bio-krona 0.0.1 → 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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
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@@ -30,12 +30,11 @@ require 'rspec/core/rake_task'
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RSpec::Core::RakeTask.new(:spec) do |spec|
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spec.pattern = FileList['spec/**/*_spec.rb']
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end
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-
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-
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spec.pattern = 'spec/**/*_spec.rb'
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spec.rcov = true
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RSpec::Core::RakeTask.new(:test_without_wrapper) do |spec|
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spec.pattern = FileList['spec/**/*_spec.rb'].reject{|f| f=='spec/bio-krona_wrapper_spec.rb'}
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end
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+
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require 'cucumber/rake/task'
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Cucumber::Rake::Task.new(:features)
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data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.0
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1
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+
0.1.0
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data/lib/bio-krona/krona.rb
CHANGED
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@@ -7,41 +7,46 @@ module Bio
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# * 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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# * options:
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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)
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# ** :resources_url: URL of krona resources (i.e. the -u option of ktImportText)
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def self.html(count_hash, options={})
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raise unless count_hash.kind_of?(Hash)
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options[:krona_path] ||= %(ktImportText)
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-
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+
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Tempfile.open('krona') do |tempfile|
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count_hash.each do |array, count|
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raise unless array.kind_of?(Array)
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raise unless count.kind_of?(Numeric)
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-
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+
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tempfile.puts [
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count,
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array
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].flatten.join("\t")
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end
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tempfile.close
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-
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+
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Tempfile.open('krona_out') do |output|
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output.close
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-
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+
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command = [
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options[:krona_path],
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'-o',
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output.path,
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tempfile.path,
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].flatten
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if options[:resources_url]
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command.push '-u'
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command.push options[:resources_url]
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end
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Bio::Command.call_command_open3(command) do |stdin, stdout, stderr|
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err = stderr.read
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raise err unless err==''
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end
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-
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+
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return File.open(output.path).read
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end
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end
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end
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-
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+
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# 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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#
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# Returns the collapsed count_hash
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@@ -51,7 +56,7 @@ module Bio
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count_hash.each do |array, count|
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raise unless array.kind_of?(Array)
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raise unless count.kind_of?(Numeric)
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-
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+
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new_count_hash[array[0...max_level]] ||= 0
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new_count_hash[array[0...max_level]] += count
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end
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data/spec/bio-krona_spec.rb
CHANGED
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@@ -1,64 +1,6 @@
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require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
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describe "BioKrona" do
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it "should give a html when you give it a simple hash" do
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html = Bio::Krona.html({
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['Sponge','Amphimedon']=>3,
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['Sponge','Calciums']=>4,
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})
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expected = <<EOF
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-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<meta charset="utf-8"/>
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<link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
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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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<script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
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</head>
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<body>
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<img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
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<img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
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<noscript>Javascript must be enabled to view this page.</noscript>
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<div style="display:none">
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<krona collapse="true" key="true">
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<attributes magnitude="magnitude">
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<list>members</list>
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<attribute display="Total">magnitude</attribute>
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</attributes>
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-
<datasets>
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<dataset>input</dataset>
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</datasets>
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<node name="all">
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<magnitude><val>7</val></magnitude>
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<node name="Sponge">
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<magnitude><val>7</val></magnitude>
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<node name="Amphimedon">
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<magnitude><val>3</val></magnitude>
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</node>
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<node name="Calciums">
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<magnitude><val>4</val></magnitude>
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</node>
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</node>
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</node>
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</krona>
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</div></body></html>
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-
EOF
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-
make_comparable = lambda do |string|
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string.split("\n").reject{|line| line.match(/<dataset>/)}
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-
end
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expected = make_comparable.call(expected)
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html = make_comparable.call(html)
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-
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html.should eq(expected)
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end
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-
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# it "should give back the html split up for re-use" do
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# h = Bio::Krona.reusable_html_chunks({
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# ['Sponge','Amphimedon']=>3,
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# ['Sponge','Calciums']=>4,
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# })
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# end
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-
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it "should collapse hashes right" do
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big = {%w(a b c)=>2, %w(a b f)=>4, %w(g)=>5}
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@@ -0,0 +1,71 @@
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require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
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describe "BioKronaWrapper" do
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it "should give a html when you give it a simple hash" do
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html = Bio::Krona.html({
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['Sponge','Amphimedon']=>3,
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['Sponge','Calciums']=>4,
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})
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expected = <<EOF
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<meta charset="utf-8"/>
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<link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
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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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<script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
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</head>
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<body>
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<img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
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<img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
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<img id="logo" src="http://krona.sourceforge.net/img/logo.png" style="display:none"/>
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<noscript>Javascript must be enabled to view this page.</noscript>
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<div style="display:none">
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<krona collapse="true" key="true">
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<attributes magnitude="magnitude">
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<list>members</list>
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<attribute display="Total">magnitude</attribute>
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</attributes>
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<datasets>
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<dataset>input</dataset>
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</datasets>
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<node name="all">
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<magnitude><val>7</val></magnitude>
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<node name="Sponge">
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<magnitude><val>7</val></magnitude>
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<node name="Amphimedon">
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<magnitude><val>3</val></magnitude>
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</node>
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<node name="Calciums">
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<magnitude><val>4</val></magnitude>
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</node>
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</node>
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</node>
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</krona>
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</div></body></html>
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EOF
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make_comparable = lambda do |string|
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string.split("\n").reject{|line| line.match(/<dataset>/)}
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end
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expected = make_comparable.call(expected)
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html = make_comparable.call(html)
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html.should eq(expected)
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end
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+
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# it "should give back the html split up for re-use" do
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# h = Bio::Krona.reusable_html_chunks({
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# ['Sponge','Amphimedon']=>3,
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# ['Sponge','Calciums']=>4,
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# })
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# end
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it 'should use a specified URL for the krona assets when set to' do
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html = Bio::Krona.html({
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['Sponge','Amphimedon']=>3,
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['Sponge','Calciums']=>4,
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}, :resources_url => 'http://dummy.com')
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html.should match('script src="http://dummy.com')
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end
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end
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
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--- !ruby/object:Gem::Specification
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name: bio-krona
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version: !ruby/object:Gem::Version
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-
version: 0.0
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+
version: 0.1.0
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5
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prerelease:
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platform: ruby
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authors:
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@@ -9,11 +9,11 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date:
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+
date: 2013-07-17 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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-
requirement:
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+
requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -21,10 +21,15 @@ dependencies:
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version: '0'
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22
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type: :runtime
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23
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prerelease: false
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24
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-
version_requirements:
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+
version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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25
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- !ruby/object:Gem::Dependency
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26
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name: rspec
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27
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-
requirement:
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+
requirement: !ruby/object:Gem::Requirement
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28
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none: false
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29
34
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requirements:
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30
35
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- - ~>
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|
@@ -32,10 +37,15 @@ dependencies:
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32
37
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version: 2.8.0
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33
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type: :development
|
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34
39
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prerelease: false
|
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35
|
-
version_requirements:
|
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40
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+
version_requirements: !ruby/object:Gem::Requirement
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+
none: false
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42
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+
requirements:
|
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43
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+
- - ~>
|
|
44
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+
- !ruby/object:Gem::Version
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45
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+
version: 2.8.0
|
|
36
46
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- !ruby/object:Gem::Dependency
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37
47
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name: yard
|
|
38
|
-
requirement:
|
|
48
|
+
requirement: !ruby/object:Gem::Requirement
|
|
39
49
|
none: false
|
|
40
50
|
requirements:
|
|
41
51
|
- - ~>
|
|
@@ -43,10 +53,15 @@ dependencies:
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|
|
43
53
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version: '0.7'
|
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44
54
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type: :development
|
|
45
55
|
prerelease: false
|
|
46
|
-
version_requirements:
|
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56
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+
version_requirements: !ruby/object:Gem::Requirement
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+
none: false
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58
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+
requirements:
|
|
59
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+
- - ~>
|
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+
- !ruby/object:Gem::Version
|
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61
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+
version: '0.7'
|
|
47
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- !ruby/object:Gem::Dependency
|
|
48
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name: rdoc
|
|
49
|
-
requirement:
|
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+
requirement: !ruby/object:Gem::Requirement
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50
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none: false
|
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51
66
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requirements:
|
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52
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- - ~>
|
|
@@ -54,10 +69,15 @@ dependencies:
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version: '3.12'
|
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type: :development
|
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56
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prerelease: false
|
|
57
|
-
version_requirements:
|
|
72
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version_requirements: !ruby/object:Gem::Requirement
|
|
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+
none: false
|
|
74
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+
requirements:
|
|
75
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+
- - ~>
|
|
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- !ruby/object:Gem::Version
|
|
77
|
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version: '3.12'
|
|
58
78
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- !ruby/object:Gem::Dependency
|
|
59
79
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name: cucumber
|
|
60
|
-
requirement:
|
|
80
|
+
requirement: !ruby/object:Gem::Requirement
|
|
61
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none: false
|
|
62
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requirements:
|
|
63
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- - ! '>='
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@@ -65,10 +85,15 @@ dependencies:
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version: '0'
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type: :development
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prerelease: false
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68
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-
version_requirements:
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88
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+
version_requirements: !ruby/object:Gem::Requirement
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none: false
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90
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+
requirements:
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+
- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: jeweler
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-
requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -76,10 +101,15 @@ dependencies:
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version: 1.8.3
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type: :development
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prerelease: false
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-
version_requirements:
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+
version_requirements: !ruby/object:Gem::Requirement
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+
none: false
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+
requirements:
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+
- - ~>
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+
- !ruby/object:Gem::Version
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+
version: 1.8.3
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- !ruby/object:Gem::Dependency
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name: bundler
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-
requirement:
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+
requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -87,10 +117,15 @@ dependencies:
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version: 1.0.21
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type: :development
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prerelease: false
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90
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-
version_requirements:
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+
version_requirements: !ruby/object:Gem::Requirement
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+
none: false
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+
requirements:
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123
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+
- - ! '>='
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124
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+
- !ruby/object:Gem::Version
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+
version: 1.0.21
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91
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- !ruby/object:Gem::Dependency
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92
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name: rdoc
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93
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-
requirement:
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128
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+
requirement: !ruby/object:Gem::Requirement
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94
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none: false
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95
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requirements:
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- - ~>
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@@ -98,7 +133,12 @@ dependencies:
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version: '3.12'
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type: :development
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prerelease: false
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101
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-
version_requirements:
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+
version_requirements: !ruby/object:Gem::Requirement
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137
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+
none: false
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138
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+
requirements:
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139
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+
- - ~>
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+
- !ruby/object:Gem::Version
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+
version: '3.12'
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description: This biogem is built around Krona, a flashy way of representing hierarchical
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103
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data.
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104
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email: donttrustben near gmail.com
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@@ -119,6 +159,7 @@ files:
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119
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- lib/bio-krona.rb
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120
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- lib/bio-krona/krona.rb
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121
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- spec/bio-krona_spec.rb
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162
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+
- spec/bio-krona_wrapper_spec.rb
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122
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- spec/data/krona/input.txt
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123
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- spec/data/krona/input.txt.krona
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124
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- spec/spec_helper.rb
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@@ -137,7 +178,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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137
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version: '0'
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138
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segments:
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139
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- 0
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140
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-
hash:
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181
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+
hash: -576254847
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141
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required_rubygems_version: !ruby/object:Gem::Requirement
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142
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none: false
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requirements:
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@@ -146,7 +187,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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146
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version: '0'
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147
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requirements: []
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rubyforge_project:
|
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149
|
-
rubygems_version: 1.8.
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190
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+
rubygems_version: 1.8.25
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150
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signing_key:
|
|
151
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|
specification_version: 3
|
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152
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summary: This biogem is built around Krona, a flashy way of representing hierarchical
|