def setUp(self):
self.settings = {'jobfactory.root_dir': '/somedir',
'restricted': False,
'ncpus': 1}
self.config = testing.setUp(settings=self.settings)
self.config.add_route('status.json', '/status/{jobid}.json')
self.jobid = '3ad25048-26f6-11e1-851e-00012e260790'
self.post = {'key': 'value'}
self.jq = Mock(JobQuery)
self.jobquery = Mock(JobQuery)
jobmeta = JobMeta(uuid.UUID(self.jobid), owner='bob')
self.job = Job(jobmeta, '/mydir', Mock(JobDb))
self.job.jobquery = Mock(return_value=self.jobquery)
self.job.db.maxMSLevel.return_value = 1
self.job.db.moleculesTotalCount.return_value = 1
self.jobid2 = 'fe144547-cf16-44bb-8e97-e2ffe5675154'
jobmeta2 = JobMeta(uuid.UUID(self.jobid2), owner='bob')
self.job2 = Job(jobmeta2, '/mydir', Mock(JobDb))
self.job2.jobquery = Mock(return_value=self.jobquery)
self.job2.db.maxMSLevel.return_value = 1
self.job2.db.moleculesTotalCount.return_value = 1
self.rpc = RpcViews(self.job, testing.DummyRequest(post=self.post))
self.rpc.new_job = Mock(return_value=self.job2)
self.rpc.job_factory.submitQuery = Mock()
def test_new_job(self):
request = testing.DummyRequest()
request.user = User('bob', 'Bob Example', '*****@*****.**')
parent_job = self.job
rpc = RpcViews(parent_job, request)
rpc.job_factory.cloneJob = Mock(return_value=self.job2)
job = rpc.new_job()
self.assertEqual(job, self.job2)
rpc.job_factory.cloneJob.assert_called_with(parent_job, 'bob')
def test_new_job(self):
request = testing.DummyRequest()
request.user = User('bob', 'Bob Example', '*****@*****.**')
parent_job = self.job
rpc = RpcViews(parent_job, request)
rpc.job_factory.cloneJob = Mock(return_value=self.job2)
job = rpc.new_job()
self.assertEqual(job, self.job2)
rpc.job_factory.cloneJob.assert_called_with(parent_job, 'bob')
def setUp(self):
self.settings = {'jobfactory.root_dir': '/somedir',
'restricted': False,
}
self.config = testing.setUp(settings=self.settings)
self.config.add_route('status.json', '/status/{jobid}.json')
self.jobid = '3ad25048-26f6-11e1-851e-00012e260790'
self.post = {'key': 'value'}
self.jq = Mock(JobQuery)
self.jobquery = Mock(JobQuery)
jobmeta = JobMeta(uuid.UUID(self.jobid), owner='bob')
self.job = Job(jobmeta, '/mydir', Mock(JobDb))
self.job.jobquery = Mock(return_value=self.jobquery)
self.job.db.maxMSLevel.return_value = 1
self.job.db.moleculesTotalCount.return_value = 1
self.jobid2 = 'fe144547-cf16-44bb-8e97-e2ffe5675154'
jobmeta2 = JobMeta(uuid.UUID(self.jobid2), owner='bob')
self.job2 = Job(jobmeta2, '/mydir', Mock(JobDb))
self.job2.jobquery = Mock(return_value=self.jobquery)
self.job2.db.maxMSLevel.return_value = 1
self.job2.db.moleculesTotalCount.return_value = 1
self.rpc = RpcViews(self.job, testing.DummyRequest(post=self.post))
self.rpc.new_job = Mock(return_value=self.job2)
self.rpc.job_factory.submitQuery = Mock()
def test_construct(self):
request = testing.DummyRequest()
rpc = RpcViews(self.job, request)
self.assertIsInstance(rpc.job_factory, JobFactory)
self.assertEqual(request, rpc.request)
self.assertEqual(self.job, rpc.job)
class RpcViewsTestCase(unittest.TestCase):
def setUp(self):
self.settings = {'jobfactory.root_dir': '/somedir',
'restricted': False,
}
self.config = testing.setUp(settings=self.settings)
self.config.add_route('status.json', '/status/{jobid}.json')
self.jobid = '3ad25048-26f6-11e1-851e-00012e260790'
self.post = {'key': 'value'}
self.jq = Mock(JobQuery)
self.jobquery = Mock(JobQuery)
jobmeta = JobMeta(uuid.UUID(self.jobid), owner='bob')
self.job = Job(jobmeta, '/mydir', Mock(JobDb))
self.job.jobquery = Mock(return_value=self.jobquery)
self.job.db.maxMSLevel.return_value = 1
self.job.db.moleculesTotalCount.return_value = 1
self.jobid2 = 'fe144547-cf16-44bb-8e97-e2ffe5675154'
jobmeta2 = JobMeta(uuid.UUID(self.jobid2), owner='bob')
self.job2 = Job(jobmeta2, '/mydir', Mock(JobDb))
self.job2.jobquery = Mock(return_value=self.jobquery)
self.job2.db.maxMSLevel.return_value = 1
self.job2.db.moleculesTotalCount.return_value = 1
self.rpc = RpcViews(self.job, testing.DummyRequest(post=self.post))
self.rpc.new_job = Mock(return_value=self.job2)
self.rpc.job_factory.submitQuery = Mock()
def tearDown(self):
testing.tearDown()
def _assert_status_callback_url(self):
expected_cb_url = 'http://example.com/status/'
expected_cb_url += 'fe144547-cf16-44bb-8e97-e2ffe5675154.json'
self.job2.jobquery.assert_called_with(expected_cb_url, False)
def test_construct(self):
request = testing.DummyRequest()
rpc = RpcViews(self.job, request)
self.assertIsInstance(rpc.job_factory, JobFactory)
self.assertEqual(request, rpc.request)
self.assertEqual(self.job, rpc.job)
def test_new_job(self):
request = testing.DummyRequest()
request.user = User('bob', 'Bob Example', '*****@*****.**')
parent_job = self.job
rpc = RpcViews(parent_job, request)
rpc.job_factory.cloneJob = Mock(return_value=self.job2)
job = rpc.new_job()
self.assertEqual(job, self.job2)
rpc.job_factory.cloneJob.assert_called_with(parent_job, 'bob')
def test_addstructure(self):
self.jobquery.add_structures.return_value = self.jq
response = self.rpc.add_structures()
self.jobquery.add_structures.assert_called_with(self.post, True)
self.job2.db.maxMSLevel.assert_called_with()
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_addstructure_with_db(self):
from colander import Invalid, SchemaNode, String
invalid = Invalid(SchemaNode(String()))
self.jobquery.add_structures.side_effect = invalid
self.rpc.request.POST['structure_database'] = 'pubchem'
self.rpc.add_structures()
self.jobquery.annotate.assert_called_with(self.post,
False
)
def test_addstructure_with_db_and_no_msdata(self):
self.job2.db.maxMSLevel.return_value = 0
from colander import Invalid, SchemaNode, String
invalid = Invalid(SchemaNode(String()))
self.jobquery.add_structures.side_effect = invalid
with self.assertRaises(Invalid):
self.rpc.add_structures()
def test_addmsdata(self):
post = {'ms_data': 'ms data', 'ms_data_file': ''}
self.rpc.request.POST = post
self.jobquery.add_ms_data.return_value = self.jq
response = self.rpc.add_ms_data()
self.jobquery.add_ms_data.assert_called_with(post, True)
self.job2.db.moleculesTotalCount.assert_called_with()
self.assertEqual(self.job2.ms_filename, 'Uploaded as text')
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_addmsdata_as_file(self):
from cgi import FieldStorage
ms_file = FieldStorage()
ms_file.filename = 'c:\bla\bla\F1234.mzxml'
post = {'ms_data_file': ms_file}
self.rpc.request.POST = post
self.jobquery.add_ms_data.return_value = self.jq
response = self.rpc.add_ms_data()
self.jobquery.add_ms_data.assert_called_with(post, True)
self.job2.db.moleculesTotalCount.assert_called_with()
self.assertEqual(self.job2.ms_filename, 'c:\bla\bla\F1234.mzxml')
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_metabolize(self):
self.jobquery.metabolize.return_value = self.jq
response = self.rpc.metabolize()
self.jobquery.metabolize.assert_called_with(self.post, True)
self.job2.db.maxMSLevel.assert_called_with()
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_metabolize_one(self):
self.jobquery.metabolize_one.return_value = self.jq
response = self.rpc.metabolize_one()
self.jobquery.metabolize_one.assert_called_with(self.post, True)
self.job2.db.maxMSLevel.assert_called_with()
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_annotate(self):
self.jobquery.annotate.return_value = self.jq
response = self.rpc.annotate()
self.jobquery.annotate.assert_called_with(self.post)
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_submit_query_withoutjobmanager(self):
from magmaweb.job import JobSubmissionError
from pyramid.httpexceptions import HTTPInternalServerError
import json
q = Mock(side_effect=JobSubmissionError())
self.rpc.job_factory.submitQuery = q
with self.assertRaises(HTTPInternalServerError) as e:
self.rpc.submit_query({}, {})
expected_json = {'success': False, 'msg': 'Unable to submit query'}
self.assertEquals(json.loads(e.exception.body), expected_json)
def test_assign_molecule2peak(self):
self.rpc.request.POST = {'scanid': 641,
'mz': 109.029563903808,
'molid': 72}
response = self.rpc.assign_molecule2peak()
assigned_func = self.job.db.assign_molecule2peak
assigned_func.assert_called_with(641, 109.029563903808, 72)
self.assertEquals(response, {'success': True, 'jobid': self.jobid})
def test_unassign_molecule2peak(self):
self.rpc.request.POST = {'scanid': 641,
'mz': 109.029563903808}
response = self.rpc.unassign_molecule2peak()
unassign_func = self.job.db.unassign_molecule2peak
unassign_func.assert_called_with(641, 109.029563903808)
self.assertEquals(response, {'success': True, 'jobid': self.jobid})
class RpcViewsTestCase(unittest.TestCase):
def setUp(self):
self.settings = {'jobfactory.root_dir': '/somedir',
'restricted': False,
'ncpus': 1}
self.config = testing.setUp(settings=self.settings)
self.config.add_route('status.json', '/status/{jobid}.json')
self.jobid = '3ad25048-26f6-11e1-851e-00012e260790'
self.post = {'key': 'value'}
self.jq = Mock(JobQuery)
self.jobquery = Mock(JobQuery)
jobmeta = JobMeta(uuid.UUID(self.jobid), owner='bob')
self.job = Job(jobmeta, '/mydir', Mock(JobDb))
self.job.jobquery = Mock(return_value=self.jobquery)
self.job.db.maxMSLevel.return_value = 1
self.job.db.moleculesTotalCount.return_value = 1
self.jobid2 = 'fe144547-cf16-44bb-8e97-e2ffe5675154'
jobmeta2 = JobMeta(uuid.UUID(self.jobid2), owner='bob')
self.job2 = Job(jobmeta2, '/mydir', Mock(JobDb))
self.job2.jobquery = Mock(return_value=self.jobquery)
self.job2.db.maxMSLevel.return_value = 1
self.job2.db.moleculesTotalCount.return_value = 1
self.rpc = RpcViews(self.job, testing.DummyRequest(post=self.post))
self.rpc.new_job = Mock(return_value=self.job2)
self.rpc.job_factory.submitQuery = Mock()
def tearDown(self):
testing.tearDown()
def _assert_status_callback_url(self):
expected_cb_url = 'http://example.com/status/'
expected_cb_url += 'fe144547-cf16-44bb-8e97-e2ffe5675154.json'
self.job2.jobquery.assert_called_with(expected_cb_url, False, 1)
def test_construct(self):
request = testing.DummyRequest()
rpc = RpcViews(self.job, request)
self.assertIsInstance(rpc.job_factory, JobFactory)
self.assertEqual(request, rpc.request)
self.assertEqual(self.job, rpc.job)
def test_new_job(self):
request = testing.DummyRequest()
request.user = User('bob', 'Bob Example', '*****@*****.**')
parent_job = self.job
rpc = RpcViews(parent_job, request)
rpc.job_factory.cloneJob = Mock(return_value=self.job2)
job = rpc.new_job()
self.assertEqual(job, self.job2)
rpc.job_factory.cloneJob.assert_called_with(parent_job, 'bob')
def test_addstructure(self):
self.jobquery.add_structures.return_value = self.jq
response = self.rpc.add_structures()
self.jobquery.add_structures.assert_called_with(self.post, True)
self.job2.db.maxMSLevel.assert_called_with()
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_addstructure_with_db(self):
from colander import Invalid, SchemaNode, String
invalid = Invalid(SchemaNode(String()))
self.jobquery.add_structures.side_effect = invalid
self.rpc.request.POST['structure_database'] = 'pubchem'
self.rpc.add_structures()
self.jobquery.annotate.assert_called_with(self.post,
False
)
def test_addstructure_with_db_and_no_msdata(self):
self.job2.db.maxMSLevel.return_value = 0
from colander import Invalid, SchemaNode, String
invalid = Invalid(SchemaNode(String()))
self.jobquery.add_structures.side_effect = invalid
with self.assertRaises(Invalid):
self.rpc.add_structures()
def test_addmsdata(self):
post = {'ms_data': 'ms data', 'ms_data_file': ''}
self.rpc.request.POST = post
self.jobquery.add_ms_data.return_value = self.jq
response = self.rpc.add_ms_data()
self.jobquery.add_ms_data.assert_called_with(post, True)
self.job2.db.moleculesTotalCount.assert_called_with()
self.assertEqual(self.job2.ms_filename, 'Uploaded as text')
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_addmsdata_as_file(self):
from cgi import FieldStorage
ms_file = FieldStorage()
ms_file.filename = 'c:\bla\bla\F1234.mzxml'
post = {'ms_data_file': ms_file}
self.rpc.request.POST = post
self.jobquery.add_ms_data.return_value = self.jq
response = self.rpc.add_ms_data()
self.jobquery.add_ms_data.assert_called_with(post, True)
self.job2.db.moleculesTotalCount.assert_called_with()
self.assertEqual(self.job2.ms_filename, 'c:\bla\bla\F1234.mzxml')
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_metabolize(self):
self.jobquery.metabolize.return_value = self.jq
response = self.rpc.metabolize()
self.jobquery.metabolize.assert_called_with(self.post, True)
self.job2.db.maxMSLevel.assert_called_with()
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_metabolize_one(self):
self.jobquery.metabolize_one.return_value = self.jq
response = self.rpc.metabolize_one()
self.jobquery.metabolize_one.assert_called_with(self.post, True)
self.job2.db.maxMSLevel.assert_called_with()
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_annotate(self):
self.jobquery.annotate.return_value = self.jq
response = self.rpc.annotate()
self.jobquery.annotate.assert_called_with(self.post)
self.rpc.new_job.assert_called_with()
self._assert_status_callback_url()
self.rpc.job_factory.submitQuery.assert_called_with(self.jq, self.job2)
self.assertEquals(response, {'success': True, 'jobid': self.jobid2})
def test_submit_query_withoutjobmanager(self):
from magmaweb.job import JobSubmissionError
from pyramid.httpexceptions import HTTPInternalServerError
import json
q = Mock(side_effect=JobSubmissionError())
self.rpc.job_factory.submitQuery = q
with self.assertRaises(HTTPInternalServerError) as e:
self.rpc.submit_query({}, {})
expected_json = {'success': False, 'msg': 'Unable to submit query'}
self.assertEquals(json.loads(e.exception.body), expected_json)
def test_assign_molecule2peak(self):
self.rpc.request.POST = {'scanid': 641,
'mz': 109.029563903808,
'molid': 72}
response = self.rpc.assign_molecule2peak()
assigned_func = self.job.db.assign_molecule2peak
assigned_func.assert_called_with(641, 109.029563903808, 72)
self.assertEquals(response, {'success': True, 'jobid': self.jobid})
def test_unassign_molecule2peak(self):
self.rpc.request.POST = {'scanid': 641,
'mz': 109.029563903808}
response = self.rpc.unassign_molecule2peak()
unassign_func = self.job.db.unassign_molecule2peak
unassign_func.assert_called_with(641, 109.029563903808)
self.assertEquals(response, {'success': True, 'jobid': self.jobid})
