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ngi_pipeline/engines/sarek/models/sarek.py

Summary

Maintainability
D
1 day
Test Coverage

File sarek.py has 487 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import csv
import os

from ngi_pipeline.engines.sarek.database import CharonConnector, TrackingConnector
from ngi_pipeline.engines.sarek.exceptions import BestPracticeAnalysisNotRecognized, SampleNotValidForAnalysisError
Severity: Minor
Found in ngi_pipeline/engines/sarek/models/sarek.py - About 7 hrs to fix

    SarekAnalysis has 26 functions (exceeds 20 allowed). Consider refactoring.
    Open

    class SarekAnalysis(object):
    """
    Base class for the SarekAnalysis engine. This class contains the necessary methods for configuring and launching
    an analysis with the Sarek engine. However, some methods are not implemented (they are "abstract") and are
    expected to be implemented in subclasses, providing interfaces to the specialized analysis modes (e.g. Germline or
    Severity: Minor
    Found in ngi_pipeline/engines/sarek/models/sarek.py - About 3 hrs to fix

      Function get_analysis_instance_for_workflow has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def get_analysis_instance_for_workflow(
      Severity: Minor
      Found in ngi_pipeline/engines/sarek/models/sarek.py - About 45 mins to fix

        Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def __init__(
        Severity: Minor
        Found in ngi_pipeline/engines/sarek/models/sarek.py - About 45 mins to fix

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

              def seqrun_should_be_started(self,
          Severity: Minor
          Found in ngi_pipeline/engines/sarek/models/sarek.py - About 35 mins to fix

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

                def get_analysis_instance_for_project(
            Severity: Minor
            Found in ngi_pipeline/engines/sarek/models/sarek.py - About 35 mins to fix

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