Access to private and reviewer link datasets about geoquery HOT 1 CLOSED

FROM NCBI

Hi Sean,

I ran your proposal by developers, and I'm afraid it got a fairly cool
response for the reasons outlined below. However, please see the workaround
suggestion, maybe that's something to look into.

Thanks and best regards,
Tanya

Providing access to private data via FTP is not possible for us as it would
require adding each GEO user as FTP user. So GEOquery would have to use https
for everything, meaning only calls to /geo/query/acc.cgi and/or some other GEO
services. GEOquery would have to authorize user thru MyNCBI, and send us
authorization cookie along with request. We have nothing better or "formal"
for this this task, or any type of history of implementing something like this.

My alternative suggestion to solve this problem:
Make GEOquery to be able work on isolated data, meaning no ad hoc calls during
running time to outside http services.

If authorized user wants to analyze private GSE, make user download all
samples data and platform data as separate files ahead of the time. Then run
the code that with work with this local data. Of course limitation is that
GEOquery prefers matrix file over Sample soft files, and we do not generate it
ahead of time, and we could not generate it on the fly for normal size series.

from geoquery.