diff --git a/.github/workflows/Test_module.yaml b/.github/workflows/Test_module.yaml index 9e8174c..a6b7b3c 100644 --- 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 + \ No newline at end of file diff --git a/.gitignore b/.gitignore index 5b6a065..b634670 100644 --- 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 new file mode 100644 index 0000000..2ade6ad --- /dev/null +++ b/.renvignore @@ -0,0 +1,2 @@ +/extras/ +/tests/ diff --git a/Main.R b/Main.R index 435d4ca..cedc5e7 100644 --- 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 ) - - } @@ -178,24 +184,23 @@ 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$dbms - ) - + ) + PatientLevelPrediction::insertCsvToDatabase( csvFolder = resultsFolder, - conn = conn, + conn = conn, databaseSchemaSettings = databaseSchemaSettings, - modelSaveLocation = file.path(resultsFolder, 'dbmodels'), - csvTableAppend = '' + modelSaveLocation = file.path(resultsFolder, "dbmodels"), + csvTableAppend = "" ) - } createDataModelSchema <- function(jobContext) { @@ -203,13 +208,16 @@ createDataModelSchema <- function(jobContext) { moduleInfo <- ParallelLogger::loadSettingsFromJson("MetaData.json") tablePrefix <- moduleInfo$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 index b3b4b95..8fa5607 100644 --- 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 index f22560a..3295b02 100644 --- 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 index 8d6f69e..09980c6 100644 --- 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 diff --git a/compare_versions b/compare_versions new file mode 100644 index 0000000..54e5fea --- /dev/null +++ b/compare_versions @@ -0,0 +1,27 @@ +#!/usr/bin/perl + +open(R_VERSION, "grep 'Version' DESCRIPTION |"); +$version = ; +close(R_VERSION); + +$version =~ /(\d+)\.(\d+)\.(\d+)/; +$r_major = $1; +$r_minor = $2; +$r_mod = $3; + +open(GIT_VERSION, "git describe --tags |"); +$git = ; +close(GIT_VERSION); + +$git =~ /v(\d+)\.(\d+)\.(\d+)/; +$git_major = $1; +$git_minor = $2; +$git_mod = $3; + +if ($r_major > $git_major || $r_minor > $git_minor || $r_mod > $git_mod) { + $new_version = "v$r_major.$r_minor.$r_mod"; +} else { + $new_version = ""; +} + +print($new_version); diff --git a/deploy.sh b/deploy.sh new file mode 100644 index 0000000..9705725 --- /dev/null +++ b/deploy.sh @@ -0,0 +1,31 @@ +#!/bin/bash +set -o errexit -o nounset +addToDrat(){ + PKG_REPO=$PWD + + ## Build package tar ball + export PKG_TARBALL=$(ls *.tar.gz) + + cd ..; mkdir drat; cd drat + + ## Set up Repo parameters + git init + git config user.name "Martijn Schuemie" + git config user.email "schuemie@ohdsi.org" + git config --global push.default simple + + ## Get drat repo + git remote add upstream "https://$GH_TOKEN@github.com/OHDSI/drat.git" + git fetch upstream 2>err.txt + git checkout gh-pages + + ## Link to local R packages + echo 'R_LIBS=~/Rlib' > .Renviron + + Rscript -e "drat::insertPackage('$PKG_REPO/$PKG_TARBALL', \ + repodir = '.', \ + commit='GitHub Actions release: $PKG_TARBALL run $GITHUB_RUN_ID')" + git push + +} +addToDrat diff --git a/extras/CreateJobContextForTesting.R b/extras/CreateJobContextForTesting.R index 051d29a..62b037b 100644 --- a/extras/CreateJobContextForTesting.R +++ b/extras/CreateJobContextForTesting.R @@ -17,12 +17,14 @@ getSampleCohortDefintionSet <- function() { cohortJsonFileName <- cohortJsonFiles[i] cohortName <- tools::file_path_sans_ext(basename(cohortJsonFileName)) cohortJson <- readChar(cohortJsonFileName, file.info(cohortJsonFileName)$size) - sampleCohorts <- rbind(sampleCohorts, data.frame(cohortId = i, - cohortName = cohortName, - cohortDefinition = cohortJson, - stringsAsFactors = FALSE)) + sampleCohorts <- rbind(sampleCohorts, data.frame( + cohortId = i, + cohortName = cohortName, + cohortDefinition = cohortJson, + stringsAsFactors = FALSE + )) } - sampleCohorts <- apply(sampleCohorts,1,as.list) + sampleCohorts <- apply(sampleCohorts, 1, as.list) return(sampleCohorts) } @@ -34,15 +36,15 @@ createCohortSharedResource <- function(cohortDefinitionSet) { # Module Settings Spec ---------------------------- makeModelDesignSettings <- function(targetId, outcomeId, popSettings, covarSettings) { - invisible( PatientLevelPrediction::createModelDesign( - targetId = targetId, - outcomeId = outcomeId, - restrictPlpDataSettings = PatientLevelPrediction::createRestrictPlpDataSettings(), - populationSettings = popSettings, - covariateSettings = covarSettings, - preprocessSettings = PatientLevelPrediction::createPreprocessSettings(), - modelSettings = PatientLevelPrediction::setLassoLogisticRegression(), - splitSettings = PatientLevelPrediction::createDefaultSplitSetting(), + invisible(PatientLevelPrediction::createModelDesign( + targetId = targetId, + outcomeId = outcomeId, + restrictPlpDataSettings = PatientLevelPrediction::createRestrictPlpDataSettings(), + populationSettings = popSettings, + covariateSettings = covarSettings, + preprocessSettings = PatientLevelPrediction::createPreprocessSettings(), + modelSettings = PatientLevelPrediction::setLassoLogisticRegression(), + splitSettings = PatientLevelPrediction::createDefaultSplitSetting(), runCovariateSummary = T )) } @@ -57,7 +59,7 @@ plpPopulationSettings <- PatientLevelPrediction::createStudyPopulationSettings( plpCovarSettings <- FeatureExtraction::createDefaultCovariateSettings() modelDesignList <- list() -exposureOfInterestIds <- c(1,2) +exposureOfInterestIds <- c(1, 2) outcomeOfInterestIds <- c(3) for (i in 1:length(exposureOfInterestIds)) { for (j in 1:length(outcomeOfInterestIds)) { @@ -82,7 +84,7 @@ analysisSpecifications <- createEmptyAnalysisSpecificiations() %>% addSharedResources(createCohortSharedResource(getSampleCohortDefintionSet())) %>% addModuleSpecifications(plpModuleSpecifications) -executionSettings <- Strategus::createCdmExecutionSettings( +executionSettings <- Strategus::createCdmExecutionSettings( connectionDetailsReference = "dummy", workDatabaseSchema = "main", cdmDatabaseSchema = "main", diff --git a/extras/ModuleMaintenance.R b/extras/ModuleMaintenance.R index bb7414c..aae86d4 100644 --- a/extras/ModuleMaintenance.R +++ b/extras/ModuleMaintenance.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 PatientLevelPredictionModule # @@ -16,8 +16,8 @@ # Format and check code: styler::style_dir() -OhdsiRTools::updateCopyrightYearFolder() -OhdsiRTools::findNonAsciiStringsInFolder() +OhdsiRTools::updateCopyrightYearFolder(path = ".", recursive = F) +OhdsiRTools::updateCopyrightYearFolder(path = "./extras", recursive = F) # Generate settings function moduleInfo <- ParallelLogger::loadSettingsFromJson("MetaData.json") @@ -29,18 +29,150 @@ rCode <- gsub("%module%", moduleInfo$Name, rCode) rCode <- gsub("%version%", moduleInfo$Version, rCode) writeLines(rCode, "SettingsFunctions.R") -# Generate renv lock file and activate renv: -renv::deactivate() -OhdsiRTools::createRenvLockFile( - rootPackage = "PatientLevelPrediction", - includeRootPackage = TRUE, - mode = "description", - additionalRequiredPackages = c( - "DatabaseConnector", - "checkmate", - "CirceR", - "testthat", - "Eunomia" - ) +# Generate renv lock file for default & dev profiles ------------ +# updatedPackages and updatedDevPackages are those packages that either +# 1. Cannot be synced between the HADES-wide lock file and the project lock files +# since they are not in semver format +# 2. Updates to HADES packages +# NOTE: Mandatory Strategus dependencies: +# CohortGenerator +# DatabaseConnector +# keyring +# ParallelLogger +# SqlRender +# are explicitly included in Main.R as library calls to allow renv's init() +# function to find them and include them even if they are not used in the +# module code. + +# NOTE: using pre-release of Strategus for these functions +# renv::install("OHDSI/Strategus@renv_lock_validation") +updatedPackages <- list( + list( + Package = "askpass", + Version = "1.2.0", + Source = "Repository", + Repository = "CRAN" + ), + list( + Package = "Matrix", + Version = "1.6-0", + Source = "Repository", + Repository = "CRAN" + ), + list( + Package = "reticulate", + Version = "1.32.0", + Source = "Repository", + Repository = "CRAN" + ), + list( + Package = "SqlRender", + Version = "1.16.1", + Source = "Repository", + Repository = "CRAN" + ), + list( + Package = "xgboost", + Version = "1.7.5.1", + Source = "Repository", + Repository = "CRAN" + ), + list( + Package = "pool", + Version = "1.0.1", + Source = "Repository", + Repository = "CRAN" + ), + "OHDSI/PatientLevelPrediction@v6.3.6", + "OHDSI/CohortGenerator@v0.8.1", + "OHDSI/FeatureExtraction@v3.3.1", + "OHDSI/ResultModelManager@v0.5.6" +) +updatedDevPackages <- list( + list( + Package = "evaluate", + Version = "0.22", + Source = "Repository", + Repository = "CRAN" + ), + "OHDSI/Eunomia@v1.0.2" +) + +# Deactivates and cleans the project to remove any/all old references +renv::deactivate(clean = TRUE) + +# Initialize the default profile --------- +renv::activate(profile = NULL) +# Use the implicit option so renv crawls the full project. +renv::init(settings = renv::settings$snapshot.type("implicit")) +# Record the explicit package versions mentioned above +renv::record(updatedPackages) +# Force a restore for the default profile +renv::restore(prompt = FALSE) + +# Initialize the dev profile ------------ +renv::activate(profile = "dev") # Creates a new profile called "dev" for development + +# Remove the "tests" directory from the .renvignore +# so the test dependencies are included in the dev lock file +file.copy(".renvignore", ".renvignore-backup", overwrite = TRUE) +ignoreFileContents <- readLines(".renvignore") +ignoreFileContents <- ignoreFileContents[!grepl("/tests/", ignoreFileContents)] +writeLines(ignoreFileContents, ".renvignore") + +# Capture the dependencies +renv::init(profile = "dev") # Init the 'dev' profile renv.lock with the explicit DESCRIPTION references + +# Record the updated packages +renv::record(c(updatedPackages, updatedDevPackages), lockfile = "renv/profiles/dev/renv.lock") + +# Force a restore for the dev profile +renv::restore(prompt = FALSE) + +# Restore the original .renvignore +unlink(".renvignore") +file.rename(".renvignore-backup", ".renvignore") + +# Re-activate the default profile - the dev profile is only used for unit tests +renv::activate(profile = NULL) # Sets the default profile as the default for the project + +# Sync lock files with HADES-wide lock file -------------- +hadesWideLockFileName <- normalizePath("hades-wide.lock") +unlink(hadesWideLockFileName) +utils::download.file( + url = "https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q3/renv.lock", + destfile = hadesWideLockFileName +) + +# Compare HADES-wide lock file to the dev lock file +hwVsProjDevLockFile <- Strategus::compareLockFiles( + filename1 = hadesWideLockFileName, + filename2 = "renv/profiles/dev/renv.lock" +) +hwVsProjDevLockFile[!is.na(hwVsProjDevLockFile$lockfile2Version) & hwVsProjDevLockFile$lockfile1Version != hwVsProjDevLockFile$lockfile2Version, ] + +# Compare project default lock file to the dev lock file +projDevVsProjLockFile <- Strategus::compareLockFiles( + filename1 = "renv/profiles/dev/renv.lock", + filename2 = "renv.lock" ) -renv::init() +projDevVsProjLockFile[!is.na(projDevVsProjLockFile$lockfile2Version) & projDevVsProjLockFile$lockfile1Version != projDevVsProjLockFile$lockfile2Version, ] + +# Given a source of truth lock file, update the target +# lock file. Only replace the version in the target +# lock file if the version is newer. Provide a warning +# for those packages that could not be evaluated by +# version +Strategus::syncLockFile( + sourceOfTruthLockFileName = hadesWideLockFileName, + targetLockFileName = "renv/profiles/dev/renv.lock" +) + +Strategus::syncLockFile( + sourceOfTruthLockFileName = "renv/profiles/dev/renv.lock", + targetLockFileName = "renv.lock" +) + +# NOTE: Use the compare functions above to verify the files are in sync +# and add any dependencies that could not be synced automatically to the +# updatedPackages and updatedDevPackages respectively. diff --git a/extras/SettingsFunctionsStub.R b/extras/SettingsFunctionsStub.R index 530c10f..be130ef 100644 --- a/extras/SettingsFunctionsStub.R +++ b/extras/SettingsFunctionsStub.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 # diff --git a/hades-wide.lock b/hades-wide.lock new file mode 100644 index 0000000..089d5ad --- /dev/null +++ b/hades-wide.lock @@ -0,0 +1,1565 @@ +{ + "R" : { + "Version" : "4.2.3", + "Repositories" : [ + { + "Name" : "CRAN", + "URL" : "https://cloud.r-project.org" + } + ] + }, + "Packages" : { + "cli" : { + "Package" : "cli", + "Version" : "3.6.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "glue" : { + "Package" : "glue", + "Version" : "1.6.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "rlang" : { + "Package" : "rlang", + "Version" : "1.1.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "lifecycle" : { + "Package" : "lifecycle", + "Version" : "1.0.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "fansi" : { + "Package" : "fansi", + "Version" : "1.0.4", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "ps" : { + "Package" : "ps", + "Version" : "1.7.5", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "R6" : { + "Package" : "R6", + "Version" : "2.5.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "utf8" : { + "Package" : "utf8", + "Version" : "1.2.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "vctrs" : { + "Package" : "vctrs", + "Version" : "0.6.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "base64enc" : { + "Package" : "base64enc", + "Version" : "0.1-3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "digest" : { + "Package" : "digest", + "Version" : "0.6.33", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "ellipsis" : { + "Package" : "ellipsis", + "Version" : "0.3.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "fastmap" : { + "Package" : "fastmap", + "Version" : "1.1.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "magrittr" : { + "Package" : "magrittr", + "Version" : "2.0.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "pillar" : { + "Package" : "pillar", + "Version" : "1.9.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "pkgconfig" : 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b/renv/profiles/dev/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/profiles/dev/renv/settings.json b/renv/profiles/dev/renv/settings.json new file mode 100644 index 0000000..ffdbb32 --- /dev/null +++ b/renv/profiles/dev/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/renv/settings.dcf b/renv/settings.dcf deleted file mode 100644 index 169d82f..0000000 --- a/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.cellar: TRUE -vcs.ignore.library: TRUE -vcs.ignore.local: TRUE diff --git a/tests/test-eunomia.R b/tests/test-eunomia.R index deff9fd..c5f8614 100644 --- a/tests/test-eunomia.R +++ b/tests/test-eunomia.R @@ -1,3 +1,6 @@ +# Use this profile when testing +# Sys.setenv(RENV_PROFILE = "dev") +# renv::restore(prompt = FALSE) library(testthat) library(Eunomia) connectionDetails <- getEunomiaConnectionDetails() @@ -17,7 +20,7 @@ jobContext$moduleExecutionSettings$resultsDatabaseSchema <- jobContext$moduleExe test_that("Test createDataModelSchema", { source("Main.R") createDataModelSchema(jobContext) - + # Verify that the table(s) are created connection <- DatabaseConnector::connect( connectionDetails = jobContext$moduleExecutionSettings$resultsConnectionDetails