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.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.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);
public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
{
- super(service.getName(), action, service.getLabel(), "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) throws IOException
{
- Optional<RemoteFile> logFile = client.getJobResults(job.getJobId()).stream()
- .filter(f -> f.getLabel() == "log").findFirst();
- if (logFile.isPresent())
+ List<RemoteFile> files = client.getJobResults(job.getJobId());
+ RemoteFile logFile=null;
+ for (RemoteFile f : files)
{
- InputStream stream = logFile.get().getContent();
- long nextChunk = stream.skip(job.getNextChunk());
- job.setnextChunk(nextChunk + appendJobStatus(job, stream));
+ if (f.getLabel().equals("log"))
+ {
+ logFile = f; break;
+ }
}
- if (failedStates.contains(job.getJobState()))
+
+ boolean newContent = false;
+ if (logFile!=null)
{
- Optional<RemoteFile> errLogFile = client.getJobResults(job.getJobId()).stream()
- .filter(f -> f.getLabel() == "error-log").findFirst();
- if (errLogFile.isPresent())
+ ByteArrayOutputStream output = new ByteArrayOutputStream();
+ logFile.writeTo(output);
+ if (output.size() > job.getNextChunk())
{
- appendJobStatus(job, errLogFile.get().getContent());
+ newContent = true;
+ job.setStatus(output.toString("UTF-8"));
+ job.setnextChunk(output.size());
}
}
- return false;
- }
-
- 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)
+ if (failedStates.contains(job.getJobState()))
{
- chunkLen += len;
- builder.append(buffer, 0, len);
+
+ 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"));
+ }
+ }
}
- job.setStatus(builder.toString());
- return chunkLen;
+ return newContent;
}
@Override