public List<ShowSimple> list(String status) {
    BasicDBObject criteria = new BasicDBObject();

    // FIXME
    if (!"all".equals(status)) {
      criteria.put("status", ShowStatus.ACTIVE.ordinal());
    }
    DBCursor selectedShows =
        db.getCollection("show").find(criteria).sort(new BasicDBObject("name", 1));

    List<ShowSimple> mappedShows = new ArrayList<>();
    for (DBObject show : selectedShows) {
      mappedShows.add(mapper.map(show, ShowSimple.class));
    }
    Collections.sort(
        mappedShows,
        new Comparator<ShowSimple>() {
          @Override
          public int compare(ShowSimple s1, ShowSimple s2) {
            return s1.getName().toLowerCase().compareTo(s2.getName().toLowerCase());
          }
        });
    return mappedShows;
  }
  public QueryResult<VariantAnalysisInfo> getAnalysisInfo(String studyId) {

    long start = System.currentTimeMillis();
    QueryResult<VariantAnalysisInfo> qres = new QueryResult<>();
    VariantAnalysisInfo vi = new VariantAnalysisInfo();

    DBCollection coll = db.getCollection("sources");
    DBCollection collV = db.getCollection("variants");

    long dbStart = System.currentTimeMillis();
    DBObject study = coll.findOne(new BasicDBObject("alias", studyId));

    if (study != null) {
      Iterator<Object> it = ((BasicDBList) study.get("samples")).iterator();

      while (it.hasNext()) {
        vi.addSample((String) it.next());
      }

      BasicDBObject gs = (BasicDBObject) study.get("globalStats");

      for (String elem : gs.keySet()) {
        if (!elem.equalsIgnoreCase("consequenceTypes")) {
          double val = gs.getDouble(elem);
          vi.addGlobalStats(elem, val);
        } else {

          BasicDBObject cts = (BasicDBObject) gs.get("consequenceTypes");
          for (String ct : cts.keySet()) {
            vi.addConsequenceType(ct, cts.getInt(ct));
          }
        }
      }
    }
    qres.setDbTime(System.currentTimeMillis() - dbStart);

    qres.setResult(Arrays.asList(vi));

    qres.setTime(System.currentTimeMillis() - start);

    return qres;
  }
示例#3
0
    public TaskWrite(Map map1, Map m_max, Map m_min, DBCollection coll, ModbusSlaveSet slave) {

      try {
        synchronized (slave) {
          Calendar calener = Calendar.getInstance();
          Date d1 = calener.getTime();
          Date d2 = new Date(calener.getTime().getTime() - 5000);
          BasicDBObject b2 = new BasicDBObject();
          b2.put("$gte", d2);
          b2.put("$lte", d1);
          DBCursor cursor =
              coll.find(new BasicDBObject("_id", b2)).sort(new BasicDBObject("_id", -1)).limit(1);
          while (cursor.hasNext()) {
            DBObject dbo = cursor.next();
            Set set1 = map1.entrySet();
            Iterator it1 = set1.iterator();
            while (it1.hasNext()) {
              Map.Entry<String, Map<String, String>> entry =
                  (Map.Entry<String, Map<String, String>>) it1.next();
              Map<String, String> map2 = entry.getValue();
              for (Iterator it2 = map2.entrySet().iterator(); it2.hasNext(); ) {
                Map.Entry<String, String> entry2 = (Map.Entry<String, String>) it2.next();
                String name = entry2.getKey().toString();
                String paramAddr = entry2.getValue().toString();
                int fun = (int) (Double.parseDouble(paramAddr));
                if (paramAddr.substring(0, 1).equals("4")) {
                  double value = Double.parseDouble(dbo.get(name).toString());
                  double dmax = (Double) m_max.get(name);
                  double dmin = (Double) m_min.get(name);
                  double dValue = 0;
                  if (value > dmax || value < dmin) {
                    if (value >= 0) {
                      dValue = 32000 * (int) (value / dmax);
                    }
                    if (value < 0) {
                      dValue = -32000 * (int) (value / dmin);
                    }
                    // slave.getProcessImage(3).setInputRegister(fun % 10000, (short) dValue);
                  } else { /// 参数超限报警
                    JOptionPane.showMessageDialog(null, "参数超限");
                    slave.stop();
                  }
                }
                if (paramAddr.substring(0, 1).equals("3")) {
                  double value = Double.parseDouble(dbo.get(name).toString());
                  double dmax = (Double) m_max.get(name);
                  double dmin = (Double) m_min.get(name);
                  double dValue = 0;
                  if (value > dmax || value < dmin) {
                    if (value >= 0) {
                      dValue = 32000 * (int) (value / dmax);
                    }
                    if (value < 0) {
                      dValue = -32000 * (int) (value / dmin);
                    }
                    // slave.getProcessImage(3).setHoldingRegister(fun % 10000, (short) dValue);
                  } else { /// 参数超限报警
                    JOptionPane.showMessageDialog(null, "参数超限");
                    slave.stop();
                  }
                  ;
                }
                if (paramAddr.substring(0, 1).equals("2")) {
                  String value = dbo.get(name).toString();
                  /// slave.getProcessImage(4).setInput(fun % 10000, Boolean.valueOf(value));
                }
                if (paramAddr.substring(0, 1).equals("1")) {
                  String value = dbo.get(name).toString();
                  // slave.getProcessImage(4).setCoil(fun % 10000, Boolean.valueOf(value));
                }
              }
            }
          }
        }
      } catch (Exception ex) {
      }
    }
示例#4
0
    public TaskRead(Map map1, Map m_max, Map m_min, DBCollection coll, ModbusSlaveSet slave) {
      try {
        //// 此处只要点击开始就能保存数据
        /// 方案:利用数据源发送单个布尔型变量(1,0)交替,链接成功,先判断是否链接成功,然后在保存数据
        synchronized (slave) {
          Map map = new HashMap();
          Set set1 = map1.entrySet();
          Iterator it1 = set1.iterator();
          while (it1.hasNext()) {
            Map.Entry<String, Map<String, String>> entry =
                (Map.Entry<String, Map<String, String>>) it1.next();
            Map<String, String> map2 = entry.getValue();
            for (Iterator it2 = map2.entrySet().iterator(); it2.hasNext(); ) {
              Map.Entry<String, String> entry2 = (Map.Entry<String, String>) it2.next();
              String name = entry2.getKey().toString();
              String paramAddr = entry2.getValue().toString();
              int fun = (int) (Double.parseDouble(paramAddr));
              if (paramAddr.substring(0, 1).equals("4")) {
                Short d4 = slave.getProcessImage(1).getInputRegister(fun % 10000);
                double dmax = (Double) m_max.get(name);
                double dmin = (Double) m_min.get(name);
                double dValue = 0;
                if (d4 >= 0) {
                  dValue = dmax * d4 / 32000;
                } else {
                  dValue = dmin * d4 / (-32000);
                }
                map.put(name, dValue);
              }
              if (paramAddr.substring(0, 1).equals("3")) {
                Short d3 = slave.getProcessImage(1).getHoldingRegister(fun % 10000);
                double dmax = (Double) m_max.get(name);
                double dmin = (Double) m_min.get(name);
                double dValue = 0;

                if (d3 >= 0) {
                  dValue = dmax * d3 / 32000;
                } else {
                  dValue = dmin * d3 / (-32000);
                }
                map.put(name, dValue);
              }
              if (paramAddr.substring(0, 1).equals("2")) {
                map.put(name, slave.getProcessImage(2).getInput(fun % 10000));
              }
              if (paramAddr.substring(0, 1).equals("1")) {
                Boolean a = slave.getProcessImage(2).getCoil(fun % 10000 - 1);
                map.put(name, a);
              }
            }
          }

          Calendar calendar = Calendar.getInstance();
          Date dd = calendar.getTime();

          BasicDBObject doc = new BasicDBObject();
          doc.put("_id", dd);

          Set set = map.entrySet();
          Iterator it = set.iterator();
          while (it.hasNext()) {
            Map.Entry<String, String> entry1 = (Map.Entry<String, String>) it.next();
            doc.put(entry1.getKey(), entry1.getValue());
          }
          coll.insert(doc);
        }
      } catch (Exception ex) {
      }
    }
  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;
  }
  public QueryResult getSimpleVariantsByRegion(
      Region region, String sourceId, QueryOptions options) {
    Long start, end, dbstart, dbend;
    start = System.currentTimeMillis();
    boolean includeStats;
    boolean includeEffects;
    if (!options.containsKey("stats") && !options.containsKey("effects")) {
      includeStats = true;
      includeEffects = true;
    } else {
      includeStats = options.containsKey("stats") && options.getBoolean("stats");
      includeEffects = options.containsKey("effects") && options.getBoolean("effects");
    }

    QueryResult<Variant> queryResult =
        new QueryResult<>(
            String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
    List<Variant> results = new ArrayList<>();
    String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
    String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
    BasicDBObject query =
        new BasicDBObject("position", new BasicDBObject("$gte", startRow).append("$lte", stopRow))
            .append("sources.sourceId", sourceId);
    DBCollection collection = db.getCollection("variants");
    dbstart = System.currentTimeMillis();
    DBCursor variantInStudies = collection.find(query);
    dbend = System.currentTimeMillis();
    queryResult.setDbTime(dbend - dbstart);

    for (DBObject result : variantInStudies) {
      String[] rowkeyParts = result.get("position").toString().split("_");
      String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", "");
      int position = Integer.parseInt(rowkeyParts[1]);
      BasicDBList studies = (BasicDBList) result.get("sources");
      BasicDBObject st = (BasicDBObject) studies.get(0);
      String ref = (String) st.get("ref");
      String alt = StringUtils.join((ArrayList<String>) st.get("alt"), ",");

      // TODO Needs rework
      Variant variant = new Variant(chromosome, position, position, ref, alt);

      // Set stats informations
      if (includeStats) {
        VariantStats stats = new VariantStats();
        BasicDBObject mongoStats = (BasicDBObject) st.get("stats");
        stats.setMaf((float) (double) mongoStats.get("maf"));
        stats.setMafAllele((String) mongoStats.get("alleleMaf"));
        stats.setMissingGenotypes((int) mongoStats.get("missing"));
        List<Genotype> genotypeCount = new ArrayList<>();
        for (BasicDBObject s : (List<BasicDBObject>) mongoStats.get("genotypeCount")) {
          for (Map.Entry<String, Object> entry : s.entrySet()) {
            Genotype genotype = new Genotype(entry.getKey());
            genotype.setCount((Integer) entry.getValue());
            genotypeCount.add(genotype);
          }
        }
        stats.setGenotypes(genotypeCount);
        variant.setStats(stats);
      }

      // TODO Set consequence type names
      if (includeEffects) {
        BasicDBList mongoEffects = (BasicDBList) st.get("effects");
        if (mongoEffects != null) {
          for (Object e : mongoEffects) {
            String effectObo = e.toString();
            VariantEffect effect = new VariantEffect();
            effect.setConsequenceTypeObo(effectObo);
            variant.addEffect(effect);
          }
        }
      }

      results.add(variant);
    }

    queryResult.setResult(results);
    queryResult.setNumResults(results.size());
    end = System.currentTimeMillis();
    queryResult.setTime(end - start);
    return queryResult;
  }