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.IOError;
import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+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.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.INTERRUPED, 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)
{
this.service = service;
}
+ protected final JobId submit(List<SequenceI> sequences,
+ WsParamSetI preset, List<ArgumentI> args) throws Throwable
+ {
+ SlivkaForm form = service.getForm();
+ Optional<FormField> inputField = form.getFields().stream()
+ .filter(f -> f.getType() == FieldType.FILE).findFirst();
+ if (inputField.isPresent())
+ {
+ StringBuilder builder = new StringBuilder();
+ for (SequenceI seq : sequences)
+ {
+ builder.append(">").append(seq.getName()).append("\n")
+ .append(seq.getSequence()).append("\n");
+ }
+ InputStream stream = new ByteArrayInputStream(
+ builder.toString().getBytes());
+ RemoteFile file = client.uploadFile(stream, "input.fa",
+ "application/fasta");
+ form.insert(inputField.get().getName(), file);
+ }
+ 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, field.valueOf(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());
+ Optional<RemoteFile> logFile = files.stream()
+ .filter(f -> f.getLabel().equals("log")).findFirst();
+ boolean newContent = false;
+ if (logFile.isPresent())
+ {
+ InputStream stream = logFile.get().getContent();
+ long nextChunk = stream.skip(job.getNextChunk());
+ int len = appendJobStatus(job, stream);
+ job.setnextChunk(nextChunk + len);
+ newContent |= len > 0;
+ }
+ if (failedStates.contains(job.getJobState()))
+ {
+ Optional<RemoteFile> errLogFile = files.stream()
+ .filter(f -> f.getLabel().equals("error-log")).findFirst();
+ if (errLogFile.isPresent())
+ {
+ newContent |= appendJobStatus(job, errLogFile.get().getContent()) > 0;
+ }
+ }
+ return newContent;
+ }
+
+ private int appendJobStatus(WsJob job, InputStream stream) throws IOException
+ {
+ StringBuilder builder = new StringBuilder(job.getStatus());
+ InputStreamReader reader = new InputStreamReader(stream);
+ char[] buffer = new char[4096];
+ int chunkLen = 0;
+ int len = 0;
+ while ((len = reader.read(buffer)) != -1)
+ {
+ chunkLen += len;
+ builder.append(buffer, 0, len);
+ }
+ job.setStatus(builder.toString());
+ return chunkLen;
}
@Override