Prepare for release on CRAN

- Included URL in DESCRIPTION
- Ignore generated README.Rmd

.Rbuildignore

 ^.*\.Rproj$
 ^\.Rproj\.user$
+^README\.Rmd$
+^README-.*\.png$
+^cran-comments\.md$

.gitignore

@@ -3,3 +3,5 @@
 .RData
 .Ruserdata
 man
+README.Rmd
+cran-comments.md

DESCRIPTION

 Package: genesysr
-Title: R client for Genesys PGR (www.genesys-pgr.org)
-Version: 0.1
+Version: 0.9.1
+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",
                   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)
-License: Apache License 2.0
-LazyData: true
 Imports:
-  httr
+  httr,
+  jsonlite
+License: Apache License 2.0 + see LICENSE
 RoxygenNote: 6.0.1
+URL: https://gitlab.croptrust.org/genesys-pgr/genesysr

NEWS.md

+
+# June 2018
+
+First version of the Genesys API client for R is released.
+

R/api-client.R

@@ -21,7 +21,7 @@
 
 #' 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
 setup_production <- function() {
@@ -30,7 +30,7 @@ setup_production <- function() {
 
 #' 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
 setup_sandbox <- function() {
@@ -39,7 +39,7 @@ setup_sandbox <- function() {
 
 #' 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_secret OAuth client secret
 #'
@@ -67,7 +67,9 @@ print_setup <- function() {
 
 #' 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
 authorization <- function(authorization) {
   assign("Authorization", authorization, envir = .genesysEnv)
@@ -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(
     Authorization = .genesysEnv$Authorization
     )
@@ -162,7 +164,7 @@ api_call <- function(path, method = "get", server = GENESYS_SERVER) {
 
 #' 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
 #' @export

R/filters.R

@@ -17,6 +17,7 @@
 #' See FAO/Bioversity Multi-Crop Passport Descriptors.
 #'
 #' @param filter Existing filters (or blank list if not provided)
+#' @param DOI Accession DOI
 #' @param ORIGCTY Country of origin
 #' @param SAMPSTAT Biological status of sample
 #'
@@ -37,6 +38,8 @@ mcpd_filter <- function(filter = list(), DOI = NULL, ORIGCTY = NULL, SAMPSTAT =
 }
 
 #' Add filter on accession DOI
+#' @param filter Existing filters (or blank list if not provided)
+#' @param DOI Accession DOI
 #' @export
 filter_DOI <- function(filter = list(), DOI) {
   f <- c(filter)
@@ -47,6 +50,8 @@ filter_DOI <- function(filter = list(), DOI) {
 }
 
 #' Add filter on Country of origin of material
+#' @param filter Existing filters (or blank list if not provided)
+#' @param ORIGCTY Country of origin
 #' @export
 filter_ORIGCTY <- function(filter = list(), ORIGCTY) {
   f <- c(filter)
@@ -57,6 +62,8 @@ filter_ORIGCTY <- function(filter = list(), ORIGCTY) {
 }
 
 #' Add filter on Biological status of sample
+#' @param filter Existing filters (or blank list if not provided)
+#' @param SAMPSTAT Biological status of sample
 #' @export
 filter_SAMPSTAT <- function(filter = list(), SAMPSTAT) {
   f <- c(filter)