New shiny app

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DataQualityDashboard
 Type: Package
 Title: Execute and View Data Quality Checks on OMOP CDM Database
-Version: 1.3.1
+Version: 1.4.0
 Date: 2020-02-28
 Authors@R: c(
   person("Clair", "Blacketer", , "[email protected]", role = c("aut", "cre")),
@@ -35,5 +35,5 @@ Suggests:
   rmarkdown,
   shiny,
   ggplot2
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Encoding: UTF-8

NAMESPACE

@@ -4,3 +4,4 @@ export(executeDqChecks)
 export(listDqChecks)
 export(viewDqDashboard)
 export(writeJsonResultsToTable)
+export(writeJsonResultsToCsv)

R/view.R

@@ -24,16 +24,51 @@
 #'
 #' @export
 viewDqDashboard <- function(jsonPath, launch.browser=NULL, display.mode=NULL, ...) {
+
+  ensure_installed("shiny")
+
   Sys.setenv(jsonPath = jsonPath)
-  appDir <- system.file("shinyApps", package = "DataQualityDashboard")
-
+  appDir <- system.file("ResultsV2", package = "DataQualityDashboard")
+  
   if(is.null(display.mode)){
-      display.mode="normal"
+    display.mode="normal"
   }
-
+  
   if(is.null(launch.browser)){
-      launch.browser=TRUE
+    launch.browser=TRUE
   }
-
+  
   shiny::runApp(appDir = appDir, launch.browser = launch.browser, display.mode = display.mode, ...)
 }
+
+
+# Borrowed from devtools:
+# https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L44
+is_installed <- function(pkg, version = 0) {
+  installed_version <-
+    tryCatch(
+      utils::packageVersion(pkg),
+      error = function(e)
+        NA
+    )
+  ! is.na(installed_version) && installed_version >= version
+}
+
+# Borrowed and adapted from devtools:
+# https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L74
+ensure_installed <- function(pkg) {
+  if (!is_installed(pkg)) {
+    msg <-
+      paste0(sQuote(pkg), " must be installed for this functionality.")
+    if (interactive()) {
+      message(msg, "\nWould you like to install it?")
+      if (menu(c("Yes", "No")) == 1) {
+        install.packages(pkg)
+      } else {
+        stop(msg, call. = FALSE)
+      }
+    } else {
+      stop(msg, call. = FALSE)
+    }
+  }
+}

README.md

@@ -9,7 +9,7 @@ The goal of the Data Quality Dashboard (DQD) project is to design and develop an
 Introduction
 ============
 
-This package will run a series of data quality checks against an OMOP CDM instance (currently supports v5.3.1 and v5.2.2). It systematically runs the checks, evaluates the checks against some pre-specified threshold, and then communicates what was done in a transparent and easily understandable way. 
+This package will run a series of data quality checks against an OMOP CDM instance (currently supports v5.4, v5.3.1 and v5.2.2). It systematically runs the checks, evaluates the checks against some pre-specified threshold, and then communicates what was done in a transparent and easily understandable way. 
 
 Overview
 ========
@@ -33,7 +33,7 @@ Version 1 of the tool includes 20 different check types organized into Kahn cont
 After systematically applying the 20 check types to an OMOP CDM version approximately 3,351 individual data quality checks are resolved, run against the database, and evaluated based on a pre-specified threshold. The R package then creates a json object that is read into an RShiny application to view the results.
 
 
-<img src="https://github.com/OHDSI/DataQualityDashboard/raw/master/extras/dqDashboardScreenshot.png"/>
+<img src="https://github.com/OHDSI/DataQualityDashboard/raw/main/extras/dqDashboardScreenshot.png"/>
 
 
 Features
@@ -42,6 +42,24 @@ Features
 - Analyzes data in the OMOP Common Data Model format for all data checks
 - Produces a set of data check results with supplemental investigation assets.
 
+Data Requirements
+=================
+
+Prior to execution the DataQualityDashboard package requires that the CDM_SOURCE table is properly populated.  The following table is a guide to the expected contents of the CDM_SOURCE table.
+
+cdmFieldName | userGuidance | etlConventions
+-- | -- | --
+cdm_source_name | The name of the CDM instance. | Descriptive name for the source   data.
+cdm_source_abbreviation | The abbreviation of the CDM   instance. | The abbreviation should   consistent for different release from the same source.
+cdm_holder | The holder of the CDM instance. | The institution that controls   access to the data.  If possible   include contact information for who to contact to request access to the data.
+source_description | The description of the CDM   instance. | Add notes, caveats, special   characteristics about the source data that would not be assumed from the   general descriptive name.  This   description intended to help analysists determine if the data is suitable for   the problem they are studying.
+source_documentation_reference | Reference to where one can find   documentation about the source data. | Can include URL's, file name,   source data experts contact information (if they agree to it)
+cdm_etl_reference | Reference to where one can find   documentation about the source to ETL into OMOP CDM. | Assuming there is a document or   files (such as Rabbit in the Hat) describing the ETL.  May be the location of the ETL source and   documentation repository.
+source_release_date | The release date of the source   data. | When the source data was made   available for ETL'ing.  For sites doing   incremental updates, the date the last increment made available.  This implies that for sites doing incremental   updates the CDM Source table should be updated to reflect that changes were   made to the CDM.
+cdm_release_date | The release date of the CDM   instance. | When the source data was made   available for general use.  For sites   doing incremental updates, this implies that the CDM Source table should be   updated to reflect that changes were made to the CDM.
+cdm_version | Identifies the CDM version | Enter the numeric portion of the   version, e.g. 5.4
+cdm_version_concept_id | The Concept Id representing the   version of the CDM. | SELECT concept_id WHERE domain =   Metadata and vocabulary_id = CDM and concept_code like %[numeric portion of   the version]%
+vocabulary_version | The vocabulary version used in   the ETL | Obtained by SELECT   vocabulary_version FROM vocabulary WHERE vocabulary_id = 'None'
 
 Technology
 ==========
@@ -63,7 +81,7 @@ DataQualityDashboard is licensed under Apache License 2.0
 
 ### Development status
 
-V1.0 ready for use. 
+V1.4 ready for use. 
 
 # Acknowledgements
 

_pkgdown.yml

@@ -6,6 +6,8 @@ home:
   links:
   - text: Ask a question
     href: http://forums.ohdsi.org
+  - text: DQD Example Output
+    href: https://data.ohdsi.org/DataQualityDashboardMDCD/
 
 navbar:
   structure: