Version 212 hotfix (#534)

* Changes to diagnostics explorer when index event/orphan are not run * Package maintenance
OHDSI · Sep 15, 2021 · 6c4415d · 6c4415d
1 parent 0610260
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: CohortDiagnostics
 Type: Package
 Title: Diagnostics for OHDSI Cohorts
-Version: 2.1.1
-Date: 2021-09-01
+Version: 2.1.2
+Date: 2021-09-15
 Authors@R: c(
     person("Gowtham", "Rao", email = "[email protected]", role = c("aut", "cre")),
     person("Martijn", "Schuemie", email = "[email protected]", role = c("aut")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+CohortDiagnostics 2.1.2
+=======================
+
+Bug fixes:
+1. DiagnosticsExplorer fixes a bug of app failure when runIndexEventBreakdown, runOrphanConcepts, includedSourceConcept is set to FALSE
+
+
 CohortDiagnostics 2.1.1
 =======================
 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/CohortDiagnosticsInPackageMode.html b/docs/articles/CohortDiagnosticsInPackageMode.html
diff --git a/docs/articles/CohortDiagnosticsUsingWebApi.html b/docs/articles/CohortDiagnosticsUsingWebApi.html
diff --git a/docs/articles/DatabaseModeInDiagnosticsExplorer.html b/docs/articles/DatabaseModeInDiagnosticsExplorer.html
diff --git a/docs/articles/RunningCohortDiagnostics.html b/docs/articles/RunningCohortDiagnostics.html
diff --git a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html
diff --git a/docs/articles/WhatIsCohortDiagnostics.html b/docs/articles/WhatIsCohortDiagnostics.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -8,5 +8,5 @@ articles:
   RunningCohortDiagnostics: RunningCohortDiagnostics.html
   ViewingResultsUsingDiagnosticsExplorer: ViewingResultsUsingDiagnosticsExplorer.html
   WhatIsCohortDiagnostics: WhatIsCohortDiagnostics.html
-last_built: 2021-09-01T14:23Z
+last_built: 2021-09-15T00:13Z
 
diff --git a/docs/reference/CohortDiagnostics-package.html b/docs/reference/CohortDiagnostics-package.html
diff --git a/docs/reference/checkInputFileEncoding.html b/docs/reference/checkInputFileEncoding.html
diff --git a/docs/reference/createResultsDataModel.html b/docs/reference/createResultsDataModel.html
diff --git a/docs/reference/getCohortCounts.html b/docs/reference/getCohortCounts.html
diff --git a/docs/reference/getResultsDataModelSpecifications.html b/docs/reference/getResultsDataModelSpecifications.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/instantiateCohortSet.html b/docs/reference/instantiateCohortSet.html
diff --git a/docs/reference/launchCohortExplorer.html b/docs/reference/launchCohortExplorer.html
diff --git a/docs/reference/launchDiagnosticsExplorer.html b/docs/reference/launchDiagnosticsExplorer.html
diff --git a/docs/reference/preMergeDiagnosticsFiles.html b/docs/reference/preMergeDiagnosticsFiles.html
diff --git a/docs/reference/runCohortDiagnostics.html b/docs/reference/runCohortDiagnostics.html
diff --git a/docs/reference/uploadResults.html b/docs/reference/uploadResults.html
diff --git a/extras/CohortDiagnostics.pdf b/extras/CohortDiagnostics.pdf
diff --git a/inst/doc/CohortDiagnosticsInPackageMode.pdf b/inst/doc/CohortDiagnosticsInPackageMode.pdf
diff --git a/inst/doc/CohortDiagnosticsUsingWebApi.pdf b/inst/doc/CohortDiagnosticsUsingWebApi.pdf
diff --git a/inst/doc/DatabaseModeInDiagnosticsExplorer.pdf b/inst/doc/DatabaseModeInDiagnosticsExplorer.pdf
diff --git a/inst/doc/RunningCohortDiagnostics.pdf b/inst/doc/RunningCohortDiagnostics.pdf
diff --git a/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf b/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf
diff --git a/inst/doc/WhatIsCohortDiagnostics.pdf b/inst/doc/WhatIsCohortDiagnostics.pdf
diff --git a/inst/shiny/DiagnosticsExplorer/R/Results.R b/inst/shiny/DiagnosticsExplorer/R/Results.R
@@ -237,6 +237,8 @@ getIndexEventBreakdown <- function(dataSource = .GlobalEnv,
                                         .data$vocabularyId,
                                         .data$standardConcept),
                           by = c("conceptId"))
+    } else {
+      return(NULL)
     }
   } else {
     sql <- "SELECT index_event_breakdown.*,
@@ -317,6 +319,9 @@ getIncludedConceptResult <- function(dataSource = .GlobalEnv,
                                      cohortId,
                                      databaseIds) {
   if (is(dataSource, "environment")) {
+    if (!exists("includedSourceConcept")) {
+      return(NULL)
+    }
     data <- get("includedSourceConcept", envir = dataSource) %>% 
       dplyr::filter(.data$cohortId == !!cohortId &
                       .data$databaseId %in% !!databaseIds) %>% 
@@ -371,6 +376,7 @@ getOrphanConceptResult <- function(dataSource = .GlobalEnv,
                                    cohortId,
                                    databaseIds) {
   if (is(dataSource, "environment")) {
+    if (!exists("orphanConcept")) {return(NULL)}
     data <- get("orphanConcept", envir = dataSource) %>% 
       dplyr::filter(.data$cohortId == !!cohortId &
                       .data$databaseId %in% !!databaseIds) %>% 

diff --git a/inst/shiny/DiagnosticsExplorer/server.R b/inst/shiny/DiagnosticsExplorer/server.R
@@ -920,7 +920,11 @@ shiny::shinyServer(function(input, output, session) {
 
     data <- getOrphanConceptResult(dataSource = dataSource,
                                    cohortId = row$cohortId,
-                                   databaseIds = getDatabaseIdInCohortConceptSet()) %>% 
+                                   databaseIds = getDatabaseIdInCohortConceptSet())
+    if (is.null(data)) {
+      return(NULL)
+    }
+    data <- data %>% 
       dplyr::filter(.data$conceptSetName == cohortDefinitionConceptSetExpressionRow()$name)
   })
 
@@ -2293,6 +2297,10 @@ shiny::shinyServer(function(input, output, session) {
         cohortIds = cohortId(),
         databaseIds = databaseIds()
       )
+      if (any(is.null(data),
+              nrow(data) == 0)) {
+        return(NULL)
+      }
       if (!is.null(data)) {
         if (!'domainTable' %in% colnames(data)) {
           data$domainTable <- "Not in data"