https://github.com/genome/genome
Tip revision: 6d717079e5a605f0a9fdbef83d5dd6058a6da66e authored by apregier on 02 June 2015, 22:00:49 UTC
CHANGELOG: New required param for vep
CHANGELOG: New required param for vep
Tip revision: 6d71707
test_helper.bash
function abs_path {
echo "$( cd -P "$1" && pwd )"
}
function tempdir {
set -o errexit
local TEMPDIR;
if man mktemp | grep -q BSD
then
TEMPDIR="$(mktemp -d -t genome-env-testing)"
fi
if man mktemp | grep -q GNU
then
TEMPDIR="$(mktemp --tmpdir -d genome-env-testing.XXXXXXXX)"
fi
echo "$TEMPDIR"
}
function cache_repo {
local NAME="$1"
local URL="$2"
local CLONE_BASE_DIR="$3"
# Avoid using /tmp because I think tmpreaper is partially removing the
# cached repos. `/var/cache` is probably more correct anyway.
local CACHE_BASE_DIR="/var/cache/jenkins/genome-env-cache/"
if ! test -d "$CACHE_BASE_DIR"
then
CACHE_BASE_DIR="/tmp/genome-env-cache"
fi
local CACHE_DIR="$CACHE_BASE_DIR/$NAME.git"
local CLONE_DIR="$CLONE_BASE_DIR/$NAME"
# Try to detect corrupted cache repo which has probably been happening
# because tmpreaper partially removes the cached repo.
if test -d $CACHE_DIR && ! git --git-dir $CACHE_DIR rev-parse --is-inside-git-dir 2> /dev/null
then
rm -rf $CACHE_DIR
fi
if ! test -d $CACHE_DIR
then
git clone --bare $URL $CACHE_DIR > /dev/null 2>&1
fi
git --git-dir $CACHE_DIR fetch > /dev/null 2>&1
git clone --reference $CACHE_DIR $URL $CLONE_DIR > /dev/null 2>&1
}
function init_workspace {
export WORKSPACE="$(tempdir)"
# clone from the existing genome repo instead of getting an origin/master
cache_repo genome "$(git rev-parse --git-dir)" "$WORKSPACE"
cache_repo ur https://github.com/genome/UR.git "$WORKSPACE"
cache_repo workflow https://github.com/genome/tgi-workflow.git "$WORKSPACE"
cache_repo genome-sqitch https://github.com/genome/genome-sqitch.git "$WORKSPACE"
}
function rm_workspace {
if test -n "$WORKSPACE" -a -d "$WORKSPACE"
then
rm -rf "$WORKSPACE"
fi
}
function submodule_is_clean {
if ! git diff --exit-code $1
then
echo "submodule should be clean: $1" >&2
exit 1
fi
}
function submodule_is_initialized {
if git submodule status $1 | grep -q '^-'
then
echo "submodule should be initialized: $1" >&2
exit 1
fi
}
function submodule_is_not_initialized {
if git submodule status $1 | grep -qv '^-'
then
echo "submodule should be not initialized: $1" >&2
exit 1
fi
}
function apipe_test_db_is_used {
DS_GMSCHEMA_SERVER="$(genome config get ds_gmschema_server)"
if echo "$DS_GMSCHEMA_SERVER" | grep -qv 'apipe-test-db'
then
echo "DS_GMSCHEMA_SERVER should refer to apipe-test-db" >&2
exit 1
fi
}
function apipe_test_db_is_not_used {
DS_GMSCHEMA_SERVER="$(genome config get ds_gmschema_server)"
if echo "$DS_GMSCHEMA_SERVER" | grep -q 'apipe-test-db'
then
echo "DS_GMSCHEMA_SERVER should not refer to apipe-test-db" >&2
exit 1
fi
}
function module_loaded_from_submodule {
local SUBMODULE="${1,,}"
if test "$WORKSPACE/genome/$SUBMODULE/lib/$1.pm" != "$(perl -M$1 -e "print \$INC{q($1.pm)}, qq(\\n)")"
then
echo "$1 should be loaded from submodule" >&2
exit 1
fi
}
function module_not_loaded_from_submodule {
local SUBMODULE="${1,,}"
if test "$WORKSPACE/genome/$SUBMODULE/lib/$1.pm" == "$(perl -M$1 -e "print \$INC{q($1.pm)}, qq(\\n)")"
then
echo "$1 should not be loaded from submodule" >&2
exit 1
fi
}