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import json
import time
from confluent_kafka import Consumer, Producer, KafkaException
from fatcat_tools.transforms import release_ingest_request, release_to_elasticsearch
from .worker_common import FatcatWorker, most_recent_message
class ChangelogWorker(FatcatWorker):
"""
Periodically polls the fatcat API looking for new changelogs. When they are
found, fetch them and push (as JSON) into a Kafka topic.
"""
def __init__(self, api, kafka_hosts, produce_topic, poll_interval=10.0, offset=None):
super().__init__(kafka_hosts=kafka_hosts,
produce_topic=produce_topic,
api=api)
self.poll_interval = poll_interval
self.offset = offset # the fatcat changelog offset, not the kafka offset
def run(self):
# On start, try to consume the most recent from the topic, and using
# that as the starting offset. Note that this is a single-partition
# topic
if self.offset is None:
print("Checking for most recent changelog offset...")
msg = most_recent_message(self.produce_topic, self.kafka_config)
if msg:
self.offset = json.loads(msg.decode('utf-8'))['index']
else:
self.offset = 0
print("Most recent changelog index in Kafka seems to be {}".format(self.offset))
def fail_fast(err, msg):
if err is not None:
print("Kafka producer delivery error: {}".format(err))
print("Bailing out...")
# TODO: should it be sys.exit(-1)?
raise KafkaException(err)
producer_conf = self.kafka_config.copy()
producer_conf.update({
'delivery.report.only.error': True,
'default.topic.config': {
'request.required.acks': -1, # all brokers must confirm
},
})
producer = Producer(producer_conf)
while True:
latest = int(self.api.get_changelog(limit=1)[0].index)
if latest > self.offset:
print("Fetching changelogs from {} through {}".format(
self.offset+1, latest))
for i in range(self.offset+1, latest+1):
cle = self.api.get_changelog_entry(i)
obj = self.api.api_client.sanitize_for_serialization(cle)
producer.produce(
self.produce_topic,
json.dumps(obj).encode('utf-8'),
key=str(i),
on_delivery=fail_fast,
#NOTE timestamp could be timestamp=cle.timestamp (?)
)
self.offset = i
producer.flush()
print("Sleeping {} seconds...".format(self.poll_interval))
time.sleep(self.poll_interval)
class EntityUpdatesWorker(FatcatWorker):
"""
Consumes from the changelog topic and publishes expanded entities (fetched
from API) to update topics.
"""
def __init__(self, api, kafka_hosts, consume_topic, release_topic,
file_topic, container_topic, ingest_file_request_topic, poll_interval=5.0):
super().__init__(kafka_hosts=kafka_hosts,
consume_topic=consume_topic,
api=api)
self.release_topic = release_topic
self.file_topic = file_topic
self.container_topic = container_topic
self.ingest_file_request_topic = ingest_file_request_topic
self.poll_interval = poll_interval
self.consumer_group = "entity-updates"
self.ingest_oa_only = True
self.ingest_pdf_doi_prefix_blocklist = [
# gbif.org: many DOIs, not PDF fulltext
"10.15468/",
# ssl.fao.org: gene data
"10.18730/",
# plutof.ut.ee: gene data
"10.15156/",
# ba.e-pics.ethz.ch: swiss image (photo) archive
"10.3932/",
# ccdc.cam.ac.uk: crystal structures
"10.5517/",
]
self.live_pdf_ingest_doi_prefix_acceptlist = [
# biorxiv and medrxiv
"10.1101/",
# researchgate
"10.13140/",
]
def want_live_ingest(self, release, ingest_request):
"""
This function looks at ingest requests and decides whether they are
worth enqueing for ingest.
In theory crawling all DOIs to a landing page is valuable. It is
intended to be an operational point of control to reduce load on daily
ingest crawling (via wayback SPN).
"""
link_source = ingest_request.get('ingest_request')
ingest_type = ingest_request.get('ingest_type')
doi = ingest_request.get('ext_ids', {}).get('doi')
in_acceptlist = False
if doi:
for prefix in self.live_pdf_ingest_doi_prefix_acceptlist:
if doi.startswith(prefix):
in_acceptlist = True
if self.ingest_oa_only and link_source not in ('arxiv', 'pmc'):
es = release_to_elasticsearch(release)
if not es['is_oa'] and not in_acceptlist:
return False
if ingest_type == "pdf" and doi:
for prefix in self.ingest_pdf_doi_prefix_blocklist:
if doi.startswith(prefix):
return False
return True
def run(self):
def fail_fast(err, msg):
if err is not None:
print("Kafka producer delivery error: {}".format(err))
print("Bailing out...")
# TODO: should it be sys.exit(-1)?
raise KafkaException(err)
def on_commit(err, partitions):
if err is not None:
print("Kafka consumer commit error: {}".format(err))
print("Bailing out...")
# TODO: should it be sys.exit(-1)?
raise KafkaException(err)
for p in partitions:
# check for partition-specific commit errors
print(p)
if p.error:
print("Kafka consumer commit error: {}".format(p.error))
print("Bailing out...")
# TODO: should it be sys.exit(-1)?
raise KafkaException(p.error)
print("Kafka consumer commit successful")
pass
def on_rebalance(consumer, partitions):
for p in partitions:
if p.error:
raise KafkaException(p.error)
print("Kafka partitions rebalanced: {} / {}".format(
consumer, partitions))
consumer_conf = self.kafka_config.copy()
consumer_conf.update({
'group.id': self.consumer_group,
'on_commit': fail_fast,
# messages don't have offset marked as stored until pushed to
# elastic, but we do auto-commit stored offsets to broker
'enable.auto.commit': True,
'enable.auto.offset.store': False,
# user code timeout; if no poll after this long, assume user code
# hung and rebalance (default: 5min)
'max.poll.interval.ms': 180000,
'default.topic.config': {
'auto.offset.reset': 'latest',
},
})
consumer = Consumer(consumer_conf)
producer_conf = self.kafka_config.copy()
producer_conf.update({
'delivery.report.only.error': True,
'default.topic.config': {
'request.required.acks': -1, # all brokers must confirm
},
})
producer = Producer(producer_conf)
consumer.subscribe([self.consume_topic],
on_assign=on_rebalance,
on_revoke=on_rebalance,
)
print("Kafka consuming {}".format(self.consume_topic))
while True:
msg = consumer.poll(self.poll_interval)
if not msg:
print("nothing new from kafka (poll_interval: {} sec)".format(self.poll_interval))
continue
if msg.error():
raise KafkaException(msg.error())
cle = json.loads(msg.value().decode('utf-8'))
#print(cle)
print("processing changelog index {}".format(cle['index']))
release_ids = []
new_release_ids = []
file_ids = []
container_ids = []
work_ids = []
release_edits = cle['editgroup']['edits']['releases']
for re in release_edits:
release_ids.append(re['ident'])
# filter to direct release edits which are not updates
if not re.get('prev_revision') and not re.get('redirect_ident'):
new_release_ids.append(re['ident'])
file_edits = cle['editgroup']['edits']['files']
for e in file_edits:
file_ids.append(e['ident'])
container_edits = cle['editgroup']['edits']['containers']
for e in container_edits:
container_ids.append(e['ident'])
work_edits = cle['editgroup']['edits']['works']
for e in work_edits:
work_ids.append(e['ident'])
# TODO: do these fetches in parallel using a thread pool?
for ident in set(file_ids):
file_entity = self.api.get_file(ident, expand=None)
# update release when a file changes
# TODO: fetch old revision as well, and only update
# releases for which list changed
release_ids.extend(file_entity.release_ids or [])
file_dict = self.api.api_client.sanitize_for_serialization(file_entity)
producer.produce(
self.file_topic,
json.dumps(file_dict).encode('utf-8'),
key=ident.encode('utf-8'),
on_delivery=fail_fast,
)
for ident in set(container_ids):
container = self.api.get_container(ident)
container_dict = self.api.api_client.sanitize_for_serialization(container)
producer.produce(
self.container_topic,
json.dumps(container_dict).encode('utf-8'),
key=ident.encode('utf-8'),
on_delivery=fail_fast,
)
for ident in set(release_ids):
release = self.api.get_release(ident, expand="files,filesets,webcaptures,container")
work_ids.append(release.work_id)
release_dict = self.api.api_client.sanitize_for_serialization(release)
producer.produce(
self.release_topic,
json.dumps(release_dict).encode('utf-8'),
key=ident.encode('utf-8'),
on_delivery=fail_fast,
)
# filter to "new" active releases with no matched files
if release.ident in new_release_ids:
ir = release_ingest_request(release, ingest_request_source='fatcat-changelog')
if ir and not release.files and self.want_live_ingest(release, ir):
producer.produce(
self.ingest_file_request_topic,
json.dumps(ir).encode('utf-8'),
#key=None,
on_delivery=fail_fast,
)
producer.flush()
# TODO: publish updated 'work' entities to a topic
consumer.store_offsets(message=msg)
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