def _retrieve_links(self, publications):
if self.lamr is None:
return
pubs_by_uids = {}
for pub in publications:
for id in Identifier.find_by_type(pub.identifiers, 'WOK'):
pubs_by_uids[id.value] = pub
uids = pubs_by_uids.keys()
result_by_uids = self.lamr.retrieve_by_ids(uids)
for uid, result in result_by_uids.iteritems():
pub = pubs_by_uids[uid]
if 'timesCited' in result:
pub.times_cited = int(result['timesCited'])
if 'sourceURL' in result:
pub.source_urls.append(
URL(result['sourceURL'],
type='WOK',
description=u'Web of Science®'))
if 'citingArticlesURL' in result:
pub.cite_urls.append(
URL(result['citingArticlesURL'],
type='WOK',
description=u'Web of Science®'))
if 'message' in result:
pub.errors.append(u'Failed loading article URLs: ' +
unicode(result['message']))
def populate(file):
pp.pprint("parsing file %s" % file)
file_reader = open(file, "r")
url_objects = []
for line in file_reader:
if not line.startswith("#"):
pp.pprint(line)
line = line.strip()
line = line.strip("'")
line = line.strip("\n")
pp.pprint(line)
url = URL(util.hash_domain(line), util.hash_url(line))
if (not url.hash_domain == "" and not url.hash_url == ""):
url_objects.append(url)
db_session.add(url)
db_session.commit()
pp.pprint(url_objects)
"""
TODO: this doesn't work with the large data set, perhaps there is a max without any errors?
Will create a SQL script to insert manually into DB
try:
db_session.bulk_save_objects(url_objects)
db_session.commit()
except exc.IntegrityError:
db_session.rollback()
"""
results = URL.query.all()
pp.pprint("Inserted %d rows" % len(results))
def get(self):
template_values = {
'tasks': Task.all(),
'urls': URL.all(),
'settings': settings,
'datetime_now': datetime.now(pytz.timezone(settings.TIMEZONE)).strftime(settings.TIMEFORMAT)
}
template = JINJA_ENVIRONMENT.get_template('templates/index.html')
self.response.write(template.render(template_values))
def search_citations(self, publications):
for publication in publications:
ut = list(Identifier.find_by_type(publication.identifiers, 'WOK'))
if len(ut) == 0:
continue
ut = ut[0].value.lstrip(u'WOS:')
for cite_url in URL.find_by_type(publication.cite_urls, 'WOK'):
for pub in self._get_citations_from_url(cite_url.value, ut):
yield pub
def add_url(self, url, title, hostmask_id, channel=None):
with self.dbcon.scoped_db_session() as session:
url_qr = session.query(URL).filter(URL.url==url).all() # One?
if len(url_qr) == 0:
url_obj = URL()
#self.connection.privmsg("jabr", type(url_obj.hostmask_id))
url_obj.url = url
url_obj.title = title
url_obj.channel = channel
url_obj.hostmask_id = hostmask_id
session.add(url_obj)
msg = "URL %s added by %d" % (url, hostmask_id)
self.connection.privmsg("jabr", msg)
elif len(url_qr) == 1:
msg = "URL %s already exist" % url
self.connection.privmsg("jabr", msg)
else:
msg = "ERROR: %d instances of URL (%s) in DB" % (len(url_qr), url)
self.connection.privmsg("jabr", msg)
def search_citations(self, publications):
for publication in publications:
eid = list(
Identifier.find_by_type(publication.identifiers, 'SCOPUS'))
if len(eid) == 0:
continue
eid = eid[0].value
detail_url = list(
URL.find_by_type(publication.source_urls, 'SCOPUS'))
if len(detail_url) == 0:
continue
detail_url = detail_url[0].value
for pub in self._get_citations_from_detail_url(detail_url, eid):
yield pub
def receive(self, message):
logging.info("Processing a message from: " + message.sender)
plaintext_bodies = message.bodies('text/plain')
for content_type, body in plaintext_bodies:
text = body.decode()
logging.info("Text: " + text)
text = text.strip().split('#')
#format: phone_number#url_id#periods#dates#sms_type#sms_sender#password
if len(text) == 7 and text[6] == settings.MAIL_PASSWORD:
logging.info('weather request...')
text[1] = URL.get_by_id(int(text[1])).url #get URL string based on id in DB
utils.addTask(*text[:6])
#format: phone_number#text#password
elif len(text) == 3 and text[2] == settings.MAIL_PASSWORD:
logging.info('sms request...')
gs = GSMService()
gs.sendSMS(text[1], text[0], 'poland')
else:
logging.error("Password or format incorrect")
def add_url(self, url, title, hostmask_id, channel=None):
with self.dbcon.scoped_db_session() as session:
url_qr = session.query(URL).filter(URL.url == url).all() # One?
if len(url_qr) == 0:
url_obj = URL()
#self.connection.privmsg("jabr", type(url_obj.hostmask_id))
url_obj.url = url
url_obj.title = title
url_obj.channel = channel
url_obj.hostmask_id = hostmask_id
session.add(url_obj)
msg = "URL %s added by %d" % (url, hostmask_id)
self.connection.privmsg("jabr", msg)
elif len(url_qr) == 1:
msg = "URL %s already exist" % url
self.connection.privmsg("jabr", msg)
else:
msg = "ERROR: %d instances of URL (%s) in DB" % (len(url_qr),
url)
self.connection.privmsg("jabr", msg)
def post(self):
url = URL(url=self.request.get('newURL').strip())
url.put()
self.redirect('/')
"""
pp = pprint.PrettyPrinter(indent=4)
def populate():
db_session.add(url1)
db_session.add(url2)
db_session.add(url3)
db_session.add(url4)
db_session.add(url5)
db_session.commit()
results = URL.query.all()
pp.pprint(results)
if __name__ == '__main__':
url1 = URL(util.hash_domain('https://googo.com/gmail'),
util.hash_url('https://googo.com/gmail'))
url2 = URL(util.hash_domain('https://docs.googo.com/spreadsheets/u/01/'),
util.hash_url('https://docs.googo.com/spreadsheets/u/01/'))
url3 = URL(util.hash_domain('https://docs.googo.com/document/u/0/1'),
util.hash_url('https://docs.googo.com/document/u/0/1'))
url4 = URL(util.hash_domain('https://www.appa.com/mac/index.html'),
util.hash_url('https://www.appa.com/mac/index.html'))
url5 = URL(util.hash_domain('https://www.appa.com/ipad/stuff.htm'),
util.hash_url('https://www.appa.com/ipad/stuff.htm'))
populate()
test_domain5 = "www2.stuffandthings.co.au"
test_parse_url1 = "https://google.com/gmail/"
test_parse_url2 = "https://go.google.com/somethingelse"
test_parse_url3 = "http://stuffandthings.co.au/somethingelse/anotherthing"
test_parse_url4 = "http://www.stuffandthings.co.au/somethingelse/anotherthing"
test_parse_url5 = "http://www.stuffandthings.co.au:8080/somethingelse/anotherthing/yaya.html"
test_parse_path1 = "httpsgoogle.com/gmail"
test_parse_path2 = "httpsgo.google.com/somethingelse"
test_parse_path3 = "httpstuffandthings.co.au/somethingelse/anotherthing"
test_parse_path4 = "httpwww.stuffandthings.co.au/somethingelse/anotherthing"
test_parse_path5 = "http8080www.stuffandthings.co.au/somethingelse/anotherthing/yaya.html"
test_list = []
url1 = URL(util.hash_domain(test_raw_url1), util.hash_url(test_raw_url1))
url2 = URL(util.hash_domain(test_raw_url2), util.hash_url(test_raw_url2))
url3 = URL(util.hash_domain(test_raw_url3), util.hash_url(test_raw_url3))
url4 = URL(util.hash_domain(test_raw_url4), util.hash_url(test_raw_url4))
url5 = URL(util.hash_domain(test_raw_url5), util.hash_url(test_raw_url5))
test_list.append(url1)
test_list.append(url2)
test_list.append(url3)
test_list.append(url4)
test_list.append(url5)
# Domain parsing tests
test_parse_domain(test_raw_url1, test_domain1)
test_parse_domain(test_raw_url2, test_domain2)
test_parse_domain(test_raw_url3, test_domain3)
def _parse_csv(self, content, encoding='UTF-8'):
csv = unicodecsv.DictReader(strip_bom(content).splitlines(),
encoding=encoding)
def empty_to_none(s):
if s == None:
return None
s = s.strip()
if len(s) == 0:
return None
return s
def list_remove_empty(l):
r = []
for x in l:
v = empty_to_none(x)
if v:
r.append(v)
return r
def to_num(x):
x = x.strip()
if len(x) == 0:
return 0
return int(x)
for line in csv:
if line['Authors'] == '[No author name available]':
authors = []
else:
# (mrshu): SCOPUS sa rozhodol oddelovat ako priezvyska, tak aj
# jednotlive mena autorov ciarkov. Toto robi problemy, preto
# preprocessujeme zoznam autorov, ktory vyzera napriklad
#
# Brejová, B., Brown, D.G., Li, M., Vinař, T.
#
# najdeme, konce celych mien, a ciarku v tomto pripade nahradime
# bodkociarkou. Nasledne potom funkcii, ktora mena autorov spracovava
# dame vediet, ze je ako separator pouzita bodkociarka.
line['Authors'] = re.sub(r'\.,', ';', line['Authors'])
authors = Author.parse_sn_first_list(line['Authors'],
separator=u';')
pub = Publication(line['Title'], authors, to_num(line['Year']))
source_title = empty_to_none(line['Source title'])
if source_title:
source_title, replacements = re.subn(
r' \(including subseries [^)]+\)', '', source_title)
source_title = source_title.strip()
if replacements:
pub.series = source_title
else:
pub.published_in = source_title
pub.volume = empty_to_none(line['Volume'])
pub.issue = empty_to_none(line['Issue'])
pub.pages = make_page_range(empty_to_none(line['Page start']),
empty_to_none(line['Page end']))
# (mrshu): z dovodu, ktory nedokazem pochopit teraz SCOPUS vracia cosi
# ako 'DOILink', kde da dohromady tieto dva fieldy. Nepodarilo sa mi
# prist na to ako to spravit rozumnejsie, tento hack to aspon rozparsuje
splits = line['DOILink'].split('"')
if len(splits) > 1:
line['Link'] = splits[1]
line['DOI'] = splits[0]
else:
line['Link'] = splits[0]
line['DOI'] = None
pub.times_cited = empty_to_none(line['Cited by'])
pub.article_no = empty_to_none(line['Art. No.'])
pub.publisher = empty_to_none(line['Publisher'])
url = empty_to_none(line['Link'])
if url:
pub.source_urls.append(
URL(url, type='SCOPUS', description='SCOPUS'))
url_parts = urlparse(url)
url_query = parse_qs(url_parts.query)
if 'eid' in url_query and len:
pub.identifiers.append(
Identifier(url_query['eid'][0], type='SCOPUS'))
for issn in list_remove_empty(line['ISSN'].split(u';')):
pub.identifiers.append(Identifier(issn, type='ISSN'))
for isbn in list_remove_empty(line['ISBN'].split(u';')):
pub.identifiers.append(Identifier(isbn, type='ISBN'))
doi = empty_to_none(line['DOI'])
if doi:
pub.identifiers.append(Identifier(doi, type='DOI'))
pub.indexes.append(Index('SCOPUS', type='SCOPUS'))
yield pub
def entries_to_publications(self, entries):
"""Prerobi data zo SCOPUS json reprezentacie na internu Publication."""
def empty_to_none(s):
if s is None:
return None
s = s.strip()
if len(s) == 0:
return None
return s
def exists_to_none(d, key):
if key in d:
if type(d[key]) is list:
return [empty_to_none(x['$']) for x in d[key]]
else:
return empty_to_none(d[key])
else:
return None
def append_identifier(d, key, obj, type):
ids = exists_to_none(d, key)
if ids:
if isinstance(ids, list):
for id in ids:
obj.identifiers.append(Identifier(id, type=type))
else:
obj.identifiers.append(Identifier(ids, type=type))
for entry in entries:
author_count = int(entry['author-count']['$'])
if author_count == 0:
authors = []
else:
authors = self.authors_from_json(entry['author'])
year = empty_to_none(entry['prism:coverDate'])
if year:
year = int(year.split('-')[0])
pub = Publication(empty_to_none(entry['dc:title']), authors, year)
pub.times_cited = empty_to_none(entry['citedby-count'])
source_title = exists_to_none(entry, 'prism:publicationName')
if source_title:
source_title, replacements = re.subn(INCLUDING_RE,
'',
source_title)
source_title = source_title.strip()
if replacements:
pub.series = source_title
else:
pub.published_in = source_title
url = self.find_next_url(entry['link'], ref='scopus')
pub.source_urls.append(URL(url,
type='SCOPUS',
description='SCOPUS'))
citedby_url = self.find_next_url(entry['link'],
ref='scopus-citedby')
if citedby_url is not None:
pub.cite_urls.append(URL(citedby_url,
type='SCOPUS',
description='SCOPUS'))
pub.pages = exists_to_none(entry, 'prism:pageRange')
pub.volume = exists_to_none(entry, 'prism:volume')
pub.issue = exists_to_none(entry, 'prism:issueIdentifier')
pub.pages = exists_to_none(entry, 'prism:pageRange')
append_identifier(entry, 'prism:doi', pub, 'DOI')
append_identifier(entry, 'prism:isbn', pub, 'ISBN')
append_identifier(entry, 'prism:issn', pub, 'ISSN')
append_identifier(entry, 'eid', pub, 'SCOPUS')
pub.indexes.append(Index('SCOPUS', type='SCOPUS'))
yield pub