def _base_qrels(self, subset): rnd, _ = subset.split('-', 1) path = os.path.join(util.path_dataset(self), f'{rnd}.qrels') if os.path.exists(path): return trec.read_qrels_dict(path) self.logger.info(f'missing qrels for {rnd} -- returning empty qrels') return {}
def init(self, force=False): base_path = util.path_dataset(self) idxs = [self.index, self.index_stem, self.doc_store] self._init_indices_parallel(idxs, self._init_iter_collection(), force) qrels_file = os.path.join(base_path, 'qrels.robust2004.txt') if (force or not os.path.exists(qrels_file)) and self._confirm_dua(): util.download(**_FILES['qrels'], file_name=qrels_file) for fold in FOLDS: fold_qrels_file = os.path.join(base_path, f'{fold}.qrels') if (force or not os.path.exists(fold_qrels_file)): all_qrels = trec.read_qrels_dict(qrels_file) fold_qrels = { qid: dids for qid, dids in all_qrels.items() if qid in FOLDS[fold] } trec.write_qrels_dict(fold_qrels_file, fold_qrels) query_file = os.path.join(base_path, 'topics.txt') if (force or not os.path.exists(query_file)) and self._confirm_dua(): query_file_stream = util.download_stream(**_FILES['queries'], encoding='utf8') with util.finialized_file(query_file, 'wt') as f: plaintext.write_tsv(f, trec.parse_query_format(query_file_stream))
def qrels_path(self, fold_qrels_file): if not fold_qrels_file.is_file(): with self.assessments.path.open("r") as fp: all_qrels = trec.read_qrels_dict(fp) fold_qrels = { qid: dids for qid, dids in all_qrels.items() if qid in self.qids } trec.write_qrels_dict(fold_qrels_file, fold_qrels) return fold_qrels_file
def calc_metrics(self, qrelsf, runf, metrics, verbose=False): rel_args = {} output_map = {} for metric in metrics: for exp in TE_METRICS: match = re.match(exp, str(metric)) if match: params = match.groupdict() rel, par, gain = params.get('rel'), params.get( 'par'), params.get('gain') rel_args.setdefault((rel, gain), {}) in_name, out_name = TE_METRICS[exp] if in_name not in rel_args[rel, gain]: rel_args[rel, gain][in_name] = in_name if par is not None: rel_args[rel, gain][in_name] += par elif par is not None: rel_args[rel, gain][in_name] += f',{par}' output_map[metric] = (rel, gain, out_name.format(**params)) break full_trec_eval_result = {} for rel_level, gains in rel_args: with ExitStack() as stack: if verbose: logger.debug( f'running trec_eval (rel_level={rel_level} gains={gains})' ) if gains: gain_map = [g.split('=') for g in gains.split(':')] gain_map = {int(k): int(v) for k, v in gain_map} tmpf = tempfile.NamedTemporaryFile() stack.enter_context(tmpf) qrels = trec.read_qrels_dict(qrelsf) for qid in qrels: for did in qrels[qid]: qrels[qid][did] = gain_map.get( qrels[qid][did], qrels[qid][did]) trec.write_run_dict(tmpf, qrels) qrelsf_run = tmpf.name else: qrelsf_run = qrelsf trec_eval_result = self._treceval( qrelsf_run, runf, rel_args[rel_level, gains].values(), rel_level) for k, v in trec_eval_result.items(): full_trec_eval_result[rel_level, gains, k] = v results = {} for onir_metric, te_metric in output_map.items(): results[str(onir_metric)] = full_trec_eval_result[te_metric] return results
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)])
def init(self, force=False): needs_docs = [] for index in [self.index_stem, self.index_stem_2020, self.doc_store]: if force or not index.built(): needs_docs.append(index) if needs_docs and self._confirm_dua(): with contextlib.ExitStack() as stack: doc_iter = self._init_iter_collection() doc_iter = self.logger.pbar(doc_iter, desc='articles') doc_iters = util.blocking_tee(doc_iter, len(needs_docs)) for idx, it in zip(needs_docs, doc_iters): if idx is self.index_stem_2020: it = (d for d in it if '2020' in d.data['date']) stack.enter_context( util.CtxtThread(functools.partial(idx.build, it))) path = os.path.join(util.path_dataset(self), 'rnd1.tsv') if not os.path.exists(path) and self._confirm_dua(): with util.download_tmp('https://ir.nist.gov/covidSubmit/data/topics-rnd1.xml', expected_md5="cf1b605222f45f7dbc90ca8e4d9b2c31") as f, \ util.finialized_file(path, 'wt') as fout: soup = BeautifulSoup(f.read(), 'lxml-xml') for topic in soup.find_all('topic'): qid = topic['number'] plaintext.write_tsv(fout, [ (qid, 'query', topic.find('query').get_text()), (qid, 'quest', topic.find('question').get_text()), (qid, 'narr', topic.find('narrative').get_text()), ]) udel_flag = path + '.includes_udel' if not os.path.exists(udel_flag): with open(path, 'at') as fout, util.finialized_file(udel_flag, 'wt'): with util.download_tmp( 'https://raw.githubusercontent.com/castorini/anserini/master/src/main/resources/topics-and-qrels/topics.covid-round1-udel.xml', expected_md5="2915cf59ae222f0aa20b2a671f67fd7a") as f: soup = BeautifulSoup(f.read(), 'lxml-xml') for topic in soup.find_all('topic'): qid = topic['number'] plaintext.write_tsv(fout, [ (qid, 'udel', topic.find('query').get_text()), ]) path = os.path.join(util.path_dataset(self), 'rnd2.tsv') if not os.path.exists(path) and self._confirm_dua(): with util.download_tmp('https://ir.nist.gov/covidSubmit/data/topics-rnd2.xml', expected_md5="550129e71c83de3fb4d6d29a172c5842") as f, \ util.finialized_file(path, 'wt') as fout: soup = BeautifulSoup(f.read(), 'lxml-xml') for topic in soup.find_all('topic'): qid = topic['number'] plaintext.write_tsv(fout, [ (qid, 'query', topic.find('query').get_text()), (qid, 'quest', topic.find('question').get_text()), (qid, 'narr', topic.find('narrative').get_text()), ]) udel_flag = path + '.includes_udel' if not os.path.exists(udel_flag): with open(path, 'at') as fout, util.finialized_file(udel_flag, 'wt'): with util.download_tmp( 'https://raw.githubusercontent.com/castorini/anserini/master/src/main/resources/topics-and-qrels/topics.covid-round2-udel.xml', expected_md5="a8988734e6f812921d5125249c197985") as f: soup = BeautifulSoup(f.read(), 'lxml-xml') for topic in soup.find_all('topic'): qid = topic['number'] plaintext.write_tsv(fout, [ (qid, 'udel', topic.find('query').get_text()), ]) path = os.path.join(util.path_dataset(self), 'rnd5.tsv') if not os.path.exists(path) and self._confirm_dua(): with util.download_tmp('https://ir.nist.gov/covidSubmit/data/topics-rnd5.xml', expected_md5="0307a37b6b9f1a5f233340a769d538ea") as f, \ util.finialized_file(path, 'wt') as fout: soup = BeautifulSoup(f.read(), 'lxml-xml') for topic in soup.find_all('topic'): qid = topic['number'] plaintext.write_tsv(fout, [ (qid, 'query', topic.find('query').get_text()), (qid, 'quest', topic.find('question').get_text()), (qid, 'narr', topic.find('narrative').get_text()), ]) udel_flag = path + '.includes_udel' if not os.path.exists(udel_flag): with open(path, 'at') as fout, util.finialized_file(udel_flag, 'wt'): with util.download_tmp( 'https://raw.githubusercontent.com/castorini/anserini/master/src/main/resources/topics-and-qrels/topics.covid-round5-udel.xml', expected_md5="966a49487348dc853634bcdd0829fd26") as f: soup = BeautifulSoup(f.read(), 'lxml-xml') for topic in soup.find_all('topic'): qid = topic['number'] plaintext.write_tsv(fout, [ (qid, 'udel', topic.find('query').get_text()), ]) qrels_file = os.path.join(util.path_dataset(self), 'rnd5.qrels') if (force or not os.path.exists(qrels_file)) and self._confirm_dua(): util.download( 'https://raw.githubusercontent.com/castorini/anserini/master/src/main/resources/topics-and-qrels/qrels.covid-round4-cumulative.txt', qrels_file) for fold in FOLDS: fold_qrels_file = os.path.join(util.path_dataset(self), f'{fold}-rnd5.qrels') if (force or not os.path.exists(fold_qrels_file)): all_qrels = trec.read_qrels_dict(qrels_file) fold_qrels = { qid: dids for qid, dids in all_qrels.items() if str(qid) in FOLDS[fold] } trec.write_qrels_dict(fold_qrels_file, fold_qrels)