Class: RDF::Tabular::Reader

Inherits:
Reader show all
Includes:
Util::Logger
Defined in:
vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb

Overview

A Tabular Data to RDF parser in Ruby.

Author:

Instance Attribute Summary collapse

Attributes inherited from Reader

#options

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Util::Logger

#log_debug, #log_depth, #log_error, #log_fatal, #log_info, #log_recover, #log_recovering?, #log_statistics, #log_warn, #logger

Methods inherited from Reader

#base_uri, #canonicalize?, #close, each, #encoding, #fail_object, #fail_predicate, #fail_subject, for, format, #intern?, #lineno, open, #prefix, #prefixes, #prefixes=, #read_statement, #read_triple, #rewind, to_sym, #to_sym, #valid?, #validate?

Methods included from Util::Aliasing::LateBound

#alias_method

Methods included from Enumerable

add_entailment, #dump, #each_graph, #each_object, #each_predicate, #each_quad, #each_subject, #each_term, #entail, #enum_graph, #enum_object, #enum_predicate, #enum_quad, #enum_statement, #enum_subject, #enum_term, #enum_triple, #graph_names, #has_graph?, #has_object?, #has_predicate?, #has_quad?, #has_statement?, #has_subject?, #has_term?, #has_triple?, #invalid?, #method_missing, #objects, #predicates, #project_graph, #quads, #respond_to_missing?, #statements, #subjects, #supports?, #terms, #to_a, #to_h, #to_set, #triples, #valid?

Methods included from Isomorphic

#bijection_to, #isomorphic_with?

Methods included from Countable

#count, #empty?

Methods included from Readable

#readable?

Constructor Details

#initialize(input = $stdin, options = {}) {|reader| ... } ⇒ Reader

Initializes the RDF::Tabular Reader instance.

Parameters:

  • input (Util::File::RemoteDoc, IO, StringIO, Array<Array<String>>, String) (defaults to: $stdin)

    An opened file possibly JSON Metadata, or an Array used as an internalized array of arrays

  • options (Hash{Symbol => Object}) (defaults to: {})

    any additional options (see RDF::Reader#initialize)

  • optinons (Hash)

    a customizable set of options

Options Hash (options):

  • :metadata (Metadata, Hash, String, RDF::URI)

    user supplied metadata, merged on top of extracted metadata. If provided as a URL, Metadata is loade from that location

  • :minimal (Boolean)

    includes only the information gleaned from the cells of the tabular data

  • :noProv (Boolean)

    do not output optional provenance information

Yields:

  • (reader)

    self

Yield Parameters:

Yield Returns:

  • (void)

    ignored

Raises:



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# File 'vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb', line 66

def initialize(input = $stdin, options = {}, &block)
  super do
    # Base would be how we are to take this
    @options[:base] ||= base_uri.to_s if base_uri
    @options[:base] ||= input.base_uri if input.respond_to?(:base_uri)
    @options[:base] ||= input.path if input.respond_to?(:path)
    @options[:base] ||= input.filename if input.respond_to?(:filename)
    if RDF::URI(@options[:base]).relative? && File.exist?(@options[:base].to_s)
      @options[:base] = "file:/#{File.expand_path(@options[:base])}"
    end

    log_debug("Reader#initialize") {"input: #{input.inspect}, base: #{@options[:base]}"}

    # Minimal implies noProv
    @options[:noProv] ||= @options[:minimal]

    @input = case input
    when String then StringIO.new(input)
    when Array then StringIO.new(input.map {|r| r.join(",")}.join("\n"))
    else input
    end

    log_depth do
      # If input is JSON, then the input is the metadata
      content_type = @input.respond_to?(:content_type) ? @input.content_type : ""
      if @options[:base] =~ /\.json(?:ld)?$/ || content_type =~ %r(application/(csvm\+|ld\+)?json)
        @metadata = Metadata.new(@input, @options.merge(filenames: @options[:base]))
        # If @metadata is for a Table, turn it into a TableGroup
        @metadata = @metadata.to_table_group if @metadata.is_a?(Table)
        @metadata.normalize!
        @input = @metadata
      elsif (@options[:base].to_s.end_with?(".html") || %w(text/html application/xhtml+html).include?(content_type)) &&
            !RDF::URI(@options[:base].to_s).fragment
        require 'nokogiri' unless defined?(:Nokogiri)
        doc = Nokogiri::HTML.parse(input)
        doc.xpath("//script[@type='application/csvm+json']/text()").each do |script|
          def script.content_type; "application/csvm+json"; end
          log_debug("Reader#initialize") {"Process HTML script block"}
          @input = script
          @metadata = Metadata.new(@input, @options.merge(filenames: @options[:base]))
          # If @metadata is for a Table, turn it into a TableGroup
          @metadata = @metadata.to_table_group if @metadata.is_a?(Table)
          @metadata.normalize!
          @input = @metadata
        end
      elsif @options[:no_found_metadata]
        # Extract embedded metadata and merge
         = @options[:metadata] || Table.new({}, context: "http://www.w3.org/ns/csvw")
        dialect = .dialect.dup

        # HTTP flags for setting header values
        dialect.header = false if (input.headers.fetch(:content_type, '').split(';').include?('header=absent') rescue false)
        dialect.encoding = input.charset if (input.charset rescue nil)
        dialect.separator = "\t" if (input.content_type == "text/tsv" rescue nil)
        embed_options = @options.dup
        embed_options[:lang] = .lang if .lang
         = dialect.(input, @options[:metadata], embed_options)

        if (@metadata = @options[:metadata]) && @metadata.tableSchema
          @metadata.verify_compatible!()
        else
          @metadata = .normalize!
        end

        lang = input.headers[:content_language] rescue nil
        lang = nil if lang.to_s.include?(',') # Not for multiple languages
        # Set language, if unset and provided
        @metadata.lang ||= lang if lang 
          
        @metadata.dialect = dialect
      else
        # It's tabluar data. Find metadata and proceed as if it was specified in the first place
        @options[:original_input] = @input unless @options[:metadata]
        @input = @metadata = Metadata.for_input(@input, @options).normalize!
      end

      log_debug("Reader#initialize") {"input: #{input}, metadata: #{.inspect}"}

      if block_given?
        case block.arity
          when 0 then instance_eval(&block)
          else block.call(self)
        end
      end
    end
  end
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class RDF::Enumerable

Instance Attribute Details

#input:read (readonly)

Input open to read

Returns:

  • (:read)


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# File 'vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb', line 21

def input
  @input
end

#metadataMetadata (readonly)

Metadata associated with the CSV

Returns:



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# File 'vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb', line 16

def 
  @metadata
end

Class Method Details

.optionsObject

Writer options



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# File 'vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb', line 26

def self.options
  super + [
    RDF::CLI::Option.new(
      symbol: :metadata,
      datatype: RDF::URI,
      control: :url2,
      on: ["--metadata URI"],
      description: "user supplied metadata, merged on top of extracted metadata. If provided as a URL, Metadata is loade from that location.") {|arg| RDF::URI(arg)},
    RDF::CLI::Option.new(
      symbol: :minimal,
      control: :checkbox,
      datatype: TrueClass,
      on: ["--minimal"],
      description: "Includes only the information gleaned from the cells of the tabular data.") {true},
    RDF::CLI::Option.new(
      symbol: :noProv,
      datatype: TrueClass,
      control: :checkbox,
      on: ["--no-prov"],
      description: "do not output optional provenance information.") {true},
  ]
end

Instance Method Details

#minimal?Boolean

Returns:

  • (Boolean)


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# File 'vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb', line 629

def minimal?; @options[:minimal]; end

#prov?Boolean

Returns:

  • (Boolean)


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# File 'vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb', line 630

def prov?; !(@options[:noProv]); end

#to_hash(options = {}) ⇒ Hash, Array

Return a hash representation of the data for JSON serialization

Produces an array if run in minimal mode.

Parameters:

Returns:



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# File 'vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb', line 446

def to_hash(options = {})
  # Construct metadata from that passed from file open, along with information from the file.
  if input.is_a?(Metadata)
    log_debug("each_statement: metadata") {input.inspect}
    log_depth do
      # Get Metadata to invoke and open referenced files
      begin
        # Validate metadata
        input.validate!

        tables = []
        table_group = {}
        table_group['@id'] = input.id.to_s if input.id

        # Common Properties
        input.each do |key, value|
          next unless key.to_s.include?(':') || key == :notes
          table_group[key] = input.common_properties(nil, key, value)
          table_group[key] = [table_group[key]] if key == :notes && !table_group[key].is_a?(Array)
        end

        table_group['tables'] = tables

        if options[:original_input] && !input.describes_file?(options[:base_uri])
          Reader.new(options[:original_input], options.merge(
              metadata:           input.tables.first,
              base:               input.tables.first.url,
              minimal:            minimal?,
              no_found_metadata:  true,
          )) do |r|
            case t = r.to_hash(options)
            when Array then tables += t unless input.tables.first.suppressOutput
            when Hash  then tables << t unless input.tables.first.suppressOutput
            end
          end
        else
          input.each_table do |table|
            next if table.suppressOutput && !validate?
            Reader.open(table.url, options.merge(
              metadata:           table,
              base:               table.url,
              minimal:            minimal?,
              no_found_metadata:  true,
            )) do |r|
              case t = r.to_hash(options)
              when Array then tables += t unless table.suppressOutput
              when Hash  then tables << t unless table.suppressOutput
              end
            end
          end
        end

        # Lastly, if validating, validate foreign key integrity
        validate_foreign_keys(input) if validate?

        # Result is table_group or array
        minimal? ? tables : table_group
      end
    end
  else
    rows = []
    table = {}
    table['@id'] = .id.to_s if .id
    table['url'] = .url.to_s

    table.merge!("row" => rows)

    # Input is file containing CSV data.
    # Output ROW-Level statements
    primary_keys = []
    .each_row(input) do |row|
      if row.is_a?(RDF::Statement)
        # May add additional comments
        table['rdfs:comment'] ||= []
        table['rdfs:comment'] << row.object.to_s
        next
      end

      # Collect primary and foreign keys if validating
      if validate?
        primary_keys << row.primaryKey
        collect_foreign_key_references(, options[:fks_referencing_table], row)
      end

      # Output row-level metadata
      r, a, values = {}, {}, {}
      r["url"] = row.id.to_s
      r["rownum"] = row.number

      # Row titles
      Array(row.titles).each { |t| merge_compacted_value(r, "titles", t.to_s) unless t.nil?}

      row.values.each_with_index do |cell, index|
        column = .tableSchema.columns[index]

        # Collect cell errors
        unless Array(cell.errors).empty?
          self.send(validate? ? :log_error : :log_warn,
            "Table #{.url} row #{row.number}(src #{row.sourceNumber}, col #{cell.column.sourceNumber}): ") do
            cell.errors.join("\n")
          end
        end

        # Ignore suppressed columns
        next if column.suppressOutput

        # Skip valueUrl cells where the valueUrl is null
        next if cell.column.valueUrl && cell.valueUrl.nil?

        # Skip empty sequences
        next if !cell.column.valueUrl && cell.value.is_a?(Array) && cell.value.empty?

        subject = cell.aboutUrl || 'null'
        co = (a[subject.to_s] ||= {})
        co['@id'] = subject.to_s unless subject == 'null'
        prop = case cell.propertyUrl
        when RDF.type then '@type'
        when nil then URI.decode(column.name) # Use URI-decoded name
        else
          # Compact the property to a term or prefixed name
          .context.compact_iri(cell.propertyUrl, vocab: true)
        end

        value = case
        when prop == '@type'
          .context.compact_iri(cell.valueUrl || cell.value, vocab: true)
        when cell.valueUrl
          unless subject == cell.valueUrl
            values[cell.valueUrl.to_s] ||= {o: co, prop: prop, count: 0}
            values[cell.valueUrl.to_s][:count] += 1
          end
          cell.valueUrl.to_s
        when cell.value.is_a?(RDF::Literal::Double)
          cell.value.object.nan? || cell.value.object.infinite? ? cell.value : cell.value.object
        when cell.value.is_a?(RDF::Literal::Integer)
          cell.value.object.to_i
        when cell.value.is_a?(RDF::Literal::Numeric)
          cell.value.object.to_f
        when cell.value.is_a?(RDF::Literal::Boolean)
          cell.value.object
        when cell.value
          cell.value
        end

        # Add or merge value
        merge_compacted_value(co, prop, value) unless value.nil?
      end

      # Check for nesting
      values.keys.each do |valueUrl|
        next unless a.has_key?(valueUrl)
        ref = values[valueUrl]
        co = ref[:o]
        prop = ref[:prop]
        next if ref[:count] != 1
        raise "Expected #{ref[o][prop].inspect} to include #{valueUrl.inspect}" unless Array(co[prop]).include?(valueUrl)
        co[prop] = Array(co[prop]).map {|e| e == valueUrl ? a.delete(valueUrl) : e}
        co[prop] = co[prop].first if co[prop].length == 1
      end

      r["describes"] = a.values

      if minimal?
        rows.concat(r["describes"])
      else
        rows << r
      end
    end

    # Validate primary keys
    validate_primary_keys(, primary_keys) if validate?

    # Use string values notes and common properties
    .each do |key, value|
      next unless key.to_s.include?(':') || key == :notes
      table[key] = .common_properties(nil, key, value)
      table[key] = [table[key]] if key == :notes && !table[key].is_a?(Array)
    end unless minimal?

    minimal? ? table["row"] : table
  end
end

#to_json(options = @options) ⇒ String

Transform to JSON. Note that this must be run from within the reader context if the input is an open IO stream.

Examples:

outputing annotated CSV as JSON

result = nil
RDF::Tabular::Reader.open("etc/doap.csv") do |reader|
  result = reader.to_json
end
result #=> {...}

outputing annotated CSV as JSON from an in-memory structure

csv = %(
  GID,On Street,Species,Trim Cycle,Inventory Date
  1,ADDISON AV,Celtis australis,Large Tree Routine Prune,10/18/2010
  2,EMERSON ST,Liquidambar styraciflua,Large Tree Routine Prune,6/2/2010
  3,EMERSON ST,Liquidambar styraciflua,Large Tree Routine Prune,6/2/2010
).gsub(/^\s+/, '')
r = RDF::Tabular::Reader.new(csv)
r.to_json #=> {...}

Parameters:

  • options (Hash{Symbol => Object}) (defaults to: @options)

    may also be a JSON state

Options Hash (options):

  • io (IO, StringIO)

    to output to file

  • :state (::JSON::State)

    used when dumping

  • :atd (Boolean)

    output Abstract Table representation instead

Returns:

Raises:



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# File 'vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb', line 401

def to_json(options = @options)
  io = case options
  when IO, StringIO then options
  when Hash then options[:io]
  end
  json_state = case options
  when Hash
    case
    when options.has_key?(:state) then options[:state]
    when options.has_key?(:indent) then options
    else ::JSON::LD::JSON_STATE
    end
  when ::JSON::State, ::JSON::Ext::Generator::State, ::JSON::Pure::Generator::State
    options
  else ::JSON::LD::JSON_STATE
  end
  options = {} unless options.is_a?(Hash)

  hash_fn = :to_hash
  options = options.merge(noProv: @options[:noProv])

  res = if io
    ::JSON::dump_default_options = json_state
    ::JSON.dump(self.send(hash_fn, options), io)
  else
    hash = self.send(hash_fn, options)
    ::JSON.generate(hash, json_state)
  end

  if validate? && log_statistics[:error]
    raise RDF::Tabular::Error, "Errors found during processing"
  end

  res
rescue IOError => e
  raise RDF::Tabular::Error, e.message
end

#validate!Object

Do we have valid metadata?

Raises:



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# File 'vendor/bundler/ruby/2.4.0/bundler/gems/rdf-tabular-6243d85fc308/lib/rdf/tabular/reader.rb', line 368

def validate!
  @options[:validate] = true
  each_statement {}
rescue RDF::ReaderError => e
  raise Error, e.message
end