initial commit

3 files changed, 206 insertions, 0 deletions

diff --git a/utils/R_setup.sh b/utils/R_setup.sh
new file mode 100644
index 00000000..532f6987
--- /dev/null
+++ b/utils/R_setup.sh
@@ -0,0 +1,68 @@
+#!/bin/bash
+#
+# Setup an R environment in a given directory.
+#
+# This works as follows. We create an ".Rprofile" file in the current 
+# directory that sets the .libPaths to the desired Rlib directory. We do the 
+# same with an .Renviron file because it's R so one place isn't enough. This 
+# essentially makes that the only source of packages read by anything that 
+# respects this .Rprofile. Next we install packages as normal using the 
+# install_if_not_exists.R script, which only installs packages if necessary 
+# and supports GitHub and local packages as well.
+#
+# This file is part of RSimpleVenv: https://github.com/GjjvdBurg/RSimpleVenv
+#
+# Author: G.J.J. van den Burg
+# Date: 2019-06-19
+# License: MIT
+
+res='\033[1m\033[0m'
+log() { echo -e "\e[32m$*${res}"; }
+err() { echo -e "\e[31m$*${res}"; exit 1; }
+
+install() {
+	log "Installing $1";
+	Rscript ./utils/install_if_not_exist.R "$1"
+	# exit on failure
+	if [ ! $? == 0 ]
+	then
+		err "Non-zero exit status after installing $1"
+	fi
+}
+
+if [ $# -ne 2 ]
+then
+	echo "Usage: $0 packageFile rlib_dir"
+	exit 1
+fi
+
+PACKAGE_FILE="$1"
+LIBDIR=$(realpath "$2")
+mkdir -p ${LIBDIR}
+
+# Ensure that this is the only libPath from now on.
+echo ".libPaths(c('${LIBDIR}'))" > .Rprofile
+echo "R_LIBS=${LIBDIR}" > .Renviron
+echo "R_LIBS_USER=${LIBDIR}" >> .Renviron
+
+# Here's a fun one: for some reason R tests lazy loading in vanilla mode by 
+# default, which overwrites all the environment and library stuff we just 
+# carefully set. This can break things when you have a different package 
+# version installed in your user R package library. Luckily, if you dig 
+# through the R source code (not in the documentation!), you can find out that 
+# there's an obscure environment variable that can be set to disable this 
+# behaviour. What fun! What an intuitively designed programming language! /s
+export _R_CHECK_INSTALL_DEPENDS_="TRUE"
+
+# Install devtools for GitHub-based packages
+install devtools
+
+# Install all packages from the provided package file
+while read -r pkg
+do
+	if [ -z ${pkg} ]
+	then
+		continue
+	fi
+	install "${pkg}"
+done < ${PACKAGE_FILE}
diff --git a/utils/install_if_not_exist.R b/utils/install_if_not_exist.R
new file mode 100644
index 00000000..9daf21ca
--- /dev/null
+++ b/utils/install_if_not_exist.R
@@ -0,0 +1,75 @@
+#!/usr/bin/env Rscript
+#
+# Install an R package from the command line. Supports CRAN, GitHub, and local 
+# packages.
+#
+# It is expected that this is only run through R_setup.sh.
+#
+# This file is part of RSimpleVenv: https://github.com/GjjvdBurg/RSimpleVenv
+#
+# Author: G.J.J. van den Burg
+# Date: 2019-06-20
+# License: MIT
+
+REPOS <- c("https://cran.r-project.org")
+
+# Parse args
+args <- commandArgs(trailingOnly=T)
+if (!length(args) == 1) {
+    print("Please provide a package name")
+    quit()
+}
+pkg <- args[1]
+
+# As a sanity check, ensure that nothing overwrote the R_LIBS variable
+if (Sys.getenv("R_LIBS") != .libPaths()[1]) {
+    print("Mismatch between R_LIBS and .libPaths()[1]")
+    quit(status=1, save="no")
+}
+
+# Install the package
+if (startsWith(pkg, "github:")) {
+    pkg <- substring(pkg, nchar("github:")+1, nchar(pkg))
+    # this check only works if the package name matches the repo name
+    pkgName <- basename(pkg)
+    if (pkgName %in% installed.packages()) {
+        cat("Package", pkgName, "exists.\n")
+        quit()
+    }
+    Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")
+    # install_github returns the package name (yay!)
+    pkgName <- devtools::install_github(pkg)
+} else if (startsWith(pkg, "local:")) {
+    pkgPath <- substring(pkg, nchar("local:")+1, nchar(pkg))
+    pkgName <- basename(pkgPath)
+    if (pkgName %in% installed.packages()) {
+        cat("Package", pkgName, "exists.\n")
+        quit()
+    }
+    devtools::build(pkgPath)
+    devtools::install(pkgPath)
+} else {
+    version <- NULL
+    if (grepl('==', pkg)) {
+        pkgName <- sub('==(.*)', '', pkg)
+        version <- sub('(.*)==', '', pkg)
+    } else {
+        pkgName <- pkg
+    }
+
+    if (pkgName %in% installed.packages()) {
+        cat("Package", pkg, "exists.\n")
+        quit()
+    }
+
+    if (pkgName == 'devtools') {
+        install.packages(pkgName, Sys.getenv('R_LIBS'), repos=REPOS, 
+                         dependencies=c('Depends', 'Imports', 'LinkingTo'))
+    } else {
+        devtools::install_version(pkgName, version=version, repos=REPOS)
+    }
+}
+
+# Test if it works
+if (!library(pkgName, character.only=T, logical.return=T))
+    quit(status=1, save='no')
diff --git a/utils/validate_schema.py b/utils/validate_schema.py
new file mode 100644
index 00000000..647cc310
--- /dev/null
+++ b/utils/validate_schema.py
@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+Validate all result files against a given JSON schema.
+
+Author: Gertjan van den Burg
+
+"""
+
+
+import argparse
+import json
+import jsonschema
+import os
+
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "-s", "--schema-file", help="Schema file", default="./schema.json"
+    )
+    parser.add_argument("-r", "--result-dir", help="Directory with results")
+    parser.add_argument(
+        "-v", "--verbose", help="Enable verbose mode", action="store_true"
+    )
+    return parser.parse_args()
+
+
+def load_schema(schema_file):
+    with open(schema_file, "rb") as fp:
+        schema = json.load(fp)
+    return schema
+
+
+def scantree(path):
+    """Recursively yield DirEntry objects for given directory."""
+    for entry in os.scandir(path):
+        if entry.is_dir(follow_symlinks=False):
+            yield from scantree(entry.path)
+        else:
+            yield entry
+
+
+def validate_file(filename, schema):
+    with open(filename, "rb") as fp:
+        data = json.load(fp)
+    jsonschema.validate(instance=data, schema=schema)
+
+
+def main():
+    args = parse_args()
+
+    log = lambda *a, **kw: print(*a, **kw) if args.verbose else None
+
+    schema = load_schema(args.schema_file)
+    for entry in scantree(args.result_dir):
+        log("Checking file: %s" % entry.path)
+        validate_file(entry.path, schema)
+
+
+if __name__ == "__main__":
+    main()