コード例 #1
0
ファイル: EntryController.java プロジェクト: chimaerase/ice
  public List<PartData> retrieveOwnerEntries(
      String userId, String ownerEmail, ColumnField sort, boolean asc, int start, int limit) {
    List<Entry> entries;
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);

    if (authorization.isAdmin(userId) || account.getEmail().equals(ownerEmail)) {
      entries = dao.retrieveOwnerEntries(ownerEmail, sort, asc, start, limit);
    } else {
      Set<Group> accountGroups = new HashSet<>(account.getGroups());
      GroupController controller = new GroupController();
      Group everybodyGroup = controller.createOrRetrievePublicGroup();
      accountGroups.add(everybodyGroup);
      // retrieve entries for user that can be read by others
      entries =
          dao.retrieveUserEntries(account, ownerEmail, accountGroups, sort, asc, start, limit);
    }

    ArrayList<PartData> data = new ArrayList<>();
    for (Entry entry : entries) {
      PartData info = ModelToInfoFactory.createTableViewData(userId, entry, false);
      info.setViewCount(DAOFactory.getAuditDAO().getHistoryCount(entry));
      data.add(info);
    }
    return data;
  }
コード例 #2
0
ファイル: EntryController.java プロジェクト: chimaerase/ice
  public long updatePart(String userId, long partId, PartData part) {
    Entry existing = dao.get(partId);
    authorization.expectWrite(userId, existing);

    Entry entry = InfoToModelFactory.updateEntryField(part, existing);
    entry.getLinkedEntries().clear();
    if (part.getLinkedParts() != null && part.getLinkedParts().size() > 0) {
      for (PartData data : part.getLinkedParts()) {
        Entry linked = dao.getByPartNumber(data.getPartId());

        // check permissions on link
        if (!authorization.canRead(userId, linked)) {
          continue;
        }

        if (!canLink(entry, linked)) continue;

        entry.getLinkedEntries().add(linked);
      }
    }

    entry.setModificationTime(Calendar.getInstance().getTime());
    if (entry.getVisibility() == Visibility.DRAFT.getValue()) {
      List<EntryField> invalidFields = EntryUtil.validates(part);
      if (invalidFields.isEmpty()) entry.setVisibility(Visibility.OK.getValue());
    }
    entry = dao.update(entry);

    // check pi email
    String piEmail = entry.getPrincipalInvestigatorEmail();
    if (StringUtils.isNotEmpty(piEmail)) {
      Account pi = DAOFactory.getAccountDAO().getByEmail(piEmail);
      if (pi != null) {
        // add write permission for the PI (method also checks to see if permission already exists)
        AccessPermission accessPermission = new AccessPermission();
        accessPermission.setArticle(AccessPermission.Article.ACCOUNT);
        accessPermission.setArticleId(pi.getId());
        accessPermission.setType(AccessPermission.Type.WRITE_ENTRY);
        accessPermission.setTypeId(entry.getId());
        permissionsController.addPermission(userId, accessPermission);
      }
    }

    return entry.getId();
  }
コード例 #3
0
ファイル: EntryController.java プロジェクト: chimaerase/ice
  public List<PartData> getEntriesSharedWithUser(
      String userId, ColumnField field, boolean asc, int start, int limit) {
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    GroupController groupController = new GroupController();
    Group publicGroup = groupController.createOrRetrievePublicGroup();
    Set<Group> accountGroups = account.getGroups();
    accountGroups.remove(publicGroup);
    List<Entry> entries =
        dao.sharedWithUserEntries(account, accountGroups, field, asc, start, limit);

    ArrayList<PartData> data = new ArrayList<>();
    for (Entry entry : entries) {
      PartData info = ModelToInfoFactory.createTableViewData(userId, entry, false);
      info.setViewCount(DAOFactory.getAuditDAO().getHistoryCount(entry));
      data.add(info);
    }
    return data;
  }
コード例 #4
0
ファイル: EntryController.java プロジェクト: chimaerase/ice
  /**
   * Moves the specified list of entries to the deleted folder
   *
   * @param userId unique identifier for user making the request. Must have write access privileges
   *     on the entries in the list
   * @param list unique identifiers for entries
   * @return true or false if operation succeeds on all listed entries or not
   */
  public boolean moveEntriesToTrash(String userId, ArrayList<PartData> list) {
    List<Entry> toTrash = new LinkedList<>();
    for (PartData data : list) {
      Entry entry = dao.get(data.getId());
      if (entry == null || !authorization.canWriteThoroughCheck(userId, entry)) return false;

      toTrash.add(entry);
    }

    // add to bin
    try {
      for (Entry entry : toTrash) {
        entry.setVisibility(Visibility.DELETED.getValue());
        dao.update(entry);
      }
    } catch (DAOException de) {
      Logger.error(de);
      return false;
    }

    return true;
  }
コード例 #5
0
  /**
   * sets the corresponding fields in data only if they are not null
   *
   * @param data PartData object to converted to Entry
   * @param entry if null, a new entry is created otherwise entry is used
   * @return converted PartData object
   */
  public static Entry updateEntryField(PartData data, Entry entry) {
    EntryType type = data.getType();
    if (type == null) return entry;

    switch (type) {
      case PLASMID:
        entry = setPlasmidFields(data.getPlasmidData(), entry);
        break;

      case STRAIN:
        entry = setStrainFields(data.getStrainData(), entry);
        break;

      case PART:
        break;

      case ARABIDOPSIS:
        entry = setSeedFields(data.getArabidopsisSeedData(), entry);
        break;
    }

    entry = setCommon(entry, data);
    return entry;
  }
コード例 #6
0
  public static Entry infoToEntry(PartData info) {
    EntryType type = info.getType();
    Entry entry;

    switch (type) {
      case PLASMID:
        entry = setPlasmidFields(info.getPlasmidData(), new Plasmid());
        break;

      case STRAIN:
        entry = setStrainFields(info.getStrainData(), new Strain());
        break;

      case ARABIDOPSIS:
        entry = setSeedFields(info.getArabidopsisSeedData(), new ArabidopsisSeed());
        break;

      case PART:
      default:
        entry = new Part();
        break;
    }

    if (entry == null) return null;

    // common fields
    if (StringUtils.isEmpty(info.getRecordId())) entry.setRecordId(UUID.randomUUID().toString());
    else entry.setRecordId(info.getRecordId());

    entry.setVersionId(entry.getRecordId());
    if (info.getCreationTime() == 0) entry.setCreationTime(new Date());
    else entry.setCreationTime(new Date(info.getCreationTime()));

    entry.setModificationTime(entry.getCreationTime());
    entry = setCommon(entry, info);
    return entry;
  }
コード例 #7
0
ファイル: EntryController.java プロジェクト: chimaerase/ice
  protected PartData retrieveEntryDetails(String userId, Entry entry) {
    // user must be able to read if not public entry
    if (!permissionsController.isPubliclyVisible(entry)) authorization.expectRead(userId, entry);

    PartData partData = ModelToInfoFactory.getInfo(entry);
    if (partData == null) return null;
    boolean hasSequence = sequenceDAO.hasSequence(entry.getId());

    partData.setHasSequence(hasSequence);
    boolean hasOriginalSequence = sequenceDAO.hasOriginalSequence(entry.getId());
    partData.setHasOriginalSequence(hasOriginalSequence);

    // permissions
    partData.setCanEdit(authorization.canWriteThoroughCheck(userId, entry));
    partData.setPublicRead(permissionsController.isPubliclyVisible(entry));

    // create audit event if not owner
    // todo : remote access check
    if (userId != null
        && authorization.getOwner(entry) != null
        && !authorization.getOwner(entry).equalsIgnoreCase(userId)) {
      try {
        Audit audit = new Audit();
        audit.setAction(AuditType.READ.getAbbrev());
        audit.setEntry(entry);
        audit.setUserId(userId);
        audit.setLocalUser(true);
        audit.setTime(new Date(System.currentTimeMillis()));
        auditDAO.create(audit);
      } catch (Exception e) {
        Logger.error(e);
      }
    }

    // retrieve more information about linked entries if any (default only contains id)
    if (partData.getLinkedParts() != null) {
      ArrayList<PartData> newLinks = new ArrayList<>();
      for (PartData link : partData.getLinkedParts()) {
        Entry linkedEntry = dao.get(link.getId());
        if (!authorization.canRead(userId, linkedEntry)) continue;

        link = ModelToInfoFactory.createTipView(linkedEntry);
        Sequence sequence = sequenceDAO.getByEntry(linkedEntry);
        if (sequence != null) {
          link.setBasePairCount(sequence.getSequence().length());
          link.setFeatureCount(sequence.getSequenceFeatures().size());
        }

        newLinks.add(link);
      }
      partData.getLinkedParts().clear();
      partData.getLinkedParts().addAll(newLinks);
    }

    // check if there is a parent available
    List<Entry> parents = dao.getParents(entry.getId());
    if (parents == null) return partData;

    for (Entry parent : parents) {
      if (!authorization.canRead(userId, parent)) continue;

      if (parent.getVisibility() != Visibility.OK.getValue()
          && !authorization.canWriteThoroughCheck(userId, entry)) continue;

      EntryType type = EntryType.nameToType(parent.getRecordType());
      PartData parentData = new PartData(type);
      parentData.setId(parent.getId());
      parentData.setName(parent.getName());
      parentData.setVisibility(Visibility.valueToEnum(parent.getVisibility()));
      partData.getParents().add(parentData);
    }

    return partData;
  }
コード例 #8
0
ファイル: EntryController.java プロジェクト: chimaerase/ice
  /**
   * Retrieves and sets the default values for the entry. Some of these values (e.g. PI, and Funding
   * Source) are set by individual users as part of their personal preferences
   *
   * @param userId Unique identifier for user requesting the values.
   * @param type entry type
   * @return PartData object with the retrieve part defaults
   */
  public PartData getPartDefaults(String userId, EntryType type) {
    PartData partData = new PartData(type);
    PreferencesController preferencesController = new PreferencesController();

    // pi defaults
    String value =
        preferencesController.getPreferenceValue(
            userId, PreferenceKey.PRINCIPAL_INVESTIGATOR.name());
    if (value != null) {
      Account piAccount = accountController.getByEmail(value);
      if (piAccount == null) {
        partData.setPrincipalInvestigator(value);
      } else {
        partData.setPrincipalInvestigator(piAccount.getFullName());
        partData.setPrincipalInvestigatorEmail(piAccount.getEmail());
        partData.setPrincipalInvestigatorId(piAccount.getId());
      }
    }

    // funding source defaults
    value = preferencesController.getPreferenceValue(userId, PreferenceKey.FUNDING_SOURCE.name());
    if (value != null) {
      partData.setFundingSource(value);
    }

    // owner and creator details
    Account account = accountController.getByEmail(userId);
    if (account != null) {
      partData.setOwner(account.getFullName());
      partData.setOwnerEmail(account.getEmail());
      partData.setCreator(partData.getOwner());
      partData.setCreatorEmail(partData.getOwnerEmail());
    }

    // set the entry type defaults
    return EntryUtil.setPartDefaults(partData);
  }
コード例 #9
0
  private static Entry setCommon(Entry entry, PartData info) {
    if (entry == null || info == null) return null;

    if (info.getName() != null) entry.setName(info.getName());

    if (info.getSelectionMarkers() != null) {
      Set<SelectionMarker> markers = getSelectionMarkers(info.getSelectionMarkers(), entry);
      entry.setSelectionMarkers(markers);
    }

    if (info.getReferences() != null) entry.setReferences(info.getReferences());

    if (StringUtils.isBlank(entry.getPartNumber())) entry.setPartNumber(info.getPartId());

    Date currentTime = new Date();
    if (entry.getCreationTime() == null) entry.setCreationTime(currentTime);

    entry.setModificationTime(currentTime);

    if (info.getOwnerEmail() != null) {
      entry.setOwnerEmail(info.getOwnerEmail());
    }

    if (info.getOwner() != null) entry.setOwner(info.getOwner());

    if (info.getCreatorEmail() != null) {
      entry.setCreatorEmail(info.getCreatorEmail());
    }

    if (info.getCreator() != null) entry.setCreator(info.getCreator());

    if (info.getStatus() == null) {
      if (StringUtils.isBlank(entry.getStatus())) entry.setStatus("");
    } else entry.setStatus(info.getStatus());

    if (info.getAlias() != null) entry.setAlias(info.getAlias());

    if (info.getBioSafetyLevel() == null) {
      if (entry.getBioSafetyLevel() == null) entry.setBioSafetyLevel(0);
    } else entry.setBioSafetyLevel(info.getBioSafetyLevel());

    if (info.getShortDescription() != null) entry.setShortDescription(info.getShortDescription());
    if (info.getLongDescription() != null) entry.setLongDescription(info.getLongDescription());
    if (info.getIntellectualProperty() != null)
      entry.setIntellectualProperty(info.getIntellectualProperty());

    Set<Link> links = getLinks(info.getLinks(), entry);
    entry.setLinks(links);

    Visibility visibility = info.getVisibility();
    if (visibility != null) entry.setVisibility(visibility.getValue());

    // checking for null instead of blank since it could be cleared
    if (info.getFundingSource() != null) entry.setFundingSource(info.getFundingSource());
    if (info.getPrincipalInvestigator() != null)
      entry.setPrincipalInvestigator(info.getPrincipalInvestigator());
    if (info.getPrincipalInvestigatorEmail() != null)
      entry.setPrincipalInvestigatorEmail(info.getPrincipalInvestigatorEmail());

    if (info.getKeywords() != null) entry.setKeywords(info.getKeywords());

    // parameters
    List<Parameter> parameters = getParameters(info.getCustomFields(), entry);
    entry.setParameters(parameters);
    return entry;
  }