ontopia-tldr 0.0.1-java

data/ChangeLog

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+# markup: rd
+
+= Revision history for ontopia-tldr
+
+== 0.0.1 [2013-07-30]
+
+* Birthday :-)

data/README

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+= ontopia-tldr - Tolog Document Retrieval with Ontopia
+
+== VERSION
+
+This documentation refers to ontopia-tldr version 0.0.1
+
+
+== DESCRIPTION
+
+Ontopia::TLDR is an attempt at bridging the gap between the worlds of formal
+knowledge representation (ontologies, topic maps, etc.) and bibliographic document
+retrieval (bibliographic databases). It allows for retrieving documents from
+bibliographic databases (currently, only Midos[http://progris.de] databases are
+supported) by means of tolog[http://ontopia.net/omnigator/docs/query/tutorial.html],
+Ontopia's[http://ontopia.net] topic map query language.
+
+=== Deployment
+
+Ontopia::TLDR comes as a Sinatra application, so all the standard deployment
+options apply (rackup, Passenger[https://www.phusionpassenger.com/], etc.).
+However, in order to allow for maximum flexibility, you need to supply your
+own <tt>config.ru</tt> file; e.g. (see Ontopia::TLDR for available options):
+
+  require 'ontopia/tldr'
+
+  Ontopia::TLDR.set(
+    dbm_file: File.expand_path('../tldr.dbm', __FILE__),
+    xtm_file: File.expand_path('../tldr.xtm', __FILE__),
+
+    document_keys: %w[YOUR DOCUMENT KEYS],
+    topic_keys:    %w[YOUR TOPIC KEYS],
+
+    title: 'YOUR TITLE'
+  )
+
+  run Ontopia::TLDR
+
+Assuming the following directory layout:
+
+  /srv/tldr
+    |
+    +-- config.ru
+    |
+    +-- tldr.dbm
+    |
+    +-- tldr.xtm
+    |
+    +-- tmp/
+
+Place your database and topic map files there and adjust their paths in the
+<tt>config.ru</tt> file. The <tt>tmp/</tt> directory is used by Passenger
+for the <tt>restart.txt</tt> file.
+
+To deploy Ontopia::TLDR with Passenger on Apache, create a symlink in the
+DocumentRoot pointing to the app's <tt>public/</tt> directory (this example
+makes use of current_gem[http://blackwinter.github.com/current_gem]; adjust
+the paths according to your environment):
+
+  /var/www
+    |
+    +-- tldr -> /usr/local/jruby/lib/ruby/gems/shared/current/ontopia-tldr/lib/ontopia/tldr/public
+
+Then put the following snippet in Apache's VirtualHost configuration:
+
+  <VirtualHost *:80>
+    ...
+
+    RackBaseURI /tldr
+    <Directory /var/www/tldr>
+      Options -MultiViews
+      PassengerAppRoot /srv/tldr  # <-- This (non-standard) line is important
+    </Directory>
+  </VirtualHost>
+
+
+== SUPPORTED PLATFORMS
+
+Ontopia::TLDR requires JRuby[http://jruby.org]. It has been tested with jruby
+1.7.4 (1.9.3p392) on OpenJDK 64-Bit Server VM 1.6.0_27-b27 [linux-amd64].
+
+
+== LINKS
+
+<b></b>
+Documentation:: http://blackwinter.github.com/ontopia-tldr
+Source code::   http://github.com/blackwinter/ontopia-tldr
+RubyGem::       http://rubygems.org/gems/ontopia-tldr
+Ontopia::       http://ontopia.net/
+Demo::          http://ixtrieve.fh-koeln.de/ghn
+
+
+== AUTHORS
+
+* Jens Wille <mailto:jens.wille@gmail.com>
+
+
+== LICENSE AND COPYRIGHT
+
+Copyright (C) 2013 Jens Wille
+
+ontopia-tldr is free software: you can redistribute it and/or modify it
+under the terms of the GNU Affero General Public License as published by
+the Free Software Foundation, either version 3 of the License, or (at your
+option) any later version.
+
+ontopia-tldr is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
+License for more details.
+
+You should have received a copy of the GNU Affero General Public License
+along with ontopia-tldr. If not, see <http://www.gnu.org/licenses/>.

data/Rakefile

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+require File.expand_path(%q{../lib/ontopia/tldr/version}, __FILE__)
+
+begin
+  require 'hen'
+
+  Hen.lay! {{
+    :gem => {
+      :name         => %q{ontopia-tldr},
+      :version      => Ontopia::TLDR::VERSION,
+      :summary      => %q{Tolog Document Retrieval with Ontopia.},
+      :author       => %q{Jens Wille},
+      :email        => %q{jens.wille@gmail.com},
+      :license      => %q{AGPL},
+      :homepage     => :blackwinter,
+      :platform     => 'java',
+      :dependencies => %w[json ontopia-topicmaps ruby-nuggets sinatra],
+      :extra_files  => FileList['*.sample', 'lib/ontopia/tldr/{public,views}/*'].to_a
+    }
+  }}
+rescue LoadError => err
+  warn "Please install the `hen' gem. (#{err})"
+end

data/config.ru.sample

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+require 'ontopia/tldr'
+
+Ontopia::TLDR.set(
+  #xtm_file: '...',
+  #dbm_file: '...',
+
+  #document_keys: %w[...],
+  #topic_keys:    %w[...],
+
+  #title: '...'
+)
+
+run Ontopia::TLDR

data/lib/ontopia-tldr.rb

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+require 'ontopia/tldr'

data/lib/ontopia/tldr.rb

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+# encoding: utf-8
+
+#--
+###############################################################################
+#                                                                             #
+# ontopia-tldr -- Tolog Document Retrieval with Ontopia.                      #
+#                                                                             #
+# Copyright (C) 2013 Jens Wille                                               #
+#                                                                             #
+# ontopia-tldr is free software: you can redistribute it and/or modify it     #
+# under the terms of the GNU Affero General Public License as published by    #
+# the Free Software Foundation, either version 3 of the License, or (at your  #
+# option) any later version.                                                  #
+#                                                                             #
+# ontopia-tldr is distributed in the hope that it will be useful, but WITHOUT #
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or       #
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License #
+# for more details.                                                           #
+#                                                                             #
+# You should have received a copy of the GNU Affero General Public License    #
+# along with ontopia-tldr. If not, see <http://www.gnu.org/licenses/>.        #
+#                                                                             #
+###############################################################################
+#++
+
+require 'json'
+require 'sinatra/base'
+require 'nuggets/midos'
+require 'ontopia/topicmaps'
+
+module Ontopia
+  class TLDR < Sinatra::Base
+
+    class << self
+
+      private
+
+      def jget(*a, &b)
+        jroute(:get, *a, &b)
+      end
+
+      def jpost(*a, &b)
+        jroute(:post, *a, &b)
+      end
+
+      def jroute(m, r, t, &b)
+        e = 'json'; e.prepend('.') unless r.end_with?('/')
+        send(m, "#{r}#{e}")         { instance_eval(&b); do_json }
+        send(m, r, provides: :html) { instance_eval(&b); erb(t) }
+        send(m, r, provides: :json) { instance_eval(&b); do_json }
+      end
+
+    end
+
+    set :root, __FILE__.chomp('.rb')
+
+    set :otm do
+      @__otm__ ||= Ontopia::Topicmaps::Topicmap.new(settings.xtm_file).tap {
+        Ontopia::Topicmaps.default_stringifier = :id
+      }
+    end
+
+    set :dbm do
+      @__dbm__ ||= begin
+        dbm, topic_keys = {}, settings.topic_keys
+
+        topic_index = Hash.new { |h, k| h[k] = {} }
+        dbm.define_singleton_method(:topic_index) { topic_index }
+
+        Nuggets::Midos::Parser.parse_file(settings.dbm_file, settings.dbm_opts) { |id, doc|
+          unless (topics = doc.values_at(*topic_keys).compact).empty?
+            dbm[id] = doc
+            topics.flatten.each { |topic| topic_index[topic][id] = doc }
+          end
+        }
+
+        dbm
+      end
+    end
+
+    set :topics do
+      @__topics__ ||= settings.otm.topics(:name)
+    end
+
+    set :topic_index do
+      @__topic_index__ ||= settings.dbm.topic_index
+    end
+
+    set :document_keys, %w[]
+    set :topic_keys,    %w[]
+
+    set :title, 'TLDR'
+
+    set :xtm_file, File.expand_path('../tldr.xtm', __FILE__)
+    set :dbm_file, File.expand_path('../tldr.dbm', __FILE__)
+    set :dbm_opts, { encoding: 'utf-8', vs: '|' }
+
+    set :tolog, <<-EOT
+import "http://psi.ontopia.net/tolog/string/" as s
+%s
+select %s from %s?
+    EOT
+
+    set :title_topic, 'TOPIC'
+    set :title_query, 'YOUR QUERY'
+    set :title_rules, 'CUSTOM INFERENCE RULES (optional)'
+
+    set :tolog_sample, {
+      q: <<-EOT,
+Production($_ : isProducing, $TOPIC : isProductOf),
+topic-name($TOPIC, $PRODUCTNAME),
+value($PRODUCTNAME, $PRODUCTSTRING),
+s:contains($PRODUCTSTRING, "service")
+      EOT
+      r: <<-EOT
+direct-narrower-term($A, $B) :-
+  HierarchicalRelation($A : broaderTermMember,
+                       $B : narrowerTermMember).
+
+strictly-narrower-term($A, $B) :- {
+  direct-narrower-term($A, $B) |
+  direct-narrower-term($A, $C), strictly-narrower-term($C, $B)
+}.
+
+narrower-term($A, $B) :- {
+  $A = $B | strictly-narrower-term($A, $B)
+}.
+
+narrower-term-1($A, $B) :- {
+  $A = $B | direct-narrower-term($A, $B)
+}.
+
+narrower-term-2($A, $B) :- {
+  narrower-term-1($A, $B) |
+  narrower-term-1($A, $C), narrower-term-1($C, $B)
+}.
+
+narrower-term-3($A, $B) :- {
+  narrower-term-2($A, $B) |
+  narrower-term-2($A, $C), narrower-term-1($C, $B)
+}.
+
+direct-broader-term($A, $B) :-
+  direct-narrower-term($B, $A).
+
+strictly-broader-term($A, $B) :-
+  strictly-narrower-term($B, $A).
+
+broader-term($A, $B) :-
+  narrower-term($B, $A).
+
+broader-term-1($A, $B) :-
+  narrower-term-1($B, $A).
+
+broader-term-2($A, $B) :-
+  narrower-term-2($B, $A).
+
+broader-term-3($A, $B) :-
+  narrower-term-3($B, $A).
+      EOT
+    }
+
+    tolog_maps_base = <<-EOT
+association-role($ASSOC, $ROLE),
+association-role($ASSOC, $ROLE2),
+role-player($ROLE, $TOPIC2),
+role-player($ROLE2, $TOPIC),
+type($ASSOC, $TYPE),
+$TOPIC /= $TOPIC2
+    EOT
+
+    set :tolog_maps, {
+      relations: <<-EOT,
+select $TYPE, $ROLE, $TOPIC from
+#{tolog_maps_base}, $TOPIC2 = %s?
+      EOT
+      roles: <<-EOT,
+select $ROLE, $TOPIC from
+#{tolog_maps_base}, type($ASSOC, %s)?
+      EOT
+      types: <<-EOT
+select $TYPE, $TOPIC from
+#{tolog_maps_base}, type($ROLE, %s)?
+      EOT
+    }
+
+    helpers ERB::Util
+
+    not_found do
+      @error = 'Not found!'
+      erb ''
+    end
+
+    get '/' do
+      erb :index
+    end
+
+    jpost '/', :index do
+      @query = params[:q]
+      @rules = params[:r] || ''
+      @param = params[:p] || TITLE_TOPIC
+
+      if !@query || @query.strip.empty?
+        @error = 'Query missing!'
+      elsif !@param || @param.strip.empty? || @param =~ /\W/
+        @error = 'Invalid projection!'
+      elsif (@topics = get_topics).empty?
+        @topics = nil
+      elsif (@documents = get_documents).empty?
+        @documents = nil
+      else
+        @filter = :documents
+      end
+    end
+
+    get '/xtm' do
+      do_file(settings.xtm_file, 'xml')
+    end
+
+    jget '/topics', :topics do
+      @title = "Topics (#{settings.topics.size})"
+      @topics, @filter = settings.topics.keys, :topics
+    end
+
+    jget '/topic/:i', :topic do
+      @title = topic_to_s(@topic = params[:i])
+      not_found unless settings.topics.include?(@topic)
+
+      @documents, @filter = settings.topic_index[@topic], :documents
+      @relations, @roles, @types = {}, {}, {}
+
+      get_topic_maps(:relations)
+      get_topic_maps(:roles) if @relations.empty?
+      get_topic_maps(:types) if @roles.empty?
+    end
+
+    get '/dbm' do
+      do_file(settings.dbm_file, 'txt')
+    end
+
+    jget '/documents', :documents do
+      @title = "Documents (#{settings.dbm.size})"
+      @documents, @filter = settings.dbm, :documents
+    end
+
+    jget '/document/:i', :document do
+      @title = "##{@id = params[:i].to_i}"
+      not_found unless @document = settings.dbm[@id]
+    end
+
+    private
+
+    def do_json
+      content_type :json
+
+      JSON.fast_generate({
+        d: @document || @documents,
+        e: @error,
+        i: @id,
+        l: @relations,
+        o: @roles,
+        p: @param,
+        q: @query,
+        r: @rules,
+        t: @topic || @topics,
+        y: @types
+      }.delete_if { |_, v| !v })
+    end
+
+    def do_file(file, type)
+      File.readable?(file) ? send_file(file, type: type) : not_found
+    end
+
+    def get_topics(query = @query, param = @param, rules = @rules)
+      settings.otm.query(settings.tolog % [rules, "$#{param}", query])
+    rescue => err
+      @error = err.to_s
+      []
+    end
+
+    def get_topic_maps(name, topic = @topic, hash = nil, str = nil)
+      hash ||= instance_variable_get("@#{name}")
+      str  ||= Ontopia::Topicmaps.id_stringifier
+
+      query = settings.tolog_maps[name] % topic
+      keys  = settings.otm.extract_query_projection(query)
+
+      settings.otm.query_maps(query).each { |map|
+        values = map.values_at(*keys).map!(&str)
+        topic, key = values.pop, values.pop
+
+        (values.inject(hash) { |h, k| h[k] ||= {} }[key] ||= []) << topic
+      }
+    rescue => err
+      @error = err.to_s
+    end
+
+    def get_documents(topics = @topics)
+      settings.topic_index.values_at(*topics).compact.inject(&:merge)
+    end
+
+    def render_topics(topics = @topics)
+      _ul(topics.sort, id: :topics) { |topic|
+        _li(link_to_topic(topic), ' (', settings.topic_index[topic].size, ')')
+      }
+    end
+
+    def render_documents(documents = @documents)
+      _ul(documents.sort_by { |k,| k }, id: :documents) { |id, doc|
+        _li(link_to_document(id, doc))
+      }
+    end
+
+    def render_topics_hash(hash)
+      _ul(hash.map { |k, v| [topic_to_s(k), k, v] }.sort) { |name, key, value|
+        _li(link_to_topic(key, name),
+          value.is_a?(Hash) ? render_topics_hash(value) :
+            _ul(value.sort.uniq) { |topic| _li(link_to_topic(topic)) })
+      }
+    end
+
+    def topic_to_s(topic)
+      h(settings.topics[topic] || topic.tr('_', ' '))
+    end
+
+    def doc_to_s(id, doc)
+      a, t, u, y = doc.values_at(*settings.document_keys)
+
+      a = a.join('; ') if a.is_a?(Array)
+      s = [a, t].compact.join(': ')
+
+      if s.empty?
+        s = "##{id}"
+      elsif u
+        s << " – #{u}"
+      end
+
+      s << " (#{y})" if y
+
+      h(s)
+    end
+
+    def link_to_topic(topic, text = topic_to_s(topic))
+      _a(text, href: url("/topic/#{h(topic)}"))
+    end
+
+    def link_to_document(id, doc)
+      _a(doc_to_s(id, doc), href: url("/document/#{h(id)}"))
+    end
+
+    def _a(*args)
+      _tag(:a, *args)
+    end
+
+    def _ul(list, *args)
+      _tag(:ul, *args) { |t| list.each { |*i| t << yield(*i) } }
+    end
+
+    def _li(*args)
+      _tag(:li, *args)
+    end
+
+    def _tag(name, *args)
+      a = args.pop.map { |k, v| %Q{#{h(k)}="#{h(v)}"} } if args.last.is_a?(Hash)
+
+      t = ["<#{name}#{a.unshift(nil).join(' ') if a}>"]
+
+      args.each { |s| t << s }
+      yield t if block_given?
+
+      t << "</#{name}>"
+      t.join
+    end
+
+  end
+end
+
+require_relative 'tldr/version'