Download full metadata without sequences

[Wytamma]

Currently the full metadata can only be downloaded with the sequence data. Is there a way to only get the metadata without downloading sequences? (#16)

[tomwenseleers]

I seem to have asked a similar question here
https://github.com/Wytamma/GISAIDR/issues/26
where I mention that I found a solution to do this from R using RSelenium - see answer here
https://stackoverflow.com/questions/72632118/download-covid-patient-metadata-from-gisaid-website-in-r-using-rselenium

[Wytamma]

Thanks @tomwenseleers this issue is related to downloading the full metadata without the sequences. I think this might be related to the different versions of GISAID we have (touched on here #26 )... For me and others when we download sequences from GISAID we get a zip file that contains a fasta file and a metadata.tsv i.e. it is not possible to download metadata.tsv without the fasta.

[tomwenseleers]

For the record, with my login & credentials, this is how I managed to download a separate metadatafile with all the columns I was given access to & the code given can also still be modified a bit to allow download of the FASTA; this is using RSelenium (so a bit different than your httr approach). It also shows how to get the most recently uploaded records that are absent in the download package: https://stackoverflow.com/questions/72632118/download-covid-patient-metadata-from-gisaid-website-in-r-using-rselenium

[jrotieno]

Do you know if your rselenium code can extract the sequencing technology field?

[tomwenseleers]

Right now I didn't implement that yet, but with some small modification in the code this would be possible...