Example #1
0
 public static VariantSource readVariantSource(
     CatalogManager catalogManager, Study study, File file) throws CatalogException {
   // TODO: Fix aggregate and studyType
   VariantSource source =
       new VariantSource(
           file.getName(),
           Integer.toString(file.getId()),
           Integer.toString(study.getId()),
           study.getName());
   URI fileUri = catalogManager.getFileUri(file);
   return VariantStorageManager.readVariantSource(Paths.get(fileUri.getPath()), source);
 }
Example #2
0
  public QueryResult<File> index(
      int fileId, int outDirId, String storageEngine, String sessionId, QueryOptions options)
      throws IOException, CatalogException, AnalysisExecutionException {

    if (options == null) {
      options = new QueryOptions();
    }
    final boolean execute = options.getBoolean(AnalysisJobExecuter.EXECUTE);
    final boolean simulate = options.getBoolean(AnalysisJobExecuter.SIMULATE);
    final boolean recordOutput = options.getBoolean(AnalysisJobExecuter.RECORD_OUTPUT);
    final long start = System.currentTimeMillis();

    /** Query catalog for user data. * */
    String userId = catalogManager.getUserIdBySessionId(sessionId);
    File file = catalogManager.getFile(fileId, sessionId).first();
    File outDir = catalogManager.getFile(outDirId, sessionId).first();
    int studyIdByOutDirId = catalogManager.getStudyIdByFileId(outDirId);
    Study study = catalogManager.getStudy(studyIdByOutDirId, sessionId).getResult().get(0);

    if (file.getType() != File.Type.FILE) {
      throw new CatalogException(
          "Expected file type = " + File.Type.FILE + " instead of " + file.getType());
    }

    final String dbName;
    if (options.containsKey(DB_NAME)) {
      dbName = options.getString(DB_NAME);
    } else {
      if (study.getAttributes().containsKey(DB_NAME)
          && study.getAttributes().get(DB_NAME) != null) {
        dbName = study.getAttributes().get(DB_NAME).toString();
      } else {
        int projectId = catalogManager.getProjectIdByStudyId(study.getId());
        String alias =
            catalogManager
                .getProject(projectId, new QueryOptions("include", "alias"), sessionId)
                .first()
                .getAlias();
        dbName =
            Config.getAnalysisProperties()
                    .getProperty(OPENCGA_ANALYSIS_STORAGE_DATABASE_PREFIX, "opencga_")
                + userId
                + "_"
                + alias;
      }
    }

    // TODO: Check if file can be indexed

    // ObjectMap to fill with modifications over the indexed file (like new attributes or jobId)
    ObjectMap indexFileModifyParams = new ObjectMap("attributes", new ObjectMap());

    /** Create temporal Job Outdir * */
    final URI temporalOutDirUri;
    final String randomString = "I_" + StringUtils.randomString(10);
    if (simulate) {
      temporalOutDirUri = createSimulatedOutDirUri(randomString);
    } else {
      temporalOutDirUri =
          catalogManager.createJobOutDir(studyIdByOutDirId, randomString, sessionId);
    }

    List<Sample> sampleList;

    /** Create index file* */
    final File index;
    if (options.containsKey(INDEX_FILE_ID)) {
      logger.debug("Using an existing indexedFile.");
      int indexFileId = options.getInt(INDEX_FILE_ID);
      index = catalogManager.getFile(indexFileId, sessionId).first();
      if (index.getType() != File.Type.INDEX) {
        throw new CatalogException("Expected {type: INDEX} in IndexedFile " + indexFileId);
      }
      if (index.getStatus() != File.Status.READY) {
        throw new CatalogException("Expected {status: READY} in IndexedFile " + indexFileId);
      }
      if (simulate) {
        index.setStatus(File.Status.INDEXING);
      } else {
        ObjectMap parameters = new ObjectMap("status", File.Status.INDEXING);
        catalogManager.modifyFile(index.getId(), parameters, sessionId);
      }

      /** Get file samples * */
      sampleList =
          catalogManager
              .getAllSamples(study.getId(), new QueryOptions("id", index.getSampleIds()), sessionId)
              .getResult();

    } else {

      /** Get file samples * */
      sampleList = getFileSamples(study, file, indexFileModifyParams, simulate, options, sessionId);

      String indexedFileDescription = "Indexation of " + file.getName() + " (" + fileId + ")";
      String indexedFileName = file.getName() + "." + storageEngine;
      String indexedFilePath = Paths.get(outDir.getPath(), indexedFileName).toString();

      if (simulate) {
        index =
            new File(
                -10,
                indexedFileName,
                File.Type.INDEX,
                file.getFormat(),
                file.getBioformat(),
                indexedFilePath,
                userId,
                TimeUtils.getTime(),
                indexedFileDescription,
                File.Status.INDEXING,
                -1,
                -1,
                null,
                -1,
                null,
                null,
                new HashMap<String, Object>());
      } else {
        index =
            catalogManager
                .createFile(
                    studyIdByOutDirId,
                    File.Type.INDEX,
                    file.getFormat(),
                    file.getBioformat(),
                    indexedFilePath,
                    null,
                    null,
                    indexedFileDescription,
                    File.Status.INDEXING,
                    0,
                    -1,
                    null,
                    -1,
                    null,
                    null,
                    false,
                    null,
                    sessionId)
                .first();
      }
    }

    /** Create commandLine * */
    String commandLine =
        createCommandLine(
            study,
            file,
            index,
            sampleList,
            storageEngine,
            temporalOutDirUri,
            indexFileModifyParams,
            dbName,
            options);
    if (options.containsKey(PARAMETERS)) {
      List<String> extraParams = options.getAsStringList(PARAMETERS);
      for (String extraParam : extraParams) {
        commandLine += " " + extraParam;
      }
    }

    /** Create job * */
    ObjectMap jobResourceManagerAttributes = new ObjectMap();
    jobResourceManagerAttributes.put(Job.TYPE, Job.Type.INDEX);
    jobResourceManagerAttributes.put(Job.INDEXED_FILE_ID, index.getId());

    String jobName = "index";
    String jobDescription = "Indexing file " + file.getName() + " (" + fileId + ")";
    final Job job =
        AnalysisJobExecuter.createJob(
                catalogManager,
                studyIdByOutDirId,
                jobName,
                OPENCGA_STORAGE_BIN_NAME,
                jobDescription,
                outDir,
                Collections.<Integer>emptyList(),
                sessionId,
                randomString,
                temporalOutDirUri,
                commandLine,
                execute,
                simulate,
                recordOutput,
                jobResourceManagerAttributes)
            .first();

    if (simulate) {
      index.getAttributes().put("job", job);
      //            index.getAttributes().putAll(indexFileModifyParams.getMap("attributes"));
      index.setSampleIds(indexFileModifyParams.getAsIntegerList("sampleIds"));
      //            VariantSource variantSource = (VariantSource)
      // index.getAttributes().get("variantSource");
      //            for (Map.Entry<String, Integer> entry :
      // variantSource.getSamplesPosition().entrySet()) {
      //                System.out.println("entry.getKey() = " + entry.getKey());
      //                System.out.println("entry.getValue() = " + entry.getValue());
      //            }
      //            for (String s : variantSource.getSamples()) {
      //                System.out.println("sample = " + s);
      //            }
      //            variantSource.setSamplesPosition(new HashMap<String, Integer>());
      return new QueryResult<>(
          "indexFile",
          (int) (System.currentTimeMillis() - start),
          1,
          1,
          "",
          "",
          Collections.singletonList(index));
    } else {
      /** Update IndexFile to add extra information (jobId, sampleIds, attributes, ...) * */
      indexFileModifyParams.put("jobId", job.getId());
      Set<Integer> jobIds;
      try {
        jobIds = new HashSet<>(new ObjectMap(index.getAttributes()).getAsIntegerList("jobIds"));
      } catch (Exception ignore) {
        jobIds = new HashSet<>(1);
      }
      if (index.getJobId() > 0) {
        jobIds.add(index.getJobId());
      }
      jobIds.add(job.getId());
      indexFileModifyParams.getMap("attributes").put("jobIds", jobIds);

      catalogManager.modifyFile(index.getId(), indexFileModifyParams, sessionId).getResult();

      return new QueryResult<>(
          "indexFile",
          (int) (System.currentTimeMillis() - start),
          1,
          1,
          "",
          "",
          catalogManager.getFile(index.getId(), sessionId).getResult());
    }
  }
Example #3
0
  private List<Sample> getFileSamples(
      Study study,
      File file,
      ObjectMap indexFileModifyParams,
      boolean simulate,
      QueryOptions options,
      String sessionId)
      throws CatalogException {
    List<Sample> sampleList;
    QueryOptions queryOptions =
        new QueryOptions(
            "include",
            Arrays.asList("projects.studies.samples.id", "projects.studies.samples.name"));

    if (file.getSampleIds() == null || file.getSampleIds().isEmpty()) {
      // Read samples from file
      List<String> sampleNames = null;
      switch (file.getBioformat()) {
        case VARIANT:
          {
            if (file.getAttributes().containsKey("variantSource")) {
              Object variantSource = file.getAttributes().get("variantSource");
              if (variantSource instanceof VariantSource) {
                sampleNames = ((VariantSource) variantSource).getSamples();
              } else if (variantSource instanceof Map) {
                sampleNames = new ObjectMap((Map) variantSource).getAsStringList("samples");
              } else {
                logger.warn(
                    "Unexpected object type of variantSource ({}) in file attributes. Expected {} or {}",
                    variantSource.getClass(),
                    VariantSource.class,
                    Map.class);
              }
            }
            if (sampleNames == null) {
              VariantSource variantSource = readVariantSource(catalogManager, study, file);
              indexFileModifyParams
                  .get("attributes", ObjectMap.class)
                  .put("variantSource", variantSource);
              sampleNames = variantSource.getSamples();
            }
          }
          break;
        default:
          return new LinkedList<>();
          //                    throw new CatalogException("Unknown to get samples names from
          // bioformat " + file.getBioformat());
      }

      // Find matching samples in catalog with the sampleName from the VariantSource.
      queryOptions.add("name", sampleNames);
      sampleList = catalogManager.getAllSamples(study.getId(), queryOptions, sessionId).getResult();

      // check if all file samples exists on Catalog
      if (sampleList.size()
          != sampleNames.size()) { // Size does not match. Find the missing samples.
        Set<String> set = new HashSet<>(sampleNames);
        for (Sample sample : sampleList) {
          set.remove(sample.getName());
        }
        logger.warn("Missing samples: m{}", set);
        if (options.getBoolean(CREATE_MISSING_SAMPLES, true)) {
          for (String sampleName : set) {
            if (simulate) {
              sampleList.add(new Sample(-1, sampleName, file.getName(), null, null));
            } else {
              sampleList.add(
                  catalogManager
                      .createSample(
                          study.getId(), sampleName, file.getName(), null, null, null, sessionId)
                      .first());
            }
          }
        } else {
          throw new CatalogException(
              "Can not find samples " + set + " in catalog"); // FIXME: Create missing samples??
        }
      }
    } else {
      // Get samples from file.sampleIds
      queryOptions.add("id", file.getSampleIds());
      sampleList = catalogManager.getAllSamples(study.getId(), queryOptions, sessionId).getResult();
    }

    List<Integer> sampleIdsList = new ArrayList<>(sampleList.size());
    for (Sample sample : sampleList) {
      sampleIdsList.add(sample.getId());
      //
      // sampleIdsString.append(sample.getName()).append(":").append(sample.getId()).append(",");
    }
    indexFileModifyParams.put("sampleIds", sampleIdsList);

    return sampleList;
  }
Example #4
0
  /**
   * @param study Study where file is located
   * @param file File to be indexed
   * @param indexFile Generated index file
   * @param sampleList
   * @param storageEngine StorageEngine to be used
   * @param outDirUri Index outdir
   * @param indexFileModifyParams This map will be used to modify the indexFile
   * @param dbName
   * @return CommandLine
   * @throws org.opencb.opencga.catalog.db.CatalogDBException
   * @throws CatalogIOManagerException
   */
  private String createCommandLine(
      Study study,
      File file,
      File indexFile,
      List<Sample> sampleList,
      String storageEngine,
      URI outDirUri,
      final ObjectMap indexFileModifyParams,
      final String dbName,
      QueryOptions options)
      throws CatalogException {

    // Create command line
    String userId = file.getOwnerId();
    String name = file.getName();
    String commandLine;
    ObjectMap indexAttributes = indexFileModifyParams.get("attributes", ObjectMap.class);

    String opencgaStorageBin =
        Paths.get(Config.getOpenCGAHome(), "bin", OPENCGA_STORAGE_BIN_NAME).toString();

    if (file.getBioformat() == File.Bioformat.ALIGNMENT
        || name.endsWith(".bam")
        || name.endsWith(".sam")) {
      int chunkSize = 200; // TODO: Read from properties.
      commandLine =
          new StringBuilder(opencgaStorageBin)
              .append(" --storage-engine ")
              .append(storageEngine)
              .append(" index-alignments ")
              .append(" --file-id ")
              .append(indexFile.getId())
              .append(" --database ")
              .append(dbName)
              .append(" --input ")
              .append(catalogManager.getFileUri(file))
              .append(" --calculate-coverage ")
              .append(chunkSize)
              .append(" --mean-coverage ")
              .append(chunkSize)
              .append(" --outdir ")
              .append(outDirUri)
              //                    .append(" --credentials ")
              .toString();

      indexAttributes.put("chunkSize", chunkSize);

    } else if (name.endsWith(".fasta") || name.endsWith(".fasta.gz")) {
      throw new UnsupportedOperationException();
    } else if (file.getBioformat() == File.Bioformat.VARIANT
        || name.contains(".vcf")
        || name.contains(".vcf.gz")) {

      StringBuilder sampleIdsString = new StringBuilder();
      for (Sample sample : sampleList) {
        sampleIdsString.append(sample.getName()).append(":").append(sample.getId()).append(",");
      }

      StringBuilder sb =
          new StringBuilder(opencgaStorageBin)
              .append(" --storage-engine ")
              .append(storageEngine)
              .append(" index-variants ")
              .append(" --file-id ")
              .append(indexFile.getId())
              .append(" --study-name \'")
              .append(study.getName())
              .append("\'")
              .append(" --study-id ")
              .append(study.getId())
              //                    .append(" --study-type ").append(study.getType())
              .append(" --database ")
              .append(dbName)
              .append(" --input ")
              .append(catalogManager.getFileUri(file))
              .append(" --outdir ")
              .append(outDirUri)
              .append(" --include-genotypes ")
              .append(" --compress-genotypes ")
              .append(" --include-stats ")
          //                    .append(" --sample-ids ").append(sampleIdsString)
          //                    .append(" --credentials ")
          ;
      if (options.getBoolean(VariantStorageManager.ANNOTATE, true)) {
        sb.append(" --annotate ");
      }
      if (options.getBoolean(VariantStorageManager.INCLUDE_SRC, false)) {
        sb.append(" --include-src ");
      }
      commandLine = sb.toString();

    } else {
      return null;
    }
    indexAttributes.put(INDEXED_FILE, file.getId());
    indexAttributes.put(DB_NAME, dbName);
    indexAttributes.put(STORAGE_ENGINE, storageEngine);

    return commandLine;
  }