Release v0.2.0

OHDSI · Sep 6, 2023 · 177268a · 177268a
2 parents 866a293 + db0ba7e
commit 177268a
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diff --git a/.github/workflows/Test_module.yaml b/.github/workflows/Test_module.yaml
@@ -18,9 +18,12 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release', rspm: "https://cloud.r-project.org"}
-          - {os: macOS-latest, r: 'release', rspm: "https://cloud.r-project.org"}
-          #- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
+          - {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
+          - {os: ubuntu-20.04, r: '4.2.3', rtools: '42', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
+          - {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
+          - {os: ubuntu-20.04, r: 'release', rtools: '', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
@@ -43,20 +46,22 @@ jobs:
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-
+          rtools-version: ${{ matrix.config.rtools }}
+
       - name: Install system requirements
         if: runner.os == 'Linux'
         run: |
           sudo apt-get install -y make
           sudo apt-get install -y default-jdk
           sudo apt-get install -y libcurl4-openssl-dev
           sudo apt-get install -y libssl-dev
-
+          sudo apt-get install -y libglpk-dev
+          
       - uses: r-lib/actions/setup-renv@v2
         with:
           cache-version: 4

diff --git a/Main.R b/Main.R
@@ -169,3 +169,47 @@ execute <- function(jobContext) {
 
 
 }
+
+
+uploadResultsCallback <- function(jobContext) {
+  connectionDetails <- jobContext$moduleExecutionSettings$resultsConnectionDetails
+  moduleInfo <- ParallelLogger::loadSettingsFromJson("MetaData.json")
+  tablePrefix <- moduleInfo$TablePrefix
+  schema <- jobContext$moduleExecutionSettings$resultsDatabaseSchema
+
+  resultsFolder <- jobContext$moduleExecutionSettings$resultsSubFolder
+
+  conn <- DatabaseConnector::connect(connectionDetails)
+  on.exit(DatabaseConnector::disconnect(conn))
+
+  databaseSchemaSettings <- PatientLevelPrediction::createDatabaseSchemaSettings(
+    resultSchema = schema, 
+    tablePrefix = tablePrefix, 
+    targetDialect = connectionDetails$dbms
+    )
+
+  PatientLevelPrediction::insertCsvToDatabase(
+    csvFolder = resultsFolder,
+    conn = conn, 
+    databaseSchemaSettings = databaseSchemaSettings,
+    modelSaveLocation = file.path(resultsFolder, 'dbmodels'),
+    csvTableAppend = ''
+  )
+
+}
+
+createDataModelSchema <- function(jobContext) {
+  connectionDetails <- jobContext$moduleExecutionSettings$resultsConnectionDetails
+  moduleInfo <- ParallelLogger::loadSettingsFromJson("MetaData.json")
+  tablePrefix <- moduleInfo$TablePrefix
+  schema <- jobContext$moduleExecutionSettings$resultsDatabaseSchema
+
+  PatientLevelPrediction::createPlpResultTables(
+    connectionDetails = connectionDetails, 
+    targetDialect = connectionDetails$dbms, 
+    resultSchema = schema, 
+    deleteTables = F,
+    createTables = T, 
+    tablePrefix = tablePrefix
+  )
+}
diff --git a/MetaData.json b/MetaData.json
@@ -1,6 +1,6 @@
 {
   "Name": "PatientLevelPredictionModule",
-  "Version": "0.1.0",
+  "Version": "0.2.0",
   "Dependencies": ["CohortGeneratorModule"],
   "TablePrefix": "plp_"
 }
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+PatientLevelPredictionModule 0.2.0
+=======================
+
+- Updated module to use HADES wide lock file and updated to use renv v1.0.2
+- Added functions and tests for creating the results data model for use by Strategus upload functionality
+- Added additional GitHub Action tests to unit test the module functionality on HADES supported R version (v4.2.3) and the latest release of R
+
 PatientLevelPredictionModule 0.1.0
 =======================
 

diff --git a/SettingsFunctions.R b/SettingsFunctions.R
@@ -18,7 +18,7 @@
 createPatientLevelPredictionModuleSpecifications <- function(modelDesignList) {
   specifications <- list(
     module = "PatientLevelPredictionModule",
-    version = "0.1.0",
+    version = "0.2.0",
     remoteRepo = "github.com",
     remoteUsername = "ohdsi",
     settings = modelDesignList