--- /dev/null
+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;
+
+public abstract class SlivkaWSInstance extends ServiceWithParameters
+ implements JalviewServiceEndpointProviderI, JalviewWebServiceI
+{
+ protected final SlivkaClient client;
+
+ protected final SlivkaService service;
+
+ protected SlivkaDatastore store = null;
+
+ 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)
+ {
+ super(service.getName(), 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();
+ 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)
+ {
+ try
+ {
+ job.setState(stateMap.get(client.getJobState(job.getJobId())));
+ } catch (IOException e)
+ {
+ throw new IOError(e);
+ }
+ }
+
+ @Override
+ public final boolean updateJobProgress(WsJob job) throws IOException
+ {
+ 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
+ public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
+ {
+ if (_lex instanceof FormValidationException)
+ {
+ FormValidationException formError = (FormValidationException) _lex;
+ String[] messages = new String[formError.getErrors().size()];
+ int i = 0;
+ for (ValidationException e : formError.getErrors())
+ {
+ messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
+ }
+ j.setState(WsJob.JobState.INVALID);
+ j.setStatus(String.join(", ", messages));
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
+ {
+ // TODO
+ return false;
+ }
+
+ final SlivkaService getService()
+ {
+ return service;
+ }
+
+ @Override
+ public final Object getEndpoint()
+ {
+ return this;
+ }
+
+ @Override
+ public final void initParamStore(ParamManager userParameterStore)
+ {
+ if (store == null)
+ {
+ try
+ {
+ store = new SlivkaDatastore(service);
+ } catch (IOException e)
+ {
+ throw new IOError(e);
+ }
+ }
+ }
+
+ @Override
+ public boolean hasParameters()
+ {
+ return true;
+ }
+
+ @Override
+ public final ParamDatastoreI getParamStore()
+ {
+ if (store == null)
+ {
+ initParamStore(null);
+ }
+ return store;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff