Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fixed some global variables in PEcAn.DB package #2971

Merged
merged 20 commits into from
Aug 1, 2022
Merged

Fixed some global variables in PEcAn.DB package #2971

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
20 commits
Select commit Hold shift + click to select a range
72dc9ea
some changes in the global variable "setting"
nanu1605 Jul 20, 2022
a2dc5df
Merge branch 'develop' into db_global_variable
nanu1605 Jul 20, 2022
bb36396
minor change in query.prior.R
nanu1605 Jul 21, 2022
3f9846e
Rd file updated
nanu1605 Jul 21, 2022
b14eef5
Update base/db/R/get.trait.data.pft.R
nanu1605 Jul 22, 2022
25982c6
requested changes
nanu1605 Jul 22, 2022
e54f8e3
Merge branch 'PecanProject:develop' into db_global_variable
nanu1605 Jul 26, 2022
50041a6
Merge branch 'develop' into db_global_variable
nanu1605 Jul 27, 2022
f8a7fd5
Update base/db/R/query.prior.R
nanu1605 Jul 28, 2022
8504ffd
removed settings variable
nanu1605 Jul 28, 2022
0dbbc0d
Merge branch 'develop' into db_global_variable
nanu1605 Jul 28, 2022
e90856c
some changes in the global variable "var_name" and "user.permission"
nanu1605 Jul 30, 2022
3b5f1c6
Update base/db/R/utils_db.R
nanu1605 Jul 31, 2022
88c50ef
Update base/db/R/query.dplyr.R
nanu1605 Jul 31, 2022
1ba0702
Update base/db/R/query.dplyr.R
nanu1605 Jul 31, 2022
8559a12
Update base/db/R/utils_db.R
nanu1605 Jul 31, 2022
5ed0732
Update base/db/R/utils_db.R
nanu1605 Jul 31, 2022
c451b32
removed update variable
nanu1605 Jul 31, 2022
947680a
Merge branch 'develop' into db_global_variable
nanu1605 Jul 31, 2022
1d3ae6c
Merge branch 'develop' into db_global_variable
dlebauer Aug 1, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion base/db/R/get.trait.data.pft.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,10 @@ get.trait.data.pft <- function(pft, modeltype, dbfiles, dbcon, trait.names,
dplyr::mutate_if(is.character, ~dplyr::na_if(., ""))

# get the priors
prior.distns <- PEcAn.DB::query.priors(pft = pftid, trstr = PEcAn.utils::vecpaste(trait.names), con = dbcon)
prior.distns <- PEcAn.DB::query.priors(
pft = pftid,
trstr = PEcAn.utils::vecpaste(trait.names),
con = dbcon)
prior.distns <- prior.distns[which(!rownames(prior.distns) %in% names(pft$constants)),]
traits <- rownames(prior.distns)

Expand Down
2 changes: 1 addition & 1 deletion base/db/R/query.dplyr.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -268,7 +268,7 @@ load_data_single_run <- function(bety, workflow_id, run_id) {
ncfile <- list.files(path = outputfolder, pattern = "\\.nc$", full.names = TRUE)[1]
nc <- ncdf4::nc_open(ncfile)

globalDF <- tidyr::gather(out, key = var_name, value = vals, names(out)[names(out) != "posix"]) %>%
globalDF <- tidyr::gather(out, key = "var_name", value = "vals", names(out)[names(out) != "posix"]) %>%
dplyr::rename(dates = .data$posix)
globalDF$workflow_id <- workflow_id
globalDF$run_id <- run_id
Expand Down
13 changes: 3 additions & 10 deletions base/db/R/query.prior.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,16 +41,9 @@ query.priors <- function(pft, trstr = NULL, con = NULL, ...){
if (is.null(con)) {
params <- list(...)
if (!length(params)) {
PEcAn.logger::logger.warn(paste0(
"No connection (`con`) or params (`...`) specified. ",
'Trying to connect from `settings[[c("database", "bety")]]`.'
))
if (!exists("settings")) {
PEcAn.logger::logger.severe(
"`settings` object not found. Unable to connect to database."
)
}
params <- settings[[c("database", "bety")]]
PEcAn.logger::logger.severe(
"No connection (`con`) specified and no connection parameters given in `...`.",
"Unable to connect to database.")
}
con <- db.open(params)
on.exit(db.close(con), add = TRUE)
Expand Down
2 changes: 1 addition & 1 deletion base/db/R/utils_db.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -322,7 +322,7 @@ db.exists <- function(params, write = TRUE, table = NA) {
}

#check table's privilege about read and write permission
user.permission <<- tryCatch({
user.permission <- tryCatch({
invisible(db.query(
paste0("SELECT privilege_type FROM information_schema.role_table_grants ",
"WHERE grantee='", params$user,
Expand Down