1 package jalview.ws.slivkaws;
3 import jalview.datamodel.SequenceI;
4 import jalview.gui.WebserviceInfo;
5 import jalview.ws.api.JalviewServiceEndpointProviderI;
6 import jalview.ws.api.JalviewWebServiceI;
7 import jalview.ws.api.JobId;
8 import jalview.ws.api.ServiceWithParameters;
9 import jalview.ws.gui.WsJob;
10 import jalview.ws.params.ArgumentI;
11 import jalview.ws.params.ParamDatastoreI;
12 import jalview.ws.params.ParamManager;
13 import jalview.ws.params.WsParamSetI;
15 import java.io.ByteArrayInputStream;
16 import java.io.IOError;
17 import java.io.IOException;
18 import java.io.InputStream;
19 import java.io.InputStreamReader;
20 import java.util.Arrays;
21 import java.util.EnumMap;
22 import java.util.HashSet;
23 import java.util.List;
24 import java.util.Optional;
27 import uk.ac.dundee.compbio.slivkaclient.FieldType;
28 import uk.ac.dundee.compbio.slivkaclient.FormField;
29 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
30 import uk.ac.dundee.compbio.slivkaclient.JobState;
31 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
32 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
33 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
34 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
35 import uk.ac.dundee.compbio.slivkaclient.ValidationException;
37 public abstract class SlivkaWSInstance extends ServiceWithParameters
38 implements JalviewServiceEndpointProviderI, JalviewWebServiceI
40 protected final SlivkaClient client;
42 protected final SlivkaService service;
44 protected SlivkaDatastore store = null;
46 protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
48 stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
49 stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
50 stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
51 stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
52 stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
53 stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
54 stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
56 protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
57 WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
58 WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
61 public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
63 super(service.getName(), action, service.getLabel(), "Slivka", client.getUrl().toString());
65 this.service = service;
68 protected final JobId submit(List<SequenceI> sequences,
69 WsParamSetI preset, List<ArgumentI> args) throws Throwable
71 SlivkaForm form = service.getForm();
72 Optional<FormField> inputField = form.getFields().stream()
73 .filter(f -> f.getType() == FieldType.FILE).findFirst();
74 if (inputField.isPresent())
76 StringBuilder builder = new StringBuilder();
77 for (SequenceI seq : sequences)
79 builder.append(">").append(seq.getName()).append("\n")
80 .append(seq.getSequence()).append("\n");
82 InputStream stream = new ByteArrayInputStream(
83 builder.toString().getBytes());
84 RemoteFile file = client.uploadFile(stream, "input.fa",
86 form.insert(inputField.get().getName(), file);
90 for (ArgumentI arg : args)
92 String fieldName = arg.getName().split("\\$", 2)[0];
93 FormField field = form.getField(fieldName);
94 if (field.getType() == FieldType.BOOLEAN)
96 form.insert(fieldName,
97 (arg.getValue() != null && !arg.getValue().isBlank())
103 form.insert(fieldName, field.valueOf(arg.getValue()));
107 return new JobId(service.getName(), service.getName(), form.submit());
111 public final void updateStatus(WsJob job)
115 job.setState(stateMap.get(client.getJobState(job.getJobId())));
116 } catch (IOException e)
118 throw new IOError(e);
123 public final boolean updateJobProgress(WsJob job) throws IOException
125 List<RemoteFile> files = client.getJobResults(job.getJobId());
126 Optional<RemoteFile> logFile = files.stream()
127 .filter(f -> f.getLabel().equals("log")).findFirst();
128 boolean newContent = false;
129 if (logFile.isPresent())
131 InputStream stream = logFile.get().getContent();
132 long nextChunk = stream.skip(job.getNextChunk());
133 int len = appendJobStatus(job, stream);
134 job.setnextChunk(nextChunk + len);
135 newContent |= len > 0;
137 if (failedStates.contains(job.getJobState()))
139 Optional<RemoteFile> errLogFile = files.stream()
140 .filter(f -> f.getLabel().equals("error-log")).findFirst();
141 if (errLogFile.isPresent())
143 newContent |= appendJobStatus(job, errLogFile.get().getContent()) > 0;
149 private int appendJobStatus(WsJob job, InputStream stream) throws IOException
151 StringBuilder builder = new StringBuilder(job.getStatus());
152 InputStreamReader reader = new InputStreamReader(stream);
153 char[] buffer = new char[4096];
156 while ((len = reader.read(buffer)) != -1)
159 builder.append(buffer, 0, len);
161 job.setStatus(builder.toString());
166 public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
168 if (_lex instanceof FormValidationException)
170 FormValidationException formError = (FormValidationException) _lex;
171 String[] messages = new String[formError.getErrors().size()];
173 for (ValidationException e : formError.getErrors())
175 messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
177 j.setState(WsJob.JobState.INVALID);
178 j.setStatus(String.join(", ", messages));
185 public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
191 final SlivkaService getService()
197 public final Object getEndpoint()
203 public final void initParamStore(ParamManager userParameterStore)
209 store = new SlivkaDatastore(service);
210 } catch (IOException e)
212 throw new IOError(e);
218 public boolean hasParameters()
224 public final ParamDatastoreI getParamStore()
228 initParamStore(null);