src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.api.FeatureColourI;
   4 import jalview.bin.Cache;
   5 import jalview.datamodel.Alignment;
   6 import jalview.datamodel.AlignmentAnnotation;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.datamodel.features.FeatureMatcherSetI;
   9 import jalview.io.AnnotationFile;
  10 import jalview.io.DataSourceType;
  11 import jalview.io.FeaturesFile;
  12 import jalview.util.MessageManager;
  13 import jalview.ws.api.JobId;
  14 import jalview.ws.api.SequenceAnnotationServiceI;
  15 import jalview.ws.params.ArgumentI;
  16 import jalview.ws.params.WsParamSetI;
  17 import jalview.ws.uimodel.AlignAnalysisUIText;
  18
  19 import java.io.BufferedReader;
  20 import java.io.ByteArrayInputStream;
  21 import java.io.IOError;
  22 import java.io.IOException;
  23 import java.io.InputStream;
  24 import java.io.InputStreamReader;
  25 import java.util.Arrays;
  26 import java.util.HashMap;
  27 import java.util.List;
  28 import java.util.Map;
  29
  30 import uk.ac.dundee.compbio.slivkaclient.FormField;
  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
  36 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  37 {
  38   public SlivkaAnnotationServiceInstance(SlivkaClient client,
  39           SlivkaService service, boolean conservation)
  40   {
  41     super(client, service, !conservation ? "Annotations disorder"
  42             : "Alignment Conservation");
  43     if (conservation)
  44     {
  45       setAlignAnalysisUI(new AlignAnalysisUIText(service.getName(),
  46               SlivkaAnnotationServiceInstance.class,
  47               "Slivka.AACons", false, true, true, true, true, 2,
  48               MessageManager.getString("label.aacon_calculations"),
  49               MessageManager.getString("tooltip.aacon_calculations"),
  50               MessageManager.getString("label.aacon_settings"),
  51               MessageManager.getString("tooltip.aacon_settings")));
  52     }
  53     style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
  54   }
  55
  56   @Override
  57   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  58   {
  59     StringBuilder builder = new StringBuilder();
  60     for (SequenceI seq : seqs)
  61     {
  62       builder.append(">").append(seq.getName()).append("\n");
  63       builder.append(seq.getSequence()).append("\n");
  64     }
  65     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
  66     RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
  67     SlivkaForm form = service.getForm();
  68     HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
  69     if (paramset != null)
  70     {
  71       for (ArgumentI arg : paramset)
  72       {
  73         values.put(arg.getName(), arg.getValue());
  74       }
  75     }
  76     for (FormField field : form.getFields())
  77     {
  78       switch (field.getType())
  79       {
  80       case FILE:
  81         form.insert(field.getName(), file);
  82         break;
  83       case BOOLEAN:
  84         String value = values.get(field.getName());
  85         form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
  86         break;
  87       default:
  88         form.insert(field.getName(), field.valueOf(values.get(field.getName())));
  89       }
  90     }
  91     return new JobId(service.getName(), service.getName(), form.submit());
  92   }
  93
  94   @Override
  95   public List<AlignmentAnnotation> getAnnotationResult(JobId job,
  96           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  97           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  98   {
  99     RemoteFile annotFile = null;
 100     RemoteFile featFile = null;
 101     try
 102     {
 103       List<RemoteFile> files = client.getJobResults(job.getJobId());
 104       for (RemoteFile f : files)
 105       {
 106         if (f.getMimeType().equals("application/jalview-annotations"))
 107         {
 108           annotFile = f;
 109         }
 110         else if (f.getMimeType().equals("application/jalview-features"))
 111         {
 112           featFile = f;
 113         }
 114       }
 115     } catch (IOException e)
 116     {
 117       throw new IOError(e);
 118     }
 119     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
 120     BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
 121     if (!new AnnotationFile().parseAnnotationFrom(aln, null, readerIn))
 122     {
 123       Cache.log.debug("No annotation from slivka job\n" + annotFile);
 124     }
 125     if (featFile != null)
 126     {
 127       if (!new FeaturesFile(featFile.getURL().toString(),
 128               DataSourceType.URL).parse(aln, featureColours, true))
 129       {
 130         Cache.log.debug("No features from slivka job\n" + featFile);
 131       }
 132     }
 133     return Arrays.asList(aln.getAlignmentAnnotation());
 134   }
 135 }