bio-publisci 0.0.4 → 0.0.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3cb588f4ec6cfa77e1e9011b687ca3e148c6ca6e
-  data.tar.gz: 6a257692f2317eaea75f0fe306b93e01c1de6a70
+  metadata.gz: 017f15f45cc8f40401aebe96aaf5dd886ba602e7
+  data.tar.gz: f59abde75019333ff918968a8717f51f419946ee
 SHA512:
-  metadata.gz: 163459c5c65c023475a5cb9853c7300d8b5f2a0c4afdf8a98a9f7f7f61ba9103c15e562f01c08a19f7c2d08853ce31447b0710c29e14d9c6f954705f82c26bba
-  data.tar.gz: 6e07fbb66df785ef3d15820d825823fdcd7ee18fe60cd68f8009f9f92c3204fc8945c3e0ac3bf79663b66d1259036da4f6d2749bac2d34f8870c73c25d850cbc
+  metadata.gz: 7c80715a4e5354b330c93591b812f5a6c5105fbf6be2fe3d3028721796246e8a13cd1410af29411ba46d396cb82e494319f7137cd1aa2985e0e5d6cf08ce2422
+  data.tar.gz: 96dd7d0f7fb252837524640f21ec6513197366c2455ce3691b8c2a36ba9dd7acfa438eb87cb2b0c3b6560a54fc87e3ab972fd7ae9e5ebec515f74869ac87334c

data/Rakefile

@@ -21,7 +21,7 @@ Jeweler::Tasks.new do |gem|
   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 = "0.0.4"
+  gem.version = "0.0.5"
 
   # dependencies defined in Gemfile
 end

data/examples/no_magic.prov

@@ -1,16 +1,29 @@
+# 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, steps: "spec/resource/example.Rhistory"
+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
@@ -18,23 +31,28 @@ entity :original do
   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
+  # 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
 
-generate_n3
+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

data/examples/primer.prov

@@ -1,28 +1,66 @@
-# http://www.w3.org/TR/prov-primer/images/agents.png
+# Provenance generation code for primer example at
+#  http://www.w3.org/TR/prov-primer/images/agents.png
 
-organization :chartgen
+# Set the base url
+base_url "http://example.org"
+
+# Elements can be created with an options hash
+entity :chart1, attributed_to: :derek
+
+# entity => http://www.w3.org/TR/prov-o/#Entity
+entity :composition1
+entity :regionList1
 
+# Elements can also be defined using a block
+#
+# agent => http://www.w3.org/TR/prov-o/#Agent
 agent :derek do
+
+  # name => foaf:name
   name "Derek"
+
+  # on_behalf_of => http://www.w3.org/TR/prov-o/#actedOnBehalfOf
   on_behalf_of :chartgen
 end
 
-entity :chart1, attributed_to: :derek
-entity :composition1
-entity :regionList1
-entity :dataSet1
+# Some methods are just wrappers with argument generation
+#  "organization" is short for agent :chartgen, type: "organization"
+#
+# organization => http://www.w3.org/TR/prov-o/#Organization
+organization :chartgen
+
 
+# An element of the correct type will be looked up for any
+#  method whose argument is a symbol
 activity :illustrate do
+
+  # generated => http://www.w3.org/TR/prov-o/#generated
   generated :chart1
+
+  # associated_with => http://www.w3.org/TR/prov-o/#wasAssociatedWith
   associated_with :derek
+
+  # used => http://www.w3.org/TR/prov-o/#used
   used :composition1
+
 end
 
 activity :compose1 do
   generated :composition1
   associated_with :derek
   used :regionList1
+
+  # Since symbols are lazy loaded (only when looked up by generate_n3)
+  #  you can call used here before declaring dataSet1
   used :dataSet1
 end
 
-generate_n3(true)
+# data is aliased to entity
+data :dataSet1
+
+# Returns the turtle form of each element
+generate_n3
+
+# Can return abbreviated form by passing true
+#  (easier to read, some prefixes not yet included so may not work w/ triple stores)
+#  generate_n3(true)

data/examples/prov_dsl.prov

@@ -1,10 +1,19 @@
-agent :publisci, type: "software"
+# Made up example to show generation and customization features
+
+# Set subject manually (prevents automatic generation)
 agent :R, subject: "http://r-project.org"
 
+agent :publisci, type: "software"
+
+# Define plan, load step list from file if available
 plan :R_steps, steps: "spec/resource/example.Rhistory"
 
 organization :sciruby, subject: "http://sciruby.com"
 
+# The DSL is built on top Ruby, so you can assign variables if you need to
+#   or do any other ruby thing you might like.
+#
+# The vocabulary(url) method is short for RDF::Vocabulary.new(url)
 foaf = vocabulary "http://xmlns.com/foaf/0.1/"
 
 agent :Will do
@@ -12,12 +21,39 @@ agent :Will do
   name "Will Strinz"
   on_behalf_of :sciruby
 
+  # Custom predicates can be added using the has(predicate, object) method.
   has foaf.mailbox, "wstrinz@gmail.com"
-  has foaf.homepage, "http://gsocsemantic.wordpress.com/"
+
+  # Predicates must but either a vocabulary object or a valid RDF resource,
+  #   but objects can be a resource or a literal.
+  #
+  # RDF.rb is used to assign the right type to each object (resource or literal)
+  has "http://xmlns.com/foaf/0.1/", "http://gsocsemantic.wordpress.com/"
+end
+
+data :field_work
+
+data :original do
+  # Derivations and attributions can be generated automatically
+  #  if their corresponding methods are called with a symbol
+  attributed_to :R
+
+  # derived_from will add a prov:wasDerivedFrom predicate to this entity
+  #   with the subject for the entity represented by :field_work
+  #   as its object.
+  derived_from :field_work
 end
 
 data :triplified_example do
   attributed_to :Will
+
+  # Derivations can be qualified by passing a block.
+  #   This will add a prov:qualifiedDerivation relation
+  #   to the resource for :triplified_example.
+  #   (see http://www.w3.org/TR/prov-o/#Derivation)
+  #
+  # A new Derivation resource and object will also be
+  #   created with the information in the block.
   derived_from do
     entity :original
     activity :triplify
@@ -30,20 +66,15 @@ activity :triplify do
   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 {
+  # Qualified associations for activities can also be created using blocks
+  associated_with do
     agent :R
     plan :R_steps
-  }
+  end
 
   associated_with :Will
 end

data/features/prov_dsl.feature

@@ -3,8 +3,8 @@ 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
+  Scenario: Generate based on example for w3.org
+    Given the prov DSL string from file examples/primer.prov
     When I call Prov.run on it
     Then I should receive a provenance string
 

data/lib/bio-publisci/metadata/prov/agent.rb

@@ -41,16 +41,17 @@ module Prov
       @organization = organization
     end
 
-    def on_behalf_of(agent=nil)
-      if agent
-        if agent.is_a? Symbol
-          raise "UnknownAgent: #{agent}" unless Prov.agents.has_key?(agent)
-          agent = Prov.agents[agent]
-        end
-        @on_behalf_of = agent
+    def on_behalf_of(other_agent=nil)
+      if other_agent
+        @on_behalf_of = other_agent
+      elsif @on_behalf_of.is_a? Symbol
+        raise "UnknownAgent: #{@on_behalf_of}" unless Prov.agents.has_key?(@on_behalf_of)
+        @on_behalf_of = Prov.agents[@on_behalf_of]
       else
         @on_behalf_of
       end
+
+      @on_behalf_of
     end
     alias_method :worked_for, :on_behalf_of
 

data/lib/bio-publisci/metadata/prov/dsl.rb

@@ -109,6 +109,10 @@ module PubliSci
         end
       end
 
+      def base_url(url)
+        Prov.base_url=url
+      end
+
       def generate_n3(abbreviate = false)
         entities = Prov.entities.values.map(&:to_n3).join
         agents = Prov.agents.values.map(&:to_n3).join

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-publisci
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors:
 - Will Strinz