Sign upLogin

KarrLab/datanator

View on GitHub
Star

Showing 376 of 791 total issues

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

    def parse_gene(self, lines):
        """Parse GENES category
        (http://rest.kegg.jp/get/ko:K00023)
        
        Args:
Severity: Minor
Found in datanator/data_source/kegg_orthology.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    def make_bulk(self, offset=0, bulk_size=100):
        """Make bulk objects to be inserted into MongoDB.

        Args:
            offset(:obj:`int`): Position of beginning (zero-indexed). Defaults to 0.
Severity: Minor
Found in datanator/data_source/kegg_org_code.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

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

        Args:
            sbml (:obj:`libsbml.Species`): SBML-representation of a compound or enzyme
Severity: Minor
Found in datanator/data_source/sabio_rk_nosql.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    def grab_eymdb(self, start=0):
        """Fill collection with concentration values from ec/ymdb.
        Documents in current collection all have inchikey
        """
        query = {'concentrations': {'$ne': None}}
Severity: Minor
Found in datanator/data_source/metabolite_concentration/doi_10_1038_nchembio_2077.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    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
Severity: Minor
Found in datanator/data_source/sabio_rk_nosql.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    def parse_ko_txt(self, filename):
        '''Parse kegg_ortho txt file into dictionary object
        '''
        file_path = os.path.join(self.path, filename)
        try:
Severity: Minor
Found in datanator/data_source/kegg_orthology.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    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
Severity: Minor
Found in datanator/data_source/sabio_rk.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    def load_data(self, skip=0, top_hits=10):
        """Loading data.
        
        Args:
            skip (:obj:`int`, optional): Beginning of the documents. Defaults to 0.
Severity: Minor
Found in datanator/data_source/gene_ortholog.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    def load_halflife(self, df, growth_medium='MeOH', start=0):
        df_json = json.loads(df.to_json(orient='records'))
        row_count = len(df.index)
        for i, doc in enumerate(df_json[start:]):
            if i == self.max_entries:
Severity: Minor
Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

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

        Args:
            ids (:obj:`list` of :obj:`int`): list kinetic law IDs
Severity: Minor
Found in datanator/data_source/sabio_rk.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    def fill_reactant_aggregate_name(self, start=0):
        """Fill sabio documents with reactant aggregate
        information by reactants' name.
        """
        query = {}
Severity: Minor
Found in datanator/data_source/sabio_rk_json_mongo.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    def make_doc(self, lines):
        """Turn a block of EC info into a dictionary object
        
        Args:
            lines (:obj:`list` of :obj:`str`): list consists of lines of information on one EC group.
Severity: Minor
Found in datanator/data_source/ec.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db=None,
Severity: Major
Found in datanator/data_source/sabio_rk_nosql.py - About 1 hr to fix

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

        def __init__(self, MongoDB, db, cache_dirname=None, replicaSet=None, verbose=False, max_entries=float('inf'),
    Severity: Major
    Found in datanator/data_source/kegg_org_code.py - About 1 hr to fix

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

          def __init__(self, username=None, password=None, server=None, authSource='admin',
      Severity: Major
      Found in datanator/data_source/sabio_compound.py - About 1 hr to fix

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

            def __init__(self, cache_dir=None, server=None, db=None, collection_str=None,
        Severity: Major
        Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py - About 1 hr to fix

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

              def __init__(self, name=None,
          Severity: Major
          Found in datanator/core/data_source.py - About 1 hr to fix

            Function inchi_to_inchikey has 34 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                def inchi_to_inchikey(self, szINCHISource):
        '''
            fork from git@github.com:mnowotka/chembl_ikey.git
        '''
        flagstd = 'S'
            Severity: Minor
            Found in datanator/util/chem_util.py - About 1 hr to fix

              Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def __init__(self, username=None, password=None, server=None, authSource='admin',
              Severity: Major
              Found in datanator/data_source/protein_aggregate.py - About 1 hr to fix

                Function download_fastq has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
                Open

                def download_fastq(experiment_name,  sample_name, temp_directory, fastq_urls):
    FASTQ_DIR = "{}/FASTQ_FILES".format(temp_directory)
    if not os.path.isdir(FASTQ_DIR):
        os.makedirs(FASTQ_DIR)
    for num, url in enumerate(fastq_urls.split(" ")):
                Severity: Minor
                Found in datanator/data_source/process_rna_seq/core.py - About 1 hr to fix

                Cognitive Complexity

                Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                A method's cognitive complexity is based on a few simple rules:

                • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                • Code is considered more complex for each "break in the linear flow of the code"
                • Code is considered more complex when "flow breaking structures are nested"

                Further reading

                Severity
                Category
                Status
                Source
                Language