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Applied changes as suggested by @infotroph
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Signed-off-by: Abhinav Pandey <[email protected]>
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@Sweetdevil144
Sweetdevil144 committed Oct 9, 2024
1 parent 94c92f0 commit a578be2
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Showing 2 changed files with 100 additions and 83 deletions.
161 changes: 85 additions & 76 deletions base/db/R/add.database.entries.R
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Original file line number Diff line number Diff line change
Expand Up @@ -23,99 +23,108 @@

add.database.entries <- function(
result, con, start_date,
end_date, write, overwrite,
end_date, overwrite,
insert.new.file, input.args,
machine, mimetype, formatname,
allow.conflicting.dates, ensemble,
ensemble_name, existing.input,
existing.dbfile, input) {
if (write) {
# Setup newinput. This list will contain two variables: a vector of input IDs and a vector of DB IDs for each entry in result.
# This list will be returned.
newinput <- list(input.id = NULL, dbfile.id = NULL) # Blank vectors are null.
# Setup newinput. This list will contain two variables: a vector of input IDs and a vector of DB IDs for each entry in result.
# This list will be returned.
newinput <- list(input.id = NULL, dbfile.id = NULL) # Blank vectors are null.

for (i in 1:length(result)) { # Master for loop
id_not_added <- TRUE
for (i in 1:length(result)) { # Master for loop
id_not_added <- TRUE

if (!is.null(existing.input) && nrow(existing.input[[i]]) > 0 &&
(existing.input[[i]]$start_date != start_date || existing.input[[i]]$end_date != end_date)) {
# Updating record with new dates
db.query(paste0("UPDATE inputs SET start_date='", start_date, "', end_date='", end_date, "' WHERE id=", existing.input[[i]]$id), con)
id_not_added <- FALSE
if (!is.null(existing.input) && nrow(existing.input[[i]]) > 0 &&
(existing.input[[i]]$start_date != start_date || existing.input[[i]]$end_date != end_date)) {
# Updating record with new dates
db.query(
paste0(
"UPDATE inputs SET start_date='", start_date, "', end_date='", end_date,
"' WHERE id=", existing.input[[i]]$id
),
con
)
id_not_added <- FALSE

# The overall structure of this loop has been set up so that exactly one input.id and one dbfile.id will be written to newinput every iteration.
newinput$input.id <- c(newinput$input.id, existing.input[[i]]$id)
newinput$dbfile.id <- c(newinput$dbfile.id, existing.dbfile[[i]]$id)
}

if (overwrite) {
# A bit hacky, but need to make sure that all fields are updated to expected values (i.e., what they'd be if convert_input was creating a new record)
if (!is.null(existing.input) && nrow(existing.input[[i]]) > 0) {
db.query(paste0("UPDATE inputs SET name='", basename(dirname(result[[i]]$file[1])), "' WHERE id=", existing.input[[i]]$id), con)
}
# The overall structure of this loop has been set up so that exactly one input.id and one dbfile.id will be written to newinput every iteration.
newinput$input.id <- c(newinput$input.id, existing.input[[i]]$id)
newinput$dbfile.id <- c(newinput$dbfile.id, existing.dbfile[[i]]$id)
}

if (!is.null(existing.dbfile) && nrow(existing.dbfile[[i]]) > 0) {
db.query(paste0("UPDATE dbfiles SET file_path='", dirname(result[[i]]$file[1]), "', file_name='", result[[i]]$dbfile.name[1], "' WHERE id=", existing.dbfile[[i]]$id), con)
}
if (overwrite) {
# A bit hacky, but need to make sure that all fields are updated to expected values (i.e., what they'd be if convert_input was creating a new record)
if (!is.null(existing.input) && nrow(existing.input[[i]]) > 0) {
db.query(
paste0(
"UPDATE dbfiles SET file_path='", dirname(result[[i]]$file[1]),
"', file_name='", result[[i]]$dbfile.name[1],
"' WHERE id=", existing.dbfile[[i]]$id
),
con
)
}

# If there is no ensemble then for each record there should be one parent
# But when you have ensembles, all of the members have one parent !!
parent.id <- if (is.numeric(ensemble)) {
ifelse(is.null(input[[i]]), NA, input[[1]]$id)
} else {
ifelse(is.null(input[[i]]), NA, input[[i]]$id)
if (!is.null(existing.dbfile) && nrow(existing.dbfile[[i]]) > 0) {
db.query(paste0(
"UPDATE dbfiles SET file_path='", dirname(result[[i]]$file[1]),
"', file_name='", result[[i]]$dbfile.name[1],
"' WHERE id=", existing.dbfile[[i]]$id
), con)
}
}

# If there is no ensemble then for each record there should be one parent
# But when you have ensembles, all of the members have one parent !!
parent.id <- if (is.numeric(ensemble)) {
ifelse(is.null(input[[i]]), NA, input[[1]]$id)
} else {
ifelse(is.null(input[[i]]), NA, input[[i]]$id)
}

if ("newsite" %in% names(input.args) && !is.null(input.args[["newsite"]])) {
site.id <- input.args$newsite
}

if (insert.new.file && id_not_added) {
dbfile.id <- dbfile.insert(
in.path = dirname(result[[i]]$file[1]),
in.prefix = result[[i]]$dbfile.name[1],
"Input",
existing.input[[i]]$id,
con,
reuse = TRUE,
hostname = machine$hostname
)
if ("newsite" %in% names(input.args) && !is.null(input.args[["newsite"]])) {
site.id <- input.args$newsite
}

newinput$input.id <- c(newinput$input.id, existing.input[[i]]$id)
newinput$dbfile.id <- c(newinput$dbfile.id, dbfile.id)
} else if (id_not_added) {
# This is to tell input.insert if we are writing ensembles
# Why does it need it? Because it checks for inputs with the same time period, site, and machine
# and if it returns something it does not insert anymore, but for ensembles, it needs to bypass this condition
ens.flag <- if (!is.null(ensemble) | is.null(ensemble_name)) TRUE else FALSE
if (insert.new.file && id_not_added) {
dbfile.id <- dbfile.insert(
in.path = dirname(result[[i]]$file[1]),
in.prefix = result[[i]]$dbfile.name[1],
"Input",
existing.input[[i]]$id,
con,
reuse = TRUE,
hostname = machine$hostname
)

new_entry <- dbfile.input.insert(
in.path = dirname(result[[i]]$file[1]),
in.prefix = result[[i]]$dbfile.name[1],
siteid = site.id,
startdate = start_date,
enddate = end_date,
mimetype = mimetype,
formatname = formatname,
parentid = parent.id,
con = con,
hostname = machine$hostname,
allow.conflicting.dates = allow.conflicting.dates,
ens = ens.flag
)
newinput$input.id <- c(newinput$input.id, existing.input[[i]]$id)
newinput$dbfile.id <- c(newinput$dbfile.id, dbfile.id)
} else if (id_not_added) {
# This is to tell input.insert if we are writing ensembles
# Why does it need it? Because it checks for inputs with the same time period, site, and machine
# and if it returns something it does not insert anymore, but for ensembles, it needs to bypass this condition
ens.flag <- if (!is.null(ensemble) || is.null(ensemble_name)) TRUE else FALSE

newinput$input.id <- c(newinput$input.id, new_entry$input.id)
newinput$dbfile.id <- c(newinput$dbfile.id, new_entry$dbfile.id)
}
} # End for loop
new_entry <- dbfile.input.insert(
in.path = dirname(result[[i]]$file[1]),
in.prefix = result[[i]]$dbfile.name[1],
siteid = site.id,
startdate = start_date,
enddate = end_date,
mimetype = mimetype,
formatname = formatname,
parentid = parent.id,
con = con,
hostname = machine$hostname,
allow.conflicting.dates = allow.conflicting.dates,
ens = ens.flag
)

successful <- TRUE
return(newinput)
} else {
PEcAn.logger::logger.warn("Input was not added to the database")
successful <- TRUE
return(NULL)
}
newinput$input.id <- c(newinput$input.id, new_entry$input.id)
newinput$dbfile.id <- c(newinput$dbfile.id, new_entry$dbfile.id)
}
} # End for loop
return(newinput)
}
22 changes: 15 additions & 7 deletions base/db/R/convert_input.R
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Original file line number Diff line number Diff line change
Expand Up @@ -591,13 +591,21 @@ convert_input <-

#---------------------------------------------------------------#
# New arrangement of database adding code to deal with ensembles.
return (add.database.entries(result, con, start_date,
end_date, write, overwrite,
insert.new.file, input.args,
machine, mimetype, formatname,
allow.conflicting.dates, ensemble,
ensemble_name, existing.input,
existing.dbfile, input))
if(write) {
add_entries_result <- return (add.database.entries(result, con, start_date,
end_date, overwrite,
insert.new.file, input.args,
machine, mimetype, formatname,
allow.conflicting.dates, ensemble,
ensemble_name, existing.input,
existing.dbfile, input))
} else {
PEcAn.logger::logger.warn("Input was not added to the database")
successful <- TRUE
return(NULL)
}
successful <- TRUE
return (add_entries_result)
} # convert_input


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