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-rw-r--r--python/fatcat_tools/harvest/__init__.py2
-rw-r--r--python/fatcat_tools/harvest/crossrefish.py39
-rw-r--r--python/fatcat_tools/harvest/datacite.py29
-rw-r--r--python/fatcat_tools/harvest/ingest_common.py127
-rwxr-xr-xpython/fatcat_worker.py49
5 files changed, 240 insertions, 6 deletions
diff --git a/python/fatcat_tools/harvest/__init__.py b/python/fatcat_tools/harvest/__init__.py
new file mode 100644
index 00000000..85034f04
--- /dev/null
+++ b/python/fatcat_tools/harvest/__init__.py
@@ -0,0 +1,2 @@
+
+from .crossrefish import HarvestCrossrefWorker
diff --git a/python/fatcat_tools/harvest/crossrefish.py b/python/fatcat_tools/harvest/crossrefish.py
new file mode 100644
index 00000000..a88cedbd
--- /dev/null
+++ b/python/fatcat_tools/harvest/crossrefish.py
@@ -0,0 +1,39 @@
+
+"""
+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.
+"""
+
+from fatcat_tools.harvest.ingest_common import DoiApiHarvest
+
+class HarvestCrossrefWorker(DoiApiHarvest):
+
+ def __init__(self, kafka_hosts, produce_topic, state_topic, contact_email,
+ api_host_url="https://api.crossref.org/works",
+ is_update_filter=None,
+ 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)
+
+ self.is_update_filter = is_update_filter
+
diff --git a/python/fatcat_tools/harvest/datacite.py b/python/fatcat_tools/harvest/datacite.py
new file mode 100644
index 00000000..12860810
--- /dev/null
+++ b/python/fatcat_tools/harvest/datacite.py
@@ -0,0 +1,29 @@
+
+"""
+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?
+"""
+
+from fatcat_tools.harvest.ingest_common import DoiApiHarvest
+
+class HarvestDataciteWorker(DoiApiHarvest):
+
+ 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)
+
+ self.update_filter_name = "update"
+
diff --git a/python/fatcat_tools/harvest/ingest_common.py b/python/fatcat_tools/harvest/ingest_common.py
new file mode 100644
index 00000000..67ff3dc3
--- /dev/null
+++ b/python/fatcat_tools/harvest/ingest_common.py
@@ -0,0 +1,127 @@
+
+"""
+logic:
+- 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
+"""
+
+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 DoiApiHarvest:
+ """
+ This class supports core features for both the Crossref and Datacite REST
+ APIs for fetching updated metadata (the Datacite API seems to be moduled on
+ the Crossref API).
+
+ Implementations must provide the push results function.
+ """
+
+ def __init__(self, kafka_hosts, produce_topic, state_topic, api_host_url,
+ contact_email, start_date=None, end_date=None):
+ self.loop_sleep = 60*60 # how long to wait, in seconds, between date checks
+ self.api_batch_size = 50
+ 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 = None
+ self.update_filter_name = "index"
+
+ # these are both optional, and should be datetime.date
+ self.start_date = start_date
+ self.end_date = end_date
+
+ 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 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)
+ filter_param = 'from-{index}-date:{},until-{index}-date:{}'.format(
+ date_str, date_str, index=self.update_filter_name)
+ if self.is_update_filter is not None:
+ filter_param += ',is_update:{}'.format(bool(is_update))
+ params = {
+ 'filter': filter_param,
+ 'rows': self.api_batch_size,
+ 'cursor': '*',
+ }
+ 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)
+ assert http_resp.status_code is 200
+ resp = http_resp.json()
+ items = resp['message']['items']
+ count += len(items)
+ print("... got {} ({} of {}) in {}".format(len(items), count,
+ resp['message']['total-results']), http_resp.elapsed)
+ #print(json.dumps(resp))
+ for work in items:
+ producer.produce(json.dumps(work).encode('utf-8'))
+ if len(items) < params['rows']:
+ break
+ params['cursor'] = resp['message']['next-cursor']
+
+ # record our completion state
+ with state_topic.get_sync_producer() as producer:
+ producer.produce(date.strftime(DATE_FMT).encode('utf-8'))
+
+
+ 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("Crossref DOI ingest caught up through {}".format(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())
+
diff --git a/python/fatcat_worker.py b/python/fatcat_worker.py
index 611c8e1b..f68b0606 100755
--- a/python/fatcat_worker.py
+++ b/python/fatcat_worker.py
@@ -2,29 +2,51 @@
import sys
import argparse
+import datetime
from fatcat_tools.workers.changelog import FatcatChangelogWorker, FatcatEntityUpdatesWorker
from fatcat_tools.workers.elastic import FatcatElasticReleaseWorker
+from fatcat_tools.harvest import HarvestCrossrefWorker
-def run_changelog_worker(args):
+def run_changelog(args):
topic = "fatcat-{}.changelog".format(args.env)
worker = FatcatChangelogWorker(args.api_host_url, args.kafka_hosts, topic,
args.poll_interval)
worker.run()
-def run_entity_updates_worker(args):
+def run_entity_updates(args):
changelog_topic = "fatcat-{}.changelog".format(args.env)
release_topic = "fatcat-{}.release-updates".format(args.env)
worker = FatcatEntityUpdatesWorker(args.api_host_url, args.kafka_hosts,
changelog_topic, release_topic)
worker.run()
-def run_elastic_release_worker(args):
+def run_elastic_release(args):
consume_topic = "fatcat-{}.release-updates".format(args.env)
worker = FatcatElasticReleaseWorker(args.kafka_hosts,
consume_topic, elastic_backend=args.elastic_backend,
elastic_index=args.elastic_index)
worker.run()
+def run_harvest_crossref(args):
+ worker = HarvestCrossrefWorker(
+ args.kafka_hosts,
+ produce_topic="fatcat-{}.crossref".format(args.env),
+ state_topic="fatcat-{}.crossref-state".format(args.env),
+ contact_email=args.contact_email,
+ start_date=args.start_date,
+ end_date=args.end_date)
+ worker.run_once()
+
+def run_harvest_datacite(args):
+ worker = HarvestDataciteWorker(
+ args.kafka_hosts,
+ produce_topic="fatcat-{}.datacite".format(args.env),
+ state_topic="fatcat-{}.datacite-state".format(args.env),
+ contact_email=args.contact_email,
+ start_date=args.start_date,
+ end_date=args.end_date)
+ worker.run_once()
+
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--debug',
@@ -42,16 +64,16 @@ def main():
subparsers = parser.add_subparsers()
sub_changelog = subparsers.add_parser('changelog')
- sub_changelog.set_defaults(func=run_changelog_worker)
+ sub_changelog.set_defaults(func=run_changelog)
sub_changelog.add_argument('--poll-interval',
help="how long to wait between polling (seconds)",
default=10.0, type=float)
sub_entity_updates = subparsers.add_parser('entity-updates')
- sub_entity_updates.set_defaults(func=run_entity_updates_worker)
+ sub_entity_updates.set_defaults(func=run_entity_updates)
sub_elastic_release = subparsers.add_parser('elastic-release')
- sub_elastic_release.set_defaults(func=run_elastic_release_worker)
+ sub_elastic_release.set_defaults(func=run_elastic_release)
sub_elastic_release.add_argument('--elastic-backend',
help="elasticsearch backend to connect to",
default="http://localhost:9200")
@@ -59,6 +81,21 @@ def main():
help="elasticsearch index to push into",
default="fatcat")
+ def mkdate(raw):
+ return datetime.datetime.strptime(raw, "%Y-%m-%d").date()
+
+ sub_harvest_crossref = subparsers.add_parser('harvest-crossref')
+ sub_harvest_crossref.set_defaults(func=run_harvest_crossref)
+ sub_harvest_crossref.add_argument('--contact-email',
+ default="undefined", # better?
+ help="contact email to use in API header")
+ sub_harvest_crossref.add_argument('--start-date',
+ default=None, type=mkdate,
+ help="begining of harvest period")
+ sub_harvest_crossref.add_argument('--end-date',
+ default=None, type=mkdate,
+ help="end of harvest period")
+
args = parser.parse_args()
if not args.__dict__.get("func"):
print("tell me what to do!")
generated by cgit v1.2.3 (git 2.39.1) at 2024-12-04 08:11:08 +0000