standardizing sccs

- standardizing sccs
OHDSI · Aug 4, 2023 · 00842e1 · 00842e1
1 parent c82addd
commit 00842e1
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Showing 10 changed files with 825 additions and 761 deletions.
diff --git a/R/helpers-sccsDataPulls.R b/R/helpers-sccsDataPulls.R
@@ -130,76 +130,7 @@ sccsGetAnalyses <- function(
   return(result2)
 }
 
-getSccsResults <- function(connectionHandler,
-                           resultDatabaseSettings,
-                           exposureIds,
-                           outcomeIds,
-                           databaseIds,
-                           analysisIds) {
-  sql <- "
-  SELECT
-  sr.*,
-  ds.cdm_source_abbreviation as database_name,
-  sds.mdrr,
-  sds.ease,
-  sds.time_trend_p,
-  sds.pre_exposure_p,
-  sds.mdrr_diagnostic,
-  sds.ease_diagnostic,
-  sds.time_trend_diagnostic,
-  sds.pre_exposure_diagnostic,
-  sds.unblind,
-  sc.covariate_name,
-  sc.era_id,
-  sc.covariate_analysis_id,
-  a.description,
-  eos.outcome_id
-  FROM @schema.@sccs_table_prefixresult sr
-  INNER JOIN 
-  @schema.@database_table_prefix@database_table ds 
-  ON sr.database_id = ds.database_id
-  INNER JOIN 
-  @schema.@sccs_table_prefixdiagnostics_summary sds ON (
-    sds.exposures_outcome_set_id = sr.exposures_outcome_set_id AND
-    sds.database_id = sr.database_id AND
-    sds.analysis_id = sr.analysis_id AND
-    sds.covariate_id = sr.covariate_id
-  )
-  INNER JOIN 
-  @schema.@sccs_table_prefixcovariate sc ON (
-    sc.exposures_outcome_set_id = sr.exposures_outcome_set_id AND
-    sc.database_id = sr.database_id AND
-    sc.analysis_id = sr.analysis_id AND
-    sc.covariate_id = sr.covariate_id
-  )
-  INNER JOIN @schema.@sccs_table_prefixexposures_outcome_set eos
-  ON 
-  eos.exposures_outcome_set_id = sr.exposures_outcome_set_id
-  INNER JOIN
-  @schema.@sccs_table_prefixanalysis a
-  on a.analysis_id = sr.analysis_id
-  
-  WHERE sr.analysis_id IN (@analysis_ids)
-  AND sr.database_id IN (@database_ids)
-  AND eos.outcome_id IN (@outcome_ids)
-  AND sc.era_id IN (@exposure_ids)
-  "
 
-  results <- connectionHandler$queryDb(
-    sql,
-    schema = resultDatabaseSettings$schema,
-    database_table_prefix = resultDatabaseSettings$databaseTablePrefix,
-    database_table = resultDatabaseSettings$databaseTable,
-    sccs_table_prefix = resultDatabaseSettings$sccsTablePrefix,
-    database_ids = paste(quoteLiterals(databaseIds), collapse = ','),
-    analysis_ids = analysisIds,
-    outcome_ids = paste(outcomeIds, collapse = ','),
-    exposure_ids = paste(exposureIds, collapse = ','),
-    snakeCaseToCamelCase = TRUE
-  )
-
-  return(results)
-}
 
 getSccsModel <- function(connectionHandler,
                          resultDatabaseSettings,

diff --git a/R/helpers-sccsPlots.R b/R/helpers-sccsPlots.R
@@ -1,9 +1,3 @@
-prettyHr <- function(x) {
-  result <- sprintf("%.2f", x)
-  result[is.na(x) | x > 100] <- "NA"
-  return(result)
-}
-
 convertToStartDate <- function(year, month) {
   return(as.Date(sprintf(
     "%s-%s-%s",

diff --git a/R/sccs-diagnosticsSummary.R b/R/sccs-diagnosticsSummary.R
@@ -20,13 +20,12 @@
 sccsDiagnosticsSummaryViewer <- function(id) {
   ns <- shiny::NS(id)
 
-  shiny::div(
-    inputSelectionViewer(ns("input-selection")),
+  shinydashboard::box(
+    status = 'info', 
+    width = '100%',
+    title = shiny::span('Diagnostic Results'),
+    solidHeader = TRUE,
 
-    shiny::conditionalPanel(
-      condition = 'input.generate != 0',
-      ns = shiny::NS(ns("input-selection")),
-
       shiny::tabsetPanel(
         type = 'pills',
         id = ns('diagnosticsTablePanel'),
@@ -40,107 +39,29 @@ sccsDiagnosticsSummaryViewer <- function(id) {
         )
       )
     )
-  )
 
 }
 
 sccsDiagnosticsSummaryServer <- function(
     id,
     connectionHandler,
-    resultDatabaseSettings
+    resultDatabaseSettings,
+    inputSelected
 ) {
 
   shiny::moduleServer(
     id,
     function(input, output, session) {
 
-      targetIds <- getSccsDiagTargets(
-        connectionHandler = connectionHandler,
-        resultDatabaseSettings = resultDatabaseSettings
-      )
-      outcomeIds <- getSccsDiagOutcomes(
-        connectionHandler = connectionHandler,
-        resultDatabaseSettings = resultDatabaseSettings
-      )
-      analysisIds <- getSccsDiagAnalyses(
-        connectionHandler = connectionHandler,
-        resultDatabaseSettings = resultDatabaseSettings
-      )
 
-      inputSelected <- inputSelectionServer(
-        id = "input-selection", 
-        inputSettingList = list(
-          createInputSetting(
-            rowNumber = 1,                           
-            columnWidth = 6,
-            varName = 'targetIds',
-            uiFunction = 'shinyWidgets::pickerInput',
-            uiInputs = list(
-              label = 'Target: ',
-              choices = targetIds,
-              selected = targetIds[1],
-              multiple = T,
-              options = shinyWidgets::pickerOptions(
-                actionsBox = TRUE,
-                liveSearch = TRUE,
-                size = 10,
-                liveSearchStyle = "contains",
-                liveSearchPlaceholder = "Type here to search",
-                virtualScroll = 50
-              )
-            )
-          ),
-          createInputSetting(
-            rowNumber = 1,                           
-            columnWidth = 6,
-            varName = 'outcomeIds',
-            uiFunction = 'shinyWidgets::pickerInput',
-            uiInputs = list(
-              label = 'Outcome: ',
-              choices = outcomeIds,
-              selected = outcomeIds[1],
-              multiple = T,
-              options = shinyWidgets::pickerOptions(
-                actionsBox = TRUE,
-                liveSearch = TRUE,
-                size = 10,
-                liveSearchStyle = "contains",
-                liveSearchPlaceholder = "Type here to search",
-                virtualScroll = 50
-              )
-            )
-          ),
-
-          createInputSetting(
-            rowNumber = 2,                           
-            columnWidth = 12,
-            varName = 'analysisIds',
-            uiFunction = 'shinyWidgets::pickerInput',
-            uiInputs = list(
-              label = 'Analysis: ',
-              choices = analysisIds,
-              selected = analysisIds[1],
-              multiple = T,
-              options = shinyWidgets::pickerOptions(
-                actionsBox = TRUE,
-                liveSearch = TRUE,
-                size = 10,
-                liveSearchStyle = "contains",
-                liveSearchPlaceholder = "Type here to search",
-                virtualScroll = 50
-              )
-            )
-          )
-        )
-      )
-
       data <- shiny::reactive({
+
         getSccsAllDiagnosticsSummary(
           connectionHandler = connectionHandler,
           resultDatabaseSettings = resultDatabaseSettings,
-          targetIds = inputSelected()$targetIds,
-          outcomeIds = inputSelected()$outcomeIds,
-          analysisIds = inputSelected()$analysisIds
+          targetIds = inputSelected()$exposure,
+          outcomeIds = inputSelected()$outcome,
+          analysisIds = inputSelected()$analysis
         )
       })
 
@@ -370,6 +291,11 @@ getSccsAllDiagnosticsSummary <- function(
     outcomeIds,
     analysisIds = NULL
 ) {
+
+  if(is.null(targetIds)){
+    return(NULL)
+  }
+
   sql <- "
   SELECT 
   d.cdm_source_abbreviation as database_name,