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Merge pull request #305 from OHDSI/hotfix-2.1.5-develop-merge
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Hotfix 2.1.5 develop merge
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azimov authored Jul 15, 2024
2 parents 1f90210 + a594c22 commit 05da629
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Showing 31 changed files with 153 additions and 23 deletions.
2 changes: 1 addition & 1 deletion R/cohort-diagnostics-main-ui.R
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Expand Up @@ -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())
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2 changes: 2 additions & 0 deletions R/cohort-diagnostics-main.R
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Expand Up @@ -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,
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2 changes: 1 addition & 1 deletion R/cohort-diagnostics-orphanConcepts.R
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Expand Up @@ -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) {
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4 changes: 2 additions & 2 deletions R/components-data-viewer.R
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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4 changes: 4 additions & 0 deletions R/components-largeTableViewer.R
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Expand Up @@ -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(
Expand Down Expand Up @@ -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,
Expand All @@ -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)
Expand Down Expand Up @@ -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,
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6 changes: 3 additions & 3 deletions R/datasources-main.R
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Expand Up @@ -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")
Expand All @@ -38,7 +38,7 @@ datasourcesHelperFile <- function() {
#'
#' @return The UI for the datasources module
#' @export
#'
#' @family {Utils}
datasourcesViewer <- function(id) {
ns <- shiny::NS(id)

Expand Down Expand Up @@ -72,7 +72,7 @@ datasourcesViewer <- function(id) {
#'
#' @return The server for the datasources module
#' @export
#'
#' @family {Utils}
datasourcesServer <- function(
id,
connectionHandler,
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4 changes: 2 additions & 2 deletions R/helpers-componentsCreateCustomColDefList.R
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Expand Up @@ -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) {
Expand Down Expand Up @@ -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))))
}
7 changes: 3 additions & 4 deletions R/phevaluator-main.R
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Expand Up @@ -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")
Expand All @@ -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)

Expand Down Expand Up @@ -134,8 +134,7 @@ phevaluatorViewer <- function(id) {
#' @return The phevaluator main module server
#'
#' @export
#'

#' @family {PheValuator}
phevaluatorServer <- function(
id,
connectionHandler,
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2 changes: 1 addition & 1 deletion docs/404.html

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6 changes: 3 additions & 3 deletions docs/authors.html

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2 changes: 1 addition & 1 deletion docs/index.html

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4 changes: 2 additions & 2 deletions docs/pkgdown.yml
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@@ -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

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2 changes: 1 addition & 1 deletion extras/PackageMaintenance.R
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Expand Up @@ -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,
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5 changes: 3 additions & 2 deletions man/LargeDataTable.Rd

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6 changes: 6 additions & 0 deletions man/cohortDiagnosticsHelperFile.Rd

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6 changes: 6 additions & 0 deletions man/cohortDiagnosticsServer.Rd

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10 changes: 10 additions & 0 deletions man/createCustomColDefList.Rd

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6 changes: 6 additions & 0 deletions man/createLargeSqlQueryDt.Rd

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10 changes: 10 additions & 0 deletions man/datasourcesHelperFile.Rd

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10 changes: 10 additions & 0 deletions man/datasourcesServer.Rd

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10 changes: 10 additions & 0 deletions man/datasourcesViewer.Rd

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6 changes: 6 additions & 0 deletions man/largeTableServer.Rd

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6 changes: 6 additions & 0 deletions man/largeTableView.Rd

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10 changes: 10 additions & 0 deletions man/makeButtonLabel.Rd

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6 changes: 6 additions & 0 deletions man/orpahanConceptsView.Rd

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6 changes: 6 additions & 0 deletions man/phevaluatorHelperFile.Rd

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6 changes: 6 additions & 0 deletions man/phevaluatorServer.Rd

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6 changes: 6 additions & 0 deletions man/phevaluatorViewer.Rd

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