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Showing 36 of 36 total issues

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

    for l in ('rec', 'recording'):
        if l in bidsmeta:
            info['Parameter Value[recording label]'] = bidsmeta[l]
Severity: Minor
Found in datalad_neuroimaging/bids2scidata.py and 1 other location - About 50 mins to fix
datalad_neuroimaging/bids2scidata.py on lines 240..242

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 36.

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

    for l in ('acq', 'acquisition'):
        if l in bidsmeta:
            info['Parameter Value[acquisition label]'] = bidsmeta[l]
Severity: Minor
Found in datalad_neuroimaging/bids2scidata.py and 1 other location - About 50 mins to fix
datalad_neuroimaging/bids2scidata.py on lines 237..239

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 36.

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

Avoid deeply nested control flow statements.
Open

                            if fg_color:
                                self.fg_color = fg_color
                            elif bg_color:
                                self.bg_color = bg_color
                            elif value == 1:
Severity: Major
Found in docs/utils/pygments_ansi_color.py - About 45 mins to fix

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

    def split_term_source_accession(val):
    if val is None:
        return '', ''
    if not r_url.match(val):
        # no URL
    Severity: Minor
    Found in datalad_neuroimaging/bids2scidata.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 _format_action_invocation has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

        def _format_action_invocation(self, action):
        if not action.option_strings:
            metavar, = self._metavar_formatter(action, action.dest)(1)
            return metavar
    Severity: Minor
    Found in formatters.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 _get_assay_df has 6 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def _get_assay_df(
    Severity: Minor
    Found in datalad_neuroimaging/bids2scidata.py - About 45 mins to fix

      Function __call__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __call__(repo_name, repo_accession, repo_url, path=None, output=None, dataset=None):
      Severity: Minor
      Found in datalad_neuroimaging/bids2scidata.py - About 35 mins to fix

        Function _struct2dict has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

        def _struct2dict(struct):
    out = {}
    for k in struct.dir():
        if hasattr(struct, k):
            value = getattr(struct, k)
        Severity: Minor
        Found in datalad_neuroimaging/extractors/dicom.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

        Avoid too many return statements within this function.
        Open

                    return '', val
        Severity: Major
        Found in datalad_neuroimaging/bids2scidata.py - About 30 mins to fix

          Function _get_dsmeta has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
          Open

              def _get_dsmeta(self, bids):
        context = {}
        if hasattr(bids, 'get_dataset_description'):
            # post 0.9.1
            # https://github.com/bids-standard/pybids/pull/444
          Severity: Minor
          Found in datalad_neuroimaging/extractors/bids.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

          Function _get_bids_entities has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
          Open

              def _get_bids_entities(self, bids):
        """Get dataset-specific entities from BIDSLayout"""
        ds_entities = list(bids.entities.keys())
        new_entities = {}
        # If the entity is in the main list AND in the list
          Severity: Minor
          Found in datalad_neuroimaging/extractors/bids_dataset.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

          Try, Except, Pass detected.
          Open

                      except Exception as e:
          Severity: Info
          Found in datalad_neuroimaging/extractors/bids_dataset.py by bandit

          Starting a process with a shell, possible injection detected, security issue.
          Open

                      os.system(
                '{} build_examples --expath {} --rstpath {}'.format(
                    setup_py_path,
                    abspath(opj(dirname(__file__), pardir, 'examples')),
                    opj(dirname(__file__), 'generated', 'examples')))
          Severity: Major
          Found in docs/source/conf.py by bandit

          Starting a process with a shell, possible injection detected, security issue.
          Open

                      os.system(
                '{} build_manpage --cmdsuite {} --manpath {} --rstpath {}'.format(
                    setup_py_path,
                    'datalad_neuroimaging:command_suite',
                    abspath(opj(dirname(setup_py_path), 'build', 'man')),
          Severity: Major
          Found in docs/source/conf.py by bandit

          Try, Except, Pass detected.
          Open

                  except:
          Severity: Info
          Found in docs/source/conf.py by bandit

          Try, Except, Pass detected.
          Open

                  except:
          Severity: Info
          Found in docs/source/conf.py by bandit
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