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remove deprecated cohortId param #245

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remove deprecated cohortId param #245

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a84e5c3
remove deprecated param
ginberg Apr 16, 2024
28f16f8
Merge branch 'develop' into issue244
ginberg Apr 19, 2024
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8 changes: 0 additions & 8 deletions R/GetCovariates.R
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Original file line number Diff line number Diff line change
Expand Up @@ -46,9 +46,6 @@
#' specify both the database and the schema, so for example
#' 'cdm_instance.dbo'.
#' @param cohortTableIsTemp Is the cohort table a temp table?
#' @param cohortId DEPRECATED:For which cohort ID(s) should covariates be constructed? If set to -1,
#' covariates will be constructed for all cohorts in the specified cohort
#' table.
#' @param cohortIds For which cohort ID(s) should covariates be constructed? If set to c(-1),
#' covariates will be constructed for all cohorts in the specified cohort
#' table.
Expand Down Expand Up @@ -100,7 +97,6 @@ getDbCovariateData <- function(connectionDetails = NULL,
cohortTable = "cohort",
cohortDatabaseSchema = cdmDatabaseSchema,
cohortTableIsTemp = FALSE,
cohortId = -1,
cohortIds = c(-1),
rowIdField = "subject_id",
covariateSettings,
Expand All @@ -115,10 +111,6 @@ getDbCovariateData <- function(connectionDetails = NULL,
if (cdmVersion == "4") {
stop("CDM version 4 is not supported any more")
}
if (!missing(cohortId)) {
warning("cohortId argument has been deprecated, please use cohortIds")
cohortIds <- cohortId
}
errorMessages <- checkmate::makeAssertCollection()
minCharacterizationMean <- utils::type.convert(minCharacterizationMean, as.is = TRUE)
checkmate::assertNumeric(x = minCharacterizationMean, lower = 0, add = errorMessages)
Expand Down
5 changes: 0 additions & 5 deletions R/GetCovariatesFromCohortAttributes.R
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Expand Up @@ -73,7 +73,6 @@ getDbCohortAttrCovariatesData <- function(connection,
oracleTempSchema = NULL,
cdmDatabaseSchema,
cohortTable = "#cohort_person",
cohortId = -1,
cohortIds = c(-1),
cdmVersion = "5",
rowIdField = "subject_id",
Expand All @@ -85,10 +84,6 @@ getDbCohortAttrCovariatesData <- function(connection,
if (cdmVersion == "4") {
stop("Common Data Model version 4 is not supported")
}
if (!missing(cohortId)) {
warning("cohortId argument has been deprecated, please use cohortIds")
cohortIds <- cohortId
}
start <- Sys.time()
writeLines("Constructing covariates from cohort attributes table")

Expand Down
9 changes: 2 additions & 7 deletions R/GetCovariatesFromOtherCohorts.R
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Expand Up @@ -32,7 +32,6 @@ getDbCohortBasedCovariatesData <- function(connection,
oracleTempSchema = NULL,
cdmDatabaseSchema,
cohortTable = "#cohort_person",
cohortId = -1,
cohortIds = c(-1),
cdmVersion = "5",
rowIdField = "subject_id",
Expand All @@ -44,18 +43,14 @@ getDbCohortBasedCovariatesData <- function(connection,
checkmate::assertCharacter(oracleTempSchema, len = 1, null.ok = TRUE, add = errorMessages)
checkmate::assertCharacter(cdmDatabaseSchema, len = 1, null.ok = TRUE, add = errorMessages)
checkmate::assertCharacter(cohortTable, len = 1, add = errorMessages)
checkmate::assertIntegerish(cohortId, add = errorMessages)
# checkmate::assertCharacter(cdmVersion, len = 1, add = errorMessages)
checkmate::assertIntegerish(cohortIds, add = errorMessages)
checkmate::assertCharacter(cdmVersion, len = 1, add = errorMessages)
checkmate::assertCharacter(rowIdField, len = 1, add = errorMessages)
checkmate::assertClass(covariateSettings, "covariateSettings", add = errorMessages)
checkmate::assertLogical(aggregated, len = 1, add = errorMessages)
minCharacterizationMean <- utils::type.convert(minCharacterizationMean, as.is = TRUE)
checkmate::assertNumeric(x = minCharacterizationMean, lower = 0, add = errorMessages)
checkmate::reportAssertions(collection = errorMessages)
if (!missing(cohortId)) {
warning("cohortId argument has been deprecated, please use cohortIds")
cohortIds <- cohortId
}

start <- Sys.time()
message("Constructing covariates from other cohorts")
Expand Down
5 changes: 0 additions & 5 deletions R/GetDefaultCovariates.R
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Expand Up @@ -59,7 +59,6 @@ getDbDefaultCovariateData <- function(connection,
oracleTempSchema = NULL,
cdmDatabaseSchema,
cohortTable = "#cohort_person",
cohortId = -1,
cohortIds = c(-1),
cdmVersion = "5",
rowIdField = "subject_id",
Expand All @@ -79,10 +78,6 @@ getDbDefaultCovariateData <- function(connection,
if (!missing(targetCovariateTable) && !is.null(targetCovariateTable) && aggregated) {
stop("Writing aggregated results to database is currently not supported")
}
if (!missing(cohortId)) {
warning("cohortId argument has been deprecated, please use cohortIds")
cohortIds <- cohortId
}
errorMessages <- checkmate::makeAssertCollection()
minCharacterizationMean <- utils::type.convert(minCharacterizationMean, as.is = TRUE)
checkmate::assertNumeric(x = minCharacterizationMean, lower = 0, add = errorMessages)
Expand Down
10 changes: 2 additions & 8 deletions R/HelperFunctions.R
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Expand Up @@ -65,7 +65,6 @@ filterByRowId <- function(covariateData, rowIds) {
#' Filter covariates by cohort definition IDs
#'
#' @param covariateData An object of type \code{CovariateData}
#' @param cohortId DEPRECATED The cohort definition IDs to keep.
#' @param cohortIds The cohort definition IDs to keep.
#'
#' @return
Expand All @@ -86,8 +85,7 @@ filterByRowId <- function(covariateData, rowIds) {
#' }
#'
#' @export
filterByCohortDefinitionId <- function(covariateData,
cohortId = 1,
filterByCohortDefinitionId <- function(covariateData,
cohortIds = c(1)) {
if (!isCovariateData(covariateData)) {
stop("Data not of class CovariateData")
Expand All @@ -98,11 +96,7 @@ filterByCohortDefinitionId <- function(covariateData,
if (!isAggregatedCovariateData(covariateData)) {
stop("Can only filter aggregated data by cohortIds")
}
if (!missing(cohortId)) {
warning("cohortId argument has been deprecated, please use cohortIds")
cohortIds <- cohortId
}


if (is.null(covariateData$covariates)) {
covariates <- NULL
} else {
Expand Down
2 changes: 1 addition & 1 deletion R/UnitTestHelperFunctions.R
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Expand Up @@ -80,7 +80,7 @@
#' oracleTempSchema = NULL,
#' cdmDatabaseSchema = "main",
#' cohortTable = "cohort",
#' cohortId = 1,
#' cohortIds = 1,
#' cdmVersion = "5",
#' rowIdField = "subject_id",
#' covariateSettings = covSettings,
Expand Down
5 changes: 0 additions & 5 deletions extras/GetHdpsCovariates.R
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Expand Up @@ -36,16 +36,11 @@ getDbHdpsCovariateData <- function(connection,
oracleTempSchema = NULL,
cdmDatabaseSchema,
cohortTable = "cohort_person",
cohortId = -1,
cohortIds = c(-1),
cdmVersion = "5",
rowIdField = "subject_id",
covariateSettings,
aggregated = FALSE) {
if (!missing(cohortId)) {
warning("cohortId argument has been deprecated, please use cohortIds")
cohortIds <- cohortId
}
if (cohortIds != -1)
stop("Haven't implemented restricting to cohort ID yet.")
if (aggregated)
Expand Down
3 changes: 0 additions & 3 deletions man-roxygen/GetCovarParams.R
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Expand Up @@ -16,9 +16,6 @@
#' covariates. If it is a temp table, the name should have a hash prefix,
#' e.g. '#temp_table'. If it is a non-temp table, it should include the
#' database schema, e.g. 'cdm_database.cohort'.
#' @param cohortId DEPRECATED:For which cohort ID should covariates be constructed? If set to -1,
#' covariates will be constructed for all cohorts in the specified cohort
#' table.
#' @param cohortIds For which cohort ID(s) should covariates be constructed? If set to c(-1),
#' covariates will be constructed for all cohorts in the specified cohort
#' table.
Expand Down
2 changes: 1 addition & 1 deletion man/dot-getDbLooCovariateData.Rd
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4 changes: 1 addition & 3 deletions man/filterByCohortDefinitionId.Rd
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5 changes: 0 additions & 5 deletions man/getDbCohortAttrCovariatesData.Rd
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5 changes: 0 additions & 5 deletions man/getDbCohortBasedCovariatesData.Rd
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5 changes: 0 additions & 5 deletions man/getDbCovariateData.Rd
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5 changes: 0 additions & 5 deletions man/getDbDefaultCovariateData.Rd
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11 changes: 0 additions & 11 deletions tests/testthat/test-CovariateData.R
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Expand Up @@ -144,17 +144,6 @@ test_that("Test show method", {
on.exit(rm(cvData))
})

test_that("getDbCovariateData cohortId warning", {
skip_if_not(dbms == "sqlite")
settings <- createDefaultCovariateSettings()
expect_warning(getDbCovariateData(connectionDetails = eunomiaConnectionDetails,
cdmDatabaseSchema = eunomiaCdmDatabaseSchema,
cohortDatabaseSchema = eunomiaOhdsiDatabaseSchema,
cohortId = c(1),
covariateSettings = settings,
aggregated = FALSE), "cohortId argument has been deprecated, please use cohortIds")
})

test_that("getDbCovariateData settings list - check metaData", {
skip_if_not(dbms == "sqlite")
looCovSet <- FeatureExtraction:::.createLooCovariateSettings(useLengthOfObs = TRUE)
Expand Down
20 changes: 0 additions & 20 deletions tests/testthat/test-GetCovariatesFromCohortAttributes.R
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Expand Up @@ -72,23 +72,3 @@ test_that("createCohortAttrCovariateSettings check", {
result <- createCohortAttrCovariateSettings(attrDatabaseSchema = "main")
expect_equal(class(result), "covariateSettings")
})

test_that("getDbCohortAttrCovariatesData cohortId warning", {
skip_if_not(dbms == "sqlite")
covariateSettings <- createCohortAttrCovariateSettings(
attrDatabaseSchema = eunomiaOhdsiDatabaseSchema,
cohortAttrTable = cohortAttributeTable,
attrDefinitionTable = attributeDefinitionTable,
includeAttrIds = c(1),
isBinary = FALSE,
missingMeansZero = TRUE
)
# cohortId argument
expect_warning(getDbCohortAttrCovariatesData(
connection = eunomiaConnection,
cdmDatabaseSchema = eunomiaCdmDatabaseSchema,
cohortTable = cohortTable,
covariateSettings = covariateSettings,
cohortId = 1
), "cohortId argument has been deprecated, please use cohortIds")
})
2 changes: 1 addition & 1 deletion tests/testthat/test-GetDefaultCovariates.R
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Expand Up @@ -31,7 +31,7 @@ test_that("Test exit conditions", {
expect_error(getDbDefaultCovariateData(
connection = eunomiaConnection,
cdmDatabaseSchema = "main",
cohortId = -1,
cohortIds = -1,
covariateSettings = createDefaultCovariateSettings(),
targetDatabaseSchema = "main",
targetCovariateTable = "cov",
Expand Down
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