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datanator/data_source/intact_nosql.py

Summary

Maintainability
C
1 day
Test Coverage
A
93%

Function add_complexes has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

    def add_complexes(self):
        """ Parse complexes from data and add complexes to MongoDB """
        raw_columns = [
            '#Complex ac', 'Recommended name', 'Taxonomy identifier',
            'Identifiers (and stoichiometry) of molecules in complex', 'Experimental evidence',
Severity: Minor
Found in datanator/data_source/intact_nosql.py - About 3 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 9 arguments (exceeds 4 allowed). Consider refactoring.
Open

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

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

        def find_protein_gene(self, interactor, alias):
        """ Parse the protein and gene identifiers from key-value pairs of interactors and their aliases

        Args:
            interactor (:obj:`str`): key-value pairs of interactor
    Severity: Minor
    Found in datanator/data_source/intact_nosql.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 download_content has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def download_content(self):
        """ Download data from FTP server """
        if not os.path.exists(os.path.join(self.cache_dirname, 'intact')):
            os.makedirs(os.path.join(self.cache_dirname, 'intact'))
        if not os.path.exists(os.path.join(self.cache_dirname, 'intact', 'complextab')):
    Severity: Minor
    Found in datanator/data_source/intact_nosql.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

            if not os.path.exists(os.path.join(self.cache_dirname, 'intact', 'psimitab')):
            os.makedirs(os.path.join(self.cache_dirname, 'intact', 'psimitab'))
    Severity: Major
    Found in datanator/data_source/intact_nosql.py and 1 other location - About 1 hr to fix
    datanator/data_source/intact_nosql.py on lines 43..44

    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 49.

    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 not os.path.exists(os.path.join(self.cache_dirname, 'intact', 'complextab')):
            os.makedirs(os.path.join(self.cache_dirname, 'intact', 'complextab'))
    Severity: Major
    Found in datanator/data_source/intact_nosql.py and 1 other location - About 1 hr to fix
    datanator/data_source/intact_nosql.py on lines 45..46

    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 49.

    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 7 locations. Consider refactoring.
    Open

            super(IntActNoSQL, self).__init__(cache_dirname=cache_dirname, MongoDB=MongoDB, replicaSet=replicaSet, db=db,
    Severity: Major
    Found in datanator/data_source/intact_nosql.py and 6 other locations - About 1 hr to fix
    datanator/data_source/corum_nosql.py on lines 26..26
    datanator/data_source/kegg_orthology.py on lines 26..26
    datanator/data_source/metabolites_meta_collection.py on lines 27..27
    datanator/data_source/pax_nosql.py on lines 25..25
    datanator/data_source/taxon_tree.py on lines 27..27
    datanator/util/index_collection.py on lines 19..19

    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 40.

    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

                interaction['protein_b'], interaction['gene_b'] = self.find_protein_gene(row['ID(s) interactor B'], row['Alias(es) interactor B'])
    Severity: Major
    Found in datanator/data_source/intact_nosql.py and 1 other location - About 1 hr to fix
    datanator/data_source/intact_nosql.py on lines 129..129

    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 39.

    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

                interaction['protein_a'], interaction['gene_a'] = self.find_protein_gene(row['#ID(s) interactor A'], row['Alias(es) interactor A'])
    Severity: Major
    Found in datanator/data_source/intact_nosql.py and 1 other location - About 1 hr to fix
    datanator/data_source/intact_nosql.py on lines 130..130

    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 39.

    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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