From e590eec544ab6f2e54e8770f01e64eef3158fdaa Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Mon, 19 Nov 2018 23:04:18 -0800 Subject: initial OAI-PMH harvesters --- python/Pipfile | 1 + python/Pipfile.lock | 320 ++++++++++++++++---------- python/fatcat_harvest.py | 57 ++++- python/fatcat_tools/harvest/__init__.py | 2 + python/fatcat_tools/harvest/doi_registrars.py | 13 +- python/fatcat_tools/harvest/oaipmh.py | 157 +++++++++++++ 6 files changed, 417 insertions(+), 133 deletions(-) create mode 100644 python/fatcat_tools/harvest/oaipmh.py (limited to 'python') diff --git a/python/Pipfile b/python/Pipfile index f4137dca..04b5c5ef 100644 --- a/python/Pipfile +++ b/python/Pipfile @@ -31,6 +31,7 @@ flask-uuid = "*" flask-debugtoolbar = "*" pykafka = "*" python-dateutil = "*" +sickle = "*" [requires] # Python 3.5 is the bundled (system) version of python for Ubuntu 16.04 diff --git a/python/Pipfile.lock b/python/Pipfile.lock index da96a24f..fa597faa 100644 --- a/python/Pipfile.lock +++ b/python/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "c99945057fc87c7a825a76cfe4d1abdcb99d0e70dc71db770cf259b761c6835c" + "sha256": "f3c3ce52dc614cb4514b4d637732e705815403f9181c142aea59a7feaa51f355" }, "pipfile-spec": 6, "requires": { @@ -110,11 +110,73 @@ ], "version": "==2.5.0" }, + "lxml": { + "hashes": [ + "sha256:02bc220d61f46e9b9d5a53c361ef95e9f5e1d27171cd461dddb17677ae2289a5", + "sha256:22f253b542a342755f6cfc047fe4d3a296515cf9b542bc6e261af45a80b8caf6", + "sha256:2f31145c7ff665b330919bfa44aacd3a0211a76ca7e7b441039d2a0b0451e415", + "sha256:36720698c29e7a9626a0dc802ef8885f8f0239bfd1689628ecd459a061f2807f", + "sha256:438a1b0203545521f6616132bfe0f4bca86f8a401364008b30e2b26ec408ce85", + "sha256:4815892904c336bbaf73dafd54f45f69f4021c22b5bad7332176bbf4fb830568", + "sha256:5be031b0f15ad63910d8e5038b489d95a79929513b3634ad4babf77100602588", + "sha256:5c93ae37c3c588e829b037fdfbd64a6e40c901d3f93f7beed6d724c44829a3ad", + 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b/python/fatcat_harvest.py index f1bb3416..6ecc3ec6 100755 --- a/python/fatcat_harvest.py +++ b/python/fatcat_harvest.py @@ -3,11 +3,13 @@ import sys import argparse import datetime -from fatcat_tools.harvest import HarvestCrossrefWorker, HarvestDataciteWorker +from fatcat_tools.harvest import HarvestCrossrefWorker, HarvestDataciteWorker,\ + HarvestArxivWorker, HarvestPubmedWorker, HarvestDoajArticleWorker,\ + HarvestDoajJournalWorker def run_crossref(args): worker = HarvestCrossrefWorker( - args.kafka_hosts, + kafka_hosts=args.kafka_hosts, produce_topic="fatcat-{}.crossref".format(args.env), state_topic="fatcat-{}.crossref-state".format(args.env), contact_email=args.contact_email, @@ -17,7 +19,7 @@ def run_crossref(args): def run_datacite(args): worker = HarvestDataciteWorker( - args.kafka_hosts, + kafka_hosts=args.kafka_hosts, produce_topic="fatcat-{}.datacite".format(args.env), state_topic="fatcat-{}.datacite-state".format(args.env), contact_email=args.contact_email, @@ -25,6 +27,43 @@ def run_datacite(args): end_date=args.end_date) worker.run() +def run_arxiv(args): + worker = HarvestArxivWorker( + kafka_hosts=args.kafka_hosts, + produce_topic="fatcat-{}.arxiv".format(args.env), + state_topic="fatcat-{}.arxiv-state".format(args.env), + start_date=args.start_date, + end_date=args.end_date) + worker.run() + +def run_pubmed(args): + worker = HarvestPubmedWorker( + kafka_hosts=args.kafka_hosts, + produce_topic="fatcat-{}.pubmed".format(args.env), + state_topic="fatcat-{}.pubmed-state".format(args.env), + start_date=args.start_date, + end_date=args.end_date) + worker.run() + +def run_doaj_article(args): + worker = HarvestDoajArticleWorker( + kafka_hosts=args.kafka_hosts, + produce_topic="fatcat-{}.doaj-article".format(args.env), + state_topic="fatcat-{}.doaj-article-state".format(args.env), + start_date=args.start_date, + end_date=args.end_date) + worker.run() + +def run_doaj_journal(args): + worker = HarvestDoajJournalWorker( + kafka_hosts=args.kafka_hosts, + produce_topic="fatcat-{}.doaj-journal".format(args.env), + state_topic="fatcat-{}.doaj-journal-state".format(args.env), + start_date=args.start_date, + end_date=args.end_date) + worker.run() + + def mkdate(raw): return datetime.datetime.strptime(raw, "%Y-%m-%d").date() @@ -59,6 +98,18 @@ def main(): sub_datacite = subparsers.add_parser('datacite') sub_datacite.set_defaults(func=run_datacite) + sub_arxiv = subparsers.add_parser('arxiv') + sub_arxiv.set_defaults(func=run_arxiv) + + sub_pubmed = subparsers.add_parser('pubmed') + sub_pubmed.set_defaults(func=run_pubmed) + + # DOAJ stuff disabled because API range-requests are broken + #sub_doaj_article = subparsers.add_parser('doaj-article') + #sub_doaj_article.set_defaults(func=run_doaj_article) + #sub_doaj_journal = subparsers.add_parser('doaj-journal') + #sub_doaj_journal.set_defaults(func=run_doaj_journal) + args = parser.parse_args() if not args.__dict__.get("func"): print("tell me what to do!") diff --git a/python/fatcat_tools/harvest/__init__.py b/python/fatcat_tools/harvest/__init__.py index 4de2cbde..7d814696 100644 --- a/python/fatcat_tools/harvest/__init__.py +++ b/python/fatcat_tools/harvest/__init__.py @@ -1,3 +1,5 @@ from .harvest_common import HarvestState from .doi_registrars import HarvestCrossrefWorker, HarvestDataciteWorker +from .oaipmh import HarvestArxivWorker, HarvestPubmedWorker,\ + HarvestDoajArticleWorker, HarvestDoajJournalWorker diff --git a/python/fatcat_tools/harvest/doi_registrars.py b/python/fatcat_tools/harvest/doi_registrars.py index d5e4b7ec..10492c17 100644 --- a/python/fatcat_tools/harvest/doi_registrars.py +++ b/python/fatcat_tools/harvest/doi_registrars.py @@ -10,15 +10,13 @@ import datetime from pykafka import KafkaClient from fatcat_tools.workers import most_recent_message -from .harvest_common import HarvestState +from .harvest_common import HarvestState, DATE_FMT # Skip pylint due to: # AttributeError: 'NoneType' object has no attribute 'scope' # in 'astroid/node_classes.py' # pylint: skip-file -DATE_FMT = "%Y-%m-%d" - class HarvestCrossrefWorker: """ @@ -68,7 +66,6 @@ class HarvestCrossrefWorker: 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 params(self, date_str): @@ -86,6 +83,9 @@ class HarvestCrossrefWorker: params['cursor'] = resp['message']['next-cursor'] return params + def extract_key(self, obj): + return obj['DOI'].encode('utf-8') + def fetch_date(self, date): produce_topic = self.kafka.topics[self.produce_topic] @@ -112,7 +112,7 @@ class HarvestCrossrefWorker: self.extract_total(resp), http_resp.elapsed)) #print(json.dumps(resp)) for work in items: - producer.produce(json.dumps(work).encode('utf-8')) + producer.produce(json.dumps(work).encode('utf-8'), partition_key=self.extract_key(work)) if len(items) < self.api_batch_size: break params = self.update_params(params, resp) @@ -181,6 +181,9 @@ class HarvestDataciteWorker(HarvestCrossrefWorker): def extract_total(self, resp): return resp['meta']['total'] + def extract_key(self, obj): + return obj['doi'].encode('utf-8') + def update_params(self, params, resp): params['page[number]'] = resp['meta']['page'] + 1 return params diff --git a/python/fatcat_tools/harvest/oaipmh.py b/python/fatcat_tools/harvest/oaipmh.py new file mode 100644 index 00000000..c3cb90db --- /dev/null +++ b/python/fatcat_tools/harvest/oaipmh.py @@ -0,0 +1,157 @@ + +""" +OAI-PMH protocol: + https://sickle.readthedocs.io/en/latest/ + +Pubmed + 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 + +arxiv + some APIs work on a per-version basis, others do not + + 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 + +doaj + https://github.com/miku/doajfetch + +----- + +actually, just going to re-use https://github.com/miku/metha for OAI-PMH stuff + => shell script from cronjob + => call metha-sync daily + => metha-cat -since | kafkacat output + => echo "date" | kafkat state + => some shell trick (comm?) to find missing dates; for each, do metha-cat into kafka + +or, just skip kafka for this stuff for now? hrm. + +crossref-like stuff is far enough along to keep + +## More Miku Magic! + +wowa, JSTOR KBART files! + http://www.jstor.org/kbart/collections/all-archive-titles + +https://github.com/miku/ldjtab: faster than jq for just grabbing + +sort can be told how much memory to use; eg: `sort -S50%`, and threads to use + +""" + +import re +import sys +import csv +import json +import time +import requests +import itertools +import datetime +from pykafka import KafkaClient +import sickle + +from fatcat_tools.workers import most_recent_message +from .harvest_common import HarvestState, DATE_FMT + + +class HarvestOaiPmhWorker: + """ + Base class for OAI-PMH harvesters. + + Based on Crossref importer + """ + + + 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 = KafkaClient(hosts=kafka_hosts, broker_version="1.0.0") + + 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.state = HarvestState(start_date, end_date) + self.state.initialize_from_kafka(self.kafka.topics[self.state_topic]) + + + def fetch_date(self, date): + + api = sickle.Sickle(self.endpoint_url) + date_str = date.strftime(DATE_FMT) + produce_topic = self.kafka.topics[self.produce_topic] + # this dict kwargs hack is to work around 'from' as a reserved python keyword + # recommended by sickle docs + records = api.ListRecords(**{ + 'metadataPrefix': self.metadata_prefix, + 'from': date_str, + 'until': date_str, + }) + + count = 0 + with produce_topic.get_producer() as producer: + for item in records: + count += 1 + if count % 50 == 0: + print("... up to {}".format(count)) + producer.produce(item.raw.encode('utf-8'), partition_key=item.header.identifier.encode('utf-8')) + + 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.kafka.topics[self.state_topic]) + continue + + if continuous: + print("Sleeping {} seconds...".format(self.loop_sleep)) + time.sleep(self.loop_sleep()) + else: + break + print("{} DOI ingest caught up".format(self.name)) + + +class HarvestArxivWorker(HarvestOaiPmhWorker): + + def __init__(self, **kwargs): + super().__init__(**kwargs) + self.endpoint_url = "https://export.arxiv.org/oai2" + self.metadata_prefix = "arXiv" + + +class HarvestPubmedWorker(HarvestOaiPmhWorker): + + 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" + + +class HarvestDoajJournalWorker(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" + self.metadata_prefix = "oai_dc" + + +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" + -- cgit v1.2.3