biovision 0.4.210512.0 → 0.12.211124.0

data/app/lib/biovision/components/content_component.rb

@@ -5,7 +5,18 @@ module Biovision
     # Content
     class ContentComponent < BaseComponent
       def self.dependent_models
-        [DynamicPage, NavigationGroup, NavigationGroupPage, DynamicBlock]
+        [
+          DynamicPage, NavigationGroup, NavigationGroupPage, DynamicBlock,
+          OembedReceiver, OembedDomain, OembedLink
+        ]
+      end
+
+      def self.seed
+        [
+          Biovision::Components::Content::Oembed::VimeoReceiver,
+          Biovision::Components::Content::Oembed::YoutubeReceiver,
+          Biovision::Components::Content::Oembed::TwitterReceiver
+        ].each(&:seed)
       end
 
       def use_parameters?
@@ -17,11 +28,11 @@ module Biovision
       end
 
       def crud_table_names
-        super - %w[navigation_group_pages]
+        super - %w[navigation_group_pages oembed_receivers oembed_domains]
       end
 
       def administrative_parts
-        %w[navigation_groups dynamic_blocks dynamic_pages]
+        %w[navigation_groups dynamic_blocks dynamic_pages oembed_links]
       end
 
       def navigation

data/app/lib/biovision/components/users_component.rb

@@ -124,6 +124,12 @@ module Biovision
         user.attributes[attribute_name.to_s]
       end
 
+      def role_tree
+        result = super
+        result['users'] << 'log_in'
+        result
+      end
+
       def crud_table_names
         super - %w[user_languages biovision_component_users]
       end

data/app/lib/biovision/helpers/data_helper.rb

@@ -7,18 +7,25 @@ module Biovision
       attr_reader :model_class
 
       # @param [ApplicationRecord] model_class
-      def initialize(model_class)
+      # @param [Hash] filters
+      def initialize(model_class, filters = {})
         @model_class = model_class
+        @filters = filters
       end
 
       # @param [Integer] page
-      # @param [Hash] filters
-      def administrative_collection(page = 1, filters = {})
-        @filters = filters
+      def administrative_collection(page = 1)
         paginates = model_class.respond_to?(:page_for_administration)
         paginates ? administrative_page(page) : administrative_list
       end
 
+      # @param [User] user
+      # @param [Integer] page
+      def personal_collection(user, page = 1)
+        paginates = model_class.respond_to?(:page_for_owner)
+        paginates ? personal_page(user, page) : personal_list(user)
+      end
+
       private
 
       def administrative_list
@@ -38,6 +45,26 @@ module Biovision
           model_class.page_for_administration(page)
         end
       end
+
+      # @param [User] user
+      def personal_list(user)
+        if model_class.respond_to?(:filtered)
+          model_class.filtered(@filters).list_for_owner(user)
+        else
+          model_class.list_for_owner(user)
+        end
+      end
+
+      # @param [User] user
+      # @param [Integer] page
+      def personal_page(user, page)
+        reflection = model_class.singleton_method(:page_for_owner)
+        if reflection.parameters.include?(%i[key filters])
+          model_class.page_for_owner(user, page, filters: @filters)
+        else
+          model_class.page_for_owner(user, page)
+        end
+      end
     end
   end
 end

data/app/lib/biovision/helpers/export_helper.rb

@@ -0,0 +1,97 @@
+# frozen_string_literal: true
+
+module Biovision
+  module Helpers
+    # Helper for exporting model data
+    class ExportHelper
+      EXPORT_DIR = "#{Rails.root}/tmp/export"
+      SPECIAL_FIELDS = %w[id agent_id ip_address_id image attachment].freeze
+
+      # @param [Class] model
+      def export_model(model)
+        puts "Exporting model #{model}..."
+        FileUtils.mkdir_p(EXPORT_DIR) unless Dir.exist?(EXPORT_DIR)
+        file_name = "#{EXPORT_DIR}/#{model.table_name}.yml"
+        File.open(file_name, 'wb') do |file|
+          @file = file
+          model.order(:id).each do |entity|
+            @entity = entity
+            export_entity
+          end
+        end
+      end
+
+      private
+
+      def export_entity
+        print "\r#{@entity.id}  "
+        @file.puts "#{@entity.id}:"
+        export_attributes
+      end
+
+      def export_attributes
+        filtered = @entity.attributes.reject { |a, v| ignored?(a) || v.nil? }
+        filtered.each do |attribute, value|
+          export_attribute(attribute, value)
+        end
+        export_track
+        export_media('image') if @entity.attributes.key?('image')
+        export_media('attachment') if @entity.attributes.key?('attachment')
+      end
+
+      # @param [String] attribute
+      # @param value
+      def export_attribute(attribute, value)
+        @file.print "  #{attribute}: "
+        if value.is_a?(Hash)
+          if value.blank?
+            @file.puts '{}'
+          else
+            @file.puts value.to_yaml.gsub(/\A---|\n\z/, '').gsub("\n", "\n    ")
+          end
+        else
+          @file.puts value.inspect
+        end
+      end
+
+      def export_track
+        return unless @entity.is_a?(HasTrack)
+
+        unless @entity.ip_address.nil?
+          @file.puts "  ip_address: #{@entity.ip_address.ip.to_s.inspect}"
+        end
+
+        return if @entity.agent.blank?
+
+        @file.puts "  agent: #{@entity.agent.name.inspect}"
+      end
+
+      def media_dir
+        "#{EXPORT_DIR}/#{@entity.class.table_name}"
+      end
+
+      def export_media(type)
+        media = @entity.send(type.to_sym)
+
+        return if media.blank?
+
+        media_name = File.basename(media.path)
+        dir_name = "#{media_dir}/#{@entity.id}"
+        FileUtils.mkdir_p(dir_name) unless Dir.exist?(dir_name)
+        FileUtils.copy(media.path, "#{dir_name}/#{media_name}")
+        @file.puts "  #{type}: #{media_name.inspect}"
+      end
+
+      # @param [String] attribute
+      def ignored?(attribute)
+        return true if SPECIAL_FIELDS.include?(attribute)
+
+        %w[count cache].each do |ending|
+          return true if attribute.end_with?("_#{ending}")
+        end
+
+        false
+      end
+    end
+  end
+end

data/app/lib/biovision/migrations/component_migration.rb

@@ -22,7 +22,9 @@ module Biovision
           message = "create_#{model.table_name}".to_sym
           send(message) if respond_to?(message, true)
         end
-        component[nil].create_roles
+        handler = component[nil]
+        handler.create_roles
+        handler.seed if handler.respond_to?(:seed)
       end
 
       # Drops tables for each dependent model

data/app/lib/biovision/stories/component_story.rb

@@ -0,0 +1,55 @@
+# frozen_string_literal: true
+
+module Biovision
+  module Stories
+    # Base component story
+    class ComponentStory
+      attr_accessor :component_handler, :entity
+
+      # @param [Biovision::Components::BaseComponent] handler
+      # @param [ApplicationRecord|String|nil] entity
+      def initialize(handler, entity = nil)
+        self.component_handler = handler
+        return if entity.blank?
+
+        if entity.is_a?(ApplicationRecord)
+          self.entity = entity
+        else
+          self.entity_id = entity.to_s
+        end
+      end
+
+      # Get associated model class
+      #
+      # This method should be implemented in children if story name
+      # does not match model name.
+      # The result is used in #entity_id=
+      def model_class
+        model_name = to_s.demodulize.to_s.underscore.gsub('_story', '')
+        model_name.classify.safe_constantize
+      end
+
+      # @param [Hash] parameters
+      def perform(parameters)
+        @parameters = parameters
+        # implement in children and return hash
+        { result: 'Nothing was processed.' }
+      end
+
+      # Set entity identified by value
+      #
+      # This method can be implemented in child classes
+      #
+      # @param [String] value
+      def entity_id=(value)
+        return if model_class.nil?
+
+        if model_class.respond_to?(:[])
+          self.entity = model_class[value]
+        elsif model_class.respond_to?(:find_by)
+          self.entity = model_class.find_by(id: value)
+        end
+      end
+    end
+  end
+end

data/app/models/biovision_component.rb

@@ -13,12 +13,15 @@
 class BiovisionComponent < ApplicationRecord
   include FlatPriority
   include RequiredUniqueSlug
+  include Toggleable
 
   SLUG_LIMIT = 250
   SLUG_PATTERN_HTML = '^[a-zA-Z][-a-zA-Z0-9_]+[a-zA-Z0-9]$'
 
-  has_many :biovision_component_users, dependent: :delete_all
+  toggleable :active
+
   has_many :simple_images, dependent: :destroy
+  has_many :uploaded_files, dependent: :destroy
   has_many :codes, dependent: :delete_all
   has_many :roles, dependent: :destroy
   has_many :groups, dependent: :destroy
@@ -42,6 +45,8 @@ class BiovisionComponent < ApplicationRecord
 
   # @param [String] slug
   # @param value
+  #
+  # @deprecated use parameters[slug.to_s] = value
   def []=(slug, value)
     parameters[slug.to_s] = value
     save!
@@ -65,4 +70,12 @@ class BiovisionComponent < ApplicationRecord
 
     code
   end
+
+  def text_for_link
+    I18n.t("biovision.components.#{slug}.name", default: slug)
+  end
+
+  def admin_url
+    "/admin/components/#{slug}"
+  end
 end

data/app/models/code.rb

@@ -17,7 +17,7 @@ class Code < ApplicationRecord
   include HasTrack
 
   BODY_LIMIT = 50
-  QUANTITY_RANGE = (0..32_767).freeze
+  QUANTITY_RANGE = (0..32_767)
 
   belongs_to :biovision_component
   belongs_to :user, optional: true
@@ -80,10 +80,10 @@ class Code < ApplicationRecord
     return unless body.nil?
 
     if phone?
+      self.body = SecureRandom.random_number(1_000_000).to_s.rjust(6, '0')
+    else
       number = SecureRandom.random_number(0xffff_ffff_ffff_ffff)
       self.body = number.to_s(36).scan(/.{4}/).join('-').upcase
-    else
-      self.body = SecureRandom.random_number(1_000_000).to_s.rjust(6, '0')
     end
   end
 

data/app/models/concerns/checkable.rb

@@ -13,7 +13,8 @@ module Checkable
       if id.blank?
         entity = new(parameters)
       else
-        entity = find_by(id: id)
+        key = column_names.include?('uuid') && id.include?('-') ? :uuid : :id
+        entity = find_by(key => id)
         entity.assign_attributes(parameters)
       end
       entity

data/app/models/concerns/has_uploaded_file.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+# Model references to uploaded file
+module HasUploadedFile
+  extend ActiveSupport::Concern
+
+  included do
+    belongs_to :uploaded_file, optional: true, counter_cache: :object_count
+
+    scope :included_file, -> { includes(:uploaded_file) }
+  end
+
+  def attachment_name
+    uploaded_file&.name
+  end
+
+  def attachment_size
+    uploaded_file&.file_size
+  end
+
+  def attachment_url
+    return if uploaded_file&.attachment.blank?
+
+    uploaded_file.attachment.url
+  end
+end

data/app/models/concerns/simple_tag.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+# Adds list of toggleable attributes to model
+#
+# @author Maxim Khan-Magomedov <maxim.km@gmail.com>
+module SimpleTag
+  extend ActiveSupport::Concern
+
+  included do
+
+    before_validation :normalize_name
+    validates_uniqueness_of :name, case_sensitive: false
+
+    scope :list_for_administration, -> { order(:name) }
+
+    def self.entity_parameters
+      %i[name]
+    end
+
+    def self.name_limit
+      100
+    end
+
+    private
+
+    def normalize_name
+      self.name = name.to_s[0..name_limit]
+    end
+  end
+end

data/app/models/concerns/toggleable.rb

@@ -14,7 +14,8 @@ module Toggleable
     def toggle_parameter(attribute)
       return unless toggleable_attributes.include? attribute.to_sym
 
-      toggle! attribute
+      assign_attributes(attribute => !attributes[attribute.to_s])
+      save!
       { attribute => self[attribute] }
     end
   end

data/app/models/concerns/tree_structure.rb

@@ -13,6 +13,8 @@ module TreeStructure
     after_destroy { parent&.cache_children! unless ENV['SKIP_CHILDREN_CACHE'] }
     after_save { parent&.cache_children! unless ENV['SKIP_CHILDREN_CACHE'] }
 
+    scope :with_parent_id, ->(v) { where(parent_id: v) }
+
     def self.tree(collection)
       result = {}
 

data/app/models/metric.rb

@@ -25,6 +25,10 @@ class Metric < ApplicationRecord
 
   validates_length_of :name, maximum: NAME_LIMIT
 
+  # @param [String] name
+  def self.[](name)
+    find_by(name: name)
+  end
 
   def quantity
     metric_values.sum(:quantity)

data/app/models/oembed_domain.rb

@@ -0,0 +1,25 @@
+# frozen_string_literal: true
+
+# Domain for OEmbed receiver
+#
+# Attributes:
+#   name [String]
+#   oembed_receiver_id [OembedReceiver]
+class OembedDomain < ApplicationRecord
+  include RequiredUniqueName
+
+  NAME_LIMIT = 255
+
+  belongs_to :oembed_receiver
+
+  validates_length_of :name, maximum: NAME_LIMIT
+
+  # @param [String] name
+  def self.[](name)
+    find_by(name: name.to_s.downcase)
+  end
+
+  def receiver_slug
+    oembed_receiver&.slug
+  end
+end

data/app/models/oembed_link.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+# Link from oembed tag
+#
+# Attributes:
+#   code [Text], optional
+#   created_at [DateTime]
+#   updated_at [DateTime]
+#   url [String]
+class OembedLink < ApplicationRecord
+  URL_LIMIT = 255
+
+  validates_presence_of :url
+  before_save { self.url = url.to_s[0..(URL_LIMIT - 1)] }
+
+  def self.[](url)
+    find_or_initialize_by(url: url)
+  end
+end

data/app/models/oembed_receiver.rb

@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+# Receiver for OEmbed links
+#
+# Attributes:
+#   slug [String]
+class OembedReceiver < ApplicationRecord
+  include RequiredUniqueSlug
+
+  SLUG_PATTERN = /\A[a-z]+(_?[a-z]+){2,49}\z/
+
+  has_many :oembed_domains, dependent: :delete_all
+
+  validates_format_of :slug, with: SLUG_PATTERN
+end

data/app/models/role.rb

@@ -44,12 +44,7 @@ class Role < ApplicationRecord
   end
 
   def user_ids
-    # direct_inclusive = user_roles.where(inclusive: true).pluck(:user_id).uniq
-    # direct_exclusive = user_roles.where(inclusive: false).pluck(:user_id).uniq
-    # group_inclusive = groups.map(&:user_ids).flatten
-    #
-    # group_inclusive + direct_inclusive - direct_exclusive
-    []
+    (user_roles.pluck(:user_id).uniq + groups.map(&:user_ids).flatten).uniq
   end
 
   def count_users!
@@ -76,12 +71,9 @@ class Role < ApplicationRecord
   end
 
   # @param [User] user
-  # @param [Hash] options
-  def add_user(user, options = { inclusive: true })
-    inclusive = !options[:inclusive].blank?
-
-    user_roles.create(user: user, inclusive: inclusive)
-    inclusive ? add_to_cache!(user) : remove_from_cache!(user)
+  def add_user(user)
+    user_roles.create(user: user)
+    add_to_cache!(user)
   end
 
   # @param [User] user

data/app/models/simple_image.rb

@@ -6,7 +6,9 @@
 #   agent_id [Agent], optional
 #   biovision_component_id [BiovisionComponent]
 #   caption [string], optional
+#   checksum [String], optional
 #   created_at [DateTime]
+#   data [jsonb]
 #   image [SimpleImageUploader]
 #   image_alt_text [string]
 #   ip_address_id [IpAddress], optional
@@ -16,7 +18,6 @@
 #   updated_at [DateTime]
 #   user_id [User], optional
 #   uuid [uuid]
-#   data [jsonb]
 class SimpleImage < ApplicationRecord
   include Checkable
   include HasOwner
@@ -24,6 +25,7 @@ class SimpleImage < ApplicationRecord
   include HasUuid
 
   META_LIMIT = 255
+  ORIGINAL_CHECKSUM = 'original_checksum'
 
   mount_uploader :image, SimpleImageUploader
 
@@ -33,6 +35,8 @@ class SimpleImage < ApplicationRecord
   has_many :simple_image_tag_images, dependent: :destroy
   has_many :simple_image_tags, through: :simple_image_tag_images
 
+  before_save :calculate_checksum
+
   validates_presence_of :image
   validates_length_of :caption, maximum: META_LIMIT
   validates_length_of :image_alt_text, maximum: META_LIMIT
@@ -41,12 +45,27 @@ class SimpleImage < ApplicationRecord
 
   scope :in_component, ->(v) { where(biovision_component: v) }
   scope :filtered, ->(v) { where('image ilike ? or caption ilike ?', "%#{v}%", "%#{v}%") unless v.blank? }
-  scope :list_for_administration, -> { order('image asc') }
+  scope :list_for_administration, -> { order(:image) }
+
+  # @param [String] input
+  def self.[](input)
+    case input
+    when /\A\h{8}-\h{4}-4\h{3}-[89ab]\h{3}-\h{12}\Z/i
+      find_by(uuid: input)
+    when /\A[a-f0-9]{64}\z/i
+      key = "data->>'#{ORIGINAL_CHECKSUM}'"
+      find_by(checksum: input) || find_by("#{key} = ?", input)
+    end
+  end
 
   def self.entity_parameters
     %i[caption image image_alt_text source_link source_name]
   end
 
+  def self.json_attributes
+    %i[caption image_alt_text source_link source_name]
+  end
+
   def name
     File.basename(image.path)
   end
@@ -58,4 +77,12 @@ class SimpleImage < ApplicationRecord
   def image_slug
     "#{uuid[0..2]}/#{uuid[3..5]}/#{uuid}"
   end
+
+  private
+
+  def calculate_checksum
+    return if image&.path.blank?
+
+    self.checksum = Digest::SHA256.file(image.path).hexdigest
+  end
 end

data/app/models/simple_image_tag.rb

@@ -9,22 +9,7 @@
 #   updated_at [DateTime]
 class SimpleImageTag < ApplicationRecord
   include Checkable
-  NAME_LIMIT = 100
+  include SimpleTag
 
   has_many :simple_image_tag_images, dependent: :delete_all
-
-  before_validation :normalize_name
-  validates_uniqueness_of :name, case_sensitive: false
-
-  scope :list_for_administration, -> { order('name asc') }
-
-  def self.entity_parameters
-    %i[name]
-  end
-
-  private
-
-  def normalize_name
-    self.name = name.to_s[0..NAME_LIMIT]
-  end
 end

data/app/models/uploaded_file.rb

@@ -0,0 +1,62 @@
+# frozen_string_literal: true
+
+# Uploaded file
+#
+# Attributes:
+#   attachment [SimpleFileUploader]
+#   agent_id [Agent], optional
+#   biovision_component_id [BiovisionComponent]
+#   checksum [String]
+#   created_at [DateTime]
+#   data [jsonb]
+#   description [String], optional
+#   ip_address_id [IpAddress], optional
+#   object_count [Integer]
+#   updated_at [DateTime]
+#   user_id [User], optional
+#   uuid [uuid]
+class UploadedFile < ApplicationRecord
+  include Checkable
+  include HasOwner
+  include HasTrack
+  include HasUuid
+
+  META_LIMIT = 255
+
+  mount_uploader :attachment, SimpleFileUploader
+
+  belongs_to :agent, optional: true
+  belongs_to :biovision_component
+  belongs_to :user, optional: true
+  has_many :uploaded_file_tag_files, dependent: :destroy
+  has_many :uploaded_file_tags, through: :uploaded_file_tag_files
+
+  before_save :calculate_checksum
+
+  validates_presence_of :attachment
+  validates_length_of :description, maximum: META_LIMIT
+
+  scope :in_component, ->(v) { where(biovision_component: v) }
+  scope :filtered, ->(v) { where('description ilike ? or attachment ilike ?', "%#{v}%", "%#{v}%") unless v.blank? }
+  scope :list_for_administration, -> { order('attachment asc') }
+
+  def self.entity_parameters
+    %i[attachment description]
+  end
+
+  def name
+    File.basename(attachment.path)
+  end
+
+  def file_size
+    File.size(attachment.path)
+  end
+
+  private
+
+  def calculate_checksum
+    return if attachment&.path.blank?
+
+    self.checksum = Digest::SHA256.file(attachment.path).hexdigest
+  end
+end