Update docs example script to generate Ares files

docs/docs/ares-docs.md

@@ -86,37 +86,31 @@ existing OMOP CDM database and require
 both [Achilles](https://github.com/ohdsi/achilles)
 and [DataQualityDashboard](https://github.com/ohdsi/dataqualitydashboard).
 
-Here's an example script to generate Ares files based on a sample dataset (replace connectionDetails to generate results
-for your database).
+Here's an example script to generate Ares files (replace connectionDetails with your own)
 
 ```r
-# DatabaseConnector::downloadJdbcDrivers("postgresql","D:/OHDSI/Drivers") - use it to download the JDBC driver
+# DatabaseConnector::downloadJdbcDrivers("postgresql","./") - use it to download the JDBC driver
 options(connectionObserver = NULL)
 
-cdmDatabaseSchema = "main" #indicate the name of the cdm schema you created
-resultsDatabaseSchema = "main" #indicate the name of the results schema you created
-vocabDatabaseSchema = "main" #vocab should be located in the cdm schema
-numThreads = 1 #i only managed to get till the end in single-threaded mode, had problems utilizing 2 or more
+cdmDatabaseSchema = "cdm"
+resultsDatabaseSchema = "results" # used to store Achilles output
+vocabDatabaseSchema = "cdm" #usually located within the cdm schema
+numThreads = 1
 cdmSourceName = 'synthea'
-cdmVersion = "5.4" #do not change
+cdmVersion = "5.4"
 
-aresDataDirectory = "./data" #output directory
-sourceFolders = "./data" #source files folder for indexers.
+aresDataDirectory = "./data" #Achilles output directory
 
-connectionDetails <- Eunomia::getEunomiaConnectionDetails() #Provides a sample dataset
-
-sourceReleaseKey = AresIndexer::getSourceReleaseKey(connectionDetails, cdmDatabaseSchema)
-
-
-# Example connection details 
-#connectionDetails <- DatabaseConnector::createConnectionDetails(
-#  dbms     = dbms, #your database management system
-#  server   = server, #server address
-#  user     = user,
-#  password = password,
-#  pathToDriver = pathToDriver #location of the JDBC driver
-#)
+#connectionDetails <- Eunomia::getEunomiaConnectionDetails() #Provides a sample dataset
 
+connectionDetails <- DatabaseConnector::createConnectionDetails(
+  dbms     = "postgresql",
+  server   = "localhost/synthea",
+  user     = "postgres",
+  password = "12345",
+  port     = 5432,
+  pathToDriver = "./" #indicate path to your chosen dbms JDBC driver
+) #Used to connect to your existing CDM
 
 # Run Achilles
 Achilles::achilles(
@@ -125,23 +119,25 @@ Achilles::achilles(
   resultsDatabaseSchema= resultsDatabaseSchema,
   vocabDatabaseSchema = vocabDatabaseSchema,
   numThreads = 1,
-  cdmVersion = "5.4.0",
+  cdmVersion = cdmVersion,
   createIndices = F,
   createTable = T,
   smallCellCount = 0,
 )
-# Export statistics generated by Achilles
+
+# Export Achilles results to Ares supported format
 Achilles::exportToAres(
   connectionDetails = connectionDetails,
   cdmDatabaseSchema = cdmDatabaseSchema,
   resultsDatabaseSchema = resultsDatabaseSchema,
   vocabDatabaseSchema = vocabDatabaseSchema,
-  outputPath = sourceFolders,
+  outputPath = aresDataDirectory,
 )
 
-datasourceReleaseOutputFolder <- file.path(aresDataDirectory, releaseKey)
+sourceReleaseKey = AresIndexer::getSourceReleaseKey(connectionDetails, cdmDatabaseSchema)
+datasourceReleaseOutputFolder <- file.path(aresDataDirectory, sourceReleaseKey)
 
-# Run Data Quality Dashboard
+#Run data quality checks
 DataQualityDashboard::executeDqChecks(
   connectionDetails = connectionDetails,
   cdmDatabaseSchema = cdmDatabaseSchema,
@@ -152,15 +148,35 @@ DataQualityDashboard::executeDqChecks(
   outputFolder = datasourceReleaseOutputFolder,
   outputFile = "dq-result.json",
   verboseMode = T,
-  writeToTable = F
+  writeToTable = F,
+  cdmVersion = cdmVersion
+
+)
+# Run Achilles temporal characterization
+outputFile <- file.path(datasourceReleaseOutputFolder, "temporal-characterization.csv")
+Achilles::performTemporalCharacterization(
+  connectionDetails = connectionDetails,
+  cdmDatabaseSchema = cdmDatabaseSchema,
+  resultsDatabaseSchema = resultsDatabaseSchema,
+  outputFile = outputFile,
 )
 
+# Get a list of sources generated by the exportToAres function
+list <- list.dirs(aresDataDirectory, recursive = FALSE)
 
-list <- list.dirs(sourceFolders, recursive = FALSE)
-AresIndexer::augmentConceptFiles(sourceFolders = list)
+# Augment concept files with data quality details
+AresIndexer::augmentConceptFiles(releaseFolder = file.path(aresDataDirectory, cdmSourceName, sourceReleaseKey))
+# Export index of all sql functions used in data processing
 AresIndexer::buildExportQueryIndex(aresDataDirectory)
+# Compare data quality issues with previous source releases (used to display the issue delta)
+AresIndexer::augmentDataQualityFiles(sourceFolders = list)
+# Create index of quality issues across releases (used to render data quality delta chart)
+AresIndexer::buildSourceDataQualityDelta(sourceFolders = list)
+# Create index of all available sources and releases
 AresIndexer::buildNetworkIndex(list, outputFolder = aresDataDirectory)
+# Create quality index across network
 AresIndexer::buildDataQualityIndex(list, outputFolder = aresDataDirectory)
+# Create index of unmapped source codes across the network
 AresIndexer::buildNetworkUnmappedSourceCodeIndex(list, outputFolder = aresDataDirectory)
 ```