Merge pull request #98 from OHDSI/shiny_no_path

no default path for shiny
OHDSI · Nov 1, 2024 · 2d40429 · 2d40429
2 parents a4d290b + 2c11fa8
commit 2d40429
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Showing 5 changed files with 12 additions and 10 deletions.
diff --git a/R/addCodelistAttribute.R b/R/addCodelistAttribute.R
@@ -65,7 +65,7 @@ addCodelistAttribute <- function(cohort,
     }
 
     cohortCodelist <- dplyr::bind_rows(currentCohortCodelist |>
-      dplyr::filter(!cohort_definition_id %in%
+      dplyr::filter(!.data$cohort_definition_id %in%
                       unique(cohortCodelist$cohort_definition_id)),
                     cohortCodelist)
   }

diff --git a/R/shinyDiagnostics.R b/R/shinyDiagnostics.R
@@ -47,10 +47,10 @@
 #'                                  schema ="main",
 #'                                  overwrite = TRUE)
 #'   my_result_cohort_diag <- cdm$my_cohort |> phenotypeDiagnostics()
-#'   shinyDiagnostics(my_result_cohort_diag)
+#'   shinyDiagnostics(my_result_cohort_diag, here::here())
 #' }
 shinyDiagnostics <- function(result,
-                             directory = here::here()){
+                             directory){
 
   rlang::check_installed("OmopViewer")
 

diff --git a/man/shinyDiagnostics.Rd b/man/shinyDiagnostics.Rd
diff --git a/tests/testthat/test-dbms.R b/tests/testthat/test-dbms.R
@@ -18,7 +18,7 @@ test_that("eunomia", {
                                conceptSet = meds_cs,
                                name = "meds")
   results <- phenotypeDiagnostics(cdm$meds)
-  expect_no_error(shinyDiagnostics(result = results))
+  expect_no_error(shinyDiagnostics(result = results, directory = here::here()))
 })
 
 test_that("postgres test", {
@@ -49,7 +49,7 @@ test_that("postgres test", {
   cdm <- omopgenerics::bind(cdm$asthma, cdm$drugs, name = "my_cohort")
 
   results <- phenotypeDiagnostics(cdm$my_cohort)
-  expect_no_error(shinyDiagnostics(result = results))
+  expect_no_error(shinyDiagnostics(result = results, directory = here::here()))
   expect_no_error(CodelistGenerator::tableCohortCodeUse(results))
   expect_no_error(CodelistGenerator::tableAchillesCodeUse(results))
   expect_no_error(CodelistGenerator::tableOrphanCodes(results))
@@ -60,7 +60,7 @@ test_that("postgres test", {
   expect_no_error(CohortCharacteristics::tableCohortTiming(results))
   expect_no_error(CohortCharacteristics::tableLargeScaleCharacteristics(results))
   # omopViewer::exportStaticApp(results)
-  expect_no_error(shinyDiagnostics(result = results))
+  expect_no_error(shinyDiagnostics(result = results, directory = here::here()))
 
   CDMConnector::cdm_disconnect(cdm = cdm)
 

diff --git a/tests/testthat/test-shinyDiagnostics.R b/tests/testthat/test-shinyDiagnostics.R
@@ -4,7 +4,8 @@ test_that("basic working example with one cohort", {
 
   # empty result - should still work without error
   expect_no_error(
-    shinyDiagnostics(result = omopgenerics::emptySummarisedResult())
+    shinyDiagnostics(result = omopgenerics::emptySummarisedResult(),
+                     directory = here::here())
     )
 
   # with results
@@ -38,7 +39,8 @@ test_that("basic working example with one cohort", {
 
   my_result_cohort_diag <- cdm$my_cohort |> phenotypeDiagnostics()
 
-  expect_no_error(shinyDiagnostics(my_result_cohort_diag))
+  expect_no_error(shinyDiagnostics(my_result_cohort_diag,
+                                   directory = here::here()))
 
 
 })