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app_utils.py
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app_utils.py
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import re
import sys
import time
import traceback
from os import listdir, rename, fdopen, pardir
from os.path import join, walk, exists, abspath
from invenio.bibrecord import record_add_field, record_xml_output
from invenio.errorlib import register_exception
from invenio.minidom_utils import (get_value_in_tag,
xml_to_text,
NoDOIError,
format_arxiv_id)
from xml.dom.minidom import parse
RE_ARXIV_ID = re.compile(r"\d+.\d+")
class APPParser(object):
def __init__(self):
self.references = None
def get_article(self, path):
return parse(open(path))
def get_title(self, xml):
try:
return get_value_in_tag(xml, "ArticleTitle")
except Exception, err:
print >> sys.stderr, "Can't find title"
def get_publication_information(self, xml):
try:
doi = get_value_in_tag(xml, "ArticleDOI")
if not doi:
raise ValueError("DOI not found")
except Exception, err:
print >> sys.stderr, "Can't find doi: %s" % err
raise
#journal, issn, volume, issue, first_page, last_page, year
journal = get_value_in_tag(xml, "JournalAbbreviatedTitle")
if journal == 'J. High Energ. Phys.':
journal = 'JHEP'
issn = get_value_in_tag(xml, "JournalAbbreviatedTitle")
volume = get_value_in_tag(xml, "VolumeIDStart")[2:] + "%02d" % int(get_value_in_tag(xml, "IssueIDStart"))
issue = ""
first_page = "%03d" % int(get_value_in_tag(xml, "ArticleSequenceNumber"))
pages = get_value_in_tag(xml, "ArticleLastPage")
year = get_value_in_tag(xml, "VolumeIDStart")
return journal, issn, volume, issue, first_page, pages, year, doi
def get_authors(self, xml):
authors = []
for author in xml.getElementsByTagName("Author"):
tmp = {}
surname = get_value_in_tag(author, "FamilyName")
if surname:
tmp["surname"] = surname
given_name = get_value_in_tag(author, "GivenName")
if given_name:
tmp["given_name"] = given_name.replace('\n', ' ')
# initials = get_value_in_tag(author, "ce:initials")
# if initials:
# tmp["initials"] = initials
# It's not there
# orcid = author.getAttribute('orcid').encode('utf-8')
# if orcid:
# tmp["orcid"] = orcid
emails = author.getElementsByTagName("Email")
for email in emails:
if email.getAttribute("type").encode('utf-8') in ('email', ''):
tmp["email"] = xml_to_text(email)
break
# cross_refs = author.getElementsByTagName("ce:cross-ref")
# if cross_refs:
# tmp["cross_ref"] = []
# for cross_ref in cross_refs:
# tmp["cross_ref"].append(cross_ref.getAttribute("refid").encode('utf-8'))
tmp["affiliations_ids"] = []
aids = author.getAttribute("AffiliationIDS").split()
for aid in aids:
tmp["affiliations_ids"].append(aid.encode('utf-8'))
authors.append(tmp)
affiliations = {}
for affiliation in xml.getElementsByTagName("Affiliation"):
aff_id = affiliation.getAttribute("ID").encode('utf-8')
text = xml_to_text(affiliation, delimiter=', ')
affiliations[aff_id] = text
implicit_affilations = True
for author in authors:
matching_ref = [ref for ref in author.get("affiliations_ids") if ref in affiliations]
if matching_ref:
implicit_affilations = False
author["affiliation"] = []
for i in xrange(0, len(matching_ref)):
author["affiliation"].append(affiliations[matching_ref[i]])
if implicit_affilations and len(affiliations) > 1:
print >> sys.stderr, "Implicit affiliations are used, but there's more than one affiliation: %s" % affiliations
if implicit_affilations and len(affiliations) >= 1:
for author in authors:
author["affiliation"] = []
for aff in affiliations.values():
author["affiliation"].append(aff)
return authors
def get_publication_date(self, xml):
article_info = xml.getElementsByTagName("ArticleInfo")[0]
article_history = article_info.getElementsByTagName("ArticleHistory")[0]
online_date = article_history.getElementsByTagName("OnlineDate")
if online_date:
online_date = online_date[0]
year = get_value_in_tag(online_date, "Year")
month = get_value_in_tag(online_date, "Month")
day = get_value_in_tag(online_date, "Day")
try:
return "%04d-%02d-%02d" % (int(year), int(month), int(day))
except Exception, err:
print >> sys.stderr, "Can't reliably extract the publication date: %s" % err
return ""
return err
def get_abstract(self, xml):
try:
return get_value_in_tag(xml.getElementsByTagName("Abstract")[0], "Para")
except Exception, err:
print >> sys.stderr, "Can't find abstract"
def get_copyright(self, xml):
try:
return get_value_in_tag(xml.getElementsByTagName("ArticleCopyright")[0], "CopyrightHolderName")
except Exception, err:
print >> sys.stderr, "Can't find copyright. %s" % (err, )
def get_keywords(self, xml):
try:
return [xml_to_text(keyword) for keyword in xml.getElementsByTagName("Keyword")]
except Exception, err:
print >> sys.stderr, "Can't find keywords. %s" % (err,)
def get_body_ref(self, xml):
try:
ref = xml.getElementsByTagName('BodyRef')[0]
return ref.getAttribute('FileRef').encode('utf-8')
except Exception, err:
print >> sys.stderr, "Can't find reference to XML file."
def get_arxiv_id(self, xml):
article_note = xml.getElementsByTagName('ArticleNote')
if article_note:
article_note = article_note[0]
else:
return ""
arxiv_id = get_value_in_tag(article_note, "RefSource")
if RE_ARXIV_ID.match(arxiv_id):
return "arXiv:%s" % arxiv_id
return ""
def get_references(self, xml):
references = []
for reference in xml.getElementsByTagName("Citation"):
if not reference.getElementsByTagName("BibArticle"):
references.append((get_value_in_tag(reference,
"BibUnstructured"),
'', '', '', '', '', '', ''))
else:
label = get_value_in_tag(reference, "ArticleTitle")
authors = []
for author in reference.getElementsByTagName("BibAuthorName"):
given_name = get_value_in_tag(author, "Initials")
surname = get_value_in_tag(author, "FamilyName")
if given_name:
name = "%s, %s" % (surname, given_name)
else:
name = surname
authors.append(name)
doi_tag = reference.getElementsByTagName("Occurrence")
doi = ""
for tag in doi_tag:
if tag.getAttribute("Type") == "DOI":
doi = xml_to_text(tag)
## What is it exactly?
# issue = get_value_in_tag(reference, "sb:issue")
issue = ""
page = get_value_in_tag(reference, "FirstPage")
title = get_value_in_tag(reference, "JournalTitle")
volume = get_value_in_tag(reference, "VolumeID")
year = get_value_in_tag(reference, "Year")
references.append((label, authors, doi, issue, page, title, volume, year))
return references
def get_record(self, f_path, publisher=None, collection=None, logger=None):
#path = abspath(join(f_path, pardir))
xml = self.get_article(f_path)
rec = {}
title = self.get_title(xml)
if title:
record_add_field(rec, '245', subfields=[('a', title)])
publication_date = self.get_publication_date(xml)
if publication_date:
record_add_field(rec, '260', subfields=[('c', publication_date)])
journal, issn, volume, issue, first_page, pages, year, doi = self.get_publication_information(xml)
if doi:
record_add_field(rec, '024', ind1='7', subfields=[('a', doi), ('2', 'DOI')])
arxiv_id = self.get_arxiv_id(xml)
if arxiv_id:
record_add_field(rec, '037', subfields=[('a', arxiv_id), ('9', 'arXiv')])
if logger:
logger.info("Creating record: %s %s" % (f_path, doi))
authors = self.get_authors(xml)
first_author = True
for author in authors:
subfields = [('a', '%s, %s' % (author['surname'], author.get('given_name') or author.get('initials')))]
if 'orcid' in author:
subfields.append(('j', author['orcid']))
if 'affiliation' in author:
for aff in author["affiliation"]:
subfields.append(('v', aff))
if first_author:
record_add_field(rec, '100', subfields=subfields)
first_author = False
else:
record_add_field(rec, '700', subfields=subfields)
abstract = self.get_abstract(xml)
if abstract:
record_add_field(rec, '520', subfields=[('a', abstract)])
record_add_field(rec, '540', subfields=[('a', 'CC-BY-4.0'), ('u', 'http://creativecommons.org/licenses/by/4.0/')])
copyright = self.get_copyright(xml)
if copyright:
record_add_field(rec, '542', subfields=[('f', copyright)])
keywords = self.get_keywords(xml)
if keywords:
for keyword in keywords:
record_add_field(rec, '653', ind1='1', subfields=[('a', keyword), ('9', 'author')])
record_add_field(rec, "260", subfields=[('c', year)])
record_add_field(rec, "300", subfields=[('a', pages)])
record_add_field(rec, '773', subfields=[('p', journal), ('v', volume), ('c', first_page), ('y', year)])
references = self.get_references(xml)
for label, authors, doi, issue, page, title, volume, year in references:
subfields = []
if doi:
subfields.append(('a', doi))
for author in authors:
subfields.append(('h', author))
if issue:
subfields.append(('n', issue))
if label:
subfields.append(('o', label))
if page:
subfields.append(('p', page))
subfields.append(('s', '%s %s (%s) %s' % (title, volume, year, page)))
if title:
subfields.append(('t', title))
if volume:
subfields.append(('v', volume))
if year:
subfields.append(('y', year))
if subfields:
record_add_field(rec, '999', ind1='C', ind2='5', subfields=subfields)
folder_name = join('/', *(f_path.split('/')[0:-1]))
pdf_name = f_path.split('/')[-1].rstrip('.xml.scoap') + '.pdf'
pdf_path = join(folder_name, 'BodyRef/PDF', pdf_name)
print pdf_path
if exists(pdf_path):
record_add_field(rec, 'FFT', subfields=[('a', pdf_path), ('n', 'main'), ('f', '.pdf;pdfa')])
else:
# Don't know why it doesn't work????????????
# register_exception(alert_admin=True)
if logger:
logger.error("Record %s doesn't contain PDF file." % (doi,))
record_add_field(rec, 'FFT', subfields=[('a', self.get_body_ref(xml)), ('n', 'main')])
record_add_field(rec, '980', subfields=[('a', collection), ('b', publisher)])
return record_xml_output(rec)