From b2029cd7c83075a4a5565b07bd49493efc8f914e Mon Sep 17 00:00:00 2001
From: Admin_mschuemi <Admin_mschuemi@its.jnj.com>
Date: Thu, 12 Oct 2023 05:26:34 -0400
Subject: [PATCH] Trying to adapt shiny viewer to new ShinyAppBuilder interface

---
 NEWS.md                                 |  1 +
 R/Viewer.R                              | 11 +----
 extras/MultiAnalysesVignetteDataFetch.R | 55 +++++++++++++++++++++++++
 3 files changed, 58 insertions(+), 9 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index deafa169..f5eba7ef 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -15,6 +15,7 @@ Changes:
 
 6. The results schema specifications of the `exportToCsv()` function has changed:
     - Removed the `attrition_fraction` and `attrition_diagnostic` fields from the `cm_diagnostics_summary ` table.
+    - Added the `target_estimator` field to the `cm_result` add `cm_interaction_result` tables.
     - Added the `generalizability_max_sdm` and `generalizabiltiy_diagnostic` fields to the `cm_diagnostics_summary` table.
     - Added the `mean_before`, `mean_after`, `target_std_diff`, `comparator_std_diff`, and `target_comparator_std_diff` fields to both the `cm_covariate_balance` and `cm_shared_covariate_balance` tables.
     
diff --git a/R/Viewer.R b/R/Viewer.R
index 8df13b59..7a170a98 100644
--- a/R/Viewer.R
+++ b/R/Viewer.R
@@ -208,10 +208,7 @@ launchResultsViewer <- function(connectionDetails, databaseSchema) {
 
   ensureInstalled("ShinyAppBuilder")
   ensureInstalled("markdown")
-  aboutModule <- ShinyAppBuilder::createDefaultAboutConfig(
-    resultDatabaseDetails = NULL,
-    useKeyring = TRUE
-  )
+  aboutModule <- ShinyAppBuilder::createDefaultAboutConfig()
   resultDatabaseDetails <- list(
     dbms = connectionDetails$dbms,
     tablePrefix = 'cm_',
@@ -220,13 +217,9 @@ launchResultsViewer <- function(connectionDetails, databaseSchema) {
     schema = databaseSchema,
     databaseTable = 'DATABASE_META_DATA'
   )
-  cohortMethodModule <- ShinyAppBuilder::createDefaultCohortMethodConfig(
-    resultDatabaseDetails = resultDatabaseDetails,
-    useKeyring = TRUE
-  )
+  cohortMethodModule <- ShinyAppBuilder::createDefaultCohortMethodConfig()
   shinyAppConfig <- ShinyAppBuilder::initializeModuleConfig() %>%
     ShinyAppBuilder::addModuleConfig(aboutModule) %>%
-    # addModuleConfig(cohortGeneratorModule) %>%
     ShinyAppBuilder::addModuleConfig(cohortMethodModule)
   connectionHandler <- ResultModelManager::ConnectionHandler$new(connectionDetails)
   ShinyAppBuilder::viewShiny(shinyAppConfig, connectionHandler)
diff --git a/extras/MultiAnalysesVignetteDataFetch.R b/extras/MultiAnalysesVignetteDataFetch.R
index 238c4d20..145015af 100644
--- a/extras/MultiAnalysesVignetteDataFetch.R
+++ b/extras/MultiAnalysesVignetteDataFetch.R
@@ -311,3 +311,58 @@ insertExportedResultsInSqlite(sqliteFileName = file.path(folder, "export", "resu
                               exportFolder = file.path(folder, "export"),
                               cohorts = cohorts)
 launchResultsViewerUsingSqlite(sqliteFileName = file.path(folder, "export", "results.sqlite"))
+
+# Upload results to SQLite using RMM -------------------------------------------
+databaseFile <-  file.path(folder, "export", "CohortMethodResults.sqlite")
+connectionDetails <- DatabaseConnector::createConnectionDetails(
+  dbms = "sqlite",
+  server = databaseFile
+)
+createResultsDataModel(
+  connectionDetails = connectionDetails,
+  databaseSchema = "main",
+  tablePrefix = ""
+)
+uploadResults(
+  connectionDetails = connectionDetails,
+  schema = "main",
+  zipFileName = file.path(folder, "export", "Results_MDCD.zip"),
+  purgeSiteDataBeforeUploading = FALSE
+)
+# Add cohort and database tables:
+connection <- DatabaseConnector::connect(connectionDetails)
+cohorts <- data.frame(
+  cohortId = c(
+    1118084,
+    1124300,
+    192671),
+  cohortName = c(
+    "Celecoxib",
+    "Diclofenac",
+    "GI Bleed"
+  )
+)
+DatabaseConnector::insertTable(
+  connection = connection,
+  databaseSchema = "main",
+  tableName = "cg_cohort_definition",
+  data = cohorts,
+  dropTableIfExists = TRUE,
+  createTable = TRUE,
+  camelCaseToSnakeCase = TRUE
+)
+databases <- tibble(
+  database_id = "MDCR",
+  cdm_source_name = "Merative Marketscan MDCR",
+  cdm_source_abbreviation = "MDCR"
+)
+DatabaseConnector::insertTable(
+  connection = connection,
+  databaseSchema = "main",
+  tableName = "databases",
+  data = databases,
+  dropTableIfExists = TRUE,
+  createTable = TRUE
+)
+DatabaseConnector::disconnect(connection)
+