def _init_qrels(self, subset, qrels_files, force=False, expected_md5=None):
qrelsf = os.path.join(util.path_dataset(self), f'{subset}.qrels')
if (force or not os.path.exists(qrelsf)) and self._confirm_dua():
qrels = itertools.chain(*(trec.read_qrels(
util.download_stream(f, 'utf8', expected_md5=expected_md5))
for f in qrels_files))
trec.write_qrels(qrelsf, qrels)
def init(self, force=False):
idxs = [self.index_stem, self.doc_store]
self._init_indices_parallel(idxs, self._init_iter_collection(), force)
base_path = util.path_dataset(self)
needs_queries = []
if force or not os.path.exists(
os.path.join(base_path, 'train.queries.tsv')):
needs_queries.append(lambda it: plaintext.write_tsv(
os.path.join(base_path, 'train.queries.tsv'),
((qid, txt) for file, qid, txt in it
if file == 'queries.train.tsv' and qid not in MINI_DEV)))
if force or not os.path.exists(
os.path.join(base_path, 'minidev.queries.tsv')):
needs_queries.append(lambda it: plaintext.write_tsv(
os.path.join(base_path, 'minidev.queries.tsv'),
((qid, txt) for file, qid, txt in it
if file == 'queries.train.tsv' and qid in MINI_DEV)))
if force or not os.path.exists(
os.path.join(base_path, 'dev.queries.tsv')):
needs_queries.append(lambda it: plaintext.write_tsv(
os.path.join(base_path, 'dev.queries.tsv'),
((qid, txt) for file, qid, txt in it
if file == 'queries.dev.tsv')))
if force or not os.path.exists(
os.path.join(base_path, 'eval.queries.tsv')):
needs_queries.append(lambda it: plaintext.write_tsv(
os.path.join(base_path, 'eval.queries.tsv'),
((qid, txt) for file, qid, txt in it
if file == 'queries.eval.tsv')))
if needs_queries and self._confirm_dua():
with util.download_tmp(_SOURCES['queries']) as f, \
tarfile.open(fileobj=f) as tarf, \
contextlib.ExitStack() as ctxt:
def _extr_subf(subf):
for qid, txt in plaintext.read_tsv(
io.TextIOWrapper(tarf.extractfile(subf))):
yield subf, qid, txt
query_iter = [
_extr_subf('queries.train.tsv'),
_extr_subf('queries.dev.tsv'),
_extr_subf('queries.eval.tsv')
]
query_iter = tqdm(itertools.chain(*query_iter), desc='queries')
query_iters = util.blocking_tee(query_iter, len(needs_queries))
for fn, it in zip(needs_queries, query_iters):
ctxt.enter_context(
util.CtxtThread(functools.partial(fn, it)))
file = os.path.join(base_path, 'train.qrels')
if (force or not os.path.exists(file)) and self._confirm_dua():
stream = util.download_stream(_SOURCES['train-qrels'], 'utf8')
with util.finialized_file(file, 'wt') as out:
for qid, _, did, score in plaintext.read_tsv(stream):
if qid not in MINI_DEV:
trec.write_qrels(out, [(qid, did, score)])
file = os.path.join(base_path, 'minidev.qrels')
if (force or not os.path.exists(file)) and self._confirm_dua():
stream = util.download_stream(_SOURCES['train-qrels'], 'utf8')
with util.finialized_file(file, 'wt') as out:
for qid, _, did, score in plaintext.read_tsv(stream):
if qid in MINI_DEV:
trec.write_qrels(out, [(qid, did, score)])
file = os.path.join(base_path, 'dev.qrels')
if (force or not os.path.exists(file)) and self._confirm_dua():
stream = util.download_stream(_SOURCES['dev-qrels'], 'utf8')
with util.finialized_file(file, 'wt') as out:
for qid, _, did, score in plaintext.read_tsv(stream):
trec.write_qrels(out, [(qid, did, score)])
file = os.path.join(base_path, 'train.mspairs.gz')
if not os.path.exists(file) and os.path.exists(
os.path.join(base_path, 'qidpidtriples.train.full')):
# legacy
os.rename(os.path.join(base_path, 'qidpidtriples.train.full'),
file)
if (force or not os.path.exists(file)) and self._confirm_dua():
util.download(_SOURCES['qidpidtriples.train.full'], file)
if not self.config['init_skip_msrun']:
for file_name, subf in [('dev.msrun', 'top1000.dev'),
('eval.msrun', 'top1000.eval'),
('train.msrun', 'top1000.train.txt')]:
file = os.path.join(base_path, file_name)
if (force or not os.path.exists(file)) and self._confirm_dua():
run = {}
with util.download_tmp(_SOURCES[file_name]) as f, \
tarfile.open(fileobj=f) as tarf:
for qid, did, _, _ in tqdm(
plaintext.read_tsv(
io.TextIOWrapper(tarf.extractfile(subf)))):
if qid not in run:
run[qid] = {}
run[qid][did] = 0.
if file_name == 'train.msrun':
minidev = {
qid: dids
for qid, dids in run.items() if qid in MINI_DEV
}
with self.logger.duration('writing minidev.msrun'):
trec.write_run_dict(
os.path.join(base_path, 'minidev.msrun'),
minidev)
run = {
qid: dids
for qid, dids in run.items() if qid not in MINI_DEV
}
with self.logger.duration(f'writing {file_name}'):
trec.write_run_dict(file, run)
query_path = os.path.join(base_path, 'trec2019.queries.tsv')
if (force or not os.path.exists(query_path)) and self._confirm_dua():
stream = util.download_stream(_SOURCES['trec2019.queries'], 'utf8')
plaintext.write_tsv(query_path, plaintext.read_tsv(stream))
msrun_path = os.path.join(base_path, 'trec2019.msrun')
if (force or not os.path.exists(msrun_path)) and self._confirm_dua():
run = {}
with util.download_stream(_SOURCES['trec2019.msrun'],
'utf8') as stream:
for qid, did, _, _ in plaintext.read_tsv(stream):
if qid not in run:
run[qid] = {}
run[qid][did] = 0.
with util.finialized_file(msrun_path, 'wt') as f:
trec.write_run_dict(f, run)
qrels_path = os.path.join(base_path, 'trec2019.qrels')
if not os.path.exists(qrels_path) and self._confirm_dua():
util.download(_SOURCES['trec2019.qrels'], qrels_path)
qrels_path = os.path.join(base_path, 'judgedtrec2019.qrels')
if not os.path.exists(qrels_path):
os.symlink('trec2019.qrels', qrels_path)
query_path = os.path.join(base_path, 'judgedtrec2019.queries.tsv')
judged_qids = util.Lazy(
lambda: trec.read_qrels_dict(qrels_path).keys())
if (force or not os.path.exists(query_path)):
with util.finialized_file(query_path, 'wt') as f:
for qid, qtext in plaintext.read_tsv(
os.path.join(base_path, 'trec2019.queries.tsv')):
if qid in judged_qids():
plaintext.write_tsv(f, [(qid, qtext)])
msrun_path = os.path.join(base_path, 'judgedtrec2019.msrun')
if (force or not os.path.exists(msrun_path)) and self._confirm_dua():
with util.finialized_file(msrun_path, 'wt') as f:
for qid, dids in trec.read_run_dict(
os.path.join(base_path, 'trec2019.msrun')).items():
if qid in judged_qids():
trec.write_run_dict(f, {qid: dids})
# A subset of dev that only contains queries that have relevance judgments
judgeddev_path = os.path.join(base_path, 'judgeddev')
judged_qids = util.Lazy(lambda: trec.read_qrels_dict(
os.path.join(base_path, 'dev.qrels')).keys())
if not os.path.exists(f'{judgeddev_path}.qrels'):
os.symlink('dev.qrels', f'{judgeddev_path}.qrels')
if not os.path.exists(f'{judgeddev_path}.queries.tsv'):
with util.finialized_file(f'{judgeddev_path}.queries.tsv',
'wt') as f:
for qid, qtext in plaintext.read_tsv(
os.path.join(base_path, 'dev.queries.tsv')):
if qid in judged_qids():
plaintext.write_tsv(f, [(qid, qtext)])
if self.config['init_skip_msrun']:
if not os.path.exists(f'{judgeddev_path}.msrun'):
with util.finialized_file(f'{judgeddev_path}.msrun',
'wt') as f:
for qid, dids in trec.read_run_dict(
os.path.join(base_path, 'dev.msrun')).items():
if qid in judged_qids():
trec.write_run_dict(f, {qid: dids})
if not self.config['init_skip_train10']:
file = os.path.join(base_path, 'train10.queries.tsv')
if not os.path.exists(file):
with util.finialized_file(file, 'wt') as fout:
for qid, qtext in self.logger.pbar(
plaintext.read_tsv(
os.path.join(base_path, 'train.queries.tsv')),
desc='filtering queries for train10'):
if int(qid) % 10 == 0:
plaintext.write_tsv(fout, [(qid, qtext)])
file = os.path.join(base_path, 'train10.qrels')
if not os.path.exists(file):
with util.finialized_file(file, 'wt') as fout, open(
os.path.join(base_path, 'train.qrels'), 'rt') as fin:
for line in self.logger.pbar(
fin, desc='filtering qrels for train10'):
qid = line.split()[0]
if int(qid) % 10 == 0:
fout.write(line)
if not self.config['init_skip_msrun']:
file = os.path.join(base_path, 'train10.msrun')
if not os.path.exists(file):
with util.finialized_file(file, 'wt') as fout, open(
os.path.join(base_path, 'train.msrun'),
'rt') as fin:
for line in self.logger.pbar(
fin, desc='filtering msrun for train10'):
qid = line.split()[0]
if int(qid) % 10 == 0:
fout.write(line)
file = os.path.join(base_path, 'train10.mspairs.gz')
if not os.path.exists(file):
with gzip.open(file, 'wt') as fout, gzip.open(
os.path.join(base_path, 'train.mspairs.gz'),
'rt') as fin:
for qid, did1, did2 in self.logger.pbar(
plaintext.read_tsv(fin),
desc='filtering mspairs for train10'):
if int(qid) % 10 == 0:
plaintext.write_tsv(fout, [(qid, did1, did2)])
if not self.config['init_skip_train_med']:
med_qids = util.Lazy(
lambda: {
qid.strip()
for qid in util.download_stream(
'https://raw.githubusercontent.com/Georgetown-IR-Lab/covid-neural-ir/master/med-msmarco-train.txt',
'utf8',
expected_md5="dc5199de7d4a872c361f89f08b1163ef")
})
file = os.path.join(base_path, 'train_med.queries.tsv')
if not os.path.exists(file):
with util.finialized_file(file, 'wt') as fout:
for qid, qtext in self.logger.pbar(
plaintext.read_tsv(
os.path.join(base_path, 'train.queries.tsv')),
desc='filtering queries for train_med'):
if qid in med_qids():
plaintext.write_tsv(fout, [(qid, qtext)])
file = os.path.join(base_path, 'train_med.qrels')
if not os.path.exists(file):
with util.finialized_file(file, 'wt') as fout, open(
os.path.join(base_path, 'train.qrels'), 'rt') as fin:
for line in self.logger.pbar(
fin, desc='filtering qrels for train_med'):
qid = line.split()[0]
if qid in med_qids():
fout.write(line)
if not self.config['init_skip_msrun']:
file = os.path.join(base_path, 'train_med.msrun')
if not os.path.exists(file):
with util.finialized_file(file, 'wt') as fout, open(
os.path.join(base_path, 'train.msrun'),
'rt') as fin:
for line in self.logger.pbar(
fin, desc='filtering msrun for train_med'):
qid = line.split()[0]
if qid in med_qids():
fout.write(line)
file = os.path.join(base_path, 'train_med.mspairs.gz')
if not os.path.exists(file):
with gzip.open(file, 'wt') as fout, gzip.open(
os.path.join(base_path, 'train.mspairs.gz'),
'rt') as fin:
for qid, did1, did2 in self.logger.pbar(
plaintext.read_tsv(fin),
desc='filtering mspairs for train_med'):
if qid in med_qids():
plaintext.write_tsv(fout, [(qid, did1, did2)])