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Coverage Report

  1. Project Clover database Wed Dec 3 2025 17:03:17 GMT
  2. Package jalview.ws.slivkaws

File SlivkaWSInstance.java

 

Coverage histogram

../../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

32
98
13
1
266
237
34
0.35
7.54
13
2.62

Classes

Class Line # Actions
SlivkaWSInstance 39 98 34
0.00%
 

Contributing tests

No tests hitting this source file were found.

Source view

1    package jalview.ws.slivkaws;
2   
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.Set;
13   
14    import jalview.datamodel.AlignmentI;
15    import jalview.datamodel.SequenceI;
16    import jalview.gui.WebserviceInfo;
17    import jalview.io.DataSourceType;
18    import jalview.io.FileFormat;
19    import jalview.io.FormatAdapter;
20    import jalview.ws.api.JalviewServiceEndpointProviderI;
21    import jalview.ws.api.JalviewWebServiceI;
22    import jalview.ws.api.JobId;
23    import jalview.ws.api.ServiceWithParameters;
24    import jalview.ws.gui.WsJob;
25    import jalview.ws.params.ArgumentI;
26    import jalview.ws.params.ParamDatastoreI;
27    import jalview.ws.params.ParamManager;
28    import jalview.ws.params.WsParamSetI;
29    import javajs.http.ClientProtocolException;
30   
31    import java.util.Collection;
32    import uk.ac.dundee.compbio.slivkaclient.Job;
33    import uk.ac.dundee.compbio.slivkaclient.RequestValues;
34    import uk.ac.dundee.compbio.slivkaclient.Parameter;
35    import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
36    import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
37    import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
38   
 
39    public abstract class SlivkaWSInstance extends ServiceWithParameters
40    implements JalviewServiceEndpointProviderI, JalviewWebServiceI
41    {
42    protected final SlivkaClient client;
43   
44    protected final SlivkaService service;
45   
46    protected SlivkaDatastore store = null;
47   
48    protected static final EnumMap<Job.Status, WsJob.JobState> stateMap = new EnumMap<>(Job.Status.class);
 
49  0 toggle {
50  0 stateMap.put(Job.Status.PENDING, WsJob.JobState.QUEUED);
51  0 stateMap.put(Job.Status.REJECTED, WsJob.JobState.INVALID);
52  0 stateMap.put(Job.Status.ACCEPTED, WsJob.JobState.QUEUED);
53  0 stateMap.put(Job.Status.QUEUED, WsJob.JobState.QUEUED);
54  0 stateMap.put(Job.Status.RUNNING, WsJob.JobState.RUNNING);
55  0 stateMap.put(Job.Status.COMPLETED, WsJob.JobState.FINISHED);
56  0 stateMap.put(Job.Status.INTERRUPTED, WsJob.JobState.CANCELLED);
57  0 stateMap.put(Job.Status.DELETED, WsJob.JobState.CANCELLED);
58  0 stateMap.put(Job.Status.FAILED, WsJob.JobState.FAILED);
59  0 stateMap.put(Job.Status.ERROR, WsJob.JobState.SERVERERROR);
60  0 stateMap.put(Job.Status.UNKNOWN, WsJob.JobState.UNKNOWN);
61    }
62    protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
63    WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
64    WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
65    ));
66   
 
67  0 toggle public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
68    {
69  0 super(action, action, service.getName(), "Slivka", client.getUrl().toString());
70  0 this.client = client;
71  0 this.service = service;
72    }
73   
 
74  0 toggle protected final JobId submit(List<SequenceI> sequences,
75    WsParamSetI preset, List<ArgumentI> args) throws Throwable
76    {
77  0 var parameters = service.getParameters();
78  0 var request = new RequestValues();
79  0 for (Parameter param : parameters)
80    {
81  0 if (param instanceof Parameter.FileParameter)
82    {
83  0 FormatAdapter fa = new FormatAdapter();
84  0 fa.setNewlineString("\r\n");
85  0 Parameter.FileParameter fileParam = (Parameter.FileParameter) param;
86  0 FileFormat format;
87  0 switch (fileParam.getMediaType())
88    {
89  0 case "application/pfam":
90  0 format = FileFormat.Pfam;
91  0 break;
92  0 case "application/stockholm":
93  0 format = FileFormat.Stockholm;
94  0 break;
95  0 default:
96  0 case "application/fasta":
97  0 format = FileFormat.Fasta;
98  0 break;
99    }
100   
101    // we avoid any use of Jalview's user facing export routines here
102   
103  0 InputStream stream = new ByteArrayInputStream(format.getWriter(null)
104    .print(sequences.toArray(new SequenceI[0]), false)
105    .getBytes());
106  0 request.addFile(param.getId(), stream);
107    }
108    }
109  0 if (args != null)
110    {
111  0 for (ArgumentI arg : args)
112    {
113    // multiple choice field names are name$number to avoid duplications
114    // the number is stripped here
115  0 String paramId = arg.getName().split("\\$", 2)[0];
116  0 Parameter param = service.getParameter(paramId);
117  0 if (param instanceof Parameter.FlagParameter) {
118  0 if (arg.getValue() != null && !arg.getValue().isBlank())
119  0 request.addData(paramId, true);
120    else
121  0 request.addData(paramId, false);
122    }
123    else
124    {
125  0 request.addData(paramId, arg.getValue());
126    }
127    }
128    }
129  0 var jobId = client.submitJob(service, request);
130  0 return new JobId(service.getName(), service.getName(), jobId);
131    }
132   
 
133  0 toggle @Override
134    public final void updateStatus(WsJob job)
135    {
136  0 try
137    {
138  0 job.setState(stateMap.get(client.fetchJobStatus(job.getJobId())));
139    } catch (IOException e)
140    {
141  0 throw new IOError(e);
142    }
143    }
144   
 
145  0 toggle @Override
146    public final boolean updateJobProgress(WsJob job) throws IOException
147    {
148  0 Collection<RemoteFile> files = client.fetchFilesList(job.getJobId());
149  0 RemoteFile logFile=null;
150  0 for (RemoteFile f : files)
151    {
152  0 if (f.getLabel().equals("log"))
153    {
154  0 logFile = f; break;
155    }
156    }
157   
158  0 boolean newContent = false;
159  0 if (logFile!=null)
160    {
161  0 ByteArrayOutputStream output = new ByteArrayOutputStream();
162  0 client.writeFileTo(logFile, output);
163  0 if (output.size() > job.getNextChunk())
164    {
165  0 newContent = true;
166  0 job.setStatus(output.toString("UTF-8"));
167  0 job.setnextChunk(output.size());
168    }
169    }
170  0 if (failedStates.contains(job.getJobState()))
171    {
172   
173  0 RemoteFile errLogFile = null;
174  0 for (RemoteFile f : files)
175    {
176  0 if (f.getLabel().equals("error-log"))
177    {
178  0 errLogFile = f;
179  0 break;
180    }
181    }
182   
183  0 if (errLogFile!=null)
184    {
185  0 ByteArrayOutputStream output = new ByteArrayOutputStream();
186  0 client.writeFileTo(errLogFile, output);
187  0 if (output.size() > 0)
188    {
189  0 newContent = true;
190  0 job.setStatus(job.getStatus() + "\n" + output.toString("UTF-8"));
191    }
192    }
193    }
194  0 return newContent;
195    }
196   
 
197  0 toggle @Override
198    public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
199    {
200  0 if (_lex instanceof ClientProtocolException)
201    {
202  0 j.setState(WsJob.JobState.INVALID);
203  0 j.setStatus(_lex.getMessage());
204  0 return true;
205    }
206  0 return false;
207    }
208   
 
209  0 toggle @Override
210    public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
211    {
212    // TODO
213  0 return false;
214    }
215   
 
216  0 toggle final SlivkaService getService()
217    {
218  0 return service;
219    }
220   
 
221  0 toggle @Override
222    public final Object getEndpoint()
223    {
224  0 return this;
225    }
226   
 
227  0 toggle @Override
228    public final void initParamStore(ParamManager userParameterStore)
229    {
230  0 if (store == null)
231    {
232  0 store = new SlivkaDatastore(service);
233    }
234    }
235   
 
236  0 toggle @Override
237    public boolean hasParameters()
238    {
239  0 return true;
240    }
241   
 
242  0 toggle @Override
243    public final ParamDatastoreI getParamStore()
244    {
245  0 if (store == null)
246    {
247  0 initParamStore(null);
248    }
249  0 return store;
250    }
251   
 
252  0 toggle public static AlignmentI readAlignment(RemoteFile f) throws IOException
253    {
254  0 final var mimetype = f.getMediaType();
255  0 FileFormat format;
256  0 if (mimetype.equals("application/clustal"))
257  0 format = FileFormat.Clustal;
258  0 else if (mimetype.equals("application/fasta"))
259  0 format = FileFormat.Fasta;
260    else
261  0 return null;
262  0 return new FormatAdapter().readFile(f.getContentUrl().toString(),
263    DataSourceType.URL, format);
264    }
265   
266    }
  • Report generated by OpenClover v 4.4.1 on Wed Dec 3 2025 17:13:21 GMT using coverage data from Wed Dec 3 2025 17:13:06 GMT.
  • OpenClover is free and open-source software.