Examples with PublicationRep cbit.vcell.modeldb.PublicationRep used on opensource projects

Example 1 with PublicationRep

use of cbit.vcell.modeldb.PublicationRep in project vcell by virtualcell.

the class PublicationServerResource method getPublicationRepresentation.

private static PublicationRepresentation getPublicationRepresentation(RestDatabaseService restDatabaseService, User vcellUser, KeyValue pubID) {
    // RestDatabaseService restDatabaseService = ((VCellApiApplication)getApplication()).getRestDatabaseService();
    try {
        PublicationRep publicationRep = restDatabaseService.getPublicationRep(pubID, vcellUser);
        PublicationRepresentation publicationRepresentation = new PublicationRepresentation(publicationRep);
        return publicationRepresentation;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "publication not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 2 with PublicationRep

use of cbit.vcell.modeldb.PublicationRep in project vcell by virtualcell.

the class RestDatabaseService method getPublicationRep.

public PublicationRep getPublicationRep(KeyValue pubKey, User vcellUser) throws SQLException, ObjectNotFoundException, DataAccessException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    ArrayList<String> conditions = new ArrayList<String>();
    if (pubKey != null) {
        conditions.add("(" + PublicationTable.table.id.getQualifiedColName() + " = " + pubKey.toString() + ")");
    } else {
        throw new RuntimeException("bioModelID not specified");
    }
    StringBuffer conditionsBuffer = new StringBuffer();
    for (String condition : conditions) {
        if (conditionsBuffer.length() > 0) {
            conditionsBuffer.append(" AND ");
        }
        conditionsBuffer.append(condition);
    }
    PublicationRep[] publicationReps = databaseServerImpl.getPublicationReps(vcellUser, conditionsBuffer.toString(), null);
    if (publicationReps == null || publicationReps.length != 1) {
        throw new ObjectNotFoundException("failed to get publication");
    }
    return publicationReps[0];
}

Example 3 with PublicationRep

use of cbit.vcell.modeldb.PublicationRep in project vcell by virtualcell.

the class RestDatabaseService method query.

public PublicationRep[] query(PublicationsServerResource resource, User vcellUser) throws SQLException, DataAccessException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    Long pubID = resource.getLongQueryValue(PublicationsServerResource.PARAM_PUB_ID);
    // it is ok if the orderBy is null;
    String orderByParam = resource.getQueryValue(PublicationsServerResource.PARAM_ORDERBY);
    ArrayList<String> conditions = new ArrayList<String>();
    java.text.SimpleDateFormat df = new java.text.SimpleDateFormat("MM/dd/yyyy HH:mm:ss", java.util.Locale.US);
    if (pubID != null) {
        conditions.add("(" + PublicationTable.table.id.getQualifiedColName() + " = " + pubID + ")");
    }
    StringBuffer conditionsBuffer = new StringBuffer();
    for (String condition : conditions) {
        if (conditionsBuffer.length() > 0) {
            conditionsBuffer.append(" AND ");
        }
        conditionsBuffer.append(condition);
    }
    // default
    OrderBy orderBy = OrderBy.year_desc;
    if (orderByParam != null) {
        if (orderByParam.equals(BiomodelsServerResource.PARAM_ORDERBY_YEAR_ASC)) {
            orderBy = OrderBy.year_asc;
        } else if (orderByParam.equals(BiomodelsServerResource.PARAM_ORDERBY_YEAR_DESC)) {
            orderBy = OrderBy.year_desc;
        } else if (orderByParam.equals(BiomodelsServerResource.PARAM_ORDERBY_NAME_ASC)) {
            orderBy = OrderBy.name_asc;
        } else if (orderByParam.equals(BiomodelsServerResource.PARAM_ORDERBY_NAME_DESC)) {
            orderBy = OrderBy.name_desc;
        }
    }
    PublicationRep[] publicationReps = databaseServerImpl.getPublicationReps(vcellUser, conditionsBuffer.toString(), orderBy);
    return publicationReps;
}

Example 4 with PublicationRep

use of cbit.vcell.modeldb.PublicationRep in project vcell by virtualcell.

the class PublicationServerResource method getPublicationRepresentation.

private PublicationRepresentation getPublicationRepresentation(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        PublicationRep publicationRep = restDatabaseService.query(this, vcellUser);
        PublicationRepresentation publicationRepresentation = new PublicationRepresentation(publicationRep);
        return publicationRepresentation;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "publication not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 5 with PublicationRep

use of cbit.vcell.modeldb.PublicationRep in project vcell by virtualcell.

the class PublicationsServerResource method getPublicationRepresentations.

private PublicationRepresentation[] getPublicationRepresentations(User vcellUser) {
    ArrayList<PublicationRepresentation> publicationRepresentations = new ArrayList<PublicationRepresentation>();
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        PublicationRep[] publicationReps = restDatabaseService.query(this, vcellUser);
        for (PublicationRep publicationRep : publicationReps) {
            PublicationRepresentation publicationRepresentation = new PublicationRepresentation(publicationRep);
            publicationRepresentations.add(publicationRepresentation);
        }
    } catch (PermissionException ee) {
        ee.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "not authorized");
    } catch (DataAccessException | SQLException | ExpressionException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to retrieve biomodels from VCell Database : " + e.getMessage());
    }
    return publicationRepresentations.toArray(new PublicationRepresentation[0]);
}