BF: workaround singularity bug to be able to run under /tmp/subdirectory

scripts/singularity_cmd

@@ -34,7 +34,7 @@
 set -eu
 
 function info() {
-	: # echo -e "I: $@" >&2
+	: #	echo -e "I: " "$@" >&2
 }
 
 #
@@ -72,17 +72,52 @@ pass_git_config "user.name" "ReproNim User"
 pass_git_config "user.email" "nobody@example.com"
 
 # Common arguments for the singularity run
-SARGS=( -e -c -B "$PWD" -H "$BHOME" --pwd "$PWD" "$@" )
+SARGS=( -e -B "$PWD" -H "$BHOME" --pwd "$PWD" "$@" )
 
+# Due to https://github.com/sylabs/singularity/issues/3949
+# which was fixed only in v3.3.0-rc.1-431-g40331a5b1
+# for now we need to avoid using `-c` in such cases and
+# just create those needed bind points manually and bind mount
+# /tmp manually (apparently -W is not in effect really without -c).
+# TODO: make it also check/depend on current version of singularity
+need_no_c=
+for d in "$PWD" "$updir"; do
+	if [ "${d##/tmp/}" != "$d" ]; then
+		# we should create that one within our $tmpdir
+		info "Creating $d under $tmpdir"
+		mkdir -p "$tmpdir/$d" "$tmpdir/var/tmp"
+		need_no_c=1
+	fi
+done
+
+if [ -z "$need_no_c" ]; then
+	SARGS=( -c "${SARGS[@]}" )
+else
+	SARGS=( -B "$tmpdir/tmp:/tmp" -B "$tmpdir/var/tmp:/var/tmp" "${SARGS[@]}" )
+fi
+
+# set -x
 if [ "$OSTYPE" == "linux-gnu" ] && [ -z "${REPRONIM_USE_DOCKER:-}" ]; then
 	singularity "$cmd" -W "$tmpdir" "${SARGS[@]}"
 else
-	docker run --privileged --rm \
-	-e "UID=$(id -u)" \
-	-e "GID=$(id -g)" \
-	-v "$PWD:$PWD" \
-	-v "$BHOME:$BHOME" \
-	-w "$PWD" \
-	mjtravers/singularity-shim:latest \
-	"$cmd" "${SARGS[@]}"
+	DARGS=(
+	--privileged
+	--rm
+	-e "UID=$(id -u)"
+	-e "GID=$(id -g)"
+	-v "$PWD:$PWD"
+	-v "$updir:$updir"
+	-v "$BHOME:$BHOME"
+	-w "$PWD")
+
+	# Bind mount present /etc/localtime inside the docker container to be
+	# passed into singularity env
+	if [ -e "/etc/localtime" ]; then
+		DARGS=( "${DARGS[@]}" -v /etc/localtime )
+	fi
+
+	docker run \
+		   "${DARGS[@]}" \
+		   mjtravers/singularity-shim:latest \
+		   "$cmd" "${SARGS[@]}"
 fi

scripts/tests/test_helpers.bash

@@ -0,0 +1,62 @@
+# Messaging
+debug () {
+	[ -z "$DEBUG_BATS" ] || echo "	DEBUG: $@" >&3
+}
+
+debug_run () {
+	debug "> lines=${lines[@]}"
+	debug "> STATUS=$status"
+}
+
+fail_msg () {
+	echo -e "FAIL: $@" >&3
+}
+
+fail () {
+	fail_msg "$@"
+	exit 1
+}
+
+error () {
+	echo -e "ERROR: $@" >&3
+	exit 2
+}
+
+# Assertion helpers
+
+assert_equal () {
+	if [ "$#" != 2 ]; then
+		error "Got $# arguments to eq whenever expected 2"
+	fi
+	if [ "$1" != "$2" ]; then
+		fail "Arguments are not equal.\n #1=<<$1>>\n #2=<<$2>>"
+	fi
+}
+
+assert_python_re_match () {
+	if ! python -c 'import re, sys; assert re.match(sys.argv[1], sys.argv[2], flags=re.DOTALL)' "$1" "$2"; then
+		fail "<<$2>>\ndid not match\n<<$1>>"
+	fi
+}
+
+assert_clean_exit () {
+	assert_equal "$status" 0
+}
+
+
+# Misc helpers
+
+pull_singularity_shim () {
+	# make sure that we have our shim docker image so its pulling does not
+	# leak into output of scripts/singularity_cmd
+	if ! docker pull mjtravers/singularity-shim:latest; then
+		skip "Failed to pull singularity shim"
+	fi
+}
+
+skip_if_travis_osx() {
+	if [ "$TRAVIS_OS_NAME" = osx ]
+	then
+		skip "$@"
+	fi
+}

scripts/tests/test_singularity_cmd.bats

@@ -13,27 +13,96 @@
 #   bats test_singularity_cmd.bats
 #   bats .
 
+load test_helpers
+
+arg_test_img="$BATS_TEST_DIRNAME/arg-test.simg"
+topdir="$BATS_TEST_DIRNAME/../.."
+
+cd "$BATS_TEST_DIRNAME"
+git annex get "$arg_test_img"
+
+
 @test "verifying arguments passed to singularity_cmd Docker shim" {
-    # make sure that we have the singularity image
-    img="$BATS_TEST_DIRNAME/arg-test.simg"
-    cd "$BATS_TEST_DIRNAME"
-    git annex get "$img"
-    cd ../..
-    # make sure that we have our shim docker image so its pulling does not
-    # leak into output of scripts/singularity_cmd
-    docker pull mjtravers/singularity-shim:latest
-
-    export REPRONIM_USE_DOCKER=1
-    run scripts/singularity_cmd \
-        exec "$img" /singularity "foo bar" blah 45.5 /dir "bar;" "foo&" '${foo}'
-    echo "> STATUS=$status" >&3
-    echo "> lines=${lines[@]}" >&3
-    [ "$status" -eq 0 ]
-    [ "${lines[0]}" = 'arg #1=<foo bar>' ]
-    [ "${lines[1]}" = 'arg #2=<blah>' ]
-    [ "${lines[2]}" = 'arg #3=<45.5>' ]
-    [ "${lines[3]}" = 'arg #4=</dir>' ]
-    [ "${lines[4]}" = 'arg #5=<bar;>' ]
-    [ "${lines[5]}" = 'arg #6=<foo&>' ]
-    [ "${lines[6]}" = 'arg #7=<${foo}>' ]
+	pull_singularity_shim
+
+	cd "$topdir"
+	export REPRONIM_USE_DOCKER=1
+	run scripts/singularity_cmd \
+		exec "$arg_test_img" /singularity "foo bar" blah 45.5 /dir "bar;" "foo&" '${foo}'
+
+	debug_run
+
+	assert_clean_exit
+	assert_equal "${lines[0]}"	'arg #1=<foo bar>'
+	assert_equal "${lines[1]}"	'arg #2=<blah>'
+	assert_equal "${lines[2]}"	'arg #3=<45.5>'
+	assert_equal "${lines[3]}"	'arg #4=</dir>'
+	assert_equal "${lines[4]}"	'arg #5=<bar;>'
+	assert_equal "${lines[5]}"	'arg #6=<foo&>'
+	assert_equal "${lines[6]}"	'arg #7=<${foo}>'
+}
+
+
+@test "verifying ability to singularity exec under /tmp subdir" {
+	skip_if_travis_osx "skipping Singularity directory test on Travis OSX"
+	check_subdir "$(_mktemp_dir_under /tmp)"
+}
+
+@test "verifying ability to singularity exec under /tmp subdir (explicit use of docker)" {
+	skip_if_travis_osx "skipping Singularity directory test on Travis OSX"
+	export REPRONIM_USE_DOCKER=1
+	check_subdir "$(_mktemp_dir_under /tmp)"
+}
+
+@test "verifying ability to singularity exec under $HOME subdir" {
+	skip_if_travis_osx "skipping Singularity directory test on Travis OSX"
+	check_subdir "$(_mktemp_dir_under $HOME)"
+}
+
+@test "verifying ability to singularity exec under $HOME subdir (explicit use of docker)" {
+	skip_if_travis_osx "skipping Singularity directory test on Travis OSX"
+	export REPRONIM_USE_DOCKER=1
+	check_subdir "$(_mktemp_dir_under $HOME)"
+}
+
+
+_mktemp_dir_under () {
+	subdir="$1/$(mktemp -t "tmp dir.XXXXXX" -u | sed -e 's,.*/,,g')"
+	mkdir -p "$subdir"
+	debug "subdir: $subdir"
+	echo "$subdir"
+}
+
+check_subdir () {
+	subdir="$1"
+	cd "$subdir"
+	echo "content" > "$subdir/file"
+
+	# Our arg_test image has no /etc/localtime so singularity might complain
+	# about inability to bind mount that one
+	#  \S* to swallow ANSI coloring
+	target_out=( '(\S*WARNING:\S* skipping mount of /etc/localtime: no such file or directory\n)?/tmp'
+"$subdir"
+"$subdir/file"
+/var/tmp
+content )
+
+	if [ -n "${REPRONIM_USE_DOCKER:-}" ]; then
+		pull_singularity_shim
+	fi
+	run_cmd="find /tmp"
+	if [ "${subdir##/tmp/}" = "$subdir" ]; then
+		# We are not under /tmp so find will not find our directory, add it explicitly to the list
+		# for find
+		run_cmd+=" \"$subdir\""
+	fi
+	run_cmd+=" /var/tmp && cat \"$subdir/file\""
+	run "$topdir/scripts/singularity_cmd" exec "$arg_test_img" sh -c "$run_cmd"
+
+	rm -rf "$subdir"  # cleanup asap
+
+	debug_run
+
+	assert_clean_exit
+	assert_python_re_match "${target_out[*]}" "${lines[*]}"
 }

travis/dummy_docker

@@ -28,21 +28,25 @@ elif [ "$1" = "run" -a \
        "$7" = "GID=20" -a \
        "$8" = "-v" -a \
        "${10}" = "-v" -a \
-       "${12}" = "-w" -a \
-       "${15}" = "exec" -a \
-       "${16}" = "-e" -a \
-       "${17}" = "-c" -a \
-       "${18}" = "-B" -a \
-       "${20}" = "-H" -a \
-       "${22}" = "--pwd" -a \
-       "${25}" = "/singularity" -a \
-       "${26}" = "foo bar" -a \
-       "${27}" = "blah" -a \
-       "${28}" = "45.5" -a \
-       "${29}" = "/dir" -a \
-       "${30}" = "bar;" -a \
-       "${31}" = "foo&" -a \
-       "${32}" = "\${foo}" ]
+       "${12}" = "-v" -a \
+       "${14}" = "-w" -a \
+       "${16}" = "-v" -a \
+       "${17}" = "/etc/localtime" -a \
+       "${18}" = "mjtravers/singularity-shim:latest" -a \
+       "${19}" = "exec" -a \
+       "${20}" = "-c" -a \
+       "${21}" = "-e" -a \
+       "${22}" = "-B" -a \
+       "${24}" = "-H" -a \
+       "${26}" = "--pwd" -a \
+       "${29}" = "/singularity" -a \
+       "${30}" = "foo bar" -a \
+       "${31}" = "blah" -a \
+       "${32}" = "45.5" -a \
+       "${33}" = "/dir" -a \
+       "${34}" = "bar;" -a \
+       "${35}" = "foo&" -a \
+       "${36}" = "\${foo}" ]
 then
     cat << EOF
 arg #1=<foo bar>