Function download_cdna has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

def download_cdna(ref_genome, strain_name, url, temp_directory):
    CDNA_DIR = "{}/CDNA_FILES".format(temp_directory)
    if not os.path.isdir(CDNA_DIR):
        os.makedirs(CDNA_DIR)
    file_name = "{}/{}.cdna.all.fa.gz".format(CDNA_DIR, strain_name)

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Function reset_cellular_locations has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def reset_cellular_locations(self, start=0):
        """Github (https://github.com/KarrLab/datanator_rest_api/issues/69)
        """
        query = {'cellular_locations': {'$ne': None}}
        count = self.collection.count_documents(query) - start

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Function load_abundance_from_pax has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def load_abundance_from_pax(self):
        '''
            Load protein abundance data but interating from pax collection.
        '''
        _, _, col_pax = self.mongo_manager.con_db('pax')

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Function calc_enzyme_molecular_weights has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def calc_enzyme_molecular_weights(self, enzymes, length):
        """ Calculate the molecular weight of each enzyme

        Args:
            enzymes (:obj:`list` of :obj:`dict`): list of enzymes

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Function quant has 15 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def quant(self, fastq_filenames, index_filename=None, output_dirname=None,

Function fill_abundance_publication has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def fill_abundance_publication(self, start=0):
        """(https://github.com/KarrLab/datanator/issues/51)

        Args:
            start(:obj:`int`, optional): beginning of documents.

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Function load_abundance_from_pax has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def load_abundance_from_pax(self):
        '''Load protein abundance data but interating from pax collection.
        '''
        _, _, col_pax = self.con_db('pax')
        query = {}

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Function load_uniprot has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def load_uniprot(self, query=False, msg='', species=None):
        """Build dataframe
        
        Args:
            query (:obj:`bool`, optional): Whether download all reviewed entries of perform individual queries. Defaults to False.

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Function load_missing_enzyme_information_from_html has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def load_missing_enzyme_information_from_html(self, ids, start=0):
        """ Loading enzyme subunit information from html

        Args:
            ids (:obj:`list` of :obj:`int`): list of IDs of kinetic laws to download

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Function __init__ has 14 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self, name=None, cache_dirname=None, clear_content=False, load_content=False, max_entries=float('inf'),

Function fill_rna_halflife has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def fill_rna_halflife(self, df, species):
        """load data into rna_halflife collection
        
        Args:
            df (:obj:`pandas.DataFrame`): dataframe to be loaded into the database

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Function __init__ has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(self, name=None, cache_dirname=None, clear_content=False, load_content=False, max_entries=float('inf'),
                 commit_intermediate_results=False, download_backups=True, verbose=False,
                 quilt_owner=None, quilt_package=None):
        """
        Args:

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Function quant has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def quant(self, fastq_filenames, index_filename=None, output_dirname=None,
              bias=False, bootstrap_samples=0, seed=42, plaintext=False, fusion=False,
              single_end_reads=False, forward_stranded=False, reverse_stranded=False,
              fragment_length=None, fragment_length_std=None,
              threads=1, pseudobam=False):

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Function extract_values has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def extract_values(self, obj, key):
        """Pull all values of specified key from nested JSON.
        """
        arr = []

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Function process_docs has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def process_docs(self, skip=0):
        query = {}
        projection = {"_id": 0}
        docs = self.client["datanator-test"]["metabolite_concentrations"].find(filter=query, projection=projection)
        for i, doc in enumerate(docs):

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Function one_to_many has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def one_to_many(self, inchi, collection_str='metabolites_meta',
                    field='inchi', lookup='InChI_Key', num=100):
        ''' Calculate tanimoto coefficients between one
        metabolite and the rest of the 'collection_str'
        Args:

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Function run has 42 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def run(self):
        # create dict of MODOMICS single character monomer codes
        modomics_short_code_to_monomer = {}
        for monomer in bpforms.rna_alphabet.monomers.values():
            for identifier in monomer.identifiers:

Function build_obs has 42 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def build_obs(self, data, i, doc):
        """Build observation objects from obj.
        Go into observations collection.
        Args:
            data (:obj:`Obj`): source object.

Function _flatten_conc_obj has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def _flatten_conc_obj(self, obj, ncbi_id, species_name, _id, source='ECMDB'):
        """Flatten concentrations object in ec/ymdb.

        Args:
            obj(:obj:`Obj`): concentrations object.

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Function get_ftp_url has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

def get_ftp_url(url):
    ftp_url = None
    attempts = 0
    while attempts < 10:
        try:

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