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Merge pull request #1 from DrTTrousers/develop(ru)
Fixes snowflake duplication error
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| # Copyright 2023 Observational Health Data Sciences and Informatics | ||
| # | ||
| # This file is part of Strategus | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
|
|
||
| .handleInjectVar <- function (x) { | ||
| hVar <- function(x) { | ||
| if (is.character(x)) { | ||
| return(sprintf('"%s"', x)) | ||
| } else { | ||
| return(sprintf('%s', x)) | ||
| } | ||
| } | ||
|
|
||
| if (length(x) == 1) { | ||
| return(hVar(x)) | ||
| } else if (is.vector(x)) { | ||
| innerVars <- hVar(x) | ||
| return(paste0("c(", paste(innerVars, collapse = ", "), ")")) | ||
| } else { | ||
| stop("cannot handle complex data structures in variable injection") | ||
| } | ||
| } | ||
|
|
||
| #' Load module execution space inside and renv | ||
| #' inspired by targets::tar_script but allowing custom variable execution | ||
| #' | ||
| #' Designed to allow more human readable code that is executed inside a module as well as simple variable substituion | ||
| #' for injecting constants (e.g. simple parameters or file paths used inside and outside of modules) | ||
| #' | ||
| #' This pattern also allows dependency injection which could be used if you don't want to use and renv and (instead) | ||
| #' would like to use docker images or just execution in the base environment for testing/debugging | ||
| #' | ||
| #' @param code code block to execute | ||
| #' @param moduleFolder Instantiated Strategus module folder | ||
| #' @param injectVars list of var names list(name=value) to replace (e.g. replace list(foo = "some string") will | ||
| #' find the pattern foo and replace it with the string some string - be careful! | ||
| #' @param tempScriptFile tempFile to write script to (ret | ||
| #' @param job run as rstudio job | ||
| #' @param processName String name for process | ||
| #' @returns NULL invisibly | ||
| withModuleRenv <- function(code, | ||
| moduleFolder, | ||
| injectVars = list(), | ||
| tempScriptFile = tempfile(fileext = ".R"), | ||
| useLocalStrategusLibrary = TRUE, | ||
| job = FALSE, | ||
| processName = paste(moduleFolder, "_renv_run")) { | ||
| # convert human readable code to a string for writing | ||
| script <- as.character(substitute(code))[-1] | ||
| # Insert variables | ||
| for (name in names(injectVars)) { | ||
| rep <- .handleInjectVar(injectVars[[name]]) | ||
| script <- gsub(name, rep, script) | ||
| } | ||
|
|
||
| # Enforce attachment of Strategus from calling process - note one inside the renv | ||
| if (useLocalStrategusLibrary) { | ||
| libPath <- file.path(find.package("Strategus"), "../") | ||
| script <- c(sprintf("library(Strategus, lib.loc = '%s')", libPath), | ||
| script) | ||
| } | ||
|
|
||
| # Write file and execute script inside an renv | ||
| fileConn <- file(tempScriptFile) | ||
| writeLines(script, fileConn) | ||
| close(fileConn) | ||
| renv::run( | ||
| script = tempScriptFile, | ||
| job = job, | ||
| name = processName, | ||
| project = moduleFolder | ||
| ) | ||
| return(invisible(NULL)) | ||
| } |
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