Instructions would be nice

[rtaylorzfin]

Hi,

Thanks for writing this validation library. Could you include instructions on how to use it? I have some sssom files that I would like to validate.

Thanks,
Ryan

[matentzn]

@rtaylorzfin Thank you for reaching out!

I would recommend the following:

1. For simple command line usage do

pip install sssom
sssom validate my.sssom.tsv

For Continuous Integration I would recommand setting up a Mapping Registry which comes with a GitHub action that will do the checking for you whenever you make a pull request (see action here).

The repo you found here is a bad attempt of me to write a webtool for validating SSSOM. Something like https://jsonlint.com/ for sssom files. Would you still be interested in this?

[rtaylorzfin]

@matentzn
Thanks for the reply. The command line tool is great. Thanks!

[matentzn]

I would be amiss to say that the validator does not catch all important errors.

Please feel free to open issues to things you think are wrong and should be validated.

Also, for a well rounded picture, we use

1. tsvalid to check for basic TSV issues like redundant whitespace
2. do a test conversion into RDF
3. run sssom validate

(https://github.com/monarch-initiative/monarch-mapping-commons/blob/62a76081a4cf326ee7fc48add6d2bb9439b30a22/Makefile#L43)

All of these should give you a good level of security. Looking forward to your issues!

[rtaylorzfin]

Great tips! Thank you!