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.Optional;
+import java.util.Set;
+
import jalview.datamodel.AlignmentI;
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.MultipleSequenceAlignmentI;
import jalview.ws.api.ServiceWithParameters;
import jalview.ws.gui.WsJob;
import jalview.ws.params.ArgumentI;
-import jalview.ws.params.InvalidArgumentException;
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.rmi.ServerError;
-import java.util.EnumMap;
-import java.util.HashMap;
-import java.util.List;
-
+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.SlivkaService;
import uk.ac.dundee.compbio.slivkaclient.ValidationException;
-public class SlivkaWSInstance extends ServiceWithParameters
- implements MultipleSequenceAlignmentI, JalviewServiceEndpointProviderI
+public abstract class SlivkaWSInstance extends ServiceWithParameters
+ implements JalviewServiceEndpointProviderI, JalviewWebServiceI
{
- private SlivkaClient client;
- private SlivkaService service;
- private SlivkaDatastore store = null;
+ protected final SlivkaClient client;
+
+ protected final SlivkaService service;
+
+ protected SlivkaDatastore store = null;
- private EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
+ 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
+ ));
- SlivkaWSInstance(SlivkaClient client, SlivkaService service) {
- super(service.getName(), "Alignment", service.getName(), "Slivka", client.getUrl().toString());
+ public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
+ {
+ 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 void updateStatus(WsJob job)
+ public final void updateStatus(WsJob job)
{
try
{
job.setState(stateMap.get(client.getJobState(job.getJobId())));
} catch (IOException e)
{
- throw new RuntimeException(e);
+ throw new IOError(e);
}
}
- SlivkaService getService()
- {
- return service;
- }
-
@Override
- public 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
- public boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
+ public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
{
if (_lex instanceof FormValidationException)
{
}
@Override
- public boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
+ public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
{
+ // TODO
return false;
}
- @Override
- public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
+ final SlivkaService getService()
{
- StringBuilder builder = new StringBuilder();
- for (SequenceI seq : toalign)
- {
- builder.append(">").append(seq.getName()).append("\n");
- builder.append(seq.getSequence()).append("\n");
- }
- InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
- RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
- SlivkaForm form = service.getForm();
- HashMap<String, String> values = new HashMap<>(list != null ? list.size() : 0);
- if (list != null)
- {
- for (ArgumentI arg : list)
- {
- values.put(arg.getName(), arg.getValue());
- }
- }
- for (FormField field : form.getFields())
- {
- switch (field.getType()) {
- case FILE:
- form.insert(field.getName(), file);
- break;
- case BOOLEAN:
- String value = values.get(field.getName());
- form.insert(field.getName(), (value != null && !value.isBlank()) ? true : false);
- break;
- default:
- form.insert(field.getName(), field.valueOf(values.get(field.getName())));
- }
- }
- return new JobId(service.getName(), service.getName(), form.submit());
- }
-
- @Override
- public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
- {
- List<RemoteFile> files;
- try
- {
- files = client.getJobResults(jobId.getJobId());
- for (RemoteFile f : files)
- {
- if (f.getMimeType().equals("application/clustal"))
- {
- return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
- }
- else if (f.getMimeType().equals("application/fasta"))
- {
- return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
- }
- }
- } catch (IOException e)
- {
- throw new IOError(e);
- }
- return null;
+ return service;
}
@Override
- public Object getEndpoint()
+ public final Object getEndpoint()
{
return this;
}
@Override
- public void initParamStore(ParamManager userParameterStore)
+ public final void initParamStore(ParamManager userParameterStore)
{
if (store == null)
{
}
@Override
- public ParamDatastoreI getParamStore()
+ public final ParamDatastoreI getParamStore()
{
+ if (store == null)
+ {
+ initParamStore(null);
+ }
return store;
}
+
+ public static AlignmentI readAlignment(RemoteFile f) throws IOException
+ {
+ final var mimetype = f.getMimeType();
+ 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.getURL().toString(),
+ DataSourceType.URL, format);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff