def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
"""Upload compiled parts for the given prefix to AWS."""
if s3_client is None:
s3_client = boto3.client("s3")
logger.info("[%s] getting id->name mapping", prefix)
get_id_name_mapping(prefix)
id_name_path = prefix_cache_join(prefix, name="names.tsv", version=get_version(prefix))
if not id_name_path.exists():
raise FileNotFoundError
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, s3_client=s3_client)
logger.info("[%s] getting id->synonyms mapping", prefix)
get_id_synonyms_mapping(prefix)
id_synonyms_path = prefix_cache_join(prefix, name="synonyms.tsv", version=get_version(prefix))
if not id_synonyms_path.exists():
raise FileNotFoundError
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, s3_client=s3_client)
logger.info("[%s] getting xrefs", prefix)
get_xrefs_df(prefix)
xrefs_path = prefix_cache_join(prefix, name="xrefs.tsv", version=get_version(prefix))
if not xrefs_path.exists():
raise FileNotFoundError
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, s3_client=s3_client)
logger.info("[%s] getting relations", prefix)
get_relations_df(prefix)
relations_path = prefix_cache_join(prefix, name="relations.tsv", version=get_version(prefix))
if not relations_path.exists():
raise FileNotFoundError
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, s3_client=s3_client)
logger.info("[%s] getting properties", prefix)
get_properties_df(prefix)
properties_path = prefix_cache_join(prefix, name="properties.tsv", version=get_version(prefix))
if not properties_path.exists():
raise FileNotFoundError
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, s3_client=s3_client)
logger.info("[%s] getting alternative identifiers", prefix)
get_id_to_alts(prefix)
alts_path = prefix_cache_join(prefix, name="alt_ids.tsv", version=get_version(prefix))
if not alts_path.exists():
raise FileNotFoundError
alts_key = os.path.join(prefix, "cache", "alt_ids.tsv")
logger.info("[%s] uploading alternative identifiers", prefix)
upload_file(path=alts_path, bucket=bucket, key=alts_key)
def get_reactome_mapping() -> Mapping[str, str]:
"""Get IntAct to Reactome mapping.
Is basically equivalent to:
.. code-block:: python
from pyobo import get_filtered_xrefs
intact_complexportal_mapping = get_filtered_xrefs('intact', 'reactome')
"""
@cached_mapping(
path=prefix_cache_join('intact',
'xrefs',
name='reactome.tsv',
version=get_version('intact')),
header=['intact_id', 'reactome_id'],
)
def _cache():
df = _get_complexportal_df()
return dict(df.values)
return _cache()
def get_complexportal_mapping() -> Mapping[str, str]:
"""Get IntAct to Complex Portal mapping.
Is basically equivalent to:
.. code-block:: python
from pyobo import get_filtered_xrefs
intact_complexportal_mapping = get_filtered_xrefs('intact', 'complexportal')
"""
@cached_mapping(
path=prefix_cache_join(
"intact", "xrefs", name="complexportal.tsv", version=get_version("intact")
),
header=["intact_id", "complexportal_id"],
)
def _cache():
df = _get_complexportal_df()
return dict(df.values)
return _cache()