import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
+import java.util.Arrays;
+import java.util.Collections;
import java.util.EnumMap;
import java.util.List;
+import java.util.Map;
import java.util.regex.Pattern;
+import jalview.api.FeatureColourI;
import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.io.AnnotationFile;
import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.ws.params.ArgumentI;
import jalview.ws2.api.JobStatus;
import jalview.ws2.api.WebServiceJobHandle;
import jalview.ws2.client.api.AlignmentWebServiceClientI;
+import jalview.ws2.client.api.AnnotationWebServiceClientI;
import jalview.ws2.client.api.WebServiceClientI;
import uk.ac.dundee.compbio.slivkaclient.Job;
import uk.ac.dundee.compbio.slivkaclient.Parameter;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
+import static java.lang.String.format;
+
public class SlivkaWSClient implements WebServiceClientI
{
final SlivkaService service;
final SlivkaClient client;
- SlivkaWSClient(SlivkaService service)
+ SlivkaWSClient(SlivkaClient client, SlivkaService service)
{
this.service = service;
- this.client = service.getClient();
+ this.client = client;
}
@Override
}
// pattern for matching media types
- static final Pattern mediaTypePattern = Pattern.compile("(?:text|application)\\/(?:x-)?(\\w+)");
+ static final Pattern mediaTypePattern = Pattern.compile(
+ "(?:text|application)\\/(?:x-)?([\\w-]+)");
@Override
public WebServiceJobHandle submit(List<SequenceI> sequences,
List<ArgumentI> args, Credentials credentials) throws IOException
{
- var request = new uk.ac.dundee.compbio.slivkaclient.JobRequest();
+ var request = new uk.ac.dundee.compbio.slivkaclient.RequestValues();
for (Parameter param : service.getParameters())
{
// TODO: restrict input sequences parameter name to "sequences"
}
if (format == null)
{
- Cache.log.warn(String.format(
+ Console.warn(String.format(
"Unknown input format %s, assuming fasta.",
fileParam.getMediaType()));
format = FileFormat.Fasta;
Parameter param = service.getParameter(paramId);
if (param instanceof Parameter.FlagParameter)
{
- if (arg.getValue() != null && !arg.getValue().isBlank())
+ if (arg.getValue() != null && !arg.getValue().isEmpty())
request.addData(paramId, true);
else
request.addData(paramId, false);
}
}
}
- var job = service.submitJob(request);
- return createJobHandle(job.getId());
+ var jobId = client.submitJob(service, request);
+ return createJobHandle(jobId);
}
protected WebServiceJobHandle createJobHandle(String jobId)
@Override
public JobStatus getStatus(WebServiceJobHandle job) throws IOException
{
- var slivkaJob = client.getJob(job.getJobId());
- return statusMap.getOrDefault(slivkaJob.getStatus(), JobStatus.UNKNOWN);
+ return statusMap.getOrDefault(client.fetchJobStatus(job.getJobId()), JobStatus.UNKNOWN);
}
protected static final EnumMap<Job.Status, JobStatus> statusMap = new EnumMap<>(Job.Status.class);
@Override
public String getLog(WebServiceJobHandle job) throws IOException
{
- var slivkaJob = client.getJob(job.getJobId());
- for (var f : slivkaJob.getResults())
+ for (var f : client.fetchFilesList(job.getJobId()))
{
if (f.getLabel().equals("log"))
{
ByteArrayOutputStream stream = new ByteArrayOutputStream();
- f.writeTo(stream);
- return stream.toString(StandardCharsets.UTF_8);
+ client.writeFileTo(f, stream);
+ return stream.toString("UTF-8");
}
}
return "";
@Override
public String getErrorLog(WebServiceJobHandle job) throws IOException
{
- var slivkaJob = client.getJob(job.getJobId());
- for (var f : slivkaJob.getResults())
+ for (var f : client.fetchFilesList(job.getJobId()))
{
if (f.getLabel().equals("error-log"))
{
ByteArrayOutputStream stream = new ByteArrayOutputStream();
- f.writeTo(stream);
- return stream.toString(StandardCharsets.UTF_8);
+ client.writeFileTo(f, stream);
+ return stream.toString("UTF-8");
}
}
return "";
public void cancel(WebServiceJobHandle job)
throws IOException, UnsupportedOperationException
{
- throw new UnsupportedOperationException(
+ Console.warn(
"slivka client does not support job cancellation");
}
}
implements AlignmentWebServiceClientI
{
- SlivkaAlignmentWSClient(SlivkaService service)
+ SlivkaAlignmentWSClient(SlivkaClient client, SlivkaService service)
{
- super(service);
+ super(client, service);
}
@Override
public AlignmentI getAlignment(WebServiceJobHandle job) throws IOException
{
- var slivkaJob = client.getJob(job.getJobId());
- for (var f : slivkaJob.getResults())
+ for (var f : client.fetchFilesList(job.getJobId()))
{
// TODO: restrict result file label to "alignment"
FileFormat format;
return new FormatAdapter().readFile(f.getContentUrl().toString(),
DataSourceType.URL, format);
}
- Cache.log.warn("No alignment found on the server");
+ Console.warn("No alignment found on the server");
throw new IOException("no alignment found");
}
-}
\ No newline at end of file
+}
+
+class SlivkaAnnotationWSClient extends SlivkaWSClient
+ implements AnnotationWebServiceClientI
+{
+ SlivkaAnnotationWSClient(SlivkaClient client, SlivkaService service)
+ {
+ super(client, service);
+ }
+
+ @Override
+ public List<AlignmentAnnotation> attachAnnotations(WebServiceJobHandle job,
+ List<SequenceI> sequences, Map<String, FeatureColourI> colours,
+ Map<String, FeatureMatcherSetI> filters) throws IOException
+ {
+ var aln = new Alignment(sequences.toArray(new SequenceI[sequences.size()]));
+ boolean featPresent = false, annotPresent = false;
+ for (var f : client.fetchFilesList(job.getJobId()))
+ {
+ // TODO: restrict file label to "annotations" or "features"
+ var match = mediaTypePattern.matcher(f.getMediaType());
+ if (!match.find())
+ continue;
+ String fmt = match.group(1);
+ if (fmt.equalsIgnoreCase("jalview-annotations"))
+ {
+ annotPresent = new AnnotationFile().readAnnotationFileWithCalcId(
+ aln, service.getId(), f.getContentUrl().toString(),
+ DataSourceType.URL);
+ if (annotPresent)
+ Console.debug(format("loaded annotations for %s", service.getId()));
+ }
+ else if (fmt.equalsIgnoreCase("jalview-features"))
+ {
+ FeaturesFile ff = new FeaturesFile(f.getContentUrl().toString(),
+ DataSourceType.URL);
+ featPresent = ff.parse(aln, colours, true);
+ if (featPresent)
+ Console.debug(format("loaded features for %s", service.getId()));
+ }
+ }
+ if (!annotPresent)
+ Console.debug(format("no annotations found for %s", service.getId()));
+ if (!featPresent)
+ Console.debug(format("no features found for %s", service.getId()));
+ return aln.getAlignmentAnnotation() != null ? Arrays.asList(aln.getAlignmentAnnotation())
+ : Collections.emptyList();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff