bio-publisci 0.0.1

data/lib/vocabs/ma.rb

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+module RDF
+  ##
+  # W3C Media Annotation vocabulary.
+  # @see www.w3.org/ns/ma-ont.rdf
+  class MA < Vocabulary("http://www.w3.org/ns/ma-ont#")
+    property :IsRatingOf
+    property :alternativeTitle
+    property :averageBitRate
+    property :collectionName
+    property :copyright
+    property :createdIn
+    property :creationDate
+    property :date
+    property :depictsFictionalLocation
+    property :description
+    property :duration
+    property :editDate
+    property :features
+    property :fragmentName
+    property :frameHeight
+    property :frameRate
+    property :frameSizeUnit
+    property :frameWidth
+    property :hasAccessConditions
+    property :hasAudioDescription
+    property :hasCaptioning
+    property :hasChapter
+    property :hasClassification
+    property :hasClassificationSystem
+    property :hasCompression
+    property :hasContributor
+    property :hasCreator
+    property :hasFormat
+    property :hasFragment
+    property :hasGenre
+    property :hasKeyword
+    property :hasLanguage
+    property :hasLocationCoordinateSystem
+    property :hasNamedFragment
+    property :hasPermissions
+    property :hasPolicy
+    property :hasPublished
+    property :hasPublisher
+    property :hasRating
+    property :hasRatingSystem
+    property :hasRelatedImage
+    property :hasRelatedLocation
+    property :hasRelatedResource
+    property :hasSigning
+    property :hasSource
+    property :hasSubtitling
+    property :hasTargetAudience
+    property :hasTrack
+    property :isChapterOf
+    property :isCopyrightedBy
+    property :isLocationRelatedTo
+    property :isMemberOf
+    property :isProvidedBy
+    property :isRelatedTo
+    property :isSourceOf
+    property :isTargetAudienceOf
+    property :locationAltitude
+    property :locationLatitude
+    property :locationLongitude
+    property :locationName
+    property :locator
+    property :mainOriginalTitle
+    property :numberOfTracks
+    property :ratingScaleMax
+    property :ratingScaleMin
+    property :ratingValue
+    property :recordDate
+    property :releaseDate
+    property :samplingRate
+    property :title
+    property :trackName
+  end
+end

data/lib/vocabs/owl.rb

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+module RDF
+  ##
+  # Web Ontology Language (OWL) vocabulary.
+  #
+  # @see http://www.w3.org/TR/owl-overview/
+  class OWL < Vocabulary("http://www.w3.org/2002/07/owl#")
+    property :allValuesFrom
+    property :annotatedProperty
+    property :annotatedSource
+    property :annotatedTarget
+    property :assertionProperty
+    property :backwardCompatibleWith
+    property :bottomDataProperty
+    property :bottomObjectProperty
+    property :cardinality
+    property :complementOf
+    property :datatypeComplementOf
+    property :deprecated
+    property :differentFrom
+    property :disjointUnionOf
+    property :disjointWith
+    property :distinctMembers
+    property :equivalentClass
+    property :equivalentProperty
+    property :hasKey
+    property :hasSelf
+    property :hasValue
+    property :imports
+    property :incompatibleWith
+    property :intersectionOf
+    property :inverseOf
+    property :maxCardinality
+    property :maxQualifiedCardinality
+    property :members
+    property :minCardinality
+    property :minQualifiedCardinality
+    property :onClass
+    property :onDataRange
+    property :onDatatype
+    property :onProperties
+    property :onProperty
+    property :oneOf
+    property :priorVersion
+    property :propertyChainAxiom
+    property :propertyDisjointWith
+    property :qualifiedCardinality
+    property :sameAs
+    property :someValuesFrom
+    property :sourceIndividual
+    property :targetIndividual
+    property :targetValue
+    property :topDataProperty
+    property :topObjectProperty
+    property :unionOf
+    property :versionIRI
+    property :versionInfo
+    property :withRestrictions
+  end
+end

data/lib/vocabs/rdfs.rb

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+module RDF
+  ##
+  # RDF Schema (RDFS) vocabulary.
+  #
+  # @see http://www.w3.org/TR/rdf-schema/
+  class RDFS < Vocabulary("http://www.w3.org/2000/01/rdf-schema#")
+    property :comment
+    property :domain
+    property :isDefinedBy
+    property :label
+    property :member
+    property :range
+    property :seeAlso
+    property :subClassOf
+    property :subPropertyOf
+  end
+end

data/lib/vocabs/rsa.rb

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+module RDF
+  ##
+  # W3 RSA Keys (RSA) vocabulary.
+  #
+  # @see   http://www.w3.org/ns/auth/rsa#
+  # @since 0.2.0
+  class RSA < Vocabulary("http://www.w3.org/ns/auth/rsa#")
+    property :modulus
+    property :private_exponent
+    property :public_exponent
+  end
+end

data/lib/vocabs/rss.rb

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+module RDF
+  ##
+  # RDF Site Summary (RSS) vocabulary.
+  #
+  # @see http://web.resource.org/rss/1.0/
+  class RSS < Vocabulary("http://purl.org/rss/1.0/")
+    property :description
+    property :items
+    property :link
+    property :name
+    property :title
+    property :url
+  end
+end

data/lib/vocabs/sioc.rb

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+module RDF
+  ##
+  # Semantically-Interlinked Online Communities (SIOC) vocabulary.
+  #
+  # @see http://rdfs.org/sioc/spec/
+  class SIOC < Vocabulary("http://rdfs.org/sioc/ns#")
+    property :about
+    property :account_of
+    property :administrator_of
+    property :attachment
+    property :avatar
+    property :container_of
+    property :content
+    property :content_encoded    # @deprecated
+    property :created_at         # @deprecated
+    property :creator_of
+    property :description        # @deprecated
+    property :earlier_version
+    property :email
+    property :email_sha1
+    property :feed
+    property :first_name         # @deprecated
+    property :follows
+    property :function_of
+    property :group_of           # @deprecated
+    property :has_administrator
+    property :has_container
+    property :has_creator
+    property :has_discussion
+    property :has_function
+    property :has_group          # @deprecated
+    property :has_host
+    property :has_member
+    property :has_moderator
+    property :has_modifier
+    property :has_owner
+    property :has_parent
+    property :has_part           # @deprecated
+    property :has_reply
+    property :has_scope
+    property :has_space
+    property :has_subscriber
+    property :has_usergroup
+    property :host_of
+    property :id
+    property :ip_address
+    property :last_activity_date
+    property :last_item_date
+    property :last_name          # @deprecated
+    property :last_reply_date
+    property :later_version
+    property :latest_version
+    property :link
+    property :links_to
+    property :member_of
+    property :moderator_of
+    property :modified_at        # @deprecated
+    property :modifier_of
+    property :name
+    property :next_by_date
+    property :next_version
+    property :note
+    property :num_authors
+    property :num_items
+    property :num_replies
+    property :num_threads
+    property :num_views
+    property :owner_of
+    property :parent_of
+    property :part_of            # @deprecated
+    property :previous_by_date
+    property :previous_version
+    property :reference          # @deprecated
+    property :related_to
+    property :reply_of
+    property :scope_of
+    property :sibling
+    property :space_of
+    property :subject            # @deprecated
+    property :subscriber_of
+    property :title              # @deprecated
+    property :topic
+    property :usergroup_of
+
+    ##
+    # Semantically-Interlinked Online Communities (SIOC) types vocabulary.
+    #
+    # @see http://rdfs.org/sioc/spec/#sec-modules
+    class Types < RDF::Vocabulary("http://rdfs.org/sioc/types#")
+      # TODO
+    end
+  end
+end

data/lib/vocabs/skos.rb

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+module RDF
+  ##
+  # Simple Knowledge Organization System (SKOS) vocabulary.
+  #
+  # @see http://www.w3.org/TR/skos-reference/skos.html
+  class SKOS < Vocabulary("http://www.w3.org/2004/02/skos/core#")
+    property :altLabel
+    property :broadMatch
+    property :broader
+    property :broaderTransitive
+    property :changeNote
+    property :closeMatch
+    property :definition
+    property :editorialNote
+    property :exactMatch
+    property :example
+    property :hasTopConcept
+    property :hiddenLabel
+    property :historyNote
+    property :inScheme
+    property :mappingRelation
+    property :member
+    property :memberList
+    property :narrowMatch
+    property :narrower
+    property :narrowerTransitive
+    property :notation
+    property :note
+    property :prefLabel
+    property :related
+    property :relatedMatch
+    property :scopeNote
+    property :semanticRelation
+    property :topConceptOf
+  end
+end

data/lib/vocabs/wot.rb

@@ -0,0 +1,21 @@
+module RDF
+  ##
+  # Web of Trust (WOT) vocabulary.
+  #
+  # @see http://xmlns.com/wot/0.1/
+  class WOT < Vocabulary("http://xmlns.com/wot/0.1/")
+    property :assurance
+    property :encryptedTo
+    property :encrypter
+    property :fingerprint
+    property :hasKey
+    property :hex_id
+    property :identity
+    property :length
+    property :pubkeyAddress
+    property :sigdate
+    property :signed
+    property :signer
+    property :sigtime
+  end
+end

data/lib/vocabs/xhtml.rb

@@ -0,0 +1,9 @@
+module RDF
+  ##
+  # Extensible HyperText Markup Language (XHTML) vocabulary.
+  #
+  # @see http://www.w3.org/1999/xhtml/
+  class XHTML < Vocabulary("http://www.w3.org/1999/xhtml#")
+    # TODO
+  end
+end

data/lib/vocabs/xsd.rb

@@ -0,0 +1,58 @@
+module RDF
+  ##
+  # XML Schema (XSD) vocabulary.
+  #
+  # @see http://www.w3.org/XML/Schema
+  # @see http://www.w3.org/TR/xmlschema-2/#built-in-datatypes
+  class XSD < Vocabulary("http://www.w3.org/2001/XMLSchema#")
+    # XML Schema built-in primitive types
+    # @see http://www.w3.org/TR/xmlschema-2/#built-in-primitive-datatypes
+    property :NOTATION
+    property :QName
+    property :anyURI
+    property :base64Binary
+    property :boolean
+    property :date
+    property :dateTime
+    property :decimal
+    property :double
+    property :duration
+    property :float
+    property :gDay
+    property :gMonth
+    property :gMonthDay
+    property :gYear
+    property :gYearMonth
+    property :hexBinary
+    property :string
+    property :time
+
+    # XML Schema built-in derived types
+    # @see http://www.w3.org/TR/xmlschema-2/#built-in-derived
+    property :ENTITIES
+    property :ENTITY
+    property :ID
+    property :IDREF
+    property :IDREFS
+    property :NCName
+    property :NMTOKEN
+    property :NMTOKENS
+    property :Name
+    property :byte
+    property :int
+    property :integer
+    property :language
+    property :long
+    property :negativeInteger
+    property :nonNegativeInteger
+    property :nonPositiveInteger
+    property :normalizedString
+    property :positiveInteger
+    property :short
+    property :token
+    property :unsignedByte
+    property :unsignedInt
+    property :unsignedLong
+    property :unsignedShort
+  end
+end

data/resources/queries/codes.rq

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+PREFIX qb:   <http://purl.org/linked-data/cube#> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
+PREFIX skos:  <http://www.w3.org/2004/02/skos/core#> 
+
+
+SELECT DISTINCT ?dimension ?code ?codeLabel WHERE{
+	?dim a qb:DimensionProperty;
+		rdfs:label ?dimension;
+		qb:codeList ?codes.
+
+	?codes skos:hasTopConcept ?code. 
+	?code skos:prefLabel ?codeLabel.
+}

data/resources/queries/dataset.rq

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+PREFIX qb:   <http://purl.org/linked-data/cube#> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
+
+SELECT DISTINCT ?dataset ?label WHERE{
+	?dataset a qb:DataSet;
+		rdfs:label ?label.		
+}

data/resources/queries/dimension_ranges.rq

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+PREFIX qb:   <http://purl.org/linked-data/cube#> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
+
+SELECT DISTINCT ?dimension ?range WHERE {
+	?dim a qb:DimensionProperty;
+		rdfs:label ?dimension;
+		rdfs:range ?range.
+}

data/resources/queries/dimensions.rq

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+PREFIX qb:   <http://purl.org/linked-data/cube#> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
+
+SELECT DISTINCT ?dimension WHERE{
+	?dim a qb:DimensionProperty;
+		rdfs:label ?dimension.		
+}

data/resources/queries/measures.rq

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+PREFIX qb:   <http://purl.org/linked-data/cube#> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
+
+SELECT DISTINCT ?measure WHERE{
+	?meas a qb:MeasureProperty;
+		rdfs:label ?measure.
+}

data/resources/queries/observations.rq

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+PREFIX qb:   <http://purl.org/linked-data/cube#> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
+PREFIX prop:  <http://www.rqtl.org/dc/properties/> 
+
+SELECT DISTINCT ?observation ?property ?value WHERE{
+	?observation a qb:Observation;
+		?property ?value.
+
+	{ ?property a qb:DimensionProperty. }
+	UNION
+	{ ?property a qb:MeasureProperty. }
+}

data/resources/queries/test.rq

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+SELECT * WHERE{
+	?s ?p ?o
+}LIMIT 10

data/resources/weather.numeric.arff

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+@relation weather
+
+@attribute outlook {sunny, overcast, rainy}
+@attribute temperature real
+@attribute humidity real
+@attribute windy {TRUE, FALSE}
+@attribute play {yes, no}
+
+@data
+sunny,85,85,FALSE,no
+sunny,80,90,TRUE,no
+overcast,83,86,FALSE,yes
+rainy,70,96,FALSE,yes
+rainy,68,80,FALSE,yes
+rainy,65,70,TRUE,no
+overcast,64,65,TRUE,yes
+sunny,72,95,FALSE,no
+sunny,69,70,FALSE,yes
+rainy,75,80,FALSE,yes
+sunny,75,70,TRUE,yes
+overcast,72,90,TRUE,yes
+overcast,81,75,FALSE,yes
+rainy,71,91,TRUE,no

data/spec/analyzer_spec.rb

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+require_relative '../lib/bio-publisci.rb'
+
+describe R2RDF::Analyzer do
+	class Ana 
+		include R2RDF::Analyzer
+	end
+
+	before(:all) do
+		@analyzer = Ana.new
+		
+		@measures = ['chunkiness','deliciousness']
+		@dimensions = ['producer', 'pricerange']
+		@labels = %w(hormel newskies whys)
+		@data = 
+		{
+			"producer" =>      ["hormel","newskies",  "whys"],
+			"pricerange" =>    ["low",   "medium",    "nonexistant"],
+			"chunkiness"=>     [1,         6,          9001],
+			"deliciousness"=>  [1,         9,          6]  
+		}
+	end
+	
+	it "should run a basic validation" do
+		newdata = []
+
+		@data.keys.size.times{|i|
+			obs = {}
+			@data.map{|k,v|
+				obs[k] = v[i]
+			}
+			newdata << obs
+		}
+
+		@analyzer.check_integrity(newdata, @measures, @dimensions)
+	end
+end

data/spec/bio-publisci_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioPublisci" do
+  it "fails" do
+    fail "hey buddy, you should probably rename this file and start specing for real"
+  end
+end

data/spec/csv/bacon.csv

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+producer,pricerange,chunkiness,deliciousness
+hormel,low,1,1
+newskies,medium,6,9
+whys,nonexistant,9001,6

data/spec/csv/moar_bacon.csv

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+producer,pricerange,chunkiness,deliciousness
+hormel,low,1,1
+oscar_mayer,low,6,3
+newskies,medium,2,5
+hormel,low,2,2
+DArtagnan,medium,6,9
+oscar_mayer,low,5,4
+hormel,low,2,1
+farmland,high,6,9
+newskies,medium,6,9
+whys,nonexistant,9001,6