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run_tests.sh
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run_tests.sh
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#!/bin/sh
pwd_dir=$(pwd)
cd `dirname $0`
# A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/
rm -f run_functional_tests.log
show_help() {
cat <<EOF
'${0##*/} -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)
'${0##*/} -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')
'${0##*/} -list' for listing all the tool ids
'${0##*/} -api (test_path)' for running all the test scripts in the ./test/api directory
'${0##*/} -toolshed (test_path)' for running all the test scripts in the ./test/shed_functional/functional directory
'${0##*/} -installed' for running tests of Tool Shed installed tools
'${0##*/} -framework' for running through example tool tests testing framework features in test/functional/tools"
'${0##*/} -framework -id toolid' for testing one framework tool (in test/functional/tools/) with id 'toolid'
'${0##*/} -data_managers -id data_manager_id' for testing one Data Manager with id 'data_manager_id'
'${0##*/} -unit' for running all unit tests (doctests and tests in test/unit)
'${0##*/} -unit (test_path)' for running unit tests on specified test path
'${0##*/} -qunit' for running qunit JavaScript tests
'${0##*/} -qunit testname' for running single JavaScript test with given name
'${0##*/} -selenium' for running all selenium web tests (in test/selenium_tests)
'${0##*/} -selenium (test_path)' for running specified selenium web tests (use nosetest path)
This wrapper script largely serves as a point documentation and convenience -
most tests shipped with Galaxy can be run with nosetests or qunit directly.
The main test types are as follows:
- API: These tests are located in test/api and test various aspects of the Galaxy
API and test general backend aspects of Galaxy using the API.
- Integration: These tests are located in test/integration and test special
configurations of Galaxy. All API tests assume a particular Galaxy configuration
defined by test/base/driver_util.py and integration tests can be used to
launch and test Galaxy in other configurations.
- Framework: These tests are all Galaxy tool tests and can be found in
test/functional/tools. These are for the most part meant to test and
demonstrate features of the tool evaluation environment and of Galaxy tool XML
files.
- Unit: These are Python unit tests either defined as doctests or inside of
test/unit. These should generally not require a Galaxy instance and should
quickly test just a component or a few components of Galaxy's backend code.
- QUnit: These are JavaScript unit tests defined in test/qunit.
- Selenium: These are full stack tests meant to test the Galaxy UI with real
browsers and are located in test/selenium_tests.
- ToolShed: These are web tests that use the older Python web testing
framework twill to test ToolShed related functionality. These are
located in test/shed_functional.
Nose tests will allow specific tests to be selected per the documentation at
https://nose.readthedocs.org/en/latest/usage.html#selecting-tests. These are
indicated with the optional parameter (test_path). A few examples are:
Run all API tests:
./run_tests.sh -api
The same test as above can be run using nosetests directly as follows:
nosetests test/api
However when using nosetests directly output options defined in this
file aren't respected and a new Galaxy instance will be created for each
TestCase class (this scripts optimizes it so all tests can share a Galaxy
instance).
Run a full class of API tests:
./run_tests.sh -api test/api/test_tools.py:ToolsTestCase
Run a specific API test:
./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_map_over_with_output_format_actions
Run all selenium tests (Under Linux using Docker):
# Start selenium chrome Docker container
docker run -d -p 4444:4444 -v /dev/shm:/dev/shm selenium/standalone-chrome:3.0.1-aluminum
GALAXY_TEST_SELENIUM_REMOTE=1 ./run_tests.sh -selenium
Run a specific selenium test (under Linux or Mac OS X after installing geckodriver or chromedriver):
./run_tests.sh -selenium test/selenium_tests/test_registration.py:RegistrationTestCase.test_reregister_username_fails
Note About Selenium Tests:
If using a local selenium driver such as a Chrome or Firefox based one
either chromedriver or geckodriver needs to be installed an placed on
the PATH.
More information on geckodriver can be found at
https://github.com/mozilla/geckodriver and more information on
chromedriver can be found at
https://sites.google.com/a/chromium.org/chromedriver/.
By default Galaxy will check the PATH for these and pick
whichever it finds. This can be overridden by setting
GALAXY_TEST_SELENIUM_BROWSER to either FIREFOX, CHROME, or something
more esoteric (including OPERA and PHANTOMJS).
If PyVirtualDisplay is installed Galaxy will attempt to run this
browser in a headless mode. This can be disabled by setting
GALAXY_TEST_SELENIUM_HEADLESS to 0 however.
Selenium can also be setup a remote service - to target a service set
GALAXY_TEST_SELENIUM_REMOTE to 1. The target service may be configured
with GALAXY_TEST_SELENIUM_REMOTE_PORT and
GALAXY_TEST_SELENIUM_REMOTE_HOST. By default Galaxy will assume the
remote service being targetted is CHROME - but this can be overridden
with GALAXY_TEST_SELENIUM_BROWSER.
In this remote mode, please ensure that GALAXY_TEST_HOST is set to a
host that is accessible from the Selenium host. By default under Linux
if GALAXY_TEST_SELENIUM_REMOTE is set, Galaxy will set this to be the IP
address Docker exposes localhost on to its child containers. This trick
doesn't work on Mac OS X and so GALAXY_TEST_HOST will need to be crafted
carefully ahead of time.
For Selenium test cases a stack trace is usually insufficient to diagnose
problems. For this reason, GALAXY_TEST_ERRORS_DIRECTORY is populated with
a new directory of information for each failing test case. This information
includes a screenshot, a stack trace, and the DOM of the currently rendered
Galaxy instance. The new directories are created with names that include
information about the failed test method name and the timestamp. By default,
GALAXY_TEST_ERRORS_DIRECTORY will be set to database/errors.
The Selenium tests seem to be subject to transient failures at a higher
rate than the rest of the tests in Galaxy. Though this is unfortunate,
they have more moving pieces so this is perhaps not surprising. One can
set the GALAXY_TEST_SELENIUM_RETRIES to a number greater than 0 to
automatically retry every failed test case the specified number of times.
External Tests:
A small subset of tests can be run against an existing Galaxy
instance. The external Galaxy instance URL can be configured with
--external_url. If this is set, either --external_master_key or
--external_user_key must be set as well - more tests can be executed
with --external_master_key than with a user key.
Extra options:
--verbose_errors Force some tests produce more verbose error reporting.
--no_cleanup Do not delete temp files for Python functional tests
(-toolshed, -framework, etc...)
--debug On python test error or failure invoke a pdb shell for
interactive debugging of the test
--report_file Path of HTML report to produce (for Python Galaxy
functional tests). If not given, a default filename will
be used, and reported on stderr at the end of the run.
--xunit_report_file Path of XUnit report to produce (for Python Galaxy
functional tests).
--skip-venv Do not create .venv (passes this flag to
common_startup.sh)
--dockerize Run tests in a pre-configured Docker container (must be
first argument if present).
--db <type> For use with --dockerize, run tests using partially
migrated 'postgres', 'mysql', or 'sqlite' databases.
--external_url External URL to use for Galaxy testing (only certain
tests).
--external_master_key Master API key used to configure external tests.
--external_user_key User API used for external tests - not required if
external_master_key is specified.
Environment Variables:
In addition to the above command-line options, many environment variables
can be used to control the Galaxy functional testing processing. Command-line
options above like (--external_url) will set environment variables - in such
cases the command line argument takes precedent over environment variables set
at the time of running this script.
Functional Test Environment Variables
GALAXY_TEST_DBURI Database connection string used for functional
test database for Galaxy.
GALAXY_TEST_INSTALL_DBURI Database connection string used for functional
test database for Galaxy's install framework.
GALAXY_TEST_INSTALL_DB_MERGED Set to use same database for Galaxy and install
framework, this defaults to True for Galaxy
tests an False for shed tests.
GALAXY_TEST_DB_TEMPLATE If GALAXY_TEST_DBURI is unset, this URL can be
retrieved and should be an sqlite database that
will be upgraded and tested against.
GALAXY_TEST_TMP_DIR Temp directory used for files required by
Galaxy server setup for Galaxy functional tests.
GALAXY_TEST_SAVE Location to save certain test files (such as
tool outputs).
GALAXY_TEST_EXTERNAL Target an external Galaxy as part of testing.
GALAXY_TEST_JOB_CONFIG_FILE Job config file to use for the test.
GALAXY_CONFIG_MASTER_KEY Master or admin API key to use as part of
testing with GALAXY_TEST_EXTERNAL.
GALAXY_TEST_USER_API_KEY User API key to use as part of testing with
GALAXY_TEST_EXTERNAL.
GALAXY_TEST_VERBOSE_ERRORS Enable more verbose errors during API tests.
GALAXY_TEST_UPLOAD_ASYNC Upload tool test inputs asynchronously (may
overwhelm sqlite database).
GALAXY_TEST_RAW_DIFF Don't slice up tool test diffs to keep output
managable - print all output. (default off)
GALAXY_TEST_DEFAULT_WAIT Max time allowed for a tool test before Galaxy
gives up (default 86400) - tools may define a
maxseconds attribute to extend this.
GALAXY_TEST_TOOL_DEPENDENCY_DIR tool dependency dir to use for Galaxy during
functional tests.
GALAXY_TEST_FILE_DIR Test data sources (default to
test-data,https://github.com/galaxyproject/galaxy-test-data.git)
GALAXY_TEST_DIRECTORY $GALAXY_ROOT/test
GALAXY_TEST_TOOL_DATA_PATH Set to override tool data path during tool
shed tests.
GALAXY_TEST_FETCH_DATA Fetch remote test data to
GALAXY_TEST_DATA_REPO_CACHE as part of tool
tests if it is not available locally (default
to True). Requires git to be available on the
command-line.
GALAXY_TEST_DATA_REPO_CACHE Where to cache remote test data to (default to
test-data-cache).
HTTP_ACCEPT_LANGUAGE Defaults to 'en'
GALAXY_TEST_NO_CLEANUP Do not cleanup main test directory after tests,
the deprecated option TOOL_SHED_TEST_NO_CLEANUP
does the same thing.
GALAXY_TEST_HOST Host to use for Galaxy server setup for
testing.
GALAXY_TEST_PORT Port to use for Galaxy server setup for
testing.
GALAXY_TEST_TOOL_PATH Path defaulting to 'tools'.
GALAXY_TEST_SHED_TOOL_CONF Shed toolbox conf (defaults to
config/shed_tool_conf.xml) used when testing
installed to tools with -installed.
TOOL_SHED_TEST_HOST Host to use for shed server setup for testing.
TOOL_SHED_TEST_PORT Port to use for shed server setup for testing.
TOOL_SHED_TEST_FILE_DIR Defaults to test/shed_functional/test_data.
TOOL_SHED_TEST_TMP_DIR Defaults to random /tmp directory - place for
tool shed test server files to be placed.
TOOL_SHED_TEST_OMIT_GALAXY Do not launch a Galaxy server for tool shed
testing.
Unit Test Environment Variables
GALAXY_TEST_INCLUDE_SLOW - Used in unit tests to trigger slower tests that
aren't included by default with --unit/-u.
EOF
}
show_list() {
python tool_list.py
echo "==========================================================================================================================================="
echo "'${0##*/} -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)"
echo "'${0##*/} -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')"
}
exists() {
type "$1" >/dev/null 2>/dev/null
}
ensure_grunt_for_qunit() {
if ! exists "grunt";
then
PATH="$PATH:./test/qunit/node_modules/grunt/bin"
export PATH
if ! exists "grunt";
then
echo "Grunt not on path, cannot run these tests."
exit 1
fi
fi
}
DOCKER_DEFAULT_IMAGE='galaxy/testing-base:17.05.0'
test_script="./scripts/functional_tests.py"
report_file="run_functional_tests.html"
xunit_report_file=""
structured_data_report_file=""
with_framework_test_tools_arg=""
driver="python"
if [ "$1" = "--dockerize" ];
then
shift
DOCKER_EXTRA_ARGS=${DOCKER_ARGS:-""}
DOCKER_RUN_EXTRA_ARGS=${DOCKER_RUN_EXTRA_ARGS:-""}
DOCKER_IMAGE=${DOCKER_IMAGE:-${DOCKER_DEFAULT_IMAGE}}
if [ "$1" = "--db" ]; then
db_type=$2
shift 2
else
db_type="sqlite"
fi
if [ "$1" = "--external_tmp" ]; then
# If /tmp is a tmpfs there may be better performance by reusing
# the parent's temp file system. Also, it seems to decrease the
# frequency or errors such as the following:
# /bin/sh: 1: /tmp/tmpiWU3kJ/tmp_8zLxx/job_working_directory_mwwDmg/000/274/galaxy_274.sh: Text file busy
tmp=$(mktemp -d)
chmod 1777 $tmp
DOCKER_RUN_EXTRA_ARGS="-v ${tmp}:/tmp ${DOCKER_RUN_EXTRA_ARGS}"
shift
fi
MY_UID=$(id -u)
DOCKER_RUN_EXTRA_ARGS="-e GALAXY_TEST_UID=${MY_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 $?
fi
# If in Jenkins environment, create xunit-${BUILD_NUMBER}.xml by default.
if [ -n "$BUILD_NUMBER" ];
then
xunit_report_file="xunit-${BUILD_NUMBER}.xml"
fi
# Loop through and consume the main arguments.
# Some loops will consume more than one argument (there are extra "shift"s in some cases).
while :
do
case "$1" in
-h|--help|-\?)
show_help
exit 0
;;
-l|-list|--list)
show_list
exit 0
;;
-id|--id)
if [ $# -gt 1 ]; then
test_id=$2;
shift 2
else
echo "--id requires an argument" 1>&2
exit 1
fi
;;
-s|-sid|--sid)
if [ $# -gt 1 ]; then
section_id=$2
shift 2
else
echo "--sid requires an argument" 1>&2
exit 1
fi
;;
-a|-api|--api)
with_framework_test_tools_arg="-with_framework_test_tools"
test_script="./scripts/functional_tests.py"
report_file="./run_api_tests.html"
if [ $# -gt 1 ]; then
api_script=$2
shift 2
else
api_script="./test/api"
shift 1
fi
;;
-selenium|--selenium)
with_framework_test_tools_arg="-with_framework_test_tools"
test_script="./scripts/functional_tests.py"
report_file="./run_selenium_tests.html"
selenium_test=1;
if [ $# -gt 1 ]; then
selenium_script=$2
shift 2
else
selenium_script="./test/selenium_tests"
shift 1
fi
;;
-t|-toolshed|--toolshed)
test_script="./test/shed_functional/functional_tests.py"
report_file="run_toolshed_tests.html"
if [ $# -gt 1 ]; then
toolshed_script=$2
shift 2
else
toolshed_script="./test/shed_functional/functional"
shift 1
fi
;;
-clean_pyc|--clean_pyc)
find lib -iname '*pyc' -exec rm -rf {} \;
find test -iname '*pyc' -exec rm -rf {} \;
shift
;;
-with_framework_test_tools|--with_framework_test_tools)
with_framework_test_tools_arg="-with_framework_test_tools"
shift
;;
--external_url)
GALAXY_TEST_EXTERNAL=$2
shift 2
;;
--external_master_key)
GALAXY_CONFIG_MASTER_KEY=$2
shift 2
;;
--external_user_key)
GALAXY_TEST_USER_API_KEY=$2
shift 2
;;
-f|-framework|--framework)
report_file="run_framework_tests.html"
framework_test=1;
shift 1
;;
-d|-data_managers|--data_managers)
data_managers_test=1;
shift 1
;;
-j|-casperjs|--casperjs)
# TODO: Support running casper tests against existing
# Galaxy instances.
with_framework_test_tools_arg="-with_framework_test_tools"
if [ $# -gt 1 ]; then
casperjs_test_name=$2
shift 2
else
shift 1
fi
report_file="run_casperjs_tests.html"
casperjs_test=1;
;;
-m|-migrated|--migrated)
migrated_test=1;
shift
;;
-i|-installed|--installed)
installed_test=1;
shift
;;
-r|--report_file)
if [ $# -gt 1 ]; then
report_file=$2
shift 2
else
echo "--report_file requires an argument" 1>&2
exit 1
fi
;;
--xunit_report_file)
if [ $# -gt 1 ]; then
xunit_report_file=$2
shift 2
else
echo "--xunit_report_file requires an argument" 1>&2
exit 1
fi
;;
--structured_data_report_file)
if [ $# -gt 1 ]; then
structured_data_report_file=$2
shift 2
else
echo "--structured_data_report_file requires an argument" 1>&2
exit 1
fi
;;
--verbose_errors)
GALAXY_TEST_VERBOSE_ERRORS=True
export GALAXY_TEST_VERBOSE_ERRORS
shift
;;
-c|--coverage)
# Must have coverage installed (try `which coverage`) - only valid with --unit
# for now. Would be great to get this to work with functional tests though.
coverage_arg="--with-coverage"
NOSE_WITH_COVERAGE=true
shift
;;
--debug)
#TODO ipdb would be nicer.
NOSE_PDB=True
export NOSE_PDB
shift
;;
-u|-unit|--unit)
report_file="run_unit_tests.html"
test_script="./scripts/nosetests.py"
if [ $# -gt 1 ]; then
unit_extra=$2
shift 2
else
unit_extra='--exclude=functional --exclude="^get" --exclude=controllers --exclude=runners --exclude dictobj --exclude=jstree lib test/unit'
shift 1
fi
;;
-i|-integration|--integration)
report_file="run_integration_tests.html"
test_script="./scripts/nosetests.py"
if [ $# -gt 1 ]; then
integration_extra=$2
shift 2
else
integration_extra='test/integration'
shift 1
fi
;;
-q|-qunit|--qunit)
# Requires grunt installed and dependencies configured see
# test/qunit/README.txt for more information.
driver="grunt"
gruntfile="./test/qunit/Gruntfile.js"
if [ $# -gt 1 ]; then
qunit_name=$2
shift 2
else
shift 1
fi
;;
--no_cleanup)
GALAXY_TEST_NO_CLEANUP=1
export GALAXY_TEST_NO_CLEANUP
TOOL_SHED_TEST_NO_CLEANUP=1
export TOOL_SHED_TEST_NO_CLEANUP
GALAXY_INSTALL_TEST_NO_CLEANUP=1
export GALAXY_INSTALL_TEST_NO_CLEANUP
echo "Skipping Python test clean up."
shift
;;
-watch|--watch)
# Have grunt watch test or directory for changes, only
# valid for javascript testing.
watch=1
shift
;;
--skip-venv)
skip_venv='--skip-venv'
shift
;;
--no-create-venv)
no_create_venv='--no-create-venv'
shift
;;
--no-replace-pip)
no_replace_pip='--no-replace-pip'
shift
;;
--replace-pip)
replace_pip='--replace-pip'
shift
;;
--skip-common-startup)
# Don't run ./scripts/common_startup.sh (presumably it has already
# been done, or you know what you're doing).
skip_common_startup=1
shift
;;
--)
shift
break
;;
-*)
echo "invalid option: $1" 1>&2;
show_help
exit 1
;;
*)
break;
;;
esac
done
if [ -z "$skip_common_startup" ]; then
if [ -n "$GALAXY_TEST_DBURI" ]; then
GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=$GALAXY_TEST_DBURI
export GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
fi
./scripts/common_startup.sh $skip_venv $no_create_venv $no_replace_pip $replace_pip --dev-wheels || exit 1
fi
GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-.venv}"
if [ -z "$skip_venv" -a -d "$GALAXY_VIRTUAL_ENV" ];
then
printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
. "$GALAXY_VIRTUAL_ENV/bin/activate"
fi
if [ -n "$migrated_test" ] ; then
[ -n "$test_id" ] && class=":TestForTool_$test_id" || class=""
extra_args="functional.test_toolbox$class -migrated"
elif [ -n "$installed_test" ] ; then
[ -n "$test_id" ] && class=":TestForTool_$test_id" || class=""
extra_args="functional.test_toolbox$class -installed"
elif [ -n "$framework_test" ] ; then
[ -n "$test_id" ] && class=":TestForTool_$test_id" || class=""
extra_args="functional.test_toolbox$class -framework"
elif [ -n "$selenium_test" ] ; then
extra_args="$selenium_script -selenium"
elif [ -n "$data_managers_test" ] ; then
[ -n "$test_id" ] && class=":TestForDataManagerTool_$test_id" || class=""
extra_args="functional.test_data_managers$class -data_managers"
elif [ -n "$toolshed_script" ]; then
extra_args="$toolshed_script"
elif [ -n "$api_script" ]; then
extra_args="$api_script"
elif [ -n "$casperjs_test" ]; then
# TODO: Ensure specific versions of casperjs and phantomjs are
# available. Some option for leveraging npm to automatically
# install these dependencies would be nice as well.
if [ -n "$casperjs_test_name" ]; then
extra_args="test/casperjs/casperjs_runner.py:$casperjs_test_name"
else
extra_args="test/casperjs/casperjs_runner.py"
fi
elif [ -n "$section_id" ]; then
extra_args=`python tool_list.py $section_id`
elif [ -n "$test_id" ]; then
class=":TestForTool_$test_id"
extra_args="functional.test_toolbox$class"
elif [ -n "$unit_extra" ]; then
extra_args="--with-doctest $unit_extra"
elif [ -n "$integration_extra" ]; then
extra_args="$integration_extra"
elif [ -n "$1" ] ; then
extra_args="$1"
else
extra_args='--exclude="^get" functional'
fi
if [ "$driver" = "python" ]; then
if [ -n "$xunit_report_file" ]; then
xunit_args="--with-xunit --xunit-file $xunit_report_file"
else
xunit_args=""
fi
if [ -n "$structured_data_report_file" ]; then
structured_data_args="--with-structureddata --structured-data-file $structured_data_report_file"
else
structured_data_args=""
fi
if [ -n "$with_framework_test_tools_arg" ]; then
GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
export GALAXY_TEST_TOOL_CONF
fi
python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $extra_args
exit_status=$?
echo "Testing complete. HTML report is in \"$report_file\"." 1>&2
exit ${exit_status}
else
ensure_grunt_for_qunit
if [ -n "$watch" ]; then
grunt_task="watch"
else
grunt_task=""
fi
if [ -n "$qunit_name" ]; then
grunt_args="--test=$qunit_name"
else
grunt_args=""
fi
# TODO: Exapnd javascript helpers to include setting up
# grunt deps in npm, "watch"ing directory, and running casper
# functional tests.
grunt --gruntfile=$gruntfile $grunt_task $grunt_args
fi