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, 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, 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
transaction.commit()
# We should have only one SDM
sdmexp = self.experiments.values()[0]
self.form = EnsembleExperimentHelper(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
transaction.commit()
# We should have only one SDM
sdmexp = self.experiments.values()[0]
self.form = EnsembleExperimentHelper(self.portal, sdmexp)
class ExperimentSDMAddTest(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]
self.datasets = self.portal[defaults.DATASETS_FOLDER_ID]
self.form = SDMExperimentHelper(self.portal)
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-experiment', self.experiments)
exp = self.experiments['my-experiment']
self.assertEqual(exp.environmental_datasets.keys(),
[unicode(self.form.current.UID())])
self.assertEqual(exp.environmental_datasets.values(),
[set([u'B01', u'B02'])])
# 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['function'], 'bioclim')
self.assertEqual(result.job_params[
'environmental_datasets'], exp.environmental_datasets)
# 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 sholud finish
transaction.commit()
self.assertEqual(jt.state, u'COMPLETED')
# and we should have a result as well
self.assertGreaterEqual(len(result.keys()), 1)
# TODO: assrt two result folders,....
# TODO: check mix of jt.state (in multistate scenario with queued,
# running etc. mixed)
@mock.patch('org.bccvl.tasks.compute.run_script')
def test_run_experiment_twice(self, mock_run_script):
# create experiment
form = self.form.get_form()
form.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
form.update()
# start experiment
jt = IExperimentJobTracker(self.experiments['my-experiment'])
self.assertEqual(jt.state, u'QUEUED')
# error
state = jt.start_job(form.request)
self.assertEqual(state[0], 'error')
# setup mock_run_script
mock_run_script.side_effect = self.form.mock_run_script
# finish current job
transaction.commit()
self.assertEqual(jt.state, u'COMPLETED')
# TODO: after commit tasks cause site to disappear and the
# following code will fail, bceause without site we can't find
# a catalog without whchi we can't finde the toolkit by uuid
jt.start_job(form.request)
self.assertEqual(jt.state, u'PARTIAL')
transaction.commit()
self.assertEqual(jt.state, u'COMPLETED')
def test_mixed_resolution_highest(self):
current_1k_uuid = unicode(
self.datasets[defaults.DATASETS_ENVIRONMENTAL_FOLDER_ID]['current_1k'].UID())
form = self.form.get_form()
form.request.form.update({
'form.buttons.create': 'Create',
# select 1k dataset as well
'form.widgets.scale_down': 'true',
'form.widgets.scale_down-empty-marker': 1,
'form.widgets.environmental_datasets.item.2': current_1k_uuid,
'form.widgets.environmental_datasets.item.2.item': [u'B01'],
'form.widgets.environmental_datasets.count': '3',
})
form.update()
# resolution should be set to the lowest of selected datasets
expmd = IBCCVLMetadata(self.experiments['my-experiment'])
self.assertEqual(expmd['resolution'], 'Resolution30s')
def test_mixed_resolution_lowest(self):
current_1k_uuid = unicode(
self.datasets[defaults.DATASETS_ENVIRONMENTAL_FOLDER_ID]['current_1k'].UID())
form = self.form.get_form()
form.request.form.update({
'form.buttons.create': 'Create',
# select 1k dataset as well
'form.widgets.scale_down': 'false',
'form.widgets.scale_down-empty-marker': 1,
'form.widgets.environmental_datasets.item.2': current_1k_uuid,
'form.widgets.environmental_datasets.item.2.item': [u'B01'],
'form.widgets.environmental_datasets.count': '3',
})
form.update()
# resolution should be set to the lowest of selected datasets
expmd = IBCCVLMetadata(self.experiments['my-experiment'])
self.assertEqual(expmd['resolution'], 'Resolution2_5m')
class ExperimentSDMAddTest(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]
self.datasets = self.portal[defaults.DATASETS_FOLDER_ID]
self.form = SDMExperimentHelper(self.portal)
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-experiment', self.experiments)
exp = self.experiments['my-experiment']
self.assertEqual(exp.environmental_datasets.keys(),
[unicode(self.form.current.UID())])
self.assertEqual(exp.environmental_datasets.values(),
[set([u'B01', u'B02'])])
# 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['function'], 'bioclim')
self.assertEqual(result.job_params['environmental_datasets'],
exp.environmental_datasets)
# 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 sholud finish
transaction.commit()
self.assertEqual(jt.state, u'COMPLETED')
# and we should have a result as well
self.assertGreaterEqual(len(result.keys()), 1)
# TODO: assrt two result folders,....
# TODO: check mix of jt.state (in multistate scenario with queued,
# running etc. mixed)
@mock.patch('org.bccvl.tasks.compute.run_script')
def test_run_experiment_twice(self, mock_run_script):
# create experiment
form = self.form.get_form()
form.request.form.update({
'form.buttons.save': 'Create and start',
})
# update form with updated request
form.update()
# start experiment
jt = IExperimentJobTracker(self.experiments['my-experiment'])
self.assertEqual(jt.state, u'QUEUED')
# error
state = jt.start_job(form.request)
self.assertEqual(state[0], 'error')
# setup mock_run_script
mock_run_script.side_effect = self.form.mock_run_script
# finish current job
transaction.commit()
self.assertEqual(jt.state, u'COMPLETED')
# TODO: after commit tasks cause site to disappear and the
# following code will fail, bceause without site we can't find
# a catalog without whchi we can't finde the toolkit by uuid
jt.start_job(form.request)
self.assertEqual(jt.state, u'PARTIAL')
transaction.commit()
self.assertEqual(jt.state, u'COMPLETED')
def test_mixed_resolution_highest(self):
current_1k_uuid = unicode(self.datasets[
defaults.DATASETS_ENVIRONMENTAL_FOLDER_ID]['current_1k'].UID())
form = self.form.get_form()
form.request.form.update({
'form.buttons.create':
'Create',
# select 1k dataset as well
'form.widgets.scale_down':
'true',
'form.widgets.scale_down-empty-marker':
1,
'form.widgets.environmental_datasets.item.2':
current_1k_uuid,
'form.widgets.environmental_datasets.item.2.item': [u'B01'],
'form.widgets.environmental_datasets.count':
'3',
})
form.update()
# resolution should be set to the lowest of selected datasets
expmd = IBCCVLMetadata(self.experiments['my-experiment'])
self.assertEqual(expmd['resolution'], 'Resolution30s')
def test_mixed_resolution_lowest(self):
current_1k_uuid = unicode(self.datasets[
defaults.DATASETS_ENVIRONMENTAL_FOLDER_ID]['current_1k'].UID())
form = self.form.get_form()
form.request.form.update({
'form.buttons.create':
'Create',
# select 1k dataset as well
'form.widgets.scale_down':
'false',
'form.widgets.scale_down-empty-marker':
1,
'form.widgets.environmental_datasets.item.2':
current_1k_uuid,
'form.widgets.environmental_datasets.item.2.item': [u'B01'],
'form.widgets.environmental_datasets.count':
'3',
})
form.update()
# resolution should be set to the lowest of selected datasets
expmd = IBCCVLMetadata(self.experiments['my-experiment'])
self.assertEqual(expmd['resolution'], 'Resolution2_5m')