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datanator/data_source/corum_nosql.py

Summary

Maintainability
C
1 day
Test Coverage
A
90%

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

    def load_content(self, endpoint='corum'):
        """ Collect and parse all data from CORUM website into JSON files and add to NoSQL database """
        database_url = self.ENDPOINT_DOMAINS[endpoint]
        _, _, collection = self.con_db(self.collection)
        os.makedirs(os.path.join(
Severity: Minor
Found in datanator/data_source/corum_nosql.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 9 arguments (exceeds 4 allowed). Consider refactoring.
Open

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

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

                    if len(su_uniprot_list) != len(su_entrez_list):
                    msg = 'Unequal number of uniprot/entrezs subunits at line {}\n  {}\n  {}'.format(
                        i_entry, '; '.join(su_uniprot_list), '; '.join(su_entrez_list))
                    raise Exception(msg)
    Severity: Major
    Found in datanator/data_source/corum_nosql.py and 1 other location - About 2 hrs to fix
    datanator/data_source/corum_nosql.py on lines 144..147

    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 50.

    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 len(protein_name_list) != len(su_entrez_list):
                    msg = 'Unequal number of uniprot/entrez subunits at line {}\n  {}\n  {}'.format(
                        i_entry, '; '.join(protein_name_list), '; '.join(su_entrez_list))
                    raise Exception(msg)
    Severity: Major
    Found in datanator/data_source/corum_nosql.py and 1 other location - About 2 hrs to fix
    datanator/data_source/corum_nosql.py on lines 149..152

    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 50.

    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(CorumNoSQL, self).__init__(cache_dirname=cache_dirname, MongoDB=MongoDB, replicaSet=replicaSet, db=db,
    Severity: Major
    Found in datanator/data_source/corum_nosql.py and 6 other locations - About 1 hr to fix
    datanator/data_source/intact_nosql.py on lines 23..23
    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

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