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galaxy/run_tests.sh
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John E 5d0c27c902 docs: fix some typos 
Signed-off-by: John E <jeis4wpi@outlook.com>
2026-05-22 11:27:36 -04:00

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#!/bin/bash
cd "$(dirname "$0")"
show_help() {
cat <<EOF
'${0##*/} -api (test_path)' for running all the test scripts in the ./lib/galaxy_test/api directory, test_path
can be pytest selector
'${0##*/} -cwl (test_path)' for running all the test scripts in the ./lib/galaxy_test/api/cwl directory, test_path
can be pytest selector
'${0##*/} -integration (test_path)' for running all integration test scripts in the ./test/integration directory, test_path
can be pytest selector
'${0##*/} -toolshed (test_path)' for running all the test scripts in the ./lib/tool_shed/test directory
'${0##*/} -main' for running tests of tools shipped with Galaxy
'${0##*/} -framework' for running through example tool tests testing framework features in test/functional/tools"
'${0##*/} -framework -id toolid' for testing one framework tool (in test/functional/tools/) with id 'toolid'
'${0##*/} -framework-workflows' for running through workflow tests to test correctness of workflow evaluation
'${0##*/} -framework-workflows -id workflow_name' test single workflow framework test
'${0##*/} -data_managers -id data_manager_id' for testing one Data Manager with id 'data_manager_id'
'${0##*/} -unit' for running all unit tests (doctests and tests in test/unit)
'${0##*/} -unit (test_selector)' for running unit tests on specified test path (using pytest selector syntax)
'${0##*/} -selenium' for running all selenium web tests (in lib/galaxy_test/selenium)
'${0##*/} -selenium (test_selector)' for running specified selenium web tests (using pytest selector syntax)
'${0##*/} -playwright' for running all end2end web tests (in lib/galaxy_test/selenium) using Playwright
'${0##*/} -playwright (test_selector)' for running specified end2end web tests (using pytest selector syntax) using Playwright
This wrapper script largely serves as a point documentation and convenience for
running Galaxy's Python tests. All Python tests shipped with Galaxy can be run with
pytest directly. Galaxy's client unit tests can be run with ``make client-test``
or ``pnpm`` directly as documented in detail in ``client/README.md``.
The main test types are as follows:
- API: These tests are located in lib/galaxy_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.
- Selenium: These are full stack tests meant to test the Galaxy UI with real
browsers and are located in lib/galaxy_test/selenium.
- ToolShed: These are tests that test ToolShed related functionality. These are
located in lib/tool_shed/test.
Python testing is done via pytest. Specific tests can be selected
using the syntax described at https://docs.pytest.org/en/latest/how-to/usage.html .
A few examples are shown below.
Run all API tests:
./run_tests.sh -api
The same test as above can be run using pytest directly as follows:
pytest lib/galaxy_test/api
However, when using pytest directly, output options defined in this
file aren't respected and a new Galaxy instance will be created for each
Test class (this scripts optimizes it so all tests can share a Galaxy
instance).
Run a full class of API tests:
./run_tests.sh -api lib/galaxy_test/api/test_tools.py::TestToolsApi
Run a specific API test:
./run_tests.sh -api lib/galaxy_test/api/test_tools.py::TestToolsApi::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 lib/galaxy_test/selenium/test_registration.py::TestRegistration::test_reregister_username_fails
Run an end-to-end test using Selenium against a running server while watching client (fastest iterating on client tests):
GALAXY_SKIP_CLIENT_BUILD=1 GALAXY_RUN_WITH_TEST_TOOLS=1 ./run.sh & # run Galaxy on 8080 with test tools and skip client build
make client-dev-server & # watch for client changes and serve on 8081
export GALAXY_TEST_EXTERNAL=http://localhost:8081/ # Target tests at server.
. .venv/bin/activate # source the virtualenv so can skip run_tests.sh.
pytest lib/galaxy_test/selenium/test_workflow_editor.py::TestWorkflowEditor::test_data_input
Some tests create new users but most tests can just use a single user - you can adjust
these end-to-end tests to use a specific user by copying and updating the sample config:
cp lib/galaxy_test/selenium/jupyter/galaxy_selenium_context.yml.sample ./galaxy_selenium_context.yml
vi galaxy_selenium_context.yml # edit user and password, target galaxy server, etc..
Config keys map to environment variables:
local_galaxy_url -> GALAXY_TEST_SELENIUM_URL
login_email -> GALAXY_TEST_SELENIUM_USER_EMAIL
login_password -> GALAXY_TEST_SELENIUM_USER_PASSWORD
admin_api_key -> GALAXY_TEST_SELENIUM_ADMIN_API_KEY
selenium_galaxy_url -> GALAXY_TEST_EXTERNAL_FROM_SELENIUM
If you've setup this config file, the file can be used with any end-to-end/selenium/playwright test by
setting GALAXY_TEST_END_TO_END_CONFIG when calling pytest or run_tests.sh. So for example
the last line in that previous example run could become:
GALAXY_TEST_END_TO_END_CONFIG=./galaxy_selenium_context.yml pytest lib/galaxy_test/selenium/test_workflow_editor.py::TestWorkflowEditor::test_data_input
Run an end-to-end test using Playwright against a running server while watching client (fastest iterating on client tests):
GALAXY_SKIP_CLIENT_BUILD=1 GALAXY_RUN_WITH_TEST_TOOLS=1 ./run.sh & # run Galaxy on 8080 with test tools and skip client build
make client-dev-server & # watch for client changes and serve on 8081
export GALAXY_TEST_EXTERNAL=http://localhost:8081/ # Target tests at server.
. .venv/bin/activate # source the virtualenv so can skip run_tests.sh.
GALAXY_TEST_DRIVER_BACKEND=playwright pytest lib/galaxy_test/selenium/test_workflow_editor.py::TestWorkflowEditor::test_data_input
Playwright will probably require a browser installation:
. .venv/bin/activate
playwright install --with-deps
To run the tool tests for a specific framework test tool
listed in test/functional/tools/sample_tool_conf.xml.
./run_tests.sh -framework -id <tool_id>
If you'd like to skip this script and run it with pytest
directly a command like the following can be used. Note
the framework tools run with conda installation on but 99%
of the tools do not require this so this example includes
disabling that.
GALAXY_TEST_TOOL_CONF="test/functional/tools/sample_tool_conf.xml" GALAXY_CONFIG_OVERRIDE_CONDA_AUTO_INIT=false pytest test/functional/test_toolbox_pytest.py -k <tool_id> -m tool
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/chromium.org/driver/ .
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).
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 targeted 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...)
--coverage Generate a test coverage report. This option currently
works with every Python test, but the
results may not be reliable with Selenium or other
frameworks that primarily test the client.
--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)
--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.
--skip_flakey_fails Skip flakey tests on error (sets
GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR=1).
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.
General Test Environment Variables
GALAXY_TEST_COVERAGE If set, it is equivalent to passing the
--coverage option.
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_API_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
manageable - 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).
GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR
Skip tests annotated with @flakey on test errors.
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.
GALAXY_TEST_HISTORY_ID Some tests can target existing history ids, this option
is fairly limited and not compatible with parallel testing
so should be limited to debugging one-off tests.
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 lib/tool_shed/test/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.
GALAXY_TEST_DISABLE_ACCESS_LOG Do not log access messages.
GALAXY_TEST_LOG_LEVEL Set Galaxy server log level for tests
(default: DEBUG). E.g. WARNING to reduce output.
GALAXY_TEST_AXE_SCRIPT_URL URL of aXe script to use for accessibility testing.
GALAXY_TEST_SKIP_AXE Set this to '1' to skip aXe accessibility testing when
running selenium tests.
We're trying annotate API and Selenium tests with the resources they require
and create to make them more appropriate to run on established Galaxy instances.
The following variables can be used to disable certain classes of properly tests.
GALAXY_TEST_SKIP_IF_REQUIRES_ADMIN
GALAXY_TEST_SKIP_IF_REQUIRES_NEW_HISTORY
GALAXY_TEST_SKIP_IF_REQUIRES_NEW_LIBRARY
GALAXY_TEST_SKIP_IF_REQUIRES_NEW_USER
GALAXY_TEST_SKIP_IF_REQUIRES_NEW_PUBLISHED_OBJECTS
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 "$1" >/dev/null 2>/dev/null
}
debug=""
test_script="pytest"
report_file="run_functional_tests.html"
if [ -n "$GALAXY_TEST_COVERAGE" ]; then
coverage_arg="--with-coverage"
else
coverage_arg=""
fi
xunit_report_file=""
structured_data_report_file=""
structured_data_html=0
# Detect blocking I/O in async handlers during tests via aiocop
# (https://github.com/Feverup/aiocop). Set to 0 to disable.
GALAXY_TEST_AIOCOP=${GALAXY_TEST_AIOCOP:-1}
export GALAXY_TEST_AIOCOP
SKIP_CLIENT_BUILD=${GALAXY_SKIP_CLIENT_BUILD:-1}
if [ "$SKIP_CLIENT_BUILD" = "1" ]; then
skip_client_build="--skip-client-build"
else
skip_client_build=""
fi
# If in Jenkins environment, create xunit-${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
;;
-id|--id)
if [ $# -gt 1 ]; then
test_id=$2
shift 2
else
echo "ERROR: --id requires an argument" 1>&2
exit 1
fi
;;
-a|-api|--api)
GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE="True" # Run these tests with a non-trivial object store.
export GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE
GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/sample_tool_conf.xml"
marker="not cwl_conformance"
report_file="./run_api_tests.html"
if [ $# -gt 1 ]; then
api_script=$2
shift 2
else
api_script="./lib/galaxy_test/api"
shift 1
fi
;;
-cwl|--cwl)
GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE="True" # Run these tests with a non-trivial object store.
export GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE
GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/sample_tool_conf.xml"
marker="cwl_conformance"
report_file="./run_cwl_tests.html"
generate_cwl_conformance_tests=1
if [ $# -gt 1 ]; then
api_script=$2
shift 2
else
api_script="./lib/galaxy_test/api/cwl"
shift 1
fi
;;
-selenium|--selenium)
GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/sample_tool_conf.xml"
report_file="./run_selenium_tests.html"
skip_client_build=""
if [ $# -gt 1 ]; then
selenium_script=$2
shift 2
else
selenium_script="./lib/galaxy_test/selenium"
shift 1
fi
;;
-playwright|--playwright)
GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/sample_tool_conf.xml"
GALAXY_TEST_DRIVER_BACKEND="playwright"
export GALAXY_TEST_DRIVER_BACKEND
report_file="./run_playwright_tests.html"
skip_client_build=""
install_playwright_browers=(chromium)
if [ $# -gt 1 ]; then
selenium_script=$2
shift 2
else
selenium_script="./lib/galaxy_test/selenium"
shift 1
fi
;;
-t|-toolshed|--toolshed)
report_file="run_toolshed_tests.html"
if [ $# -gt 1 ]; then
toolshed_script=$2
shift 2
else
toolshed_script="./lib/tool_shed/test/functional"
shift 1
fi
;;
-clean_pyc|--clean_pyc)
find lib -iname '*pyc' -exec rm -rf {} \;
find test -iname '*pyc' -exec rm -rf {} \;
shift
;;
-skip_flakey_fails|--skip_flakey_fails)
GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR=1
export GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR
shift
;;
--external_url)
export GALAXY_TEST_EXTERNAL=$2
shift 2
;;
--external_master_key)
export GALAXY_CONFIG_MASTER_API_KEY=$2
shift 2
;;
--external_user_key)
export GALAXY_TEST_USER_API_KEY=$2
shift 2
;;
-f|-framework|--framework|--framework-tools)
GALAXY_TEST_TOOL_CONF="test/functional/tools/sample_tool_conf.xml"
marker="tool"
report_file="run_framework_tests.html"
framework_test=1
shift 1
;;
-w|-framework-workflows|--framework-workflows)
marker="workflow"
report_file="run_framework_workflows_tests.html"
framework_workflows_test=1
shift 1
;;
-d|-data_managers|--data_managers)
marker="data_manager"
report_file="run_data_managers_tests.html"
data_managers_test=1
shift 1
;;
-main|-main_tools|--main_tools)
GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample"
marker="tool"
report_file="run_framework_tests.html"
framework_test=1
shift 1
;;
-r|--report_file)
if [ $# -gt 1 ]; then
report_file=$2
shift 2
else
echo "ERROR: --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 "ERROR: --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 "ERROR: --structured_data_report_file requires an argument" 1>&2
exit 1
fi
;;
--structured_data_html)
structured_data_html=1
shift
;;
--verbose_errors)
GALAXY_TEST_VERBOSE_ERRORS=True
export GALAXY_TEST_VERBOSE_ERRORS
shift
;;
--ci_test_metrics)
GALAXY_CONFIG_OVERRIDE_STATSD_PREFIX="galaxy"
export GALAXY_CONFIG_OVERRIDE_STATSD_PREFIX
GALAXY_CONFIG_OVERRIDE_STATSD_HOST="localhost"
export GALAXY_CONFIG_OVERRIDE_STATSD_HOST
GALAXY_CONFIG_OVERRIDE_STATSD_INFLUXDB="true"
export GALAXY_CONFIG_OVERRIDE_STATSD_INFLUXDB
GALAXY_CONFIG_OVERRIDE_DATABASE_LOG_QUERY_COUNTS="true"
export GALAXY_CONFIG_OVERRIDE_DATABASE_LOG_QUERY_COUNTS
GALAXY_CONFIG_OVERRIDE_ENABLE_PER_REQUEST_SQL_DEBUGGING="true"
export GALAXY_CONFIG_OVERRIDE_ENABLE_PER_REQUEST_SQL_DEBUGGING
GALAXY_CONFIG_OVERRIDE_STATSD_MOCK_CALLS="true"
export GALAXY_CONFIG_OVERRIDE_STATSD_MOCK_CALLS
shift
;;
-c|--coverage)
# Must have coverage installed (try `which coverage`) - only works with pytest
# for now. Would be great to get this to work with functional tests though.
coverage_arg="--with-coverage"
shift
;;
--debug)
debug="--pdb"
shift
;;
-u|-unit|--unit)
report_file="run_unit_tests.html"
unit_extra='--doctest-modules
--ignore lib/galaxy/datatypes/converters/
--ignore lib/galaxy/jobs/runners/chronos.py
--ignore lib/galaxy/model/migrations/alembic
--ignore lib/galaxy/tools/bundled
--ignore lib/galaxy/web/proxy/js/node_modules/
--ignore lib/galaxy_test
--ignore lib/tool_shed/test
--ignore lib/tool_shed/webapp/controllers
--ignore=lib/tool_shed/webapp/model/migrations/alembic/'
generate_cwl_conformance_tests=1
install_playwright_browers=(chromium firefox)
if [ $# -gt 1 ]; then
unit_extra="$unit_extra $2"
shift 2
else
unit_extra="$unit_extra lib test/unit"
shift 1
fi
;;
-i|-integration|--integration)
GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/sample_tool_conf.xml"
report_file="./run_integration_tests.html"
if [ $# -gt 1 ]; then
integration_extra=$2
shift 2
else
integration_extra="./test/integration"
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
;;
--skip-venv)
skip_venv='--skip-venv'
shift
;;
--no-create-venv)
no_create_venv='--no-create-venv'
shift
;;
--no-replace-pip|--replace-pip)
# Deprecated options
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
;;
--)
# Do not default to running the functional tests in this case, caller
# is opting to run specific tests so don't interfere with that by default.
shift
break
;;
-*)
echo "ERROR: Invalid option $1" 1>&2
show_help
exit 1
;;
*)
if [ -n "$1" ]; then
test_target="$1"
shift
fi
# Maybe we shouldn't break here but for now to pass more than one argument to the
# underlying test driver use -- instead.
break
;;
esac
done
if [ -z "$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 $skip_client_build --dev-wheels || exit 1
unset GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
fi
. ./scripts/common_startup_functions.sh
setup_python
if [ -n "$install_playwright_browers" ]; then
playwright install "${install_playwright_browers[@]}"
fi
if [ -n "$framework_test" ] || [ -n "$data_managers_test" ] ; then
if [ -n "$test_id" ]; then
selector="-k $test_id"
else
selector=""
fi
extra_args="test/functional/test_toolbox_pytest.py $selector"
elif [ -n "$framework_workflows_test" ]; then
if [ -n "$test_id" ]; then
selector="-k $test_id"
else
selector=""
fi
extra_args="lib/galaxy_test/workflow/test_framework_workflows.py $selector"
elif [ -n "$selenium_script" ]; then
extra_args="$selenium_script"
elif [ -n "$toolshed_script" ]; then
extra_args="$toolshed_script"
elif [ -n "$api_script" ]; then
extra_args="$api_script"
elif [ -n "$unit_extra" ]; then
extra_args="$unit_extra"
elif [ -n "$integration_extra" ]; then
extra_args="$integration_extra"
elif [ -n "$test_target" ] ; then
extra_args="$test_target"
else
echo "ERROR: No testing mode selected!" 1>&2
show_help
exit 1
fi
if [ -n "$xunit_report_file" ]; then
xunit_args="--junit-xml $xunit_report_file"
else
xunit_args=""
fi
if [ -n "$structured_data_report_file" ]; then
structured_data_args="--json-report --json-report-file $structured_data_report_file"
else
structured_data_args=""
fi
if [ -n "$generate_cwl_conformance_tests" ]; then
make generate-cwl-conformance-tests
fi
export GALAXY_TEST_TOOL_CONF
if [ "$coverage_arg" = '--with-coverage' ]; then
coverage_arg="--cov-report xml --cov=lib"
fi
if [ -n "$marker" ]; then
marker_args=(-m "$marker")
else
marker_args=()
fi
args=(-v $debug $structured_data_args --html "$report_file" --self-contained-html $coverage_arg $xunit_args $extra_args "${marker_args[@]}" "$@")
"$test_script" "${args[@]}"
exit_status=$?
echo "Testing complete. HTML report is in \"$report_file\"." 1>&2
if [ -n "$coverage_arg" ] && [ -f .coverage ]; then
echo "Total coverage: $(coverage report --format=total)%" 1>&2
fi
if [ "$structured_data_html" = '1' ]; then
python scripts/tests_markdown.py --output_path "${structured_data_report_file%.json}.html" "$structured_data_report_file"
fi
exit ${exit_status}
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