Add migration scripts [SCI-3539]

.gitignore

@@ -35,6 +35,9 @@ ehthumbs.db
 # Ignore temporary files
 public/system/*
 
+# Ignore ActiveStorage Disc service storage directory
+storage/
+
 # Ignore robots.txt
 public/robots.txt
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM ruby:2.5.5
+FROM ruby:2.6.3
 MAINTAINER BioSistemika <info@biosistemika.com>
 
 # Get version of Debian (lsb_release substitute) and save it to /tmp/lsb_release for further commands

Dockerfile.production

@@ -1,4 +1,4 @@
-FROM ruby:2.5.5
+FROM ruby:2.6.3
 MAINTAINER BioSistemika <info@biosistemika.com>
 
 RUN echo deb "http://http.debian.net/debian stretch-backports main" >> /etc/apt/sources.list

Gemfile

@@ -2,7 +2,7 @@
 
 source 'http://rubygems.org'
 
-ruby '2.5.5'
+ruby '2.6.3'
 
 
 gem 'bootsnap', require: false
@@ -80,7 +80,9 @@ gem 'underscore-rails'
 gem 'wicked_pdf', '~> 1.1.0'
 gem 'wkhtmltopdf-heroku'
 
+gem 'aws-sdk-rails'
 gem 'aws-sdk-s3'
+gem 'mini_magick'
 gem 'paperclip', '~> 6.1' # File attachment, image attachment library
 gem 'delayed_job_active_record'
 gem 'devise-async',

Gemfile.lock

@@ -115,10 +115,16 @@ GEM
     aws-sdk-kms (1.21.0)
       aws-sdk-core (~> 3, >= 3.53.0)
       aws-sigv4 (~> 1.1)
+    aws-sdk-rails (2.1.0)
+      aws-sdk-ses (~> 1)
+      railties (>= 3)
     aws-sdk-s3 (1.42.0)
       aws-sdk-core (~> 3, >= 3.53.0)
       aws-sdk-kms (~> 1)
       aws-sigv4 (~> 1.1)
+    aws-sdk-ses (1.22.0)
+      aws-sdk-core (~> 3, >= 3.53.0)
+      aws-sigv4 (~> 1.1)
     aws-sigv4 (1.1.0)
       aws-eventstream (~> 1.0, >= 1.0.2)
     backports (3.15.0)
@@ -310,6 +316,7 @@ GEM
     method_source (0.9.2)
     mime-types (1.25.1)
     mimemagic (0.3.3)
+    mini_magick (4.9.3)
     mini_mime (1.0.1)
     mini_portile2 (2.3.0)
     minitest (5.11.3)
@@ -567,6 +574,7 @@ DEPENDENCIES
   auto_strip_attributes (~> 2.1)
   autosize-rails
   awesome_print
+  aws-sdk-rails
   aws-sdk-s3
   base62
   bcrypt (~> 3.1.10)
@@ -610,6 +618,7 @@ DEPENDENCIES
   kaminari
   listen (~> 3.0)
   logging (~> 2.0.0)
+  mini_magick
   momentjs-rails (~> 2.17.1)
   nested_form_fields
   newrelic_rpm
@@ -664,7 +673,7 @@ DEPENDENCIES
   yomu
 
 RUBY VERSION
-   ruby 2.5.5p157
+   ruby 2.6.3p62
 
 BUNDLED WITH
    1.17.3

app/models/asset.rb

@@ -6,48 +6,51 @@ class Asset < ApplicationRecord
 
   require 'tempfile'
   # Lock duration set to 30 minutes
-  LOCK_DURATION = 60*30
+  LOCK_DURATION = 60 * 30
+
+  # ActiveStorage configuration
+  has_one_attached :file
 
   # Paperclip validation
-  has_attached_file :file,
+  # has_attached_file :file,
-                    styles: lambda { |a|
+  #                   styles: lambda { |a|
-                      if a.previewable_document?
+  #                     if a.previewable_document?
-                        {
+  #                       {
-                          large: { processors: [:custom_file_preview],
+  #                         large: { processors: [:custom_file_preview],
-                                   geometry: Constants::LARGE_PIC_FORMAT,
+  #                                  geometry: Constants::LARGE_PIC_FORMAT,
-                                   format: :jpg },
+  #                                  format: :jpg },
-                          medium: { processors: [:custom_file_preview],
+  #                         medium: { processors: [:custom_file_preview],
-                                    geometry: Constants::MEDIUM_PIC_FORMAT,
+  #                                   geometry: Constants::MEDIUM_PIC_FORMAT,
-                                    format: :jpg }
+  #                                   format: :jpg }
-                        }
+  #                       }
-                      else
+  #                     else
-                        {
+  #                       {
-                          large: [Constants::LARGE_PIC_FORMAT, :jpg],
+  #                         large: [Constants::LARGE_PIC_FORMAT, :jpg],
-                          medium: [Constants::MEDIUM_PIC_FORMAT, :jpg]
+  #                         medium: [Constants::MEDIUM_PIC_FORMAT, :jpg]
-                        }
+  #                       }
-                      end
+  #                     end
-                    },
+  #                   },
-                    convert_options: {
+  #                   convert_options: {
-                      medium: '-quality 70 -strip',
+  #                     medium: '-quality 70 -strip',
-                      all: '-background "#d2d2d2" -flatten +matte'
+  #                     all: '-background "#d2d2d2" -flatten +matte'
-                    }
+  #                   }
 
-  before_post_process :previewable?
+  # before_post_process :previewable?
-  before_post_process :extract_image_quality
+  # before_post_process :extract_image_quality
 
   # adds image processing in background job
-  process_in_background :file, processing_image_url: '/images/:style/processing.gif'
+  # process_in_background :file, processing_image_url: '/images/:style/processing.gif'
 
-  validates_attachment :file,
+  # validates_attachment :file,
-                       presence: true,
+  #                      presence: true,
-                       size: {
+  #                      size: {
-                         less_than: Rails.configuration.x.file_max_size_mb.megabytes
+  #                        less_than: Rails.configuration.x.file_max_size_mb.megabytes
-                       }
+  #                      }
-  validates :estimated_size, presence: true
+  # validates :estimated_size, presence: true
-  validates :file_present, inclusion: { in: [true, false] }
+  # validates :file_present, inclusion: { in: [true, false] }
 
   # Should be checked for any security leaks
-  do_not_validate_attachment_file_type :file
+  # do_not_validate_attachment_file_type :file
 
   # Asset validation
   # This could cause some problems if you create empty asset and want to
@@ -200,6 +203,18 @@ class Asset < ApplicationRecord
     end
   end
 
+  def medium_preview
+    file.variant(resize: Constants::MEDIUM_PIC_FORMAT)
+  end
+
+  def large_preview
+    file.variant(resize: Constants::LARGE_PIC_FORMAT)
+  end
+
+  def file_size
+    file.blob.byte_size
+  end
+
   def extract_image_quality
     return unless ['image/jpeg', 'image/pjpeg'].include? file_content_type
 

config/storage.yml

@@ -6,13 +6,13 @@ local:
   service: Disk
   root: <%= Rails.root.join("storage") %>
 
-# Use rails credentials:edit to set the AWS secrets (as aws:access_key_id|secret_access_key)
+amazon:
-# amazon:
+  service: CustomS3
-#   service: S3
+  access_key_id: <%= ENV["AWS_ACCESS_KEY_ID"] %>
-#   access_key_id: <%= Rails.application.credentials.dig(:aws, :access_key_id) %>
+  secret_access_key: <%= ENV["AWS_SECRET_ACCESS_KEY"] %>
-#   secret_access_key: <%= Rails.application.credentials.dig(:aws, :secret_access_key) %>
+  region: <%= ENV["AWS_REGION"] %>
-#   region: us-east-1
+  bucket: <%= ENV["S3_BUCKET"] %>
-#   bucket: your_own_bucket
+  subfolder: <%= ENV["S3_SUBFOLDER"] %>
 
 # Remember not to checkin your GCS keyfile to a repository
 # google:

db/migrate/20190613134100_convert_to_active_storage.rb

@@ -0,0 +1,117 @@
+# frozen_string_literal: true
+
+class ConvertToActiveStorage < ActiveRecord::Migration[5.2]
+  require 'open-uri'
+
+  ID_PARTITION_LIMIT = 1_000_000_000
+  DIGEST = OpenSSL::Digest.const_get('SHA1').new
+
+  def up
+    ActiveRecord::Base.connection.raw_connection.prepare('active_storage_blob_statement', <<-SQL)
+      INSERT INTO active_storage_blobs (
+        key, filename, content_type, metadata, byte_size, checksum, created_at
+      ) VALUES ($1, $2, $3, '{}', $4, $5, $6)
+      RETURNING id;
+    SQL
+
+    ActiveRecord::Base.connection.raw_connection.prepare('active_storage_attachment_statement', <<-SQL)
+      INSERT INTO active_storage_attachments (
+        name, record_type, record_id, blob_id, created_at
+      ) VALUES ($1, $2, $3, $4, $5)
+    SQL
+
+    Rails.application.eager_load!
+    models = ApplicationRecord.descendants.reject(&:abstract_class?)
+
+    transaction do
+      models.each do |model|
+        attachments = model.column_names.map do |c|
+          $1 if c =~ /(.+)_file_name$/
+        end.compact
+
+        next if attachments.blank?
+
+        model.find_each.each do |instance|
+          attachments.each do |attachment|
+            next if instance.__send__("#{attachment}_file_name").blank?
+
+            res = ActiveRecord::Base.connection.raw_connection.exec_prepared(
+              'active_storage_blob_statement', [
+                key(instance, attachment),
+                instance.__send__("#{attachment}_file_name"),
+                instance.__send__("#{attachment}_content_type"),
+                instance.__send__("#{attachment}_file_size") || 0,
+                checksum(instance.__send__(attachment)),
+                instance.updated_at.iso8601
+              ]
+            )
+
+            ActiveRecord::Base.connection.raw_connection.exec_prepared(
+              'active_storage_attachment_statement', [
+                attachment,
+                model.name,
+                instance.id,
+                res[0]['id'],
+                instance.updated_at.iso8601
+              ]
+            )
+          end
+        end
+      end
+    end
+  end
+
+  def down
+    # raise ActiveRecord::IrreversibleMigration
+  end
+
+  private
+
+  ID_PARTITION_LIMIT = 1_000_000_000
+  DIGEST = OpenSSL::Digest.const_get('SHA1').new
+
+  def id_partition(id)
+    if id < ID_PARTITION_LIMIT
+      format('%09d', id).scan(/\d{3}/).join('/')
+    else
+      format('%012d', id).scan(/\d{3}/).join('/')
+    end
+  end
+
+  def hash_data(instance, attachment)
+    "#{instance.class.to_s.underscore.pluralize}/#{attachment.pluralize}/#{instance.id}/original"
+  end
+
+  def interpolate(pattern, instance, attachment)
+    path = pattern
+    path = path.gsub(':class', instance.class.to_s.underscore.pluralize)
+    path = path.gsub(':attachment', attachment.pluralize)
+    path = path.gsub(':id_partition', id_partition(instance.id))
+    path = path.gsub(':hash', OpenSSL::HMAC.hexdigest(DIGEST,
+                                                      ENV['PAPERCLIP_HASH_SECRET'],
+                                                      hash_data(instance, attachment)))
+    path.gsub(':filename', instance.__send__("#{attachment}_file_name"))
+  end
+
+  def key(instance, attachment)
+    # SecureRandom.uuid
+    # Alternatively:
+    pattern = if ENV['PAPERCLIP_STORAGE'] == 's3'
+                ':class/:attachment/:id_partition/:hash/original/:filename'
+              else
+                "#{Rails.root}/public/system/:class/:attachment/:id_partition/:hash/original/:filename"
+              end
+    interpolate(pattern, instance, attachment)
+  end
+
+  def checksum(_attachment)
+    'dummy'
+    # local files stored on disk:
+    # url = attachment.path
+    # Digest::MD5.base64digest(File.read(url))
+
+    # remote files stored on another person's computer:
+    # url = attachment.url
+    # Digest::MD5.base64digest(Net::HTTP.get(URI(url)))
+  end
+end

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: 2019_06_13_094834) do
+ActiveRecord::Schema.define(version: 2019_06_13_134100) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "btree_gist"

lib/active_storage/service/custom_s3_service.rb

@@ -0,0 +1,172 @@
+# frozen_string_literal: true
+
+# Copyright (c) 2017-2019 David Heinemeier Hansson, Basecamp
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+# LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+# OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+# WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+gem 'aws-sdk-s3', '~> 1.14'
+
+require 'aws-sdk-s3'
+require 'active_support/core_ext/numeric/bytes'
+
+module ActiveStorage
+  # Wraps the Amazon Simple Storage Service (S3) as an Active Storage service.
+  # See ActiveStorage::Service for the generic API documentation that applies to all services.
+  class Service::CustomS3Service < Service
+    attr_reader :client, :bucket
+    attr_reader :multipart_upload_threshold, :upload_options
+    attr_reader :subfolder
+
+    def initialize(bucket:, upload: {}, **options)
+      @subfolder = options.delete(:subfolder)
+
+      @client = Aws::S3::Resource.new(**options)
+      @bucket = @client.bucket(bucket)
+
+      @multipart_upload_threshold = upload.fetch(:multipart_threshold, 100.megabytes)
+      @upload_options = upload
+    end
+
+    def upload(key, io, checksum: nil, content_type: nil, **)
+      instrument :upload, key: key, checksum: checksum do
+        if io.size < multipart_upload_threshold
+          upload_with_single_part key, io, checksum: checksum, content_type: content_type
+        else
+          upload_with_multipart key, io, content_type: content_type
+        end
+      end
+    end
+
+    def download(key, &block)
+      if block_given?
+        instrument :streaming_download, key: key do
+          stream(key, &block)
+        end
+      else
+        instrument :download, key: key do
+          object_for(key).get.body.string.force_encoding(Encoding::BINARY)
+        rescue Aws::S3::Errors::NoSuchKey
+          raise ActiveStorage::FileNotFoundError
+        end
+      end
+    end
+
+    def download_chunk(key, range)
+      instrument :download_chunk, key: key, range: range do
+        object_for(key).get(range: "bytes=#{range.begin}-#{range.exclude_end? ? range.end - 1 : range.end}")
+                       .body
+                       .string
+                       .force_encoding(Encoding::BINARY)
+      rescue Aws::S3::Errors::NoSuchKey
+        raise ActiveStorage::FileNotFoundError
+      end
+    end
+
+    def delete(key)
+      instrument :delete, key: key do
+        object_for(key).delete
+      end
+    end
+
+    def delete_prefixed(prefix)
+      instrument :delete_prefixed, prefix: prefix do
+        prefix = subfolder.present? ? File.join(subfolder, prefix) : prefix
+        bucket.objects(prefix: prefix).batch_delete!
+      end
+    end
+
+    def exist?(key)
+      instrument :exist, key: key do |payload|
+        answer = object_for(key).exists?
+        payload[:exist] = answer
+        answer
+      end
+    end
+
+    def url(key, expires_in:, filename:, disposition:, content_type:)
+      instrument :url, key: key do |payload|
+        generated_url = object_for(key).presigned_url :get, expires_in: expires_in.to_i,
+          response_content_disposition: content_disposition_with(type: disposition, filename: filename),
+          response_content_type: content_type
+
+        payload[:url] = generated_url
+
+        generated_url
+      end
+    end
+
+    def url_for_direct_upload(key, expires_in:, content_type:, content_length:, checksum:)
+      instrument :url, key: key do |payload|
+        generated_url = object_for(key).presigned_url :put, expires_in: expires_in.to_i,
+          content_type: content_type, content_length: content_length, content_md5: checksum
+
+        payload[:url] = generated_url
+
+        generated_url
+      end
+    end
+
+    def headers_for_direct_upload(_key, content_type:, checksum:, **)
+      { 'Content-Type' => content_type, 'Content-MD5' => checksum }
+    end
+
+    private
+
+    MAXIMUM_UPLOAD_PARTS_COUNT = 10000
+    MINIMUM_UPLOAD_PART_SIZE   = 5.megabytes
+
+    def upload_with_single_part(key, io, checksum: nil, content_type: nil)
+      object_for(key).put(body: io, content_md5: checksum, content_type: content_type, **upload_options)
+    rescue Aws::S3::Errors::BadDigest
+      raise ActiveStorage::IntegrityError
+    end
+
+    def upload_with_multipart(key, io, content_type: nil)
+      part_size = [io.size.fdiv(MAXIMUM_UPLOAD_PARTS_COUNT).ceil, MINIMUM_UPLOAD_PART_SIZE].max
+
+      object_for(key).upload_stream(content_type: content_type, part_size: part_size, **upload_options) do |out|
+        IO.copy_stream(io, out)
+      end
+    end
+
+    def object_for(key)
+      key = subfolder.present? ? File.join(subfolder, key) : key
+      bucket.object(key)
+    end
+
+    # Reads the object for the given key in chunks, yielding each to the block.
+    def stream(key)
+      object = object_for(key)
+
+      chunk_size = 5.megabytes
+      offset = 0
+
+      raise ActiveStorage::FileNotFoundError unless object.exists?
+
+      while offset < object.content_length
+        yield object.get(range: "bytes=#{offset}-#{offset + chunk_size - 1}")
+                    .body
+                    .string
+                    .force_encoding(Encoding::BINARY)
+        offset += chunk_size
+      end
+    end
+  end
+end

lib/tasks/active_storage.rake

@@ -0,0 +1,69 @@
+# frozen_string_literal: true
+
+namespace :active_storage do
+  ID_PARTITION_LIMIT = 1_000_000_000
+  DIGEST = OpenSSL::Digest.const_get('SHA1').new
+
+  def id_partition(id)
+    if id < ID_PARTITION_LIMIT
+      format('%09d', id).scan(/\d{3}/).join('/')
+    else
+      format('%012d', id).scan(/\d{3}/).join('/')
+    end
+  end
+
+  def hash_data(attachment)
+    "#{attachment.record_type.underscore.pluralize}/#{attachment.name.pluralize}/#{attachment.record.id}/original"
+  end
+
+  def interpolate(pattern, attachment)
+    path = pattern
+    path = path.gsub(':class', attachment.record_type.underscore.pluralize)
+    path = path.gsub(':attachment', attachment.name.pluralize)
+    path = path.gsub(':id_partition', id_partition(attachment.record.id))
+    path = path.gsub(':hash', OpenSSL::HMAC.hexdigest(DIGEST, ENV['PAPERCLIP_HASH_SECRET'], hash_data(attachment)))
+    path.gsub(':filename', attachment.blob.filename.to_s)
+  end
+
+  desc 'Copy all files from Paperclip to ActiveStorage'
+  task :migrate_files, [:before] => :environment do |_, _args|
+    if ENV['PAPERCLIP_STORAGE'] == 'filesystem'
+      local_path = "#{Rails.root}/public/system/:class/:attachment/:id_partition/:hash/original/:filename"
+
+      ActiveStorage::Attachment.find_each do |attachment|
+        src = interpolate(local_path, attachment)
+        dst_dir = File.join(
+          'storage',
+          attachment.blob.key.first(2),
+          attachment.blob.key.first(4).last(2)
+        )
+        dst = File.join(dst_dir, attachment.blob.key)
+
+        FileUtils.mkdir_p(dst_dir)
+        puts "Copying #{src} to #{dst}"
+        FileUtils.cp(src, dst)
+      end
+    elsif ENV['PAPERCLIP_STORAGE'] == 's3'
+
+      s3_path = ':class/:attachment/:id_partition/:hash/original/:filename'
+      s3_path = "#{ENV['S3_SUBFOLDER']}/" + s3_path if ENV['S3_SUBFOLDER']
+
+      ActiveStorage::Attachment.find_each do |attachment|
+        src_path = interpolate(s3_path, attachment)
+
+        next unless S3_BUCKET.object(src_path).exists?
+
+        dst_path = ENV['S3_SUBFOLDER'] ? File.join(ENV['S3_SUBFOLDER'], attachment.blob.key) : attachment.blob.key
+
+        puts "Copying #{src_path} to #{dst_path}"
+
+        s3.copy_object(bucket: S3_BUCKET.name,
+                       copy_source: S3_BUCKET.name + src_path,
+                       key: dst_path)
+      rescue StandardError => e
+        puts 'Caught exception copying object ' + src_path + ':'
+        puts e.message
+      end
+    end
+  end
+end