fixed db warnings and other minor annoyances

OHDSI · Oct 5, 2023 · d17ba1e · d17ba1e
1 parent d898d56
commit d17ba1e
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Showing 6 changed files with 7 additions and 27 deletions.
diff --git a/R/cohort-diagnostics-cohort-overlap.R b/R/cohort-diagnostics-cohort-overlap.R
@@ -211,18 +211,17 @@ cohortOverlapView <- function(id) {
               id = ns("overlapPlotContainer"),
               plotly::plotlyOutput(ns("overlapPlot"), width = "100%", height = "300px")
             )
-          )
-        ),
-
-          # complicated way of setting plot height based on number of rows and selection type
+          ),
+           # complicated way of setting plot height based on number of rows and selection type
           # Note that this code is only used because renderUI/ uiOutput didn't seem to update with plotly
           shiny::tags$script(sprintf("
         Shiny.addCustomMessageHandler('%s', function(height) {
           let plotSpace = document.getElementById('%s');
           plotSpace.querySelector('.svg-container').style.height = height;
           plotSpace.querySelector('.js-plotly-plot').style.height = height;
         });
-      ", ns("overlapPlotHeight"), ns("overlapPlotContainer"))),
+      ", ns("overlapPlotHeight"), ns("overlapPlotContainer")))
+        ),
         shiny::tabPanel(
           title = "Table",
           shiny::fluidRow(

diff --git a/R/cohort-diagnostics-main-ui.R b/R/cohort-diagnostics-main-ui.R
@@ -182,7 +182,7 @@ cohortDiagnosticsView <- function(id = "DiagnosticsExplorer") {
         )
       )
     ),
-    shiny::fluidPage(
+    shiny::tagList(
       shiny::conditionalPanel(
         ns = ns,
         condition = "input.tabs == 'cohortDefinitions'",

diff --git a/R/cohort-diagnostics-main.R b/R/cohort-diagnostics-main.R
@@ -273,24 +273,8 @@ createCdDatabaseDataSource <- function(
   return(dataSource)
 }
 
-# SO much of the app requires this table in memory - it would be much better to re-write queries to not need it!
 getDatabaseTable <- function(dataSource) {
-
-  # hot fix
-  if(tolower(paste0(dataSource$databaseTablePrefix, dataSource$databaseTable)) == 'database_meta_data'){
-    databaseTable <- dataSource$connectionHandler$queryDb(
-      "SELECT *, cdm_source_abbreviation as database_name FROM @schema.@table_name",
-      schema = dataSource$schema,
-      table_name = paste0(dataSource$databaseTablePrefix, dataSource$databaseTable)
-    ) # end hot fix
-  } else{
-  databaseTable <- loadResultsTable(
-    dataSource = dataSource, 
-    tableName = paste0(dataSource$databaseTablePrefix, dataSource$databaseTable), 
-    required = TRUE
-    )
-  }
-
+  databaseTable <- loadResultsTable(dataSource, dataSource$databaseTable, required = TRUE)
   if (nrow(databaseTable) > 0 &
     "vocabularyVersion" %in% colnames(databaseTable)) {
     databaseTable <- databaseTable %>%

diff --git a/tests/resources/cdDatabase/databaseFile.sqlite b/tests/resources/cdDatabase/databaseFile.sqlite
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -133,10 +133,6 @@ resultDatabaseSettingsCohortDiag <- list(
   dbms = 'sqlite',
   cdTablePrefix = '',
   schema = "main",
-  cgTablePrefix = '',
-  cgTable = "cohort",
-  databaseTablePrefix = '',
-  databaseTable = "database",
   vocabularyDatabaseSchema = "main"
 )
 

diff --git a/tests/testthat/test-cohort-diagnostics-main.R b/tests/testthat/test-cohort-diagnostics-main.R
@@ -6,6 +6,7 @@ shiny::testServer(cohortDiagnosticsServer, args = list(
   resultDatabaseSettings = resultDatabaseSettingsCohortDiag,
   dataSource = dataSourceCd
 ), {
+
   ## input tests will go here
   session$setInputs(
     tabs = "cohortCounts",