private void cacheTypeDescriptor(SpaceTypeDescriptor typeDescriptor) {

    if (typeDescriptor == null)
      throw new IllegalArgumentException("typeDescriptor can not be null");

    if (!types.containsKey(typeDescriptor.getTypeName())) introduceType(typeDescriptor);

    types.put(typeDescriptor.getTypeName(), new SpaceTypeDescriptorContainer(typeDescriptor));
  }
Example #2
0
  // --------------------------------------------------------------------------------
  private void drawItem(String parentFieldName, TreeItem parentItem, Map data, boolean expand) {
    Iterator p = data.keySet().iterator();
    while (p.hasNext()) {
      String key = (String) p.next();
      if (!data.containsKey(key)) {
        continue;
      }
      Object value = data.get(key);

      TreeItem newItem = new TreeItem(parentItem, SWT.NONE);
      newItem.setText(1, getClassName(value));

      String fieldName = parentFieldName + "." + key;
      if (fieldName.startsWith(".")) {
        fieldName = fieldName.substring(1);
      }
      newItem.setData("fieldName", fieldName);
      newItem.setData("value", value);
      fieldNameTreeItemMap.put(fieldName, newItem);

      if (value == null) {
        newItem.setText(key + " : null");
        newItem.setImage(nullImage);
      } else if (value instanceof Map) {
        newItem.setText(key);
        newItem.setImage(mapImage);
        drawItem(fieldName, newItem, (Map) value, expand);
      } else if (value instanceof List) {
        newItem.setText(key);
        newItem.setImage(listImage);
        drawItem(fieldName, newItem, (List) value, expand);
      } else {
        setItemInfo(newItem, key, value);
      }

      if (expand) {
        parentItem.setExpanded(expand);
        newItem.setExpanded(expand);
      }
    }
  }
  public QueryResult<VariantInfo> getRecordsMongo(
      int page, int start, int limit, MutableInt count, Map<String, String> options) {

    long startTime = System.currentTimeMillis();
    QueryResult<VariantInfo> queryResult = new QueryResult<>();

    List<VariantInfo> res = new ArrayList<>();
    String sourceId = options.get("studyId");
    DBCollection coll = db.getCollection("variants");

    BasicDBObject elemMatch = new BasicDBObject("sourceId", sourceId);
    DBObject query = new BasicDBObject();
    BasicDBList orList = new BasicDBList();

    Map<String, List<String>> sampleGenotypes = processSamplesGT(options);

    System.out.println("map = " + options);

    if (options.containsKey("region") && !options.get("region").equals("")) {
      String[] regions = options.get("region").split(",");
      Pattern pattern = Pattern.compile("(\\w+):(\\d+)-(\\d+)");
      Matcher matcher, matcherChr;

      for (int i = 0; i < regions.length; i++) {
        String region = regions[i];
        matcher = pattern.matcher(region);
        if (matcher.find()) {
          String chr = matcher.group(1);
          int s = Integer.valueOf(matcher.group(2));
          int e = Integer.valueOf(matcher.group(3));

          DBObject regionClause = new BasicDBObject("chr", chr);
          regionClause.put("pos", new BasicDBObject("$gte", s).append("$lte", e));
          orList.add(regionClause);
        } else {

          Pattern patternChr = Pattern.compile("(\\w+)");
          matcherChr = patternChr.matcher(region);

          if (matcherChr.find()) {
            String chr = matcherChr.group();
            DBObject regionClause = new BasicDBObject("chr", chr);
            orList.add(regionClause);
          }
        }
      }
      query.put("$or", orList);

    } else if (options.containsKey("genes") && !options.get("genes").equals("")) {
      orList = processGeneList(options.get("genes"));
      if (orList.size() > 0) {
        query.put("$or", orList);
      } else {
        queryResult.setWarningMsg("Wrong gene name");
        queryResult.setResult(res);
        queryResult.setNumResults(res.size());
        return queryResult;
      }
    }

    if (options.containsKey("conseq_type") && !options.get("conseq_type").equals("")) {
      String[] cts = options.get("conseq_type").split(",");

      BasicDBList ctList = new BasicDBList();
      for (String ct : cts) {
        ctList.add(ct);
      }
      elemMatch.put("effects", new BasicDBObject("$in", ctList));
    }

    if (sampleGenotypes.size() > 0) {
      for (Map.Entry<String, List<String>> entry : sampleGenotypes.entrySet()) {
        BasicDBList gtList = new BasicDBList();
        for (String gt : entry.getValue()) {
          gtList.add(gt);
        }
        elemMatch.put("samples." + entry.getKey() + ".GT", new BasicDBObject("$in", gtList));
      }
    }

    if (options.containsKey("miss_gt") && !options.get("miss_gt").equalsIgnoreCase("")) {
      Integer val = Integer.valueOf(options.get("miss_gt"));
      Object missGt = getMongoOption(options.get("option_miss_gt"), val);
      elemMatch.put("stats.missGenotypes", missGt);
    }

    BasicDBList andControls = new BasicDBList();

    if (options.containsKey("maf_1000g_controls")
        && !options.get("maf_1000g_controls").equalsIgnoreCase("")) {
      BasicDBList or = new BasicDBList();
      or.add(new BasicDBObject("attributes.1000G_maf", new BasicDBObject("$exists", false)));
      or.add(
          new BasicDBObject(
              "attributes.1000G_maf",
              new BasicDBObject("$lte", options.get("maf_1000g_controls"))));

      andControls.add(new BasicDBObject("$or", or));
    }

    if (options.containsKey("maf_1000g_afr_controls")
        && !options.get("maf_1000g_afr_controls").equalsIgnoreCase("")) {
      BasicDBList or = new BasicDBList();
      or.add(new BasicDBObject("attributes.1000G_AFR_maf", new BasicDBObject("$exists", false)));
      or.add(
          new BasicDBObject(
              "attributes.1000G_AFR_maf",
              new BasicDBObject("$lte", options.get("maf_1000g_afr_controls"))));

      andControls.add(new BasicDBObject("$or", or));
    }

    if (options.containsKey("maf_1000g_asi_controls")
        && !options.get("maf_1000g_asi_controls").equalsIgnoreCase("")) {
      BasicDBList or = new BasicDBList();
      or.add(new BasicDBObject("attributes.1000G_ASI_maf", new BasicDBObject("$exists", false)));
      or.add(
          new BasicDBObject(
              "attributes.1000G_ASI_maf",
              new BasicDBObject("$lte", options.get("maf_1000g_asi_controls"))));

      andControls.add(new BasicDBObject("$or", or));
    }

    if (options.containsKey("maf_1000g_eur_controls")
        && !options.get("maf_1000g_eur_controls").equalsIgnoreCase("")) {
      System.out.print("EUR");
      BasicDBList or = new BasicDBList();
      or.add(new BasicDBObject("attributes.1000G_EUR_maf", new BasicDBObject("$exists", false)));
      or.add(
          new BasicDBObject(
              "attributes.1000G_EUR_maf",
              new BasicDBObject("$lte", options.get("maf_1000g_eur_controls"))));

      andControls.add(new BasicDBObject("$or", or));
    }
    if (options.containsKey("maf_1000g_ame_controls")
        && !options.get("maf_1000g_ame_controls").equalsIgnoreCase("")) {
      System.out.print("AME");
      BasicDBList or = new BasicDBList();
      or.add(new BasicDBObject("attributes.1000G_AME_maf", new BasicDBObject("$exists", false)));
      or.add(
          new BasicDBObject(
              "attributes.1000G_AME_maf",
              new BasicDBObject("$lte", options.get("maf_1000g_ame_controls"))));

      andControls.add(new BasicDBObject("$or", or));
    }
    if (options.containsKey("maf_evs_controls")
        && !options.get("maf_evs_controls").equalsIgnoreCase("")) {
      BasicDBList or = new BasicDBList();
      or.add(new BasicDBObject("attributes.EVS_maf", new BasicDBObject("$exists", false)));
      or.add(
          new BasicDBObject(
              "attributes.EVS_maf", new BasicDBObject("$lte", options.get("maf_evs_controls"))));

      andControls.add(new BasicDBObject("$or", or));
    }

    if (options.containsKey("maf_bier_controls")
        && !options.get("maf_bier_controls").equalsIgnoreCase("")) {
      BasicDBList or = new BasicDBList();
      or.add(new BasicDBObject("attributes.BIER_maf", new BasicDBObject("$exists", false)));
      or.add(
          new BasicDBObject(
              "attributes.BIER_maf", new BasicDBObject("$lte", options.get("maf_bier_controls"))));

      andControls.add(new BasicDBObject("$or", or));
    }

    if (andControls.size() > 0) {
      elemMatch.append("$and", andControls);
    }

    query.put("sources", new BasicDBObject("$elemMatch", elemMatch));

    System.out.println("#############################");
    System.out.println(query);
    System.out.println("#############################");

    long dbStart = System.currentTimeMillis();

    DBObject sort = null;
    DBCursor cursor;

    if (options.containsKey("sort")) {
      sort = getQuerySort(options.get("sort"));
      cursor = coll.find(query).sort(sort).skip(start).limit(limit);
    } else {
      cursor = coll.find(query).skip(start).limit(limit);
    }

    count.setValue(cursor.count());

    queryResult.setDbTime(dbStart - System.currentTimeMillis());

    for (DBObject obj : cursor) {

      BasicDBObject elem = (BasicDBObject) obj;
      VariantInfo vi = new VariantInfo();
      VariantStats vs = new VariantStats();

      String chr = elem.getString("chr");
      int pos = elem.getInt("pos");

      vi.setChromosome(chr);
      vi.setPosition(pos);

      BasicDBList studies = (BasicDBList) elem.get("sources");

      Iterator<Object> it = studies.iterator();
      while (it.hasNext()) {
        BasicDBObject study = (BasicDBObject) it.next();

        if (study.getString("sourceId").equalsIgnoreCase(sourceId)) {

          BasicDBObject stats = (BasicDBObject) study.get("stats");

          String ref = study.getString("ref");
          BasicDBList alt = (BasicDBList) study.get("alt");
          vi.setRef(ref);
          vi.setAlt(Joiner.on(",").join(alt.toArray()));
          vs.setMaf((float) stats.getDouble("maf"));
          vs.setMgf((float) stats.getDouble("mgf"));
          vs.setMafAllele(stats.getString("alleleMaf"));
          vs.setMgfAllele(stats.getString("genotypeMaf"));
          vs.setMissingAlleles(stats.getInt("missAllele"));
          vs.setMissingGenotypes(stats.getInt("missGenotypes"));
          vs.setMendelinanErrors(stats.getInt("mendelErr"));
          vs.setCasesPercentDominant((float) stats.getDouble("casesPercentDominant"));
          vs.setControlsPercentDominant((float) stats.getDouble("controlsPercentDominant"));
          vs.setCasesPercentRecessive((float) stats.getDouble("casesPercentRecessive"));
          vs.setControlsPercentRecessive((float) stats.getDouble("controlsPercentRecessive"));

          BasicDBObject samples = (BasicDBObject) study.get("samples");

          for (String sampleName : samples.keySet()) {

            DBObject sample = (DBObject) samples.get(sampleName);

            if (sample.containsField("GT")) {
              String sampleGT = (String) sample.get("GT");
              vi.addSammpleGenotype(sampleName, sampleGT);
            }
          }

          vi.setSnpid((String) study.get("snpId"));

          if (study.containsField("effects")) {
            BasicDBList conseqTypes = (BasicDBList) study.get("effects");
            conseqTypes.remove("");
            String cts = Joiner.on(",").join(conseqTypes.iterator());
            vi.addConsequenceTypes(cts);
          }

          if (study.containsField("genes")) {
            BasicDBList genesList = (BasicDBList) study.get("genes");
            String genes = Joiner.on(",").join(genesList.iterator());
            vi.addGenes(genes);
          }

          if (study.containsField("attributes")) {

            BasicDBObject attr = (BasicDBObject) study.get("attributes");

            if (attr.containsField("1000G_maf")) {
              vi.addControl("1000G_maf", (String) attr.get("1000G_maf"));
              vi.addControl("1000G_amaf", (String) attr.get("1000G_amaf"));
              vi.addControl("1000G_gt", (String) attr.get("1000G_gt"));
            }

            if (attr.containsField("1000G_ASI_maf")) {
              vi.addControl("1000G-ASI_maf", (String) attr.get("1000G_ASI_maf"));
              vi.addControl("1000G-ASI_amaf", (String) attr.get("1000G_ASI_amaf"));
              vi.addControl("1000G-ASI_gt", (String) attr.get("1000G_ASI_gt"));
            }

            if (attr.containsField("1000G_AFR_maf")) {
              vi.addControl("1000G-AFR_maf", (String) attr.get("1000G_AFR_maf"));
              vi.addControl("1000G-AFR_amaf", (String) attr.get("1000G_AFR_amaf"));
              vi.addControl("1000G-AFR_gt", (String) attr.get("1000G_AFR_gt"));
            }

            if (attr.containsField("1000G_AME_maf")) {
              vi.addControl("1000G-AME_maf", (String) attr.get("1000G_AME_maf"));
              vi.addControl("1000G-AME_amaf", (String) attr.get("1000G_AME_amaf"));
              vi.addControl("1000G-AME_gt", (String) attr.get("1000G_AME_gt"));
            }

            if (attr.containsField("1000G_EUR_maf")) {
              vi.addControl("1000G-EUR_maf", (String) attr.get("1000G_EUR_maf"));
              vi.addControl("1000G-EUR_amaf", (String) attr.get("1000G_EUR_amaf"));
              vi.addControl("1000G-EUR_gt", (String) attr.get("1000G_EUR_gt"));
            }

            if (attr.containsField("EVS_maf")) {
              vi.addControl("EVS_maf", (String) attr.get("EVS_maf"));
              vi.addControl("EVS_amaf", (String) attr.get("EVS_amaf"));
              vi.addControl("EVS_gt", (String) attr.get("EVS_gt"));
            }

            if (attr.containsField("BIER_maf")) {
              vi.addControl("BIER_maf", (String) attr.get("BIER_maf"));
              vi.addControl("BIER_amaf", (String) attr.get("BIER_amaf"));
              vi.addControl("BIER_gt", (String) attr.get("BIER_gt"));
            }

            if (attr.containsField("PolyphenScore")) {
              vi.setPolyphen_score(Double.parseDouble(attr.getString("PolyphenScore")));
              vi.setPolyphen_effect(Integer.parseInt(attr.getString("PolyphenEffect")));
            }

            if (attr.containsField("SIFTScore")) {
              vi.setSift_score(Double.parseDouble(attr.getString("SIFTScore")));
              vi.setSift_effect(Integer.parseInt(attr.getString("SIFTEffect")));
            }
          }
          continue;
        }
      }
      vi.addStats(vs);
      res.add(vi);
    }

    queryResult.setResult(res);
    queryResult.setTime(startTime - System.currentTimeMillis());

    return queryResult;
  }