annotations2triannon 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: f33ee86839aa0422e2b9d4f65c3e7d4eb8d43abd
+  data.tar.gz: 3734d6618c18d16162ef9d547f477181cd8093cd
+SHA512:
+  metadata.gz: 6fdaa5ff288ba974553e1888cd0d9ae1217aa47f0b2e53880977d9c1155b85f1fb1ad90caeed670ec10168acec7fe2db31b39653969632465992b593d86504ea
+  data.tar.gz: 7efdb3d2eae0d633a61a1238de7a996edb66251fccc6ecbe446ad24dd422f2875d87c038fd09fa71e1fe9f90116d037550b3421a577907b4962be2de4246f035

data/.env_example

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+# https://github.com/bkeepers/dotenv is used for
+# default configuration options.  The values in
+# this file do not replace existing values in
+# the shell ENV.
+
+# Uncomment and set values as required.  See used settings in
+# lib/marc2linkeddata/configuration.rb
+
+export DEBUG=false
+
+# limit the depth of IIIF navigation; useful for development
+# or testing a new data source.
+export ANNO_LIMIT_MANIFESTS=0   # 0 is all of them
+export ANNO_LIMIT_ANNOLISTS=0   # 0 is all of them
+export ANNO_LIMIT_OPENANNOS=0   # 0 is all of them
+
+export ANNO_LOG_FILE='log/annotations2triannon.log'
+
+# RestClient/Rack-Cache configs, see
+# http://rtomayko.github.io/rack-cache/configuration
+# http://rtomayko.github.io/rack-cache/storage
+export RACK_CACHE_ENABLED=true
+export RACK_CACHE_VERBOSE=false
+export RACK_CACHE_METASTORE='memcached://localhost:11211/anno_meta'
+#export RACK_CACHE_METASTORE='file:/tmp/cache/anno_meta'
+export RACK_CACHE_ENTITYSTORE='file:/tmp/cache/anno_body'
+
+# Configure the triannon service
+export TRIANNON_LOG_FILE='log/triannon_client.log'
+export TRIANNON_HOST='triannon.example.org'
+export TRIANNON_USER=''
+export TRIANNON_PASS=''
+
+# Configure the revs database for annotations and users
+export REVS_ENABLED=false
+export REVS_SRC_USER='libuser'
+export REVS_SRC_HOST='revs.example.org'
+export REVS_DB_HOST='localhost'
+export REVS_DB_PORT='3306'
+export REVS_DB_USER='revs'
+export REVS_DB_PASSWORD=''
+export REVS_DB_DATABASE='revs'
+
+

data/.travis.yml

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+language: ruby
+
+install: ./bin/setup.sh
+
+script: ./bin/test.sh
+
+notifications:
+  email: false
+
+rvm:
+  - 1.9.3
+  - 2.0.0
+  - 2.1.5
+  - 2.2.0
+

data/Gemfile

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+source "https://rubygems.org"
+
+# Dependencies are defined in *.gemspec
+gemspec
+

data/LICENSE

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data/README.md

@@ -0,0 +1,31 @@
+# Utilities for Bulk Loading Open Annotations into Triannon and Fedora4
+
+[![Build Status](https://travis-ci.org/sul-dlss/annotations2triannon.svg?branch=master)](https://travis-ci.org/sul-dlss/annotations2triannon)
+
+## A work in progress
+
+- rapidly evolving code (as of early 2015)
+- no gems published yet
+- no stable API
+
+## Open Annotation Resources
+
+- http://www.openannotation.org/spec/core/
+- http://austese.net/lorestore/validate.html
+
+## Triannon Resources
+
+- https://github.com/sul-dlss/triannon-service
+    - README has useful info
+
+- Triannon gem
+    - https://github.com/sul-dlss/triannon
+    - has annotation specific graph manipulations:
+        - https://github.com/sul-dlss/triannon/blob/master/lib/triannon/graph.rb
+    - also RDF vocabs, four small gems for easy ruby RDF vocabulary access:
+        - https://github.com/sul-dlss?query=rdf
+    - also has specs that show posting annos and looking at http return codes, etc
+        - https://github.com/sul-dlss/triannon/blob/master/spec/integration
+    - http status codes:
+        - https://github.com/sul-dlss/triannon/search?utf8=%E2%9C%93&q=status
+

data/Rakefile

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+require 'bundler/gem_tasks'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec)
+
+require 'rdf'
+require 'linkeddata'
+require 'rdf/cli/vocab-loader'
+
+desc 'Default: run specs.'
+task :default => :spec
+task :specs => :spec
+
+# Derived from https://raw.githubusercontent.com/ruby-rdf/rdf/develop/Rakefile
+desc "Generate Vocabularies"
+vocab_sources = {
+  #oa:  {
+  #  uri: 'http://www.w3.org/ns/oa#',
+  #  source: 'http://www.openannotation.org/spec/core/20130208/oa.owl',
+  #  strict: true
+  #},
+  Content: {
+    uri: 'http://www.w3.org/2011/content#',
+    source: 'http://www.w3.org/2011/content',
+    strict: true
+  },
+}
+
+task :gen_vocabs => vocab_sources.keys.map {|v| "lib/rdf/vocab/#{v}.rb"}
+
+vocab_sources.each do |id, v|
+  file "lib/rdf/vocab/#{id}.rb" => :do_build do
+    puts "Generate lib/rdf/vocab/#{id}.rb"
+    begin
+      out = StringIO.new
+      loader = RDF::VocabularyLoader.new(id.to_s.upcase)
+      loader.uri = v[:uri]
+      loader.source = v[:source] if v[:source]
+      loader.extra = v[:extra] if v[:extra]
+      loader.strict = v.fetch(:strict, true)
+      loader.output = out
+      loader.run
+      out.rewind
+      File.open("lib/rdf/vocab/#{id}.rb", "w") {|f| f.write out.read}
+    rescue
+      puts "Failed to load #{id}: #{$!.message}"
+    end
+  end
+end
+
+task :do_build

data/annotations2triannon.gemspec

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+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name        = 'annotations2triannon'
+  s.version     = '0.1.0'
+  s.licenses    = ['Apache-2.0']
+  s.platform    = Gem::Platform::RUBY
+
+  s.authors     = ['Darren Weber',]
+  s.email       = ['darren.weber@stanford.edu']
+
+  s.homepage    = 'https://github.com/sul-dlss/triannon'
+  s.summary     = 'bulk load annotations into triannon'
+  s.description = 'Utilities for bulk loading annotations into triannon'
+
+  s.required_rubygems_version = '>= 1.3.6'
+
+  s.extra_rdoc_files = ['README.md', 'LICENSE']
+
+  # general utils
+  s.add_dependency 'json'
+  s.add_dependency 'uuid'
+  # Use ENV for config
+  s.add_dependency 'dotenv'
+  # RDF linked data
+  s.add_dependency 'addressable', '~> 2.3'
+  s.add_dependency 'linkeddata', '~> 1.0'
+  s.add_dependency 'rdf-iiif'
+  s.add_dependency 'rdf-vocab', '~> 0.5'
+  # HTTP client and rack cache components
+  s.add_dependency 'triannon-client'
+  s.add_dependency 'rest-client', '~> 1.7.0'
+  s.add_dependency 'rest-client-components', '~> 1.3.0'
+  s.add_dependency 'rack-cache', '~> 1.2'
+  # dalli is a memcached ruby client
+  s.add_dependency 'dalli', '~> 2.7.2'
+  # Use pry for console and debug config
+  s.add_dependency 'pry'
+  s.add_dependency 'pry-doc'
+  # database gems
+  s.add_dependency 'mysql2'
+  s.add_dependency 'sequel'
+
+  s.add_development_dependency 'coveralls'
+  s.add_development_dependency 'guard'
+  s.add_development_dependency 'guard-ctags-bundler'
+  s.add_development_dependency 'rake'
+  s.add_development_dependency 'rspec'
+
+  s.files   = `git ls-files`.split($/)
+  dev_files = %w(.gitignore bin/setup.sh bin/test.sh)
+  dev_files.each {|f| s.files.delete f }
+
+  s.executables = s.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  s.test_files  = s.files.grep(%r{^(test|spec|features)/})
+
+end
+

data/bin/console

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+#!/usr/bin/env ruby
+require 'annotations2triannon'
+CONFIG = Annotations2triannon.configuration
+binding.pry
+

data/bin/ctags.rb

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+#!/usr/bin/env ruby
+system "find . -name '*.rb' | ctags -f .tags --languages=Ruby -L -"
+
+if File.exist? './Gemfile'
+  require 'bundler'
+  paths = Bundler.load.specs.map(&:full_gem_path).join(' ')
+  system "ctags -R -f .gemtags --languages=Ruby #{paths}"
+end

data/bin/dms.rb

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+#!/usr/bin/env ruby
+require 'annotations2triannon'
+CONFIG = Annotations2triannon.configuration
+
+
+# https://jirasul.stanford.edu/jira/browse/DT-5
+# Annotation lists:
+# 1) http://dms-data.stanford.edu/data/manifests/BnF/jr903ng8662/list/
+# 2) http://dms-data.stanford.edu/data/manifests/Stanford/kq131cs7229/list/
+
+# 3) http://dms-data.stanford.edu/data/data/yale/yale_cs_annotations_for_stanford.json
+
+# Stanford manifests associated with 1) and 2)
+# 1) http://dms-data.stanford.edu/data/manifests/BnF/jr903ng8662/manifest.json
+# 2) http://dms-data.stanford.edu/data/manifests/Stanford/kq131cs7229/manifest.json
+
+# Additional PURL manifest
+# http://purl.stanford.edu/jr903ng8662/iiif/manifest.json
+
+# Mirador viewer
+# http://sul-reader-test.stanford.edu/m2/#6c45932d-2276-4699-9203-a9133181c2a1
+
+
+
+IIIF_COLLECTION='http://dms-data.stanford.edu/data/manifests/collections/collection.json'
+puts "\nCollection:\n#{IIIF_COLLECTION}"
+
+iiif_navigator = Annotations2triannon::IIIFNavigator.new(IIIF_COLLECTION);
+
+puts "\nManifests:"
+manifests = iiif_navigator.manifests;
+manifests.each {|m| puts m.iri}
+
+puts "\nAnnotation List counts:"
+annotation_lists = iiif_navigator.annotation_lists;
+annotation_lists.each_pair {|m,alist| puts "#{m} => #{alist.length}"}
+
+puts "\nOpen Annotation counts:"
+open_annotations = iiif_navigator.open_annotations;
+open_annotations.each_pair do |m,alists|
+  puts "\n#{m}"
+  alists.each_pair do |alist, oa_arr|
+    puts "\t#{alist}\t=> #{oa_arr.length}"
+  end
+end
+
+# Find all annotations where the body is text
+text_annotations = {}
+manifest_keys = open_annotations.keys
+manifest_keys.each do |mk|
+  text_annotations[mk] = {}
+  anno_list_keys = open_annotations[mk].keys
+  anno_list_keys.each do |ak|
+    anno_list = open_annotations[mk][ak]
+    anno_text_list = anno_list.select {|oa| oa if oa.body_contentAsText? }
+    text_annotations[mk][ak] = anno_text_list
+  end
+end
+
+# text_anno_list = text_annotations.values.first.values.first
+# oa = text_anno_list.sample(1).first
+# puts oa.body_contentChars
+# puts oa.to_jsonld_iiif
+# puts oa.to_jsonld_oa
+# binding.pry
+
+
+# -----------------------------------------------------------------------
+# POST annotations to triannon and track the triannon URIs
+
+tc = TriannonClient::TriannonClient.new
+
+# cleanup any prior annotations in triannon
+puts "\nText Annotation cleanup:"
+anno_tracking_file = File.join(CONFIG.log_path, 'dms_annotation_tracking.json')
+if File.exists? anno_tracking_file
+  if File.size(anno_tracking_file).to_i > 0
+    anno_tracking = JSON.parse( File.read(anno_tracking_file) )
+    anno_tracking.each_pair do |manifest_uri,anno_lists|
+      puts "\n#{manifest_uri}"
+      anno_lists.each_pair do |anno_list_uri, anno_list|
+        puts "Removing:\t#{anno_list_uri}\t=> #{anno_list.length}"
+        anno_list.each do |anno_data|
+          success = tc.delete_annotation(anno_data['uri'])
+          CONFIG.logger.error("FAILURE to delete #{anno_data['uri']}") unless success
+        end
+      end
+    end
+  else
+    puts "Nothing to delete."
+  end
+else
+  puts "Nothing to delete."
+end
+
+
+puts "\nText Annotation posts:"
+anno_tracking = {}
+text_annotations.each_pair do |m,anno_lists|
+  puts "\n#{m}"
+  anno_tracking[m] = {}
+  anno_lists.each_pair do |anno_list_uri, anno_list|
+    puts "Posting:\t#{anno_list_uri}\t=> #{anno_list.length}"
+    anno_tracking[m][anno_list_uri] = []
+    anno_list.each do |oa|
+      response = tc.post_annotation(oa.to_jsonld_oa)
+      # parse the response into an RDF::Graph
+      g = RDF::Graph.new
+      RDF::Reader.for(:rdfxml).new(response) do |reader|
+        reader.each_statement {|s| g << s }
+      end
+      # query the graph to extract the annotation URI
+      q = [:s, RDF.type, RDF::Vocab::OA.Annotation]
+      uris = g.query(q).collect {|s| s.subject }
+      if uris.length != 1
+        #TODO issue an error
+      else
+        anno_data = {
+          uri: uris.first,
+          chars: oa.body_contentChars.first
+        }
+        anno_tracking[m][anno_list_uri].push(anno_data)
+      end
+    end
+  end
+end
+
+# persist the anno_tracking data
+File.open(anno_tracking_file,'w') do |f|
+  f.write(JSON.pretty_generate(anno_tracking))
+end
+puts "Annotation records saved to: #{anno_tracking_file}"
+
+
+# For conversion of IIIF to OA context, see
+# https://github.com/sul-dlss/triannon/blob/master/lib/triannon/graph.rb#L36-50
+# https://jirasul.stanford.edu/jira/browse/DT-6
+
+
+# These notes below are left here to document code that filters manifests and
+# based on the RDF type of the manifest (vs. the RDF type for the manifest in
+# the parent collection, which can differ from the manifest itself).
+
+# # Explore the collection to resolve IIIF and Shared Canvas (SC) manifests.
+# iiif_manifests = []
+# sc_manifests = []
+
+# # Examine IIIF manifests in the collection
+# iiif_manifests.push(* iiif_navigator.iiif_manifests)
+# # A IIIF collection might contain a IIIF manifest that itself
+# # could be typed as an SC manifest.
+# tmp = iiif_manifests.select {|m| m if m.sc_manifest? }
+# tmp.each do |m|
+#   sc_manifests << Annotations2triannon::SharedCanvasManifest.new(m.iri.to_s)
+# end
+# iiif_manifests = iiif_manifests.select {|m| m if m.iiif_manifest? }
+
+# # Examine SC manifests in the collection
+# sc_manifests.push(* iiif_navigator.sc_manifests)
+# # A IIIF collection might contain an SC manifest that itself
+# # could be typed as a IIIF manifest.
+# iiif_manifests.push(* sc_manifests.select {|m| m if m.iiif_manifest? } )
+# tmp = sc_manifests.select {|m| m if m.iiif_manifest? }
+# tmp.each do |m|
+#   iiif_manifests << Annotations2triannon::IIIFManifest.new(m.iri.to_s)
+# end
+# sc_manifests = sc_manifests.select {|m| m if m.sc_manifest? }
+
+# # The collection should be now resolved into IIIF and SC manifests.
+
+# # Looking at examples of IIIF and SC manifests:
+# sc_manifest = sc_manifests.sample(1).first rescue nil
+# # iiif_manifest = iiif_manifests.sample(1).first rescue nil
+# # There are no IIIF manifests in this data?
+

data/bin/revs.rb

@@ -0,0 +1,17 @@
+#!/usr/bin/env ruby
+
+ENV['REVS_ENABLED'] = 'true'
+
+require 'annotations2triannon'
+CONFIG = Annotations2triannon.configuration
+
+revs = Annotations2triannon::Revs.new
+
+tc = TriannonClient::TriannonClient.new
+puts "\nRevs open annotation posts:"
+revs.open_annotations.each do |oa|
+  binding.pry
+  tc.post_annotation(oa.to_jsonld_oa)
+end
+
+