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.bin.Console;
  19 import jalview.datamodel.Alignment;
  20 import jalview.datamodel.AlignmentAnnotation;
  21 import jalview.datamodel.AlignmentI;
  22 import jalview.datamodel.SequenceI;
  23 import jalview.datamodel.features.FeatureMatcherSetI;
  24 import jalview.io.AnnotationFile;
  25 import jalview.io.DataSourceType;
  26 import jalview.io.FeaturesFile;
  27 import jalview.io.FileFormat;
  28 import jalview.io.FormatAdapter;
  29 import jalview.ws.params.ArgumentI;
  30 import jalview.ws2.api.Credentials;
  31 import jalview.ws2.api.JobStatus;
  32 import jalview.ws2.api.WebServiceJobHandle;
  33 import jalview.ws2.client.api.AlignmentWebServiceClientI;
  34 import jalview.ws2.client.api.AnnotationWebServiceClientI;
  35 import jalview.ws2.client.api.WebServiceClientI;
  36 import uk.ac.dundee.compbio.slivkaclient.Job;
  37 import uk.ac.dundee.compbio.slivkaclient.Parameter;
  38 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  39 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  40
  41 import static java.lang.String.format;
  42
  43 public class SlivkaWSClient implements WebServiceClientI
  44 {
  45   final SlivkaService service;
  46
  47   final SlivkaClient client;
  48
  49   SlivkaWSClient(SlivkaService service)
  50   {
  51     this.service = service;
  52     this.client = service.getClient();
  53   }
  54
  55   @Override
  56   public String getUrl()
  57   {
  58     return client.getUrl().toString();
  59   }
  60
  61   @Override
  62   public String getClientName()
  63   {
  64     return "slivka";
  65   }
  66
  67   // pattern for matching media types
  68   static final Pattern mediaTypePattern = Pattern.compile(
  69       "(?:text|application)\\/(?:x-)?([\\w-]+)");
  70
  71   @Override
  72   public WebServiceJobHandle submit(List<SequenceI> sequences,
  73       List<ArgumentI> args, Credentials credentials) throws IOException
  74   {
  75     var request = new uk.ac.dundee.compbio.slivkaclient.JobRequest();
  76     for (Parameter param : service.getParameters())
  77     {
  78       // TODO: restrict input sequences parameter name to "sequences"
  79       if (param instanceof Parameter.FileParameter)
  80       {
  81         Parameter.FileParameter fileParam = (Parameter.FileParameter) param;
  82         FileFormat format = null;
  83         var match = mediaTypePattern.matcher(fileParam.getMediaType());
  84         if (match.find())
  85         {
  86           String fmt = match.group(1);
  87           if (fmt.equalsIgnoreCase("pfam"))
  88             format = FileFormat.Pfam;
  89           else if (fmt.equalsIgnoreCase("stockholm"))
  90             format = FileFormat.Stockholm;
  91           else if (fmt.equalsIgnoreCase("clustal"))
  92             format = FileFormat.Clustal;
  93           else if (fmt.equalsIgnoreCase("fasta"))
  94             format = FileFormat.Fasta;
  95         }
  96         if (format == null)
  97         {
  98           Console.warn(String.format(
  99               "Unknown input format %s, assuming fasta.",
 100               fileParam.getMediaType()));
 101           format = FileFormat.Fasta;
 102         }
 103         InputStream stream = new ByteArrayInputStream(format.getWriter(null)
 104             .print(sequences.toArray(new SequenceI[0]), false)
 105             .getBytes());
 106         request.addFile(param.getId(), stream);
 107       }
 108     }
 109     if (args != null)
 110     {
 111       for (ArgumentI arg : args)
 112       {
 113         // multiple choice field names are name$number to avoid duplications
 114         // the number is stripped here
 115         String paramId = arg.getName().split("\\$", 2)[0];
 116         Parameter param = service.getParameter(paramId);
 117         if (param instanceof Parameter.FlagParameter)
 118         {
 119           if (arg.getValue() != null && !arg.getValue().isEmpty())
 120             request.addData(paramId, true);
 121           else
 122             request.addData(paramId, false);
 123         }
 124         else if (param instanceof Parameter.FileParameter)
 125         {
 126           request.addFile(paramId, new File(arg.getValue()));
 127         }
 128         else
 129         {
 130           request.addData(paramId, arg.getValue());
 131         }
 132       }
 133     }
 134     var job = service.submitJob(request);
 135     return createJobHandle(job.getId());
 136   }
 137
 138   protected WebServiceJobHandle createJobHandle(String jobId)
 139   {
 140     return new WebServiceJobHandle(
 141         getClientName(), service.getName(), client.getUrl().toString(),
 142         jobId);
 143   }
 144
 145   @Override
 146   public JobStatus getStatus(WebServiceJobHandle job) throws IOException
 147   {
 148     var slivkaJob = client.getJob(job.getJobId());
 149     return statusMap.getOrDefault(slivkaJob.getStatus(), JobStatus.UNKNOWN);
 150   }
 151
 152   protected static final EnumMap<Job.Status, JobStatus> statusMap = new EnumMap<>(Job.Status.class);
 153   static
 154   {
 155     statusMap.put(Job.Status.PENDING, JobStatus.SUBMITTED);
 156     statusMap.put(Job.Status.REJECTED, JobStatus.INVALID);
 157     statusMap.put(Job.Status.ACCEPTED, JobStatus.SUBMITTED);
 158     statusMap.put(Job.Status.QUEUED, JobStatus.QUEUED);
 159     statusMap.put(Job.Status.RUNNING, JobStatus.RUNNING);
 160     statusMap.put(Job.Status.COMPLETED, JobStatus.COMPLETED);
 161     statusMap.put(Job.Status.INTERRUPTED, JobStatus.CANCELLED);
 162     statusMap.put(Job.Status.DELETED, JobStatus.CANCELLED);
 163     statusMap.put(Job.Status.FAILED, JobStatus.FAILED);
 164     statusMap.put(Job.Status.ERROR, JobStatus.SERVER_ERROR);
 165     statusMap.put(Job.Status.UNKNOWN, JobStatus.UNKNOWN);
 166   }
 167
 168   @Override
 169   public String getLog(WebServiceJobHandle job) throws IOException
 170   {
 171     var slivkaJob = client.getJob(job.getJobId());
 172     for (var f : slivkaJob.getResults())
 173     {
 174       if (f.getLabel().equals("log"))
 175       {
 176         ByteArrayOutputStream stream = new ByteArrayOutputStream();
 177         f.writeTo(stream);
 178         return stream.toString("UTF-8");
 179       }
 180     }
 181     return "";
 182   }
 183
 184   @Override
 185   public String getErrorLog(WebServiceJobHandle job) throws IOException
 186   {
 187     var slivkaJob = client.getJob(job.getJobId());
 188     for (var f : slivkaJob.getResults())
 189     {
 190       if (f.getLabel().equals("error-log"))
 191       {
 192         ByteArrayOutputStream stream = new ByteArrayOutputStream();
 193         f.writeTo(stream);
 194         return stream.toString("UTF-8");
 195       }
 196     }
 197     return "";
 198   }
 199
 200   @Override
 201   public void cancel(WebServiceJobHandle job)
 202       throws IOException, UnsupportedOperationException
 203   {
 204     Console.warn(
 205         "slivka client does not support job cancellation");
 206   }
 207 }
 208
 209 class SlivkaAlignmentWSClient extends SlivkaWSClient
 210     implements AlignmentWebServiceClientI
 211 {
 212
 213   SlivkaAlignmentWSClient(SlivkaService service)
 214   {
 215     super(service);
 216   }
 217
 218   @Override
 219   public AlignmentI getAlignment(WebServiceJobHandle job) throws IOException
 220   {
 221     var slivkaJob = client.getJob(job.getJobId());
 222     for (var f : slivkaJob.getResults())
 223     {
 224       // TODO: restrict result file label to "alignment"
 225       FileFormat format;
 226       var match = mediaTypePattern.matcher(f.getMediaType());
 227       if (!match.find())
 228         continue;
 229       String fmt = match.group(1);
 230       if (fmt.equalsIgnoreCase("clustal"))
 231         format = FileFormat.Clustal;
 232       else if (fmt.equalsIgnoreCase("fasta"))
 233         format = FileFormat.Fasta;
 234       else
 235         continue;
 236       return new FormatAdapter().readFile(f.getContentUrl().toString(),
 237           DataSourceType.URL, format);
 238     }
 239     Console.warn("No alignment found on the server");
 240     throw new IOException("no alignment found");
 241   }
 242
 243 }
 244
 245 class SlivkaAnnotationWSClient extends SlivkaWSClient
 246     implements AnnotationWebServiceClientI
 247 {
 248   SlivkaAnnotationWSClient(SlivkaService service)
 249   {
 250     super(service);
 251   }
 252
 253   @Override
 254   public List<AlignmentAnnotation> attachAnnotations(WebServiceJobHandle job,
 255       List<SequenceI> sequences, Map<String, FeatureColourI> colours,
 256       Map<String, FeatureMatcherSetI> filters) throws IOException
 257   {
 258     var slivkaJob = client.getJob(job.getJobId());
 259     var aln = new Alignment(sequences.toArray(new SequenceI[sequences.size()]));
 260     boolean featPresent = false, annotPresent = false;
 261     for (var f : slivkaJob.getResults())
 262     {
 263       // TODO: restrict file label to "annotations" or "features"
 264       var match = mediaTypePattern.matcher(f.getMediaType());
 265       if (!match.find())
 266         continue;
 267       String fmt = match.group(1);
 268       if (fmt.equalsIgnoreCase("jalview-annotations"))
 269       {
 270         annotPresent = new AnnotationFile().readAnnotationFileWithCalcId(
 271             aln, service.getId(), f.getContentUrl().toString(),
 272             DataSourceType.URL);
 273         if (annotPresent)
 274           Console.debug(format("loaded annotations for %s", service.getId()));
 275       }
 276       else if (fmt.equalsIgnoreCase("jalview-features"))
 277       {
 278         FeaturesFile ff = new FeaturesFile(f.getContentUrl().toString(),
 279             DataSourceType.URL);
 280         featPresent = ff.parse(aln, colours, true);
 281         if (featPresent)
 282           Console.debug(format("loaded features for %s", service.getId()));
 283       }
 284     }
 285     if (!annotPresent)
 286       Console.debug(format("no annotations found for %s", service.getId()));
 287     if (!featPresent)
 288       Console.debug(format("no features found for %s", service.getId()));
 289     return aln.getAlignmentAnnotation() != null ? Arrays.asList(aln.getAlignmentAnnotation())
 290         : Collections.emptyList();
 291   }
 292 }