Source code for cmapPy.clue_api_client.gene_queries

import logging
import cmapPy.pandasGEXpress.setup_GCToo_logger as setup_logger

__authors__ = "David L. Lahr"
__email__ = "dlahr@broadinstitute.org"


logger = logging.getLogger(setup_logger.LOGGER_NAME)

resource_name = "genes"


def are_genes_in_api(my_clue_api_client, gene_symbols):
    """determine if genes are present in the API

    Args:
        my_clue_api_client:
        gene_symbols: collection of gene symbols to query the API with

    Returns: set of the found gene symbols

    """
    if len(gene_symbols) > 0:
        query_gene_symbols = gene_symbols if type(gene_symbols) is list else list(gene_symbols)

        query_result = my_clue_api_client.run_filter_query(resource_name,
            {"where":{"gene_symbol":{"inq":query_gene_symbols}}, "fields":{"gene_symbol":True}})
        logger.debug("query_result:  {}".format(query_result))

        r = set([x["gene_symbol"] for x in query_result])
        return r
    else:
        logger.warning("provided gene_symbols was empty, cannot run query")
        return set()