def __init__(self,
collection,
issns=None,
output_file=None,
from_date=FROM,
user=None,
password=None,
api_token=None):
self._articlemeta = utils.articlemeta_server()
self.collection = collection
self.from_date = from_date
self.user = user
self.password = password
self.issns = issns or [None]
self.session = self.authenticated_session()
self.parse_schema()
self.doaj_articles = Articles(usertoken=api_token)
def __init__(self, collection, issns=None, output_file=None, from_date=FROM,
user=None, password=None, api_token=None):
self._articlemeta = utils.articlemeta_server()
self.collection = collection
self.from_date = from_date
self.user = user
self.password = password
self.issns = issns or [None]
self.session = self.authenticated_session()
self.parse_schema()
self.doaj_articles = Articles(usertoken=api_token)
class ArticlesTest(unittest.TestCase):
def setUp(self):
self.ac = Articles()
def test_get_article(self):
response = self.ac.get('255723f2f2374f1fbb8865eeb044c9d2')
self.assertTrue('bibjson' in response)
def test_get_article_not_available(self):
response = self.ac.get('not available')
self.assertEqual(response['status'], 'not_found')
def test_search_invalid_page_size(self):
with self.assertRaises(ValueError):
[x for x in self.ac.search('issn:1806-9940', pagesize='invalid')]
def test_search_invalid_page_size_1(self):
"""
not between 10 and 100.
"""
with self.assertRaises(ValueError):
[x for x in self.ac.search('issn:1806-9940', pagesize=9)]
def test_search_invalid_page_size_2(self):
"""
not between 10 and 100.
"""
with self.assertRaises(ValueError):
[x for x in self.ac.search('issn:1806-9940', pagesize=101)]
def test_search(self):
articles = [x for x in self.ac.search('id:255723f2f2374f1fbb8865eeb044c9d2')]
self.assertEqual(1, len(articles))
def setUp(self):
self.ac = Articles()
class Dumper(object):
def __init__(self, collection, issns=None, output_file=None, from_date=FROM,
user=None, password=None, api_token=None):
self._articlemeta = utils.articlemeta_server()
self.collection = collection
self.from_date = from_date
self.user = user
self.password = password
self.issns = issns or [None]
self.session = self.authenticated_session()
self.parse_schema()
self.doaj_articles = Articles(usertoken=api_token)
def _doaj_id_by_meta(self, issn, publication_year, title):
### Query by metadata
escaped_title = ''
for char in title:
if char in ['+','-','&','|','!','(',')','{','}','[',']','^','"','~','*','?',':','\\']:
escaped_title += u'\\'+char
continue
escaped_title += char
query = 'issn:%s AND year:%s AND title:%s' % (
issn,
publication_year,
escaped_title
)
result = []
try:
result = [i for i in self.doaj_articles.search(query)]
except:
logger.debug('Fail to query DOAJ API using metadata: %s' % query)
if len(result) == 1:
return result[0].get('id', None)
def _doaj_id_by_doi(self, doi):
### Query by doi
query = 'doi:%s' % (doi)
result = []
try:
result = [i for i in self.doaj_articles.search(query)]
except:
logger.debug('Fail to query DOAJ API using DOI: %s' % query)
if len(result) == 1:
return result[0].get('id', None)
def _doaj_id(self, document):
doaj_id = None
if document.original_title():
doaj_id = self._doaj_id_by_meta(
document.scielo_issn,
document.publication_date[0:4],
document.original_title()
)
if doaj_id:
return doaj_id
if document.doi:
return self._doaj_id_by_doi(document.doi)
def parse_schema(self):
xsd = BytesIO(DOAJ_XSD.encode('utf-8'))
try:
sch_doc = etree.parse(xsd)
sch = etree.XMLSchema(sch_doc)
except Exception as e:
logger.exception(e)
logger.error('Fail to parse XML')
return False
self.doaj_schema = sch
def authenticated_session(self):
auth_url = 'https://doaj.org/account/login'
login = {'username': self.user, 'password': self.password}
session = requests.Session()
try:
request = session.post(auth_url, data=login)
except requests.exceptions.SSLError:
logger.debug('Authentication without SSL validation')
request = session.post(auth_url, data=login, verify=False)
if request.status_code != 200:
logger.debug('Authentication attempt done')
return None
if u'Incorrect' in request.text:
logger.debug('Incorrect username or password')
return None
logger.debug('Authenticated successfully')
return session
def xml_is_valid(self, xml):
try:
xml = StringIO(xml)
xml_doc = etree.parse(xml)
logger.debug('XML is well formed')
except Exception as e:
logger.exception(e)
logger.error('Fail to parse XML')
return False
try:
result = self.doaj_schema.assertValid(xml_doc)
logger.debug('XML is valid')
return True
except Exception as e:
logger.exception(e)
logger.error('Fail to parse XML')
return False
def send_xml(self, file_name, file_data):
files = {'file': (file_name, file_data)}
try:
response = self.session.post(
'https://doaj.org/publisher/uploadfile',
data={'schema': 'doaj'},
files=files
)
except requests.ConnectionError:
logger.debug('Fail to send document to DOAJ')
return False
if u'successfully uploaded' in response.text:
logger.info('Document Sent')
return True
else:
self.authenticated_session()
logger.error('Document not Sent: %s' % response.status_code)
return False
def run(self):
if not self.session:
return None
for issn in self.issns:
for document in self._articlemeta.documents(collection=self.collection, issn=issn, from_date=self.from_date):
logger.info('Reading document: %s_%s' % (document.publisher_id, document.collection_acronym))
if document.data.get('doaj_id', None):
logger.debug('Document already available in DOAJ: %s_%s' % (document.publisher_id, document.collection_acronym))
continue
doaj_id = self._doaj_id(document)
if doaj_id:
logger.debug('Document already available in DOAJ, setting id on Article Meta for: %s_%s' % (document.publisher_id, document.collection_acronym))
self._articlemeta.set_doaj_id(document.publisher_id, document.collection_acronym, doaj_id)
continue
try:
xml = self._articlemeta.document(document.publisher_id, document.collection_acronym, fmt='xmldoaj')
except Exception as e:
logger.exception(e)
logger.error('Fail to read document: %s_%s' % (document.publisher_id, document.collection_acronym))
xml = u''
if not self.xml_is_valid(xml):
logger.error('Fail to parse xml document: %s_%s' % (document.publisher_id, document.collection_acronym))
continue
logger.info('Sending document: %s_%s' % (document.publisher_id, document.collection_acronym))
filename = '%s_%s.xml' % (document.publisher_id, document.collection_acronym)
self.send_xml(filename, xml)
class Dumper(object):
def __init__(self,
collection,
issns=None,
output_file=None,
from_date=FROM,
user=None,
password=None,
api_token=None):
self._articlemeta = utils.articlemeta_server()
self.collection = collection
self.from_date = from_date
self.user = user
self.password = password
self.issns = issns or [None]
self.session = self.authenticated_session()
self.parse_schema()
self.doaj_articles = Articles(usertoken=api_token)
def _doaj_id_by_meta(self, issn, publication_year, title):
### Query by metadata
escaped_title = ''
for char in title:
if char in [
'+', '-', '&', '|', '!', '(', ')', '{', '}', '[', ']', '^',
'"', '~', '*', '?', ':', '\\'
]:
escaped_title += u'\\' + char
continue
escaped_title += char
query = 'issn:%s AND year:%s AND title:%s' % (issn, publication_year,
escaped_title)
result = []
try:
result = [i for i in self.doaj_articles.search(query)]
except:
logger.debug('Fail to query DOAJ API using metadata: %s' % query)
if len(result) == 1:
return result[0].get('id', None)
def _doaj_id_by_doi(self, doi):
### Query by doi
query = 'doi:%s' % (doi)
result = []
try:
result = [i for i in self.doaj_articles.search(query)]
except:
logger.debug('Fail to query DOAJ API using DOI: %s' % query)
if len(result) == 1:
return result[0].get('id', None)
def _doaj_id(self, document):
doaj_id = None
if document.original_title():
doaj_id = self._doaj_id_by_meta(document.journal.scielo_issn,
document.publication_date[0:4],
document.original_title())
if doaj_id:
return doaj_id
if document.doi:
return self._doaj_id_by_doi(document.doi)
def parse_schema(self):
xsd = BytesIO(DOAJ_XSD.encode('utf-8'))
try:
sch_doc = etree.parse(xsd)
sch = etree.XMLSchema(sch_doc)
except Exception as e:
logger.exception(e)
logger.error('Fail to parse XML')
return False
self.doaj_schema = sch
def authenticated_session(self):
auth_url = 'https://doaj.org/account/login'
login = {'username': self.user, 'password': self.password}
session = requests.Session()
try:
request = session.post(auth_url, data=login)
except requests.exceptions.SSLError:
logger.debug('Authentication without SSL validation')
request = session.post(auth_url, data=login, verify=False)
if request.status_code != 200:
logger.debug('Authentication attempt done')
return None
if u'Incorrect' in request.text:
logger.debug('Incorrect username or password')
return None
logger.debug('Authenticated successfully')
return session
def xml_is_valid(self, xml):
try:
xml = StringIO(xml)
xml_doc = etree.parse(xml)
logger.debug('XML is well formed')
except Exception as e:
logger.exception(e)
logger.error('Fail to parse XML')
return False
try:
result = self.doaj_schema.assertValid(xml_doc)
logger.debug('XML is valid')
return True
except Exception as e:
logger.exception(e)
logger.error('Fail to parse XML')
return False
def send_xml(self, file_name, file_data):
files = {'file': (file_name, file_data)}
try:
response = self.session.post(
'https://doaj.org/publisher/uploadfile',
data={'schema': 'doaj'},
files=files)
except requests.ConnectionError:
logger.debug('Fail to send document to DOAJ')
return False
if u'File uploaded and waiting to be processed' in response.text:
logger.info('Document Sent')
return True
else:
self.authenticated_session()
logger.error('Document not Sent: %s' % response.status_code)
return False
def run(self):
if not self.session:
return None
extra_filter = json.dumps({'doaj_id': {'$exists': 0}})
for issn in self.issns:
for document in self._articlemeta.documents(
collection=self.collection,
issn=issn,
from_date=self.from_date,
extra_filter=extra_filter):
logger.info(
'Reading document: %s_%s' %
(document.publisher_id, document.collection_acronym))
if document.data.get('doaj_id', None):
logger.debug(
'Document already available in DOAJ: %s_%s' %
(document.publisher_id, document.collection_acronym))
continue
doaj_id = self._doaj_id(document)
if doaj_id:
logger.debug(
'Document already available in DOAJ, setting id on Article Meta for: %s_%s'
% (document.publisher_id, document.collection_acronym))
self._articlemeta.set_doaj_id(document.publisher_id,
document.collection_acronym,
doaj_id)
continue
try:
xml = self._articlemeta.document(
document.publisher_id,
document.collection_acronym,
fmt='xmldoaj')
except Exception as e:
logger.exception(e)
logger.error(
'Fail to read document: %s_%s' %
(document.publisher_id, document.collection_acronym))
xml = u''
if not self.xml_is_valid(xml):
logger.error(
'Fail to parse xml document: %s_%s' %
(document.publisher_id, document.collection_acronym))
continue
logger.info(
'Sending document: %s_%s' %
(document.publisher_id, document.collection_acronym))
filename = '%s_%s.xml' % (document.publisher_id,
document.collection_acronym)
self.send_xml(filename, xml)