2025 02 17 issue 12 automation gresh

CreateResultsDataModel.R

@@ -1,40 +1,57 @@
-################################################################################
-# INSTRUCTIONS: The code below assumes you have access to a PostgreSQL database
-# and permissions to create tables in an existing schema specified by the
-# resultsDatabaseSchema parameter.
-# 
-# See the Working with results section
-# of the UsingThisTemplate.md for more details.
-# 
-# More information about working with results produced by running Strategus 
-# is found at:
-# https://ohdsi.github.io/Strategus/articles/WorkingWithResults.html
-# ##############################################################################
-
-# Code for creating the result schema and tables in a PostgreSQL database
-resultsDatabaseSchema <- "results"
-analysisSpecifications <- ParallelLogger::loadSettingsFromJson(
-  fileName = "inst/sampleStudy/sampleStudyAnalysisSpecification.json"
-)
-
-resultsDatabaseConnectionDetails <- DatabaseConnector::createConnectionDetails(
-  dbms = "postgresql",
-  server = Sys.getenv("OHDSI_RESULTS_DATABASE_SERVER"),
-  user = Sys.getenv("OHDSI_RESULTS_DATABASE_USER"),
-  password = Sys.getenv("OHDSI_RESULTS_DATABASE_PASSWORD")
-)
-
-# Create results data model -------------------------
-
-# Use the 1st results folder to define the results data model
-resultsFolder <- list.dirs(path = "results", full.names = T, recursive = F)[1]
-resultsDataModelSettings <- Strategus::createResultsDataModelSettings(
-  resultsDatabaseSchema = resultsDatabaseSchema,
-  resultsFolder = file.path(resultsFolder, "strategusOutput")
-)
-
-Strategus::createResultDataModel(
-  analysisSpecifications = analysisSpecifications,
-  resultsDataModelSettings = resultsDataModelSettings,
-  resultsConnectionDetails = resultsDatabaseConnectionDetails
-)
+# Create database objects for results ------------------------------------------
+
+# libraries --------------------------------------------------------------------
+
+source("./_StartHere/03-upload-results/config/01-UploadResultsConfig.R")
+source("./util/database/StrategusDatabaseUtil.R")
+
+# implementation ---------------------------------------------------------------
+
+# create a connection to use to create the schema if it does not exist ----
+bootStrapConnectionDetails <- StrategusDatabaseUtil$getConnectionDetails (
+  dbms = dbms,
+  connectionString = bootStrapConnectionString
+)
+
+# create the database if it does not exist ----
+conn <- DatabaseConnector::connect(bootStrapConnectionDetails)
+StrategusDatabaseUtil$createDatabaseIfItDoesNotExist(dbName, conn)
+DatabaseConnector::disconnect(conn)
+
+# resultsConnectionDetails ----
+resultsConnectionDetails <- StrategusDatabaseUtil$getConnectionDetails (
+  dbms = dbms,
+  connectionString = connectionString
+)
+
+# create the schema if it does not exist ----
+conn <- DatabaseConnector::connect(resultsConnectionDetails)
+StrategusDatabaseUtil$createSchemaIfItDoesNotExist(schemaName, conn)
+DatabaseConnector::disconnect(conn)
+
+# analysisSpecifications ----
+analysisSpecifications <- ParallelLogger::loadSettingsFromJson (
+  fileName = analysisSpecificationFilePath
+)
+
+# resultsDataModelSettings ---- 
+resultsDataModelSettings <- Strategus::createResultsDataModelSettings (
+  resultsDatabaseSchema = schemaName,
+  resultsFolder = resultsPath
+)
+
+# Create results data model -------------------------
+
+# Use the 1st results folder to define the results data model
+resultsFolder <- list.dirs(path = resultsPath, full.names = T, recursive = F)[1]
+resultsDataModelSettings <- Strategus::createResultsDataModelSettings(
+  resultsDatabaseSchema = schemaName,
+  resultsFolder = file.path(resultsFolder, "strategusOutput")
+)
+
+Strategus::createResultDataModel(
+  analysisSpecifications = analysisSpecifications,
+  resultsDataModelSettings = resultsDataModelSettings,
+  resultsConnectionDetails = resultsConnectionDetails
+)
+