src/jalview/ws2/client/slivka/SlivkaWSClient.java

   1 package jalview.ws2.client.slivka;
   2
   3 import java.io.ByteArrayInputStream;
   4 import java.io.ByteArrayOutputStream;
   5 import java.io.File;
   6 import java.io.IOException;
   7 import java.io.InputStream;
   8 import java.nio.charset.StandardCharsets;
   9 import java.util.Arrays;
  10 import java.util.Collections;
  11 import java.util.EnumMap;
  12 import java.util.List;
  13 import java.util.Map;
  14 import java.util.regex.Pattern;
  15
  16 import jalview.api.FeatureColourI;
  17 import jalview.bin.Cache;
  18 import jalview.datamodel.Alignment;
  19 import jalview.datamodel.AlignmentAnnotation;
  20 import jalview.datamodel.AlignmentI;
  21 import jalview.datamodel.SequenceI;
  22 import jalview.datamodel.features.FeatureMatcherSetI;
  23 import jalview.io.AnnotationFile;
  24 import jalview.io.DataSourceType;
  25 import jalview.io.FeaturesFile;
  26 import jalview.io.FileFormat;
  27 import jalview.io.FormatAdapter;
  28 import jalview.ws.params.ArgumentI;
  29 import jalview.ws2.api.Credentials;
  30 import jalview.ws2.api.JobStatus;
  31 import jalview.ws2.api.WebServiceJobHandle;
  32 import jalview.ws2.client.api.AlignmentWebServiceClientI;
  33 import jalview.ws2.client.api.AnnotationWebServiceClientI;
  34 import jalview.ws2.client.api.WebServiceClientI;
  35 import uk.ac.dundee.compbio.slivkaclient.Job;
  36 import uk.ac.dundee.compbio.slivkaclient.Parameter;
  37 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  38 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  39
  40 import static java.lang.String.format;
  41
  42 public class SlivkaWSClient implements WebServiceClientI
  43 {
  44   final SlivkaService service;
  45
  46   final SlivkaClient client;
  47
  48   SlivkaWSClient(SlivkaService service)
  49   {
  50     this.service = service;
  51     this.client = service.getClient();
  52   }
  53
  54   @Override
  55   public String getUrl()
  56   {
  57     return client.getUrl().toString();
  58   }
  59
  60   @Override
  61   public String getClientName()
  62   {
  63     return "slivka";
  64   }
  65
  66   // pattern for matching media types
  67   static final Pattern mediaTypePattern = Pattern.compile(
  68       "(?:text|application)\\/(?:x-)?([\\w-]+)");
  69
  70   @Override
  71   public WebServiceJobHandle submit(List<SequenceI> sequences,
  72       List<ArgumentI> args, Credentials credentials) throws IOException
  73   {
  74     var request = new uk.ac.dundee.compbio.slivkaclient.JobRequest();
  75     for (Parameter param : service.getParameters())
  76     {
  77       // TODO: restrict input sequences parameter name to "sequences"
  78       if (param instanceof Parameter.FileParameter)
  79       {
  80         Parameter.FileParameter fileParam = (Parameter.FileParameter) param;
  81         FileFormat format = null;
  82         var match = mediaTypePattern.matcher(fileParam.getMediaType());
  83         if (match.find())
  84         {
  85           String fmt = match.group(1);
  86           if (fmt.equalsIgnoreCase("pfam"))
  87             format = FileFormat.Pfam;
  88           else if (fmt.equalsIgnoreCase("stockholm"))
  89             format = FileFormat.Stockholm;
  90           else if (fmt.equalsIgnoreCase("clustal"))
  91             format = FileFormat.Clustal;
  92           else if (fmt.equalsIgnoreCase("fasta"))
  93             format = FileFormat.Fasta;
  94         }
  95         if (format == null)
  96         {
  97           Cache.log.warn(String.format(
  98               "Unknown input format %s, assuming fasta.",
  99               fileParam.getMediaType()));
 100           format = FileFormat.Fasta;
 101         }
 102         InputStream stream = new ByteArrayInputStream(format.getWriter(null)
 103             .print(sequences.toArray(new SequenceI[0]), false)
 104             .getBytes());
 105         request.addFile(param.getId(), stream);
 106       }
 107     }
 108     if (args != null)
 109     {
 110       for (ArgumentI arg : args)
 111       {
 112         // multiple choice field names are name$number to avoid duplications
 113         // the number is stripped here
 114         String paramId = arg.getName().split("\\$", 2)[0];
 115         Parameter param = service.getParameter(paramId);
 116         if (param instanceof Parameter.FlagParameter)
 117         {
 118           if (arg.getValue() != null && !arg.getValue().isBlank())
 119             request.addData(paramId, true);
 120           else
 121             request.addData(paramId, false);
 122         }
 123         else if (param instanceof Parameter.FileParameter)
 124         {
 125           request.addFile(paramId, new File(arg.getValue()));
 126         }
 127         else
 128         {
 129           request.addData(paramId, arg.getValue());
 130         }
 131       }
 132     }
 133     var job = service.submitJob(request);
 134     return createJobHandle(job.getId());
 135   }
 136
 137   protected WebServiceJobHandle createJobHandle(String jobId)
 138   {
 139     return new WebServiceJobHandle(
 140         getClientName(), service.getName(), client.getUrl().toString(),
 141         jobId);
 142   }
 143
 144   @Override
 145   public JobStatus getStatus(WebServiceJobHandle job) throws IOException
 146   {
 147     var slivkaJob = client.getJob(job.getJobId());
 148     return statusMap.getOrDefault(slivkaJob.getStatus(), JobStatus.UNKNOWN);
 149   }
 150
 151   protected static final EnumMap<Job.Status, JobStatus> statusMap = new EnumMap<>(Job.Status.class);
 152   static
 153   {
 154     statusMap.put(Job.Status.PENDING, JobStatus.SUBMITTED);
 155     statusMap.put(Job.Status.REJECTED, JobStatus.INVALID);
 156     statusMap.put(Job.Status.ACCEPTED, JobStatus.SUBMITTED);
 157     statusMap.put(Job.Status.QUEUED, JobStatus.QUEUED);
 158     statusMap.put(Job.Status.RUNNING, JobStatus.RUNNING);
 159     statusMap.put(Job.Status.COMPLETED, JobStatus.COMPLETED);
 160     statusMap.put(Job.Status.INTERRUPTED, JobStatus.CANCELLED);
 161     statusMap.put(Job.Status.DELETED, JobStatus.CANCELLED);
 162     statusMap.put(Job.Status.FAILED, JobStatus.FAILED);
 163     statusMap.put(Job.Status.ERROR, JobStatus.SERVER_ERROR);
 164     statusMap.put(Job.Status.UNKNOWN, JobStatus.UNKNOWN);
 165   }
 166
 167   @Override
 168   public String getLog(WebServiceJobHandle job) throws IOException
 169   {
 170     var slivkaJob = client.getJob(job.getJobId());
 171     for (var f : slivkaJob.getResults())
 172     {
 173       if (f.getLabel().equals("log"))
 174       {
 175         ByteArrayOutputStream stream = new ByteArrayOutputStream();
 176         f.writeTo(stream);
 177         return stream.toString(StandardCharsets.UTF_8);
 178       }
 179     }
 180     return "";
 181   }
 182
 183   @Override
 184   public String getErrorLog(WebServiceJobHandle job) throws IOException
 185   {
 186     var slivkaJob = client.getJob(job.getJobId());
 187     for (var f : slivkaJob.getResults())
 188     {
 189       if (f.getLabel().equals("error-log"))
 190       {
 191         ByteArrayOutputStream stream = new ByteArrayOutputStream();
 192         f.writeTo(stream);
 193         return stream.toString(StandardCharsets.UTF_8);
 194       }
 195     }
 196     return "";
 197   }
 198
 199   @Override
 200   public void cancel(WebServiceJobHandle job)
 201       throws IOException, UnsupportedOperationException
 202   {
 203     throw new UnsupportedOperationException(
 204         "slivka client does not support job cancellation");
 205   }
 206 }
 207
 208 class SlivkaAlignmentWSClient extends SlivkaWSClient
 209     implements AlignmentWebServiceClientI
 210 {
 211
 212   SlivkaAlignmentWSClient(SlivkaService service)
 213   {
 214     super(service);
 215   }
 216
 217   @Override
 218   public AlignmentI getAlignment(WebServiceJobHandle job) throws IOException
 219   {
 220     var slivkaJob = client.getJob(job.getJobId());
 221     for (var f : slivkaJob.getResults())
 222     {
 223       // TODO: restrict result file label to "alignment"
 224       FileFormat format;
 225       var match = mediaTypePattern.matcher(f.getMediaType());
 226       if (!match.find())
 227         continue;
 228       String fmt = match.group(1);
 229       if (fmt.equalsIgnoreCase("clustal"))
 230         format = FileFormat.Clustal;
 231       else if (fmt.equalsIgnoreCase("fasta"))
 232         format = FileFormat.Fasta;
 233       else
 234         continue;
 235       return new FormatAdapter().readFile(f.getContentUrl().toString(),
 236           DataSourceType.URL, format);
 237     }
 238     Cache.log.warn("No alignment found on the server");
 239     throw new IOException("no alignment found");
 240   }
 241
 242 }
 243
 244 class SlivkaAnnotationWSClient extends SlivkaWSClient
 245     implements AnnotationWebServiceClientI
 246 {
 247   SlivkaAnnotationWSClient(SlivkaService service)
 248   {
 249     super(service);
 250   }
 251
 252   @Override
 253   public List<AlignmentAnnotation> attachAnnotations(WebServiceJobHandle job,
 254       List<SequenceI> sequences, Map<String, FeatureColourI> colours,
 255       Map<String, FeatureMatcherSetI> filters) throws IOException
 256   {
 257     var slivkaJob = client.getJob(job.getJobId());
 258     var aln = new Alignment(sequences.toArray(new SequenceI[sequences.size()]));
 259     boolean featPresent = false, annotPresent = false;
 260     for (var f : slivkaJob.getResults())
 261     {
 262       // TODO: restrict file label to "annotations" or "features"
 263       var match = mediaTypePattern.matcher(f.getMediaType());
 264       if (!match.find())
 265         continue;
 266       String fmt = match.group(1);
 267       if (fmt.equalsIgnoreCase("jalview-annotations"))
 268       {
 269         annotPresent = new AnnotationFile().readAnnotationFileWithCalcId(
 270             aln, service.getId(), f.getContentUrl().toString(),
 271             DataSourceType.URL);
 272         if (annotPresent)
 273           Cache.log.debug(format("loaded annotations for %s", service.getId()));
 274       }
 275       else if (fmt.equalsIgnoreCase("jalview-features"))
 276       {
 277         FeaturesFile ff = new FeaturesFile(f.getContentUrl().toString(),
 278             DataSourceType.URL);
 279         featPresent = ff.parse(aln, colours, true);
 280         if (featPresent)
 281           Cache.log.debug(format("loaded features for %s", service.getId()));
 282       }
 283     }
 284     if (!annotPresent)
 285       Cache.log.debug(format("no annotations found for %s", service.getId()));
 286     if (!featPresent)
 287       Cache.log.debug(format("no features found for %s", service.getId()));
 288     return aln.getAlignmentAnnotation() != null ? Arrays.asList(aln.getAlignmentAnnotation())
 289         : Collections.emptyList();
 290   }
 291 }