active-fedora 12.0.3 → 12.1.0

data/LICENSE

@@ -1,14 +1,16 @@
-##########################################################################
-# Copyright 2011 Stanford University Libraries (SULAIR) and MediaShelf, LLC
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+Copyright 2011 Stanford University Libraries (SULAIR) and MediaShelf, LLC
+Copyright 2011 The Pennsylvania State University
+Copyright 2012 University of Notre Dame
+Additional copyright may be held by others, as reflected in the commit history.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

data/README.md

@@ -1,40 +1,54 @@
-Description
------------
+# ActiveFedora
 
-[![Build Status](https://travis-ci.org/samvera/active_fedora.png?branch=master)](https://travis-ci.org/samvera/active\_fedora)
-[![Version](https://badge.fury.io/rb/active-fedora.png)](http://badge.fury.io/rb/active-fedora)
-[![Dependencies](https://gemnasium.com/samvera/active_fedora.png)](https://gemnasium.com/samvera/active\_fedora)
-[![Coverage Status](https://img.shields.io/coveralls/samvera/active_fedora.svg)](https://coveralls.io/r/samvera/active_fedora)
+Code: [![Version](https://badge.fury.io/rb/active-fedora.png)](http://badge.fury.io/rb/active-fedora)
+[![Build Status](https://travis-ci.org/samvera/active_fedora.png?branch=master)](https://travis-ci.org/samvera/active_fedora)
+[![Coverage Status](https://coveralls.io/repos/github/samvera/active_fedora/badge.svg?branch=master)](https://coveralls.io/github/samvera/active_fedora?branch=master)
+
+Docs: [![Contribution Guidelines](http://img.shields.io/badge/CONTRIBUTING-Guidelines-blue.svg)](./CONTRIBUTING.md)
+[![Apache 2.0 License](http://img.shields.io/badge/APACHE2-license-blue.svg)](./LICENSE)
+
+Jump in: [![Slack Status](http://slack.samvera.org/badge.svg)](http://slack.samvera.org/)
+
+# What is ActiveFedora?
 
 ActiveFedora is a Ruby gem for creating and
 managing objects in the Fedora Repository Architecture
 ([http://fedora-commons.org](http://fedora-commons.org)). ActiveFedora
 is loosely based on “ActiveRecord” in Rails. Version 9.0+ works with Fedora 4 and prior versions work on Fedora 3. Version 9.2+ works with Solr 4.10. Version 10.0+ works with Fedora >= 4.5.1.
 
-Getting Help
-------------
+## Product Owner & Maintenance
+ActiveFedora is a Core Component of the Samvera community. The documentation for
+what this means can be found
+[here](http://samvera.github.io/core_components.html#requirements-for-a-core-component).
 
--   Community Discussions & Mailing List are located at
-    [http://groups.google.com/group/samvera-tech](http://groups.google.com/group/samvera-tech)
--   Developers hang out on [slack.samvera.org](http://slack.samvera.org/)
+### Product Owner
 
-Installation
-------------
+[no-reply](https://github.com/no-reply)
 
-The gem is hosted on rubygems.
+# Help
 
-```bash
-gem install active-fedora
-```
+The Samvera community is here to help. Please see our [support guide](./SUPPORT.md).
 
-Getting Started
----------------
+# Getting Started
 
 The [Dive into Hydra](https://github.com/samvera/hydra/wiki/Dive-into-Hydra)
 gives you a brief tour through ActiveFedora’s features on the command line.
 
-Generators
-----------
+## Prerequisites
+
+- A Fedora Commons Repository installation (configured by URL in fedora.yml)
+- A Solr index (configured by URL in solr.yml)
+- A JDK8+ installation (if running the test suite)
+
+## Installation
+
+The gem is hosted on rubygems.
+
+```bash
+gem install active-fedora
+```
+
+## Generators
 
 You can generate a model inheriting from ActiveFedora::Base.
 
@@ -42,8 +56,7 @@ You can generate a model inheriting from ActiveFedora::Base.
 rails generate active_fedora:model Book
 ```
 
-Testing (this Gem)
-------------------
+## Testing (this Gem)
 
 In order to run the RSpec tests, you need to have a copy of the
 ActiveFedora source code, and then run bundle install in the source
@@ -88,11 +101,9 @@ is installed, run:
 rake spec
 ```
 
-Acknowledgements
-----------------
+# Acknowledgments
 
-Creator: Matt Zumwalt ([MediaShelf](http://yourmediashelf.com))
+This software has been developed by and is brought to you by the Samvera community.  Learn more at the
+[Samvera website](http://samvera.org/).
 
-Developers:
-Justin Coyne, McClain Looney & Eddie Shin
-([MediaShelf](http://yourmediashelf.com)), Rick Johnson (Notre Dame)
+![Samvera Logo](https://wiki.duraspace.org/download/thumbnails/87459292/samvera-fall-font2-200w.png?version=1&modificationDate=1498550535816&api=v2)

data/SUPPORT.md

@@ -0,0 +1,5 @@
+If you would like to report an issue, first search [the list of issues](https://github.com/samvera/active_fedora/issues/) to see if someone else has already reported it, and then feel free to [create a new issue](https://github.com/samvera/active_fedora/issues/new).
+
+If you have questions or need help, please email [the Samvera community tech list](https://groups.google.com/forum/#!forum/samvera-tech) or stop by the #dev channel in [the Samvera community Slack team](https://wiki.duraspace.org/pages/viewpage.action?pageId=87460391#Getintouch!-Slack).
+
+You can learn more about the various Samvera communication channels on the [Get in touch!](https://wiki.duraspace.org/pages/viewpage.action?pageId=87460391) wiki page.

data/active-fedora.gemspec

@@ -8,7 +8,7 @@ Gem::Specification.new do |s|
   s.platform    = Gem::Platform::RUBY
   s.authors     = ["Matt Zumwalt", "McClain Looney", "Justin Coyne"]
   s.email       = ["samvera-tech@googlegroups.com"]
-  s.homepage    = %q{https://github.com/projecthydra/active_fedora}
+  s.homepage    = %q{https://github.com/samvera/active_fedora}
   s.summary     = %q{A convenience libary for manipulating documents in the Fedora Repository.}
   s.description = %q{ActiveFedora provides for creating and managing objects in the Fedora Repository Architecture.}
   s.license = "Apache-2.0"
@@ -16,16 +16,16 @@ Gem::Specification.new do |s|
 
   s.add_dependency 'rsolr', '>= 1.1.2', '< 3'
   s.add_dependency 'solrizer', '>= 3.4', '< 5'
-  s.add_dependency "activesupport", '>= 4.2.4', '< 5.2'
-  s.add_dependency "activemodel", '>= 4.2', '< 5.2'
+  s.add_dependency "activesupport", '>= 4.2.4', '< 5.3'
+  s.add_dependency "activemodel", '>= 4.2.10', '< 5.3'
   s.add_dependency "active-triples", '>= 0.11.0', '< 2.0.0'
   s.add_dependency "deprecation"
-  s.add_dependency "ldp", '~> 0.7.0'
+  s.add_dependency "ldp", '>= 0.7.0', '< 2'
   s.add_dependency "ruby-progressbar", '~> 1.0'
-  s.add_dependency 'faraday', '~> 0.12.1'
+  s.add_dependency 'faraday', '~> 0.12'
   s.add_dependency 'faraday-encoding', '0.0.4'
 
-  s.add_development_dependency "rails", ">= 4.2", "< 5.2"
+  s.add_development_dependency "rails"
   s.add_development_dependency "rdoc"
   s.add_development_dependency "yard"
   s.add_development_dependency "rake"
@@ -35,7 +35,7 @@ Gem::Specification.new do |s|
   s.add_development_dependency "rspec-its"
   s.add_development_dependency "equivalent-xml"
   s.add_development_dependency "simplecov", '~> 0.8'
-  s.add_development_dependency "rubocop", '~> 0.47.1'
+  s.add_development_dependency "rubocop", '~> 0.56.0'
   s.add_development_dependency "rubocop-rspec", '~> 1.12.0'
 
   s.files         = `git ls-files`.split("\n")

data/lib/active_fedora.rb

@@ -9,7 +9,7 @@ require 'active_support/core_ext/hash/except'
 require 'active_triples'
 
 # Monkey patching RDF::Literal::DateTime to support fractional seconds.
-# See https://github.com/projecthydra/active_fedora/issues/497
+# See https://github.com/samvera/active_fedora/issues/497
 # Also monkey patches in a fix for timezones to be stored properly.
 module RDF
   class Literal

data/lib/active_fedora/aggregation/list_source.rb

@@ -15,7 +15,7 @@ module ActiveFedora
       # Overriding so that we don't track previously_changed, which was
       # rather expensive.
       def clear_changed_attributes
-        @changed_attributes.clear
+        clear_changes_information
       end
 
       def changed?
@@ -36,7 +36,7 @@ module ActiveFedora
       # Serializing head/tail/nodes slows things down CONSIDERABLY, and is not
       # useful.
       # @note This method is used by ActiveFedora::Base upstream for indexing,
-      #   at https://github.com/projecthydra/active_fedora/blob/master/lib/active_fedora/profile_indexing_service.rb.
+      #   at https://github.com/samvera/active_fedora/blob/master/lib/active_fedora/indexing_service.rb.
       def serializable_hash(_options = nil)
         {}
       end
@@ -80,6 +80,7 @@ module ActiveFedora
           # Set node subjects to a term in AF JUST so that AF will persist the
           # sub-graphs.
           # TODO: Find a way to fix this.
+          # See https://github.com/samvera/active_fedora/issues/1337
           resource.set_value(:nodes, [])
           self.nodes += graph.subjects.to_a
           ordered_self.changes_committed!

data/lib/active_fedora/associations/builder/collection_association.rb

@@ -26,6 +26,7 @@ module ActiveFedora::Associations::Builder
       full_callback_name = "#{callback_name}_for_#{name}"
 
       # TODO : why do i need method_defined? I think its because of the inheritance chain
+      # See https://github.com/samvera/active_fedora/issues/1333
       model.class_attribute full_callback_name.to_sym unless model.method_defined?(full_callback_name)
 
       callbacks = Array(options[callback_name.to_sym]).map do |callback|

data/lib/active_fedora/associations/collection_association.rb

@@ -43,6 +43,7 @@ module ActiveFedora
         ids = Array(ids).reject(&:blank?)
         replace(klass.find(ids)) # .index_by { |r| r.id }.values_at(*ids))
         # TODO, like this when find() can return multiple records
+        # See https://github.com/samvera/active_fedora/issues/1340
         # send("#{reflection.name}=", reflection.klass.find(ids))
         # send("#{reflection.name}=", ids.collect { |id| reflection.klass.find(id)})
       end
@@ -171,6 +172,7 @@ module ActiveFedora
       # See delete for more info.
       def delete_all
         # TODO: load_target causes extra loads. Can't we just send delete requests?
+        # See https://github.com/samvera/active_fedora/issues/1341
         delete(load_target).tap do
           reset
           loaded!
@@ -301,6 +303,7 @@ module ActiveFedora
         def find_target
           # TODO: don't reify, just store the solr results and lazily reify.
           # For now, we set a hard limit of 1000 results.
+          # See https://github.com/samvera/active_fedora/issues/1358
           records = ActiveFedora::QueryResultBuilder.reify_solr_results(load_from_solr(rows: SolrService::MAX_ROWS))
           records.each { |record| set_inverse_instance(record) }
           records

data/lib/active_fedora/associations/collection_proxy.rb

@@ -41,6 +41,8 @@ module ActiveFedora
         merge! association.scope(nullify: false)
       end
 
+      delegate :each, to: :to_a
+
       def target
         @association.target
       end

data/lib/active_fedora/associations/directly_contains_one_association.rb

@@ -4,6 +4,7 @@ module ActiveFedora
     class DirectlyContainsOneAssociation < SingularAssociation #:nodoc:
       # Finds objects contained by the container predicate (either the configured has_member_relation or ldp:contains)
       # TODO: Refactor this to use solr (for efficiency) instead of parsing the RDF graph.  Requires indexing ActiveFedora::File objects into solr, including their RDF.type and, if possible, the id of their container
+      # See https://github.com/samvera/active_fedora/issues/1335
       def find_target
         # filtered_objects = container_association_proxy.to_a.select { |o| o.metadata_node.type.include?(options[:type]) }
         query_node = if container_predicate = options[:has_member_relation]

data/lib/active_fedora/associations/indirectly_contains_association.rb

@@ -2,6 +2,7 @@ module ActiveFedora
   module Associations
     # TODO: we may want to split this into two subclasses, one for has_member_relation
     # and the other for is_member_of_relation
+    # See https://github.com/samvera/active_fedora/issues/1332
     class IndirectlyContainsAssociation < ContainsAssociation #:nodoc:
       # Add +records+ to this association.  Returns +self+ so method calls may be chained.
       # Since << flattens its argument list and inserts each record, +push+ and +concat+ behave identically.
@@ -40,6 +41,7 @@ module ActiveFedora
           uris.map { |object_uri| klass.find(klass.uri_to_id(object_uri)) }
         else # is_member_of_relation
           # TODO this is a lot of reads. Avoid this path
+          # See https://github.com/samvera/active_fedora/issues/1345
           container_predicate = ::RDF::Vocab::LDP.contains
           proxy_uris = container.resource.query(predicate: container_predicate).map { |r| r.object.to_s }
           proxy_uris.map { |uri| proxy_class.find(proxy_class.uri_to_id(uri))[options[:foreign_key]] }

data/lib/active_fedora/associations/singular_association.rb

@@ -33,6 +33,7 @@ module ActiveFedora
 
         def find_target
           # TODO: this forces a solr query, but I think it's likely we can just lookup from Fedora.
+          # See https://github.com/samvera/active_fedora/issues/1330
           rec = scope.take
           rec.tap { |record| set_inverse_instance(record) }
         end

data/lib/active_fedora/attribute_methods.rb

@@ -136,7 +136,7 @@ module ActiveFedora
     #   person.attribute_names
     #   # => ["id", "created_at", "updated_at", "name", "age"]
     def attribute_names
-      @attributes.keys
+      @local_attributes.keys
     end
 
     # Returns a hash of all the attributes with their names as keys and the values of the attributes as values.

data/lib/active_fedora/attribute_methods/read.rb

@@ -36,7 +36,7 @@ module ActiveFedora
       end
 
       def _read_attribute(attr_name) # :nodoc:
-        @attributes.fetch(attr_name.to_s) { |n| yield n if block_given? }
+        attributes.fetch(attr_name.to_s) { |n| yield n if block_given? }
       end
 
       alias attribute _read_attribute

data/lib/active_fedora/attribute_methods/write.rb

@@ -28,7 +28,7 @@ module ActiveFedora
 
       def write_attribute(attribute_name, value)
         if self.class.properties.key?(attribute_name)
-          @attributes[attribute_name] = value
+          attributes[attribute_name] = value
         else
           raise ActiveModel::MissingAttributeError, "can't write unknown attribute `#{attribute_name}'"
         end

data/lib/active_fedora/attributes.rb

@@ -12,7 +12,7 @@ module ActiveFedora
       after_save :clear_changed_attributes
       def clear_changed_attributes
         @previously_changed = changes
-        @changed_attributes.clear
+        clear_attribute_changes(changes.keys)
       end
     end
 

data/lib/active_fedora/attributes/property_builder.rb

@@ -57,6 +57,7 @@ module ActiveFedora::Attributes
 
     def build(&block)
       # TODO: remove this block stuff
+      # See https://github.com/samvera/active_fedora/issues/1336
       NodeConfig.new(name, options[:predicate], options.except(:predicate)) do |config|
         config.with_index(&block) if block_given?
       end

data/lib/active_fedora/callbacks.rb

@@ -215,7 +215,8 @@ module ActiveFedora
       :after_initialize, :after_find, :before_validation, :after_validation,
       :before_save, :around_save, :after_save, :before_create, :around_create,
       :after_create, :before_update, :around_update, :after_update,
-      :before_destroy, :around_destroy, :after_destroy
+      :before_destroy, :around_destroy, :after_destroy,
+      :before_update_index, :around_update_index, :after_update_index
     ].freeze
 
     included do
@@ -223,13 +224,17 @@ module ActiveFedora
       include ActiveModel::Validations::Callbacks
 
       define_model_callbacks :initialize, :find, only: :after
-      define_model_callbacks :save, :create, :update, :destroy
+      define_model_callbacks :save, :create, :update, :destroy, :update_index
     end
 
     def destroy(*) #:nodoc:
       _run_destroy_callbacks { super }
     end
 
+    def update_index(*args)
+      _run_update_index_callbacks { super(*args) }
+    end
+
     private
 
       def create_or_update(*)

data/lib/active_fedora/fedora.rb

@@ -103,5 +103,13 @@ module ActiveFedora
         ActiveFedora::Base.logger.warn "Fedora URL (#{host}) does not end with /rest. This could be a problem. Check your fedora.yml config"
       end
     end
+
+    def ntriples_connection
+      authorized_connection.tap { |conn| conn.headers['Accept'] = 'application/n-triples' }
+    end
+
+    def build_ntriples_connection
+      ActiveFedora::InitializingConnection.new(ActiveFedora::CachingConnection.new(ntriples_connection, omit_ldpr_interaction_model: true), root_resource_path)
+    end
   end
 end

data/lib/active_fedora/file.rb

@@ -43,7 +43,7 @@ module ActiveFedora
           raise "The first argument to #{self} must be a Hash, String or RDF::URI. You provided a #{identifier.class}"
         end
 
-        @attributes = {}.with_indifferent_access
+        @local_attributes = {}.with_indifferent_access
         @readonly = false
         yield self if block_given?
       end
@@ -86,7 +86,7 @@ module ActiveFedora
       @content = nil
       @metadata = nil
       @ds_content = nil
-      changed_attributes.clear
+      clear_attribute_changes(changes.keys)
     end
 
     def check_fixity
@@ -94,12 +94,12 @@ module ActiveFedora
     end
 
     def datastream_will_change!
-      attribute_will_change! :profile
+      attribute_will_change! :ldp_source
     end
 
     def attribute_will_change!(attr)
       return super unless attr == 'content'
-      changed_attributes['content'] = true
+      attributes_changed_by_setter[:content] = true
     end
 
     def remote_content
@@ -196,7 +196,9 @@ module ActiveFedora
       end
 
       def local_or_remote_content(ensure_fetch = true)
-        @content ||= ensure_fetch ? remote_content : @ds_content unless new_record?
+        return @content if new_record?
+
+        @content ||= ensure_fetch ? remote_content : @ds_content
         @content.rewind if behaves_like_io?(@content)
         @content
       end

data/lib/active_fedora/indexing/descendant_fetcher.rb

@@ -77,7 +77,7 @@ module ActiveFedora
       protected
 
         def rdf_resource
-          @rdf_resource ||= Ldp::Resource::RdfSource.new(ActiveFedora.fedora.connection, uri)
+          @rdf_resource ||= Ldp::Resource::RdfSource.new(ActiveFedora.fedora.build_ntriples_connection, uri)
         end
 
         def rdf_graph

data/lib/active_fedora/indexing/field_mapper.rb

@@ -22,6 +22,7 @@ module ActiveFedora
       # @api
       # Given a field name, index_type, etc., returns the corresponding Solr name.
       # TODO field type is the input format, maybe we could just detect that?
+      # See https://github.com/samvera/active_fedora/issues/1338
       # @param [String] field_name the ruby (term) name which will get a suffix appended to become a Solr field name
       # @param opts - index_type is only needed if the FieldDescriptor requires it (e.g. :searcahble)
       # @return [String] name of the solr field, based on the params
@@ -69,6 +70,7 @@ module ActiveFedora
 
             # Is there a custom converter?
             # TODO instead of a custom converter, look for input data type and output data type. Create a few methods that can do that cast.
+            # See https://github.com/samvera/active_fedora/issues/1339
 
             value = if converter
                       if converter.arity == 1