Feature/versioning

.eslintrc

@@ -12,6 +12,7 @@
     "no-console": ["off"],
     "comma-dangle": [1,"only-multiline"],
     "react/jsx-filename-extension": [1, { "extensions": [".js", ".jsx"] }],
-    "prefer-destructuring": ["error", {"object": true, "array": false}]
+    "prefer-destructuring": ["error", {"object": true, "array": false}],
+    "react/forbid-prop-types": ["off"]
   }
 }

Gemfile

@@ -111,6 +111,8 @@ gem 'whenever', require: false
 
 gem 'yaml_db'
 
+gem 'logidze'
+
 group :development do
   gem 'better_errors' # allows to debug exception on backend from browser
 

Gemfile.lock

@@ -429,6 +429,10 @@ GEM
     listen (3.3.1)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
+    logidze (1.2.0)
+      activerecord (>= 5.0)
+      railties (>= 5.0)
+      ruby-next-core (~> 0.9)
     loofah (2.17.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
@@ -641,6 +645,7 @@ GEM
       activesupport
       memoist
     ruby-mailchecker (3.2.29)
+    ruby-next-core (0.13.1)
     ruby-ole (1.2.12.2)
     ruby-progressbar (1.10.1)
     ruby2_keywords (0.0.2)
@@ -828,6 +833,7 @@ DEPENDENCIES
   ketcherails!
   launchy (~> 2.4.3)
   listen
+  logidze
   memory_profiler
   meta_request
   net-sftp

app/api/api.rb

@@ -3,6 +3,8 @@
 require 'grape-swagger'
 
 class API < Grape::API
+  include LogidzeModule
+
   format :json
   prefix :api
   version 'v1'
@@ -143,6 +145,7 @@ def to_json_camel_case(val)
   mount Chemotion::NmrdbAPI
   mount Chemotion::MeasurementsAPI
   mount Chemotion::ConverterAPI
+  mount Chemotion::VersionAPI
 
   add_swagger_documentation(info: {
     "title": "Chemotion ELN",

app/api/chemotion/version_api.rb

@@ -0,0 +1,126 @@
+require 'open-uri'
+
+module Chemotion
+  class VersionAPI < Grape::API
+    include Grape::Kaminari
+    helpers ParamsHelpers
+
+    namespace :versions do
+      resource :samples do
+        desc 'Return versions of the given sample'
+
+        params do
+          requires :id, type: Integer, desc: 'Sample id'
+        end
+
+        paginate per_page: 10, offset: 0, max_per_page: 100
+
+        route_param :id do
+          get do
+            # find specific sample and load only required data
+            sample = Sample.select(:id, :name, :log_data, :updated_at).find(params[:id])
+
+            analyses = sample.analyses.flat_map { |analysis| analysis.self_and_descendants.select(:id, :name, :updated_at, :log_data) }
+
+            # create cache key for sample
+            timestamp = [
+              sample.updated_at,
+              analyses.map(&:updated_at).max,
+              Attachment.where(attachable_id: analyses.map(&:id), attachable_type: 'Container').maximum(:updated_at)
+            ].reject(&:nil?).max.to_i
+            cache_key = "versions/samples/#{sample.id}/#{timestamp}"
+
+            # cache processed and sorted versions to speed up pagination
+            versions = Rails.cache.fetch cache_key do
+              all_versions = sample.versions_hash
+              all_versions += sample.residues.select(:sample_id, :log_data).flat_map do |residue|
+                residue.versions_hash(sample.name)
+              end
+              all_versions += sample.elemental_compositions.select(:sample_id, :log_data).flat_map do |elemental_composition|
+                elemental_composition.versions_hash(sample.name)
+              end
+
+              analyses.each do |analysis|
+                all_versions += analysis.versions_hash
+                all_versions += analysis.attachments.select(:attachable_id, :attachable_type, :filename, :log_data).flat_map do |attachment|
+                  attachment.versions_hash(attachment.filename)
+                end
+              end
+
+              all_versions.sort_by! { |version| -version['t'].to_i } # sort versions with the latest changes in the first place
+                          .each_with_index { |record, index| record['v'] = all_versions.length - index } # adjust v to be uniq and in right order
+            end
+
+            { versions: paginate(Kaminari.paginate_array(versions)) }
+          end
+        end
+      end
+
+      resource :reactions do
+        desc 'Return versions of the given reaction'
+
+        params do
+          requires :id, type: Integer, desc: 'Reaction id'
+        end
+
+        paginate per_page: 10, offset: 0, max_per_page: 100
+
+        route_param :id do
+          get do
+            # find specific sample and load only required data
+            reaction = Reaction.select(:id, :name, :log_data, :updated_at).find(params[:id])
+
+            analyses = (
+              reaction.analyses +
+              reaction.samples.includes(:container).pluck('containers.id').flat_map { |container_id| Container.analyses_for_root(container_id) }
+            ).flat_map { |analysis| analysis.self_and_descendants.select(:id, :name, :updated_at, :log_data) }
+
+            # create cache key for reaction
+            timestamp = [
+              reaction.updated_at,
+              reaction.samples.with_deleted.maximum(:updated_at),
+              reaction.reactions_samples.with_deleted.maximum(:updated_at),
+              analyses.map(&:updated_at).max,
+              Attachment.where(attachable_id: analyses.map(&:id), attachable_type: 'Container').maximum(:updated_at)
+            ].reject(&:nil?).max.to_i
+            cache_key = "versions/reactions/#{reaction.id}/#{timestamp}"
+
+            # cache processed and sorted versions of all reaction dependent records and merge them into one list to speed up pagination
+            versions = Rails.cache.fetch cache_key do
+              all_versions = reaction.versions_hash
+
+              analyses.each do |analysis|
+                all_versions += analysis.versions_hash
+                all_versions += analysis.attachments.select(:attachable_id, :attachable_type, :filename, :log_data).flat_map do |attachment|
+                  attachment.versions_hash(attachment.filename)
+                end
+              end
+
+              samples = reaction.samples.with_deleted.select('samples.id, samples.name, samples.log_data')
+              samples.each do |sample|
+                all_versions += sample.versions_hash
+                all_versions += sample.residues.select(:sample_id, :log_data).flat_map do |residue|
+                  residue.versions_hash(sample.name)
+                end
+                all_versions += sample.elemental_compositions.select(:sample_id, :log_data).flat_map do |elemental_composition|
+                  elemental_composition.versions_hash(sample.name)
+                end
+              end
+
+              reactions_samples = reaction.reactions_samples.with_deleted.select(:sample_id, :log_data, :type)
+              all_versions += reactions_samples.flat_map do |reactions_sample|
+                sample = samples.detect { |s| s.id == reactions_sample.sample_id }
+                reactions_sample.versions_hash(sample.name)
+              end
+
+              all_versions.sort_by! { |version| -version['t'].to_i } # sort versions with the latest changes in the first place
+                          .each_with_index { |record, index| record['v'] = all_versions.length - index } # adjust v to be uniq and in right order
+            end
+
+            { versions: paginate(Kaminari.paginate_array(versions)) }
+          end
+        end
+      end
+    end
+  end
+end

app/api/modules/logidze_module.rb

@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+# A helper to help logidize track current_user
+module LogidzeModule
+  extend ActiveSupport::Concern
+
+  included do
+    before do
+      if current_user.present? && request.request_method.in?(%w[PATCH POST PUT DELETE])
+        @logidze_meta_set ||= begin
+          Logidze.with_responsible!(current_user.id)
+          true
+        end
+      end
+    end
+
+    after do
+      Logidze.clear_responsible! if @logidze_meta_set.present?
+    end
+  end
+end

app/assets/stylesheets/version.scss

@@ -0,0 +1,24 @@
+.row.row-version-history { // overwrite bootstrap
+  display: flex;
+  flex-wrap: wrap;
+  font-size: 10px;
+  margin: 0;
+  word-break: break-all;
+
+  & + .row-version-history {
+    margin-top: 15px;
+  }
+
+  & > [class*="col-"] {
+    padding: 10px;
+  }
+
+  .ql-editor {
+    padding: 0;
+  }
+
+  .ql-tooltip.ql-hidden {
+    height: 0;
+    padding-top: 10px;
+  }
+}

app/models/attachment.rb

@@ -30,6 +30,8 @@
 
 
 class Attachment < ApplicationRecord
+  include Versionable
+
   include AttachmentJcampAasm
   include AttachmentJcampProcess
   include AttachmentConverter
@@ -52,6 +54,10 @@ class Attachment < ApplicationRecord
 
   belongs_to :attachable, polymorphic: true, optional: true
   has_one :report_template
+<<<<<<< HEAD
+=======
+
+>>>>>>> Add a change history /w logidze
 
   scope :where_research_plan, lambda { |c_id|
     where(attachable_id: c_id, attachable_type: 'ResearchPlan')