From 5ce01ab8ca992023c320294f20356735d550d4d9 Mon Sep 17 00:00:00 2001
From: Bryan Newbold <bnewbold@archive.org>
Date: Wed, 10 Nov 2021 15:16:58 -0800
Subject: simple persist worker/tool to backfill grobid_refs

---
 python/persist_tool.py        | 22 ++++++++++++++++++++++
 python/sandcrawler/persist.py | 40 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 62 insertions(+)

(limited to 'python')

diff --git a/python/persist_tool.py b/python/persist_tool.py
index 069bef7..e08d66c 100755
--- a/python/persist_tool.py
+++ b/python/persist_tool.py
@@ -139,6 +139,18 @@ def run_crossref(args):
     pusher.run()
 
 
+def run_grobid_refs(args):
+    worker = PersistGrobidRefsWorker(
+        db_url=args.db_url,
+    )
+    pusher = JsonLinePusher(
+        worker,
+        args.json_file,
+        batch_size=100,
+    )
+    pusher.run()
+
+
 def main():
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser.add_argument(
@@ -277,6 +289,16 @@ def main():
         help="use GROBID to parse any unstructured references (default is to not)",
     )
 
+    sub_grobid_refs = subparsers.add_parser(
+        "grobid-refs", help="backfill a grobid_refs JSON dump into postgresql"
+    )
+    sub_grobid_refs.set_defaults(func=run_grobid_refs)
+    sub_grobid_refs.add_argument(
+        "json_file",
+        help="grobid_refs to import from (or '-' for stdin)",
+        type=argparse.FileType("r"),
+    )
+
     args = parser.parse_args()
     if not args.__dict__.get("func"):
         print("Tell me what to do!", file=sys.stderr)
diff --git a/python/sandcrawler/persist.py b/python/sandcrawler/persist.py
index 6847e2e..d753380 100644
--- a/python/sandcrawler/persist.py
+++ b/python/sandcrawler/persist.py
@@ -678,6 +678,12 @@ class PersistHtmlTeiXmlWorker(GenericPersistDocWorker):
 
 
 class PersistCrossrefWorker(SandcrawlerWorker):
+    """
+    Pushes Crossref API JSON records into postgresql. Can also talk to GROBID,
+    parsed 'unstructured' references, and push the results in to postgresql at
+    the same time.
+    """
+
     def __init__(
         self,
         db_url: str,
@@ -739,3 +745,37 @@ class PersistCrossrefWorker(SandcrawlerWorker):
 
         self.db.commit()
         return []
+
+
+class PersistGrobidRefsWorker(SandcrawlerWorker):
+    """
+    Simple persist worker to backfill GROBID references in to postgresql
+    locally. Consumes the JSON output from GROBID CrossrefRefsWorker.
+    """
+
+    def __init__(self, db_url: str, **kwargs):
+        super().__init__(**kwargs)
+        self.db = SandcrawlerPostgresClient(db_url)
+        self.cur = self.db.conn.cursor()
+
+    def process(self, record: Any, key: Optional[str] = None) -> Any:
+        """Only do batches (as transactions)"""
+        raise NotImplementedError
+
+    def push_batch(self, batch: list) -> list:
+        self.counts["total"] += len(batch)
+
+        refs_batch = []
+        for record in batch:
+            assert record["source"]
+            assert record["source_id"]
+            refs_batch.append(record)
+
+        resp = self.db.insert_grobid_refs(self.cur, refs_batch)
+        if len(refs_batch) < len(batch):
+            self.counts["skip"] += len(batch) - len(refs_batch)
+        self.counts["insert-grobid_refs"] += resp[0]
+        self.counts["update-grobid_refs"] += resp[1]
+
+        self.db.commit()
+        return []
-- 
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