package jalview.ws.slivkaws;
+import jalview.datamodel.SequenceI;
import jalview.gui.WebserviceInfo;
+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 java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
import java.io.IOError;
import java.io.IOException;
+import java.io.InputStream;
+import java.util.Arrays;
import java.util.EnumMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Optional;
+import java.util.Set;
+import uk.ac.dundee.compbio.slivkaclient.FieldType;
+import uk.ac.dundee.compbio.slivkaclient.FileField;
+import uk.ac.dundee.compbio.slivkaclient.FormField;
import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
import uk.ac.dundee.compbio.slivkaclient.JobState;
+import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
import uk.ac.dundee.compbio.slivkaclient.ValidationException;
protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
{
stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
+ stateMap.put(JobState.REJECTED, WsJob.JobState.INVALID);
+ stateMap.put(JobState.ACCEPTED, WsJob.JobState.QUEUED);
stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
+ stateMap.put(JobState.INTERRUPTED, WsJob.JobState.CANCELLED);
+ stateMap.put(JobState.DELETED, WsJob.JobState.CANCELLED);
stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
}
+ protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
+ WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
+ WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
+ ));
public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
{
- super(service.getLabel(), action, service.getName(), "Slivka",
- client.getUrl().toString());
+ super(action, action, service.getLabel(), "Slivka", client.getUrl().toString());
this.client = client;
this.service = service;
}
+ protected final JobId submit(List<SequenceI> sequences,
+ WsParamSetI preset, List<ArgumentI> args) throws Throwable
+ {
+ SlivkaForm form = service.getForm();
+ for (FormField field : form.getFields())
+ {
+ if (field.getType() == FieldType.FILE)
+ {
+ FormatAdapter fa = new FormatAdapter();
+ fa.setNewlineString("\r\n");
+ FileField fileField = (FileField) field;
+ FileFormat format;
+ switch (fileField.getMediaType())
+ {
+ case "application/pfam":
+ format = FileFormat.Pfam;
+ break;
+ case "application/stockholm":
+ format = FileFormat.Stockholm;
+ break;
+ default:
+ case "application/fasta":
+ format = FileFormat.Fasta;
+ break;
+ }
+ InputStream stream = new ByteArrayInputStream(
+ fa.formatSequences(format, sequences.toArray(new SequenceI[0]))
+ .getBytes());
+ RemoteFile rf = client.uploadFile(stream, "input",
+ fileField.getMediaType());
+ form.insert(field.getName(), rf);
+ }
+ }
+ if (args != null)
+ {
+ for (ArgumentI arg : args)
+ {
+ // multiple choice field names are name$number to avoid duplications
+ // the number is stripped here
+ String fieldName = arg.getName().split("\\$", 2)[0];
+ FormField field = form.getField(fieldName);
+ if (field.getType() == FieldType.BOOLEAN)
+ {
+ form.insert(fieldName,
+ (arg.getValue() != null && !arg.getValue().isBlank())
+ ? true
+ : false);
+ }
+ else
+ {
+ form.insert(fieldName, arg.getValue());
+ }
+ }
+ }
+ return new JobId(service.getName(), service.getName(), form.submit());
+ }
+
@Override
public final void updateStatus(WsJob job)
{
}
@Override
- public final boolean updateJobProgress(WsJob job)
+ public final boolean updateJobProgress(WsJob job) throws IOException
{
- return false;
+ List<RemoteFile> files = client.getJobResults(job.getJobId());
+ RemoteFile logFile=null;
+ for (RemoteFile f : files)
+ {
+ if (f.getLabel().equals("log"))
+ {
+ logFile = f; break;
+ }
+ }
+
+ boolean newContent = false;
+ if (logFile!=null)
+ {
+ ByteArrayOutputStream output = new ByteArrayOutputStream();
+ logFile.writeTo(output);
+ if (output.size() > job.getNextChunk())
+ {
+ newContent = true;
+ job.setStatus(output.toString("UTF-8"));
+ job.setnextChunk(output.size());
+ }
+ }
+ if (failedStates.contains(job.getJobState()))
+ {
+
+ RemoteFile errLogFile = null;
+ for (RemoteFile f : files)
+ {
+ if (f.getLabel().equals("error-log"))
+ {
+ errLogFile = f;
+ break;
+ }
+ }
+
+ if (errLogFile!=null)
+ {
+ ByteArrayOutputStream output = new ByteArrayOutputStream();
+ errLogFile.writeTo(output);
+ if (output.size() > 0)
+ {
+ newContent = true;
+ job.setStatus(job.getStatus() + "\n" + output.toString("UTF-8"));
+ }
+ }
+ }
+ return newContent;
}
@Override