Genesys PGR Client

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Documentation for package ‘genesysr’ version 2.1.1

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api1_url Get partial API v1 URL for the provided path
api2_url Get partial API v2 URL for the provided path
authorization Provide OAuth2 token to use for authorization with Genesys
check_country Run Land-or-Sea check on MCPD data. Uploads only rows where ORIGCTY, DECLATITUDE and DECLONGITUDE are provided.
check_landorsea 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_taxonomy Check MCPD taxonomic data (GENUS, SPECIES, SPAUTHOR, SUBTAXA, SUBTAUTHOR) using https://validator.genesys-pgr.org.
client_login Login to Genesys as a service client (system-to-system)
download_mcpd Download passport data for one genebank in Excel format and save it to disk
download_pdci Download PDCI data for one genebank in Excel format and save it to disk.
fetch_accessions 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.
filter_DOI Add filter on accession DOI
filter_GENUS Add filter by genus
filter_INSTCODE Add filter by genus
filter_ORIGCTY Add filter on Country of origin of material
filter_SAMPSTAT Add filter on Biological status of sample
filter_SPECIES Add filter on specific epithet
get_accessions Get accession passport data as a data table.
list_crops Fetch Genesys crops. Note that the list of Genesys crops does not fully correspond with various CROPNAME in MCPD provided by genebanks.
list_institutes List FAO WIEWS institutes.
list_species Fetch taxonomic data of selected accessions.
mcpd_filter Make or adjust filter using MCPD terminology
me Who am i? Loads and prints the user profile from Genesys as JSON. You need to be logged in.
print_setup Print Genesys client configuration
setup Configure the Genesys environment
setup_production Setup for Genesys Production
setup_sandbox Setup for Genesys Sandbox
user_login Login to Genesys as a user