Release v0.3.0

OHDSI · Jan 26, 2024 · 67cef19 · 67cef19
2 parents 92c64c2 + c95d0c1
commit 67cef19
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diff --git a/.github/workflows/Test_module.yaml b/.github/workflows/Test_module.yaml
@@ -12,7 +12,7 @@ jobs:
   Test-module:
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    name: unit-test-${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
@@ -22,7 +22,7 @@ jobs:
           - {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: 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:
@@ -64,7 +64,48 @@ jobs:
           
       - uses: r-lib/actions/setup-renv@v2
         with:
+          profile: '"dev"'
           cache-version: 4
 
       - name: Run module test script
         run: Rscript tests/testScript.R
+
+  Test-default-module-restore:
+    needs: Test-module
+
+    name: module-restore-${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {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"}
+
+    runs-on: ${{ matrix.config.os }}
+
+    steps:
+      - 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/.gitignore b/.gitignore
@@ -1,4 +1,43 @@
-.Rproj.user
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
+
+# User-specific files
 .Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# Project specific
+/extras/test/output
+/_targets/
diff --git a/.renvignore b/.renvignore
@@ -0,0 +1,2 @@
+/extras/
+/tests/
diff --git a/Main.R b/Main.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortGeneratorModule
 #
@@ -14,6 +14,16 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+# Adding library references that are required for Strategus
+library(CohortGenerator)
+library(DatabaseConnector)
+library(keyring)
+library(ParallelLogger)
+library(SqlRender)
+
+# Adding RSQLite so that we can test modules with Eunomia
+library(RSQLite)
+
 # Module methods -------------------------
 getModuleInfo <- function() {
   checkmate::assert_file_exists("MetaData.json")
@@ -36,8 +46,10 @@ createCohortDefinitionSetFromJobContext <- function(sharedResources, settings) {
   if (length(sharedResources) <= 0) {
     stop("No shared resources found")
   }
-  cohortDefinitionSharedResource <- getSharedResourceByClassName(sharedResources = sharedResources, 
-                                                                 class = "CohortDefinitionSharedResources")
+  cohortDefinitionSharedResource <- getSharedResourceByClassName(
+    sharedResources = sharedResources,
+    class = "CohortDefinitionSharedResources"
+  )
   if (is.null(cohortDefinitionSharedResource)) {
     stop("Cohort definition shared resource not found!")
   }
@@ -59,43 +71,39 @@ createCohortDefinitionSetFromJobContext <- function(sharedResources, settings) {
 }
 
 setCovariateSchemaTable <- function(
-    modelDesignList, 
+    modelDesignList,
     cohortDatabaseSchema,
-    cohortTable
-    ){
-
-  if(inherits(modelDesignList, 'modelDesign')){
+    cohortTable) {
+  if (inherits(modelDesignList, "modelDesign")) {
     modelDesignList <- list(modelDesignList)
   }
-  
-  for(i in 1:length(modelDesignList)){
+
+  for (i in 1:length(modelDesignList)) {
     covariateSettings <- modelDesignList[[i]]$covariateSettings
-    
-    if(inherits(covariateSettings, 'covariateSettings')){
+
+    if (inherits(covariateSettings, "covariateSettings")) {
       covariateSettings <- list(covariateSettings)
     }
-
-    for(j in 1:length(covariateSettings)){
-
-      if('cohortDatabaseSchema' %in% names(covariateSettings[[j]])){
+
+    for (j in 1:length(covariateSettings)) {
+      if ("cohortDatabaseSchema" %in% names(covariateSettings[[j]])) {
         covariateSettings[[j]]$cohortDatabaseSchema <- cohortDatabaseSchema
       }
-      if('cohortTable' %in% names(covariateSettings[[j]])){
+      if ("cohortTable" %in% names(covariateSettings[[j]])) {
         covariateSettings[[j]]$cohortTable <- cohortTable
       }
-
     }
-    
+
     modelDesignList[[i]]$covariateSettings <- covariateSettings
   }
-  
+
   return(modelDesignList)
 }
 
 # Module methods -------------------------
 execute <- function(jobContext) {
   rlang::inform("Validating inputs")
-  inherits(jobContext, 'list')
+  inherits(jobContext, "list")
 
   if (is.null(jobContext$settings)) {
     stop("Analysis settings not found in job context")
@@ -106,68 +114,66 @@ execute <- function(jobContext) {
   if (is.null(jobContext$moduleExecutionSettings)) {
     stop("Execution settings not found in job context")
   }
-  
+
   workFolder <- jobContext$moduleExecutionSettings$workSubFolder
   resultsFolder <- jobContext$moduleExecutionSettings$resultsSubFolder
-  
+
   rlang::inform("Executing PLP")
   moduleInfo <- getModuleInfo()
-  
+
   # Creating database details
   databaseDetails <- PatientLevelPrediction::createDatabaseDetails(
-    connectionDetails = jobContext$moduleExecutionSettings$connectionDetails, 
+    connectionDetails = jobContext$moduleExecutionSettings$connectionDetails,
     cdmDatabaseSchema = jobContext$moduleExecutionSettings$cdmDatabaseSchema,
     cohortDatabaseSchema = jobContext$moduleExecutionSettings$workDatabaseSchema,
     cdmDatabaseName = jobContext$moduleExecutionSettings$connectionDetailsReference,
     cdmDatabaseId = jobContext$moduleExecutionSettings$databaseId,
-    #tempEmulationSchema =  , is there s temp schema specified anywhere?
-    cohortTable = jobContext$moduleExecutionSettings$cohortTableNames$cohortTable, 
-    outcomeDatabaseSchema = jobContext$moduleExecutionSettings$workDatabaseSchema, 
+    # tempEmulationSchema =  , is there s temp schema specified anywhere?
+    cohortTable = jobContext$moduleExecutionSettings$cohortTableNames$cohortTable,
+    outcomeDatabaseSchema = jobContext$moduleExecutionSettings$workDatabaseSchema,
     outcomeTable = jobContext$moduleExecutionSettings$cohortTableNames$cohortTable
   )
-  
+
   # find where cohortDefinitions are as sharedResources is a list
   cohortDefinitionSet <- createCohortDefinitionSetFromJobContext(
     sharedResources = jobContext$sharedResources,
     settings = jobContext$settings
-    )
-  
-  # set the covariate settings schema and tables 
+  )
+
+  # set the covariate settings schema and tables
   jobContext$settings <- setCovariateSchemaTable(
-    modelDesignList = jobContext$settings, 
+    modelDesignList = jobContext$settings,
     cohortDatabaseSchema = jobContext$moduleExecutionSettings$workDatabaseSchema,
     cohortTable = jobContext$moduleExecutionSettings$cohortTableNames$cohortTable
-    )
-  
+  )
+
   # run the models
   PatientLevelPrediction::runMultiplePlp(
-    databaseDetails = databaseDetails, 
-    modelDesignList = jobContext$settings, 
+    databaseDetails = databaseDetails,
+    modelDesignList = jobContext$settings,
     cohortDefinitions = cohortDefinitionSet,
     saveDirectory = workFolder
-      )
-  
+  )
+
   # Export the results
   rlang::inform("Export data to csv files")
 
   sqliteConnectionDetails <- DatabaseConnector::createConnectionDetails(
-    dbms = 'sqlite',
-    server = file.path(workFolder, "sqlite","databaseFile.sqlite")
+    dbms = "sqlite",
+    server = file.path(workFolder, "sqlite", "databaseFile.sqlite")
   )
-    
+
   PatientLevelPrediction::extractDatabaseToCsv(
-    connectionDetails = sqliteConnectionDetails, 
+    connectionDetails = sqliteConnectionDetails,
     databaseSchemaSettings = PatientLevelPrediction::createDatabaseSchemaSettings(
-      resultSchema = 'main', # sqlite settings
-      tablePrefix = '', # sqlite settings
-      targetDialect = 'sqlite', 
+      resultSchema = "main", # sqlite settings
+      tablePrefix = "", # sqlite settings
+      targetDialect = "sqlite",
       tempEmulationSchema = NULL
-    ), 
+    ),
     csvFolder = file.path(resultsFolder),
     fileAppend = NULL
   )
-
-
 }
 
 
@@ -178,38 +184,40 @@ uploadResultsCallback <- function(jobContext) {
   schema <- jobContext$moduleExecutionSettings$resultsDatabaseSchema
 
   resultsFolder <- jobContext$moduleExecutionSettings$resultsSubFolder
-  
+
   conn <- DatabaseConnector::connect(connectionDetails)
   on.exit(DatabaseConnector::disconnect(conn))
-  
+
   databaseSchemaSettings <- PatientLevelPrediction::createDatabaseSchemaSettings(
-    resultSchema = schema, 
-    tablePrefix = tablePrefix, 
+    resultSchema = schema,
+    tablePrefix = tablePrefix,
     targetDialect = connectionDetails$dbms
-    )
-  
+  )
+
   PatientLevelPrediction::insertCsvToDatabase(
     csvFolder = resultsFolder,
-    conn = conn, 
+    conn = conn,
     databaseSchemaSettings = databaseSchemaSettings,
-    modelSaveLocation = file.path(resultsFolder, 'dbmodels'),
-    csvTableAppend = ''
+    modelSaveLocation = file.path(resultsFolder, "dbmodels"),
+    csvTableAppend = ""
   )
-
 }
 
 createDataModelSchema <- function(jobContext) {
   connectionDetails <- jobContext$moduleExecutionSettings$resultsConnectionDetails
   moduleInfo <- ParallelLogger::loadSettingsFromJson("MetaData.json")
   tablePrefix <- moduleInfo$TablePrefix
   schema <- jobContext$moduleExecutionSettings$resultsDatabaseSchema
-
+
+  # Workaround for issue https://github.com/tidyverse/vroom/issues/519:
+  readr::local_edition(1)
+
   PatientLevelPrediction::createPlpResultTables(
-    connectionDetails = connectionDetails, 
-    targetDialect = connectionDetails$dbms, 
-    resultSchema = schema, 
+    connectionDetails = connectionDetails,
+    targetDialect = connectionDetails$dbms,
+    resultSchema = schema,
     deleteTables = F,
-    createTables = T, 
+    createTables = T,
     tablePrefix = tablePrefix
   )
 }
diff --git a/MetaData.json b/MetaData.json
@@ -1,6 +1,6 @@
 {
   "Name": "PatientLevelPredictionModule",
-  "Version": "0.2.1",
+  "Version": "0.3.0",
   "Dependencies": ["CohortGeneratorModule"],
   "TablePrefix": "plp_"
 }
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+PatientLevelPredictionModule 0.3.0
+=======================
+- Using renv project profiles to manage core packages required for module execution vs. those that are needed for development purposes.
+
 PatientLevelPredictionModule 0.2.1
 =======================
 

diff --git a/SettingsFunctions.R b/SettingsFunctions.R
@@ -1,5 +1,5 @@
 # This file has been autogenerated in 'extras/ModuleMaintenance.R'. Do not change by hand. 
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortGeneratorModule
 #
@@ -18,7 +18,7 @@
 createPatientLevelPredictionModuleSpecifications <- function(modelDesignList) {
   specifications <- list(
     module = "PatientLevelPredictionModule",
-    version = "0.2.1",
+    version = "0.3.0",
     remoteRepo = "github.com",
     remoteUsername = "ohdsi",
     settings = modelDesignList