def fetch_details(options):
"""
Fetch details call for a BrAPI object (ex: /brapi/v1/studies/{id})
"""
source, logger, entity, object_id = options
if 'detail' not in entity:
return
detail_call_group = entity['detail']
in_store = object_id in entity['store']
skip_if_in_store = detail_call_group.get('skip-if-in-store')
already_detailed = get_in(entity['store'], [object_id, 'etl:detailed'])
if in_store and (skip_if_in_store or already_detailed):
return
entity_name = entity['name']
entity_id = entity_name + 'DbId'
detail_call = get_implemented_call(source, detail_call_group, {entity_id: object_id})
if not detail_call:
return
details = BreedingAPIIterator.fetch_all(source['brapi:endpointUrl'], detail_call, logger).__next__()
details['etl:detailed'] = True
return entity_name, [details]
def fetch_all_links(source, logger, entities):
"""
Link objects across entities.
- Internal: link an object (ex: study) to another using an identifier inside the JSON object
(ex: link a location via study.locationDbId)
- Internal object: link an object (ex: study) to another contained inside the first
(ex: link a location via study.location.locationDbId)
- External object: link an object (ex: study) to another using a dedicated call
(ex: link to observation variables via /brapi/v1/studies/{id}/observationVariables)
"""
for (entity_name, entity) in entities.items():
if 'links' not in entity:
continue
for link in entity['links']:
for (object_id, object) in entity['store'].items():
linked_entity_name = link['entity']
linked_entity = entities[linked_entity_name]
linked_objects_by_id = {}
if link['type'].startswith('internal'):
link_path = link['json-path']
link_path_list = remove_empty(link_path.split('.'))
link_values = remove_none(as_list(get_in(object, link_path_list)))
if not link_values:
if link.get('required'):
raise BrokenLink("Could not find required field '{}' in {} object id '{}'"
.format(link_path, entity_name, object_id))
continue
if link['type'] == 'internal-object':
for link_value in link_values:
link_id = get_identifier(linked_entity_name, link_value)
linked_objects_by_id[link_id] = link_value
elif link['type'] == 'internal':
link_id_field = linked_entity['name'] + 'DbId'
link_name_field = linked_entity['name'] + 'Name'
for link_value in link_values:
link_id = link_value.get(link_id_field)
link_name = link_value.get(link_name_field)
if link_id:
linked_objects_by_id[link_id] = {link_id_field: link_id, link_name_field: link_name}
elif link['type'] == 'external-object':
call = get_implemented_call(source, link, context=object)
if not call:
continue
link_values = list(BreedingAPIIterator.fetch_all(source['brapi:endpointUrl'], call, logger))
for link_value in link_values:
link_id = get_identifier(linked_entity_name, link_value)
linked_objects_by_id[link_id] = link_value
link_objects(entity, object, linked_entity, linked_objects_by_id)
def list_object(options):
"""
Fetch list for one entity (studies-search, germplasm-search, etc.)
"""
source, logger, entity = options
if 'list' not in entity:
return
call = get_implemented_call(source, entity['list'])
if call is None:
return
data_list = list(BreedingAPIIterator.fetch_all(source['brapi:endpointUrl'], call, logger))
return entity['name'], data_list
def fetch_details(options):
"""
Fetch details call for a BrAPI object (ex: /brapi/v1/studies/{id})
"""
source, logger, entity, object_id = options
if 'detail' not in entity:
return
detail_call_group = entity['detail']
in_store = object_id in entity['store']
skip_if_in_store = detail_call_group.get('skip-if-in-store')
already_detailed = get_in(entity['store'], [object_id, 'etl:detailed'])
if in_store and (skip_if_in_store or already_detailed):
return
entity_name = entity['name']
entity_id = entity_name + 'DbId'
detail_call = get_implemented_call(source, detail_call_group,
{entity_id: object_id})
if not detail_call:
return
details = BreedingAPIIterator.fetch_all(source['brapi:endpointUrl'],
detail_call, logger).__next__()
details['etl:detailed'] = True
# -----------------------------------------------------------------
# Detect bugy endpoints that returns several studies instead of one.
if "expect-single-result" in detail_call_group and detail_call_group[
"expect-single-result"] and 'data' in details and len(
details['data']) != 1:
logger.debug(f"More than one results for {detail_call}")
raise EndPointError(f"More than one results for {detail_call}")
if 'data' in details and len(details['data']) == 1:
details = details['data'][0]
# -----------------------------------------------------------------
return entity_name, [details]