* @version 1.0
*/
class MsaWSThread
- extends Thread implements WSClientI
+ extends WSThread implements WSClientI
{
- jalview.gui.AlignFrame alignFrame;
-
- WebserviceInfo wsInfo = null;
-
- String WebServiceName = null;
-
- String OutputHeader;
- AlignmentView input;
boolean submitGaps = false; // pass sequences including gaps to alignment
// service
// order
- class MsaWSJob
+ class MsaWSJob extends WSThread.WSJob
{
- int jobnum = 0; // WebServiceInfo pane for this job
-
- String jobId; // ws job ticket
-
- vamsas.objects.simple.MsaResult result = null;
-
+ // hold special input for this
vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
SequenceSet();
}
- int allowedServerExceptions = 3; // thread dies if too many
-
- // exceptions.
- boolean submitted = false;
- boolean subjobComplete = false;
-
Hashtable SeqNames = new Hashtable();
Vector emptySeqs = new Vector();
/**
public boolean hasResults()
{
if (subjobComplete && result != null && result.isFinished()
- && result.getMsa() != null && result.getMsa().getSeqs() != null)
+ && ((MsaResult) result).getMsa() != null && ((MsaResult) result).getMsa().getSeqs() != null)
{
return true;
}
SequenceI[] alseqs = null;
char alseq_gapchar = '-';
int alseq_l = 0;
- if (result.getMsa() != null)
+ if (((MsaResult) result).getMsa() != null)
{
- alseqs = getVamsasAlignment(result.getMsa());
- alseq_gapchar = result.getMsa().getGapchar().charAt(0);
+ alseqs = getVamsasAlignment(((MsaResult) result).getMsa());
+ alseq_gapchar = ((MsaResult) result).getMsa().getGapchar().charAt(0);
alseq_l = alseqs.length;
}
if (emptySeqs.size() > 0)
}
return null;
}
-
- boolean cancelled = false;
/**
* mark subjob as cancelled and set result object appropriatly
*/
subjobComplete = true;
result = null;
}
+ /**
+ *
+ * @return boolean true if job can be submitted.
+ */
+ boolean hasValidInput() {
+ if (seqs.getSeqs()!=null)
+ return true;
+ return false;
+ }
}
- MsaWSJob jobs[] = null;
String alTitle; // name which will be used to form new alignment window.
-
- boolean jobComplete = false;
-
Alignment dataset; // dataset to which the new alignment will be
// associated.
ext.vamsas.MuscleWS server = null;
-
- String WsUrl = null;
-
/**
* set basic options for this (group) of Msa jobs
*
{
// CANCELLED_JOB
cancelledMessage = "Job cancelled.";
- jobs[job].cancel();
+ ((MsaWSJob) jobs[job]).cancel();
wsInfo.setStatus(jobs[job].jobnum,
WebserviceInfo.STATE_CANCELLED_OK);
}
}
}
}
-
- class JobStateSummary {
- int running = 0;
- int queuing = 0;
- int finished = 0;
- int error = 0;
- int serror = 0;
- int cancelled=0;
- int results=0;
- void updateJobPanelState(WebserviceInfo wsInfo, MsaWSJob j) {
- if (j.result != null)
- {
- String progheader = "";
- // Parse state of job[j]
- if (j.result.isRunning())
- {
- running++;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
- }
- else if (j.result.isQueued())
- {
- queuing++;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
- }
- else if (j.result.isFinished())
- {
- finished++;
- j.subjobComplete = true;
- if (j.hasResults())
- results++;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
- }
- else if (j.result.isFailed())
- {
- progheader += "Job failed.\n";
- j.subjobComplete = true;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
- error++;
- }
- else if (j.result.isServerError())
- {
- serror++;
- j.subjobComplete = true;
- wsInfo.setStatus(j.jobnum,
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- else if (j.result.isBroken() || j.result.isFailed())
- {
- error++;
- j.subjobComplete = true;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
- }
- // and pass on any sub-job messages to the user
- wsInfo.setProgressText(j.jobnum, OutputHeader);
- wsInfo.appendProgressText(j.jobnum, progheader);
- if (j.result.getStatus() != null)
- {
- wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
- }
- }
- else
- {
- if (j.submitted && j.subjobComplete)
- {
- if (j.allowedServerExceptions == 0)
- {
- serror++;
- }
- else if (j.result == null)
- {
- error++;
- }
- }
- }
- }
+ void pollJob(WSJob job) throws Exception {
+ ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);
}
- public void run()
+ void StartJob(WSJob job)
{
- JobStateSummary jstate=null;
- while (!jobComplete)
- {
- jstate = new JobStateSummary();
- for (int j = 0; j < jobs.length; j++)
- {
-
- if (!jobs[j].submitted && jobs[j].seqs.getSeqs() != null)
- {
- StartJob(jobs[j]);
- }
-
- if (jobs[j].submitted && !jobs[j].subjobComplete)
- {
- try
- {
- if ( (jobs[j].result = server.getResult(jobs[j].jobId)) == null)
- {
- throw (new Exception(
- "Timed out when communicating with server\nTry again later.\n"));
- }
- jalview.bin.Cache.log.debug("Job " + j + " Result state " +
- jobs[j].result.getState()
- + "(ServerError=" +
- jobs[j].result.isServerError() + ")");
- }
- catch (Exception ex)
- {
- // Deal with Transaction exceptions
- wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
- + " Server exception!\n" + ex.getMessage());
- Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
- + ") Server exception: " + ex.getMessage());
-
- if (jobs[j].allowedServerExceptions > 0)
- {
- jobs[j].allowedServerExceptions--;
- Cache.log.debug("Sleeping after a server exception.");
- try
- {
- Thread.sleep(5000);
- }
- catch (InterruptedException ex1)
- {
- }
- }
- else
- {
- Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
- jobs[j].subjobComplete = true;
- wsInfo.setStatus(jobs[j].jobnum,
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- }
- catch (OutOfMemoryError er)
- {
- jobComplete = true;
- jobs[j].subjobComplete = true;
- jobs[j].result = null; // may contain out of date result object
- wsInfo.setStatus(jobs[j].jobnum,
- WebserviceInfo.STATE_STOPPED_ERROR);
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Out of memory handling result for job !!"
- +
- "\nSee help files for increasing Java Virtual Machine memory.",
- "Out of memory", JOptionPane.WARNING_MESSAGE);
- Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
- WsUrl + "/" + jobs[j].jobId, er);
- System.gc();
- }
- }
- jstate.updateJobPanelState(wsInfo, jobs[j]);
- }
- // Decide on overall state based on collected jobs[] states
- if (jstate.running > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
- }
- else if (jstate.queuing > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
- }
- else
- {
- jobComplete = true;
- if (jstate.finished > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- }
- else if (jstate.error > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- }
- else if (jstate.serror > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- }
- if (!jobComplete)
- {
- try
- {
- Thread.sleep(5000);
- }
- catch (InterruptedException e)
- {
- Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
- }
- // System.out.println("I'm alive "+alTitle);
- }
+ if (!(job instanceof MsaWSJob)) {
+ throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "+job.getClass());
}
- if (jobComplete)
- {
- parseResult(); // tidy up and make results available to user
- }
- }
-
- void StartJob(MsaWSJob j)
- {
+ MsaWSJob j = (MsaWSJob) job;
if (j.submitted)
{
if (Cache.log.isDebugEnabled())
j.result = new MsaResult();
j.result.setFinished(true);
j.result.setStatus("Empty Alignment Job");
- j.result.setMsa(null);
+ ((MsaResult) j.result).setMsa(null);
}
try
{
{
for (int j = 0; j < jobs.length; j++)
{
- finalState.updateJobPanelState(wsInfo, jobs[j]);
+ finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
{
results++;
- vamsas.objects.simple.Alignment valign = jobs[j].result.getMsa();
+ vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result).getMsa();
if (valign != null)
{
wsInfo.appendProgressText(jobs[j].jobnum,
}
});
wsInfo.setResultsReady();
- }
+ } else
+ wsInfo.setFinishedNoResults();
}
void displayResults(boolean newFrame)
int width = 0; // subalignment width
if (jobs[j].hasResults())
{
- Object[] subalg = jobs[j++].getAlignment();
+ Object[] subalg = ((MsaWSJob) jobs[j++]).getAlignment();
alorders.add(subalg[1]);
SequenceI mseq[] = (SequenceI[]) subalg[0];
width = mseq[0].getLength();
int width = 0;
if (jobs[j].hasResults())
{
- Object[] subalg = jobs[j].getAlignment();
+ Object[] subalg = ((MsaWSJob) jobs[j]).getAlignment();
alorders.add(subalg[1]);
SequenceI mseq[] = (SequenceI[]) subalg[0];
width = mseq[0].getLength();
{
if (jobs[0].hasResults())
{
- Object[] alg = jobs[0].getAlignment();
+ Object[] alg = ((MsaWSJob) jobs[0]).getAlignment();
alignment = (SequenceI[]) alg[0];
alorders.add(alg[1]);
}
--- /dev/null
+package jalview.ws;
+
+import jalview.gui.AlignFrame;
+import jalview.gui.WebserviceInfo;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.Desktop;
+import javax.swing.JOptionPane;
+import jalview.bin.Cache;
+
+public abstract class WSThread extends Thread
+{
+ /**
+ * Generic properties for Web Service Client threads.
+ */
+ AlignFrame alignFrame;
+ WebserviceInfo wsInfo = null;
+ AlignmentView input;
+ boolean jobComplete = false;
+ abstract class WSJob {
+ /**
+ * Generic properties for an individual job within a Web Service Client thread
+ */
+ int jobnum = 0; // WebServiceInfo pane for this job
+ String jobId; // ws job ticket
+ boolean cancelled = false;
+ int allowedServerExceptions = 3; // job dies if too many exceptions.
+ boolean submitted = false;
+ boolean subjobComplete = false;
+ /**
+ *
+ * @return true if job has completed and valid results are available
+ */
+ abstract boolean hasResults();
+ /**
+ *
+ * @return boolean true if job can be submitted.
+ */
+ abstract boolean hasValidInput();
+ vamsas.objects.simple.Result result;
+ }
+ class JobStateSummary {
+ int running = 0;
+ int queuing = 0;
+ int finished = 0;
+ int error = 0;
+ int serror = 0;
+ int cancelled = 0;
+ int results = 0;
+ void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
+ WSJob j)
+ {
+ if (j.result != null)
+ {
+ String progheader = "";
+ // Parse state of job[j]
+ if (j.result.isRunning())
+ {
+ running++;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
+ }
+ else if (j.result.isQueued())
+ {
+ queuing++;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
+ }
+ else if (j.result.isFinished())
+ {
+ finished++;
+ j.subjobComplete = true;
+ if (j.hasResults())
+ results++;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else if (j.result.isFailed())
+ {
+ progheader += "Job failed.\n";
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ error++;
+ }
+ else if (j.result.isServerError())
+ {
+ serror++;
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum,
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ else if (j.result.isBroken() || j.result.isFailed())
+ {
+ error++;
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ // and pass on any sub-job messages to the user
+ wsInfo.setProgressText(j.jobnum, OutputHeader);
+ wsInfo.appendProgressText(j.jobnum, progheader);
+ if (j.result.getStatus() != null)
+ {
+ wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
+ }
+ }
+ else
+ {
+ if (j.submitted && j.subjobComplete)
+ {
+ if (j.allowedServerExceptions == 0)
+ {
+ serror++;
+ }
+ else if (j.result == null)
+ {
+ error++;
+ }
+ }
+ }
+ }
+ }
+
+ WSJob jobs[] = null;
+ String WebServiceName = null;
+ String OutputHeader;
+ String WsUrl = null;
+ abstract void pollJob(WSJob job) throws Exception;
+ public void run()
+ {
+ JobStateSummary jstate=null;
+ if (jobs==null)
+ jobComplete=true;
+ while (!jobComplete)
+ {
+ jstate = new JobStateSummary();
+ for (int j = 0; j < jobs.length; j++)
+ {
+
+ if (!jobs[j].submitted && jobs[j].hasValidInput())
+ {
+ StartJob(jobs[j]);
+ }
+
+ if (jobs[j].submitted && !jobs[j].subjobComplete)
+ {
+ try
+ {
+ pollJob(jobs[j]);
+ if (jobs[j].result == null)
+ {
+ throw (new Exception(
+ "Timed out when communicating with server\nTry again later.\n"));
+ }
+ jalview.bin.Cache.log.debug("Job " + j + " Result state " +
+ jobs[j].result.getState()
+ + "(ServerError=" +
+ jobs[j].result.isServerError() + ")");
+ }
+ catch (Exception ex)
+ {
+ // Deal with Transaction exceptions
+ wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
+ + " Server exception!\n" + ex.getMessage());
+ Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ + ") Server exception: " + ex.getMessage());
+
+ if (jobs[j].allowedServerExceptions > 0)
+ {
+ jobs[j].allowedServerExceptions--;
+ Cache.log.debug("Sleeping after a server exception.");
+ try
+ {
+ Thread.sleep(5000);
+ }
+ catch (InterruptedException ex1)
+ {
+ }
+ }
+ else
+ {
+ Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+ jobs[j].subjobComplete = true;
+ wsInfo.setStatus(jobs[j].jobnum,
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ }
+ catch (OutOfMemoryError er)
+ {
+ jobComplete = true;
+ jobs[j].subjobComplete = true;
+ jobs[j].result = null; // may contain out of date result object
+ wsInfo.setStatus(jobs[j].jobnum,
+ WebserviceInfo.STATE_STOPPED_ERROR);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "Out of memory handling result for job !!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory.",
+ "Out of memory", JOptionPane.WARNING_MESSAGE);
+ Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
+ WsUrl + "/" + jobs[j].jobId, er);
+ System.gc();
+ }
+ }
+ jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+ }
+ // Decide on overall state based on collected jobs[] states
+ if (jstate.running > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+ }
+ else if (jstate.queuing > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+ }
+ else
+ {
+ jobComplete = true;
+ if (jstate.finished > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else if (jstate.error > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ else if (jstate.serror > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ }
+ if (!jobComplete)
+ {
+ try
+ {
+ Thread.sleep(5000);
+ }
+ catch (InterruptedException e)
+ {
+ Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
+ }
+ // System.out.println("I'm alive "+alTitle);
+ }
+ }
+ if (jobComplete)
+ {
+ parseResult(); // tidy up and make results available to user
+ }
+}
+abstract void StartJob(WSJob job);
+abstract void parseResult();
+}
git://source.jalview.org / jalview.git / commitdiff