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-rw-r--r--python/fatcat_tools/importers/__init__.py3
-rw-r--r--python/fatcat_tools/importers/common.py36
-rw-r--r--python/fatcat_tools/importers/jalc.py310
3 files changed, 348 insertions, 1 deletions
diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index f5ff43e5..ecbfe38e 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -12,8 +12,9 @@ To run an import you combine two classes; one each of:
"""
-from .common import EntityImporter, JsonLinePusher, LinePusher, CsvPusher, SqlitePusher, KafkaJsonPusher, make_kafka_consumer, clean
+from .common import EntityImporter, JsonLinePusher, LinePusher, CsvPusher, SqlitePusher, Bs4XmlFilePusher, KafkaJsonPusher, make_kafka_consumer, clean, is_cjk
from .crossref import CrossrefImporter, CROSSREF_TYPE_MAP
+from .jalc import JalcImporter
from .grobid_metadata import GrobidMetadataImporter
from .journal_metadata import JournalMetadataImporter
from .matched import MatchedImporter
diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py
index 282f775c..7fca38cf 100644
--- a/python/fatcat_tools/importers/common.py
+++ b/python/fatcat_tools/importers/common.py
@@ -7,13 +7,16 @@ import ftfy
import sqlite3
import itertools
import subprocess
+import unicodedata
from collections import Counter
import pykafka
+from bs4 import BeautifulSoup
import fatcat_client
from fatcat_client.rest import ApiException
+DATE_FMT = "%Y-%m-%d"
SANE_MAX_RELEASES = 200
SANE_MAX_URLS = 100
@@ -52,6 +55,23 @@ def test_clean():
assert clean('<b>a&amp;b</b>') == '<b>a&amp;b</b>'
assert clean('<b>a&amp;b</b>', force_xml=True) == '<b>a&b</b>'
+def is_cjk(s):
+ if not s:
+ return False
+ return unicodedata.name(s[0]).startswith("CJK")
+
+def test_is_cjk():
+ assert is_cjk(None) == False
+ assert is_cjk('') == False
+ assert is_cjk('blah') == False
+ assert is_cjk('岡, 鹿, 梨, 阜, 埼') == True
+ assert is_cjk('菊') == True
+ assert is_cjk('ひヒ') == True
+ assert is_cjk('english with ひヒ') == True
+ assert is_cjk('き゚ゅ') == True
+ assert is_cjk('水道') == True
+ assert is_cjk('ㄴ, ㄹ, ㅁ, ㅂ, ㅅ') == True
+
DOMAIN_REL_MAP = {
"archive.org": "archive",
# LOCKSS, Portico, DuraSpace, etc would also be "archive"
@@ -456,6 +476,22 @@ class SqlitePusher(RecordPusher):
return counts
+class Bs4XmlFilePusher(RecordPusher):
+
+ def __init__(self, importer, xml_file, record_tag, **kwargs):
+ self.importer = importer
+ self.xml_file = xml_file
+ self.record_tag = record_tag
+
+ def run(self):
+ soup = BeautifulSoup(self.xml_file, "xml")
+ for record in soup.find_all(self.record_tag):
+ self.importer.push_record(record)
+ counts = self.importer.finish()
+ print(counts)
+ return counts
+
+
class KafkaJsonPusher(RecordPusher):
def __init__(self, importer, kafka_hosts, kafka_env, topic_suffix, group, **kwargs):
diff --git a/python/fatcat_tools/importers/jalc.py b/python/fatcat_tools/importers/jalc.py
new file mode 100644
index 00000000..d7b89727
--- /dev/null
+++ b/python/fatcat_tools/importers/jalc.py
@@ -0,0 +1,310 @@
+
+import sys
+import json
+import sqlite3
+import datetime
+import itertools
+import subprocess
+from bs4 import BeautifulSoup
+
+import fatcat_client
+from .common import EntityImporter, clean, is_cjk, DATE_FMT
+
+
+class JalcImporter(EntityImporter):
+ """
+ Importer for JALC DOI metadata.
+
+ NOTE: some JALC DOIs seem to get cross-registered with Crossref
+ """
+
+ def __init__(self, api, issn_map_file, **kwargs):
+
+ eg_desc = kwargs.get('editgroup_description',
+ "Automated import of JALC DOI metadata")
+ eg_extra = kwargs.get('editgroup_extra', dict())
+ eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.JalcImporter')
+ super().__init__(api,
+ issn_map_file=issn_map_file,
+ editgroup_description=eg_desc,
+ editgroup_extra=eg_extra,
+ **kwargs)
+
+ self.create_containers = kwargs.get('create_containers')
+ extid_map_file = kwargs.get('extid_map_file')
+ self.extid_map_db = None
+ if extid_map_file:
+ db_uri = "file:{}?mode=ro".format(extid_map_file)
+ print("Using external ID map: {}".format(db_uri))
+ self.extid_map_db = sqlite3.connect(db_uri, uri=True)
+ else:
+ print("Not using external ID map")
+
+ self.read_issn_map_file(issn_map_file)
+
+ def lookup_ext_ids(self, doi):
+ if self.extid_map_db is None:
+ return dict(core_id=None, pmid=None, pmcid=None, wikidata_qid=None, arxiv_id=None, jstor_id=None)
+ row = self.extid_map_db.execute("SELECT core, pmid, pmcid, wikidata FROM ids WHERE doi=? LIMIT 1",
+ [doi.lower()]).fetchone()
+ if row is None:
+ return dict(core_id=None, pmid=None, pmcid=None, wikidata_qid=None, arxiv_id=None, jstor_id=None)
+ row = [str(cell or '') or None for cell in row]
+ return dict(
+ core_id=row[0],
+ pmid=row[1],
+ pmcid=row[2],
+ wikidata_qid=row[3],
+ # TODO:
+ arxiv_id=None,
+ jstor_id=None,
+ )
+
+ def want(self, obj):
+ return True
+
+ def parse_record(self, record):
+ """
+ record is a beautiful soup object
+ returns a ReleaseEntity, or None
+
+ In JALC metadata, both English and Japanese records are given for most
+ fields.
+ """
+
+ extra = dict()
+ extra_jalc = dict()
+
+ titles = record.find_all("title")
+ title = titles[0].string.strip()
+ original_title = None
+ if title.endswith('.'):
+ title = title[:-1]
+ if len(titles) > 1:
+ original_title = titles[1].string.strip()
+ if original_title.endswith('.'):
+ original_title = original_title[:-1]
+
+ doi = None
+ if record.doi:
+ doi = record.doi.string.lower().strip()
+ assert doi.startswith('10.')
+
+ contribs = []
+ people = record.find_all("Person")
+ if people and (len(people) % 2 == 0) and is_cjk(people[1].find('name').string):
+ # both english and japanese names are included for every author
+ for i in range(int(len(people)/2)):
+ eng = people[i*2]
+ jpn = people[i*2 + 1]
+ # there isn't always an english name though? TODO
+ name = eng
+ if not name.find('name'):
+ name = jpn
+ contrib = fatcat_client.ReleaseContrib(
+ raw_name=clean(name.find('name').string),
+ given_name=clean(name.find('givenName').string),
+ surname=clean(name.find('familyName').string),
+ role='author',
+ )
+ if eng.find('name') and jpn.find('name'):
+ contrib.extra = {
+ 'original_name': {
+ 'lang': 'ja',
+ 'raw_name': clean(jpn.find('name').string),
+ 'given_name': clean(jpn.find('givenName').string),
+ 'surname': clean(jpn.find('familyName').string),
+ }}
+ contribs.append(contrib)
+ elif people:
+ # TODO: test for this codepath?
+ for eng in people:
+ contrib = dict(
+ raw_name=clean(eng.find('name').string),
+ given_name=clean(eng.find('givenName').string),
+ surname=clean(eng.find('familyName').string),
+ role='author',
+ )
+ contribs.append(contrib)
+
+ release_year = None
+ release_date = None
+ date = record.date or None
+ if date:
+ date = date.string
+ if len(date) is 10:
+ release_date = datetime.datetime.strptime(date['completed-date'], DATE_FMT).date()
+ release_year = release_date.year
+ release_date = release_date.isoformat()
+ elif len(date) is 4:
+ release_year = int(date)
+
+ pages = None
+ if record.startingPage:
+ pages = record.startingPage.string
+ if record.endingPage:
+ pages = "{}-{}".format(pages, record.endingPage.string)
+ volume = None
+ if record.volume:
+ volume = record.volume.string
+ issue = None
+ if record.number:
+ # note: number/issue transform
+ issue = record.number.string
+
+ # container
+ issn = None
+ issn_list = record.find_all("issn")
+ if issn_list:
+ # if we wanted the other ISSNs, would also need to uniq the list.
+ # But we only need one to lookup ISSN-L/container
+ issn = issn_list[0].string
+ issnl = self.issn2issnl(issn)
+ container_id = None
+ if issnl:
+ container_id = self.lookup_issnl(issnl)
+
+ publisher = None
+ container_name = None
+ container_extra = dict()
+
+ if record.publicationName:
+ pubs = [p.string.strip() for p in record.find_all("publicationName")]
+ pubs = [p for p in pubs if p]
+ assert(pubs)
+ if len(pubs) > 1 and pubs[0] == pubs[1]:
+ pubs = [pubs[0]]
+ elif len(pubs) > 1 and is_cjk(pubs[0]):
+ # ordering is not reliable
+ pubs = [pubs[1], pubs[0]]
+ container_name = clean(pubs[0])
+ if len(pubs) > 1:
+ orig_container_name = pubs[1]
+ container_extra['original_name'] = clean(pubs[1])
+
+ if record.publisher:
+ pubs = [p.string.strip() for p in record.find_all("publisher")]
+ pubs = [p for p in pubs if p]
+ if len(pubs) > 1 and pubs[0] == pubs[1]:
+ pubs = [pubs[0]]
+ elif len(pubs) > 1 and is_cjk(pubs[0]):
+ # ordering is not reliable
+ pubs = [pubs[1], pubs[0]]
+ publisher = clean(pubs[0])
+ if len(pubs) > 1:
+ container_extra['publisher_alt_name'] = pubs[1]
+
+ if (container_id is None and self.create_containers and (issnl is not None)
+ and container_name):
+ # name, type, publisher, issnl
+ # extra: issnp, issne, original_name, languages, country
+ container_extra['country'] = 'jp'
+ container_extra['languages'] = ['ja']
+ ce = fatcat_client.ContainerEntity(
+ name=container_name,
+ container_type='journal',
+ publisher=publisher,
+ issnl=issnl,
+ extra=(container_extra or None))
+ ce_edit = self.create_container(ce)
+ container_id = ce_edit.ident
+
+ # the vast majority of works are in japanese
+ # TODO: any indication when *not* in japanese?
+ lang = "ja"
+
+ # reasonable default for this collection
+ release_type = "article-journal"
+
+ # external identifiers
+ extids = self.lookup_ext_ids(doi=doi)
+
+ # extra:
+ # translation_of
+ # aliases
+ # container_name
+ # group-title
+ # always put at least an empty dict here to indicate the DOI registrar
+ # (informally)
+ extra['jalc'] = extra_jalc
+
+ re = fatcat_client.ReleaseEntity(
+ work_id=None,
+ title=title,
+ original_title=original_title,
+ release_type="article-journal",
+ release_stage='published',
+ release_date=release_date,
+ release_year=release_year,
+ ext_ids=fatcat_client.ReleaseExtIds(
+ doi=doi,
+ pmid=extids['pmid'],
+ pmcid=extids['pmcid'],
+ wikidata_qid=extids['wikidata_qid'],
+ core=extids['core_id'],
+ arxiv=extids['arxiv_id'],
+ jstor=extids['jstor_id'],
+ ),
+ volume=volume,
+ issue=issue,
+ pages=pages,
+ publisher=publisher,
+ language=lang,
+ #license_slug
+
+ # content, mimetype, lang
+ #abstracts=abstracts,
+
+ # raw_name, role, raw_affiliation, extra
+ contribs=contribs,
+
+
+ extra=extra,
+ )
+ return re
+
+ def try_update(self, re):
+
+ # lookup existing DOI
+ existing = None
+ try:
+ existing = self.api.lookup_release(doi=re.ext_ids.doi)
+ except fatcat_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+ # doesn't exist, need to insert
+ return True
+
+ # eventually we'll want to support "updates", but for now just skip if
+ # entity already exists
+ if existing:
+ self.counts['exists'] += 1
+ return False
+ return False
+
+ def insert_batch(self, batch):
+ self.api.create_release_auto_batch(fatcat_client.ReleaseAutoBatch(
+ editgroup=fatcat_client.Editgroup(
+ description=self.editgroup_description,
+ extra=self.editgroup_extra),
+ entity_list=batch))
+
+ def parse_file(self, handle):
+ """
+ Helper for testing; can run this file stand-alone instead of using a pusher
+ """
+
+ # 1. open with beautiful soup
+ soup = BeautifulSoup(handle, "xml")
+
+ # 2. iterate over articles, call parse_article on each
+ for record in soup.find_all("Description"):
+ resp = self.parse_record(record)
+ #print(json.dumps(resp))
+ print(resp)
+ #sys.exit(-1)
+
+
+if __name__=='__main__':
+ parser = JalcXmlParser()
+ parser.parse_file(open(sys.argv[1]))
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-23 06:55:29 +0000