Thanks to visit codestin.com
Credit goes to github.com

Skip to content

682 redundant checks #689

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

Merged
cristinamullin merged 15 commits into from
Oct 17, 2025
Merged

682 redundant checks #689

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
393410e
Run checks/tests on push to this branch while working on it
jbousquin Oct 15, 2025
f930ba0
Use TADA_CheckType() for .data in TADA_CheckColumns()
jbousquin Oct 15, 2025
9913dac
TADA_CheckColumns() checks type
jbousquin Oct 15, 2025
87fb8f2
TADA_CheckColumns() is checking type
jbousquin Oct 15, 2025
a7eada4
Bring up to date w/ develop
jbousquin Oct 16, 2025
bec9c6f
Update expected error for TADA_CheckColumns when input is not dataframe
jbousquin Oct 16, 2025
b6784e8
missed one file update
jbousquin Oct 16, 2025
4afb70a
Resolve merge conflcits
jbousquin Oct 16, 2025
8a4d1f1
Styler (files w/ minor changes)
jbousquin Oct 16, 2025
7d39ca5
styler - whitespace
jbousquin Oct 16, 2025
c606f63
Styler changes to vignettes rmd files
jbousquin Oct 16, 2025
3faa190
Lost expected_ref_cols def in merge
jbousquin Oct 16, 2025
bd6aeac
All calls to TADA_CheckColumns() should follow a similar structure (i…
jbousquin Oct 16, 2025
c4828f3
Prep for PR
jbousquin Oct 16, 2025
9f3283b
Missed one use of required_cols
jbousquin Oct 17, 2025
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
3 changes: 1 addition & 2 deletions .github/workflows/R-CMD-check.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,7 @@
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches:
[develop]
branches: [develop]
pull_request:
branches: develop
# allow manual action trigger
Expand Down
3 changes: 1 addition & 2 deletions .github/workflows/test-coverage.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,7 @@
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches:
[develop]
branches: [develop]
pull_request:
branches: [develop]

Expand Down
30 changes: 15 additions & 15 deletions R/ATTAINSCrosswalks.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1257,10 +1257,10 @@ TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assi
# Excel ref files to be stored in the Downloads folder location.
# Define the OneDrive Downloads path
onedrive_downloads_path <- file.path(Sys.getenv("USERPROFILE"), "OneDrive", "Downloads", "myfileRef.xlsx")

# Define the default Downloads path
default_downloads_path <- file.path(Sys.getenv("USERPROFILE"), "Downloads", "myfileRef.xlsx")

# Check if the OneDrive Downloads path exists, and prioritize it
if (file.exists(onedrive_downloads_path)) {
downloads_path <- onedrive_downloads_path
Expand Down Expand Up @@ -1706,7 +1706,7 @@ TADA_CreateUseParamRef <- function(.data, org_id = NULL, paramRef = NULL, usePar

if (is.data.frame(useParamRef)) {
col.names <- c(
"ATTAINS.OrganizationIdentifier",
"ATTAINS.OrganizationIdentifier",
"ATTAINS.ParameterName", "ATTAINS.UseName"
)

Expand Down Expand Up @@ -1940,7 +1940,7 @@ TADA_CreateUseParamRef <- function(.data, org_id = NULL, paramRef = NULL, usePar
!paste(ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName, ATTAINS.UseName) %in% paste(ATTAINS_param_all$ATTAINS.OrganizationIdentifier, ATTAINS_param_all$ATTAINS.ParameterName, ATTAINS_param_all$ATTAINS.UseName) &
ATTAINS.UseName %in% ATTAINS_param_all$ATTAINS.UseName ~
"Use name is listed as a prior cause in ATTAINS for this organization, but not for this parameter name.",
TRUE ~
TRUE ~
"Use name is not listed as a prior cause in ATTAINS."
)) %>%
dplyr::mutate(Flag.UseInput = dplyr::case_when(
Expand Down Expand Up @@ -1970,10 +1970,10 @@ TADA_CreateUseParamRef <- function(.data, org_id = NULL, paramRef = NULL, usePar

# Define the OneDrive Downloads path
onedrive_downloads_path <- file.path(Sys.getenv("USERPROFILE"), "OneDrive", "Downloads", "myfileRef.xlsx")

# Define the default Downloads path
default_downloads_path <- file.path(Sys.getenv("USERPROFILE"), "Downloads", "myfileRef.xlsx")

# Check if the OneDrive Downloads path exists, and prioritize it
if (file.exists(onedrive_downloads_path)) {
downloads_path <- onedrive_downloads_path
Expand Down Expand Up @@ -2859,10 +2859,10 @@ TADA_CreateMLSummaryRef <- function(.data, org_id = NULL, useParamRef = NULL, di
# default Downloads file location.
# Define the OneDrive Downloads path
onedrive_downloads_path <- file.path(Sys.getenv("USERPROFILE"), "OneDrive", "Downloads", "myfileRef.xlsx")

# Define the default Downloads path
default_downloads_path <- file.path(Sys.getenv("USERPROFILE"), "Downloads", "myfileRef.xlsx")

# Check if the OneDrive Downloads path exists, and prioritize it
if (file.exists(onedrive_downloads_path)) {
downloads_path <- onedrive_downloads_path
Expand Down Expand Up @@ -2968,7 +2968,7 @@ TADA_CreateMLSummaryRef <- function(.data, org_id = NULL, useParamRef = NULL, di
LongitudeMeasure, LatitudeMeasure, IncludeOrExclude, UniqueSpatialCriteria
) %>%
dplyr::distinct()

# data frame to only display sites that contains the parameter
CreateMLSummaryRef2 <- useParamRef %>%
tidyr::uncount(weights = length(unique_ML)) %>%
Expand All @@ -2988,7 +2988,7 @@ TADA_CreateMLSummaryRef <- function(.data, org_id = NULL, useParamRef = NULL, di
LongitudeMeasure, LatitudeMeasure, TADA.ParameterInSite.Flag, IncludeOrExclude, UniqueSpatialCriteria
) %>%
dplyr::distinct()

# joins the table back together and flag appropriately
CreateMLSummaryRef <- CreateMLSummaryRef %>%
# dplyr::bind_rows(CreateMLSummaryRef2)
Expand All @@ -3008,17 +3008,17 @@ TADA_CreateMLSummaryRef <- function(.data, org_id = NULL, useParamRef = NULL, di
) %>%
dplyr::arrange(MonitoringLocationIdentifier)
}

if (displayNA == TRUE && nrow(useParamRef) > 2000 || length(unique_ML) > 2000) {
warning(paste0(
"displayNA = TRUE: ",
"Too many sites or uses and parameters. Cannot assign all uses and parameters to each monitoring sites in the output. ",
"Defaulting to displayNA = FALSE"
))
displayNA = FALSE

displayNA <- FALSE
}

# If we want to exclude rows of sites with no specified parameters
if (displayNA == FALSE) {
print(paste0(
Expand All @@ -3044,7 +3044,7 @@ TADA_CreateMLSummaryRef <- function(.data, org_id = NULL, useParamRef = NULL, di
LongitudeMeasure, LatitudeMeasure, TADA.ParameterInSite.Flag, IncludeOrExclude, UniqueSpatialCriteria
) %>%
dplyr::distinct()

CreateMLSummaryRef <- CreateMLSummaryRef2 %>%
dplyr::arrange(MonitoringLocationIdentifier)
}
Expand Down
34 changes: 14 additions & 20 deletions R/CensoredDataSuite.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,22 +40,19 @@
#'
#'
TADA_IDCensoredData <- function(.data) {
# check .data is data.frame
TADA_CheckType(.data, "data.frame", "Input object")

# Check if the input data frame is empty
if (nrow(.data) == 0) {
message("The entered data frame is empty. The function will not run.")
return(NULL) # Exit the function early
}

# check .data has all of the required columns
# check .data is data.frame and has required columns
expected_cols <- c(
"ResultDetectionConditionText",
"DetectionQuantitationLimitTypeName",
"TADA.ResultMeasureValueDataTypes.Flag"
)
TADA_CheckColumns(.data, expected_cols)
# Check if the input data frame is empty
if (nrow(.data) == 0) {
message("The entered data frame is empty. The function will not run.")
return(NULL) # Exit the function early
}


# this copies det lim result value and unit over to TADA result value and unit
# when the result value is TEXT but there is a specific text value that indicates
Expand Down Expand Up @@ -398,23 +395,20 @@ TADA_SimpleCensoredMethods <- function(.data, nd_method = "multiplier",
nd_multiplier = 0.5,
od_method = "as-is",
od_multiplier = "null") {
# check .data is data.frame
TADA_CheckType(.data, "data.frame", "Input object")

# Check if the input data frame is empty
if (nrow(.data) == 0) {
message("The entered data frame is empty. The function will not run.")
return(NULL) # Exit the function early
}

# check .data has all of the required columns
# check .data is data.frame and has required columns
expected_cols <- c(
"ResultDetectionConditionText",
"DetectionQuantitationLimitTypeName",
"TADA.ResultMeasureValueDataTypes.Flag"
)
TADA_CheckColumns(.data, expected_cols)

# Check if the input data frame is empty
if (nrow(.data) == 0) {
message("The entered data frame is empty. The function will not run.")
return(NULL) # Exit the function early
}

# check that multiplier is provided if method = "multiplier"
if (nd_method == "multiplier" & nd_multiplier == "null") {
stop("Please provide a multiplier for the lower detection limit handling method of 'multiplier'. Typically, the multiplier value is between 0 and 1.")
Expand Down
Loading