def get_reader_output(db,
ref_id,
ref_type='tcid',
reader=None,
reader_version=None):
"""Return reader output for a given text content.
Parameters
----------
db : :py:class:`DatabaseManager`
Reference to the DB to query
ref_id : int or str
The text reference ID whose reader output should be returned
ref_type : Optional[str]
The type of ID to look for, options include
'tcid' for the database's internal unique text content ID,
or 'pmid', 'pmcid', 'doi, 'pii', 'manuscript_id'
Default: 'tcid'
reader : Optional[str]
The name of the reader whose output is of interest
reader_version : Optional[str]
The specific version of the reader
Returns
-------
reading_results : dict{dict{list[str]}}
A dict of reader outputs that match the query criteria, indexed first
by text content id, then by reader.
"""
if ref_type == 'tcid':
clauses = [db.Reading.text_content_id == ref_id]
else:
trids = _get_trids(db, ref_id, ref_type)
if not trids:
return []
logger.debug("Found %d text ref ids." % len(trids))
clauses = [
db.TextContent.text_ref_id.in_(trids),
db.Reading.text_content_id == db.TextContent.id
]
if reader:
clauses.append(db.Reading.reader == reader.upper())
if reader_version:
clauses.append(db.Reading.reader_version == reader_version)
res = db.select_all(
[db.Reading.text_content_id, db.Reading.reader, db.Reading.bytes],
*clauses)
reading_dict = defaultdict(lambda: defaultdict(lambda: []))
for tcid, reader, result in res:
unpacked_result = None
if len(result) == 0:
logger.warning("Got reading result with zero content.")
else:
unpacked_result = unpack(result)
reading_dict[tcid][reader].append(unpacked_result)
return reading_dict
def add_paper_ids(self, initial_ids, id_type='pmid'):
"""Convert if needed and save paper IDs.
Parameters
----------
initial_ids : set(str)
A set of paper IDs.
id_type : str
What type the given IDs are (e.g. pmid, doi, pii). All IDs except
for PIIs will be converted into TextRef IDs before saving.
"""
logger.info(f'Adding new paper IDs from {len(initial_ids)} {id_type}s')
if id_type in {'pii', 'TRID'}:
self.paper_ids.update(set(initial_ids))
else:
db = get_db('primary')
for paper_id in initial_ids:
trids = _get_trids(db, paper_id, id_type)
# Some papers might be not in the database yet
if trids:
self.paper_ids.add(trids[0])