Add rake task for creation and syncing structure of BMT inventory [SCI-6010]

app/controllers/bio_eddie_assets_controller.rb

@@ -56,14 +56,16 @@ class BioEddieAssetsController < ApplicationController
   end
 
   def bmt_request
-    return render_404 unless ENV['BIOMOLECULE_TOOLKIT_BASE_URL']
+    return render_404 unless Rails.application.config.x.biomolecule_toolkit_base_url
 
-    uri = URI.parse(ENV['BIOMOLECULE_TOOLKIT_BASE_URL'])
+    uri = URI.parse(Rails.application.config.x.biomolecule_toolkit_base_url)
     uri.path = request.original_fullpath.remove('/biomolecule_toolkit')
 
     Net::HTTP.start(uri.host, uri.port, use_ssl: uri.scheme == 'https') do |http|
       api_request = "Net::HTTP::#{request.request_method.capitalize}".constantize.new(uri)
-      api_request['x-api-key'] = ENV['BIOMOLECULE_TOOLKIT_API_KEY'] if ENV['BIOMOLECULE_TOOLKIT_API_KEY']
+      if Rails.application.config.x.biomolecule_toolkit_api_key
+        api_request['x-api-key'] = if Rails.application.config.x.biomolecule_toolkit_api_key
+      end
       api_request['Content-Type'] = 'application/json'
       request_body = request.body.read
 

app/services/biomolecule_toolkit_client.rb

@@ -2,15 +2,14 @@
 
 class BiomoleculeToolkitClient
   MACROMOLECULES_PATH = '/api/macromolecules'
+  MACROMOLECULES_ATTRIBUTES_PATH = '/api/admin/attributes/MACROMOLECULE'
 
   class BiomoleculeToolkitClientException < StandardError; end
 
   def initialize
-    @host = Rails.configuration.x.biomolecule_toolkit_host
-    @http = Net::HTTP.new(
-      Rails.configuration.x.biomolecule_toolkit_host,
-      Rails.application.config.x.biomolecule_toolkit_port
-    )
+    uri = URI.parse(Rails.application.config.x.biomolecule_toolkit_base_url)
+    @http = Net::HTTP.new(uri.host, uri.port)
+    @http.use_ssl = (uri.scheme == 'https')
   end
 
   def healthy?
@@ -18,13 +17,18 @@ class BiomoleculeToolkitClient
     process_request(request)&.dig('status') == 'UP'
   end
 
+  def list_attributes
+    request = Net::HTTP::Get.new(MACROMOLECULES_ATTRIBUTES_PATH)
+    process_request(request)
+  end
+
   def list
     request = Net::HTTP::Get.new(MACROMOLECULES_PATH)
     process_request(request)
   end
 
   def create(params:)
-    request = Net::HTTP::Post.new(MACROMOLECULES_PATH, 'Content-Type': 'application/json')
+    request = Net::HTTP::Post.new(MACROMOLECULES_PATH)
     request.body = params
     process_request(request)
   end
@@ -35,7 +39,7 @@ class BiomoleculeToolkitClient
   end
 
   def update(cid:, params:)
-    request = Net::HTTP::Put.new("#{MACROMOLECULES_PATH}/#{CGI.escape(cid)}", 'Content-Type': 'application/json')
+    request = Net::HTTP::Put.new("#{MACROMOLECULES_PATH}/#{CGI.escape(cid)}")
     request.body = params
     process_request(request)
   end
@@ -48,9 +52,13 @@ class BiomoleculeToolkitClient
   private
 
   def process_request(request)
+    if Rails.application.config.x.biomolecule_toolkit_api_key
+      request['x-api-key'] = Rails.application.config.x.biomolecule_toolkit_api_key
+    end
+    request['Content-Type'] = 'application/json'
     response = @http.request(request)
 
-    case response.class
+    case response
     when Net::HTTPOK
       JSON.parse(response.body)
     when Net::HTTPNoContent

config/initializers/biomolecule_toolkit_client.rb

@@ -1,4 +1,4 @@
 # frozen_string_literal: true
 
-Rails.application.config.x.biomolecule_toolkit_host = ENV['BIOMOLECULE_TOOLKIT_HOST']
-Rails.application.config.x.biomolecule_toolkit_port = ENV['BIOMOLECULE_TOOLKIT_PORT'] || 80
+Rails.application.config.x.biomolecule_toolkit_base_url = ENV['BIOMOLECULE_TOOLKIT_BASE_URL']
+Rails.application.config.x.biomolecule_toolkit_api_key = ENV['BIOMOLECULE_TOOLKIT_API_KEY']

lib/tasks/biomolecule_toolkit.rake

@@ -0,0 +1,46 @@
+# frozen_string_literal: true
+
+namespace :biomolecule_toolkit do
+  desc 'Creates new BMT inventory and maps BMT macromolecules attributes to its columns'
+  task :init_repository, [:team_id] => :environment do |_, args|
+    raise StandardError, 'BMT repository already exists!' if BmtRepository.any?
+
+    bmt_client = BiomoleculeToolkitClient.new
+    attributes = bmt_client.list_attributes
+
+    team = Team.find(args[:team_id])
+    BmtRepository.transaction do
+      repository = BmtRepository.create!(name: 'Molecules', team: team, created_by: team.created_by)
+      attributes.each do |attribute|
+        repository.repository_columns.create!(name: attribute['name'],
+                                              data_type: 'RepositoryTextValue',
+                                              created_by: team.created_by)
+      end
+    end
+  end
+
+  desc 'Syncs BMT inventory columns with BMT macromolecules attributes'
+  task sync_repository: :environment do
+    raise StandardError, 'BMT repository does not exist!' if BmtRepository.none?
+
+    bmt_client = BiomoleculeToolkitClient.new
+    attributes = bmt_client.list_attributes
+
+    BmtRepository.transaction do
+      repository = BmtRepository.take
+      attributes.each do |attribute|
+        next if repository.repository_columns.find_by(name: attribute['name']).present?
+
+        repository.repository_columns.create!(name: attribute['name'],
+                                              data_type: 'RepositoryTextValue',
+                                              created_by: repository.created_by)
+      end
+
+      repository.repository_columns.each do |repository_column|
+        next if attributes.pluck('name').include?(repository_column.name)
+
+        repository_column.destroy!
+      end
+    end
+  end
+end