package jalview.ws.slivkaws;
-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.JobId;
-import jalview.ws.api.MultipleSequenceAlignmentI;
+import jalview.ws.api.JalviewWebServiceI;
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.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 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;
- private EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
+ 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.QUEUED, WsJob.JobState.QUEUED);
stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
}
- SlivkaWSInstance(SlivkaClient client, SlivkaService service) {
- super(service.getName(), "Alignment", service.getName(), "Slivka", client.getUrl().toString());
+ public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
+ {
+ super(service.getLabel(), action, service.getName(), "Slivka",
+ client.getUrl().toString());
this.client = client;
this.service = service;
}
@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)
{
return false;
}
@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;
}
+
}