def test_json_schema__raises_error__when_version_from_path_is_not_found(
self):
# given
schema_path = 'type/project/project'
schema_json = load_json(f'{self.test_dir}/files/project.json')
# when/then
with self.assertRaises(MetadataSchemaError):
schema = MetadataSchema(schema_json, schema_path)
schema.get_json_schema({'version_numbers': {}},
self.schema_base_url)
def _process_directory(repo,
branch_name,
base_server_path,
server_path,
version_numbers,
context,
dryrun=False):
print("Processing " + server_path + " in " + branch_name + " branch of " +
repo.name)
created_list = []
contents = repo.get_dir_contents(server_path, branch_name)
for content in contents:
if content.type == 'dir':
created_list.extend(
_process_directory(repo, branch_name, base_server_path,
content.path, version_numbers, context,
dryrun))
else:
try:
path = content.path
file_root, file_extension = os.path.splitext(path)
if file_extension == '.json' and not path.endswith(
'versions.json'):
print("- processing: " + path)
file_content = repo.get_contents(path, branch_name)
data = base64.b64decode(file_content.content)
json_data = json.loads(data.decode('utf8'))
relative_path = path.replace(base_server_path + "/", "")
relative_path = relative_path.replace(".json", "")
key = None
if relative_path in UNVERSIONED_FILES:
key = relative_path
else:
schema_base_url = SCHEMA_URL.get(branch_name)
metadata_schema = MetadataSchema(
json_data, relative_path)
json_data = metadata_schema.get_json_schema(
version_numbers, schema_base_url)
key = get_relative_url(relative_path, version_numbers)
if key is None:
print("- could not find key for: " + path)
else:
created = _upload(key, branch_name, json_data, context,
dryrun)
if created:
created_list.append(key)
else:
print("- skipping: " + path)
except (GithubException, IOError) as e:
print('Error processing %s: %s', content.path, e)
return created_list
def test_json_schema__returns_dict_with_schema_urls_in_id_and_refs__when_version_from_path_is_found(
self):
# given
schema_path = 'type/project/project'
schema_json = load_json(f'{self.test_dir}/files/project.json')
# when
schema = MetadataSchema(schema_json, schema_path)
# then
expected = load_json(f'{self.test_dir}/files/project-schema.json')
self.assertEqual(
schema.get_json_schema(self.version_map, self.schema_base_url),
expected)
def test_update_refs_urls__raises_error__when_not_all_ref_versions_found(
self):
# given
schema_json = {
'$schema': 'http://json-schema.org/draft-04/schema#',
'properties': {
'provenance': {
'description':
'Provenance information provided by the system.',
'type': 'object',
'$ref': 'system/provenance.json'
},
}
}
version_map = {
'version_numbers': {
'type': {
'biomaterial': {
'donor': '1.2.3'
}
},
}
}
schema_path = 'type/biomaterial/donor'
# when / then
with self.assertRaises(MetadataSchemaError):
MetadataSchema(schema_json, schema_path).update_refs_urls(
version_map, self.schema_base_url)
def test_get_relative_url__returns_path__id_is_found(self):
# given
schema_json = {'$schema': 'http://json-schema.org/draft-07/schema#'}
version_map = {
'version_numbers': {
'type': {
'biomaterial': {
'donor': '1.2.3'
}
}
}
}
schema_path = 'type/biomaterial/donor'
# when
metadata_schema = MetadataSchema(schema_json, schema_path)
json_schema = metadata_schema.get_json_schema(version_map,
self.schema_base_url)
# then
self.assertEqual(get_relative_url(schema_path, version_map),
'type/biomaterial/1.2.3/donor')
def test_insert_id_url__inserts_old_id_key__when_draft_04(self):
# given
schema_json = {
'$schema': 'http://json-schema.org/draft-04/schema#',
}
version_map = {
'version_numbers': {
'type': {
'biomaterial': {
'donor': '1.2.3'
}
}
}
}
schema_path = 'type/biomaterial/donor'
# when
schema = MetadataSchema(schema_json, schema_path).insert_id_url(
version_map, self.schema_base_url)
# then
self.assertEqual(
schema.get('id'),
'https://schema.humancellatlas.org/type/biomaterial/1.2.3/donor')
def test_update_refs_urls__returns_json_with_updated_refs__when_all_ref_versions_found(
self):
# given
schema_json = {
'$schema': 'http://json-schema.org/draft-04/schema#',
'properties': {
'provenance': {
'description':
'Provenance information provided by the system.',
'type': 'object',
'$ref': 'system/provenance.json'
},
}
}
version_map = {
'version_numbers': {
'type': {
'biomaterial': {
'donor': '1.2.3'
}
},
'system': {
'provenance': '1.0.0'
}
}
}
schema_path = 'type/biomaterial/donor'
# when
schema = MetadataSchema(schema_json, schema_path).update_refs_urls(
version_map, self.schema_base_url)
# then
expected = {
'$schema': 'http://json-schema.org/draft-04/schema#',
'properties': {
'provenance': {
'description':
'Provenance information provided by the system.',
'type':
'object',
'$ref':
'https://schema.humancellatlas.org/system/1.0.0/provenance'
},
}
}
self.assertEqual(expected, schema)
def test_insert_id_url__raises_error__when_version_from_path_is_not_found(
self):
# given
schema_json = {
'$schema': 'http://json-schema.org/draft-07/schema#',
}
version_map = {
'version_numbers': {
'type': {
'biomaterial': {
'donor': '1.2.3'
}
}
}
}
schema_path = 'type/biomaterial/cell_suspension'
# when/then
with self.assertRaises(MetadataSchemaError):
MetadataSchema(schema_json, schema_path).get_json_schema(
version_map, self.schema_base_url)
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('path',
help="Base path to the HCA metadata schemas",
metavar="FILE")
parser.add_argument('schema_base_url',
help="Base url of the schema server")
args = parser.parse_args()
if "~" in args.path:
path = os.path.expanduser(args.path)
else:
path = args.path
version_map = load_json(path + "/versions.json")
schemas = get_schema_paths(path)
for schema in schemas:
raw_schema_json = load_json(schema)
metadata_schema = MetadataSchema(path, raw_schema_json)
new_json = metadata_schema.get_json_schema(version_map,
args.schema_base_url)
dump_json(schema, new_json)