def testGirderInputSpec(models):
# Set an API_URL so we can use the spec outside of a rest request
Setting().set(PluginSettings.API_URL, 'http://127.0.0.1')
Setting().set(PluginSettings.DIRECT_PATH, True)
spec = utils.girderInputSpec(models['adminFolder'], resourceType='folder')
assert spec['id'] == str(models['adminFolder']['_id'])
assert spec['resource_type'] == 'folder'
assert not spec['fetch_parent']
assert 'direct_path' not in spec
spec = utils.girderInputSpec(models['sampleFile'], resourceType='file')
assert spec['id'] == str(models['sampleFile']['_id'])
assert spec['resource_type'] == 'file'
assert not spec['fetch_parent']
assert 'direct_path' in spec
Setting().set(PluginSettings.DIRECT_PATH, False)
spec = utils.girderInputSpec(models['sampleFile'], resourceType='file')
assert not spec['fetch_parent']
assert 'direct_path' not in spec
Setting().set(PluginSettings.DIRECT_PATH, True)
spec = utils.girderInputSpec(models['sampleFile'], resourceType='file', fetchParent=True)
assert spec['fetch_parent']
assert 'direct_path' not in spec
def _transformInputs(self, inputs, token):
"""
Validates and sanitizes the input bindings. If they are Girder inputs, adds
the necessary token info. If the token does not allow DATA_READ, or if the user
does not have read access to the resource, raises an AccessException.
"""
transformed = {}
for k, v in six.viewitems(inputs):
if v['mode'] == 'girder':
ensureTokenScopes(token, TokenScope.DATA_READ)
rtype = v.get('resource_type', 'file')
if rtype not in {'file', 'item', 'folder'}:
raise ValidationException(
'Invalid input resource_type: %s.' % rtype)
resource = self.model(rtype).load(v['id'],
level=AccessType.READ,
user=self.getCurrentUser(),
exc=True)
transformed[k] = utils.girderInputSpec(resource,
resourceType=rtype,
token=token,
dataFormat='none')
elif v['mode'] == 'inline':
transformed[k] = {'mode': 'inline', 'data': v['data']}
else:
raise ValidationException('Invalid input mode: %s.' %
v['mode'])
return transformed
def _transformInputs(self, inputs, token):
"""
Validates and sanitizes the input bindings. If they are Girder inputs, adds
the necessary token info. If the token does not allow DATA_READ, or if the user
does not have read access to the resource, raises an AccessException.
"""
transformed = {}
for k, v in six.viewitems(inputs):
if v['mode'] == 'girder':
ensureTokenScopes(token, TokenScope.DATA_READ)
rtype = v.get('resource_type', 'file')
if rtype not in {'file', 'item', 'folder'}:
raise ValidationException('Invalid input resource_type: %s.' % rtype)
resource = self.model(rtype).load(
v['id'], level=AccessType.READ, user=self.getCurrentUser(), exc=True)
transformed[k] = utils.girderInputSpec(
resource, resourceType=rtype, token=token, dataFormat='none')
elif v['mode'] == 'inline':
transformed[k] = {
'mode': 'inline',
'data': v['data']
}
else:
raise ValidationException('Invalid input mode: %s.' % v['mode'])
return transformed
def testWorkerStatusEndpoint(server, models):
# Create a job to be handled by the worker plugin
job = Job().createJob(
title='title', type='foo', handler='worker_handler',
user=models['admin'], public=False, args=(), kwargs={})
job['kwargs'] = {
'jobInfo': utils.jobInfoSpec(job),
'inputs': [
utils.girderInputSpec(models['adminFolder'], resourceType='folder')
],
'outputs': [
utils.girderOutputSpec(models['adminFolder'], token=models['adminToken'])
]
}
job = Job().save(job)
assert job['status'] == JobStatus.INACTIVE
# Schedule the job
with mock.patch('celery.Celery') as celeryMock:
instance = celeryMock.return_value
instance.send_task.return_value = FakeAsyncResult()
Job().scheduleJob(job)
# Call the worker status endpoint
resp = server.request('/worker/status', method='GET', user=models['admin'])
assertStatusOk(resp)
for key in ['report', 'stats', 'ping', 'active', 'reserved']:
assert key in resp.json
def testWorkerCancel(models):
jobModel = Job()
job = jobModel.createJob(
title='title', type='foo', handler='worker_handler',
user=models['admin'], public=False, args=(), kwargs={})
job['kwargs'] = {
'jobInfo': utils.jobInfoSpec(job),
'inputs': [
utils.girderInputSpec(models['adminFolder'], resourceType='folder')
],
'outputs': [
utils.girderOutputSpec(models['adminFolder'], token=models['adminToken'])
]
}
job = jobModel.save(job)
assert job['status'] == JobStatus.INACTIVE
# Schedule the job, make sure it is sent to celery
with mock.patch('celery.Celery') as celeryMock, \
mock.patch('girder_worker.girder_plugin.event_handlers.AsyncResult') as asyncResult:
instance = celeryMock.return_value
instance.send_task.return_value = FakeAsyncResult()
jobModel.scheduleJob(job)
jobModel.cancelJob(job)
asyncResult.assert_called_with('fake_id', app=mock.ANY)
# Check we called revoke
asyncResult.return_value.revoke.assert_called_once()
job = jobModel.load(job['_id'], force=True)
assert job['status'] == CustomJobStatus.CANCELING
def testWorker(server, models):
# Test the settings
resp = server.request('/system/setting', method='PUT', params={
'list': json.dumps([{
'key': PluginSettings.BROKER,
'value': 'amqp://[email protected]'
}, {
'key': PluginSettings.BACKEND,
'value': 'amqp://[email protected]'
}])
}, user=models['admin'])
assertStatusOk(resp)
# Create a job to be handled by the worker plugin
jobModel = Job()
job = jobModel.createJob(
title='title', type='foo', handler='worker_handler',
user=models['admin'], public=False, args=(), kwargs={})
job['kwargs'] = {
'jobInfo': utils.jobInfoSpec(job),
'inputs': [
utils.girderInputSpec(models['adminFolder'], resourceType='folder')
],
'outputs': [
utils.girderOutputSpec(models['adminFolder'], token=models['adminToken'])
]
}
job = jobModel.save(job)
assert job['status'] == JobStatus.INACTIVE
# Schedule the job, make sure it is sent to celery
with mock.patch('celery.Celery') as celeryMock:
instance = celeryMock.return_value
instance.send_task.return_value = FakeAsyncResult()
jobModel.scheduleJob(job)
# Make sure we sent the job to celery
assert len(celeryMock.mock_calls) == 2
assert celeryMock.mock_calls[0][1] == ('girder_worker',)
assert celeryMock.mock_calls[0][2] == {
'broker': 'amqp://[email protected]',
'backend': 'amqp://[email protected]'
}
sendTaskCalls = celeryMock.return_value.send_task.mock_calls
assert len(sendTaskCalls) == 1
assert sendTaskCalls[0][1] == (
'girder_worker.run', job['args'], job['kwargs'])
assert 'headers' in sendTaskCalls[0][2]
assert 'jobInfoSpec' in sendTaskCalls[0][2]['headers']
# Make sure we got and saved the celery task id
job = jobModel.load(job['_id'], force=True)
assert job['celeryTaskId'] == 'fake_id'
assert job['status'] == JobStatus.QUEUED
def testWorkerDifferentTask(server, models):
# Test the settings
resp = server.request('/system/setting', method='PUT', params={
'key': PluginSettings.API_URL,
'value': 'bad value'
}, user=models['admin'])
assertStatus(resp, 400)
assert resp.json['message'] == 'API URL must start with http:// or https://.'
resp = server.request('/system/setting', method='PUT', params={
'list': json.dumps([{
'key': PluginSettings.BROKER,
'value': 'amqp://[email protected]'
}, {
'key': PluginSettings.BACKEND,
'value': 'amqp://[email protected]'
}])
}, user=models['admin'])
assertStatusOk(resp)
# Create a job to be handled by the worker plugin
jobModel = Job()
job = jobModel.createJob(
title='title', type='foo', handler='worker_handler',
user=models['admin'], public=False, args=(), kwargs={},
otherFields={
'celeryTaskName': 'some_other.task',
'celeryQueue': 'my_other_q'
})
job['kwargs'] = {
'jobInfo': utils.jobInfoSpec(job),
'inputs': [
utils.girderInputSpec(models['adminFolder'], resourceType='folder')
],
'outputs': [
utils.girderOutputSpec(models['adminFolder'], token=models['adminToken'])
]
}
job = jobModel.save(job)
# Schedule the job, make sure it is sent to celery
app = celery.getCeleryApp()
with mock.patch.object(app, 'send_task') as sendTask:
sendTask.return_value = FakeAsyncResult()
jobModel.scheduleJob(job)
sendTaskCalls = sendTask.mock_calls
assert len(sendTaskCalls) == 1
assert sendTaskCalls[0][1] == (
'some_other.task', job['args'], job['kwargs'])
assert 'queue' in sendTaskCalls[0][2]
assert sendTaskCalls[0][2]['queue'] == 'my_other_q'
def scoreSubmission(self, submission, apiUrl):
"""
Run a Girder Worker job to score a submission.
"""
phase = Phase().load(submission['phaseId'], force=True)
folder = Folder().load(submission['folderId'], force=True)
user = User().load(submission['creatorId'], force=True)
otherFields = {}
if 'overallScore' in submission:
otherFields['rescoring'] = True
jobTitle = '%s submission: %s' % (phase['name'], folder['name'])
job = Job().createJob(
title=jobTitle, type='covalic_score', handler='worker_handler', user=user,
otherFields=otherFields)
scoreUserId = Setting().get(PluginSettings.SCORING_USER_ID)
if not scoreUserId:
raise GirderException(
'No scoring user ID is set. Please set one on the plugin configuration page.')
scoreUser = User().load(scoreUserId, force=True)
if not scoreUser:
raise GirderException('Invalid scoring user setting (%s).' % scoreUserId)
scoreToken = Token().createToken(user=scoreUser, days=7)
Folder().setUserAccess(
folder, user=scoreUser, level=AccessType.READ, save=True)
groundTruth = Folder().load(phase['groundTruthFolderId'], force=True)
if not Phase().hasAccess(phase, user=scoreUser, level=AccessType.ADMIN):
Phase().setUserAccess(
phase, user=scoreUser, level=AccessType.ADMIN, save=True)
if not Folder().hasAccess(groundTruth, user=scoreUser, level=AccessType.READ):
Folder().setUserAccess(
groundTruth, user=scoreUser, level=AccessType.READ, save=True)
task = phase.get('scoreTask', {})
image = task.get('dockerImage') or 'girder/covalic-metrics:latest'
containerArgs = task.get('dockerArgs') or [
'--groundtruth=$input{groundtruth}',
'--submission=$input{submission}'
]
kwargs = {
'task': {
'name': jobTitle,
'mode': 'docker',
'docker_image': image,
'container_args': containerArgs,
'inputs': [{
'id': 'submission',
'type': 'string',
'format': 'text',
'target': 'filepath',
'filename': 'submission.zip'
}, {
'id': 'groundtruth',
'type': 'string',
'format': 'text',
'target': 'filepath',
'filename': 'groundtruth.zip'
}],
'outputs': [{
'id': '_stdout',
'format': 'string',
'type': 'string'
}]
},
'inputs': {
'submission': utils.girderInputSpec(
folder, 'folder', token=scoreToken),
'groundtruth': utils.girderInputSpec(
groundTruth, 'folder', token=scoreToken)
},
'outputs': {
'_stdout': {
'mode': 'http',
'method': 'POST',
'format': 'string',
'url': '/'.join((apiUrl, 'covalic_submission',
str(submission['_id']), 'score')),
'headers': {'Girder-Token': scoreToken['_id']}
}
},
'jobInfo': utils.jobInfoSpec(job),
'validate': False,
'auto_convert': False,
'cleanup': True
}
job['kwargs'] = kwargs
job['covalicSubmissionId'] = submission['_id']
job = Job().save(job)
Job().scheduleJob(job)
submission['jobId'] = job['_id']
return self.save(submission, validate=False)