https://github.com/galaxyproject/galaxy
Tip revision: 95daf69b372fa829325be561dc0a9907da0bea81 authored by Nate Coraor on 15 December 2016, 17:49:39 UTC
Merge branch 'release_15.07' into release_15.10
Merge branch 'release_15.07' into release_15.10
Tip revision: 95daf69
run_tests.sh
#!/bin/sh
pwd_dir=$(pwd)
cd `dirname $0`
./scripts/common_startup.sh
# A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/
rm -f run_functional_tests.log
show_help() {
cat <<EOF
'${0##*/} (test_path)' for testing all the tools in functional directory
'${0##*/} -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)
'${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
'${0##*/} -toolshed (test_path)' for running all the test scripts in the ./test/tool_shed/functional directory
'${0##*/} -workflow test.xml' for running a workflow test case as defined by supplied workflow xml test file (experimental)
'${0##*/} -installed' for running tests of Tool Shed installed tools
'${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'
'${0##*/} -unit (test_path)' for running all unit tests (doctests in lib and tests in test/unit)
'${0##*/} -qunit' for running qunit JavaScript tests
'${0##*/} -qunit testname' for running single JavaScript test with given name
'${0##*/} -casperjs (py_test_path)' for running casperjs JavaScript tests using a Python wrapper for consistency. py_test_path in casperjs_runner.py e.g. 'Test_04_HDAs' or 'Test_04_HDAs.test_00_HDA_states'.
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 TestUserInfo functional tests:
./run_tests.sh test/functional/test_user_info.py:TestUserInfo
Run a specific API test requiring the framework test tools:
./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_map_over_with_output_format_actions
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).
--xunit_report_file Path of XUnit report to produce (for Python Galaxy functional tests).
--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.
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() {
if ! exists "grunt";
then
echo "Grunt not on path, cannot run these tests."
exit 1
fi
}
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:-"galaxy/testing-base:15.10.0"}
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
docker $DOCKER_EXTRA_ARGS run $DOCKER_RUN_EXTRA_ARGS -e "GALAXY_TEST_DATABASE_TYPE=$db_type" --rm -v `pwd`:/galaxy $DOCKER_IMAGE "$@"
exit $?
fi
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
;;
-t|-toolshed|--toolshed)
test_script="./test/tool_shed/functional_tests.py"
report_file="run_toolshed_tests.html"
if [ $# -gt 1 ]; then
toolshed_script=$2
shift 2
else
toolshed_script="./test/tool_shed/functional"
shift 1
fi
;;
-with_framework_test_tools|--with_framework_test_tools)
with_framework_test_tools_arg="-with_framework_test_tools"
shift
;;
-w|-workflow|--workflow)
if [ $# -gt 1 ]; then
workflow_file=$2
workflow_test=1
shift 2
else
echo "--workflow requires an argument" 1>&2
exit 1
fi
;;
-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
;;
-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
;;
--)
shift
break
;;
-*)
echo "invalid option: $1" 1>&2;
show_help
exit 1
;;
*)
break;
;;
esac
done
if [ -n "$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$class -framework"
elif [ -n "$data_managers_test" ] ; then
[ -n "$test_id" ] && class=":TestForDataManagerTool_$test_id" || class=""
extra_args="functional.test_data_managers$class -data_managers"
elif [ -n "$workflow_test" ]; then
extra_args="functional.workflow:WorkflowTestCase $workflow_file"
elif [ -n "$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 "$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
python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $with_framework_test_tools_arg $extra_args
else
ensure_grunt
if [ -n "$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