Merge pull request #303 from OHDSI/hotfix-2.1.5

Hotfix 2.1.5

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OhdsiShinyModules
 Type: Package
 Title: Repository of Shiny Modules for OHDSI Result Viewers
-Version: 2.1.4
+Version: 2.1.5
 Author: Jenna Reps
 Maintainer: Jenna Reps <reps@ohdsi.org>
 Description: Install this package to access useful shiny modules for building shiny apps to explore results using the OHDSI tools .
@@ -54,6 +54,5 @@ Suggests:
     testthat,
     withr
 Remotes:
-    ohdsi/CirceR,
     ohdsi/ResultModelManager
 RoxygenNote: 7.3.1

NEWS.md

@@ -1,3 +1,7 @@
+OhdsiShinyModules v2.1.5
+========================
+Fixed issue in DatabaseConnector check for pooled connections of sqlite databases on cohort diagnotiscs load
+
 OhdsiShinyModules v2.1.4
 ========================
 Fixed missing call to dplyr in CohortDiagnostics load up

R/OhdsiShinyModules.R

@@ -19,9 +19,7 @@
 #' OhdsiShinyModules
 #' 
 #' @description A selection of shiny modules for exploring standardized OHDSI results 
-#'
-#' @docType package
 #' @name OhdsiShinyModules
 #' @importFrom dplyr %>%
 #' @importFrom rlang .data
-NULL
+"_PACKAGE"

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())

R/cohort-diagnostics-main.R

@@ -20,14 +20,16 @@
     tables <- connectionHandler$queryDb(sql, schema = schema) |>
       dplyr::pull("tableName") |>
       tolower()
-    return(tables)
-  }
-
-  return(
-    DatabaseConnector::getTableNames(connectionHandler$getConnection(),
+
+  } else if (connectionHandler$dbms() != "sqlite") {
+    tables <- DatabaseConnector::getTableNames(connectionHandler$getConnection(),
                                      databaseSchema = schema) |>
       tolower()
-  )
+  } else {
+    tables <- DatabaseConnector::getTableNames(connectionHandler$getConnection()) |>
+      tolower()
+  }
+  return(tables)
 }
 
 
@@ -410,6 +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,

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) {

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

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,

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)
 
@@ -80,7 +80,7 @@ datasourcesViewer <- function(id) {
 #'
 #' @return The server for the datasources module
 #' @export
-#'
+#' @family {Utils}
 datasourcesServer <- function(
   id, 
   connectionHandler, 

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) {
@@ -86,7 +86,7 @@ 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))))
 }

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)
 
@@ -141,8 +141,7 @@ phevaluatorViewer <- function(id) {
 #' @return The phevaluator main module server
 #' 
 #' @export
-#'
-
+#' @family {PheValuator}
 phevaluatorServer <- function(
   id, 
   connectionHandler, 

_pkgdown.yml

@@ -110,12 +110,12 @@ reference:
       - cohortMethodServer
       - cohortMethodAttritionViewer
       - cohortMethodAttritionServer
+      - cohortMethodResultSummaryViewer
+      - cohortMethodResultSummaryServer
       - cohortMethodCovariateBalanceViewer
       - cohortMethodCovariateBalanceServer
       - cohortMethodDiagnosticsSummaryViewer
       - cohortMethodDiagnosticsSummaryServer
-      - cohortMethodForestPlotViewer
-      - cohortMethodForestPlotServer
       - cohortMethodKaplanMeierViewer
       - cohortMethodKaplanMeierServer
       - cohortMethodPopulationCharacteristicsViewer
@@ -126,14 +126,14 @@ reference:
       - cohortMethodPropensityModelServer
       - cohortMethodPropensityScoreDistViewer
       - cohortMethodPropensityScoreDistServer
-      - cohortMethodResultsTableViewer
-      - cohortMethodResultsTableServer
-      - cohortMethodSubgroupsViewer
-      - cohortMethodSubgroupsServer
       - cohortMethodSystematicErrorViewer
       - cohortMethodSystematicErrorServer
-      - cohortMethodTitlePanelViewer
-      - cohortMethodTitlePanelServer
+      - evidenceSynthesisHelperFile
+      - evidenceSynthesisServer
+      - evidenceSynthesisViewer
+      - sccsHelperFile
+      - sccsServer
+      - sccsView
   - title: "Data diagnostics module"
     desc: >
       Modules for the DataDiagnostics package.
@@ -149,7 +149,7 @@ reference:
     desc: >
       Modules for the CohortDiagnostics package.
     contents:
-      - cohortDiagnosticsSever 
+      - cohortDiagnosticsServer
       - cohortDiagnosticsView
       - cohortDiagnosticsHelperFile      
       - cohortDiagCharacterizationView
@@ -170,4 +170,15 @@ reference:
       - timeDistributionsView
       - visitContextView
       - inclusionRulesView
-
+  - title: Cohort Diagnostics
+    desc: "Run cohort diagnostics, deploy shiny"
+    contents: has_concept("CohortDiagnostics")
+  - title: "PheValuator module"
+    desc: "PheValuator module"
+    contents: has_concept("PheValuator")
+  - title: Large Table
+    desc: "Utilities for tables that contain large amounts of rows"
+    contents: has_concept("LargeTables")
+  - title: Utils
+    desc: "Shared usable utility functions"
+    contents: has_concept("Utils")