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KarrLab/datanator_query_python

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datanator_query_python/query/query_sabiork.py

Summary

Maintainability
F
3 days
Test Coverage
A
96%

Function get_kinlawid_by_name has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
Open

    def get_kinlawid_by_name(self, substrates, products):
        ''' Get kinlaw_id from substrates and products, all in one reaction

            Args:
                substrates: (:obj:`list` of :obj:`str`): list of substrate names
Severity: Minor
Found in datanator_query_python/query/query_sabiork.py - About 2 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 get_kinlawid_by_rxn has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

    def get_kinlawid_by_rxn(self, substrates, products):
        ''' Find the kinlaw_id defined in sabio_rk using 
            rxn participants' inchi string

            Args:
Severity: Minor
Found in datanator_query_python/query/query_sabiork.py - About 2 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 __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
Open

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

    Function get_kinlaw_by_environment has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def get_kinlaw_by_environment(self, taxon=None, taxon_wildtype=None, ph_range=None, temp_range=None,
    Severity: Major
    Found in datanator_query_python/query/query_sabiork.py - About 50 mins to fix

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

          def find_reaction_participants(self, kinlaw_id):
        ''' Find the reaction participants defined in sabio_rk using kinetic law id
        
            Args:
                kinlaw_id (:obj:`list` of :obj:`int`) list of kinlaw_id to search for
      Severity: Minor
      Found in datanator_query_python/query/query_sabiork.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

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

          def get_kinlaw_by_environment(self, taxon=None, taxon_wildtype=None, ph_range=None, temp_range=None,
                          name_space=None, observed_type=None, projection={'_id': 0}):
        """get kinlaw info based on experimental conditions
        
        Args:
      Severity: Minor
      Found in datanator_query_python/query/query_sabiork.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

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

          def get_subunit_by_id(self, _id):
        """Get protein subunit information by kinlaw_id.
        
        Args:
            _id (:obj:`int`): kinlaw_id.
      Severity: Minor
      Found in datanator_query_python/query/query_sabiork.py - About 25 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

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

                      for name in compounds:
                    ids = []
                    query = {products: name}
                    cursor = self.collection.find(
                        filter=query, projection=projection, collation=collation)
      Severity: Major
      Found in datanator_query_python/query/query_sabiork.py and 1 other location - About 3 hrs to fix
      datanator_query_python/query/query_sabiork.py on lines 189..196

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 71.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

                      for name in compounds:
                    ids = []
                    query = {substrates: name}
                    cursor = self.collection.find(
                        filter=query, projection=projection, collation=collation)
      Severity: Major
      Found in datanator_query_python/query/query_sabiork.py and 1 other location - About 3 hrs to fix
      datanator_query_python/query/query_sabiork.py on lines 201..208

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 71.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

                      for inchi in hashed_inchi:
                    ids = []
                    query = {substrate: inchi}
                    cursor = self.collection.find(
                        filter=query, projection=projection)
      Severity: Major
      Found in datanator_query_python/query/query_sabiork.py and 1 other location - About 3 hrs to fix
      datanator_query_python/query/query_sabiork.py on lines 141..148

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 68.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

                      for inchi in hashed_inchi:
                    ids = []
                    query = {product: inchi}
                    cursor = self.collection.find(
                        filter=query, projection=projection)
      Severity: Major
      Found in datanator_query_python/query/query_sabiork.py and 1 other location - About 3 hrs to fix
      datanator_query_python/query/query_sabiork.py on lines 129..136

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 68.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

              super().__init__(cache_dirname=cache_dirname, MongoDB=MongoDB,
      Severity: Minor
      Found in datanator_query_python/query/query_sabiork.py and 1 other location - About 55 mins to fix
      datanator_query_python/query/query_sabio_compound.py on lines 12..12

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 37.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

              if substrates == None:
            sub_id = self.collection.distinct('kinlaw_id')
        else:
            sub_id = get_kinlawid(substrates, side='substrate')
      Severity: Minor
      Found in datanator_query_python/query/query_sabiork.py and 1 other location - About 55 mins to fix
      datanator_query_python/query/query_sabiork.py on lines 217..220

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 37.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

              if products == None:
            pro_id = self.collection.distinct('kinlaw_id')
        else:
            pro_id = get_kinlawid(products, side='product')
      Severity: Minor
      Found in datanator_query_python/query/query_sabiork.py and 1 other location - About 55 mins to fix
      datanator_query_python/query/query_sabiork.py on lines 212..215

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 37.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

              if temp_range:    
            all_constraints.append({'temperature': {'$gte': temp_range[0], '$lte': temp_range[1]}})
      Severity: Major
      Found in datanator_query_python/query/query_sabiork.py and 3 other locations - About 45 mins to fix
      datanator_query_python/query/query_sabiork.py on lines 247..248
      datanator_query_python/query/query_sabiork_old.py on lines 60..61
      datanator_query_python/query/query_sabiork_old.py on lines 62..63

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 35.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

              if ph_range:
            all_constraints.append({'ph': {'$gte': ph_range[0], '$lte': ph_range[1]}})
      Severity: Major
      Found in datanator_query_python/query/query_sabiork.py and 3 other locations - About 45 mins to fix
      datanator_query_python/query/query_sabiork.py on lines 249..250
      datanator_query_python/query/query_sabiork_old.py on lines 60..61
      datanator_query_python/query/query_sabiork_old.py on lines 62..63

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 35.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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