Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.
is basically an SQL-like interface (see #32) that allows a CSV export. I wonder whether it would be possible to formulate the query URL in R, auto-download the offered CSV & then call retrieve_data(... , searchType = "bacdive_id") on the hits.
In any case:
add the advanced search to the README.Rmd as a possible source for ID lists
try a read_ID_list() function or retrieve_IDs(adv_search_URL = "...") as a 2nd step after manually puzzling together a query on https://bacdive.dsmz.de/advsearch
[x] take semi-automatic approach: user formulates query, copy-paste URL to a BacDiveR function (i.e. retrieve_search_results()), then append ?download, readLines() & purrr::map(retrieve_data(..., searchType = "bacdive_id))
Problem: multiple large lists => EITHER refactor r_d to take ID vector, OR construct large list within r_s_r.
[x] write vignette about this use-case after implementing #60
https://bacdive.dsmz.de/advsearch?advsearch=search&site=advsearch&searchparams%5B20%5D%5Bcontenttype%5D=text&searchparams%5B20%5D%5Btypecontent%5D=contains&searchparams%5B20%5D%5Bsearchterm%5D=pacific&searchparams%5B100%5D%5Bcontenttype%5D=text&searchparams%5B100%5D%5Btypecontent%5D=beginswith&searchparams%5B100%5D%5Bsearchterm%5D=Russ&searchparams%5B17%5D%5Bsearchterm%5D=Europe
is basically an SQL-like interface (see #32) that allows a CSV export. I wonder whether it would be possible to formulate the query URL in R, auto-download the offered CSV & then call
retrieve_data(... , searchType = "bacdive_id")on the hits.In any case:
add the advanced search to theREADME.Rmdas a possible source for ID liststry aread_ID_list()function orretrieve_IDs(adv_search_URL = "...")as a 2nd step after manually puzzling together a query on https://bacdive.dsmz.de/advsearchretrieve_search_results()), then append?download,readLines()&purrr::map(retrieve_data(..., searchType = "bacdive_id))r_dto take ID vector, OR construct large list withinr_s_r.