Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

get_names 'could not convert string' error with NCBI #117

Open
miistakis opened this issue Apr 8, 2023 · 2 comments
Open

get_names 'could not convert string' error with NCBI #117

miistakis opened this issue Apr 8, 2023 · 2 comments

Comments

@miistakis
Copy link

Using ‘taxadb’ version 0.2.1.99
Have no issues with col, or otis, but for NCBI I get the following error when it attempts to do get_names():

i In argument: accepted_name = get_names(id, "ncbi").
Caused by error in collect():
! Failed to collect lazy table.
Caused by error:
! rapi_execute: Failed to run query
Error: Conversion Error: Could not convert string 'NCBI:181977' to INT32

Also, when I try to td_create("ott") I get the error:
Error: no match found for schema: common provider: ott version: 22.12

@cboettig
Copy link
Member

cboettig commented May 1, 2023

apologies for the slow reply but thanks for reporting these bugs introduced in the recent release, we'll fix these ASAP.

Meanwhile, with ott you can work around by explicitly requesting only the darwin core data, td_create("ott", "dwc")

Looks like NCBI snapshot currently only has accepted IDs, obviously a bug so we'll fix. meanwhile you can filter on those, e.g.

taxadb::taxa_tbl("ncbi") |> dplyr::filter(acceptedNameUsageID == "NCBI:9606")

@miistakis
Copy link
Author

Thanks!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants