publisci 0.1.2

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 276af2e741bcad49c2e8ff5c6b2e83dbfc331ba1
+  data.tar.gz: 289f4d7eda9047fcf18b626a9d66def6d033f3f7
+SHA512:
+  metadata.gz: a4437108c231668ebe168d74ebb4e1027556c875f96ff49104c471e03922936de82d6d7a52beb6cfe28067b523d82f8aa890c1c0453a48db6260d40954795d30
+  data.tar.gz: 3dbbb11bb94f7a86e7a938b78fe9c72a177bc87b163bfea300670fab6c43e8deb440ff5017e5017a59c369bcbdf063bab894184fd3fe324fcde282fae07f8dfc

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.3
+  - 2.0.0
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+#
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# 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 "rdoc", "~> 3.12"
+  gem "cucumber", ">= 0"
+  gem "jeweler", "~> 1.8.4", :git => "https://github.com/technicalpickles/jeweler.git"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+  gem "spoon"
+  gem "spira", git: "https://github.com/ruby-rdf/spira.git"
+end
+
+
+gem 'rdf'
+gem 'rdf-4store', :git => "https://github.com/fumi/rdf-4store.git"
+gem 'rdf-turtle'
+gem 'rdf-rdfxml'
+gem 'json-ld'
+gem 'rserve-client'
+gem 'sparql'
+
+gem 'slop'
+
+gem 'sinatra'
+gem 'sinatra-contrib'
+gem 'sinatra-linkeddata'
+gem 'sinatra-cross_origin'
+gem 'rack-flash3'
+gem 'rest-client'

data/LICENSE.txt

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+Copyright (c) 2013 wstrinz
+
+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.

data/README.md

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+# PubliSci
+
+[![Build Status](https://secure.travis-ci.org/wstrinz/bioruby-publisci.png)](http://travis-ci.org/wstrinz/bioruby-publisci)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-publisci
+```
+
+## Usage
+
+```ruby
+require 'bio-publisci'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wstrinz/bioruby-publisci
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite
+
+* [The Ruby Science Foundation. 2013. SciRuby: Tools for scientific computing in Ruby. http://sciruby.com.](http://sciruby.com)
+
+and one of
+
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-publisci)
+
+## Copyright
+
+Copyright (c) 2013 wstrinz. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-publisci
+
+{<img
+src="https://secure.travis-ci.org/wstrinz/bioruby-publisci.png"
+/>}[http://travis-ci.org/#!/wstrinz/bioruby-publisci]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-publisci
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-publisci'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/wstrinz/bioruby-publisci
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-publisci
+
+== Copyright
+
+Copyright (c) 2013 wstrinz. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "publisci"
+  gem.homepage = "http://github.com/wstrinz/bioruby-publisci"
+  gem.license = "MIT"
+  gem.summary = %Q{Publish scientific results to the semantic web}
+  gem.description = %Q{A toolkit for publishing scientific results and datasets using RDF, OWL, and related technologies }
+  gem.email = "wstrinz@gmail.com"
+  gem.authors = ["Will Strinz"]
+  gem.version = "0.1.2"
+
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.rspec_opts = "--tag ~no_travis"
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new(:features)
+
+# task :default => :spec
+
+task :default => [] do
+  Rake::Task[:spec].invoke
+end
+
+task :test => [] do
+  begin
+    Rake::Task[:spec].invoke
+  rescue
+  end
+  Rake::Task[:features].invoke
+end
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : "0.0.1"
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "publisci #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/bin/bio-publisci

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+#!/usr/bin/env ruby
+#
+# BioRuby bio-publisci Plugin BioPublisci
+# Author:: wstrinz
+# Copyright:: 2013
+
+version = "0.0.4" #File.new(VERSION_FILENAME).read.chomp
+
+USAGE = <<-EOF
+  bio-publisci #{version} by Will Strinz 2013
+
+  Usage:
+
+  bio-publisci file
+  (execute PROV dsl file)
+EOF
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+require 'bio-publisci'
+
+#VERSION_FILENAME=File.join(gempath,'VERSION')
+
+# print banner
+
+if ARGV.size == 0
+  print USAGE
+elsif ARGV.size == 1
+  #assume file, run DSL (prov for now)
+  if File.exist? ARGV[0]
+    puts "#{PubliSci::Prov.prefixes}\n#{PubliSci::Prov.run(ARGV[0])}"
+  else
+    puts "(no file #{ARGV[0]})"
+    print USAGE
+  end
+else
+  if ARGV.size % 2 == 0
+    opts=Hash[*ARGV]
+    puts "got options #{opts}"
+  else
+    print USAGE
+  end
+end
+
+require 'bio-publisci'
+require 'optparse'
+
+# Uncomment when using the bio-logger
+# require 'bio-logger'
+# Bio::Log::CLI.logger('stderr')
+# Bio::Log::CLI.trace('info')
+
+options = {:example_switch=>false,:show_help=>false}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
+
+  o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
+    # TODO: your logic here, below an example
+    options[:example_parameter] = 'this is a parameter'
+  end
+
+  o.separator ""
+  o.on("--switch-example", 'TODO: put a description for the SWITCH') do
+    # TODO: your logic here, below an example
+    self[:example_switch] = true
+  end
+
+  # Uncomment the following when using the bio-logger
+  # o.separator ""
+  # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
+  #   Bio::Log::CLI.logger(name)
+  # end
+  #
+  # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
+  #   Bio::Log::CLI.trace(s)
+  # end
+  #
+  # o.on("-q", "--quiet", "Run quietly") do |q|
+  #   Bio::Log::CLI.trace('error')
+  # end
+  #
+  # o.on("-v", "--verbose", "Run verbosely") do |v|
+  #   Bio::Log::CLI.trace('info')
+  # end
+  #
+  # o.on("--debug", "Show debug messages") do |v|
+  #   Bio::Log::CLI.trace('debug')
+  # end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+begin
+  opts.parse!(ARGV)
+
+  # Uncomment the following when using the bio-logger
+  # Bio::Log::CLI.configure('bio-publisci')
+
+  # TODO: your code here
+  # use options for your logic
+rescue OptionParser::InvalidOption => e
+  options[:invalid_argument] = e.message
+end

data/bin/bio-publisci-server

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+#!/usr/bin/env ruby
+require 'cgi'
+require 'yaml'
+
+require 'bio-publisci'
+require 'slop'
+
+require 'sinatra/base'
+require "sinatra/linkeddata"
+require "sinatra/cross_origin"
+require 'rack-flash'
+
+class PubliSciServer < Sinatra::Base
+  configure do
+    enable :sessions
+    enable :cross_origin
+  end
+
+  set :views, File.dirname(__FILE__) + '/../server/views'
+  # set :repository, RDF::Repository.new
+  set :sudo_pass, nil
+
+  use Rack::Flash
+
+  require_relative '../server/helpers.rb'
+
+  if ARGV[0]
+    opts = Slop.parse do
+      banner 'Usage: bio-publisci-server [options]'
+
+      on 'uri', 'Store URI', argument: :optional
+      on 't', 'type', 'The repository type', argument: :optional
+      on 'a', 'sudo_pass', 'Password for sudo (currently needed to clear 4store)', argument: :optional
+      on 'p', 'port', 'Sinatra port', argument: :optional
+      on 'o', 'bind', 'Bind address ', argument: :optional
+    end
+
+    configure_server(opts)
+  else
+    # set :repository, RDF::FourStore::Repository.new('http://localhost:8080')
+    set :repository, RDF::Repository.new
+
+    settings.repository.load(File.dirname(__FILE__) + '/../resources/primer.ttl')
+  end
+
+  require_relative '../server/routes.rb'
+
+
+  run!
+end

data/examples/bio-band_integration.rb

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+require 'bio-band'
+require 'bio-publisci'
+
+f = open(File.dirname(__FILE__) + '/../resources/weather.numeric.arff')
+clustering = Weka::Clusterer::SimpleKMeans::Base
+clustering.set_options "-N 5"
+clustering.set_data(Core::Parser::parse_ARFF(f.path))
+clustered = clustering.new
+puts clustered

data/examples/no_magic.prov

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+# Example using as little generation "magic" as possible, for execution
+# as plain Ruby script.
+#
+# Run using "ruby no_magic.prov"
+
+require 'bio-publisci'
+include PubliSci::Prov::DSL
+
+
+# Subject and type for most elements can be set manually
+agent :publisci, subject: 'http://gsocsemantic.wordpress.com/publisci', type: "software"
+agent :R, subject: "http://r-project.org"
+agent :sciruby, subject: "http://sciruby.com", type: "organization"
+
+plan :R_steps, subject: "http://example.org/plan/R_steps", steps: "spec/resource/example.Rhistory"
+
+agent :Will do
+  # subject can be called within a block as well
+  subject "http://gsocsemantic.wordpress.com/me"
+  type "person"
+  name "Will Strinz"
+  on_behalf_of "http://sciruby.com"
+end
+
+# The wasGeneratedBy relationship is usually created automatically when an activitiy
+#   is associated with an entity, but it can be specified manually
+entity :triplified_example, subject: "http://example.org/dataset/ex", generated_by: :triplify
+
+entity :original do
+  generated_by :use_R
+  subject "http://example.org/R/ex"
+  source "./example.RData"
+
+  # Custom predicates and objects can be used for flexibility and extensibility
+  has "http://purl.org/dc/terms/title", "original data object"
+end
+
+activity :triplify do
+  # Most methods will take either Symbols or Strings, and correctly handle
+  #   resources vs literals
+  subject "http://example.org/activity/triplify"
+  generated "http://example.org/dataset/ex"
+  associated_with :publisci
+  used :original
+end
+
+activity :use_R do
+  subject "http://example.org/activity/use_R"
+  generated "http://example.org/R/ex"
+
+  associated_with :R
+  associated_with :Will
+end
+
+# Running a prov script using the gem executable will print the result, but
+#   if you use the DSL you'll have to do it manually. You also read out to a file
+#   or other method/object of course (eg "open('out.ttl','w'){|file| file.write generate_n3}")
+puts generate_n3