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import re
import sys
import csv
import json
import requests
import itertools
import datetime
from pykafka import KafkaClient
from fatcat_tools.workers.worker_common import most_recent_message
DATE_FMT = "%Y-%m-%d"
class HarvestCrossrefWorker:
"""
Notes on crossref API:
- from-index-date is the updated time
- is-update can be false, to catch only new or only old works
https://api.crossref.org/works?filter=from-index-date:2018-11-14,is-update:false&rows=2
I think the design is going to have to be a cronjob or long-running job
(with long sleeps) which publishes "success through" to a separate state
queue, as simple YYYY-MM-DD strings.
Within a day, will need to use a resumption token. Maybe should use a
crossref library... meh.
will want to have some mechanism in kafka consumer (pushing to fatcat) to group
in batches as well. maybe even pass through as batches? or just use timeouts on
iteration.
logic of this worker:
- on start, fetch latest date from state feed
- in a function (unit-testable), decide which dates to ingest
- for each date needing update:
- start a loop for just that date, using resumption token for this query
- when done, publish to state feed, with immediate sync
TODO: what sort of parallelism? I guess multi-processing on dates, but need
to be careful how state is serialized back into kafka.
"""
def __init__(self, kafka_hosts, produce_topic, state_topic, contact_email,
api_host_url="https://api.crossref.org/works", start_date=None,
end_date=None, is_update_filter=None):
self.api_host_url = api_host_url
self.produce_topic = produce_topic
self.state_topic = state_topic
self.contact_email = contact_email
self.kafka = KafkaClient(hosts=kafka_hosts, broker_version="1.0.0")
self.is_update_filter = is_update_filter
# these are both optional, and should be datetime.date
self.start_date = start_date
self.end_date = end_date
self.loop_sleep = 60*60 # how long to wait, in seconds, between date checks
self.api_batch_size = 50
# for crossref, it's "from-index-date"
self.name = "Crossref"
def get_latest_date(self):
state_topic = self.kafka.topics[self.state_topic]
latest = most_recent_message(state_topic)
if latest:
latest = datetime.datetime.strptime(latest.decode('utf-8'), DATE_FMT).date()
print("Latest date found: {}".format(latest))
return latest
def params(self, date_str):
filter_param = 'from-index-date:{},until-index-date:{}'.format(
date_str, date_str)
if self.is_update_filter is not None:
filter_param += ',is_update:{}'.format(bool(self.is_update_filter))
params = {
'filter': filter_param,
'rows': self.api_batch_size,
'cursor': '*',
}
def update_params(self, params, resp):
params['cursor'] = resp['message']['next-cursor']
return params
def fetch_date(self, date):
state_topic = self.kafka.topics[self.state_topic]
produce_topic = self.kafka.topics[self.produce_topic]
date_str = date.strftime(DATE_FMT)
params = self.params(date_str)
headers = {
'User-Agent': 'fatcat_tools/0.1.0 (https://fatcat.wiki; mailto:{}) python-requests'.format(self.contact_email),
}
count = 0
with produce_topic.get_producer() as producer:
while True:
http_resp = requests.get(self.api_host_url, params, headers=headers)
if http_resp.status_code is 503:
# crud backoff
print("got HTTP {}, pausing for 30 seconds".format(http_resp.status_code))
time.sleep(30.0)
continue
assert http_resp.status_code is 200
resp = http_resp.json()
items = self.extract_items(resp)
count += len(items)
print("... got {} ({} of {}) in {}".format(len(items), count,
self.extract_total(resp), http_resp.elapsed))
#print(json.dumps(resp))
for work in items:
producer.produce(json.dumps(work).encode('utf-8'))
if len(items) < self.api_batch_size:
break
params = self.update_params(params, resp)
# record our completion state
with state_topic.get_sync_producer() as producer:
producer.produce(date.strftime(DATE_FMT).encode('utf-8'))
def extract_items(self, resp):
return resp['message']['items']
def extract_total(self, resp):
return resp['message']['total-results']
def run_once(self):
today_utc = datetime.datetime.utcnow().date()
if self.start_date is None:
self.start_date = self.get_latest_date()
if self.start_date:
# if we are continuing, start day after last success
self.start_date = self.start_date + datetime.timedelta(days=1)
if self.start_date is None:
# bootstrap to yesterday (don't want to start on today until it's over)
self.start_date = datetime.datetime.utcnow().date()
if self.end_date is None:
# bootstrap to yesterday (don't want to start on today until it's over)
self.end_date = today_utc - datetime.timedelta(days=1)
print("Harvesting from {} through {}".format(self.start_date, self.end_date))
current = self.start_date
while current <= self.end_date:
print("Fetching DOIs updated on {} (UTC)".format(current))
self.fetch_date(current)
current += datetime.timedelta(days=1)
print("{} DOI ingest caught up through {}".format(self.name, self.end_date))
return self.end_date
def run_loop(self):
while True:
last = self.run_once()
self.start_date = last
self.end_date = None
print("Sleeping {} seconds...".format(self.loop_sleep))
time.sleep(self.loop_sleep())
class HarvestDataciteWorker(HarvestCrossrefWorker):
"""
datacite has a REST API as well as OAI-PMH endpoint.
have about 8 million
bulk export notes: https://github.com/datacite/datacite/issues/188
fundamentally, very similar to crossref. don't have a scrape... maybe
could/should use this script for that, and dump to JSON?
"""
def __init__(self, kafka_hosts, produce_topic, state_topic, contact_email,
api_host_url="https://api.datacite.org/works",
start_date=None, end_date=None):
super().__init__(kafka_hosts=kafka_hosts,
produce_topic=produce_topic,
state_topic=state_topic,
api_host_url=api_host_url,
contact_email=contact_email,
start_date=start_date,
end_date=end_date)
# for datecite, it's "from-update-date"
self.name = "Datacite"
def params(self, date_str):
return {
'from-update-date': date_str,
'until-update-date': date_str,
'page[size]': self.api_batch_size,
'page[number]': 1,
}
def extract_items(self, resp):
return resp['data']
def extract_total(self, resp):
return resp['meta']['total']
def update_params(self, params, resp):
params['page[number]'] = resp['meta']['page'] + 1
return params
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