReader(istream)); // TODO: verify only one VAMSAS element per vamsas.xml entry.
- docroot.getProvenance().addEntry(ProvenanceStuff.newProvenanceEntry("ArchiveWriter", "user", "added vamsas.xml from "+argv[argpos-1]));
- docroot.addVAMSAS(root);
- }
- }
- } else {
- // Begin a new vamsas document
- PrintWriter docwriter = varc.getDocumentOutputStream();
- }
- }
- } catch (Exception e) {
- log.error("Whilst manipulating "+argv[0], e);
- }
- }
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import uk.ac.vamsas.client.IClientAppdata;
-import uk.ac.vamsas.client.Vobject;
-import uk.ac.vamsas.client.VorbaId;
-import uk.ac.vamsas.client.simpleclient.ClientDocument;
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-import uk.ac.vamsas.objects.utils.ProvenanceStuff;
-
-// simple holder to pass to client.
-public class ClientDoc extends uk.ac.vamsas.client.ClientDocument {
- /* (non-Javadoc)
- * @see uk.ac.vamsas.client.IClientDocument#getClientAppdata()
- */
- public IClientAppdata getClientAppdata() {
- throw new Error("Appdata access is not implemented in the test.simpleclient.ClientDoc instance."); // TODO Auto-generated method stub
- }
- protected boolean isModified=false;
- private Log log = LogFactory.getLog(ClientDoc.class);
- protected VamsasDocument doc;
- public uk.ac.vamsas.objects.core.VAMSAS[] _VamsasRoots;
- protected VamsasArchive iohandler=null;
- protected VamsasArchiveReader reader=null;
- private String user=null;
- private String app=null;
-
- /**
- * @param doc
- * @param iohandler
- * @param reader
- * @param app
- * @param user
- */
- public ClientDoc(VamsasDocument doc, VamsasArchive iohandler, VamsasArchiveReader reader, String app, String user, Hashtable objrefs) {
- super(objrefs, (iohandler!=null) ? iohandler.getVorba() : null);
- this.doc = doc;
- this.iohandler = iohandler;
- this.reader = reader;
- this.app = app;
- this.user = user;
- this.objrefs = objrefs;
- _VamsasRoots = doc.getVAMSAS();
- }
- // AppDataOutputStream appd;
- //AppDataOutputStream userd;
- /* (non-Javadoc)
- * @see java.lang.Object#finalize()
- */
- protected Entry getProvenanceEntry(String action) {
- // VAMSAS: modify schema to allow referencing of user field (plus other issues, ClientUrn field, machine readable action, input parameters, additional data generated notes
- Entry prov = ProvenanceStuff.newProvenanceEntry(app, user, action);
- return prov;
- }
- public VAMSAS[] getVamsasRoots() {
- if (doc==null) {
- log.debug("Null document for getVamsasRoots(), returning null");
- return null;
- }
- if (iohandler==null) {
- // LATER: decide on read-only status of ClientDocument object
- log.warn("getVamsasRoots() called on possibly read-only document.");
- }
- if (_VamsasRoots!=null)
- return _VamsasRoots;
- VAMSAS[] roots = doc.getVAMSAS();
- if (roots == null) {
- // Make a new one to return to client to get filled.
- _VamsasRoots = new VAMSAS[] { new VAMSAS() };
- // Do provenance now. just in case.
- doc.getProvenance().addEntry(getProvenanceEntry("Created new document root [id="+_VamsasRoots[0].getId()+"]"));
- doc.addVAMSAS(_VamsasRoots[0]);
- } else {
- _VamsasRoots = new VAMSAS[roots.length];
- for (int r=0;r<roots.length; r++)
- _VamsasRoots[r] = roots[r];
- }
- return _VamsasRoots;
- }
-
- private int _contains(VAMSAS root, VAMSAS[] docRoots) {
- if (root==null)
- return -1;
- if (docRoots==null || docRoots.length==0)
- return -1;
- VorbaId r_id = root.getVorbaId();
- for (int i=0,j=docRoots.length; i<j; i++) {
- VorbaId n_id=null;
- if (docRoots[i]==root || (docRoots[i]!=null && (n_id=docRoots[i].getVorbaId())!=null && n_id.equals(r_id)))
- return i;
- }
- return -1;
- }
-/**
- * verify that newr version is really an intact version of the
- * @param newVersion (may be modified)
- * @param oldVersion
- * @return true if newVersion is a valid root that preserves original references
- */
- private boolean isValidUpdate(VAMSAS newVersion, final VAMSAS oldVersion) {
- // ideal - this cascades down the two structures, ensuring that all ID'd objects in one are present in the other.
- if (oldVersion==newVersion) {
- // may be a virgin root element.
- if (!newVersion.isRegistered())
- iohandler.getVorba().makeVorbaId(newVersion);
- // Should retrieve original version and compare - unless local hashes can be used to determine if resultSet has been truncated.
- // just do internal validation for moment.
- if (newVersion.isValid())
- return true;
- return false;
- } else {
- // redundant ? if (oldVersion.is__stored_in_document())
- if (!newVersion.isRegistered())
- iohandler.getVorba().makeVorbaId(newVersion);
- if (newVersion.isValid())
- return true;
- }
- return false;
- }
- /**
- /**
- * merge old and new root vectors
- * @param newr This array may be written to
- * @param original
- * @param the client document (usually this) which this root set belongs to.
- * @return merged vector of vamsas roots
- */
- private VAMSAS[] _combineRoots(VAMSAS[] newr, final VAMSAS[] original, ClientDoc modflag) {
- Vector rts = new Vector();
- boolean modified=false;
- for (int i=0,j=original.length; i<j; i++) {
- int k = _contains(original[i], newr);
- if (k>-1) {
- if (isValidUpdate(newr[k], original[i])) {
- modified=true;
- rts.add(newr[k]);
- newr[k]=null;
- } else {
- // LATER: try harder to merge ducument roots.
- log.warn("Couldn't merge new VAMSAS root "+newr[k].getId());
- newr[k] = null; // LATER: this means we ignore mangled roots. NOT GOOD
- }
- } else {
- // add in order.
- rts.add(original[i]);
- }
- }
- // add remaining (new) roots
- for (int i=0,j=newr.length; i<j; i++) {
- if (newr[i]!=null) {
- rts.add(newr[i]);
- modified=true;
- }
- }
- newr = new VAMSAS[rts.size()];
- for (int i=0,j=rts.size(); i<j; i++)
- newr[i] = (VAMSAS) rts.get(i);
- if (modflag!=null)
- modflag.isModified = modified;
- return newr;
- }
-
- /**
- * update the document with new roots.
- * LATER: decide: this affects the next call to getVamsasRoots()
- * @see org.vamsas.IClientDocument.setVamsasRoots
- */
- public void setVamsasRoots(VAMSAS[] newroots) {
- if (doc==null) {
- log.debug("setVamsasRoots called on null document.");
- return;
- }
- VAMSAS[] newr;
- if (newroots==null) {
- log.debug("setVamsasRoots(null) - do nothing.");
- return;
- }
- // are we dealing with same array ?
- if (_VamsasRoots!=newroots) {
- // merge roots into local version.
- newr = new VAMSAS[newroots.length];
- for (int i=0;i<newr.length;i++)
- newr[i] = newroots[i];
- newr=_combineRoots(newr,_VamsasRoots,this);
- } else {
- newr = new VAMSAS[_VamsasRoots.length];
- for (int i=0;i<newr.length;i++)
- newr[i]=_VamsasRoots[i];
- }
- // actually compare with document root set for final combination (to ensure nothing is lost)
- _VamsasRoots = _combineRoots(newr, doc.getVAMSAS(), this);
- }
-
-
- /* (non-Javadoc)
- * LATER: decide: this affects the next call to getVamsasRoots()
- * @see uk.ac.vamsas.client.IClientDocument#addVamsasRoot(uk.ac.vamsas.objects.core.VAMSAS)
- */
- public void addVamsasRoot(VAMSAS newroot) {
- if (doc==null) {
- log.debug("addVamsasRoots called on null document.");
- return;
- }
- VAMSAS[] newroots = _combineRoots(new VAMSAS[] {newroot}, _VamsasRoots, this);
- _VamsasRoots = newroots;
- }
-
- public VamsasArchiveReader getReader() {
- return reader;
- }
- private void _finalize() {
- log.debug("finalizing clientDoc");
- if (doc!=null) {
- doc = null;
- }
- if (_VamsasRoots!=null) {
- for (int i=0; i<_VamsasRoots.length; i++)
- _VamsasRoots[i]=null;
- _VamsasRoots=null;
-
- }
-
- if (reader!=null) {
- log.debug("Closing and removing reader reference");
- reader.close();
- reader=null;
- }
- if (iohandler!=null) {
- log.debug("Removing ioHandler reference.");
- iohandler.cancelArchive();
- iohandler=null;
- }
- }
- protected void finalize() throws Throwable {
- _finalize();
- super.finalize();
- }
- private java.util.Hashtable objrefs=null;
-
- public VorbaId[] registerObjects(Vobject[] unregistered) {
- if (doc==null) {
- log.warn("registerObjects[] called on null document.");
- return null;
- }
- if (objrefs==null) {
- log.warn("registerObjects[] called for null objrefs hasharray.");
- return null;
- }
- if (unregistered!=null) {
- VorbaId ids[] = new VorbaId[unregistered.length];
- for (int i=0,k=unregistered.length; i<k; i++)
- if (unregistered[i]!=null) {
- log.warn("Null Vobject passed to registerObject[] at position "+i);
- return null;
- } else {
- ids[i]=registerObject(unregistered[i]);
- }
- log.debug("Registered "+unregistered.length+" objects - total of "+objrefs.size()+" ids.");
- return ids;
- }
- return null;
- }
- /* (non-Javadoc)
- * @see uk.ac.vamsas.client.IClientDocument#registerObject(uk.ac.vamsas.client.Vobject)
- */
- public VorbaId registerObject(Vobject unregistered) {
- if (doc==null) {
- log.warn("registerObjects called on null document.");
- return null;
- }
- if (objrefs==null) {
- log.warn("registerObjects called for null objrefs hasharray.");
- return null;
- }
- if (iohandler==null) {
- log.warn("registerObjects called for read only document.");
- return null;
- }
-
- if (unregistered!=null) {
- VorbaId id = this._registerObject(unregistered);
- log.debug("Registered object - total of "+objrefs.size()+" ids.");
- return id;
- }
- log.warn("Null Vobject passed to registerObject.");
- return null;
- }
- /*
- * (non-Javadoc)
- *
- * @see uk.ac.vamsas.client.IClientDocument#getObject(uk.ac.vamsas.client.VorbaId)
- */
- public Vobject getObject(VorbaId id) {
- if (objrefs==null) {
- log.debug("getObject called on null objrefs list.");
- return null;
- }
- if (objrefs.containsKey(id.getId()))
- return (Vobject) objrefs.get(id.getId());
- log.debug("Returning null Vobject reference for id "+id.getId());
- return null;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see uk.ac.vamsas.client.IClientDocument#getObjects(uk.ac.vamsas.client.VorbaId[])
- */
- public Vobject[] getObjects(VorbaId[] ids) {
- if (objrefs==null) {
- log.debug("getObject[] called on null objrefs list.");
- return null;
- }
- Vobject[] vo = new Vobject[ids.length];
- for (int i=0,j=ids.length; i<j;i++)
- if (objrefs.containsKey(ids[i]))
- vo[i] = (Vobject) objrefs.get(ids[i]);
- else
- log.debug("Returning null Vobject reference for id "+ids[i].getId());
- return vo;
- }
- protected void updateDocumentRoots() {
- if (doc==null) {
- log.error("updateDocumentRoots called on null document. Probably an implementation error.");
- return;
- }
- if (isModified) {
- if (_VamsasRoots!=null) {
- doc.setVAMSAS(_VamsasRoots);
- _VamsasRoots=null;
- }
- }
- }
- /**
- * tell vamsas client to close the document and reset the object. Once closed, nothing can be done with the object.
- *
- */
- public void closeDoc() {
- if (doc!=null) {
- log.debug("Closing open document.");
- _finalize();
- } else {
- log.warn("Ignoring closeDoc on invalid document.");
- }
- }
-
-}
\ No newline at end of file
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.util.Iterator;
-import java.util.Vector;
-
-
-import uk.ac.vamsas.client.ClientHandle;
-import uk.ac.vamsas.client.simpleclient.ClientsFile;
-import uk.ac.vamsas.client.simpleclient.FileWatcher;
-import uk.ac.vamsas.client.simpleclient.Lock;
-
-public class ClientsFileTest {
- private static CommandProcessor cproc;
-
- private static Vector commands;
- static {
- cproc = new CommandProcessor();
- ClientsFileTest.commands = new Vector();
- ClientsFileTest.commands.add(new String("add"));
- cproc.addCommand("add", 2, "for the Client's 'Name' and 'Version'");
- ClientsFileTest.commands.add(new String("remove"));
- cproc.addCommand("remove", 3, "for the Client's 'Name', Version and URN");
- ClientsFileTest.commands.add(new String("list"));
- cproc.addCommand("list", 0, "no args needed");
- ClientsFileTest.commands.add(new String("clear"));
- cproc.addCommand("clear", 0, "no args needed");
- ClientsFileTest.commands.add(new String("watch"));
- cproc.addCommand("watch", 0, "no args needed");
- ClientsFileTest.commands.add(new String("monitor"));
- cproc.addCommand("monitor", 2, "for the Client's 'Name' and 'Version'");
- }
-
- private static void complainArgs(int argl, int argpos, String cmd,
- int argneed, String msg) {
- if (argl - argpos < argneed)
- throw new Error(cmd + " needs " + argneed + " arguments : " + msg);
- }
-
- public static void main(String[] args) {
- java.io.File cf = new java.io.File(args[0]);
- System.out.println("Connecting to clientFile " + args[0]);
- ClientsFile cfhand;
- try {
- cfhand = new ClientsFile(cf);
- } catch (Exception e) {
- e.printStackTrace(System.err);
- return;
- }
- int argc = 1;
- while (argc < args.length) {
- // vars needed for operations
- ClientHandle ch;
- int com = cproc.getCommand(args, argc);
- argc++;
- switch (com) {
- case 0:
- // Add
- int pos = cfhand.addClient(ch = new ClientHandle(args[argc],
- args[argc + 1]));
- argc += 2;
- if (pos != 0)
- System.out.println("Client added at " + pos + " as urn:"
- + ch.getClientUrn());
- else
- System.out.println("Client was not added.");
- break;
- case 1:
- // remove
- ch = new ClientHandle(args[argc], args[argc + 1]);
- ch.setClientUrn(args[argc + 2]);
- argc += 3;
- cfhand.removeClient(ch, null);
- System.out.println("Client removed (apparently)");
- break;
- case 2:
- // list
- ClientHandle[] chlist = cfhand.retrieveClientList();
- if (chlist != null) {
- for (int chi = 0, che = chlist.length; chi < che; chi++) {
- System.out.println("Client " + chi + " ("
- + chlist[chi].getClientName() + " " + chlist[chi].getVersion()
- + " " + chlist[chi].getClientUrn() + ")");
- }
- } else {
- System.out.println("Client list is empty.");
- }
- break;
- case 3:
- // clear
- //cfhand.get = null;
- //cf.delete();
- try {
-
- cfhand.clearList();
-
- } catch (Exception e) {
- System.err.println("Failed on new empty clientfile creation!");
- e.printStackTrace(System.err);
- }
- break;
- case 4:
- // watch
- FileWatcher w = new FileWatcher(cf);
- while (cf.exists()) {
- // get watcher's lock to ensure state change is fixed for retrieval
- Lock chlock = w.getChangedState();
- if (chlock != null) {
- ClientHandle[] cl = cfhand.retrieveClientList(chlock);
- System.out.println("-- Watching " + cf.getName());
- //while (w.hasChanged())
- // ;
- if (cl != null) {
- for (int chi = 0, che = cl.length; chi < che; chi++) {
- System.out.println("Client " + chi + " ("
- + cl[chi].getClientName() + " " + cl[chi].getVersion()
- + " " + cl[chi].getClientUrn() + ")");
- }
- } else {
- System.out.println("Client list is empty.");
- }
- }
-
- }
- break;
- case 5:
- // monitor
- int clpos = cfhand.addClient(ch = new ClientHandle(args[argc],
- args[argc + 1]));
- argc += 2;
- if (clpos != 0)
- System.out.println("Monitor Client added at " + clpos + " as urn:"
- + ch.getClientUrn());
- else {
- System.err.println("Monitor Client was not added.");
- break;
- }
- FileWatcher mon = new FileWatcher(cf);
- while (cf.exists()) {
- // get watcher's lock to ensure state change is fixed for retrieval
- Lock chlock = mon.getChangedState();
- if (chlock != null) {
- ClientHandle[] cl = cfhand.retrieveClientList(chlock);
- System.out.println("-- Monitor " + cf.getName());
- //while (w.hasChanged())
- // ;
- int newpos = -1;
- if (cl != null) {
- for (int chi = 0, che = cl.length; chi < che; chi++) {
- if (ch.equals(cl[chi]))
- newpos = chi + 1;
- }
- }
- if (newpos == -1) {
- // add self again to cleared list.
- newpos = cfhand.addClient(ch);
- mon.setState();
- if (newpos == 0) {
- System.err
- .println("Monitor client could not be re-added to list.");
- break;
- }
- }
- if (newpos != clpos) {
- System.out.println("Monitor client moved from " + clpos + " to "
- + newpos);
- clpos = newpos;
- }
- }
- }
- break;
- default:
- if (com == -1) {
- System.err
- .println("Unknown command : " + args[argc++] + "*Ignored!*");
- } else
- System.err.println("Command " + args[argc++]
- + " *Ignored!* - its not implemented.");
- }
-
- for (int j = 0; j < 900000; j++) {
- Integer i = Integer.getInteger("1");
- Integer q = i;
- }
- }
-
- }
-
- /* Iterator coms = commands.iterator();
- int com=-1;
- while ((coms!=null) && coms.hasNext()) {
- com++;
- if (args[argc].toLowerCase().equals((String) coms.next())) {
- System.out.println("Doing "+args[argc]);
- ClientHandle ch;
- argc++;
- switch (com) {
- case 0:
- // Add
- ClientsFileTest.complainArgs(args.length, argc, "add", 2, "for the Client's 'Name' and 'Version'");
- int pos = cfhand.addClient(ch=new ClientHandle(args[argc],args[argc+1]));
- argc+=2;
- if (pos!=0)
- System.out.println("Client added at "+pos+" as urn:"+ch.getClientUrn());
- else
- System.out.println("Client was not added.");
- break;
- case 1:
- // remove
- ClientsFileTest.complainArgs(args.length, argc, "remove", 3, "for the Client's 'Name', Version and URN");
- ch=new ClientHandle(args[argc], args[argc+1]);
- ch.setClientUrn(args[argc+2]);
- argc+=3;
- cfhand.removeClient(ch, null);
- System.out.println("Client removed (apparently)");
- break;
- case 2:
- // list
- ClientHandle[] chlist = cfhand.retrieveClientList();
- if (chlist!=null) {
- for (int chi=0,che=chlist.length; chi<che; chi++) {
- System.out.println("Client "+chi+" ("+chlist[chi].getClientName()+" "+chlist[chi].getVersion()+" "+chlist[chi].getClientUrn()+")");
- }
- } else {
- System.out.println("Client list is empty.");
- }
- break;
- case 3:
- // clear
- cfhand = null;
- cf.delete();
- try {
- cf.createNewFile();
- cfhand = new ClientsFile(cf);
- }
- catch (Exception e) {
- System.err.println("Failed on new empty clientfile creation!");
- e.printStackTrace(System.err);
- }
- break;
- case 4:
- // watch
- FileWatcher w=new FileWatcher(cf);
- while (cf.exists()) {
- // get watcher's lock to ensure state change is fixed for retrieval
- Lock chlock=w.getChangedState();
- if (chlock!=null) {
- ClientHandle[] cl = cfhand.retrieveClientList(chlock);
- System.out.println("-- Watching "+cf.getName());
- //while (w.hasChanged())
- // ;
- if (cl!=null) {
- for (int chi=0,che=cl.length; chi<che; chi++) {
- System.out.println("Client "+chi+" ("+cl[chi].getClientName()+" "+cl[chi].getVersion()+" "+cl[chi].getClientUrn()+")");
- }
- } else {
- System.out.println("Client list is empty.");
- }
- }
-
- }
- break;
- case 5:
- // monitor
- ClientsFileTest.complainArgs(args.length, argc, "monitor", 2, "for the Client's 'Name' and 'Version'");
- int clpos = cfhand.addClient(ch=new ClientHandle(args[argc],args[argc+1]));
- argc+=2;
- if (clpos!=0)
- System.out.println("Monitor Client added at "+clpos+" as urn:"+ch.getClientUrn());
- else {
- System.err.println("Monitor Client was not added.");
- break;
- }
- FileWatcher mon=new FileWatcher(cf);
- while (cf.exists()) {
- // get watcher's lock to ensure state change is fixed for retrieval
- Lock chlock=mon.getChangedState();
- if (chlock!=null) {
- ClientHandle[] cl = cfhand.retrieveClientList(chlock);
- System.out.println("-- Monitor "+cf.getName());
- //while (w.hasChanged())
- // ;
- int newpos=-1;
- if (cl!=null) {
- for (int chi=0,che=cl.length; chi<che; chi++) {
- if (ch.equals(cl[chi]))
- newpos=chi+1;
- }
- }
- if (newpos==-1) {
- // add self again to cleared list.
- newpos=cfhand.addClient(ch);
- mon.setState();
- if (newpos==0) {
- System.err.println("Monitor client could not be re-added to list.");
- break;
- }
- }
- if (newpos!=clpos) {
- System.out.println("Monitor client moved from "+clpos+" to "+newpos);
- clpos=newpos;
- }
- }
- }
-
- }
- coms = null;
- }
- } */
-
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.util.Iterator;
-import java.util.Vector;
-
-public class CommandProcessor {
- /**
- * this is not getOPT!!!! - processes a *series* of space separated commands - some of which take arguments.
- */
- private Vector commands;
- /* static {
- ClientsFileTest.commands=new Vector();
- ClientsFileTest.commands.add(new String("add"));
- ClientsFileTest.commands.add(new String("remove"));
- ClientsFileTest.commands.add(new String("list"));
- ClientsFileTest.commands.add(new String("clear"));
- ClientsFileTest.commands.add(new String("watch"));
- ClientsFileTest.commands.add(new String("monitor"));
- } */
-
- public int addCommand(String cmd, int argneed, String complainString) {
- int cnum=0;
- if (commands==null)
- commands = new Vector();
- else
- cnum = commands.size();
- Vector cv = new Vector();
- cv.add(new String(cmd));
- cv.add(new Integer(argneed));
- cv.add(new String(complainString));
- commands.add(cv);
- return cnum;
- }
-
- /**
- * Integer argl, Integer argpos, String cmd, Integer argneed, String msg in vector
- */
- public void complainArgs(int argl, int argpos, Vector ca) {
- int argneed = ((Integer) ca.get(1)).intValue();
- if (argl-argpos<argneed)
- throw new Error(((String) ca.get(0))+" at position "+argpos+" needs "+argneed+" arguments : "+(String) ca.get(2));
- }
- /**
- * find and verify a command
- * @param args argstring
- * @param argpos position to check for command
- * @return matching command or -1
- */
- public int getCommand(String[]args, int argpos) {
- Iterator coms = commands.iterator();
- int com=-1, argc;
- argc=argpos;
- while ((coms!=null) && coms.hasNext()) {
- com++;
- Vector comnext = (Vector) coms.next();
- if (args[argc].toLowerCase().equals((String) comnext.get(0))) {
- if (comnext.size()>2)
- complainArgs(args.length, argc+1, comnext);
- return com;
- }
- }
- return -1;
-
- }
-}
+++ /dev/null
-package org.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("org.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,
- "org.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,
- "org.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);
- }
- }
-}
git://source.jalview.org / vamsas.git / commitdiff