NationalGenomicsInfrastructure/ngi_pipeline

View on GitHub
ngi_pipeline/engines/rna_ngi/local_process_tracking.py

Summary

Maintainability
C
1 day
Test Coverage

Function record_project_job has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

def record_project_job(project, job_id, analysis_dir, workflow=None, engine='rna_ngi', run_mode='local', config=None, config_file_path=None):
    with get_session() as db_session:
        project_db_obj=ProjectAnalysis(project_id=project.project_id,
                                        job_id=job_id,
                                        project_name=project.name,
Severity: Minor
Found in ngi_pipeline/engines/rna_ngi/local_process_tracking.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

Function update_analysis has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

def update_analysis(project_id, status):
    charon_session=CharonSession()
    mail_analysis(project_id, engine_name='rna_ngi', level='INFO' if status else 'ERROR')
    new_sample_status='ANALYZED' if status else 'FAILED'
    new_seqrun_status='DONE' if status else 'FAILED'
Severity: Minor
Found in ngi_pipeline/engines/rna_ngi/local_process_tracking.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

Function update_charon_with_local_jobs_status has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

def update_charon_with_local_jobs_status(quiet=False, config=None, config_file_path=None):
    jobs=[]
    with get_session() as db_session:
        jobs=db_session.query(ProjectAnalysis).filter(ProjectAnalysis.engine=='rna_ngi').all()

Severity: Minor
Found in ngi_pipeline/engines/rna_ngi/local_process_tracking.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 record_project_job has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

def record_project_job(project, job_id, analysis_dir, workflow=None, engine='rna_ngi', run_mode='local', config=None, config_file_path=None):
Severity: Major
Found in ngi_pipeline/engines/rna_ngi/local_process_tracking.py - About 1 hr to fix

    Avoid deeply nested control flow statements.
    Open

                            if CharonSession().libprep_get(project.project_id, sample.name, libprep.name).get('qc') != "FAILED":
                                for seqrun in libprep:
                                    if seqrun.being_analyzed:
                                        CharonSession().seqrun_update(project.project_id, sample.name, libprep.name, seqrun.name, alignment_status="RUNNING")
                    except Exception as e:
    Severity: Major
    Found in ngi_pipeline/engines/rna_ngi/local_process_tracking.py - About 45 mins to fix

      Avoid deeply nested control flow statements.
      Open

                          for seqrun in charon_session.libprep_get_seqruns(project_id, sample.get('sampleid'),libprep.get('libprepid')).get('seqruns', {}):
                              if seqrun.get('alignment_status')=="RUNNING":
                                  LOG.info("Marking analysis of seqrun {}/{}/{}/{} as {}".format(project_id, sample.get('sampleid'),libprep.get('libprepid'), seqrun.get('seqrunid'), new_seqrun_status))
                                  charon_session.seqrun_update(project_id, sample.get('sampleid'),libprep.get('libprepid'), seqrun.get('seqrunid'), alignment_status=new_seqrun_status)
      
      
      Severity: Major
      Found in ngi_pipeline/engines/rna_ngi/local_process_tracking.py - About 45 mins to fix

        There are no issues that match your filters.

        Category
        Status