immunoscore_results_aggregator 0.0.3

data/lib/semicolon_cleaner.rb

@@ -0,0 +1,68 @@
+#Copyright (c) 2014, Carlo B. Bifulco. All rights reserved.
+
+### Cleaning of the Definines semicolon junk
+class DefinensCSV
+
+  def initialize file_path
+    @file_path=file_path
+    @text=File.read @file_path
+    #puts @text.encode("UTF-8")
+    #clean utf not sure why
+    _digest_utf
+    #header_line
+    csv=CSV.read(@file_path)
+    if (csv and csv.count !=0)
+      puts @file_path
+      header=csv[0][0]
+      if header.count(";")>header.count(",") then _parse_semicolon end
+    end
+
+    #parse_semicolon
+  end
+
+
+  def _digest_utf
+    text=File.read @file_path
+    text=text.encode("UTF-16BE", :invalid=>:replace, :replace=>"?").encode("UTF-8")
+    fh=File.new @file_path, "w"
+    fh.write text
+    fh.close
+    self
+  end
+
+  #replaces ; from definins csv with ,
+  def _parse_semicolon
+    #puts "removing semicolons"
+    c=CSV.table @file_path, :col_sep=> ";"
+    fh=File.new @file_path, "w"
+    fh.write c.to_csv
+    fh.close
+    self
+  end
+
+  def table
+    c=CSV.table @file_path
+  end
+
+  def get_dictionary
+    table =self.table
+    dictionary={}
+    table.headers.each do |h|
+      dictionary[h]=table[h][0] if table[h]
+    end
+    dictionary
+  end
+end
+
+
+def csv_clean_all match_pattern="*.csv", root_directory_path=BASE_DIR
+  csv_matches=Dir.glob "#{File.absolute_path root_directory_path}/**/#{match_pattern}"
+  csv_matches.each do |cm|
+    begin
+      DefinensCSV.new cm
+    rescue
+      puts "FAILED on #{cm}"
+    end
+  end
+end
+

data/license.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2014 Carlo B. Bifulco, MD
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

metadata

@@ -0,0 +1,243 @@
+--- !ruby/object:Gem::Specification
+name: immunoscore_results_aggregator
+version: !ruby/object:Gem::Version
+  version: 0.0.3
+  prerelease: 
+platform: ruby
+authors:
+- Carlo Bifulco
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-10-01 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bson_ext
+  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: mongo_mapper
+  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: bson_ext
+  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: gibberish
+  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: bicrypt
+  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: chronic
+  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: thor
+  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: mm-versionable
+  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: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  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'
+description: immunoscore_results_aggregator
+email: carlobif@gmail.com
+executables:
+- immunoscore_cli.rb
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- Gemfile.lock
+- README.md
+- Rakefile
+- bin/immunoscore_cli.rb
+- config.rb
+- data_struct.rb
+- docs/aggregator.html
+- docs/analyzer.html
+- docs/data_struct.html
+- docs/database_connection.html
+- docs/docco.css
+- docs/exporter.html
+- docs/immunoscore_results_loader.html
+- docs/public/fonts/aller-bold.eot
+- docs/public/fonts/aller-bold.ttf
+- docs/public/fonts/aller-bold.woff
+- docs/public/fonts/aller-light.eot
+- docs/public/fonts/aller-light.ttf
+- docs/public/fonts/aller-light.woff
+- docs/public/fonts/novecento-bold.eot
+- docs/public/fonts/novecento-bold.ttf
+- docs/public/fonts/novecento-bold.woff
+- docs/public/stylesheets/normalize.css
+- docs/semicolon_cleaner.html
+- immunoscore_results_aggregator.gemspec
+- immunoscore_results_aggregator.rb
+- lib/analyzer.rb
+- lib/data_struct.rb
+- lib/database_connection.rb
+- lib/exporter.rb
+- lib/immunoscore_results_aggregator/version.rb
+- lib/immunoscore_results_loader.rb
+- lib/mongo_aggregator.rb
+- lib/semicolon_cleaner.rb
+- license.txt
+homepage: https://github.com/carlobifulco/immunoscore_results
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23.2
+signing_key: 
+specification_version: 3
+summary: immunoscore_results_aggregator
+test_files: []