updates

.github/workflows/R-CMD-check.yaml

@@ -18,11 +18,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-13,   r: 'release'}
+          - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'release'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.0.10
-Date: 2024-11-22 12:14:07 UTC
-SHA: 79e20aa7cada9614032930f494936f1431d04efd
+Version: 1.1.1
+Date: 2025-02-06 10:46:22 UTC
+SHA: 074c44dfb7ece3f7d4a4373c2b17a6b6be288367

DESCRIPTION

@@ -90,6 +90,7 @@ Collate:
     'obscureCounts.R'
     'runBenchmark.R'
     'shiny.R'
+    'shinyApp.R'
     'summariseChecks.R'
     'utils-pipe.R'
     'utils.R'

NEWS.md

@@ -1,5 +1,10 @@
 # DrugExposureDiagnostics (development version)
 
+# DrugExposureDiagnostics 1.1.1
+* Update shiny app: fix NA in boxplots and add dropdown drugs-missing
+* CDMConnector v2 changes
+* Add shiny modules
+
 # DrugExposureDiagnostics 1.1.0
 * Add params to executeChecks so it will write results to disk, no need to separately call writeResultToDisk
 

R/metaDataPanel.R

@@ -69,8 +69,8 @@ metaDataPanel <- R6::R6Class(
           data <- getData()
           if (!is.null(data) && nrow(data) > 0) {
             shinyWidgets::downloadBttn(shiny::NS(private$.namespace, "downloadButton"),
-                                       size = "xs",
-                                       label = "Download"
+              size = "xs",
+              label = "Download"
             )
           }
         })

R/shinyApp.R

@@ -0,0 +1,291 @@
+# Copyright 2024 DARWIN EU®
+#
+# This file is part of DrugExposureDiagnostics
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+#' @title ShinyApp
+#'
+#' @description
+#' R6 ShinyApp class.
+#'
+#' @noRd
+ShinyApp <- R6::R6Class(
+  classname = "ShinyApp",
+  inherit = ShinyModule,
+  public = list(
+
+    #' @description
+    #' Initializer method
+    #'
+    #' @param resultList (`list`) List containing the output of the checks
+    #' @param database_id (`character`)
+    #'
+    #' @return (`invisible(self)`)
+    initialize = function(resultList, database_id) {
+      super$initialize()
+      private$.resultList <- resultList
+      private$.database_id <- database_id
+      lapply(names(private$.resultList), FUN = function(name) {
+        private$.resultList[[name]] <- dplyr::bind_cols(
+          database_id = database_id,
+          private$.resultList[[name]]
+        )
+      })
+      if (nrow(private$.resultList$conceptSummary) > 0) {
+        ingredientConceptsColumnsToHide <- c(
+          "concept_code", "valid_start_date", "valid_end_date",
+          "invalid_reason", "amount_value", "amount_unit_concept_id", "numerator_value",
+          "numerator_unit_concept_id", "numerator_unit", "denominator_value",
+          "denominator_unit_concept_id", "denominator_unit", "box_size", "amount_unit"
+        )
+        ingredientConceptColumnsSelected <- colnames(private$.resultList$conceptSummary)
+        ingredientConceptColumnsSelected <- setdiff(ingredientConceptColumnsSelected, ingredientConceptsColumnsToHide)
+        private$.ingredientConceptsTab <- dataPlotPanel$new(
+          data = private$.resultList$conceptSummary,
+          id = "ingredientConcepts",
+          title = "Ingredient concepts",
+          description = "Ingredient concepts",
+          plotPercentage = FALSE,
+          byConcept = FALSE,
+          downloadFilename = "IngredientConcepts.csv",
+          selectedColumns = ingredientConceptColumnsSelected
+        )
+        private$.ingredientConceptsTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$drugRoutesOverall) > 0) {
+        private$.drugRoutesTab <- dataPlotPanel$new(
+          data = private$.resultList$drugRoutesOverall,
+          dataByConcept = private$.resultList$drugRoutesByConcept,
+          id = "drugRoutes",
+          title = "Drug routes",
+          description = "Drug routes",
+          plotPercentage = FALSE,
+          byConcept = TRUE,
+          downloadFilename = "DrugRoutes.csv"
+        )
+        private$.drugRoutesTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$drugTypesOverall) > 0) {
+        private$.drugTypesTab <- dataPlotPanel$new(
+          data = private$.resultList$drugTypesOverall,
+          dataByConcept = private$.resultList$drugTypesByConcept,
+          id = "drugTypes",
+          title = "Drug types",
+          description = "Drug types",
+          plotPercentage = FALSE,
+          byConcept = TRUE,
+          downloadFilename = "DrugTypes.csv"
+        )
+        private$.drugTypesTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$drugSourceConceptsOverall) > 0) {
+        private$.drugSourceConceptsTab <- dataPlotPanel$new(
+          data = private$.resultList$drugSourceConceptsOverall,
+          id = "drugSourceConcepts",
+          title = "Drug source concepts",
+          description = "Drug source concepts",
+          plotPercentage = FALSE,
+          byConcept = FALSE,
+          downloadFilename = "DrugSourceConcepts.csv"
+        )
+        private$.drugSourceConceptsTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$drugExposureDurationOverall) > 0) {
+        private$.drugExposureDurationTab <- dataPlotPanel$new(
+          data = private$.resultList$drugExposureDurationOverall,
+          dataByConcept = private$.resultList$drugExposureDurationByConcept,
+          id = "drugExposureDuration",
+          title = "Drug exposure duration",
+          description = "Drug exposure duration",
+          plotPercentage = FALSE,
+          byConcept = TRUE,
+          downloadFilename = "DrugExposureDuration.csv"
+        )
+        private$.drugExposureDurationTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$missingValuesOverall) > 0) {
+        private$.drugVariablesMissingTab <- dataPlotPanel$new(
+          data = private$.resultList$missingValuesOverall,
+          dataByConcept = private$.resultList$missingValuesByConcept,
+          id = "drugVariablesMissing",
+          title = "Drug variables missing",
+          description = "Drug variables missing",
+          plotPercentage = TRUE,
+          byConcept = TRUE,
+          downloadFilename = "DrugVariablesMissing.csv"
+        )
+        private$.drugVariablesMissingTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$drugDaysSupply) > 0) {
+        private$.drugDaysSupplyTab <- dataPlotPanel$new(
+          data = private$.resultList$drugDaysSupply,
+          dataByConcept = private$.resultList$drugDaysSupplyByConcept,
+          id = "drugDaysSupply",
+          title = "Drug days supply",
+          description = "Drug days supply",
+          plotPercentage = FALSE,
+          byConcept = TRUE,
+          downloadFilename = "DrugDaysSupply.csv"
+        )
+        private$.drugDaysSupplyTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$drugQuantity) > 0) {
+        private$.drugQuantityTab <- dataPlotPanel$new(
+          data = private$.resultList$drugQuantity,
+          dataByConcept = private$.resultList$drugQuantityByConcept,
+          id = "drugQuantity",
+          title = "Drug quantity",
+          description = "Drug quantity",
+          plotPercentage = FALSE,
+          byConcept = TRUE,
+          downloadFilename = "DrugQuantity.csv"
+        )
+        private$.drugQuantityTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$drugSig) > 0) {
+        private$.drugSigTab <- dataPlotPanel$new(
+          data = private$.resultList$drugSig,
+          dataByConcept = private$.resultList$drugSigByConcept,
+          id = "drugSig",
+          title = "Drug sig",
+          description = "Drug sig",
+          plotPercentage = FALSE,
+          byConcept = TRUE,
+          downloadFilename = "DrugSig.csv"
+        )
+        private$.drugSigTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$drugVerbatimEndDate) > 0) {
+        private$.drugVerbatimEndDateTab <- dataPlotPanel$new(
+          data = private$.resultList$drugVerbatimEndDate,
+          dataByConcept = private$.resultList$drugVerbatimEndDateByConcept,
+          id = "drugVerbatimEndDate",
+          title = "Drug verbatim end date",
+          description = "Drug verbatim end date",
+          plotPercentage = FALSE,
+          byConcept = TRUE,
+          downloadFilename = "DrugVerbatimEndDate.csv"
+        )
+        private$.drugVerbatimEndDateTab$parentNamespace <- self$namespace
+      }
+      if (nrow(private$.resultList$drugDose) > 0) {
+        private$.drugDailyDoseTab <- dataPlotPanel$new(
+          data = private$.resultList$drugDose,
+          id = "drugDailyDose",
+          title = "Drug daily dose",
+          description = "Drug daily dose",
+          plotPercentage = FALSE,
+          byConcept = FALSE,
+          downloadFilename = "DrugDailyDose.csv"
+        )
+        private$.drugDailyDoseTab$parentNamespace <- self$namespace
+      }
+      # metadata
+      if (nrow(private$.resultList$metadata) > 0) {
+        private$.metaDataTab <- metaDataPanel$new(
+          data = private$.resultList$metadata,
+          id = "metaData",
+          title = "Metadata",
+          description = "Metadata",
+          downloadFilename = "metaData.csv"
+        )
+        private$.metaDataTab$parentNamespace <- self$namespace
+      }
+      return(invisible(self))
+    }
+  ),
+
+  ## Private ----
+  private = list(
+    ### Fields ----
+    .resultList = NULL,
+    .database_id = NULL,
+    .ingredientConceptsTab = NULL,
+    .drugRoutesTab = NULL,
+    .drugTypesTab = NULL,
+    .drugSourceConceptsTab = NULL,
+    .drugExposureDurationTab = NULL,
+    .drugVariablesMissingTab = NULL,
+    .drugDaysSupplyTab = NULL,
+    .drugQuantityTab = NULL,
+    .drugSigTab = NULL,
+    .drugVerbatimEndDateTab = NULL,
+    .drugDailyDoseTab = NULL,
+    .metaDataTab = NULL,
+
+    ### Methods ----
+    .UI = function() {
+      allTabsList <- list(widths = c(2, 10))
+      if (!is.null(private$.ingredientConceptsTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.ingredientConceptsTab$uiBody()
+      }
+      if (!is.null(private$.drugRoutesTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugRoutesTab$uiBody()
+      }
+      if (!is.null(private$.drugTypesTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugTypesTab$uiBody()
+      }
+      if (!is.null(private$.drugSourceConceptsTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugSourceConceptsTab$uiBody()
+      }
+      if (!is.null(private$.drugExposureDurationTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugExposureDurationTab$uiBody()
+      }
+      if (!is.null(private$.drugVariablesMissingTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugVariablesMissingTab$uiBody()
+      }
+      if (!is.null(private$.drugDaysSupplyTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugDaysSupplyTab$uiBody()
+      }
+      if (!is.null(private$.drugQuantityTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugQuantityTab$uiBody()
+      }
+      if (!is.null(private$.drugSigTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugSigTab$uiBody()
+      }
+      if (!is.null(private$.drugVerbatimEndDateTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugVerbatimEndDateTab$uiBody()
+      }
+      if (!is.null(private$.drugDailyDoseTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.drugDailyDoseTab$uiBody()
+      }
+      if (!is.null(private$.metaDataTab)) {
+        allTabsList[[length(allTabsList) + 1]] <- private$.metaDataTab$uiBody()
+      }
+      shiny::fluidPage(
+        theme = bslib::bs_theme(version = "5", bootswatch = "spacelab"),
+        shinyjs::useShinyjs(),
+        shiny::titlePanel(
+          title = shiny::h2("Drug Exposure Diagnostics Dashboard", align = "center"),
+          windowTitle = "Drug Exposure Diagnostics Dashboard"
+        ),
+        do.call(navlistPanel, allTabsList)
+      )
+    },
+    .server = function(input, output, session) {
+      private$.ingredientConceptsTab$server(input, output, session)
+      private$.drugRoutesTab$server(input, output, session)
+      private$.drugTypesTab$server(input, output, session)
+      private$.drugSourceConceptsTab$server(input, output, session)
+      private$.drugExposureDurationTab$server(input, output, session)
+      private$.drugVariablesMissingTab$server(input, output, session)
+      private$.drugDaysSupplyTab$server(input, output, session)
+      private$.drugQuantityTab$server(input, output, session)
+      private$.drugSigTab$server(input, output, session)
+      private$.drugVerbatimEndDateTab$server(input, output, session)
+      private$.drugDailyDoseTab$server(input, output, session)
+      private$.metaDataTab$server(input, output, session)
+    }
+  )
+)