1 package jalview.ws.slivkaws;
3 import jalview.gui.WebserviceInfo;
4 import jalview.ws.api.JalviewServiceEndpointProviderI;
5 import jalview.ws.api.JalviewWebServiceI;
6 import jalview.ws.api.ServiceWithParameters;
7 import jalview.ws.gui.WsJob;
8 import jalview.ws.params.ParamDatastoreI;
9 import jalview.ws.params.ParamManager;
11 import java.io.IOError;
12 import java.io.IOException;
13 import java.io.InputStream;
14 import java.io.InputStreamReader;
15 import java.util.Arrays;
16 import java.util.EnumMap;
17 import java.util.HashSet;
18 import java.util.Optional;
21 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
22 import uk.ac.dundee.compbio.slivkaclient.JobState;
23 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
24 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
25 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
26 import uk.ac.dundee.compbio.slivkaclient.ValidationException;
28 public abstract class SlivkaWSInstance extends ServiceWithParameters
29 implements JalviewServiceEndpointProviderI, JalviewWebServiceI
31 protected final SlivkaClient client;
33 protected final SlivkaService service;
35 protected SlivkaDatastore store = null;
37 protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
39 stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
40 stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
41 stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
42 stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
43 stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
44 stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
45 stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
47 protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
48 WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
49 WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
52 public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
54 super(service.getName(), action, service.getLabel(), "Slivka", client.getUrl().toString());
56 this.service = service;
60 public final void updateStatus(WsJob job)
64 job.setState(stateMap.get(client.getJobState(job.getJobId())));
65 } catch (IOException e)
72 public final boolean updateJobProgress(WsJob job) throws IOException
74 Optional<RemoteFile> logFile = client.getJobResults(job.getJobId()).stream()
75 .filter(f -> f.getLabel() == "log").findFirst();
76 if (logFile.isPresent())
78 InputStream stream = logFile.get().getContent();
79 long nextChunk = stream.skip(job.getNextChunk());
80 job.setnextChunk(nextChunk + appendJobStatus(job, stream));
82 if (failedStates.contains(job.getJobState()))
84 Optional<RemoteFile> errLogFile = client.getJobResults(job.getJobId()).stream()
85 .filter(f -> f.getLabel() == "error-log").findFirst();
86 if (errLogFile.isPresent())
88 appendJobStatus(job, errLogFile.get().getContent());
94 private int appendJobStatus(WsJob job, InputStream stream) throws IOException
96 StringBuilder builder = new StringBuilder(job.getStatus());
97 InputStreamReader reader = new InputStreamReader(stream);
98 char[] buffer = new char[4096];
101 while ((len = reader.read(buffer)) != -1)
104 builder.append(buffer, 0, len);
106 job.setStatus(builder.toString());
111 public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
113 if (_lex instanceof FormValidationException)
115 FormValidationException formError = (FormValidationException) _lex;
116 String[] messages = new String[formError.getErrors().size()];
118 for (ValidationException e : formError.getErrors())
120 messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
122 j.setState(WsJob.JobState.INVALID);
123 j.setStatus(String.join(", ", messages));
130 public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
136 final SlivkaService getService()
142 public final Object getEndpoint()
148 public final void initParamStore(ParamManager userParameterStore)
154 store = new SlivkaDatastore(service);
155 } catch (IOException e)
157 throw new IOError(e);
163 public boolean hasParameters()
169 public final ParamDatastoreI getParamStore()
173 initParamStore(null);