1 package jalview.ws.slivkaws;
3 import java.io.ByteArrayInputStream;
4 import java.io.ByteArrayOutputStream;
5 import java.io.IOError;
6 import java.io.IOException;
7 import java.io.InputStream;
8 import java.util.Arrays;
9 import java.util.EnumMap;
10 import java.util.HashSet;
11 import java.util.List;
12 import java.util.Optional;
15 import jalview.datamodel.AlignmentI;
16 import jalview.datamodel.SequenceI;
17 import jalview.gui.WebserviceInfo;
18 import jalview.io.DataSourceType;
19 import jalview.io.FileFormat;
20 import jalview.io.FormatAdapter;
21 import jalview.ws.api.JalviewServiceEndpointProviderI;
22 import jalview.ws.api.JalviewWebServiceI;
23 import jalview.ws.api.JobId;
24 import jalview.ws.api.ServiceWithParameters;
25 import jalview.ws.gui.WsJob;
26 import jalview.ws.params.ArgumentI;
27 import jalview.ws.params.ParamDatastoreI;
28 import jalview.ws.params.ParamManager;
29 import jalview.ws.params.WsParamSetI;
30 import uk.ac.dundee.compbio.slivkaclient.FieldType;
31 import uk.ac.dundee.compbio.slivkaclient.FormField;
32 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
33 import uk.ac.dundee.compbio.slivkaclient.JobState;
34 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
35 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
36 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
37 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
38 import uk.ac.dundee.compbio.slivkaclient.ValidationException;
40 public abstract class SlivkaWSInstance extends ServiceWithParameters
41 implements JalviewServiceEndpointProviderI, JalviewWebServiceI
43 protected final SlivkaClient client;
45 protected final SlivkaService service;
47 protected SlivkaDatastore store = null;
49 protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
51 stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
52 stateMap.put(JobState.REJECTED, WsJob.JobState.INVALID);
53 stateMap.put(JobState.ACCEPTED, WsJob.JobState.QUEUED);
54 stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
55 stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
56 stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
57 stateMap.put(JobState.INTERRUPTED, WsJob.JobState.CANCELLED);
58 stateMap.put(JobState.DELETED, WsJob.JobState.CANCELLED);
59 stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
60 stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
61 stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
63 protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
64 WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
65 WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
68 public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
70 super(action, action, service.getLabel(), "Slivka", client.getUrl().toString());
72 this.service = service;
75 protected final JobId submit(List<SequenceI> sequences,
76 WsParamSetI preset, List<ArgumentI> args) throws Throwable
78 SlivkaForm form = service.getForm();
79 Optional<FormField> inputField = form.getFields().stream()
80 .filter(f -> f.getType() == FieldType.FILE).findFirst();
81 if (inputField.isPresent())
83 StringBuilder builder = new StringBuilder();
84 for (SequenceI seq : sequences)
86 builder.append(">").append(seq.getName()).append("\n")
87 .append(seq.getSequence()).append("\n");
89 InputStream stream = new ByteArrayInputStream(
90 builder.toString().getBytes());
91 RemoteFile file = client.uploadFile(stream, "input.fa",
93 form.insert(inputField.get().getName(), file);
97 for (ArgumentI arg : args)
99 // multiple choice field names are name$number to avoid duplications
100 // the number is stripped here
101 String fieldName = arg.getName().split("\\$", 2)[0];
102 FormField field = form.getField(fieldName);
103 if (field.getType() == FieldType.BOOLEAN)
105 form.insert(fieldName,
106 (arg.getValue() != null && !arg.getValue().isBlank())
112 form.insert(fieldName, arg.getValue());
116 return new JobId(service.getName(), service.getName(), form.submit());
120 public final void updateStatus(WsJob job)
124 job.setState(stateMap.get(client.getJobState(job.getJobId())));
125 } catch (IOException e)
127 throw new IOError(e);
132 public final boolean updateJobProgress(WsJob job) throws IOException
134 List<RemoteFile> files = client.getJobResults(job.getJobId());
135 RemoteFile logFile=null;
136 for (RemoteFile f : files)
138 if (f.getLabel().equals("log"))
144 boolean newContent = false;
147 ByteArrayOutputStream output = new ByteArrayOutputStream();
148 logFile.writeTo(output);
149 if (output.size() > job.getNextChunk())
152 job.setStatus(output.toString("UTF-8"));
153 job.setnextChunk(output.size());
156 if (failedStates.contains(job.getJobState()))
159 RemoteFile errLogFile = null;
160 for (RemoteFile f : files)
162 if (f.getLabel().equals("error-log"))
169 if (errLogFile!=null)
171 ByteArrayOutputStream output = new ByteArrayOutputStream();
172 errLogFile.writeTo(output);
173 if (output.size() > 0)
176 job.setStatus(job.getStatus() + "\n" + output.toString("UTF-8"));
184 public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
186 if (_lex instanceof FormValidationException)
188 FormValidationException formError = (FormValidationException) _lex;
189 String[] messages = new String[formError.getErrors().size()];
191 for (ValidationException e : formError.getErrors())
193 messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
195 j.setState(WsJob.JobState.INVALID);
196 j.setStatus(String.join(", ", messages));
203 public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
209 final SlivkaService getService()
215 public final Object getEndpoint()
221 public final void initParamStore(ParamManager userParameterStore)
227 store = new SlivkaDatastore(service);
228 } catch (IOException e)
230 throw new IOError(e);
236 public boolean hasParameters()
242 public final ParamDatastoreI getParamStore()
246 initParamStore(null);
251 public static AlignmentI readAlignment(RemoteFile f) throws IOException
253 final var mimetype = f.getMimeType();
255 if (mimetype == "application/clustal")
256 format = FileFormat.Clustal;
257 else if (mimetype == "application/fasta")
258 format = FileFormat.Fasta;
261 return new FormatAdapter().readFile(f.getURL().toString(),
262 DataSourceType.URL, format);