def setUp(self):
self.user = User(username='******',
password='******',
email='*****@*****.**')
self.user.save()
self.exp = Experiment(approved=True,
title='title1',
institution_name='institution1',
description='description1',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.uid = 0
self.url = 'http://remotetardis:8080'
self.mock_ts = flexmock()
flexmock(TransferClient).new_instances(self.mock_ts)
self.mock_integrity = flexmock()
flexmock(IntegrityCheck).new_instances(self.mock_integrity)
self.status = {
'human_status': 'this is a readable status',
'message': 'this is a message'
}
def setUp(self):
# create a test user
self.user = User.objects.create_user(username='******',
email='',
password='******')
# create a public experiment
self.experiment1 = Experiment(title='Experiment 1',
created_by=self.user,
public=True)
self.experiment1.save()
# create a non-public experiment
self.experiment2 = Experiment(title='Experiment 2',
created_by=self.user,
public=False)
self.experiment2.save()
# dataset1 belongs to experiment1
self.dataset1 = Dataset(experiment=self.experiment1)
self.dataset1.save()
# dataset2 belongs to experiment2
self.dataset2 = Dataset(experiment=self.experiment2)
self.dataset2.save()
# absolute path first
filename = 'testfile.txt'
self.dest1 = abspath(
join(settings.FILE_STORE_PATH,
'%s/%s/' % (self.experiment1.id, self.dataset1.id)))
self.dest2 = abspath(
join(settings.FILE_STORE_PATH,
'%s/%s/' % (self.experiment2.id, self.dataset2.id)))
if not exists(self.dest1):
makedirs(self.dest1)
if not exists(self.dest2):
makedirs(self.dest2)
testfile1 = abspath(join(self.dest1, filename))
f = open(testfile1, 'w')
f.write("Hello World!\n")
f.close()
testfile2 = abspath(join(self.dest2, filename))
f = open(testfile2, 'w')
f.write("Hello World!\n")
f.close()
self.dataset_file1 = Dataset_File(dataset=self.dataset1,
filename=filename,
protocol='tardis',
url='tardis://%s' % filename)
self.dataset_file1.save()
self.dataset_file2 = Dataset_File(dataset=self.dataset2,
filename=basename(filename),
protocol='tardis',
url='tardis://%s' % filename)
self.dataset_file2.save()
def setUp(self):
# Create test owner without enough details
username, email, password = ("testuser", "*****@*****.**", "password")
user = User.objects.create_user(username, email, password)
# Need UserAuthentication
UserAuthentication(userProfile=user.userprofile, username=username, authenticationMethod="localdb").save()
# Create staging dir
from os import path, makedirs
staging_dir = path.join(settings.STAGING_PATH, username)
if not path.exists(staging_dir):
makedirs(staging_dir)
# Ensure that staging dir is set up properly
expect(get_full_staging_path(username)).to_be_truthy()
# Create test experiment and make user the owner of it
experiment = Experiment(title="Text Experiment", institution_name="Test Uni", created_by=user)
experiment.save()
acl = ObjectACL(
pluginId=django_user,
entityId=str(user.id),
content_object=experiment,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
acl.save()
self.dataset = Dataset(description="dataset description...")
self.dataset.save()
self.dataset.experiments.add(experiment)
self.dataset.save()
self.username, self.password = (username, password)
def setUp(self):
self.user = User(username='******',
password='******',
email='*****@*****.**')
self.user.save()
self.bad_exp = Experiment(approved=True,
title='title1',
institution_name='institution1',
description='description1',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.bad_exp.save()
self.bad_dataset = self._make_dataset(self.bad_exp, [
'file_that_exists',
'file_that_exists_too',
'file_that_exists_but_is_empty',
'file_that_doesnt_exist',
])
self.good_exp = Experiment(approved=True,
title='title1',
institution_name='institution1',
description='description1',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.good_exp.save()
self.good_dataset = self._make_dataset(
self.good_exp, ['file_that_exists', 'file_that_exists_too'])
class MRtaskTestCase(TestCase):
def setUp(self):
from django.contrib.auth.models import User
from tardis.tardis_portal.models import Experiment
from tardis.tardis_portal.models import ExperimentACL
from tardis.tardis_portal.models import Dataset
from tardis.apps.mrtardis.mrtask import MRtask
user = '******'
pwd = 'secret'
email = ''
self.user = User.objects.create_user(user, email, pwd)
self.experiment = Experiment(approved=True,
title="Test Experiment",
institution_name="Test Institution",
created_by=self.user,
public=False)
self.experiment.save()
acl = ExperimentACL(pluginId="django_user",
entityId="1",
experiment=self.experiment,
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True)
acl.save()
self.test_dataset = Dataset(experiment=self.experiment,
description="test dataset")
self.test_dataset.save()
self.test_mrtask = MRtask(dataset=self.test_dataset)
def test_mrtask(self):
self.assertEqual(len(self.test_mrtask.parameters), 0)
def testRightsRequireValidOwner(self):
# Create test owner without enough details
username, email, password = ("testuser", "*****@*****.**", "password")
user = User.objects.create_user(username, email, password)
# Create test experiment and make user the owner of it
experiment = Experiment(title="Text Experiment", institution_name="Test Uni", created_by=user)
experiment.save()
acl = ObjectACL(
pluginId=django_user,
entityId=str(user.id),
content_object=experiment,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
acl.save()
# Create client and login as user
client = Client()
login = client.login(username=username, password=password)
self.assertTrue(login)
# Get "Choose Rights" page, and check that we're forbidden
rights_url = reverse("tardis.tardis_portal.views.choose_rights", args=[str(experiment.id)])
response = client.get(rights_url)
expect(response.status_code).to_equal(403)
# Fill in remaining details
user.first_name = "Voltaire" # Mononymous persons are just fine
user.save()
# Get "Choose Rights" page, and check that we're now allowed access
response = client.get(rights_url)
expect(response.status_code).to_equal(200)
def setUp(self):
# create a test user
self.user = User.objects.create_user(username='******',
email='',
password='******')
# create a public experiment
self.experiment1 = Experiment(
title='Experiment 1',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.experiment1.save()
# create a non-public experiment
self.experiment2 = Experiment(
title='Experiment 2',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_NONE)
self.experiment2.save()
# dataset1 belongs to experiment1
self.dataset1 = Dataset()
self.dataset1.save()
self.dataset1.experiments.add(self.experiment1)
self.dataset1.save()
# dataset2 belongs to experiment2
self.dataset2 = Dataset()
self.dataset2.save()
self.dataset2.experiments.add(self.experiment2)
self.dataset2.save()
# absolute path first
filename1 = 'testfile.txt'
filename2 = 'testfile.tiff'
self.dest1 = abspath(join(settings.FILE_STORE_PATH, '%s/%s/'
% (self.experiment1.id,
self.dataset1.id)))
self.dest2 = abspath(join(settings.FILE_STORE_PATH,
'%s/%s/'
% (self.experiment2.id,
self.dataset2.id)))
if not exists(self.dest1):
makedirs(self.dest1)
if not exists(self.dest2):
makedirs(self.dest2)
testfile1 = abspath(join(self.dest1, filename1))
f = open(testfile1, 'w')
f.write("Hello World!\n")
f.close()
testfile2 = abspath(join(self.dest2, filename2))
_generate_test_image(testfile2)
self.datafile1 = self._build_datafile(testfile1, filename1,
self.dataset1)
self.datafile2 = self._build_datafile(testfile2, filename2,
self.dataset2)
def setUp(self):
"""
setting up essential objects, copied from tests above
"""
user = '******'
pwd = 'secret'
email = ''
self.user = User.objects.create_user(user, email, pwd)
self.userProfile = self.user.userprofile
self.exp = Experiment(title='test exp1',
institution_name='monash',
created_by=self.user)
self.exp.save()
self.acl = ObjectACL(
pluginId=django_user,
entityId=str(self.user.id),
content_object=self.exp,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
self.acl.save()
self.dataset = Dataset(description='dataset description...')
self.dataset.save()
self.dataset.experiments.add(self.exp)
self.dataset.save()
self.datafile = DataFile(dataset=self.dataset,
size=42,
filename="foo",
md5sum="junk")
self.datafile.save()
def _get_experiment(self, entry, user):
experimentId, title, public_access = \
self._get_experiment_details(entry, user)
try:
try:
param_name = ParameterName.objects.\
get(name=self.PARAM_EXPERIMENT_ID, \
schema=AtomImportSchemas.get_schema(Schema.EXPERIMENT))
parameter = ExperimentParameter.objects.\
get(name=param_name, string_value=experimentId)
except ExperimentParameter.DoesNotExist:
raise Experiment.DoesNotExist
return parameter.parameterset.experiment
except Experiment.DoesNotExist:
experiment = Experiment(title=title,
created_by=user,
public_access=public_access)
experiment.save()
self._create_experiment_id_parameter_set(experiment, experimentId)
acl = ExperimentACL(experiment=experiment,
pluginId=django_user,
entityId=user.id,
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True,
aclOwnershipType=ExperimentACL.OWNER_OWNED)
acl.save()
return experiment
def _get_experiment(self, entry, user):
experimentId, title, public_access = \
self._get_experiment_details(entry, user)
try:
try:
param_name = ParameterName.objects.\
get(name=self.PARAM_EXPERIMENT_ID, \
schema=AtomImportSchemas.get_schema(Schema.EXPERIMENT))
parameter = ExperimentParameter.objects.\
get(name=param_name, string_value=experimentId)
except ExperimentParameter.DoesNotExist:
raise Experiment.DoesNotExist
return parameter.parameterset.experiment
except Experiment.DoesNotExist:
experiment = Experiment(title=title,
created_by=user,
public_access=public_access)
experiment.save()
self._create_experiment_id_parameter_set(experiment, experimentId)
acl = ObjectACL(content_object=experiment,
pluginId=django_user,
entityId=user.id,
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED)
acl.save()
return experiment
def _create_experiment(user, bad):
experiment = Experiment(title='Norwegian Blue',
description='Parrot + 40kV',
created_by=user)
experiment.public_access = Experiment.PUBLIC_ACCESS_METADATA
experiment.save()
experiment.author_experiment_set.create(
order=0, author="John Cleese", url="http://nla.gov.au/nla.party-1")
experiment.author_experiment_set.create(
order=1, author="Michael Palin", url="http://nla.gov.au/nla.party-2")
psm = ParameterSetManager(parentObject=experiment, schema=SCHEMA_URI)
if bad:
params = {
'type': 'website',
'identifier': 'https://www.badexample.com/'
}
else:
params = {
'type': 'website',
'identifier': 'https://www.example.com/',
'title': 'Google',
'notes': 'This is a note.'
}
for k, v in params.items():
psm.set_param(k, v)
return experiment
def _create_test_data():
user = User(username='******',
first_name='Thomas',
last_name='Atkins',
email='*****@*****.**')
user.save()
license_ = License(name='Creative Commons Attribution-NoDerivs 2.5 Australia',
url='http://creativecommons.org/licenses/by-nd/2.5/au/',
internal_description='CC BY 2.5 AU',
allows_distribution=True)
license_.save()
experiment = Experiment(title='Norwegian Blue',
description='Parrot + 40kV',
created_by=user)
experiment.public_access = Experiment.PUBLIC_ACCESS_FULL
experiment.license = license_
experiment.save()
experiment.experimentauthor_set.create(order=0,
author="John Cleese",
url="http://nla.gov.au/nla.party-1")
experiment.experimentauthor_set.create(order=1,
author="Michael Palin",
url="http://nla.gov.au/nla.party-2")
acl = ObjectACL(content_object=experiment,
pluginId='django_user',
entityId=str(user.id),
isOwner=True,
canRead=True,
canWrite=True,
canDelete=True,
aclOwnershipType=ObjectACL.OWNER_OWNED)
acl.save()
return user, experiment
def _create_test_data():
user = User(username='******',
first_name='Thomas',
last_name='Atkins',
email='*****@*****.**')
user.save()
user2 = User(username='******', email='*****@*****.**')
user2.save()
map(lambda u: UserProfile(user=u).save(), [user, user2])
license_ = License(name='Creative Commons Attribution-NoDerivs 2.5 Australia',
url='http://creativecommons.org/licenses/by-nd/2.5/au/',
internal_description='CC BY 2.5 AU',
allows_distribution=True)
license_.save()
experiment = Experiment(title='Norwegian Blue',
description='Parrot + 40kV',
created_by=user)
experiment.public_access = Experiment.PUBLIC_ACCESS_FULL
experiment.license = license_
experiment.save()
acl = ExperimentACL(experiment=experiment,
pluginId='django_user',
entityId=str(user2.id),
isOwner=True,
canRead=True,
canWrite=True,
canDelete=True,
aclOwnershipType=ExperimentACL.OWNER_OWNED)
acl.save()
return (user, experiment)
def setUp(self):
# create user
self.testuser = User(username='******')
self.testuser.save()
# create test experiment
self.exp = Experiment(title='tar download test' * 15,
created_by=self.testuser,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.exp.save()
# create test dataset
self.ds = self.exp.datasets.create(
description="testing tar download dataset")
datafile_content = "\n".join(['some data %d' % i for i in range(1000)])
filesize = len(datafile_content)
md5sum = hashlib.md5(datafile_content).hexdigest()
# create test datafiles and datafile objects
self.dfs = []
for i in range(20):
df = self.ds.datafile_set.create(
filename='testfile%d.txt' % i,
mimetype='text/plain',
size=filesize,
md5sum=md5sum,
directory='/'.join(['testdir%d' % i for i in range(i, i + 4)]))
df.file_object = StringIO(datafile_content)
df.refresh_from_db()
self.dfs.append(df)
# mock client
self.client = Client()
def setUp(self):
self.client = Client()
# old_user
user_old_username = '******'
# new_user
user_new_username = '******'
pwd = 'secret'
email = '*****@*****.**'
self.user_new = User.objects.create_user(user_new_username, email, pwd)
self.user_old = User.objects.create_user(user_old_username, email, pwd)
# create group
self.group = Group.objects.create(name='test group')
# add old user to group
self.group.user_set.add(self.user_old)
# add user auth
user_auth = UserAuthentication(userProfile=UserProfile.objects.get(user=self.user_old),
username= self.user_old.username,
authenticationMethod='localdb')
user_auth.save()
# add experiments
experiment = Experiment(title='Text Experiment',
institution_name='Test Uni',
created_by=self.user_old)
experiment.save()
acl = ObjectACL(
pluginId='django_user',
entityId=str(self.user_old.id),
content_object=experiment,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
acl.save()
def setUp(self):
self.user = User(username='******', password='******', email='*****@*****.**')
self.user.save()
self.bad_exp = Experiment(
approved = True,
title = 'title1',
institution_name = 'institution1',
description = 'description1',
created_by = self.user,
public_access = Experiment.PUBLIC_ACCESS_FULL
)
self.bad_exp.save()
self.bad_dataset = self._make_dataset(self.bad_exp, [
'file_that_exists',
'file_that_exists_too',
'file_that_exists_but_is_empty',
'file_that_doesnt_exist',
])
self.good_exp = Experiment(
approved = True,
title = 'title1',
institution_name = 'institution1',
description = 'description1',
created_by = self.user,
public_access = Experiment.PUBLIC_ACCESS_FULL
)
self.good_exp.save()
self.good_dataset = self._make_dataset(self.good_exp, [
'file_that_exists',
'file_that_exists_too'
])
class IntegrityCheckTestCase(TestCase):
def _make_dataset(self, exp, filenames):
dataset = Dataset(experiment=exp)
dataset.save()
for filename in filenames:
df = Dataset_File(dataset=dataset, size=41, protocol='file')
df.filename = filename
df.url = 'file://' + path.join(path.dirname(__file__), 'data', df.filename)
df.save()
def setUp(self):
self.user = User(username='******', password='******', email='*****@*****.**')
self.user.save()
self.bad_exp = Experiment(
approved = True,
title = 'title1',
institution_name = 'institution1',
description = 'description1',
created_by = self.user,
public_access = Experiment.PUBLIC_ACCESS_FULL
)
self.bad_exp.save()
self.bad_dataset = self._make_dataset(self.bad_exp, [
'file_that_exists',
'file_that_exists_too',
'file_that_exists_but_is_empty',
'file_that_doesnt_exist',
])
self.good_exp = Experiment(
approved = True,
title = 'title1',
institution_name = 'institution1',
description = 'description1',
created_by = self.user,
public_access = Experiment.PUBLIC_ACCESS_FULL
)
self.good_exp.save()
self.good_dataset = self._make_dataset(self.good_exp, [
'file_that_exists',
'file_that_exists_too'
])
def testBadExperimentFails(self):
result = IntegrityCheck(self.bad_exp).get_datafiles_integrity()
self.assertEqual(result['files_ok'], 2)
self.assertEqual(result['files_incomplete'], 1)
self.assertEqual(result['files_missing'], 1)
good_or_bad = IntegrityCheck(self.bad_exp).all_files_complete()
self.assertFalse(good_or_bad)
def testGoodExperimentPasses(self):
result = IntegrityCheck(self.good_exp).get_datafiles_integrity()
self.assertEqual(result['files_ok'], 2)
self.assertEqual(result['files_incomplete'], 0)
self.assertEqual(result['files_missing'], 0)
good_or_bad = IntegrityCheck(self.good_exp).all_files_complete()
self.assertTrue(good_or_bad)
def _create_test_experiment(user, license_):
experiment = Experiment(title='Norwegian Blue',
description='Parrot + 40kV',
created_by=user)
experiment.public_access = Experiment.PUBLIC_ACCESS_FULL
experiment.license = license_
experiment.save()
experiment.experimentauthor_set.create(
order=0,
author="John Cleese",
url="http://nla.gov.au/nla.party-1")
experiment.experimentauthor_set.create(
order=1,
author="Michael Palin",
url="http://nla.gov.au/nla.party-2")
acl = ObjectACL(content_object=experiment,
pluginId='django_user',
entityId=str(user.id),
isOwner=True,
canRead=True,
canWrite=True,
canDelete=True,
aclOwnershipType=ObjectACL.OWNER_OWNED)
acl.save()
return experiment
def setUp(self):
self.client = Client()
# old_user
user_old_username = '******'
# new_user
user_new_username = '******'
pwd = 'secret'
email = '*****@*****.**'
self.user_new = User.objects.create_user(user_new_username, email, pwd)
self.user_old = User.objects.create_user(user_old_username, email, pwd)
# create group
self.group = Group.objects.create(name='test group')
# add old user to group
self.group.user_set.add(self.user_old)
# add user auth
user_auth = UserAuthentication(userProfile=UserProfile.objects.get(user=self.user_old),
username= self.user_old.username,
authenticationMethod='localdb')
user_auth.save()
# add experiments
experiment = Experiment(title='Text Experiment',
institution_name='Test Uni',
created_by=self.user_old)
experiment.save()
acl = ObjectACL(
pluginId='django_user',
entityId=str(self.user_old.id),
content_object=experiment,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
acl.save()
def setUp(self):
from os import path, mkdir
from tempfile import mkdtemp
user = '******'
pwd = 'secret'
email = ''
self.user = User.objects.create_user(user, email, pwd)
self.userProfile = UserProfile(user=self.user).save()
self.test_dir = mkdtemp()
Location.force_initialize()
self.exp = Experiment(title='test exp1',
institution_name='monash',
created_by=self.user)
self.exp.save()
acl = ObjectACL(
pluginId=django_user,
entityId=str(self.user.id),
content_object=self.exp,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
acl.save()
self.dataset = \
Dataset(description='dataset description...')
self.dataset.save()
self.dataset.experiments.add(self.exp)
self.dataset.save()
self.experiment_path = path.join(
settings.FILE_STORE_PATH,
str(self.dataset.get_first_experiment().id))
self.dataset_path = path.join(self.experiment_path,
str(self.dataset.id))
if not path.exists(self.experiment_path):
mkdir(self.experiment_path)
if not path.exists(self.dataset_path):
mkdir(self.dataset_path)
# write test file
self.filename = 'testfile.txt'
self.f1 = open(path.join(self.test_dir, self.filename), 'w')
self.f1.write('Test file 1')
self.f1.close()
self.f1_size = path.getsize(path.join(self.test_dir, self.filename))
self.f1 = open(path.join(self.test_dir, self.filename), 'r')
def setUp(self):
# Create test owner without enough details
username, email, password = ('testuser',
'*****@*****.**',
'password')
user = User.objects.create_user(username, email, password)
profile = UserProfile(user=user, isDjangoAccount=True)
profile.save()
Location.force_initialize()
# Create test experiment and make user the owner of it
experiment = Experiment(title='Text Experiment',
institution_name='Test Uni',
created_by=user)
experiment.save()
acl = ObjectACL(
pluginId='django_user',
entityId=str(user.id),
content_object=experiment,
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED)
acl.save()
dataset = Dataset(description='dataset description...')
dataset.save()
dataset.experiments.add(experiment)
dataset.save()
def create_datafile(filename):
testfile = path.join(path.dirname(__file__), 'fixtures',
filename)
size, sha512sum = get_size_and_sha512sum(testfile)
datafile = Dataset_File(dataset=dataset,
filename=path.basename(testfile),
size=size,
sha512sum=sha512sum)
datafile.save()
base_url = 'file://' + path.abspath(path.dirname(testfile))
location = Location.load_location({
'name': 'test-grabber', 'url': base_url, 'type': 'external',
'priority': 10, 'transfer_provider': 'local'})
replica = Replica(datafile=datafile,
url='file://'+path.abspath(testfile),
protocol='file',
location=location)
replica.verify()
replica.save()
return Dataset_File.objects.get(pk=datafile.pk)
self.dataset = dataset
self.datafiles = [create_datafile('data_grabber_test1.admin'),
create_datafile('testfile.txt')
]
def createhpcexperiment(request, user, dl):
from django.contrib.auth.models import User
from tardis.tardis_portal.views import _registerExperimentDocument
import os
import tempfile
# TODO
temp = tempfile.TemporaryFile()
for chunk in dl.chunks():
temp.write(chunk)
temp.seek(0)
metadata = {}
for line in temp:
key, value = line.split("~")
metadata[key] = value
temp.close()
author = metadata["Name"]
title = metadata["Experiment"]
ds_desc = metadata["Facility"]
desc = metadata["Description"]
fname = metadata["FolderName"]
counter = metadata["Counter"]
package = metadata["Package"]
exp = Experiment(
title=title, institution_name="RMIT University", description=desc, created_by=User.objects.get(id=user.pk)
)
exp.save()
eid = exp.id
# Store the author for the dataset
ae = models.Author_Experiment(experiment=exp, author=author, order="1")
ae.save()
auth_key = settings.DEFAULT_AUTH
try:
e = Experiment.objects.get(pk=eid)
except Experiment.DoesNotExist:
logger.exception("Experiment for eid %i in CreateHPCExperiment does not exist" % eid)
acl = ExperimentACL(
experiment=e,
pluginId=django_user,
entityId=str(user.id),
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True,
aclOwnershipType=ExperimentACL.OWNER_OWNED,
)
acl.save()
folder_desc = "%s.%s.%s.%s" % (ds_desc.strip(), package.strip(), fname.strip(), counter.strip())
logger.debug("folder_desc = %s" % folder_desc)
return eid, exp, folder_desc
def setUp(self):
# Create test owner without enough details
username, email, password = ('testuser', '*****@*****.**',
'password')
user = User.objects.create_user(username, email, password)
profile = UserProfile(user=user, isDjangoAccount=True)
profile.save()
Location.force_initialize()
# Create test experiment and make user the owner of it
experiment = Experiment(title='Text Experiment',
institution_name='Test Uni',
created_by=user)
experiment.save()
acl = ObjectACL(
pluginId='django_user',
entityId=str(user.id),
content_object=experiment,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
acl.save()
dataset = Dataset(description='dataset description...')
dataset.save()
dataset.experiments.add(experiment)
dataset.save()
def create_datafile(index):
testfile = path.join(path.dirname(__file__), 'fixtures',
'jeol_sem_test%d.txt' % index)
size, sha512sum = get_size_and_sha512sum(testfile)
datafile = Dataset_File(dataset=dataset,
filename=path.basename(testfile),
size=size,
sha512sum=sha512sum)
datafile.save()
base_url = 'file://' + path.abspath(path.dirname(testfile))
location = Location.load_location({
'name': 'test-jeol',
'url': base_url,
'type': 'external',
'priority': 10,
'transfer_provider': 'local'
})
replica = Replica(datafile=datafile,
url='file://' + path.abspath(testfile),
protocol='file',
location=location)
replica.verify()
replica.save()
return Dataset_File.objects.get(pk=datafile.pk)
self.dataset = dataset
self.datafiles = [create_datafile(i) for i in (1, 2)]
def setUp(self):
# create a test user
self.user = User.objects.create_user(username='******',
email='',
password='******')
# create a public experiment
self.experiment1 = Experiment(
title='Experiment 1',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.experiment1.save()
# create a non-public experiment
self.experiment2 = Experiment(
title='Experiment 2',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_NONE)
self.experiment2.save()
# dataset1 belongs to experiment1
self.dataset1 = Dataset(description='dangerous;name')
self.dataset1.save()
self.dataset1.experiments.add(self.experiment1)
self.dataset1.save()
# dataset2 belongs to experiment2
self.dataset2 = Dataset(description='terrible\nname')
self.dataset2.save()
self.dataset2.experiments.add(self.experiment2)
self.dataset2.save()
# absolute path first
filename1 = 'testfile.txt'
filename2 = 'testfile.tiff'
self.dest1 = abspath(
join(settings.FILE_STORE_PATH,
'%s/%s/' % (self.experiment1.id, self.dataset1.id)))
self.dest2 = abspath(
join(settings.FILE_STORE_PATH,
'%s/%s/' % (self.experiment2.id, self.dataset2.id)))
if not exists(self.dest1):
makedirs(self.dest1)
if not exists(self.dest2):
makedirs(self.dest2)
testfile1 = abspath(join(self.dest1, filename1))
f = open(testfile1, 'w')
f.write("Hello World!\n")
f.close()
testfile2 = abspath(join(self.dest2, filename2))
_generate_test_image(testfile2)
self.datafile1 = self._build_datafile(testfile1, filename1,
self.dataset1)
self.datafile2 = self._build_datafile(testfile2, filename2,
self.dataset2)
class IntegrityCheckTestCase(TestCase):
def _make_dataset(self, exp, filenames):
dataset = Dataset()
dataset.save()
dataset.experiments.add(exp)
dataset.save()
for filename in filenames:
df = Dataset_File(dataset=dataset, size=41, protocol='file')
df.filename = filename
df.url = 'file://' + path.join(path.dirname(__file__), 'data',
df.filename)
df.save()
def setUp(self):
self.user = User(username='******',
password='******',
email='*****@*****.**')
self.user.save()
self.bad_exp = Experiment(approved=True,
title='title1',
institution_name='institution1',
description='description1',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.bad_exp.save()
self.bad_dataset = self._make_dataset(self.bad_exp, [
'file_that_exists',
'file_that_exists_too',
'file_that_exists_but_is_empty',
'file_that_doesnt_exist',
])
self.good_exp = Experiment(approved=True,
title='title1',
institution_name='institution1',
description='description1',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.good_exp.save()
self.good_dataset = self._make_dataset(
self.good_exp, ['file_that_exists', 'file_that_exists_too'])
def testBadExperimentFails(self):
result = IntegrityCheck(self.bad_exp).get_datafiles_integrity()
self.assertEqual(result['files_ok'], 2)
self.assertEqual(result['files_incomplete'], 1)
self.assertEqual(result['files_missing'], 1)
good_or_bad = IntegrityCheck(self.bad_exp).all_files_complete()
self.assertFalse(good_or_bad)
def testGoodExperimentPasses(self):
result = IntegrityCheck(self.good_exp).get_datafiles_integrity()
self.assertEqual(result['files_ok'], 2)
self.assertEqual(result['files_incomplete'], 0)
self.assertEqual(result['files_missing'], 0)
good_or_bad = IntegrityCheck(self.good_exp).all_files_complete()
self.assertTrue(good_or_bad)
def _create_test_data():
"""
Create Single experiment with two owners
"""
user1 = User(username='******',
first_name='Thomas',
last_name='Atkins',
email='*****@*****.**')
user1.save()
UserProfile(user=user1).save()
user2 = User(username='******',
first_name='Joe',
last_name='Bloggs',
email='*****@*****.**')
user2.save()
UserProfile(user=user2).save()
license_ = License(name='Creative Commons Attribution-NoDerivs '
+ '2.5 Australia',
url='http://creativecommons.org/licenses/by-nd/2.5/au/',
internal_description='CC BY 2.5 AU',
allows_distribution=True)
license_.save()
experiment = Experiment(title='Norwegian Blue',
description='Parrot + 40kV',
created_by=user1)
experiment.public_access = Experiment.PUBLIC_ACCESS_FULL
experiment.license = license_
experiment.save()
experiment.author_experiment_set.create(order=0,
author="John Cleese",
url="http://nla.gov.au/nla.party-1")
experiment.author_experiment_set.create(order=1,
author="Michael Palin",
url="http://nla.gov.au/nla.party-2")
acl1 = ExperimentACL(experiment=experiment,
pluginId='django_user',
entityId=str(user1.id),
isOwner=True,
canRead=True,
canWrite=True,
canDelete=True,
aclOwnershipType=ExperimentACL.OWNER_OWNED)
acl1.save()
acl2 = ExperimentACL(experiment=experiment,
pluginId='django_user',
entityId=str(user2.id),
isOwner=True,
canRead=True,
canWrite=True,
canDelete=True,
aclOwnershipType=ExperimentACL.OWNER_OWNED)
acl2.save()
return (user1, user2, experiment)
class TarDownloadTestCase(TestCase):
def setUp(self):
# create user
self.testuser = User(username="******")
self.testuser.save()
# create test experiment
self.exp = Experiment(
title="tar download test" * 15, created_by=self.testuser, public_access=Experiment.PUBLIC_ACCESS_FULL
)
self.exp.save()
# create test dataset
self.ds = self.exp.datasets.create(description="testing tar download dataset")
datafile_content = "\n".join(["some data %d" % i for i in range(1000)])
filesize = len(datafile_content)
md5sum = hashlib.md5(datafile_content).hexdigest()
# create test datafiles and datafile objects
self.dfs = []
for i in range(20):
df = self.ds.datafile_set.create(
filename="testfile%d.txt" % i,
mimetype="text/plain",
size=filesize,
md5sum=md5sum,
directory="/".join(["testdir%d" % i for i in range(i, i + 4)]),
)
df.file_object = StringIO(datafile_content)
df.refresh_from_db()
self.dfs.append(df)
# mock client
self.client = Client()
def tearDown(self):
# delete created objects and files
[ds.delete() for ds in self.exp.datasets.all()]
self.exp.delete()
def test_tar_experiment_download(self):
self.assertTrue(all(df.verified for df in self.dfs))
response = self.client.get(
reverse("tardis.tardis_portal.download.streaming_download_experiment", args=(self.exp.id, "tar"))
)
with NamedTemporaryFile("w") as tarfile:
for c in response.streaming_content:
tarfile.write(c)
tarfile.flush()
self.assertEqual(int(response["Content-Length"]), os.stat(tarfile.name).st_size)
tf = TarFile(tarfile.name)
for df in self.dfs:
full_path = os.path.join(
self.exp.title.replace(" ", "_"), self.ds.description, df.directory, df.filename
)
tf.extract(full_path, "/tmp")
self.assertEqual(os.stat(os.path.join("/tmp", full_path)).st_size, int(df.size))
def setUp(self):
# create a test user
self.user = User.objects.create_user(username='******',
email='',
password='******')
# create a public experiment
self.experiment1 = Experiment(title='Experiment 1',
created_by=self.user,
public=True)
self.experiment1.save()
# create a non-public experiment
self.experiment2 = Experiment(title='Experiment 2',
created_by=self.user,
public=False)
self.experiment2.save()
# dataset1 belongs to experiment1
self.dataset1 = Dataset(experiment=self.experiment1)
self.dataset1.save()
# dataset2 belongs to experiment2
self.dataset2 = Dataset(experiment=self.experiment2)
self.dataset2.save()
# absolute path first
filename = 'testfile.txt'
self.dest1 = abspath(join(settings.FILE_STORE_PATH, '%s'
% self.experiment1.id))
self.dest2 = abspath(join(settings.FILE_STORE_PATH, '%s'
% self.experiment2.id))
if not exists(self.dest1):
mkdir(self.dest1)
if not exists(self.dest2):
mkdir(self.dest2)
testfile1 = abspath(join(self.dest1, filename))
f = open(testfile1, 'w')
f.write("Hello World!\n")
f.close()
testfile2 = abspath(join(self.dest2, filename))
f = open(testfile2, 'w')
f.write("Hello World!\n")
f.close()
self.dataset_file1 = Dataset_File(dataset=self.dataset1,
filename=filename,
protocol='tardis',
url='tardis://%s' % filename)
self.dataset_file1.save()
self.dataset_file2 = Dataset_File(dataset=self.dataset2,
filename=basename(filename),
protocol='tardis',
url='tardis://%s' % filename)
self.dataset_file2.save()
def setUp(self):
self.user = User.objects.create_user('test', '', 'test')
self.expt = Experiment(title='test exp1',
institution_name='monash',
created_by=self.user,
)
self.schema, _ = Schema.objects.get_or_create(namespace=settings.DOI_NAMESPACE)
self.doi_name, _ = ParameterName.objects.get_or_create(schema=self.schema, full_name='DOI', name='doi')
self.expt.save()
def setUp(self):
"""Setup test fixtures if needed."""
self.user = User.objects.create_user("doctor", '', "pwd")
self.exp = Experiment(title="Wonderful",
institution_name="Monash University",
created_by=self.user)
self.exp.save()
group = Group(name="Group1")
group.save()
facility = Facility(name="Test Facility", manager_group=group)
facility.save()
self.inst = Instrument(name="Test Instrument1", facility=facility)
self.inst.save()
self.dataset = Dataset(description="Dataset1", instrument=self.inst)
self.dataset.save()
storage_classes = getattr(settings, "HSM_STORAGE_CLASSES",
DEFAULT_HSM_CLASSES)
self.sbox1 = StorageBox(name="SBOX1",
django_storage_class=storage_classes[0],
status='online',
max_size=256)
self.sbox1.save()
sbox1_attr = StorageBoxAttribute(storage_box=self.sbox1,
key='type',
value=StorageBox.DISK)
sbox1_attr.save()
sbox1_loc_opt = StorageBoxOption(storage_box=self.sbox1,
key="location",
value="/dummy/path")
sbox1_loc_opt.save()
self.sbox2 = StorageBox(
name="SBOX2",
django_storage_class="any.non.disk.StorageSystem",
status='offline',
max_size=256)
self.sbox2.save()
sbox2_attr = StorageBoxAttribute(storage_box=self.sbox2,
key='type',
value=StorageBox.TAPE)
sbox2_attr.save()
self.df1 = DataFile(dataset=self.dataset, filename="test_df.jpg")
self.df1.save()
self.dfo1 = DataFileObject(datafile=self.df1,
storage_box=self.sbox1,
uri="stream/test.jpg",
verified=True)
self.dfo1.save()
self.df1.verify()
def testNeverExpire(self):
experiment = Experiment(created_by=self.user, end_time=dt.datetime(1999,4,3))
experiment.save()
eh = EmbargoHandler(experiment.id, True)
self.assertFalse(eh.never_expires())
eh.prevent_expiry()
self.assertTrue(eh.never_expires())
self.assertFalse(eh.because_no_end_date())
def setUp(self):
raise SkipTest # temporarily disabling this feature, needs coding
from tempfile import mkdtemp, mktemp
from django.conf import settings
import os
# Disconnect post_save signal
from django.db.models.signals import post_save
from tardis.tardis_portal.models import Experiment, \
staging_hook, Dataset, DataFile, DataFileObject, StorageBox
post_save.disconnect(staging_hook, sender=DataFileObject)
from django.contrib.auth.models import User
user = '******'
pwd = 'secret'
email = ''
self.user = User.objects.create_user(user, email, pwd)
try:
os.makedirs(settings.GET_FULL_STAGING_PATH_TEST)
except OSError:
pass
self.temp = mkdtemp(dir=settings.GET_FULL_STAGING_PATH_TEST)
self.filepath = mktemp(dir=self.temp)
content = 'test file'
with open(self.filepath, "w+b") as f:
f.write(content)
# make datafile
exp = Experiment(title='test exp1',
institution_name='monash',
created_by=self.user)
exp.save()
# make dataset
dataset = Dataset(description="dataset description...")
dataset.save()
dataset.experiments.add(exp)
dataset.save()
# create datafile
df = DataFile(dataset=dataset, size=len(content),
filename=path.basename(self.file),
md5sum='f20d9f2072bbeb6691c0f9c5099b01f3')
df.save()
# create replica
base_url = settings.GET_FULL_STAGING_PATH_TEST
s_box = StorageBox.get_default_storage(location=base_url)
dfo = DataFileObject(datafile=df,
uri=self.filepath,
storage_box=s_box)
dfo.save()
self.dfo = dfo
def create_draft_publication(user, publication_title, publication_description):
# Note: Maybe this logic can be taken from the tardis_portal/views.py?
experiment = Experiment(created_by=user,
title=publication_title,
description=publication_description)
experiment.save()
ObjectACL(content_object=experiment,
pluginId=django_user,
entityId=str(user.id),
canRead=True,
canWrite=False,
canDelete=False,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED).save()
ObjectACL(content_object=experiment,
pluginId=django_group,
entityId=str(
Group.objects.get_or_create(
name=getattr(
settings, 'PUBLICATION_OWNER_GROUP',
default_settings.PUBLICATION_OWNER_GROUP))[0].id),
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED).save()
publication_schema = Schema.objects.get(
namespace=getattr(settings, 'PUBLICATION_SCHEMA_ROOT',
default_settings.PUBLICATION_SCHEMA_ROOT))
# Attach draft schema
draft_publication_schema = Schema.objects.get(
namespace=getattr(settings, 'PUBLICATION_DRAFT_SCHEMA',
default_settings.PUBLICATION_DRAFT_SCHEMA))
ExperimentParameterSet(schema=draft_publication_schema,
experiment=experiment).save()
# Attach root schema and blank form_state parameter
publication_root_schema = Schema.objects.get(
namespace=getattr(settings, 'PUBLICATION_SCHEMA_ROOT',
default_settings.PUBLICATION_SCHEMA_ROOT))
publication_root_parameter_set = ExperimentParameterSet(
schema=publication_schema,
experiment=experiment)
publication_root_parameter_set.save()
form_state_param_name = ParameterName.objects.get(
schema=publication_root_schema, name='form_state')
ExperimentParameter(name=form_state_param_name,
parameterset=publication_root_parameter_set).save()
return experiment
def create_draft_publication(user, publication_title, publication_description):
# Note: Maybe this logic can be taken from the tardis_portal/views.py?
experiment = Experiment(created_by=user,
title=publication_title,
description=publication_description)
experiment.save()
ObjectACL(content_object=experiment,
pluginId=django_user,
entityId=str(user.id),
canRead=True,
canWrite=False,
canDelete=False,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED).save()
ObjectACL(content_object=experiment,
pluginId=django_group,
entityId=str(
Group.objects.get_or_create(
name=getattr(
settings, 'PUBLICATION_OWNER_GROUP',
default_settings.PUBLICATION_OWNER_GROUP))[0].id),
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED).save()
publication_schema = Schema.objects.get(
namespace=getattr(settings, 'PUBLICATION_SCHEMA_ROOT',
default_settings.PUBLICATION_SCHEMA_ROOT))
# Attach draft schema
draft_publication_schema = Schema.objects.get(
namespace=getattr(settings, 'PUBLICATION_DRAFT_SCHEMA',
default_settings.PUBLICATION_DRAFT_SCHEMA))
ExperimentParameterSet(schema=draft_publication_schema,
experiment=experiment).save()
# Attach root schema and blank form_state parameter
publication_root_schema = Schema.objects.get(
namespace=getattr(settings, 'PUBLICATION_SCHEMA_ROOT',
default_settings.PUBLICATION_SCHEMA_ROOT))
publication_root_parameter_set = ExperimentParameterSet(
schema=publication_schema,
experiment=experiment)
publication_root_parameter_set.save()
form_state_param_name = ParameterName.objects.get(
schema=publication_root_schema, name='form_state')
ExperimentParameter(name=form_state_param_name,
parameterset=publication_root_parameter_set).save()
return experiment
def setUp(self):
from django.contrib.auth.models import User
from tardis.tardis_portal.models import Experiment
user = '******'
pwd = 'secret'
email = ''
self.user = User.objects.create_user(user, email, pwd)
self.experiment = Experiment(created_by=self.user)
self.experiment.save()
sys.modules['datetime'].datetime = FrozenTime
def _create_test_data():
user = User(username='******',
first_name="Voltaire",
email='*****@*****.**')
user.save()
UserProfile(user=user).save()
experiment = Experiment(title='Norwegian Blue',
description='Parrot + 40kV',
created_by=user)
experiment.public_access = Experiment.PUBLIC_ACCESS_METADATA
experiment.save()
return (experiment, user)
def _create_test_data():
user = User(username='******',
first_name="Voltaire",
email='*****@*****.**')
user.save()
UserProfile(user=user).save()
experiment = Experiment(title='Norwegian Blue',
description='Parrot + 40kV',
created_by=user)
experiment.public_access = Experiment.PUBLIC_ACCESS_METADATA
experiment.save()
return (experiment, user)
def setUp(self):
# Create test owner without enough details
username, email, password = ('testuser',
'*****@*****.**',
'password')
user = User.objects.create_user(username, email, password)
# Create test experiment and make user the owner of it
experiment = Experiment(title='Text Experiment',
institution_name='Test Uni',
created_by=user)
experiment.save()
acl = ObjectACL(
pluginId='django_user',
entityId=str(user.id),
content_object=experiment,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
acl.save()
dataset = Dataset(description='dataset description...')
dataset.save()
dataset.experiments.add(experiment)
dataset.save()
base_path = path.join(path.dirname(__file__), 'fixtures')
s_box = StorageBox.get_default_storage(location=base_path)
def create_datafile(index):
testfile = path.join(base_path, 'middleware_test%d.txt' % index)
size, sha512sum = get_size_and_sha512sum(testfile)
datafile = DataFile(dataset=dataset,
filename=path.basename(testfile),
size=size,
sha512sum=sha512sum)
datafile.save()
dfo = DataFileObject(
datafile=datafile,
storage_box=s_box,
uri=path.basename(testfile))
dfo.save()
if index != 1:
dfo.verified = False
dfo.save(update_fields=['verified'])
return DataFile.objects.get(pk=datafile.pk)
self.dataset = dataset
self.datafiles = [create_datafile(i) for i in (1, 2)]
def setUp(self):
# Load schemas for test
from django.core.management import call_command
call_command('loaddata', 'as_schemas')
self.client = Client()
self.experiments = []
try:
user = User.objects.get(username='******')
except User.DoesNotExist:
user = User.objects.create_user('test', '', 'test')
user.save()
self.userprofile = user.userprofile
# base_path = path.abspath(path.dirname(__file__))
experiment = Experiment(title='SAXS Test',
created_by=user)
experiment.save()
acl = ObjectACL(pluginId=django_user,
entityId=str(user.id),
content_object=experiment,
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True)
acl.save()
self.experiments += [experiment]
schema = Schema.objects.get(type=Schema.DATAFILE, subtype='saxs')
parameter = ParameterName.objects.get(schema=schema, name='io')
parameter.is_searchable = True
parameter.save()
self.io_param_name = parameter.getUniqueShortName()
schema = Schema.objects.get(type=Schema.DATASET, subtype='saxs')
parameter = ParameterName.objects.get(schema=schema, name='frqimn')
parameter.is_searchable = True
parameter.save()
self.frqimn_param_name = parameter.getUniqueShortName()
new_schema = Schema()
new_schema.namespace = 'testschemawithduplicatename'
new_schema.save()
new_param = ParameterName(
schema=new_schema,
name='title',
full_name='Duplicate title parametername',
is_searchable=True)
new_param.save()
def create_experiment(i):
experiment = Experiment(title="Text Experiment #%d" % i, institution_name="Test Uni", created_by=user)
experiment.save()
acl = ObjectACL(
pluginId=django_user,
entityId=str(user.id),
content_object=experiment,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
acl.save()
return experiment
def test_create_index(self):
self.exp1 = Experiment(title='test exp1',
institution_name='monash',
description='Test Description',
created_by=self.user)
self.exp2 = Experiment(title='test exp2',
institution_name='monash',
description='Test Description',
created_by=self.user)
self.exp1.save()
self.exp2.save()
# get search instance
search = ExperimentDocument.search()
# query for title(exact matching)
query = search.query("match", title='test exp1')
result = query.execute(ignore_cache=True)
self.assertEqual(result.hits[0].title, 'test exp1')
# query for description
query = search.query("match", description='Test Description')
result = query.execute(ignore_cache=True)
self.assertEqual(result.hits[0].description, 'Test Description')
# query for created_time
query = search.query("match", created_time=self.exp1.created_time)
result = query.execute(ignore_cache=True)
self.assertEqual(result.hits[0].created_time, self.exp1.created_time)
# dataset
# dataset1 belongs to experiment1
self.dataset1 = Dataset(description='test_dataset')
self.dataset1.save()
self.dataset1.experiments.add(self.exp1)
self.dataset1.save()
# dataset2 belongs to experiment2
self.dataset2 = Dataset(description='test_dataset2')
self.dataset2.save()
self.dataset2.experiments.add(self.exp2)
self.dataset2.save()
# search on dataset
search = DatasetDocument.search()
query = search.query("match", description='test_dataset')
result = query.execute(ignore_cache=True)
self.assertEqual(result.hits.total.value, 1)
# search on datafile
settings.REQUIRE_DATAFILE_SIZES = False
settings.REQUIRE_DATAFILE_CHECKSUMS = False
self.datafile = DataFile(dataset=self.dataset1, filename='test.txt')
self.datafile.save()
search = DataFileDocument.search()
query = search.query("match", filename='test.txt')
result = query.execute(ignore_cache=True)
self.assertEqual(result.hits[0].filename, self.datafile.filename)
class ANDSDOITestCase(TestCase):
def setUp(self):
self.user = User.objects.create_user("test", "", "test")
self.expt = Experiment(title="test exp1", institution_name="monash", created_by=self.user)
self.schema, _ = Schema.objects.get_or_create(namespace=settings.DOI_NAMESPACE)
self.doi_name, _ = ParameterName.objects.get_or_create(schema=self.schema, full_name="DOI", name="doi")
self.expt.save()
def test_init(self):
doi_service = DOIService(self.expt)
def test_get_doi_none(self):
doi_service = DOIService(self.expt)
self.assertEquals(None, doi_service.get_doi())
def test_authors(self):
exp = Experiment(
title='test exp2',
institution_name='monash',
created_by=self.user,
)
exp.save()
ExperimentAuthor(experiment=exp, author='nigel', order=0).save()
exp = Experiment(
title='test exp1',
institution_name='monash',
created_by=self.user,
)
exp.save()
ae1 = ExperimentAuthor(experiment=exp, author='steve', order=100)
ae1.save()
ae2 = ExperimentAuthor(experiment=exp, author='russell', order=1)
ae2.save()
ae3 = ExperimentAuthor(experiment=exp, author='uli', order=50)
ae3.save()
authors = exp.experimentauthor_set.all()
# confirm that there are 2 authors
self.assertEqual(len(authors), 3)
self.assertTrue(ae1 in authors)
self.assertTrue(ae2 in authors)
self.assertTrue(ae3 == authors[1])
def testCleanExperiment(self):
experiment = Experiment(created_by=self.user)
experiment.save()
eh = EmbargoHandler(experiment.id)
self.assertTrue(eh.never_expires())
self.assertFalse(eh.has_any_expiry())
self.assertFalse(eh.can_be_defaulted())
self.assertTrue(eh.because_no_end_date())
self.assertEqual(None, eh.get_expiry_date())
self.assertRaises(Exception, eh.prevent_expiry)
eh.reset_to_default() # should not raise Exception
self.assertRaises(Exception, eh.set_expiry)
def _get_experiment(self, entry, user):
'''
Finds the Experiment corresponding to this entry.
If it doesn't exist, a new Experiment is created and given
an appropriate ACL for the user.
'''
experimentId, title, public_access = self._get_experiment_details(entry, user)
if (experimentId, title) == (None, None):
return None
if experimentId:
try:
# Try and match ExperimentID if we have one.
param_name = ParameterName.objects.\
get(name=IngestOptions.PARAM_EXPERIMENT_ID, \
schema=AtomImportSchemas.get_schema(Schema.EXPERIMENT))
parameter = ExperimentParameter.objects.\
get(name=param_name, string_value=experimentId)
return parameter.parameterset.experiment
except ExperimentParameter.DoesNotExist:
pass
# Failing that, match ExperimentTitle if possible
if title:
try:
experiment = Experiment.objects.get(title=title, created_by=user)
return experiment
except Experiment.DoesNotExist:
pass
# No existing expriment - shall we create a new one?
if not IngestOptions.ALLOW_EXPERIMENT_CREATION:
logging.getLogger(__name__).info("Skipping dataset. ALLOW_EXPERIMENT_CREATION disabled, so ignoring (experimentId: {0}, title: {1}, user: {2})".format(
experimentId, title, user))
return None
experiment = Experiment(title=title, created_by=user, public_access=public_access)
experiment.save()
self._create_experiment_id_parameter_set(experiment, experimentId)
logging.getLogger(__name__).info("Created experiment {0} (title: {1}, user: {2}, experimentId: {3})".format(
experiment.id, experiment.title, experiment.created_by, experimentId))
acl = ExperimentACL(experiment=experiment,
pluginId=django_user,
entityId=user.id,
canRead=True,
canWrite=True,
canDelete=True,
isOwner=True,
aclOwnershipType=ExperimentACL.OWNER_OWNED)
acl.save()
return experiment
def setUp(self):
self.user = User(username='******',
password='******',
email='*****@*****.**')
self.user.save()
self.exp = Experiment(approved=True,
title='title1',
institution_name='institution1',
description='description1',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.exp.save()
self.uid = 0
self.url = 'http://remotetardis:8080'
def setUp(self):
self.hostname = '127.0.0.1'
self.username = '******'
self.password = '******'
email = ''
self.user = User.objects.create_user(self.username, email,
self.password)
self.exp = Experiment(title='test exp1',
institution_name='monash',
created_by=self.user)
self.exp.save()
self.acl = ObjectACL(content_object=self.exp,
pluginId='django_user',
entityId=str(self.user.id),
isOwner=True,
canRead=True,
canWrite=True,
canDelete=True,
aclOwnershipType=ObjectACL.OWNER_OWNED)
self.acl.save()
self.dataset = Dataset(description='test dataset1')
self.dataset.save()
self.dataset.experiments.set([self.exp])
self.dataset.save()
def _build(dataset, filename, url):
datafile_content = b"\n".join(
[b'some data %d' % i for i in range(1000)])
filesize = len(datafile_content)
datafile = DataFile(dataset=dataset,
filename=filename,
size=filesize)
datafile.save()
dfo = DataFileObject(
datafile=datafile,
storage_box=datafile.get_default_storage_box(),
uri=url)
dfo.file_object = BytesIO(datafile_content)
dfo.save()
return datafile
saved_setting = settings.REQUIRE_DATAFILE_CHECKSUMS
try:
settings.REQUIRE_DATAFILE_CHECKSUMS = False
_build(self.dataset, 'file.txt', 'path/file.txt')
finally:
settings.REQUIRE_DATAFILE_CHECKSUMS = saved_setting
def create_experiment(i):
experiment = Experiment(title='Text Experiment #%d' % i,
institution_name='Test Uni',
created_by=user)
experiment.save()
acl = ExperimentACL(
pluginId=django_user,
entityId=str(user.id),
experiment=experiment,
canRead=True,
isOwner=True,
aclOwnershipType=ExperimentACL.OWNER_OWNED,
)
acl.save()
return experiment
def testResetToDefault(self):
expiry = dt.datetime(2034,12,4)
expiry_as_string = '2034/12/04'
experiment = Experiment(created_by=self.user)
experiment.save()
eh = EmbargoHandler(experiment.id, True)
eh.set_expiry(expiry_as_string)
self.assertEqual(expiry, eh.get_expiry_date())
eh = EmbargoHandler(experiment.id, True)
eh.reset_to_default()
self.assertEqual(None, eh.get_expiry_date())
def setUp(self):
# create user
self.testuser = User(username="******")
self.testuser.save()
# create test experiment
self.exp = Experiment(
title="tar download test" * 15, created_by=self.testuser, public_access=Experiment.PUBLIC_ACCESS_FULL
)
self.exp.save()
# create test dataset
self.ds = self.exp.datasets.create(description="testing tar download dataset")
datafile_content = "\n".join(["some data %d" % i for i in range(1000)])
filesize = len(datafile_content)
md5sum = hashlib.md5(datafile_content).hexdigest()
# create test datafiles and datafile objects
self.dfs = []
for i in range(20):
df = self.ds.datafile_set.create(
filename="testfile%d.txt" % i,
mimetype="text/plain",
size=filesize,
md5sum=md5sum,
directory="/".join(["testdir%d" % i for i in range(i, i + 4)]),
)
df.file_object = StringIO(datafile_content)
df.refresh_from_db()
self.dfs.append(df)
# mock client
self.client = Client()
def setUp(self):
"""
setting up essential objects, copied from tests above
"""
user = '******'
pwd = 'secret'
email = ''
self.user = User.objects.create_user(user, email, pwd)
self.userProfile = self.user.userprofile
self.exp = Experiment(title='test exp1',
institution_name='monash', created_by=self.user)
self.exp.save()
self.acl = ObjectACL(
pluginId=django_user,
entityId=str(self.user.id),
content_object=self.exp,
canRead=True,
isOwner=True,
aclOwnershipType=ObjectACL.OWNER_OWNED,
)
self.acl.save()
self.dataset = Dataset(description='dataset description...')
self.dataset.save()
self.dataset.experiments.add(self.exp)
self.dataset.save()
self.datafile = DataFile(dataset=self.dataset,
size=42, filename="foo",
md5sum="junk")
self.datafile.save()
def setUp(self):
self.user = User(username='******', password='******', email='*****@*****.**')
self.user.save()
self.exp = Experiment(
approved = True,
title = 'title1',
institution_name = 'institution1',
description = 'description1',
created_by = self.user,
public_access = Experiment.PUBLIC_ACCESS_FULL
)
self.uid = 0
self.url = 'http://remotetardis:8080'
self.mock_ts = flexmock()
flexmock(TransferClient).new_instances(self.mock_ts)
self.mock_integrity = flexmock()
flexmock(IntegrityCheck).new_instances(self.mock_integrity)
self.status = {
'human_status': 'this is a readable status',
'message': 'this is a message'
}
def setUp(self):
# Create test owner without enough details
username, email, password = ('testuser',
'*****@*****.**',
'password')
user = User.objects.create_user(username, email, password)
profile = UserProfile(user=user, isDjangoAccount=True)
profile.save()
# Create test experiment and make user the owner of it
experiment = Experiment(title='Text Experiment',
institution_name='Test Uni',
created_by=user)
experiment.save()
acl = ExperimentACL(
pluginId='django_user',
entityId=str(user.id),
experiment=experiment,
canRead=True,
isOwner=True,
aclOwnershipType=ExperimentACL.OWNER_OWNED,
)
acl.save()
dataset = Dataset(description='dataset description...')
dataset.save()
dataset.experiments.add(experiment)
dataset.save()
def create_datafile(index):
testfile = path.join(path.dirname(__file__), 'fixtures',
'jeol_sem_test%d.txt' % index)
size, sha512sum = get_size_and_sha512sum(testfile)
datafile = Dataset_File(dataset=dataset,
filename=path.basename(testfile),
url='file://'+path.abspath(testfile),
protocol='file',
size=size,
sha512sum=sha512sum)
datafile.verify()
datafile.save()
return datafile
self.dataset = dataset
self.datafiles = [create_datafile(i) for i in (1,2)]
def has_experiment_download_access(request, experiment_id):
if Experiment.safe.owned_and_shared(request) \
.filter(id=experiment_id) \
.exists():
return True
else:
exp = Experiment.objects.get(id=experiment_id)
return Experiment.public_access_implies_distribution(exp.public_access)
def setUp(self):
self.user = User(username='******',
password='******',
email='*****@*****.**')
self.user.save()
self.exp = Experiment(approved=True,
title='title1',
institution_name='institution1',
description='description1',
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_FULL)
self.exp.save()
self.synced_exp = SyncedExperiment(uid='tardis.1',
experiment=self.exp,
provider_url='url')
self.synced_exp.msg = '{"message": "You broke everything!"}'
self.synced_exp.save()
def generate_experiment(datasets=[], users=[]):
from tardis.tardis_portal.models import Experiment, ObjectACL
experiment = Experiment(created_by=users[0])
experiment.save()
for ds in datasets:
ds.experiments.add(experiment)
ds.save()
for user in users:
acl = ObjectACL(content_object=experiment,
pluginId='django_user',
entityId=str(user.id),
isOwner=True,
canRead=True,
canWrite=True,
canDelete=True,
aclOwnershipType=ObjectACL.OWNER_OWNED)
acl.save()
return experiment
def setUp(self):
user, client = _create_user_and_login()
experiment = Experiment(title='Norwegian Blue',
description='Parrot + 40kV',
created_by=user)
experiment.save()
acl = ObjectACL(content_object=experiment,
pluginId='django_user',
entityId=str(user.id),
isOwner=False,
canRead=True,
canWrite=False,
canDelete=False,
aclOwnershipType=ObjectACL.OWNER_OWNED)
acl.save()
self.client = client
self.experiment = experiment
def setUp(self):
self.user = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
self.settings = ('tardis.tardis_portal.tests.test_publishservice.MockRifCsProvider',)
self.e1 = Experiment(id="1", title="Experiment 1",
description="This is my description.",
created_by=self.user,
public_access=Experiment.PUBLIC_ACCESS_NONE)
class ANDSDOITestCase(TestCase):
def setUp(self):
self.user = User.objects.create_user('test', '', 'test')
self.expt = Experiment(title='test exp1',
institution_name='monash',
created_by=self.user,
)
self.schema, _ = Schema.objects.get_or_create(namespace=settings.DOI_NAMESPACE)
self.doi_name, _ = ParameterName.objects.get_or_create(schema=self.schema, full_name='DOI', name='doi')
self.expt.save()
def test_init(self):
doi_service = DOIService(self.expt)
def test_get_doi_none(self):
doi_service = DOIService(self.expt)
self.assertEquals(None, doi_service.get_doi())