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Clean balsamic analysis api #5161

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3 changes: 3 additions & 0 deletions cg/meta/workflow/balsamic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -566,6 +566,7 @@
)
return config_data["analysis"]["BALSAMIC_version"]

# TODO: Remove this method

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codefactor.io / CodeFactor

cg/meta/workflow/balsamic.py#L569 

Unresolved comment '# TODO: Remove this method'. (C100)

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SonarQubeCloud / SonarCloud Code Analysis

Complete the task associated to this "TODO" comment. 


See more on https://sonarcloud.io/project/issues?id=Clinical-Genomics_cg&issues=AZ8ES9lCmADGP9d-JE1x&open=AZ8ES9lCmADGP9d-JE1x&pullRequest=5161
def config_case(
self,
case_id: str,
Expand Down Expand Up @@ -628,6 +629,7 @@
parameters = command + options
self.process.run_command(parameters=parameters, dry_run=dry_run)

# TODO: Remove this method

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codefactor.io / CodeFactor

cg/meta/workflow/balsamic.py#L632 

Unresolved comment '# TODO: Remove this method'. (C100)

Check warning on line 632 in cg/meta/workflow/balsamic.py

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SonarQubeCloud / SonarCloud Code Analysis

Complete the task associated to this "TODO" comment. 


See more on https://sonarcloud.io/project/issues?id=Clinical-Genomics_cg&issues=AZ8ES9lCmADGP9d-JE1y&open=AZ8ES9lCmADGP9d-JE1y&pullRequest=5161
def run_analysis(
self,
case_id: str,
Expand Down Expand Up @@ -712,6 +714,7 @@
"""Return data analysis type carried out."""
return self.get_bundle_deliverables_type(case_id)

# TODO: Remove this method

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codefactor.io / CodeFactor

cg/meta/workflow/balsamic.py#L717 

Unresolved comment '# TODO: Remove this method'. (C100)

Check warning on line 717 in cg/meta/workflow/balsamic.py

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SonarQubeCloud / SonarCloud Code Analysis

Complete the task associated to this "TODO" comment. 


See more on https://sonarcloud.io/project/issues?id=Clinical-Genomics_cg&issues=AZ8ES9lCmADGP9d-JE1z&open=AZ8ES9lCmADGP9d-JE1z&pullRequest=5161
def is_analysis_normal_only(self, case_id: str) -> bool:
"""Return whether the analysis is normal only."""
case: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
Expand Down
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