--- /dev/null
+package jalview.ws;
+
+import javax.swing.JMenuItem;
+
+import jalview.analysis.SeqsetUtils;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.ws.api.JPredMutlipleAlignmentServiceI;
+import jalview.ws.api.ServiceWithParameters;
+
+public class JPredClient extends WSClient
+{
+ JPredMutlipleAlignmentServiceI server;
+
+ public JPredClient(ServiceWithParameters sh, String title,
+ AlignmentView alView, AlignFrame alFrame, boolean viewOnly)
+ {
+ server = (JPredMutlipleAlignmentServiceI) sh.getEndpoint();
+ wsInfo = setWebService(sh, false);
+ startClient(title, alView, alFrame, viewOnly);
+ }
+
+ private void startClient(String title, AlignmentView view,
+ AlignFrame frame, boolean viewOnly)
+ {
+ var msf = view.getSequences();
+ var seq = msf[0].getSeq('-');
+ if (msf.length <= 1)
+ throw new RuntimeException("You need more than one sequence.");
+ var aln = new SequenceI[msf.length];
+ for (int i = 0; i < msf.length; i++)
+ {
+ aln[i] = msf[i].getSeq('-');
+ }
+ int[] delMap = viewOnly ?
+ view.getVisibleContigMapFor(seq.gapMap()) : null;
+ var sequenceInfo = SeqsetUtils.uniquify(aln, true);
+ var thread = new JPredThread(wsInfo, title, server, sequenceInfo, aln,
+ delMap, view, frame, WsURL);
+ wsInfo.setthisService(thread);
+ wsInfo.setVisible(true);
+ thread.start();
+ }
+
+ // sh parameter should be moved to the WSMenuEntryProvider interface
+ public static WSMenuEntryProviderI getMenuEntryProvider(ServiceWithParameters sh)
+ {
+ return (menu, frame) -> {
+ final JMenuItem mi = new JMenuItem(sh.getName());
+ mi.setToolTipText(sh.getHostURL());
+ mi.addActionListener((event) -> {
+ var view = frame.gatherSeqOrMsaForSecStrPrediction();
+ if (view.getSequences().length > 1)
+ {
+ new JPredClient(sh, frame.getTitle(), view, frame, true);
+ }
+ else
+ {
+ Cache.log.error("Single sequence not supported");
+ }
+ });
+ menu.add(mi);
+ };
+ }
+}
--- /dev/null
+package jalview.ws;
+
+import static java.lang.String.format;
+
+import java.util.Hashtable;
+import java.util.List;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+import jalview.ws.api.CancellableI;
+import jalview.ws.api.JPredMutlipleAlignmentServiceI;
+import jalview.ws.gui.WsJob;
+import jalview.ws.gui.WsJob.JobState;
+
+
+class JPredJob extends WsJob
+{
+ Hashtable<?, ?> sequenceInfo;
+ List<SequenceI> msf;
+ int[] delMap;
+ public AlignmentI alignment;
+
+ public JPredJob(Hashtable<?, ?> sequenceInfo, SequenceI[] msf, int[] delMap)
+ {
+ this.sequenceInfo = sequenceInfo;
+ this.msf = List.of(msf);
+ this.delMap = delMap;
+ }
+
+ @Override
+ public boolean hasValidInput()
+ {
+ return true;
+ }
+}
+
+
+public class JPredThread extends AWSThread implements WSClientI
+{
+
+ private JPredMutlipleAlignmentServiceI server;
+ private String title;
+ private Hashtable<?, ?> sequenceInfo;
+ private SequenceI[] msf;
+ private int[] delMap;
+
+ public JPredThread(WebserviceInfo wsInfo, String title,
+ JPredMutlipleAlignmentServiceI server, Hashtable<?, ?> sequenceInfo,
+ SequenceI[] msf, int[] delMap, AlignmentView view, AlignFrame frame,
+ String wsURL)
+ {
+ super(frame, wsInfo, view, wsURL);
+ this.server = server;
+ this.title = title;
+ this.sequenceInfo = sequenceInfo;
+ this.msf = msf;
+ this.delMap = delMap;
+ JPredJob job = new JPredJob(sequenceInfo, msf, delMap);
+ this.jobs = new JPredJob[] { job };
+ }
+
+ @Override
+ public boolean isCancellable()
+ {
+ return server instanceof CancellableI;
+ }
+
+ @Override
+ public boolean canMergeResults()
+ {
+ return false;
+ }
+
+ @Override
+ public void cancelJob()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void pollJob(AWsJob job_) throws Exception
+ {
+ var job = (JPredJob) job_;
+ server.updateStatus(job);
+ server.updateJobProgress(job);
+ }
+
+ @Override
+ public void StartJob(AWsJob job_)
+ {
+ if (!(job_ instanceof JPredJob))
+ throw new RuntimeException("Invalid job type");
+ var job = (JPredJob) job_;
+ if (job.isSubmitted())
+ {
+ return;
+ }
+ try {
+ try
+ {
+ var jobHandle = server.align(job.msf);
+ if (jobHandle != null)
+ job.setJobHandle(jobHandle);
+ }
+ catch (Throwable th) {
+ if (!server.handleSubmitError(th, job, wsInfo)) {
+ throw th;
+ }
+ }
+ if (job.getJobId() != null) {
+ job.setSubmitted(true);
+ job.setSubjobComplete(false);
+ return;
+ }
+ else {
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[]
+ { WsUrl }));
+ }
+ }
+ catch (Throwable th)
+ {
+ // For unexpected errors
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n");
+ th.printStackTrace(System.err);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setStatus(job.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+
+ }
+ finally
+ {
+ if (!job.isSubmitted())
+ {
+ job.setAllowedServerExceptions(0);
+ wsInfo.appendProgressText(job.getJobnum(), MessageManager.getString(
+ "info.failed_to_submit_sequences_for_alignment"));
+ }
+ }
+ }
+
+ @Override
+ public void parseResult()
+ {
+ long progbar = (long) (Math.random() * ~(1L << 63));
+ wsInfo.setProgressBar(
+ MessageManager.getString("status.collecting_job_results"), progbar);
+ int results = 0;
+ var finalState = new JobStateSummary();
+ try
+ {
+ for (int i = 0; i < jobs.length; i++) {
+ final var job = (JPredJob) jobs[i];
+ finalState.updateJobPanelState(wsInfo, OutputHeader, job);
+ if (job.isFinished()) {
+ try {
+ server.updateJobProgress(job);
+ }
+ catch (Exception e) {
+ Cache.log.warn(format(
+ "Exception when retrieving remaining Job progress data " +
+ "for job %s on server %s", job.getJobId(), WsUrl));
+ e.printStackTrace();
+ }
+ // removed the waiting loop
+ Cache.log.debug(format("Job Execution file for job: %s " +
+ "on server %s%n%s", job.getJobId(), WsUrl, job.getStatus()));
+ try {
+ job.alignment = server.getResult(job.getJobHandle());
+ }
+ catch (Exception e) {
+ if (!server.handleCollectionException(e, job, wsInfo)) {
+ Cache.log.error("Could not get alignment for job.", e);
+ job.setState(JobState.SERVERERROR);
+ }
+ }
+ }
+ finalState.updateJobPanelState(wsInfo, OutputHeader, job);
+ if (job.isSubmitted() && job.isSubjobComplete() && job.hasResults()) {
+ results++;
+ }
+ }
+ }
+ catch (Exception e) {
+ Cache.log.error(
+ "Unexpected exception when processing results for " + title, e);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ if (results > 0) {
+ wsInfo.showResultsNewFrame.addActionListener(
+ (evt) -> displayResults(true));
+ wsInfo.mergeResults.addActionListener(
+ (evt) -> displayResults(false));
+ wsInfo.setResultsReady();
+ }
+ else {
+ wsInfo.setFinishedNoResults();
+ }
+ updateGlobalStatus(finalState);
+ wsInfo.removeProgressBar(progbar);
+ }
+
+
+
+ private void displayResults(boolean newWindow)
+ {
+ System.out.println("DISPLAYING THE RESULT");
+ }
+
+}
--- /dev/null
+package jalview.ws.api;
+
+import java.util.List;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+public interface JPredMutlipleAlignmentServiceI extends JalviewWebServiceI
+{
+ public JobId align(List<SequenceI> sequences) throws Throwable;
+
+ public AlignmentI getResult(JobId jobId) throws Exception;
+}
import jalview.bin.Cache;
import jalview.gui.AlignFrame;
+import jalview.ws.JPredClient;
import jalview.ws.jws2.MsaWSClient;
import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.params.ParamManager;
import javax.swing.JMenu;
public abstract class ServiceWithParameters extends UIinfo
+ implements JalviewServiceEndpointProviderI
{
protected jalview.ws.uimodel.AlignAnalysisUIText aaui;
protected enum ServiceClient
{
- MSAWSCLIENT, SEQUENCEANNOTATIONWSCLIENT;
+ MSAWSCLIENT, SEQUENCEANNOTATIONWSCLIENT, JPREDWSCLIENT;
};
protected ServiceClient style = null;
case MSAWSCLIENT:
new MsaWSClient().attachWSMenuEntry(atpoint, this, alignFrame);
break;
+ case JPREDWSCLIENT:
+ JPredClient.getMenuEntryProvider(this).attachWSMenuEntry(atpoint, alignFrame);
+ break;
case SEQUENCEANNOTATIONWSCLIENT:
new SequenceAnnotationWSClient().attachWSMenuEntry(atpoint, this,
alignFrame);
import compbio.metadata.RunnerConfig;
public class Jws2Instance extends ServiceWithParameters
- implements JalviewServiceEndpointProviderI, AutoCloseable
+ implements AutoCloseable
{
public JABAService service;
--- /dev/null
+package jalview.ws.slivkaws;
+
+import java.io.IOError;
+import java.io.IOException;
+import java.util.List;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.ws.api.JPredMutlipleAlignmentServiceI;
+import jalview.ws.api.JobId;
+import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
+
+public class SlivkaJPredServiceInstance extends SlivkaWSInstance
+ implements JPredMutlipleAlignmentServiceI
+{
+
+ public SlivkaJPredServiceInstance(SlivkaClient client,
+ SlivkaService service, String action)
+ {
+ super(client, service, action);
+ style = ServiceClient.JPREDWSCLIENT;
+ }
+
+ @Override
+ public JobId align(List<SequenceI> sequences) throws Throwable
+ {
+ return super.submit(sequences, null, null);
+ }
+
+ @Override
+ public AlignmentI getResult(JobId jobId) throws Exception
+ {
+ List<RemoteFile> files;
+ try {
+ files = client.getJobResults(jobId.getJobId());
+ for (RemoteFile f : files) {
+ return readAlignment(f);
+ }
+ }
+ catch (IOException e) {
+ throw new IOError(e);
+ }
+ return null;
+ }
+}
package jalview.ws.slivkaws;
+import java.io.IOError;
+import java.io.IOException;
+import java.rmi.ServerError;
+import java.util.List;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;
-
-import java.io.IOError;
-import java.io.IOException;
-import java.rmi.ServerError;
-import java.util.List;
-
-import compbio.data.msa.Category;
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
files = client.getJobResults(jobId.getJobId());
for (RemoteFile f : files)
{
- if (f.getMimeType().equals("application/clustal"))
- {
- return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
- }
- else if (f.getMimeType().equals("application/fasta"))
- {
- return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
- }
+ return readAlignment(f);
}
} catch (IOException e)
{
service, Category.CATEGORY_DISORDER);
break;
case "protein secondary structure prediction":
- newInstance = new SlivkaAnnotationServiceInstance(client,
+ newInstance = new SlivkaJPredServiceInstance(client,
service, "Secondary Structure Prediction");
break;
case "multiple sequence alignment":
package jalview.ws.slivkaws;
-import jalview.datamodel.SequenceI;
-import jalview.gui.WebserviceInfo;
-import jalview.ws.api.JalviewServiceEndpointProviderI;
-import jalview.ws.api.JalviewWebServiceI;
-import jalview.ws.api.JobId;
-import jalview.ws.api.ServiceWithParameters;
-import jalview.ws.gui.WsJob;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParamManager;
-import jalview.ws.params.WsParamSetI;
-
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOError;
import java.util.Optional;
import java.util.Set;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.WebserviceInfo;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.ws.api.JalviewServiceEndpointProviderI;
+import jalview.ws.api.JalviewWebServiceI;
+import jalview.ws.api.JobId;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.gui.WsJob;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.WsParamSetI;
import uk.ac.dundee.compbio.slivkaclient.FieldType;
import uk.ac.dundee.compbio.slivkaclient.FormField;
import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
}
return store;
}
+
+ public static AlignmentI readAlignment(RemoteFile f) throws IOException
+ {
+ final var mimetype = f.getMimeType();
+ FileFormat format;
+ if (mimetype == "application/clustal")
+ format = FileFormat.Clustal;
+ else if (mimetype == "application/fasta")
+ format = FileFormat.Fasta;
+ else
+ return null;
+ return new FormatAdapter().readFile(f.getURL().toString(),
+ DataSourceType.URL, format);
+ }
}
git://source.jalview.org / jalview.git / commitdiff