hyrax 3.0.0.pre.rc2 → 3.0.0.pre.rc3

data/app/services/hyrax/workflow/action_taken_service.rb

@@ -32,7 +32,7 @@ module Hyrax
           status
         end
 
-        return target.save if success
+        return save_target if success
         Rails.logger.error "Not all workflow methods were successful, so not saving (#{target.id})"
         false
       end
@@ -63,6 +63,19 @@ module Hyrax
         Rails.logger.error "Expected '#{class_name}' to respond to 'call', but it didn't, so not running workflow callback"
         nil
       end
+
+      private
+
+      ##
+      # @api private
+      def save_target
+        case target
+        when ActiveFedora::Base
+          target.save
+        else
+          Hyrax.persister.save(resource: target)
+        end
+      end
     end
   end
 end

data/app/services/hyrax/workflow/grant_edit_to_depositor.rb

@@ -7,7 +7,9 @@ module Hyrax
       # @param [#read_users=, #read_users] target (likely an ActiveRecord::Base) to which we are adding edit_users for the depositor
       # @return void
       def self.call(target:, **)
-        target.edit_users += [target.depositor]
+        return true unless target.try(:depositor)
+        target.edit_users = target.edit_users.to_a + Array.wrap(target.depositor) # += works in Ruby 2.6+
+        target.try(:permission_manager)&.acl&.save
         # If there are a lot of members, granting access to each could take a
         # long time. Do this work in the background.
         GrantEditToMembersJob.perform_later(target, target.depositor)

data/app/services/hyrax/workflow/permission_generator.rb

@@ -3,6 +3,7 @@ require 'active_support/core_ext/array/wrap'
 
 module Hyrax
   module Workflow
+    ##
     # @api public
     #
     # This has three major uses:
@@ -17,28 +18,32 @@ module Hyrax
     # information.
     #
     # See the specs for more on what is happening, however the general idea is
-    # to encapsulate the logic of assigning :agents to the :role either for
-    # the :entity or the :workflow. Then creating the given :action_names for
-    # the :workflow and :workflow_state and granting permission in that
-    # :workflow_state for the given :role.
+    # to encapsulate the logic of assigning +:agents+ to the +:role+ either for
+    # the +:entity+ or the +:workflow+. Then creating the given +:action_names+ for
+    # the +:workflow+ and +:workflow_state+ and granting permission in that
+    # +:workflow_state+ for the given :role.
     #
     # @see Sipity::WorkflowResponsibility
     # @see Sipity::EntitySpecificResponsibility
-    # @note And yes this violates some kind of single responsibility principle as it has many different access points
+    # @note Yes this violates some kind of single responsibility principle as it has many different access points
     class PermissionGenerator
+      ##
       # @todo Extract public class level methods that expose each of the primary purposes (instead of relying on parameters)
       def self.call(**keywords, &block)
         new(**keywords, &block).call
       end
 
+      ##
       # @param [Array<Sipity::Role, #string>] roles - converted to Sipity::Role
       # @param [Sipity::Workflow] workflow -
       # @param [Array<Object>] agents -
-      # @param [Sipity::Entity] entity - if given
-      #                                          - will grant the given :agents the given :roles for the given :entity (e.g. Sipity::EntitySpecificResponsibility)
+      # @param keywords
+      # @option keywords [Sipity::Entity] :entity - if given
+      #                                          - will grant the given +:agents+ the given +:roles+ for the given +:entity+ (e.g. Sipity::EntitySpecificResponsibility)
       #                                  if NOT given
-      #                                          - will grant the given :agents the given :roles for the given :workflow (e.g. Sipity::WorkflowResponsibility)
-      # @param [Array<String>] action_names - it will wire-up the workflow, allowing the given :roles to take the given :actions
+      #                                          - will grant the given +:agents+ the given +:roles+ for the given +:workflow+ (e.g. Sipity::WorkflowResponsibility)
+      # @option keywords [Array<String>] action_names - it will wire-up the workflow, allowing the given +:roles+ to take the given +:actions+
+      #
       # @todo Extract public class level methods that expose each of the options (and don't rely on an external parameter list)
       def initialize(roles:, workflow:, agents: [], **keywords)
         self.roles = roles

data/app/services/hyrax/workflow/workflow_action_service.rb

@@ -20,7 +20,7 @@ module Hyrax
         comment = create_sipity_comment
         handle_sipity_notifications(comment: comment)
         handle_additional_sipity_workflow_action_processing(comment: comment)
-        subject.work.update_index # So that the new actions and state are written into solr.
+        subject.work.try(:update_index) # So that the new actions and state are written into solr.
       end
 
       private

data/app/services/hyrax/workflow/workflow_factory.rb

@@ -40,16 +40,17 @@ module Hyrax
       # The Sipity::Entity acts as a proxy to a work within a workflow
       # @return [TrueClass]
       def create
+        action = find_deposit_action
         entity = create_workflow_entity!
         assign_specific_roles_to(entity: entity)
-        run_workflow_action!
+        run_workflow_action!(action: action)
         true
       end
 
       private
 
       def create_workflow_entity!
-        Sipity::Entity.create!(proxy_for_global_id: work.to_global_id.to_s,
+        Sipity::Entity.create!(proxy_for_global_id: Hyrax::GlobalID(work).to_s,
                                workflow: workflow_for(work),
                                workflow_state: nil)
       end
@@ -61,23 +62,24 @@ module Hyrax
                                                   workflow: workflow_for(work))
       end
 
-      def run_workflow_action!
+      def run_workflow_action!(action:)
         subject = WorkflowActionInfo.new(work, user)
         Workflow::WorkflowActionService.run(subject: subject,
-                                            action: find_deposit_action)
+                                            action: action)
       end
 
       # Find an action that has no starting state. This is the deposit action.
-      # # @return [Sipity::WorkflowAction]
+      # @return [Sipity::WorkflowAction]
+      # @raise [Sipity::StateError]
       def find_deposit_action
-        actions_that_lead_to_states = Sipity::WorkflowStateAction.all.pluck(:workflow_action_id)
-        relation = Sipity::WorkflowAction.where(workflow: workflow_for(work))
-        relation = relation.where('id NOT IN (?)', actions_that_lead_to_states) if actions_that_lead_to_states.any?
-        relation.first!
+        workflow_for(work).find_deposit_action
       end
 
+      ##
+      # @return [Sipity::Workflow]
+      # @raise [Sipity::StateError]
       def workflow_for(work)
-        Sipity::Workflow.find_active_workflow_for(admin_set_id: work.admin_set_id)
+        Sipity::Workflow.find_active_workflow_for(admin_set_id: work.try(:admin_set_id))
       end
     end
   end

data/app/services/hyrax/working_directory.rb

@@ -25,7 +25,6 @@ module Hyrax
       # @return [String] path of the working file
       def copy_repository_resource_to_working_directory(file, id)
         Rails.logger.debug "Loading #{file.original_name} (#{file.id}) from the repository to the working directory"
-        # TODO: this causes a load into memory, which we'd like to avoid
         copy_stream_to_working_directory(id, file.original_name, StringIO.new(file.content))
       end
 

data/app/services/hyrax/works/managed_works_service.rb

@@ -9,8 +9,20 @@ module Hyrax
       # @param scope [Object] Typically a controller object that responds to `repository`, `can?`, `blacklight_config`, `current_ability`
       # @return [Array<SolrDocument>]
       def self.managed_works_count(scope:)
-        query_builder = Hyrax::Dashboard::WorksSearchBuilder.new(scope).rows(0)
-        scope.repository.search(query_builder.query).response["numFound"]
+        response, _docs = search_service(scope).search_results do |builder|
+          builder.rows(0)
+        end
+        response.response["numFound"]
+      end
+
+      def self.search_service(scope)
+        Hyrax::SearchService.new(
+          config: scope.blacklight_config,
+          user_params: scope.params,
+          scope: scope,
+          current_ability: scope.current_ability,
+          search_builder_class: Hyrax::Dashboard::WorksSearchBuilder
+        )
       end
     end
   end

data/app/views/_controls.html.erb

@@ -1,4 +1,4 @@
-<nav class="navbar navbar-default navbar-static-top" role="navigation">
+<nav class="navbar navbar-default navbar-static-top" role="navigation" aria-label="Root Menu">
   <div class="container-fluid">
     <div class="row">
       <ul class="nav navbar-nav col-sm-5">

data/app/views/hyrax/admin/collection_types/index.html.erb

@@ -40,7 +40,7 @@
                  <% unless collection_type.admin_set? || collection_type.user_collection? %>
                   <button class="btn btn-danger btn-sm delete-collection-type"
                           data-collection-type="<%= collection_type.to_json %>"
-                          data-collection-type-index="<%= hyrax.dashboard_collections_path({ 'f[collection_type_gid_ssim][]' => collection_type.gid, 'f[has_model_ssim][]' => 'Collection' }) %>"
+                          data-collection-type-index="<%= hyrax.dashboard_collections_path({ 'f[collection_type_gid_ssim][]' => collection_type.to_global_id.to_s, 'f[has_model_ssim][]' => 'Collection' }) %>"
                           data-has-collections="<%= collection_type.collections? %>">
                     <%= t('helpers.action.delete') %>
                   </button>

data/app/views/hyrax/base/_member.html.erb

@@ -1,6 +1,6 @@
 <tr class="<%= dom_class(member) %> attributes">
   <td class="thumbnail">
-    <%= render_thumbnail_tag member %>
+    <%= render_thumbnail_tag member, { alt: "file details" } %>
   </td>
   <td class="attribute attribute-filename ensure-wrapped"><%= link_to(member.link_name, contextual_path(member, @presenter)) %></td>
   <td class="attribute attribute-date_uploaded"><%= member.try(:date_uploaded) %></td>

data/app/views/hyrax/base/_representative_media.html.erb

@@ -5,5 +5,5 @@
     <%= media_display presenter.representative_presenter %>
   <% end %>
 <% else %>
-  <%= image_tag 'default.png', class: "canonical-image" %>
+  <%= image_tag 'default.png', class: "canonical-image", alt: 'default representative image' %>
 <% end %>

data/app/views/hyrax/base/iiif_viewers/_universal_viewer.html.erb

@@ -1,5 +1,5 @@
 <div class="viewer-wrapper">
-  <iframe
+  <iframe aria-label="image view" 
     src="<%= universal_viewer_base_url %>#?manifest=<%= main_app.polymorphic_url [main_app, :manifest, presenter], { locale: nil } %>&config=<%= universal_viewer_config_url %>" 
     allowfullscreen="true" 
     frameborder="0" 

data/app/views/hyrax/base/show.html.erb

@@ -33,7 +33,7 @@
 
     <div class="panel panel-default">
       <div class="panel-heading">
-        <h3 class="panel-title"><%= t('hyrax.base.show.relationships') %></h3>
+        <h1 class="panel-title"><%= t('hyrax.base.show.relationships') %></h1>
       </div>
       <div class="panel-body">
         <%= render 'relationships', presenter: @presenter %>
@@ -42,7 +42,7 @@
 
     <div class="panel panel-default">
       <div class="panel-heading">
-        <h3 class="panel-title"><%= t('.items') %></h3>
+        <h1 class="panel-title"><%= t('.items') %></h1>
       </div>
       <div class="panel-body">
         <%= render 'items', presenter: @presenter %>

data/app/views/hyrax/batch_select/_add_button.html.erb

@@ -1,3 +1,3 @@
 <div data-behavior="batch-add-button">
-  <%= check_box_tag "batch_document_#{document.id}", document.id, false, class:"batch_document_selector", id: "batch_document_#{document.id}", checks: "active" %>
+  <%= check_box_tag "batch_document_ids[]", document.id, false, class:"batch_document_selector", id: "batch_document_#{document.id}", checks: "active" %>
 </div>

data/app/views/hyrax/collections/_default_group.html.erb

@@ -1,3 +1,4 @@
+<fieldset>
 <table class="table table-striped">
   <caption class="sr-only"><%= t("hyrax.dashboard.my.sr.listing") %> <%= application_name %></caption>
   <thead>
@@ -20,3 +21,4 @@
   <% end %>
   </tbody>
 </table>
+</fieldset>

data/app/views/hyrax/collections/show.html.erb

@@ -47,7 +47,7 @@
           </div>
       <% end %>
 
-      </header>
+      </div>
 
     </div>
   </div>

data/app/views/hyrax/dashboard/works/_default_group.html.erb

@@ -1,3 +1,4 @@
+<fieldset>
 <table class="table table-striped works-list">
   <caption class="sr-only"><%= t("hyrax.dashboard.my.sr.listing") %> <%= application_name %></caption>
   <thead>
@@ -18,3 +19,4 @@
   <% end %>
   </tbody>
 </table>
+</fieldset>

data/app/views/hyrax/embargoes/_list_expired_active_embargoes.html.erb

@@ -40,7 +40,7 @@
         <tr data-behavior="extra" data-id="<%= curation_concern.id %>" class="extra-embargo-info">
           <td></td>
           <td colspan=5>
-            <%= check_box_tag "embargoes[#{i}][copy_visibility]", curation_concern.id, false %>
+            <%= check_box_tag "embargoes[#{i}][copy_visibility]", curation_concern.id, true %>
             <%= t('.change_all', cc: curation_concern) %>
             <%= visibility_badge(curation_concern.visibility_after_embargo) %>?
           </td>

data/app/views/hyrax/leases/_list_expired_active_leases.html.erb

@@ -17,6 +17,7 @@
 <% else %>
 
   <%= form_tag leases_path, method: :patch do %>
+    <fieldset>
     <%= submit_tag t('.deactivate_selected'), class: 'btn btn-primary' %>
     <table class="leases table">
       <thead>
@@ -49,5 +50,5 @@
       </tbody>
     </table>
   <% end %>
-
+  </fieldset>
 <% end %>

data/app/views/hyrax/my/works/_default_group.html.erb

@@ -1,3 +1,4 @@
+<fieldset>
 <table class="table table-striped works-list">
   <caption class="sr-only"><%= t("hyrax.dashboard.my.sr.listing") %> <%= application_name %></caption>
   <thead>
@@ -16,3 +17,4 @@
   <% end %>
   </tbody>
 </table>
+</fieldset>

data/app/views/layouts/hyrax.html.erb

@@ -29,19 +29,4 @@
     <%= render 'shared/footer' %>
     <%= render 'shared/ajax_modal' %>
   </body>
-  <script type="text/javascript">
-    $( document ).ready(function() {
-      $(".skip-to-content").click(function(event) {
-        event.preventDefault();
-        // element to focus on
-        let skipTo = '#' + $(this)[0].firstElementChild.hash.split('#')[1];
-
-        // Setting 'tabindex' to -1 takes an element out of normal 
-        // tab flow but allows it to be focused via javascript
-        $(skipTo).attr('tabindex', -1).on('blur focusout', function () {
-          $(this).removeAttr('tabindex');
-        }).focus();
-      });
-    });
-  </script>
 </html>

data/bin/db-migrate-seed.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+set -e
+
+db-wait.sh "$DB_HOST:$DB_PORT"
+db-wait.sh "$FCREPO_HOST:$FCREPO_PORT"
+db-wait.sh "$SOLR_HOST:$SOLR_PORT"
+
+bundle exec rails db:migrate
+bundle exec rails db:seed

data/bin/db-wait.sh

@@ -0,0 +1,14 @@
+#!/bin/sh
+
+host=$(printf "%s\n" "$1"| cut -d : -f 1)
+port=$(printf "%s\n" "$1"| cut -d : -f 2)
+
+shift 1
+
+while ! nc -z "$host" "$port"
+do
+  echo "waiting for $host:$port"
+  sleep 1
+done
+
+exec "$@"

data/bin/hyrax-entrypoint.sh

@@ -0,0 +1,15 @@
+#!/bin/sh
+set -e
+
+# Make sure common volume points have the app permission
+chown -fR app:app /app/samvera/hyrax-webapp/tmp
+chown -fR app:app /app/samvera/hyrax-webapp/public
+
+chown -fR app:app $HYRAX_DERIVATIVES_PATH
+chown -fR app:app $HYRAX_UPLOAD_PATH
+
+mkdir -p /app/samvera/hyrax-webapp/tmp/pids
+rm -f /app/samvera/hyrax-webapp/tmp/pids/*
+
+# Run the command
+exec "$@"

data/chart/fcrepo/.gitignore

@@ -0,0 +1,2 @@
+charts/*
+Chart.lock

data/chart/fcrepo/.helmignore

@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

data/chart/fcrepo/Chart.yaml

@@ -0,0 +1,11 @@
+apiVersion: v2
+name: fcrepo
+description: Fedora Commons Repository 4
+type: application
+version: 0.4.1
+appVersion: 4.7
+dependencies:
+  - name: postgresql
+    version: 9.3.3
+    repository: https://charts.bitnami.com/bitnami
+    condition: postgresql.enabled

data/chart/fcrepo/README.md

@@ -0,0 +1,50 @@
+Fedora Commons Helm Chart
+=========================
+
+Fedora is the flexible, modular, open source repository platform with native
+linked data support.
+
+## Installation
+
+```sh
+helm dep up chart/fcrepo
+helm install fcrepo chart/fcrepo
+```
+
+## Configuration
+
+By default, this chart deploys with Postgresql as the backend for Fedora.
+Without other configuration, it will deploy a new Postgresql instance/database
+as a service available to the `fcrepo` deployment.
+
+In practice, users may want to forego installing postgres for two reasons:
+
+_First_, when you are deploying Fedora into a more complex application
+environment you may wish to reuse an existing Postgres instance already
+maintained with that environment.
+
+In this case, `fcrepo` should be deployed with postgresql explictly disabled, an
+`exernalDatabaseUsername`, and an `fcrepoSecretName`. `fcrepoSecretName` must
+correspond to an existing secret providing `DATABASE_PASSWORD`, `DATABASE_HOST`,
+and `JAVA_OPTS`.
+
+Optionally, a `externalDatabaseName` may be given to avoid collissions in the
+case that the default `fcrepo` is not an acceptable database name.
+
+This is usually done in the context of a parent chart which provides the postgresql instance, for example:
+
+```yaml
+fcrepo:
+  enabled: true
+  fcrepoSecretName: "mychart.fcrepo.fullname"
+  externalDatabaseUsername: "mydbuser"
+  servicePort: 8080
+  postgresql:
+    enabled: false
+```
+
+_Second_, because they want to use another backend for Fedora. This use case is broadly unsupported here. In theory, you can get a default (Infinispan) configuration by setting `postgresql.enabled` to `false`. **THIS CONFIGURATION IS UNTESTED AND UNSUPPORTED**:
+
+```sh
+helm install --set postgresql.enabled=false fcrepo-test chart/fcrepo
+```