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JAL-3848 Update slivka client library.
[jalview.git]
/
src
/
jalview
/
ws
/
slivkaws
/
SlivkaMsaServiceInstance.java
diff --git
a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
index
9a33b04
..
03dda3f
100644
(file)
--- a/
src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
+++ b/
src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
@@
-1,5
+1,6
@@
package jalview.ws.slivkaws;
package jalview.ws.slivkaws;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
@@
-14,6
+15,7
@@
import jalview.ws.params.WsParamSetI;
import java.io.IOError;
import java.io.IOException;
import java.rmi.ServerError;
import java.io.IOError;
import java.io.IOException;
import java.rmi.ServerError;
+import java.util.Collection;
import java.util.List;
import compbio.data.msa.Category;
import java.util.List;
import compbio.data.msa.Category;
@@
-37,19
+39,20
@@
public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements Multip
@Override
public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
{
@Override
public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
{
- List<RemoteFile> files;
+ Collection<RemoteFile> files;
try
{
try
{
- files = client.getJobResults(jobId.getJobId());
+ var slivkaJob = client.getJob(jobId.getJobId());
+ files = slivkaJob.getResults();
for (RemoteFile f : files)
{
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)
}
}
} catch (IOException e)