hyrax 5.0.0.rc1 → 5.0.0.rc3

data/.koppie/db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 2021_12_07_172259) do
+ActiveRecord::Schema.define(version: 2023_08_03_165135) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -140,6 +140,17 @@ ActiveRecord::Schema.define(version: 2021_12_07_172259) do
     t.index ["machine_id"], name: "index_hyrax_collection_types_on_machine_id", unique: true
   end
 
+  create_table "hyrax_counter_metrics", force: :cascade do |t|
+    t.string "worktype"
+    t.string "resource_type"
+    t.string "work_id"
+    t.date "date"
+    t.integer "total_item_investigations"
+    t.integer "total_item_requests"
+    t.datetime "created_at", precision: 6, null: false
+    t.datetime "updated_at", precision: 6, null: false
+  end
+
   create_table "hyrax_default_administrative_set", force: :cascade do |t|
     t.string "default_admin_set_id", null: false
     t.datetime "created_at", null: false

data/CONTAINERS.md

@@ -5,10 +5,11 @@ Our goal is to provide a practical, reusable reference environment for applicati
 
 The [Hyrax Engine Development](#hyrax-engine-development) is further along than the [Docker Image for Hyrax-based Applications](#docker-image-for-hyrax-based-applications) which is further along than [Deploying to Production](#deploying-to-production).
 
-There are two options for development environments to run:
+There are three options for development environments to run:
 
 - [Dassie](#dassie-internal-test-app-with-activefedora) is the default internal test app that will run an ActiveFedora-based Hyrax web application using Fedora 4 as the backend storage. See [Troubleshooting Dassie](#troubleshooting-dassie) if you encounter any issues.
 - [Koppie](#koppie-internal-test-app-with-valkyrie-connector-to-postgres) is a newer internal test app that is a Valkyrie-based Hyrax web application that runs with PostGres as backend storage. It does not run ActiveFedora or use Fedora 4. See [Troubleshooting Koppie](#troubleshooting-koppie) if you encounter any issues.
+- [Sirenia](#sirenia-internal-test-app-with-valkyrie-connector-to-fedora) is Koppie but with Valkyrie configured to use Fedora 6 metadata and storage adapters.
 
 <!-- NOTE: This title is referenced in the top-level README.md. Keep that in mind if you change it. -->
 ## Hyrax Engine Development
@@ -37,6 +38,7 @@ This starts containers for:
   - Redis
   - Memcached
   - SideKiq (for background jobs)
+  - Chrome (for feature tests)
 
 It also runs database migrations. This will also bring up a development application on `http://localhost:3000`.
 
@@ -71,8 +73,6 @@ Let's break down the above command:
 
 _**Note:**_ The `bundle exec rspec` portion of the command runs the whole test suite. See the [rspec command documentation](https://github.com/rspec/rspec-core#the-rspec-command) for how to refine your test runs.
 
-_**Note**: The `/app/samvera/hyrax-webapp` is analogous to the `.internal_test_app` that we generate as part of the Hyrax engine Continuous Integration._
-
 #### The Docker Container Named "app"
 
 As a developer, you may need to run commands against the Hyrax-based application and/or the Hyrax engine.  Examples
@@ -149,6 +149,7 @@ This starts containers for:
   - Redis
   - Memcached
   - SideKiq (for background jobs)
+  - Chrome (for feature tests)
 
 It also runs database migrations. This will also bring up a development application on `http://localhost:3001`.
 
@@ -185,13 +186,47 @@ echo "FROM samveralabs/hyrax" > Dockerfile
 
 _This is for applications that mount Hyrax and is separate from the docker containers for Hyrax engine development._
 
+### Sirenia Internal Test App with Valkyrie Connector to Fedora
+
+Sirenia uses the same image as koppie. If you have not already done so, follow the build instructions for koppie above.
+
+Start Sirenia: `docker compose -f docker-compose-sirenia.yml up`
+
+This starts containers for:
+
+  - a `hyrax` test application (`.sirenia`);
+  - Fedora
+  - Solr
+  - Postgresql
+  - Redis
+  - Memcached
+  - SideKiq (for background jobs)
+  - Chrome (for feature tests)
+
+It also runs database migrations. This will also bring up a development application on `http://localhost:3002`.
+
+To stop the containers for the Hyrax-based application, type <kbd>Ctrl</kbd>+<kbd>c</kbd>. To restart the containers run `docker compose -f docker-compose-sirenia.yml up`.
+
+_**Note:** Starting and stopping Docker in this way will preserve your data between restarts._
+
+Sirenia runs as a different project than Dassie and Koppie, so it should be possible to run both concurrently (assuming your workstation has enough RAM).
+
+#### Run rails console on Sirenia
+
+Currently Sirenia should not be used for running specs. See [Code Changes and Testing](#code-changes-and-testing) under Dassie instead until the specs can be updated for a valkyrie only environment.
+
+```sh
+docker compose -f docker-compose-sirenia.yml up
+docker compose -f docker-compose-sirenia.yml exec app bundle exec rails c
+```
+
 ### Maintaining
 
 We publish several Hyrax images to the [GitHub container registry][ghcr] under
 the [Samvera organization][samvera-packages].  To build them:
 
 ```sh
-export HYRAX_VERSION=v5.0.0.rc1 # or desired version
+export HYRAX_VERSION=v5.0.0.rc3 # or desired version
 git checkout hyrax-$HYRAX_VERSION
 
 docker build --target hyrax-base --tag ghcr.io/samvera/hyrax/hyrax-base:$(git rev-parse HEAD) .

data/Dockerfile

@@ -1,8 +1,5 @@
-ARG ALPINE_VERSION=3.18
-ARG RUBY_VERSION=3.2.2
-
-FROM ruby:$RUBY_VERSION-alpine$ALPINE_VERSION as builder
-RUN apk add build-base curl jemalloc
+ARG ALPINE_VERSION=3.19
+ARG RUBY_VERSION=3.2.3
 
 FROM ruby:$RUBY_VERSION-alpine$ALPINE_VERSION as hyrax-base
 
@@ -16,6 +13,14 @@ RUN apk --no-cache upgrade && \
   curl \
   gcompat \
   imagemagick \
+  imagemagick-heic \
+  imagemagick-jpeg \
+  imagemagick-jxl \
+  imagemagick-pdf \
+  imagemagick-svg \
+  imagemagick-tiff \
+  imagemagick-webp \
+  jemalloc \
   tzdata \
   nodejs \
   yarn \
@@ -33,13 +38,11 @@ USER app
 RUN mkdir -p /app/samvera/hyrax-webapp
 WORKDIR /app/samvera/hyrax-webapp
 
-COPY --chown=1001:101 ./bin /app/samvera
-ENV PATH="/app/samvera:$PATH"
-ENV RAILS_ROOT="/app/samvera/hyrax-webapp"
-ENV RAILS_SERVE_STATIC_FILES="1"
-
-COPY --from=builder /usr/lib/libjemalloc.so.2 /usr/local/lib/
-ENV LD_PRELOAD="/usr/local/lib/libjemalloc.so.2"
+COPY --chown=1001:101 ./bin/*.sh /app/samvera/
+ENV PATH="/app/samvera:$PATH" \
+    RAILS_ROOT="/app/samvera/hyrax-webapp" \
+    RAILS_SERVE_STATIC_FILES="1" \
+    LD_PRELOAD="/usr/local/lib/libjemalloc.so.2"
 
 ENTRYPOINT ["hyrax-entrypoint.sh"]
 CMD ["bundle", "exec", "puma", "-v", "-b", "tcp://0.0.0.0:3000"]
@@ -89,6 +92,13 @@ ONBUILD RUN RAILS_ENV=production SECRET_KEY_BASE=`bin/rake secret` DB_ADAPTER=nu
 
 FROM hyrax-base as hyrax-engine-dev
 
+USER root
+RUN apk --no-cache add bash \
+  ffmpeg \
+  mediainfo \
+  perl
+USER app
+
 ARG APP_PATH=.dassie
 ARG BUNDLE_WITHOUT=
 
@@ -100,7 +110,9 @@ COPY --chown=1001:101 . /app/samvera/hyrax-engine
 RUN bundle -v && \
   bundle install --jobs "$(nproc)" && \
   cd $HYRAX_ENGINE_PATH && \
-  bundle install --jobs "$(nproc)"
+  bundle install --jobs "$(nproc)" && \
+  yarn
+
 RUN RAILS_ENV=production SECRET_KEY_BASE='fakesecret1234' DB_ADAPTER=nulldb DATABASE_URL='postgresql://fake' bundle exec rake assets:precompile
 
 

data/Gemfile

@@ -1,7 +1,14 @@
 # frozen_string_literal: true
 source 'https://rubygems.org'
+
 # Please see hyrax.gemspec for dependency information.
-gemspec
+# Install gems from test app
+if ENV['RAILS_ROOT']
+  test_app_gemfile_path = File.expand_path('Gemfile', ENV['RAILS_ROOT'])
+  eval_gemfile test_app_gemfile_path
+else
+  gemspec
+end
 
 group :development, :test do
   gem 'benchmark-ips'
@@ -13,26 +20,3 @@ group :development, :test do
   gem 'ruby-prof', require: false
   gem "simplecov", require: false
 end
-
-test_app_path = ENV['RAILS_ROOT'] ||
-                ENV.fetch('ENGINE_CART_DESTINATION', File.expand_path('.internal_test_app', File.dirname(__FILE__)))
-test_app_gemfile = File.expand_path('Gemfile', test_app_path)
-
-# rubocop:disable Bundler/DuplicatedGem
-if File.exist?(test_app_gemfile)
-  begin
-    Bundler.ui.info "[Hyrax] Including test application dependencies from #{test_app_gemfile}"
-    eval_gemfile test_app_gemfile
-  rescue Bundler::GemfileError => e
-    Bundler.ui.warn '[Hyrax] Skipping Rails application dependencies:'
-    Bundler.ui.warn e.message
-  end
-elsif ENV['RAILS_VERSION'] == 'edge'
-  gem 'rails', github: 'rails/rails', source: 'https://rubygems.org'
-  ENV['ENGINE_CART_RAILS_OPTIONS'] = '--edge --skip-turbolinks'
-elsif ENV['RAILS_VERSION']
-  gem 'rails', ENV['RAILS_VERSION'], source: 'https://rubygems.org'
-else
-  Bundler.ui.warn '[Hyrax] Skipping all Rails dependency injection'
-end
-# rubocop:enable Bundler/DuplicatedGem

data/Gemfile.dassie

@@ -0,0 +1,2 @@
+# Use dedicated lock files for dassie/koppie to avoid gem mismatches
+eval_gemfile 'Gemfile'

data/Gemfile.koppie

@@ -0,0 +1,2 @@
+# Use dedicated lock files for dassie/koppie to avoid gem mismatches
+eval_gemfile 'Gemfile'

data/README.md

@@ -50,7 +50,6 @@ More detailed documentation about Hyrax is available on the [Hyrax Github Wiki](
 
 Hyrax can also work running prerequisite dependencies separately. The following describe ways to do this:
 * [Developing Your Hyrax-based Application](./documentation/developing-your-hyrax-based-app.md)
-* [Development setup using Engine Cart and Solr Fedora wrapper](https://github.com/samvera/hyrax/wiki/Development-setup-using-Engine-Cart-and-Solr---Fedora-wrapper)
 
 ## Contribute
 
@@ -77,6 +76,8 @@ This software has been developed by and is brought to you by the Samvera communi
 
 ![Samvera Logo](./samvera-fall-TM3.svg)
 
+This project is tested with Browserstack.
+
 ## License
 
 Hyrax is available under [the Apache 2.0 license](LICENSE).

data/Rakefile

@@ -9,17 +9,6 @@ end
 
 Bundler::GemHelper.install_tasks
 
-task :setup_test_server do
-  require 'engine_cart'
-  EngineCart.load_application!
-end
-
 Dir.glob('tasks/*.rake').each { |r| import r }
 
 task default: :ci
-
-# Load the test app's rake tasks so they can be run from the app namespace (e.g. app:db:migrate)
-if File.exist?(File.expand_path(".internal_test_app/Rakefile", __dir__))
-  APP_RAKEFILE = File.expand_path(".internal_test_app/Rakefile", __dir__)
-  load 'rails/tasks/engine.rake'
-end

data/app/actors/hyrax/actors/base_actor.rb

@@ -69,10 +69,13 @@ module Hyrax
       end
 
       def save(env, use_valkyrie: false)
-        return env.curation_concern.save unless use_valkyrie
+        # NOTE: You must call env.curation_concern.save before you attempt to coerce the curation
+        # concern into a valkyrie resource.
+        is_valid = env.curation_concern.save
+        return is_valid unless use_valkyrie
 
         # don't run validations again on the converted object if they've already passed
-        resource = valkyrie_save(resource: env.curation_concern.valkyrie_resource, is_valid: env.curation_concern.save)
+        resource = valkyrie_save(resource: env.curation_concern.valkyrie_resource, is_valid: is_valid)
 
         # we need to manually set the id and reload, because the actor stack requires
         # `env.curation_concern` to be the exact same instance throughout.
@@ -83,7 +86,7 @@ module Hyrax
         # for now, just hit the validation error again
         # later we should capture the _err.obj and pass it back
         # through the environment
-        env.curation_concern.save
+        is_valid
       end
 
       def apply_save_data_to_curation_concern(env)

data/app/actors/hyrax/actors/embargo_actor.rb

@@ -14,12 +14,9 @@ module Hyrax
       def destroy
         case work
         when Valkyrie::Resource
-          embargo_manager = Hyrax::EmbargoManager.new(resource: work)
-          return if embargo_manager.embargo.embargo_release_date.blank?
-
-          embargo_manager.deactivate!
-          work.embargo = Hyrax.persister.save(resource: embargo_manager.embargo)
-          Hyrax::AccessControlList(work).save
+          Hyrax::EmbargoManager.deactivate_embargo_for(resource: work) &&
+            Hyrax.persister.save(resource: work.embargo) &&
+            Hyrax::AccessControlList(work).save
         else
           work.embargo_visibility! # If the embargo has lapsed, update the current visibility.
           work.deactivate_embargo!

data/app/actors/hyrax/actors/file_actor.rb

@@ -80,7 +80,7 @@ module Hyrax
           :original_file
         when Hyrax::FileMetadata::Use::EXTRACTED_TEXT
           :extracted_file
-        when Hyrax::FileMetadata::Use::THUMBNAIL
+        when Hyrax::FileMetadata::Use::THUMBNAIL_IMAGE
           :thumbnail_file
         else
           :original_file

data/app/actors/hyrax/actors/lease_actor.rb

@@ -14,12 +14,9 @@ module Hyrax
       def destroy
         case work
         when Valkyrie::Resource
-          lease_manager = Hyrax::LeaseManager.new(resource: work)
-          return if lease_manager.lease.lease_expiration_date.blank?
-
-          lease_manager.deactivate!
-          work.lease = Hyrax.persister.save(resource: lease_manager.lease)
-          Hyrax::AccessControlList(work).save
+          Hyrax::LeaseManager.deactivate_lease_for(resource: work) &&
+            Hyrax.persister.save(resource: work.lease) &&
+            Hyrax::AccessControlList(work).save
         else
           work.lease_visibility! # If the lease has lapsed, update the current visibility.
           work.deactivate_lease!

data/app/assets/javascripts/hyrax/batch_select_all.js

@@ -41,7 +41,7 @@
     var checked = $("#check_all")[0]['checked'];
 
     // check each individual box
-    $("input[type='checkbox'].batch_document_selector").each(function(index, value) {
+    $("input[type='checkbox'].batch_document_selector:not(.disabled)").each(function(index, value) {
        value['checked'] = checked;
     });
     toggleButtons();

data/app/assets/javascripts/hyrax/file_manager/member.es6

@@ -10,7 +10,7 @@ export class InputTracker {
     this.notifier = notifier
     this.element.data("initial-value", this.element.val())
     this.element.data("tracker", this)
-    this.element.trigger("change", this.value_changed)
+    this.element.on("change", this.value_changed)
   }
 
   reset() {

data/app/assets/javascripts/hyrax/save_work/uploaded_files.es6

@@ -3,7 +3,15 @@ export class UploadedFiles {
   constructor(form, callback) {
     this.form = form
     this.element = $('#fileupload')
-    this.element.on('fileuploadcompleted', callback)
+    this.uploadsInProgress = 0
+    this.element.on('fileuploadadded', (e, data) => {
+      this.uploadsInProgress += 1
+      callback(e, data)
+    })
+    this.element.on('fileuploadcompleted', (e, data) => {
+      this.uploadsInProgress -= 1
+      callback(e, data)
+    })
     this.element.on('fileuploaddestroyed', callback)
   }
 
@@ -13,7 +21,7 @@ export class UploadedFiles {
   }
 
   get inProgress() {
-    return this.element.fileupload('active') > 0
+    return this.uploadsInProgress > 0;
   }
 
   get hasFiles() {

data/app/assets/stylesheets/hyrax/_file-listing.scss

@@ -70,8 +70,6 @@ h4 .small {
 .batch-info {
 
   .sort-toggle {
-    height: 5.1em;
-
     button {
       margin-left: 10px;
     }

data/app/assets/stylesheets/hyrax/_work-show.scss

@@ -116,6 +116,21 @@ ul.tabular {
   background: #fff;
   border-color: #e0e0e0;
 
+  & > .btn {
+    padding: 0;
+    border: 0;
+  }
+
+  .btn-primary {
+    margin-bottom: 1rem;
+  }
+
+  .workflow-comments {
+    label {
+      font-weight: bold;
+    }
+  }
+
   .card-header {
     background-color: #e6ab5f;
     color: #ffffff;
@@ -128,8 +143,9 @@ ul.tabular {
   .card-body {
     background-color: #f2f1eb;
   }
-}
 
-.workflow-actions {
-  background-color: #f8f8f8;
+  .workflow-actions {
+    background-color: #f8f8f8;
+    padding: 1rem;
+  }
 }

data/app/assets/stylesheets/hyrax/sidebar.scss

@@ -56,6 +56,29 @@ $gutter-width: $grid-gutter-width/2;
     }
   }
 
+  &:not(.maximized) {
+    .sidebar-action-text,
+    a span + span,
+    h5 {
+      display: none;
+    }
+
+    .nav li {
+      text-align: center;
+      a {
+        padding-left: 0;
+        padding-right: 0;
+      }
+      .fa {
+        margin-right: 0;
+      }
+    }
+
+    .nav-item {
+      width: $drawer-small;
+    }
+  }
+
   .sidebar-toggle {
     cursor: pointer;
     background-color: $body-background-color;
@@ -114,9 +137,14 @@ $gutter-width: $grid-gutter-width/2;
     li {
       white-space: nowrap;
 
-      > a:hover, > a:focus {
+      > a:focus {
+        color: $admin-sidebar-link-color;
+      }
+
+      > a:hover {
         text-decoration: none;
         background-color: $admin-sidebar-link-background-color;
+        color: $admin-sidebar-link-hover-color;
       }
     }
     

data/app/controllers/concerns/hyrax/collections_controller_behavior.rb

@@ -39,7 +39,7 @@ module Hyrax
 
       respond_to do |format|
         format.html
-        format.json { render json: @curation_concern }
+        format.json { render 'hyrax/base/show' }
       end
     end
 

data/app/controllers/concerns/hyrax/embargoes_controller_behavior.rb

@@ -31,7 +31,13 @@ module Hyrax
       filter_docs_with_edit_access!
       copy_visibility = []
       copy_visibility = params[:embargoes].values.map { |h| h[:copy_visibility] } if params[:embargoes]
-      resources = Hyrax.custom_queries.find_many_by_alternate_ids(alternate_ids: batch, use_valkyrie: Hyrax.config.use_valkyrie?)
+
+      resources = if Hyrax.config.use_valkyrie?
+                    Hyrax.query_service.find_many_by_ids(ids: batch)
+                  else
+                    Hyrax.custom_queries.find_many_by_alternate_ids(alternate_ids: batch, use_valkyrie: false)
+                  end
+
       resources.each do |resource|
         if Hyrax.config.use_valkyrie?
           EmbargoManager.new(resource: resource).release!

data/app/controllers/concerns/hyrax/leases_controller_behavior.rb

@@ -29,7 +29,13 @@ module Hyrax
       filter_docs_with_edit_access!
       copy_visibility = []
       copy_visibility = params[:leases].values.map { |h| h[:copy_visibility] } if params[:leases]
-      resources = Hyrax.custom_queries.find_many_by_alternate_ids(alternate_ids: batch, use_valkyrie: Hyrax.config.use_valkyrie?)
+
+      resources = if Hyrax.config.use_valkyrie?
+                    Hyrax.query_service.find_many_by_ids(ids: batch)
+                  else
+                    Hyrax.custom_queries.find_many_by_alternate_ids(alternate_ids: batch, use_valkyrie: false)
+                  end
+
       resources.each do |resource|
         if Hyrax.config.use_valkyrie?
           LeaseManager.new(resource: resource).release!

data/app/controllers/concerns/hyrax/local_file_downloads_controller_behavior.rb

@@ -6,9 +6,7 @@ module Hyrax
     # Handle the HTTP show request
     def send_local_content
       response.headers['Accept-Ranges'] = 'bytes'
-      if request.head?
-        local_content_head
-      elsif request.headers['Range']
+      if request.headers['Range']
         send_range_for_local_file
       else
         send_local_file_contents
@@ -26,7 +24,11 @@ module Hyrax
       self.status = 206
       prepare_local_file_headers
       # For derivatives stored on the local file system
-      send_data IO.binread(file, length, from), local_derivative_download_options.merge(status: status)
+      if request.head?
+        head status
+      else
+        send_data IO.binread(file, length, from), local_derivative_download_options.merge(status: status)
+      end
     end
 
     def send_local_file_contents
@@ -34,7 +36,11 @@ module Hyrax
       self.status = 200
       prepare_local_file_headers
       # For derivatives stored on the local file system
-      send_file file, local_derivative_download_options
+      if request.head?
+        head status
+      else
+        send_file file, local_derivative_download_options
+      end
     end
 
     def local_file_size
@@ -54,16 +60,9 @@ module Hyrax
       File.mtime(file) if file.is_a? String
     end
 
-    # Override
-    # render an HTTP HEAD response
-    def local_content_head
-      response.headers['Content-Length'] = local_file_size.to_s
-      head :ok, content_type: local_file_mime_type
-    end
-
     # Override
     def prepare_local_file_headers
-      send_file_headers! local_content_options
+      send_file_headers! local_derivative_download_options
       response.headers['Content-Type'] = local_file_mime_type
       response.headers['Content-Length'] ||= local_file_size.to_s
       # Prevent Rack::ETag from calculating a digest over body
@@ -73,12 +72,6 @@ module Hyrax
 
     private
 
-    # Override the Hydra::Controller::DownloadBehavior#content_options so that
-    # we have an attachement rather than 'inline'
-    def local_content_options
-      { type: local_file_mime_type, filename: local_file_name, disposition: 'attachment' }
-    end
-
     # Override this method if you want to change the options sent when downloading
     # a derivative file
     def local_derivative_download_options

data/app/controllers/concerns/hyrax/stream_file_downloads_controller_behavior.rb

@@ -0,0 +1,54 @@
+# frozen_string_literal: true
+module Hyrax
+  # Overrides Hydra::Controller:DownloadBehavior handing of HEAD requests to
+  # respond with same headers as a GET request would receive.
+  module StreamFileDownloadsControllerBehavior
+    protected
+
+    # Handle the HTTP show request
+    def send_content
+      response.headers['Accept-Ranges'] = 'bytes'
+      if request.headers['HTTP_RANGE']
+        send_range
+      else
+        send_file_contents
+      end
+    end
+
+    # rubocop:disable Metrics/AbcSize
+    def send_range
+      _, range = request.headers['HTTP_RANGE'].split('bytes=')
+      from, to = range.split('-').map(&:to_i)
+      to = file.size - 1 unless to
+      length = to - from + 1
+      response.headers['Content-Range'] = "bytes #{from}-#{to}/#{file.size}"
+      response.headers['Content-Length'] = length.to_s
+      self.status = 206
+      prepare_file_headers
+
+      if request.head?
+        head status
+      else
+        stream_body file.stream(request.headers['HTTP_RANGE'])
+      end
+    end
+    # rubocop:enable Metrics/AbcSize
+
+    def send_file_contents
+      return unless stale?(last_modified: file_last_modified, template: false)
+
+      self.status = 200
+      prepare_file_headers
+
+      if request.head?
+        head status
+      else
+        stream_body file.stream
+      end
+    end
+
+    def file_last_modified
+      file.modified_date
+    end
+  end
+end