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import sys
import json
import datetime
import warnings
from bs4 import BeautifulSoup
import fatcat_client
from .common import EntityImporter, clean, LANG_MAP_MARC
# TODO: more entries?
JSTOR_CONTRIB_MAP = {
'author': 'author',
'editor': 'editor',
'translator': 'translator',
'illustrator': 'illustrator',
}
class JstorImporter(EntityImporter):
"""
Importer for JSTOR bulk XML metadata (eg, from their Early Journals
Collection)
"""
def __init__(self, api, issn_map_file, **kwargs):
eg_desc = kwargs.get('editgroup_description',
"Automated import of JSTOR XML metadata")
eg_extra = kwargs.get('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.JstorImporter')
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', True)
self.read_issn_map_file(issn_map_file)
def want(self, obj):
return True
def parse_record(self, article):
journal_meta = article.front.find("journal-meta")
article_meta = article.front.find("article-meta")
extra = dict()
extra_jstor = dict()
title = article_meta.find("article-title")
if title:
title = title.string.strip()
if title.endswith('.'):
title = title[:-1]
release_type = "article-journal"
if "[Abstract]" in title:
# TODO: strip the "[Abstract]" bit?
release_type = "abstract"
elif "[Editorial" in title:
release_type = "editorial"
elif "[Letter" in title:
release_type = "letter"
elif "[Poem" in title or "[Photograph" in title:
release_type = None
if title.startswith("[") and title.endswith("]"):
# strip brackets if that is all that is there (eg, translation or non-english)
title = title[1:-1]
# JSTOR journal-id
journal_ids = [j.string for j in journal_meta.find_all('journal-id')]
if journal_ids:
extra_jstor['journal_ids'] = journal_ids
journal_title = journal_meta.find("journal-title").string
publisher = journal_meta.find("publisher-name").string
issn = journal_meta.find("issn")
if issn:
issn = issn.string
if len(issn) == 8:
issn = "{}-{}".format(issn[0:4], issn[4:8])
else:
assert len(issn) == 9
issnl = self.issn2issnl(issn)
container_id = None
if issnl:
container_id = self.lookup_issnl(issnl)
# create container if it doesn't exist
if (container_id is None and self.create_containers and (issnl is not None)
and journal_title):
ce = fatcat_client.ContainerEntity(
issnl=issnl,
publisher=publisher,
container_type=self.map_container_type(release_type),
name=clean(journal_title, force_xml=True))
ce_edit = self.create_container(ce)
container_id = ce_edit.ident
self._issnl_id_map[issnl] = container_id
doi = article_meta.find("article-id", {"pub-id-type": "doi"})
if doi:
doi = doi.string.lower().strip()
jstor_id = article_meta.find("article-id", {"pub-id-type": "jstor"})
if jstor_id:
jstor_id = jstor_id.string
contribs = []
cgroup = article_meta.find("contrib-group")
if cgroup:
for c in cgroup.find_all("contrib"):
given = c.find("given-names")
surname = c.find("surname")
if given and surname:
name = "{} {}".format(given.string, surname.string)
elif surname:
name = surname.string
else:
name = None
role = JSTOR_CONTRIB_MAP.get(c['contrib-type'])
if not role and c['contrib-type']:
sys.stderr.write("NOT IN JSTOR_CONTRIB_MAP: {}".format(c['contrib-type']))
contribs.append(fatcat_client.ReleaseContrib(
role=JSTOR_CONTRIB_MAP.get(c['contrib-type']),
raw_name=clean(name),
given_name=clean(given.string),
surname=clean(surname.string),
))
release_year = None
release_date = None
pub_date = article_meta.find('pub-date')
if pub_date and pub_date.year:
release_year = int(pub_date.year.string)
if pub_date.month and pub_date.day:
release_date = datetime.date(
release_year,
int(pub_date.month.string),
int(pub_date.day.string))
if release_date.day == 1 and release_date.month == 1:
# suspect jan 1st dates get set by JSTOR when actual
# date not known (citation needed), so drop them
release_date = None
volume = None
if article_meta.volume:
volume = article_meta.volume.string or None
issue = None
if article_meta.issue:
issue = article_meta.issue.string or None
pages = None
if article_meta.find("page-range"):
pages = article_meta.find("page-range").string
elif article_meta.fpage:
pages = article_meta.fpage.string
language = None
cm = article_meta.find("custom-meta")
if cm.find("meta-name").string == "lang":
language = cm.find("meta-value").string
language = LANG_MAP_MARC.get(language)
if not language:
warnings.warn("MISSING MARC LANG: {}".format(cm.find("meta-value").string))
# JSTOR issue-id
if article_meta.find('issue-id'):
issue_id = clean(article_meta.find('issue-id').string)
if issue_id:
extra_jstor['issue_id'] = issue_id
# everything in JSTOR is published
release_stage = "published"
# extra:
# withdrawn_date
# translation_of
# subtitle
# aliases
# container_name
# group-title
# pubmed: retraction refs
if extra_jstor:
extra['jstor'] = extra_jstor
if not extra:
extra = None
re = fatcat_client.ReleaseEntity(
#work_id
title=title,
#original_title
release_type=release_type,
release_stage=release_stage,
release_date=release_date,
release_year=release_year,
ext_ids=fatcat_client.ReleaseExtIds(
doi=doi,
jstor=jstor_id,
),
volume=volume,
issue=issue,
pages=pages,
publisher=publisher,
language=language,
#license_slug
# content, mimetype, lang
#abstracts=abstracts,
contribs=contribs,
# key, year, container_name, title, locator
# extra: volume, authors, issue, publisher, identifiers
#refs=refs,
# name, type, publisher, issnl
# extra: issnp, issne, original_name, languages, country
container_id=container_id,
extra=extra,
)
return re
def try_update(self, re):
# first, lookup existing by JSTOR id (which much be defined)
existing = None
try:
existing = self.api.lookup_release(jstor=re.ext_ids.jstor)
except fatcat_client.rest.ApiException as err:
if err.status != 404:
raise err
# then try DOI lookup if there is one (try JSTOR prefix+jstor_id if
# there isn't a DOI set)
if not existing:
doi = re.ext_ids.doi
if not doi:
doi = "10.2307/{}".format(re.ext_ids.jstor)
try:
existing = self.api.lookup_release(doi=doi)
except fatcat_client.rest.ApiException as err:
if err.status != 404:
raise err
if existing and existing.ext_ids.jstor:
# don't update if it already has JSTOR ID
self.counts['exists'] += 1
return False
elif existing:
# but do update if only DOI was set
existing.ext_ids.jstor = re.ext_ids.jstor
existing.extra['jstor'] = re.extra['jstor']
self.api.update_release(self.get_editgroup_id(), existing.ident, existing)
self.counts['update'] += 1
return False
return True
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):
# 1. open with beautiful soup
soup = BeautifulSoup(handle, "xml")
# 2. iterate over articles, call parse_article on each
for article in soup.find_all("article"):
resp = self.parse_record(article)
print(json.dumps(resp))
#sys.exit(-1)
if __name__=='__main__':
parser = JstorImporter(None, None)
parser.parse_file(open(sys.argv[1]))
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