def testListCLI(self):
"""
Test that we can list clis, get help for each, and get the xml spec for
each.
"""
from girder.plugins.slicer_cli_web import rest_slicer_cli
from girder.api.rest import Resource
restResource = Resource()
cli_args = ('--list_cli', )
cli_list = self._runTest(cli_args, contains=['"NucleiDetection"'])
cli_list = json.loads(cli_list)
self.assertIn('NucleiDetection', cli_list)
for cli in cli_list:
cli_args = (cli, '--help')
# Each cli's help must mention usage, its own name, and that you
# can output xml
self._runTest(cli_args, contains=['usage:', cli, '--xml'])
cli_args = (cli, '--xml')
# The xml output needs to have a tile and an executable tag
xml = self._runTest(cli_args,
contains=[
'<executable>', '<title>', '</executable>',
'</title>'
])
if '<' in xml:
xml = xml[xml.index('<'):]
try:
rest_slicer_cli.genHandlerToRunDockerCLI(
'dockerimage', os.environ.get('CLI_CWD'), xml,
restResource)
except Exception:
sys.stderr.write('Failed in generating endpoints for %s' % cli)
raise
def test_genHandlerToRunDockerCLI(self):
from girder.plugins.slicer_cli_web import docker_resource
from girder.plugins.slicer_cli_web import rest_slicer_cli
xmlpath = os.path.join(os.path.dirname(__file__), 'data', 'ExampleSpec.xml')
cliXML = open(xmlpath, 'rb').read()
resource = docker_resource.DockerResource('test')
handlerFunc = rest_slicer_cli.genHandlerToRunDockerCLI(
'dockerImage', 'data', cliXML, resource)
self.assertIsNotNone(handlerFunc)
job = handlerFunc(params={
'inputImageFile_girderFileId': str(self.file['_id']),
'secondImageFile_girderFileId': str(self.file['_id']),
'outputStainImageFile_1_girderFolderId': str(self.folder['_id']),
'outputStainImageFile_1_name': 'sample1.png',
'outputStainImageFile_2_girderFolderId': str(self.folder['_id']),
'outputStainImageFile_2_name': 'sample2.png',
'stainColor_1': '[0.5, 0.5, 0.5]',
'stainColor_2': '[0.2, 0.3, 0.4]',
'returnparameterfile_girderFolderId': str(self.folder['_id']),
'returnparameterfile_name': 'output.data',
})
self.assertHasKeys(
job['kwargs']['inputs'],
['inputImageFile', 'stainColor_1', 'stainColor_2'])
self.assertEqual(job['kwargs']['inputs']['inputImageFile']['id'], str(self.file['_id']))
self.assertEqual(job['kwargs']['inputs']['stainColor_1']['data'], '[0.5, 0.5, 0.5]')
self.assertEqual(job['kwargs']['inputs']['stainColor_1']['type'], 'number_list')
self.assertHasKeys(
job['kwargs']['outputs'],
['outputStainImageFile_1', 'outputStainImageFile_2', 'returnparameterfile'])
self.assertEqual(len(job['kwargs']['task']['inputs']), 5)
self.assertEqual(len(job['kwargs']['task']['outputs']), 3)
