search

LRGASP / lrgasp-submissions

Definition and validators for LRGASP submissions
MIT License
8 stars 2 forks source link

Comma-separated column names do not match libraries in experiment.json #44

Closed andrewprzh closed 2 years ago

andrewprzh commented 2 years ago

Dear Mark,

a small problem regarding R2C2 submission for challenge 2: as indicated here, column names in expression.tsv should be comma-separated: https://lrgasp.github.io/lrgasp-submissions/docs/faq.html

But when comma separated libraries are provided in libraries section in experiment.json, the validation reports

caused by: experiment field 'libraries' is not valid, value is 'ENCFF379KHH,ENCFF694JLN'
caused by: not a valid symbolic identifier 'ENCFF379KHH,ENCFF694JLN'

When libraries are listed one by one in experiment.json, validation fails with: caused by: matrix column 'ENCFF379KHH,ENCFF694JLN' is not listed in experiment_md.libraries for 'H1_mix_r2c2_ont'

Thanks a lot! Andrey

diekhans commented 2 years ago

this is fixed in 1.8.0 release

Andrey Prjibelski @.***> writes:

Dear Mark,

a small problem regarding R2C2 submission for challenge 2: as indicated here, column names in expression.tsv should be comma-separated: https://lrgasp.github.io/lrgasp-submissions/docs/faq.html

But when comma separated libraries are provided in libraries section in experiment.json, the validation reports

caused by: experiment field 'libraries' is not valid, value is 'ENCFF379KHH,ENCFF694JLN'
caused by: not a valid symbolic identifier 'ENCFF379KHH,ENCFF694JLN'

When libraries are listed one by one in experiment.json, validation fails with: caused by: matrix column 'ENCFF379KHH,ENCFF694JLN' is not listed in experiment_md.libraries for 'H1_mix_r2c2_ont'

Thanks a lot! Andrey

andrewprzh commented 2 years ago

I've checked the version before reporting the issue and it was 1.8. However, it looks like we had some mix-up between locally install 1.8 and system-wide one, for some reason pip only installs 1.7 if not directly specified. Sorry for reporting this!