testing_queries.py

import settings
import logging
import coloredlogs
from intermine.webservice import Service


logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
coloredlogs.install(level='DEBUG')

logging.getLogger('intermine').setLevel(logging.INFO)
logging.getLogger('JSONIterator').setLevel(logging.INFO)
logging.getLogger('Model').setLevel(logging.INFO)


def assert_result(query_number, number_of_rows, expected_result, model):

    try:
        assert len(number_of_rows) == expected_result
        logger.info('Query #' + query_number + ' ' + model + ' PASSED. Returned ' + str(len(number_of_rows)))
        return 'Query #' + query_number + ' ' + model + ' PASSED. Returned ' + str(len(number_of_rows))
    except Exception as e:
        logger.info(str(e))
        # settings.to_check.append(('query_' + str(query_number), model))
        logger.warning('Query #' + query_number + ' ' + model + ' FAILED. Expected ' + str(expected_result) + ' returned ' + str(len(number_of_rows)))
        return 'Query #' + query_number + ' ' + model + ' FAILED. Expected ' + str(expected_result) + ' returned ' + str(len(number_of_rows))


def assert_greater(query_number, number_of_rows, minimum, model):

    try:
        assert len(number_of_rows) >= minimum
        logger.info('Query #' + query_number + ' ' + model + '  PASSED. Returned ' + str(len(number_of_rows)))
        return 'Query #' + query_number + ' PASSED. Returned ' + str(len(number_of_rows))
    except Exception as e:
        logger.info(str(e))
        # settings.to_check.append(('query_' + str(query_number), model))
        logger.warning('Query #' + query_number + ' FAILED. Expected ' + str(minimum) + ' returned ' + str(len(number_of_rows)))
        return 'Query #' + query_number + ' ' + model + ' FAILED. Expected ' + str(minimum) + ' returned ' + str(len(number_of_rows))


def save_txt_file(my_class, rows):

    output_file = open('to_remove_' + my_class + '.txt', 'a+')
    for row in rows:
        output_file.write(row['primaryIdentifier'] + '\n')
    output_file.close()


def query_01(service, save_file=False):

    query = service.new_query('Gene')
    query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol', 'organism.name')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('primaryIdentifier', 'NOT LIKE', 'WBGene*', code='B')

    if save_file:
        save_txt_file('gene', query.rows())
        logger.info('File saved')

    return assert_result('01', query.rows(), 0, 'Gene')


def query_02(service, save_file=False):

    query = service.new_query('Gene')
    query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol', 'organism.name')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('symbol', 'IS NULL', code='B')

    if save_file:
        save_txt_file('gene', query.rows())
        logger.info('File saved')

    return assert_result('02', query.rows(), 0, 'Gene')


def query_03(service, save_file=False):

    query = service.new_query('Gene')
    query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol', 'organism.name')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('primaryIdentifier', 'IS NULL', code='B')

    if save_file:
        save_txt_file('gene', query.rows())
        logger.info('File saved')

    return assert_result('03', query.rows(), 0, 'Gene')


def query_04(service, save_file=False):

    query = service.new_query('Transcript')
    query.add_view('primaryIdentifier', 'symbol', 'organism.name')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('chromosome', 'IS NULL', code='B')

    if save_file:
        save_txt_file('transcript', query.rows())
        logger.info('File saved')

    return assert_result('04', query.rows(), 0, 'Transcript')


def query_05(service, save_file=False):

    query = service.new_query('CDS')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('primaryIdentifier', 'CONTAINS', '2L52.1a', code='A')

    if save_file:
        save_txt_file('cds', query.rows())
        logger.info('File saved')

    return assert_result('05', query.rows(), 1, 'CDS')


def query_06(service, save_file=False):

    query = service.new_query('Transcript')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('primaryIdentifier', 'CONTAINS', 'B0207.4', code='B')
    query.add_constraint('symbol', 'CONTAINS', 'B0207.4', code='A')
    query.set_logic('A or B')

    if save_file:
        save_txt_file('transcript', query.rows())
        logger.info('File saved')

    return assert_result('06', query.rows(), 2, 'Transcript')


def query_07(service, save_file=False):

    query = service.new_query('Allele')
    query.add_view('primaryIdentifier', 'gene.primaryIdentifier', 'gene.secondaryIdentifier')
    query.add_constraint('primaryIdentifier', '=', 'WBVar01498288', code='A')

    if save_file:
        save_txt_file('allele', query.rows())
        logger.info('File saved')

    return assert_result('07', query.rows(), 76, 'Allele')


def query_08(service, save_file=False):

    query = service.new_query('Gene')
    query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol')
    query.add_constraint('secondaryIdentifier', 'CONTAINS', 'WBGene', code='A')

    if save_file:
        save_txt_file('gene', query.rows())
        logger.info('File saved')

    return assert_result('08', query.rows(), 0, 'Gene')


def query_09(service, save_file=False):

    query = service.new_query('Gene')
    query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol')
    query.add_constraint('symbol', 'CONTAINS', 'WBGene', code='A')

    if save_file:
        save_txt_file('gene', query.rows())
        logger.info('File saved')

    return assert_result('09', query.rows(), 0, 'Gene')


def query_10(service, save_file=False):

    query = service.new_query('Transcript')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('primaryIdentifier', 'NOT LIKE', 'Transcript:*', code='A')

    if save_file:
        save_txt_file('transcript', query.rows())
        logger.info('File saved')

    return assert_result('10', query.rows(), 0, 'Transcript')


def query_11(service, save_file=False):

    query = service.new_query('CDS')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('primaryIdentifier', 'NOT LIKE', 'CDS:*', code='A')

    if save_file:
        save_txt_file('cds', query.rows())
        logger.info('File saved')

    return assert_result('11', query.rows(), 0, 'CDS')


def query_12(service, save_file=False):

    query = service.new_query('Gene')
    query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('CDSs', 'IS NOT NULL', code='B')

    if save_file:
        save_txt_file('gene', query.rows())
        logger.info('File saved')

    return assert_greater('12', query.rows(), 19984, 'Gene')


def query_13(service, save_file=False):

    query = service.new_query('CDS')
    query.add_view('primaryIdentifier', 'symbol', 'sequence.length')
    query.add_constraint('symbol', '=', 'ZC416.4', code='A')

    for row in query.rows():
        try:
            assert (row['length'] >= 999)
            return 'Query #13' + ' PASSED. Returned ' + str(row['length'])
        except Exception as e:
            logger.info(e)
            return 'Query #13' + ' FAILED. Returned ' + str(row['length'])


def query_14(service, save_file=False):

    query = service.new_query('Gene')
    query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol', 'length')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('length', 'IS NOT NULL', code='B')

    if save_file:
        save_txt_file('gene', query.rows())
        logger.info('File saved')

    return assert_greater('14', query.rows(), 46500, 'Gene')


def query_15(service, save_file=False):

    query = service.new_query('Gene')
    query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol')
    query.add_constraint('organism', 'IS NULL', code='A')

    if save_file:
        save_txt_file('gene', query.rows())
        logger.info('File saved')

    return assert_result('15', query.rows(), 0, 'Gene')


def query_16(service, save_file=False):

    query = service.new_query('CDS')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('gene', 'IS NULL', code='B')

    if save_file:
        save_txt_file('cds', query.rows())
        logger.info('File saved')

    return assert_result('16', query.rows(), 0, 'CDS')


def query_17(service, save_file=False):

    query = service.new_query('Transcript')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('gene', 'IS NULL', code='B')

    if save_file:
        save_txt_file('transcript', query.rows())
        logger.info('File saved')

    return assert_result('17', query.rows(), 0, 'Transcript')


def query_18(service, save_file=False):

    query = service.new_query('CDS')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('protein', 'IS NULL', code='B')

    if save_file:
        save_txt_file('cds', query.rows())
        logger.info('File saved')

    return assert_result('18', query.rows(), 0, 'CDS')


def query_19(service, save_file=False):

    query = service.new_query('CDS')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('transcripts', 'IS NULL', code='B')

    if save_file:
        save_txt_file('cds', query.rows())
        logger.info('File saved')

    return assert_result('19', query.rows(), 0, 'CDS')


def query_20(service, save_file=False):

    query = service.new_query('Transcript')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('CDSs', 'IS NOT NULL', code='A')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='B')

    if save_file:
        save_txt_file('transcript', query.rows())
        logger.info('File saved')

    return assert_greater('20', query.rows(), 31000, 'Transcript')


def query_21(service, save_file=False):

    query = service.new_query('Protein')
    query.add_view('primaryAccession', 'primaryIdentifier', 'secondaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('primaryAccession', 'NOT LIKE', 'CE*', code='B')

    if save_file:
        save_txt_file('protein', query.rows())
        logger.info('File saved')

    return assert_result('21', query.rows(), 0, 'Protein')


def query_22(service, save_file=False):

    query = service.new_query('Protein')
    query.add_view('primaryAccession', 'primaryIdentifier', 'secondaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('primaryIdentifier', 'NOT LIKE', 'CE*', code='B')

    if save_file:
        save_txt_file('protein', query.rows())
        logger.info('File saved')

    return assert_result('22', query.rows(), 0, 'Protein')


def query_23(service, save_file=False):

    query = service.new_query('Protein')
    query.add_view('primaryAccession', 'primaryIdentifier', 'secondaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('CDSs', 'IS NULL', code='B')

    if save_file:
        save_txt_file('protein', query.rows())
        logger.info('File saved')

    return assert_result('23', query.rows(), 0, 'Protein')


def query_24(service, save_file=False):

    query = service.new_query('Protein')
    query.add_view('primaryAccession', 'primaryIdentifier', 'secondaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('sequence', 'IS NULL', code='B')

    if save_file:
        save_txt_file('protein', query.rows())
        logger.info('File saved')

    return assert_result('24', query.rows(), 0, 'Protein')


def query_25(service, save_file=False):

    query = service.new_query('CDS')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('organism', 'IS NULL', code='A')

    if save_file:
        save_txt_file('cds', query.rows())
        logger.info('File saved')

    return assert_result('25', query.rows(), 0, 'CDS')


def query_26(service, save_file=False):

    query = service.new_query('Transcript')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('organism', 'IS NULL', code='A')

    if save_file:
        save_txt_file('transcript', query.rows())
        logger.info('File saved')

    return assert_result('26', query.rows(), 0, 'Transcript')


def query_27(service, save_file=False):

    query = service.new_query('Protein')
    query.add_view('primaryAccession', 'primaryIdentifier', 'secondaryIdentifier', 'symbol')
    query.add_sort_order('Protein.primaryIdentifier', 'ASC')
    query.add_constraint('primaryIdentifier', 'IS NULL', code='A')

    if save_file:
        save_txt_file('protein', query.rows())
        logger.info('File saved')

    return assert_result('27', query.rows(), 0, 'Protein')


def query_28(service, save_file=False):

    query = service.new_query('Allele')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('symbol', '=', 'e1370', code='A')

    if save_file:
        save_txt_file('allele', query.rows())
        logger.info('File saved')

    return assert_result('28', query.rows(), 1, 'Allele')


def query_29(service, save_file=False):

    query = service.new_query('CDS')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('primaryIdentifier', 'LIKE', 'CDS:CDS:*', code='A')

    if save_file:
        save_txt_file('cds', query.rows())
        logger.info('File saved')

    return assert_result('29', query.rows(), 0, 'CDS')


def query_30(service, save_file=False):

    query = service.new_query('MRNA')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    query.add_constraint('gene', 'IS NULL', code='B')

    if save_file:
        save_txt_file('mrna', query.rows())
        logger.info('File saved')

    return assert_result('30', query.rows(), 0, 'MRNA')


def query_31(service, save_file=False):

    query = service.new_query('MRNA')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('organism', 'IS NULL', code='A')

    if save_file:
        save_txt_file('mrna', query.rows())
        logger.info('File saved')

    return assert_result('31', query.rows(), 0, 'MRNA')


def query_32(service, save_file=False):

    query = service.new_query('MRNA')
    query.add_view('primaryIdentifier', 'symbol')
    query.add_constraint('CDSs', 'IS NULL', code='A')

    if save_file:
        save_txt_file('mrna', query.rows())
        logger.info('File saved')

    return assert_result('32', query.rows(), 0, 'MRNA')


def query_33(service, save_file=False):

    query = service.new_query('Protein')
    query.add_view('primaryIdentifier', 'CDSs.primaryIdentifier', 'CDSs.symbol')
    query.add_constraint('primaryIdentifier', '=', 'CE46852', code='A')

    if save_file:
        save_txt_file('protein', query.rows())
        logger.info('File saved')

    return assert_result('33', query.rows(), 1, 'PROTEIN')


def query_34(service, save_file=False):

    query = service.new_query('CDS')
    query.add_view('primaryIdentifier', 'symbol', 'protein.primaryIdentifier')
    query.add_constraint('protein.primaryIdentifier', '=', 'CE46852', code='A')

    if save_file:
        save_txt_file('cds', query.rows())
        logger.info('File saved')

    return assert_result('34', query.rows(), 1, 'CDS')


def query_35(service, save_file=False):

    query = service.new_query('Organism')
    query.add_view('name', 'taxonId')
    query.add_constraint('name', 'IS NULL', code='A')

    if save_file:
        save_txt_file('organism', query.rows())
        logger.info('File saved')

    return assert_result('35', query.rows(), 0, 'Organism')


def query_36(service, save_file=False):

    query = service.new_query('Organism')
    query.add_view('name', 'taxonId')
    print('Query #36')
    result = {}
    for row in query.rows():
        result[row['name']] = row['taxonId']

    to_return = 'Query #36<br>'
    for i in result:
        print('\t' + i + '\t' + str(result[i]))
        to_return += '&nbsp' + i + '&nbsp' + str(result[i]) + '<br>'

    return to_return


def query_37(service, save_file=False):

    query = service.new_query('Chromosome')
    query.add_view('primaryIdentifier', 'organism.name')
    query.add_constraint('organism.name', '=', 'Caenorhabditis elegans', code='A')
    print('Query #37')

    result = {}
    for row in query.rows():
        result[row['primaryIdentifier']] = row['organism.name']

    to_return = 'Query #37<br>'
    for i in result:
        try:
            print('\t' + i + '\t' + str(result[i]))
            to_return += '&nbsp' + i + '&nbsp' + str(result[i]) + '<br>'
        except Exception as e:
            logger.info(e)
            print('\t' + i)
            to_return += '\t' + i

    return to_return


def query_38(service, save_file=False):

    query = service.new_query('Allele')
    query.add_view('primaryIdentifier', 'symbol', 'phenotype.identifier', 'phenotype.name')
    query.add_constraint('primaryIdentifier', '=', 'WBVar00143949', code='A')

    if save_file:
        save_txt_file('allele', query.rows())
        logger.info('File saved')

    return assert_result('38', query.rows(), 94, 'Allele')


def query_39(service, save_file=False):

    query = service.new_query('ExpressionPattern')
    query.add_view('primaryIdentifier', 'genes.primaryIdentifier', 'genes.secondaryIdentifier', 'genes.symbol')
    query.add_constraint('primaryIdentifier', '=', 'Expr3417', code='A')

    if save_file:
        save_txt_file('expression_pattern', query.rows())
        logger.info('File saved')

    return assert_result('39', query.rows(), 47, 'ExpressionPattern')


def query_40(service, save_file=False):

    query = service.new_query('Gene')
    query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol', 'allele.primaryIdentifier', 'allele.symbol')
    query.add_constraint('symbol', '=', 'cdk-4', code='A')
    query.add_constraint('allele.primaryIdentifier', '=', 'WBVar02146689', code='B')

    if save_file:
        save_txt_file('gene', query.rows())
        logger.info('File saved')

    return assert_result('40', query.rows(), 1, 'Gene')


def query_41(service, save_file=False):
    query = service.new_query('AnatomyTerm')
    query.add_view('primaryIdentifier', 'name', 'synonym', 'definition')
    query.add_constraint('definition', 'CONTAINS', 'CDATA', code='A')

    if save_file:
        save_txt_file('anatomy_term', query.rows())
        logger.info('File saved')

    return assert_result('41', query.rows(), 0, 'AnatomyTerm')

    # print('\nTesting complete')
    # print('These queries need to be checked: {0}'.format(', '.join(to_check)))


# if __name__ == '__main__':

#     service = Service('http://im-dev1.wormbase.org/tools/wormmine/service')

#     def inner():
#         for x in dir(testing_queries):
#             item = getattr(testing_queries, x)
#             print(item)
#             if callable(item):
#                 if not item.__name__ in ['assert_result', 'Service', 'assert_greater', 'save_txt_file']:
#                     time.sleep(1)
#                     print '%s<br/>\n' % item(service)