From 9870fb8571e553cfc8c581c1981bbd664560a220 Mon Sep 17 00:00:00 2001 From: Anthony Sena Date: Fri, 1 Sep 2023 08:30:17 -0400 Subject: [PATCH] Create results data model tests and renv.lock update (#11) --- Main.R | 5 +- MetaData.json | 2 +- SettingsFunctions.R | 2 +- renv.lock | 2955 +++++++++++++++++++++--------------------- renv/activate.R | 70 +- tests/test-eunomia.R | 18 + 6 files changed, 1546 insertions(+), 1506 deletions(-) diff --git a/Main.R b/Main.R index e9b4875..435d4ca 100644 --- a/Main.R +++ b/Main.R @@ -204,11 +204,8 @@ createDataModelSchema <- function(jobContext) { tablePrefix <- moduleInfo$TablePrefix schema <- jobContext$moduleExecutionSettings$resultsDatabaseSchema - conn <- DatabaseConnector::connect(connectionDetails) - on.exit(DatabaseConnector::disconnect(conn)) - PatientLevelPrediction::createPlpResultTables( - conn = conn, + connectionDetails = connectionDetails, targetDialect = connectionDetails$dbms, resultSchema = schema, deleteTables = F, diff --git a/MetaData.json b/MetaData.json index 21caae1..23c172e 100644 --- a/MetaData.json +++ b/MetaData.json @@ -1,6 +1,6 @@ { "Name": "PatientLevelPredictionModule", - "Version": "0.2.0-1", + "Version": "0.2.0-3", "Dependencies": ["CohortGeneratorModule"], "TablePrefix": "plp_" } diff --git a/SettingsFunctions.R b/SettingsFunctions.R index e62809d..77b482b 100644 --- a/SettingsFunctions.R +++ b/SettingsFunctions.R @@ -18,7 +18,7 @@ createPatientLevelPredictionModuleSpecifications <- function(modelDesignList) { specifications <- list( module = "PatientLevelPredictionModule", - version = "0.2.0-1", + version = "0.2.0-3", remoteRepo = "github.com", remoteUsername = "ohdsi", settings = modelDesignList diff --git a/renv.lock b/renv.lock index ab16903..934c9f7 100644 --- a/renv.lock +++ b/renv.lock @@ -1,1477 +1,1482 @@ { - "R" : { - "Version" : "4.2.3", - "Repositories" : [ - { - "Name" : "CRAN", - "URL" : "https://packagemanager.posit.co/cran/latest" - } - ] - }, - "Packages" : { - "cli" : { - 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"reticulate": { + "Package": "reticulate", + "Version": "1.31", + "Source": "Repository", + "Repository": "CRAN" + }, + "rlang": { + "Package": "rlang", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "rmarkdown": { + "Package": "rmarkdown", + "Version": "2.21", + "Source": "Repository", + "Repository": "CRAN" + }, + "rprojroot": { + "Package": "rprojroot", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "CRAN" + }, + "rstatix": { + "Package": "rstatix", + "Version": "0.7.2", + "Source": "Repository", + "Repository": "CRAN" + }, + "sass": { + "Package": "sass", + "Version": "0.4.5", + "Source": "Repository", + "Repository": "CRAN" + }, + "scales": { + "Package": "scales", + "Version": "1.2.1", + "Source": "Repository", + "Repository": "CRAN" + }, + "shiny": { + "Package": "shiny", + "Version": "1.7.4", + "Source": "Repository", + "Repository": "CRAN" + }, + "shinyWidgets": { + "Package": "shinyWidgets", + "Version": "0.7.6", + "Source": "Repository", + "Repository": "CRAN" + }, + "shinycssloaders": { + "Package": "shinycssloaders", + "Version": "1.0.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "shinydashboard": { + "Package": "shinydashboard", + "Version": "0.7.2", + "Source": "Repository", + "Repository": "CRAN" + }, + "snow": { + "Package": "snow", + "Version": "0.4-4", + "Source": "Repository", + "Repository": "CRAN" + }, + "sodium": { + "Package": "sodium", + "Version": "1.2.1", + "Source": "Repository", + "Repository": "CRAN" + }, + "sourcetools": { + "Package": "sourcetools", + "Version": "0.1.7-1", + "Source": "Repository", + "Repository": "CRAN" + }, + "stringi": { + "Package": "stringi", + "Version": "1.7.12", + "Source": "Repository", + "Repository": "CRAN" + }, + "stringr": { + "Package": "stringr", + "Version": "1.5.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "survMisc": { + "Package": "survMisc", + "Version": "0.5.6", + "Source": "Repository", + "Repository": "CRAN" + }, + "survival": { + "Package": "survival", + "Version": "3.5-3", + "Source": "Repository", + "Repository": "CRAN" + }, + "survminer": { + "Package": "survminer", + "Version": "0.4.9", + "Source": "Repository", + "Repository": "CRAN" + }, + "sys": { + "Package": "sys", + "Version": "3.4.1", + "Source": "Repository", + "Repository": "CRAN" + }, + "testthat": { + "Package": "testthat", + "Version": "3.1.7", + "Source": "Repository", + "Repository": "CRAN" + }, + "tibble": { + "Package": "tibble", + "Version": "3.2.1", + "Source": "Repository", + "Repository": "CRAN" + }, + "tidyr": { + "Package": "tidyr", + "Version": "1.3.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "tidyselect": { + "Package": "tidyselect", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "timechange": { + "Package": "timechange", + "Version": "0.2.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "tinytex": { + "Package": "tinytex", + "Version": "0.44", + "Source": "Repository", + "Repository": "CRAN" + }, + "tippy": { + "Package": "tippy", + "Version": "0.1.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "torch": { + "Package": "torch", + "Version": "0.9.1", + "Source": "Repository", + "Repository": "CRAN" + }, + "torchopt": { + "Package": "torchopt", + "Version": "0.1.3", + "Source": "Repository", + "Repository": "CRAN" + }, + "triebeard": { + "Package": "triebeard", + "Version": "0.4.1", + "Source": "Repository", + "Repository": "CRAN" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.3.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "urltools": { + "Package": "urltools", + "Version": "1.7.3", + "Source": "Repository", + "Repository": "CRAN" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "CRAN" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.1", + "Source": "Repository", + "Repository": "CRAN" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.1", + "Source": "Repository", + "Repository": "CRAN" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.1", + "Source": "Repository", + "Repository": "CRAN" + }, + "waldo": { + "Package": "waldo", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "withr": { + "Package": "withr", + "Version": "2.5.0", + "Source": "Repository", + "Repository": "CRAN" + }, + "xfun": { + "Package": "xfun", + "Version": "0.38", + "Source": "Repository", + "Repository": "CRAN" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.3", + "Source": "Repository", + "Repository": "CRAN" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Repository": "CRAN" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.7", + "Source": "Repository", + "Repository": "CRAN" + }, + "zip": { + "Package": "zip", + "Version": "2.2.2", + "Source": "Repository", + "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-11", + "Source": "Repository", + "Repository": "CRAN" + } + } } diff --git a/renv/activate.R b/renv/activate.R index 03f9289..2969c73 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,12 +2,27 @@ local({ # the requested version of renv - version <- "1.0.0" + version <- "1.0.2" attr(version, "sha") <- NULL # the project directory project <- getwd() + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + # figure out whether the autoloader is enabled enabled <- local({ @@ -504,7 +519,7 @@ local({ # open the bundle for reading # We use gzcon for everything because (from ?gzcon) - # > Reading from a connection which does not supply a ‘gzip’ magic + # > Reading from a connection which does not supply a 'gzip' magic # > header is equivalent to reading from the original connection conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) on.exit(close(conn)) @@ -767,10 +782,12 @@ local({ renv_bootstrap_validate_version <- function(version, description = NULL) { # resolve description file - description <- description %||% { - path <- getNamespaceInfo("renv", "path") - packageDescription("renv", lib.loc = dirname(path)) - } + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") # check whether requested version 'version' matches loaded version of renv sha <- attr(version, "sha", exact = TRUE) @@ -841,7 +858,7 @@ local({ hooks <- getHook("renv::autoload") for (hook in hooks) if (is.function(hook)) - tryCatch(hook(), error = warning) + tryCatch(hook(), error = warnify) # load the project renv::load(project) @@ -982,10 +999,15 @@ local({ } - renv_bootstrap_version_friendly <- function(version, sha = NULL) { + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { sha <- sha %||% attr(version, "sha", exact = TRUE) - parts <- c(version, sprintf("[sha: %s]", substring(sha, 1L, 7L))) - paste(parts, collapse = " ") + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) } renv_bootstrap_run <- function(version, libpath) { @@ -1017,6 +1039,14 @@ local({ commandArgs()[[1]] == "RStudio" } + # Used to work around buglet in RStudio if hook uses readline + renv_bootstrap_flush_console <- function() { + tryCatch({ + tools <- as.environment("tools:rstudio") + tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE) + }, error = function(cnd) {}) + } + renv_json_read <- function(file = NULL, text = NULL) { jlerr <- NULL @@ -1155,25 +1185,15 @@ local({ # construct full libpath libpath <- file.path(root, prefix) - # attempt to load - if (renv_bootstrap_load(project, libpath, version)) - return(TRUE) - if (renv_bootstrap_in_rstudio()) { + # RStudio only updates console once .Rprofile is finished, so + # instead run code on sessionInit setHook("rstudio.sessionInit", function(...) { - renv_bootstrap_run(version, libpath) - - # Work around buglet in RStudio if hook uses readline - tryCatch( - { - tools <- as.environment("tools:rstudio") - tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE) - }, - error = function(cnd) {} - ) + renv_bootstrap_exec(project, libpath, version) + renv_bootstrap_flush_console() }) } else { - renv_bootstrap_run(version, libpath) + renv_bootstrap_exec(project, libpath, version) } invisible() diff --git a/tests/test-eunomia.R b/tests/test-eunomia.R index b4536f5..deff9fd 100644 --- a/tests/test-eunomia.R +++ b/tests/test-eunomia.R @@ -11,6 +11,24 @@ jobContext <- readRDS("tests/testJobContext.rds") jobContext$moduleExecutionSettings$workSubFolder <- workFolder jobContext$moduleExecutionSettings$resultsSubFolder <- resultsfolder jobContext$moduleExecutionSettings$connectionDetails <- connectionDetails +jobContext$moduleExecutionSettings$resultsConnectionDetails <- connectionDetails +jobContext$moduleExecutionSettings$resultsDatabaseSchema <- jobContext$moduleExecutionSettings$workDatabaseSchema + +test_that("Test createDataModelSchema", { + source("Main.R") + createDataModelSchema(jobContext) + + # Verify that the table(s) are created + connection <- DatabaseConnector::connect( + connectionDetails = jobContext$moduleExecutionSettings$resultsConnectionDetails + ) + on.exit(DatabaseConnector::disconnect(connection)) + tableList <- DatabaseConnector::getTableNames( + connection = connection + ) + resultsTablesCreated <- tableList[grep(getModuleInfo()$TablePrefix, tableList)] + expect_true(length(resultsTablesCreated) > 0) +}) test_that("Run module", { source("Main.R")