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ngi_pipeline/utils/parsers.py

Summary

Maintainability
D
2 days
Test Coverage

File parsers.py has 376 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import collections
import csv
import glob
import gzip
import os
Severity: Minor
Found in ngi_pipeline/utils/parsers.py - About 5 hrs to fix

    Function determine_library_prep_from_fcid has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
    Open

    def determine_library_prep_from_fcid(project_id, sample_name, fcid):
    """Use the information in the database to get the library prep id
    from the project name, sample name, and flowcell id.

    :param str project_id: The ID of the project
    Severity: Minor
    Found in ngi_pipeline/utils/parsers.py - About 2 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

    Function determine_library_prep_from_samplesheet has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
    Open

    def determine_library_prep_from_samplesheet(samplesheet_path, project_id, sample_id, lane_num):
    lane_num = int(lane_num) # Raises ValueError if it can't convert. Handy
    samplesheet = parse_samplesheet(samplesheet_path)
    for row in samplesheet:
        if not row.get("Description"):
    Severity: Minor
    Found in ngi_pipeline/utils/parsers.py - About 2 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

    Function __init__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
    Open

        def __init__(self, aList):
        for element in aList:
            if element:
                # treat like dict
                if len(element) == 1 or element[0].tag != element[1].tag:
    Severity: Minor
    Found in ngi_pipeline/utils/parsers.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 __init__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
    Open

        def __init__(self, parent_element):
        if list(parent_element.items()):
            self.update(dict(list(parent_element.items())))
        for element in parent_element:
            if element:
    Severity: Minor
    Found in ngi_pipeline/utils/parsers.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 parse_samplesheet has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

    def parse_samplesheet(samplesheet_path):
    """Parses an Illumina SampleSheet.csv and returns a list of dicts
    """
    try:
        # try opening as a gzip file (Uppsala)
    Severity: Minor
    Found in ngi_pipeline/utils/parsers.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 find_fastq_read_pairs has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

    def find_fastq_read_pairs(file_list):
    """
    Given a list of file names, finds read pairs (based on _R1_/_R2_ file naming)
    and returns a dict of {base_name: [ file_read_one, file_read_two ]}
    Filters out files not ending with .fastq[.gz|.gzip|.bz2].
    Severity: Minor
    Found in ngi_pipeline/utils/parsers.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

    Avoid deeply nested control flow statements.
    Open

                            if seqrun_runid == fcid:
                            ## BUG if we have one sample with two libpreps on the same flowcell,
                            ##     this just picks the first one it encounters; instead,
                            ##     it should raise an Exception. Requires restructuring.
                            return libprep['libprepid']
    Severity: Major
    Found in ngi_pipeline/utils/parsers.py - About 45 mins to fix

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

                      if len(element) == 1 or element[0].tag != element[1].tag:
      Severity: Major
      Found in ngi_pipeline/utils/parsers.py and 1 other location - About 1 hr to fix
      ngi_pipeline/utils/parsers.py on lines 312..312

      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 38.

      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 len(element) == 1 or element[0].tag != element[1].tag:
      Severity: Major
      Found in ngi_pipeline/utils/parsers.py and 1 other location - About 1 hr to fix
      ngi_pipeline/utils/parsers.py on lines 274..274

      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 38.

      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

                      if list(element.items()):
                    aDict.update(dict(list(element.items())))
      Severity: Minor
      Found in ngi_pipeline/utils/parsers.py and 1 other location - About 35 mins to fix
      ngi_pipeline/utils/parsers.py on lines 306..307

      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 33.

      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

              if list(parent_element.items()):
            self.update(dict(list(parent_element.items())))
      Severity: Minor
      Found in ngi_pipeline/utils/parsers.py and 1 other location - About 35 mins to fix
      ngi_pipeline/utils/parsers.py on lines 322..323

      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 33.

      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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