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NationalGenomicsInfrastructure/ngi_pipeline

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ngi_pipeline/engines/sarek/models/resources.py

Summary

Maintainability
D
1 day
Test Coverage

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

    def sample_fastq_file_pair(sample_fastqs):
        """
        Take a list of SampleFastq objects and return a generator where each element is a list containing a fastq file
        pair (if paired-end, for single-end the list will just contain one entry), with first element being R1 and
        second element being R2.
Severity: Minor
Found in ngi_pipeline/engines/sarek/models/resources.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

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

    def __init__(self, path):
        """
        Creates a Runfolder object representing a runfolder directory.

        :param path: the path to the runfolder where the name will be used to identify properties
Severity: Major
Found in ngi_pipeline/engines/sarek/models/resources.py and 1 other location - About 4 hrs to fix
ngi_pipeline/engines/sarek/models/resources.py on lines 15..28

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 80.

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

    def __init__(self, path):
        """
        Creates a SampleFastq object representing a fastq file.

        :param path: the path to the fastq file, where the file name will be used to identify properties
Severity: Major
Found in ngi_pipeline/engines/sarek/models/resources.py and 1 other location - About 4 hrs to fix
ngi_pipeline/engines/sarek/models/resources.py on lines 76..89

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 80.

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

    def split_filename(self, filename):
        """
        Split the filename according to the regexp and return the identified groups. If the regexp was not matched,
        None will be returned for all properties.
Severity: Major
Found in ngi_pipeline/engines/sarek/models/resources.py and 1 other location - About 2 hrs to fix
ngi_pipeline/engines/sarek/models/resources.py on lines 91..101

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 55.

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

    def split_runfolder_name(self, runfolder_name):
        """
        Split the runfolder name according to the regexp and return the identified groups. If the regexp was not
        matched, None will be returned for all properties.
Severity: Major
Found in ngi_pipeline/engines/sarek/models/resources.py and 1 other location - About 2 hrs to fix
ngi_pipeline/engines/sarek/models/resources.py on lines 30..40

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 55.

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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