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authorMartin Czygan <martin.czygan@gmail.com>2020-02-14 14:32:57 +0100
committerMartin Czygan <martin.czygan@gmail.com>2020-02-19 01:07:46 +0100
commit519b90d7f539b667e919c220a53626e7a4ac48bf (patch)
treeb7c3beed283d7dca732a8f2ab5b1dfe283bb69f3 /python/fatcat_tools/importers
parent4cbc94cd708c1db80a232150ab2cf56dddf83e62 (diff)
downloadfatcat-519b90d7f539b667e919c220a53626e7a4ac48bf.tar.gz
fatcat-519b90d7f539b667e919c220a53626e7a4ac48bf.zip
pubmed ftp harvest and KafkaBs4XmlPusher
* add PubmedFTPWorker * utils are currently stored alongside pubmed (e.g. ftpretr, xmlstream) but may live elsewhere, as they are more generic * add KafkaBs4XmlPusher
Diffstat (limited to 'python/fatcat_tools/importers')
-rw-r--r--python/fatcat_tools/importers/__init__.py2
-rw-r--r--python/fatcat_tools/importers/common.py65
2 files changed, 66 insertions, 1 deletions
diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index d936605f..03c7cbcc 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -12,7 +12,7 @@ To run an import you combine two classes; one each of:
"""
-from .common import EntityImporter, JsonLinePusher, LinePusher, CsvPusher, SqlitePusher, Bs4XmlFilePusher, Bs4XmlLargeFilePusher, Bs4XmlLinesPusher, Bs4XmlFileListPusher, KafkaJsonPusher, make_kafka_consumer, clean, is_cjk, LANG_MAP_MARC
+from .common import EntityImporter, JsonLinePusher, LinePusher, CsvPusher, SqlitePusher, Bs4XmlFilePusher, Bs4XmlLargeFilePusher, Bs4XmlLinesPusher, Bs4XmlFileListPusher, KafkaJsonPusher, KafkaBs4XmlPusher, make_kafka_consumer, clean, is_cjk, LANG_MAP_MARC
from .crossref import CrossrefImporter, CROSSREF_TYPE_MAP, lookup_license_slug
from .datacite import DataciteImporter
from .jalc import JalcImporter
diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py
index 1ffbd6e7..1cb5529e 100644
--- a/python/fatcat_tools/importers/common.py
+++ b/python/fatcat_tools/importers/common.py
@@ -721,6 +721,71 @@ class Bs4XmlFileListPusher(RecordPusher):
print(counts)
return counts
+class KafkaBs4XmlPusher(RecordPusher):
+ """
+ Fetch XML for an article from Kafka, parse via Bs4.
+ """
+ def __init__(self, importer, kafka_hosts, kafka_env, topic_suffix, group, **kwargs):
+ self.importer = importer
+ self.consumer = make_kafka_consumer(
+ kafka_hosts,
+ kafka_env,
+ topic_suffix,
+ group,
+ kafka_namespace=kwargs.get('kafka_namespace', 'fatcat')
+ )
+ self.poll_interval = kwargs.get('poll_interval', 5.0)
+ self.consume_batch_size = kwargs.get('consume_batch_size', 100)
+
+ def run(self):
+ count = 0
+ last_push = datetime.datetime.now()
+ while True:
+ # Note: this is batch-oriented, because underlying importer is
+ # often batch-oriented, but this doesn't confirm that entire batch
+ # has been pushed to fatcat before commiting offset. Eg, consider
+ # case where there there is one update and thousands of creates;
+ # update would be lingering in importer, and if importer crashed
+ # never created.
+ # This is partially mitigated for the worker case by flushing any
+ # outstanding editgroups every 5 minutes, but there is still that
+ # window when editgroups might be hanging (unsubmitted).
+ batch = self.consumer.consume(
+ num_messages=self.consume_batch_size,
+ timeout=self.poll_interval)
+ print("... got {} kafka messages ({}sec poll interval)".format(
+ len(batch), self.poll_interval))
+ if not batch:
+ if datetime.datetime.now() - last_push > datetime.timedelta(minutes=5):
+ # it has been some time, so flush any current editgroup
+ self.importer.finish()
+ last_push = datetime.datetime.now()
+ #print("Flushed any partial import batch: {}".format(self.importer.counts))
+ continue
+ # first check errors on entire batch...
+ for msg in batch:
+ if msg.error():
+ raise KafkaException(msg.error())
+ # ... then process
+ for msg in batch:
+ soup = BeautifulSoup(msg.value().decode('utf-8'), "xml")
+ self.importer.push_record(soup)
+ soup.decompose()
+ count += 1
+ if count % 500 == 0:
+ print("Import counts: {}".format(self.importer.counts))
+ last_push = datetime.datetime.now()
+ for msg in batch:
+ # locally store offsets of processed messages; will be
+ # auto-commited by librdkafka from this "stored" value
+ self.consumer.store_offsets(message=msg)
+
+ # TODO: should catch UNIX signals (HUP?) to shutdown cleanly, and/or
+ # commit the current batch if it has been lingering
+ counts = self.importer.finish()
+ print(counts)
+ self.consumer.close()
+ return counts
class KafkaJsonPusher(RecordPusher):