Genesys PGR Client


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Documentation for package ‘genesysr’ version 1.0.0

Help Pages

api1_url Get full Genesys API v1 URL for a specific path
api2_url Get full Genesys API v1 URL for a specific 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 all 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
filter_DOI Add filter on accession DOI
filter_GENUS 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 Fetch accession passport data
mcpd_filter Make or adjust filter using MCPD terminology
me Who am i?
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