def id_url(ag):
# Return identifier URLs in a prioritized order
# TODO: we should add handling for UPPRO here, however, that would require
# access to UniProt client resources in the context of the DB REST API
# which could be problematic
for db_name in link_namespace_order:
if db_name in ag.db_refs:
# Handle a special case where a list of IDs is given
if isinstance(ag.db_refs[db_name], list):
db_id = ag.db_refs[db_name][0]
if db_name == 'WM':
db_id = db_id[0]
else:
db_id = ag.db_refs[db_name]
# We can add more name spaces here if there are issues
if db_name in {'CHEBI'}:
db_id = ensure_prefix('CHEBI', db_id)
# Here we validate IDs to make sure we don't surface invalid
# links.
if not validate_id(db_name, db_id):
logger.debug('Invalid grounding encountered: %s:%s' %
(db_name, db_id))
continue
# Finally, we return a valid identifiers.org URL
return get_identifiers_url(db_name, db_id)
def extract_context(annotations, annot_manager):
"""Return a BioContext object extracted from the annotations.
The entries that are extracted into the BioContext are popped from the
annotations.
Parameters
----------
annotations : dict
PyBEL annotations dict
annot_manager : AnnotationManager
An annotation manager to get name/db reference mappings for each ot the
annotation types.
Returns
-------
bc : BioContext
An INDRA BioContext object
"""
def get_annot(annotations, key):
"""Return a specific annotation given a key."""
val = annotations.pop(key, None)
if val:
val_list = [v for v, tf in val.items() if tf]
if len(val_list) > 1:
logger.warning('More than one "%s" in annotations' % key)
elif not val_list:
return None
return val_list[0]
return None
bc = BioContext()
species = get_annot(annotations, 'Species')
if species:
name = annot_manager.get_mapping('Species', species)
bc.species = RefContext(name=name, db_refs={'TAXONOMY': species})
mappings = (('CellLine', 'cell_line', None), ('Disease', 'disease', None),
('Anatomy', 'organ', None), ('Cell', 'cell_type', None),
('CellStructure', 'location', 'MESH'))
for bel_name, indra_name, ns in mappings:
ann = get_annot(annotations, bel_name)
if ann:
ref = annot_manager.get_mapping(bel_name, ann)
if ref is None:
continue
if not ns:
db_ns, db_id = ref.split('_', 1)
else:
db_ns, db_id = ns, ref
if db_ns == 'CLO':
db_ns = 'CL'
if db_ns in {'CL', 'UBERON', 'DOID'}:
db_id = identifiers.ensure_prefix(db_ns, db_id)
setattr(bc, indra_name, RefContext(name=ann,
db_refs={db_ns: db_id}))
# Overwrite blank BioContext
if not bc:
bc = None
return bc
def get_ref_context(db_ns, db_id):
db_id = db_id.strip()
if db_ns in {'BTO'}:
db_id = ensure_prefix(db_ns, db_id)
standard_name, db_refs = standardize_name_db_refs({db_ns: db_id})
return RefContext(standard_name, db_refs)
