package jalview.ws.jws2.jabaws2;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.gui.WebserviceInfo;
-import jalview.util.MessageManager;
import jalview.ws.api.CancellableI;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
-import jalview.ws.gui.WsJob;
-import jalview.ws.gui.WsJob.JobState;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;
import java.io.IOError;
import java.rmi.ServerError;
import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
-import java.util.Map;
-import compbio.data.msa.MsaWS;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.FastaSequence;
-import compbio.metadata.Argument;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.Preset;
import compbio.metadata.ResultNotAvailableException;
public class JabawsMsaInstance
+ extends JabawsServiceInstance<compbio.data.msa.MsaWS>
implements MultipleSequenceAlignmentI, CancellableI
{
- /**
- * our service instance handler generated by the discoverer
- */
- Jws2Instance our;
-
- MsaWS<?> service;
-
@Override
public JobId align(List<SequenceI> toalign, WsParamSetI parameters,
List<ArgumentI> arguments) throws Throwable
public JabawsMsaInstance(Jws2Instance handle)
{
- our = handle;
- service = (MsaWS<?>) our.service;
- }
-
- @Override
- public boolean cancel(WsJob job)
- {
- service.cancelJob(job.getJobId());
- // 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.
-
- return true;
- }
-
- Map<JobStatus, JobState> jwsState = new HashMap<>();
- {
- jwsState.put(JobStatus.CANCELLED, JobState.CANCELLED);
- jwsState.put(JobStatus.COLLECTED, JobState.FINISHED);
- jwsState.put(JobStatus.FAILED, JobState.FAILED);
- jwsState.put(JobStatus.FINISHED, JobState.FINISHED);
- jwsState.put(JobStatus.PENDING, JobState.QUEUED);
- jwsState.put(JobStatus.RUNNING, JobState.RUNNING);
- jwsState.put(JobStatus.STARTED, JobState.RUNNING);
- jwsState.put(JobStatus.SUBMITTED, JobState.SUBMITTED);
- jwsState.put(JobStatus.UNDEFINED, JobState.UNKNOWN);
- }
- @Override
- public void updateStatus(WsJob job)
- {
- JobStatus jwsstatus = service.getJobStatus(job.getJobId());
- job.setState(jwsState.get(jwsstatus));
- }
-
- @Override
- public boolean updateJobProgress(WsJob job) throws Exception
- {
- StringBuilder response = new StringBuilder(job.getStatus());
- long lastchunk = job.getNextChunk();
- boolean changed = false;
- do
- {
- ChunkHolder chunk = service.pullExecStatistics(job.getJobId(),
- lastchunk);
- if (chunk != null)
- {
- changed |= chunk.getChunk().length() > 0;
- response.append(chunk.getChunk());
- lastchunk = chunk.getNextPosition();
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException x)
- {
- }
- ;
- }
- ;
- job.setnextChunk(lastchunk);
- } while (lastchunk >= 0 && job.getNextChunk() != lastchunk);
- if (job instanceof WsJob)
- {
- // TODO decide if WsJob will be the bean for all ng-webservices
- job.setStatus(response.toString());
- }
- return changed;
- }
-
- public boolean isPresetJob(WsJob job)
- {
- return job.getPreset() != null && job.getPreset() instanceof JabaPreset;
- }
-
- public Preset getServerPreset(WsJob job)
- {
- return (isPresetJob(job))
- ? ((JabaPreset) job.getPreset()).getJabaPreset()
- : null;
- }
-
- public List<Argument> getJabaArguments(WsParamSetI preset)
- {
- List<Argument> newargs = new ArrayList<>();
- if (preset != null)
- {
- if (preset instanceof JabaWsParamSet)
- {
- newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
- }
- else
- {
- newargs.addAll(
- JabaParamStore.getJabafromJwsArgs(preset.getArguments()));
- }
- }
- return newargs;
+ super(handle);
}
- @Override
- public boolean handleSubmitError(Throwable _lex, WsJob j,
- WebserviceInfo wsInfo) throws Exception, Error
- {
- if (_lex instanceof compbio.metadata.UnsupportedRuntimeException)
- {
- 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);
- return true;
- }
- if (_lex instanceof compbio.metadata.LimitExceededException)
- {
- 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);
- return true;
- }
- if (_lex instanceof compbio.metadata.WrongParameterException)
- {
- 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);
- return true;
- }
- // pass on to generic error handler
- return false;
- }
-
- @Override
- public boolean handleCollectionException(Exception ex, WsJob msjob,
- WebserviceInfo wsInfo)
- {
- if (ex instanceof compbio.metadata.ResultNotAvailableException)
- {
- // job has failed for some reason - probably due to invalid
- // parameters
- Cache.log.debug(
- "Results not available for finished job - marking as broken job.",
- ex);
- String status = msjob.getStatus();
-
- msjob.setStatus(status
- +
- "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
- + ex.getLocalizedMessage());
- msjob.setState(WsJob.JobState.BROKEN);
- return true;
- }
- return false;
- }
}
git://source.jalview.org / jalview.git / blobdiff