From 4a3505a864651146b16c4c4951499a5418016771 Mon Sep 17 00:00:00 2001
From: Anthony Sena <anthonysena@users.noreply.github.com>
Date: Mon, 16 Sep 2024 16:34:28 -0400
Subject: [PATCH] Add PLP RDMS to results (#166)

* Add RDMS to PLP results

* Update GHA dependencies
---
 .github/workflows/R_CMD_check_Hades.yaml |  4 ++--
 R/Module-PatientLevelPrediction.R        | 22 +++++++++++++++++++++-
 2 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml
index 5887ede7..f5cf2832 100644
--- a/.github/workflows/R_CMD_check_Hades.yaml
+++ b/.github/workflows/R_CMD_check_Hades.yaml
@@ -85,7 +85,7 @@ jobs:
 
       - name: Upload source package
         if: success() && runner.os == 'Windows' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: package_tarball
           path: check/*.tar.gz
@@ -156,7 +156,7 @@ jobs:
       #
       # - name: Download package tarball
       #   if: ${{ env.new_version != '' }}
-      #   uses: actions/download-artifact@v2
+      #   uses: actions/download-artifact@v4
       #   with:
       #     name: package_tarball
       #
diff --git a/R/Module-PatientLevelPrediction.R b/R/Module-PatientLevelPrediction.R
index cfeefcef..7c63443f 100644
--- a/R/Module-PatientLevelPrediction.R
+++ b/R/Module-PatientLevelPrediction.R
@@ -34,7 +34,7 @@ PatientLevelPredictionModule <- R6::R6Class(
         cohortDatabaseSchema = jobContext$moduleExecutionSettings$workDatabaseSchema,
         cdmDatabaseName = jobContext$moduleExecutionSettings$connectionDetailsReference,
         cdmDatabaseId = jobContext$moduleExecutionSettings$cdmDatabaseMetaData$databaseId,
-        # tempEmulationSchema =  , is there s temp schema specified anywhere?
+        tempEmulationSchema = jobContext$moduleExecutionSettings$tempEmulationSchema,
         cohortTable = jobContext$moduleExecutionSettings$cohortTableNames$cohortTable,
         outcomeDatabaseSchema = jobContext$moduleExecutionSettings$workDatabaseSchema,
         outcomeTable = jobContext$moduleExecutionSettings$cohortTableNames$cohortTable
@@ -73,6 +73,13 @@ PatientLevelPredictionModule <- R6::R6Class(
         fileAppend = NULL
       )
 
+      resultsDataModel <- private$.getResultsDataModelSpecification()
+      CohortGenerator::writeCsv(
+        x = resultsDataModel,
+        file = file.path(resultsFolder, "resultsDataModelSpecification.csv"),
+        warnOnFileNameCaseMismatch = F
+      )
+
       private$.message(paste("Results available at:", resultsFolder))
     },
     #' @description Create the results data model for the module
@@ -166,6 +173,19 @@ PatientLevelPredictionModule <- R6::R6Class(
       }
 
       return(modelDesignList)
+    },
+    .getResultsDataModelSpecification = function() {
+      rdms <- CohortGenerator::readCsv(
+        file = private$.getResultsDataModelSpecificationFileLocation()
+      )
+      rdms$tableName <-paste0(self$tablePrefix, rdms$tableName)
+      return(rdms)
+    },
+    .getResultsDataModelSpecificationFileLocation = function() {
+      return(system.file(
+        file.path("settings", "resultsDataModelSpecification.csv"),
+        package = "PatientLevelPrediction"
+      ))
     }
   )
 )