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Various fixes for test image Docker user switching.

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- Fix if testing as user with GID 109 (fixes #3425).
- Fix if testing as a user with any UID or GID that already exists in the container.
- More logging to indicate the "problems" being printed to standard output in these cases are not problems.
- Fix sqlite being readonly in the container for the test user.
This commit is contained in:
John Chilton
2017-01-17 16:56:51 -05:00
parent 910bbdfc54
commit 5c48402b02
1 changed files with 14 additions and 8 deletions
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test/docker/base/run_test_wrapper.sh
+14 -8
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@@ -1,11 +1,16 @@
#!/bin/bash
set -e
echo "Deleting galaxy user - it may not exist and this is fine."
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
echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and this is fine."
groupadd -r galaxy -g "$GALAXY_TEST_UID" | true
echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and this is fine."
useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash | true
echo "Setting galaxy user password - the operation may fail."
echo "galaxy:galaxy" | chpasswd | true
chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" /galaxy_venv
GALAXY_TEST_DATABASE_TYPE=${GALAXY_TEST_DATABASE_TYPE:-"postgres"}
if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
@@ -26,6 +31,7 @@ then
GALAXY_TEST_INSTALL_DB_MERGED="true"
GALAXY_TEST_DBURI="sqlite:////opt/galaxy/galaxy.sqlite"
TOOL_SHED_TEST_DBURI="sqlite:////opt/galaxy/toolshed.sqlite"
chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" /opt/galaxy
else
echo "Unknown database type"
exit 1
@@ -42,19 +48,19 @@ export TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION
: ${GALAXY_VIRTUAL_ENV:=.venv}
sudo -E -u galaxy ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
sudo -E -u "#${GALAXY_TEST_UID}" ./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 $dev_requirements
echo "Upgrading test database..."
sudo -E -u galaxy sh manage_db.sh upgrade
sudo -E -u "#${GALAXY_TEST_UID}" sh manage_db.sh upgrade
echo "Upgrading tool shed database... $TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION"
sudo -E -u galaxy sh manage_db.sh upgrade tool_shed
sudo -E -u "#${GALAXY_TEST_UID}" sh manage_db.sh upgrade tool_shed
if [ -z "$GALAXY_NO_TESTS" ];
then
sudo -E -u galaxy sh run_tests.sh --skip-common-startup $@
sudo -E -u "#${GALAXY_TEST_UID}" 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}