def test_flatten__entities_has_input(self):
# given
with open(self.script_dir +
'/entities-with-inputs-specimen.json') as file:
metadata_entity = Entity.from_json(json.load(file))
with open(self.script_dir +
'/entities-with-inputs-donor.json') as file:
input_entity = Entity.from_json(json.load(file))
with open(self.script_dir +
'/entities-with-inputs-process.json') as file:
process = Entity.from_json(json.load(file))
with open(self.script_dir +
'/entities-with-inputs-protocols.json') as file:
protocols = Entity.from_json_list(json.load(file))
metadata_entity.set_input([input_entity], [], process, protocols)
# when
flattener = Flattener()
actual = flattener.flatten([metadata_entity, process] + protocols)
with open(self.script_dir +
'/entities-with-inputs-flattened.json') as file:
expected = json.load(file)
self.assertEqual(actual, expected)
def test_flatten__has_string_arrays(self):
# given
self.content.update({
"insdc_project_accessions": ["SRP180337"],
"geo_series_accessions": ["GSE124298", "GSE124299"]
})
self.metadata_entity = {'content': self.content, 'uuid': self.uuid}
entity_list = [Entity.from_json(self.metadata_entity)]
# when
flattener = Flattener()
actual = flattener.flatten(entity_list)
self.flattened_metadata_entity['Project']['values'][0].update({
'project.insdc_project_accessions':
'SRP180337',
'project.geo_series_accessions':
"GSE124298||GSE124299"
})
self.flattened_metadata_entity['Project']['headers'].extend([
'project.insdc_project_accessions', 'project.geo_series_accessions'
])
self.assertEqual(actual, self.flattened_metadata_entity)
def __build_entity_dict(self, submission):
data_by_submission = self.__get_submission_data(submission)
entity_dict = {}
for entity_json in data_by_submission:
entity = Entity.from_json(entity_json)
entity_dict[entity.id] = entity
linking_map = self.__get_linking_map(submission)
self.__set_inputs(entity_dict, linking_map)
return entity_dict
def test_flatten__has_no_modules(self):
# given
metadata_entity = {'content': self.content, 'uuid': self.uuid}
entity_list = [Entity.from_json(metadata_entity)]
# when
flattener = Flattener()
actual = flattener.flatten(entity_list)
self.assertEqual(actual, self.flattened_metadata_entity)
def test_flatten__has_list_property_with_elements(self):
# given
content = {
"describedBy":
"https://schema.humancellatlas.org/type/project/14.2.0/collection_protocol",
"schema_type":
"protocol",
"organ_parts": [{
"field_1": "UBERON:0000376",
"field_2": "hindlimb stylopod",
"field_3": "hindlimb stylopod"
}]
}
metadata_entity = {'content': content, 'uuid': self.uuid}
entity_list = [Entity.from_json(metadata_entity)]
# when
flattener = Flattener()
actual = flattener.flatten(entity_list)
flattened_metadata_entity = {
'Collection protocol': {
'values': [{
'collection_protocol.organ_parts.field_1':
'UBERON:0000376',
'collection_protocol.organ_parts.field_2':
'hindlimb stylopod',
'collection_protocol.organ_parts.field_3':
'hindlimb stylopod',
'collection_protocol.uuid': 'uuid1'
}],
'headers': [
'collection_protocol.uuid',
'collection_protocol.organ_parts.field_1',
'collection_protocol.organ_parts.field_2',
'collection_protocol.organ_parts.field_3'
]
},
'Schemas': [
'https://schema.humancellatlas.org/type/project/14.2.0/collection_protocol'
]
}
# then
self.assertEqual(actual, flattened_metadata_entity)
def test_flatten__has_boolean(self):
# given
self.content.update({'boolean_field': True})
self.metadata_entity = {'content': self.content, 'uuid': self.uuid}
entity_list = [Entity.from_json(self.metadata_entity)]
# when
flattener = Flattener()
actual = flattener.flatten(entity_list)
self.flattened_metadata_entity['Project']['values'][0].update(
{'project.boolean_field': 'True'})
self.flattened_metadata_entity['Project']['headers'].append(
'project.boolean_field')
# then
self.assertEqual(actual, self.flattened_metadata_entity)
def test_flatten__rows_have_different_columns(self):
# given
entity_json_list = [
{
'content': {
"describedBy":
"https://schema.humancellatlas.org/type/project/14.2.0/project",
"schema_type": "project",
"project_core": {
"project_short_name": "label1",
}
},
'uuid': {
'uuid': 'uuid1'
}
},
{
'content': {
"describedBy":
"https://schema.humancellatlas.org/type/project/14.2.0/project",
"schema_type": "project",
"project_core": {
"project_short_name": "label2",
"project_title": "title",
"project_description": "desc"
}
},
'uuid': {
'uuid': 'uuid2'
}
},
]
# when
flattener = Flattener()
entity_list = [
Entity.from_json(entity_json) for entity_json in entity_json_list
]
actual = flattener.flatten(entity_list)
expected = {
'Project': {
'headers': [
'project.uuid', 'project.project_core.project_short_name',
'project.project_core.project_title',
'project.project_core.project_description'
],
'values': [{
'project.uuid': 'uuid1',
'project.project_core.project_short_name': 'label1'
}, {
'project.uuid': 'uuid2',
'project.project_core.project_short_name': 'label2',
'project.project_core.project_title': 'title',
'project.project_core.project_description': 'desc'
}]
},
'Schemas':
['https://schema.humancellatlas.org/type/project/14.2.0/project']
}
# then
self.assertEqual(actual, expected)