1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
|
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/",
]
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')
if self.ingest_oa_only and link_source not in ('arxiv', 'pmc'):
es = release_to_elasticsearch(release)
if not es['is_oa']:
return False
doi = ingest_request.get('ext_ids', {}).get('doi')
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(err)
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)
|
