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_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_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_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 _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
