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.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.ws.api.JalviewServiceEndpointProviderI;
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.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;
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.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);
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;
}
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();
+ 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;
}
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);
+ }
}