import os import sys import json import argparse from typing import List, Any import requests from requests.adapters import HTTPAdapter from requests.packages.urllib3.util.retry import Retry # pylint: disable=import-error import elasticsearch from elasticsearch_dsl import Search, Q def requests_retry_session( retries: int = 2, backoff_factor: int = 3, status_forcelist: List[int] = [500, 502, 504], ) -> requests.Session: """ From: https://www.peterbe.com/plog/best-practice-with-retries-with-requests """ session = requests.Session() retry = Retry( total=retries, read=retries, connect=retries, backoff_factor=backoff_factor, status_forcelist=status_forcelist, ) adapter = HTTPAdapter(max_retries=retry) session.mount("http://", adapter) session.mount("https://", adapter) return session def run_query_fatcat(query: str, fulltext_only: bool, json_output: Any) -> None: """ Queries fatcat search index (the full regular fatcat.wiki release index) for search string passed (and some filters), iterates over the result set (using scroll), and fetches full release entity (via api.fatcat.wik) for each. TODO: group by work_id """ api_session = requests_retry_session() es_backend = os.environ.get( "ELASTICSEARCH_BACKEND", default="https://search.fatcat.wiki", ) es_index = "fatcat_release" es_client = elasticsearch.Elasticsearch(es_backend) search = Search(using=es_client, index=es_index) search = search.exclude("terms", release_type=["stub", "component", "abstract"]) # "Emerald Expert Briefings" search = search.exclude("terms", container_id=["fnllqvywjbec5eumrbavqipfym"]) # ResearchGate search = search.exclude("terms", doi_prefix=["10.13140"]) if fulltext_only: search = search.filter("terms", in_ia=True) search = search.query( Q("query_string", query=query, default_operator="AND", fields=["biblio"]) ) print("Expecting {} search hits".format(search.count()), file=sys.stderr) search = search.params(clear_scroll=False) search = search.params(_source=False) results = search.scan() for hit in results: release_id = hit.meta.id resp = api_session.get( "https://api.fatcat.wiki/v0/release/{}".format(release_id), params={ "expand": "container,files,filesets,webcaptures", "hide": "references", }, ) resp.raise_for_status() row = dict( fatcat_hit=hit.meta._d_, release_id=release_id, fatcat_release=resp.json(), ) print(json.dumps(row, sort_keys=True), file=json_output) def main() -> None: """ Run this command like: python -m fatcat_scholar.query_fatcat """ parser = argparse.ArgumentParser( formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser.add_argument( "query", help="base query string to use", type=str, ) parser.add_argument( "--fulltext-only", help="flag to filter to only documents with fulltext available", action="store_true", ) args = parser.parse_args() run_query_fatcat(args.query, args.fulltext_only, sys.stdout) if __name__ == "__main__": main()