Merge pull request #305 from OHDSI/hotfix-2.1.5-develop-merge

Hotfix 2.1.5 develop merge
OHDSI · Jul 15, 2024 · 05da629 · 05da629
2 parents 1f90210 + a594c22
commit 05da629
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Showing 31 changed files with 153 additions and 23 deletions.
diff --git a/R/cohort-diagnostics-main-ui.R b/R/cohort-diagnostics-main-ui.R
@@ -145,7 +145,7 @@ cdUiControls <- function(ns) {
 #'
 #' @return
 #' string location of the description helper file
-#'
+#' @family {CohortDiagnostics}
 #' @export
 cohortDiagnosticsHelperFile <- function() {
   fileLoc <- system.file('cohort-diagnostics-www', "cohort-diagnostics.html", package = utils::packageName())

diff --git a/R/cohort-diagnostics-main.R b/R/cohort-diagnostics-main.R
@@ -412,6 +412,8 @@ getResultsTemporalTimeRef <- function(dataSource) {
 #' @param connectionHandler             ResultModelManager ConnectionHander instance
 #' @param resultDatabaseSettings        results database settings
 #' @param dataSource                    dataSource optionally created with createCdDatabaseDataSource
+#'
+#' @family {CohortDiagnostics}
 #' @export
 cohortDiagnosticsServer <- function(id,
                                     connectionHandler,

diff --git a/R/cohort-diagnostics-orphanConcepts.R b/R/cohort-diagnostics-orphanConcepts.R
@@ -17,7 +17,7 @@
 #' Orphan Concepts View
 #' @description
 #' Use for customizing UI
-#'
+#' @family {CohortDiagnostics}
 #' @param id    Namespace Id - use namespaced id ns("orphanConcepts") inside diagnosticsExplorer module
 #' @export
 orpahanConceptsView <- function(id) {

diff --git a/R/components-data-viewer.R b/R/components-data-viewer.R
@@ -11,7 +11,7 @@
 #' @param downloadedFileName string, desired name of downloaded data file. can use the name from the module that is being used
 #'
 #' @return shiny module UI
-#'
+#' @family {Utils}
 resultTableViewer <- function(
     id = "result-table",
     downloadedFileName = NULL
@@ -158,7 +158,7 @@ ohdsiReactableTheme <- reactable::reactableTheme(
 #' @param groupBy The columns to group by 
 #'
 #' @return shiny module server
-#'
+#' @family {Utils}
 resultTableServer <- function(
     id, #string
     df, #data.frame

diff --git a/R/components-largeTableViewer.R b/R/components-largeTableViewer.R
@@ -19,6 +19,7 @@
 #' @field countQuery        count query string (should match query). Can be auto generated with sub query (default) but
 #'                          this will likely result in slow results
 #' @field connectionHandler ResultModelManager connection handler to execute query inside
+#' @family {LargeTables}
 LargeDataTable <- R6::R6Class(
   classname = "LargeDataTable",
   public = list(
@@ -102,6 +103,7 @@ LargeDataTable <- R6::R6Class(
 #' @param baseQuery                 base sql query
 #' @param countQuery                count query string (should match query). Can be auto generated with sub query
 #'                                  (default) but this will likely result in slow results
+#' @family {LargeTables}
 createLargeSqlQueryDt <- function(connectionHandler = NULL,
                                   connectionDetails = NULL,
                                   baseQuery,
@@ -126,6 +128,7 @@ createLargeSqlQueryDt <- function(connectionHandler = NULL,
 #' @param pageSizeChoices    numeric selection options for pages
 #' @param selectedPageSize   numeric selection options for pages
 #' @param fullDownloads     allow download button of full dataset from query
+#' @family {LargeTables}
 largeTableView <- function(id, pageSizeChoices = c(10,25,50,100), selectedPageSize = 10, fullDownloads = TRUE) {
   ns <- shiny::NS(id)
   checkmate::assertNumeric(pageSizeChoices, min.len = 1, finite = TRUE, lower = 1)
@@ -209,6 +212,7 @@ largeTableView <- function(id, pageSizeChoices = c(10,25,50,100), selectedPageSi
 #'
 #' @param columns       List or reactable returning list of reactable::columnDef objects
 #' @param ...           Additional reactable options (searchable, sortable
+#' @family {LargeTables}
 largeTableServer <- function(id,
                              ldt,
                              inputParams,

diff --git a/R/datasources-main.R b/R/datasources-main.R
@@ -23,7 +23,7 @@
 #'
 #' @return The helper html file for the datasources module
 #' @export
-#'
+#' @family {Utils}
 datasourcesHelperFile <- function() {
   fileLoc <-
     system.file('datasources-www', "datasources.html", package = "OhdsiShinyModules")
@@ -38,7 +38,7 @@ datasourcesHelperFile <- function() {
 #'
 #' @return The UI for the datasources module
 #' @export
-#'
+#' @family {Utils}
 datasourcesViewer <- function(id) {
   ns <- shiny::NS(id)
 
@@ -72,7 +72,7 @@ datasourcesViewer <- function(id) {
 #'
 #' @return The server for the datasources module
 #' @export
-#'
+#' @family {Utils}
 datasourcesServer <- function(
   id, 
   connectionHandler, 

diff --git a/R/helpers-componentsCreateCustomColDefList.R b/R/helpers-componentsCreateCustomColDefList.R
@@ -13,7 +13,7 @@
 #'
 #' @return A named list of reactable::colDef objects
 #' @export 
-#' 
+#' @family {Utils}
 createCustomColDefList <- function(rawColNames, niceColNames = NULL,
                                    tooltipText = NULL, case = NULL,
                                    customColDefOptions = NULL) {
@@ -105,7 +105,7 @@ createCustomColDefList <- function(rawColNames, niceColNames = NULL,
 #'
 #' @return html code to make a button label
 #' @export
-#'
+#' @family {Utils}
 makeButtonLabel <- function(label) {
   as.character(htmltools::tags$div(htmltools::tags$button(paste(label))))
 }
diff --git a/R/phevaluator-main.R b/R/phevaluator-main.R
@@ -25,7 +25,7 @@
 #' @return String location of the phevaluator helper file
 #' 
 #' @export 
-#'
+#' @family {PheValuator}
 phevaluatorHelperFile <- function() {
   fileLoc <-
     system.file('phevaluator-www', "phevaluator.html", package = "OhdsiShinyModules")
@@ -40,7 +40,7 @@ phevaluatorHelperFile <- function() {
 #' @return The user interface to the phevaluator results viewer
 #' 
 #' @export
-#'
+#' @family {PheValuator}
 phevaluatorViewer <- function(id) {
   ns <- shiny::NS(id)
 
@@ -134,8 +134,7 @@ phevaluatorViewer <- function(id) {
 #' @return The phevaluator main module server
 #' 
 #' @export
-#'
-
+#' @family {PheValuator}
 phevaluatorServer <- function(
   id, 
   connectionHandler, 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,7 +1,7 @@
-pandoc: 3.1.12.3
+pandoc: '3.2'
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   AddingShinyModules: AddingShinyModules.html
-last_built: 2024-04-25T21:46Z
+last_built: 2024-07-15T14:49Z
 
diff --git a/extras/OhdsiShinyModules.pdf b/extras/OhdsiShinyModules.pdf
diff --git a/extras/PackageMaintenance.R b/extras/PackageMaintenance.R
@@ -26,7 +26,7 @@ unlink("extras/OhdsiShinyModules.pdf")
 system("R CMD Rd2pdf ./ --output=extras/OhdsiShinyModules.pdf")
 
 rmarkdown::render("vignettes/AddingShinyModules.Rmd",
-                  output_file = "inst/doc/AddingShinyModules.pdf",
+                  output_file = "../inst/doc/AddingShinyModules.pdf",
                   rmarkdown::pdf_document(latex_engine = "pdflatex",
                                           toc = TRUE,
                                           toc_depth = 3,

diff --git a/man/LargeDataTable.Rd b/man/LargeDataTable.Rd
diff --git a/man/cohortDiagnosticsHelperFile.Rd b/man/cohortDiagnosticsHelperFile.Rd
diff --git a/man/cohortDiagnosticsServer.Rd b/man/cohortDiagnosticsServer.Rd
diff --git a/man/createCustomColDefList.Rd b/man/createCustomColDefList.Rd
diff --git a/man/createLargeSqlQueryDt.Rd b/man/createLargeSqlQueryDt.Rd
diff --git a/man/datasourcesHelperFile.Rd b/man/datasourcesHelperFile.Rd
diff --git a/man/datasourcesServer.Rd b/man/datasourcesServer.Rd
diff --git a/man/datasourcesViewer.Rd b/man/datasourcesViewer.Rd
diff --git a/man/largeTableServer.Rd b/man/largeTableServer.Rd
diff --git a/man/largeTableView.Rd b/man/largeTableView.Rd
diff --git a/man/makeButtonLabel.Rd b/man/makeButtonLabel.Rd
diff --git a/man/orpahanConceptsView.Rd b/man/orpahanConceptsView.Rd
diff --git a/man/phevaluatorHelperFile.Rd b/man/phevaluatorHelperFile.Rd
diff --git a/man/phevaluatorServer.Rd b/man/phevaluatorServer.Rd
diff --git a/man/phevaluatorViewer.Rd b/man/phevaluatorViewer.Rd