Examples with Account org.jbei.ice.storage.model.Account used on opensource projects

Example 76 with Account

use of org.jbei.ice.storage.model.Account in project ice by JBEI.

the class GroupControllerTest method testRetrieveGroupMembers.

@Test
public void testRetrieveGroupMembers() throws Exception {
    Account a1 = AccountCreator.createTestAccount("testRetrieveGroupMembers1", false);
    AccountCreator.createTestAccount("testRetrieveGroupMembers2", false);
    AccountCreator.createTestAccount("testRetrieveGroupMembers3", false);
    UserGroup user = new UserGroup();
    user.setDescription("desc");
    user.setLabel("label");
    user.setType(GroupType.PRIVATE);
    // create group
    user = controller.createGroup(a1.getEmail(), user);
    Assert.assertNotNull(user);
}

Example 77 with Account

use of org.jbei.ice.storage.model.Account in project ice by JBEI.

the class FolderAuthorization method canRead.

public boolean canRead(String userId, Folder folder) {
    if (controller.isPublicVisible(folder))
        return true;
    Account account = getAccount(userId);
    if (account == null)
        return false;
    if (folder.getType() == FolderType.PUBLIC)
        return true;
    if (super.canRead(userId, folder))
        return true;
    // now check actual permissions
    Set<Folder> folders = new HashSet<>();
    folders.add(folder);
    if (controller.groupHasReadPermission(new ArrayList<>(account.getGroups()), folders) || controller.groupHasWritePermission(new ArrayList<>(account.getGroups()), folders))
        return true;
    return controller.accountHasReadPermission(account, folders) || controller.accountHasWritePermission(account, folders);
}

Example 78 with Account

use of org.jbei.ice.storage.model.Account in project ice by JBEI.

the class PartDefaults method get.

/**
     * 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 type entry type
     * @return PartData object with the retrieve part defaults
     */
public PartData get(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 = this.accountDAO.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 = this.accountDAO.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);
}

Example 79 with Account

use of org.jbei.ice.storage.model.Account in project ice by JBEI.

the class EntryPermissionTask method addPermissions.

protected void addPermissions(Entry entry) {
    for (AccessPermission access : permissions) {
        // account or group
        Account account = null;
        Group group = null;
        switch(access.getArticle()) {
            case ACCOUNT:
            default:
                account = accountDAO.get(access.getArticleId());
                break;
            case GROUP:
                group = groupDAO.get(access.getArticleId());
                break;
        }
        // does the permissions already exists
        if (permissionDAO.hasPermission(entry, null, null, account, group, access.isCanRead(), access.isCanWrite()))
            return;
        // add the permission if not
        Permission permission = new Permission();
        permission.setEntry(entry);
        entry.getPermissions().add(permission);
        permission.setGroup(group);
        permission.setFolder(null);
        permission.setUpload(null);
        permission.setAccount(account);
        permission.setCanRead(access.isCanRead());
        permission.setCanWrite(access.isCanWrite());
        permissionDAO.create(permission);
    }
}

Example 80 with Account

use of org.jbei.ice.storage.model.Account in project ice by JBEI.

the class SBOLParser method createNewEntry.

protected long createNewEntry(TopLevel moduleDefinition, SBOLDocument document) {
    String identity = moduleDefinition.getIdentity().toString();
    String description = moduleDefinition.getDescription();
    String name = moduleDefinition.getName();
    Part part = new Part();
    part.setOwner(partData.getOwner());
    part.setOwnerEmail(partData.getOwnerEmail());
    part.setCreator(partData.getCreator());
    part.setCreatorEmail(partData.getCreatorEmail());
    part.setPrincipalInvestigator(partData.getPrincipalInvestigator());
    part.setPrincipalInvestigatorEmail(partData.getPrincipalInvestigatorEmail());
    part.setBioSafetyLevel(partData.getBioSafetyLevel());
    part.setStatus(partData.getStatus());
    description = StringUtils.isEmpty(description) ? partData.getShortDescription() : description;
    name = StringUtils.isEmpty(name) ? moduleDefinition.getDisplayId() : name;
    part.setShortDescription(description);
    part.setName(name);
    EntryCreator entryCreator = new EntryCreator();
    Account account = DAOFactory.getAccountDAO().getByEmail(part.getCreatorEmail());
    Entry entry = entryCreator.createEntry(account, part, null);
    parseToGenBank(document, entry.getName(), entry, moduleDefinition.getIdentity().toString());
    identityEntryMap.put(identity, entry.getId());
    return entry.getId();
}