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Trying to adapt shiny viewer to new ShinyAppBuilder interface
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Admin_mschuemi authored and Admin_mschuemi committed Oct 12, 2023
1 parent 4c3c32e commit b2029cd
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Showing 3 changed files with 58 additions and 9 deletions.
1 change: 1 addition & 0 deletions NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.

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11 changes: 2 additions & 9 deletions R/Viewer.R
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Expand Up @@ -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$dbms,
tablePrefix = 'cm_',
Expand All @@ -220,13 +217,9 @@ launchResultsViewer <- function(connectionDetails, databaseSchema) {
schema = databaseSchema,
databaseTable = 'DATABASE_META_DATA'
)
cohortMethodModule <- ShinyAppBuilder::createDefaultCohortMethodConfig(
resultDatabaseDetails = resultDatabaseDetails,
useKeyring = TRUE
)
cohortMethodModule <- ShinyAppBuilder::createDefaultCohortMethodConfig()
shinyAppConfig <- ShinyAppBuilder::initializeModuleConfig() %>%
ShinyAppBuilder::addModuleConfig(aboutModule) %>%
# addModuleConfig(cohortGeneratorModule) %>%
ShinyAppBuilder::addModuleConfig(cohortMethodModule)
connectionHandler <- ResultModelManager::ConnectionHandler$new(connectionDetails)
ShinyAppBuilder::viewShiny(shinyAppConfig, connectionHandler)
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55 changes: 55 additions & 0 deletions extras/MultiAnalysesVignetteDataFetch.R
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Expand Up @@ -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)

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