Commit 7ac98123 authored by Matija Obreza's avatar Matija Obreza
Browse files

Prepare for release on CRAN

- Included URL in DESCRIPTION
- Ignore generated README.Rmd
parent 65c5af5a
^.*\.Rproj$ ^.*\.Rproj$
^\.Rproj\.user$ ^\.Rproj\.user$
^README\.Rmd$
^README-.*\.png$
^cran-comments\.md$
...@@ -3,3 +3,5 @@ ...@@ -3,3 +3,5 @@
.RData .RData
.Ruserdata .Ruserdata
man man
README.Rmd
cran-comments.md
Package: genesysr Package: genesysr
Title: R client for Genesys PGR (www.genesys-pgr.org) Version: 0.9.1
Version: 0.1 Title: Genesys PGR Client
Description: Access data on plant genetic resources from genebanks around the world published on Genesys (<https://www.genesys-pgr.org>).
Your use of data is subject to terms and conditions available at <https://www.genesys-pgr.org/content/legal/terms>.
Authors@R: person("Matija", "Obreza", email = "matija.obreza@croptrust.org", Authors@R: person("Matija", "Obreza", email = "matija.obreza@croptrust.org",
role = c("aut", "cre")) role = c("aut", "cre"))
Description: Selected Genesys API calls implemented in R.
Allows for authentication and exposes common API calls.
Depends: R (>= 3.1.0) Depends: R (>= 3.1.0)
License: Apache License 2.0
LazyData: true
Imports: Imports:
httr httr,
jsonlite
License: Apache License 2.0 + see LICENSE
RoxygenNote: 6.0.1 RoxygenNote: 6.0.1
URL: https://gitlab.croptrust.org/genesys-pgr/genesysr
# June 2018
First version of the Genesys API client for R is released.
...@@ -21,7 +21,7 @@ ...@@ -21,7 +21,7 @@
#' Setup for Genesys Production #' Setup for Genesys Production
#' #'
#' Use the Genesys R Client with \link{https://www.genesys-pgr.org} requiring \code{\link{user_login}} #' Use the Genesys R Client with <https://www.genesys-pgr.org> requiring \code{\link{user_login}}
#' #'
#' @export #' @export
setup_production <- function() { setup_production <- function() {
...@@ -30,7 +30,7 @@ setup_production <- function() { ...@@ -30,7 +30,7 @@ setup_production <- function() {
#' Setup for Genesys Sandbox #' Setup for Genesys Sandbox
#' #'
#' Use the Genesys R Client with \link{https://sandbox.genesys-pgr.org} requiring \code{\link{user_login}} #' Use the Genesys R Client with <https://sandbox.genesys-pgr.org> requiring \code{\link{user_login}}
#' #'
#' @export #' @export
setup_sandbox <- function() { setup_sandbox <- function() {
...@@ -39,7 +39,7 @@ setup_sandbox <- function() { ...@@ -39,7 +39,7 @@ setup_sandbox <- function() {
#' Configure the Genesys environment #' Configure the Genesys environment
#' #'
#' @param server Server base URL (e.g. \link{https://www.genesys-pgr.org} or \link{https://sandbox.genesys-pgr.org}) #' @param server Server base URL (e.g. "https://www.genesys-pgr.org" or "https://sandbox.genesys-pgr.org")
#' @param client_id OAuth client ID #' @param client_id OAuth client ID
#' @param client_secret OAuth client secret #' @param client_secret OAuth client secret
#' #'
...@@ -67,7 +67,9 @@ print_setup <- function() { ...@@ -67,7 +67,9 @@ print_setup <- function() {
#' Provide OAuth2 token to use for authorization with Genesys #' Provide OAuth2 token to use for authorization with Genesys
#' #'
#' @seealso \code{\link{login}} #' @param authorization OAuth2 Authorization header obtained from somewhere else (e.g. an ENV variable)
#'
#' @seealso \code{\link{user_login}}, \code{\link{client_login}}
#' @export #' @export
authorization <- function(authorization) { authorization <- function(authorization) {
assign("Authorization", authorization, envir = .genesysEnv) assign("Authorization", authorization, envir = .genesysEnv)
...@@ -145,7 +147,7 @@ client_login <- function() { ...@@ -145,7 +147,7 @@ client_login <- function() {
} }
api_call <- function(path, method = "get", server = GENESYS_SERVER) { api_call <- function(path, method = "get") {
resp <- httr::GET(api_url(path), httr::add_headers( resp <- httr::GET(api_url(path), httr::add_headers(
Authorization = .genesysEnv$Authorization Authorization = .genesysEnv$Authorization
) )
...@@ -162,7 +164,7 @@ api_call <- function(path, method = "get", server = GENESYS_SERVER) { ...@@ -162,7 +164,7 @@ api_call <- function(path, method = "get", server = GENESYS_SERVER) {
#' Get full Genesys API URL for a specific path #' Get full Genesys API URL for a specific path
#' #'
#' @param path #' @param path relative path of the API endpoint (e.g. \code{/me})
#' #'
#' @return Absolute URL to an API call #' @return Absolute URL to an API call
#' @export #' @export
......
...@@ -17,6 +17,7 @@ ...@@ -17,6 +17,7 @@
#' See FAO/Bioversity Multi-Crop Passport Descriptors. #' See FAO/Bioversity Multi-Crop Passport Descriptors.
#' #'
#' @param filter Existing filters (or blank list if not provided) #' @param filter Existing filters (or blank list if not provided)
#' @param DOI Accession DOI
#' @param ORIGCTY Country of origin #' @param ORIGCTY Country of origin
#' @param SAMPSTAT Biological status of sample #' @param SAMPSTAT Biological status of sample
#' #'
...@@ -37,6 +38,8 @@ mcpd_filter <- function(filter = list(), DOI = NULL, ORIGCTY = NULL, SAMPSTAT = ...@@ -37,6 +38,8 @@ mcpd_filter <- function(filter = list(), DOI = NULL, ORIGCTY = NULL, SAMPSTAT =
} }
#' Add filter on accession DOI #' Add filter on accession DOI
#' @param filter Existing filters (or blank list if not provided)
#' @param DOI Accession DOI
#' @export #' @export
filter_DOI <- function(filter = list(), DOI) { filter_DOI <- function(filter = list(), DOI) {
f <- c(filter) f <- c(filter)
...@@ -47,6 +50,8 @@ filter_DOI <- function(filter = list(), DOI) { ...@@ -47,6 +50,8 @@ filter_DOI <- function(filter = list(), DOI) {
} }
#' Add filter on Country of origin of material #' Add filter on Country of origin of material
#' @param filter Existing filters (or blank list if not provided)
#' @param ORIGCTY Country of origin
#' @export #' @export
filter_ORIGCTY <- function(filter = list(), ORIGCTY) { filter_ORIGCTY <- function(filter = list(), ORIGCTY) {
f <- c(filter) f <- c(filter)
...@@ -57,6 +62,8 @@ filter_ORIGCTY <- function(filter = list(), ORIGCTY) { ...@@ -57,6 +62,8 @@ filter_ORIGCTY <- function(filter = list(), ORIGCTY) {
} }
#' Add filter on Biological status of sample #' Add filter on Biological status of sample
#' @param filter Existing filters (or blank list if not provided)
#' @param SAMPSTAT Biological status of sample
#' @export #' @export
filter_SAMPSTAT <- function(filter = list(), SAMPSTAT) { filter_SAMPSTAT <- function(filter = list(), SAMPSTAT) {
f <- c(filter) f <- c(filter)
......
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