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Merge pull request #3342 from jmchilton/remove_workflow_testing

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Remove workflow testing stuff in test/functional and references.
This commit is contained in:
Martin Cech
2016-12-23 23:09:20 +01:00
committed by GitHub
parent 8463c8a202 a7818e3065
commit 58c1828c4c
3 changed files with 0 additions and 212 deletions
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run_tests.sh
-14
View File
@@ -14,7 +14,6 @@ cat <<EOF
'${0##*/} -list' for listing all the tool ids
'${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##*/} -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'
@@ -346,16 +345,6 @@ do
GALAXY_TEST_USER_API_KEY=$2
shift 2
;;
-w|-workflow|--workflow)
if [ $# -gt 1 ]; then
workflow_file=$2
workflow_test=1
shift 2
else
echo "--workflow requires an argument" 1>&2
exit 1
fi
;;
-f|-framework|--framework)
report_file="run_framework_tests.html"
framework_test=1;
@@ -547,9 +536,6 @@ elif [ -n "$selenium_test" ] ; then
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 "$workflow_test" ]; then
GALAXY_TEST_WORKFLOW_FILE="$workflow_file"
extra_args="functional.workflow:WorkflowTestCase"
elif [ -n "$toolshed_script" ]; then
extra_args="$toolshed_script"
elif [ -n "$api_script" ]; then
scripts/functional_tests.py
-11
View File
@@ -88,22 +88,11 @@ class DataManagersGalaxyTestDriver(driver_util.GalaxyTestDriver):
)
class WorkflowGalaxyTestDriver(driver_util.GalaxyTestDriver):
"""Galaxy-style nose TestDriver for testing a Galaxy workflow."""
def build_tests(self):
"""Setup WorkflowTestCase for test execution."""
import functional.workflow
functional.workflow.WorkflowTestCase.master_api_key = get_master_api_key()
functional.workflow.WorkflowTestCase.user_api_key = get_user_api_key()
TEST_DRIVERS = {
'-migrated': MigratedToolsGalaxyTestDriver,
'-installed': InstalledToolsGalaxyTestDriver,
'-framework': FrameworkToolsGalaxyTestDriver,
'-data_managers': DataManagersGalaxyTestDriver,
'-workflow': WorkflowGalaxyTestDriver,
'-selenium': SeleniumGalaxyTestDriver,
}
test/functional/workflow.py
-187
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@@ -1,187 +0,0 @@
from __future__ import print_function
import os
import sys
from json import dumps, load
from logging import getLogger
from base.interactor import GalaxyInteractorApi, stage_data_in_history
from base.twilltestcase import TwillTestCase
from galaxy.tools.test import parse_output_elems, parse_param_elem, require_file, test_data_iter
from galaxy.util import bunch, parse_xml
log = getLogger( __name__ )
class WorkflowTestCase( TwillTestCase ):
"""
Kind of a shell of a test case for running workflow tests. Probably
needs to look more like test_toolbox.
"""
workflow_test_file = os.environ.get("GALAXY_TEST_WORKFLOW_FILE", None)
user_api_key = None
master_api_key = None
def test_workflow( self, workflow_test_file=None ):
maxseconds = 120
workflow_test_file = workflow_test_file or WorkflowTestCase.workflow_test_file
assert workflow_test_file
workflow_test = parse_test_file( workflow_test_file )
galaxy_interactor = GalaxyWorkflowInteractor( self )
# Calling workflow https://github.com/jmchilton/blend4j/blob/master/src/test/java/com/github/jmchilton/blend4j/galaxy/WorkflowsTest.java
# Import workflow
workflow_id, step_id_map, output_defs = self.__import_workflow( galaxy_interactor, workflow_test.workflow )
# Stage data and history for workflow
test_history = galaxy_interactor.new_history()
stage_data_in_history( galaxy_interactor, workflow_test.test_data(), test_history )
# Build workflow parameters
uploads = galaxy_interactor.uploads
ds_map = {}
for step_index, input_dataset_label in workflow_test.input_datasets():
# Upload is {"src": "hda", "id": hid}
try:
upload = uploads[ workflow_test.upload_name( input_dataset_label ) ]
except KeyError:
raise AssertionError( "Failed to find upload with label %s in uploaded datasets %s" % ( input_dataset_label, uploads ) )
ds_map[ step_id_map[ step_index ] ] = upload
payload = {
"history": "hist_id=%s" % test_history,
"ds_map": dumps( ds_map ),
"workflow_id": workflow_id,
}
run_response = galaxy_interactor.run_workflow( payload ).json()
outputs = run_response[ 'outputs' ]
if not len( outputs ) == len( output_defs ):
msg_template = "Number of outputs [%d] created by workflow execution does not equal expected number from input file [%d]."
msg = msg_template % ( len( outputs ), len( output_defs ) )
raise AssertionError( msg )
galaxy_interactor.wait_for_ids( test_history, outputs )
for expected_output_def in workflow_test.outputs:
# Get the correct hid
name, outfile, attributes = expected_output_def
output_testdef = bunch.Bunch( name=name, outfile=outfile, attributes=attributes )
output_data = outputs[ int( name ) ]
try:
galaxy_interactor.verify_output( test_history, output_data, output_testdef=output_testdef, shed_tool_id=None, maxseconds=maxseconds )
except Exception:
for stream in ['stdout', 'stderr']:
stream_output = galaxy_interactor.get_job_stream( test_history, output_data, stream=stream )
print(self._format_stream( stream_output, stream=stream, format=True ), file=sys.stderr)
raise
def __import_workflow( self, galaxy_interactor, workflow ):
"""
Import workflow into Galaxy and return id and mapping of step ids.
"""
workflow_info = galaxy_interactor.import_workflow( workflow ).json()
try:
workflow_id = workflow_info[ 'id' ]
except KeyError:
raise AssertionError( "Failed to find id for workflow import response %s" % workflow_info )
# Well ideally the local copy of the workflow would have the same step ids
# as the one imported through the API, but API workflow imports are 1-indexed
# and GUI exports 0-indexed as of mid-november 2013.
imported_workflow = galaxy_interactor.read_workflow( workflow_id )
step_id_map = {}
local_steps_ids = sorted( int( step_id ) for step_id in workflow[ 'steps' ].keys() )
imported_steps_ids = sorted( int( step_id ) for step_id in imported_workflow[ 'steps' ].keys() )
for local_step_id, imported_step_id in zip( local_steps_ids, imported_steps_ids ):
step_id_map[ local_step_id ] = imported_step_id
output_defs = []
for local_step_id in local_steps_ids:
step_def = workflow['steps'][ str( local_step_id ) ]
output_defs.extend( step_def.get( "outputs", [] ) )
return workflow_id, step_id_map, output_defs
def parse_test_file( workflow_test_file ):
tree = parse_xml( workflow_test_file )
root = tree.getroot()
input_elems = root.findall( "input" )
required_files = []
dataset_dict = {}
for input_elem in input_elems:
name, value, attrib = parse_param_elem( input_elem )
require_file( name, value, attrib, required_files )
dataset_dict[ name ] = value
outputs = parse_output_elems( root )
workflow_file_rel_path = root.get( 'file' )
if not workflow_file_rel_path:
raise Exception( "Workflow test XML must declare file attribute pointing to workflow under test." )
# TODO: Normalize this path, prevent it from accessing arbitrary files on system.
worfklow_file_abs_path = os.path.join( os.path.dirname( workflow_test_file ), workflow_file_rel_path )
return WorkflowTest(
dataset_dict,
required_files,
worfklow_file_abs_path,
outputs=outputs,
)
class WorkflowTest( object ):
def __init__( self, dataset_dict, required_files, workflow_file, outputs ):
self.dataset_dict = dataset_dict
self.required_files = required_files
self.workflow = load( open( workflow_file, "r" ) )
self.outputs = outputs
def test_data( self ):
return test_data_iter( self.required_files )
def upload_name( self, input_dataset_label ):
return self.dataset_dict[ input_dataset_label ]
def input_datasets( self ):
steps = self.workflow[ "steps" ]
log.info("in input_datasets with steps %s" % steps)
for step_index, step_dict in steps.items():
if step_dict.get( "name", None ) == "Input dataset":
yield int( step_index ), step_dict[ "inputs" ][0][ "name" ]
class GalaxyWorkflowInteractor(GalaxyInteractorApi):
def __init__( self, twill_test_case ):
super(GalaxyWorkflowInteractor, self).__init__( twill_test_case )
def import_workflow( self, workflow_rep ):
payload = { "workflow": dumps( workflow_rep ) }
return self._post( "workflows/upload", data=payload )
def run_workflow( self, data ):
return self._post( "workflows", data=data )
def read_workflow( self, id ):
return self._get( "workflows/%s" % id ).json()
def wait_for_ids( self, history_id, ids ):
self.twill_test_case.wait_for( lambda: not all( [ self.__dataset_ready( history_id, id ) for id in ids ] ), maxseconds=120 )
def __dataset_ready( self, history_id, id ):
contents = self._get( 'histories/%s/contents' % history_id ).json()
for content in contents:
if content["id"] == id:
state = content[ 'state' ]
state_ready = self._state_ready( state, error_msg="Dataset creation failed for dataset with name %s." % content[ 'name' ] )
return state_ready
return False