version 0.9.2

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: genesysr
-Version: 0.9.1
+Version: 0.9.2
 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>.
@@ -10,15 +10,15 @@ Maintainer: Matija Obreza <matija.obreza@croptrust.org>
 Depends: R (>= 3.1.0)
 Imports: httr, jsonlite
 License: Apache License 2.0
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
 URL: https://gitlab.croptrust.org/genesys-pgr/genesysr
 BugReports: https://gitlab.croptrust.org/genesys-pgr/genesysr/issues
 Suggests: knitr, rmarkdown
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2018-06-12 19:12:29 UTC; mobreza
+Packaged: 2019-09-02 09:32:51 UTC; mobreza
 Author: Global Crop Diversity Trust [cph],
   Matija Obreza [aut, cre],
   Nora Castaneda [ctb]
 Repository: CRAN
-Date/Publication: 2018-06-14 19:24:54 UTC
+Date/Publication: 2019-09-02 15:20:02 UTC

MD5

@@ -1,25 +1,30 @@
-a86defb48d4d5b6930386bf4709d9833 *DESCRIPTION
+b79f7b6b1bb4ee7f122d15e2dc5c09cd *DESCRIPTION
 95e36a55ec470fcfdd38b16d4fe61245 *NAMESPACE
-3d49656b4c304602fa0bbe2e22627d29 *NEWS.md
-e3fc67b971ebed3dbaecdd817078bf93 *R/api-client.R
-aafaf7b9f67fc8451ef3640c80485443 *R/filters.R
+3e34da3f556f9b453bb93da2503a2dcf *NEWS.md
+6f8999f55812e6b15ff82a19d734adc6 *R/api-client.R
+6867b32775e64efe5bd34b29363324a4 *R/filters.R
 73128a079eef5a8f628ec1e17158304c *R/genesys.R
-7e0493a9e4c33ae5be92580b72ccd46f *README.md
-ea3b12fe2a55e424552ab1e32780fbee *build/vignette.rds
-bf6557dda1549bec046340a92c9292f2 *inst/doc/tutorial.Rmd
-db1df546d28bfd7e25a2f871ecc24c05 *inst/doc/tutorial.html
+a6cd114243bc980b433d12c648844fc2 *README.md
+89e54575a73d1df3d124692c6aee6c17 *build/vignette.rds
+446d14ec0ec67ebe43439dd2eebe93b3 *inst/doc/tutorial.Rmd
+f65491305d51068c3c4688c53c0edc6b *inst/doc/tutorial.html
 a59a638d633133520d47af9af3e8556f *man/api_url.Rd
 3c89e0e5581c109333bd2c32c8affd80 *man/authorization.Rd
 b977ae83784900d75d756d2946920d63 *man/client_login.Rd
+614d434792f634e542f152dd7ec7ec8f *man/dot-MAX_ALLOWED_PAGES.Rd
+1a9125f6ae1a357530bfb1253beba86c *man/dot-check_auth.Rd
+8c2e55f11a4626ad66c77d73ff319642 *man/dot-fetch_accessions_page.Rd
+0012e14aa882077b9aac609b77704593 *man/dot-onLoad.Rd
+c546c4641530df70c79f983290e95879 *man/dot-post.Rd
 a4e2f7a68c9b341c04a80b23844ae3f0 *man/fetch_accessions.Rd
 2db62806b45ddc904228f7dad30cb932 *man/filter_DOI.Rd
 1a26ce7d5cd01e2375640e029940359f *man/filter_ORIGCTY.Rd
 f5e9d08ec3ee48022daea3ba8491c9b8 *man/filter_SAMPSTAT.Rd
 991994b8a7a65b025e6b161b4a25c5c1 *man/mcpd_filter.Rd
 2ba6fb516ae56d6124cb4b514ebf6b4e *man/me.Rd
 8a6fbe344291d152f27e1329998747d7 *man/print_setup.Rd
-1ea2a1c45d29721ff4961042e87ed1cc *man/setup.Rd
-cf8ee093227e205ff3f6677a2d410588 *man/setup_production.Rd
-88d5cc71d196bc775a7bf85aa83ab6ca *man/setup_sandbox.Rd
+f562d7cc9ec22b8e692370d584361330 *man/setup.Rd
+a5d181cf2b629e0fd4d28356bd185422 *man/setup_production.Rd
+5c09b4337f8f2c69dad1d9c47427ef08 *man/setup_sandbox.Rd
 8e92387d911827f80c26ef8ce7ee7a9e *man/user_login.Rd
-bf6557dda1549bec046340a92c9292f2 *vignettes/tutorial.Rmd
+446d14ec0ec67ebe43439dd2eebe93b3 *vignettes/tutorial.Rmd

NEWS.md

@@ -1,3 +1,6 @@
+# August 2019
+
+Updated for API at api.genesys-pgr.org
 
 # June 2018
 

R/api-client.R

@@ -14,32 +14,35 @@
 
 .genesysEnv <- new.env(parent = emptyenv())
 
-#' Configure package defaults
+#' Configure package defaults on load
+#' 
+#' @param libname Library name
+#' @param pkgname Package name
 .onLoad <- function(libname, pkgname) {
   setup_production()
 }
 
 #' Setup for Genesys Production
 #'
-#' Use the Genesys R Client with <https://www.genesys-pgr.org> requiring \code{\link{user_login}}
+#' Use the Genesys R Client with <https://api.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(server = "https://api.genesys-pgr.org", client_id = "oHgJR.NjcdJAIB175gBDbuLEK3@www.genesys-pgr.org", client_secret = "public")
 }
 
 #' Setup for Genesys Sandbox
 #'
-#' Use the Genesys R Client with <https://sandbox.genesys-pgr.org> requiring \code{\link{user_login}}
+#' Use the Genesys R Client with <https://api.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)
+  setup(server = "https://api.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. "https://www.genesys-pgr.org" or "https://sandbox.genesys-pgr.org")
+#' @param server Server base URL (e.g. "https://api.genesys-pgr.org" or "https://api.sandbox.genesys-pgr.org")
 #' @param client_id OAuth client ID
 #' @param client_secret OAuth client secret
 #'

R/filters.R

@@ -12,6 +12,30 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+
+MCPD <- list(
+  SAMPSTAT = list("Wild" = list(100, "Natural" = 110, "Semi-natural/wild"=120, "Semi-natural/sown"=130),
+                  "Weedy" = 200, 
+                  "Traditional cultivar/landrace" = 300,
+                  "Breeding/research material"= list(400, "Breeder's line"=410,"Synthetic population"=411,"Hybrid"=412,"Founder stock/base population"=413,"Inbred line (parent of hybrid cultivar)"=414,"Segregating population"=415,"Clonal selection"=416,"Genetic stock"=420,"Mutant (e.g. induced/insertion mutant, tilling population)"=421,"Cytogenetic stock (e.g. chromosome addition/substitution, aneuploids, amphiploids)"=422,"Other genetic stocks (e.g. mapping populations)"=423),
+                  "Advanced or improved cultivar (conventional breeding methods)"=500,
+                  "GMO (by genetic engineering)"=600,
+                  "Other (elaborate in REMARKS field)"=999),
+  STORAGE = list("Seed collection"=list(10,"Short term"=11,"Medium term"=12,"Long term"=13),
+                 "Field collection"=20,
+                 "In vitro collection"=30,
+                 "Cryopreserved collection"=40,
+                 "DNA collection"=50,
+                 "Other (elaborate in REMARKS field)"=99),
+  COLLSRC = list("Wild habitat"=list(10,"Forest or woodland"=11,"Shrubland"=12,"Grassland"=13,"Desert or tundra"=14,"Aquatic habitat"=15),
+                 "Farm or cultivated habitat"=list(20,"Field"=21,"Orchard"=22,"Backyard, kitchen or home garden (urban, peri-urban or rural)"=23,"Fallow land"=24,"Pasture"=25,"Farm store"=26,"Threshing floor"=27,"Park"=28),
+                 "Market or shop"=30,
+                 "Institute, Experimental station, Research organization, Genebank"=40,
+                 "Seed company"=50,
+                 "Weedy, disturbed or ruderal habitat"=list(60,"Roadside"=61,"Field margin"=62),
+                 "Other (Elaborate in REMARKS field)"=99)
+)
+
 #' Make or adjust filter using MCPD terminology
 #'
 #' See FAO/Bioversity Multi-Crop Passport Descriptors.

README.md

@@ -51,7 +51,7 @@ Accessing Genesys **without user interaction** requires that a client is registe
 ```R
 # Setup
 library('genesysr')
-genesysr::setup(server = "https://www.genesys-pgr.org",
+genesysr::setup(server = "https://api.genesys-pgr.org",
   client_id = "someId.....@www.genesys-pgr.org",
   client_secret = "your-private-secret")
 

inst/doc/tutorial.Rmd

@@ -16,6 +16,7 @@ Querying Genesys PGR
 maintained *ex situ* in national, regional and international genebanks around the world.
 
 **genesysr** uses the [Genesys API](https://www.genesys-pgr.org/doc/0/apis) to query Genesys data.
+The API is accessible at https://api.genesys-pgr.org.
 
 Accessing data with **genesysr** is similar to downloading data in CSV or Excel format and loading
 it into R.
@@ -28,7 +29,7 @@ The database is queried by providing a `filter` (see Filters below):
 
 ```
 ## Setup: use Genesys Sandbox environment
-# genesysr::setup_sandbox() 
+# genesysr::setup_sandbox()
 # genesysr::setup_production() # This is initialized by default when loading genesysr
 
 # Open a browser: login to Genesys and authorize access
@@ -44,7 +45,7 @@ itc <- fetch_accessions(list(institute.code = c('BEL084')))
 some <- fetch_accessions(list(institute.code = c('BEL084','COL003')))
 ```
 
-**genesysr** provides utility functions to create `filter` objects using [Multi-Crop Passport Descriptors (MCPD)](https://www.genesys-pgr.org/doc/0/basics#mcpd) definitions:
+**genesysr** provides utility functions to create `filter` objects using [Multi-Crop Passport Descriptors (MCPD)](https://www.genesys-pgr.org/documentation/basics) definitions:
 
 ```
 # Retrieve data by country of origin (MCPD)
@@ -63,7 +64,7 @@ musa.flatten <- musa.flatten %>% map_df(bind_rows)
 
 # Filters
 
-The records returned by Genesys match all filters provided (*AND* operation), while individual filters 
+The records returned by Genesys match all filters provided (*AND* operation), while individual filters
 allow for specifying multiple criteria (*OR* operation):
 
 ```r

inst/doc/tutorial.html

@@ -7,22 +7,23 @@
 <meta charset="utf-8" />
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 <meta name="generator" content="pandoc" />
+<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
 <meta name="viewport" content="width=device-width, initial-scale=1">
 
 <meta name="author" content="Nora Castaneda &amp; Matija Obreza" />
 
-<meta name="date" content="2018-06-12" />
+<meta name="date" content="2019-09-02" />
 
 <title>genesysr Tutorial</title>
 
 
 
 <style type="text/css">code{white-space: pre;}</style>
-<style type="text/css">
+<style type="text/css" data-origin="pandoc">
 a.sourceLine { display: inline-block; line-height: 1.25; }
 a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; position: absolute; }
+a.sourceLine:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 div.sourceCode { margin: 1em 0; }
@@ -35,13 +36,11 @@
 a.sourceLine { text-indent: -1em; padding-left: 1em; }
 }
 pre.numberSource a.sourceLine
-  { position: relative; }
-pre.numberSource a.sourceLine:empty
-  { position: absolute; }
+  { position: relative; left: -4em; }
 pre.numberSource a.sourceLine::before
   { content: attr(data-line-number);
-    position: absolute; left: -5em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all;
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; pointer-events: all; display: inline-block;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;
@@ -83,7 +82,29 @@
 code span.va { color: #19177c; } /* Variable */
 code span.vs { color: #4070a0; } /* VerbatimString */
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+
 </style>
+<script>
+// apply pandoc div.sourceCode style to pre.sourceCode instead
+(function() {
+  var sheets = document.styleSheets;
+  for (var i = 0; i < sheets.length; i++) {
+    if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
+    try { var rules = sheets[i].cssRules; } catch (e) { continue; }
+    for (var j = 0; j < rules.length; j++) {
+      var rule = rules[j];
+      // check if there is a div.sourceCode rule
+      if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") continue;
+      var style = rule.style.cssText;
+      // check if color or background-color is set
+      if (rule.style.color === '' && rule.style.backgroundColor === '') continue;
+      // replace div.sourceCode by a pre.sourceCode rule
+      sheets[i].deleteRule(j);
+      sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
+    }
+  }
+})();
+</script>
 
 
 
@@ -271,6 +292,9 @@
 code > span.fu { color: #900; font-weight: bold; }  code > span.er { color: #a61717; background-color: #e3d2d2; } 
 </style>
 
+
+
+
 </head>
 
 <body>
@@ -279,22 +303,22 @@
 
 
 <h1 class="title toc-ignore">genesysr Tutorial</h1>
-<h4 class="author"><em>Nora Castaneda &amp; Matija Obreza</em></h4>
-<h4 class="date"><em>2018-06-12</em></h4>
+<h4 class="author">Nora Castaneda &amp; Matija Obreza</h4>
+<h4 class="date">2019-09-02</h4>
 
 
 
 <div id="querying-genesys-pgr" class="section level1">
 <h1>Querying Genesys PGR</h1>
 <p><a href="https://www.genesys-pgr.org">Genesys PGR</a> is the global database on plant genetic resources maintained <em>ex situ</em> in national, regional and international genebanks around the world.</p>
-<p><strong>genesysr</strong> uses the <a href="https://www.genesys-pgr.org/doc/0/apis">Genesys API</a> to query Genesys data.</p>
+<p><strong>genesysr</strong> uses the <a href="https://www.genesys-pgr.org/doc/0/apis">Genesys API</a> to query Genesys data. The API is accessible at <a href="https://api.genesys-pgr.org" class="uri">https://api.genesys-pgr.org</a>.</p>
 <p>Accessing data with <strong>genesysr</strong> is similar to downloading data in CSV or Excel format and loading it into R.</p>
 <div id="for-the-impatient" class="section level2">
 <h2>For the impatient</h2>
 <p>Accession passport data is retrieved with the <code>fetch_accessions</code> function.</p>
 <p>The database is queried by providing a <code>filter</code> (see Filters below):</p>
 <pre><code>## Setup: use Genesys Sandbox environment
-# genesysr::setup_sandbox() 
+# genesysr::setup_sandbox()
 # genesysr::setup_production() # This is initialized by default when loading genesysr
 
 # Open a browser: login to Genesys and authorize access
@@ -308,7 +332,7 @@ <h2>For the impatient</h2>
 
 # Retrieve all accession data for the Musa International Transit Center, Bioversity International (BEL084) and the International Center for Tropical Agriculture (COL003)
 some &lt;- fetch_accessions(list(institute.code = c('BEL084','COL003')))</code></pre>
-<p><strong>genesysr</strong> provides utility functions to create <code>filter</code> objects using <a href="https://www.genesys-pgr.org/doc/0/basics#mcpd">Multi-Crop Passport Descriptors (MCPD)</a> definitions:</p>
+<p><strong>genesysr</strong> provides utility functions to create <code>filter</code> objects using <a href="https://www.genesys-pgr.org/documentation/basics">Multi-Crop Passport Descriptors (MCPD)</a> definitions:</p>
 <pre><code># Retrieve data by country of origin (MCPD)
 fetch_accessions(mcpd_filter(ORIGCTY = c(&quot;DEU&quot;, &quot;SVN&quot;)))</code></pre>
 </div>
@@ -392,6 +416,9 @@ <h1>Step-by-step example</h1>
 
 
 
+<!-- code folding -->
+
+
 <!-- dynamically load mathjax for compatibility with self-contained -->
 <script>
   (function () {