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ArXivDirect.py
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ArXivDirect.py
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# on localhost:
# uses libxml2 via virtualenv --system-site-packages
# and adspy via mount of /proj
import sys
try:
import ads.ADSCachedExports as ads_ex
import ads.journal_parser as ads_jp
import ads.Keywords as kw_normalizer
import ads.ArtDefs as ArtDefs
except ImportError:
sys.path.append('/proj/ads/soft/python/lib/site-packages')
try:
import ads.ADSCachedExports as ads_ex
import ads.journal_parser as ads_jp
import ads.Keywords as kw_normalizer
import ads.ArtDefs as ArtDefs
except ImportError as e:
print 'Unable to import ads libraries: {}'.format(e)
def add_direct(record, json_timestamp=None, current_record=None,
origin=None, matched_preprint=False, fulltext=None):
"""
return a complete ADSRecords instance from direct data with xml
"""
bibcode = record['bibcode']
if not bibcode:
raise ads_ex.InvalidBibcode('Empty bibcode.')
adsr = ads_ex.ADSRecords('full', 'XML', cacheLooker=False)
bibliographic_info = ads_ex.get_bibliographic_info(bibcode)
# create a new record for the Direct entry
if current_record is None:
rec_properties = {'bibcode': bibcode, 'entry_date': record['pubdate']}
adsr.current_record = ads_ex.xml_node(adsr.xml_records, 'record', properties=rec_properties)
else:
adsr.current_record = current_record
# create a new metadata tag for the Direct entry abstract
datasource = 'ARXIV'
abs_properties = {'origin': datasource, 'type': 'general', 'primary': 'True', 'alternate_journal': 'False'}
adsr.current_abstract = ads_ex.xml_node(adsr.current_record, 'metadata', properties=abs_properties)
# begin creating subfields under this metadata tag
creation_time = ads_ex.iso_8601_time(None)
modif_time = creation_time
ads_ex.xml_node(adsr.current_abstract, 'creation_time', creation_time)
ads_ex.xml_node(adsr.current_abstract, 'modification_time', modif_time)
ads_ex.xml_node(adsr.current_abstract, 'bibcode', bibcode)
(year, month, dum) = record['pubdate'].split('-')
dates = {'date-preprint': '%s-%s-00' % (year, month)}
ads_ex.add_dates(adsr.current_abstract, dates)
title = record['title'].replace('\n ','')
ads_ex.xml_node(adsr.current_abstract, 'title', title)
abstract_field = record['abstract']
abstract_field = ads_ex.UNICODE_HANDLER.remove_control_chars(abstract_field)
try:
abstract_field = ads_ex.UNICODE_HANDLER.ent2xml(abstract_field)
except:
pass
ads_ex.xml_node(adsr.current_abstract, 'abstract', abstract_field.strip())
authors = ads_ex.UNICODE_HANDLER.ent2u(record['authors'])
authors = ads_ex.UNICODE_HANDLER.remove_control_chars(authors)
authors = ads_ex.RE_INITIAL.sub('. ', authors)
authors = authors.strip().strip(';')
author_number = 0
for index, author_name in enumerate(authors.split(';')):
normalized_author = ads_ex.normalize_author(author_name)
author_number += 1
author = {
'nr': str(author_number),
'western': author_name.strip(),
'normalized': normalized_author,
'affiliation': None,
'id': None,
'email': None,
'native': None,
'author_id': None,
'type': 'regular'
}
ads_ex.add_author(adsr.current_abstract, author, 'full')
journal = record['publication']
ads_ex.xml_node(adsr.current_abstract, 'journal', journal)
canonical_journal = ads_jp.get_canonical_journal(bibcode)
ads_ex.xml_node(adsr.current_abstract, 'canonical_journal', canonical_journal)
electronic_id = journal.replace('eprint ', '')
ads_ex.xml_node(adsr.current_abstract, 'electronic_id', electronic_id)
number_pages = 0
ads_ex.xml_node(adsr.current_abstract, 'number_pages', str(number_pages))
databases = set()
try:
field = ads_ex.UNICODE_HANDLER.ent2xml(record['keywords'])
except:
try:
field = record['keywords']
except:
pass
if len(field) > 0:
adsr.arxiv_categories = ads_ex.xml_node(adsr.current_abstract, 'arxivcategories')
all_keywords = {}
keywords = []
main_category = 'main'
for keyword in field.split(';'):
keyword = keyword.strip()
try:
category = ArtDefs.cat2channel[keyword]
except:
pass
else:
ads_ex.xml_node(adsr.arxiv_categories, 'arxivcategory', category, {'type': main_category})
if category.find('.') >= 0:
category = category.split('.')[0]
try:
databases.add(ads_ex.ARXIV_DATABASE[category])
except:
pass
main_category = None
keywords.append((keyword, kw_normalizer.get_normalized_keyword(keyword)))
all_keywords.setdefault('arXiv', []).extend(keywords)
ads_ex.add_keywords(adsr.current_abstract, all_keywords)
pubnote = "; ".join([x.replace('\n', '') for x in record['comments']])
ads_ex.xml_node(adsr.current_abstract,'pubnote', pubnote.replace(' ', ' '))
# Properties
adsr.current_properties = ads_ex.xml_node(adsr.current_record, 'metadata',
properties={'type': 'properties',
'primary': 'False',
'origin': 'ADS metadata',
'alternate_journal': 'False'})
ads_ex.xml_node(adsr.current_properties, 'JSON_timestamp', ' dummy string')
ads_ex.add_databases(adsr.current_properties, databases)
ads_ex.xml_node(adsr.current_properties, 'pubtype', 'eprint')
ads_ex.xml_node(adsr.current_properties, 'private', 0)
ads_ex.xml_node(adsr.current_properties, 'ocrabstract', 0)
# preprint_id = electronic_id.replace('arXiv:', '')
preprint_id = electronic_id
ads_ex.xml_node(adsr.current_properties, 'preprint', preprint_id)
ads_ex.xml_node(adsr.current_properties, 'nonarticle', 0)
ads_ex.xml_node(adsr.current_properties, 'refereed', 0)
ads_ex.xml_node(adsr.current_properties, 'openaccess', 1)
ads_ex.xml_node(adsr.current_properties, 'eprint_openaccess', 1)
ads_ex.xml_node(adsr.current_properties, 'pub_openaccess', 0)
ads_ex.xml_node(adsr.current_properties, 'note', 0)
ads_ex.xml_node(adsr.current_properties, 'ads_openaccess', 0)
# Relations
adsr.current_relations = ads_ex.xml_node(adsr.current_record, 'metadata',
properties={'type': 'relations',
'primary': 'False',
'origin': 'ADS metadata',
'alternate_journal': 'False'})
ads_ex.xml_node(adsr.current_relations, 'preprintid', preprint_id, {'ecode': bibcode})
ads_ex.xml_node(adsr.current_relations, 'alternates', None)
adsr.linksection = ads_ex.xml_node(adsr.current_relations, 'links')
ads_ex.xml_node(adsr.linksection, 'link',
properties={'type': 'preprint',
'url': record['properties']['HTML'],
'access': 'open'})
return adsr
#def main():
#
# import gzip
#
# reclist = list()
## meta_dir = '/proj/ads/abstracts/sources/ArXiv/oai/arXiv.org/'
## reclist.append(meta_dir + '1711/05739')
## reclist.append(meta_dir + '1710/08505')
#
# caldate = '2018-07-10'
#
# ARXIV_INCOMING_ABS_DIR = '/proj/ads/abstracts/sources/ArXiv'
# ARXIV_UPDATE_AGENT_DIR = ARXIV_INCOMING_ABS_DIR + '/UpdateAgent'
# ARXIV_ARCHIVE_ABS_DIR = ARXIV_INCOMING_ABS_DIR + '/oai/arXiv.org'
#
# logfile = ARXIV_UPDATE_AGENT_DIR + '/UpdateAgent.out.' + caldate + '.gz'
# with gzip.open(logfile,'r') as flist:
# for l in flist.readlines():
# # sample line: oai/arXiv.org/0706/2491 2018-06-13T01:00:29
# a = ARXIV_INCOMING_ABS_DIR + '/' + l.split()[0]
# reclist.append(a)
#
# for f in reclist:
# with open(f,'rU') as fp:
# input_doc = arxiv.ArxivParser()
# r = input_doc.parse(fp)
# output = adsDirectRecord('full','XML',cacheLooker=False)
# output.addDirect(r)
## print output.root.serialize()
# if r['bibcode'] == '2018arXiv180703779S':
# print r
#
#if __name__ == '__main__':
# main()