colons in values
nsheff opened this issue · comments
geofetch should quote any constant columns its sticking in the config, since embedded colons are causing problems.
Do you have an GSE example to check if it is still a problem?
GSE181846
In geofetch0.11.0 this error is solved by deleting all special characters. Not sure if it's the best solution, but I decided to do this, as quoted text was causing errors, because some of the text in GEO and NCBI had double or single quotes.
geofetch -i GSE181846 --metadata-folder `pwd` --just-metadata --const-limit-project 1 --const-limit-discard 10000 --attr-limit-truncate 10000
You can run this command using geofetch from this branch: https://github.com/pepkit/geofetch/tree/refactoring
I would suggest:
- quote the fields
- escape any internal quotes.
Would that work? I think it's better than stripping characters.