def test_object_ids_for_location(user: User, action: Action):
data = {'name': {'_type': 'text', 'text': 'Object'}}
object1 = objects.create_object(user_id=user.id,
action_id=action.id,
data=data)
object2 = objects.create_object(user_id=user.id,
action_id=action.id,
data=data)
object3 = objects.create_object(user_id=user.id,
action_id=action.id,
data=data)
location1 = locations.create_location("Location",
"This is an example location", None,
user.id)
location2 = locations.create_location("Location",
"This is an example location", None,
user.id)
assert locations.get_object_ids_at_location(location1.id) == set()
assert locations.get_object_ids_at_location(location2.id) == set()
locations.assign_location_to_object(object1.id, location1.id, None,
user.id, "")
assert locations.get_object_ids_at_location(location1.id) == {object1.id}
assert locations.get_object_ids_at_location(location2.id) == set()
locations.assign_location_to_object(object2.id, location1.id, None,
user.id, "")
assert locations.get_object_ids_at_location(
location1.id) == {object1.id, object2.id}
assert locations.get_object_ids_at_location(location2.id) == set()
locations.assign_location_to_object(object3.id, location2.id, user.id,
user.id, "")
assert locations.get_object_ids_at_location(
location1.id) == {object1.id, object2.id}
assert locations.get_object_ids_at_location(location2.id) == {object3.id}
def test_validate_object_reference_invalid_type():
from sampledb.models.users import User, UserType
from sampledb.models.actions import Action
schema = {'title': 'Example', 'type': 'object_reference'}
user = User("User", "*****@*****.**", UserType.OTHER)
action = Action(sampledb.models.ActionType.SAMPLE_CREATION,
"Example Action",
schema={
"title": "Sample Information",
"type": "object",
"properties": {
"name": {
"title": "Sample Name",
"type": "text"
}
},
'required': ['name']
})
sampledb.db.session.add(user)
sampledb.db.session.add(action)
sampledb.db.session.commit()
object_id = create_object(
data={'name': {
'_type': 'text',
'text': 'example'
}},
user_id=user.id,
action_id=action.id)
instance = object_id
with pytest.raises(ValidationError):
validate(instance, schema)
def test_validate_measurement_wrong_object_id_type():
from sampledb.models.users import User, UserType
from sampledb.models.actions import Action
schema = {'title': 'Example', 'type': 'measurement'}
user = User("User", "*****@*****.**", UserType.OTHER)
action = Action(sampledb.models.ActionType.MEASUREMENT,
"Example Action",
schema={
"title": "Measurement Information",
"type": "object",
"properties": {
"name": {
"title": "Measurement Name",
"type": "text"
}
},
"required": ["name"]
})
sampledb.db.session.add(user)
sampledb.db.session.add(action)
sampledb.db.session.commit()
object = create_object(data={'name': {
'_type': 'text',
'text': 'example'
}},
user_id=user.id,
action_id=action.id)
instance = {'_type': 'measurement', 'object_id': object}
with pytest.raises(ValidationError):
validate(instance, schema)
def test_validate_sample():
from sampledb.models.users import User, UserType
from sampledb.models.actions import Action
schema = {
'title': 'Example',
'type': 'sample'
}
user = User("User", "*****@*****.**", UserType.OTHER)
action = Action(sampledb.models.ActionType.SAMPLE_CREATION, "Example Action", schema={
"title": "Sample Information",
"type": "object",
"properties": {
"name": {
"title": "Sample Name",
"type": "text"
}
},
'required': ['name']
})
sampledb.db.session.add(user)
sampledb.db.session.add(action)
sampledb.db.session.commit()
object = create_object(data={'name': {'_type': 'text', 'text': 'example'}}, user_id=user.id, action_id=action.id)
instance = {
'_type': 'sample',
'object_id': object.id
}
validate(instance, schema)
def post(self):
if flask.g.user.is_readonly:
return {'message': 'user has been marked as read only'}, 400
request_json = flask.request.get_json(force=True)
if not isinstance(request_json, dict):
return {"message": "JSON object body required"}, 400
for key in request_json:
if key not in {
'object_id', 'version_id', 'action_id', 'schema', 'data'
}:
return {"message": "invalid key '{}'".format(key)}, 400
if 'object_id' in request_json:
return {"message": "object_id cannot be set"}, 400
if 'version_id' in request_json:
if request_json['version_id'] != 0:
return {"message": "version_id must be 0"}, 400
if 'action_id' in request_json:
if not isinstance(request_json['action_id'], int):
return {"message": "action_id must be an integer"}, 400
action_id = request_json['action_id']
try:
action = get_action(action_id=action_id)
except errors.ActionDoesNotExistError:
return {
"message": "action {} does not exist".format(action_id)
}, 400
else:
return {"message": "action_id must be set"}, 400
if 'schema' in request_json:
if request_json['schema'] != action.schema:
return {
"message":
"schema must be:\n{}".format(
json.dumps(action.schema, indent=4))
}, 400
schema = action.schema
if 'data' not in request_json:
return {"message": "data must be set"}, 400
data = request_json['data']
try:
object = create_object(action_id=action_id,
data=data,
user_id=flask.g.user.id,
schema=schema)
except errors.ValidationError as e:
messages = e.message.splitlines()
return {
"message":
"validation failed:\n - {}".format('\n - '.join(messages))
}, 400
except Exception:
return {"message": "failed to create object"}, 400
object_version_url = flask.url_for('api.object_version',
object_id=object.object_id,
version_id=object.version_id)
return flask.redirect(object_version_url, code=201)
def test_validate_object_reference_wrong_action():
from sampledb.models.users import User, UserType
from sampledb.models.actions import Action
user = User("User", "*****@*****.**", UserType.OTHER)
action = Action(sampledb.models.ActionType.SAMPLE_CREATION, "Example Action", schema={
"title": "Sample Information",
"type": "object",
"properties": {
"name": {
"title": "Sample Name",
"type": "text"
}
},
"required": ["name"]
})
sampledb.db.session.add(user)
sampledb.db.session.add(action)
sampledb.db.session.commit()
object = create_object(data={'name': {'_type': 'text', 'text': 'example'}}, user_id=user.id, action_id=action.id)
instance = {
'_type': 'object_reference',
'object_id': object.id
}
schema = {
'title': 'Example',
'type': 'object_reference',
'action_id': action.id
}
validate(instance, schema)
schema = {
'title': 'Example',
'type': 'object_reference',
'action_id': action.id + 1
}
with pytest.raises(ValidationError):
validate(instance, schema)
def object(user: User, action: Action):
data = {'name': {'_type': 'text', 'text': 'Object'}}
return objects.create_object(user_id=user.id,
action_id=action.id,
data=data)
def set_up_state(user: User):
action = actions.create_action(
action_type_id=sampledb.models.ActionType.SAMPLE_CREATION,
name='Example Action',
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Sample Name',
'type': 'text'
}
},
'required': ['name']
},
description='',
instrument_id=None
)
actions.create_action(
action_type_id=sampledb.models.ActionType.SAMPLE_CREATION,
name='Irrelevant Action',
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Sample Name',
'type': 'text'
}
},
'required': ['name']
},
description='',
instrument_id=None
)
data = {'name': {'_type': 'text', 'text': 'Object'}}
object = objects.create_object(user_id=user.id, action_id=action.id, data=data)
def save_content(file): file.write("This is a test file.".encode('utf-8'))
files.create_local_file(object.id, user.id, "test.txt", save_content)
files.create_url_file(object.id, user.id, "https://example.com")
instrument = sampledb.logic.instruments.create_instrument(
name="Example Instrument",
description="Example Instrument Description",
users_can_view_log_entries=True
)
category = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title="Category",
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.RED
)
log_entry = sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument_id=instrument.id,
user_id=user.id,
content="Example Log Entry Text",
category_ids=[category.id]
)
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="example.txt",
content=b'Example Content'
)
sampledb.logic.instrument_log_entries.create_instrument_log_object_attachment(
instrument_log_entry_id=log_entry.id,
object_id=object.id
)
def test_generate_rdf(flask_server, user, other_user):
action = actions.create_action(
action_type=ActionType.SAMPLE_CREATION,
name='Example Action',
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Sample Name',
'type': 'text'
}
},
'required': ['name']
},
description='',
instrument_id=None
)
data = {'name': {'_type': 'text', 'text': 'Example Object'}}
object = objects.create_object(user_id=user.id, action_id=action.id, data=data)
comments.create_comment(object.id, other_user.id, 'Example Comment')
objects.update_object(object.id, data, user.id)
objects.update_object(object.id, data, other_user.id)
flask_server.app.config['SERVER_NAME'] = urlparse(flask_server.base_url).netloc
with flask_server.app.app_context():
rdf_document = rdf.generate_rdf(user.id, object.id)
etree.register_namespace('dcterms', 'http://purl.org/dc/terms/')
et = etree.fromstring(rdf_document)
assert next(et.iter('{*}title')).text == 'Example Object'
assert next(et.iter('{*}identifier')).text == f'{flask_server.base_url}objects/{object.id}'
creators = list(et.iter('{*}creator'))
assert len(creators) == 2
assert creators[0][0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about') == f'{flask_server.base_url}users/{user.id}'
assert creators[0][0][0].text == user.name
assert creators[1][0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about') == f'{flask_server.base_url}users/{other_user.id}'
assert creators[1][0][0].text == other_user.name
contributors = list(et.iter('{*}contributor'))
assert len(contributors) == 0
versions = list(et.iter('{*}hasVersion'))
assert len(versions) == 3
assert versions[0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource') == f'{flask_server.base_url}objects/{object.id}/versions/0'
assert versions[1].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource') == f'{flask_server.base_url}objects/{object.id}/versions/1'
assert versions[2].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource') == f'{flask_server.base_url}objects/{object.id}/versions/2'
is_version_of = list(et.iter('{*}isVersionOf'))
assert len(is_version_of) == 0
flask_server.app.config['SERVER_NAME'] = urlparse(flask_server.base_url).netloc
with flask_server.app.app_context():
rdf_document = rdf.generate_rdf(user.id, object.id, 1)
etree.register_namespace('dcterms', 'http://purl.org/dc/terms/')
et = etree.fromstring(rdf_document)
assert next(et.iter('{*}title')).text == 'Example Object'
assert next(et.iter('{*}identifier')).text == f'{flask_server.base_url}objects/{object.id}/versions/1'
creators = list(et.iter('{*}creator'))
assert len(creators) == 1
assert creators[0][0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about') == f'{flask_server.base_url}users/{user.id}'
assert creators[0][0][0].text == user.name
contributors = list(et.iter('{*}contributor'))
assert len(contributors) == 1
assert contributors[0][0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about') == f'{flask_server.base_url}users/{other_user.id}'
assert contributors[0][0][0].text == other_user.name
versions = list(et.iter('{*}hasVersion'))
assert len(versions) == 0
is_version_of = list(et.iter('{*}isVersionOf'))
assert len(is_version_of) == 1
assert is_version_of[0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource') == f'{flask_server.base_url}objects/{object.id}'
