import os import sys from pathlib import Path import datetime import tarfile import xml.etree.ElementTree as ET from tqdm import tqdm import re from itertools import chain, islice import requests import time import shutil import arxiv import langdetect from langdetect import detect from utils import Loader as Loader from utils import make_archive def batch_loader(seq, size): """ Iterator that takes in a list `seq` and returns chunks of size `size` """ return [seq[pos:pos + size] for pos in range(0, len(seq), size)] def _delete_files_except_pattern(path, pattern, transform = lambda x: None, verbose=False): """ recursively """ for f in os.listdir(path): f_path = os.path.join(path, f) if verbose: print(f_path) if os.path.isfile(f_path): if not re.search(pattern, f): os.chmod(f_path, 0o755) os.remove(f_path) else: transform(f_path) elif os.path.isdir(f_path): try: print(f_path) except UnicodeEncodeError: new_path = f_path.encode("utf-8", 'replace').decode() os.system(f"mv \"{f_path}\" \"{new_path}\"") f_path = new_path _delete_files_except_pattern(f_path, pattern, transform=transform, verbose=verbose) def _download_with_progress_bar(url): response = requests.get(url, stream=True) total_size_in_bytes = int(response.headers.get("content-length", 0)) block_size = 1024 # 1 Kibibyte progress_bar = tqdm(total=total_size_in_bytes, unit="iB", unit_scale=True) to_return = bytearray() for data in response.iter_content(block_size): progress_bar.update(len(data)) to_return += data progress_bar.close() if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: raise AssertionError("ERROR, something went wrong") return to_return def get_math_ids(resumption_token="init"): with Loader(f"fetching metadata shard {resumption_token}..."): if resumption_token=="init": resp = requests.get("https://export.arxiv.org/oai2?verb=ListIdentifiers&set=math&metadataPrefix=oai_dc") else: time.sleep(5) resp = requests.get(f"https://export.arxiv.org/oai2?verb=ListIdentifiers&resumptionToken={resumption_token}") root = ET.fromstring(resp.content.decode("utf-8")) articles = root[2] math_ids = {} for article in articles: if article.tag == "{http://www.openarchives.org/OAI/2.0/}resumptionToken": if article.text: return math_ids | get_math_ids(resumption_token=article.text) else: return math_ids db_id = article[0].text eyed = db_id[db_id.rindex(":")+1:] math_ids[eyed] = True def clean_tex_file(path): with open(path, encoding="utf-8") as f: try: src = f.read() except (UnicodeDecodeError, UnicodeError): print(f"Decoding error at {path} with utf-8. Trying latin-1") try: with open(path, encoding="latin-1") as fle: src = fle.read() #print("latin-1 successful\n") except (UnicodeDecodeError, UnicodeError): #print(f"Decoding error at {path} with latin-1. Trying utf-16") try: with open(path, encoding="utf-16") as fl: src = fl.read() #print("utf-16 successful\n") except (UnicodeDecodeError, UnicodeError): #print(f"Decoding error at {path} with utf-16. Trying utf-32") try: with open(path, encoding="utf-32") as f: src = f.read() except (UnicodeDecodeError, UnicodeError): print(f"Decoding error at {path} with all of utf-8, 16, 32 and latin-1. Deleting this file") print("This issue should only occur with a handful of quite old files. Continuing...\n") return end = re.search(r"\\end\{document\}", src) if end: src = src[:end.span()[1]] bib = re.search(r"\\Refs|\\begin\{thebibliography\}", src) if bib: src = src[:bib.span()[0]] os.chmod(path, 0o755) with open(path, "w", encoding="utf-8") as f: f.write(src) def clean_tex_file_some_more(path): with open(path) as f: text = f.read() text = re.sub(r"(?280: try: print(path) except UnicodeEncodeError: path = path.encode('utf-8', 'replace').decode() try: lang = detect(text) except langdetect.lang_detect_exception.LangDetectException: # no linguistic features to analyze, delete return if lang=="en": with open(path, "w") as f: f.write(text) else: print("HIT NONENGLISH ARTICLE") def process_tarball_old_scheme(tarball_name, save_dir): tarball_path = os.path.join(save_dir, tarball_name) os.system("tar -xf " + tarball_path + " -C " + save_dir) last_ = tarball_name.rfind("_") second_last_ = tarball_name.rfind("_", 0, last_) subdir = tarball_name[second_last_+1:last_] subpath = os.path.join(save_dir, subdir) zipped_names = os.listdir(subpath) for zipped_name in zipped_names: if zipped_name[-len(".gz"):]==".gz": zipped_path = os.path.join(subpath, zipped_name) if re.match(r"math", zipped_name): eyed = zipped_name[:-len(".gz")] if tarfile.is_tarfile(zipped_path): article_dir = os.path.join(subpath, eyed) Path(article_dir).mkdir() os.system("tar -xzf " + zipped_path + " -C " + article_dir) os.remove(zipped_path) else: os.system("gzip -d " + zipped_path) unzipped_path = os.path.join(subpath, eyed) os.rename(unzipped_path, unzipped_path + ".tex") else: os.remove(zipped_path) _delete_files_except_pattern(subpath, r".*\.tex", transform=clean_tex_file) os.remove(tarball_path) def process_tarball(tarball_name, save_dir, math_ids): tarball_path = os.path.join(save_dir, tarball_name) untar_cmd = "tar -xf " + tarball_path + " -C " + save_dir os.system(untar_cmd) last_ = tarball_name.rfind("_") second_last_ = tarball_name.rfind("_", 0, last_) subdir = tarball_name[second_last_+1:last_] subpath = os.path.join(save_dir, subdir) listdir = os.listdir(subpath) ids = [x[:-3] for x in listdir if x[-3:]==".gz"] for eyed in ids: if eyed in math_ids: zipped_path = os.path.join(subpath, eyed + ".gz") if tarfile.is_tarfile(zipped_path): article_dir = os.path.join(subpath, eyed) Path(article_dir).mkdir() os.system("tar -xzf " + zipped_path + " -C " + article_dir) os.remove(zipped_path) else: os.system("gzip -d " + zipped_path) unzipped_path = os.path.join(subpath, eyed) os.rename(unzipped_path, unzipped_path + ".tex") _delete_files_except_pattern(subpath, r".*\.tex", transform=clean_tex_file) os.remove(tarball_path) def main(): """ Warning: this code is *extremely* brittle """ math_ids = get_math_ids() save_dir = "arxiv" Path(save_dir).mkdir(exist_ok=True) manifest_path = os.path.join(save_dir, "manifest.xml") os.system(f"s3cmd get s3://arxiv/src/arXiv_src_manifest.xml --requester-pays {manifest_path}") tree = ET.parse(manifest_path) root = tree.getroot() shards_and_dates = [] for child in root: if child.tag == "file": shard = child[1].text # the index of filename yymm = child[9].text # the index of yymm shards_and_dates.append((shard, yymm)) format_cutoff = datetime.datetime(2007, 3, 1) # arXiv switches from old to new format for shard, yymm in tqdm(shards_and_dates): print("SHARD: ", shard) os.system(f"s3cmd get s3://arxiv/" + shard + \ " --requester-pays " + save_dir) tarball_name=shard[shard.rindex("/")+1:] # nb this code will stop working in 2051 ;) year = int("19" + yymm[:2]) if int(yymm[:2])>50 else int("20"+yymm[:2]) if datetime.datetime(year, int(yymm[2:]), 1)<=format_cutoff: process_tarball_old_scheme(tarball_name, save_dir) else: process_tarball(tarball_name, save_dir, math_ids) os.remove(manifest_path) if __name__=="__main__": main() _delete_files_except_pattern("arxiv", r".*\.tex$", transform=clean_tex_file_some_more) for f in tqdm(os.listdir("arxiv")): f_path = os.path.join("arxiv", f) make_archive(f_path)