triannon 1.0.1 → 1.1.0

data/app/services/triannon/solr_writer.rb

@@ -4,9 +4,9 @@ module Triannon
     # DO NOT CALL before anno is stored: the graph should have an assigned url for the
     #   @id of the root;  it shouldn't be a blank node
     #
-    # Convert a Triannon::Graph object into a Hash suitable for writing to Solr.
+    # Convert a OA::Graph object into a Hash suitable for writing to Solr.
     #
-    # @param [Triannon::Graph] triannon_graph a populated Triannon::Graph object for a *stored* anno
+    # @param [OA::Graph] triannon_graph a populated OA::Graph object for a *stored* anno
     # @return [Hash] a hash to be written to Solr, populated appropriately
     def self.solr_hash(triannon_graph)
       doc_hash = {}
@@ -18,7 +18,7 @@ module Triannon
         doc_hash[:id] = solr_id.sub(/^\/*/, "") # remove first char slash(es) if present
 
         # use short strings for motivation field
-        doc_hash[:motivation] = triannon_graph.motivated_by.map { |m| m.sub(RDF::OpenAnnotation.to_s, "") }
+        doc_hash[:motivation] = triannon_graph.motivated_by.map { |m| m.sub(RDF::Vocab::OA.to_s, "") }
 
         # date field format: 1995-12-31T23:59:59Z; or w fractional seconds: 1995-12-31T23:59:59.999Z
         if triannon_graph.annotated_at
@@ -31,11 +31,11 @@ module Triannon
         end
         #doc_hash[:annotated_by_stem] # not yet implemented
 
-        doc_hash[:target_url] = triannon_graph.predicate_urls RDF::OpenAnnotation.hasTarget
+        doc_hash[:target_url] = triannon_graph.predicate_urls RDF::Vocab::OA.hasTarget
         # TODO: recognize more target types
         doc_hash[:target_type] = ['external_URI'] if doc_hash[:target_url].size > 0
 
-        doc_hash[:body_url] = triannon_graph.predicate_urls RDF::OpenAnnotation.hasBody
+        doc_hash[:body_url] = triannon_graph.predicate_urls RDF::Vocab::OA.hasBody
         doc_hash[:body_type] = []
         doc_hash[:body_type] << 'external_URI' if doc_hash[:body_url].size > 0
         doc_hash[:body_chars_exact] = triannon_graph.body_chars.map {|bc| bc.strip}
@@ -57,9 +57,9 @@ module Triannon
       @max_sleep_seconds = Triannon.config[:max_sleep_seconds] || 5
     end
 
-    # Convert the Triannon::Graph to a Solr document hash, then call RSolr.add
+    # Convert the OA::Graph to a Solr document hash, then call RSolr.add
     #  with the doc hash
-    # @param [Triannon::Graph] tgraph anno represented as a Triannon::Graph
+    # @param [OA::Graph] tgraph anno represented as a OA::Graph
     def write(tgraph)
       doc_hash = self.class.solr_hash(tgraph) if tgraph && !tgraph.id_as_url.empty?
       add(doc_hash) if doc_hash && !doc_hash.empty?
@@ -75,9 +75,9 @@ module Triannon
         @logger.debug "#{exception.inspect} on Solr add attempt #{attempt_cnt} for #{id}"
         if exception.kind_of?(RSolr::Error::Http)
           # Note there are extra shenanigans b/c RSolr hijacks the Solr error to return RSolr Error
-          raise Triannon::SearchError.new("error adding doc #{id} to Solr #{doc.inspect}; #{exception.message}", exception.response[:status], exception.response[:body])
+          fail Triannon::SearchError.new("error adding doc #{id} to Solr #{doc.inspect}; #{exception.message}", exception.response[:status], exception.response[:body])
         elsif exception.kind_of?(StandardError)
-          raise Triannon::SearchError.new("error adding doc #{id} to Solr #{doc.inspect}; #{exception.message}")
+          fail Triannon::SearchError.new("error adding doc #{id} to Solr #{doc.inspect}; #{exception.message}")
         end
       end
 
@@ -101,9 +101,9 @@ module Triannon
         @logger.debug "#{exception.inspect} on Solr delete attempt #{attempt_cnt} for #{id}"
         if exception.kind_of?(RSolr::Error::Http)
           # Note there are extra shenanigans b/c RSolr hijacks the Solr error to return RSolr Error
-          raise Triannon::SearchError.new("error deleting doc #{id} from Solr: #{exception.message}", exception.response[:status], exception.response[:body])
+          fail Triannon::SearchError.new("error deleting doc #{id} from Solr: #{exception.message}", exception.response[:status], exception.response[:body])
         elsif exception.kind_of?(StandardError)
-          raise Triannon::SearchError.new("error deleting doc #{id} from Solr: #{exception.message}")
+          fail Triannon::SearchError.new("error deleting doc #{id} from Solr: #{exception.message}")
         end
       end
 
@@ -120,4 +120,4 @@ module Triannon
     end
 
   end
-end
+end

data/config/jetty/etc/fedora-override-web.xml

@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<web-app xmlns="http://java.sun.com/xml/ns/javaee"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd"
+  version="3.0">
+
+  <display-name>Fedora 4</display-name>
+
+  <context-param>
+    <param-name>contextConfigLocation</param-name>
+    <param-value>WEB-INF/classes/spring/master.xml</param-value>
+  </context-param>
+
+  <listener>
+    <listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
+  </listener>
+
+  <servlet>
+    <servlet-name>jersey-servlet</servlet-name>
+    <servlet-class>org.glassfish.jersey.servlet.ServletContainer</servlet-class>
+
+    <init-param>
+      <param-name>javax.ws.rs.Application</param-name>
+      <param-value>org.fcrepo.http.commons.FedoraApplication</param-value>
+    </init-param>
+
+    <load-on-startup>1</load-on-startup>
+    <async-supported>true</async-supported>
+  </servlet>
+
+  <servlet-mapping>
+    <servlet-name>jersey-servlet</servlet-name>
+    <url-pattern>/rest/*</url-pattern>
+
+  </servlet-mapping>
+
+  <!-- commenting out to disable Basic-Authentication -->
+  <!--
+  <security-constraint>
+    <web-resource-collection>
+      <web-resource-name>Fedora4</web-resource-name>
+      <url-pattern>/*</url-pattern>
+      <http-method>DELETE</http-method>
+      <http-method>PUT</http-method>
+      <http-method>HEAD</http-method>
+      <http-method>OPTIONS</http-method>
+      <http-method>PATCH</http-method>
+      <http-method>GET</http-method>
+      <http-method>POST</http-method>
+    </web-resource-collection>
+    <auth-constraint>
+      <role-name>fedoraUser</role-name>
+      <role-name>fedoraAdmin</role-name>
+    </auth-constraint>
+    <user-data-constraint>
+      <transport-guarantee>NONE</transport-guarantee>
+    </user-data-constraint>
+  </security-constraint>
+  -->
+
+  <login-config>
+    <auth-method>BASIC</auth-method>
+    <realm-name>fcrepo</realm-name>
+  </login-config>
+
+</web-app>

data/config/routes.rb

@@ -7,7 +7,7 @@ Triannon::Engine.routes.draw do
     constraints: lambda { |request|
                             id = request.env["action_dispatch.request.path_parameters"][:id]
                             id !~ /^iiif$/ && id !~ /^oa$/ && id !~ /^search$/
-                        } do
+                 } do
     collection do
       get 'search', to: 'search#find'
     end
@@ -26,6 +26,6 @@ Triannon::Engine.routes.draw do
                           jsonld_context = request.env["action_dispatch.request.path_parameters"][:jsonld_context]
                           id = request.env["action_dispatch.request.path_parameters"][:id]
                           (jsonld_context =~ /^iiif$/ || jsonld_context =~ /^oa$/ ) && id !~ /^new$/
-                      }
+                 }
 
 end

data/config/triannon.yml

@@ -1,15 +1,38 @@
 development:
-  ldp_url: yer_ldp_store_url_here
-  solr_url: yer_triannon_solr_url_here
+  ldp:
+    url: http://your.ldp_store_url.here
+    # uber_container:  LDP BasicContainer that will have anno containers as members
+    uber_container:  anno
+    # anno_containers:  LDP BasicContainers that will have individual annotations as members
+    #  the container names here will also map to paths in the triannon url, e.g.
+    #  "foo" here will mean you add a foo anno by POST to http://your.triannon-server.com/annotations/foo
+    #  and you get the foo anno by GET to http://your.triannon-server.com/annotations/foo/(anno_uuid)
+    anno_containers:
+      - foo
+      - blah
+  solr_url: http://your.triannon_solr_url.here
+  # triannon_base_url:  the prefix for the urls for your annos
   triannon_base_url: http://your.triannon-server.com/annotations/
   max_solr_retries: 5
   base_sleep_seconds: 1
   max_sleep_seconds: 5
+
 test: &test
-  ldp_url: yer_ldp_url_here
-  solr_url: yer_triannon_solr_url_here
+  ldp:
+    url: http://your.ldp_store_url.here
+    uber_container:  anno
+    anno_containers:
+      - foo
+      - blah
+  solr_url: http://your.triannon_solr_url.here
   triannon_base_url: http://your.triannon-server.com/annotations/
+
 production:
-  ldp_url: yer_ldp_url_here
-  solr_url: yer_triannon_solr_url_here
+  ldp:
+    url: http://your.ldp_store_url.here
+    uber_container:  anno
+    anno_containers:
+      - foo
+      - blah
+  solr_url: http://your.triannon_solr_url.here
   triannon_base_url: http://your.triannon-server.com/annotations/

data/lib/generators/triannon/install_generator.rb

@@ -11,18 +11,38 @@ module Triannon
     def create_triannon_yml_file
       default_yml =<<-YML
 development:
-  ldp_url: http://localhost:8983/fedora/rest/anno
+  ldp:
+    url: http://localhost:8983/fedora/rest
+    # uber_container:  LDP BasicContainer that will have anno containers as members
+    uber_container:  anno
+    # anno_containers:  LDP BasicContainers that will have individual annotations as members
+    #  the container names here will also map to paths in the triannon url, e.g.
+    #  "foo" here will mean you add a foo anno by POST to http://your.triannon-server.com/annotations/foo
+    #  and you get the foo anno by GET to http://your.triannon-server.com/annotations/foo/(anno_uuid)
+    anno_containers:
+      - foo
+      - blah
   solr_url: http://localhost:8983/solr/triannon
   triannon_base_url: http://your.triannon-server.com/annotations/
   max_solr_retries: 5
   base_sleep_seconds: 1
   max_sleep_seconds: 5
 test: &test
-  ldp_url: http://localhost:8983/fedora/rest/anno
+  ldp:
+    url: http://localhost:8983/fedora/rest
+    uber_container:  anno
+    anno_containers:
+      - foo
+      - blah
   solr_url: http://localhost:8983/solr/triannon
   triannon_base_url: http://your.triannon-server.com/annotations/
 production:
-  ldp_url:
+  ldp:
+    url:
+    uber_container:  anno
+    anno_containers:
+      - foo
+      - blah
   solr_url:
   triannon_base_url:
       YML

data/lib/rdf/triannon_vocab.rb

@@ -1,6 +1,6 @@
 require 'rdf'
 module RDF
-  # contains RDF predefined terms and properties for Triannon 
+  # contains RDF predefined terms and properties for Triannon
   class Triannon < RDF::StrictVocabulary("http://triannon.stanford.edu/ns/")
 
     # Property definitions
@@ -11,4 +11,4 @@ module RDF
       range: "xsd:anyURI".freeze,  # rdf:URI?  rdfs:Resource?
       type: "rdf:Property".freeze
   end
-end
+end

data/lib/tasks/triannon_tasks.rake

@@ -1,11 +1,25 @@
-require_relative '../../app/services/triannon/root_annotation_creator'
+require_relative '../../app/services/triannon/ldp_writer'
 
 namespace :triannon do
-  desc "Create the root annotation container"
-  task :create_root_container do
-    unless File.exists? Triannon.triannon_file
+  desc "set up jetty for triannon"
+  task :jetty_setup => [:solr_jetty_setup, :disable_fedora_auth_in_jetty]
+
+  desc "set up triannon Solr in jetty"
+  task :solr_jetty_setup do
+    `cp -r config/solr/triannon-core jetty/solr`
+    `cp config/solr/solr.xml jetty/solr`
+  end
+
+  desc "disable fedora basic authorization in jetty"
+  task :disable_fedora_auth_in_jetty do
+    `cp config/jetty/etc/* jetty/etc`
+  end
+
+  desc 'Create the uber root annotation container'
+  task :create_uber_root_container do
+    unless File.exist? Triannon.triannon_file
       puts "Triannon config file missing: #{Triannon.triannon_file}"
     end
-    Triannon::RootAnnotationCreator.create
+    Triannon::LdpWriter.create_basic_container(nil, Triannon.config[:ldp]['uber_container'])
   end
 end

data/lib/triannon.rb

@@ -1,8 +1,6 @@
 require 'linkeddata'
-require 'rdf/open_annotation'
+require 'oa/graph'
 require 'rdf/iiif'
-require 'rdf/ldp'
-require 'rdf/fcrepo4'
 require 'rdf/triannon_vocab'
 require 'bootstrap-sass'
 require 'faraday' # for writing to LDP store
@@ -10,23 +8,22 @@ require 'rsolr'
 require 'retries' # for writing to Solr
 
 module Triannon
-  require "triannon/engine"
-  require "triannon/error"
-  require "triannon/graph"
-  require "triannon/iiif_anno_list"
-  require "triannon/jsonld_context"
+  require 'triannon/engine'
+  require 'triannon/error'
+  require 'triannon/iiif_anno_list'
+  require 'triannon/oa_graph_helper.rb'
 
   class << self
     attr_accessor :config
   end
 
   def self.triannon_file
-    "#{::Rails.root.to_s}/config/triannon.yml"
+    "#{::Rails.root}/config/triannon.yml"
   end
 
   def self.config
     @triannon_config ||= begin
-        raise "The #{::Rails.env} environment settings were not found in the triannon.yml config" unless config_yml[::Rails.env]
+        fail "The #{::Rails.env} environment settings were not found in the triannon.yml config" unless config_yml[::Rails.env]
         config_yml[::Rails.env].symbolize_keys
       end
   end
@@ -36,23 +33,19 @@ module Triannon
     require 'yaml'
 
     return @triannon_yml if @triannon_yml
-    unless File.exists?(triannon_file)
-      raise "You are missing the triannon configuration file: #{triannon_file}."
-    end
+    fail "You are missing the triannon configuration file: #{triannon_file}." unless File.exist?(triannon_file)
 
     begin
-      @triannon_yml = YAML::load_file(triannon_file)
-    rescue => e
-      raise("triannon.yml was found, but could not be parsed.\n")
+      @triannon_yml = YAML.load_file(triannon_file)
+    rescue
+      raise 'triannon.yml was found, but could not be parsed.'
     end
 
     if @triannon_yml.nil? || !@triannon_yml.is_a?(Hash)
-      raise("triannon.yml was found, but was blank or malformed.\n")
+      fail 'triannon.yml was found, but was blank or malformed.'
     end
 
-    return @triannon_yml
+    @triannon_yml
   end
 
-
-
 end

data/lib/triannon/iiif_anno_list.rb

@@ -27,14 +27,14 @@ module Triannon
 
 # Class Methods ----------------------------------------------------------------
 
-    # take an Array of annos as Triannon::Graph objects and return a Hash representation
+    # take an Array of annos as OA::Graph objects and return a Hash representation
     #    of IIIF Annotation List
-    # @param [Array<Triannon::Graph>] tgraph_array annotations as Triannon::Graph objects
+    # @param [Array<OA::Graph>] tgraph_array annotations as OA::Graph objects
     # @return [Hash] IIIF Annotation List as a Hash, containing the annotations in the array
     def self.anno_list(tgraph_array)
       if tgraph_array
         result = {
-          "@context" => Triannon::JsonldContext::IIIF_CONTEXT_URL,
+          "@context" => OA::Graph::IIIF_CONTEXT_URL,
           "@type" => "sc:AnnotationList",
           "within" => {"@type" => "sc:Layer", "total" => tgraph_array.size },
           "resources" => tgraph_array.map { |g|
@@ -56,4 +56,4 @@ module Triannon
     end
 
   end
-end
+end

data/lib/triannon/oa_graph_helper.rb

@@ -0,0 +1,51 @@
+require 'oa/graph'
+
+# mixin methods
+module OA
+  class Graph
+
+    # returns graph without any LDP-specific triples
+    def self.remove_ldp_triples graph
+      if graph && graph.is_a?(RDF::Graph) && graph.count > 0
+        no_ldp_graph = RDF::Graph.new
+        ldp_props = RDF::Vocab::LDP.properties.map {|p| p.to_s}
+        graph.each { |stmt|
+          no_ldp_graph << stmt unless ldp_props.include?(stmt.predicate.to_s) ||
+                                      ldp_props.include?(stmt.object.to_s) ||
+                                      ldp_props.include?(stmt.subject.to_s)
+        }
+        no_ldp_graph
+      else
+        graph
+      end
+    end
+
+    # returns graph without any fedora-specific triples
+    #  note that the Fedora vocab is not complete and also doesn't include modeshape
+    def self.remove_fedora_triples graph
+      if graph && graph.is_a?(RDF::Graph) && graph.count > 0
+        no_fedora_graph = RDF::Graph.new
+        fedora_props = RDF::Vocab::Fcrepo4.properties.map {|p| p.to_s}
+        fedora_ns = "http://fedora.info/definitions"
+        modeshape_ns = "http://www.jcp.org/jcr"
+         # describable predates Fedora 4.1.1, but just in case ...
+        fedora_describable = "http://purl.org/dc/elements/1.1/describable"
+        graph.each { |stmt|
+          no_fedora_graph << stmt unless fedora_props.include?(stmt.predicate.to_s) ||
+                                      fedora_props.include?(stmt.object.to_s) ||
+                                      fedora_props.include?(stmt.subject.to_s) ||
+                                      stmt.predicate.to_s.match(fedora_ns) ||
+                                      stmt.predicate.to_s.match(modeshape_ns) ||
+                                      stmt.subject.to_s.match(fedora_ns) ||
+                                      stmt.object.to_s.match(fedora_ns) ||
+                                      stmt.object.to_s.match(modeshape_ns) ||
+                                      stmt.object.to_s == (fedora_describable)
+        }
+        no_fedora_graph
+      else
+        graph
+      end
+    end
+
+  end
+end

data/lib/triannon/version.rb

@@ -1,3 +1,3 @@
 module Triannon
-  VERSION = "1.0.1"
+  VERSION = "1.1.0"
 end

metadata

@@ -1,16 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: triannon
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.1.0
 platform: ruby
 authors:
-- Chris Beer
 - Naomi Dushay
 - Willy Mene
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-21 00:00:00.000000000 Z
+date: 2015-05-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -41,7 +40,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: rdf-open_annotation
+  name: oa-graph
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -68,34 +67,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: rdf-ldp
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rdf-fcrepo4
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
 - !ruby/object:Gem::Dependency
   name: bootstrap-sass
   requirement: !ruby/object:Gem::Requirement
@@ -278,6 +249,34 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rubocop-rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
@@ -322,9 +321,7 @@ dependencies:
         version: '0'
 description: 
 email:
-- cabeer@stanford.edu
-- ndushay@stanford.edu
-- wmene@stanford.edu
+- triannon-commits@lists.stanford.edu
 executables: []
 extensions: []
 extra_rdoc_files: []
@@ -345,7 +342,6 @@ files:
 - app/services/triannon/ldp_loader.rb
 - app/services/triannon/ldp_to_oa_mapper.rb
 - app/services/triannon/ldp_writer.rb
-- app/services/triannon/root_annotation_creator.rb
 - app/services/triannon/solr_searcher.rb
 - app/services/triannon/solr_writer.rb
 - app/views/layouts/triannon/application.html.erb
@@ -355,6 +351,7 @@ files:
 - app/views/triannon/annotations/show.html.erb
 - app/views/triannon/search/find.html.erb
 - config/initializers/mime_types.rb
+- config/jetty/etc/fedora-override-web.xml
 - config/routes.rb
 - config/solr/solr.xml
 - config/solr/triannon-core/conf/schema.xml
@@ -367,11 +364,10 @@ files:
 - lib/triannon.rb
 - lib/triannon/engine.rb
 - lib/triannon/error.rb
-- lib/triannon/graph.rb
 - lib/triannon/iiif_anno_list.rb
-- lib/triannon/jsonld_context.rb
+- lib/triannon/oa_graph_helper.rb
 - lib/triannon/version.rb
-homepage: 
+homepage: https://github.com/sul-dlss/triannon
 licenses:
 - Apache-2.0
 metadata: {}