Package 'genesysr'

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: Global Crop Diversity Trust [cph], Matija Obreza [aut, cre], Nora Castaneda [ctb]
Maintainer: Matija Obreza <[email protected]>
License: Apache License 2.0
Version: 2.1.1
Built: 2025-02-18 03:56:04 UTC
Source: https://github.com/cran/genesysr

Help Index

Get partial API v1 URL for the provided path

Description

Get partial API v1 URL for the provided path

Usage

api1_url(path)

Arguments

path

relative path of the API v1 endpoint (e.g. /me)

Value

Returns "/api/v1" + path

Examples

api1_url("/me")

Get partial API v2 URL for the provided path

Description

Get partial API v2 URL for the provided path

Usage

api2_url(path)

Arguments

path

relative path of the API v2 endpoint (e.g. /me)

Value

Returns "/api/v2" + path

Examples

api2_url("/me")

Provide OAuth2 token to use for authorization with Genesys

Description

Provide OAuth2 token to use for authorization with Genesys

Usage

authorization(authorization)

Arguments

authorization

OAuth2 Authorization header obtained from somewhere else (e.g. an ENV variable)

See Also

user_login, client_login

Run Land-or-Sea check on MCPD data. Uploads only rows where ORIGCTY, DECLATITUDE and DECLONGITUDE are provided.

Description

Run Land-or-Sea check on MCPD data. Uploads only rows where ORIGCTY, DECLATITUDE and DECLONGITUDE are provided.

Usage

check_country(mcpd)

Arguments

mcpd

Accession passport data in MCPD format

Value

Results from validator

Examples

## Not run: 
  geoCheck <- genesysr::check_country(mcpd)

## End(Not run)

Run Land-or-Sea check on MCPD data using https://validator.genesys-pgr.org. Uploads only rows where DECLATITUDE and DECLONGITUDE are provided. In practice it is better to use 'check_country' if ORIGCTY data exists.

Description

Run Land-or-Sea check on MCPD data using https://validator.genesys-pgr.org. Uploads only rows where DECLATITUDE and DECLONGITUDE are provided. In practice it is better to use 'check_country' if ORIGCTY data exists.

Usage

check_landorsea(mcpd)

Arguments

mcpd

Accession passport data in MCPD format

Value

Results from validator

Examples

## Not run: 
  waterCheck <- genesysr::check_landorsea(mcpd)

## End(Not run)

Check MCPD taxonomic data (GENUS, SPECIES, SPAUTHOR, SUBTAXA, SUBTAUTHOR) using https://validator.genesys-pgr.org.

Description

Duplicate input rows are removed using dplyr::distinct() and results are returned for unique rows.

Usage

check_taxonomy(mcpd, toCurrentTaxa = FALSE)

Arguments

mcpd

Accession passport data in MCPD format
toCurrentTaxa

Should obsoleted names be reported?

Value

Results from validator

Examples

## Not run: 
  taxaCheck <- genesysr::check_taxonomy(mcpd)

## End(Not run)

Login to Genesys as a service client (system-to-system)

Description

The client must be enabled for Client Credential grant on Genesys.

Usage

client_login()

See Also

setup

Download passport data for one genebank in Excel format and save it to disk

Description

Download passport data for one genebank in Excel format and save it to disk

Usage

download_mcpd(instituteCode, file = NULL)

Arguments

instituteCode

FAO WIEWS institute code
file

Target file name. Defaults to Genesys-provided file name in the current working directory.

Value

The downloaded MCPD file name

Examples

## Not run: 
  # Download MCPD passport data for NGA039
  excelFile <- download_mcpd("NGA039")

## End(Not run)

Download PDCI data for one genebank in Excel format and save it to disk.

Description

Download PDCI data for one genebank in Excel format and save it to disk.

Usage

download_pdci(instituteCode, file = NULL)

Arguments

instituteCode

FAO WIEWS institute code
file

Target file name. Defaults to Genesys-provided file name in the current working directory.

Value

The downloaded PDCI file name

Examples

## Not run: 
  # Download PDCI  data for NGA039
  excelData <- download_pdci("NGA039")

## End(Not run)

Fetch accession passport data and return the paged data structure for further processing. get_accessions might be more useful as it returns a data table.

Description

Fetch accession passport data and return the paged data structure for further processing. get_accessions might be more useful as it returns a data table.

Usage

fetch_accessions(
  filters = list(),
  page = NULL,
  size = 1000,
  selector = NULL,
  at.least = NULL
)

Arguments

filters

an R structure with Genesys filters
page

the page index (0-based)
size

number of records to load per page (page size)
selector

NULL or a function to "select" variables of interest
at.least

stop fetching when at.least records are received from Genesys

Value

Paged data structure

See Also

get_accessions

Examples

## Not run: 
  # Retrieve all accession data by country of origin
  accessions <- genesysr::fetch_accessions(mcpd_filter(ORIGCTY = c("DEU", "SVN")))

  # Fetch Musa
  musa <- genesysr::fetch_accessions(list(taxonomy.genus = c('Musa')))

  # Apply selector function
  accessions <- genesysr::fetch_accessions(
    mcpd_filter(ORIGCTY = c("DEU", "SVN")),
    selector = function(x) {
      list(id = x$id, acceNumb = x$acceNumb, instCode = x$institute$code)
    }
  )

## End(Not run)

Add filter on accession DOI

Description

Add filter on accession DOI

Usage

filter_DOI(filter = list(), DOI)

Arguments

filter

Existing filters (or blank list if not provided)
DOI

Accession DOI

Add filter by genus

Description

Add filter by genus

Usage

filter_GENUS(filter = list(), GENUS)

Arguments

filter

Existing filters (or blank list if not provided)
GENUS

List of genera

Add filter by genus

Description

Add filter by genus

Usage

filter_INSTCODE(filter = list(), INSTCODE)

Arguments

filter

Existing filters (or blank list if not provided)
INSTCODE

List of WIEWS institute codes

Add filter on Country of origin of material

Description

Add filter on Country of origin of material

Usage

filter_ORIGCTY(filter = list(), ORIGCTY)

Arguments

filter

Existing filters (or blank list if not provided)
ORIGCTY

Country of origin

Add filter on Biological status of sample

Description

Add filter on Biological status of sample

Usage

filter_SAMPSTAT(filter = list(), SAMPSTAT)

Arguments

filter

Existing filters (or blank list if not provided)
SAMPSTAT

Biological status of sample

Add filter on specific epithet

Description

Add filter on specific epithet

Usage

filter_SPECIES(filter = list(), SPECIES)

Arguments

filter

Existing filters (or blank list if not provided)
SPECIES

List of specific epithets

Get accession passport data as a data table.

Description

Get accession passport data as a data table.

Usage

get_accessions(
  filters = list(),
  page = 0,
  size = 1000,
  fields = NULL,
  exclude = NULL,
  selector = NULL,
  at.least = NULL
)

Arguments

filters

an R structure with Genesys filters
page

the page index (0-based)
size

number of records to load per page (page size)
fields

list of fields to fetch from Genesys
exclude

list of field prefixes to exclude from the Genesys response
selector

NULL or a function to "select" variables of interest
at.least

stop fetching when at.least records are received from Genesys

Value

Data table

See Also

mcpd_filter

Examples

## Not run: 
  # Retrieve all accession data by country of origin (Slovenia, Ivory Coast)
  accessions <- genesysr::get_accessions(list(countryOfOrigin = list(code3 = c('SVN', 'CIV'))))

  # Fetch Musa, but only geographic data and accessionNumber
  musa <- genesysr::get_accessions(list(taxonomy = list(genus = c('Musa'))),
    fields = c("accessionNumber", "geo"))

  # Apply selector function
  accessions <- genesysr::get_accessions(mcpd_filter(ORIGCTY = c('DEU', 'SVN')),
    selector = function(x) {
      list(id = x$id, acceNumb = x$accessionNumber, instCode = x$instituteCode)
    }, at.least = 100)

## End(Not run)

Fetch Genesys crops. Note that the list of Genesys crops does not fully correspond with various CROPNAME in MCPD provided by genebanks.

Description

Fetch Genesys crops. Note that the list of Genesys crops does not fully correspond with various CROPNAME in MCPD provided by genebanks.

Usage

list_crops()

Value

Genesys crops

Examples

## Not run: 
  # Retrieve all Genesys crops
  crops <- genesysr::list_crops()

## End(Not run)

List FAO WIEWS institutes.

Description

Institute filters: - code: list of WIEWS institute codes - accessions: boolean, TRUE list only institutes with accessions in Genesys, FALSE without accessions - country$code3: list of ISO3166 country codes

Usage

list_institutes(filters = list(), at.least = NULL)

Arguments

filters

an R structure with Institute filters
at.least

stop fetching when at.least records are received from Genesys

Value

List of institutes

See Also

mcpd_filter

Examples

## Not run: 
  # Retrieve taxa of selected accessions
  filters <- c();
  filters$accessions = TRUE; # Has accessions in Genesys
  institutes <- genesysr::list_institutes(filters)

## End(Not run)

Fetch taxonomic data of selected accessions.

Description

Fetch taxonomic data of selected accessions.

Usage

list_species(filters = list())

Arguments

filters

an R structure with Genesys filters

Value

Taxonomic records of selected accessions

See Also

mcpd_filter

Examples

## Not run: 
  # Retrieve taxa of selected accessions
  taxa <- genesysr::list_species(mcpd_filter(INSTCODE = c("LBN002", "MEX002")))

## End(Not run)

Make or adjust filter using MCPD terminology

Description

See FAO/Bioversity Multi-Crop Passport Descriptors.

Usage

mcpd_filter(
  filter = list(),
  INSTCODE = NULL,
  DOI = NULL,
  ORIGCTY = NULL,
  SAMPSTAT = NULL,
  GENUS = NULL,
  SPECIES = NULL
)

Arguments

filter

Existing filters (or blank list if not provided)
INSTCODE

WIEWS Institute Code of the holding institute
DOI

Accession DOI
ORIGCTY

Country of origin
SAMPSTAT

Biological status of sample
GENUS

List of genera
SPECIES

List of specific epithets (within specified genera)

Examples

# Filter accessions from Mexico and Slovenia
 mcpd_filter(ORIGCTY = c("MEX", "SVN"))

Who am i? Loads and prints the user profile from Genesys as JSON. You need to be logged in.

Description

Who am i? Loads and prints the user profile from Genesys as JSON. You need to be logged in.

Usage

me()

Examples

## Not run: 
  # Login
  setup_production()
  user_login()
  me()

## End(Not run)

Print Genesys client configuration

Description

Print Genesys client configuration

Usage

print_setup()

Configure the Genesys environment

Description

Configure the Genesys environment

Usage

setup(server = NULL, client_id = NULL, client_secret = NULL)

Arguments

server

Server base URL (e.g. "https://api.genesys-pgr.org" or "https://api.sandbox.genesys-pgr.org")
client_id

OAuth client ID
client_secret

OAuth client secret

See Also

See utility methods setup_production, setup_sandbox

Examples

# Link with sandbox
  setup_sandbox()

Setup for Genesys Production

Description

Use the Genesys R Client with <https://api.genesys-pgr.org> requiring user_login

Usage

setup_production()

Setup for Genesys Sandbox

Description

Use the Genesys R Client with <https://api.sandbox.genesys-pgr.org> requiring user_login

Usage

setup_sandbox()

Login to Genesys as a user

Description

The authorization URL will open in a browser, ask the user to grant permissions to R. After successful authentication the browser will display a message:

Usage

user_login(redirect_uri = "http://127.0.0.1:48913")

Arguments

redirect_uri

a custom redirect_uri to submit as part of the authentication request. This is most useful if the default port is blocked and you wish to specify another port: redirect_uri = "http://127.0.0.1:44211" Note that "http://127.0.0.1" is requred and that "http://localhost" will not work.

Details

“' Authentication complete. Please close this page and return to R. “'

Close the browser and return to R.

See Also

setup