def test_add_default_group_permissions(flask_server, user):
with flask_server.app.app_context():
group_id = groups.create_group("Example Group", "", user.id).id
session = requests.session()
assert session.get(flask_server.base_url +
'users/{}/autologin'.format(user.id)).status_code == 200
r = session.get(flask_server.base_url +
'users/{}/preferences'.format(user.id))
assert r.status_code == 200
document = BeautifulSoup(r.content, 'html.parser')
default_permissions_form = document.find(attrs={
'name': 'add_group_permissions',
'value': 'add_group_permissions'
}).find_parent('form')
data = {}
for hidden_field in default_permissions_form.find_all(
'input', {'type': 'hidden'}):
data[hidden_field['name']] = hidden_field['value']
data['group_id'] = str(group_id)
data['permissions'] = 'read'
data['add_group_permissions'] = 'add_group_permissions'
assert session.post(flask_server.base_url +
'users/{}/preferences'.format(user.id),
data=data).status_code == 200
with flask_server.app.app_context():
assert object_permissions.get_default_permissions_for_groups(
creator_id=user.id).get(
group_id) == object_permissions.Permissions.READ
def test_group_permissions(users, independent_action_object):
user, creator = users
object_id = independent_action_object.object_id
group_id = groups.create_group("Example Group", "", creator.id).id
assert object_permissions.get_object_permissions_for_users(object_id=object_id) == {
creator.id: Permissions.GRANT
}
assert not object_permissions.object_is_public(object_id)
assert object_permissions.get_user_object_permissions(object_id=object_id, user_id=user.id) == Permissions.NONE
object_permissions.set_group_object_permissions(object_id=object_id, group_id=group_id, permissions=Permissions.WRITE)
assert object_permissions.get_object_permissions_for_users(object_id=object_id) == {
creator.id: Permissions.GRANT
}
assert not object_permissions.object_is_public(object_id)
assert object_permissions.get_user_object_permissions(object_id=object_id, user_id=user.id) == Permissions.NONE
groups.add_user_to_group(group_id=group_id, user_id=user.id)
assert object_permissions.get_object_permissions_for_users(object_id=object_id) == {
creator.id: Permissions.GRANT,
user.id: Permissions.WRITE
}
assert not object_permissions.object_is_public(object_id)
assert object_permissions.get_user_object_permissions(object_id=object_id, user_id=user.id) == Permissions.WRITE
object_permissions.set_user_object_permissions(object_id=object_id, user_id=user.id, permissions=Permissions.READ)
assert object_permissions.get_object_permissions_for_users(object_id=object_id) == {
creator.id: Permissions.GRANT,
user.id: Permissions.WRITE
}
assert not object_permissions.object_is_public(object_id)
assert object_permissions.get_user_object_permissions(object_id=object_id, user_id=user.id) == Permissions.WRITE
object_permissions.set_group_object_permissions(object_id=object_id, group_id=group_id, permissions=Permissions.READ)
object_permissions.set_user_object_permissions(object_id=object_id, user_id=user.id, permissions=Permissions.WRITE)
assert object_permissions.get_object_permissions_for_users(object_id=object_id) == {
creator.id: Permissions.GRANT,
user.id: Permissions.WRITE
}
assert not object_permissions.object_is_public(object_id)
assert object_permissions.get_user_object_permissions(object_id=object_id, user_id=user.id) == Permissions.WRITE
object_permissions.set_user_object_permissions(object_id=object_id, user_id=user.id, permissions=Permissions.READ)
object_permissions.set_group_object_permissions(object_id=object_id, group_id=group_id, permissions=Permissions.GRANT)
groups.remove_user_from_group(group_id=group_id, user_id=user.id)
assert object_permissions.get_object_permissions_for_users(object_id=object_id) == {
creator.id: Permissions.GRANT,
user.id: Permissions.READ
}
assert not object_permissions.object_is_public(object_id)
assert object_permissions.get_user_object_permissions(object_id=object_id, user_id=user.id) == Permissions.READ
def test_group_permissions(users, user_action):
user, creator = users
action_id = user_action.id
group_id = groups.create_group("Example Group", "", creator.id).id
assert action_permissions.get_action_permissions_for_users(action_id=action_id) == {
creator.id: Permissions.GRANT
}
assert not action_permissions.action_is_public(action_id)
assert action_permissions.get_user_action_permissions(action_id=action_id, user_id=user.id) == Permissions.NONE
action_permissions.set_group_action_permissions(action_id=action_id, group_id=group_id, permissions=Permissions.WRITE)
assert action_permissions.get_action_permissions_for_users(action_id=action_id) == {
creator.id: Permissions.GRANT
}
assert not action_permissions.action_is_public(action_id)
assert action_permissions.get_user_action_permissions(action_id=action_id, user_id=user.id) == Permissions.NONE
groups.add_user_to_group(group_id=group_id, user_id=user.id)
assert action_permissions.get_action_permissions_for_users(action_id=action_id) == {
creator.id: Permissions.GRANT,
user.id: Permissions.WRITE
}
assert not action_permissions.action_is_public(action_id)
assert action_permissions.get_user_action_permissions(action_id=action_id, user_id=user.id) == Permissions.WRITE
action_permissions.set_user_action_permissions(action_id=action_id, user_id=user.id, permissions=Permissions.READ)
assert action_permissions.get_action_permissions_for_users(action_id=action_id) == {
creator.id: Permissions.GRANT,
user.id: Permissions.WRITE
}
assert not action_permissions.action_is_public(action_id)
assert action_permissions.get_user_action_permissions(action_id=action_id, user_id=user.id) == Permissions.WRITE
action_permissions.set_group_action_permissions(action_id=action_id, group_id=group_id, permissions=Permissions.READ)
action_permissions.set_user_action_permissions(action_id=action_id, user_id=user.id, permissions=Permissions.WRITE)
assert action_permissions.get_action_permissions_for_users(action_id=action_id) == {
creator.id: Permissions.GRANT,
user.id: Permissions.WRITE
}
assert not action_permissions.action_is_public(action_id)
assert action_permissions.get_user_action_permissions(action_id=action_id, user_id=user.id) == Permissions.WRITE
action_permissions.set_user_action_permissions(action_id=action_id, user_id=user.id, permissions=Permissions.READ)
action_permissions.set_group_action_permissions(action_id=action_id, group_id=group_id, permissions=Permissions.GRANT)
groups.remove_user_from_group(group_id=group_id, user_id=user.id)
assert action_permissions.get_action_permissions_for_users(action_id=action_id) == {
creator.id: Permissions.GRANT,
user.id: Permissions.READ
}
assert not action_permissions.action_is_public(action_id)
assert action_permissions.get_user_action_permissions(action_id=action_id, user_id=user.id) == Permissions.READ
def test_object_permissions_for_groups_with_project(users,
independent_action_object):
user, creator = users
object_id = independent_action_object.object_id
group_id = groups.create_group("Example Group", "", creator.id).id
object_permissions.set_group_object_permissions(
object_id=object_id, group_id=group_id, permissions=Permissions.READ)
assert object_permissions.get_object_permissions_for_groups(object_id) == {
group_id: Permissions.READ
}
project_id = sampledb.logic.projects.create_project(
"Example Project", "", creator.id).id
object_permissions.set_project_object_permissions(
object_id=object_id,
project_id=project_id,
permissions=Permissions.GRANT)
assert object_permissions.get_object_permissions_for_groups(object_id) == {
group_id: Permissions.READ
}
sampledb.logic.projects.add_group_to_project(project_id=project_id,
group_id=group_id,
permissions=Permissions.WRITE)
assert object_permissions.get_object_permissions_for_groups(object_id) == {
group_id: Permissions.READ
}
assert object_permissions.get_object_permissions_for_groups(
object_id, include_projects=True) == {
group_id: Permissions.WRITE
}
sampledb.logic.projects.update_group_project_permissions(
project_id=project_id,
group_id=group_id,
permissions=Permissions.GRANT)
assert object_permissions.get_object_permissions_for_groups(
object_id, include_projects=True) == {
group_id: Permissions.GRANT
}
sampledb.logic.projects.remove_group_from_project(project_id=project_id,
group_id=group_id)
assert object_permissions.get_object_permissions_for_groups(
object_id, include_projects=True) == {
group_id: Permissions.READ
}
def test_edit_default_group_permissions(flask_server, user):
with flask_server.app.app_context():
group_id = groups.create_group("Example Group", "", user.id).id
object_permissions.set_default_permissions_for_group(
creator_id=user.id,
group_id=group_id,
permissions=object_permissions.Permissions.WRITE)
assert object_permissions.get_default_permissions_for_groups(
creator_id=user.id).get(
group_id) == object_permissions.Permissions.WRITE
session = requests.session()
assert session.get(flask_server.base_url +
'users/{}/autologin'.format(user.id)).status_code == 200
r = session.get(flask_server.base_url +
'users/{}/preferences'.format(user.id))
assert r.status_code == 200
document = BeautifulSoup(r.content, 'html.parser')
default_permissions_form = document.find(attrs={
'name': 'edit_user_permissions',
'value': 'edit_user_permissions'
}).find_parent('form')
data = {}
group_field_name = None
for hidden_field in default_permissions_form.find_all(
'input', {'type': 'hidden'}):
data[hidden_field['name']] = hidden_field['value']
if hidden_field['name'].endswith(
'group_id') and hidden_field['value'] == str(group_id):
# the associated radio button is the first radio button in the same table row
group_field_name = hidden_field.find_parent('tr').find(
'input', {'type': 'radio'})['name']
for radio_button in default_permissions_form.find_all(
'input', {'type': 'radio'}):
if radio_button.has_attr(
'checked') and not radio_button.has_attr('disabled'):
data[radio_button['name']] = radio_button['value']
assert group_field_name is not None
assert data[group_field_name] == 'write'
data[group_field_name] = 'read'
data['edit_user_permissions'] = 'edit_user_permissions'
assert session.post(flask_server.base_url +
'users/{}/preferences'.format(user.id),
data=data).status_code == 200
with flask_server.app.app_context():
assert object_permissions.get_default_permissions_for_groups(
creator_id=user.id).get(
group_id) == object_permissions.Permissions.READ
def test_default_permissions_for_groups(users, independent_action):
user, creator = users
group_id = groups.create_group("Example Group", "", creator.id).id
assert object_permissions.get_default_permissions_for_groups(
creator_id=creator.id) == {}
object = sampledb.logic.objects.create_object(
user_id=creator.id,
action_id=independent_action.id,
data={'name': {
'_type': 'text',
'text': 'Name'
}})
assert object_permissions.get_object_permissions_for_groups(
object_id=object.id) == {}
object_permissions.set_default_permissions_for_group(
creator_id=creator.id, group_id=group_id, permissions=Permissions.READ)
assert object_permissions.get_default_permissions_for_groups(
creator_id=creator.id) == {
group_id: Permissions.READ
}
object = sampledb.logic.objects.create_object(
user_id=creator.id,
action_id=independent_action.id,
data={'name': {
'_type': 'text',
'text': 'Name'
}})
assert object_permissions.get_object_permissions_for_groups(
object_id=object.id) == {
group_id: Permissions.READ
}
# the default permissions are only used when creating a new object.
object_permissions.set_default_permissions_for_group(
creator_id=creator.id,
group_id=group_id,
permissions=Permissions.WRITE)
assert object_permissions.get_default_permissions_for_groups(
creator_id=creator.id) == {
group_id: Permissions.WRITE
}
assert object_permissions.get_object_permissions_for_groups(
object_id=object.id) == {
group_id: Permissions.READ
}
def test_object_permissions_for_groups(users, independent_action_object):
user, creator = users
object_id = independent_action_object.object_id
group_id = groups.create_group("Example Group", "", creator.id).id
assert object_permissions.get_object_permissions_for_groups(object_id) == {}
object_permissions.set_group_object_permissions(object_id=object_id, group_id=group_id, permissions=Permissions.WRITE)
assert object_permissions.get_object_permissions_for_groups(object_id) == {
group_id: Permissions.WRITE
}
object_permissions.set_group_object_permissions(object_id=object_id, group_id=group_id, permissions=Permissions.NONE)
assert object_permissions.get_object_permissions_for_groups(object_id) == {}
def test_action_permissions_for_groups(users, user_action):
user, creator = users
action_id = user_action.id
group_id = groups.create_group("Example Group", "", creator.id).id
assert action_permissions.get_action_permissions_for_groups(action_id) == {}
action_permissions.set_group_action_permissions(action_id=action_id, group_id=group_id, permissions=Permissions.WRITE)
assert action_permissions.get_action_permissions_for_groups(action_id) == {
group_id: Permissions.WRITE
}
action_permissions.set_group_action_permissions(action_id=action_id, group_id=group_id, permissions=Permissions.NONE)
assert action_permissions.get_action_permissions_for_groups(action_id) == {}
def setup_data(app):
# TODO: replace using user management logic
admin = User(name="Administrator",
email="*****@*****.**",
type=UserType.PERSON)
admin.is_admin = True
instrument_responsible_user = User(name="Instrument Responsible User",
email="*****@*****.**",
type=UserType.PERSON)
basic_user = User(name="Basic User",
email="*****@*****.**",
type=UserType.PERSON)
for user in (admin, instrument_responsible_user, basic_user):
sampledb.db.session.add(user)
sampledb.db.session.commit()
api_user = sampledb.logic.users.create_user(name="API User",
email="*****@*****.**",
type=UserType.OTHER)
sampledb.logic.authentication.add_other_authentication(
api_user.id, 'api', 'password')
group_id = groups.create_group(
"Example Group", "This is an example group for testing purposes.",
instrument_responsible_user.id).id
project_id = projects.create_project("Example Project",
"This is an example project",
instrument_responsible_user.id).id
project_id2 = projects.create_project("Example Project 2",
"This is another example project",
instrument_responsible_user.id).id
projects.create_subproject_relationship(parent_project_id=project_id,
child_project_id=project_id2,
child_can_add_users_to_parent=True)
# Setup autologin for testing
@app.route('/users/me/autologin')
@app.route('/users/<int:user_id>/autologin')
def autologin(user_id=instrument_responsible_user.id):
user = User.query.get(user_id)
assert user is not None
flask_login.login_user(user)
return flask.redirect(
flask.url_for('frontend.new_action', previous_action_id=4))
sampledb.login_manager.login_view = 'autologin'
instrument = create_instrument(
name="OMBE I", description="This is an example instrument.")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('sampledb/schemas/ombe_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.SAMPLE_CREATION,
"Sample Creation",
"This is an example action", schema,
instrument.id)
independent_action = create_action(ActionType.SAMPLE_CREATION,
"Alternative Process",
"This is an example action", schema)
with open('sampledb/schemas/ombe_measurement_batch.sampledb.json',
'r') as schema_file:
batch_schema = json.load(schema_file)
create_action(ActionType.SAMPLE_CREATION, "Sample Creation (Batch)",
"This is an example action", batch_schema, instrument.id)
sampledb.db.session.commit()
with open('example_data/ombe-1.sampledb.json', 'r') as data_file:
data = json.load(data_file)
instrument_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=instrument_action.id,
connection=sampledb.db.engine)
create_object(object_id=instrument_object.object_id,
user_id=instrument_responsible_user.id)
data['multilayer'][0]['repetitions']['magnitude_in_base_units'] = 20000
data['multilayer'][1]['films'][0]['thickness'][
'magnitude_in_base_units'] = 1
independent_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=independent_action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
comments.create_comment(
instrument_object.id, instrument_responsible_user.id,
'This comment is very long. ' * 20 + '\n' +
'This comment has three paragraphs. ' * 20 + '\n' + '\n' +
'This comment has three paragraphs. ' * 20)
comments.create_comment(instrument_object.id,
instrument_responsible_user.id,
'This is another, shorter comment')
files.create_local_file(
instrument_object.id, instrument_responsible_user.id, 'example.txt',
lambda stream: stream.write("Dies ist ein Test".encode('utf-8')))
files.create_local_file(
instrument_object.id, instrument_responsible_user.id, 'demo.png',
lambda stream: stream.write(
open('sampledb/static/img/ghs01.png', 'rb').read()))
files.update_file_information(instrument_object.id, 1,
instrument_responsible_user.id,
'Example File',
'This is a file description.')
files.create_url_file(instrument_object.id, instrument_responsible_user.id,
'http://iffsamples.fz-juelich.de/')
with open('server_schemas/ombe_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
sampledb.logic.actions.update_action(instrument_action.id,
"Updated Sample Creation", "", schema)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
instrument = create_instrument(name="XRR",
description="X-Ray Reflectometry")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('sampledb/schemas/xrr_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"XRR Measurement", "", schema,
instrument.id)
with open('sampledb/schemas/searchable_quantity.json', 'r') as schema_file:
schema = json.load(schema_file)
action = create_action(ActionType.SAMPLE_CREATION, "Searchable Object", "",
schema, None)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-1"
},
"tags": {
"_type": "tags",
"tags": ["tag1", "tag2"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.00001,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
object_permissions.set_user_object_permissions(
independent_object.object_id, api_user.id,
object_permissions.Permissions.WRITE)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-2"
},
"tags": {
"_type": "tags",
"tags": ["tag2", "tag3"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.000005,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
sampledb.db.session.commit()
instrument = create_instrument(
name="MPMS SQUID", description="MPMS SQUID Magnetometer JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/squid_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="Powder Diffractometer",
description="Huber Imaging Plate Guinier Camera G670 at JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/powder_diffractometer_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="GALAXI", description="Gallium Anode Low-Angle X-ray Instrument")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/galaxi_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
with open('server_schemas/other_sample.sampledb.json', 'r') as schema_file:
schema = json.load(schema_file)
create_action(ActionType.SAMPLE_CREATION, "Other Sample", "", schema, None)
sampledb.db.session.commit()
sample_action = sampledb.logic.actions.create_action(
action_type=ActionType.SAMPLE_CREATION,
name="sample_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
}
},
'required': ['name']
})
measurement_action = sampledb.logic.actions.create_action(
action_type=ActionType.MEASUREMENT,
name="measurement_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
},
'comment': {
'title': 'Comment',
'type': 'text',
'multiline': True
}
},
'required': ['name']
})
data = {'name': {'_type': 'text', 'text': 'Object 1'}}
object = sampledb.logic.objects.create_object(sample_action.id, data,
user.id)
sampledb.logic.object_permissions.set_object_public(object.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 2'
},
'sample': {
'_type': 'sample',
'object_id': object.id
}
}
sample = sampledb.logic.objects.create_object(sample_action.id, data,
user.id)
sampledb.logic.object_permissions.set_object_public(sample.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 1'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
}
}
sampledb.logic.objects.update_object(object.id, data, user.id)
data = {
'name': {
'_type': 'text',
'text': 'Measurement'
},
'sample': {
'_type': 'sample',
'object_id': object.id
},
'comment': {
'_type':
'text',
'text':
'This is a test.\nThis is a second line.\n\nThis line follows an empty line.'
}
}
measurement = sampledb.logic.objects.create_object(measurement_action.id,
data, user.id)
sampledb.logic.object_permissions.set_object_public(measurement.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Measurement 2'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
},
'comment': {
'_type':
'text',
'text':
'This is a test.\nThis is a second line.\n\nThis line follows an empty line.'
}
}
measurement = sampledb.logic.objects.create_object(
measurement_action.id, data, instrument_responsible_user.id)
sampledb.logic.object_permissions.set_object_public(measurement.id, True)
juelich = sampledb.logic.locations.create_location(
"FZJ", "Forschungszentrum Jülich", None,
instrument_responsible_user.id)
building_04_8 = sampledb.logic.locations.create_location(
"Building 04.8", "Building 04.8 at Forschungszentrum Jülich",
juelich.id, instrument_responsible_user.id)
room_139 = sampledb.logic.locations.create_location(
"Room 139b", "Building 04.8, Room 139", building_04_8.id,
instrument_responsible_user.id)
room_141 = sampledb.logic.locations.create_location(
"Room 141", "Building 04.8, Room 141", building_04_8.id,
instrument_responsible_user.id)
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_141.id, None, instrument_responsible_user.id,
"Temporarily stored on table\n\nSome other text")
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_141.id, instrument_responsible_user.id,
basic_user.id, "Stored in shelf K")
sampledb.logic.notifications.create_other_notification(
instrument_responsible_user.id, "This is a demo.")
sampledb.logic.object_permissions.set_user_object_permissions(
independent_object.id, instrument_responsible_user.id,
sampledb.models.Permissions.GRANT)
sampledb.logic.notifications.create_notification_for_having_received_an_objects_permissions_request(
instrument_responsible_user.id, independent_object.id, admin.id)
def setup_data(app):
# TODO: replace using user management logic
admin = User(name="Administrator",
email="*****@*****.**",
type=UserType.PERSON)
admin.is_admin = True
instrument_responsible_user = User(name="Instrument Responsible User",
email="*****@*****.**",
type=UserType.PERSON)
basic_user = User(name="Basic User",
email="*****@*****.**",
type=UserType.PERSON)
for user in (admin, instrument_responsible_user, basic_user):
sampledb.db.session.add(user)
sampledb.db.session.commit()
api_user = sampledb.logic.users.create_user(name="API User",
email="*****@*****.**",
type=UserType.OTHER)
sampledb.logic.authentication.add_other_authentication(
api_user.id, 'api', 'password')
group_id = groups.create_group(
"Example Group", "This is an example group for testing purposes.",
instrument_responsible_user.id).id
project_id = projects.create_project("Example Project",
"This is an example project",
instrument_responsible_user.id).id
project_id2 = projects.create_project("Example Project 2",
"This is another example project",
instrument_responsible_user.id).id
projects.create_subproject_relationship(parent_project_id=project_id,
child_project_id=project_id2,
child_can_add_users_to_parent=True)
# Setup autologin for testing
@app.route('/users/me/autologin')
@app.route('/users/<int:user_id>/autologin')
def autologin(user_id=instrument_responsible_user.id):
user = User.query.get(user_id)
assert user is not None
flask_login.login_user(user)
# Remove the message asking the user to sign in
flask.session.pop('_flashes', None)
flask.flash(
'You have been signed in automatically as part of the SampleDB Demo.',
'info')
return flask.redirect(
os.environ.get('SAMPLEDB_DEMO_REDIRECT_URI',
flask.url_for('frontend.index')))
sampledb.login_manager.login_view = 'autologin'
markdown_notes = """
This example shows how Markdown can be used for instrument Notes.
## Header
*italics* **bold**
| A | B | C |
|--:|:-:|---|
| Example | 100˚C | 5µm |
| Data | 110˚C | 6µm |
"""
instrument = create_instrument(
name="OMBE I",
description="This is an example instrument.",
users_can_create_log_entries=True,
notes=markdown_notes,
notes_as_html=sampledb.frontend.utils.markdown_to_safe_html(
markdown_notes))
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
log_category_error = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Error',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
RED)
log_category_warning = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Warning',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
YELLOW)
log_category_success = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Success',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
GREEN)
log_category_other = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Other',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
BLUE)
log_category_normal = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Normal',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
GRAY)
for category in sampledb.logic.instrument_log_entries.get_instrument_log_categories(
instrument.id):
sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry", [category.id])
sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry")
log_entry = sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry", [
log_category_error.id, log_category_warning.id,
log_category_normal.id, log_category_success.id
])
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="ghs01.png",
content=open('sampledb/static/img/ghs01.png', 'rb').read())
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="ghs02.png",
content=open('sampledb/static/img/ghs02.png', 'rb').read())
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="test.txt",
content="This is a test".encode('utf-8'))
with open('sampledb/schemas/ombe_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.SAMPLE_CREATION,
"Sample Creation",
"This is an example action", schema,
instrument.id)
independent_action = create_action(ActionType.SAMPLE_CREATION,
"Alternative Process",
"This is an example action", schema)
with open('sampledb/schemas/ombe_measurement_batch.sampledb.json',
'r') as schema_file:
batch_schema = json.load(schema_file)
create_action(ActionType.SAMPLE_CREATION, "Sample Creation (Batch)",
"This is an example action", batch_schema, instrument.id)
sampledb.db.session.commit()
with open('example_data/ombe-1.sampledb.json', 'r') as data_file:
data = json.load(data_file)
instrument_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=instrument_action.id,
connection=sampledb.db.engine)
create_object(object_id=instrument_object.object_id,
user_id=instrument_responsible_user.id)
data['multilayer'][0]['repetitions']['magnitude_in_base_units'] = 20000
data['multilayer'][1]['films'][0]['thickness'][
'magnitude_in_base_units'] = 1
independent_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=independent_action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
comments.create_comment(
instrument_object.id, instrument_responsible_user.id,
'This comment is very long. ' * 20 + '\n' +
'This comment has three paragraphs. ' * 20 + '\n' + '\n' +
'This comment has three paragraphs. ' * 20)
comments.create_comment(instrument_object.id,
instrument_responsible_user.id,
'This is another, shorter comment')
files.create_local_file(
instrument_object.id, instrument_responsible_user.id, 'example.txt',
lambda stream: stream.write("Dies ist ein Test".encode('utf-8')))
files.create_local_file(
instrument_object.id, instrument_responsible_user.id, 'demo.png',
lambda stream: stream.write(
open('sampledb/static/img/ghs01.png', 'rb').read()))
files.update_file_information(instrument_object.id, 1,
instrument_responsible_user.id,
'Example File',
'This is a file description.')
files.create_url_file(instrument_object.id, instrument_responsible_user.id,
'http://iffsamples.fz-juelich.de/')
with open('server_schemas/ombe_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
sampledb.logic.actions.update_action(instrument_action.id,
"Updated Sample Creation", "", schema)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
instrument = create_instrument(name="XRR",
description="X-Ray Reflectometry")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('sampledb/schemas/xrr_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"XRR Measurement", "", schema,
instrument.id)
with open('sampledb/schemas/searchable_quantity.json', 'r') as schema_file:
schema = json.load(schema_file)
action = create_action(ActionType.SAMPLE_CREATION, "Searchable Object", "",
schema, None)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-1"
},
"tags": {
"_type": "tags",
"tags": ["tag1", "tag2"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.00001,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
object_permissions.set_user_object_permissions(
independent_object.object_id, api_user.id,
object_permissions.Permissions.WRITE)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-2"
},
"tags": {
"_type": "tags",
"tags": ["tag2", "tag3"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.000005,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
sampledb.db.session.commit()
instrument = create_instrument(
name="MPMS SQUID", description="MPMS SQUID Magnetometer JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/squid_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="Powder Diffractometer",
description="Huber Imaging Plate Guinier Camera G670 at JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/powder_diffractometer_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="GALAXI", description="Gallium Anode Low-Angle X-ray Instrument")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/galaxi_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
with open('server_schemas/other_sample.sampledb.json', 'r') as schema_file:
schema = json.load(schema_file)
create_action(ActionType.SAMPLE_CREATION, "Other Sample", "", schema, None)
sampledb.db.session.commit()
sample_action = sampledb.logic.actions.create_action(
action_type_id=ActionType.SAMPLE_CREATION,
name="sample_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
}
},
'required': ['name']
})
measurement_action = sampledb.logic.actions.create_action(
action_type_id=ActionType.MEASUREMENT,
name="measurement_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
},
'comment': {
'title': 'Comment',
'type': 'text',
'multiline': True
}
},
'required': ['name']
})
data = {'name': {'_type': 'text', 'text': 'Object 1'}}
object = sampledb.logic.objects.create_object(sample_action.id, data,
user.id)
sampledb.logic.object_permissions.set_object_public(object.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 2'
},
'sample': {
'_type': 'sample',
'object_id': object.id
}
}
sample = sampledb.logic.objects.create_object(sample_action.id, data,
user.id)
sampledb.logic.object_permissions.set_object_public(sample.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 1'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
}
}
sampledb.logic.objects.update_object(object.id, data, user.id)
data = {
'name': {
'_type': 'text',
'text': 'Measurement'
},
'sample': {
'_type': 'sample',
'object_id': object.id
},
'comment': {
'_type':
'text',
'text':
'This is a test.\nThis is a second line.\n\nThis line follows an empty line.'
}
}
measurement = sampledb.logic.objects.create_object(measurement_action.id,
data, user.id)
sampledb.logic.object_permissions.set_object_public(measurement.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Measurement 2'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
},
'comment': {
'_type':
'text',
'text':
'This is a test.\nThis is a second line.\n\nThis line follows an empty line.'
}
}
measurement = sampledb.logic.objects.create_object(
measurement_action.id, data, instrument_responsible_user.id)
sampledb.logic.object_permissions.set_object_public(measurement.id, True)
juelich = sampledb.logic.locations.create_location(
"FZJ", "Forschungszentrum Jülich", None,
instrument_responsible_user.id)
building_04_8 = sampledb.logic.locations.create_location(
"Building 04.8", "Building 04.8 at Forschungszentrum Jülich",
juelich.id, instrument_responsible_user.id)
room_139 = sampledb.logic.locations.create_location(
"Room 139b", "Building 04.8, Room 139", building_04_8.id,
instrument_responsible_user.id)
room_141 = sampledb.logic.locations.create_location(
"Room 141", "Building 04.8, Room 141", building_04_8.id,
instrument_responsible_user.id)
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_141.id, None, instrument_responsible_user.id,
"Temporarily stored on table\n\nSome other text")
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_141.id, instrument_responsible_user.id,
basic_user.id, "Stored in shelf K")
sampledb.logic.notifications.create_other_notification(
instrument_responsible_user.id, "This is a demo.")
sampledb.logic.object_permissions.set_user_object_permissions(
independent_object.id, instrument_responsible_user.id,
sampledb.models.Permissions.GRANT)
sampledb.logic.notifications.create_notification_for_having_received_an_objects_permissions_request(
instrument_responsible_user.id, independent_object.id, admin.id)
for i in range(1, 8):
sampledb.logic.instrument_log_entries.create_instrument_log_object_attachment(
instrument_log_entry_id=log_entry.id, object_id=i)
