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import re
import sys
import csv
import json
import time
import itertools
import datetime
import requests
import sickle
from confluent_kafka import Producer, KafkaException
from fatcat_tools.workers import most_recent_message
from .harvest_common import HarvestState
class HarvestOaiPmhWorker:
"""
Base class for OAI-PMH harvesters. Uses the 'sickle' protocol library.
Typically run as a single process; harvests records and publishes in raw
(XML) format to a Kafka topic, one-message-per-document.
Based on Crossref importer, with the HarvestState internal class managing
progress with day-level granularity. Note that this depends on the OAI-PMH
endpoint being correct! In that it must be possible to poll for only
records updated on a particular date (typically "yesterday").
Was very tempted to re-use <https://github.com/miku/metha> for this OAI-PMH
stuff to save on dev time, but i'd already built the Crossref harvester and
would want something similar operationally. Oh well!
"""
def __init__(self, kafka_hosts, produce_topic, state_topic,
start_date=None, end_date=None):
self.produce_topic = produce_topic
self.state_topic = state_topic
self.kafka_config = {
'bootstrap.servers': kafka_hosts,
'message.max.bytes': 20000000, # ~20 MBytes; broker is ~50 MBytes
}
self.loop_sleep = 60*60 # how long to wait, in seconds, between date checks
self.endpoint_url = None # needs override
self.metadata_prefix = None # needs override
self.name = "unnamed"
self.state = HarvestState(start_date, end_date)
self.state.initialize_from_kafka(self.state_topic, self.kafka_config)
def fetch_date(self, date):
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)
api = sickle.Sickle(self.endpoint_url)
date_str = date.isoformat()
# this dict kwargs hack is to work around 'from' as a reserved python keyword
# recommended by sickle docs
try:
records = api.ListRecords(**{
'metadataPrefix': self.metadata_prefix,
'from': date_str,
'until': date_str,
})
except sickle.oaiexceptions.NoRecordsMatch:
print("WARN: no OAI-PMH records for this date: {} (UTC)".format(date_str))
return
count = 0
for item in records:
count += 1
if count % 50 == 0:
print("... up to {}".format(count))
producer.produce(
self.produce_topic,
item.raw.encode('utf-8'),
key=item.header.identifier.encode('utf-8'),
on_delivery=fail_fast)
producer.flush()
def run(self, continuous=False):
while True:
current = self.state.next(continuous)
if current:
print("Fetching DOIs updated on {} (UTC)".format(current))
self.fetch_date(current)
self.state.complete(current,
kafka_topic=self.state_topic,
kafka_config=self.kafka_config)
continue
if continuous:
print("Sleeping {} seconds...".format(self.loop_sleep))
time.sleep(self.loop_sleep)
else:
break
print("{} OAI-PMH ingest caught up".format(self.name))
class HarvestArxivWorker(HarvestOaiPmhWorker):
"""
Arxiv refs:
- http://export.arxiv.org/oai2?verb=GetRecord&identifier=oai:arXiv.org:0804.2273&metadataPrefix=arXiv
- http://export.arxiv.org/oai2?verb=GetRecord&identifier=oai:arXiv.org:0804.2273&metadataPrefix=arXivRaw
All records are work-level. Some metadata formats have internal info about
specific versions. The 'arXivRaw' format does, so i'm using that.
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.endpoint_url = "https://export.arxiv.org/oai2"
self.metadata_prefix = "arXivRaw"
self.name = "arxiv"
class HarvestPubmedWorker(HarvestOaiPmhWorker):
"""
Will likely be doing MEDLINE daily batch imports for primary metadata, but
might also want to run a PMC importer to update fulltext and assign OA
licenses (when appropriate).
Pubmed refs:
- https://www.ncbi.nlm.nih.gov/pmc/tools/oai/
- https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:152494&metadataPrefix=pmc_fm
- https://github.com/titipata/pubmed_parser
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.endpoint_url = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi"
self.metadata_prefix = "pmc_fm"
self.name = "pubmed"
class HarvestDoajJournalWorker(HarvestOaiPmhWorker):
"""
WARNING: DOAJ OAI-PMH doesn't seem to respect 'from' and 'until' params
As an alternative, could use:
- https://github.com/miku/doajfetch
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.endpoint_url = "https://www.doaj.org/oai"
self.metadata_prefix = "oai_dc"
self.name = "doaj-journal"
class HarvestDoajArticleWorker(HarvestOaiPmhWorker):
"""
WARNING: DOAJ OAI-PMH doesn't seem to respect 'from' and 'until' params
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.endpoint_url = "https://www.doaj.org/oai.article"
self.metadata_prefix = "oai_doaj"
self.name = "doaj-article"
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