onebox 1.2.2 → 1.2.3
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- checksums.yaml +4 -4
- data/README.md +2 -2
- data/lib/onebox/engine.rb +1 -0
- data/lib/onebox/engine/pubmed_onebox.rb +58 -0
- data/lib/onebox/engine/youtube_onebox.rb +8 -3
- data/lib/onebox/version.rb +1 -1
- data/spec/fixtures/pubmed-xml.response +122 -0
- data/spec/fixtures/pubmed.response +300 -0
- data/spec/lib/onebox/engine/pubmed_onebox_spec.rb +33 -0
- data/templates/amazon.mustache +1 -1
- data/templates/pubmed.mustache +12 -0
- metadata +10 -2
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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|
4
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-
data.tar.gz:
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3
|
+
metadata.gz: d9dbbcef9ad30d0ab30cf3b5392f01b781dca291
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4
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+
data.tar.gz: 7cd665b5a0d344b702fe7df32b6c691010539028
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
|
|
6
|
+
metadata.gz: 8bd2e6ed6565c4df9114a62e4628affb6b6227a40bfbd5e483f9ef0d73f8fb196d5dca3034ba46bd30173099d9a5647522dd9e307cf0918057fd1a137da7b892
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7
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+
data.tar.gz: a80fa2616b82977524212e8d084849910558e9910f385d8b943c5805f4791e06056bc21974bb9de40660a84fecc4c43703ddc1bc16f69c3ffa9255a58ec20ce2
|
data/README.md
CHANGED
|
@@ -107,7 +107,7 @@ Adding Support for a new URL
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107
107
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end
|
|
108
108
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```
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109
109
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110
|
-
3. Create new onebox spec
|
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110
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+
3. Create new onebox spec using [FakeWeb](https://github.com/chrisk/fakeweb)
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|
111
111
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|
|
112
112
|
``` ruby
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113
113
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# in spec/lib/onebox/engine/name_spec.rb
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@@ -153,7 +153,7 @@ Adding Support for a new URL
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153
153
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</div>
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|
154
154
|
```
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|
155
155
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156
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-
5. Create new fixture from HTML response
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|
156
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+
5. Create new fixture from HTML response for your FakeWeb request(s)
|
|
157
157
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|
|
158
158
|
``` bash
|
|
159
159
|
curl --output spec/fixtures/oneboxname.response -L -X -GET http://example.com
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data/lib/onebox/engine.rb
CHANGED
|
@@ -0,0 +1,58 @@
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1
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+
module Onebox
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2
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+
module Engine
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3
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+
class PubmedOnebox
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|
4
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+
include Engine
|
|
5
|
+
include LayoutSupport
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|
6
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+
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7
|
+
matches do
|
|
8
|
+
http
|
|
9
|
+
domain("www.ncbi.nlm.nih")
|
|
10
|
+
tld("gov")
|
|
11
|
+
has("/pubmed/")
|
|
12
|
+
end
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|
13
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+
|
|
14
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+
private
|
|
15
|
+
|
|
16
|
+
def get_xml
|
|
17
|
+
doc = Nokogiri::XML(open(@url + "?report=xml&format=text"))
|
|
18
|
+
pre = doc.xpath("//pre")
|
|
19
|
+
Nokogiri::XML("<root>" + pre.text + "</root>")
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
def authors_of_xml(xml)
|
|
23
|
+
initials = xml.css("Initials").map{|x| x.content}
|
|
24
|
+
last_names = xml.css("LastName").map{|x| x.content}
|
|
25
|
+
author_list = (initials.zip(last_names)).map{|i,l| i + " " + l}
|
|
26
|
+
if author_list.length > 1 then
|
|
27
|
+
author_list[-2] = author_list[-2] + " and " + author_list[-1]
|
|
28
|
+
author_list.pop
|
|
29
|
+
end
|
|
30
|
+
author_list.join(", ")
|
|
31
|
+
end
|
|
32
|
+
|
|
33
|
+
def date_of_xml(xml)
|
|
34
|
+
date_arr = (xml.css("PubDate")[0].children).map{|x| x.content}
|
|
35
|
+
date_arr = date_arr.select{|s| !s.match(/^\s+$/)}
|
|
36
|
+
date_arr = (date_arr.map{|s| s.split}).flatten
|
|
37
|
+
date_arr.sort.reverse.join(" ") # Reverse sort so month before year.
|
|
38
|
+
end
|
|
39
|
+
|
|
40
|
+
def data
|
|
41
|
+
xml = get_xml()
|
|
42
|
+
{
|
|
43
|
+
title: xml.css("ArticleTitle")[0].content,
|
|
44
|
+
authors: authors_of_xml(xml),
|
|
45
|
+
journal: xml.css("Title")[0].content,
|
|
46
|
+
abstract: xml.css("AbstractText")[0].content,
|
|
47
|
+
date: date_of_xml(xml),
|
|
48
|
+
link: @url,
|
|
49
|
+
pmid: match[:pmid]
|
|
50
|
+
}
|
|
51
|
+
end
|
|
52
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+
|
|
53
|
+
def match
|
|
54
|
+
@match ||= @url.match(%r{www\.ncbi\.nlm\.nih\.gov/pubmed/(?<pmid>[0-9]+)})
|
|
55
|
+
end
|
|
56
|
+
end
|
|
57
|
+
end
|
|
58
|
+
end
|
|
@@ -7,11 +7,16 @@ module Onebox
|
|
|
7
7
|
matches_regexp /^https?:\/\/(?:www\.)?(?:youtube\.com|youtu\.be)\/.+$/
|
|
8
8
|
|
|
9
9
|
def to_html
|
|
10
|
-
rewrite_agnostic(
|
|
10
|
+
rewrite_agnostic(append_params(raw[:html]))
|
|
11
11
|
end
|
|
12
12
|
|
|
13
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-
def
|
|
14
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-
|
|
13
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+
def append_params(html)
|
|
14
|
+
result = html.dup
|
|
15
|
+
result.gsub! /(src="[^"]+)/, '\1&wmode=opaque'
|
|
16
|
+
if url =~ /t=(\d+)/
|
|
17
|
+
result.gsub! /(src="[^"]+)/, '\1&start=' + Regexp.last_match[1]
|
|
18
|
+
end
|
|
19
|
+
result
|
|
15
20
|
end
|
|
16
21
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|
|
17
22
|
def rewrite_agnostic(html)
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data/lib/onebox/version.rb
CHANGED
|
@@ -0,0 +1,122 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="utf-8"?>
|
|
2
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
3
|
+
<pre>
|
|
4
|
+
<PubmedArticle>
|
|
5
|
+
<MedlineCitation Owner="NLM" Status="MEDLINE">
|
|
6
|
+
<PMID Version="1">7288891</PMID>
|
|
7
|
+
<DateCreated>
|
|
8
|
+
<Year>1981</Year>
|
|
9
|
+
<Month>12</Month>
|
|
10
|
+
<Day>22</Day>
|
|
11
|
+
</DateCreated>
|
|
12
|
+
<DateCompleted>
|
|
13
|
+
<Year>1981</Year>
|
|
14
|
+
<Month>12</Month>
|
|
15
|
+
<Day>22</Day>
|
|
16
|
+
</DateCompleted>
|
|
17
|
+
<DateRevised>
|
|
18
|
+
<Year>2010</Year>
|
|
19
|
+
<Month>11</Month>
|
|
20
|
+
<Day>18</Day>
|
|
21
|
+
</DateRevised>
|
|
22
|
+
<Article PubModel="Print">
|
|
23
|
+
<Journal>
|
|
24
|
+
<ISSN IssnType="Print">0022-2844</ISSN>
|
|
25
|
+
<JournalIssue CitedMedium="Print">
|
|
26
|
+
<Volume>17</Volume>
|
|
27
|
+
<Issue>6</Issue>
|
|
28
|
+
<PubDate>
|
|
29
|
+
<Year>1981</Year>
|
|
30
|
+
</PubDate>
|
|
31
|
+
</JournalIssue>
|
|
32
|
+
<Title>Journal of molecular evolution</Title>
|
|
33
|
+
<ISOAbbreviation>J. Mol. Evol.</ISOAbbreviation>
|
|
34
|
+
</Journal>
|
|
35
|
+
<ArticleTitle>Evolutionary trees from DNA sequences: a maximum likelihood approach.</ArticleTitle>
|
|
36
|
+
<Pagination>
|
|
37
|
+
<MedlinePgn>368-76</MedlinePgn>
|
|
38
|
+
</Pagination>
|
|
39
|
+
<Abstract>
|
|
40
|
+
<AbstractText>The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.</AbstractText>
|
|
41
|
+
</Abstract>
|
|
42
|
+
<AuthorList CompleteYN="Y">
|
|
43
|
+
<Author ValidYN="Y">
|
|
44
|
+
<LastName>Felsenstein</LastName>
|
|
45
|
+
<ForeName>J</ForeName>
|
|
46
|
+
<Initials>J</Initials>
|
|
47
|
+
</Author>
|
|
48
|
+
</AuthorList>
|
|
49
|
+
<Language>eng</Language>
|
|
50
|
+
<PublicationTypeList>
|
|
51
|
+
<PublicationType>Journal Article</PublicationType>
|
|
52
|
+
<PublicationType>Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
|
|
53
|
+
</PublicationTypeList>
|
|
54
|
+
</Article>
|
|
55
|
+
<MedlineJournalInfo>
|
|
56
|
+
<Country>GERMANY, WEST</Country>
|
|
57
|
+
<MedlineTA>J Mol Evol</MedlineTA>
|
|
58
|
+
<NlmUniqueID>0360051</NlmUniqueID>
|
|
59
|
+
<ISSNLinking>0022-2844</ISSNLinking>
|
|
60
|
+
</MedlineJournalInfo>
|
|
61
|
+
<ChemicalList>
|
|
62
|
+
<Chemical>
|
|
63
|
+
<RegistryNumber>9007-49-2</RegistryNumber>
|
|
64
|
+
<NameOfSubstance>DNA</NameOfSubstance>
|
|
65
|
+
</Chemical>
|
|
66
|
+
</ChemicalList>
|
|
67
|
+
<CitationSubset>IM</CitationSubset>
|
|
68
|
+
<MeshHeadingList>
|
|
69
|
+
<MeshHeading>
|
|
70
|
+
<DescriptorName MajorTopicYN="Y">Base Sequence</DescriptorName>
|
|
71
|
+
</MeshHeading>
|
|
72
|
+
<MeshHeading>
|
|
73
|
+
<DescriptorName MajorTopicYN="Y">Biological Evolution</DescriptorName>
|
|
74
|
+
</MeshHeading>
|
|
75
|
+
<MeshHeading>
|
|
76
|
+
<DescriptorName MajorTopicYN="N">Computers</DescriptorName>
|
|
77
|
+
</MeshHeading>
|
|
78
|
+
<MeshHeading>
|
|
79
|
+
<DescriptorName MajorTopicYN="N">DNA</DescriptorName>
|
|
80
|
+
<QualifierName MajorTopicYN="Y">genetics</QualifierName>
|
|
81
|
+
</MeshHeading>
|
|
82
|
+
<MeshHeading>
|
|
83
|
+
<DescriptorName MajorTopicYN="N">Mathematics</DescriptorName>
|
|
84
|
+
</MeshHeading>
|
|
85
|
+
<MeshHeading>
|
|
86
|
+
<DescriptorName MajorTopicYN="N">Models, Biological</DescriptorName>
|
|
87
|
+
</MeshHeading>
|
|
88
|
+
<MeshHeading>
|
|
89
|
+
<DescriptorName MajorTopicYN="N">Phylogeny</DescriptorName>
|
|
90
|
+
</MeshHeading>
|
|
91
|
+
</MeshHeadingList>
|
|
92
|
+
</MedlineCitation>
|
|
93
|
+
<PubmedData>
|
|
94
|
+
<History>
|
|
95
|
+
<PubMedPubDate PubStatus="pubmed">
|
|
96
|
+
<Year>1981</Year>
|
|
97
|
+
<Month>1</Month>
|
|
98
|
+
<Day>1</Day>
|
|
99
|
+
</PubMedPubDate>
|
|
100
|
+
<PubMedPubDate PubStatus="medline">
|
|
101
|
+
<Year>1981</Year>
|
|
102
|
+
<Month>1</Month>
|
|
103
|
+
<Day>1</Day>
|
|
104
|
+
<Hour>0</Hour>
|
|
105
|
+
<Minute>1</Minute>
|
|
106
|
+
</PubMedPubDate>
|
|
107
|
+
<PubMedPubDate PubStatus="entrez">
|
|
108
|
+
<Year>1981</Year>
|
|
109
|
+
<Month>1</Month>
|
|
110
|
+
<Day>1</Day>
|
|
111
|
+
<Hour>0</Hour>
|
|
112
|
+
<Minute>0</Minute>
|
|
113
|
+
</PubMedPubDate>
|
|
114
|
+
</History>
|
|
115
|
+
<PublicationStatus>ppublish</PublicationStatus>
|
|
116
|
+
<ArticleIdList>
|
|
117
|
+
<ArticleId IdType="pubmed">7288891</ArticleId>
|
|
118
|
+
</ArticleIdList>
|
|
119
|
+
</PubmedData>
|
|
120
|
+
</PubmedArticle>
|
|
121
|
+
|
|
122
|
+
</pre>
|
|
@@ -0,0 +1,300 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="utf-8"?>
|
|
2
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
3
|
+
<html xmlns="http://www.w3.org/1999/xhtml">
|
|
4
|
+
<head xmlns:xi="http://www.w3.org/2001/XInclude"><meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
5
|
+
<!-- meta -->
|
|
6
|
+
<meta name="author" content="pubmeddev" /><meta name="keywords" content="PubMed, National Center for Biotechnology Information, NCBI, United States National Library of Medicine, NLM, MEDLINE, Medical Journals, pub med, Entrez, Journal Articles, Citation search" /><meta name="description" content="PubMed comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites." /><meta name="robots" content="index,nofollow,noarchive" />
|
|
7
|
+
<meta name="ncbi_app" content="entrez" /><meta name="ncbi_db" content="pubmed" /><meta name="ncbi_report" content="abstract" /><meta name="ncbi_format" content="html" /><meta name="ncbi_pagesize" content="20" /><meta name="ncbi_sortorder" content="default" /><meta name="ncbi_pageno" content="1" /><meta name="ncbi_resultcount" content="1" /><meta name="ncbi_op" content="retrieve" /><meta name="ncbi_pdid" content="abstract" /><meta name="ncbi_sessionid" content="396A07392FFBFC81_0249SID" /><meta name="ncbi_uidlist" content="7288891" /><meta name="ncbi_filter" content="all" /><meta name="ncbi_stat" content="false" /><meta name="ncbi_hitstat" content="false" />
|
|
8
|
+
|
|
9
|
+
|
|
10
|
+
<!-- title -->
|
|
11
|
+
<title>Evolutionary trees from DNA sequences: a maximum ... [J Mol Evol. 1981] - PubMed - NCBI</title>
|
|
12
|
+
|
|
13
|
+
<!-- Common JS and CSS -->
|
|
14
|
+
|
|
15
|
+
<script type="text/javascript">
|
|
16
|
+
var ncbi_startTime = new Date();
|
|
17
|
+
</script>
|
|
18
|
+
|
|
19
|
+
<link rel="alternate" type="application/rss+xml" title="PubMed New and Noteworthy" href="/feed/rss.cgi?ChanKey=PubMedNews" />
|
|
20
|
+
<link rel="search" type="application/opensearchdescription+xml" href="/corehtml/query/static/pubmedsearch.xml" title="PubMed search" />
|
|
21
|
+
|
|
22
|
+
<script type="text/javascript" src="//static.pubmed.gov/core/jig/1.13/js/jig.min.js"></script>
|
|
23
|
+
|
|
24
|
+
<link xmlns="http://www.w3.org/1999/xhtml" type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/3968188/css/3881636/3579733.css" xml:base="http://127.0.0.1/sites/static/header_footer/" /><link xmlns="http://www.w3.org/1999/xhtml" type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/3968188/css/3529739.css" media="print" xml:base="http://127.0.0.1/sites/static/header_footer/" />
|
|
25
|
+
<link rel="shortcut icon" href="//www.ncbi.nlm.nih.gov/favicon.ico" /><meta name="ncbi_phid" content="396A07392FFBE7610000000000F9D8FF" /><script type="text/javascript"><!--
|
|
26
|
+
var ScriptUrl = 'http://www.ncbi.nlm.nih.gov/pubmed';
|
|
27
|
+
var ScriptPath = '/portal/';
|
|
28
|
+
var objHierarchy = {"name":"EntrezSystem2","type":"Layout","realname":"EntrezSystem2",
|
|
29
|
+
"children":[{"name":"EntrezSystem2.PEntrez","type":"Cluster","realname":"EntrezSystem2.PEntrez",
|
|
30
|
+
"children":[{"name":"EntrezSystem2.PEntrez.DbConnector","type":"Portlet","realname":"EntrezSystem2.PEntrez.PEntrez.DbConnector","shortname":"DbConnector"},
|
|
31
|
+
{"name":"EntrezSystem2.PEntrez.ParamContainer","type":"Portlet","realname":"EntrezSystem2.PEntrez.PEntrez.ParamContainer","shortname":"ParamContainer"},
|
|
32
|
+
{"name":"EntrezSystem2.PEntrez.MyNcbi","type":"Portlet","realname":"EntrezSystem2.PEntrez.PEntrez.MyNcbi","shortname":"MyNcbi"},
|
|
33
|
+
{"name":"EntrezSystem2.PEntrez.UserPreferenceUrlParamContainer","type":"Portlet","realname":"EntrezSystem2.PEntrez.PEntrez.UserPreferenceUrlParamContainer","shortname":"UserPreferenceUrlParamContainer"},
|
|
34
|
+
{"name":"EntrezSystem2.PEntrez.GridProperty","type":"Portlet","realname":"EntrezSystem2.PEntrez.PEntrez.GridProperty","shortname":"GridProperty"},
|
|
35
|
+
{"name":"EntrezSystem2.PEntrez.PubMed","type":"Cluster","realname":"EntrezSystem2.PEntrez.PubMed",
|
|
36
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">SNP Submission Tool</a></li><li><a href="/sutils/splign/" title=" Tool for aligning transcripts to genomic DNA ">Splign</a></li><li><a href="/Structure/VAST/vast.html" title=" Tool that generates 3D structural alignments ">Vector Alignment Search Tool (VAST)</a></li><li><a href="/guide/data-software/">All Data & Software Resources...</a></li></ul></li><li><a href="#domains-structures">Domains & Structures</a><ul class="actual-resources-submenu domains-structures"><li><a href="/biosystems/" title=" Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships. ">BioSystems</a></li><li><a href="/Structure/CN3D/cn3d.shtml" title=" Program for viewing 3D structures and alignments ">Cn3D</a></li><li><a href="/cdd" title=" Database of conserved protein domains represented by multiple sequence alignments ">Conserved Domain Database (CDD)</a></li><li><a href="/Structure/cdd/wrpsb.cgi" title=" Locates conserved domains within a protein sequence ">Conserved Domain Search Service (CD Search)</a></li><li><a href="/structure/" title=" Database of 3D macromolecular structures derived from PDB ">Structure (Molecular Modeling Database)</a></li><li><a href="/Structure/VAST/vast.html" title=" Tool that generates 3D structural alignments ">Vector Alignment Search Tool (VAST)</a></li><li><a href="/guide/domains-structures/">All Domains & Structures Resources...</a></li></ul></li><li><a href="#genes-expression">Genes & Expression</a><ul class="actual-resources-submenu genes-expression"><li><a href="/biosystems/" title=" Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships. ">BioSystems</a></li><li><a href="/gap" title=" Genotype/Phenotype association studies ">Database of Genotypes and Phenotypes (dbGaP)</a></li><li><a href="/books/NBK25501/ " title=" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system ">E-Utilities</a></li><li><a href="/gene" title=" Database of gene loci and associated transcripts and proteins ">Gene</a></li><li><a href="/geo/" title=" Gene Expression Omnibus (GEO) Database ">Gene Expression Omnibus (GEO) Database </a></li><li><a href="/gds" title=" Curated collections of gene expression data sets ">Gene Expression Omnibus (GEO) Datasets</a></li><li><a href="/geoprofiles/" title=" Database of gene expression Profiles for individual sequences ">Gene Expression Omnibus (GEO) Profiles</a></li><li><a href="/tools/gbench/" title=" Stand-alone application for analyzing sequence data ">Genome Workbench</a></li><li><a href="/homologene" title=" Sets of homologous eukaryotic genes ">HomoloGene</a></li><li><a href="/mapview/" title=" Tool for searching, viewing and downloading genomic maps and related data ">Map Viewer</a></li><li><a href="/omim" title=" Database of human genes and genetic disorders ">Online Mendelian Inheritance in Man (OMIM)</a></li><li><a href="/refseq/rsg/" title=" RefSeqGene reference standards for genomic sequences of well-characterized genes ">RefSeqGene</a></li><li><a href="/unigene" title=" Gene-centered clusters of transcripts and ESTs ">UniGene</a></li><li><a href="/guide/genes-expression/">All Genes & Expression Resources...</a></li></ul></li><li><a href="#genetics-medicine">Genetics & Medicine</a><ul class="actual-resources-submenu genetics-medicine"><li><a href="/books" title=" Online biomedical books ">Bookshelf</a></li><li><a href="/gap" title=" Genotype/Phenotype association studies ">Database of Genotypes and Phenotypes (dbGaP)</a></li><li><a href="/gtr/" title=" Detailed information about genetic tests and labs ">Genetic Testing Registry</a></li><li><a href="/genomes/FLU/" title=" Data from the NIAID Influenza Genome Sequencing Project ">Influenza Virus</a></li><li><a href="/mapview/" title=" Tool for searching, viewing and downloading genomic maps and related data ">Map Viewer</a></li><li><a href="/omim" title=" Database of human genes and genetic disorders ">Online Mendelian Inheritance in Man (OMIM)</a></li><li><a href="/pubmed" title=" Biomedical literature abstracts ">PubMed</a></li><li><a href="/pmc/" title=" Free, full-text articles ">PubMed Central (PMC)</a></li><li><a href="/pubmed/clinical " title=" Directory of PubMed queries about clinical topics ">PubMed Clinical Queries</a></li><li><a href="/refseq/rsg/" title=" RefSeqGene reference standards for genomic sequences of well-characterized genes ">RefSeqGene</a></li><li><a href="/guide/genetics-medicine/">All Genetics & Medicine Resources...</a></li></ul></li><li><a href="#genomes-maps">Genomes & Maps</a><ul class="actual-resources-submenu genomes-maps"><li><a href="/dbvar" title=" A database of genomic structural variation ">Database of Genomic Structural Variation (dbVar)</a></li><li><a href="/genbank/tbl2asn2/" title=" Command-line program for submitting sequence data ">GenBank: tbl2asn</a></li><li><a href="/sites/genome" title=" Curated genomic DNA sequences ">Genome</a></li><li><a href="/bioproject/" title=" Central status pages for genome sequencing projects ">Genome Project</a></li><li><a href="/sutils/protmap.cgi" title=" Maps proteins from a COG/VOG back to its genome ">Genome ProtMap</a></li><li><a href="/tools/gbench/" title=" Stand-alone application for analyzing sequence data ">Genome Workbench</a></li><li><a href="/genomes/FLU/" title=" Data from the NIAID Influenza Genome Sequencing Project ">Influenza Virus</a></li><li><a href="/mapview/" title=" Tool for searching, viewing and downloading genomic maps and related data ">Map Viewer</a></li><li><a href="/nuccore" title=" Nucleotide sequence data in GenBank and RefSeq ">Nucleotide Database</a></li><li><a href="/popset" title=" Sets of nucleotide sequences representing a population ">PopSet</a></li><li><a href="/sutils/static/prosplign/prosplign.html" title=" Tool for aligning proteins to genomic DNA ">ProSplign</a></li><li><a href="/Traces/sra/sra.cgi?" title=" Database of sequences reads from next generation sequencing technologies ">Sequence Read Archive (SRA)</a></li><li><a href="/sutils/splign/" title=" Tool for aligning transcripts to genomic DNA ">Splign</a></li><li><a href="/Traces/trace.cgi" title=" DNA chromatograms, base calls, and quality estimates for single-pass reads. ">Trace Archive</a></li><li><a href="/unists" title=" Database of Sequence Tagged Sites ">UniSTS</a></li><li><a href="/guide/genomes-maps/">All Genomes & Maps Resources...</a></li></ul></li><li><a href="#homology">Homology</a><ul class="actual-resources-submenu homology"><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" title=" Tool for finding local regions of sequence similarity ">BLAST (Basic Local Alignment Search Tool)</a></li><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download" title=" BLAST programs for a local computer ">BLAST (Stand-alone)</a></li><li><a href="/sutils/blink.cgi?mode=query" title=" Pre-computed reports showing proteins with similar sequences ">BLAST Link (BLink)</a></li><li><a href="/cdd" title=" Database of conserved protein domains represented by multiple sequence alignments ">Conserved Domain Database (CDD)</a></li><li><a href="/Structure/cdd/wrpsb.cgi" title=" Locates conserved domains within a protein sequence ">Conserved Domain Search Service (CD Search)</a></li><li><a href="/sutils/protmap.cgi" title=" Maps proteins from a COG/VOG back to its genome ">Genome ProtMap</a></li><li><a href="/homologene" title=" Sets of homologous eukaryotic genes ">HomoloGene</a></li><li><a href="/proteinclusters" title=" Clusters of related proteins from prokaryotes and organelles ">Protein Clusters</a></li><li><a href="/guide/homology/">All Homology Resources...</a></li></ul></li><li><a href="#literature">Literature</a><ul class="actual-resources-submenu literature"><li><a href="/books" title=" Online biomedical books ">Bookshelf</a></li><li><a href="/books/NBK25501/ " title=" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system ">E-Utilities</a></li><li><a href="/nlmcatalog/journals" title=" Information on journals cited by NCBI records ">Journals in NCBI Databases</a></li><li><a href="/mesh" title=" Controlled vocabulary for MEDLINE ">MeSH Database</a></li><li><a href="/books/NBK143764/" title=" Introductory articles about NCBI resources ">NCBI Handbook</a></li><li><a href="/books/NBK3831/" title=" Online, searchable help documentation ">NCBI Help Manual</a></li><li><a href="/books/NBK1969/" title=" NCBI's monthly newsletter ">NCBI News</a></li><li><a href="/pubmed" title=" Biomedical literature abstracts ">PubMed</a></li><li><a href="/pmc/" title=" Free, full-text articles ">PubMed Central (PMC)</a></li><li><a href="/pubmed/clinical " title=" Directory of PubMed queries about clinical topics ">PubMed Clinical Queries</a></li><li><a href="/pubmedhealth/" title=" Reviews of clinical effectiveness research ">PubMed Health</a></li><li><a href="/guide/literature/">All Literature Resources...</a></li></ul></li><li><a href="#proteins">Proteins</a><ul class="actual-resources-submenu proteins"><li><a href="/biosystems/" title=" Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships. ">BioSystems</a></li><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" title=" Tool for finding local regions of sequence similarity ">BLAST (Basic Local Alignment Search Tool)</a></li><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download" title=" BLAST programs for a local computer ">BLAST (Stand-alone)</a></li><li><a href="/sutils/blink.cgi?mode=query" title=" Pre-computed reports showing proteins with similar sequences ">BLAST Link (BLink)</a></li><li><a href="/cdd" title=" Database of conserved protein domains represented by multiple sequence alignments ">Conserved Domain Database (CDD)</a></li><li><a href="/Structure/cdd/wrpsb.cgi" title=" Locates conserved domains within a protein sequence ">Conserved Domain Search Service (CD Search)</a></li><li><a href="/books/NBK25501/ " title=" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system ">E-Utilities</a></li><li><a href="/sutils/static/prosplign/prosplign.html" title=" Tool for aligning proteins to genomic DNA ">ProSplign</a></li><li><a href="/proteinclusters" title=" Clusters of related proteins from prokaryotes and organelles ">Protein Clusters</a></li><li><a href="/protein" title=" Protein sequence data ">Protein Database</a></li><li><a href="/refseq/" title=" Curated nucleotide and protein sequences produced by NCBI ">Reference Sequence (RefSeq)</a></li><li><a href="/guide/proteins/">All Proteins Resources...</a></li></ul></li><li><a href="#sequence-analysis">Sequence Analysis</a><ul class="actual-resources-submenu sequence-analysis"><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" title=" Tool for finding local regions of sequence similarity ">BLAST (Basic Local Alignment Search Tool)</a></li><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download" title=" BLAST programs for a local computer ">BLAST (Stand-alone)</a></li><li><a href="/sutils/blink.cgi?mode=query" title=" Pre-computed reports showing proteins with similar sequences ">BLAST Link (BLink)</a></li><li><a href="/Structure/cdd/wrpsb.cgi" title=" Locates conserved domains within a protein sequence ">Conserved Domain Search Service (CD Search)</a></li><li><a href="/sutils/protmap.cgi" title=" Maps proteins from a COG/VOG back to its genome ">Genome ProtMap</a></li><li><a href="/tools/gbench/" title=" Stand-alone application for analyzing sequence data ">Genome Workbench</a></li><li><a href="/genomes/FLU/" title=" Data from the NIAID Influenza Genome Sequencing Project ">Influenza Virus</a></li><li><a href="/tools/primer-blast/" title=" Designs PCR primers and analyzes them for target specificity using BLAST. ">Primer-BLAST</a></li><li><a href="/sutils/static/prosplign/prosplign.html" title=" Tool for aligning proteins to genomic DNA ">ProSplign</a></li><li><a href="/sutils/splign/" title=" Tool for aligning transcripts to genomic DNA ">Splign</a></li><li><a href="/guide/sequence-analysis/">All Sequence Analysis Resources...</a></li></ul></li><li><a href="#taxonomy">Taxonomy</a><ul class="actual-resources-submenu taxonomy"><li><a href="/taxonomy" title=" The NCBI taxonomy tree in Entrez ">Taxonomy</a></li><li><a href="/Taxonomy/Browser/wwwtax.cgi?mode=Root" title=" Displays and links Entrez data to each taxonomic node ">Taxonomy Browser</a></li><li><a href="/Taxonomy/CommonTree/wwwcmt.cgi" title=" Creates custom taxonomic trees ">Taxonomy Common Tree</a></li><li><a href="/guide/taxonomy/">All Taxonomy Resources...</a></li></ul></li><li><a href="#training-tutorials">Training & Tutorials</a><ul class="actual-resources-submenu training-tutorials"><li><a href="/education/" title=" Central page providing links to tutorials and training materials ">NCBI Education Page</a></li><li><a href="/books/NBK143764/" title=" Introductory articles about NCBI resources ">NCBI Handbook</a></li><li><a href="/books/NBK3831/" title=" Online, searchable help documentation ">NCBI Help Manual</a></li><li><a href="/books/NBK1969/" title=" NCBI's monthly newsletter ">NCBI News</a></li><li><a href="/guide/training-tutorials/">All Training & Tutorials Resources...</a></li></ul></li><li><a href="#variation">Variation</a><ul class="actual-resources-submenu variation"><li><a href="/dbvar" title=" A database of genomic structural variation ">Database of Genomic Structural Variation (dbVar)</a></li><li><a href="/gap" title=" Genotype/Phenotype association studies ">Database of Genotypes and Phenotypes (dbGaP)</a></li><li><a href="/snp" title=" Database of nucleotide sequence polymorphisms ">Database of Single Nucleotide Polymorphisms (dbSNP)</a></li><li><a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" title=" The SNP database tools page provides links to the general submission guidelines and to the submission handle request. 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<div class="rprt_all"><div class="rprt abstract"><div class="cit"><a href="#" title="Journal of molecular evolution." abstractLink="yes" alsec="jour" alterm="J Mol Evol.">J Mol Evol.</a> 1981;17(6):368-76.</div><h1>Evolutionary trees from DNA sequences: a maximum likelihood approach.</h1><div class="auths"><a href="/pubmed?term=Felsenstein%20J%5BAuthor%5D&cauthor=true&cauthor_uid=7288891">Felsenstein J</a>.</div><div class="abstr"><h3>Abstract</h3><div class=""><p>The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.</p></div></div><div class="aux"><div class="resc"><dl class="rprtid"><dt>PMID:</dt> <dd>7288891</dd> <dd> [PubMed - indexed for MEDLINE] </dd><dd> </dd></dl></div><div class="links"></div></div><div class="morecit"><h3><a title="Supplemental information" class="jig-ncbitoggler ui-ncbitoggler" href="#"><span class="ui-ncbitoggler-master-text">Publication Types, MeSH Terms, Substances</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></h3><div class="ui-ncbi-toggler-slave"><h4>Publication Types</h4><ul><li><a href="#" abstractLink="yes" alsec="ptyp" alterm="Research Support, U.S. Gov't, Non-P.H.S.">Research Support, U.S. Gov't, Non-P.H.S.</a></li></ul><h4>MeSH Terms</h4><ul><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Base Sequence*">Base Sequence*</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Biological Evolution*">Biological Evolution*</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Computers">Computers</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="DNA/genetics*">DNA/genetics*</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Mathematics">Mathematics</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Models, Biological">Models, Biological</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Phylogeny">Phylogeny</a></li></ul><h4>Substances</h4><ul><li><a href="#" abstractLink="yes" alsec="subs" alterm="DNA">DNA</a></li></ul></div></div><div class="morecit"><h3><a title="Links to resources such as full text articles and biological data" class="jig-ncbitoggler ui-ncbitoggler" href="#"><span class="ui-ncbitoggler-master-text">LinkOut - more resources</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></h3><div class="ui-ncbi-toggler-slave"><div class="linkoutlist"><h4>Other Literature Sources</h4><ul><li><a title="Free resource" href="http://www.scholaruniverse.com/ncbi-linkout?id=7288891" ref="itool=Abstract&PrId=3087&uid=7288891&db=pubmed&log$=linkoutlink&nlmid=0360051" target="_blank">COS Scholar Universe</a></li></ul></div></div></div><div id="comments_panel" data-recid="7288891" data-exp="true" data-rsys="1"><div id="comments_panel_head"><a id="coments_panel_anchor" href="/pubmedcommons/" name="comments">PubMed Commons home</a><h2><span id="show_comments" title="Shows comments">
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<a href="http://www.nlm.nih.gov/privacy.html" class="newdomain">Privacy</a> |
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<a href="/guide/browsers/">Browsers</a> | <a href="http://www.nlm.nih.gov/accessibility.html">Accessibility</a> | <a href="/About/glance/contact_info.html">Contact</a>
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</span> <span class="org url"><a href="http://www.nlm.nih.gov/">U.S. National Library of Medicine</a></span>
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<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIConfigJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js?v=1"> </script>
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<script type="text/javascript" src="/portal/portal3rc.fcgi/static/js/hfjs2.js"> </script>
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<div><input name="EntrezSystem2.PEntrez.DbConnector.Db" sid="1" type="hidden" value="pubmed" /><input name="EntrezSystem2.PEntrez.DbConnector.LastDb" sid="1" type="hidden" value="pubmed" /><input name="EntrezSystem2.PEntrez.DbConnector.Term" sid="1" type="hidden" value="" /><input name="EntrezSystem2.PEntrez.DbConnector.LastTabCmd" sid="1" type="hidden" value="" /><input name="EntrezSystem2.PEntrez.DbConnector.LastQueryKey" sid="1" type="hidden" value="1" /><input name="EntrezSystem2.PEntrez.DbConnector.IdsFromResult" sid="1" type="hidden" value="" /><input name="EntrezSystem2.PEntrez.DbConnector.LastIdsFromResult" sid="1" type="hidden" value="" /><input name="EntrezSystem2.PEntrez.DbConnector.LinkName" sid="1" type="hidden" /><input name="EntrezSystem2.PEntrez.DbConnector.LinkReadableName" sid="1" type="hidden" /><input name="EntrezSystem2.PEntrez.DbConnector.LinkSrcDb" sid="1" type="hidden" /><input name="EntrezSystem2.PEntrez.DbConnector.Cmd" sid="1" type="hidden" /><input name="EntrezSystem2.PEntrez.DbConnector.TabCmd" sid="1" type="hidden" /><input name="EntrezSystem2.PEntrez.DbConnector.QueryKey" sid="1" type="hidden" /></div>
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<input type="hidden" name="p$a" id="p$a" /><input type="hidden" name="p$l" id="p$l" value="EntrezSystem2" /><input type="hidden" name="p$st" id="p$st" value="pubmed" /><input name="SessionId" id="SessionId" value="396A07392FFBFC81_0249SID" disabled="disabled" type="hidden" /><input name="Snapshot" id="Snapshot" value="/projects/entrez/pubmed/PubMedGroup@2.13" disabled="disabled" type="hidden" /></form>
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<!-- 396A07392FFBFC81_0249SID /projects/entrez/pubmed/PubMedGroup@2.13 portal202 v4.0.1.r425050:TC Fri, Jan 24 2014 02:40:33 -->
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<script type='text/javascript' src='/portal/js/portal.js?v4%2E0%2E1%2Er425050%3ATC+Fri%2C+Jan+24+2014+02%3A40%3A33'></script><script type="text/javascript" src="//static.pubmed.gov/portal/portal3rc.fcgi/3963835/js/3812534/3923183/3812535/3759173/3916331/3456248/3812251/3936369/3908752/2868104/2486879/2600938/3758627/20927/3963834/3423/31971/31967/2692675/3801193/3838067/648425/3890977/3920825/3929876/3922903/3783853.js" snapshot="pubmed"></script></body>
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@@ -0,0 +1,33 @@
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1
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+
require "spec_helper"
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+
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3
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+
describe Onebox::Engine::PubmedOnebox do
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4
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+
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5
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+
let(:link) { "http://www.ncbi.nlm.nih.gov/pubmed/7288891" }
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+
let(:xml_link) { "http://www.ncbi.nlm.nih.gov/pubmed/7288891?report=xml&format=text" }
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+
let(:html) { described_class.new(link).to_html }
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+
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9
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+
before do
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10
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+
fake(link, response("pubmed"))
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+
fake(xml_link, response("pubmed-xml"))
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+
end
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13
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+
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14
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+
it "has the paper's title" do
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15
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+
expect(html).to include("Evolutionary trees from DNA sequences: a maximum likelihood approach.")
|
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+
end
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18
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+
it "has the paper's author" do
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+
expect(html).to include("Felsenstein")
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+
end
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it "has the paper's abstract" do
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expect(html).to include("The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed.") end
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+
it "has the paper's date" do
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+
expect(html).to include("1981")
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|
+
end
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+
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it "has the URL to the resource" do
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expect(html).to include(link)
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end
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end
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|
data/templates/amazon.mustache
CHANGED
metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: onebox
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3
3
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version: !ruby/object:Gem::Version
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-
version: 1.2.
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4
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+
version: 1.2.3
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5
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platform: ruby
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6
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authors:
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7
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- Joanna Zeta
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@@ -10,7 +10,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2014-02-
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+
date: 2014-02-24 00:00:00.000000000 Z
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14
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dependencies:
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15
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- !ruby/object:Gem::Dependency
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name: multi_json
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@@ -267,6 +267,7 @@ files:
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- lib/onebox/engine/html.rb
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- lib/onebox/engine/json.rb
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+
- lib/onebox/engine/pubmed_onebox.rb
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@@ -287,6 +288,8 @@ files:
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- spec/fixtures/googleplayapp.response
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- spec/fixtures/pubmed.response
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@@ -303,6 +306,7 @@ files:
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- spec/lib/onebox/engine/html_spec.rb
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+
- spec/lib/onebox/engine/pubmed_onebox_spec.rb
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- spec/lib/onebox/engine/stack_exchange_onebox_spec.rb
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@@ -321,6 +325,7 @@ files:
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- templates/githubcommit.mustache
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|
- templates/githubpullrequest.mustache
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+
- templates/pubmed.mustache
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|
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|
@@ -356,6 +361,8 @@ test_files:
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|
- spec/fixtures/githubpullrequest.response
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|
- spec/fixtures/googleplayapp.response
|
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|
- spec/fixtures/image.response
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|
+
- spec/fixtures/pubmed-xml.response
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+
- spec/fixtures/pubmed.response
|
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|
- spec/fixtures/stackexchange.response
|
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|
- spec/fixtures/twitterstatus.response
|
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|
- spec/fixtures/video.response
|
|
@@ -372,6 +379,7 @@ test_files:
|
|
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|
- spec/lib/onebox/engine/google_play_app_onebox_spec.rb
|
|
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|
- spec/lib/onebox/engine/html_spec.rb
|
|
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381
|
- spec/lib/onebox/engine/json_spec.rb
|
|
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|
+
- spec/lib/onebox/engine/pubmed_onebox_spec.rb
|
|
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383
|
- spec/lib/onebox/engine/stack_exchange_onebox_spec.rb
|
|
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384
|
- spec/lib/onebox/engine/twitter_status_onebox_spec.rb
|
|
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385
|
- spec/lib/onebox/engine/whitelisted_generic_onebox_spec.rb
|