Initial R client code

.Rbuildignore

+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+man

DESCRIPTION

+Package: genesysr
+Title: R client for Genesys PGR (www.genesys-pgr.org)
+Version: 0.1
+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
+RoxygenNote: 6.0.1

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(api_url)
+export(authorization)
+export(client_login)
+export(fetch_accessions)
+export(filter_DOI)
+export(filter_ORIGCTY)
+export(filter_SAMPSTAT)
+export(mcpd_filter)
+export(me)
+export(print_setup)
+export(setup)
+export(setup_production)
+export(setup_sandbox)
+export(user_login)

R/api-client.R

+# Copyright 2018 Global Crop Diversity Trust
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+.genesysEnv <- new.env(parent = emptyenv())
+
+#' Configure package defaults
+.onLoad <- function(libname, pkgname) {
+  setup_production()
+}
+
+#' Setup for Genesys Production
+#'
+#' Use the Genesys R Client with \link{https://www.genesys-pgr.org} requiring \code{\link{user_login}}
+#'
+#' @export
+setup_production <- function() {
+  setup(server = "https://www.genesys-pgr.org", client_id = "oHgJR.NjcdJAIB175gBDbuLEK3@www.genesys-pgr.org", client_secret = "public")
+}
+
+#' Setup for Genesys Sandbox
+#'
+#' Use the Genesys R Client with \link{https://sandbox.genesys-pgr.org} requiring \code{\link{user_login}}
+#'
+#' @export
+setup_sandbox <- function() {
+  setup(server = "https://sandbox.genesys-pgr.org", client_id = "cCS6e.BAn9u2WkhIwgxBLxOVqZ@sandbox.genesys-pgr.org", client_secret = NULL)
+}
+
+#' 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 client_id OAuth client ID
+#' @param client_secret OAuth client secret
+#'
+#' @export
+#' @seealso See utility methods \code{\link{setup_production}}, \code{\link{setup_sandbox}}
+#'
+#' @examples
+#'   # Link with sandbox
+#'   setup_sandbox()
+#'
+setup <- function(server = NULL, client_id = NULL, client_secret = NULL) {
+  assign("server", server, envir = .genesysEnv)
+  assign("client_id", client_id, envir = .genesysEnv)
+  assign("client_secret", client_secret, envir = .genesysEnv)
+}
+
+#' Print Genesys client configuration
+#'
+#' @export
+print_setup <- function() {
+  message(paste("Genesys URL:", .genesysEnv$server))
+  message(paste("Client ID:", .genesysEnv$client_id))
+  message(paste("Client secret:", .genesysEnv$client_secret))
+}
+
+#' Provide OAuth2 token to use for authorization with Genesys
+#'
+#' @seealso \code{\link{login}}
+#' @export
+authorization <- function(authorization) {
+  assign("Authorization", authorization, envir = .genesysEnv)
+  message(paste('Genesys Authorization:', authorization))
+}
+
+#' Login to Genesys as a user
+#'
+#' The authorization URL will open in a browser, ask the user to grant
+#' permissions to R and the verification code must be copy-pasted after
+#' you grant access to the client.
+#'
+#' @seealso \code{\link{setup}}
+#'
+#' @export
+user_login <- function() {
+  url <- paste0(.genesysEnv$server, "/oauth/authorize")
+  browseURL(httr::modify_url(url, query = list(
+    client_id = .genesysEnv$client_id, client_secret = .genesysEnv$client_secret,
+    redirect_uri = "oob",
+    scope = "read",
+    response_type= "code"
+    )))
+
+  code <- readline("Enter the authorization code: ");
+
+  url <- paste0(.genesysEnv$server, "/oauth/token")
+  resp <- httr::POST(url, body = list(
+    client_id = .genesysEnv$client_id, client_secret = .genesysEnv$client_secret,
+    redirect_uri = "oob",
+    grant_type = "authorization_code", code = code
+    ), encode = "form")
+
+  if (httr::http_type(resp) != "application/json" || httr::status_code(resp) != 200) {
+    stop(paste("API did not return json", httr::content(resp, "text")), call. = FALSE)
+  }
+
+  parsed <- jsonlite::fromJSON(httr::content(resp, "text"), simplifyVector = FALSE)
+
+  authorization(paste("Bearer", parsed$access_token))
+
+  invisible(structure(
+    parsed,
+    class = "genesys_auth"
+  ))
+}
+
+
+#' Login to Genesys as a service client (system-to-system)
+#'
+#' The client must be enabled for Client Credential grant on Genesys.
+#'
+#' @seealso \code{\link{setup}}
+#'
+#' @export
+client_login <- function() {
+  url <- paste0(.genesysEnv$server, "/oauth/token")
+  resp <- httr::POST(url, body = list(
+    client_id = .genesysEnv$client_id, client_secret = .genesysEnv$client_secret,
+    grant_type = "client_credentials"
+  ), encode = "form")
+
+  if (httr::http_type(resp) != "application/json" || httr::status_code(resp) != 200) {
+    stop("API did not return json", call. = FALSE)
+  }
+
+  parsed <- jsonlite::fromJSON(httr::content(resp, "text"), simplifyVector = FALSE)
+
+  authorization(paste("Bearer", parsed$access_token))
+
+  invisible(structure(
+    parsed,
+    class = "genesys_auth"
+  ))
+}
+
+
+api_call <- function(path, method = "get", server = GENESYS_SERVER) {
+  resp <- httr::GET(api_url(path), httr::add_headers(
+    Authorization = .genesysEnv$Authorization
+    )
+  )
+  resp
+  if (httr::http_type(resp) != "application/json") {
+    stop("API did not return json", call. = FALSE)
+  }
+  # return(resp)
+  parsed <- jsonlite::fromJSON(httr::content(resp, "text"), simplifyVector = FALSE)
+  return(parsed)
+}
+
+
+#' Get full Genesys API URL for a specific path
+#'
+#' @param path
+#'
+#' @return Absolute URL to an API call
+#' @export
+#'
+#' @examples
+#'  api_url("/me")
+api_url <- function(path) {
+  paste0(.genesysEnv$server, "/api/v0", path)
+}
+
+get <- function(path, query = NULL) {
+  resp <- httr::GET(api_url(path), httr::add_headers(
+    Authorization = .genesysEnv$Authorization
+  ))
+  if (httr::http_type(resp) != "application/json") {
+    stop("API did not return json", call. = FALSE)
+  }
+  resp
+}
+
+post <- function(path, query = NULL, body) {
+  resp <- httr::POST(api_url(path), httr::add_headers(
+    Authorization = .genesysEnv$Authorization,
+    "Content-Type" = "application/json"
+  ), body = jsonlite::toJSON(body))
+  if (httr::http_type(resp) != "application/json") {
+    stop("API did not return json", call. = FALSE)
+  }
+  resp
+}

R/filters.R

+# Copyright 2018 Global Crop Diversity Trust
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+#' Make or adjust filter using MCPD terminology
+#'
+#' See FAO/Bioversity Multi-Crop Passport Descriptors.
+#'
+#' @param filter Existing filters (or blank list if not provided)
+#' @param ORIGCTY Country of origin
+#' @param SAMPSTAT Biological status of sample
+#'
+#' @examples
+#'  # Filter accessions from Mexico and Slovenia
+#'  mcpd_filter(ORIGCTY = c("MEX", "SVN"))
+#'
+#'
+#' @export
+mcpd_filter <- function(filter = list(), DOI = NULL, ORIGCTY = NULL, SAMPSTAT = NULL) {
+  f <- c(filter)
+
+  f <- filter_DOI(f, DOI)
+  f <- filter_ORIGCTY(f, ORIGCTY)
+  f <- filter_SAMPSTAT(f, SAMPSTAT)
+
+  f
+}
+
+#' Add filter on accession DOI
+#' @export
+filter_DOI <- function(filter = list(), DOI) {
+  f <- c(filter)
+  if (!is.null(DOI)) {
+    f$doi = c(f$doi, DOI)
+  }
+  f
+}
+
+#' Add filter on Country of origin of material
+#' @export
+filter_ORIGCTY <- function(filter = list(), ORIGCTY) {
+  f <- c(filter)
+  if (!is.null(ORIGCTY)) {
+    f$orgCty.iso3 = c(f$orgCty.iso3, ORIGCTY)
+  }
+  f
+}
+
+#' Add filter on Biological status of sample
+#' @export
+filter_SAMPSTAT <- function(filter = list(), SAMPSTAT) {
+  f <- c(filter)
+  if (!is.null(SAMPSTAT)) {
+    f$sampStat = c(f$sampStat, SAMPSTAT)
+  }
+  f
+}

R/genesys.R

+# Copyright 2018 Global Crop Diversity Trust
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+#' Who am i?
+#'
+#' @export
+me <- function() {
+  resp <- api_call("/me")
+  message(jsonlite::toJSON(resp, pretty = TRUE))
+  invisible(resp)
+}
+
+#' Fetch accession passport data
+#'
+#' @param filters an R \code{structure} with Genesys filters
+#' @param size number of records to load per page (page size)
+#' @param page the page index (0-based)
+#'
+#' @seealso \code{\link{mcpd_filter}}
+#'
+#' @examples
+#'   # Retrieve accession data by DOI
+#'   accessions <- fetch_accessions(mcpd_filter(DOI = c("10.1010/DUMMY", "10.1010/DUNNY")))
+#'
+#' @export
+#' @return Paged data structure
+fetch_accessions <- function(filters = list(), page = 0, size = 100) {
+  resp <- post(path = "/acn/filter", query=list(p = page, s = size), body = filters)
+  jsonlite::fromJSON(httr::content(resp, "text"), simplifyVector = FALSE)
+}

genesys-R-client.Rproj

+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace