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NationalGenomicsInfrastructure/ngi_pipeline

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ngi_pipeline/engines/utils.py

Summary

Maintainability
C
1 day
Test Coverage

Function handle_sample_status has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
Open

def handle_sample_status(analysis_object, sample, charon_reported_status):
    """ returns true of false wether the sample should be analyzed"""
    if charon_reported_status == "UNDER_ANALYSIS":
        if not analysis_object.restart_running_jobs:
            error_text = ('Charon reports seqrun analysis for project "{}" '
Severity: Minor
Found in ngi_pipeline/engines/utils.py - About 3 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

Avoid too many return statements within this function.
Open

            return True
Severity: Major
Found in ngi_pipeline/engines/utils.py - About 30 mins to fix

    Avoid too many return statements within this function.
    Open

            return True
    Severity: Major
    Found in ngi_pipeline/engines/utils.py - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

                  return False
      Severity: Major
      Found in ngi_pipeline/engines/utils.py - About 30 mins to fix

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

                    if not analysis_object.config.get('quiet'):
                mail_analysis(project_name=analysis_object.project.name, sample_name=sample.name,
                              engine_name=analysis_module.__name__,
        Severity: Major
        Found in ngi_pipeline/engines/utils.py and 1 other location - About 1 hr to fix
        ngi_pipeline/engines/utils.py on lines 35..37

        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 not analysis_object.config.get('quiet'):
                mail_analysis(project_name=analysis_object.project.name, sample_name=sample.name,
                              engine_name=analysis_module.__name__,
        Severity: Major
        Found in ngi_pipeline/engines/utils.py and 1 other location - About 1 hr to fix
        ngi_pipeline/engines/utils.py on lines 60..62

        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

        Similar blocks of code found in 3 locations. Consider refactoring.
        Open

            elif charon_reported_status == 'DONE' and not analysis_object.restart_finished_jobs:
        LOG.info("seqrun {}/{}/{}/{} has been analyzed and no restart_analyzed flag was given, skipping.".format(analysis_object.project.project_id, sample.name, libprep.name, seqrun.name))
        return False
        Severity: Minor
        Found in ngi_pipeline/engines/utils.py and 2 other locations - About 30 mins to fix
        ngi_pipeline/engines/utils.py on lines 8..10
        ngi_pipeline/engines/utils.py on lines 14..16

        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 3 locations. Consider refactoring.
        Open

            elif charon_reported_status == 'FAILED' and not analysis_object.restart_failed_jobs:
        LOG.info("seqrun {}/{}/{}/{} analysis has failed, but no restart_failed flag was given, skipping.".format(analysis_object.project.project_id, sample.name, libprep.name, seqrun.name))
        return False
        Severity: Minor
        Found in ngi_pipeline/engines/utils.py and 2 other locations - About 30 mins to fix
        ngi_pipeline/engines/utils.py on lines 8..10
        ngi_pipeline/engines/utils.py on lines 11..13

        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 3 locations. Consider refactoring.
        Open

            if charon_reported_status == 'RUNNING' and not analysis_object.restart_running_jobs:
        LOG.info("seqrun {}/{}/{}/{} is being analyzed and no restart_running flag was given, skipping.".format(analysis_object.project.project_id, sample.name, libprep.name, seqrun.name))
        return False
        Severity: Minor
        Found in ngi_pipeline/engines/utils.py and 2 other locations - About 30 mins to fix
        ngi_pipeline/engines/utils.py on lines 11..13
        ngi_pipeline/engines/utils.py on lines 14..16

        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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