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_fragments_badmolecule_notfound(self):
from magmaweb.job import FragmentNotFound
request = testing.DummyRequest(matchdict={
'molid': 72,
'scanid': 641
},
params={'node': ''})
job = self.fake_job()
job.db.fragments.side_effect = FragmentNotFound
views = JobViews(job, request)
from pyramid.httpexceptions import HTTPNotFound
with self.assertRaises(HTTPNotFound):
views.fragments()
def test_incompletejob(self):
request = testing.DummyRequest(params={'start': 0, 'limit': 10})
job = self.fake_job()
job.is_complete = Mock()
JobViews(job, request)
job.is_complete.assert_called_with()
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'])
def test_runinfojson(self):
request = testing.DummyRequest()
job = self.fake_job()
from magmaweb.models import Run
job.db.runInfo.return_value = Run(
ionisation_mode=-1,
skip_fragmentation=True,
ms_intensity_cutoff=200000.0,
msms_intensity_cutoff=50,
mz_precision=4.0,
mz_precision_abs=0.002,
use_all_peaks=True,
ms_filename='F123456.mzxml',
abs_peak_cutoff=1000,
max_ms_level=3,
precursor_mz_precision=0.01,
max_broken_bonds=4,
description='My first description',
max_water_losses=1,
)
views = JobViews(job, request)
response = views.runinfojson()
self.assertEqual(
response, {
'success':
True,
'data':
dict(
ms_data_area='',
ms_data_format='mzxml',
ionisation_mode=-1,
ms_intensity_cutoff=200000.0,
msms_intensity_cutoff=50,
mz_precision=4.0,
mz_precision_abs=0.002,
abs_peak_cutoff=1000,
max_ms_level=3,
precursor_mz_precision=0.01,
max_broken_bonds=4,
max_water_losses=1,
)
})
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_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)
