1 package jalview.ws2.slivka;
3 import java.io.ByteArrayInputStream;
4 import java.io.ByteArrayOutputStream;
5 import java.io.IOException;
6 import java.io.InputStream;
7 import java.util.ArrayList;
8 import java.util.Arrays;
9 import java.util.Collection;
10 import java.util.EnumMap;
11 import java.util.HashSet;
12 import java.util.List;
15 import jalview.api.AlignViewportI;
16 import jalview.bin.Cache;
17 import jalview.datamodel.Alignment;
18 import jalview.datamodel.AlignmentAnnotation;
19 import jalview.datamodel.AlignmentI;
20 import jalview.datamodel.SequenceI;
21 import jalview.io.AnnotationFile;
22 import jalview.io.DataSourceType;
23 import jalview.io.FeaturesFile;
24 import jalview.io.FileFormat;
25 import jalview.io.FileFormatI;
26 import jalview.io.FormatAdapter;
27 import jalview.ws.gui.WsJob;
28 import jalview.ws.params.ArgumentI;
29 import jalview.ws.params.ParamDatastoreI;
30 import jalview.ws.params.WsParamSetI;
31 import jalview.ws.slivkaws.SlivkaDatastore;
32 import jalview.ws2.WebServiceI;
33 import jalview.ws2.operations.Operation;
34 import jalview.ws2.ResultSupplier;
35 import jalview.ws2.WSJob;
36 import jalview.ws2.WSJobStatus;
37 import javajs.http.ClientProtocolException;
38 import uk.ac.dundee.compbio.slivkaclient.Job;
39 import uk.ac.dundee.compbio.slivkaclient.Parameter;
40 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
41 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
42 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
44 public class SlivkaWebService implements WebServiceI
46 protected final SlivkaClient client;
48 protected final SlivkaService service;
50 protected SlivkaDatastore store = null;
52 protected final ArrayList<Operation> operations = new ArrayList<>();
54 protected int typeFlags = 0;
56 protected static final EnumMap<Job.Status, WSJobStatus> statusMap = new EnumMap<>(
59 statusMap.put(Job.Status.PENDING, WSJobStatus.SUBMITTED);
60 statusMap.put(Job.Status.REJECTED, WSJobStatus.INVALID);
61 statusMap.put(Job.Status.ACCEPTED, WSJobStatus.QUEUED);
62 statusMap.put(Job.Status.QUEUED, WSJobStatus.QUEUED);
63 statusMap.put(Job.Status.RUNNING, WSJobStatus.RUNNING);
64 statusMap.put(Job.Status.COMPLETED, WSJobStatus.FINISHED);
65 statusMap.put(Job.Status.INTERRUPTED, WSJobStatus.CANCELLED);
66 statusMap.put(Job.Status.DELETED, WSJobStatus.CANCELLED);
67 statusMap.put(Job.Status.FAILED, WSJobStatus.FAILED);
68 statusMap.put(Job.Status.ERROR, WSJobStatus.SERVER_ERROR);
69 statusMap.put(Job.Status.UNKNOWN, WSJobStatus.UNKNOWN);
72 public SlivkaWebService(SlivkaClient client, SlivkaService service)
75 this.service = service;
79 public String getHostName()
81 return client.getUrl().toString();
85 public String getProviderName()
91 public String getName()
93 return service.getName();
97 public String getDescription()
99 return service.getDescription();
103 public List<Operation> getOperations()
108 void addOperation(Operation operation)
110 operations.add(operation);
113 void removeOperation(Operation operation)
115 operations.remove(operation);
119 public boolean hasParameters()
121 return getParamStore().getServiceParameters().size() > 0;
125 public ParamDatastoreI getParamStore()
129 store = new SlivkaDatastore(service);
135 public String submit(List<SequenceI> sequences, List<ArgumentI> args)
138 var request = new uk.ac.dundee.compbio.slivkaclient.JobRequest();
139 for (Parameter param : service.getParameters())
141 if (param instanceof Parameter.FileParameter)
143 // if finds a file input, gives it sequences stream
144 Parameter.FileParameter fileParam = (Parameter.FileParameter) param;
146 switch (fileParam.getMediaType())
148 case "application/pfam":
149 format = FileFormat.Pfam;
151 case "application/stockholm":
152 format = FileFormat.Stockholm;
154 case "application/clustal":
155 format = FileFormat.Clustal;
157 case "application/fasta":
159 format = FileFormat.Fasta;
162 InputStream stream = new ByteArrayInputStream(format.getWriter(null)
163 .print(sequences.toArray(new SequenceI[0]), false)
165 request.addFile(param.getId(), stream);
170 for (ArgumentI arg : args)
172 // multiple choice field names are name$number to avoid duplications
173 // the number is stripped here
174 String paramId = arg.getName().split("\\$", 2)[0];
175 Parameter param = service.getParameter(paramId);
176 if (param instanceof Parameter.FlagParameter)
178 if (arg.getValue() != null && !arg.getValue().isBlank())
179 request.addData(paramId, true);
181 request.addData(paramId, false);
185 request.addData(paramId, arg.getValue());
189 var job = service.submitJob(request);
194 public void updateProgress(WSJob job) throws IOException
196 var slivkaJob = client.getJob(job.getJobId());
197 job.setStatus(statusMap.get(slivkaJob.getStatus()));
198 Collection<RemoteFile> files = slivkaJob.getResults();
199 for (RemoteFile f : files)
201 if (f.getLabel().equals("log"))
203 ByteArrayOutputStream stream = new ByteArrayOutputStream();
205 job.setLog(stream.toString("UTF-8"));
207 else if (f.getLabel().equals("error-log"))
209 ByteArrayOutputStream stream = new ByteArrayOutputStream();
211 job.setErrorLog(stream.toString("UTF-8"));
217 public void cancel(WSJob job) throws IOException
219 job.setStatus(WSJobStatus.CANCELLED);
220 Cache.log.warn("Slivka does not support job cancellation yet.");
224 public boolean handleSubmissionError(WSJob job, Exception ex)
226 if (ex instanceof ClientProtocolException)
228 Cache.log.error("Job submission failed due to exception.", ex);
235 public boolean handleCollectionError(WSJob job, Exception ex)
237 // TODO Auto-generated method stub
241 public AlignmentI getAlignment(WSJob job, List<SequenceI> dataset,
242 AlignViewportI viewport) throws IOException
244 Collection<RemoteFile> files;
245 var slivkaJob = client.getJob(job.getJobId());
246 files = slivkaJob.getResults();
247 for (RemoteFile f : files)
249 if (f.getMediaType().equals("application/clustal"))
251 return new FormatAdapter().readFile(f.getContentUrl().toString(),
252 DataSourceType.URL, FileFormat.Clustal);
254 else if (f.getMediaType().equals("application/fasta"))
256 return new FormatAdapter().readFile(f.getContentUrl().toString(),
257 DataSourceType.URL, FileFormat.Fasta);
263 public FeaturesFile getFeaturesFile(WSJob job,
264 List<SequenceI> dataset, AlignViewportI viewport) throws IOException
266 var slivkaJob = client.getJob(job.getJobId());
267 Collection<RemoteFile> files = slivkaJob.getResults();
268 for (RemoteFile f : files)
270 if (f.getMediaType().equals("application/jalview-features"))
272 return new FeaturesFile(f.getContentUrl().toString(), DataSourceType.URL);
278 public List<AlignmentAnnotation> getAnnotations(WSJob job,
279 List<SequenceI> dataset, AlignViewportI viewport) throws IOException
281 var slivkaJob = client.getJob(job.getJobId());
282 Collection<RemoteFile> files = slivkaJob.getResults();
283 for (RemoteFile f : files)
285 if (f.getMediaType().equals("application/jalview-annotations"))
287 Alignment aln = new Alignment(dataset.toArray(new SequenceI[0]));
288 AnnotationFile af = new AnnotationFile();
289 boolean valid = af.readAnnotationFileWithCalcId(aln, service.getId(),
290 f.getContentUrl().toString(), DataSourceType.URL);
293 return Arrays.asList(aln.getAlignmentAnnotation());
297 throw new IOException("Unable to read annotations from file " +
298 f.getContentUrl().toString());
306 public String toString()
308 return String.format("SlivkaWebService[%s]", getName());