Merge pull request #2010 from seek4science/emt-json-creation

System Admin has right to create, manage (enable, disable), and delete extended metadata types via user interface #1999

app/assets/javascripts/application.js

@@ -78,3 +78,4 @@
 //= require select2.full.min
 //= require licenses
 //= require svg-pan-zoom-3.6.1/svg-pan-zoom.min
+//= require extended_metadata_type

app/assets/javascripts/extended_metadata_type.js

@@ -0,0 +1,13 @@
+var ExtendedMetadataType = {
+
+    addNewMarker: function(new_id, type) {
+        var isNested = (type === "ExtendedMetadata");
+        $j("#nested-tab, #nested-tab").parent().toggleClass("active", isNested);
+        $j("#nested-metadata-table").toggleClass("active in", isNested);
+        $j("#top-level-tab, #top-level-tab").parent().toggleClass("active", !isNested);
+        $j("#top-level-metadata-table").toggleClass("active in", !isNested);
+
+        var table = isNested ? $j("#nested-metadata-table") : $j("#top-level-metadata-table");
+        table.find("tbody td#" + new_id).append(' <sup style="color:red; font-weight:bold; font-size: 12px">new</sup>');
+    }
+};

app/controllers/extended_metadata_types_controller.rb

@@ -1,8 +1,10 @@
 class ExtendedMetadataTypesController < ApplicationController
-  respond_to :json
+  respond_to :json, :html
+  skip_before_action :project_membership_required
   before_action :is_user_admin_auth, except: [:form_fields, :show, :index]
-  before_action :find_requested_item, only: [:administer_update, :show]
+  before_action :find_requested_item, only: [:administer_update, :show, :destroy]
   include Seek::IndexPager
+  after_action :log_event, only: [:create, :destroy]
 
   api_actions :index, :show
 
@@ -25,10 +27,40 @@ def form_fields
     end
   end
 
+  def create
+
+    if params[:emt_json_file].blank?
+      flash[:error] = 'Please select a file to upload!'
+      redirect_to new_extended_metadata_type_path and return
+    end
+
+    uploaded_file = params[:emt_json_file]
+    @extended_metadata_type = Seek::ExtendedMetadataType::EMTExtractor.extract_extended_metadata_type(uploaded_file)
+
+    if @extended_metadata_type.save
+      flash[:notice] = 'Extended metadata type was successfully created.'
+       redirect_to administer_extended_metadata_types_path(emt: @extended_metadata_type.id)
+    else
+      flash[:error] = @extended_metadata_type.errors.full_messages.join(', ')
+      redirect_to new_extended_metadata_type_path
+    end
+  rescue StandardError => e
+    flash[:error] = e.message
+    redirect_to new_extended_metadata_type_path
+  end
+
+
+  def new
+    respond_to do |format|
+      format.html
+    end
+  end
+
   def show
-     respond_to do |format|
-        format.json {render json: @extended_metadata_type}
-      end
+    respond_to do |format|
+      format.json {render json: @extended_metadata_type}
+      format.html
+    end
   end
 
   def index
@@ -46,6 +78,26 @@ def index
      end
   end
 
+  def destroy
+
+    # if a nested metadata type is linked by other metadata types
+    return if @extended_metadata_type.linked_metadata_attributes.any?
+
+    # if a top level metadata type has been used to create metadatas
+    return if @extended_metadata_type.extended_metadatas.present?
+
+    if @extended_metadata_type.destroy
+      flash[:notice] = 'Extended metadata type was successfully deleted.'
+    else
+      flash[:alert] = 'Failed to delete the extended metadata type.'
+    end
+
+    respond_to do |format|
+      format.html { redirect_to administer_extended_metadata_types_path }
+    end
+
+  end
+
   def administer_update
     @extended_metadata_type.update(extended_metadata_type_params)
     unless @extended_metadata_type.save
@@ -57,6 +109,9 @@ def administer_update
   end
 
   def administer
+    if params[:emt]
+      @extended_metadata_type = ExtendedMetadataType.find(params[:emt])
+    end
     @extended_metadata_types = ExtendedMetadataType.order(:supported_type)
     respond_to do |format|
       format.html
@@ -69,4 +124,17 @@ def extended_metadata_type_params
     params.require(:extended_metadata_type).permit(:title, :enabled)
   end
 
+  def log_event
+
+    return if object_invalid_or_unsaved?(@extended_metadata_type)
+
+    ActivityLog.create(action: action_name.downcase,
+                       culprit: current_user,
+                       controller_name: self.controller_name.downcase,
+                       activity_loggable: object_for_request,
+                        data: object_for_request.title,
+                        user_agent: request.env['HTTP_USER_AGENT'])
+
+  end
+
 end

app/models/extended_metadata.rb

@@ -23,4 +23,8 @@ def attribute_class
     ExtendedMetadataAttribute
   end
 
+  def self.supports_extended_metadata?
+    true
+  end
+
 end

app/models/extended_metadata_type.rb

@@ -4,9 +4,9 @@ class ExtendedMetadataType < ApplicationRecord
   validates :title, presence: true
   validates :extended_metadata_attributes, presence: true
   validates :supported_type, presence: true
-  validate :supported_type_must_be_valid_type
   validate :unique_titles_for_extended_metadata_attributes
   validate :cannot_disable_nested_extended_metadata
+  validate :supports_extended_metadata
 
   alias_method :metadata_attributes, :extended_metadata_attributes
 
@@ -34,13 +34,11 @@ def extended_type?
     supported_type == 'ExtendedMetadata'
   end
 
-  def supported_type_must_be_valid_type
-    return if supported_type.blank? # already convered by presence validation
-    unless Seek::Util.lookup_class(supported_type, raise: false)
-      errors.add(:supported_type, 'is not a type that can supported extended metadata')
-    end
+  def linked_metadata_attributes
+    ExtendedMetadataAttribute.where(linked_extended_metadata_type_id: id)
   end
 
+
   def unique_titles_for_extended_metadata_attributes
     titles = extended_metadata_attributes.collect(&:title)
     if titles != titles.uniq
@@ -54,6 +52,16 @@ def cannot_disable_nested_extended_metadata
     end
   end
 
+  def supports_extended_metadata
+    begin
+      unless Seek::Util.lookup_class(self.supported_type).supports_extended_metadata?
+        errors.add(:supported_type, " '#{self.supported_type}' does not support extended metadata!")
+      end
+    rescue NameError
+      errors.add(:supported_type, "'#{self.supported_type}' is not a valid support type!")
+    end
+  end
+
   def usage
     extended_metadatas.count
   end
@@ -66,7 +74,4 @@ def self.disabled_but_in_use
     disabled.select{|emt| emt.disabled_but_used?}
   end
 
-
-
-
 end

app/models/file_template.rb

@@ -41,5 +41,9 @@ def supports_spreadsheet_explore?
   def self.user_creatable?
     Seek::Config.file_templates_enabled
   end
+
+  def self.supports_extended_metadata?
+    false
+  end
 
 end

app/models/placeholder.rb

@@ -28,4 +28,8 @@ def self.user_creatable?
     Seek::Config.placeholders_enabled
   end
 
+  def self.supports_extended_metadata?
+    false
+  end
+
 end

app/models/publication.rb

@@ -171,6 +171,10 @@ def contributor_credited?
     false
   end
 
+  def self.supports_extended_metadata?
+    false
+  end
+
   def is_in_isa_publishable?
     false
   end

app/models/sample.rb

@@ -65,6 +65,10 @@ def self.can_create?
     User.logged_in_and_member? && Seek::Config.samples_enabled
   end
 
+  def self.supports_extended_metadata?
+    false
+  end
+
   def related_data_files
     [originating_data_file].compact + linked_data_files
   end

app/models/sample_attribute_type.rb

@@ -68,6 +68,10 @@ def linked_extended_metadata_multi?
     base_type == Seek::Samples::BaseType::LINKED_EXTENDED_METADATA_MULTI
   end
 
+  def linked_extended_metadata_or_multi?
+    [Seek::Samples::BaseType::LINKED_EXTENDED_METADATA, Seek::Samples::BaseType::LINKED_EXTENDED_METADATA_MULTI].include?(base_type)
+  end
+
   def seek_sample?
     base_type == Seek::Samples::BaseType::SEEK_SAMPLE
   end

app/models/sample_type.rb

@@ -274,5 +274,9 @@ def validate_title_is_not_type_of_seek_sample_multi
     end
   end
 
+  def self.supports_extended_metadata?
+    false
+  end
+
   class UnknownAttributeException < RuntimeError; end
 end

app/models/template.rb

@@ -111,4 +111,9 @@ def isa_tag_white_list(template_level)
       []
     end
   end
+
+  def self.supports_extended_metadata?
+    false
+  end
+
 end

app/models/workflow.rb

@@ -211,6 +211,10 @@ def contributor_credited?
     false
   end
 
+  def self.supports_extended_metadata?
+    false
+  end
+
   MATURITY_LEVELS = {
       0 => :work_in_progress,
       1 => :released,