package jalview.ws.slivkaws;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.ws.params.InvalidArgumentException;
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.Collection;
import java.util.List;
-import java.util.Optional;
-import uk.ac.dundee.compbio.slivkaclient.FieldType;
-import uk.ac.dundee.compbio.slivkaclient.FormField;
+import compbio.data.msa.Category;
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;
public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
{
- SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service) {
- super(client, service, "Sequence Alignment");
+ SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
+ super(client, service, category);
style = ServiceClient.MSAWSCLIENT;
}
@Override
public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
{
- 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();
- Optional<FormField> inputField = form.getFields().stream()
- .filter(f -> f.getType() == FieldType.FILE).findFirst();
- if (inputField.isPresent())
- {
- form.insert(inputField.get().getName(), file);
- }
- if (list != null)
- {
- for (ArgumentI arg : list)
- {
- FormField field = form.getField(arg.getName());
- if (field.getType() == FieldType.BOOLEAN)
- {
- form.insert(arg.getName(), (arg.getValue() != null && !arg.getValue().isBlank()) ? true : false);
- }
- else
- {
- form.insert(arg.getName(), field.valueOf(arg.getValue()));
- }
- }
- }
- return new JobId(service.getName(), service.getName(), form.submit());
+ return super.submit(toalign, parameters, list);
}
@Override
public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
{
- List<RemoteFile> files;
+ Collection<RemoteFile> files;
try
{
- files = client.getJobResults(jobId.getJobId());
+ var slivkaJob = client.getJob(jobId.getJobId());
+ files = slivkaJob.getResults();
for (RemoteFile f : files)
{
- if (f.getMimeType().equals("application/clustal"))
+ if (f.getMediaType().equals("application/clustal"))
{
- return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
+ return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Clustal);
}
- else if (f.getMimeType().equals("application/fasta"))
+ else if (f.getMediaType().equals("application/fasta"))
{
- return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
+ return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Fasta);
}
}
} catch (IOException e)