1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
|
###############################################################################
#
# This file is part of the Utopia Documents application.
# Copyright (c) 2008-2014 Lost Island Labs
# <info@utopiadocs.com>
#
# Utopia Documents is free software: you can redistribute it and/or modify
# it under the terms of the GNU GENERAL PUBLIC LICENSE VERSION 3 as
# published by the Free Software Foundation.
#
# Utopia Documents 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.
#
# In addition, as a special exception, the copyright holders give
# permission to link the code of portions of this program with the OpenSSL
# library under certain conditions as described in each individual source
# file, and distribute linked combinations including the two.
#
# You must obey the GNU General Public License in all respects for all of
# the code used other than OpenSSL. If you modify file(s) with this
# exception, you may extend this exception to your version of the file(s),
# but you are not obligated to do so. If you do not wish to do so, delete
# this exception statement from your version.
#
# You should have received a copy of the GNU General Public License
# along with Utopia Documents. If not, see <http://www.gnu.org/licenses/>
#
###############################################################################
#? name: ScienceWISE
#? www: http://sciencewise.info/
#? urls: http://beta.sciencewise.info/ http://sciencewise.info/
import common.utils
import hashlib
import json
import spineapi
import urllib
import utopia.document
import urllib2
class ScienceWISE(utopia.document.Annotator, utopia.document.Visualiser):
"""Annotate with ScienceWISE"""
@utopia.document.buffer
def on_activate_event(self, document):
text = document.text().encode('utf8')
text_hash = hashlib.md5(text).hexdigest()
url = 'http://beta.sciencewise.info/api/utopia'
payload = urllib.urlencode({ 'text': text, 'chksum': text_hash })
response = urllib2.urlopen(url, payload, timeout=8).read()
results = json.loads(response)
annotations = []
for result in results:
before = result.get('context', {}).get('before', '')
term = result.get('value', '')
after = result.get('context', {}).get('after', '')
link = result.get('link')
definitions = []
for definition in result.get('definitions', []):
definitions.append((definition.get('url'), definition.get('title')))
if len(term) > 0 and len(before) + len(term) + len(after) > 0 and link is not None:
matches = document.findInContext(before, term, after)
if len(matches) > 0:
annotation = spineapi.Annotation()
annotation['concept'] = 'ScienceWISE'
annotation['property:webpageUrl'] = link
annotation['property:term'] = term
annotation['property:name'] = 'Definitions of {0}'.format(term)
annotation['property:description'] = 'ScienceWISE ontology definitions'
annotation['property:sourceDatabase'] = 'sciencewise'
annotation['property:sourceDescription'] = '<p><a href="http://sciencewise.info/">ScienceWISE</a> provides phycists with article annotation and scientific bookmarking.</p>'
for url, title in definitions:
annotation.insertProperty('property:definitions', '{0} {1}'.format(url, title))
for match in matches:
annotation.addExtent(match)
annotations.append(annotation)
if len(annotations) > 0:
document.addAnnotations(annotations)
def visualisable(self, annotation):
return annotation.get('concept') == 'ScienceWISE'
def visualise(self, annotation):
xhtml = '<div>Term: <strong>{0}</strong></div>{1}<div><br /><a href="{2}">See term in ScienceWISE</a></div>'
definitions_xhtml = ''
if 'property:definitions' in annotation:
definitions = []
for definition in annotation.getAllProperties('property:definitions'):
url, _, title = definition.partition(' ')
definitions.append(' — <a href="{0}">{1}</a>'.format(url, title))
if len(definitions) > 0:
definitions_xhtml += '<br/>External definitions:<br/>'
definitions_xhtml += '<br/>'.join(definitions)
xhtml = xhtml.format(annotation['property:term'], definitions_xhtml, annotation['property:webpageUrl'])
return xhtml
|
