Source code for capreolus.benchmark.covid

import json
import os
from pathlib import Path

from bs4 import BeautifulSoup

from capreolus import ConfigOption, Dependency, constants
from capreolus.utils.common import download_file, get_udel_query_expander
from capreolus.utils.loginit import get_logger
from capreolus.utils.trec import load_qrels, topic_to_trectxt

from . import Benchmark

[docs]logger = get_logger(__name__)
[docs]PACKAGE_PATH = constants["PACKAGE_PATH"]
[docs]@Benchmark.register class COVID(Benchmark): """Ongoing TREC-COVID bechmark from https://ir.nist.gov/covidSubmit that uses documents from CORD, the COVID-19 Open Research Dataset (https://www.semanticscholar.org/cord19)."""
[docs] module_name = "covid"
[docs] dependencies = [Dependency(key="collection", module="collection", name="covid")]
[docs] data_dir = PACKAGE_PATH / "data" / "covid"
[docs] topic_url = "https://ir.nist.gov/covidSubmit/data/topics-rnd%d.xml"
[docs] qrel_url_v1 = "https://ir.nist.gov/covidSubmit/data/qrels-rnd%d.txt"
[docs] qrel_url_v2 = "https://ir.nist.gov/covidSubmit/data/qrels-covid_d%d_j0.5-%d.txt"
[docs] lastest_round = 5
[docs] query_type = "title"
[docs] config_spec = [ConfigOption("udelqexpand", False), ConfigOption("useprevqrels", True)]
[docs] def build(self): if self.collection.config["round"] == self.lastest_round and not self.config["useprevqrels"]: logger.warning(f"No evaluation can be done for the lastest round without using previous qrels") data_dir = self.get_cache_path() / "documents" data_dir.mkdir(exist_ok=True, parents=True) self.qrel_ignore = f"{data_dir}/ignore.qrel.txt" self.qrel_file = f"{data_dir}/qrel.txt" self.topic_file = f"{data_dir}/topic.txt" self.fold_file = f"{data_dir}/fold.json" self.download_if_missing()
[docs] def download_if_missing(self): if all([os.path.exists(fn) for fn in [self.qrel_file, self.qrel_ignore, self.topic_file, self.fold_file]]): return rnd_i, useprevqrels = self.collection.config["round"], self.config["useprevqrels"] if rnd_i > self.lastest_round: raise ValueError(f"round {rnd_i} is unavailable") logger.info(f"Preparing files for covid round-{rnd_i}") # topic file topic_url = self.topic_url % rnd_i tmp_dir = self.get_cache_path() / "tmp" topic_tmp = tmp_dir / f"topic.round.{rnd_i}.xml" if not os.path.exists(topic_tmp): tmp_dir.mkdir(exist_ok=True, parents=True) download_file(topic_url, topic_tmp) all_qids = self.xml2trectopic(topic_tmp) # will update self.topic_file labeled_qids = set() # put qrels from previous round into qrel_file if using previous judgement, else into qrel_ignore_file prev_qrel_urls = ( [self.qrel_url_v1 % i for i in range(1, rnd_i)] if rnd_i <= 3 else [self.qrel_url_v2 % (rnd_i - 1, rnd_i - 1)] ) # qrels before current run # if rnd_i < 4: # prev_qrel_urls = [self.qrel_url_v1 % i if rnd_i != 4 else self.qrel_url_v2 % (rnd_i-1, rnd_i-1) for i in range(1, rnd_i)] # elif rnd_i == 5: # prev_qrel_urls = [self.qrel_url_v2 % (4, 4), self.qrel_url_v1 % 5] qrel_fn = open(self.qrel_file, "w") if useprevqrels else open(self.qrel_ignore, "w") for qrel_url in prev_qrel_urls: qrel_tmp = tmp_dir / qrel_url.split("/")[-1] if not os.path.exists(qrel_tmp): download_file(qrel_url, qrel_tmp) with open(qrel_tmp) as f: for line in f: labeled_qids.add(line.strip().split()[0]) qrel_fn.write(line) qrel_fn.close() if useprevqrels: # for rounds without available qrels f = open(self.qrel_ignore, "w") # no qrels to remove after search f.close() # if not use previous qrels: use judgement in current round to evaluate elif rnd_i == self.lastest_round: logger.warn(f"No evaluation qrel is available for current round {rnd_i}") f = open(self.qrel_file, "w") f.close() elif rnd_i >= 3: # special case since document id changes a lot from rnd 2 -> 3, or rnd 3 -> 4 self.prep_backward_compatible_qrels(tmp_dir, self.qrel_ignore, self.qrel_file) # write results to self.qrel else: # not useprevqrels and rnd_i == 2, qrel_tmp = tmp_dir / f"qrel-{rnd_i}" if not os.path.exists(qrel_tmp): qrel_url = self.qrel_url_v1 % rnd_i if rnd_i != 4 else self.qrel_url_v2 % (4, 4) download_file(qrel_url, qrel_tmp) with open(qrel_tmp) as fin, open(self.qrel_file, "w") as fout: for line in fin: fout.write(line) folds = {"s1": {"train_qids": list(labeled_qids), "predict": {"dev": list(labeled_qids), "test": all_qids}}} json.dump(folds, open(self.fold_file, "w"))
[docs] def prep_backward_compatible_qrels(self, tmp_dir, prev_qrels_fn, tgt_qrel_fn): """ Prepare qrels file for round 3 adaptable to previous rounds: convert the new docids in qrels-covid_d3_j0.5-3.txt back to its old id remove judgement existed in round1 and round2 Warning: this function should not be used when search / training is done on collection released since round 4, where docids are already updated :param tmp_dir: pathlib.Path object, sthe directory to store downloaded files :param prev_qrels_fn: qrels file which store the qrels from previous rounds (round 1 and round 2) :param tgt_qrel_fn: qrels file path where to store the processed round 3 qrels file """ DOCID2URL = { "rnd-3": "https://ir.nist.gov/covidSubmit/data/changedIds-May19.csv", "rnd-4": "https://ir.nist.gov/covidSubmit/data/changedIds-Jun19.csv", } rnd_i = self.collection.config["round"] assert rnd_i in [3, 4, 5] # assert self.collection.config["round"] == 3 # donwload files qrel_url = f"https://ir.nist.gov/covidSubmit/data/qrels-covid_d{rnd_i}_j0.5-{rnd_i}.txt" docid_map_url = DOCID2URL[f"rnd-{rnd_i}"] qrel_tmp, docid_map_tmp = tmp_dir / f"qrel-{rnd_i}.before-convert", tmp_dir / f"round{rnd_i-1}-{rnd_i}.docid.map" if not qrel_tmp.exists(): download_file(qrel_url, qrel_tmp) if not docid_map_tmp.exists(): download_file(docid_map_url, docid_map_tmp) with open(docid_map_tmp) as f: # docids to revert in current qrels file new2old = {line.split(",")[1]: line.split(",")[0] for line in f} # each line: old_docid, new_docid, type with open(prev_qrels_fn) as f: # qrels to exclude from current qrels file prev_qrels = [line for line in f] with open(qrel_tmp) as fin, open(tgt_qrel_fn, "w") as fout: for line in fin: qid, tag, docid, label = line.strip().split() docid = new2old.get(docid, docid) line = f"{qid} {tag} {docid} {label}\n" # covid qrel files have two whitespace between tag and docid if line not in prev_qrels: fout.write(line)
[docs] def xml2trectopic(self, xmlfile): with open(xmlfile, "r") as f: topic = f.read() all_qids = [] soup = BeautifulSoup(topic, "lxml") topics = soup.find_all("topic") expand_query = get_udel_query_expander() with open(self.topic_file, "w") as fout: for topic in topics: qid = topic["number"] title = topic.find_all("query")[0].text.strip() desc = topic.find_all("question")[0].text.strip() narr = topic.find_all("narrative")[0].text.strip() if self.config["udelqexpand"]: title = expand_query(title, rm_sw=True) desc = expand_query(desc, rm_sw=False) title = title + " " + desc desc = " " topic_line = topic_to_trectxt(qid, title, desc=desc, narr=narr) fout.write(topic_line) all_qids.append(qid) return all_qids
[docs]@Benchmark.register class CovidQA(Benchmark):
[docs] module_name = "covidqa"
[docs] dependencies = [Dependency(key="collection", module="collection", name="covid")]
[docs] url = "https://raw.githubusercontent.com/castorini/pygaggle/master/data/kaggle-lit-review-%s.json"
[docs] available_versions = ["0.1", "0.2"]
[docs] datadir = PACKAGE_PATH / "data" / "covidqa"
[docs] config_spec = [ConfigOption("version", "0.1+0.2")]
[docs] def build(self): os.makedirs(self.datadir, exist_ok=True) version = self.config["version"] self.qrel_file = self.datadir / f"qrels.v{version}.txt" self.topic_file = self.datadir / f"topics.v{version}.txt" self.fold_file = self.datadir / f"v{version}.json" # HOW TO SPLIT THE FOLD HERE? self.download_if_missing()
[docs] def download_if_missing(self): if all([os.path.exists(f) for f in [self.qrel_file, self.topic_file, self.fold_file]]): return tmp_dir = self.get_cache_path() / "tmp" os.makedirs(tmp_dir, exist_ok=True) topic_f = open(self.topic_file, "w", encoding="utf-8") qrel_f = open(self.qrel_file, "w", encoding="utf-8") all_qids = [] qid = 2001 # to distingsuish queries here from queries in TREC-covid versions = self.config["version"].split("+") if isinstance(self.config["version"], str) else str(self.config["version"]) for v in versions: if v not in self.available_versions: vs = " ".join(self.available_versions) logger.warning(f"Invalid version {v}, should be one of {vs}") continue url = self.url % v target_fn = tmp_dir / f"covidqa-v{v}.json" if not os.path.exists(target_fn): download_file(url, target_fn) qa = json.load(open(target_fn)) for subcate in qa["categories"]: name = subcate["name"] for qa in subcate["sub_categories"]: nq_name, kq_name = qa["nq_name"], qa["kq_name"] query_line = topic_to_trectxt(qid, kq_name, nq_name) # kq_name == "query", nq_name == "question" topic_f.write(query_line) for ans in qa["answers"]: docid = ans["id"] qrel_f.write(f"{qid} Q0 {docid} 1\n") all_qids.append(qid) qid += 1 json.dump({"s1": {"train_qids": all_qids, "predict": {"dev": all_qids, "test": all_qids}}}, open(self.fold_file, "w")) topic_f.close() qrel_f.close()