pagination

[max-mapper]

for e.g. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?&retmode=json&version=2.0&db=gds&term=GSE48968&field=ACCN&usehistory=y which has 2428 results but we can only do 1000 at a time we should implement a batched fetcher that basically paginates through all of the result ids

[bmpvieira]

I'm not sure I get the issue, if I do:

bionode-ncbi search gds GSE48968 | wc

I get 2427 12786 1677177

I might be missing one result, need to check, but otherwise it fetches everything.

[bmpvieira]

I've done bionode-ncbi search gds GSE48968 | json -ga0 uid > list1.txt and checked against the IDs in http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?&retmode=json&retmax=2428&version=2.0&db=gds&term=GSE48968&field=ACCN&usehistory=y and got exactly the same 2428 IDs. I'm still not sure why piping directly to wc gives 2427 instead of 2428, but at least pagination is working so I'm closing this.