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obj_tables/web_service.py

Summary

Maintainability
D
2 days
Test Coverage
A
100%

File web_service.py has 590 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Web service

:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2019-09-15
:Copyright: 2019, Karr Lab
Severity: Major
Found in obj_tables/web_service.py - About 1 day to fix

    Function save_in_workbook has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

    def save_in_workbook(file_storage):
    """ Save workbook to a temporary directory

    Args:
        file_storage (:obj:`FileStorage`): uploaded file
    Severity: Minor
    Found in obj_tables/web_service.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 save_out_workbook has 11 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def save_out_workbook(format, objs, schema_name, doc_metadata, model_metadata, models,
    Severity: Major
    Found in obj_tables/web_service.py - About 1 hr to fix

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

      def save_out_workbook(format, objs, schema_name, doc_metadata, model_metadata, models,
                      write_toc=False, write_schema=False, write_empty_models=True, write_empty_cols=True,
                      protected=True):
    """
    Args:
      Severity: Minor
      Found in obj_tables/web_service.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

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

                  out_wb_dir, out_wb_filename, out_wb_mimetype = save_out_workbook(
                format, objs, schema_name, doc_metadata, model_metadata, models=models,
                write_toc=args['write-toc'],
                write_schema=args['write-schema'],
                protected=args['protected'],
      Severity: Major
      Found in obj_tables/web_service.py and 1 other location - About 2 hrs to fix
      obj_tables/web_service.py on lines 394..398

      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

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

              out_wb_dir, out_wb_filename, out_wb_mimetype = save_out_workbook(
            format, objs, schema_name, doc_metadata, model_metadata, models=models,
            write_toc=args['write-toc'],
            write_schema=args['write-schema'],
            protected=args['protected'],
      Severity: Major
      Found in obj_tables/web_service.py and 1 other location - About 2 hrs to fix
      obj_tables/web_service.py on lines 113..117

      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

              try:
            _, schema, _ = get_schema_models(schema_filename)
        except Exception as err:
            flask_restplus.abort(400, str(err))
        finally:
      Severity: Major
      Found in obj_tables/web_service.py and 1 other location - About 1 hr to fix
      obj_tables/web_service.py on lines 244..249

      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 48.

      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

              try:
            schema_name, schema, models = get_schema_models(schema_filename)
        except Exception as err:
            flask_restplus.abort(400, str(err))
        finally:
      Severity: Major
      Found in obj_tables/web_service.py and 1 other location - About 1 hr to fix
      obj_tables/web_service.py on lines 493..498

      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 48.

      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

                      has_csv = has_csv or os.path.splitext(f.filename)[1] == '.csv'
      Severity: Minor
      Found in obj_tables/web_service.py and 1 other location - About 30 mins to fix
      obj_tables/web_service.py on lines 578..578

      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 32.

      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

                      has_tsv = has_tsv or os.path.splitext(f.filename)[1] == '.tsv'
      Severity: Minor
      Found in obj_tables/web_service.py and 1 other location - About 30 mins to fix
      obj_tables/web_service.py on lines 577..577

      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 32.

      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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