bio-krona 0.0.1 → 0.1.0
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- data/.travis.yml +1 -1
- data/Rakefile +3 -4
- data/VERSION +1 -1
- data/lib/bio-krona/krona.rb +12 -7
- data/spec/bio-krona_spec.rb +0 -58
- data/spec/bio-krona_wrapper_spec.rb +71 -0
- metadata +61 -20
data/.travis.yml
CHANGED
data/Rakefile
CHANGED
|
@@ -30,12 +30,11 @@ require 'rspec/core/rake_task'
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30
30
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RSpec::Core::RakeTask.new(:spec) do |spec|
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31
31
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spec.pattern = FileList['spec/**/*_spec.rb']
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32
32
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end
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33
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-
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34
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-
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35
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-
spec.pattern = 'spec/**/*_spec.rb'
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36
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-
spec.rcov = true
|
|
33
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+
RSpec::Core::RakeTask.new(:test_without_wrapper) do |spec|
|
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34
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+
spec.pattern = FileList['spec/**/*_spec.rb'].reject{|f| f=='spec/bio-krona_wrapper_spec.rb'}
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|
37
35
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end
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38
36
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|
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37
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+
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39
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require 'cucumber/rake/task'
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40
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Cucumber::Rake::Task.new(:features)
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|
41
40
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data/VERSION
CHANGED
|
@@ -1 +1 @@
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|
|
1
|
-
0.0
|
|
1
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+
0.1.0
|
data/lib/bio-krona/krona.rb
CHANGED
|
@@ -7,41 +7,46 @@ module Bio
|
|
|
7
7
|
# * count_hash: hash of Array => Numeric, where the array is a list of descriptors (e.g. [Eukaryota, Metazoa, Chordata]), and the Numeric is a count for the number of observations of that description
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|
8
8
|
# * options:
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9
9
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# ** :krona_path: path to the ktImportText script in the krona directory (default 'ktImportText' i.e. assuming it is already in the PATH)
|
|
10
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+
# ** :resources_url: URL of krona resources (i.e. the -u option of ktImportText)
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|
10
11
|
def self.html(count_hash, options={})
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|
11
12
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raise unless count_hash.kind_of?(Hash)
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|
12
13
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options[:krona_path] ||= %(ktImportText)
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13
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-
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14
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+
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14
15
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Tempfile.open('krona') do |tempfile|
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15
16
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count_hash.each do |array, count|
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16
17
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raise unless array.kind_of?(Array)
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17
18
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raise unless count.kind_of?(Numeric)
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18
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-
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19
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+
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19
20
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tempfile.puts [
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20
21
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count,
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21
22
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array
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22
23
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].flatten.join("\t")
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23
24
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end
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24
25
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tempfile.close
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25
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-
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26
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+
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26
27
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Tempfile.open('krona_out') do |output|
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27
28
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output.close
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28
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-
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29
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+
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29
30
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command = [
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30
31
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options[:krona_path],
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31
32
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'-o',
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32
33
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output.path,
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33
34
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tempfile.path,
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34
35
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].flatten
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36
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+
if options[:resources_url]
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37
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+
command.push '-u'
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|
38
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+
command.push options[:resources_url]
|
|
39
|
+
end
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35
40
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Bio::Command.call_command_open3(command) do |stdin, stdout, stderr|
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|
36
41
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err = stderr.read
|
|
37
42
|
raise err unless err==''
|
|
38
43
|
end
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|
39
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-
|
|
44
|
+
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|
40
45
|
return File.open(output.path).read
|
|
41
46
|
end
|
|
42
47
|
end
|
|
43
48
|
end
|
|
44
|
-
|
|
49
|
+
|
|
45
50
|
# Take a count_hash (hash of Array => Numeric), and collapse the array down to some maximum number of levels. In krona, the collapsed output would now have less (max_level) rings.
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|
46
51
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#
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|
47
52
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# Returns the collapsed count_hash
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|
@@ -51,7 +56,7 @@ module Bio
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51
56
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count_hash.each do |array, count|
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52
57
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raise unless array.kind_of?(Array)
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|
53
58
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raise unless count.kind_of?(Numeric)
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54
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-
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|
59
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+
|
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55
60
|
new_count_hash[array[0...max_level]] ||= 0
|
|
56
61
|
new_count_hash[array[0...max_level]] += count
|
|
57
62
|
end
|
data/spec/bio-krona_spec.rb
CHANGED
|
@@ -1,64 +1,6 @@
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1
1
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require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
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2
2
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3
3
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describe "BioKrona" do
|
|
4
|
-
it "should give a html when you give it a simple hash" do
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|
5
|
-
html = Bio::Krona.html({
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|
6
|
-
['Sponge','Amphimedon']=>3,
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|
7
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-
['Sponge','Calciums']=>4,
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8
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-
})
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9
|
-
expected = <<EOF
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|
10
|
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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11
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-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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12
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-
<head>
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13
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-
<meta charset="utf-8"/>
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14
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-
<link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
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15
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-
<script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \\"http://krona.sourceforge.net\\"."}</script>
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16
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-
<script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
|
|
17
|
-
</head>
|
|
18
|
-
<body>
|
|
19
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-
<img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
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20
|
-
<img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
|
|
21
|
-
<noscript>Javascript must be enabled to view this page.</noscript>
|
|
22
|
-
<div style="display:none">
|
|
23
|
-
<krona collapse="true" key="true">
|
|
24
|
-
<attributes magnitude="magnitude">
|
|
25
|
-
<list>members</list>
|
|
26
|
-
<attribute display="Total">magnitude</attribute>
|
|
27
|
-
</attributes>
|
|
28
|
-
<datasets>
|
|
29
|
-
<dataset>input</dataset>
|
|
30
|
-
</datasets>
|
|
31
|
-
<node name="all">
|
|
32
|
-
<magnitude><val>7</val></magnitude>
|
|
33
|
-
<node name="Sponge">
|
|
34
|
-
<magnitude><val>7</val></magnitude>
|
|
35
|
-
<node name="Amphimedon">
|
|
36
|
-
<magnitude><val>3</val></magnitude>
|
|
37
|
-
</node>
|
|
38
|
-
<node name="Calciums">
|
|
39
|
-
<magnitude><val>4</val></magnitude>
|
|
40
|
-
</node>
|
|
41
|
-
</node>
|
|
42
|
-
</node>
|
|
43
|
-
</krona>
|
|
44
|
-
</div></body></html>
|
|
45
|
-
EOF
|
|
46
|
-
make_comparable = lambda do |string|
|
|
47
|
-
string.split("\n").reject{|line| line.match(/<dataset>/)}
|
|
48
|
-
end
|
|
49
|
-
expected = make_comparable.call(expected)
|
|
50
|
-
html = make_comparable.call(html)
|
|
51
|
-
|
|
52
|
-
html.should eq(expected)
|
|
53
|
-
end
|
|
54
|
-
|
|
55
|
-
# it "should give back the html split up for re-use" do
|
|
56
|
-
# h = Bio::Krona.reusable_html_chunks({
|
|
57
|
-
# ['Sponge','Amphimedon']=>3,
|
|
58
|
-
# ['Sponge','Calciums']=>4,
|
|
59
|
-
# })
|
|
60
|
-
# end
|
|
61
|
-
|
|
62
4
|
it "should collapse hashes right" do
|
|
63
5
|
big = {%w(a b c)=>2, %w(a b f)=>4, %w(g)=>5}
|
|
64
6
|
|
|
@@ -0,0 +1,71 @@
|
|
|
1
|
+
require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
|
|
2
|
+
|
|
3
|
+
describe "BioKronaWrapper" do
|
|
4
|
+
it "should give a html when you give it a simple hash" do
|
|
5
|
+
html = Bio::Krona.html({
|
|
6
|
+
['Sponge','Amphimedon']=>3,
|
|
7
|
+
['Sponge','Calciums']=>4,
|
|
8
|
+
})
|
|
9
|
+
expected = <<EOF
|
|
10
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
|
11
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
12
|
+
<head>
|
|
13
|
+
<meta charset="utf-8"/>
|
|
14
|
+
<link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
|
|
15
|
+
<script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \\"http://krona.sourceforge.net\\"."}</script>
|
|
16
|
+
<script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
|
|
17
|
+
</head>
|
|
18
|
+
<body>
|
|
19
|
+
<img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
|
|
20
|
+
<img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
|
|
21
|
+
<img id="logo" src="http://krona.sourceforge.net/img/logo.png" style="display:none"/>
|
|
22
|
+
<noscript>Javascript must be enabled to view this page.</noscript>
|
|
23
|
+
<div style="display:none">
|
|
24
|
+
<krona collapse="true" key="true">
|
|
25
|
+
<attributes magnitude="magnitude">
|
|
26
|
+
<list>members</list>
|
|
27
|
+
<attribute display="Total">magnitude</attribute>
|
|
28
|
+
</attributes>
|
|
29
|
+
<datasets>
|
|
30
|
+
<dataset>input</dataset>
|
|
31
|
+
</datasets>
|
|
32
|
+
<node name="all">
|
|
33
|
+
<magnitude><val>7</val></magnitude>
|
|
34
|
+
<node name="Sponge">
|
|
35
|
+
<magnitude><val>7</val></magnitude>
|
|
36
|
+
<node name="Amphimedon">
|
|
37
|
+
<magnitude><val>3</val></magnitude>
|
|
38
|
+
</node>
|
|
39
|
+
<node name="Calciums">
|
|
40
|
+
<magnitude><val>4</val></magnitude>
|
|
41
|
+
</node>
|
|
42
|
+
</node>
|
|
43
|
+
</node>
|
|
44
|
+
</krona>
|
|
45
|
+
</div></body></html>
|
|
46
|
+
EOF
|
|
47
|
+
make_comparable = lambda do |string|
|
|
48
|
+
string.split("\n").reject{|line| line.match(/<dataset>/)}
|
|
49
|
+
end
|
|
50
|
+
expected = make_comparable.call(expected)
|
|
51
|
+
html = make_comparable.call(html)
|
|
52
|
+
|
|
53
|
+
html.should eq(expected)
|
|
54
|
+
end
|
|
55
|
+
|
|
56
|
+
# it "should give back the html split up for re-use" do
|
|
57
|
+
# h = Bio::Krona.reusable_html_chunks({
|
|
58
|
+
# ['Sponge','Amphimedon']=>3,
|
|
59
|
+
# ['Sponge','Calciums']=>4,
|
|
60
|
+
# })
|
|
61
|
+
# end
|
|
62
|
+
|
|
63
|
+
it 'should use a specified URL for the krona assets when set to' do
|
|
64
|
+
html = Bio::Krona.html({
|
|
65
|
+
['Sponge','Amphimedon']=>3,
|
|
66
|
+
['Sponge','Calciums']=>4,
|
|
67
|
+
}, :resources_url => 'http://dummy.com')
|
|
68
|
+
|
|
69
|
+
html.should match('script src="http://dummy.com')
|
|
70
|
+
end
|
|
71
|
+
end
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-krona
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.0
|
|
4
|
+
version: 0.1.0
|
|
5
5
|
prerelease:
|
|
6
6
|
platform: ruby
|
|
7
7
|
authors:
|
|
@@ -9,11 +9,11 @@ authors:
|
|
|
9
9
|
autorequire:
|
|
10
10
|
bindir: bin
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date:
|
|
12
|
+
date: 2013-07-17 00:00:00.000000000 Z
|
|
13
13
|
dependencies:
|
|
14
14
|
- !ruby/object:Gem::Dependency
|
|
15
15
|
name: bio
|
|
16
|
-
requirement:
|
|
16
|
+
requirement: !ruby/object:Gem::Requirement
|
|
17
17
|
none: false
|
|
18
18
|
requirements:
|
|
19
19
|
- - ! '>='
|
|
@@ -21,10 +21,15 @@ dependencies:
|
|
|
21
21
|
version: '0'
|
|
22
22
|
type: :runtime
|
|
23
23
|
prerelease: false
|
|
24
|
-
version_requirements:
|
|
24
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
25
|
+
none: false
|
|
26
|
+
requirements:
|
|
27
|
+
- - ! '>='
|
|
28
|
+
- !ruby/object:Gem::Version
|
|
29
|
+
version: '0'
|
|
25
30
|
- !ruby/object:Gem::Dependency
|
|
26
31
|
name: rspec
|
|
27
|
-
requirement:
|
|
32
|
+
requirement: !ruby/object:Gem::Requirement
|
|
28
33
|
none: false
|
|
29
34
|
requirements:
|
|
30
35
|
- - ~>
|
|
@@ -32,10 +37,15 @@ dependencies:
|
|
|
32
37
|
version: 2.8.0
|
|
33
38
|
type: :development
|
|
34
39
|
prerelease: false
|
|
35
|
-
version_requirements:
|
|
40
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
41
|
+
none: false
|
|
42
|
+
requirements:
|
|
43
|
+
- - ~>
|
|
44
|
+
- !ruby/object:Gem::Version
|
|
45
|
+
version: 2.8.0
|
|
36
46
|
- !ruby/object:Gem::Dependency
|
|
37
47
|
name: yard
|
|
38
|
-
requirement:
|
|
48
|
+
requirement: !ruby/object:Gem::Requirement
|
|
39
49
|
none: false
|
|
40
50
|
requirements:
|
|
41
51
|
- - ~>
|
|
@@ -43,10 +53,15 @@ dependencies:
|
|
|
43
53
|
version: '0.7'
|
|
44
54
|
type: :development
|
|
45
55
|
prerelease: false
|
|
46
|
-
version_requirements:
|
|
56
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
57
|
+
none: false
|
|
58
|
+
requirements:
|
|
59
|
+
- - ~>
|
|
60
|
+
- !ruby/object:Gem::Version
|
|
61
|
+
version: '0.7'
|
|
47
62
|
- !ruby/object:Gem::Dependency
|
|
48
63
|
name: rdoc
|
|
49
|
-
requirement:
|
|
64
|
+
requirement: !ruby/object:Gem::Requirement
|
|
50
65
|
none: false
|
|
51
66
|
requirements:
|
|
52
67
|
- - ~>
|
|
@@ -54,10 +69,15 @@ dependencies:
|
|
|
54
69
|
version: '3.12'
|
|
55
70
|
type: :development
|
|
56
71
|
prerelease: false
|
|
57
|
-
version_requirements:
|
|
72
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
73
|
+
none: false
|
|
74
|
+
requirements:
|
|
75
|
+
- - ~>
|
|
76
|
+
- !ruby/object:Gem::Version
|
|
77
|
+
version: '3.12'
|
|
58
78
|
- !ruby/object:Gem::Dependency
|
|
59
79
|
name: cucumber
|
|
60
|
-
requirement:
|
|
80
|
+
requirement: !ruby/object:Gem::Requirement
|
|
61
81
|
none: false
|
|
62
82
|
requirements:
|
|
63
83
|
- - ! '>='
|
|
@@ -65,10 +85,15 @@ dependencies:
|
|
|
65
85
|
version: '0'
|
|
66
86
|
type: :development
|
|
67
87
|
prerelease: false
|
|
68
|
-
version_requirements:
|
|
88
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
89
|
+
none: false
|
|
90
|
+
requirements:
|
|
91
|
+
- - ! '>='
|
|
92
|
+
- !ruby/object:Gem::Version
|
|
93
|
+
version: '0'
|
|
69
94
|
- !ruby/object:Gem::Dependency
|
|
70
95
|
name: jeweler
|
|
71
|
-
requirement:
|
|
96
|
+
requirement: !ruby/object:Gem::Requirement
|
|
72
97
|
none: false
|
|
73
98
|
requirements:
|
|
74
99
|
- - ~>
|
|
@@ -76,10 +101,15 @@ dependencies:
|
|
|
76
101
|
version: 1.8.3
|
|
77
102
|
type: :development
|
|
78
103
|
prerelease: false
|
|
79
|
-
version_requirements:
|
|
104
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
105
|
+
none: false
|
|
106
|
+
requirements:
|
|
107
|
+
- - ~>
|
|
108
|
+
- !ruby/object:Gem::Version
|
|
109
|
+
version: 1.8.3
|
|
80
110
|
- !ruby/object:Gem::Dependency
|
|
81
111
|
name: bundler
|
|
82
|
-
requirement:
|
|
112
|
+
requirement: !ruby/object:Gem::Requirement
|
|
83
113
|
none: false
|
|
84
114
|
requirements:
|
|
85
115
|
- - ! '>='
|
|
@@ -87,10 +117,15 @@ dependencies:
|
|
|
87
117
|
version: 1.0.21
|
|
88
118
|
type: :development
|
|
89
119
|
prerelease: false
|
|
90
|
-
version_requirements:
|
|
120
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
121
|
+
none: false
|
|
122
|
+
requirements:
|
|
123
|
+
- - ! '>='
|
|
124
|
+
- !ruby/object:Gem::Version
|
|
125
|
+
version: 1.0.21
|
|
91
126
|
- !ruby/object:Gem::Dependency
|
|
92
127
|
name: rdoc
|
|
93
|
-
requirement:
|
|
128
|
+
requirement: !ruby/object:Gem::Requirement
|
|
94
129
|
none: false
|
|
95
130
|
requirements:
|
|
96
131
|
- - ~>
|
|
@@ -98,7 +133,12 @@ dependencies:
|
|
|
98
133
|
version: '3.12'
|
|
99
134
|
type: :development
|
|
100
135
|
prerelease: false
|
|
101
|
-
version_requirements:
|
|
136
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
137
|
+
none: false
|
|
138
|
+
requirements:
|
|
139
|
+
- - ~>
|
|
140
|
+
- !ruby/object:Gem::Version
|
|
141
|
+
version: '3.12'
|
|
102
142
|
description: This biogem is built around Krona, a flashy way of representing hierarchical
|
|
103
143
|
data.
|
|
104
144
|
email: donttrustben near gmail.com
|
|
@@ -119,6 +159,7 @@ files:
|
|
|
119
159
|
- lib/bio-krona.rb
|
|
120
160
|
- lib/bio-krona/krona.rb
|
|
121
161
|
- spec/bio-krona_spec.rb
|
|
162
|
+
- spec/bio-krona_wrapper_spec.rb
|
|
122
163
|
- spec/data/krona/input.txt
|
|
123
164
|
- spec/data/krona/input.txt.krona
|
|
124
165
|
- spec/spec_helper.rb
|
|
@@ -137,7 +178,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
|
137
178
|
version: '0'
|
|
138
179
|
segments:
|
|
139
180
|
- 0
|
|
140
|
-
hash:
|
|
181
|
+
hash: -576254847
|
|
141
182
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
142
183
|
none: false
|
|
143
184
|
requirements:
|
|
@@ -146,7 +187,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
146
187
|
version: '0'
|
|
147
188
|
requirements: []
|
|
148
189
|
rubyforge_project:
|
|
149
|
-
rubygems_version: 1.8.
|
|
190
|
+
rubygems_version: 1.8.25
|
|
150
191
|
signing_key:
|
|
151
192
|
specification_version: 3
|
|
152
193
|
summary: This biogem is built around Krona, a flashy way of representing hierarchical
|