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Fixes a few issues related to TADA Shiny app option C #552

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Merged
cristinamullin merged 3 commits into from
Dec 12, 2024
Merged

Fixes a few issues related to TADA Shiny app option C #552

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991891e
Update RequiredCols.R
cristinamullin Dec 5, 2024
b4ee026
apply column structure in autoclean instead of DR, export req col fun…
cristinamullin Dec 5, 2024
884db2c
Update Utilities.R
cristinamullin Dec 6, 2024
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1 change: 1 addition & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ export(TADA_BigDataRetrieval)
export(TADA_Boxplot)
export(TADA_CalculateTotalNP)
export(TADA_CharStringRemoveNA)
export(TADA_CheckRequiredFields)
export(TADA_ColorPalette)
export(TADA_ConvertDepthUnits)
export(TADA_ConvertResultUnits)
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6 changes: 0 additions & 6 deletions R/DataDiscoveryRetrieval.R
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Expand Up @@ -308,12 +308,6 @@ TADA_DataRetrieval <- function(startDate = "null",
Projects = projects.DR
)

# 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(TADAprofile)

TADAprofile <- TADAprofile %>% dplyr::mutate_at(cols, as.character)

# run TADA_AutoClean function
if (applyautoclean == TRUE) {
print("Data successfully downloaded. Running TADA_AutoClean function.")
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8 changes: 5 additions & 3 deletions R/RequiredCols.R
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Expand Up @@ -130,6 +130,7 @@ require.cols <- c(

# Result Quality
"MeasureQualifierCode", # required, could be replaced by TADA.MeasureQualifierCode.Def in future mods
"ResultStatusIdentifier",
"TADA.MeasureQualifierCode.Flag", # generated
"TADA.MeasureQualifierCode.Def", # generated, could replace MeasureQualifierCode in future mods
"ResultCommentText",
Expand Down Expand Up @@ -181,8 +182,7 @@ require.cols <- c(
"HUCEightDigitCode",
"MonitoringLocationIdentifier", # required
"TADA.MonitoringLocationIdentifier",

# Groundwater fields
# Groundwater fields, used for auto filtering for assessment use case but should not be required to have in TADA template
"AquiferName", # filter, groundwater
"AquiferTypeName", # filter
"LocalAqfrName", # filter, groundwater
Expand All @@ -195,6 +195,7 @@ require.cols <- c(

# ordered list of non-essential WQP columns that can be removed from df
extra.cols <- c(
# Others
"ActivityDepthAltitudeReferencePointText",
"ActivityEndDate",
"ActivityEndTime.Time",
Expand All @@ -204,7 +205,6 @@ extra.cols <- c(
"SampleAquifer",
"ActivityLocation.LatitudeMeasure",
"ActivityLocation.LongitudeMeasure",
"ResultStatusIdentifier",
"ResultWeightBasisText",
"ResultTemperatureBasisText",
"ResultParticleSizeBasisText",
Expand Down Expand Up @@ -349,6 +349,8 @@ TADA_GetTemplate <- function() {
#' @param .data A dataframe
#'
#' @return Boolean result indicating whether or not the input dataframe contains all of the TADA profile fields.
#'
#' @export
#'
#' @examples
#' \dontrun{
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7 changes: 7 additions & 0 deletions R/Utilities.R
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Expand Up @@ -201,6 +201,11 @@ VATribeUrl <- "https://geopub.epa.gov/arcgis/rest/services/EMEF/Tribal/MapServer
#' }
#'
TADA_AutoClean <- function(.data) {
# 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(.data)
.data <- .data %>% dplyr::mutate_at(cols, as.character)

# check .data is data.frame
TADA_CheckType(.data, "data.frame", "Input object")

Expand All @@ -217,6 +222,8 @@ TADA_AutoClean <- function(.data) {
TADA_CheckColumns(.data, required_cols)

# execute function after checks are passed



# check to make sure columns do not already exist and capitalize fields with known synonyms that
# only differ in caps
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