bio-krona 0.1.1 → 0.2.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 5b05815b00deb3388e4c80630a62aa09eed51007
+  data.tar.gz: af4bf2f1f0101424c60c3a33f8b2af9f5456204b
+SHA512:
+  metadata.gz: 60240f084a744c257bd5aa0f921593aebf2ec885b9d23f5b886c08c1372d99f910faffcb62affa65f8871695f60b683ac67ae5a6bbf1b6f52b1cac7ffe86a888
+  data.tar.gz: c5467498399e8578c52d46ad7db63433cbe0ebc05feb432982849ad0c96441ada4249c6b53384bb61993690294e64c4364682d964367be36253ebc62e599a132

data/Gemfile

@@ -7,11 +7,10 @@ gem 'bio'
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "rspec", ">= 2.8.0"
+  gem "rspec", "~> 2.8.0"
   gem "yard", ">= 0.7"
   gem "rdoc", ">= 3.12"
-  gem "cucumber", ">= 0"
   gem "jeweler", ">= 1.8.3"
   gem "bundler", ">= 1.0.21"
-  gem "rdoc", ">= 3.12"
+  gem 'pry'
 end

data/Rakefile

@@ -34,10 +34,6 @@ RSpec::Core::RakeTask.new(:test_without_wrapper) do |spec|
   spec.pattern = FileList['spec/**/*_spec.rb'].reject{|f| f=='spec/bio-krona_wrapper_spec.rb'}
 end
 
-
-require 'cucumber/rake/task'
-Cucumber::Rake::Task.new(:features)
-
 task :default => :spec
 
 require 'yard'

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.2.0

data/lib/bio-krona/krona.rb

@@ -8,12 +8,14 @@ module Bio
     # * options:
     # ** :krona_path: path to the ktImportText script in the krona directory (default 'ktImportText' i.e. assuming it is already in the PATH)
     # ** :resources_url: URL of krona resources (i.e. the -u option of ktImportText)
+    # ** :multiple_samples: count_hash is a hash of sample names to hash of Array => Numeric, when multiple samples are to be included [default false]
     def self.html(count_hash, options={})
       raise unless count_hash.kind_of?(Hash)
       options[:krona_path] ||= %(ktImportText)
 
-      Tempfile.open('krona') do |tempfile|
-        count_hash.each do |array, count|
+      get_tempfile_from_count_hash = lambda do |ch|
+        tempfile = Tempfile.new('krona')
+        ch.each do |array, count|
           raise unless array.kind_of?(Array)
           raise unless count.kind_of?(Numeric)
 
@@ -23,27 +25,49 @@ module Bio
           ].flatten.join("\t")
         end
         tempfile.close
+        tempfile
+      end
 
-        Tempfile.open('krona_out') do |output|
-          output.close
+      input_tempfiles = []
+      input_names = []
+      if options[:multiple_samples]
+        input_names = count_hash.keys
+        input_tempfiles = count_hash.values.collect{|ch| get_tempfile_from_count_hash.call(ch)}
+      else
+        input_names = [nil]
+        input_tempfiles = [get_tempfile_from_count_hash.call(count_hash)]
+      end
 
-          command = [
-            options[:krona_path],
-            '-o',
-            output.path,
-            tempfile.path,
-          ].flatten
-          if options[:resources_url]
-            command.push '-u'
-            command.push options[:resources_url]
-          end
-          Bio::Command.call_command_open3(command) do |stdin, stdout, stderr|
-            err = stderr.read
-            raise err unless err==''
-          end
+      pairs = []
+      input_names.each_with_index do |name, i|
+        tmpname = input_tempfiles[i].path
+        if name.nil?
+          pairs.push tmpname
+        else
+          pairs.push "#{tmpname},#{name}"
+        end
+      end
 
-          return File.open(output.path).read
+      Tempfile.open('krona_out') do |output|
+        output.close
+
+        command = [
+          options[:krona_path],
+          '-o',
+          output.path,
+          pairs,
+          ].flatten
+        if options[:resources_url]
+          command.push '-u'
+          command.push options[:resources_url]
         end
+        Bio::Command.call_command_open3(command) do |stdin, stdout, stderr|
+          err = stderr.read
+          raise err unless err==''
+        end
+
+        input_tempfiles.each{|t| t.close}
+        return File.open(output.path).read
       end
     end
 

data/spec/bio-krona_wrapper_spec.rb

@@ -68,4 +68,55 @@ EOF
 
     html.should match('script src="http://dummy.com')
   end
+
+  it "should give a html with multiple samples" do
+    html = Bio::Krona.html({'sample1' => {
+      ['Sponge','Amphimedon']=>3,
+      ['Sponge','Calciums']=>4,
+      },
+      'sample2' => {
+        ['Sponge','Amphimedon']=>30,
+      ['Sponge','Calciums']=>45,
+      }
+      }, :multiple_samples => true)
+    html.should == '<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Strict//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd\">\n<html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\">\n <head>\n  <meta charset=\"utf-8\"/>\n  <link rel=\"shortcut icon\" href=\"http://krona.sourceforge.net/img/favicon.ico\"/>\n  <script id=\"notfound\">window.onload=function(){document.body.innerHTML=\"Could not get resources from \\\"http://krona.sourceforge.net\\\".\"}</script>\n  <script src=\"http://krona.sourceforge.net/src/krona-2.0.js\"></script>\n </head>\n <body>\n  <img id=\"hiddenImage\" src=\"http://krona.sourceforge.net/img/hidden.png\" style=\"display:none\"/>\n  <img id=\"loadingImage\" src=\"http://krona.sourceforge.net/img/loading.gif\" style=\"display:none\"/>\n  <noscript>Javascript must be enabled to view this page.</noscript>\n  <div style=\"display:none\">\n  <krona collapse=\"true\" key=\"true\">\n   <attributes magnitude=\"magnitude\">\n    <list>members</list>\n    <attribute display=\"Total\">magnitude</attribute>\n   </attributes>\n   <datasets>\n    <dataset>sample1</dataset>\n    <dataset>sample2</dataset>\n   </datasets>\n<node name=\"all\">\n <magnitude><val>7</val><val>75</val></magnitude>\n <node name=\"Sponge\">\n  <magnitude><val>7</val><val>75</val></magnitude>\n  <node name=\"Amphimedon\">\n   <magnitude><val>3</val><val>30</val></magnitude>\n  </node>\n  <node name=\"Calciums\">\n   <magnitude><val>4</val><val>45</val></magnitude>\n  </node>\n </node>\n</node>\n  </krona>\n</div></body></html>\n" (using ==)
+       Diff:
+       @@ -1 +1,37 @@
+       <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+       <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+        <head>
+         <meta charset="utf-8"/>
+         <link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
+         <script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \"http://krona.sourceforge.net\"."}</script>
+         <script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
+        </head>
+        <body>
+         <img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
+         <img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
+         <noscript>Javascript must be enabled to view this page.</noscript>
+         <div style="display:none">
+         <krona collapse="true" key="true">
+          <attributes magnitude="magnitude">
+           <list>members</list>
+           <attribute display="Total">magnitude</attribute>
+          </attributes>
+          <datasets>
+           <dataset>sample1</dataset>
+           <dataset>sample2</dataset>
+          </datasets>
+       <node name="all">
+        <magnitude><val>7</val><val>75</val></magnitude>
+        <node name="Sponge">
+         <magnitude><val>7</val><val>75</val></magnitude>
+         <node name="Amphimedon">
+          <magnitude><val>3</val><val>30</val></magnitude>
+         </node>
+         <node name="Calciums">
+          <magnitude><val>4</val><val>45</val></magnitude>
+         </node>
+        </node>
+       </node>
+         </krona>
+       +</div></body></html>'
+  end
 end

metadata

@@ -1,144 +1,113 @@
 --- !ruby/object:Gem::Specification
 name: bio-krona
 version: !ruby/object:Gem::Version
-  version: 0.1.1
-  prerelease: 
+  version: 0.2.0
 platform: ruby
 authors:
 - Ben J. Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-16 00:00:00.000000000 Z
+date: 2015-12-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.8.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.8.0
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0.7'
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '3.12'
-- !ruby/object:Gem::Dependency
-  name: cucumber
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.3
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.21
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.21
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: pry
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: '0'
 description: This biogem is built around Krona, a flashy way of representing hierarchical
   data.
 email: donttrustben near gmail.com
@@ -148,9 +117,9 @@ extra_rdoc_files:
 - LICENSE.txt
 - README.md
 files:
-- .document
-- .rspec
-- .travis.yml
+- ".document"
+- ".rspec"
+- ".travis.yml"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -166,30 +135,26 @@ files:
 homepage: http://github.com/wwood/bioruby-krona
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -432620685
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.25
+rubygems_version: 2.2.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: This biogem is built around Krona, a flashy way of representing hierarchical
   data.
 test_files: []