private void doMatches(Map<String, Object> ret, BagQueryResult bqr) {

    for (Entry<Integer, List> pair : bqr.getMatches().entrySet()) {
      Map<String, Object> resultItem;
      InterMineObject imo;
      try {
        imo = im.getObjectStore().getObjectById(pair.getKey());
      } catch (ObjectStoreException e) {
        throw new IllegalStateException("Could not retrieve object reported as match", e);
      }
      String idKey = String.valueOf(imo.getId());
      if (ret.containsKey(idKey)) {
        resultItem = (Map<String, Object>) ret.get(idKey);
      } else {
        resultItem = new HashMap<String, Object>();
        resultItem.put("identifiers", new HashMap<String, Object>());
      }
      if (!resultItem.containsKey("summary")) {
        resultItem.put("summary", getObjectDetails(imo));
      }
      Map<String, Object> identifiers = (Map<String, Object>) resultItem.get("identifiers");
      for (Object o : pair.getValue()) {
        String ident = (String) o;
        if (!identifiers.containsKey(ident)) {
          identifiers.put(ident, new HashSet<String>());
        }
        Set<String> categories = (Set<String>) identifiers.get(ident);
        categories.add("MATCH");
      }
      String className = DynamicUtil.getSimpleClassName(imo.getClass());
      resultItem.put("type", className.replaceAll("^.*\\.", ""));
      ret.put(idKey, resultItem);
    }
  }
Пример #2
0
  /**
   * Adds objects to the a bag for the matches against a set of identifiers.
   *
   * @param ids A collection of identifiers
   * @param bag The bag to add the objects to
   * @param type The type of this bag
   * @param extraFieldValue An extra value for disambiguation.
   * @param unmatchedIds An accumulator to store the failed matches.
   * @param acceptableIssues the list of issues that are OK to ignore.
   * @throws ClassNotFoundException if the type is not a valid class.
   * @throws InterMineException If something goes wrong building the bag.
   * @throws ObjectStoreException If there is a problem on the database level.
   */
  protected void addIdsToList(
      final Collection<? extends String> ids,
      final InterMineBag bag,
      final String type,
      final String extraFieldValue,
      final Set<String> unmatchedIds,
      final Collection<String> acceptableIssues)
      throws ClassNotFoundException, InterMineException, ObjectStoreException {
    final BagQueryResult result =
        runner.searchForBag(
            type,
            new ArrayList<String>(ids),
            extraFieldValue,
            acceptableIssues.contains(BagQueryResult.WILDCARD));
    bag.addIdsToBag(result.getMatches().keySet(), type);

    for (final String issueType : result.getIssues().keySet()) {
      if (acceptableIssues.contains(issueType)) {
        bag.addIdsToBag(result.getIssueIds(issueType), type);
      } else {
        unmatchedIds.addAll(result.getInputIdentifiersForIssue(issueType));
      }
    }
    unmatchedIds.addAll(result.getUnresolvedIdentifiers());
  }
  private void doDuplicates(final Map<String, Object> ret, BagQueryResult bqr, String key) {
    Map<String, Map<String, List>> issues = bqr.getIssues().get(key);
    if (issues == null) {
      return;
    }
    for (Map<String, List> issueSet : issues.values()) {
      for (Entry<String, List> identToObjects : issueSet.entrySet()) {
        String ident = identToObjects.getKey();
        for (Object o : identToObjects.getValue()) {
          InterMineObject imo;
          Map<String, Object> resultItem;
          if (o instanceof Integer) {
            try {
              imo = im.getObjectStore().getObjectById((Integer) o);
            } catch (ObjectStoreException e) {
              throw new IllegalStateException("Could not retrieve object reported as match", e);
            }
          } else if (o instanceof ConvertedObjectPair) {
            imo = ((ConvertedObjectPair) o).getNewObject();
          } else {
            imo = (InterMineObject) o;
          }
          String idKey = String.valueOf(imo.getId());
          if (ret.containsKey(idKey)) {
            resultItem = (Map<String, Object>) ret.get(idKey);
          } else {
            resultItem = new HashMap<String, Object>();
            resultItem.put("identifiers", new HashMap<String, Object>());
          }
          if (!resultItem.containsKey("summary")) {
            resultItem.put("summary", getObjectDetails(imo));
          }
          Map<String, Object> identifiers = (Map<String, Object>) resultItem.get("identifiers");

          if (!identifiers.containsKey(ident)) {
            identifiers.put(ident, new HashSet<String>());
          }
          Set<String> categories = (Set<String>) identifiers.get(ident);
          categories.add(key);
          String className = DynamicUtil.getSimpleClassName(imo.getClass());
          resultItem.put("type", className.replaceAll("^.*\\.", ""));
          ret.put(idKey, resultItem);
        }
      }
    }
  }