Add function to remove protocols declared but not used
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- Dominant language
- Python
- Stars
- 48
- Forks
- 42
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Description
This is not critical as it would be extra information in the ISA files (and the validator only gives a warning), but within the set of curation functions, we can consider adding one to remove those protocols declarations that are never used.
An example warning in this case is:
WARNING:isatools.isatab:(W) Some protocols declared in the file s_gsk_longitudinal.txt are not used in any assay file: ['', 'data transformation', 'extraction', 'labeling']
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First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
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Research direction
Start by locating the existing set of curation functions and the validator logic that reports unused protocol declarations. Trace how protocol declarations are compared with protocols used in assay files, then define the function's behavior for declarations such as those shown in the warning. Done means the unused declarations can be removed without affecting used protocols or ISA file validation.
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Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100