Comments (3)
We are kinda limited in how we can do this because the parsers are designed to handle streaming data.
The validity is inherently checked by the putting it in the hamronised format and raising an error if there is an issue, I don't really think wrapping that in try except to give a cleaner error message really adds much (just obfuscation) but if you think that's better it can be easily done.
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I would like to get some more opinios on this. Indeed it adds an obfuscation but I think a custom error message would be helful for a user as the general key error doesn't actually explain much. Personally I would prefer a more informative error message but I'm good with what you decide on!
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Created a new issue with a plan to improve this (adding a debug flag for full traceback and logging library to handle the different levels.)
Will close and redirect to #56
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Related Issues (20)
- help understanding resfinder run HOT 1
- ORF_ID missing once RGI report hAMRonized HOT 1
- RgiIO.py: Typo in line 79 HOT 1
- Fix issue of very similar runs falsely combining results in summary
- Genetic_variation_type HOT 1
- hamronize summarize - local variable 'parsed_report' reference before assignment HOT 3
- Flag overlapping ranges in hAMRonization
- AMR Variant detection - Parsers to be updated HOT 1
- Obtain specification field data information from JSON schema HOT 1
- Update README
- Add xlsx output HOT 1
- Add CONTRIBUTING.md
- Add fARGene
- PyPi not updated, 1.0.4 tarball reports version 1.0.3 HOT 2
- [BUG] `KeyError: 'reference_database_name'` when running summarize HOT 9
- [BUG] Generated output does not follow CSP rules HOT 1
- Request for Zenodo archive
- [BUG] - RGI bwt gene_mapping HOT 3
- Updating version support for starmar, amrfinderplus, kmerresistance - summarize output breaks HOT 4
- nucleotide specific fileds are empty while importing AmrFinderPlus results based on nucleotide sequences HOT 2
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