class ProjectServiceTest(TransactionalTestCase):
"""
This class contains tests for the tvb.core.services.project_service module.
"""
def setUp(self):
"""
Reset the database before each test.
"""
config.EVENTS_FOLDER = ''
self.project_service = ProjectService()
self.structure_helper = FilesHelper()
self.test_user = TestFactory.create_user()
def tearDown(self):
"""
Remove project folders and clean up database.
"""
created_projects = dao.get_projects_for_user(self.test_user.id)
for project in created_projects:
self.structure_helper.remove_project_structure(project.name)
self.delete_project_folders()
def test_create_project_happy_flow(self):
"""
Standard flow for creating a new project.
"""
user1 = TestFactory.create_user('test_user1')
user2 = TestFactory.create_user('test_user2')
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 0, "Database reset probably failed!")
TestFactory.create_project(self.test_user, 'test_project', users=[user1.id, user2.id])
resulting_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(resulting_projects), 1, "Project with valid data not inserted!")
project = resulting_projects[0]
if project.name == "test_project":
self.assertEqual(project.description, "description", "Description do no match")
users_for_project = dao.get_members_of_project(project.id)
for user in users_for_project:
self.assertTrue(user.id in [user1.id, user2.id], "Users not stored properly.")
self.assertTrue(os.path.exists(os.path.join(TvbProfile.current.TVB_STORAGE, FilesHelper.PROJECTS_FOLDER,
"test_project")), "Folder for project was not created")
def test_create_project_empty_name(self):
"""
Creating a project with an empty name.
"""
data = dict(name="", description="test_description", users=[])
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 0, "Database reset probably failed!")
self.assertRaises(ProjectServiceException, self.project_service.store_project,
self.test_user, True, None, **data)
def test_edit_project_happy_flow(self):
"""
Standard flow for editing an existing project.
"""
selected_project = TestFactory.create_project(self.test_user, 'test_proj')
proj_root = self.structure_helper.get_project_folder(selected_project)
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 1, "Database initialization probably failed!")
edited_data = dict(name="test_project", description="test_description", users=[])
edited_project = self.project_service.store_project(self.test_user, False, selected_project.id, **edited_data)
self.assertFalse(os.path.exists(proj_root), "Previous folder not deleted")
proj_root = self.structure_helper.get_project_folder(edited_project)
self.assertTrue(os.path.exists(proj_root), "New folder not created!")
self.assertNotEqual(selected_project.name, edited_project.name, "Project was no changed!")
def test_edit_project_unexisting(self):
"""
Trying to edit an un-existing project.
"""
selected_project = TestFactory.create_project(self.test_user, 'test_proj')
self.structure_helper.get_project_folder(selected_project)
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 1, "Database initialization probably failed!")
data = dict(name="test_project", description="test_description", users=[])
self.assertRaises(ProjectServiceException, self.project_service.store_project,
self.test_user, False, 99, **data)
def test_find_project_happy_flow(self):
"""
Standard flow for finding a project by it's id.
"""
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 0, "Database reset probably failed!")
inserted_project = TestFactory.create_project(self.test_user, 'test_project')
self.assertTrue(self.project_service.find_project(inserted_project.id) is not None, "Project not found !")
dao_returned_project = dao.get_project_by_id(inserted_project.id)
service_returned_project = self.project_service.find_project(inserted_project.id)
self.assertEqual(dao_returned_project.id, service_returned_project.id,
"Data returned from service is different from data returned by DAO.")
self.assertEqual(dao_returned_project.name, service_returned_project.name,
"Data returned from service is different than data returned by DAO.")
self.assertEqual(dao_returned_project.description, service_returned_project.description,
"Data returned from service is different from data returned by DAO.")
self.assertEqual(dao_returned_project.members, service_returned_project.members,
"Data returned from service is different from data returned by DAO.")
def test_find_project_unexisting(self):
"""
Searching for an un-existing project.
"""
data = dict(name="test_project", description="test_description", users=[])
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 0, "Database reset probably failed!")
self.project_service.store_project(self.test_user, True, None, **data)
self.assertRaises(ProjectServiceException, self.project_service.find_project, 99)
def test_retrieve_projects_for_user(self):
"""
Test for retrieving the projects for a given user. One page only.
"""
initial_projects = self.project_service.retrieve_projects_for_user(self.test_user.id)[0]
self.assertEqual(len(initial_projects), 0, "Database was not reset properly!")
TestFactory.create_project(self.test_user, 'test_proj')
TestFactory.create_project(self.test_user, 'test_proj1')
TestFactory.create_project(self.test_user, 'test_proj2')
user1 = TestFactory.create_user('another_user')
TestFactory.create_project(user1, 'test_proj3')
projects = self.project_service.retrieve_projects_for_user(self.test_user.id)[0]
self.assertEqual(len(projects), 3, "Projects not retrieved properly!")
for project in projects:
self.assertNotEquals(project.name, "test_project3", "This project should not have been retrieved")
def test_retrieve_1project_3usr(self):
"""
One user as admin, two users as members, getting projects for admin and for any of
the members should return one.
"""
member1 = TestFactory.create_user("member1")
member2 = TestFactory.create_user("member2")
TestFactory.create_project(self.test_user, 'Testproject', users=[member1.id, member2.id])
projects = self.project_service.retrieve_projects_for_user(self.test_user.id, 1)[0]
self.assertEqual(len(projects), 1, "Projects not retrieved properly!")
projects = self.project_service.retrieve_projects_for_user(member1.id, 1)[0]
self.assertEqual(len(projects), 1, "Projects not retrieved properly!")
projects = self.project_service.retrieve_projects_for_user(member2.id, 1)[0]
self.assertEqual(len(projects), 1, "Projects not retrieved properly!")
def test_retrieve_3projects_3usr(self):
"""
Three users, 3 projects. Structure of db:
proj1: {admin: user1, members: [user2, user3]}
proj2: {admin: user2, members: [user1]}
proj3: {admin: user3, members: [user1, user2]}
Check valid project returns for all the users.
"""
member1 = TestFactory.create_user("member1")
member2 = TestFactory.create_user("member2")
member3 = TestFactory.create_user("member3")
TestFactory.create_project(member1, 'TestProject1', users=[member2.id, member3.id])
TestFactory.create_project(member2, 'TestProject2', users=[member1.id])
TestFactory.create_project(member3, 'TestProject3', users=[member1.id, member2.id])
projects = self.project_service.retrieve_projects_for_user(member1.id, 1)[0]
self.assertEqual(len(projects), 3, "Projects not retrieved properly!")
projects = self.project_service.retrieve_projects_for_user(member2.id, 1)[0]
self.assertEqual(len(projects), 3, "Projects not retrieved properly!")
projects = self.project_service.retrieve_projects_for_user(member3.id, 1)[0]
self.assertEqual(len(projects), 2, "Projects not retrieved properly!")
def test_retrieve_projects_random(self):
"""
Generate a large number of users/projects, and validate the results.
"""
ExtremeTestFactory.generate_users(NR_USERS, MAX_PROJ_PER_USER)
for i in range(NR_USERS):
current_user = dao.get_user_by_name("gen" + str(i))
expected_projects = ExtremeTestFactory.VALIDATION_DICT[current_user.id]
if expected_projects % PROJECTS_PAGE_SIZE == 0:
expected_pages = expected_projects / PROJECTS_PAGE_SIZE
exp_proj_per_page = PROJECTS_PAGE_SIZE
else:
expected_pages = expected_projects / PROJECTS_PAGE_SIZE + 1
exp_proj_per_page = expected_projects % PROJECTS_PAGE_SIZE
if expected_projects == 0:
expected_pages = 0
exp_proj_per_page = 0
projects, pages = self.project_service.retrieve_projects_for_user(current_user.id, expected_pages)
self.assertEqual(len(projects), exp_proj_per_page, "Projects not retrieved properly! Expected:" +
str(exp_proj_per_page) + "but got:" + str(len(projects)))
self.assertEqual(pages, expected_pages, "Pages not retrieved properly!")
for folder in os.listdir(TvbProfile.current.TVB_STORAGE):
full_path = os.path.join(TvbProfile.current.TVB_STORAGE, folder)
if os.path.isdir(full_path) and folder.startswith('Generated'):
shutil.rmtree(full_path)
def test_retrieve_projects_page2(self):
"""
Test for retrieving the second page projects for a given user.
"""
for i in range(PROJECTS_PAGE_SIZE + 3):
TestFactory.create_project(self.test_user, 'test_proj' + str(i))
projects, pages = self.project_service.retrieve_projects_for_user(self.test_user.id, 2)
self.assertEqual(len(projects), (PROJECTS_PAGE_SIZE + 3) % PROJECTS_PAGE_SIZE, "Pagination inproper.")
self.assertEqual(pages, 2, 'Wrong number of pages retrieved.')
def test_retrieve_projects_and_del(self):
"""
Test for retrieving the second page projects for a given user.
"""
created_projects = []
for i in range(PROJECTS_PAGE_SIZE + 1):
created_projects.append(TestFactory.create_project(self.test_user, 'test_proj' + str(i)))
projects, pages = self.project_service.retrieve_projects_for_user(self.test_user.id, 2)
self.assertEqual(len(projects), (PROJECTS_PAGE_SIZE + 1) % PROJECTS_PAGE_SIZE, "Pagination improper.")
self.assertEqual(pages, (PROJECTS_PAGE_SIZE + 1) / PROJECTS_PAGE_SIZE + 1, 'Wrong number of pages')
self.project_service.remove_project(created_projects[1].id)
projects, pages = self.project_service.retrieve_projects_for_user(self.test_user.id, 2)
self.assertEqual(len(projects), 0, "Pagination improper.")
self.assertEqual(pages, 1, 'Wrong number of pages retrieved.')
projects, pages = self.project_service.retrieve_projects_for_user(self.test_user.id, 1)
self.assertEqual(len(projects), PROJECTS_PAGE_SIZE, "Pagination improper.")
self.assertEqual(pages, 1, 'Wrong number of pages retrieved.')
def test_empty_project_has_zero_disk_size(self):
TestFactory.create_project(self.test_user, 'test_proj')
projects, pages = self.project_service.retrieve_projects_for_user(self.test_user.id)
self.assertEqual(0, projects[0].disk_size)
self.assertEqual('0.0 KiB', projects[0].disk_size_human)
def test_project_disk_size(self):
project1 = TestFactory.create_project(self.test_user, 'test_proj1')
zip_path = os.path.join(os.path.dirname(tvb_data.__file__), 'connectivity', 'connectivity_66.zip')
TestFactory.import_zip_connectivity(self.test_user, project1, 'testSubject', zip_path)
project2 = TestFactory.create_project(self.test_user, 'test_proj2')
TestFactory.import_cff(test_user=self.test_user, test_project=project2)
projects = self.project_service.retrieve_projects_for_user(self.test_user.id)[0]
self.assertNotEqual(projects[0].disk_size, projects[1].disk_size, "projects should have different size")
for project in projects:
self.assertNotEqual(0, project.disk_size)
self.assertNotEqual('0.0 KiB', project.disk_size_human)
prj_folder = self.structure_helper.get_project_folder(project)
actual_disk_size = self.compute_recursive_h5_disk_usage(prj_folder)[0]
ratio = float(actual_disk_size) / project.disk_size
msg = "Real disk usage: %s The one recorded in the db : %s" % (actual_disk_size, project.disk_size)
self.assertTrue(ratio < 1.4, msg)
def test_get_linkable_projects(self):
"""
Test for retrieving the projects for a given user.
"""
initial_projects = self.project_service.retrieve_projects_for_user(self.test_user.id)[0]
self.assertEqual(len(initial_projects), 0, "Database was not reset!")
test_proj = []
user1 = TestFactory.create_user("another_user")
for i in range(4):
test_proj.append(TestFactory.create_project(self.test_user if i < 3 else user1, 'test_proj' + str(i)))
project_storage = self.structure_helper.get_project_folder(test_proj[0])
operation = TestFactory.create_operation(test_user=self.test_user, test_project=test_proj[0])
project_storage = os.path.join(project_storage, str(operation.id))
os.makedirs(project_storage)
datatype = dao.store_entity(model.DataType(module="test_data", subject="subj1",
state="test_state", operation_id=operation.id))
linkable = self.project_service.get_linkable_projects_for_user(self.test_user.id, str(datatype.id))[0]
self.assertEqual(len(linkable), 2, "Wrong count of link-able projects!")
proj_names = [project.name for project in linkable]
self.assertTrue(test_proj[1].name in proj_names)
self.assertTrue(test_proj[2].name in proj_names)
self.assertFalse(test_proj[3].name in proj_names)
def test_remove_project_happy_flow(self):
"""
Standard flow for deleting a project.
"""
inserted_project = TestFactory.create_project(self.test_user, 'test_proj')
project_root = self.structure_helper.get_project_folder(inserted_project)
projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(projects), 1, "Initializations failed!")
self.assertTrue(os.path.exists(project_root), "Something failed at insert time!")
self.project_service.remove_project(inserted_project.id)
projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(projects), 0, "Project was not deleted!")
self.assertFalse(os.path.exists(project_root), "Root folder not deleted!")
def test_remove_project_wrong_id(self):
"""
Flow for deleting a project giving an un-existing id.
"""
TestFactory.create_project(self.test_user, 'test_proj')
projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(projects), 1, "Initializations failed!")
self.assertRaises(ProjectServiceException, self.project_service.remove_project, 99)
@staticmethod
def _create_value_wrapper(test_user, test_project=None):
"""
Creates a ValueWrapper dataType, and the associated parent Operation.
This is also used in ProjectStructureTest.
"""
if test_project is None:
test_project = TestFactory.create_project(test_user, 'test_proj')
operation = TestFactory.create_operation(test_user=test_user, test_project=test_project)
value_wrapper = ValueWrapper(data_value=5.0, data_name="my_value")
value_wrapper.type = "ValueWrapper"
value_wrapper.module = "tvb.datatypes.mapped_values"
value_wrapper.subject = "John Doe"
value_wrapper.state = "RAW_STATE"
value_wrapper.set_operation_id(operation.id)
adapter_instance = StoreAdapter([value_wrapper])
OperationService().initiate_prelaunch(operation, adapter_instance, {})
all_value_wrappers = FlowService().get_available_datatypes(test_project.id,
"tvb.datatypes.mapped_values.ValueWrapper")[0]
if len(all_value_wrappers) != 1:
raise Exception("Should be only one value wrapper.")
result_vw = ABCAdapter.load_entity_by_gid(all_value_wrappers[0][2])
return test_project, result_vw.gid, operation.gid
def __check_meta_data(self, expected_meta_data, new_datatype):
"""Validate Meta-Data"""
mapp_keys = {DataTypeMetaData.KEY_SUBJECT: "subject", DataTypeMetaData.KEY_STATE: "state"}
for key, value in expected_meta_data.iteritems():
if key in mapp_keys:
self.assertEqual(value, getattr(new_datatype, mapp_keys[key]))
elif key == DataTypeMetaData.KEY_OPERATION_TAG:
if DataTypeMetaData.KEY_OP_GROUP_ID in expected_meta_data:
## We have a Group to check
op_group = new_datatype.parent_operation.fk_operation_group
op_group = dao.get_generic_entity(model.OperationGroup, op_group)[0]
self.assertEqual(value, op_group.name)
else:
self.assertEqual(value, new_datatype.parent_operation.user_group)
def test_remove_project_node(self):
"""
Test removing of a node from a project.
"""
inserted_project, gid, gid_op = self._create_value_wrapper(self.test_user)
project_to_link = model.Project("Link", self.test_user.id, "descript")
project_to_link = dao.store_entity(project_to_link)
exact_data = dao.get_datatype_by_gid(gid)
dao.store_entity(model.Links(exact_data.id, project_to_link.id))
self.assertTrue(dao.get_datatype_by_gid(gid) is not None, "Initialization problem!")
operation_id = dao.get_generic_entity(model.Operation, gid_op, 'gid')[0].id
op_folder = self.structure_helper.get_project_folder("test_proj", str(operation_id))
self.assertTrue(os.path.exists(op_folder))
sub_files = os.listdir(op_folder)
self.assertEqual(2, len(sub_files))
### Validate that no more files are created than needed.
self.project_service._remove_project_node_files(inserted_project.id, gid)
sub_files = os.listdir(op_folder)
self.assertEqual(1, len(sub_files))
### operation.xml file should still be there
op_folder = self.structure_helper.get_project_folder("Link", str(operation_id + 1))
sub_files = os.listdir(op_folder)
self.assertEqual(2, len(sub_files))
self.assertTrue(dao.get_datatype_by_gid(gid) is not None, "Data should still be in DB, because of links")
self.project_service._remove_project_node_files(project_to_link.id, gid)
self.assertTrue(dao.get_datatype_by_gid(gid) is None)
sub_files = os.listdir(op_folder)
self.assertEqual(1, len(sub_files))
### operation.xml file should still be there
def test_update_meta_data_simple(self):
"""
Test the new update metaData for a simple data that is not part of a group.
"""
inserted_project, gid, _ = self._create_value_wrapper(self.test_user)
new_meta_data = {DataTypeOverlayDetails.DATA_SUBJECT: "new subject",
DataTypeOverlayDetails.DATA_STATE: "second_state",
DataTypeOverlayDetails.CODE_GID: gid,
DataTypeOverlayDetails.CODE_OPERATION_TAG: 'new user group'}
self.project_service.update_metadata(new_meta_data)
new_datatype = dao.get_datatype_by_gid(gid)
self.__check_meta_data(new_meta_data, new_datatype)
op_path = FilesHelper().get_operation_meta_file_path(inserted_project.name, new_datatype.parent_operation.id)
op_meta = XMLReader(op_path).read_metadata()
self.assertEqual(op_meta['user_group'], 'new user group', 'UserGroup not updated!')
def test_update_meta_data_group(self):
"""
Test the new update metaData for a group of dataTypes.
"""
datatypes, group_id = TestFactory.create_group(self.test_user, subject="test-subject-1")
new_meta_data = {DataTypeOverlayDetails.DATA_SUBJECT: "new subject",
DataTypeOverlayDetails.DATA_STATE: "updated_state",
DataTypeOverlayDetails.CODE_OPERATION_GROUP_ID: group_id,
DataTypeOverlayDetails.CODE_OPERATION_TAG: 'newGroupName'}
self.project_service.update_metadata(new_meta_data)
for datatype in datatypes:
new_datatype = dao.get_datatype_by_id(datatype.id)
self.assertEqual(group_id, new_datatype.parent_operation.fk_operation_group)
new_group = dao.get_generic_entity(model.OperationGroup, group_id)[0]
self.assertEqual(new_group.name, "newGroupName")
self.__check_meta_data(new_meta_data, new_datatype)
def _create_datatypes(self, dt_factory, nr_of_dts):
for idx in range(nr_of_dts):
dt = Datatype1()
dt.row1 = "value%i" % (idx,)
dt.row2 = "value%i" % (idx + 1,)
dt_factory._store_datatype(dt)
def test_retrieve_project_full(self):
"""
Tests full project information is retrieved by method `ProjectService.retrieve_project_full(...)`
"""
dt_factory = datatypes_factory.DatatypesFactory()
self._create_datatypes(dt_factory, 3)
_, ops_nr, operations, pages_no = self.project_service.retrieve_project_full(dt_factory.project.id)
self.assertEqual(ops_nr, 1, "DataType Factory should only use one operation to store all it's datatypes.")
self.assertEqual(pages_no, 1, "DataType Factory should only use one operation to store all it's datatypes.")
resulted_dts = operations[0]['results']
self.assertEqual(len(resulted_dts), 3, "3 datatypes should be created.")
def test_get_project_structure(self):
"""
Tests project structure is as expected and contains all datatypes
"""
SELF_DTS_NUMBER = 3
dt_factory_1 = datatypes_factory.DatatypesFactory()
self._create_datatypes(dt_factory_1, SELF_DTS_NUMBER)
dt_group = dt_factory_1.create_datatype_group()
link_ids, expected_links = [], []
# Prepare link towards a simple DT
dt_factory_2 = datatypes_factory.DatatypesFactory()
dt_to_link = dt_factory_2.create_simple_datatype()
link_ids.append(dt_to_link.id)
expected_links.append(dt_to_link.gid)
# Prepare links towards a full DT Group, but expecting only the DT_Group in the final tree
link_gr = dt_factory_2.create_datatype_group()
dts = dao.get_datatype_in_group(datatype_group_id=link_gr.id)
link_ids.extend([dt_to_link.id for dt_to_link in dts])
link_ids.append(link_gr.id)
expected_links.append(link_gr.gid)
# Prepare link towards a single DT inside a group, and expecting to find the DT in the final tree
link_gr = dt_factory_2.create_datatype_group()
dt_to_link = dao.get_datatype_in_group(datatype_group_id=link_gr.id)[0]
link_ids.append(dt_to_link.id)
expected_links.append(dt_to_link.gid)
# Actually create the links from Prj2 into Prj1
FlowService().create_link(link_ids, dt_factory_1.project.id)
# Retrieve the raw data used to compose the tree (for easy parsing)
dts_in_tree = dao.get_data_in_project(dt_factory_1.project.id)
dts_in_tree = [dt.gid for dt in dts_in_tree]
# Retrieve the tree json (for trivial validations only, as we can not decode)
node_json = self.project_service.get_project_structure(dt_factory_1.project, None, DataTypeMetaData.KEY_STATE,
DataTypeMetaData.KEY_SUBJECT, None)
self.assertEqual(len(expected_links) + SELF_DTS_NUMBER + 2, len(dts_in_tree), "invalid number of nodes in tree")
self.assertFalse(link_gr.gid in dts_in_tree, "DT_group where a single DT is linked is not expected.")
self.assertTrue(dt_group.gid in dts_in_tree, "DT_Group should be in the Project Tree!")
self.assertTrue(dt_group.gid in node_json, "DT_Group should be in the Project Tree JSON!")
project_dts = dao.get_datatypes_in_project(dt_factory_1.project.id)
for dt in project_dts:
if dt.fk_datatype_group is not None:
self.assertFalse(dt.gid in node_json, "DTs part of a group should not be")
self.assertFalse(dt.gid in dts_in_tree, "DTs part of a group should not be")
else:
self.assertTrue(dt.gid in node_json, "Simple DTs and DT_Groups should be")
self.assertTrue(dt.gid in dts_in_tree, "Simple DTs and DT_Groups should be")
for link_gid in expected_links:
self.assertTrue(link_gid in node_json, "Expected Link not present")
self.assertTrue(link_gid in dts_in_tree, "Expected Link not present")
class ProjectController(BaseController):
"""
Displays pages which deals with Project data management.
"""
PRROJECTS_FOR_LINK_KEY = "projectsforlink"
PRROJECTS_LINKED_KEY = "projectslinked"
KEY_OPERATION_FILTERS = "operationfilters"
def __init__(self):
super(ProjectController, self).__init__()
self.project_service = ProjectService()
@expose_page
@settings
def index(self):
"""
Display project main-menu. Choose one project to work with.
"""
current_project = common.get_current_project()
if current_project is None:
raise cherrypy.HTTPRedirect("/project/viewall")
template_specification = dict(mainContent="project_submenu", title="TVB Project Menu")
return self.fill_default_attributes(template_specification)
@expose_page
@settings
def viewall(self, create=False, page=1, selected_project_id=None, **_):
"""
Display all existent projects. Choose one project to work with.
"""
page = int(page)
if cherrypy.request.method == 'POST' and create:
raise cherrypy.HTTPRedirect('/project/editone')
current_user_id = common.get_logged_user().id
## Select project if user choose one.
if selected_project_id is not None:
try:
selected_project = self.project_service.find_project(selected_project_id)
self._mark_selected(selected_project)
except ProjectServiceException as excep:
self.logger.error(excep)
self.logger.warning("Could not select project: " + str(selected_project_id))
common.set_error_message("Could not select project: " + str(selected_project_id))
#Prepare template response
prjs, pages_no = self.project_service.retrieve_projects_for_user(current_user_id, page)
template_specification = dict(mainContent="project/viewall", title="Available TVB Projects",
projectsList=prjs, page_number=page, total_pages=pages_no)
return self.fill_default_attributes(template_specification, 'list')
@cherrypy.expose
@handle_error(redirect=True)
@check_user
@settings
def projectupload(self, **data):
"""Upload Project from TVB ZIP."""
self.logger.debug("Uploading ..." + str(data))
try:
upload_param = "uploadedfile"
if upload_param in data and data[upload_param]:
import_service = ImportService()
import_service.import_project_structure(data[upload_param], common.get_logged_user().id)
except ServicesBaseException as excep:
self.logger.warning(excep.message)
common.set_error_message(excep.message)
raise cherrypy.HTTPRedirect('/project/viewall')
def _remove_project(self, project_id):
"""Private method for removing project."""
try:
self.project_service.remove_project(project_id)
except ServicesBaseException as exc:
self.logger.error("Could not delete project!")
self.logger.exception(exc)
common.set_error_message(exc.message)
prj = common.get_current_project()
if prj is not None and prj.id == int(project_id):
common.remove_from_session(common.KEY_PROJECT)
def _persist_project(self, data, project_id, is_create, current_user):
"""Private method to persist"""
data = EditForm().to_python(data)
saved_project = self.project_service.store_project(current_user, is_create, project_id, **data)
selected_project = common.get_current_project()
if len(self.project_service.retrieve_projects_for_user(current_user.id, 1)) == 1:
selected_project = saved_project
if selected_project is None or (saved_project.id == selected_project.id):
self._mark_selected(saved_project)
@expose_page
@settings
def editone(self, project_id=None, cancel=False, save=False, delete=False, **data):
"""
Create or change Project. When project_id is empty we create a
new entity, otherwise we are to edit and existent one.
"""
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect('/project')
if cherrypy.request.method == 'POST' and delete:
self._remove_project(project_id)
raise cherrypy.HTTPRedirect('/project/viewall')
current_user = common.get_logged_user()
is_create = False
if project_id is None or not int(project_id):
is_create = True
data["administrator"] = current_user.username
else:
current_project = self.project_service.find_project(project_id)
if not save:
# Only when we do not have submitted data,
# populate fields with initial values for edit.
data = dict(name=current_project.name, description=current_project.description)
data["administrator"] = current_project.administrator.username
self._mark_selected(current_project)
data["project_id"] = project_id
template_specification = dict(mainContent="project/editone", data=data, isCreate=is_create,
title="Create new project" if is_create else "Edit " + data["name"],
editUsersEnabled=(current_user.username == data['administrator']))
try:
if cherrypy.request.method == 'POST' and save:
common.remove_from_session(common.KEY_PROJECT)
common.remove_from_session(common.KEY_CACHED_SIMULATOR_TREE)
self._persist_project(data, project_id, is_create, current_user)
raise cherrypy.HTTPRedirect('/project/viewall')
except formencode.Invalid as excep:
self.logger.debug(str(excep))
template_specification[common.KEY_ERRORS] = excep.unpack_errors()
except ProjectServiceException as excep:
self.logger.debug(str(excep))
common.set_error_message(excep.message)
raise cherrypy.HTTPRedirect('/project/viewall')
all_users, members, pages = self.user_service.get_users_for_project(current_user.username, project_id)
template_specification['usersList'] = all_users
template_specification['usersMembers'] = [m.id for m in members]
template_specification['usersPages'] = pages
template_specification['usersCurrentPage'] = 1
return self.fill_default_attributes(template_specification, 'properties')
@expose_fragment('project/project_members')
def getmemberspage(self, page, project_id=None):
"""Retrieve a new page of Project members."""
current_name = common.get_logged_user().username
all_users, members, _ = self.user_service.get_users_for_project(current_name, project_id, int(page))
edit_enabled = True
if project_id is not None:
current_project = self.project_service.find_project(project_id)
edit_enabled = (current_name == current_project.administrator.username)
return dict(usersList=all_users, usersMembers=[m.id for m in members],
usersCurrentPage=page, editUsersEnabled=edit_enabled)
@expose_json
def set_visibility(self, entity_type, entity_gid, to_de_relevant):
"""
Method used for setting the relevancy/visibility on a DataType(Group)/Operation(Group.
"""
to_de_relevant = string2bool(to_de_relevant)
is_operation, is_group = False, False
if entity_type == graph_structures.NODE_OPERATION_TYPE:
is_group = False
is_operation = True
elif entity_type == graph_structures.NODE_OPERATION_GROUP_TYPE:
is_group = True
is_operation = True
if is_operation:
self.project_service.set_operation_and_group_visibility(entity_gid, to_de_relevant, is_group)
else:
self.project_service.set_datatype_visibility(entity_gid, to_de_relevant)
@expose_page
@settings
def viewoperations(self, project_id=None, page=1, filtername=None, reset_filters=None):
"""
Display table of operations for a given project selected
"""
if (project_id is None) or (not int(project_id)):
raise cherrypy.HTTPRedirect('/project')
## Toggle filters
filters = self.__get_operations_filters()
selected_filters = None
for my_filter in filters:
if cherrypy.request.method == 'POST' and (filtername is not None):
if reset_filters:
my_filter.selected = False
elif my_filter.display_name == filtername:
my_filter.selected = not my_filter.selected
if my_filter.selected:
selected_filters = my_filter + selected_filters
## Iterate one more time, to update counters
for my_filter in filters:
if not my_filter.selected:
new_count = self.project_service.count_filtered_operations(project_id, my_filter + selected_filters)
my_filter.passes_count = new_count
else:
my_filter.passes_count = ''
page = int(page)
project, total_op_count, filtered_ops, pages_no = self.project_service.retrieve_project_full(
project_id, selected_filters, page)
## Select current project
self._mark_selected(project)
template_specification = dict(mainContent="project/viewoperations", project=project,
title='Past operations for " ' + project.name + '"', operationsList=filtered_ops,
total_op_count=total_op_count, total_pages=pages_no, page_number=page,
filters=filters, no_filter_selected=(selected_filters is None), model=model)
return self.fill_default_attributes(template_specification, 'operations')
@expose_fragment("call_out_project")
def generate_call_out_control(self):
"""
Returns the content of a confirmation dialog, with a given question.
"""
self.update_operations_count()
return {'selectedProject': common.get_current_project()}
def __get_operations_filters(self):
"""
Filters for VIEW_ALL_OPERATIONS page.
Get from session currently selected filters, or build a new set of filters.
"""
session_filtes = common.get_from_session(self.KEY_OPERATION_FILTERS)
if session_filtes:
return session_filtes
else:
sim_group = self.flow_service.get_algorithm_by_module_and_class(IntrospectionRegistry.SIMULATOR_MODULE,
IntrospectionRegistry.SIMULATOR_CLASS)
new_filters = StaticFiltersFactory.build_operations_filters(sim_group, common.get_logged_user().id)
common.add2session(self.KEY_OPERATION_FILTERS, new_filters)
return new_filters
@expose_fragment("overlay_confirmation")
def show_confirmation_overlay(self, **data):
"""
Returns the content of a confirmation dialog, with a given question.
"""
if not data:
data = {}
question = data.get('question', "Are you sure ?")
data['question'] = question
return self.fill_default_attributes(data)
@expose_fragment("overlay")
def get_datatype_details(self, entity_gid, back_page='null', exclude_tabs=None):
"""
Returns the HTML which contains the details for the given dataType.
:param back_page: if different from 'null' (the default) it will redirect to it after saving metedata changes
"""
if exclude_tabs is None:
exclude_tabs = []
selected_project = common.get_current_project()
datatype_details, states, entity = self.project_service.get_datatype_details(entity_gid)
### Load DataType categories
current_type = datatype_details.data_type
datatype_gid = datatype_details.gid
categories = {}
if not entity.invalid:
categories = self.flow_service.get_launchable_algorithms(datatype_gid)
is_group = False
if datatype_details.operation_group_id is not None:
## Is a DataTypeGroup
is_group = True
### Retrieve links
linkable_projects_dict = self._get_linkable_projects_dict(entity.id)
### Load all exporters
exporters = {}
if not entity.invalid:
exporters = ExportManager().get_exporters_for_data(entity)
is_relevant = entity.visible
template_specification = {"entity_gid": entity_gid,
"nodeFields": datatype_details.get_ui_fields(),
"allStates": states,
"project": selected_project,
"categories": categories,
"exporters": exporters,
"datatype_id": entity.id,
"isGroup": is_group,
"isRelevant": is_relevant,
"nodeType": 'datatype',
"backPageIdentifier": back_page}
template_specification.update(linkable_projects_dict)
overlay_class = "can-browse editor-node node-type-" + str(current_type).lower()
if is_relevant:
overlay_class += " node-relevant"
else:
overlay_class += " node_irrelevant"
overlay_title = current_type
if datatype_details.datatype_tag_1:
overlay_title += " " + datatype_details.datatype_tag_1
tabs = []
overlay_indexes = []
if "Metadata" not in exclude_tabs:
tabs.append(OverlayTabDefinition("Metadata", "metadata"))
overlay_indexes.append(0)
if "Analyzers" not in exclude_tabs:
tabs.append(OverlayTabDefinition("Analyzers", "analyzers", enabled=categories and 'Analyze' in categories))
overlay_indexes.append(1)
if "Visualizers" not in exclude_tabs:
tabs.append(OverlayTabDefinition("Visualizers", "visualizers", enabled=categories and 'View' in categories))
overlay_indexes.append(2)
enable_link_tab = False
if (not entity.invalid) and (linkable_projects_dict is not None):
projects_for_link = linkable_projects_dict.get(self.PRROJECTS_FOR_LINK_KEY)
if projects_for_link is not None and len(projects_for_link) > 0:
enable_link_tab = True
projects_linked = linkable_projects_dict.get(self.PRROJECTS_LINKED_KEY)
if projects_linked is not None and len(projects_linked) > 0:
enable_link_tab = True
if "Links" not in exclude_tabs:
tabs.append(OverlayTabDefinition("Links", "link_to", enabled=enable_link_tab))
overlay_indexes.append(3)
if "Export" not in exclude_tabs:
tabs.append(OverlayTabDefinition("Export", "export", enabled=(exporters and len(exporters) > 0)))
overlay_indexes.append(4)
if "Derived DataTypes" not in exclude_tabs:
tabs.append(OverlayTabDefinition("Derived DataTypes", "result_dts",
enabled=self.project_service.count_datatypes_generated_from(entity_gid)))
overlay_indexes.append(5)
template_specification = self.fill_overlay_attributes(template_specification, "DataType Details",
overlay_title, "project/details_datatype_overlay",
overlay_class, tabs, overlay_indexes)
template_specification['baseUrl'] = TvbProfile.current.web.BASE_URL
return FlowController().fill_default_attributes(template_specification)
@expose_fragment('project/linkable_projects')
def get_linkable_projects(self, datatype_id, is_group, entity_gid):
"""
Returns the HTML which displays the link-able projects for the given dataType
"""
template_specification = self._get_linkable_projects_dict(datatype_id)
template_specification["entity_gid"] = entity_gid
template_specification["isGroup"] = is_group
return template_specification
def _get_linkable_projects_dict(self, datatype_id):
"""" UI ready dictionary with projects in which current DataType can be linked."""
self.logger.debug("Searching projects to link for DT " + str(datatype_id))
for_link, linked = self.project_service.get_linkable_projects_for_user(common.get_logged_user().id, datatype_id)
projects_for_link, linked_projects = None, None
if for_link:
projects_for_link = {}
for project in for_link:
projects_for_link[project.id] = project.name
if linked:
linked_projects = {}
for project in linked:
linked_projects[project.id] = project.name
template_specification = {self.PRROJECTS_FOR_LINK_KEY: projects_for_link,
self.PRROJECTS_LINKED_KEY: linked_projects,
"datatype_id": datatype_id}
return template_specification
@expose_fragment("overlay")
def get_operation_details(self, entity_gid, is_group=False, back_page='burst'):
"""
Returns the HTML which contains the details for the given operation.
"""
if string2bool(str(is_group)):
### we have an OperationGroup entity.
template_specification = self._compute_operation_details(entity_gid, True)
#I expect that all the operations from a group are visible or not
template_specification["nodeType"] = graph_structures.NODE_OPERATION_GROUP_TYPE
else:
### we have a simple Operation
template_specification = self._compute_operation_details(entity_gid)
template_specification["displayRelevantButton"] = True
template_specification["nodeType"] = graph_structures.NODE_OPERATION_TYPE
template_specification["backPageIdentifier"] = back_page
overlay_class = "can-browse editor-node node-type-" + template_specification["nodeType"]
if template_specification["isRelevant"]:
overlay_class += " node-relevant"
else:
overlay_class += " node_irrelevant"
template_specification = self.fill_overlay_attributes(template_specification, "Details", "Operation",
"project/details_operation_overlay", overlay_class)
return FlowController().fill_default_attributes(template_specification)
def _compute_operation_details(self, entity_gid, is_group=False):
"""
Returns a dictionary which contains the details for the given operation.
"""
selected_project = common.get_current_project()
op_details = self.project_service.get_operation_details(entity_gid, is_group)
operation_id = op_details.operation_id
display_reload_btn = True
operation = self.flow_service.load_operation(operation_id)
if (operation.fk_operation_group is not None) or (operation.burst is not None):
display_reload_btn = False
else:
op_categ_id = operation.algorithm.fk_category
raw_categories = self.flow_service.get_raw_categories()
for category in raw_categories:
if category.id == op_categ_id:
display_reload_btn = False
break
template_specification = {"entity_gid": entity_gid,
"nodeFields": op_details.get_ui_fields(),
"operationId": operation_id,
"displayReloadBtn": display_reload_btn,
"project": selected_project,
"isRelevant": operation.visible}
return template_specification
def get_project_structure_grouping(self):
user = common.get_logged_user()
return user.get_project_structure_grouping()
def set_project_structure_grouping(self, first, second):
user = common.get_logged_user()
user.set_project_structure_grouping(first, second)
self.user_service.edit_user(user)
@expose_page
@settings
def editstructure(self, project_id=None, last_selected_tab="treeTab", first_level=None,
second_level=None, filter_input="", visibility_filter=None, **_ignored):
"""
Return the page skeleton for displaying the project structure.
"""
try:
int(project_id)
except (ValueError, TypeError):
raise cherrypy.HTTPRedirect('/project')
if first_level is None or second_level is None:
first_level, second_level = self.get_project_structure_grouping()
selected_project = self.project_service.find_project(project_id)
self._mark_selected(selected_project)
data = self.project_service.get_filterable_meta()
filters = StaticFiltersFactory.build_datatype_filters(selected=visibility_filter)
template_specification = dict(mainContent="project/structure", baseUrl=TvbProfile.current.web.BASE_URL,
title=selected_project.name,
project=selected_project, data=data,
lastSelectedTab=last_selected_tab, firstLevelSelection=first_level,
secondLevelSelection=second_level, filterInputValue=filter_input, filters=filters)
return self.fill_default_attributes(template_specification, 'data')
@expose_fragment("overlay")
def get_data_uploader_overlay(self, project_id):
"""
Returns the html which displays a dialog which allows the user
to upload certain data into the application.
"""
upload_algorithms = self.flow_service.get_upload_algorithms()
flow_controller = FlowController()
algorithms_interface = {}
tabs = []
for algorithm in upload_algorithms:
adapter_template = flow_controller.get_adapter_template(project_id, algorithm.id, True, None)
algorithms_interface['template_for_algo_' + str(algorithm.id)] = adapter_template
tabs.append(OverlayTabDefinition(algorithm.displayname, algorithm.subsection_name,
description=algorithm.description))
template_specification = self.fill_overlay_attributes(None, "Upload", "Upload data for this project",
"project/upload_data_overlay", "dialog-upload",
tabs_vertical=tabs)
template_specification['uploadAlgorithms'] = upload_algorithms
template_specification['projectId'] = project_id
template_specification['algorithmsInterface'] = algorithms_interface
return flow_controller.fill_default_attributes(template_specification)
@expose_fragment("overlay")
def get_project_uploader_overlay(self):
"""
Returns the html which displays a dialog which allows the user
to upload an entire project.
"""
template_specification = self.fill_overlay_attributes(None, "Upload", "Project structure",
"project/upload_project_overlay", "dialog-upload")
return FlowController().fill_default_attributes(template_specification)
@expose_page
def launchloader(self, project_id, algorithm_id, cancel=False, **data):
"""
Start Upload mechanism
"""
success_link = "/project/editstructure/" + str(project_id)
# do not allow GET
if cherrypy.request.method != 'POST' or cancel:
raise cherrypy.HTTPRedirect(success_link)
try:
int(project_id)
int(algorithm_id)
except (ValueError, TypeError):
raise cherrypy.HTTPRedirect(success_link)
project = self.project_service.find_project(project_id)
algorithm = self.flow_service.get_algorithm_by_identifier(algorithm_id)
FlowController().execute_post(project.id, success_link, algorithm.fk_category, algorithm, **data)
raise cherrypy.HTTPRedirect(success_link)
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def readjsonstructure(self, project_id, visibility_filter=StaticFiltersFactory.FULL_VIEW,
first_level=None, second_level=None, filter_value=None):
"""
AJAX exposed method.
Will return the complete JSON for Project's structure, or filtered tree
(filter only Relevant entities or Burst only Data).
"""
if first_level is None or second_level is None:
first_level, second_level = self.get_project_structure_grouping()
else:
self.set_project_structure_grouping(first_level, second_level)
selected_filter = StaticFiltersFactory.build_datatype_filters(single_filter=visibility_filter)
project = self.project_service.find_project(project_id)
json_structure = self.project_service.get_project_structure(project, selected_filter,
first_level, second_level, filter_value)
# This JSON encoding is necessary, otherwise we will get an error
# from JSTree library while trying to load with AJAX
# the content of the tree.
encoder = JSONEncoder()
return encoder.iterencode(json_structure)
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def createlink(self, link_data, project_id, is_group):
"""
Delegate the creation of the actual link to the flow service.
"""
if not string2bool(str(is_group)):
self.flow_service.create_link([link_data], project_id)
else:
all_data = self.project_service.get_datatype_in_group(link_data)
# Link all Dts in group and the DT_Group entity
data_ids = [data.id for data in all_data]
data_ids.append(int(link_data))
self.flow_service.create_link(data_ids, project_id)
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def removelink(self, link_data, project_id, is_group):
"""
Delegate the creation of the actual link to the flow service.
"""
if not string2bool(str(is_group)):
self.flow_service.remove_link(link_data, project_id)
else:
all_data = self.project_service.get_datatype_in_group(link_data)
for data in all_data:
self.flow_service.remove_link(data.id, project_id)
self.flow_service.remove_link(int(link_data), project_id)
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def noderemove(self, project_id, node_gid):
"""
AJAX exposed method, to execute operation of data removal.
"""
try:
if node_gid is None:
return "Remove can only be applied on a Node with GID!"
self.logger.debug("Removing data with GID=" + str(node_gid))
self.project_service.remove_datatype(project_id, node_gid)
except RemoveDataTypeException as excep:
self.logger.exception("Could not execute operation Node Remove!")
return excep.message
except ServicesBaseException as excep:
self.logger.exception("Could not execute operation Node Remove!")
return excep.message
return None
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def updatemetadata(self, **data):
""" Submit MetaData edited for DataType(Group) or Operation(Group). """
try:
self.project_service.update_metadata(data)
except ServicesBaseException as excep:
self.logger.error("Could not execute MetaData update!")
self.logger.exception(excep)
common.set_error_message(excep.message)
return excep.message
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def downloaddata(self, data_gid, export_module):
""" Export the data to a default path of TVB_STORAGE/PROJECTS/project_name """
current_prj = common.get_current_project()
# Load data by GID
entity = ABCAdapter.load_entity_by_gid(data_gid)
# Do real export
export_mng = ExportManager()
file_name, file_path, delete_file = export_mng.export_data(entity, export_module, current_prj)
if delete_file:
# We force parent folder deletion because export process generated it.
self.mark_file_for_delete(file_path, True)
self.logger.debug("Data exported in file: " + str(file_path))
return serve_file(file_path, "application/x-download", "attachment", file_name)
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def downloadproject(self, project_id):
"""
Export the data from a whole project.
"""
current_project = self.project_service.find_project(project_id)
export_mng = ExportManager()
export_file = export_mng.export_project(current_project)
# Register export file for delete when download complete
# We force parent folder deletion because export process generated it.
self.mark_file_for_delete(export_file, True)
return serve_file(export_file, "application/x-download", "attachment")
#methods related to data structure - graph
@expose_json
def create_json(self, item_gid, item_type, visibility_filter):
"""
Method used for creating a JSON representation of a graph.
"""
selected_filter = StaticFiltersFactory.build_datatype_filters(single_filter=visibility_filter)
project = common.get_current_project()
is_upload_operation = (item_type == graph_structures.NODE_OPERATION_TYPE) and \
(self.project_service.is_upload_operation(item_gid) or item_gid == "firstOperation")
if is_upload_operation:
graph_branches = []
uploader_operations = self.project_service.get_all_operations_for_uploaders(project.id)
for operation in uploader_operations:
dt_outputs = self.project_service.get_results_for_operation(operation.id, selected_filter)
dt_outputs = self._create_datatype_nodes(dt_outputs)
parent_op = self._create_operation_nodes([operation], item_gid)
branch = graph_structures.GraphComponent([], parent_op, dt_outputs, [])
graph_branches.append(branch)
graph = graph_structures.FullGraphStructure(graph_branches)
return graph.prepare_for_json()
dt_inputs, parent_op, dt_outputs, op_inputs = [], [], [], []
if item_type == graph_structures.NODE_OPERATION_TYPE:
dt_inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(item_gid, selected_filter)
parent_op = self.project_service.load_operation_by_gid(item_gid)
dt_outputs = self.project_service.get_results_for_operation(parent_op.id, selected_filter)
#create graph nodes
dt_inputs, parent_op, dt_outputs, op_inputs = self._create_nodes(dt_inputs, [parent_op],
dt_outputs, [], item_gid)
elif item_type == graph_structures.NODE_OPERATION_GROUP_TYPE:
parent_op_group = self.project_service.get_operation_group_by_gid(item_gid)
dt_inputs = self.project_service.get_datatypes_inputs_for_operation_group(parent_op_group.id,
selected_filter)
datatype_group = self.project_service.get_datatypegroup_by_op_group_id(parent_op_group.id)
datatype = self.project_service.get_datatype_by_id(datatype_group.id)
dt_inputs = self._create_datatype_nodes(dt_inputs)
parent_op = graph_structures.NodeStructure.build_structure_for_operation_group(parent_op_group.gid)
parent_op.selected = True
parent_op = [parent_op]
if selected_filter.display_name == StaticFiltersFactory.RELEVANT_VIEW and datatype.visible is False:
dt_outputs = []
else:
dt_outputs = self._create_datatype_nodes([datatype])
elif item_type == graph_structures.NODE_DATATYPE_TYPE:
selected_dt = ABCAdapter.load_entity_by_gid(item_gid)
if self.project_service.is_datatype_group(item_gid):
datatype_group = self.project_service.get_datatypegroup_by_gid(selected_dt.gid)
parent_op_group = self.project_service.get_operation_group_by_id(datatype_group.fk_operation_group)
dt_inputs = self.project_service.get_datatypes_inputs_for_operation_group(parent_op_group.id,
selected_filter)
op_inputs = self.project_service.get_operations_for_datatype_group(selected_dt.id, selected_filter)
op_inputs_in_groups = self.project_service.get_operations_for_datatype_group(selected_dt.id,
selected_filter,
only_in_groups=True)
#create graph nodes
dt_inputs, parent_op, dt_outputs, op_inputs = self._create_nodes(dt_inputs, [], [selected_dt],
op_inputs, item_gid)
parent_op = [graph_structures.NodeStructure.build_structure_for_operation_group(parent_op_group.gid)]
op_inputs_in_groups = self._create_operation_group_nodes(op_inputs_in_groups)
op_inputs.extend(op_inputs_in_groups)
else:
parent_op = self.flow_service.load_operation(selected_dt.fk_from_operation)
dt_inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(parent_op.gid,
selected_filter)
op_inputs = self.project_service.get_operations_for_datatype(selected_dt.gid, selected_filter)
op_inputs_in_groups = self.project_service.get_operations_for_datatype(selected_dt.gid, selected_filter,
only_in_groups=True)
dt_outputs = self.project_service.get_results_for_operation(parent_op.id, selected_filter)
#create graph nodes
dt_inputs, parent_op, dt_outputs, op_inputs = self._create_nodes(dt_inputs, [parent_op], dt_outputs,
op_inputs, item_gid)
op_inputs_in_groups = self._create_operation_group_nodes(op_inputs_in_groups)
op_inputs.extend(op_inputs_in_groups)
else:
self.logger.error("Invalid item type: " + str(item_type))
raise Exception("Invalid item type.")
branch = graph_structures.GraphComponent(dt_inputs, parent_op, dt_outputs, op_inputs)
graph = graph_structures.FullGraphStructure([branch])
return graph.prepare_for_json()
def _create_nodes(self, dt_inputs, parent_op, dt_outputs, op_inputs, item_gid=None):
"""Expected a list of DataTypes, Parent Operation, Outputs, and returns NodeStructure entities."""
dt_inputs = self._create_datatype_nodes(dt_inputs, item_gid)
parent_op = self._create_operation_nodes(parent_op, item_gid)
dt_outputs = self._create_datatype_nodes(dt_outputs, item_gid)
op_inputs = self._create_operation_nodes(op_inputs, item_gid)
return dt_inputs, parent_op, dt_outputs, op_inputs
@staticmethod
def _create_datatype_nodes(datatypes_list, selected_item_gid=None):
""" Expects a list of DataTypes and returns a list of NodeStructures """
nodes = []
if datatypes_list is None:
return nodes
for data_type in datatypes_list:
node = graph_structures.NodeStructure.build_structure_for_datatype(data_type.gid)
if data_type.gid == selected_item_gid:
node.selected = True
nodes.append(node)
return nodes
@staticmethod
def _create_operation_nodes(operations_list, selected_item_gid=None):
"""
Expects a list of operations and returns a list of NodeStructures
"""
nodes = []
for operation in operations_list:
node = graph_structures.NodeStructure.build_structure_for_operation(operation)
if operation.gid == selected_item_gid:
node.selected = True
nodes.append(node)
return nodes
def _create_operation_group_nodes(self, operations_list, selected_item_gid=None):
"""
Expects a list of operations that are part of some operation groups.
"""
groups = dict()
for operation in operations_list:
if operation.fk_operation_group not in groups:
group = self.project_service.get_operation_group_by_id(operation.fk_operation_group)
groups[group.id] = group.gid
nodes = []
for _, group in groups.items():
node = graph_structures.NodeStructure.build_structure_for_operation_group(group)
if group == selected_item_gid:
node.selected = True
nodes.append(node)
return nodes
def fill_default_attributes(self, template_dictionary, subsection='project'):
"""
Overwrite base controller to add required parameters for adapter templates.
"""
template_dictionary[common.KEY_SECTION] = 'project'
template_dictionary[common.KEY_SUB_SECTION] = subsection
template_dictionary[common.KEY_INCLUDE_RESOURCES] = 'project/included_resources'
BaseController.fill_default_attributes(self, template_dictionary)
return template_dictionary
class TestProjectService(TransactionalTestCase):
"""
This class contains tests for the tvb.core.services.project_service module.
"""
def transactional_setup_method(self):
"""
Reset the database before each test.
"""
self.project_service = ProjectService()
self.structure_helper = FilesHelper()
self.test_user = TestFactory.create_user()
def transactional_teardown_method(self):
"""
Remove project folders and clean up database.
"""
created_projects = dao.get_projects_for_user(self.test_user.id)
for project in created_projects:
self.structure_helper.remove_project_structure(project.name)
self.delete_project_folders()
def test_create_project_happy_flow(self):
user1 = TestFactory.create_user('test_user1')
user2 = TestFactory.create_user('test_user2')
initial_projects = dao.get_projects_for_user(self.test_user.id)
assert len(initial_projects) == 0, "Database reset probably failed!"
TestFactory.create_project(self.test_user,
'test_project',
"description",
users=[user1.id, user2.id])
resulting_projects = dao.get_projects_for_user(self.test_user.id)
assert len(
resulting_projects) == 1, "Project with valid data not inserted!"
project = resulting_projects[0]
assert project.name == "test_project", "Invalid retrieved project name"
assert project.description == "description", "Description do no match"
users_for_project = dao.get_members_of_project(project.id)
for user in users_for_project:
assert user.id in [user1.id, user2.id,
self.test_user.id], "Users not stored properly."
assert os.path.exists(
os.path.join(TvbProfile.current.TVB_STORAGE,
FilesHelper.PROJECTS_FOLDER,
"test_project")), "Folder for project was not created"
def test_create_project_empty_name(self):
"""
Creating a project with an empty name.
"""
data = dict(name="", description="test_description", users=[])
initial_projects = dao.get_projects_for_user(self.test_user.id)
assert len(initial_projects) == 0, "Database reset probably failed!"
with pytest.raises(ProjectServiceException):
self.project_service.store_project(self.test_user, True, None,
**data)
def test_edit_project_happy_flow(self):
"""
Standard flow for editing an existing project.
"""
selected_project = TestFactory.create_project(self.test_user,
'test_proj')
proj_root = self.structure_helper.get_project_folder(selected_project)
initial_projects = dao.get_projects_for_user(self.test_user.id)
assert len(
initial_projects) == 1, "Database initialization probably failed!"
edited_data = dict(name="test_project",
description="test_description",
users=[])
edited_project = self.project_service.store_project(
self.test_user, False, selected_project.id, **edited_data)
assert not os.path.exists(proj_root), "Previous folder not deleted"
proj_root = self.structure_helper.get_project_folder(edited_project)
assert os.path.exists(proj_root), "New folder not created!"
assert selected_project.name != edited_project.name, "Project was no changed!"
def test_edit_project_unexisting(self):
"""
Trying to edit an un-existing project.
"""
selected_project = TestFactory.create_project(self.test_user,
'test_proj')
self.structure_helper.get_project_folder(selected_project)
initial_projects = dao.get_projects_for_user(self.test_user.id)
assert len(
initial_projects) == 1, "Database initialization probably failed!"
data = dict(name="test_project",
description="test_description",
users=[])
with pytest.raises(ProjectServiceException):
self.project_service.store_project(self.test_user, False, 99,
**data)
def test_find_project_happy_flow(self):
"""
Standard flow for finding a project by it's id.
"""
initial_projects = dao.get_projects_for_user(self.test_user.id)
assert len(initial_projects) == 0, "Database reset probably failed!"
inserted_project = TestFactory.create_project(self.test_user,
'test_project')
assert self.project_service.find_project(
inserted_project.id) is not None, "Project not found !"
dao_returned_project = dao.get_project_by_id(inserted_project.id)
service_returned_project = self.project_service.find_project(
inserted_project.id)
assert dao_returned_project.id == service_returned_project.id, \
"Data returned from service is different from data returned by DAO."
assert dao_returned_project.name == service_returned_project.name, \
"Data returned from service is different than data returned by DAO."
assert dao_returned_project.description == service_returned_project.description, \
"Data returned from service is different from data returned by DAO."
assert dao_returned_project.members == service_returned_project.members, \
"Data returned from service is different from data returned by DAO."
def test_find_project_unexisting(self):
"""
Searching for an un-existing project.
"""
data = dict(name="test_project",
description="test_description",
users=[])
initial_projects = dao.get_projects_for_user(self.test_user.id)
assert len(initial_projects) == 0, "Database reset probably failed!"
project = self.project_service.store_project(self.test_user, True,
None, **data)
# fetch a likely non-existing project. Previous project id plus a 'big' offset
with pytest.raises(ProjectServiceException):
self.project_service.find_project(project.id + 1033)
def test_retrieve_projects_for_user(self):
"""
Test for retrieving the projects for a given user. One page only.
"""
initial_projects = self.project_service.retrieve_projects_for_user(
self.test_user.id)[0]
assert len(initial_projects) == 0, "Database was not reset properly!"
TestFactory.create_project(self.test_user, 'test_proj')
TestFactory.create_project(self.test_user, 'test_proj1')
TestFactory.create_project(self.test_user, 'test_proj2')
user1 = TestFactory.create_user('another_user')
TestFactory.create_project(user1, 'test_proj3')
projects = self.project_service.retrieve_projects_for_user(
self.test_user.id)[0]
assert len(projects) == 3, "Projects not retrieved properly!"
for project in projects:
assert project.name != "test_project3", "This project should not have been retrieved"
def test_retrieve_1project_3usr(self):
"""
One user as admin, two users as members, getting projects for admin and for any of
the members should return one.
"""
member1 = TestFactory.create_user("member1")
member2 = TestFactory.create_user("member2")
TestFactory.create_project(self.test_user,
'Testproject',
users=[member1.id, member2.id])
projects = self.project_service.retrieve_projects_for_user(
self.test_user.id, 1)[0]
assert len(projects) == 1, "Projects not retrieved properly!"
projects = self.project_service.retrieve_projects_for_user(
member1.id, 1)[0]
assert len(projects) == 1, "Projects not retrieved properly!"
projects = self.project_service.retrieve_projects_for_user(
member2.id, 1)[0]
assert len(projects) == 1, "Projects not retrieved properly!"
def test_retrieve_3projects_3usr(self):
"""
Three users, 3 projects. Structure of db:
proj1: {admin: user1, members: [user2, user3]}
proj2: {admin: user2, members: [user1]}
proj3: {admin: user3, members: [user1, user2]}
Check valid project returns for all the users.
"""
member1 = TestFactory.create_user("member1")
member2 = TestFactory.create_user("member2")
member3 = TestFactory.create_user("member3")
TestFactory.create_project(member1,
'TestProject1',
users=[member2.id, member3.id])
TestFactory.create_project(member2, 'TestProject2', users=[member1.id])
TestFactory.create_project(member3,
'TestProject3',
users=[member1.id, member2.id])
projects = self.project_service.retrieve_projects_for_user(
member1.id, 1)[0]
assert len(projects) == 3, "Projects not retrieved properly!"
projects = self.project_service.retrieve_projects_for_user(
member2.id, 1)[0]
assert len(projects) == 3, "Projects not retrieved properly!"
projects = self.project_service.retrieve_projects_for_user(
member3.id, 1)[0]
assert len(projects) == 2, "Projects not retrieved properly!"
def test_retrieve_projects_random(self):
"""
Generate a large number of users/projects, and validate the results.
"""
ExtremeTestFactory.generate_users(NR_USERS, MAX_PROJ_PER_USER)
for i in range(NR_USERS):
current_user = dao.get_user_by_name("gen" + str(i))
expected_projects = ExtremeTestFactory.VALIDATION_DICT[
current_user.id]
if expected_projects % PROJECTS_PAGE_SIZE == 0:
expected_pages = expected_projects / PROJECTS_PAGE_SIZE
exp_proj_per_page = PROJECTS_PAGE_SIZE
else:
expected_pages = expected_projects // PROJECTS_PAGE_SIZE + 1
exp_proj_per_page = expected_projects % PROJECTS_PAGE_SIZE
if expected_projects == 0:
expected_pages = 0
exp_proj_per_page = 0
projects, pages = self.project_service.retrieve_projects_for_user(
current_user.id, expected_pages)
assert len(projects) == exp_proj_per_page, "Projects not retrieved properly! Expected:" + \
str(exp_proj_per_page) + "but got:" + str(len(projects))
assert pages == expected_pages, "Pages not retrieved properly!"
for folder in os.listdir(TvbProfile.current.TVB_STORAGE):
full_path = os.path.join(TvbProfile.current.TVB_STORAGE, folder)
if os.path.isdir(full_path) and folder.startswith('Generated'):
shutil.rmtree(full_path)
def test_retrieve_projects_page2(self):
"""
Test for retrieving the second page projects for a given user.
"""
for i in range(PROJECTS_PAGE_SIZE + 3):
TestFactory.create_project(self.test_user, 'test_proj' + str(i))
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id, 2)
assert len(projects) == (PROJECTS_PAGE_SIZE + 3
) % PROJECTS_PAGE_SIZE, "Pagination inproper."
assert pages == 2, 'Wrong number of pages retrieved.'
def test_retrieve_projects_and_del(self):
"""
Test for retrieving the second page projects for a given user.
"""
created_projects = []
for i in range(PROJECTS_PAGE_SIZE + 1):
created_projects.append(
TestFactory.create_project(self.test_user,
'test_proj' + str(i)))
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id, 2)
assert len(projects) == (PROJECTS_PAGE_SIZE + 1
) % PROJECTS_PAGE_SIZE, "Pagination improper."
assert pages == (PROJECTS_PAGE_SIZE +
1) // PROJECTS_PAGE_SIZE + 1, 'Wrong number of pages'
self.project_service.remove_project(created_projects[1].id)
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id, 2)
assert len(projects) == 0, "Pagination improper."
assert pages == 1, 'Wrong number of pages retrieved.'
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id, 1)
assert len(projects) == PROJECTS_PAGE_SIZE, "Pagination improper."
assert pages == 1, 'Wrong number of pages retrieved.'
def test_empty_project_has_zero_disk_size(self):
TestFactory.create_project(self.test_user, 'test_proj')
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id)
assert 0 == projects[0].disk_size
assert '0.0 KiB' == projects[0].disk_size_human
def test_project_disk_size(self):
project1 = TestFactory.create_project(self.test_user, 'test_proj1')
zip_path = os.path.join(os.path.dirname(tvb_data.__file__),
'connectivity', 'connectivity_66.zip')
TestFactory.import_zip_connectivity(self.test_user, project1, zip_path,
'testSubject')
project2 = TestFactory.create_project(self.test_user, 'test_proj2')
zip_path = os.path.join(os.path.dirname(tvb_data.__file__),
'connectivity', 'connectivity_76.zip')
TestFactory.import_zip_connectivity(self.test_user, project2, zip_path,
'testSubject')
projects = self.project_service.retrieve_projects_for_user(
self.test_user.id)[0]
assert projects[0].disk_size != projects[
1].disk_size, "projects should have different size"
for project in projects:
assert 0 != project.disk_size
assert '0.0 KiB' != project.disk_size_human
prj_folder = self.structure_helper.get_project_folder(project)
actual_disk_size = FilesHelper.compute_recursive_h5_disk_usage(
prj_folder)
ratio = float(actual_disk_size) / project.disk_size
msg = "Real disk usage: %s The one recorded in the db : %s" % (
actual_disk_size, project.disk_size)
assert ratio < 1.1, msg
def test_get_linkable_projects(self):
"""
Test for retrieving the projects for a given user.
"""
initial_projects = self.project_service.retrieve_projects_for_user(
self.test_user.id)[0]
assert len(initial_projects) == 0, "Database was not reset!"
test_proj = []
user1 = TestFactory.create_user("another_user")
for i in range(4):
test_proj.append(
TestFactory.create_project(self.test_user if i < 3 else user1,
'test_proj' + str(i)))
operation = TestFactory.create_operation(test_user=self.test_user,
test_project=test_proj[0])
datatype = dao.store_entity(
model_datatype.DataType(module="test_data",
subject="subj1",
state="test_state",
operation_id=operation.id))
linkable = self.project_service.get_linkable_projects_for_user(
self.test_user.id, str(datatype.id))[0]
assert len(linkable) == 2, "Wrong count of link-able projects!"
proj_names = [project.name for project in linkable]
assert test_proj[1].name in proj_names
assert test_proj[2].name in proj_names
assert not test_proj[3].name in proj_names
def test_remove_project_happy_flow(self):
"""
Standard flow for deleting a project.
"""
inserted_project = TestFactory.create_project(self.test_user,
'test_proj')
project_root = self.structure_helper.get_project_folder(
inserted_project)
projects = dao.get_projects_for_user(self.test_user.id)
assert len(projects) == 1, "Initializations failed!"
assert os.path.exists(project_root), "Something failed at insert time!"
self.project_service.remove_project(inserted_project.id)
projects = dao.get_projects_for_user(self.test_user.id)
assert len(projects) == 0, "Project was not deleted!"
assert not os.path.exists(project_root), "Root folder not deleted!"
def test_remove_project_wrong_id(self):
"""
Flow for deleting a project giving an un-existing id.
"""
TestFactory.create_project(self.test_user, 'test_proj')
projects = dao.get_projects_for_user(self.test_user.id)
assert len(projects) == 1, "Initializations failed!"
with pytest.raises(ProjectServiceException):
self.project_service.remove_project(99)
def __check_meta_data(self, expected_meta_data, new_datatype):
"""Validate Meta-Data"""
mapp_keys = {
DataTypeOverlayDetails.DATA_SUBJECT: "subject",
DataTypeOverlayDetails.DATA_STATE: "state"
}
for key, value in expected_meta_data.items():
if key in mapp_keys:
assert value == getattr(new_datatype, mapp_keys[key])
elif key == DataTypeMetaData.KEY_OPERATION_TAG:
if DataTypeMetaData.KEY_OP_GROUP_ID in expected_meta_data:
# We have a Group to check
op_group = new_datatype.parent_operation.fk_operation_group
op_group = dao.get_generic_entity(
model_operation.OperationGroup, op_group)[0]
assert value == op_group.name
else:
assert value == new_datatype.parent_operation.user_group
def test_remove_project_node(self):
"""
Test removing of a node from a project.
"""
inserted_project, gid, op = TestFactory.create_value_wrapper(
self.test_user)
project_to_link = model_project.Project("Link", self.test_user.id,
"descript")
project_to_link = dao.store_entity(project_to_link)
exact_data = dao.get_datatype_by_gid(gid)
assert exact_data is not None, "Initialization problem!"
dao.store_entity(
model_datatype.Links(exact_data.id, project_to_link.id))
vw_h5_path = h5.path_for_stored_index(exact_data)
assert os.path.exists(vw_h5_path)
if dao.get_system_user() is None:
dao.store_entity(
model_operation.User(
TvbProfile.current.web.admin.SYSTEM_USER_NAME,
TvbProfile.current.web.admin.SYSTEM_USER_NAME, None, None,
True, None))
self.project_service._remove_project_node_files(
inserted_project.id, gid)
assert not os.path.exists(vw_h5_path)
exact_data = dao.get_datatype_by_gid(gid)
assert exact_data is not None, "Data should still be in DB, because of links"
vw_h5_path_new = h5.path_for_stored_index(exact_data)
assert os.path.exists(vw_h5_path_new)
assert vw_h5_path_new != vw_h5_path
self.project_service._remove_project_node_files(
project_to_link.id, gid)
assert dao.get_datatype_by_gid(gid) is None
def test_update_meta_data_simple(self):
"""
Test the new update metaData for a simple data that is not part of a group.
"""
inserted_project, gid, _ = TestFactory.create_value_wrapper(
self.test_user)
new_meta_data = {
DataTypeOverlayDetails.DATA_SUBJECT: "new subject",
DataTypeOverlayDetails.DATA_STATE: "second_state",
DataTypeOverlayDetails.CODE_GID: gid,
DataTypeOverlayDetails.CODE_OPERATION_TAG: 'new user group'
}
self.project_service.update_metadata(new_meta_data)
new_datatype = dao.get_datatype_by_gid(gid)
self.__check_meta_data(new_meta_data, new_datatype)
new_datatype_h5 = h5.h5_file_for_index(new_datatype)
assert new_datatype_h5.subject.load(
) == 'new subject', 'UserGroup not updated!'
def test_update_meta_data_group(self, test_adapter_factory):
"""
Test the new update metaData for a group of dataTypes.
"""
test_adapter_factory(adapter_class=TestAdapter3)
op_group_id = TestFactory.create_group(test_user=self.test_user)[1]
new_meta_data = {
DataTypeOverlayDetails.DATA_SUBJECT: "new subject",
DataTypeOverlayDetails.DATA_STATE: "updated_state",
DataTypeOverlayDetails.CODE_OPERATION_GROUP_ID: op_group_id,
DataTypeOverlayDetails.CODE_OPERATION_TAG: 'newGroupName'
}
self.project_service.update_metadata(new_meta_data)
datatypes = dao.get_datatype_in_group(op_group_id)
for datatype in datatypes:
new_datatype = dao.get_datatype_by_id(datatype.id)
assert op_group_id == new_datatype.parent_operation.fk_operation_group
new_group = dao.get_generic_entity(model_operation.OperationGroup,
op_group_id)[0]
assert new_group.name == "newGroupName"
self.__check_meta_data(new_meta_data, new_datatype)
def test_retrieve_project_full(self, dummy_datatype_index_factory):
"""
Tests full project information is retrieved by method `ProjectService.retrieve_project_full(...)`
"""
project = TestFactory.create_project(self.test_user)
operation = TestFactory.create_operation(test_user=self.test_user,
test_project=project)
dummy_datatype_index_factory(project=project, operation=operation)
dummy_datatype_index_factory(project=project, operation=operation)
dummy_datatype_index_factory(project=project, operation=operation)
_, ops_nr, operations, pages_no = self.project_service.retrieve_project_full(
project.id)
assert ops_nr == 1, "DataType Factory should only use one operation to store all it's datatypes."
assert pages_no == 1, "DataType Factory should only use one operation to store all it's datatypes."
resulted_dts = operations[0]['results']
assert len(resulted_dts) == 3, "3 datatypes should be created."
def test_get_project_structure(self, datatype_group_factory,
dummy_datatype_index_factory,
project_factory, user_factory):
"""
Tests project structure is as expected and contains all datatypes and created links
"""
user = user_factory()
project1 = project_factory(user, name="TestPS1")
project2 = project_factory(user, name="TestPS2")
dt_group = datatype_group_factory(project=project1)
dt_simple = dummy_datatype_index_factory(state="RAW_DATA",
project=project1)
# Create 3 DTs directly in Project 2
dummy_datatype_index_factory(state="RAW_DATA", project=project2)
dummy_datatype_index_factory(state="RAW_DATA", project=project2)
dummy_datatype_index_factory(state="RAW_DATA", project=project2)
# Create Links from Project 1 into Project 2
link_ids, expected_links = [], []
link_ids.append(dt_simple.id)
expected_links.append(dt_simple.gid)
# Prepare links towards a full DT Group, but expecting only the DT_Group in the final tree
dts = dao.get_datatype_in_group(datatype_group_id=dt_group.id)
link_ids.extend([dt_to_link.id for dt_to_link in dts])
link_ids.append(dt_group.id)
expected_links.append(dt_group.gid)
# Actually create the links from Prj1 into Prj2
AlgorithmService().create_link(link_ids, project2.id)
# Retrieve the raw data used to compose the tree (for easy parsing)
dts_in_tree = dao.get_data_in_project(project2.id)
dts_in_tree = [dt.gid for dt in dts_in_tree]
# Retrieve the tree json (for trivial validations only, as we can not decode)
node_json = self.project_service.get_project_structure(
project2, None, DataTypeMetaData.KEY_STATE,
DataTypeMetaData.KEY_SUBJECT, None)
assert len(expected_links) + 3 == len(
dts_in_tree), "invalid number of nodes in tree"
assert dt_group.gid in dts_in_tree, "DT_Group should be in the Project Tree!"
assert dt_group.gid in node_json, "DT_Group should be in the Project Tree JSON!"
project_dts = dao.get_datatypes_in_project(project2.id)
for dt in project_dts:
if dt.fk_datatype_group is not None:
assert not dt.gid in node_json, "DTs part of a group should not be"
assert not dt.gid in dts_in_tree, "DTs part of a group should not be"
else:
assert dt.gid in node_json, "Simple DTs and DT_Groups should be"
assert dt.gid in dts_in_tree, "Simple DTs and DT_Groups should be"
for link_gid in expected_links:
assert link_gid in node_json, "Expected Link not present"
assert link_gid in dts_in_tree, "Expected Link not present"
class ProjectServiceTest(TransactionalTestCase):
"""
This class contains tests for the tvb.core.services.project_service module.
"""
def setUp(self):
"""
Reset the database before each test.
"""
config.EVENTS_FOLDER = ''
self.project_service = ProjectService()
self.structure_helper = FilesHelper()
self.test_user = TestFactory.create_user()
def tearDown(self):
"""
Remove project folders and clean up database.
"""
created_projects = dao.get_projects_for_user(self.test_user.id)
for project in created_projects:
self.structure_helper.remove_project_structure(project.name)
self.delete_project_folders()
def test_create_project_happy_flow(self):
"""
Standard flow for creating a new project.
"""
user1 = TestFactory.create_user('test_user1')
user2 = TestFactory.create_user('test_user2')
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 0,
"Database reset probably failed!")
TestFactory.create_project(self.test_user,
'test_project',
users=[user1.id, user2.id])
resulting_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(resulting_projects), 1,
"Project with valid data not inserted!")
project = resulting_projects[0]
if project.name == "test_project":
self.assertEqual(project.description, "description",
"Description do no match")
users_for_project = dao.get_members_of_project(project.id)
for user in users_for_project:
self.assertTrue(user.id in [user1.id, user2.id],
"Users not stored properly.")
self.assertTrue(
os.path.exists(
os.path.join(TvbProfile.current.TVB_STORAGE,
FilesHelper.PROJECTS_FOLDER, "test_project")),
"Folder for project was not created")
def test_create_project_empty_name(self):
"""
Creating a project with an empty name.
"""
data = dict(name="", description="test_description", users=[])
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 0,
"Database reset probably failed!")
self.assertRaises(ProjectServiceException,
self.project_service.store_project, self.test_user,
True, None, **data)
def test_edit_project_happy_flow(self):
"""
Standard flow for editing an existing project.
"""
selected_project = TestFactory.create_project(self.test_user,
'test_proj')
proj_root = self.structure_helper.get_project_folder(selected_project)
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 1,
"Database initialization probably failed!")
edited_data = dict(name="test_project",
description="test_description",
users=[])
edited_project = self.project_service.store_project(
self.test_user, False, selected_project.id, **edited_data)
self.assertFalse(os.path.exists(proj_root),
"Previous folder not deleted")
proj_root = self.structure_helper.get_project_folder(edited_project)
self.assertTrue(os.path.exists(proj_root), "New folder not created!")
self.assertNotEqual(selected_project.name, edited_project.name,
"Project was no changed!")
def test_edit_project_unexisting(self):
"""
Trying to edit an un-existing project.
"""
selected_project = TestFactory.create_project(self.test_user,
'test_proj')
self.structure_helper.get_project_folder(selected_project)
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 1,
"Database initialization probably failed!")
data = dict(name="test_project",
description="test_description",
users=[])
self.assertRaises(ProjectServiceException,
self.project_service.store_project, self.test_user,
False, 99, **data)
def test_find_project_happy_flow(self):
"""
Standard flow for finding a project by it's id.
"""
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 0,
"Database reset probably failed!")
inserted_project = TestFactory.create_project(self.test_user,
'test_project')
self.assertTrue(
self.project_service.find_project(inserted_project.id) is not None,
"Project not found !")
dao_returned_project = dao.get_project_by_id(inserted_project.id)
service_returned_project = self.project_service.find_project(
inserted_project.id)
self.assertEqual(
dao_returned_project.id, service_returned_project.id,
"Data returned from service is different from data returned by DAO."
)
self.assertEqual(
dao_returned_project.name, service_returned_project.name,
"Data returned from service is different than data returned by DAO."
)
self.assertEqual(
dao_returned_project.description,
service_returned_project.description,
"Data returned from service is different from data returned by DAO."
)
self.assertEqual(
dao_returned_project.members, service_returned_project.members,
"Data returned from service is different from data returned by DAO."
)
def test_find_project_unexisting(self):
"""
Searching for an un-existing project.
"""
data = dict(name="test_project",
description="test_description",
users=[])
initial_projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(initial_projects), 0,
"Database reset probably failed!")
project = self.project_service.store_project(self.test_user, True,
None, **data)
# fetch a likely non-existing project. Previous project id plus a 'big' offset
self.assertRaises(ProjectServiceException,
self.project_service.find_project, project.id + 1033)
def test_retrieve_projects_for_user(self):
"""
Test for retrieving the projects for a given user. One page only.
"""
initial_projects = self.project_service.retrieve_projects_for_user(
self.test_user.id)[0]
self.assertEqual(len(initial_projects), 0,
"Database was not reset properly!")
TestFactory.create_project(self.test_user, 'test_proj')
TestFactory.create_project(self.test_user, 'test_proj1')
TestFactory.create_project(self.test_user, 'test_proj2')
user1 = TestFactory.create_user('another_user')
TestFactory.create_project(user1, 'test_proj3')
projects = self.project_service.retrieve_projects_for_user(
self.test_user.id)[0]
self.assertEqual(len(projects), 3, "Projects not retrieved properly!")
for project in projects:
self.assertNotEquals(
project.name, "test_project3",
"This project should not have been retrieved")
def test_retrieve_1project_3usr(self):
"""
One user as admin, two users as members, getting projects for admin and for any of
the members should return one.
"""
member1 = TestFactory.create_user("member1")
member2 = TestFactory.create_user("member2")
TestFactory.create_project(self.test_user,
'Testproject',
users=[member1.id, member2.id])
projects = self.project_service.retrieve_projects_for_user(
self.test_user.id, 1)[0]
self.assertEqual(len(projects), 1, "Projects not retrieved properly!")
projects = self.project_service.retrieve_projects_for_user(
member1.id, 1)[0]
self.assertEqual(len(projects), 1, "Projects not retrieved properly!")
projects = self.project_service.retrieve_projects_for_user(
member2.id, 1)[0]
self.assertEqual(len(projects), 1, "Projects not retrieved properly!")
def test_retrieve_3projects_3usr(self):
"""
Three users, 3 projects. Structure of db:
proj1: {admin: user1, members: [user2, user3]}
proj2: {admin: user2, members: [user1]}
proj3: {admin: user3, members: [user1, user2]}
Check valid project returns for all the users.
"""
member1 = TestFactory.create_user("member1")
member2 = TestFactory.create_user("member2")
member3 = TestFactory.create_user("member3")
TestFactory.create_project(member1,
'TestProject1',
users=[member2.id, member3.id])
TestFactory.create_project(member2, 'TestProject2', users=[member1.id])
TestFactory.create_project(member3,
'TestProject3',
users=[member1.id, member2.id])
projects = self.project_service.retrieve_projects_for_user(
member1.id, 1)[0]
self.assertEqual(len(projects), 3, "Projects not retrieved properly!")
projects = self.project_service.retrieve_projects_for_user(
member2.id, 1)[0]
self.assertEqual(len(projects), 3, "Projects not retrieved properly!")
projects = self.project_service.retrieve_projects_for_user(
member3.id, 1)[0]
self.assertEqual(len(projects), 2, "Projects not retrieved properly!")
def test_retrieve_projects_random(self):
"""
Generate a large number of users/projects, and validate the results.
"""
ExtremeTestFactory.generate_users(NR_USERS, MAX_PROJ_PER_USER)
for i in range(NR_USERS):
current_user = dao.get_user_by_name("gen" + str(i))
expected_projects = ExtremeTestFactory.VALIDATION_DICT[
current_user.id]
if expected_projects % PROJECTS_PAGE_SIZE == 0:
expected_pages = expected_projects / PROJECTS_PAGE_SIZE
exp_proj_per_page = PROJECTS_PAGE_SIZE
else:
expected_pages = expected_projects / PROJECTS_PAGE_SIZE + 1
exp_proj_per_page = expected_projects % PROJECTS_PAGE_SIZE
if expected_projects == 0:
expected_pages = 0
exp_proj_per_page = 0
projects, pages = self.project_service.retrieve_projects_for_user(
current_user.id, expected_pages)
self.assertEqual(
len(projects), exp_proj_per_page,
"Projects not retrieved properly! Expected:" +
str(exp_proj_per_page) + "but got:" + str(len(projects)))
self.assertEqual(pages, expected_pages,
"Pages not retrieved properly!")
for folder in os.listdir(TvbProfile.current.TVB_STORAGE):
full_path = os.path.join(TvbProfile.current.TVB_STORAGE, folder)
if os.path.isdir(full_path) and folder.startswith('Generated'):
shutil.rmtree(full_path)
def test_retrieve_projects_page2(self):
"""
Test for retrieving the second page projects for a given user.
"""
for i in range(PROJECTS_PAGE_SIZE + 3):
TestFactory.create_project(self.test_user, 'test_proj' + str(i))
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id, 2)
self.assertEqual(len(projects),
(PROJECTS_PAGE_SIZE + 3) % PROJECTS_PAGE_SIZE,
"Pagination inproper.")
self.assertEqual(pages, 2, 'Wrong number of pages retrieved.')
def test_retrieve_projects_and_del(self):
"""
Test for retrieving the second page projects for a given user.
"""
created_projects = []
for i in range(PROJECTS_PAGE_SIZE + 1):
created_projects.append(
TestFactory.create_project(self.test_user,
'test_proj' + str(i)))
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id, 2)
self.assertEqual(len(projects),
(PROJECTS_PAGE_SIZE + 1) % PROJECTS_PAGE_SIZE,
"Pagination improper.")
self.assertEqual(pages,
(PROJECTS_PAGE_SIZE + 1) / PROJECTS_PAGE_SIZE + 1,
'Wrong number of pages')
self.project_service.remove_project(created_projects[1].id)
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id, 2)
self.assertEqual(len(projects), 0, "Pagination improper.")
self.assertEqual(pages, 1, 'Wrong number of pages retrieved.')
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id, 1)
self.assertEqual(len(projects), PROJECTS_PAGE_SIZE,
"Pagination improper.")
self.assertEqual(pages, 1, 'Wrong number of pages retrieved.')
def test_empty_project_has_zero_disk_size(self):
TestFactory.create_project(self.test_user, 'test_proj')
projects, pages = self.project_service.retrieve_projects_for_user(
self.test_user.id)
self.assertEqual(0, projects[0].disk_size)
self.assertEqual('0.0 KiB', projects[0].disk_size_human)
def test_project_disk_size(self):
project1 = TestFactory.create_project(self.test_user, 'test_proj1')
zip_path = os.path.join(os.path.dirname(tvb_data.__file__),
'connectivity', 'connectivity_66.zip')
TestFactory.import_zip_connectivity(self.test_user, project1,
'testSubject', zip_path)
project2 = TestFactory.create_project(self.test_user, 'test_proj2')
TestFactory.import_cff(test_user=self.test_user, test_project=project2)
projects = self.project_service.retrieve_projects_for_user(
self.test_user.id)[0]
self.assertNotEqual(projects[0].disk_size, projects[1].disk_size,
"projects should have different size")
for project in projects:
self.assertNotEqual(0, project.disk_size)
self.assertNotEqual('0.0 KiB', project.disk_size_human)
prj_folder = self.structure_helper.get_project_folder(project)
actual_disk_size = self.compute_recursive_h5_disk_usage(
prj_folder)[0]
ratio = float(actual_disk_size) / project.disk_size
msg = "Real disk usage: %s The one recorded in the db : %s" % (
actual_disk_size, project.disk_size)
self.assertTrue(ratio < 1.4, msg)
def test_get_linkable_projects(self):
"""
Test for retrieving the projects for a given user.
"""
initial_projects = self.project_service.retrieve_projects_for_user(
self.test_user.id)[0]
self.assertEqual(len(initial_projects), 0, "Database was not reset!")
test_proj = []
user1 = TestFactory.create_user("another_user")
for i in range(4):
test_proj.append(
TestFactory.create_project(self.test_user if i < 3 else user1,
'test_proj' + str(i)))
project_storage = self.structure_helper.get_project_folder(
test_proj[0])
operation = TestFactory.create_operation(test_user=self.test_user,
test_project=test_proj[0])
project_storage = os.path.join(project_storage, str(operation.id))
os.makedirs(project_storage)
datatype = dao.store_entity(
model.DataType(module="test_data",
subject="subj1",
state="test_state",
operation_id=operation.id))
linkable = self.project_service.get_linkable_projects_for_user(
self.test_user.id, str(datatype.id))[0]
self.assertEqual(len(linkable), 2,
"Wrong count of link-able projects!")
proj_names = [project.name for project in linkable]
self.assertTrue(test_proj[1].name in proj_names)
self.assertTrue(test_proj[2].name in proj_names)
self.assertFalse(test_proj[3].name in proj_names)
def test_remove_project_happy_flow(self):
"""
Standard flow for deleting a project.
"""
inserted_project = TestFactory.create_project(self.test_user,
'test_proj')
project_root = self.structure_helper.get_project_folder(
inserted_project)
projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(projects), 1, "Initializations failed!")
self.assertTrue(os.path.exists(project_root),
"Something failed at insert time!")
self.project_service.remove_project(inserted_project.id)
projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(projects), 0, "Project was not deleted!")
self.assertFalse(os.path.exists(project_root),
"Root folder not deleted!")
def test_remove_project_wrong_id(self):
"""
Flow for deleting a project giving an un-existing id.
"""
TestFactory.create_project(self.test_user, 'test_proj')
projects = dao.get_projects_for_user(self.test_user.id)
self.assertEqual(len(projects), 1, "Initializations failed!")
self.assertRaises(ProjectServiceException,
self.project_service.remove_project, 99)
@staticmethod
def _create_value_wrapper(test_user, test_project=None):
"""
Creates a ValueWrapper dataType, and the associated parent Operation.
This is also used in ProjectStructureTest.
"""
if test_project is None:
test_project = TestFactory.create_project(test_user, 'test_proj')
operation = TestFactory.create_operation(test_user=test_user,
test_project=test_project)
value_wrapper = ValueWrapper(data_value=5.0, data_name="my_value")
value_wrapper.type = "ValueWrapper"
value_wrapper.module = "tvb.datatypes.mapped_values"
value_wrapper.subject = "John Doe"
value_wrapper.state = "RAW_STATE"
value_wrapper.set_operation_id(operation.id)
adapter_instance = StoreAdapter([value_wrapper])
OperationService().initiate_prelaunch(operation, adapter_instance, {})
all_value_wrappers = FlowService().get_available_datatypes(
test_project.id, "tvb.datatypes.mapped_values.ValueWrapper")[0]
if len(all_value_wrappers) != 1:
raise Exception("Should be only one value wrapper.")
result_vw = ABCAdapter.load_entity_by_gid(all_value_wrappers[0][2])
return test_project, result_vw.gid, operation.gid
def __check_meta_data(self, expected_meta_data, new_datatype):
"""Validate Meta-Data"""
mapp_keys = {
DataTypeMetaData.KEY_SUBJECT: "subject",
DataTypeMetaData.KEY_STATE: "state"
}
for key, value in expected_meta_data.iteritems():
if key in mapp_keys:
self.assertEqual(value, getattr(new_datatype, mapp_keys[key]))
elif key == DataTypeMetaData.KEY_OPERATION_TAG:
if DataTypeMetaData.KEY_OP_GROUP_ID in expected_meta_data:
## We have a Group to check
op_group = new_datatype.parent_operation.fk_operation_group
op_group = dao.get_generic_entity(model.OperationGroup,
op_group)[0]
self.assertEqual(value, op_group.name)
else:
self.assertEqual(value,
new_datatype.parent_operation.user_group)
def test_remove_project_node(self):
"""
Test removing of a node from a project.
"""
inserted_project, gid, gid_op = self._create_value_wrapper(
self.test_user)
project_to_link = model.Project("Link", self.test_user.id, "descript")
project_to_link = dao.store_entity(project_to_link)
exact_data = dao.get_datatype_by_gid(gid)
dao.store_entity(model.Links(exact_data.id, project_to_link.id))
self.assertTrue(
dao.get_datatype_by_gid(gid) is not None,
"Initialization problem!")
operation_id = dao.get_generic_entity(model.Operation, gid_op,
'gid')[0].id
op_folder = self.structure_helper.get_project_folder(
"test_proj", str(operation_id))
self.assertTrue(os.path.exists(op_folder))
sub_files = os.listdir(op_folder)
self.assertEqual(2, len(sub_files))
### Validate that no more files are created than needed.
self.project_service._remove_project_node_files(
inserted_project.id, gid)
sub_files = os.listdir(op_folder)
self.assertEqual(1, len(sub_files))
### operation.xml file should still be there
op_folder = self.structure_helper.get_project_folder(
"Link", str(operation_id + 1))
sub_files = os.listdir(op_folder)
self.assertEqual(2, len(sub_files))
self.assertTrue(
dao.get_datatype_by_gid(gid) is not None,
"Data should still be in DB, because of links")
self.project_service._remove_project_node_files(
project_to_link.id, gid)
self.assertTrue(dao.get_datatype_by_gid(gid) is None)
sub_files = os.listdir(op_folder)
self.assertEqual(1, len(sub_files))
### operation.xml file should still be there
def test_update_meta_data_simple(self):
"""
Test the new update metaData for a simple data that is not part of a group.
"""
inserted_project, gid, _ = self._create_value_wrapper(self.test_user)
new_meta_data = {
DataTypeOverlayDetails.DATA_SUBJECT: "new subject",
DataTypeOverlayDetails.DATA_STATE: "second_state",
DataTypeOverlayDetails.CODE_GID: gid,
DataTypeOverlayDetails.CODE_OPERATION_TAG: 'new user group'
}
self.project_service.update_metadata(new_meta_data)
new_datatype = dao.get_datatype_by_gid(gid)
self.__check_meta_data(new_meta_data, new_datatype)
op_path = FilesHelper().get_operation_meta_file_path(
inserted_project.name, new_datatype.parent_operation.id)
op_meta = XMLReader(op_path).read_metadata()
self.assertEqual(op_meta['user_group'], 'new user group',
'UserGroup not updated!')
def test_update_meta_data_group(self):
"""
Test the new update metaData for a group of dataTypes.
"""
datatypes, group_id = TestFactory.create_group(
self.test_user, subject="test-subject-1")
new_meta_data = {
DataTypeOverlayDetails.DATA_SUBJECT: "new subject",
DataTypeOverlayDetails.DATA_STATE: "updated_state",
DataTypeOverlayDetails.CODE_OPERATION_GROUP_ID: group_id,
DataTypeOverlayDetails.CODE_OPERATION_TAG: 'newGroupName'
}
self.project_service.update_metadata(new_meta_data)
for datatype in datatypes:
new_datatype = dao.get_datatype_by_id(datatype.id)
self.assertEqual(group_id,
new_datatype.parent_operation.fk_operation_group)
new_group = dao.get_generic_entity(model.OperationGroup,
group_id)[0]
self.assertEqual(new_group.name, "newGroupName")
self.__check_meta_data(new_meta_data, new_datatype)
def _create_datatypes(self, dt_factory, nr_of_dts):
for idx in range(nr_of_dts):
dt = Datatype1()
dt.row1 = "value%i" % (idx, )
dt.row2 = "value%i" % (idx + 1, )
dt_factory._store_datatype(dt)
def test_retrieve_project_full(self):
"""
Tests full project information is retrieved by method `ProjectService.retrieve_project_full(...)`
"""
dt_factory = datatypes_factory.DatatypesFactory()
self._create_datatypes(dt_factory, 3)
_, ops_nr, operations, pages_no = self.project_service.retrieve_project_full(
dt_factory.project.id)
self.assertEqual(
ops_nr, 1,
"DataType Factory should only use one operation to store all it's datatypes."
)
self.assertEqual(
pages_no, 1,
"DataType Factory should only use one operation to store all it's datatypes."
)
resulted_dts = operations[0]['results']
self.assertEqual(len(resulted_dts), 3,
"3 datatypes should be created.")
def test_get_project_structure(self):
"""
Tests project structure is as expected and contains all datatypes
"""
SELF_DTS_NUMBER = 3
dt_factory_1 = datatypes_factory.DatatypesFactory()
self._create_datatypes(dt_factory_1, SELF_DTS_NUMBER)
dt_group = dt_factory_1.create_datatype_group()
link_ids, expected_links = [], []
# Prepare link towards a simple DT
dt_factory_2 = datatypes_factory.DatatypesFactory()
dt_to_link = dt_factory_2.create_simple_datatype()
link_ids.append(dt_to_link.id)
expected_links.append(dt_to_link.gid)
# Prepare links towards a full DT Group, but expecting only the DT_Group in the final tree
link_gr = dt_factory_2.create_datatype_group()
dts = dao.get_datatype_in_group(datatype_group_id=link_gr.id)
link_ids.extend([dt_to_link.id for dt_to_link in dts])
link_ids.append(link_gr.id)
expected_links.append(link_gr.gid)
# Prepare link towards a single DT inside a group, and expecting to find the DT in the final tree
link_gr = dt_factory_2.create_datatype_group()
dt_to_link = dao.get_datatype_in_group(datatype_group_id=link_gr.id)[0]
link_ids.append(dt_to_link.id)
expected_links.append(dt_to_link.gid)
# Actually create the links from Prj2 into Prj1
FlowService().create_link(link_ids, dt_factory_1.project.id)
# Retrieve the raw data used to compose the tree (for easy parsing)
dts_in_tree = dao.get_data_in_project(dt_factory_1.project.id)
dts_in_tree = [dt.gid for dt in dts_in_tree]
# Retrieve the tree json (for trivial validations only, as we can not decode)
node_json = self.project_service.get_project_structure(
dt_factory_1.project, None, DataTypeMetaData.KEY_STATE,
DataTypeMetaData.KEY_SUBJECT, None)
self.assertEqual(
len(expected_links) + SELF_DTS_NUMBER + 2, len(dts_in_tree),
"invalid number of nodes in tree")
self.assertFalse(
link_gr.gid in dts_in_tree,
"DT_group where a single DT is linked is not expected.")
self.assertTrue(dt_group.gid in dts_in_tree,
"DT_Group should be in the Project Tree!")
self.assertTrue(dt_group.gid in node_json,
"DT_Group should be in the Project Tree JSON!")
project_dts = dao.get_datatypes_in_project(dt_factory_1.project.id)
for dt in project_dts:
if dt.fk_datatype_group is not None:
self.assertFalse(dt.gid in node_json,
"DTs part of a group should not be")
self.assertFalse(dt.gid in dts_in_tree,
"DTs part of a group should not be")
else:
self.assertTrue(dt.gid in node_json,
"Simple DTs and DT_Groups should be")
self.assertTrue(dt.gid in dts_in_tree,
"Simple DTs and DT_Groups should be")
for link_gid in expected_links:
self.assertTrue(link_gid in node_json, "Expected Link not present")
self.assertTrue(link_gid in dts_in_tree,
"Expected Link not present")