bio-publisci 0.0.1

data/lib/r2rdf.rb

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+require 'rserve'
+require 'rdf/4store'
+Dir[File.dirname(__FILE__) + '/vocabs/*.rb'].each {|file| require file }
+
+class QTL2RDF
+
+  attr_accessor :port_4s
+
+  def initialize(dir='.')
+    @dir = File.absolute_path(dir)
+    @R = Rserve::Connection.new()
+    if File.exist?(dir + "/.RData")
+      # puts "loading workspace #{dir}/.RData"
+      @R.eval("load('#{dir}/.RData')")
+    end
+
+    if File.exist?(dir + "/.Rhistory")
+      # puts "loading history #{dir}/.Rhistory"
+      @R.eval("loadhistory('#{dir}/.Rhistory')")
+    end
+
+    @port_4s = 8080
+  end
+
+  def load_workspace(dir=@dir,file='.RData')
+    path = File.join(File.absolute_path(dir),file)
+      if File.exist?(path)
+        # puts "loading workspace #{dir}/.RData"
+        @R.eval("load('#{path}')")
+      else
+        puts "Couldn't find #{path}"
+      end
+  end
+
+  def load_history(dir=@dir,file='.Rhistory')
+    path = File.join(File.absolute_path(dir),file)
+    if File.exist?(path)
+      # puts "loading history #{dir}/.Rhistory"
+      @R.eval("loadhistory('#{path}')")
+    else
+      puts "Couldn't find #{path}"
+    end
+  end
+
+  def dump_dataframe(var)
+    h = {}
+    h[var] = {"attr" => {}, "rows"=>{}}
+
+    x = @R.eval(var)
+
+    x.attr.payload.keys.map{ |a|
+      h[var]["attr"][a] = x.attr.payload[a].to_ruby
+    }
+
+    rownames = x.attr.payload["row.names"].to_ruby
+    colnames = x.payload.keys
+    rownames.each_with_index.map{ |row,i|
+      rh = {}
+      colnames.map{ |col|
+        rh[col] = x.payload[col].to_a[i].to_f
+      }
+      h[var]["rows"][row] = rh
+    }
+
+    h
+  end
+
+  def dump(var)
+    x = @R.eval(var)
+    if x.attr
+      # if x.attr.payload["class"].to_a.include? 'data.frame'
+        dump_dataframe var
+      # end
+    else
+      if x.list?
+        type = x.payload.class.to_s.split("::").last # seems hacky, but probably only temporary
+        value = x.payload.map(&:payload).flatten
+      elsif x.payload.size == 1
+        type = x.class.to_s.split("::").last 
+        value = x.payload.first
+      else
+        type = x.class.to_s.split("::").last 
+        value = x.payload
+      end
+      {var => {"attr"=>{"class" => type}, :value => value}}
+    end
+  end
+
+  def triples_for(h)
+    statements = []
+    base_n = RDF::Node.new
+    attr_n = RDF::Node.new
+    vocab = RDF::Vocabulary.new('http://www.placeholder.com/rqtl#')
+    base_uri = RDF::URI.new('http://www.placeholder.com/')
+    var = h.keys.first
+
+    statements << RDF::Statement.new(base_n, RDF::DC.title, RDF::Literal.new(var))
+
+    if h[var].is_a? Hash
+      if(h[var]["attr"])
+        statements << RDF::Statement.new(base_n, vocab.attributes, attr_n)
+        h[var]["attr"].map{ |k,v| statements << RDF::Statement.new(attr_n, vocab[k], RDF::Literal.new(v)) }
+      end
+
+      if h[var]["rows"]
+        h[var]["rows"].map{ |k,v|
+          row_uri = base_uri.join("row#{k}")
+          statements << RDF::Statement.new(row_uri, vocab.row_of, base_n)
+          statements << RDF::Statement.new(row_uri, RDF::DC.title, k)
+          num = 1 # maybe container support exists in RDF.rb?
+          v.map { |j,u|
+            n = RDF::Node.new
+            statements << RDF::Statement.new(n, vocab.entry_of, row_uri)
+            statements << RDF::Statement.new(n, RDF::DC.title, j)
+            statements << RDF::Statement.new(n, RDF::DC.title, j)
+            statements << RDF::Statement.new(n, vocab["_#{num}"], RDF::Literal.new(u))
+            num += 1
+          }
+        }
+      end
+
+      if h[var].has_key? :value        
+        statements << RDF::Statement.new(base_n, vocab.has_value, RDF::Literal.new(h[var][:value]))
+      end
+    else
+      statements << RDF::Statement.new(base_n, vocab.has_value, RDF::Literal.new(h[var]))
+    end
+    statements
+  end
+
+  #get n3 for a dataframe using datacube vocabulary
+  #still needs range for measures and dimensions, sdmx-dimension equivalent for rows
+  def n3_for(h)
+    str = <<-EOF
+@prefix : <http://www.rqtl.org/ns/#> .
+@prefix qb: <http://purl.org/linked-data/cube#> .
+@prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix prop: <http://www.rqtl.org/dc/properties/> .
+@prefix cs: <http://www.rqtl.org/dc/cs/> .
+
+    EOF
+    #@prefix sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#>
+    var = h.keys.first
+    names = h[var]["attr"]["names"]
+
+    #generate data structure definition
+    str << ":dsd-#{var} a qb:DataStructureDefinition ;\n"
+    str << "\tqb:component cs:refRow ,\n"
+    names.map{ |n|
+      str << "\t\tcs:#{n} ,\n\n"
+    }
+    str[-3]="."
+
+    #generate component specifications
+    str << "cs:refRow a qb:ComponentSpecification ;\n\trdfs:label \"Component Specification for Row\" ;\n\tqb:dimension prop:refRow .\n\n"
+    names.map{ |n|
+      str << "cs:#{n} a qb:ComponentSpecification ;\n\trdfs:label \"Component Specification for #{n}\" ;\n\tqb:measure prop:#{n} .\n\n"
+    }
+
+    #generate dataset definition
+    str << ":dataset-#{var} a qb:DataSet ;\n\trdfs:label \"#{var}\"@en ;\n\tqb:structure :dsd-#{var} .\n\n"
+
+    #add DimensionProperty for row
+    str << <<-EOF
+:refRow a rdf:Property, qb:DimensionProperty ;
+\trdfs:label "Row"@en .
+
+    EOF
+
+    #generate MeasureProperties
+    names.map{ |n|
+      str << ":#{n} a rdf:Property, qb:MeasureProperty ;\n\trdfs:label \"#{n}\"@en .\n\n"
+    }
+
+    #add observations
+    h[var]["rows"].map{|k,v|
+      str << ":obs#{k} a qb:Observation ;\n\tqb:dataSet :dataset-#{var} ;\n\tprop:refRow :#{k} ;\n"
+      v.map{|l,w|
+        str << "\tprop:#{l} #{w} ;\n"
+      }
+      str << "\t.\n\n"
+    }
+
+    #add row property definitions
+    h[var]["rows"].map{|k,v|
+      str << ":#{k} a prop:refRow ;\n\trdfs:label \"#{k}\" .\n\n"
+    }
+
+    str
+  end
+
+  def statements_for(string,type=:turtle)
+    statements = []
+    RDF::Reader.for(:turtle).new(string) do |reader|
+      reader.each_statement do |statement|
+        # puts statement.inspect
+        statements << statement
+      end
+    end
+    statements
+  end
+
+  def turtletype_for(value)
+    #use for providing ranges to better define data (later)
+  end
+
+  def load_statements(statements)
+    #maybe a better way than inserting statements one at a time?
+    repo = RDF::FourStore::Repository.new("http://localhost:#{@port_4s}")
+    statements.each{|s| repo.insert(s)}
+  end
+
+  def to_store(var, parse_type=:turtle)
+    load_statements(triples_for(dump(var))) if parse_type==:ntriples
+    
+    #TODO: this doesn't work (needs to be converted to statments or 
+    # a way of inserting raw strings needs to be figured out.
+    load_statements(n3_for(dump(var))) if parse_type==:turtle
+  end
+
+  def vars
+    @R.eval("ls()").payload
+  end
+
+end

data/lib/template_bak/publisci.rb

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+
+module BioPublisci
+end

data/lib/template_bak.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-publisci/publisci.rb'
+

data/lib/vocabs/cc.rb

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+module RDF
+  ##
+  # Creative Commons (CC) vocabulary.
+  #
+  # @see http://creativecommons.org/ns
+  class CC < Vocabulary("http://creativecommons.org/ns#")
+    property :attributionName
+    property :attributionURL
+    property :deprecatedOn
+    property :jurisdiction
+    property :legalcode
+    property :license
+    property :morePermissions
+    property :permits
+    property :prohibits
+    property :requires
+  end
+end

data/lib/vocabs/cert.rb

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+module RDF
+  ##
+  # W3 Authentication Certificates (CERT) vocabulary.
+  #
+  # @see   http://www.w3.org/ns/auth/cert#
+  # @since 0.2.0
+  class CERT < Vocabulary("http://www.w3.org/ns/auth/cert#")
+    property :decimal
+    property :hex
+    property :identity
+    property :public_key
+  end
+end

data/lib/vocabs/dc.rb

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+module RDF
+  ##
+  # Dublin Core (DC) vocabulary.
+  #
+  # @see http://dublincore.org/schemas/rdfs/
+  class DC < Vocabulary("http://purl.org/dc/terms/")
+    property :abstract
+    property :accessRights
+    property :accrualMethod
+    property :accrualPeriodicity
+    property :accrualPolicy
+    property :alternative
+    property :audience
+    property :available
+    property :bibliographicCitation
+    property :conformsTo
+    property :contributor
+    property :coverage
+    property :created
+    property :creator
+    property :date
+    property :dateAccepted
+    property :dateCopyrighted
+    property :dateSubmitted
+    property :description
+    property :educationLevel
+    property :extent
+    property :format
+    property :hasFormat
+    property :hasPart
+    property :hasVersion
+    property :identifier
+    property :instructionalMethod
+    property :isFormatOf
+    property :isPartOf
+    property :isReferencedBy
+    property :isReplacedBy
+    property :isRequiredBy
+    property :isVersionOf
+    property :issued
+    property :language
+    property :license
+    property :mediator
+    property :medium
+    property :modified
+    property :provenance
+    property :publisher
+    property :references
+    property :relation
+    property :replaces
+    property :requires
+    property :rights
+    property :rightsHolder
+    property :source
+    property :spatial
+    property :subject
+    property :tableOfContents
+    property :temporal
+    property :title
+    property :type
+    property :valid
+  end
+end

data/lib/vocabs/dc11.rb

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+module RDF
+  ##
+  # Dublin Core (DC) legacy vocabulary.
+  #
+  # @see http://dublincore.org/schemas/rdfs/
+  class DC11 < Vocabulary("http://purl.org/dc/elements/1.1/")
+    property :contributor
+    property :coverage
+    property :creator
+    property :date
+    property :description
+    property :format
+    property :identifier
+    property :language
+    property :publisher
+    property :relation
+    property :rights
+    property :source
+    property :subject
+    property :title
+    property :type
+  end
+end

data/lib/vocabs/doap.rb

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+module RDF
+  ##
+  # Description of a Project (DOAP) vocabulary.
+  #
+  # @see http://trac.usefulinc.com/doap
+  class DOAP < Vocabulary("http://usefulinc.com/ns/doap#")
+    property :'anon-root'
+    property :audience
+    property :blog
+    property :browse
+    property :'bug-database'
+    property :category
+    property :created
+    property :description
+    property :developer
+    property :documenter
+    property :'download-mirror'
+    property :'download-page'
+    property :'file-release'
+    property :helper
+    property :homepage
+    property :implements
+    property :language
+    property :license
+    property :location
+    property :'mailing-list'
+    property :maintainer
+    property :module
+    property :name
+    property :'old-homepage'
+    property :os
+    property :platform
+    property :'programming-language'
+    property :release
+    property :repository
+    property :revision
+    property :screenshots
+    property :'service-endpoint'
+    property :shortdesc
+    property :tester
+    property :translator
+    property :vendor
+    property :wiki
+  end
+end

data/lib/vocabs/exif.rb

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+module RDF
+  ##
+  # Exchangeable Image File Format (EXIF) vocabulary.
+  #
+  # @see http://www.w3.org/2003/12/exif/
+  class EXIF < Vocabulary("http://www.w3.org/2003/12/exif/ns#")
+    property :_unknown
+    property :apertureValue
+    property :artist
+    property :bitsPerSample
+    property :brightnessValue
+    property :cfaPattern
+    property :colorSpace
+    property :componentsConfiguration
+    property :compressedBitsPerPixel
+    property :compression
+    property :contrast
+    property :copyright
+    property :customRendered
+    property :datatype
+    property :date
+    property :dateAndOrTime
+    property :dateTime
+    property :dateTimeDigitized
+    property :dateTimeOriginal
+    property :deviceSettingDescription
+    property :digitalZoomRatio
+    property :exifAttribute
+    property :exifVersion
+    property :exif_IFD_Pointer
+    property :exifdata
+    property :exposureBiasValue
+    property :exposureIndex
+    property :exposureMode
+    property :exposureProgram
+    property :exposureTime
+    property :fNumber
+    property :fileSource
+    property :flash
+    property :flashEnergy
+    property :flashpixVersion
+    property :focalLength
+    property :focalLengthIn35mmFilm
+    property :focalPlaneResolutionUnit
+    property :focalPlaneXResolution
+    property :focalPlaneYResolution
+    property :gainControl
+    property :geo
+    property :gpsAltitude
+    property :gpsAltitudeRef
+    property :gpsAreaInformation
+    property :gpsDOP
+    property :gpsDateStamp
+    property :gpsDestBearing
+    property :gpsDestBearingRef
+    property :gpsDestDistance
+    property :gpsDestDistanceRef
+    property :gpsDestLatitude
+    property :gpsDestLatitudeRef
+    property :gpsDestLongitude
+    property :gpsDestLongitudeRef
+    property :gpsDifferential
+    property :gpsImgDirection
+    property :gpsImgDirectionRef
+    property :gpsInfo
+    property :gpsInfo_IFD_Pointer
+    property :gpsLatitude
+    property :gpsLatitudeRef
+    property :gpsLongitude
+    property :gpsLongitudeRef
+    property :gpsMapDatum
+    property :gpsMeasureMode
+    property :gpsProcessingMethod
+    property :gpsSatellites
+    property :gpsSpeed
+    property :gpsSpeedRef
+    property :gpsStatus
+    property :gpsTimeStamp
+    property :gpsTrack
+    property :gpsTrackRef
+    property :gpsVersionID
+    property :height
+    property :ifdPointer
+    property :imageConfig
+    property :imageDataCharacter
+    property :imageDataStruct
+    property :imageDescription
+    property :imageLength
+    property :imageUniqueID
+    property :imageWidth
+    property :interopInfo
+    property :interoperabilityIndex
+    property :interoperabilityVersion
+    property :interoperability_IFD_Pointer
+    property :isoSpeedRatings
+    property :jpegInterchangeFormat
+    property :jpegInterchangeFormatLength
+    property :length
+    property :lightSource
+    property :make
+    property :makerNote
+    property :maxApertureValue
+    property :meter
+    property :meteringMode
+    property :mm
+    property :model
+    property :oecf
+    property :orientation
+    property :photometricInterpretation
+    property :pictTaking
+    property :pimBrightness
+    property :pimColorBalance
+    property :pimContrast
+    property :pimInfo
+    property :pimSaturation
+    property :pimSharpness
+    property :pixelXDimension
+    property :pixelYDimension
+    property :planarConfiguration
+    property :primaryChromaticities
+    property :printImageMatching_IFD_Pointer
+    property :recOffset
+    property :referenceBlackWhite
+    property :relatedFile
+    property :relatedImageFileFormat
+    property :relatedImageLength
+    property :relatedImageWidth
+    property :relatedSoundFile
+    property :resolution
+    property :resolutionUnit
+    property :rowsPerStrip
+    property :samplesPerPixel
+    property :saturation
+    property :sceneCaptureType
+    property :sceneType
+    property :seconds
+    property :sensingMethod
+    property :sharpness
+    property :shutterSpeedValue
+    property :software
+    property :spatialFrequencyResponse
+    property :spectralSensitivity
+    property :stripByteCounts
+    property :stripOffsets
+    property :subSecTime
+    property :subSecTimeDigitized
+    property :subSecTimeOriginal
+    property :subjectArea
+    property :subjectDistance
+    property :subjectDistanceRange
+    property :subjectLocation
+    property :subseconds
+    property :tag_number
+    property :tagid
+    property :transferFunction
+    property :userComment
+    property :userInfo
+    property :versionInfo
+    property :whiteBalance
+    property :whitePoint
+    property :width
+    property :xResolution
+    property :yCbCrCoefficients
+    property :yCbCrPositioning
+    property :yCbCrSubSampling
+    property :yResolution
+  end
+end

data/lib/vocabs/foaf.rb

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+module RDF
+  ##
+  # Friend of a Friend (FOAF) vocabulary.
+  #
+  # @see http://xmlns.com/foaf/spec/
+  class FOAF < Vocabulary("http://xmlns.com/foaf/0.1/")
+    property :account
+    property :accountName
+    property :accountServiceHomepage
+    property :age
+    property :aimChatID
+    property :based_near
+    property :birthday
+    property :currentProject
+    property :depiction
+    property :depicts
+    property :dnaChecksum
+    property :familyName
+    property :family_name
+    property :firstName
+    property :fundedBy
+    property :geekcode
+    property :gender
+    property :givenName
+    property :givenname
+    property :holdsAccount
+    property :homepage
+    property :icqChatID
+    property :img
+    property :interest
+    property :isPrimaryTopicOf
+    property :jabberID
+    property :knows
+    property :lastName
+    property :logo
+    property :made
+    property :maker
+    property :mbox
+    property :mbox_sha1sum
+    property :member
+    property :membershipClass
+    property :msnChatID
+    property :myersBriggs
+    property :name
+    property :nick
+    property :openid
+    property :page
+    property :pastProject
+    property :phone
+    property :plan
+    property :primaryTopic
+    property :publications
+    property :schoolHomepage
+    property :sha1
+    property :skypeID
+    property :status
+    property :surname
+    property :theme
+    property :thumbnail
+    property :tipjar
+    property :title
+    property :topic
+    property :topic_interest
+    property :weblog
+    property :workInfoHomepage
+    property :workplaceHomepage
+    property :yahooChatID
+  end
+end

data/lib/vocabs/geo.rb

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+module RDF
+  ##
+  # WGS84 Geo Positioning (GEO) vocabulary.
+  #
+  # @see   http://www.w3.org/2003/01/geo/wgs84_pos#
+  # @since 0.2.0
+  class GEO < Vocabulary("http://www.w3.org/2003/01/geo/wgs84_pos#")
+    property :lat
+    property :location
+    property :long
+    property :lat_long
+  end
+end

data/lib/vocabs/http.rb

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+module RDF
+  ##
+  # Hypertext Transfer Protocol (HTTP) vocabulary.
+  #
+  # @see http://www.w3.org/2006/http
+  class HTTP < Vocabulary("http://www.w3.org/2006/http#")
+    property :abs_path
+    property :absoluteURI
+    property :authority
+    property :body
+    property :connectionAuthority
+    property :elementName
+    property :elementValue
+    property :fieldName
+    property :fieldValue
+    property :header
+    property :param
+    property :paramName
+    property :paramValue
+    property :request
+    property :requestURI
+    property :response
+    property :responseCode
+    property :version
+  end
+end