hyrax 3.0.0.pre.rc2 → 3.0.0.pre.rc3

data/chart/hyrax/templates/tests/test-connection.yaml

@@ -0,0 +1,15 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  name: "{{ include "hyrax.fullname" . }}-test-connection"
+  labels:
+    {{- include "hyrax.labels" . | nindent 4 }}
+  annotations:
+    "helm.sh/hook": test-success
+spec:
+  containers:
+    - name: wget
+      image: busybox
+      command: ['wget']
+      args: ['{{ include "hyrax.fullname" . }}:{{ .Values.service.port }}']
+  restartPolicy: Never

data/chart/hyrax/values.yaml

@@ -0,0 +1,97 @@
+# Default values for hyrax.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+image:
+  repository: samveralabs/dassie
+  pullPolicy: IfNotPresent
+  # Overrides the image tag whose default is the chart appVersion.
+  tag: ""
+
+imagePullSecrets: []
+nameOverride: ""
+fullnameOverride: ""
+
+serviceAccount:
+  # Specifies whether a service account should be created
+  create: true
+  # Annotations to add to the service account
+  annotations: {}
+  # The name of the service account to use.
+  # If not set and create is true, a name is generated using the fullname template
+  name: ""
+
+podAnnotations: {}
+
+podSecurityContext: {}
+  # fsGroup: 2000
+
+securityContext: {}
+  # capabilities:
+  #   drop:
+  #   - ALL
+  # readOnlyRootFilesystem: true
+  # runAsNonRoot: true
+  # runAsUser: 1000
+
+service:
+  type: ClusterIP
+  port: 80
+
+ingress:
+  enabled: false
+  annotations: {}
+    # kubernetes.io/ingress.class: nginx
+    # kubernetes.io/tls-acme: "true"
+  hosts:
+    - host: hyrax.local
+      paths: []
+  tls: []
+
+resources: {}
+
+fcrepo:
+  enabled: true
+  fcrepoSecretName: "hyrax.fcrepo.fullname"
+  externalDatabaseUsername: "hyrax"
+  servicePort: 8080
+  postgresql:
+    enabled: false
+
+memcached:
+  enabled: false
+
+postgresql:
+  enabled: true
+  image:
+    repository: bitnami/postgresql
+    tag: 12.3.0
+  postgresqlUsername: hyrax
+  postgresqlPassword: hyrax_pass
+  postgresqlDatabase: hyrax
+  servicePort: 5432
+  # cpu: 1000m
+  # memory: 1Gi
+  # persistence:
+  #   size: 10Gi
+
+redis:
+  enabled: true
+
+solr:
+  enabled: true
+
+autoscaling:
+  enabled: false
+  minReplicas: 1
+  maxReplicas: 100
+  targetCPUUtilizationPercentage: 80
+  # targetMemoryUtilizationPercentage: 80
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}

data/config/initializers/indexing_adapter_initializer.rb

@@ -1,14 +1,9 @@
 # frozen_string_literal: true
-require 'valkyrie/indexing_adapter'
-require 'valkyrie/indexing/solr/indexing_adapter'
-require 'valkyrie/indexing/null_indexing_adapter'
 
-Rails.application.config.to_prepare do
-  Valkyrie::IndexingAdapter.register(
-    Valkyrie::Indexing::Solr::IndexingAdapter.new,
-    :solr_index
-  )
-  Valkyrie::IndexingAdapter.register(
-    Valkyrie::Indexing::NullIndexingAdapter.new, :null_index
-  )
-end
+Valkyrie::IndexingAdapter.register(
+  Valkyrie::Indexing::Solr::IndexingAdapter.new,
+  :solr_index
+)
+Valkyrie::IndexingAdapter.register(
+  Valkyrie::Indexing::NullIndexingAdapter.new, :null_index
+)

data/config/initializers/listeners.rb

@@ -6,6 +6,8 @@ Hyrax.publisher.subscribe(Hyrax::Listeners::BatchNotificationListener.new)
 Hyrax.publisher.subscribe(Hyrax::Listeners::ObjectLifecycleListener.new)
 Hyrax.publisher.subscribe(Hyrax::Listeners::FileSetLifecycleListener.new)
 Hyrax.publisher.subscribe(Hyrax::Listeners::FileSetLifecycleNotificationListener.new)
+Hyrax.publisher.subscribe(Hyrax::Listeners::ProxyDepositListener.new)
+Hyrax.publisher.subscribe(Hyrax::Listeners::WorkflowListener.new)
 
 # Publish events from old style Hyrax::Callbacks to trigger the listeners
 # When callbacks are removed and replaced with direct event publication, drop these blocks

data/config/locales/hyrax.en.yml

@@ -576,7 +576,7 @@ en:
           desc: Deposit new work through this collection
           label: Deposit new work through this collection
         delete:
-          confirmation: Delete this collection?
+          confirmation: Deleting this collection will permanently remove this collection from the repository. Any items in this collection will remain in the repository. Are you sure you want to delete this collection?
           desc: Delete this collection
           label: Delete collection
         edit:

data/config/metadata/basic_metadata.yaml

@@ -19,6 +19,9 @@ attributes:
     multiple: true
     form:
       primary: false
+    index_keys:
+      - "based_near_sim"
+      - "based_near_tesim"
   bibliographic_citation:
     type: string
     multiple: true
@@ -33,11 +36,15 @@ attributes:
     form:
       required: true
       primary: true
+    index_keys:
+      - "creator_tesim"
   date_created:
     type: date_time
     multiple: true
     form:
       primary: false
+    index_keys:
+      - "date_created_tesim"
   description:
     type: string
     multiple: true
@@ -55,6 +62,7 @@ attributes:
     multiple: true
     index_keys:
       - "keyword_sim"
+      - "keyword_tesim"
     form:
       primary: false
   publisher:
@@ -83,11 +91,16 @@ attributes:
     multiple: true
     form:
       primary: false
+    index_keys:
+      - "related_url_tesim"
   resource_type:
     type: string
     multiple: true
     form:
       primary: false
+    index_keys:
+      - "resource_type_sim"
+      - "resource_type_tesim"
   rights_notes:
     type: string
     multiple: true

data/db/seeds.rb

@@ -0,0 +1,20 @@
+ActiveFedora.fedora.connection.send(:init_base_path)
+
+puts "\n== Creating default collection types"
+Hyrax::CollectionType.find_or_create_default_collection_type
+Hyrax::CollectionType.find_or_create_admin_set_type
+
+puts "\n== Loading workflows"
+Hyrax::Workflow::WorkflowImporter.load_workflows
+errors = Hyrax::Workflow::WorkflowImporter.load_errors
+abort("Failed to process all workflows:\n  #{errors.join('\n  ')}") unless errors.empty?
+
+puts "\n== Creating default admin set"
+admin_set_id = AdminSet.find_or_create_default_admin_set_id
+
+# I have found that when I come back to a development
+# environment, that I may have an AdminSet in Fedora, but it is
+# not indexed in Solr.  This remediates that situation by
+# ensuring we have an indexed AdminSet
+puts "\n== Ensuring the found or created admin set is indexed"
+AdminSet.find(admin_set_id).update_index

data/docker-compose.yml

@@ -0,0 +1,132 @@
+version: '3.7'
+
+services:
+  app: &app
+    build:
+      context: .
+      target: hyrax-engine-dev
+      args:
+        - EXTRA_APK_PACKAGES=git less
+    image: hyrax-engine-dev
+    stdin_open: true
+    tty: true
+    user: root
+    env_file:
+      - .env
+      - .dassie/.env
+    environment:
+      - RAILS_ROOT=/app/samvera/hyrax-webapp
+    depends_on:
+      - chrome
+      - db_migrate
+      - fcrepo
+      - memcached
+      - postgres
+      - redis
+      - solr
+    ports:
+      - 3000:3000
+    volumes:
+      - .dassie:/app/samvera/hyrax-webapp:cached
+      - .:/app/samvera/hyrax-engine:cached
+      - hyrax-derivatives:/app/samvera/hyrax-webapp/derivatives
+      - hyrax-uploads:/app/samvera/hyrax-webapp/uploads
+      - rails-public:/app/samvera/hyrax-webapp/public
+      - rails-tmp:/app/samvera/hyrax-webapp/tmp
+
+  chrome:
+    image: selenium/standalone-chrome:3.141
+    logging:
+      driver: none
+    volumes:
+      - /dev/shm:/dev/shm
+    shm_size: 2G
+    ports:
+      - "4444:4444"
+      - "5959:5900"
+
+  db_migrate:
+    image: hyrax-engine-dev
+    user: root
+    env_file:
+      - .env
+    entrypoint: ["sh", "-c"]
+    command: db-migrate-seed.sh
+    depends_on:
+      - postgres
+    volumes:
+      - .dassie:/app/samvera/hyrax-webapp:cached
+      - .:/app/samvera/hyrax-engine:cached
+      - rails-public:/app/samvera/hyrax-webapp/public
+      - rails-tmp:/app/samvera/hyrax-webapp/tmp
+
+  postgres:
+    image: postgres:latest
+    restart: always
+    environment:
+      - POSTGRES_USER=hyrax_user
+      - POSTGRES_PASSWORD=hyrax_password
+      - POSTGRES_DB=hyrax
+      - POSTGRES_HOST_AUTH_METHOD=trust
+    ports:
+      - "5432:5432"
+    volumes:
+      - db:/var/lib/postgresql/data
+
+  fcrepo:
+    image: cbeer/fcrepo4:4.7
+    volumes:
+      - fcrepo:/data
+    ports:
+      - 8080:8080
+    environment:
+      - JAVA_OPTS=${JAVA_OPTS} -Dfcrepo.modeshape.configuration="classpath:/config/file-simple/repository.json" -Dfcrepo.object.directory="/data/objects" -Dfcrepo.binary.directory="/data/binaries"
+
+  memcached:
+    image: bitnami/memcached
+    ports:
+      - '11211:11211'
+
+  redis:
+    image: redis:5-alpine
+    volumes:
+      - redis:/data
+
+  sidekiq:
+    build:
+      context: .
+      target: hyrax-engine-dev-worker
+    env_file:
+      - .env
+      - .dassie/.env
+    volumes:
+      - .dassie:/app/samvera/hyrax-webapp:cached
+      - .:/app/samvera/hyrax-engine:cached
+      - hyrax-derivatives:/app/samvera/hyrax-webapp/derivatives
+      - hyrax-uploads:/app/samvera/hyrax-webapp/uploads
+      - sidekiq-public:/app/samvera/hyrax-webapp/public
+      - sidekiq-tmp:/app/samvera/hyrax-webapp/tmp
+
+  solr:
+    image: solr:8.7
+    ports:
+      - 8983:8983
+    command:
+      - sh
+      - "-c"
+      - "precreate-core hyrax_test /opt/solr/server/configsets/hyraxconf; precreate-core hyrax-valkyrie-test /opt/solr/server/configsets/hyraxconf; solr-precreate hyrax /opt/solr/server/configsets/hyraxconf"
+    volumes:
+      - solr_home:/opt/solr/server/solr
+      - .dassie/solr/conf:/opt/solr/server/configsets/hyraxconf
+
+volumes:
+  db:
+  fcrepo:
+  hyrax-derivatives:
+  hyrax-uploads:
+  rails-public:
+  rails-tmp:
+  redis:
+  sidekiq-public:
+  sidekiq-tmp:
+  solr_home:

data/documentation/developing-your-hyrax-based-app.md

@@ -0,0 +1,271 @@
+# Developing Your Hyrax-based Application
+
+## Table of Contents
+
+* [Introduction](#introduction)
+* [Prerequisites](#prerequisites)
+  * [Characterization](#characterization)
+  * [Derivatives](#derivatives)
+  * [Transcoding](#transcoding)
+* [Environments](#environments)
+* [Ruby](#ruby)
+* [Redis](#redis)
+* [Rails](#rails)
+  * [JavaScript runtime](#javascript-runtime)
+* [Creating a Hyrax\-based app](#creating-a-hyrax-based-app)
+  * [Start servers](#start-servers)
+  * [Start background workers](#start-background-workers)
+  * [Create default administrative set](#create-default-administrative-set)
+  * [Generate a work type](#generate-a-work-type)
+  * [Enable notifications](#enable-notifications)
+* [Managing a Hyrax\-based app](#managing-a-hyrax-based-app)
+  * [Toggling Features](#toggling-features)
+
+## Introduction
+
+A Hyrax-based application includes lots of dependencies. We provide a [Docker image for getting started with your Hyrax-based application](/CONTAINERS.md#docker-image-for-hyrax-based-applications).
+
+<aside><p><em><strong>Note:</em></strong> The Docker image describes the canonical dependencies. In a way, it is executable documentation. The following documentation is our best effort to transcribe that executable documentation into a narrative. In other words, this documentation may drift away from the Docker details.</p></aside>
+
+You can also try [Running Hyrax-based application in local VM](https://github.com/samvera/hyrax/wiki/Hyrax-Development-Guide#running-hyrax-based-application-in-local-vm) which uses Ubuntu.
+
+This document contains instructions specific to setting up an app with __Hyrax
+v3.0.0-rc3__. If you are looking for instructions on installing a different
+version, be sure to select the appropriate branch or tag from the drop-down
+menu above.
+
+## Prerequisites
+
+Prerequisites are required for both creating a Hyrax\-based app and contributing new features to Hyrax. After installing the prerequisites...
+
+ * If you would like to create a new application using Hyrax follow the instructions for [Creating a Hyrax\-based app](#creating-a-hyrax-based-app).
+ * If you would like to create new features for Hyrax follow the instructions for [Developing the Hyrax Engine](/README.md#developing-the-hyrax-engine).
+
+Hyrax requires the following software to work:
+
+1. [Solr](http://lucene.apache.org/solr/) version >= 5.x (tested up to 8.7.0)
+1. [Fedora Commons](http://www.fedora-commons.org/) digital repository version >= 4.5.1 (tested up to 4.7.5)
+1. A SQL RDBMS (MySQL, PostgreSQL), though **note** that SQLite will be used by default if you're looking to get up and running quickly
+1. [Redis](http://redis.io/), a key-value store
+1. [ImageMagick](http://www.imagemagick.org/) with JPEG-2000 support
+1. [FITS](#characterization) version 1.0.x (1.0.5 is known to be good, 1.1.0 is known to be bad: https://github.com/harvard-lts/fits/issues/140)
+1. [LibreOffice](#derivatives)
+1. [ffmpeg](#transcoding)
+
+**NOTE: The [Hyrax Development Guide](https://github.com/samvera/hyrax/wiki/Hyrax-Development-Guide) has instructions for installing Solr and Fedora in a development environment.**
+
+### Characterization
+
+FITS can be installed on OSX using Homebrew by running the command: `brew install fits`
+
+**OR**
+
+1. Go to http://projects.iq.harvard.edu/fits/downloads and download a copy of FITS (see above to pick a known working version) & unpack it somewhere on your machine.
+1. Mark fits.sh as executable: `chmod a+x fits.sh`
+1. Run `fits.sh -h` from the command line and see a help message to ensure FITS is properly installed
+1. Give your Hyrax app access to FITS by:
+    1. Adding the full fits.sh path to your PATH (e.g., in your .bash\_profile), **OR**
+    1. Changing `config/initializers/hyrax.rb` to point to your FITS location:  `config.fits_path = "/<your full path>/fits.sh"`
+
+### Derivatives
+
+Install [LibreOffice](https://www.libreoffice.org/). If `which soffice` returns a path, you're done. Otherwise, add the full path to soffice to your PATH (in your `.bash_profile`, for instance). On OSX, soffice is **inside** LibreOffice.app. Your path may look like "/path/to/LibreOffice.app/Contents/MacOS/"
+
+You may also require [ghostscript](http://www.ghostscript.com/) if it does not come with your compiled version LibreOffice. `brew install ghostscript` should resolve the dependency on an OSX-based machine with Homebrew installed.
+
+**NOTE**: Derivatives are served from the filesystem in Hyrax.
+
+### Transcoding
+
+Hyrax includes support for transcoding audio and video files with ffmpeg > 1.0 installed.
+
+On OSX, you can use Homebrew to install ffmpeg:
+
+`brew install libvpx ffmpeg`
+
+Otherwise, to compile ffmpeg yourself, see the [ffmpeg compilation guide](https://trac.ffmpeg.org/wiki/CompilationGuide).
+
+Once ffmpeg has been installed, enable transcoding by setting `config.enable_ffmpeg = true` in `config/initializers/hyrax.rb`.  You may also configure the location of ffmpeg using `config.ffmpeg_path`.
+
+## Environments
+
+Note here that the following commands assume you're setting up Hyrax in a development environment (using the Rails built-in development environment). If you're setting up a production or production-like environment, you may wish to tell Rails that by prepending `RAILS_ENV=production` to the commands that follow, e.g., `rails`, `rake`, `bundle`, and so on.
+
+## Ruby
+
+First, you'll need a working Ruby installation. You can install this via your operating system's package manager -- you are likely to get farther with OSX, Linux, or UNIX than Windows but your mileage may vary -- but we recommend using a Ruby version manager such as [RVM](https://rvm.io/) or [rbenv](https://github.com/sstephenson/rbenv).
+
+Hyrax supports Ruby 2.5, 2.6, and 2.7. When starting a new project, we recommend using the latest Ruby 2.7 version.
+
+## Redis
+
+[Redis](http://redis.io/) is a key-value store that Hyrax uses to provide activity streams on repository objects and users, and helps when modifying order-persisting objects by managing multi-threaded actions on data (preventing race conditions as a global mutex).
+
+Starting up Redis will depend on your operating system, and may in fact already be started on your system. You may want to consult the [Redis documentation](http://redis.io/documentation) for help doing this.
+
+## Rails
+
+Hyrax requires Rails 5. We recommend the latest Rails 5.2 release.
+
+```
+# If you don't already have Rails at your disposal...
+gem install rails -v 5.2.4.4
+```
+
+### JavaScript runtime
+
+Rails requires that you have a JavaScript runtime installed (e.g. nodejs or rubyracer). Either install nodejs or uncomment the `rubyracer` line in your Gemfile and run `bundle install` before running Hyrax's install generator.
+
+NOTE: [nodejs](https://nodejs.org/en/) is preinstalled on most Mac computers and doesn't require a gem.  To test if nodejs is already installed, execute `node -v` in the terminal and the version of nodejs will be displayed if it is installed.
+
+## Creating a Hyrax-based app
+
+NOTE: The steps need to be done in order to create a new Hyrax based app.
+
+Generate a new Rails application using the template.
+
+```
+rails _5.2.4.4_ new my_app -m https://raw.githubusercontent.com/samvera/hyrax/v3.0.0-rc3/template.rb
+```
+
+Generating a new Rails application using Hyrax's template above takes cares of a number of steps for you, including:
+
+* Adding Hyrax (and any of its dependencies) to your application `Gemfile`, to declare that Hyrax is a dependency of your application
+* Running `bundle install`, to install Hyrax and its dependencies
+* Running Hyrax's install generator, to add a number of files that Hyrax requires within your Rails app, including e.g. database migrations
+* Loading all of Hyrax's database migrations into your application's database
+* Loading Hyrax's default workflows into your application's database
+* Create default collection types (e.g. Admin Set, User Collection)
+
+### Start servers
+
+To test-drive your new Hyrax application in development mode, spin up the servers that Hyrax needs (Solr, Fedora, and Rails):
+
+```
+bin/rails hydra:server
+```
+
+And now you should be able to browse to [localhost:3000](http://localhost:3000/) and see the application.
+
+Notes:
+* This web server is purely for development purposes. You will want to use a more fully featured [web server](https://github.com/samvera/hyrax/wiki/Hyrax-Management-Guide#web-server) for production-like environments.
+* You have the option to start each of these services individually.  More information on [solr_wrapper](https://github.com/cbeer/solr_wrapper) and [fcrepo_wrapper](https://github.com/cbeer/fcrepo_wrapper) will help you set this up.  Start rails with `rails s`.
+
+### Start background workers
+
+Many of the services performed by Hyrax are resource intensive, and therefore are well suited to running as background jobs that can be managed and executed by a message queuing system. Examples include:
+
+* File ingest
+* Derivative generation
+* Characterization
+* Fixity
+* Solr indexing
+
+Hyrax implements these jobs using the Rails [ActiveJob](http://edgeguides.rubyonrails.org/active_job_basics.html) framework, allowing you to choose the message queue system of your choice.
+
+For initial development, it is recommended that you change the default ActiveJob adapter from `:async` to `:inline`. This adapter will execute jobs immediately (in the foreground) as they are received. This can be accomplished by adding the following to your `config/environments/development.rb`
+
+```
+class Application < Rails::Application
+  # ...
+  config.active_job.queue_adapter = :inline
+  # ...
+end
+```
+
+For testing, it is recommended that you use the [built-in `:test` adapter](http://api.rubyonrails.org/classes/ActiveJob/QueueAdapters/TestAdapter.html) which stores enqueued and performed jobs, running only those configured to run during test setup. To do this, add the following to `config/environments/test.rb`:
+
+```ruby
+Rails.application.configure do
+  # ...
+  config.active_job.queue_adapter = :test
+  # ...
+end
+```
+
+**For production applications** you will want to use a more robust message queue system such as [Sidekiq](http://sidekiq.org/). The Hyrax Development Guide has a detailed walkthrough of [installing and configuring Sidekiq](https://github.com/samvera/hyrax/wiki/Using-Sidekiq-with-Hyrax).
+
+### Create default administrative set
+
+**After** Fedora and Solr are running, create the default administrative set -- into which all works will be deposited unless assigned to other administrative sets -- by running the following command:
+
+```
+rails hyrax:default_admin_set:create
+```
+
+This command also makes sure that Hyrax's built-in workflows are loaded for your application and available for the default administrative set.
+
+**NOTE**: You will want to run this command the first time this code is deployed to a new environment as well.
+
+### Generate a work type
+
+Using Hyrax requires generating at least one type of repository object, or "work type." Hyrax allows you to generate the work types required in your application by using a Rails generator-based tool. You may generate one or more of these work types.
+
+Pass a (CamelCased) model name to Hyrax's work generator to get started, e.g.:
+
+```
+rails generate hyrax:work Work
+```
+
+or
+
+```
+rails generate hyrax:work MovingImage
+```
+
+If your applications requires your work type to be namespaced, namespaces can be included by adding a slash to the model name which creates a new class called `MovingImage` within the `My` namespace:
+
+```
+rails generate hyrax:work My/MovingImage
+```
+
+You may wish to [customize your work type](https://github.com/samvera/hyrax/wiki/Customizing-your-work-types) now that it's been generated.
+
+### Enable notifications
+
+Hyrax 2 uses a WebSocket-based user notifications system, which requires Redis. To enable user notifications, make sure that you have configured ActionCable to use Redis as the adapter in your application's `config/cable.yml`. E.g., for the `development` Rails environment:
+
+```yaml
+development:
+  adapter: redis
+  url: redis://localhost:6379
+```
+
+Using Rails up to version 5.1.4, ActionCable will not work with the 4.x series of the `redis` gem, so you will also need to pin your application to a 3.x release by adding this to your `Gemfile`:
+
+```ruby
+gem 'redis', '~> 3.0'
+```
+
+And then run `bundle update redis`.
+
+Note that the Hyrax Management Guide contains additional information on [how to configure ActionCable in production environments](https://github.com/samvera/hyrax/wiki/Hyrax-Management-Guide#notifications).
+
+## Managing a Hyrax-based app
+
+The [Hyrax Management Guide](https://github.com/samvera/hyrax/wiki/Hyrax-Management-Guide) provides tips for how to manage, customize, and enhance your Hyrax application, including guidance specific to:
+
+* Production implementations
+* Configuration of background workers
+* Integration with e.g., Dropbox, Google Analytics, and Zotero
+* Audiovisual transcoding with `ffmpeg`
+* Setting up administrative users
+* Metadata customization
+* Virus checking
+* Workflows
+
+### Toggling Features
+
+Some features in Hyrax can be flipped on and off from either the Administrative
+Dashboard or via a YAML configuration file at `config/features.yml`. An example
+of the YAML file is below:
+
+```yaml
+assign_admin_set:
+  enabled: "false"
+proxy_deposit:
+  enabled: "false"
+```
+
+If both options exist, whichever option is set from the Administrative Dashboard
+will take precedence.