def test_datasetwrapper(self):
from mecat.models import DatasetWrapper, Sample
sample_desc = "My Description for Sample created in test_datasetwrapper()"
sample = Sample(experiment=self.experiment, description=sample_desc)
sample.save()
self.assertEqual(sample.description, sample_desc)
self.assertEqual(sample.experiment, self.experiment)
from tardis.tardis_portal.models import Dataset
dataset_desc = "My Description for Dataset created in test_datasetwrapper()"
dataset = Dataset(description=dataset_desc, experiment=self.experiment)
dataset.save()
sample_from_db = Sample.objects.get(description=sample_desc)
dataset_from_db = Dataset.objects.get(description=dataset_desc)
datasetwrapper = DatasetWrapper(sample=sample_from_db, dataset=dataset_from_db)
datasetwrapper.save()
self.assertEqual(datasetwrapper.sample, sample_from_db)
self.assertEqual(datasetwrapper.dataset, dataset_from_db)
datasetwrapper_from_db = DatasetWrapper.objects.get(sample__description=sample_desc)
self.assertEqual(datasetwrapper_from_db.dataset.pk, dataset_from_db.pk)
def test_sample(self):
from mecat.models import Sample
desc = "My Description for Sample created in test_sample()"
sample = Sample(experiment=self.experiment, description=desc)
name = "Sample 1"
forcode1 = "0001"
forcode2 = "0002"
forcode3 = "0003 - three"
notes = "A note that is not that long"
sample.name = name
sample.forcode1 = forcode1
sample.forcode2 = forcode2
sample.forcode3 = forcode3
sample.notes = notes
sample.save()
self.assertEqual(sample.description, desc)
self.assertEqual(sample.experiment, self.experiment)
self.assertEqual(sample.name, name)
self.assertEqual(sample.forcode1, forcode1)
self.assertEqual(sample.forcode2, forcode2)
self.assertEqual(sample.forcode3, forcode3)
self.assertEqual(sample.notes, notes)
sample_from_db = Sample.objects.get(description=desc)
self.assertEqual(sample_from_db.experiment, self.experiment)
def add_sample(self, cleaned_data):
logger.debug('adding sample')
logger.debug(cleaned_data)
sample_name = cleaned_data['name']
sample_description = cleaned_data['description']
sample_forcode1 = cleaned_data['forcode_1']
sample_forcode2 = cleaned_data['forcode_2']
sample_forcode3 = cleaned_data['forcode_3']
sample_notes = cleaned_data['notes']
new_sample = Sample(experiment_id=self.experiment_id,
name=sample_name,
description=sample_description,
forcode1=sample_forcode1,
forcode2=sample_forcode2,
forcode3=sample_forcode3,
notes=sample_notes)
new_sample.save()
def test_existing_datasetwrappers(self):
s1 = Sample(name="s1", description="s1 description", experiment=self._create_experiment())
s2 = Sample(name="s2", description="s2 description", experiment=self._create_experiment())
s1.save()
s2.save()
d1 = DatasetWrapper(name="dw1", description="dw1 description", sample=s1)
d2 = DatasetWrapper(name="dw2", description="dw2 description", sample=s1)
d3 = DatasetWrapper(name="dw1", description="dw1 description", sample=s2)
d4 = DatasetWrapper(name="dw2", description="dw2 description", sample=s1)
d5 = DatasetWrapper(name="", description="", sample=s1)
d1.save()
d2.save()
from mecat.forms import existing
self.assertTrue(existing(d1))
self.assertTrue(existing(d2))
self.assertFalse(existing(d3))
self.assertTrue(existing(d4)) # d4 is identical to d2 so it's considered existing
self.assertFalse(existing(d5))
d5.save()
self.assertTrue(existing(d5))
def _create_samples(self, exp):
sample_desc = {"s1 name": "s1 desc", "s2 name": "s2 desc"}
for name, desc in sample_desc.items():
sample = Sample(name=name, description=desc, experiment=exp)
sample.save()
def _registerExperimentDocument(filename, created_by, expid=None,
owners=[], username=None):
'''
Register the experiment document and return the experiment id.
:param filename: path of the document to parse (METS or notMETS)
:type filename: string
:param created_by: a User instance
:type created_by: :py:class:`django.contrib.auth.models.User`
:param expid: the experiment ID to use
:type expid: int
:param owners: a list of owners
:type owner: list
:param username: **UNUSED**
:rtype: int
'''
f = open(filename)
firstline = f.readline()
f.close()
if firstline.startswith('<experiment'):
logger.debug('processing simple xml')
processExperiment = ProcessExperiment()
eid = processExperiment.process_simple(filename, created_by, expid)
else:
logger.debug('processing METS')
eid = parseMets(filename, created_by, expid)
# Create a DatasetWrapper for each Dataset
experiment = Experiment.objects.get(pk=eid)
sample = Sample(experiment=experiment, name="Default Sample",
description="A default sample for %s" % experiment.title)
sample.save()
_create_wrappers_for_datasets(sample, experiment)
# Create a Project to wraps the experiment, then create a Sample that
# points to the experiment
project = Project(experiment=experiment)
project.save()
auth_key = ''
try:
auth_key = settings.DEFAULT_AUTH
except AttributeError:
logger.error('no default authentication for experiment ownership set (settings.DEFAULT_AUTH)')
force_user_create = False
try:
force_user_create = settings.DEFAULT_AUTH_FORCE_USER_CREATE
except AttributeError:
pass
if auth_key:
for owner in owners:
logger.debug('** Owner : %s' %owner)
# for each PI
if not owner:
continue
owner_username = None
if '@' in owner:
logger.debug('** Email as username **')
owner_username = auth_service.getUsernameByEmail(auth_key,
owner)
if not owner_username:
logger.debug('** No existing user!! **')
owner_username = owner
owner_user = auth_service.getUser(auth_key, owner_username,
force_user_create=force_user_create)
if owner_user:
# if exist, create ACL
logger.debug('registering owner: ' + owner)
e = Experiment.objects.get(pk=eid)
acl = ExperimentACL(experiment=e,
pluginId=django_user,
entityId=str(owner_user.id),
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True,
aclOwnershipType=ExperimentACL.OWNER_OWNED)
acl.save()
# Also update email
if '@' in owner:
owner_user.email = owner
owner_user.save()
return eid