File sabio_rk_nosql.py has 1090 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import datanator.config.core
from datanator.util import mongo_util
from datanator.util import file_util, chem_util
from datanator.util import molecule_util
import requests

Function normalize_parameter_value has a Cognitive Complexity of 56 (exceeds 5 allowed). Consider refactoring.

Open

    def normalize_parameter_value(self, name, type, value, error, units, enzyme_molecular_weight):
        """
        Args:
            name (:obj:`str`): parameter name
            type (:obj:`int`) parameter type (SBO term id)

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Function load_missing_kinetic_law_information_from_tsv_helper has a Cognitive Complexity of 42 (exceeds 5 allowed). Consider refactoring.

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    def load_missing_kinetic_law_information_from_tsv_helper(self, tsv, start=0):
        """ Update the properties of kinetic laws in the mongodb based on content downloaded
        from SABIO in TSV format.

        Note: this method is necessary because neither of SABIO's SBML and Excel export methods provide

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Function load_compounds has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.

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    def load_compounds(self, compounds=None):
        """ Download information from SABIO-RK about all of the compounds stored sabio_compounds
                collection
        Args:
            compounds (:obj:`list` of :obj:`obj`): list of compounds to download

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Function parse_complex_subunit_structure has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

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    def parse_complex_subunit_structure(self, text):
        """ Parse the subunit structure of complex into a dictionary of subunit coefficients

        Args:
            text (:obj:`str`): subunit structure described with nested parentheses

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Function create_kinetic_law_from_sbml has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

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    def create_kinetic_law_from_sbml(self, id, sbml, root_species, specie_properties, functions, units):
        """ Make a kinetic law doc for mongoDB

        Args:
            id (:obj:`int`): identifier

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Function create_cross_references_from_sbml has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

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    def create_cross_references_from_sbml(self, sbml):
        """ Look up cross references from an SBML object to dictionary

        Args:
            sbml (:obj:`libsbml.SBase`): object in an SBML documentation

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SabioRk has 23 functions (exceeds 20 allowed). Consider refactoring.

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class SabioRk:

    def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db=None,
                 verbose=False, max_entries=float('inf'), username=None,
                 password=None, authSource='admin', webservice_batch_size=50,

Function infer_compound_structures_from_names has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

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    def infer_compound_structures_from_names(self, compounds):
        """ Try to use PubChem to infer the structure of compounds from their names

        Notes: we don't try look up structures from their cross references because SABIO has already gathered
        all structures from their cross references to ChEBI, KEGG, and PubChem

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Function create_kinetic_laws_from_sbml has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

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    def create_kinetic_laws_from_sbml(self, ids, sbml):
        """ Add kinetic laws defined in an SBML file to the local mongodb database

        Args:
            ids (:obj:`list` of :obj:`int`): list kinetic law IDs

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Function add_inchi_hash has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

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    def add_inchi_hash(self, ids):
        '''
            Add sha224 hashed values of _value_inchi in sabio_rk collection
        '''
        query = {}

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

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

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    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 get_specie_from_sbml has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

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    def get_specie_from_sbml(self, sbml):
        """ get species information from sbml

        Args:
            sbml (:obj:`libsbml.Species`): SBML-representation of a compound or enzyme

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Function get_parameter_by_properties has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

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    def get_parameter_by_properties(self, kinetic_law, parameter_properties):
        """ Get the parameter of :obj:`kinetic_law` whose attribute values are 
                equal to that of :obj:`parameter_properties`
        Args:
            kinetic_law (:obj:`KineticLaw`): kinetic law to find parameter of

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Function __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db=None,

Function load_content has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

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    def load_content(self):
        """ Download the content of SABIO-RK and store it to a remote mongoDB. """

        def ids_to_process(total_ids, query):
            exisitng_ids = self.collection.distinct('kinlaw_id', filter=query)

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Function normalize_kinetic_laws has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def normalize_kinetic_laws(self, new_ids):
        """ Normalize parameter values.

        Args:
            new_ids (:obj:`list` of :obj:`int`): list of IDs of kinetic laws to normalize

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Function create_kinetic_law_from_sbml has 6 arguments (exceeds 4 allowed). Consider refactoring.

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    def create_kinetic_law_from_sbml(self, id, sbml, root_species, specie_properties, functions, units):

Function normalize_parameter_value has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def normalize_parameter_value(self, name, type, value, error, units, enzyme_molecular_weight):

Function load_kinetic_laws has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def load_kinetic_laws(self, ids):
        """ Download kinetic laws from SABIO-RK

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

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Avoid too many return statements within this function.

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                return ('k_cat', 25, value, error, 's^(-1)')

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

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            return parameters[0]

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

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                    return ('v_max', 186, value, error, 'mol*s^(-1)*g^(-1)')

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                return ('k_m', 27, value, error, 'M')

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                    return ('k_cat', 25, value * float(f) if value else None, error * float(f) if error else None, 's^(-1)')

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                return ('k_i', 261, value, error, 'M')

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

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                return (None, None, None, None, None)

Function calc_inchi_formula_connectivity has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def calc_inchi_formula_connectivity(self, structure):
        """ Calculate a searchable structures

        * InChI format
        * Core InChI format

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Function parse_enzyme_name has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def parse_enzyme_name(self, sbml):
        """ Parse the name of an enzyme in SBML for the enzyme name, wild type status, and variant
        description that it contains.

        Args:

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