ISA converter - use of default configuration - update needed to cope with new assay definitions
Open
@proccaserra is already working on this.
Since Jan 8, 2024.
blocker
bug
documentation
- Dominant language
- Python
- Stars
- 48
- Forks
- 42
- PR merge metrics
- No merged PRs in 30d
Description
Symptoms:
Conversion from ISA-JSON to ISA-TAB drops unrecognized assays if measurement type and technology types not found in
/resources/config/json/default by the converter
- strict requirement on
measurement type.termandtechnology type.termvalue: exact match needed. - strict requirement on
protocol_type.termvalue: exact match needed. - strict requirement on the sequence of processes and input/output (no support for optional steps, e.g. optional Labeling events during sample processing
TODO:
- add set of assay configurations to cover Metabolights definitions:
https://github.com/EBI-Metabolights/MtblsWS-Py/blob/master/resources/MetaboLightsAssayMaster.tsv - catch unrecognised assay definitions (measurement type + technology type) and raise an ERROR to users and point to curation actions to take.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
This issue has not been assessed yet.