pepkit / geofetch

Builds a PEP from SRA or GEO accessions
https://pep.databio.org/geofetch/
BSD 2-Clause "Simplified" License
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Dealing with GEO tables #103

Closed khoroshevskyi closed 1 year ago

khoroshevskyi commented 1 year ago

Adding tables to GEO (in GSM metadata) became popular in GEO. A lot of projects have tables in thair soft files. In most cases this soft files are huge (10+ MB, sometimes Gigabytes ).

I think we should disable adding tables to projects. To deal with downstream problems there is two solutions: 1) #102 2) Disable !platform_table_begin key in parsing metadata image

Project example: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199233