diff --git a/modules/webauthorlist/lib/authorlist_engine.py b/modules/webauthorlist/lib/authorlist_engine.py
index 0739ddff9..0ba68322e 100644
--- a/modules/webauthorlist/lib/authorlist_engine.py
+++ b/modules/webauthorlist/lib/authorlist_engine.py
@@ -1,833 +1,844 @@
## This file is part of Invenio.
## Copyright (C) 2011, 2012, 2013 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later version.
##
## Invenio is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with Invenio; if not, write to the Free Software Foundation, Inc.,
## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
""" Invenio Authorlist Data Conversion Engine. """
import time
try:
import json
except ImportError:
import simplejson as json
from xml.dom import minidom
try:
from xml.etree import ElementTree as ET
except ImportError:
import elementtree.ElementTree as ET
from invenio.webuser import page_not_authorized
from invenio.access_control_engine import acc_authorize_action
import invenio.authorlist_config as cfg
-from invenio.search_engine import perform_request_search
+from invenio.search_engine import perform_request_search, record_exists
from invenio.search_engine_utils import get_fieldvalues
from invenio.bibedit_utils import get_record
# from lxml import etree
from invenio.authorlist_dblayer import get_owner
from invenio.textutils import escape_latex
# default name that will be used, when affiliation name is missing
UNKNOWN_AFFILIATION = 'Unknown Affiliation'
# Namespaces used in the xml file
NAMESPACES = {'cal': 'http://www.slac.stanford.edu/spires/hepnames/authors_xml/',
'foaf': 'http://xmlns.com/foaf/0.1/',
}
def retrieve_data_from_record(recid):
"""
Extract data from a record id in order to import it to the Author list
interface
"""
+ if not record_exists(recid):
+ return
+
output = {}
- # Save the affiliatons variable, the default value for "Affiliation" column
- # will be always first value from type_of_affiliation table
- type_of_affiliation = cfg.OPTIONS.AUTHOR_AFFILIATION_TYPE[0]
- # Save the default identifier - first element from the list of identifiers
- default_identifier = cfg.OPTIONS.IDENTIFIERS_LIST[0]
- # Save identifiers mapping
- identifiers_mapping = cfg.OPTIONS.IDENTIFIERS_MAPPING
+
+ DEFAULT_AFFILIATION_TYPE = cfg.OPTIONS.AUTHOR_AFFILIATION_TYPE[0]
+ DEFAULT_IDENTIFIER = cfg.OPTIONS.IDENTIFIERS_LIST[0]
+ IDENTIFIERS_MAPPING = cfg.OPTIONS.IDENTIFIERS_MAPPING
bibrecord = get_record(recid)
- if not bibrecord:
- # record probably doesn't exist
- return output
- # Extract paper title, collaboration name, experiment number
- paper_title = get_fieldvalues(int(recid), '245__a') and get_fieldvalues(int(recid), '245__a')[0] or ''
- collaboration_name = get_fieldvalues(int(recid), '710__g') and get_fieldvalues(int(recid), '710__g')[0] or ''
- experiment_number = get_fieldvalues(int(recid), '693__e') and get_fieldvalues(int(recid), '693__e')[0] or ''
- # Extract authors
try:
- record_authors = bibrecord.get('100', [])
- record_authors.extend(bibrecord.get('700', []))
- except KeyError:
- return output
- # Extract affiliations
- record_affiliations = get_fieldvalues(int(recid), '100__u')
- record_affiliations.extend(get_fieldvalues(int(recid), '700__u'))
+ paper_title = get_fieldvalues(recid, '245__a')[0]
+ except IndexError:
+ paper_title = ""
+ try:
+ collaboration_name = get_fieldvalues(recid, '710__g')
+ except IndexError:
+ collaboration_name = ""
+ try:
+ experiment_number = get_fieldvalues(recid, '693__e')
+ except IndexError:
+ experiment_number = ""
+
+ record_authors = bibrecord.get('100', [])
+ record_authors.extend(bibrecord.get('700', []))
- # Generate all the author related information
author_list = []
- for i in xrange(len(record_authors)):
+ unique_affiliations = []
+
+ for i, field_instance in enumerate(record_authors, 1):
+ family_name = ""
+ given_name = ""
+ name_on_paper = ""
+ status = ""
+ affiliations = []
identifiers = []
- no_affiliation = True
- for field in record_authors[i][0][1:]:
- # check for affiliations and ID's
- if field[0] == 'u':
- no_affiliation = False
- if field[0] == 'i' and field[1] in identifiers_mapping:
- identifiers.append([field[1], identifiers_mapping[field[1]]])
- if not identifiers:
- # if there are no identifiers, assign the default value
- identifiers.append(['', default_identifier])
-
- if no_affiliation:
- # add this UNKNOWN_AFFILIATION to the record, because later
- # we will iterate all affiliations
- record_authors[i][0].append(('u', UNKNOWN_AFFILIATION))
- # add UNKNOWN_AFFILIATION as affiliation, so catalogers can notice
- # that something is wrong
- record_affiliations.append(UNKNOWN_AFFILIATION)
- author_info = [long(i+1), # Row number
- '',
- record_authors[i][0][0][1].split(',')[0], # Family name
- record_authors[i][0][0][1].split(',')[1].lstrip(), # Given name
- record_authors[i][0][0][1], # Name on paper
- '', # Status
- [[x[1], type_of_affiliation] for x in record_authors[i][0][1:] if x[0] == 'u'],
- identifiers]
- author_list.append(author_info)
+ field = field_instance[0]
+ for subfield_code, subfield_value in field:
+ if subfield_code == "a":
+ try:
+ family_name = subfield_value.split(',')[0]
+ given_name = subfield_value.split(',')[1].lstrip()
+ except:
+ pass
+ name_on_paper = subfield_value
+ elif subfield_code == "u":
+ affiliations.append([subfield_value, DEFAULT_AFFILIATION_TYPE])
+ unique_affiliations.append(subfield_value)
+ elif subfield_code == "i":
+ # FIXME This will currently work only with INSPIRE IDs
+ id_prefix = subfield_value.split("-")[0]
+ if id_prefix in IDENTIFIERS_MAPPING:
+ identifiers.append([subfield_value, IDENTIFIERS_MAPPING[id_prefix]])
+ else:
+ identifiers.append(['', DEFAULT_IDENTIFIER])
+ if not affiliations:
+ affiliations.append([UNKNOWN_AFFILIATION, DEFAULT_AFFILIATION_TYPE])
+ unique_affiliations.append(UNKNOWN_AFFILIATION)
+ author_list.append([
+ i, # Row number
+ '', # Place holder for the web interface
+ family_name,
+ given_name,
+ name_on_paper,
+ status,
+ affiliations,
+ identifiers
+ ])
+
+ unique_affiliations = list(set(unique_affiliations))
output.update({'authors': author_list})
# Generate all the affiliation related information
- unique_affiliations = list(set(record_affiliations))
affiliation_list = []
- for i in xrange(len(unique_affiliations)):
- institution = perform_request_search(c="Institutions", p='110__u:"' + unique_affiliations[i] + '"')
- full_name = unique_affiliations[i]
+ for i, affiliation in enumerate(unique_affiliations, 1):
+ institution = perform_request_search(c="Institutions", p='110__u:"' + affiliation + '"')
+ full_name = affiliation
if len(institution) == 1:
full_name_110_a = get_fieldvalues(institution[0], '110__a')
if full_name_110_a:
full_name = str(full_name_110_a[0])
full_name_110_b = get_fieldvalues(institution[0], '110__b')
if full_name_110_b:
full_name += ', ' + str(full_name_110_b[0])
- affiliation = [long(i+1),
+ affiliation = [i,
'',
- unique_affiliations[i],
+ affiliation,
'',
full_name,
'',
True,
'']
affiliation_list.append(affiliation)
+
output.update({'affiliations': affiliation_list})
- # Add generic information about the paper
output.update({'paper_title': paper_title,
'collaboration': collaboration_name,
'experiment_number': experiment_number,
'last_modified': int(time.time()),
'reference_ids': [],
'paper_id': '1'})
return output
def retrieve_data_from_xml(xml):
"""
Extract data from an XML file to import it to the Author list
interface
"""
def get_element_value_helper(element, tag):
"""
Helper that takes an element and returns text from the first node
of that element
"""
text = ''
elements_list = element.getElementsByTagName(tag)
if elements_list:
child = elements_list[0].firstChild
if child:
text = child.nodeValue
return text
output = {}
# Save the affiliatons variable, the default value for "Affiliation" column
# will be always first value from type_of_affiliation table
type_of_affiliation = cfg.OPTIONS.AUTHOR_AFFILIATION_TYPE
# Save the default identifier - first element from the list of identifiers
default_identifier = cfg.OPTIONS.IDENTIFIERS_LIST[0]
# Save identifiers mapping
identifiers_mapping = cfg.OPTIONS.IDENTIFIERS_MAPPING
parsed_xml = minidom.parseString(xml)
# Extract collaboration name and experiment number
collaboration_name = ''
experiment_number = ''
collaborations = parsed_xml.getElementsByTagName('cal:collaborations')
if len(collaborations) == 1:
collaboration_name = get_element_value_helper(collaborations[0], 'foaf:name')
experiment_number = get_element_value_helper(collaborations[0], 'cal:experimentNumber')
# Extract affiliations
affiliation_list = []
affiliation_id_name = {}
affiliations = parsed_xml.getElementsByTagName('foaf:Organization')
for i, affiliation in enumerate(affiliations):
affiliation_id = affiliation.getAttribute('id') or ''
affiliation_name = get_element_value_helper(affiliation, 'foaf:name')
affiliation_acronym = get_element_value_helper(affiliation, 'cal:orgName')
if not affiliation_acronym:
# No acronym ? Use the name instead
affiliation_acronym = affiliation_name
affiliation_address = get_element_value_helper(affiliation, 'cal:orgAddress')
if not affiliation_address:
affiliation_address = affiliation_name
affiliation_domain = get_element_value_helper(affiliation, 'cal:orgDomain')
# saving {id:name}, it will be needed for authors affiliations
if affiliation_id:
# According to
# http://stackoverflow.com/questions/8214932/how-to-check-if-a-value-exists-in-a-dictionary-python
# itervalues is faster than values() and viewvalues()
if affiliation_acronym in affiliation_id_name.itervalues():
# in case we have a duplicate of acronym, make it unique by
# appending the iteration number
affiliation_acronym += str(i+1)
affiliation_id_name[affiliation_id] = affiliation_acronym
affiliation_info = [long(i+1),
'',
affiliation_acronym,
'',
affiliation_address,
affiliation_domain,
True,
'']
affiliation_list.append(affiliation_info)
# Extract authors
author_list = []
authors = parsed_xml.getElementsByTagName('foaf:Person')
for i, author in enumerate(authors):
first_name = get_element_value_helper(author, 'foaf:givenName')
# In case there was no given name under previous field, we search for initials in cal:authorNamePaperGiven
if not first_name:
first_name = get_element_value_helper(author, 'cal:authorNamePaperGiven')
last_name = get_element_value_helper(author, 'foaf:familyName')
full_name = get_element_value_helper(author, 'cal:authorNamePaper')
status = get_element_value_helper(author, 'cal:authorStatus')
# Extract author affiliations
author_affiliations = []
if author.getElementsByTagName('cal:authorAffiliations'):
for afil in author.getElementsByTagName('cal:authorAffiliations')[0].getElementsByTagName('cal:authorAffiliation'):
a_id = afil.getAttribute('organizationid')
if afil.getAttribute('connection') in type_of_affiliation:
affiliation_type = afil.getAttribute('connection')
else:
affiliation_type = type_of_affiliation[0]
author_affiliations.append([affiliation_id_name.get(a_id, UNKNOWN_AFFILIATION), affiliation_type])
else:
author_affiliations = [UNKNOWN_AFFILIATION, type_of_affiliation[0]]
identifiers = []
if author.getElementsByTagName('cal:authorids'):
for author_id in author.getElementsByTagName('cal:authorids')[0].getElementsByTagName('cal:authorid'):
if author_id.getAttribute('source') in identifiers_mapping and author_id.firstChild:
identifiers.append([
author_id.firstChild.nodeValue,
identifiers_mapping[author_id.getAttribute('source')]])
if not identifiers:
identifiers.append(['', default_identifier])
author_info = [long(i+1),
'',
last_name,
first_name,
full_name,
status,
author_affiliations,
identifiers]
author_list.append(author_info)
output.update({'authors': author_list})
output.update({'affiliations': affiliation_list})
# Add generic information about the paper
output.update({'collaboration': collaboration_name,
'experiment_number': experiment_number,
'last_modified': int(time.time()),
'reference_ids': [],
'paper_id': '1',
'paper_title': ''})
return output
def user_authorization(req, ln):
""" Check user authorization to visit page """
auth_code, auth_message = acc_authorize_action(req, 'runauthorlist')
if auth_code != 0:
referer = '/authorlist/'
return page_not_authorized(req=req, referer=referer,
text=auth_message, navmenuid="authorlist")
else:
return None
def check_user_rights(user_id, paper_id):
"""Check if user can modify this paper"""
# if the paper_id is empty - user is trying to create new record
# we allow him, because everyone can do that
if not paper_id or (user_id == get_owner(paper_id)):
return True
return False
class Converter(object):
CONTENT_TYPE = 'text/plain'
FILE_NAME = 'converted.txt'
def __init__(self):
raise NotImplementedError
def dump(self, data):
raise NotImplementedError
def dumps(self, data):
raise NotImplementedError
class NA62Latex(Converter):
FILE_NAME = 'la.tex'
def __init__(self):
pass
def dump(self, data):
pass
def dumps(self, data):
pass
class ElsevierArticle(Converter):
CONTENT_TYPE = 'text/plain'
FILE_NAME = 'elsarticle.tex'
cal = '{http://www.slac.stanford.edu/spires/hepnames/authors_xml/}'
foaf = '{http://xmlns.com/foaf/0.1/}'
def __init__(self):
pass
def dictionary_to_list(self, node):
res = {}
res[node.tag] = []
self.xmltodict(node, res[node.tag])
reply = {}
reply[node.tag] = {'value': res[node.tag], 'attribs': node.attrib, 'tail': node.tail}
return reply
def xmltodict(self, node, res):
rep = {}
if len(node):
for n in list(node):
rep[node.tag] = []
value = self.xmltodict(n, rep[node.tag])
if len(n):
value = {'value': rep[node.tag], 'attributes': n.attrib, 'tail': n.tail}
res.append({n.tag: value})
else:
res.append(rep[node.tag][0])
else:
value = {}
value = {'value': node.text, 'attributes': node.attrib, 'tail': node.tail}
res.append({node.tag: value})
return
def get_organizations(self, organizations):
organization_dict = dict()
for orgs_element in organizations:
key = orgs_element.keys()[0]
if key == self.foaf + 'Organization':
for name_element in orgs_element[key]['value']:
value_key = name_element.keys()[0]
if value_key == self.cal + 'orgAddress':
if name_element[value_key]['value']:
organization_dict[orgs_element[key]['attributes']['id']] = name_element[value_key]['value'].encode('utf-8')
else:
organization_dict[orgs_element[key]['attributes']['id']] = ''
break
return organization_dict
def get_authors(self, authors):
author_list = []
for auth_element in authors:
key = auth_element.keys()[0]
if key == self.foaf + 'Person':
affiliation_list = []
given_name = ''
family_name = ''
for name_element in auth_element[key]['value']:
value_key = name_element.keys()[0]
if value_key == self.foaf + 'familyName' and name_element[value_key]['value']:
family_name = name_element[value_key]['value'].encode('utf-8')
elif value_key == self.foaf + 'givenName' and name_element[value_key]['value']:
given_name = name_element[value_key]['value'].encode('utf-8')
elif value_key == self.cal + 'authorAffiliations':
for aff_element in name_element[value_key]['value']:
aff_key = aff_element.keys()[0]
if aff_key == self.cal + 'authorAffiliation':
if aff_element[aff_key]['attributes']['connection'] == 'Affiliated with':
affiliation_list.append(aff_element[aff_key]['attributes']['organizationid'])
author_list.append([(given_name, family_name), tuple(affiliation_list)])
return author_list
def dump(self, data):
AuthorsXMLConverter = Converters.get('authorsxml')
AuthorsXML = dumps(data, AuthorsXMLConverter)
root = ET.fromstring(AuthorsXML)
tree = ET.ElementTree(root)
res = self.dictionary_to_list(tree.getroot())
collaboration_author_list_values = res['collaborationauthorlist']['value']
organization_dict = dict()
author_list = []
for element in collaboration_author_list_values:
key = element.keys()[0]
# if the value of the key is empty, start next loop cycle
if element[key]['value'] is None:
continue
if key == self.cal + 'organizations':
organization_dict = self.get_organizations(element[key]['value'])
elif key == self.cal + 'authors':
author_list = self.get_authors(element[key]['value'])
clusters = []
organization_codes = []
for element in author_list:
if len(element[1]) >= 1:
organization_code = element[1][0]
other_affiliations = element[1][1:]
author = [element[0]]
if other_affiliations:
author.extend(other_affiliations)
# if this organization already exists in the cluster
if organization_code in organization_codes:
for cluster in clusters:
if cluster[0] == organization_code:
cluster.append(author)
break
else:
organization_codes.append(organization_code)
clusters.append([organization_code, author])
myout = ""
myout += "\\documentclass[a4paper,12pt]{article}\r\n"
myout += "\\usepackage[utf8]{inputenc}\r\n"
myout += "\\begin{document}\r\n"
myout += "\\begin{center}\r\n"
myout += "{\\Large Collaboration}\\\\\r\n"
myout += "\\vspace{2mm}\r\n%\r\n"
primary_output_string = ""
secondary_affiliation_count = 1
secondary_affiliations = ""
secondary_affiliations_pos = {}
for data in clusters:
primary_output = []
organization_code = data[0]
for author in data[1:]:
name = " " + str(escape_latex(author[0][0])) + '~' + str(escape_latex(author[0][1]))
if len(author) > 1:
for sec_affiliation in author[1:]:
if sec_affiliation in organization_dict.keys():
if organization_dict[sec_affiliation] in secondary_affiliations_pos.keys():
name += "$\\,$\\footnotemark[" + str(secondary_affiliations_pos[organization_dict[sec_affiliation]]) + "]"
else:
name += "$\\,$\\footnotemark[" + str(secondary_affiliation_count) + "]"
secondary_affiliations += "%\r\n\\footnotetext[" + str(secondary_affiliation_count) + "]{" + str(escape_latex(organization_dict[sec_affiliation])) + "}\r\n"
secondary_affiliations_pos[organization_dict[sec_affiliation]] = secondary_affiliation_count
secondary_affiliation_count += 1
primary_output.append(name)
if organization_dict.get(data[0]):
organization = organization_dict.get(data[0])
else:
organization = UNKNOWN_AFFILIATION
primary_output_string += ',\r\n'.join(primary_output) + " \\\\\r\n{\\em \\small " + str(escape_latex(organization)) + "} \\\\[0.2cm]\r\n%\r\n"
myout += primary_output_string
myout += "\\end{center}\r\n"
myout += "\\setcounter{footnote}{0}\r\n"
myout += secondary_affiliations
myout += "\\end{document}\r\n"
return myout
def dumps(self, data):
return self.dump(data)
class APSpaper(Converter):
CONTENT_TYPE = 'text/plain'
FILE_NAME = 'APSpaper.tex'
def __init__(self):
pass
def dump(self, data):
AuthorsXMLConverter = Converters.get('authorsxml')
AuthorsXML = dumps(data, AuthorsXMLConverter)
organizations_list = []
authors_list = []
root = ET.fromstring(AuthorsXML)
# save affiliations
for organization in root.findall('{%s}organizations/{%s}Organization' % (NAMESPACES['cal'], NAMESPACES['foaf'])):
org_id = organization.attrib['id']
org_name = ''
if organization.find('{%s}name' % NAMESPACES['foaf']) is not None:
org_name = organization.find('{%s}name' % NAMESPACES['foaf']).text or ''
organizations_list.append([org_id, org_name.encode('utf-8')])
# save authors
for author in root.findall('{%s}authors/{%s}Person' % (NAMESPACES['cal'], NAMESPACES['foaf'])):
author_name = ''
author_affiliations = []
if author.find('{%s}authorNamePaper' % NAMESPACES['cal']) is not None:
author_name = author.find('{%s}authorNamePaper' % NAMESPACES['cal']).text or ''
for affil in author.findall('{%(cal)s}authorAffiliations/{%(cal)s}authorAffiliation' % {'cal': NAMESPACES['cal']}):
author_affiliations.append(affil.attrib['organizationid'])
authors_list.append([author_name.encode('utf-8'), author_affiliations])
myout = ''
for author in authors_list:
myout += '\\author{' + str(escape_latex(author[0])) + '$^{' + ','.join(author[1]) + '}$}\r\n'
for org in organizations_list:
myout += '\\affiliation{$^{' + str(org[0]) + '}$ ' + str(escape_latex(org[1])) + '}\r\n'
return myout
def dumps(self, data):
return self.dump(data)
class AuthorsXML(Converter):
CONTENT_TYPE = 'text/xml'
FILE_NAME = 'authors.xml'
def __init__(self):
pass
def create_affiliation(self, document, parsed, organization_ids):
affiliation = document.createElement('cal:authorAffiliation')
affiliation_acronym = parsed[cfg.JSON.AFFILIATION_ACRONYM]
affiliation_status = parsed[cfg.JSON.AFFILIATION_STATUS]
if affiliation_acronym not in organization_ids:
affiliation.setAttribute('organizationid',
'Error - there is no organization called ' +
affiliation_acronym)
else:
affiliation.setAttribute('organizationid',
organization_ids[affiliation_acronym])
affiliation.setAttribute('connection', affiliation_status)
return affiliation
def create_identifier(self, document, parsed):
identifier = document.createElement('cal:authorid')
identifier_number = parsed[cfg.JSON.IDENTIFIER_NUMBER]
identifier_name = parsed[cfg.JSON.IDENTIFIER_NAME]
identifier.setAttribute('source', identifier_name)
identifier_text = document.createTextNode(identifier_number)
identifier.appendChild(identifier_text)
return identifier
def create_authors(self, document, root, parsed, organization_ids):
parsed_authors = parsed[cfg.JSON.AUTHORS_KEY]
authors = document.createElement('cal:authors')
root.appendChild(authors)
for parsed_author in parsed_authors:
author = self.create_author(document, parsed_author, organization_ids)
authors.appendChild(author)
def create_author(self, document, parsed, organization_ids):
author = document.createElement('foaf:Person')
# paper name
paper_name = document.createElement('cal:authorNamePaper')
paper_name_info = parsed[cfg.JSON.PAPER_NAME]
paper_name_text = document.createTextNode(paper_name_info)
paper_name.appendChild(paper_name_text)
author.appendChild(paper_name)
# given name
given_name_info = parsed[cfg.JSON.GIVEN_NAME]
if (cfg.EMPTY.match(given_name_info) is None):
given_name = document.createElement('foaf:givenName')
given_name_text = document.createTextNode(given_name_info)
given_name.appendChild(given_name_text)
author.appendChild(given_name)
# family name
family_name_info = parsed[cfg.JSON.FAMILY_NAME]
if (cfg.EMPTY.match(family_name_info) is None):
family_name = document.createElement('foaf:familyName')
family_name_text = document.createTextNode(family_name_info)
family_name.appendChild(family_name_text)
author.appendChild(family_name)
# status
author_status_info = parsed[cfg.JSON.STATUS]
if (author_status_info):
author_status = document.createElement('cal:authorStatus')
author_status_text = document.createTextNode(author_status_info)
author_status.appendChild(author_status_text)
author.appendChild(author_status)
# collaboration
collaboration = document.createElement('cal:authorCollaboration')
collaboration.setAttribute('collaborationid', cfg.AuthorsXML.COLLABORATION_ID)
author.appendChild(collaboration)
# affiliations
affiliations = document.createElement('cal:authorAffiliations')
author.appendChild(affiliations)
for parsed_affiliation in parsed[cfg.JSON.AFFILIATIONS]:
affiliation = self.create_affiliation(document, parsed_affiliation, organization_ids)
affiliations.appendChild(affiliation)
# identifiers
identifiers = document.createElement('cal:authorids')
author.appendChild(identifiers)
for parsed_identifier in parsed[cfg.JSON.IDENTIFIERS]:
identifier = self.create_identifier(document, parsed_identifier)
identifiers.appendChild(identifier)
return author
def create_collaboration(self, document, root, parsed):
# collaborations
collaborations = document.createElement('cal:collaborations')
collaboration = document.createElement('cal:collaboration')
collaboration.setAttribute('id', cfg.AuthorsXML.COLLABORATION_ID)
collaborations.appendChild(collaboration)
# name
name = document.createElement('foaf:name')
name_info = parsed[cfg.JSON.COLLABORATION]
name_text = document.createTextNode(name_info)
name.appendChild(name_text)
collaboration.appendChild(name)
# experiment number
experiment_number_info = parsed[cfg.JSON.EXPERIMENT_NUMBER]
if (cfg.EMPTY.match(experiment_number_info) is None):
experiment_number = document.createElement('cal:experimentNumber')
experiment_number_text = document.createTextNode(experiment_number_info)
experiment_number.appendChild(experiment_number_text)
collaboration.appendChild(experiment_number)
root.appendChild(collaborations)
def create_document(self):
dom = minidom.getDOMImplementation()
document = dom.createDocument(None, 'collaborationauthorlist', None)
root = document.documentElement
root.setAttribute('xmlns:foaf', 'http://xmlns.com/foaf/0.1/')
root.setAttribute('xmlns:cal', 'http://www.slac.stanford.edu/spires/hepnames/authors_xml/')
return document, root
def create_header(self, document, root, parsed):
# creation date
creation_date = document.createElement('cal:creationDate')
creation_date_info = time.strftime(cfg.AuthorsXML.TIME_FORMAT)
creation_date_text = document.createTextNode(creation_date_info)
creation_date.appendChild(creation_date_text)
root.appendChild(creation_date)
# publication reference
for reference_info in parsed[cfg.JSON.REFERENCE_IDS]:
reference = document.createElement('cal:publicationReference')
reference_text = document.createTextNode(reference_info)
reference.appendChild(reference_text)
root.appendChild(reference)
def create_organizations(self, document, root, parsed, ids):
parsed_organizations = parsed[cfg.JSON.AFFILIATIONS_KEY]
# organizations container
organizations = document.createElement('cal:organizations')
root.appendChild(organizations)
# create individual organizations and append them
for parsed_organization in parsed_organizations:
organization = self.create_organization(document, parsed_organization, ids)
organizations.appendChild(organization)
def create_organization(self, document, parsed, ids):
acronym = parsed[cfg.JSON.ACRONYM]
organization = document.createElement('foaf:Organization')
organization.setAttribute('id', ids[acronym])
# create the domain node if field is set
domain_info = parsed[cfg.JSON.DOMAIN]
if (cfg.EMPTY.match(domain_info) is None):
domain = document.createElement('cal:orgDomain')
domain_text = document.createTextNode(domain_info)
domain.appendChild(domain_text)
organization.appendChild(domain)
# organization name, no presence check, already done on the client side
name = document.createElement('foaf:name')
name_info = parsed[cfg.JSON.NAME]
name_text = document.createTextNode(name_info)
name.appendChild(name_text)
organization.appendChild(name)
# organization acronym
org_acronym = document.createElement('cal:orgName')
org_acronym_text = document.createTextNode(acronym)
org_acronym.appendChild(org_acronym_text)
organization.appendChild(org_acronym)
# organization identifier
org_name_info = parsed[cfg.JSON.SPIRES_ID]
if (cfg.EMPTY.match(org_name_info) is None):
org_name = document.createElement('cal:orgName')
org_name.setAttribute('source', cfg.AuthorsXML.SPIRES)
org_name_text = document.createTextNode(org_name_info)
org_name.appendChild(org_name_text)
organization.appendChild(org_name)
else:
org_name_info = parsed[cfg.JSON.NAME]
org_address = document.createElement('cal:orgAddress')
org_address_text = document.createTextNode(org_name_info)
org_address.appendChild(org_address_text)
organization.appendChild(org_address)
# membership
org_status_info = parsed[cfg.JSON.MEMBER]
if (not org_status_info):
org_status_info = cfg.AuthorsXML.NONMEMBER
else:
org_status_info = cfg.AuthorsXML.MEMBER
org_status = document.createElement('cal:orgStatus')
org_status_text = document.createTextNode(org_status_info)
org_status.appendChild(org_status_text)
organization.appendChild(org_status)
# umbrella organization/group
group_info = parsed[cfg.JSON.UMBRELLA]
if (cfg.EMPTY.match(group_info) is None):
if group_info in ids.keys():
group = document.createElement('cal:group')
group.setAttribute('with', ids[group_info])
organization.appendChild(group)
return organization
def dump(self, data):
parsed = json.loads(data)
document, root = self.create_document()
affiliations = parsed[cfg.JSON.AFFILIATIONS_KEY]
organization_ids = self.generate_organization_ids(affiliations)
self.create_header(document, root, parsed)
self.create_collaboration(document, root, parsed)
self.create_organizations(document, root, parsed, organization_ids)
self.create_authors(document, root, parsed, organization_ids)
return document
def dumps(self, data):
# FIX for toprettyxml function from website:
# http://ronrothman.com/public/leftbraned/xml-dom-minidom-toprettyxml-and-silly-whitespace/
def fixed_writexml(self, writer, indent="", addindent="", newl=""):
# indent = current indentation
# addindent = indentation to add to higher levels
# newl = newline string
writer.write(indent+"<" + self.tagName)
attrs = self._get_attributes()
a_names = attrs.keys()
a_names.sort()
for a_name in a_names:
writer.write(" %s=\"" % a_name)
minidom._write_data(writer, attrs[a_name].value)
writer.write("\"")
if self.childNodes:
if len(self.childNodes) == 1 and self.childNodes[0].nodeType == minidom.Node.TEXT_NODE:
writer.write(">")
self.childNodes[0].writexml(writer, "", "", "")
writer.write("</%s>%s" % (self.tagName, newl))
return
writer.write(">%s" % (newl))
for node in self.childNodes:
node.writexml(writer, indent + addindent, addindent, newl)
writer.write("%s</%s>%s" % (indent, self.tagName, newl))
else:
writer.write("/>%s" % (newl))
# replace minidom's function with ours
minidom.Element.writexml = fixed_writexml
# End of FIX
return self.dump(data).toprettyxml(indent=' ', newl='\r\n', encoding='utf-8')
def generate_organization_ids(self, organizations):
ids = {}
# Map each organization acronym to an id of the kind 'o[index]'
for index, organization in enumerate(organizations):
acronym = organization[cfg.JSON.ACRONYM]
ids[acronym] = cfg.AuthorsXML.ORGANIZATION_ID + str(index)
return ids
class Converters:
__converters__ = {'authorsxml': AuthorsXML, 'elsevier': ElsevierArticle, 'aps': APSpaper}
@classmethod
def get(cls, format):
return cls.__converters__.get(format)
def dump(data, converter):
return converter().dump(data)
def dumps(data, converter):
return converter().dumps(data)