OHDSI Home | Forums | Wiki | Github

Where do I get the OHDSI Analysis Viewer?

Implementers
#1

I’m running dbDiagnostics based on the documentation here:
https://ohdsi.github.io/DbDiagnostics/index.html

In the SOS dbDiagnostics video there is mention of an OHDSI Analysis Viewer (at about 00:30:30).
https://www.youtube.com/watch?v=pmn0yUSXYgc

Google gives me links to the on line version (https://data.ohdsi.org/OhdsiPredictionTutorial/) but I’m not sure where to get a version I can use against my data, how do I do this?

#2

I believe that this is referring to the software tool named Atlas. It’s available on Github at https://github.com/OHDSI/Atlas

#3

No, it’s not Atlas. There are specific Shiny App viewers that are used to review results of a study. But I am not sure where they are hosted.

1 Like
#4

Hi @greshje.gmail I use the OHDSI Shiny Modules to view the DbDiagnostics results. It requires that your results are hosted in a database somewhere (I use sqlite). Here is my example code:

### INSTRUCTIONS - Install the dependencies, set the output folder where your results sit and then run the script without any other modifications 

remotes::install_github("OHDSI/ResultModelManager")
remotes::install_github("OHDSI/OhdsiShinyModules", ref = "develop")
remotes::install_github("OHDSI/ShinyAppBuilder")
install.packages("RSQLite")

library(magrittr)
library(ShinyAppBuilder)
library(ResultModelManager)
library(OhdsiShinyModules)

#### Create sqlite database

setwd("")
sqlLiteLocation <- ""

dd_summary <- read.csv("data_diagnostics_summary.csv")
dd_results <- read.csv("data_diagnostics_output.csv")

dataDiagnosticsResults <- RSQLite::dbConnect(RSQLite::SQLite(), "test-dd-db-example.sqlite")
RSQLite::dbWriteTable(dataDiagnosticsResults, "data_diagnostics_summary", dd_summary, overwrite = T)
RSQLite::dbWriteTable(dataDiagnosticsResults, "data_diagnostics_output", dd_results, overwrite = T)
RSQLite::dbListTables(dataDiagnosticsResults)

createDefaultDataDashboardConfig <- function(
		resultDatabaseDetails,
		useKeyring = T
){
	result <- createModuleConfig(
		moduleId = 'dataDiag',
		tabName = "DataDiagnostics",
		shinyModulePackage = 'OhdsiShinyModules',
		moduleUiFunction = "dataDiagnosticViewer",
		moduleServerFunction = "dataDiagnosticServer",
		moduleDatabaseConnectionKeyService = NULL,
		moduleDatabaseConnectionKeyUsername = NULL,
		moduleInfoBoxFile = "dataDiagnosticHelperFile()",
		moduleIcon = "stethoscope",
		resultDatabaseDetails = resultDatabaseDetails,
		useKeyring = useKeyring
	)

	return(result)
}

config <- initializeModuleConfig() %>%
	addModuleConfig(
		createDefaultAboutConfig(
			resultDatabaseDetails = list(),
			useKeyring = T
		)
	)  %>%
	addModuleConfig(
		createModuleConfig(
			moduleId = 'dataDiag',
			tabName = "DataDiagnostics",
			shinyModulePackage = 'OhdsiShinyModules',
			moduleUiFunction = "dataDiagnosticViewer",
			moduleServerFunction = "dataDiagnosticServer",
			moduleDatabaseConnectionKeyService = 'resultDatabaseDetails',
			moduleDatabaseConnectionKeyUsername = NULL,
			moduleInfoBoxFile = "dataDiagnosticHelperFile()",
			moduleIcon = "stethoscope",
			resultDatabaseDetails = list(
				dbms = 'sqlite',
				tablePrefix = '',
				schema = 'main',
				vocabularyDatabaseSchema = 'main'
			),
			useKeyring = T
		)
	)

connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sqlite",
																																server = paste0(sqlLiteLocation,"/test-dd-db-example.sqlite"))

connection <- ResultModelManager::ConnectionHandler$new(connectionDetails)
ShinyAppBuilder::viewShiny(config = config, connection = connection)
1 Like
t