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
|
"""
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 <whenever> | 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.name = "unnamed"
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
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
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("{} OAI-PMH 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"
self.name = "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"
self.name = "pubmed"
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"
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"
|
