genesysr issueshttps://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues2024-02-23T09:46:26+01:00https://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/7genesysr R package error2024-02-23T09:46:26+01:00GitLab Support Botgenesysr R package errorDear Matija,
I am unable to login to Genesys with `genesysr` R package. Running `user_login()` is giving the following error probably due to a change in the depency package `httr2`.
```R
Warning message:
The `host_name` argument of `oa...Dear Matija,
I am unable to login to Genesys with `genesysr` R package. Running `user_login()` is giving the following error probably due to a change in the depency package `httr2`.
```R
Warning message:
The `host_name` argument of `oauth_flow_auth_code()` is deprecated as of httr2 1.0.0.
Please use the `redirect_uri` argument instead.
The deprecated feature was likely used in the httr2 package.
Please report the issue at <https://github.com/r-lib/httr2/issues>.
```
Also it is not possible to report any bug via gitlab as it is crop trust repo.
I hope this is cleared up soon.
Best Regards,
J. Aravind,
Scientist,
Division of Germplasm Conservation
ICAR-National Bureau of Plant Genetic Resources,
New Delhi - 110 012https://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/6Upgrade to /acn/query2023-10-10T16:26:16+02:00Matija ObrezaUpgrade to /acn/queryThe new `.../acn/query` endpoint provides much improved performance compared to `.../acn/query`. Migrate `get_accessions()` to use the new endpoint.The new `.../acn/query` endpoint provides much improved performance compared to `.../acn/query`. Migrate `get_accessions()` to use the new endpoint.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/5Allow get the images with genesysr2023-10-10T16:24:29+02:00Miguel AcostaAllow get the images with genesysrThe objective is to allow a user to download images in bulk using `genesysr`, it can be useful both for users with some programming experience and for those who wish to share filters between users but ensuring an appropriate filter, sinc...The objective is to allow a user to download images in bulk using `genesysr`, it can be useful both for users with some programming experience and for those who wish to share filters between users but ensuring an appropriate filter, since R is a language easy to use for the scientific community.
```
filter_1 <- get_accessions(mcpd_filter(INSTCODE = 'COL003',
GENUS = 'Phaseolus',
SAMPSTAT = c('100','110','120','200'),
IMAGES=T)) # For T or F
```
In **IMAGES**, like boolean attribute use TRUE for get the files and FALSE for not including files. And download in .zip file that contain folders of each images, very similar to normal download by genesys page.https://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/4R package to query subsets and trait data2023-10-11T00:21:02+02:00Christelle RabilR package to query subsets and trait dataRequest from CIP, CIAT particiapants in the Spanish CoP to add the possibility to query subsets and trait datasets in Genesys R.Request from CIP, CIAT particiapants in the Spanish CoP to add the possibility to query subsets and trait datasets in Genesys R.Matija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/3OIDC authentication2023-07-19T06:05:07+02:00Matija ObrezaOIDC authenticationWe need to open a TCP socket on localhost so that the redirect can be done with the new authentication system.
- https://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.socket.html
- https://search.r-project.org/CRAN/refmans/opene...We need to open a TCP socket on localhost so that the redirect can be done with the new authentication system.
- https://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.socket.html
- https://search.r-project.org/CRAN/refmans/openeo/html/OIDCAuth.htmlMatija ObrezaMatija Obrezahttps://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/2Welcome2023-03-17T15:14:25+01:00Matija ObrezaWelcomeThis is to add @kaouzal to the project. Is there anything specific that you need *genesysr* to do?This is to add @kaouzal to the project. Is there anything specific that you need *genesysr* to do?Khadija AouzalKhadija Aouzalhttps://gitlab.croptrust.org/genesys-pgr/genesysr/-/issues/1Flatten nested lists2018-06-11T17:40:08+02:00Nora Castaneda-AlvarezFlatten nested lists
```r
# Digests (deep) nested lists from Genesys
# N. Castaneda
# 2018-06-11
require(devtools)
require(tidyverse)
devtools::install_git('https://gitlab.croptrust.org/genesys-pgr/genesysr')
require(genesysr)
# or sandbox.genesys-pgr.or...
```r
# Digests (deep) nested lists from Genesys
# N. Castaneda
# 2018-06-11
require(devtools)
require(tidyverse)
devtools::install_git('https://gitlab.croptrust.org/genesys-pgr/genesysr')
require(genesysr)
# or sandbox.genesys-pgr.org
genesysr::setup_sandbox()
# Open Genesys web page in browser and get verifier code
genesysr::user_login()
# Query genesys
filters <- mcpd_filter(ORIGCTY = c("DEU", "SVN")) #filter by ORIGCTY
accessions <- genesysr::fetch_accessions(filters)
filters <- jsonlite::fromJSON('{"geo.latitude":[{"range":[-180,180]}]}') #filter all records with geo.latitude
accessions <- genesysr::fetch_accessions(filters)
# Exploring the query
class(accessions)
head(accessions)
accessions$content
names(accessions$content[[1]])
# Flattening the query
gen.data <- lapply(accessions$content, unlist) #looks good
gen.data <- gen.data %>% map_df(bind_rows)
```Matija ObrezaMatija Obreza