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datanator/data_source/sabio_rk_json_mongo.py

Summary

Maintainability
F
5 days
Test Coverage
F
0%

Function make_doc has a Cognitive Complexity of 121 (exceeds 5 allowed). Consider refactoring.
Open

    def make_doc(self, file_names, file_dict):

        os.makedirs(os.path.dirname(
          self.cache_directory + 'docs/'), exist_ok=True)
        null = None
Severity: Minor
Found in datanator/data_source/sabio_rk_json_mongo.py - About 2 days 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

File sabio_rk_json_mongo.py has 652 lines of code (exceeds 250 allowed). Consider refactoring.
Open

'''Parse SabioRk json files into MongoDB documents
    (json files acquired by running sqlite_to_json.py)
:Author: Zhouyang Lian <zhouyang.lian@familian.life>
:Author: Jonathan <jonrkarr@gmail.com>
:Date: 2019-04-02
Severity: Major
Found in datanator/data_source/sabio_rk_json_mongo.py - About 1 day to fix

    Function add_inchi_hash has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.
    Open

        def add_inchi_hash(self, ids=None):
        '''
            Add inchi key values of _value_inchi in sabio_rk collection
        '''
    Severity: Minor
    Found in datanator/data_source/sabio_rk_json_mongo.py - About 4 hrs 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 __init__ has 9 arguments (exceeds 4 allowed). Consider refactoring.
    Open

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

      Function fill_kegg_meta has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
      Open

          def fill_kegg_meta(self, start=0):
        """Fill kegg information for reactions.
        
        Args:
            start (:obj:`int`, optional): Starting document. Defaults to 0.
      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

      Avoid deeply nested control flow statements.
      Open

                              for k in range(len(cur_entry_synonym_list)):
                            cur_entry_synonym_dict = cur_entry_synonym_list[k]
                            synonym__id = cur_entry_synonym_dict['synonym__id']
                            synonyms.append(
                                synonym_list[synonym__id-1]['name'])
      Severity: Major
      Found in datanator/data_source/sabio_rk_json_mongo.py - About 45 mins to fix

        Avoid deeply nested control flow statements.
        Open

                                for k in range(len(cur_compound_compound_structure_list)):
                            compound_structure__id = cur_compound_compound_structure_list[
                                k]['compound_structure__id']
                            cur_compound_structure_dict = next(
                                item for item in compound_structure_list if item['_id'] == compound_structure__id)
        Severity: Major
        Found in datanator/data_source/sabio_rk_json_mongo.py - About 45 mins to fix

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

              def fill_ec_meta(self, start=0):
        """Fill sabio documents with ec meta information.
        """
        query = {}
        docs = self.collection.find(filter=query)
          Severity: Minor
          Found in datanator/data_source/sabio_rk_json_mongo.py - About 45 mins 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 add_taxon_info has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
          Open

              def add_taxon_info(self):
        """Fill in taxonomic information
        """
        projection = {'_id': 0, 'kinlaw_id': 1, 'taxon_id': 1}
        query = {}
          Severity: Minor
          Found in datanator/data_source/sabio_rk_json_mongo.py - About 35 mins 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

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