bio-publisci 0.0.3 → 0.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f03476f5595b28e10a4cb3d950b9c454d621eb4d
-  data.tar.gz: da473d84d9c1e203de4ea1b2d7fef2579cfa8bf8
+  metadata.gz: 3cb588f4ec6cfa77e1e9011b687ca3e148c6ca6e
+  data.tar.gz: 6a257692f2317eaea75f0fe306b93e01c1de6a70
 SHA512:
-  metadata.gz: 33662112c4df2115f15d59f415329dfa11368e8bd1a47907d62c02b476bbeb4afe0a1c43599d2c215a093d1765b7ffb05320220e21888267811c86beacef8876
-  data.tar.gz: 683b5874d082ab155227ee92a1e9bfe15a66b0eaf4fe1e590db39a9391346ec31850b0a94d924c9d26b356fb6ed7f82a228c9d16afa1a67d9c6710086e849963
+  metadata.gz: 163459c5c65c023475a5cb9853c7300d8b5f2a0c4afdf8a98a9f7f7f61ba9103c15e562f01c08a19f7c2d08853ce31447b0710c29e14d9c6f954705f82c26bba
+  data.tar.gz: 6e07fbb66df785ef3d15820d825823fdcd7ee18fe60cd68f8009f9f92c3204fc8945c3e0ac3bf79663b66d1259036da4f6d2749bac2d34f8870c73c25d850cbc

data/Gemfile

@@ -13,6 +13,7 @@ group :development do
   gem "bundler", ">= 1.0.21"
   gem "bio", ">= 1.4.2"
   gem "rdoc", "~> 3.12"
+  gem "spoon"
 end
 
 

data/Rakefile

@@ -17,11 +17,11 @@ Jeweler::Tasks.new do |gem|
   gem.name = "bio-publisci"
   gem.homepage = "http://github.com/wstrinz/bioruby-publisci"
   gem.license = "MIT"
-  gem.summary = %Q{Publish science data using semantic web ontologies}
-  gem.description = %Q{A toolkit for publishing scientific results and datasets using RDF and related technologies }
+  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 = ["wstrinz"]
-  gem.version = "0.0.3"
+  gem.authors = ["Will Strinz"]
+  gem.version = "0.0.4"
 
   # dependencies defined in Gemfile
 end
@@ -50,7 +50,7 @@ task :default => [] do
 end
 
 task :test => [] do
-  begin   
+  begin
     Rake::Task[:spec].invoke
   rescue
   end

data/bin/bio-publisci

@@ -4,25 +4,48 @@
 # Author:: wstrinz
 # Copyright:: 2013
 
-USAGE = "Describe bio-publisci"
+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')
-version = File.new(VERSION_FILENAME).read.chomp
+#VERSION_FILENAME=File.join(gempath,'VERSION')
 
 # print banner
-print "bio-publisci #{version} by wstrinz 2013\n"
 
 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 
+# Uncomment when using the bio-logger
 # require 'bio-logger'
 # Bio::Log::CLI.logger('stderr')
 # Bio::Log::CLI.trace('info')
@@ -35,14 +58,14 @@ opts = OptionParser.new do |o|
     # 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 
+  # 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)
@@ -51,15 +74,15 @@ opts = OptionParser.new do |o|
   # 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
@@ -73,7 +96,7 @@ end
 begin
   opts.parse!(ARGV)
 
-  # Uncomment the following when using the bio-logger 
+  # Uncomment the following when using the bio-logger
   # Bio::Log::CLI.configure('bio-publisci')
 
   # TODO: your code here

data/examples/bio-band_integration.rb

@@ -0,0 +1,9 @@
+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

@@ -0,0 +1,40 @@
+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, steps: "spec/resource/example.Rhistory"
+
+agent :Will do
+  subject "http://gsocsemantic.wordpress.com/me"
+  type "person"
+  name "Will Strinz"
+  on_behalf_of "http://sciruby.com"
+end
+
+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"
+
+  set "http://purl.org/dc/terms/title", "original data object"
+end
+
+activity :use_R do
+  generated :original
+
+  associated_with {
+    agent :R
+  }
+
+  associated_with :Will
+end
+
+activity :triplify do
+  generated "http://example.org/dataset/ex"
+  associated_with :publisci
+  used :original
+end
+
+generate_n3

data/examples/primer.prov

@@ -0,0 +1,28 @@
+# http://www.w3.org/TR/prov-primer/images/agents.png
+
+organization :chartgen
+
+agent :derek do
+  name "Derek"
+  on_behalf_of :chartgen
+end
+
+entity :chart1, attributed_to: :derek
+entity :composition1
+entity :regionList1
+entity :dataSet1
+
+activity :illustrate do
+  generated :chart1
+  associated_with :derek
+  used :composition1
+end
+
+activity :compose1 do
+  generated :composition1
+  associated_with :derek
+  used :regionList1
+  used :dataSet1
+end
+
+generate_n3(true)

data/examples/prov_dsl.prov

@@ -0,0 +1,51 @@
+agent :publisci, type: "software"
+agent :R, subject: "http://r-project.org"
+
+plan :R_steps, steps: "spec/resource/example.Rhistory"
+
+organization :sciruby, subject: "http://sciruby.com"
+
+foaf = vocabulary "http://xmlns.com/foaf/0.1/"
+
+agent :Will do
+  type "person"
+  name "Will Strinz"
+  on_behalf_of :sciruby
+
+  has foaf.mailbox, "wstrinz@gmail.com"
+  has foaf.homepage, "http://gsocsemantic.wordpress.com/"
+end
+
+data :triplified_example do
+  attributed_to :Will
+  derived_from do
+    entity :original
+    activity :triplify
+  end
+end
+
+activity :triplify do
+  generated :triplified_example
+  associated_with :publisci
+  used :original
+end
+
+data :original do
+  derived_from :field_work
+  attributed_to :R
+end
+
+data :field_work
+
+activity :use_R do
+  generated :original
+
+  associated_with {
+    agent :R
+    plan :R_steps
+  }
+
+  associated_with :Will
+end
+
+generate_n3 true

data/features/create_generator.feature

@@ -1,7 +1,7 @@
 Feature: create generators
 
 	In order to check that objects conform to a common interface
-	I want to be able to call a generate method on various classes 
+	I want to be able to call a generate method on various classes
 
 	Scenario: create a Dataframe generator
 		Given a Dataframe generator
@@ -9,17 +9,13 @@ Feature: create generators
 
 	Scenario: create a CSV generator
 		Given a CSV generator
-		Then I should be able to call its generate_n3 method	
+		Then I should be able to call its generate_n3 method
 
 	Scenario: create a RMatrix generator
 		Given a RMatrix generator
 		Then I should be able to call its generate_n3 method
 
-	Scenario: create a Cross generator
-		Given a Cross generator
-		Then I should be able to call its generate_n3 method	
-
-	Scenario: create a BigCross generator
-		Given a BigCross generator
-		Then I should be able to call its generate_n3 method	
+	Scenario: create a RCross generator
+		Given a RCross generator
+		Then I should be able to call its generate_n3 method
 

data/features/integration_steps.rb

@@ -1,10 +1,10 @@
-
 Then(/^I should be able to cluster the result and print statistics$/) do
-  f=Tempfile.open('arff'); f.write @result; f.close
-  clustering = Weka::Clusterer::SimpleKMeans::Base
-  clustering.set_options "-N 5"
-  clustering.set_data(Core::Parser::parse_ARFF(f.path))
-  f.unlink
-  clustered = clustering.new
-  puts clustered
+  pending
+  # f=Tempfile.open('arff'); f.write @result; f.close
+  # clustering = Weka::Clusterer::SimpleKMeans::Base
+  # clustering.set_options "-N 5"
+  # clustering.set_data(Core::Parser::parse_ARFF(f.path))
+  # f.unlink
+  # clustered = clustering.new
+  # puts clustered
 end

data/features/metadata.feature

@@ -15,10 +15,23 @@ Feature: Receive metadata as user input or extract from data sources
 
   Scenario: Generate process information
     Given a class which includes the Metadata module
-    When I call its provenance method with the hash {var: "example", software: {name: "R", process: 'spec/resource/example.Rhistory'}}
+    And the source object {resource: 'http://example.org/software/R/var/ex', software:'http://r-project.org', process: 'spec/resource/example.Rhistory'}
+    And the rdf dataset {resource:'http://example.org/data'}
+    When I call its provenance method with the source object and the rdf object
     Then I should receive a metadata string
 
   Scenario: Generate organizational provenance information
     Given a class which includes the Metadata module
-    When I call its provenance method with the hash {var: "example", creator: "http://gsocsemantic.wordpress.com/me", organization: "http://sciruby.com/"}
+    And the source object {resource: 'http://example.org/software/R/var/ex', author: 'http://example.org/people/jrs', author_name: "J Random Scientist", organization: 'http://example.org/org/science', organization_name: "The League of Science" }
+    And the rdf dataset {resource:'http://example.org/data', author: 'http://gsocsemantic.wordpress.com/me', author_name: "Will Strinz", organization: 'http://sciruby.com/'}
+    When I call its provenance method with the source object and the rdf object
+    Then I should receive a metadata string
+
+  Scenario: Generate a provenance chain
+    Given a class which includes the Metadata module
+    And the source object {resource: 'http://example.org/software/R/var/ex', software:'http://r-project.org'}
+    And the rdf dataset {resource:'http://example.org/data'}
+    And the chain object {resource: 'http://example.org/lab_results/1', author: 'http://example.org/people/brl', author_name: "B Random Labtech"}
+    And the chain object {resource: 'http://example.org/field_work/1', author: 'http://example.org/people/arn', organization: 'http://example.org/org/science'}
+    When I call its provenance method with the source object, the rdf object, and the chain
     Then I should receive a metadata string

data/features/metadata_steps.rb

@@ -5,6 +5,27 @@ Given(/^a class which includes the Metadata module$/) do
   @klass = Meta
 end
 
+Given(/^the source object (\{.+\})$/) do |fields|
+  @original = eval(fields)
+end
+
+Given(/^the rdf dataset (\{.+\})$/) do |fields|
+  @rdf = eval(fields)
+end
+
+Given(/^the chain object (\{.+\})$/) do |fields|
+  (@chain ||= []) << eval(fields)
+end
+
+When(/^I call its provenance method with the source object, the rdf object, and the chain$/) do
+  @response = @klass.new.provenance(@original, @rdf, @chain)
+end
+
+
+When(/^I call its provenance method with the source object and the rdf object$/) do
+  @response = @klass.new.provenance(@original, @rdf, nil)
+end
+
 When(/^I call its basic method with the hash (\{.+\})$/) do |fields|
   fields = eval(fields)
   @response = @klass.new.basic(fields)

data/features/orm_steps.rb

@@ -1,7 +1,7 @@
 require_relative '../lib/bio-publisci.rb'
 
 Given /^an ORM::DataCube entitled "(.*?)"$/ do |name|
-	@cube = R2RDF::Dataset::ORM::DataCube.new(name: name)
+	@cube = R2RDF::ORM::DataCube.new(name: name)
 end
 
 Given /^an ORM::DataCube entitled "(.*?)" with the following options:$/ do |name, opts|
@@ -12,13 +12,13 @@ Given /^an ORM::DataCube entitled "(.*?)" with the following options:$/ do |name
 
 		v = hash["value"]
 		v = v[1..-1].to_sym if k[0] == ":"
-		
+
 		v = true if v =="true"
 		v = false if v =="false"
 
 		options_hash[k] = v
 	}
-	@cube = R2RDF::Dataset::ORM::DataCube.new(options_hash)
+	@cube = R2RDF::ORM::DataCube.new(options_hash)
 end
 
 Given(/^a turtle string from file (.*)$/) do |file|
@@ -30,7 +30,7 @@ Given(/^the URI string "(.*?)"$/) do |uri|
 end
 
 When(/^I call the ORM::DataCube class method load on it$/) do
-  @cube = R2RDF::Dataset::ORM::DataCube.load(@string)
+  @cube = R2RDF::ORM::DataCube.load(@string)
 end
 
 When /^I add a "(.*?)" dimension$/ do |dim|
@@ -70,5 +70,5 @@ Then /^the to_n3 method should return a string with a "(.*?)"$/ do |search|
 end
 
 Then(/^I should receive an ORM::DataCube object$/) do
-  @cube.is_a?(R2RDF::Dataset::ORM::DataCube).should == true
+  @cube.is_a?(R2RDF::ORM::DataCube).should == true
 end

data/features/prov_dsl.feature

@@ -0,0 +1,14 @@
+Feature: Receive metadata as user input or extract from data sources
+
+  To generate clean provenance strings through a friendly interface
+  I want to use a DSL for the PROV ontology
+
+  Scenario: Generate without any magic (more open-world)
+    Given the prov DSL string from file examples/no_magic.prov
+    When I call Prov.run on it
+    Then I should receive a provenance string
+
+  Scenario: Generate from file
+    Given the prov DSL string from file examples/prov_dsl.prov
+    When I call Prov.run on it
+    Then I should receive a provenance string

data/features/prov_dsl_steps.rb

@@ -0,0 +1,11 @@
+Given(/^the prov DSL string from file (.+)$/) do |file|
+  @dsl_string = file
+end
+
+When(/^I call Prov\.run on it$/) do
+  @turtle_string = PubliSci::Prov.run(@dsl_string)
+end
+
+Then(/^I should receive a provenance string$/) do
+  puts @turtle_string
+end