summaryrefslogtreecommitdiffstats
path: root/python/fatcat_tools/harvest/oaipmh.py
blob: ab424482b3a29df4347b1e682867bf31798962ac (plain)
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

import re
import sys
import csv
import json
import time
import itertools
import datetime
import requests
import sickle
from confluent_kafka import Producer

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,
            'delivery.report.only.error': True,
            'default.topic.config':
                {'request.required.acks': 'all'},
        }

        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 kafka_produce_delivery_callback(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 fetch_date(self, date):

        producer = Producer(self.kafka_config)

        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=self.kafka_produce_delivery_callback)
            producer.poll(0)
        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"