From b75ee68d9f6305646a55d816fb1173210e36eab9 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 5 Jan 2017 14:53:10 -0500
Subject: [PATCH] Run Galaxy tests in --dockerize mode as UID of tester.

Fixes #1541 and should really help Jenkins clean up after itself.
---
 run_tests.sh                         |  2 ++
 test/docker/base/run_test_wrapper.sh | 16 ++++++++++++----
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/run_tests.sh b/run_tests.sh
index cb892cc371bb..0144f7b17912 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -246,6 +246,8 @@ then
        DOCKER_RUN_EXTRA_ARGS="-v ${tmp}:/tmp ${DOCKER_RUN_EXTRA_ARGS}"
        shift
     fi
+    UID=$(id -u)
+    DOCKER_RUN_EXTRA_ARGS="-e GALAXY_TEST_UID=${UID} ${DOCKER_RUN_EXTRA_ARGS}"
     echo "Launching docker container for testing..."
     docker $DOCKER_EXTRA_ARGS run $DOCKER_RUN_EXTRA_ARGS -e "BUILD_NUMBER=$BUILD_NUMBER" -e "GALAXY_TEST_DATABASE_TYPE=$db_type" --rm -v `pwd`:/galaxy $DOCKER_IMAGE "$@"
     exit $?
diff --git a/test/docker/base/run_test_wrapper.sh b/test/docker/base/run_test_wrapper.sh
index 8943006145a3..27195f843a3f 100644
--- a/test/docker/base/run_test_wrapper.sh
+++ b/test/docker/base/run_test_wrapper.sh
@@ -1,6 +1,12 @@
 #!/bin/bash
 set -e
 
+deluser galaxy | true
+groupadd -r galaxy -g "$GALAXY_TEST_UID"
+useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash
+echo "galaxy:galaxy" | chpasswd
+chown -R galaxy:galaxy /galaxy_venv
+
 GALAXY_TEST_DATABASE_TYPE=${GALAXY_TEST_DATABASE_TYPE:-"postgres"}
 if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
 then
@@ -36,17 +42,19 @@ export TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION
 
 : ${GALAXY_VIRTUAL_ENV:=.venv}
 
-./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
+sudo -E -u galaxy ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
 
 dev_requirements=./lib/galaxy/dependencies/dev-requirements.txt
 [ -f $dev_requirements ] && $GALAXY_VIRTUAL_ENV/bin/pip install -r $dev_requirements
 
-sh manage_db.sh upgrade
-sh manage_db.sh upgrade tool_shed
+echo "Upgrading test database..."
+sudo -E -u galaxy sh manage_db.sh upgrade
+echo "Upgrading tool shed database... $TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION"
+sudo -E -u galaxy sh manage_db.sh upgrade tool_shed
 
 if [ -z "$GALAXY_NO_TESTS" ];
 then
-    sh run_tests.sh --skip-common-startup $@
+    sudo -E -u galaxy sh run_tests.sh --skip-common-startup $@
 else
     GALAXY_CONFIG_MASTER_API_KEY=${GALAXY_CONFIG_MASTER_API_KEY:-"testmasterapikey"}
     GALAXY_CONFIG_FILE=${GALAXY_CONFIG_FILE:-config/galaxy.ini.sample}