Refactor Strategus module approach

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Strategus
 Type: Package
 Title: Coordinating and Executing Analytics Using HADES Modules
-Version: 0.3.0
+Version: 1.0.0
 Date: 2023-06-04
 Authors@R: c(
 	person("Martijn", "Schuemie", email = "[email protected]", role = c("aut")),
@@ -17,36 +17,42 @@ BugReports: https://github.com/OHDSI/Strategus/issues
 Depends:
 	R (>= 4.2.0),
 	CohortGenerator (>= 0.8.0),
-	DatabaseConnector (>= 6.2.3)
+	DatabaseConnector (>= 6.2.3),
+	R6
 Imports:
-  targets,
-  renv (>= 1.0.0),
   ParallelLogger (>= 3.1.0),
   dplyr,
   checkmate,
-  keyring,
   rlang,
   utils,
   R.utils,
   digest,
   methods,
   tibble,
-  ResultModelManager (>= 0.3.0),
-  SqlRender (>= 1.11.0),
-  semver,
-  httr2,
-  jsonlite
+  ResultModelManager (>= 0.5.8),
+  SqlRender (>= 1.18.0)
 Suggests:
-  testthat (>= 3.0.0),
+  Characterization,
+  CohortDiagnostics,
+  CohortIncidence,
+  CohortMethod,
+  Eunomia,
   fs,
   knitr,
+  PatientLevelPrediction,
   rmarkdown,
-  Eunomia,
+  SelfControlledCaseSeries,
+  testthat (>= 3.0.0),
   withr
 Remotes:
-  ohdsi/CohortGenerator,
+  ohdsi/Characterization@372fb70c6133bdd8811f8dc1d2a2f9cb9a184345,
+  ohdsi/CohortDiagnostics,
+  ohdsi/CohortGenerator@develop,
+  ohdsi/CohortIncidence,
+  ohdsi/CohortMethod,
+  ohdsi/PatientLevelPrediction,
   ohdsi/ResultModelManager,
-  ohdsi/Eunomia
+  ohdsi/SelfControlledCaseSeries
 VignetteBuilder: knitr
 NeedsCompilation: no
 RoxygenNote: 7.3.1

NAMESPACE

@@ -1,22 +1,22 @@
 # Generated by roxygen2: do not edit by hand
 
+export(CharacterizationModule)
+export(CohortDiagnosticsModule)
+export(CohortGeneratorModule)
+export(CohortIncidenceModule)
+export(CohortMethodModule)
+export(EvidenceSynthesisModule)
+export(PatientLevelPredictionModule)
+export(SelfControlledCaseSeriesModule)
+export(StrategusModule)
 export(addModuleSpecifications)
 export(addSharedResources)
-export(compareLockFiles)
 export(createCdmExecutionSettings)
 export(createEmptyAnalysisSpecificiations)
 export(createResultDataModels)
 export(createResultsExecutionSettings)
-export(ensureAllModulesInstantiated)
 export(execute)
-export(getModuleList)
-export(installLatestModule)
-export(retrieveConnectionDetails)
-export(storeConnectionDetails)
-export(syncLockFile)
-export(unlockKeyring)
-export(validateLockFile)
-export(verifyModuleInstallation)
+export(uploadResults)
 export(zipResults)
 import(CohortGenerator)
 import(DatabaseConnector)

R/DatabaseMetaData.R

@@ -21,16 +21,12 @@
 # carefully consider serialization and deserialization to JSON, which currently
 # uses custom functionality in ParallelLogger to maintain object attributes.
 
-createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
+createDatabaseMetaData <- function(executionSettings, connectionDetails) {
   databaseMetaDataFolder <- file.path(executionSettings$resultsFolder, "DatabaseMetaData")
   if (!dir.exists(databaseMetaDataFolder)) {
     dir.create(databaseMetaDataFolder, recursive = TRUE)
   }
 
-  connectionDetails <- retrieveConnectionDetails(
-    connectionDetailsReference = executionSettings$connectionDetailsReference,
-    keyringName = keyringName
-  )
   connection <- DatabaseConnector::connect(connectionDetails)
   on.exit(DatabaseConnector::disconnect(connection))
 
@@ -54,7 +50,10 @@ createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
   }
 
   resultsDataModel <- CohortGenerator::readCsv(
-    file = system.file("databaseMetaDataRdms.csv", package = "Strategus"),
+    file = system.file(
+      file.path("csv", "databaseMetaDataRdms.csv"),
+      package = "Strategus"
+    ),
     warnOnCaseMismatch = FALSE
   )
 
@@ -132,3 +131,57 @@ createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
   )
   return(databaseId)
 }
+
+.createDatabaseMetadataTables <- function(resultsConnectionDetails,
+                                          resultsDatabaseSchema,
+                                          resultsFolder) {
+  if (dir.exists(file.path(resultsFolder, "DatabaseMetaData"))) {
+    databaseMetaDataResultsFolder <- file.path(resultsFolder, "DatabaseMetaData")
+    rdmsFile <- file.path(databaseMetaDataResultsFolder, "resultsDataModelSpecification.csv")
+    if (file.exists(rdmsFile)) {
+      rlang::inform("Creating results data model for database metadata")
+      connection <- DatabaseConnector::connect(resultsConnectionDetails)
+      on.exit(DatabaseConnector::disconnect(connection))
+
+      # Create the SQL from the resultsDataModelSpecification.csv
+      sql <- ResultModelManager::generateSqlSchema(
+        csvFilepath = rdmsFile
+      )
+      sql <- SqlRender::render(
+        sql = sql,
+        database_schema = resultsDatabaseSchema
+      )
+      DatabaseConnector::executeSql(connection = connection, sql = sql)
+    } else {
+      warning("DatabaseMetaData not found - skipping table creation")
+    }
+  }
+}
+.uploadDatabaseMetadata <- function(resultsConnectionDetails,
+                                    resultsDatabaseSchema,
+                                    resultsFolder) {
+  if (dir.exists(file.path(resultsFolder, "DatabaseMetaData"))) {
+    databaseMetaDataResultsFolder <- file.path(resultsFolder, "DatabaseMetaData")
+    rdmsFile <- file.path(databaseMetaDataResultsFolder, "resultsDataModelSpecification.csv")
+    if (file.exists(rdmsFile)) {
+      rlang::inform("Uploading database metadata")
+      connection <- DatabaseConnector::connect(resultsConnectionDetails)
+      on.exit(DatabaseConnector::disconnect(connection))
+
+      specification <- CohortGenerator::readCsv(file = rdmsFile)
+      ResultModelManager::uploadResults(
+        connection = connection,
+        schema = resultsDatabaseSchema,
+        resultsFolder = databaseMetaDataResultsFolder,
+        purgeSiteDataBeforeUploading = TRUE,
+        databaseIdentifierFile = file.path(
+          databaseMetaDataResultsFolder,
+          "database_meta_data.csv"
+        ),
+        specifications = specification
+      )
+    } else {
+      warning("DatabaseMetaData not found - skipping upload")
+    }
+  }
+}