def _handle_identifier_not_name(*, concept, prefix, identifier) -> bool:
# Some namespaces are just too much of a problem at the moment to look up
if prefix in SKIP:
return False
if prefix in NO_NAMES:
concept[NAME] = concept[IDENTIFIER]
return True
if prefix == 'uniprot':
concept[NAME] = get_mnemonic(identifier)
return True
try:
id_name_mapping = get_id_name_mapping(prefix)
except (NoOboFoundry, MissingOboBuild):
return False
if id_name_mapping is None:
logger.warning('could not get names for prefix %s', prefix)
return False
name = id_name_mapping.get(identifier)
if name is None:
logger.warning('could not get name for %s:%s', prefix, identifier)
return False
concept[NAME] = name
return True
def upload_artifacts_for_prefix(*, prefix: str, bucket: str):
"""Upload compiled parts for the given prefix to AWS."""
logger.info('[%s] getting id->name mapping', prefix)
get_id_name_mapping(prefix)
id_name_path = prefix_directory_join(prefix, 'cache', 'names.tsv')
id_name_key = os.path.join(prefix, 'cache', 'names.tsv')
logger.info('[%s] uploading id->name mapping', prefix)
upload_file(path=id_name_path, bucket=bucket, key=id_name_key)
logger.info('[%s] getting id->synonyms mapping', prefix)
get_id_synonyms_mapping(prefix)
id_synonyms_path = prefix_directory_join(prefix, 'cache', 'synonyms.tsv')
id_synonyms_key = os.path.join(prefix, 'cache', 'synonyms.tsv')
logger.info('[%s] uploading id->synonyms mapping', prefix)
upload_file(path=id_synonyms_path, bucket=bucket, key=id_synonyms_key)
logger.info('[%s] getting xrefs', prefix)
get_xrefs_df(prefix)
xrefs_path = prefix_directory_join(prefix, 'cache', 'xrefs.tsv')
xrefs_key = os.path.join(prefix, 'cache', 'xrefs.tsv')
logger.info('[%s] uploading xrefs', prefix)
upload_file(path=xrefs_path, bucket=bucket, key=xrefs_key)
logger.info('[%s] getting relations', prefix)
get_relations_df(prefix)
relations_path = prefix_directory_join(prefix, 'cache', 'relations.tsv')
relations_key = os.path.join(prefix, 'cache', 'relations.tsv')
logger.info('[%s] uploading relations', prefix)
upload_file(path=relations_path, bucket=bucket, key=relations_key)
logger.info('[%s] getting properties', prefix)
get_properties_df(prefix)
properties_path = prefix_directory_join(prefix, 'cache', 'properties.tsv')
properties_key = os.path.join(prefix, 'cache', 'properties.tsv')
logger.info('[%s] uploading properties', prefix)
upload_file(path=properties_path, bucket=bucket, key=properties_key)