Sign upLogin

KarrLab/datanator_query_python

View on GitHub
Star
datanator_query_python/util/mongo_util.py

Summary

Maintainability
C
1 day
Test Coverage
B
86%

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

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

    Function update_entity has 6 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def update_entity(self,
    Severity: Minor
    Found in datanator_query_python/util/mongo_util.py - About 45 mins to fix

      Function update_observation has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def update_observation(self,
      Severity: Minor
      Found in datanator_query_python/util/mongo_util.py - About 45 mins to fix

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

            def update_entity(self,
                      obj,
                      match,
                      db="test",
                      col="entity",
        Severity: Minor
        Found in datanator_query_python/util/mongo_util.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 update_observation has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

            def update_observation(self, 
                           obj,
                           source,
                           db="test",
                           op="update",
        Severity: Minor
        Found in datanator_query_python/util/mongo_util.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 build_taxon_object has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
        Open

            def build_taxon_object(self, _id, _format="tax_id"):
        """Build taxon object from taxon_id.
        (https://github.com/KarrLab/datanator_pattern_design/blob/master/components/taxon.json)

        Args:
        Severity: Minor
        Found in datanator_query_python/util/mongo_util.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

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

                for key, val in obj.items():
            if isinstance(val, list):
                add_to_set[key] = {"$each": val}
            else:
                _set[key] = val
        Severity: Major
        Found in datanator_query_python/util/mongo_util.py and 1 other location - About 1 hr to fix
        datanator_query_python/util/mongo_util.py on lines 154..158

        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

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

                for key, val in obj.items():
            if isinstance(val, list):
                add_to_set[key] = {"$each": val}
            else:
                _set[key] = val
        Severity: Major
        Found in datanator_query_python/util/mongo_util.py and 1 other location - About 1 hr to fix
        datanator_query_python/util/mongo_util.py on lines 118..122

        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

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

                if op == "update":
            self.client[db][col].update_one(query,
                                            _update,
                                            upsert=True)
        else:
        Severity: Major
        Found in datanator_query_python/util/mongo_util.py and 1 other location - About 1 hr to fix
        datanator_query_python/util/mongo_util.py on lines 163..168

        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 45.

        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

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

                if op == "update":
            self.client[db][col].update_one(query,
                                            _update,
                                            upsert=True)
        else:
        Severity: Major
        Found in datanator_query_python/util/mongo_util.py and 1 other location - About 1 hr to fix
        datanator_query_python/util/mongo_util.py on lines 128..133

        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 45.

        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

        There are no issues that match your filters.

        Category
        Status