publisci 0.1.2

data/examples/no_magic.rb

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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

data/examples/orm.prov

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+agent :R, subject: "http://r-project.org"
+agent :publisci, type: "software"
+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 "http://xmlns.com/foaf/0.1/", "http://gsocsemantic.wordpress.com/"
+end
+
+data :field_work
+
+data :original do
+  attributed_to :R
+  derived_from :field_work
+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
+
+
+activity :use_R do
+  generated :original
+  associated_with do
+    agent :R
+    plan :R_steps
+  end
+  associated_with :Will
+end
+
+to_repository

data/examples/primer-full.prov

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+###
+#
+# Complete PROV-O primer example,
+#   as shown in http://www.w3.org/TR/prov-primer/images/everything.png
+#   (some prefixes are different)
+#
+# See Section 3.10 of http://www.w3.org/TR/prov-primer/
+#
+
+base_url "http://example.org"
+
+dct = vocabulary "http://purl.org/dc/terms/"
+prov = vocabulary "http://www.w3.org/ns/prov#"
+
+###
+# Entities
+###
+
+entity :dataSet1
+entity :regionList
+entity :composition1
+
+entity :chart1 do
+  attributed_to :derek
+  has prov.generatedAtTime, "2012-03-02T10:30:00"
+end
+
+entity :dataSet2 do
+  has prov.wasRevisionOf, :dataSet1
+end
+
+entity :chart2 do
+  derived_from :dataSet2
+  has prov.wasRevisionOf, :chart1
+end
+
+entity :article do
+  has dct.title, "Crime rises in cities"
+end
+
+entity :articleV1 do
+  has prov.specializationOf, :article
+end
+
+entity :articleV2 do
+  has prov.specializationOf, :article
+  has prov.alternateOf, :articleV1
+end
+
+entity :quoteInBlogEntry20130326 do
+  subject "http://example.com/blog_entry"
+  has prov.wasQuotedFrom, :article
+end
+
+###
+# Agents
+###
+
+agent :edith, type: "person"
+
+organization :chartgen, name: "Chart Generators Inc"
+
+agent :derek do
+  name "Derek"
+  on_behalf_of :chartgen
+end
+
+###
+# Activities
+###
+
+activity :illustrate1 do
+  generated :chart1
+  associated_with :derek
+  used :composition1
+end
+
+activity :compose1 do
+  generated :composition1
+
+  associated_with do
+    agent :derek
+    role :analyst
+  end
+
+  used do
+    entity :regionList
+    role :regionsToAggregateBy
+  end
+
+  used do
+    entity :dataSet1
+    role :dataToCompose
+  end
+end
+
+activity :correct1 do
+  generated :dataSet2
+  used :dataSet1
+
+  associated_with do
+    agent :edith
+    plan :instructions
+  end
+
+  has prov.startedAtTime, "2012-03-31T09:21:00"
+  has prov.endedAtTime, "2012-04-01T15:21:00"
+end
+
+activity :compile1 do
+  generated :chart1
+  used :dataSet1
+end
+
+activity :compile2 do
+  generated :chart2
+  used :dataSet2
+end
+
+generate_n3 true

data/examples/primer.prov

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+# Provenance generation code for primer example at
+#  http://www.w3.org/TR/prov-primer/images/agents.png
+
+# 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
+
+# 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
+
+# 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

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+# 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
+  type "person"
+  name "Will Strinz"
+  on_behalf_of :sciruby
+
+  # Custom predicates can be added using the has(predicate, object) method.
+  has foaf.mailbox, "wstrinz@gmail.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
+  end
+end
+
+activity :triplify do
+  generated :triplified_example
+  associated_with :publisci
+  used do
+    entity :original
+    role :generation_input, comment: "source data for triplification"
+  end
+end
+
+activity :use_R do
+  generated :original
+
+  # Qualified associations for activities can also be created using blocks
+  associated_with do
+    agent :R
+    plan :R_steps
+  end
+
+  associated_with :Will
+end
+
+generate_n3
+# generate_n3 true

data/examples/safe_gen.rb

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+require 'bio-publisci'
+
+str = IO.read(ARGV[0])
+str.untaint
+$SAFE=4
+runner = PubliSci::Prov::DSL::Instance.new
+puts runner.instance_eval(str,ARGV[0])

data/examples/visualization/primer.prov

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+# Provenance generation code for primer example at
+#  http://www.w3.org/TR/prov-primer/images/agents.png
+
+# 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
+
+# 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
+
+# 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)