## load necessary packages
library(reticulate)
reticulate::use_condaenv("r-reticulate", required = T)
py_available("synapseclient") #should be check in pckg...but here for now
py_available("pandas") #should be check in pckg...but here for now
library(nfportalutils)
study_tab_id <- 'syn16787123'
portal_fileview_id <- 'syn16858331'
people_tab_id <- 'syn23564971'
## login
nfportalutils::syn_login()
## update related studies column (dry run first)
clust <- nfportalutils::calculate_related_studies(study_tab_id, n_clust = 30)
nfportalutils::calculate_related_studies(study_tab_id, n_clust = 30, dry_run = F)
## update file annotations that can be derived from study table (dry run first)
foo <- nfportalutils::update_study_annotations(study_table_id = study_tab_id,
fileview_id = portal_fileview_id,
annotations = c("studyId","studyName","fundingAgency","initiative"))
nfportalutils::update_study_annotations(study_table_id = study_tab_id,
fileview_id = portal_fileview_id,
annotations = c("studyId","studyName","fundingAgency","initiative"),
dry_run = F)
## update study "data type" submmary values (dry run first)
data_types <- get_valid_values_from_json_schema()
foo <- assign_study_data_types(study_table_id = study_tab_id,
fileview_id = portal_fileview_id,
valid_values = data_types)
assign_study_data_types(study_table_id = study_tab_id,
fileview_id = portal_fileview_id,
valid_values = data_types,
dry_run = F)
## update people table (dry run first), using both the modifiedBy and createdBy columns
peeps <- nfportalutils::add_people_from_table(source_table_id = portal_fileview_id,
source_column = "modifiedBy",
people_table_id = people_tab_id,
people_column = "ownerID")
peeps <- nfportalutils::add_people_from_table(source_table_id = portal_fileview_id,
source_column = "modifiedBy",
people_table_id = people_tab_id,
people_column = "ownerID",
dry_run = F)
peeps <- nfportalutils::add_people_from_table(source_table_id = portal_fileview_id,
source_column = "createdBy",
people_table_id = people_tab_id,
people_column = "ownerID")
peeps <- nfportalutils::add_people_from_table(source_table_id = portal_fileview_id,
source_column = "createdBy",
people_table_id = people_tab_id,
people_column = "ownerID",
dry_run = F)
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