* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.ws.jws2;
+package jalview.ws.gui;
-import jalview.analysis.AlignSeq;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.SplitFrame;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
+import jalview.ws.AWSThread;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
-import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.api.CancellableI;
+import jalview.ws.api.JobId;
+import jalview.ws.api.MultipleSequenceAlignmentI;
+import jalview.ws.gui.WsJob.JobState;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
import javax.swing.JInternalFrame;
-import compbio.data.msa.MsaWS;
-import compbio.metadata.Argument;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.Preset;
-
-class MsaWSThread extends AWS2Thread implements WSClientI
+public class MsaWSThread extends AWSThread implements WSClientI
{
boolean submitGaps = false; // pass sequences including gaps to alignment
// order
- class MsaWSJob extends JWs2Job
- {
- long lastChunk = 0;
-
- /**
- * input
- */
- ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
-
- /**
- * output
- */
- compbio.data.sequence.Alignment alignment;
-
- // set if the job didn't get run - then the input is simply returned to the
- // user
- private boolean returnInput = false;
-
- /**
- * MsaWSJob
- *
- * @param jobNum
- * int
- * @param jobId
- * String
- */
- public MsaWSJob(int jobNum, SequenceI[] inSeqs)
- {
- this.jobnum = jobNum;
- if (!prepareInput(inSeqs, 2))
- {
- submitted = true;
- subjobComplete = true;
- returnInput = true;
- }
-
- }
-
- Vector<String[]> emptySeqs = new Vector();
-
- /**
- * prepare input sequences for MsaWS service
- *
- * @param seqs
- * jalview sequences to be prepared
- * @param minlen
- * minimum number of residues required for this MsaWS service
- * @return true if seqs contains sequences to be submitted to service.
- */
- // TODO: return compbio.seqs list or nothing to indicate validity.
- private boolean prepareInput(SequenceI[] seqs, int minlen)
- {
- int nseqs = 0;
- if (minlen < 0)
- {
- throw new Error(MessageManager.getString(
- "error.implementation_error_minlen_must_be_greater_zero"));
- }
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
- {
- nseqs++;
- }
- }
- boolean valid = nseqs > 1; // need at least two seqs
- compbio.data.sequence.FastaSequence seq;
- for (int i = 0, n = 0; i < seqs.length; i++)
- {
- String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
- // for
- // any
- // subjob
- SeqNames.put(newname,
- jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
- if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
- {
- // make new input sequence with or without gaps
- seq = new compbio.data.sequence.FastaSequence(newname,
- (submitGaps) ? seqs[i].getSequenceAsString()
- : AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- seqs[i].getSequenceAsString()));
- this.seqs.add(seq);
- }
- else
- {
- String empty = null;
- if (seqs[i].getEnd() >= seqs[i].getStart())
- {
- empty = (submitGaps) ? seqs[i].getSequenceAsString()
- : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
- seqs[i].getSequenceAsString());
- }
- emptySeqs.add(new String[] { newname, empty });
- }
- }
- return valid;
- }
-
- /**
- *
- * @return true if getAlignment will return a valid alignment result.
- */
- @Override
- public boolean hasResults()
- {
- if (subjobComplete && isFinished() && (alignment != null
- || (emptySeqs != null && emptySeqs.size() > 0)))
- {
- return true;
- }
- return false;
- }
-
- /**
- *
- * get the alignment including any empty sequences in the original order
- * with original ids. Caller must access the alignment.getMetadata() object
- * to annotate the final result passsed to the user.
- *
- * @return { SequenceI[], AlignmentOrder }
- */
- public Object[] getAlignment()
- {
- // is this a generic subjob or a Jws2 specific Object[] return signature
- if (hasResults())
- {
- SequenceI[] alseqs = null;
- char alseq_gapchar = '-';
- int alseq_l = 0;
- if (alignment.getSequences().size() > 0)
- {
- alseqs = new SequenceI[alignment.getSequences().size()];
- for (compbio.data.sequence.FastaSequence seq : alignment
- .getSequences())
- {
- alseqs[alseq_l++] = new Sequence(seq.getId(),
- seq.getSequence());
- }
- alseq_gapchar = alignment.getMetadata().getGapchar();
-
- }
- // add in the empty seqs.
- if (emptySeqs.size() > 0)
- {
- SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
- // get width
- int i, w = 0;
- if (alseq_l > 0)
- {
- for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
- {
- if (w < alseqs[i].getLength())
- {
- w = alseqs[i].getLength();
- }
- t_alseqs[i] = alseqs[i];
- alseqs[i] = null;
- }
- }
- // check that aligned width is at least as wide as emptySeqs width.
- int ow = w, nw = w;
- for (i = 0, w = emptySeqs.size(); i < w; i++)
- {
- String[] es = emptySeqs.get(i);
- if (es != null && es[1] != null)
- {
- int sw = es[1].length();
- if (nw < sw)
- {
- nw = sw;
- }
- }
- }
- // make a gapped string.
- StringBuffer insbuff = new StringBuffer(w);
- for (i = 0; i < nw; i++)
- {
- insbuff.append(alseq_gapchar);
- }
- if (ow < nw)
- {
- for (i = 0; i < alseq_l; i++)
- {
- int sw = t_alseqs[i].getLength();
- if (nw > sw)
- {
- // pad at end
- alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()
- + insbuff.substring(0, sw - nw));
- }
- }
- }
- for (i = 0, w = emptySeqs.size(); i < w; i++)
- {
- String[] es = emptySeqs.get(i);
- if (es[1] == null)
- {
- t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
- insbuff.toString(), 1, 0);
- }
- else
- {
- if (es[1].length() < nw)
- {
- t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
- es[0],
- es[1] + insbuff.substring(0, nw - es[1].length()),
- 1, 1 + es[1].length());
- }
- else
- {
- t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
- es[0], es[1]);
- }
- }
- }
- alseqs = t_alseqs;
- }
- AlignmentOrder msaorder = new AlignmentOrder(alseqs);
- // always recover the order - makes parseResult()'s life easier.
- jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
- // account for any missing sequences
- jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
- return new Object[] { alseqs, msaorder };
- }
- return null;
- }
-
- /**
- * mark subjob as cancelled and set result object appropriatly
- */
- void cancel()
- {
- cancelled = true;
- subjobComplete = true;
- alignment = null;
- }
-
- /**
- *
- * @return boolean true if job can be submitted.
- */
- @Override
- public boolean hasValidInput()
- {
- // TODO: get attributes for this MsaWS instance to check if it can do two
- // sequence alignment.
- if (seqs != null && seqs.size() >= 2) // two or more sequences is valid ?
- {
- return true;
- }
- return false;
- }
-
- StringBuffer jobProgress = new StringBuffer();
-
- public void setStatus(String string)
- {
- jobProgress.setLength(0);
- jobProgress.append(string);
- }
-
- @Override
- public String getStatus()
- {
- return jobProgress.toString();
- }
-
- @Override
- public boolean hasStatus()
- {
- return jobProgress != null;
- }
-
- /**
- * @return the lastChunk
- */
- public long getLastChunk()
- {
- return lastChunk;
- }
-
- /**
- * @param lastChunk
- * the lastChunk to set
- */
- public void setLastChunk(long lastChunk)
- {
- this.lastChunk = lastChunk;
- }
-
- String alignmentProgram = null;
-
- public String getAlignmentProgram()
- {
- return alignmentProgram;
- }
-
- public boolean hasArguments()
- {
- return (arguments != null && arguments.size() > 0)
- || (preset != null && preset instanceof JabaWsParamSet);
- }
-
- public List<Argument> getJabaArguments()
- {
- List<Argument> newargs = new ArrayList<>();
- if (preset != null && preset instanceof JabaWsParamSet)
- {
- newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
- }
- if (arguments != null && arguments.size() > 0)
- {
- newargs.addAll(JabaParamStore.getJabafromJwsArgs(arguments));
- }
- return newargs;
- }
-
- /**
- * add a progess header to status string containing presets/args used
- */
- public void addInitialStatus()
- {
- if (preset != null)
- {
- jobProgress.append("Using "
- + (preset instanceof JabaPreset ? "Server" : "User")
- + "Preset: " + preset.getName());
- if (preset instanceof JabaWsParamSet)
- {
- for (Argument opt : getJabaArguments())
- {
- jobProgress.append(
- opt.getName() + " " + opt.getDefaultValue() + "\n");
- }
- }
- }
- if (arguments != null && arguments.size() > 0)
- {
- jobProgress.append("With custom parameters : \n");
- // merge arguments with preset's own arguments.
- for (Argument opt : getJabaArguments())
- {
- jobProgress.append(
- opt.getName() + " " + opt.getDefaultValue() + "\n");
- }
- }
- jobProgress.append("\nJob Output:\n");
- }
-
- public boolean isPresetJob()
- {
- return preset != null && preset instanceof JabaPreset;
- }
-
- public Preset getServerPreset()
- {
- return (isPresetJob()) ? ((JabaPreset) preset).p : null;
- }
- }
-
String alTitle; // name which will be used to form new alignment window.
AlignmentI dataset; // dataset to which the new alignment will be
// associated.
- @SuppressWarnings("unchecked")
- MsaWS server = null;
+ MultipleSequenceAlignmentI server = null;
/**
* set basic options for this (group) of Msa jobs
* @param presorder
* boolean
*/
- private MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
+ private MsaWSThread(MultipleSequenceAlignmentI server, String wsUrl,
+ WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, AlignmentView alview,
String wsname, boolean subgaps, boolean presorder)
{
}
/**
- * create one or more Msa jobs to align visible seuqences in _msa
+ * create one or more Msa jobs to align visible sequences in _msa
*
* @param title
* String
* @param seqset
* Alignment
*/
- MsaWSThread(MsaWS server2, WsParamSetI preset, List<ArgumentI> paramset,
+ public MsaWSThread(MultipleSequenceAlignmentI server2, WsParamSetI preset,
+ List<ArgumentI> paramset,
String wsUrl, WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, String wsname, String title,
AlignmentView _msa, boolean subgaps, boolean presorder,
{
if (j != 0)
{
- jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
+ jobs[j] = new MsaWSJob(this, wsinfo.addJobPane(), conmsa[j]);
}
else
{
- jobs[j] = new MsaWSJob(0, conmsa[j]);
+ jobs[j] = new MsaWSJob(this, 0, conmsa[j]);
}
if (jobs[j].hasValidInput())
{
@Override
public boolean isCancellable()
{
- return true;
+ return server instanceof CancellableI;
}
@Override
public void cancelJob()
{
+ // TODO decide if when some jobs are not cancellable to shut down the thread
+ // anyhow ?
if (!jobComplete && jobs != null)
{
boolean cancelled = true;
String cancelledMessage = "";
try
{
- boolean cancelledJob = server.cancelJob(jobs[job].getJobId());
- if (true) // cancelledJob || true)
+ CancellableI service = (CancellableI) server;
+ boolean cancelledJob = service.cancel((WsJob) jobs[job]);
+ if (cancelledJob)
{
// CANCELLED_JOB
- // if the Jaba server indicates the job can't be cancelled, its
- // because its running on the server's local execution engine
- // so we just close the window anyway.
cancelledMessage = "Job cancelled.";
((MsaWSJob) jobs[job]).cancel(); // TODO: refactor to avoid this
// ugliness -
// this is standard code, but since the interface doesn't comprise of a
// basic one that implements (getJobStatus, pullExecStatistics) we have to
// repeat the code for all jw2s services.
- j.setjobStatus(server.getJobStatus(job.getJobId()));
- updateJobProgress(j);
- }
-
- /**
- *
- * @param j
- * @return true if more job progress data was available
- * @throws Exception
- */
- protected boolean updateJobProgress(MsaWSJob j) throws Exception
- {
- StringBuffer response = j.jobProgress;
- long lastchunk = j.getLastChunk();
- boolean changed = false;
- do
- {
- j.setLastChunk(lastchunk);
- ChunkHolder chunk = server.pullExecStatistics(j.getJobId(),
- lastchunk);
- if (chunk != null)
- {
- changed |= chunk.getChunk().length() > 0;
- response.append(chunk.getChunk());
- lastchunk = chunk.getNextPosition();
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException x)
- {
- }
- ;
- }
- ;
- } while (lastchunk >= 0 && j.getLastChunk() != lastchunk);
- return changed;
+ server.updateStatus(j);
+ server.updateJobProgress(j);
}
@Override
if (j.seqs == null || j.seqs.size() == 0)
{
// special case - selection consisted entirely of empty sequences...
- j.setjobStatus(JobStatus.FINISHED);
+ j.setState(JobState.FINISHED);
j.setStatus(MessageManager.getString("label.empty_alignment_job"));
}
try
{
j.addInitialStatus(); // list the presets/parameters used for the job in
// status
- if (j.isPresetJob())
+ try
{
- j.setJobId(server.presetAlign(j.seqs, j.getServerPreset()));
- }
- else if (j.hasArguments())
- {
- j.setJobId(server.customAlign(j.seqs, j.getJabaArguments()));
- }
- else
+ JobId jobHandle = server.align(j.seqs, j.getPreset(),
+ j.getArguments());
+ if (jobHandle != null)
+ {
+ j.setJobHandle(jobHandle);
+ }
+
+ } catch (Throwable throwable)
{
- j.setJobId(server.align(j.seqs));
+ if (!server.handleSubmitError(throwable, j, wsInfo))
+ {
+ if (throwable instanceof Exception)
+ {
+ throw ((Exception) throwable);
+ }
+ if (throwable instanceof Error)
+ {
+ throw ((Error) throwable);
+ }
+ }
}
-
+ ///// generic
if (j.getJobId() != null)
{
j.setSubmitted(true);
new String[]
{ WsUrl }));
}
- } catch (compbio.metadata.UnsupportedRuntimeException _lex)
- {
- lex = _lex;
- wsInfo.appendProgressText(MessageManager.formatMessage(
- "info.job_couldnt_be_run_server_doesnt_support_program",
- new String[]
- { _lex.getMessage() }));
- wsInfo.warnUser(_lex.getMessage(),
- MessageManager.getString("warn.service_not_supported"));
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setStatus(j.getJobnum(),
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
- } catch (compbio.metadata.LimitExceededException _lex)
- {
- lex = _lex;
- wsInfo.appendProgressText(MessageManager.formatMessage(
- "info.job_couldnt_be_run_exceeded_hard_limit", new String[]
- { _lex.getMessage() }));
- wsInfo.warnUser(_lex.getMessage(),
- MessageManager.getString("warn.input_is_too_big"));
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
- } catch (compbio.metadata.WrongParameterException _lex)
- {
- lex = _lex;
- wsInfo.warnUser(_lex.getMessage(),
- MessageManager.getString("warn.invalid_job_param_set"));
- wsInfo.appendProgressText(MessageManager.formatMessage(
- "info.job_couldnt_be_run_incorrect_param_setting",
- new String[]
- { _lex.getMessage() }));
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
- } catch (Error e)
+ }
+ //// jabaws specific
+
+ //// generic
+ catch (Error e)
{
// For unexpected errors
System.err.println(WebServiceName
{
try
{
- jpchanged = updateJobProgress(msjob);
+ jpchanged = server.updateJobProgress(msjob);
jpex = false;
if (jpchanged)
{
System.out.println("*** End of status");
}
+ ///// jabaws specific(ish) Get Result from Server when available
try
{
- msjob.alignment = server.getResult(msjob.getJobId());
- } catch (compbio.metadata.ResultNotAvailableException e)
- {
- // job has failed for some reason - probably due to invalid
- // parameters
- Cache.log.debug(
- "Results not available for finished job - marking as broken job.",
- e);
- msjob.jobProgress.append(
- "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
- + e.getLocalizedMessage());
- msjob.setjobStatus(JobStatus.FAILED);
+ msjob.alignment = server.getAlignmentFor(msjob.getJobHandle());
} catch (Exception e)
{
- Cache.log.error("Couldn't get Alignment for job.", e);
- // TODO: Increment count and retry ?
- msjob.setjobStatus(JobStatus.UNDEFINED);
+ if (!server.handleCollectionException(e, msjob, wsInfo))
+ {
+ Cache.log.error("Couldn't get Alignment for job.", e);
+ // TODO: Increment count and retry ?
+ msjob.setState(JobState.SERVERERROR);
+ }
}
}
finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
&& jobs[j].hasResults())
{
results++;
- compbio.data.sequence.Alignment alignment = ((MsaWSJob) jobs[j]).alignment;
- if (alignment != null)
- {
- // server.close(jobs[j].getJobnum());
- // wsInfo.appendProgressText(jobs[j].getJobnum(),
- // "\nAlignment Object Method Notes\n");
- // wsInfo.appendProgressText(jobs[j].getJobnum(),
- // "Calculated with
- // "+alignment.getMetadata().getProgram().toString());
- // JBPNote The returned files from a webservice could be
- // hidden behind icons in the monitor window that,
- // when clicked, pop up their corresponding data
- }
}
}
} catch (Exception ex)
git://source.jalview.org / jalview.git / blobdiff