greenelab/adage-server

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adage/analyze/tests.py

Summary

Maintainability
F
4 days
Test Coverage

File tests.py has 945 lines of code (exceeds 250 allowed). Consider refactoring.
Open

# coding: utf-8 (see https://www.python.org/dev/peps/pep-0263/)

from __future__ import unicode_literals
from __future__ import print_function
import os
Severity: Major
Found in adage/analyze/tests.py - About 2 days to fix

    APIResourceTestCase has 45 functions (exceeds 20 allowed). Consider refactoring.
    Open

    class APIResourceTestCase(ResourceTestCaseMixin, TestCase):
        # API tests:
        # For most of our interfaces, we should be able to GET, but every other
        # REST API should fail: POST, PUT, PATCH, DELETE. There are a few
        # exceptions for which we allow POST but the behavior is the same as GET.
    Severity: Minor
    Found in adage/analyze/tests.py - About 6 hrs to fix

      Cyclomatic complexity is too high in method create_participations. (8)
      Open

      
          @staticmethod
          def create_participations(num_signatures, num_genes):
              """
              Static method that builds Participation table based on the input
      Severity: Minor
      Found in adage/analyze/tests.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

      Cyclomatic complexity is too high in method create_edges. (6)
      Open

      
          @staticmethod
          def create_edges(gene_counter, num_gene1, num_gene2):
              if Organism.objects.exists():
                  organism = Organism.objects.first()
      Severity: Minor
      Found in adage/analyze/tests.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

      Function create_participations has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
      Open

          def create_participations(num_signatures, num_genes):
              """
              Static method that builds Participation table based on the input
              number of signatures and number of genes.
              """
      Severity: Minor
      Found in adage/analyze/tests.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 setUp has 28 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          def setUp(self):
              super(APIResourceTestCase, self).setUp()
              # create a test experiment to retrive with the API
              self.test_experiment = ModelsTestCase.experiment_data
              ModelsTestCase.create_test_experiment(
      Severity: Minor
      Found in adage/analyze/tests.py - About 1 hr to fix

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

            def create_edges(gene_counter, num_gene1, num_gene2):
                if Organism.objects.exists():
                    organism = Organism.objects.first()
                else:
                    organism = factory.create(Organism)
        Severity: Minor
        Found in adage/analyze/tests.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 create_expressionvalue_data has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
        Open

            def create_expressionvalue_data(self, num_genes):
                """
                Generate test data for ExpressionValueResource
                """
                if Organism.objects.exists():
        Severity: Minor
        Found in adage/analyze/tests.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 3 locations. Consider refactoring.
        Open

                for i in range(gene_counter):
                    Gene.objects.create(entrezid=(i + 1),
                                        systematic_name="sys_name #" + str(i + 1),
                                        standard_name="std_name #" + str(i + 1),
        Severity: Major
        Found in adage/analyze/tests.py and 2 other locations - About 2 hrs to fix
        adage/analyze/tests.py on lines 244..247
        adage/analyze/tests.py on lines 972..975

        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 70.

        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 3 locations. Consider refactoring.
        Open

                for i in range(num_genes):
                    Gene.objects.create(entrezid=(i + 1),
                                        systematic_name="sys_name #" + str(i + 1),
                                        standard_name="std_name #" + str(i + 1),
        Severity: Major
        Found in adage/analyze/tests.py and 2 other locations - About 2 hrs to fix
        adage/analyze/tests.py on lines 175..178
        adage/analyze/tests.py on lines 972..975

        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 70.

        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 3 locations. Consider refactoring.
        Open

                for i in range(num_genes):
                    Gene.objects.create(entrezid=(i + 1),
                                        systematic_name="sys_name #" + str(i + 1),
                                        standard_name="std_name #" + str(i + 1),
        Severity: Major
        Found in adage/analyze/tests.py and 2 other locations - About 2 hrs to fix
        adage/analyze/tests.py on lines 175..178
        adage/analyze/tests.py on lines 244..247

        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 70.

        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

        Module level import not at top of file
        Open

        from adage.settings import CONFIG
        Severity: Minor
        Found in adage/analyze/tests.py by pep8

        Place imports at the top of the file.

        Always put imports at the top of the file, just after any module
        comments and docstrings, and before module globals and constants.
        
        Okay: import os
        Okay: # this is a comment\nimport os
        Okay: '''this is a module docstring'''\nimport os
        Okay: r'''this is a module docstring'''\nimport os
        Okay:
        try:\n\timport x\nexcept ImportError:\n\tpass\nelse:\n\tpass\nimport y
        Okay:
        try:\n\timport x\nexcept ImportError:\n\tpass\nfinally:\n\tpass\nimport y
        E402: a=1\nimport os
        E402: 'One string'\n"Two string"\nimport os
        E402: a=1\nfrom sys import x
        
        Okay: if x:\n    import os

        Module level import not at top of file
        Open

        import get_pseudo_sdrf as gp
        Severity: Minor
        Found in adage/analyze/tests.py by pep8

        Place imports at the top of the file.

        Always put imports at the top of the file, just after any module
        comments and docstrings, and before module globals and constants.
        
        Okay: import os
        Okay: # this is a comment\nimport os
        Okay: '''this is a module docstring'''\nimport os
        Okay: r'''this is a module docstring'''\nimport os
        Okay:
        try:\n\timport x\nexcept ImportError:\n\tpass\nelse:\n\tpass\nimport y
        Okay:
        try:\n\timport x\nexcept ImportError:\n\tpass\nfinally:\n\tpass\nimport y
        E402: a=1\nimport os
        E402: 'One string'\n"Two string"\nimport os
        E402: a=1\nfrom sys import x
        
        Okay: if x:\n    import os

        Continuation line unaligned for hanging indent
        Open

                        'and anr mutant strains under aerobic conditions',
        Severity: Minor
        Found in adage/analyze/tests.py by pep8

        Continuation lines indentation.

        Continuation lines should align wrapped elements either vertically
        using Python's implicit line joining inside parentheses, brackets
        and braces, or using a hanging indent.
        
        When using a hanging indent these considerations should be applied:
        - there should be no arguments on the first line, and
        - further indentation should be used to clearly distinguish itself
          as a continuation line.
        
        Okay: a = (\n)
        E123: a = (\n    )
        
        Okay: a = (\n    42)
        E121: a = (\n   42)
        E122: a = (\n42)
        E123: a = (\n    42\n    )
        E124: a = (24,\n     42\n)
        E125: if (\n    b):\n    pass
        E126: a = (\n        42)
        E127: a = (24,\n      42)
        E128: a = (24,\n    42)
        E129: if (a or\n    b):\n    pass
        E131: a = (\n    42\n 24)

        Module level import not at top of file
        Open

        import logging
        Severity: Minor
        Found in adage/analyze/tests.py by pep8

        Place imports at the top of the file.

        Always put imports at the top of the file, just after any module
        comments and docstrings, and before module globals and constants.
        
        Okay: import os
        Okay: # this is a comment\nimport os
        Okay: '''this is a module docstring'''\nimport os
        Okay: r'''this is a module docstring'''\nimport os
        Okay:
        try:\n\timport x\nexcept ImportError:\n\tpass\nelse:\n\tpass\nimport y
        Okay:
        try:\n\timport x\nexcept ImportError:\n\tpass\nfinally:\n\tpass\nimport y
        E402: a=1\nimport os
        E402: 'One string'\n"Two string"\nimport os
        E402: a=1\nfrom sys import x
        
        Okay: if x:\n    import os

        Continuation line unaligned for hanging indent
        Open

                        'medium with C-30',
        Severity: Minor
        Found in adage/analyze/tests.py by pep8

        Continuation lines indentation.

        Continuation lines should align wrapped elements either vertically
        using Python's implicit line joining inside parentheses, brackets
        and braces, or using a hanging indent.
        
        When using a hanging indent these considerations should be applied:
        - there should be no arguments on the first line, and
        - further indentation should be used to clearly distinguish itself
          as a continuation line.
        
        Okay: a = (\n)
        E123: a = (\n    )
        
        Okay: a = (\n    42)
        E121: a = (\n   42)
        E122: a = (\n42)
        E123: a = (\n    42\n    )
        E124: a = (24,\n     42\n)
        E125: if (\n    b):\n    pass
        E126: a = (\n        42)
        E127: a = (24,\n      42)
        E128: a = (24,\n    42)
        E129: if (a or\n    b):\n    pass
        E131: a = (\n    42\n 24)

        Continuation line unaligned for hanging indent
        Open

                    'Cystic Fibrosis patients in Denmark',
        Severity: Minor
        Found in adage/analyze/tests.py by pep8

        Continuation lines indentation.

        Continuation lines should align wrapped elements either vertically
        using Python's implicit line joining inside parentheses, brackets
        and braces, or using a hanging indent.
        
        When using a hanging indent these considerations should be applied:
        - there should be no arguments on the first line, and
        - further indentation should be used to clearly distinguish itself
          as a continuation line.
        
        Okay: a = (\n)
        E123: a = (\n    )
        
        Okay: a = (\n    42)
        E121: a = (\n   42)
        E122: a = (\n42)
        E123: a = (\n    42\n    )
        E124: a = (24,\n     42\n)
        E125: if (\n    b):\n    pass
        E126: a = (\n        42)
        E127: a = (24,\n      42)
        E128: a = (24,\n    42)
        E129: if (a or\n    b):\n    pass
        E131: a = (\n    42\n 24)

        Module level import not at top of file
        Open

        from analyze.api import SampleResource
        Severity: Minor
        Found in adage/analyze/tests.py by pep8

        Place imports at the top of the file.

        Always put imports at the top of the file, just after any module
        comments and docstrings, and before module globals and constants.
        
        Okay: import os
        Okay: # this is a comment\nimport os
        Okay: '''this is a module docstring'''\nimport os
        Okay: r'''this is a module docstring'''\nimport os
        Okay:
        try:\n\timport x\nexcept ImportError:\n\tpass\nelse:\n\tpass\nimport y
        Okay:
        try:\n\timport x\nexcept ImportError:\n\tpass\nfinally:\n\tpass\nimport y
        E402: a=1\nimport os
        E402: 'One string'\n"Two string"\nimport os
        E402: a=1\nfrom sys import x
        
        Okay: if x:\n    import os

        Continuation line unaligned for hanging indent
        Open

                        'Cystic Fibrosis patients in Denmark',
        Severity: Minor
        Found in adage/analyze/tests.py by pep8

        Continuation lines indentation.

        Continuation lines should align wrapped elements either vertically
        using Python's implicit line joining inside parentheses, brackets
        and braces, or using a hanging indent.
        
        When using a hanging indent these considerations should be applied:
        - there should be no arguments on the first line, and
        - further indentation should be used to clearly distinguish itself
          as a continuation line.
        
        Okay: a = (\n)
        E123: a = (\n    )
        
        Okay: a = (\n    42)
        E121: a = (\n   42)
        E122: a = (\n42)
        E123: a = (\n    42\n    )
        E124: a = (24,\n     42\n)
        E125: if (\n    b):\n    pass
        E126: a = (\n        42)
        E127: a = (24,\n      42)
        E128: a = (24,\n    42)
        E129: if (a or\n    b):\n    pass
        E131: a = (\n    42\n 24)

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