def test_delete(self):
from aiida.orm.group import Group
from aiida.common.exceptions import NotExistent
n = Node().store()
g = Group(name='testgroup3', description='some other desc')
g.store()
gcopy = Group.get(name='testgroup3')
self.assertEquals(g.uuid, gcopy.uuid)
g.add_nodes(n)
self.assertEquals(len(g.nodes), 1)
g.delete()
with self.assertRaises(NotExistent):
# The group does not exist anymore
Group.get(name='testgroup3')
# I should be able to restore it
g.store()
# Now, however, by deleting and recreating it, I lost the elements
self.assertEquals(len(g.nodes), 0)
self.assertEquals(g.name, 'testgroup3')
self.assertEquals(g.description, 'some other desc')
self.assertTrue(g.is_user_defined)
# To avoid to find it in further tests
g.delete()
def test_query(self):
"""
Test if queries are working
"""
g1 = Group(name='testquery1').store()
g2 = Group(name='testquery2').store()
n1 = Node().store()
n2 = Node().store()
n3 = Node().store()
n4 = Node().store()
g1.add_nodes([n1, n2])
g2.add_nodes([n1, n3])
newuser = DbUser(email='*****@*****.**', password='').save()
g3 = Group(name='testquery3', user=newuser).store()
# I should find it
g1copy = Group.get(uuid=g1.uuid)
self.assertEquals(g1.pk, g1copy.pk)
# Try queries
res = Group.query(nodes=n4)
self.assertEquals([_.pk for _ in res], [])
res = Group.query(nodes=n1)
self.assertEquals([_.pk for _ in res], [_.pk for _ in [g1, g2]])
res = Group.query(nodes=n2)
self.assertEquals([_.pk for _ in res], [_.pk for _ in [g1]])
# I try to use 'get' with zero or multiple results
with self.assertRaises(NotExistent):
Group.get(nodes=n4)
with self.assertRaises(MultipleObjectsError):
Group.get(nodes=n1)
self.assertEquals(Group.get(nodes=n2).pk, g1.pk)
# Query by user
res = Group.query(user=newuser)
self.assertEquals(set(_.pk for _ in res), set(_.pk for _ in [g3]))
# Same query, but using a string (the username=email) instead of
# a DbUser object
res = Group.query(user=newuser.email)
self.assertEquals(set(_.pk for _ in res), set(_.pk for _ in [g3]))
res = Group.query(user=get_automatic_user())
self.assertEquals(set(_.pk for _ in res), set(_.pk for _ in [g1, g2]))
# Final cleanup
g1.delete()
g2.delete()
newuser.delete()
def test_query(self):
"""
Test if queries are working
"""
from aiida.orm.group import Group
from aiida.common.exceptions import NotExistent, MultipleObjectsError
g1 = Group(name='testquery1').store()
self.addCleanup(g1.delete)
g2 = Group(name='testquery2').store()
self.addCleanup(g2.delete)
n1 = Node().store()
n2 = Node().store()
n3 = Node().store()
n4 = Node().store()
g1.add_nodes([n1, n2])
g2.add_nodes([n1, n3])
newuser = self.backend.users.create(email='*****@*****.**')
g3 = Group(name='testquery3', user=newuser).store()
# I should find it
g1copy = Group.get(uuid=g1.uuid)
self.assertEquals(g1.pk, g1copy.pk)
# Try queries
res = Group.query(nodes=n4)
self.assertEquals([_.pk for _ in res], [])
res = Group.query(nodes=n1)
self.assertEquals([_.pk for _ in res], [_.pk for _ in [g1, g2]])
res = Group.query(nodes=n2)
self.assertEquals([_.pk for _ in res], [_.pk for _ in [g1]])
# I try to use 'get' with zero or multiple results
with self.assertRaises(NotExistent):
Group.get(nodes=n4)
with self.assertRaises(MultipleObjectsError):
Group.get(nodes=n1)
self.assertEquals(Group.get(nodes=n2).pk, g1.pk)
# Query by user
res = Group.query(user=newuser)
self.assertEquals(set(_.pk for _ in res), set(_.pk for _ in [g3]))
# Same query, but using a string (the username=email) instead of
# a DbUser object
res = Group.query(user=newuser.email)
self.assertEquals(set(_.pk for _ in res), set(_.pk for _ in [g3]))
res = Group.query(user=self.backend.users.get_automatic_user())
self.assertEquals(set(_.pk for _ in res), set(_.pk for _ in [g1, g2]))
def load_example_structures():
""" Read input structures into the database
Structures are read from subfolder "example-structures"
and stored in the group "example-structures".
:return: group of available structures
"""
from aiida.orm.group import Group
try:
group = Group.get(name=group_name)
except NotExistent:
import glob
import os
from ase.io import read
from aiida.orm.data.structure import StructureData
paths = glob.glob(group_name + '/*.cif')
structure_nodes = []
for path in paths:
fname = os.path.basename(path)
name = os.path.splitext(fname)[0]
structure = StructureData(ase=read(path))
if "ML" in name:
# surface normal of monolayers should be oriented along z
structure.set_pbc([True, True, False])
else:
structure.set_pbc([True, True, True])
structure.label = name
print("Storing {} in database".format(name))
structure.store()
structure_nodes.append(structure)
group = Group(name=group_name)
group.store()
group.description = "\
Set of atomic structures used by examples for AiiDA plugins of different codes"
group.add_nodes(structure_nodes)
return group