From 4e332e9037530ebc62836acfa78896dc76700c9c Mon Sep 17 00:00:00 2001
From: Bryan Newbold <bnewbold@robocracy.org>
Date: Wed, 2 Dec 2020 10:49:35 -0800
Subject: add 'lxml' mode for large XML file import, and multi-tags

---
 python/fatcat_import.py                 |  3 +--
 python/fatcat_tools/importers/common.py | 43 +++++++++++++++++++++------------
 python/tests/import_pubmed.py           |  4 +--
 3 files changed, 31 insertions(+), 19 deletions(-)

(limited to 'python')

diff --git a/python/fatcat_import.py b/python/fatcat_import.py
index ff6c94dc..6c9e65a8 100755
--- a/python/fatcat_import.py
+++ b/python/fatcat_import.py
@@ -71,8 +71,7 @@ def run_pubmed(args):
         Bs4XmlLargeFilePusher(
             pi,
             args.xml_file,
-            "PubmedArticle",
-            record_list_tag="PubmedArticleSet",
+            ["PubmedArticle"],
         ).run()
 
 def run_jstor(args):
diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py
index 6dc2ab9e..2446cdbf 100644
--- a/python/fatcat_tools/importers/common.py
+++ b/python/fatcat_tools/importers/common.py
@@ -8,6 +8,9 @@ import datetime
 import subprocess
 from collections import Counter
 from typing import Optional, Tuple
+from confluent_kafka import Consumer, KafkaException
+import lxml
+import xml.parsers.expat
 import xml.etree.ElementTree as ET
 
 import elasticsearch
@@ -528,7 +531,7 @@ class JsonLinePusher(RecordPusher):
             record = json.loads(line)
             self.importer.push_record(record)
         counts = self.importer.finish()
-        print(counts)
+        print(counts, file=sys.stderr)
         return counts
 
 
@@ -544,7 +547,7 @@ class CsvPusher(RecordPusher):
                 continue
             self.importer.push_record(line)
         counts = self.importer.finish()
-        print(counts)
+        print(counts, file=sys.stderr)
         return counts
 
 
@@ -560,7 +563,7 @@ class LinePusher(RecordPusher):
                 continue
             self.importer.push_record(line)
         counts = self.importer.finish()
-        print(counts)
+        print(counts, file=sys.stderr)
         return counts
 
 
@@ -579,7 +582,7 @@ class SqlitePusher(RecordPusher):
         for row in cur:
             self.importer.push_record(row)
         counts = self.importer.finish()
-        print(counts)
+        print(counts, file=sys.stderr)
         return counts
 
 
@@ -600,7 +603,7 @@ class Bs4XmlLinesPusher(RecordPusher):
             self.importer.push_record(soup)
             soup.decompose()
         counts = self.importer.finish()
-        print(counts)
+        print(counts, file=sys.stderr)
         return counts
 
 
@@ -618,7 +621,7 @@ class Bs4XmlFilePusher(RecordPusher):
             record.decompose()
         counts = self.importer.finish()
         soup.decompose()
-        print(counts)
+        print(counts, file=sys.stderr)
         return counts
 
 
@@ -641,29 +644,39 @@ class Bs4XmlLargeFilePusher(RecordPusher):
     by inner container/release API lookup caches.
     """
 
-    def __init__(self, importer, xml_file, record_tag, **kwargs):
+    def __init__(self, importer, xml_file, record_tags, use_lxml=False, **kwargs):
         self.importer = importer
         self.xml_file = xml_file
-        self.record_tag = record_tag
+        self.record_tags = record_tags
+        self.use_lxml = use_lxml
 
     def run(self):
-        elem_iter = ET.iterparse(self.xml_file, ["start", "end"])
+        if self.use_lxml:
+            elem_iter = lxml.etree.iterparse(self.xml_file, ["start", "end"], load_dtd=True)
+        else:
+            elem_iter = ET.iterparse(self.xml_file, ["start", "end"])
         root = None
         for (event, element) in elem_iter:
-            if not root and event == "start":
+            if (root is not None) and event == "start":
                 root = element
                 continue
-            if not (element.tag == self.record_tag and event == "end"):
+            if not (element.tag in self.record_tags and event == "end"):
                 continue
-            soup = BeautifulSoup(ET.tostring(element), "xml")
-            for record in soup.find_all(self.record_tag):
+            if self.use_lxml:
+                soup = BeautifulSoup(lxml.etree.tostring(element), "xml")
+            else:
+                soup = BeautifulSoup(ET.tostring(element), "xml")
+            for record in soup.find_all():
+                if record.name not in self.record_tags:
+                    continue
                 self.importer.push_record(record)
                 record.decompose()
             soup.decompose()
             element.clear()
-            root.clear()
+            if root is not None:
+                root.clear()
         counts = self.importer.finish()
-        print(counts)
+        print(counts, file=sys.stderr)
         return counts
 
 
diff --git a/python/tests/import_pubmed.py b/python/tests/import_pubmed.py
index 201f533c..10ded3fc 100644
--- a/python/tests/import_pubmed.py
+++ b/python/tests/import_pubmed.py
@@ -20,7 +20,7 @@ def test_pubmed_importer(pubmed_importer):
     last_index = pubmed_importer.api.get_changelog(limit=1)[0].index
     with open('tests/files/pubmedsample_2019.xml', 'r') as f:
         pubmed_importer.bezerk_mode = True
-        counts = Bs4XmlLargeFilePusher(pubmed_importer, f, "PubmedArticle").run()
+        counts = Bs4XmlLargeFilePusher(pubmed_importer, f, ["PubmedArticle"]).run()
     assert counts['insert'] == 176
     assert counts['exists'] == 0
     assert counts['skip'] == 0
@@ -37,7 +37,7 @@ def test_pubmed_importer(pubmed_importer):
     with open('tests/files/pubmedsample_2019.xml', 'r') as f:
         pubmed_importer.bezerk_mode = False
         pubmed_importer.reset()
-        counts = Bs4XmlLargeFilePusher(pubmed_importer, f, "PubmedArticle").run()
+        counts = Bs4XmlLargeFilePusher(pubmed_importer, f, ["PubmedArticle"]).run()
     assert counts['insert'] == 0
     assert counts['exists'] == 176
     assert counts['skip'] == 0
-- 
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