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_ontology_property_with_single_element(self):
# given
self.content.update({
"organ_parts": [{
"ontology": "UBERON:0000376",
"ontology_label": "hindlimb stylopod",
"text": "hindlimb stylopod"
}]
})
metadata_entity = {'content': self.content, 'uuid': self.uuid}
entity_list = [metadata_entity]
# when
flattener = Flattener()
actual = flattener.flatten(Entity.from_json_list(entity_list))
self.flattened_metadata_entity['Project']['values'][0].update({
'project.organ_parts.ontology':
'UBERON:0000376',
'project.organ_parts.ontology_label':
'hindlimb stylopod',
'project.organ_parts.text':
'hindlimb stylopod',
})
self.flattened_metadata_entity['Project']['headers'].extend([
'project.organ_parts.ontology',
'project.organ_parts.ontology_label', 'project.organ_parts.text'
])
# then
self.assertEqual(actual, self.flattened_metadata_entity)
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 test_flatten__raises_error__given_multiple_schema_versions_of_same_concrete_entity(
self):
# given
entity_json_list = [
{
'content': {
"describedBy":
"https://schema.humancellatlas.org/type/project/14.2.0/donor_organism",
"schema_type": "biomaterial",
"field": "value"
},
'uuid': {
'uuid': 'uuid1'
}
},
{
'content': {
"describedBy":
"https://schema.humancellatlas.org/type/project/14.3.0/donor_organism",
"schema_type": "biomaterial",
"field": "value"
},
'uuid': {
'uuid': 'uuid2'
}
},
]
entity_list = Entity.from_json_list(entity_json_list)
# when/then
flattener = Flattener()
with self.assertRaisesRegex(
ValueError,
"Multiple versions of same concrete entity schema"):
flattener.flatten(entity_list)
def test_flatten__has_project_modules(self):
# given
self.content.update({
"contributors": [{
"name": "Alex A,,Pollen",
"email": "*****@*****.**",
"institution": "University of California, San Francisco (UCSF)",
"laboratory": "Department of Neurology",
"country": "USA",
"corresponding_contributor": True,
"project_role": {
"text": "experimental scientist",
"ontology": "EFO:0009741",
"ontology_label": "experimental scientist"
}
}]
})
metadata_entity = {
'content': self.content,
'uuid': self.uuid
}
entity_list = [metadata_entity]
# when
flattener = Flattener()
actual = flattener.flatten(Entity.from_json_list(entity_list))
self.flattened_metadata_entity.update({
'Project - Contributors': {
'headers': [
'project.contributors.name',
'project.contributors.email',
'project.contributors.institution',
'project.contributors.laboratory',
'project.contributors.country',
'project.contributors.corresponding_contributor',
'project.contributors.project_role.text',
'project.contributors.project_role.ontology',
'project.contributors.project_role.ontology_label'
],
'values': [{
'project.contributors.corresponding_contributor': 'True',
'project.contributors.country': 'USA',
'project.contributors.email': '*****@*****.**',
'project.contributors.institution': 'University of California, San Francisco (UCSF)',
'project.contributors.laboratory': 'Department of Neurology',
'project.contributors.name': 'Alex A,,Pollen',
'project.contributors.project_role.ontology': 'EFO:0009741',
'project.contributors.project_role.ontology_label': 'experimental scientist',
'project.contributors.project_role.text': 'experimental scientist'}
]}
})
# then
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__project_metadata(self):
# given
with open(self.script_dir + '/project-list.json') as file:
entity_list = json.load(file)
# when
flattener = Flattener()
actual = flattener.flatten(Entity.from_json_list(entity_list))
with open(self.script_dir + '/project-list-flattened.json') as file:
expected = json.load(file)
# then
self.assertEqual(actual, expected)
def test_flatten__has_different_entities(self):
# given
with open(self.script_dir + '/entities.json') as file:
entity_list = json.load(file)
# when
flattener = Flattener()
actual = flattener.flatten(Entity.from_json_list(entity_list))
with open(self.script_dir + '/entities-flattened.json') as file:
expected = json.load(file)
# then
self.assertEqual(actual, expected)
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__has_ontology_property_with_single_element_but_only_with_text_attr(
self):
# given
self.content.update({'diseases': [{'text': 'dummytext2'}]})
metadata_entity = {'content': self.content, 'uuid': self.uuid}
entity_list = [metadata_entity]
# when
flattener = Flattener()
actual = flattener.flatten(Entity.from_json_list(entity_list))
self.flattened_metadata_entity['Project']['values'][0].update({
'project.diseases.text':
'dummytext2',
})
self.flattened_metadata_entity['Project']['headers'].extend(
['project.diseases.text'])
# then
self.assertEqual(actual, self.flattened_metadata_entity)
def test_flatten__has_ontology_property_with_multiple_elements_but_with_empty_ontology_values(
self):
# given
self.content.update({
'diseases': [{
'ontology': 'UBERON:0000376',
'ontology_label': 'dummylabel1',
'text': 'dummytext1'
}, {
'ontology': '',
'ontology_label': '',
'text': 'dummytext2'
}]
})
metadata_entity = {'content': self.content, 'uuid': self.uuid}
entity_list = [metadata_entity]
# when
flattener = Flattener()
actual = flattener.flatten(Entity.from_json_list(entity_list))
self.flattened_metadata_entity['Project']['values'][0].update({
'project.diseases.ontology':
'UBERON:0000376',
'project.diseases.ontology_label':
'dummylabel1',
'project.diseases.text':
'dummytext1||dummytext2',
})
self.flattened_metadata_entity['Project']['headers'].extend([
'project.diseases.ontology', 'project.diseases.ontology_label',
'project.diseases.text'
])
# then
self.assertEqual(self.flattened_metadata_entity, actual)
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)