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
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
|
###############################################################################
#
# 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/>
#
###############################################################################
import common.eutils
import common.pubmed
import spineapi
import urllib
import utopia.document
from lxml import etree
class PubMedAnnotator(utopia.document.Annotator, utopia.document.Visualiser):
"""PubMed Recent Articles Lookup"""
def on_explore_event(self, phrase, document):
rt = ''
searchresult = common.eutils.esearch(db='pubmed', retmax=5, term=phrase)
root = etree.fromstring(searchresult)
ids = root.findall("./IdList/Id")
if len(ids) > 0:
idlist = ','.join((id.text for id in ids))
searchresult = common.eutils.efetch(db='pubmed', id=idlist)
articleset = etree.fromstring(searchresult)
for article in articleset.findall('./PubmedArticle'):
citation = common.pubmed.parse_PubmedArticle(article)
doi = citation['doi'] = citation.get('identifiers', {}).get('doi')
pmid = citation['pmid'] = citation.get('identifiers', {}).get('pubmed')
if pmid is not None:
link = '<a href="http://www.ncbi.nlm.nih.gov/pubmed/{0}">[Link]</a>'.format(pmid)
else:
link = ''
rt += u'<div class="box">{0} {1}</div>'.format(common.utils.format_citation(citation), link)
rt += '<p class="right"><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=' + urllib.quote_plus(phrase.encode('utf8')) + '">See more in PubMed...</a><p>'
annotation = spineapi.Annotation()
annotation['concept'] = 'PubMedArticleList'
annotation['property:name'] = "Articles from PubMed"
annotation['property:description'] = 'Related recent articles'
annotation['property:content'] = rt
annotation['property:sourceDatabase'] = 'pubmed'
annotation['property:sourceDescription'] = '<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/">PubMed</a> comprises more than 21 million citations for biomedical literature from MEDLINE, life science journals, and online books.</p>'
annotation['displayRelevance'] = '2000'
annotation['displayRank'] = '2000'
return [annotation]
return []
def visualisable(self, annotation):
return annotation.get('concept') == 'PubMedArticleList'
def visualise(self, annotation):
return annotation.get('property:content')
class PubMedLinkFinder(utopia.document.LinkFinder):
"""Show in PubMed"""
def findable(self, annotation):
#print '======', annotation.get('property:doi', '').encode('utf8'), annotation.get('property:pmid', '').encode('utf8'), annotation.get('property:title', '').encode('utf8')
return annotation.get('concept') in ('Citation', 'ForwardCitation') and ('property:title' in annotation or ('property:doi' in annotation and 'property:pmid' in annotation))
def findLink(self, annotation):
links = []
doi = annotation.get('property:doi')
pmid = annotation.get('property:pmid')
if doi is None and pmid is not None:
# Resolve DOI from PMID
pass # FIXME
elif pmid is None and doi is not None:
# Resolve PMID from DOI
pass # FIXME
elif doi is not None and pmid is not None:
# Resolve what can be resolved from the title
pass # FIXME
if doi is not None:
links.append(("30Show on publisher's website", 'http://dx.doi.org/{0}'.format(doi)))
if pmid is not None:
links.append(('20Show in PubMed', 'http://www.ncbi.nlm.nih.gov/pubmed/{0}'.format(pmid)))
return links
|
