diff options
Diffstat (limited to 'fatcat_scholar')
| -rw-r--r-- | fatcat_scholar/worker.py | 238 |
1 files changed, 238 insertions, 0 deletions
diff --git a/fatcat_scholar/worker.py b/fatcat_scholar/worker.py new file mode 100644 index 0000000..af84dd1 --- /dev/null +++ b/fatcat_scholar/worker.py @@ -0,0 +1,238 @@ +import os +import sys +import json +import argparse +import datetime +from typing import List, Any + +import requests +import elasticsearch +import fatcat_openapi_client +from fatcat_openapi_client import ReleaseEntity + +from fatcat_scholar.config import settings +from fatcat_scholar.issue_db import IssueDB +from fatcat_scholar.sandcrawler import ( + SandcrawlerPostgrestClient, + SandcrawlerMinioClient, +) +from fatcat_scholar.schema import ( + DocType, + IntermediateBundle, +) +from fatcat_scholar.transform import transform_heavy +from fatcat_scholar.api_entities import entity_from_json +from fatcat_scholar.work_pipeline import WorkPipeline +from fatcat_scholar.sim_pipeline import SimPipeline +from fatcat_scholar.kafka import KafkaWorker + + +class FetchDocsWorker(KafkaWorker): + def __init__( + self, + work_pipeline: WorkPipeline, + sim_pipeline: SimPipeline, + produce_docs_topic: str, + **kwargs: Any, + ): + super().__init__(**kwargs) + self.sim_pipeline = sim_pipeline + self.work_pipeline = work_pipeline + api_conf = fatcat_openapi_client.Configuration() + api_conf.host = kwargs.get("fatcat_api_host", "https://api.fatcat.wiki/v0") + self.fatcat_api = fatcat_openapi_client.DefaultApi( + fatcat_openapi_client.ApiClient(api_conf) + ) + self.producer = self.create_kafka_producer(self.kafka_brokers) + self.produce_topic = produce_docs_topic + print(f"Will produce bundles to: {self.produce_topic}", file=sys.stderr) + + def process_msg(self, msg: dict) -> None: + key = msg["key"] + if key.startswith("work_") and msg.get("work_ident"): + stubs = self.fatcat_api.get_work_releases( + ident=msg["work_ident"], hide="abstracts,references", + ) + full_releases = [] + for r in stubs: + full = self.fatcat_api.get_release( + r.ident, + expand="container,files,filesets,webcaptures", + hide="references", + ) + full_releases.append(full) + if not full_releases: + return + bundle = self.work_pipeline.process_release_list(full_releases) + bundle.fetched = datetime.datetime.utcnow() + self.producer.produce( + self.produce_topic, + bundle.json(exclude_none=True).encode("UTF-8"), + key=key, + on_delivery=self._fail_fast_produce, + ) + self.counts["works-produced"] += 1 + + # check for errors etc + self.producer.poll(0) + elif key.startswith("sim_"): + # filter out "contents" and "index" items (again) + if msg["issue_item"].endswith("_contents") or msg["issue_item"].endswith( + "_index" + ): + return + try: + full_issue = self.sim_pipeline.fetch_sim_issue( + msg["issue_item"], msg["pub_collection"] + ) + except requests.exceptions.ConnectionError as e: + print(str(e), file=sys.stderr) + raise e + except requests.exceptions.ReadTimeout as e: + print(str(e), file=sys.stderr) + raise e + if not full_issue: + return + pages = self.sim_pipeline.full_issue_to_pages(full_issue) + for bundle in pages: + bundle.fetched = datetime.datetime.utcnow() + self.producer.produce( + self.produce_topic, + bundle.json(exclude_none=True).encode("UTF-8"), + # NOTE: this isn't going to be the document key, but it will sort by issue + key=key, + on_delivery=self._fail_fast_produce, + ) + self.counts["pages-produced"] += 1 + + # check for errors etc + self.producer.poll(0) + else: + raise NotImplementedError(f"can't process updated for key={key}") + + +class IndexDocsWorker(KafkaWorker): + def __init__(self, es_client: Any, es_index: str, **kwargs: Any): + super().__init__(**kwargs) + self.es_client = es_client + self.es_index = es_index + + def process_batch(self, batch: List[dict]) -> None: + + bulk_actions = [] + for obj in batch: + bundle = IntermediateBundle( + doc_type=DocType(obj["doc_type"]), + releases=[ + entity_from_json(json.dumps(re), ReleaseEntity) + for re in obj["releases"] + ], + biblio_release_ident=obj.get("biblio_release_ident"), + grobid_fulltext=obj.get("grobid_fulltext"), + pdftotext_fulltext=obj.get("pdftotext_fulltext"), + pdf_meta=obj.get("pdf_meta"), + sim_fulltext=obj.get("sim_fulltext"), + ) + es_doc = transform_heavy(bundle) + if not es_doc: + continue + else: + bulk_actions.append(json.dumps({"index": {"_id": es_doc.key,},})) + bulk_actions.append(es_doc.json(exclude_none=True, sort_keys=True)) + self.counts["docs-indexed"] += 1 + + if not bulk_actions: + return + + self.es_client.bulk( + "\n".join(bulk_actions), self.es_index, timeout="30s", + ) + self.counts["batches-indexed"] += 1 + + +def main() -> None: + """ + Run this command like: + + python -m fatcat_scholar.work_pipeline + """ + + parser = argparse.ArgumentParser( + formatter_class=argparse.ArgumentDefaultsHelpFormatter + ) + subparsers = parser.add_subparsers() + + parser.add_argument( + "--issue-db-file", + help="sqlite3 database file to open", + default=settings.SCHOLAR_ISSUEDB_PATH, + type=str, + ) + parser.add_argument( + "--sandcrawler-db-api", + help="Sandcrawler Postgrest API endpoint", + default=settings.SANDCRAWLER_DB_API, + type=str, + ) + parser.add_argument( + "--sandcrawler-s3-api", + help="Sandcrawler S3 (minio/seaweedfs) API endpoint", + default=settings.SANDCRAWLER_S3_API, + type=str, + ) + + sub = subparsers.add_parser("fetch-docs-worker",) + sub.set_defaults(worker="fetch-docs-worker") + + sub = subparsers.add_parser("index-docs-worker",) + sub.set_defaults(worker="index-docs-worker") + + args = parser.parse_args() + if not args.__dict__.get("worker"): + parser.print_help(file=sys.stderr) + sys.exit(-1) + + if args.worker == "fetch-docs-worker": + issue_db = IssueDB(args.issue_db_file) + wp = WorkPipeline( + issue_db=issue_db, + sandcrawler_db_client=SandcrawlerPostgrestClient( + api_url=args.sandcrawler_db_api + ), + sandcrawler_s3_client=SandcrawlerMinioClient( + host_url=args.sandcrawler_s3_api, + access_key=os.environ.get("MINIO_ACCESS_KEY"), + secret_key=os.environ.get("MINIO_SECRET_KEY"), + ), + ) + sp = SimPipeline(issue_db=issue_db) + fdw = FetchDocsWorker( + kafka_brokers=settings.KAFKA_BROKERS, + consume_topics=[ + f"fatcat-{settings.SCHOLAR_ENV}.work-ident-updates", + # TODO: f"scholar-{settings.SCHOLAR_ENV}.sim-updates", + ], + consumer_group=f"scholar-{settings.SCHOLAR_ENV}-fetch-workers", + work_pipeline=wp, + sim_pipeline=sp, + produce_docs_topic=f"scholar-{settings.SCHOLAR_ENV}.update-docs", + fatcat_api_host=settings.FATCAT_API_HOST, + ) + fdw.run() + elif args.worker == "index-docs-worker": + es_client = elasticsearch.Elasticsearch( + settings.ELASTICSEARCH_BACKEND, timeout=25.0 + ) + idw = IndexDocsWorker( + kafka_brokers=settings.KAFKA_BROKERS, + batch_size=settings.INDEX_WORKER_BATCH_SIZE, + consume_topics=[f"scholar-{settings.SCHOLAR_ENV}.update-docs"], + consumer_group=f"scholar-{settings.SCHOLAR_ENV}-index-workers", + es_client=es_client, + es_index=settings.ELASTICSEARCH_FULLTEXT_INDEX, + ) + idw.run() + + +if __name__ == "__main__": + main() |