def setUp(self, mock_run_script):
self.portal = self.layer['portal']
self.experiments = self.portal[defaults.EXPERIMENTS_FOLDER_ID]
# create and run sdm experiment
formhelper = SDMExperimentHelper(self.portal)
sdmform = formhelper.get_form()
sdmform.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
sdmform.update()
# setup mock_run_script
mock_run_script.side_effect = formhelper.mock_run_script
# We should have only one SDM
sdmexp = self.experiments.values()[0]
transaction.commit()
# setup som threshold values our projection
sdmproj = sdmexp.values()[0]['proj_test.tif']
md = IBCCVLMetadata(sdmproj)
# there is only one layer
layermd = md['layers'].values()[0]
layermd['min'] = 0.0
layermd['max'] = 1.0
transaction.commit()
self.form = BiodiverseExperimentHelper(self.portal, sdmexp)
def setUp(self):
self.portal = self.layer['portal']
self.experiments = self.portal[defaults.EXPERIMENTS_FOLDER_ID]
# create and run sdm experiment
sdmform = SDMExperimentHelper(self.portal).get_form()
sdmform.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
sdmform.update()
transaction.commit()
# We should have only one SDM
sdmexp = self.experiments.values()[0]
self.form = BiodiverseExperimentHelper(self.portal, sdmexp)
def setUp(self, mock_run_script):
self.portal = self.layer['portal']
self.experiments = self.portal[defaults.EXPERIMENTS_FOLDER_ID]
# create and run sdm experiment
formhelper = SDMExperimentHelper(self.portal)
sdmform = formhelper.get_form()
sdmform.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
sdmform.update()
# setup mock_run_script
mock_run_script.side_effect = formhelper.mock_run_script
# We should have only one SDM
sdmexp = self.experiments.values()[0]
transaction.commit()
# setup som threshold values our projection
sdmproj = sdmexp.values()[0]['proj_test.tif']
md = IBCCVLMetadata(sdmproj)
# there is only one layer
layermd = md['layers'].values()[0]
layermd['min'] = 0.0
layermd['max'] = 1.0
transaction.commit()
self.form = BiodiverseExperimentHelper(self.portal, sdmexp)
class ExperimentBiodiverseAddTest(unittest.TestCase):
# Use functional layer for now to get a new demostorage layer for each test
layer = BCCVL_FUNCTIONAL_TESTING
# integration testing gives only a new transaction for each test
# (rolled back at end)
# layer = BCCVL_INTEGRATION_TESTING
@mock.patch('pwd.getpwuid',
mock.MagicMock(return_value=mock.MagicMock(pw_name='bccvl')))
@mock.patch('org.bccvl.tasks.compute.run_script')
def setUp(self, mock_run_script):
self.portal = self.layer['portal']
self.experiments = self.portal[defaults.EXPERIMENTS_FOLDER_ID]
# create and run sdm experiment
formhelper = SDMExperimentHelper(self.portal)
sdmform = formhelper.get_form()
sdmform.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
sdmform.update()
# setup mock_run_script
mock_run_script.side_effect = formhelper.mock_run_script
# We should have only one SDM
sdmexp = self.experiments.values()[0]
transaction.commit()
# setup som threshold values our projection
sdmproj = sdmexp.values()[0]['proj_test.tif']
md = IBCCVLMetadata(sdmproj)
# there is only one layer
layermd = md['layers'].values()[0]
layermd['min'] = 0.0
layermd['max'] = 1.0
transaction.commit()
self.form = BiodiverseExperimentHelper(self.portal, sdmexp)
def test_add_experiment_missing_input(self):
form = self.form.get_form()
# remove required field
del form.request.form['form.widgets.IDublinCore.title']
form.request.form.update({
'form.buttons.create': 'Create',
})
# submit form
form.update()
errors = [e for e in form.widgets.errors]
self.assertEqual(len(errors), 1)
# check self.experiments still empty
# IStatusMessage
@mock.patch('org.bccvl.tasks.compute.run_script')
def test_add_experiment(self, mock_run_script):
form = self.form.get_form()
form.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
form.update()
self.assertEqual(form.status, u'')
self.assertEqual(len(form.widgets.errors), 0)
self.assertIn('my-bd-experiment', self.experiments)
exp = self.experiments['my-bd-experiment']
# TODO: update asserts
self.assertEqual(exp.projection,
{unicode(self.form.sdmexp.UID()):
{unicode(self.form.sdmproj.UID()): {'value': Decimal('0.5'), 'label': '0.5'}}})
# FIXME: submitting with an empty model list doesn't cause form to fail
self.assertEqual(exp.cluster_size, 5000)
# get result container: (there is only one)
self.assertEqual(len(exp.objectIds()), 1)
result = exp.objectValues()[0]
# FIXME: test result.job_params
self.assertEqual(result.job_params['cluster_size'], 5000)
self.assertEqual(result.job_params['projections'], [{
"dataset": self.form.sdmproj.UID(),
"threshold": {'label': '0.5', 'value': Decimal('0.5')}}])
# no result files yet
self.assertEqual(len(result.keys()), 0)
# test job state
jt = IExperimentJobTracker(exp)
self.assertEqual(jt.state, u'QUEUED')
# setup mock_run_script
mock_run_script.side_effect = self.form.mock_run_script
# after transaction commit the job should finish
transaction.commit()
self.assertEqual(jt.state, u'COMPLETED')
# and we should have a result as well
self.assertGreaterEqual(len(result.keys()), 1)
class ExperimentBiodiverseAddTest(unittest.TestCase):
# Use functional layer for now to get a new demostorage layer for each test
layer = BCCVL_FUNCTIONAL_TESTING
# integration testing gives only a new transaction for each test
# (rolled back at end)
# layer = BCCVL_INTEGRATION_TESTING
@mock.patch('pwd.getpwuid',
mock.MagicMock(return_value=mock.MagicMock(pw_name='bccvl')))
@mock.patch('org.bccvl.tasks.compute.run_script')
def setUp(self, mock_run_script):
self.portal = self.layer['portal']
self.experiments = self.portal[defaults.EXPERIMENTS_FOLDER_ID]
# create and run sdm experiment
formhelper = SDMExperimentHelper(self.portal)
sdmform = formhelper.get_form()
sdmform.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
sdmform.update()
# setup mock_run_script
mock_run_script.side_effect = formhelper.mock_run_script
# We should have only one SDM
sdmexp = self.experiments.values()[0]
transaction.commit()
# setup som threshold values our projection
sdmproj = sdmexp.values()[0]['proj_test.tif']
md = IBCCVLMetadata(sdmproj)
# there is only one layer
layermd = md['layers'].values()[0]
layermd['min'] = 0.0
layermd['max'] = 1.0
transaction.commit()
self.form = BiodiverseExperimentHelper(self.portal, sdmexp)
def test_add_experiment_missing_input(self):
form = self.form.get_form()
# remove required field
del form.request.form['form.widgets.IDublinCore.title']
form.request.form.update({
'form.buttons.create': 'Create',
})
# submit form
form.update()
errors = [e for e in form.widgets.errors]
self.assertEqual(len(errors), 1)
# check self.experiments still empty
# IStatusMessage
@mock.patch('org.bccvl.tasks.compute.run_script')
def test_add_experiment(self, mock_run_script):
form = self.form.get_form()
form.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
form.update()
self.assertEqual(form.status, u'')
self.assertEqual(len(form.widgets.errors), 0)
self.assertIn('my-bd-experiment', self.experiments)
exp = self.experiments['my-bd-experiment']
# TODO: update asserts
self.assertEqual(
exp.projection, {
unicode(self.form.sdmexp.UID()): {
unicode(self.form.sdmproj.UID()): {
'value': Decimal('0.5'),
'label': '0.5'
}
}
})
# FIXME: submitting with an empty model list doesn't cause form to fail
self.assertEqual(exp.cluster_size, 5000)
# get result container: (there is only one)
self.assertEqual(len(exp.objectIds()), 1)
result = exp.objectValues()[0]
# FIXME: test result.job_params
self.assertEqual(result.job_params['cluster_size'], 5000)
self.assertEqual(result.job_params['projections'],
[{
"dataset": self.form.sdmproj.UID(),
"threshold": {
'label': '0.5',
'value': Decimal('0.5')
}
}])
# no result files yet
self.assertEqual(len(result.keys()), 0)
# test job state
jt = IExperimentJobTracker(exp)
self.assertEqual(jt.state, u'QUEUED')
# setup mock_run_script
mock_run_script.side_effect = self.form.mock_run_script
# after transaction commit the job should finish
transaction.commit()
self.assertEqual(jt.state, u'COMPLETED')
# and we should have a result as well
self.assertGreaterEqual(len(result.keys()), 1)
class ExperimentBiodiverseAddTest(unittest.TestCase):
# Use functional layer for now to get a new demostorage layer for each test
layer = BCCVL_FUNCTIONAL_TESTING
# integration testing gives only a new transaction for each test (rolled back at end)
#layer = BCCVL_INTEGRATION_TESTING
def setUp(self):
self.portal = self.layer['portal']
self.experiments = self.portal[defaults.EXPERIMENTS_FOLDER_ID]
# create and run sdm experiment
sdmform = SDMExperimentHelper(self.portal).get_form()
sdmform.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
sdmform.update()
transaction.commit()
# We should have only one SDM
sdmexp = self.experiments.values()[0]
self.form = BiodiverseExperimentHelper(self.portal, sdmexp)
def test_add_experiment_missing_input(self):
form = self.form.get_form()
# remove required field
del form.request.form['form.widgets.IDublinCore.title']
form.request.form.update({
'form.buttons.create': 'Create',
})
# submit form
form.update()
errors = [e for e in form.widgets.errors]
self.assertEqual(len(errors), 1)
# check self.experiments still empty
# IStatusMessage
def test_add_experiment(self):
form = self.form.get_form()
form.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
form.update()
self.assertEqual(form.status, u'')
self.assertEqual(len(form.widgets.errors), 0)
self.assertIn('my-bd-experiment', self.experiments)
exp = self.experiments['my-bd-experiment']
# TODO: update asserts
self.assertEqual(
exp.projection, {
unicode(self.form.sdmexp.UID()): {
unicode(self.form.sdmproj.UID()): {
'value': Decimal('0.0'),
'label': '0.0'
}
}
})
# FIXME: submitting with an empty model list doesn't cause form to fail
self.assertEqual(exp.cluster_size, 5000)
# get result container: (there is only one)
self.assertEqual(len(exp.objectIds()), 1)
result = exp.objectValues()[0]
# FIXME: test result.job_params
self.assertEqual(result.job_params['cluster_size'], 5000)
self.assertEqual(result.job_params['projections'],
[{
"dataset": self.form.sdmproj.UID(),
"threshold": {
'label': '0.0',
'value': Decimal('0.0')
}
}])
# no result files yet
self.assertEqual(len(result.keys()), 0)
# test job state
jt = IJobTracker(exp)
self.assertEqual(jt.state, u'QUEUED')
# after transaction commit the job should finish
transaction.commit()
self.assertEqual(jt.state, u'COMPLETED')
# and we should have a result as well
self.assertGreaterEqual(len(result.keys()), 1)
