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Fix option c #135 #194

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Fix option c #135 #194

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350e769
Update mod_query_data.R
cristinamullin Dec 5, 2024
c650cff
Merge branch 'download-template-84' into fix-option-C-#135
cristinamullin Dec 12, 2024
6427df7
update flag functions
cristinamullin Dec 13, 2024
cf20ed2
add TADA_CheckRequiredFields
cristinamullin Dec 13, 2024
f2bbaa4
Merge branch 'develop' into fix-option-C-#135
cristinamullin Dec 13, 2024
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15 changes: 13 additions & 2 deletions R/mod_query_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -305,8 +305,19 @@ mod_query_data_server <- function(id, tadat) {
)

# user uploaded data
raw <-
suppressWarnings(readxl::read_excel(input$file$datapath, sheet = 1))
raw <- suppressWarnings(readxl::read_excel(input$file$datapath, sheet = 1))

# run code included in TADA data retrieval
# need to specify this or throws error when trying to bind rows. Temporary fix for larger
# issue where data structure for all columns should be specified.
cols <- names(raw)
raw <- raw %>% dplyr::mutate_at(cols, as.character)
# check that all TADA template columns are included
raw <- EPATADA::TADA_CheckRequiredFields(raw)
# run autoclean
raw <- EPATADA::TADA_AutoClean(raw)

# other steps to prepare data for app
raw$TADA.Remove <- NULL
initializeTable(tadat, raw)
if (!is.null(tadat$original_source)) {
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5 changes: 2 additions & 3 deletions R/utils_flag_functions.R
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Expand Up @@ -90,7 +90,7 @@ applyFlags <- function(in_table, orgs) {
out <- EPATADA::TADA_FlagResultUnit(out, clean = "none")

# QC rep/blank
out <- EPATADA::TADA_FindQCActivities(out, clean = FALSE)
out <- EPATADA::TADA_FindQCActivities(out, clean = FALSE, flaggedonly = FALSE)

# Result is flagged as suspect by data submitter
out <- EPATADA::TADA_FlagMeasureQualifierCode(out, clean = FALSE, define = TRUE)
Expand All @@ -116,8 +116,7 @@ applyFlags <- function(in_table, orgs) {

# Continuous data
out <- EPATADA::TADA_FlagContinuousData(out, clean = FALSE,
flaggedonly = FALSE,
time_difference = 4)
flaggedonly = FALSE)

# Above WQX Upper Threshold
out <- EPATADA::TADA_FlagAboveThreshold(out, clean = FALSE)
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