## load necessary packages
library(reticulate)
use_condaenv("r-reticulate", required = T)
py_module_available("synapseclient")
py_module_available("pandas")
library(nfportalutils)
library(dplyr)
## login, assuming creds are set with the following env vars
nfportalutils::syn_login(Sys.getenv("SYNAPSE_USER"), Sys.getenv("SYNAPSE_PWD"))
## example to check the head set studies of the studies listed in portal studies table
study_tab_id <- 'syn16787123'
studies <- table_query(study_tab_id, "studyId") %>%
pull(studyId)
study_subset <- head(studies)
results <- check_wiki_links(study_subset)
# view
results
# Write table for reference and additional manual review
# write.csv(results, "results.csv")
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