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import re
import sys
import csv
import json
import itertools
import subprocess
from collections import Counter
import pykafka
import fatcat_client
from fatcat_client.rest import ApiException
# from: https://docs.python.org/3/library/itertools.html
def grouper(iterable, n, fillvalue=None):
"Collect data into fixed-length chunks or blocks"
args = [iter(iterable)] * n
return itertools.zip_longest(*args, fillvalue=fillvalue)
def make_kafka_consumer(hosts, env, topic_suffix, group):
topic_name = "fatcat-{}.{}".format(env, topic_suffix).encode('utf-8')
client = pykafka.KafkaClient(hosts=hosts, broker_version="1.0.0")
consume_topic = client.topics[topic_name]
print("Consuming from kafka topic {}, group {}".format(topic_name, group))
consumer = consume_topic.get_balanced_consumer(
consumer_group=group.encode('utf-8'),
managed=True,
auto_commit_enable=True,
auto_commit_interval_ms=30000, # 30 seconds
compacted_topic=True,
)
return consumer
class FatcatImporter:
"""
Base class for fatcat importers
"""
def __init__(self, api, **kwargs):
eg_extra = kwargs.get('editgroup_extra', dict())
eg_extra['git_rev'] = eg_extra.get('git_rev',
subprocess.check_output(["git", "describe", "--always"]).strip()).decode('utf-8')
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.FatcatImporter')
self.api = api
self._editgroup_description = kwargs.get('editgroup_description')
self._editgroup_extra = kwargs.get('editgroup_extra')
issn_map_file = kwargs.get('issn_map_file')
self._issnl_id_map = dict()
self._orcid_id_map = dict()
self._doi_id_map = dict()
if issn_map_file:
self.read_issn_map_file(issn_map_file)
self._orcid_regex = re.compile("^\\d{4}-\\d{4}-\\d{4}-\\d{3}[\\dX]$")
self.counts = Counter({'insert': 0, 'update': 0, 'processed_lines': 0})
def _editgroup(self):
eg = fatcat_client.Editgroup(
description=self._editgroup_description,
extra=self._editgroup_extra,
)
return self.api.create_editgroup(eg)
def describe_run(self):
print("Processed {} lines, inserted {}, updated {}.".format(
self.counts['processed_lines'], self.counts['insert'], self.counts['update']))
def create_row(self, row, editgroup_id=None):
# sub-classes expected to implement this
raise NotImplementedError
def create_batch(self, rows, editgroup_id=None):
# sub-classes expected to implement this
raise NotImplementedError
def process_source(self, source, group_size=100):
"""Creates and auto-accepts editgroup every group_size rows"""
eg = self._editgroup()
i = 0
for i, row in enumerate(source):
self.create_row(row, editgroup_id=eg.editgroup_id)
if i > 0 and (i % group_size) == 0:
self.api.accept_editgroup(eg.editgroup_id)
eg = self._editgroup()
self.counts['processed_lines'] += 1
if i == 0 or (i % group_size) != 0:
self.api.accept_editgroup(eg.editgroup_id)
def process_batch(self, source, size=50, decode_kafka=False):
"""Reads and processes in batches (not API-call-per-)"""
for rows in grouper(source, size):
if decode_kafka:
rows = [msg.value.decode('utf-8') for msg in rows]
self.counts['processed_lines'] += len(rows)
eg = self._editgroup()
self.create_batch(rows, editgroup_id=eg.editgroup_id)
def process_csv_source(self, source, group_size=100, delimiter=','):
reader = csv.DictReader(source, delimiter=delimiter)
self.process_source(reader, group_size)
def process_csv_batch(self, source, size=50, delimiter=','):
reader = csv.DictReader(source, delimiter=delimiter)
self.process_batch(reader, size)
def is_issnl(self, issnl):
return len(issnl) == 9 and issnl[4] == '-'
def lookup_issnl(self, issnl):
"""Caches calls to the ISSN-L lookup API endpoint in a local dict"""
if issnl in self._issnl_id_map:
return self._issnl_id_map[issnl]
container_id = None
try:
rv = self.api.lookup_container(issnl=issnl)
container_id = rv.ident
except ApiException as ae:
# If anything other than a 404 (not found), something is wrong
assert ae.status == 404
self._issnl_id_map[issnl] = container_id # might be None
return container_id
def is_orcid(self, orcid):
return self._orcid_regex.match(orcid) is not None
def lookup_orcid(self, orcid):
"""Caches calls to the Orcid lookup API endpoint in a local dict"""
if not self.is_orcid(orcid):
return None
if orcid in self._orcid_id_map:
return self._orcid_id_map[orcid]
creator_id = None
try:
rv = self.api.lookup_creator(orcid=orcid)
creator_id = rv.ident
except ApiException as ae:
# If anything other than a 404 (not found), something is wrong
assert ae.status == 404
self._orcid_id_map[orcid] = creator_id # might be None
return creator_id
def is_doi(self, doi):
return doi.startswith("10.") and doi.count("/") >= 1
def lookup_doi(self, doi):
"""Caches calls to the doi lookup API endpoint in a local dict"""
assert self.is_doi(doi)
doi = doi.lower()
if doi in self._doi_id_map:
return self._doi_id_map[doi]
release_id = None
try:
rv = self.api.lookup_release(doi=doi)
release_id = rv.ident
except ApiException as ae:
# If anything other than a 404 (not found), something is wrong
assert ae.status == 404
self._doi_id_map[doi] = release_id # might be None
return release_id
def read_issn_map_file(self, issn_map_file):
print("Loading ISSN map file...")
self._issn_issnl_map = dict()
for line in issn_map_file:
if line.startswith("ISSN") or len(line) == 0:
continue
(issn, issnl) = line.split()[0:2]
self._issn_issnl_map[issn] = issnl
# double mapping makes lookups easy
self._issn_issnl_map[issnl] = issnl
print("Got {} ISSN-L mappings.".format(len(self._issn_issnl_map)))
def issn2issnl(self, issn):
if issn is None:
return None
return self._issn_issnl_map.get(issn)
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