package jalview.ws.slivkaws;
+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.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.params.ParamDatastoreI;
import jalview.ws.params.ParamManager;
import jalview.ws.params.WsParamSetI;
+import javajs.http.ClientProtocolException;
-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.FormField;
-import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
-import uk.ac.dundee.compbio.slivkaclient.JobState;
+import java.util.Collection;
+import uk.ac.dundee.compbio.slivkaclient.Job;
+import uk.ac.dundee.compbio.slivkaclient.JobRequest;
+import uk.ac.dundee.compbio.slivkaclient.Parameter;
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 SlivkaDatastore store = null;
- protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
+ protected static final EnumMap<Job.Status, WsJob.JobState> stateMap = new EnumMap<>(Job.Status.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);
+ stateMap.put(Job.Status.PENDING, WsJob.JobState.QUEUED);
+ stateMap.put(Job.Status.REJECTED, WsJob.JobState.INVALID);
+ stateMap.put(Job.Status.ACCEPTED, WsJob.JobState.QUEUED);
+ stateMap.put(Job.Status.QUEUED, WsJob.JobState.QUEUED);
+ stateMap.put(Job.Status.RUNNING, WsJob.JobState.RUNNING);
+ stateMap.put(Job.Status.COMPLETED, WsJob.JobState.FINISHED);
+ stateMap.put(Job.Status.INTERRUPTED, WsJob.JobState.CANCELLED);
+ stateMap.put(Job.Status.DELETED, WsJob.JobState.CANCELLED);
+ stateMap.put(Job.Status.FAILED, WsJob.JobState.FAILED);
+ stateMap.put(Job.Status.ERROR, WsJob.JobState.SERVERERROR);
+ stateMap.put(Job.Status.UNKNOWN, WsJob.JobState.UNKNOWN);
}
protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
{
- super(service.getName(), action, service.getLabel(), "Slivka", client.getUrl().toString());
+ super(action, action, service.getName(), "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())
+ var parameters = service.getParameters();
+ var request = new JobRequest();
+ for (Parameter param : parameters)
{
- StringBuilder builder = new StringBuilder();
- for (SequenceI seq : sequences)
+ if (param instanceof Parameter.FileParameter)
{
- builder.append(">").append(seq.getName()).append("\n")
- .append(seq.getSequence()).append("\n");
+ FormatAdapter fa = new FormatAdapter();
+ fa.setNewlineString("\r\n");
+ Parameter.FileParameter fileParam = (Parameter.FileParameter) param;
+ FileFormat format;
+ switch (fileParam.getMediaType())
+ {
+ case "application/pfam":
+ format = FileFormat.Pfam;
+ break;
+ case "application/stockholm":
+ format = FileFormat.Stockholm;
+ break;
+ default:
+ case "application/fasta":
+ format = FileFormat.Fasta;
+ break;
+ }
+
+ // we avoid any use of Jalview's user facing export routines here
+
+ InputStream stream = new ByteArrayInputStream(format.getWriter(null)
+ .print(sequences.toArray(new SequenceI[0]), false)
+ .getBytes());
+ request.addFile(param.getId(), stream);
}
- 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)
{
{
// 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);
+ String paramId = arg.getName().split("\\$", 2)[0];
+ Parameter param = service.getParameter(paramId);
+ if (param instanceof Parameter.FlagParameter) {
+ if (arg.getValue() != null && !arg.getValue().isBlank())
+ request.addData(paramId, true);
+ else
+ request.addData(paramId, false);
}
else
{
- form.insert(fieldName, arg.getValue());
+ request.addData(paramId, arg.getValue());
}
}
}
- return new JobId(service.getName(), service.getName(), form.submit());
+ var job = service.submitJob(request);
+ return new JobId(service.getName(), service.getName(), job.getId());
}
@Override
{
try
{
- job.setState(stateMap.get(client.getJobState(job.getJobId())));
+ var slivkaJob = client.getJob(job.getJobId());
+ job.setState(stateMap.get(slivkaJob.getStatus()));
} 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();
+ {
+ var slivkaJob = client.getJob(job.getJobId());
+ Collection<RemoteFile> files = slivkaJob.getResults();
+ RemoteFile logFile=null;
+ for (RemoteFile f : files)
+ {
+ if (f.getLabel().equals("log"))
+ {
+ logFile = f; break;
+ }
+ }
+
boolean newContent = false;
- if (logFile.isPresent())
+ if (logFile!=null)
{
ByteArrayOutputStream output = new ByteArrayOutputStream();
- logFile.get().writeTo(output);
+ logFile.writeTo(output);
if (output.size() > job.getNextChunk())
{
newContent = true;
}
if (failedStates.contains(job.getJobState()))
{
- Optional<RemoteFile> errLogFile = files.stream()
- .filter(f -> f.getLabel().equals("error-log")).findFirst();
- if (errLogFile.isPresent())
+
+ RemoteFile errLogFile = null;
+ for (RemoteFile f : files)
+ {
+ if (f.getLabel().equals("error-log"))
+ {
+ errLogFile = f;
+ break;
+ }
+ }
+
+ if (errLogFile!=null)
{
ByteArrayOutputStream output = new ByteArrayOutputStream();
- errLogFile.get().writeTo(output);
+ errLogFile.writeTo(output);
if (output.size() > 0)
{
newContent = true;
@Override
public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
{
- if (_lex instanceof FormValidationException)
+ if (_lex instanceof ClientProtocolException)
{
- 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));
+ j.setStatus(_lex.getMessage());
return true;
}
return false;
{
if (store == null)
{
- try
- {
- store = new SlivkaDatastore(service);
- } catch (IOException e)
- {
- throw new IOError(e);
- }
+ store = new SlivkaDatastore(service);
}
}
}
return store;
}
+
+ public static AlignmentI readAlignment(RemoteFile f) throws IOException
+ {
+ final var mimetype = f.getMediaType();
+ FileFormat format;
+ if (mimetype.equals("application/clustal"))
+ format = FileFormat.Clustal;
+ else if (mimetype.equals("application/fasta"))
+ format = FileFormat.Fasta;
+ else
+ return null;
+ return new FormatAdapter().readFile(f.getContentUrl().toString(),
+ DataSourceType.URL, format);
+ }
}
git://source.jalview.org / jalview.git / blobdiff