def test_moleculesjson_nrscaneqfilter(self):
filter_in = '[{"type":"numeric","comparison":"eq",'
filter_in += '"value":1,"field":"nhits"}]'
filter_expected = [{
"type": "numeric",
"comparison": "eq",
"value": 1,
"field": "nhits"
}]
request = testing.DummyRequest(params={
'start': 0,
'limit': 10,
'filter': filter_in
})
job = self.fake_job()
views = JobViews(job, request)
views.moleculesjson()
job.db.molecules.assert_called_with(
start=0,
limit=10,
sorts=[],
scanid=None,
filters=filter_expected,
molid=None,
mz=None,
)
job.db.scansWithMolecules.assert_called_with(filters=filter_expected,
molid=None,
mz=None,
scanid=None)
def test_moleculesjson_molpage(self):
request = testing.DummyRequest(params={
'start': 0,
'limit': 10,
'molid': 1,
})
job = self.fake_job()
views = JobViews(job, request)
job.db.molecules.return_value = {
'total': 3,
'rows': [1, 2, 3],
'page': 1
}
response = views.moleculesjson()
self.assertEqual(
response, {
'totalUnfiltered': 3,
'total': 3,
'rows': [1, 2, 3],
'molid': 1,
'page': 1,
'scans': [4, 5]
})
def test_moleculesjson_scanidfilter(self):
request = testing.DummyRequest(params={
'start': 0,
'limit': 10,
'scanid': 641
})
job = self.fake_job()
views = JobViews(job, request)
views.moleculesjson()
job.db.molecules.assert_called_with(
start=0,
limit=10,
sorts=[],
scanid=641,
filters=[],
molid=None,
mz=None,
)
def test_moleculessdf(self):
job = self.fake_job()
job.db.molecules2sdf.return_value = 'bla'
request = testing.DummyRequest(params={'start': 0, 'limit': 10})
views = JobViews(job, request)
views.moleculesjson = Mock(return_value={'rows': []})
response = views.moleculessdf()
job.db.molecules2sdf.assert_called_with([], cols=[])
self.assertEqual(response.content_type, 'chemical/x-mdl-sdfile')
self.assertEqual(response.body, 'bla')
def test_moleculesjson_scansfilteredonmol(self):
request = testing.DummyRequest(params={
'start': 0,
'limit': 10,
'molid': 1,
})
job = self.fake_job()
views = JobViews(job, request)
job.db.molecules.return_value = {
'total': 3,
'rows': [1, 2, 3],
'page': 1,
'molid': 1
}
views.moleculesjson()
job.db.scansWithMolecules.assert_called_once_with(filters=[],
molid=1,
mz=None,
scanid=None)
def test_moleculessdf_somecols(self):
job = self.fake_job()
job.db.molecules2sdf.return_value = 'bla'
request = testing.DummyRequest(params={
'start': 0,
'limit': 10,
'cols': '["name","score"]'
})
views = JobViews(job, request)
views.moleculesjson = Mock(return_value={'rows': []})
views.moleculessdf()
job.db.molecules2sdf.assert_called_with([], cols=['name', 'score'])
def test_moleculescsv(self):
csv = StringIO()
csv.write('bla')
job = self.fake_job()
job.db.molecules2csv.return_value = csv
request = testing.DummyRequest(params={'start': 0, 'limit': 10})
views = JobViews(job, request)
views.moleculesjson = Mock(return_value={'rows': []})
response = views.moleculescsv()
self.assertEqual(response.content_type, 'text/csv')
self.assertEqual(response.body, b'bla')
def test_moleculesjson_notfilledreturn(self):
request = testing.DummyRequest(params={'start': 0, 'limit': 10})
job = self.fake_job()
job.db.moleculesTotalCount.return_value = 0
views = JobViews(job, request)
response = views.moleculesjson()
self.assertEqual(response, {
'totalUnfiltered': 0,
'total': 3,
'rows': [1, 2, 3],
'scans': [4, 5]
})
def test_moleculescsv_somecols(self):
csv = StringIO()
csv.write('bla')
job = self.fake_job()
job.db.molecules2csv.return_value = csv
request = testing.DummyRequest(params={
'start': 0,
'limit': 10,
'cols': '["name","score"]'
})
views = JobViews(job, request)
rows = [{'name': 'foo', 'score': 'bar', 'id': 123}]
views.moleculesjson = Mock(return_value={'rows': rows})
views.moleculescsv()
job.db.molecules2csv.assert_called_with(rows, cols=['name', 'score'])