def test_load(self):
# given:
spreadsheet_json = _create_spreadsheet_json()
# when:
entity_map = EntityMap.load(spreadsheet_json)
# then:
self.assertEqual(['project', 'biomaterial', 'file', 'protocol'],
list(entity_map.get_entity_types()))
# and:
# TODO shouldn't entity id's be unique and that there's no need to specify entity type?
biomaterial1 = entity_map.get_entity('biomaterial', 'biomaterial_id_1')
self._assert_correct_entity(biomaterial1, entity_id='biomaterial_id_1',
entity_type='biomaterial', content={'key': 'biomaterial_1'})
# and:
biomaterial2 = entity_map.get_entity('biomaterial', 'biomaterial_id_2')
links = {'biomaterial': ['biomaterial_id_1'], 'process': ['process_id_1']}
self._assert_correct_entity(biomaterial2, entity_id='biomaterial_id_2',
entity_type='biomaterial', content={'key': 'biomaterial_2'},
links=links)
# and:
protocol1 = entity_map.get_entity('protocol', 'protocol_id_1')
self.assertEqual({'key': 'protocol_1'}, protocol1.content)
def test_generate_direct_links_link_not_found_error(self):
# given
spreadsheet_json = {
'project': {
'dummy-project-id': {
'content': {
'key': 'project_1'
}
}
},
'file': {
'file_id_1': {
'content': {
'key': 'file_1'
},
'links_by_entity': {
'biomaterial': ['biomaterial_id_1'],
'protocol': ['protocol_id_1', 'protocol_id_2']
}
}
}
}
entities_dictionaries = EntityMap.load(spreadsheet_json)
entity_linker = EntityLinker(self.mocked_template_manager)
with self.assertRaises(LinkedEntityNotFound) as context:
entity_linker.process_links_from_spreadsheet(entities_dictionaries)
self.assertEqual('biomaterial', context.exception.entity)
self.assertEqual('biomaterial_id_1', context.exception.id)
def test_submit_linked_entity(self, submission_constructor):
# given:
ingest_api = MagicMock('ingest_api')
ingest_api.getSubmissionEnvelope = MagicMock()
ingest_api.patch = MagicMock()
ingest_api.get_link_from_resource = MagicMock()
submission = self._mock_submission(submission_constructor)
# and:
user = Entity('user', 'user_1', {})
entity_map = EntityMap(user)
# and:
link_to_user = {
'entity': 'user',
'id': 'user_1',
'relationship': 'wish_list'
}
linked_product = Entity('product', 'product_1', {}, direct_links=[link_to_user])
project = Entity('project', 'id', {})
entity_map.add_entity(linked_product)
entity_map.add_entity(project)
# when:
submitter = IngestSubmitter(ingest_api)
submitter.PROGRESS_CTR = 1
submitter.submit(entity_map, submission_url='url')
# then:
submission_constructor.assert_called_with(ingest_api, 'url')
submission.define_manifest.assert_called_with(entity_map)
submission.add_entity.assert_has_calls([call(user), call(linked_product)], any_order=True)
submission.link_entity.assert_called_with(linked_product, user, relationship='wish_list')
ingest_api.patch.assert_called_once()
def test_generate_direct_links_multiple_process_links(self):
# given
spreadsheet_json = {
'project': {
'dummy-project-id': {
'content': {
'key': 'project_1'
}
}
},
'biomaterial': {
'biomaterial_id_1': {
'content': {
'key': 'biomaterial_1'
},
'links_by_entity': {
'process': ['process_id_1', 'process_id_2']
}
}
},
'process': {
'process_id_1': {
'content': {
'key': 'process_1'
}
},
'process_id_2': {
'content': {
'key': 'process_2'
}
}
}
}
entities_dictionaries = EntityMap.load(spreadsheet_json)
entity_linker = EntityLinker(self.mocked_template_manager)
with self.assertRaises(MultipleProcessesFound) as context:
entity_linker.process_links_from_spreadsheet(entities_dictionaries)
self.assertEqual('biomaterial', context.exception.from_entity.type)
self.assertEqual(['process_id_1', 'process_id_2'],
context.exception.process_ids)
def test_submit(self, submission_constructor):
# given:
ingest_api = MagicMock('ingest_api')
ingest_api.getSubmissionEnvelope = MagicMock()
submission = self._mock_submission(submission_constructor)
# and:
product = Entity('product', 'product_1', {})
project = Entity('project', 'id', {})
user = Entity('user', 'user_1', {})
entity_map = EntityMap(product, user, project)
# when:
submitter = IngestSubmitter(ingest_api)
submitter.submit(entity_map, submission_url='url')
# then:
submission_constructor.assert_called_with(ingest_api, 'url')
submission.define_manifest.assert_called_with(entity_map)
submission.add_entity.assert_has_calls([call(product), call(user)], any_order=True)
def test_generate_direct_links_invalid_spreadsheet_link(self):
# given
spreadsheet_json = {
'project': {
'dummy-project-id': {
'content': {
'key': 'project_1'
}
}
},
'biomaterial': {
'biomaterial_id_1': {
'content': {
'key': 'biomaterial_1'
},
'links_by_entity': {
'file': ['file_id_1']
}
}
},
'file':{
'file_id_1': {
'content': {
'key': 'file_1'
}
}
}
}
entities_dictionaries = EntityMap.load(spreadsheet_json)
entity_linker = EntityLinker(self.mocked_template_manager)
with self.assertRaises(InvalidLinkInSpreadsheet) as context:
entity_linker.process_links_from_spreadsheet(entities_dictionaries)
self.assertEqual('biomaterial', context.exception.from_entity.type)
self.assertEqual('file', context.exception.link_entity_type)
self.assertEqual('biomaterial_id_1', context.exception.from_entity.id)
self.assertEqual('file_id_1', context.exception.link_entity_id)
def test_generate_direct_links_file_to_biomaterial_has_process(self):
# given
spreadsheet_json = {
'project': {
'dummy-project-id': {
'content': {
'key': 'project_1'
}
}
},
'file': {
'file_id_1': {
'content': {
'key': 'file_1'
},
'links_by_entity': {
'biomaterial': ['biomaterial_id_1'],
'process': ['process_id_1'],
'protocol': ['protocol_id_1', 'protocol_id_2']
}
}
},
'biomaterial': {
'biomaterial_id_1': {
'content': {
'key': 'biomaterial_1'
}
}
},
'protocol': {
'protocol_id_1': {
'content': {
'key': 'protocol_1'
}
},
'protocol_id_2': {
'content': {
'key': 'protocol_2'
}
}
}
}
expected_json = {
'project': {
'dummy-project-id': {
'content': {
'key': 'project_1'
}
}
},
'biomaterial': {
'biomaterial_id_1': {
'content': {
'key': 'biomaterial_1'
},
'direct_links': [
{
'entity': 'project',
'id': 'dummy-project-id',
'relationship': 'projects'
},
{
'entity': 'process',
'id': 'process_id_1',
'relationship': 'inputToProcesses'
}
]
}
},
'file': {
'file_id_1': {
'content': {
'key': 'file_1'
},
'direct_links': [
{
'entity': 'process',
'id': 'process_id_1',
'relationship': 'derivedByProcesses'
}
]
},
},
'process': {
'process_id_1': {
'content': {
'key': 'process_1'
},
'direct_links': [
{
'entity': 'project',
'id': 'dummy-project-id',
'relationship': 'projects'
},
{
'entity': 'protocol',
'id': 'protocol_id_1',
'relationship': 'protocols'
},
{
'entity': 'protocol',
'id': 'protocol_id_2',
'relationship': 'protocols'
}
]
}
},
'protocol': {
'protocol_id_1': {
'content': {
'key': 'protocol_1'
},
'direct_links': [
]
},
'protocol_id_2': {
'content': {
'key': 'protocol_2'
},
'direct_links': [
]
}
}
}
entity_linker = EntityLinker(self.mocked_template_manager)
entities_dictionaries = EntityMap.load(spreadsheet_json)
output = entity_linker.process_links_from_spreadsheet(entities_dictionaries)
self._assert_equal_direct_links(expected_json, output)
def test_count_links(self):
entity_map = EntityMap()
# no element
self.assertEqual(entity_map.count_links(), 0)
# has 1 element without links
entity_map.add_entity(Entity('product', 'product_0', {}))
self.assertEqual(entity_map.count_links(), 0)
# has 1 element with links
entity_map.add_entity(Entity('product', 'product_1', {}, direct_links=[{}, {}, {}]))
self.assertEqual(entity_map.count_links(), 3)
# has many element with links
entity_map.add_entity(Entity('product', 'product_2', {}, direct_links=[{}, {}, {}, {}]))
self.assertEqual(entity_map.count_links(), 7)
def test_count_total(self):
# given:
zero_map = EntityMap()
# and:
one_map = EntityMap()
one_map.add_entity(Entity('product', 'product_1', {}))
# and:
three_map = EntityMap()
three_map.add_entity(Entity('profile', 'profile_1', {}))
for product_id in range(0, 2):
three_map.add_entity(Entity('product', f'product_{product_id}', {}))
# expect:
self.assertEqual(0, zero_map.count_total())
self.assertEqual(1, one_map.count_total())
self.assertEqual(3, three_map.count_total())
def update_entities(self, dsp_submission_uuid: str, entity_map: EntityMap):
archive_submission = self.ingest_api.get_archive_submission_by_dsp_uuid(
dsp_submission_uuid)
archive_submission_url = archive_submission['_links']['self']['href']
for entity in entity_map.get_entities():
self.update_entity(archive_submission_url, entity)
def _process_links_from_spreadsheet(template_mgr, spreadsheet_json):
entity_map = EntityMap.load(spreadsheet_json)
entity_linker = EntityLinker(template_mgr)
entity_map = entity_linker.process_links_from_spreadsheet(entity_map)
return entity_map