use cdmDisconnect instead of dbDisconnect

darwin-eu · Jan 26, 2024 · 0775e78 · 0775e78
1 parent 7c9fd46
commit 0775e78
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Showing 33 changed files with 42 additions and 42 deletions.
diff --git a/R/achillesCodeUse.R b/R/achillesCodeUse.R
@@ -17,7 +17,7 @@
 #' oa <- getCandidateCodes(cdm = cdm, keywords = "osteoarthritis")
 #' result_achilles <- achillesCodeUse(list(oa = oa$concept_id), cdm = cdm)
 #' result_achilles
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 
 achillesCodeUse <- function(x,

diff --git a/R/codesFromConceptSet.R b/R/codesFromConceptSet.R
@@ -32,7 +32,7 @@
 #'                          path =  system.file(package = "CodelistGenerator",
 #'                          "concepts_for_mock"))
 #' x
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 codesFromConceptSet <- function(path, cdm, withConceptDetails = FALSE) {
   # initial checks

diff --git a/R/codesInUse.R b/R/codesInUse.R
@@ -19,7 +19,7 @@
 #'                                 cdm = cdm)
 #'
 #' x
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 restrictToCodesInUse <- function(x,
                                cdm,
@@ -71,7 +71,7 @@ x
 #' cdm <- mockVocabRef("database")
 #' x <- codesInUse(cdm = cdm)
 #' x
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 codesInUse <- function(cdm,
                        table = c("condition_occurrence",
@@ -128,7 +128,7 @@ if(!is.null(cdm[["achilles_results"]])){
 #' cdm <- mockVocabRef("database")
 #' x <- sourceCodesInUse(cdm = cdm)
 #' x
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 sourceCodesInUse <- function(cdm,
                                  table = c("condition_occurrence",

diff --git a/R/compareCodelists.R b/R/compareCodelists.R
@@ -42,7 +42,7 @@
 #'  codelist1 = codes1,
 #'  codelist2 = codes2
 #' )
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 compareCodelists <- function(codelist1,
                               codelist2) {

diff --git a/R/drugCodes.R b/R/drugCodes.R
@@ -40,7 +40,7 @@
 #' \dontrun{
 #' cdm <- mockVocabRef()
 #' getATCCodes(cdm = cdm, level = "ATC 1st")
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 getATCCodes <- function(cdm,
                         level = c("ATC 1st"),
@@ -184,7 +184,7 @@ getATCCodes <- function(cdm,
 #' \dontrun{
 #'cdm <- mockVocabRef()
 #'getDrugIngredientCodes(cdm = cdm, name = "Adalimumab")
-#'DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#'CDMConnector::cdmDisconnect(cdm)
 #'}
 getDrugIngredientCodes <- function(cdm,
                                    name = NULL,

diff --git a/R/findOrphanCodes.R b/R/findOrphanCodes.R
@@ -44,7 +44,7 @@
 #' includeAncestor = FALSE)
 #'
 #' orphan_codes
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 findOrphanCodes <- function(x,
                             cdm,

diff --git a/R/getCandidateCodes.R b/R/getCandidateCodes.R
@@ -58,7 +58,7 @@
 #'   cdm = cdm,
 #'   keywords = "osteoarthritis"
 #'  )
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 getCandidateCodes <- function(cdm,
                               keywords,

diff --git a/R/getICD10StandardCodes.R b/R/getICD10StandardCodes.R
@@ -22,7 +22,7 @@
 #'   "ICD10 Chapter",
 #'   "ICD10 SubChapter"
 #' ))
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 getICD10StandardCodes <- function(cdm,
                                   level = c(

diff --git a/R/getMappings.R b/R/getMappings.R
@@ -36,7 +36,7 @@
 #'   candidateCodelist = codes,
 #'   nonStandardVocabularies = "READ"
 #')
-#'DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#'CDMConnector::cdmDisconnect(cdm)
 #'}
 getMappings <- function(candidateCodelist,
                          cdm = NULL,

diff --git a/R/mockVocabRef.R b/R/mockVocabRef.R
@@ -25,7 +25,7 @@
 #' \dontrun{
 #' cdm <- mockVocabRef()
 #' cdm
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 mockVocabRef <- function(backend = "database") {
   errorMessage <- checkmate::makeAssertCollection()

diff --git a/R/summariseCodeUse.R b/R/summariseCodeUse.R
@@ -29,7 +29,7 @@
 #'           poliovirus_vaccine = poliovirus_vaccine)
 #'results <- summariseCodeUse(cs,cdm = cdm)
 #'results
-#'DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#'CDMConnector::cdmDisconnect(cdm)
 #'}
 #'
 summariseCodeUse <- function(x,
@@ -116,7 +116,7 @@ summariseCodeUse <- function(x,
 #'                       minCellCount = 0)
 #'
 #'results_cohort_mult
-#'DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#'CDMConnector::cdmDisconnect(cdm)
 #'}
 summariseCohortCodeUse <- function(x,
                                    cdm,

diff --git a/R/vocabUtilities.R b/R/vocabUtilities.R
@@ -25,7 +25,7 @@
 #' \dontrun{
 #' cdm <- mockVocabRef()
 #' getVocabVersion(cdm = cdm)
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 getVocabVersion <- function(cdm) {
   errorMessage <- checkmate::makeAssertCollection()
@@ -62,7 +62,7 @@ getVocabVersion <- function(cdm) {
 #' \dontrun{
 #' cdm <- mockVocabRef()
 #' getDomains(cdm = cdm)
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 getDomains <- function(cdm,
                        standardConcept = "Standard") {
@@ -134,7 +134,7 @@ getDomains <- function(cdm,
 #' \dontrun{
 #' cdm <- mockVocabRef()
 #' getVocabularies(cdm = cdm)
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 
 getVocabularies <- function(cdm) {
@@ -174,7 +174,7 @@ getVocabularies <- function(cdm) {
 #' \dontrun{
 #' cdm <- mockVocabRef()
 #' getConceptClassId(cdm = cdm, domain = "drug")
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 
 getConceptClassId <- function(cdm,
@@ -256,7 +256,7 @@ getConceptClassId <- function(cdm,
 #' \dontrun{
 #' cdm <- mockVocabRef()
 #' getDoseForm(cdm = cdm)
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 
 getDoseForm <- function(cdm) {
@@ -313,7 +313,7 @@ getDoseForm <- function(cdm) {
 #' \dontrun{
 #' cdm <- mockVocabRef()
 #' getDescendants(cdm = cdm, conceptId = 1)
-#' DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
+#' CDMConnector::cdmDisconnect(cdm)
 #' }
 
 getDescendants <- function(cdm,

diff --git a/man/achillesCodeUse.Rd b/man/achillesCodeUse.Rd
diff --git a/man/codesFromConceptSet.Rd b/man/codesFromConceptSet.Rd
diff --git a/man/codesInUse.Rd b/man/codesInUse.Rd
diff --git a/man/compareCodelists.Rd b/man/compareCodelists.Rd
diff --git a/man/findOrphanCodes.Rd b/man/findOrphanCodes.Rd
diff --git a/man/getATCCodes.Rd b/man/getATCCodes.Rd
diff --git a/man/getCandidateCodes.Rd b/man/getCandidateCodes.Rd
diff --git a/man/getDescendants.Rd b/man/getDescendants.Rd
diff --git a/man/getDomains.Rd b/man/getDomains.Rd
diff --git a/man/getDoseForm.Rd b/man/getDoseForm.Rd
diff --git a/man/getDrugIngredientCodes.Rd b/man/getDrugIngredientCodes.Rd
diff --git a/man/getICD10StandardCodes.Rd b/man/getICD10StandardCodes.Rd
diff --git a/man/getMappings.Rd b/man/getMappings.Rd
diff --git a/man/getVocabVersion.Rd b/man/getVocabVersion.Rd
diff --git a/man/getVocabularies.Rd b/man/getVocabularies.Rd
diff --git a/man/getconceptClassId.Rd b/man/getconceptClassId.Rd
diff --git a/man/mockVocabRef.Rd b/man/mockVocabRef.Rd
diff --git a/man/restrictToCodesInUse.Rd b/man/restrictToCodesInUse.Rd
diff --git a/man/sourceCodesInUse.Rd b/man/sourceCodesInUse.Rd
diff --git a/man/summariseCodeUse.Rd b/man/summariseCodeUse.Rd
diff --git a/man/summariseCohortCodeUse.Rd b/man/summariseCohortCodeUse.Rd