Package: genesysr 2.1.1

genesysr: Genesys PGR Client

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]

genesysr_2.1.1.tar.gz
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genesysr.pdf |genesysr.html✨
genesysr/json (API)
NEWS

# Install 'genesysr' in R:
install.packages('genesysr', repos = c('https://mobreza.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.00 score 6 scripts 266 downloads 27 exports 34 dependencies

Last updated 9 months agofrom:5edf6376d2. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 21 2024
R-4.5-winOKOct 21 2024
R-4.5-linuxOKOct 21 2024
R-4.4-winOKOct 21 2024
R-4.4-macOKOct 21 2024
R-4.3-winOKOct 21 2024
R-4.3-macOKOct 21 2024

Exports:api1_urlapi2_urlauthorizationcheck_countrycheck_landorseacheck_taxonomyclient_logindownload_mcpddownload_pdcifetch_accessionsfilter_DOIfilter_GENUSfilter_INSTCODEfilter_ORIGCTYfilter_SAMPSTATfilter_SPECIESget_accessionslist_cropslist_instituteslist_speciesmcpd_filtermeprint_setupsetupsetup_productionsetup_sandboxuser_login

Dependencies:askpassbitbit64clicliprcpp11crayoncurldplyrfansigenericsgluehmshttr2jsonlitelifecyclemagrittropensslpillarpkgconfigprettyunitsprogressR6rappdirsreadrrlangsystibbletidyselecttzdbutf8vctrsvroomwithr

genesysr Tutorial

Matija Obreza & Nora Castaneda

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Oct 21 2024.

Last update: 2023-10-13
Started: 2018-06-14

Validating passport data

Matija Obreza

Rendered fromvalidation.Rmdusingknitr::rmarkdownon Oct 21 2024.

Last update: 2023-10-13
Started: 2019-11-22

Readme and manuals

Help Manual

Help pageTopics
Get partial API v1 URL for the provided pathapi1_url
Get partial API v2 URL for the provided pathapi2_url
Provide OAuth2 token to use for authorization with Genesysauthorization
Run Land-or-Sea check on MCPD data. Uploads only rows where ORIGCTY, DECLATITUDE and DECLONGITUDE are provided.check_country
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.check_landorsea
Check MCPD taxonomic data (GENUS, SPECIES, SPAUTHOR, SUBTAXA, SUBTAUTHOR) using https://validator.genesys-pgr.org.check_taxonomy
Login to Genesys as a service client (system-to-system)client_login
Download passport data for one genebank in Excel format and save it to diskdownload_mcpd
Download PDCI data for one genebank in Excel format and save it to disk.download_pdci
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.fetch_accessions
Add filter on accession DOIfilter_DOI
Add filter by genusfilter_GENUS
Add filter by genusfilter_INSTCODE
Add filter on Country of origin of materialfilter_ORIGCTY
Add filter on Biological status of samplefilter_SAMPSTAT
Add filter on specific epithetfilter_SPECIES
Get accession passport data as a data table.get_accessions
Fetch Genesys crops. Note that the list of Genesys crops does not fully correspond with various CROPNAME in MCPD provided by genebanks.list_crops
List FAO WIEWS institutes.list_institutes
Fetch taxonomic data of selected accessions.list_species
Make or adjust filter using MCPD terminologymcpd_filter
Who am i? Loads and prints the user profile from Genesys as JSON. You need to be logged in.me
Print Genesys client configurationprint_setup
Configure the Genesys environmentsetup
Setup for Genesys Productionsetup_production
Setup for Genesys Sandboxsetup_sandbox
Login to Genesys as a useruser_login