From 83717e8655ce5222ed8c7642bd8b057692f1e3e7 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Mon, 10 Sep 2018 16:20:02 +0200
Subject: [PATCH 01/40] created base projects endpoint

---
 app/controllers/api/v1/projects_controller.rb | 37 +++++++++++++++++++
 app/serializers/api/v1/project_serializer.rb  | 15 ++++++++
 config/routes.rb                              |  3 +-
 3 files changed, 54 insertions(+), 1 deletion(-)
 create mode 100644 app/controllers/api/v1/projects_controller.rb
 create mode 100644 app/serializers/api/v1/project_serializer.rb

diff --git a/app/controllers/api/v1/projects_controller.rb b/app/controllers/api/v1/projects_controller.rb
new file mode 100644
index 000000000..ce0e73068
--- /dev/null
+++ b/app/controllers/api/v1/projects_controller.rb
@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProjectsController < BaseController
+      before_action :load_team
+      before_action :load_project, only: :show
+
+
+      def index
+        projects = @team.projects
+                        .page(params.dig(:page, :number))
+                        .per(params.dig(:page, :size))
+
+        render jsonapi: projects, each_serializer: ProjectSerializer
+      end
+
+      def show
+        render jsonapi: @project, serializer: ProjectSerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+    end
+  end
+end
diff --git a/app/serializers/api/v1/project_serializer.rb b/app/serializers/api/v1/project_serializer.rb
new file mode 100644
index 000000000..b1d9dede8
--- /dev/null
+++ b/app/serializers/api/v1/project_serializer.rb
@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProjectSerializer < ActiveModel::Serializer
+      type :projects
+      attributes :id, :name, :visibility, :due_date, :team_id, :created_at,
+                 :updated_at, :archived, :archived_on, :created_by_id,
+                 :last_modified_by_id, :archived_by_id, :restored_by_id,
+                 :restored_on, :experiments_order
+
+      belongs_to :team, serializer: TeamSerializer
+    end
+  end
+end
diff --git a/config/routes.rb b/config/routes.rb
index 5712f8a9a..21567b83b 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -554,7 +554,8 @@ Rails.application.routes.draw do
                         path: 'items',
                         as: :items
             end
-            resources :projects, only: %i(index show) do
+            resources :projects, only: %i(index show), path: 'projects',
+                      as: :projects do
               resources :experiments, only: %i(index show) do
                 resources :my_modules,
                           only: %i(index show),

From 44c3784977eed2a6f5871a36582a0f835951c956 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Tue, 11 Sep 2018 09:13:17 +0200
Subject: [PATCH 02/40] Created base endpoints for projects and related models

---
 .../api/v1/activities_controller.rb           | 82 +++++++++++++++++++
 .../api/v1/project_comments_controller.rb     | 43 ++++++++++
 app/controllers/api/v1/projects_controller.rb |  1 -
 app/controllers/api/v1/reports_controller.rb  | 42 ++++++++++
 .../api/v1/user_projects_controller.rb        | 42 ++++++++++
 app/serializers/api/v1/activity_serializer.rb | 14 ++++
 .../api/v1/project_comment_serializer.rb      | 13 +++
 app/serializers/api/v1/report_serializer.rb   | 13 +++
 .../api/v1/user_project_serializer.rb         | 13 +++
 config/routes.rb                              |  8 ++
 10 files changed, 270 insertions(+), 1 deletion(-)
 create mode 100644 app/controllers/api/v1/activities_controller.rb
 create mode 100644 app/controllers/api/v1/project_comments_controller.rb
 create mode 100644 app/controllers/api/v1/reports_controller.rb
 create mode 100644 app/controllers/api/v1/user_projects_controller.rb
 create mode 100644 app/serializers/api/v1/activity_serializer.rb
 create mode 100644 app/serializers/api/v1/project_comment_serializer.rb
 create mode 100644 app/serializers/api/v1/report_serializer.rb
 create mode 100644 app/serializers/api/v1/user_project_serializer.rb

diff --git a/app/controllers/api/v1/activities_controller.rb b/app/controllers/api/v1/activities_controller.rb
new file mode 100644
index 000000000..474e9726d
--- /dev/null
+++ b/app/controllers/api/v1/activities_controller.rb
@@ -0,0 +1,82 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ActivitiesController < BaseController
+      before_action :load_team
+      before_action :load_project
+      before_action :load_project_activity, only: :project_activity
+      before_action :load_experiment, except: %i(
+        project_activities project_activity
+      )
+      before_action :load_task, except: %i(project_activities project_activity)
+      before_action :load_activity, only: :show
+
+      def index
+        activities = @my_module.activities
+                               .page(params.dig(:page, :number))
+                               .per(params.dig(:page, :size))
+
+        render jsonapi: activities,
+          each_serializer: ActivitySerializer
+      end
+
+      def show
+        render jsonapi: @activity, serializer: ActivitySerializer
+      end
+
+      def project_activities
+        activities = @project.activities
+                             .page(params.dig(:page, :number))
+                             .per(params.dig(:page, :size))
+
+        render jsonapi: activities,
+          each_serializer: ActivitySerializer
+      end
+
+      def project_activity
+        render jsonapi: @project_activity, serializer: ActivitySerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+
+      def load_experiment
+        @experiment = @project.experiments.find(params.require(:experiment_id))
+        render jsonapi: {}, status: :forbidden unless can_read_experiment?(
+          @experiment
+        )
+      end
+
+      def load_task
+        @my_module = @experiment.my_modules.find(params.require(:task_id))
+        render jsonapi: {}, status: :not_found if @my_module.nil?
+      end
+
+      def load_activity
+        @activity = @my_module.activities.find(
+          params.require(:id)
+        )
+        render jsonapi: {}, status: :not_found if @activity.nil?
+      end
+
+      def load_project_activity
+        @project_activity = @project.activities.find(
+          params.require(:id)
+        )
+        render jsonapi: {}, status: :not_found if @project_activity.nil?
+      end
+    end
+  end
+end
diff --git a/app/controllers/api/v1/project_comments_controller.rb b/app/controllers/api/v1/project_comments_controller.rb
new file mode 100644
index 000000000..bca71a462
--- /dev/null
+++ b/app/controllers/api/v1/project_comments_controller.rb
@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProjectCommentsController < BaseController
+      before_action :load_team
+      before_action :load_project
+      before_action :load_project_comment, only: :show
+
+      def index
+        project_comments = @project.project_comments
+                                   .page(params.dig(:page, :number))
+                                   .per(params.dig(:page, :size))
+
+        render jsonapi: project_comments,
+          each_serializer: ProjectCommentSerializer
+      end
+
+      def show
+        render jsonapi: @project_comment, serializer: ProjectCommentSerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+
+      def load_project_comment
+        @project_comment = @project.project_comments.find(params.require(:id))
+        render jsonapi: {}, status: :not_found if @project_comment.nil?
+      end
+    end
+  end
+end
diff --git a/app/controllers/api/v1/projects_controller.rb b/app/controllers/api/v1/projects_controller.rb
index ce0e73068..0cc5c05d0 100644
--- a/app/controllers/api/v1/projects_controller.rb
+++ b/app/controllers/api/v1/projects_controller.rb
@@ -6,7 +6,6 @@ module Api
       before_action :load_team
       before_action :load_project, only: :show
 
-
       def index
         projects = @team.projects
                         .page(params.dig(:page, :number))
diff --git a/app/controllers/api/v1/reports_controller.rb b/app/controllers/api/v1/reports_controller.rb
new file mode 100644
index 000000000..01f527f53
--- /dev/null
+++ b/app/controllers/api/v1/reports_controller.rb
@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ReportsController < BaseController
+      before_action :load_team
+      before_action :load_project
+      before_action :load_report, only: :show
+
+      def index
+        reports = @project.reports
+                          .page(params.dig(:page, :number))
+                          .per(params.dig(:page, :size))
+
+        render jsonapi: reports, each_serializer: ReportSerializer
+      end
+
+      def show
+        render jsonapi: @report, serializer: ReportSerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+
+      def load_report
+        @report = @project.reports.find(params.require(:id))
+        render jsonapi: {}, status: :not_found if @report.nil?
+      end
+    end
+  end
+end
diff --git a/app/controllers/api/v1/user_projects_controller.rb b/app/controllers/api/v1/user_projects_controller.rb
new file mode 100644
index 000000000..36e3eca2b
--- /dev/null
+++ b/app/controllers/api/v1/user_projects_controller.rb
@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class UserProjectsController < BaseController
+      before_action :load_team
+      before_action :load_project
+      before_action :load_user_project, only: :show
+
+      def index
+        user_projects = @project.user_projects
+                           .page(params.dig(:page, :number))
+                           .per(params.dig(:page, :size))
+
+        render jsonapi: user_projects, each_serializer: UserProjectSerializer
+      end
+
+      def show
+        render jsonapi: @user_project, serializer: UserProjectSerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+
+      def load_user_project
+        @user_project = @project.user_projects.find(params.require(:id))
+        render jsonapi: {}, status: :not_found if @user_project.nil?
+      end
+    end
+  end
+end
diff --git a/app/serializers/api/v1/activity_serializer.rb b/app/serializers/api/v1/activity_serializer.rb
new file mode 100644
index 000000000..50b614923
--- /dev/null
+++ b/app/serializers/api/v1/activity_serializer.rb
@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ActivitySerializer < ActiveModel::Serializer
+      type :activities
+      attributes :id, :my_module_id, :user_id, :type_of, :message, :created_at,
+                 :updated_at, :project_id, :experiment_id
+      belongs_to :my_module, serializer: MyModuleSerializer, optional: true
+      belongs_to :experiment, serializer: ExperimentSerializer, optional: true
+      belongs_to :project, serializer: ProjectSerializer
+    end
+  end
+end
diff --git a/app/serializers/api/v1/project_comment_serializer.rb b/app/serializers/api/v1/project_comment_serializer.rb
new file mode 100644
index 000000000..b62ebebef
--- /dev/null
+++ b/app/serializers/api/v1/project_comment_serializer.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProjectCommentSerializer < ActiveModel::Serializer
+      type :project_comments
+      attributes :id, :message, :user_id, :created_at, :updated_at,
+                 :last_modified_by_id, :type, :associated_id
+
+      belongs_to :project, serializer: ProjectSerializer
+    end
+  end
+end
diff --git a/app/serializers/api/v1/report_serializer.rb b/app/serializers/api/v1/report_serializer.rb
new file mode 100644
index 000000000..0abff7e7e
--- /dev/null
+++ b/app/serializers/api/v1/report_serializer.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ReportSerializer < ActiveModel::Serializer
+      type :reports
+      attributes :id, :name, :description, :project_id, :user_id, :created_at,
+                 :updated_at, :last_modified_by_id, :team_id
+
+      belongs_to :project, serializer: ProjectSerializer
+    end
+  end
+end
diff --git a/app/serializers/api/v1/user_project_serializer.rb b/app/serializers/api/v1/user_project_serializer.rb
new file mode 100644
index 000000000..ba2b1899e
--- /dev/null
+++ b/app/serializers/api/v1/user_project_serializer.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class UserProjectSerializer < ActiveModel::Serializer
+      type :user_projects
+      attributes :id, :role, :user_id, :project_id, :created_at, :updated_at,
+                 :assigned_by_id
+
+      belongs_to :project, serializer: ProjectSerializer
+    end
+  end
+end
diff --git a/config/routes.rb b/config/routes.rb
index 21567b83b..45a35c544 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -556,6 +556,14 @@ Rails.application.routes.draw do
             end
             resources :projects, only: %i(index show), path: 'projects',
                       as: :projects do
+              resources :user_projects, only: %i(index show),
+                path: 'user_projects', as: :user_projects
+              resources :project_comments, only: %i(index show),
+                path: 'project_comments', as: :project_comments
+              resources :reports, only: %i(index show),
+                path: 'reports', as: :reports
+              get 'activities', to: 'activities#project_activities'
+              get 'activities/:id', to: 'activities#project_activity'
               resources :experiments, only: %i(index show) do
                 resources :my_modules,
                           only: %i(index show),

From 94a7868d6e16133f71ab41da5faf8eb04456f222 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Tue, 11 Sep 2018 09:16:59 +0200
Subject: [PATCH 03/40] Fixed hound

---
 app/controllers/api/v1/user_projects_controller.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/controllers/api/v1/user_projects_controller.rb b/app/controllers/api/v1/user_projects_controller.rb
index 36e3eca2b..dfa376a07 100644
--- a/app/controllers/api/v1/user_projects_controller.rb
+++ b/app/controllers/api/v1/user_projects_controller.rb
@@ -9,8 +9,8 @@ module Api
 
       def index
         user_projects = @project.user_projects
-                           .page(params.dig(:page, :number))
-                           .per(params.dig(:page, :size))
+                                .page(params.dig(:page, :number))
+                                .per(params.dig(:page, :size))
 
         render jsonapi: user_projects, each_serializer: UserProjectSerializer
       end

From 43e6524392697a3ff8bb55896359686c072d7f16 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Tue, 11 Sep 2018 10:31:16 +0200
Subject: [PATCH 04/40] standardized serializers by removing specified
 attributes

---
 app/serializers/api/v1/activity_serializer.rb        | 4 ++--
 app/serializers/api/v1/experiment_serializer.rb      | 3 +--
 app/serializers/api/v1/my_module_group_serializer.rb | 2 +-
 app/serializers/api/v1/project_comment_serializer.rb | 3 +--
 app/serializers/api/v1/project_serializer.rb         | 6 ++----
 app/serializers/api/v1/report_serializer.rb          | 3 +--
 app/serializers/api/v1/user_project_serializer.rb    | 3 +--
 7 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/app/serializers/api/v1/activity_serializer.rb b/app/serializers/api/v1/activity_serializer.rb
index 50b614923..e69138827 100644
--- a/app/serializers/api/v1/activity_serializer.rb
+++ b/app/serializers/api/v1/activity_serializer.rb
@@ -4,8 +4,8 @@ module Api
   module V1
     class ActivitySerializer < ActiveModel::Serializer
       type :activities
-      attributes :id, :my_module_id, :user_id, :type_of, :message, :created_at,
-                 :updated_at, :project_id, :experiment_id
+      attributes :id, :my_module_id, :user_id, :type_of, :message,
+                 :project_id, :experiment_id
       belongs_to :my_module, serializer: MyModuleSerializer, optional: true
       belongs_to :experiment, serializer: ExperimentSerializer, optional: true
       belongs_to :project, serializer: ProjectSerializer
diff --git a/app/serializers/api/v1/experiment_serializer.rb b/app/serializers/api/v1/experiment_serializer.rb
index db9c0dd7e..b1ef9023e 100644
--- a/app/serializers/api/v1/experiment_serializer.rb
+++ b/app/serializers/api/v1/experiment_serializer.rb
@@ -4,8 +4,7 @@ module Api
   module V1
     class ExperimentSerializer < ActiveModel::Serializer
       type :experiments
-      attributes :id, :name, :description, :project_id, :created_by_id,
-                 :archived, :created_at, :updated_at
+      attributes :id, :name, :description, :created_by_id, :archived
     end
   end
 end
diff --git a/app/serializers/api/v1/my_module_group_serializer.rb b/app/serializers/api/v1/my_module_group_serializer.rb
index 0ec8e2dca..4a1d5c46b 100644
--- a/app/serializers/api/v1/my_module_group_serializer.rb
+++ b/app/serializers/api/v1/my_module_group_serializer.rb
@@ -4,7 +4,7 @@ module Api
   module V1
     class MyModuleGroupSerializer < ActiveModel::Serializer
       type :task_groups
-      attributes :id, :created_at, :updated_at, :created_by_id, :experiment_id
+      attributes :id, :created_by_id, :experiment_id
       belongs_to :experiment, serializer: ExperimentSerializer
     end
   end
diff --git a/app/serializers/api/v1/project_comment_serializer.rb b/app/serializers/api/v1/project_comment_serializer.rb
index b62ebebef..a9786f316 100644
--- a/app/serializers/api/v1/project_comment_serializer.rb
+++ b/app/serializers/api/v1/project_comment_serializer.rb
@@ -4,8 +4,7 @@ module Api
   module V1
     class ProjectCommentSerializer < ActiveModel::Serializer
       type :project_comments
-      attributes :id, :message, :user_id, :created_at, :updated_at,
-                 :last_modified_by_id, :type, :associated_id
+      attributes :id, :message, :user_id, :type, :associated_id
 
       belongs_to :project, serializer: ProjectSerializer
     end
diff --git a/app/serializers/api/v1/project_serializer.rb b/app/serializers/api/v1/project_serializer.rb
index b1d9dede8..0d31b26aa 100644
--- a/app/serializers/api/v1/project_serializer.rb
+++ b/app/serializers/api/v1/project_serializer.rb
@@ -4,10 +4,8 @@ module Api
   module V1
     class ProjectSerializer < ActiveModel::Serializer
       type :projects
-      attributes :id, :name, :visibility, :due_date, :team_id, :created_at,
-                 :updated_at, :archived, :archived_on, :created_by_id,
-                 :last_modified_by_id, :archived_by_id, :restored_by_id,
-                 :restored_on, :experiments_order
+      attributes :id, :name, :visibility, :due_date,
+                 :archived, :experiments_order
 
       belongs_to :team, serializer: TeamSerializer
     end
diff --git a/app/serializers/api/v1/report_serializer.rb b/app/serializers/api/v1/report_serializer.rb
index 0abff7e7e..1d4d2509f 100644
--- a/app/serializers/api/v1/report_serializer.rb
+++ b/app/serializers/api/v1/report_serializer.rb
@@ -4,8 +4,7 @@ module Api
   module V1
     class ReportSerializer < ActiveModel::Serializer
       type :reports
-      attributes :id, :name, :description, :project_id, :user_id, :created_at,
-                 :updated_at, :last_modified_by_id, :team_id
+      attributes :id, :name, :description, :project_id
 
       belongs_to :project, serializer: ProjectSerializer
     end
diff --git a/app/serializers/api/v1/user_project_serializer.rb b/app/serializers/api/v1/user_project_serializer.rb
index ba2b1899e..e6b2dfbfe 100644
--- a/app/serializers/api/v1/user_project_serializer.rb
+++ b/app/serializers/api/v1/user_project_serializer.rb
@@ -4,8 +4,7 @@ module Api
   module V1
     class UserProjectSerializer < ActiveModel::Serializer
       type :user_projects
-      attributes :id, :role, :user_id, :project_id, :created_at, :updated_at,
-                 :assigned_by_id
+      attributes :id, :role, :user_id
 
       belongs_to :project, serializer: ProjectSerializer
     end

From 6c51a14292b28bd637c3c60dace001be5c640257 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Tue, 11 Sep 2018 13:04:40 +0200
Subject: [PATCH 05/40] Fixed oversight, added paging to connections

---
 app/controllers/api/v1/connections_controller.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/app/controllers/api/v1/connections_controller.rb b/app/controllers/api/v1/connections_controller.rb
index 740593a32..1ce2111f4 100644
--- a/app/controllers/api/v1/connections_controller.rb
+++ b/app/controllers/api/v1/connections_controller.rb
@@ -10,6 +10,8 @@ module Api
       before_action :load_connection, only: :show
 
       def index
+        @connections = @connections.page(params.dig(:page, :number))
+                                   .per(params.dig(:page, :size))
         render jsonapi: @connections, each_serializer: ConnectionSerializer
       end
 

From a086d181f58b707f0da2d76a1a46d08c663b7ec5 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Tue, 11 Sep 2018 15:37:42 +0200
Subject: [PATCH 06/40] removing attributes

---
 app/serializers/api/v1/experiment_serializer.rb      | 2 +-
 app/serializers/api/v1/my_module_group_serializer.rb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/serializers/api/v1/experiment_serializer.rb b/app/serializers/api/v1/experiment_serializer.rb
index b1ef9023e..bff94ffc1 100644
--- a/app/serializers/api/v1/experiment_serializer.rb
+++ b/app/serializers/api/v1/experiment_serializer.rb
@@ -4,7 +4,7 @@ module Api
   module V1
     class ExperimentSerializer < ActiveModel::Serializer
       type :experiments
-      attributes :id, :name, :description, :created_by_id, :archived
+      attributes :id, :name, :description, :archived
     end
   end
 end
diff --git a/app/serializers/api/v1/my_module_group_serializer.rb b/app/serializers/api/v1/my_module_group_serializer.rb
index 4a1d5c46b..06b52e31e 100644
--- a/app/serializers/api/v1/my_module_group_serializer.rb
+++ b/app/serializers/api/v1/my_module_group_serializer.rb
@@ -4,7 +4,7 @@ module Api
   module V1
     class MyModuleGroupSerializer < ActiveModel::Serializer
       type :task_groups
-      attributes :id, :created_by_id, :experiment_id
+      attributes :id, :experiment_id
       belongs_to :experiment, serializer: ExperimentSerializer
     end
   end

From dace81f72426ab43bbbc61d6b167ec1c30b3f74b Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Mon, 10 Sep 2018 16:20:02 +0200
Subject: [PATCH 07/40] created base projects endpoint

---
 app/controllers/api/v1/projects_controller.rb | 37 +++++++++++++++++++
 app/serializers/api/v1/project_serializer.rb  | 15 ++++++++
 config/routes.rb                              |  3 +-
 3 files changed, 54 insertions(+), 1 deletion(-)
 create mode 100644 app/controllers/api/v1/projects_controller.rb
 create mode 100644 app/serializers/api/v1/project_serializer.rb

diff --git a/app/controllers/api/v1/projects_controller.rb b/app/controllers/api/v1/projects_controller.rb
new file mode 100644
index 000000000..ce0e73068
--- /dev/null
+++ b/app/controllers/api/v1/projects_controller.rb
@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProjectsController < BaseController
+      before_action :load_team
+      before_action :load_project, only: :show
+
+
+      def index
+        projects = @team.projects
+                        .page(params.dig(:page, :number))
+                        .per(params.dig(:page, :size))
+
+        render jsonapi: projects, each_serializer: ProjectSerializer
+      end
+
+      def show
+        render jsonapi: @project, serializer: ProjectSerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+    end
+  end
+end
diff --git a/app/serializers/api/v1/project_serializer.rb b/app/serializers/api/v1/project_serializer.rb
new file mode 100644
index 000000000..b1d9dede8
--- /dev/null
+++ b/app/serializers/api/v1/project_serializer.rb
@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProjectSerializer < ActiveModel::Serializer
+      type :projects
+      attributes :id, :name, :visibility, :due_date, :team_id, :created_at,
+                 :updated_at, :archived, :archived_on, :created_by_id,
+                 :last_modified_by_id, :archived_by_id, :restored_by_id,
+                 :restored_on, :experiments_order
+
+      belongs_to :team, serializer: TeamSerializer
+    end
+  end
+end
diff --git a/config/routes.rb b/config/routes.rb
index 5712f8a9a..21567b83b 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -554,7 +554,8 @@ Rails.application.routes.draw do
                         path: 'items',
                         as: :items
             end
-            resources :projects, only: %i(index show) do
+            resources :projects, only: %i(index show), path: 'projects',
+                      as: :projects do
               resources :experiments, only: %i(index show) do
                 resources :my_modules,
                           only: %i(index show),

From 7f704c07e3e0de9f4045526bc9259f01c7671083 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Tue, 11 Sep 2018 09:13:17 +0200
Subject: [PATCH 08/40] Created base endpoints for projects and related models

---
 .../api/v1/activities_controller.rb           | 82 +++++++++++++++++++
 .../api/v1/project_comments_controller.rb     | 43 ++++++++++
 app/controllers/api/v1/projects_controller.rb |  1 -
 app/controllers/api/v1/reports_controller.rb  | 42 ++++++++++
 .../api/v1/user_projects_controller.rb        | 42 ++++++++++
 app/serializers/api/v1/activity_serializer.rb | 14 ++++
 .../api/v1/project_comment_serializer.rb      | 13 +++
 app/serializers/api/v1/report_serializer.rb   | 13 +++
 .../api/v1/user_project_serializer.rb         | 13 +++
 config/routes.rb                              |  8 ++
 10 files changed, 270 insertions(+), 1 deletion(-)
 create mode 100644 app/controllers/api/v1/activities_controller.rb
 create mode 100644 app/controllers/api/v1/project_comments_controller.rb
 create mode 100644 app/controllers/api/v1/reports_controller.rb
 create mode 100644 app/controllers/api/v1/user_projects_controller.rb
 create mode 100644 app/serializers/api/v1/activity_serializer.rb
 create mode 100644 app/serializers/api/v1/project_comment_serializer.rb
 create mode 100644 app/serializers/api/v1/report_serializer.rb
 create mode 100644 app/serializers/api/v1/user_project_serializer.rb

diff --git a/app/controllers/api/v1/activities_controller.rb b/app/controllers/api/v1/activities_controller.rb
new file mode 100644
index 000000000..474e9726d
--- /dev/null
+++ b/app/controllers/api/v1/activities_controller.rb
@@ -0,0 +1,82 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ActivitiesController < BaseController
+      before_action :load_team
+      before_action :load_project
+      before_action :load_project_activity, only: :project_activity
+      before_action :load_experiment, except: %i(
+        project_activities project_activity
+      )
+      before_action :load_task, except: %i(project_activities project_activity)
+      before_action :load_activity, only: :show
+
+      def index
+        activities = @my_module.activities
+                               .page(params.dig(:page, :number))
+                               .per(params.dig(:page, :size))
+
+        render jsonapi: activities,
+          each_serializer: ActivitySerializer
+      end
+
+      def show
+        render jsonapi: @activity, serializer: ActivitySerializer
+      end
+
+      def project_activities
+        activities = @project.activities
+                             .page(params.dig(:page, :number))
+                             .per(params.dig(:page, :size))
+
+        render jsonapi: activities,
+          each_serializer: ActivitySerializer
+      end
+
+      def project_activity
+        render jsonapi: @project_activity, serializer: ActivitySerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+
+      def load_experiment
+        @experiment = @project.experiments.find(params.require(:experiment_id))
+        render jsonapi: {}, status: :forbidden unless can_read_experiment?(
+          @experiment
+        )
+      end
+
+      def load_task
+        @my_module = @experiment.my_modules.find(params.require(:task_id))
+        render jsonapi: {}, status: :not_found if @my_module.nil?
+      end
+
+      def load_activity
+        @activity = @my_module.activities.find(
+          params.require(:id)
+        )
+        render jsonapi: {}, status: :not_found if @activity.nil?
+      end
+
+      def load_project_activity
+        @project_activity = @project.activities.find(
+          params.require(:id)
+        )
+        render jsonapi: {}, status: :not_found if @project_activity.nil?
+      end
+    end
+  end
+end
diff --git a/app/controllers/api/v1/project_comments_controller.rb b/app/controllers/api/v1/project_comments_controller.rb
new file mode 100644
index 000000000..bca71a462
--- /dev/null
+++ b/app/controllers/api/v1/project_comments_controller.rb
@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProjectCommentsController < BaseController
+      before_action :load_team
+      before_action :load_project
+      before_action :load_project_comment, only: :show
+
+      def index
+        project_comments = @project.project_comments
+                                   .page(params.dig(:page, :number))
+                                   .per(params.dig(:page, :size))
+
+        render jsonapi: project_comments,
+          each_serializer: ProjectCommentSerializer
+      end
+
+      def show
+        render jsonapi: @project_comment, serializer: ProjectCommentSerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+
+      def load_project_comment
+        @project_comment = @project.project_comments.find(params.require(:id))
+        render jsonapi: {}, status: :not_found if @project_comment.nil?
+      end
+    end
+  end
+end
diff --git a/app/controllers/api/v1/projects_controller.rb b/app/controllers/api/v1/projects_controller.rb
index ce0e73068..0cc5c05d0 100644
--- a/app/controllers/api/v1/projects_controller.rb
+++ b/app/controllers/api/v1/projects_controller.rb
@@ -6,7 +6,6 @@ module Api
       before_action :load_team
       before_action :load_project, only: :show
 
-
       def index
         projects = @team.projects
                         .page(params.dig(:page, :number))
diff --git a/app/controllers/api/v1/reports_controller.rb b/app/controllers/api/v1/reports_controller.rb
new file mode 100644
index 000000000..01f527f53
--- /dev/null
+++ b/app/controllers/api/v1/reports_controller.rb
@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ReportsController < BaseController
+      before_action :load_team
+      before_action :load_project
+      before_action :load_report, only: :show
+
+      def index
+        reports = @project.reports
+                          .page(params.dig(:page, :number))
+                          .per(params.dig(:page, :size))
+
+        render jsonapi: reports, each_serializer: ReportSerializer
+      end
+
+      def show
+        render jsonapi: @report, serializer: ReportSerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+
+      def load_report
+        @report = @project.reports.find(params.require(:id))
+        render jsonapi: {}, status: :not_found if @report.nil?
+      end
+    end
+  end
+end
diff --git a/app/controllers/api/v1/user_projects_controller.rb b/app/controllers/api/v1/user_projects_controller.rb
new file mode 100644
index 000000000..36e3eca2b
--- /dev/null
+++ b/app/controllers/api/v1/user_projects_controller.rb
@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class UserProjectsController < BaseController
+      before_action :load_team
+      before_action :load_project
+      before_action :load_user_project, only: :show
+
+      def index
+        user_projects = @project.user_projects
+                           .page(params.dig(:page, :number))
+                           .per(params.dig(:page, :size))
+
+        render jsonapi: user_projects, each_serializer: UserProjectSerializer
+      end
+
+      def show
+        render jsonapi: @user_project, serializer: UserProjectSerializer
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+
+      def load_user_project
+        @user_project = @project.user_projects.find(params.require(:id))
+        render jsonapi: {}, status: :not_found if @user_project.nil?
+      end
+    end
+  end
+end
diff --git a/app/serializers/api/v1/activity_serializer.rb b/app/serializers/api/v1/activity_serializer.rb
new file mode 100644
index 000000000..50b614923
--- /dev/null
+++ b/app/serializers/api/v1/activity_serializer.rb
@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ActivitySerializer < ActiveModel::Serializer
+      type :activities
+      attributes :id, :my_module_id, :user_id, :type_of, :message, :created_at,
+                 :updated_at, :project_id, :experiment_id
+      belongs_to :my_module, serializer: MyModuleSerializer, optional: true
+      belongs_to :experiment, serializer: ExperimentSerializer, optional: true
+      belongs_to :project, serializer: ProjectSerializer
+    end
+  end
+end
diff --git a/app/serializers/api/v1/project_comment_serializer.rb b/app/serializers/api/v1/project_comment_serializer.rb
new file mode 100644
index 000000000..b62ebebef
--- /dev/null
+++ b/app/serializers/api/v1/project_comment_serializer.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProjectCommentSerializer < ActiveModel::Serializer
+      type :project_comments
+      attributes :id, :message, :user_id, :created_at, :updated_at,
+                 :last_modified_by_id, :type, :associated_id
+
+      belongs_to :project, serializer: ProjectSerializer
+    end
+  end
+end
diff --git a/app/serializers/api/v1/report_serializer.rb b/app/serializers/api/v1/report_serializer.rb
new file mode 100644
index 000000000..0abff7e7e
--- /dev/null
+++ b/app/serializers/api/v1/report_serializer.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ReportSerializer < ActiveModel::Serializer
+      type :reports
+      attributes :id, :name, :description, :project_id, :user_id, :created_at,
+                 :updated_at, :last_modified_by_id, :team_id
+
+      belongs_to :project, serializer: ProjectSerializer
+    end
+  end
+end
diff --git a/app/serializers/api/v1/user_project_serializer.rb b/app/serializers/api/v1/user_project_serializer.rb
new file mode 100644
index 000000000..ba2b1899e
--- /dev/null
+++ b/app/serializers/api/v1/user_project_serializer.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class UserProjectSerializer < ActiveModel::Serializer
+      type :user_projects
+      attributes :id, :role, :user_id, :project_id, :created_at, :updated_at,
+                 :assigned_by_id
+
+      belongs_to :project, serializer: ProjectSerializer
+    end
+  end
+end
diff --git a/config/routes.rb b/config/routes.rb
index 21567b83b..45a35c544 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -556,6 +556,14 @@ Rails.application.routes.draw do
             end
             resources :projects, only: %i(index show), path: 'projects',
                       as: :projects do
+              resources :user_projects, only: %i(index show),
+                path: 'user_projects', as: :user_projects
+              resources :project_comments, only: %i(index show),
+                path: 'project_comments', as: :project_comments
+              resources :reports, only: %i(index show),
+                path: 'reports', as: :reports
+              get 'activities', to: 'activities#project_activities'
+              get 'activities/:id', to: 'activities#project_activity'
               resources :experiments, only: %i(index show) do
                 resources :my_modules,
                           only: %i(index show),

From 8ac1445acec95e8c43aea5122834733f2dfddc87 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Tue, 11 Sep 2018 09:16:59 +0200
Subject: [PATCH 09/40] Fixed hound

---
 app/controllers/api/v1/user_projects_controller.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/controllers/api/v1/user_projects_controller.rb b/app/controllers/api/v1/user_projects_controller.rb
index 36e3eca2b..dfa376a07 100644
--- a/app/controllers/api/v1/user_projects_controller.rb
+++ b/app/controllers/api/v1/user_projects_controller.rb
@@ -9,8 +9,8 @@ module Api
 
       def index
         user_projects = @project.user_projects
-                           .page(params.dig(:page, :number))
-                           .per(params.dig(:page, :size))
+                                .page(params.dig(:page, :number))
+                                .per(params.dig(:page, :size))
 
         render jsonapi: user_projects, each_serializer: UserProjectSerializer
       end

From 46d33d28a37817e79fdb02eda88f9ee9135a3413 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Tue, 11 Sep 2018 10:31:16 +0200
Subject: [PATCH 10/40] standardized serializers by removing specified
 attributes

---
 app/serializers/api/v1/activity_serializer.rb        | 4 ++--
 app/serializers/api/v1/project_comment_serializer.rb | 3 +--
 app/serializers/api/v1/project_serializer.rb         | 6 ++----
 app/serializers/api/v1/report_serializer.rb          | 3 +--
 app/serializers/api/v1/user_project_serializer.rb    | 3 +--
 5 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/app/serializers/api/v1/activity_serializer.rb b/app/serializers/api/v1/activity_serializer.rb
index 50b614923..e69138827 100644
--- a/app/serializers/api/v1/activity_serializer.rb
+++ b/app/serializers/api/v1/activity_serializer.rb
@@ -4,8 +4,8 @@ module Api
   module V1
     class ActivitySerializer < ActiveModel::Serializer
       type :activities
-      attributes :id, :my_module_id, :user_id, :type_of, :message, :created_at,
-                 :updated_at, :project_id, :experiment_id
+      attributes :id, :my_module_id, :user_id, :type_of, :message,
+                 :project_id, :experiment_id
       belongs_to :my_module, serializer: MyModuleSerializer, optional: true
       belongs_to :experiment, serializer: ExperimentSerializer, optional: true
       belongs_to :project, serializer: ProjectSerializer
diff --git a/app/serializers/api/v1/project_comment_serializer.rb b/app/serializers/api/v1/project_comment_serializer.rb
index b62ebebef..a9786f316 100644
--- a/app/serializers/api/v1/project_comment_serializer.rb
+++ b/app/serializers/api/v1/project_comment_serializer.rb
@@ -4,8 +4,7 @@ module Api
   module V1
     class ProjectCommentSerializer < ActiveModel::Serializer
       type :project_comments
-      attributes :id, :message, :user_id, :created_at, :updated_at,
-                 :last_modified_by_id, :type, :associated_id
+      attributes :id, :message, :user_id, :type, :associated_id
 
       belongs_to :project, serializer: ProjectSerializer
     end
diff --git a/app/serializers/api/v1/project_serializer.rb b/app/serializers/api/v1/project_serializer.rb
index b1d9dede8..0d31b26aa 100644
--- a/app/serializers/api/v1/project_serializer.rb
+++ b/app/serializers/api/v1/project_serializer.rb
@@ -4,10 +4,8 @@ module Api
   module V1
     class ProjectSerializer < ActiveModel::Serializer
       type :projects
-      attributes :id, :name, :visibility, :due_date, :team_id, :created_at,
-                 :updated_at, :archived, :archived_on, :created_by_id,
-                 :last_modified_by_id, :archived_by_id, :restored_by_id,
-                 :restored_on, :experiments_order
+      attributes :id, :name, :visibility, :due_date,
+                 :archived, :experiments_order
 
       belongs_to :team, serializer: TeamSerializer
     end
diff --git a/app/serializers/api/v1/report_serializer.rb b/app/serializers/api/v1/report_serializer.rb
index 0abff7e7e..1d4d2509f 100644
--- a/app/serializers/api/v1/report_serializer.rb
+++ b/app/serializers/api/v1/report_serializer.rb
@@ -4,8 +4,7 @@ module Api
   module V1
     class ReportSerializer < ActiveModel::Serializer
       type :reports
-      attributes :id, :name, :description, :project_id, :user_id, :created_at,
-                 :updated_at, :last_modified_by_id, :team_id
+      attributes :id, :name, :description, :project_id
 
       belongs_to :project, serializer: ProjectSerializer
     end
diff --git a/app/serializers/api/v1/user_project_serializer.rb b/app/serializers/api/v1/user_project_serializer.rb
index ba2b1899e..e6b2dfbfe 100644
--- a/app/serializers/api/v1/user_project_serializer.rb
+++ b/app/serializers/api/v1/user_project_serializer.rb
@@ -4,8 +4,7 @@ module Api
   module V1
     class UserProjectSerializer < ActiveModel::Serializer
       type :user_projects
-      attributes :id, :role, :user_id, :project_id, :created_at, :updated_at,
-                 :assigned_by_id
+      attributes :id, :role, :user_id
 
       belongs_to :project, serializer: ProjectSerializer
     end

From 81115f411aba45f8d2f3feb1df0bf234e861e954 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Thu, 13 Sep 2018 11:46:25 +0200
Subject: [PATCH 11/40] Renaming my module attribute to tasks

---
 app/serializers/api/v1/activity_serializer.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/serializers/api/v1/activity_serializer.rb b/app/serializers/api/v1/activity_serializer.rb
index e69138827..216372095 100644
--- a/app/serializers/api/v1/activity_serializer.rb
+++ b/app/serializers/api/v1/activity_serializer.rb
@@ -4,8 +4,9 @@ module Api
   module V1
     class ActivitySerializer < ActiveModel::Serializer
       type :activities
-      attributes :id, :my_module_id, :user_id, :type_of, :message,
+      attributes :id, :user_id, :type_of, :message,
                  :project_id, :experiment_id
+      attribute :my_module_id, key: :task_id
       belongs_to :my_module, serializer: MyModuleSerializer, optional: true
       belongs_to :experiment, serializer: ExperimentSerializer, optional: true
       belongs_to :project, serializer: ProjectSerializer

From 2e0c40ed459499467a9d770770d8fcc756b7d9db Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Wed, 26 Sep 2018 12:20:13 +0200
Subject: [PATCH 12/40] fixed merge

---
 app/controllers/api/v1/activities_controller.rb | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/app/controllers/api/v1/activities_controller.rb b/app/controllers/api/v1/activities_controller.rb
index e3b9b34a1..793794c8d 100644
--- a/app/controllers/api/v1/activities_controller.rb
+++ b/app/controllers/api/v1/activities_controller.rb
@@ -26,7 +26,6 @@ module Api
         render jsonapi: @activity, serializer: ActivitySerializer
       end
 
-<<<<<<< HEAD
       def project_activities
         activities = @project.activities
                              .page(params.dig(:page, :number))
@@ -40,8 +39,6 @@ module Api
         render jsonapi: @project_activity, serializer: ActivitySerializer
       end
 
-=======
->>>>>>> 2a1c3037b8d19dd4ba3a7ae599fe0d7e6c5a2e24
       private
 
       def load_team
@@ -74,7 +71,6 @@ module Api
         )
         render jsonapi: {}, status: :not_found if @activity.nil?
       end
-<<<<<<< HEAD
 
       def load_project_activity
         @project_activity = @project.activities.find(
@@ -82,8 +78,6 @@ module Api
         )
         render jsonapi: {}, status: :not_found if @project_activity.nil?
       end
-=======
->>>>>>> 2a1c3037b8d19dd4ba3a7ae599fe0d7e6c5a2e24
     end
   end
 end

From 2f99904000826f8e9af4d7009e412489f6258bc3 Mon Sep 17 00:00:00 2001
From: Michael <michael.chea@czbiohub.org>
Date: Thu, 27 Sep 2018 10:43:52 -0700
Subject: [PATCH 13/40] merge core-api and handle merge issues

---
 .../v1/inventory_columns_controller_spec.rb   | 74 +++++++++++++++++++
 1 file changed, 74 insertions(+)

diff --git a/spec/requests/api/v1/inventory_columns_controller_spec.rb b/spec/requests/api/v1/inventory_columns_controller_spec.rb
index 9af73ad5c..6b5b48116 100644
--- a/spec/requests/api/v1/inventory_columns_controller_spec.rb
+++ b/spec/requests/api/v1/inventory_columns_controller_spec.rb
@@ -259,4 +259,78 @@ RSpec.describe 'Api::V1::InventoryColumnsController', type: :request do
       expect(RepositoryColumn.where(id: deleted_id)).to exist
     end
   end
+
+  describe 'PATCH inventory_column, #update' do
+    before :all do
+      @valid_headers['Content-Type'] = 'application/json'
+      @inventory_column = ActiveModelSerializers::SerializableResource.new(
+        RepositoryColumn.last,
+        serializer: Api::V1::InventoryColumnSerializer
+      )
+    end
+
+    it 'Response with correctly updated inventory column' do
+      hash_body = nil
+      updated_inventory_column = @inventory_column.as_json
+      updated_inventory_column[:data][:attributes][:name] =
+        Faker::Name.unique.name
+      patch api_v1_team_inventory_column_path(
+        id: RepositoryColumn.last.id,
+        team_id: @teams.first.id,
+        inventory_id: @teams.first.repositories.first.id
+      ), params: updated_inventory_column.to_json,
+      headers: @valid_headers
+      expect(response).to have_http_status 200
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body.to_json).to match(updated_inventory_column.to_json)
+    end
+
+    it 'Invalid request, wrong team' do
+      hash_body = nil
+      updated_inventory_column = @inventory_column.as_json
+      updated_inventory_column[:data][:attributes][:name] =
+        Faker::Name.unique.name
+      patch api_v1_team_inventory_column_path(
+        id: RepositoryColumn.last.id,
+        team_id: @teams.second.id,
+        inventory_id: @teams.first.repositories.first.id
+      ), params: updated_inventory_column.to_json,
+      headers: @valid_headers
+      expect(response).to have_http_status 403
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body).to match({})
+    end
+
+    it 'Invalid request, wrong inventory' do
+      hash_body = nil
+      updated_inventory_column = @inventory_column.as_json
+      updated_inventory_column[:data][:attributes][:name] =
+        Faker::Name.unique.name
+      patch api_v1_team_inventory_column_path(
+        id: RepositoryColumn.last.id,
+        team_id: @teams.second.id,
+        inventory_id: @teams.second.repositories.first.id
+      ), params: updated_inventory_column.to_json,
+      headers: @valid_headers
+      expect(response).to have_http_status 403
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body).to match({})
+    end
+
+    it 'Invalid request, non-existent inventory' do
+      hash_body = nil
+      updated_inventory_column = @inventory_column.as_json
+      updated_inventory_column[:data][:attributes][:name] =
+        Faker::Name.unique.name
+      patch api_v1_team_inventory_column_path(
+        id: RepositoryColumn.last.id,
+        team_id: @teams.first.id,
+        inventory_id: 123
+      ), params: updated_inventory_column.to_json,
+      headers: @valid_headers
+      expect(response).to have_http_status 404
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body).to match({})
+    end
+  end
 end

From 2dc09f080d21c04a3097fe63f2d8d062da648957 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Mon, 1 Oct 2018 14:59:06 +0200
Subject: [PATCH 14/40] Revert "Revert "Merge branch 'mc-SC-2697' of
 https://github.com/czbiohub/scinote-web-1 into core-api""

This reverts commit 7ef85a9b60ff2453d4610387a117306ad17beecc.
---
 .../api/v1/inventory_items_controller_spec.rb | 70 +++++++++++++++++++
 1 file changed, 70 insertions(+)

diff --git a/spec/requests/api/v1/inventory_items_controller_spec.rb b/spec/requests/api/v1/inventory_items_controller_spec.rb
index ce1d969c7..97353307a 100644
--- a/spec/requests/api/v1/inventory_items_controller_spec.rb
+++ b/spec/requests/api/v1/inventory_items_controller_spec.rb
@@ -245,4 +245,74 @@ RSpec.describe 'Api::V1::InventoryItemsController', type: :request do
       expect(hash_body).to match({})
     end
   end
+
+  describe 'PATCH inventory_items, #update' do
+    before :all do
+      @valid_headers['Content-Type'] = 'application/json'
+      @inventory_item = ActiveModelSerializers::SerializableResource.new(
+        RepositoryRow.last,
+        serializer: Api::V1::InventoryItemSerializer,
+        include: :inventory_cells
+      )
+    end
+
+    it 'Response with correctly updated inventory item for name field' do
+      hash_body = nil
+      updated_inventory_item = @inventory_item.as_json[:data]
+      updated_inventory_item[:attributes][:name] = Faker::Name.unique.name
+      patch api_v1_team_inventory_item_path(
+        id: RepositoryRow.last.id,
+        team_id: @teams.first.id,
+        inventory_id: @valid_inventory.id
+      ), params: { data: updated_inventory_item }.to_json,
+      headers: @valid_headers
+      expect(response).to have_http_status 200
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body[:data].to_json).to match(updated_inventory_item.to_json)
+    end
+
+    it 'Response with correctly updated inventory item for list item column' do
+      hash_body = nil
+      updated_inventory_item = @inventory_item.as_json[:included]
+      updated_inventory_item.each do |cell|
+        attributes = cell[:attributes]
+        if attributes[:value_type] == 'list'
+          cell[:attributes] = {
+            value_type: 'list',
+            value: Faker::Name.unique.name,
+            column_id: 2
+          }
+        end
+      end
+      patch api_v1_team_inventory_item_path(
+        id: RepositoryRow.last.id,
+        team_id: @teams.first.id,
+        inventory_id: @valid_inventory.id
+      ), params: @inventory_item.to_json,
+      headers: @valid_headers
+      expect(response).to have_http_status 200
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body[:included].to_json).to match(updated_inventory_item.to_json)
+    end
+
+    it 'Response with correctly updated inventory item for text item column' do
+      hash_body = nil
+      updated_inventory_item = @inventory_item.as_json[:included]
+      updated_inventory_item.each do |cell|
+        attributes = cell[:attributes]
+        if attributes[:value_type] == 'text'
+          attributes[:value] = Faker::Name.unique.name
+        end
+      end
+      patch api_v1_team_inventory_item_path(
+        id: RepositoryRow.last.id,
+        team_id: @teams.first.id,
+        inventory_id: @valid_inventory.id
+      ), params: @inventory_item.to_json,
+      headers: @valid_headers
+      expect(response).to have_http_status 200
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body[:included].to_json).to match(updated_inventory_item.to_json)
+    end
+  end
 end

From 9f4cb02fba8d8de4545b045d5c7a325107a6e7eb Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Fri, 5 Oct 2018 11:50:17 +0200
Subject: [PATCH 15/40] Update doorkeeper gem to >= 4.6

---
 Gemfile      | 2 +-
 Gemfile.lock | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Gemfile b/Gemfile
index b69de8ed6..0f1ee73b3 100644
--- a/Gemfile
+++ b/Gemfile
@@ -17,7 +17,7 @@ gem 'recaptcha', require: 'recaptcha/rails'
 gem 'sanitize', '~> 4.4'
 
 # Gems for OAuth2 subsystem
-gem 'doorkeeper', '~> 4.4'
+gem 'doorkeeper', '>= 4.6'
 gem 'omniauth'
 gem 'omniauth-linkedin-oauth2'
 
diff --git a/Gemfile.lock b/Gemfile.lock
index 12e8c7223..ffbc8c0e0 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -216,7 +216,7 @@ GEM
     discard (1.0.0)
       activerecord (>= 4.2, < 6)
     docile (1.1.5)
-    doorkeeper (4.4.1)
+    doorkeeper (5.0.0)
       railties (>= 4.2)
     erubi (1.7.1)
     execjs (2.7.0)
@@ -308,7 +308,7 @@ GEM
       rails (>= 3.2.0)
     newrelic_rpm (4.7.1.340)
     nio4r (2.3.1)
-    nokogiri (1.8.4)
+    nokogiri (1.8.5)
       mini_portile2 (~> 2.3.0)
     nokogumbo (1.5.0)
       nokogiri
@@ -357,7 +357,7 @@ GEM
     public_suffix (3.0.2)
     puma (3.11.2)
     rack (2.0.5)
-    rack-test (1.0.0)
+    rack-test (1.1.0)
       rack (>= 1.0, < 3)
     rails (5.1.6)
       actioncable (= 5.1.6)
@@ -565,7 +565,7 @@ DEPENDENCIES
   devise_invitable
   devise_security_extension!
   discard (~> 1.0)
-  doorkeeper (~> 4.4)
+  doorkeeper (>= 4.6)
   factory_bot_rails
   faker
   figaro

From 7b5a65416a597d076360e4cc4613193ee4c93039 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sat, 6 Oct 2018 11:47:23 +0200
Subject: [PATCH 16/40] Update status endpoint

---
 config/initializers/extends.rb              | 2 +-
 spec/controllers/api/api_controller_spec.rb | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index d186191da..15eea86f5 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -61,7 +61,7 @@ class Extends
                                 repository_asset_value: :asset]
 
   # List of implemented core API versions
-  API_VERSIONS = ['20170715']
+  API_VERSIONS = ['v1']
 
   # Array used for injecting names of additional authentication methods for API
   API_PLUGABLE_AUTH_METHODS = [:azure_jwt_auth]
diff --git a/spec/controllers/api/api_controller_spec.rb b/spec/controllers/api/api_controller_spec.rb
index 90aa792ba..68a7ec432 100644
--- a/spec/controllers/api/api_controller_spec.rb
+++ b/spec/controllers/api/api_controller_spec.rb
@@ -16,8 +16,8 @@ describe Api::ApiController, type: :controller do
       expect { hash_body = json }.not_to raise_exception
       expect(hash_body).to match(
         'message' => I18n.t('api.core.status_ok'),
-        'versions' => [{ 'version' => '20170715',
-                         'baseUrl' => '/api/20170715/' }]
+        'versions' => [{ 'version' => 'v1',
+                         'baseUrl' => '/api/v1/' }]
       )
     end
   end

From 6faaff550b8dc3341a755e763bed4cdf4031008e Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sat, 6 Oct 2018 12:18:57 +0200
Subject: [PATCH 17/40] Update GET /teams, GET teams/:team_id endpoints
 slightly

---
 app/controllers/api/v1/teams_controller.rb | 4 +++-
 app/serializers/api/v1/team_serializer.rb  | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/app/controllers/api/v1/teams_controller.rb b/app/controllers/api/v1/teams_controller.rb
index 53e6e0c0c..40c4eefb0 100644
--- a/app/controllers/api/v1/teams_controller.rb
+++ b/app/controllers/api/v1/teams_controller.rb
@@ -13,7 +13,9 @@ module Api
       end
 
       def show
-        render jsonapi: @team, serializer: TeamSerializer
+        render jsonapi: @team,
+               serializer: TeamSerializer,
+               include: :created_by
       end
 
       private
diff --git a/app/serializers/api/v1/team_serializer.rb b/app/serializers/api/v1/team_serializer.rb
index ffe94acc0..62d13afae 100644
--- a/app/serializers/api/v1/team_serializer.rb
+++ b/app/serializers/api/v1/team_serializer.rb
@@ -4,6 +4,7 @@ module Api
   module V1
     class TeamSerializer < ActiveModel::Serializer
       attributes :id, :name, :description, :space_taken
+      belongs_to :created_by, serializer: UserSerializer
     end
   end
 end

From eaa8a627a843ff4d6766b8481e4dfc22645494db Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sat, 6 Oct 2018 12:39:44 +0200
Subject: [PATCH 18/40] Update GET /inventories, GET /inventories/:inventory_id
 endpoints

---
 app/controllers/api/v1/inventories_controller.rb | 4 +++-
 app/serializers/api/v1/inventory_serializer.rb   | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/app/controllers/api/v1/inventories_controller.rb b/app/controllers/api/v1/inventories_controller.rb
index 70fef6fea..9b901980a 100644
--- a/app/controllers/api/v1/inventories_controller.rb
+++ b/app/controllers/api/v1/inventories_controller.rb
@@ -27,7 +27,9 @@ module Api
       end
 
       def show
-        render jsonapi: @inventory, serializer: InventorySerializer
+        render jsonapi: @inventory,
+               serializer: InventorySerializer,
+               include: :created_by
       end
 
       def update
diff --git a/app/serializers/api/v1/inventory_serializer.rb b/app/serializers/api/v1/inventory_serializer.rb
index dfe55f534..88752ecf3 100644
--- a/app/serializers/api/v1/inventory_serializer.rb
+++ b/app/serializers/api/v1/inventory_serializer.rb
@@ -5,6 +5,7 @@ module Api
     class InventorySerializer < ActiveModel::Serializer
       type :inventories
       attributes :id, :name
+      belongs_to :created_by, serializer: UserSerializer
     end
   end
 end

From 6625b4019e4a4fd1121de58ecb1163b3db731d37 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sat, 6 Oct 2018 13:47:41 +0200
Subject: [PATCH 19/40] Update GET /inventory_columns, GET
 /inventory_columns/:id endpts

---
 .../api/v1/inventory_columns_controller.rb    |   9 +-
 .../api/v1/inventory_column_serializer.rb     |   4 +-
 .../v1/inventory_columns_controller_spec.rb   | 103 ++++++++++++++++--
 3 files changed, 104 insertions(+), 12 deletions(-)

diff --git a/app/controllers/api/v1/inventory_columns_controller.rb b/app/controllers/api/v1/inventory_columns_controller.rb
index 2c9ae674c..1c50924ec 100644
--- a/app/controllers/api/v1/inventory_columns_controller.rb
+++ b/app/controllers/api/v1/inventory_columns_controller.rb
@@ -14,8 +14,9 @@ module Api
                             .includes(:repository_list_items)
                             .page(params.dig(:page, :number))
                             .per(params.dig(:page, :size))
-        render jsonapi: columns, each_serializer: InventoryColumnSerializer,
-        include: :inventory_list_items
+        render jsonapi: columns,
+               each_serializer: InventoryColumnSerializer,
+               hide_list_items: true
       end
 
       def create
@@ -27,7 +28,9 @@ module Api
       end
 
       def show
-        render jsonapi: @inventory_column, serializer: InventoryColumnSerializer
+        render jsonapi: @inventory_column,
+               serializer: InventoryColumnSerializer,
+               include: :inventory_list_items
       end
 
       def update
diff --git a/app/serializers/api/v1/inventory_column_serializer.rb b/app/serializers/api/v1/inventory_column_serializer.rb
index 1d0f65b7a..347457446 100644
--- a/app/serializers/api/v1/inventory_column_serializer.rb
+++ b/app/serializers/api/v1/inventory_column_serializer.rb
@@ -7,7 +7,9 @@ module Api
       attributes :name, :data_type
       has_many :repository_list_items, key: :inventory_list_items,
                                        serializer: InventoryListItemSerializer,
-                                       class_name: 'RepositoryListItem'
+                                       class_name: 'RepositoryListItem',
+                                       if: -> { object.data_type == 'RepositoryListValue' &&
+                                                !instance_options[:hide_list_items] }
 
       def data_type
         type_id = RepositoryColumn
diff --git a/spec/requests/api/v1/inventory_columns_controller_spec.rb b/spec/requests/api/v1/inventory_columns_controller_spec.rb
index 9af73ad5c..9a8992882 100644
--- a/spec/requests/api/v1/inventory_columns_controller_spec.rb
+++ b/spec/requests/api/v1/inventory_columns_controller_spec.rb
@@ -41,16 +41,9 @@ RSpec.describe 'Api::V1::InventoryColumnsController', type: :request do
         ActiveModelSerializers::SerializableResource
           .new(@valid_inventory.repository_columns.limit(10),
                each_serializer: Api::V1::InventoryColumnSerializer,
-               include: :inventory_columns)
+               hide_list_items: true)
           .as_json[:data]
       )
-      expect(hash_body[:included]).to match(
-        ActiveModelSerializers::SerializableResource
-          .new(@valid_inventory.repository_columns.limit(10),
-               each_serializer: Api::V1::InventoryColumnSerializer,
-               include: :inventory_list_items)
-          .as_json[:included]
-      )
     end
 
     it 'When invalid request, user in not member of the team' do
@@ -87,6 +80,100 @@ RSpec.describe 'Api::V1::InventoryColumnsController', type: :request do
     end
   end
 
+  describe 'GET inventory_column, #show' do
+    it 'Valid text column response' do
+      text_column = @valid_inventory.repository_columns.first
+      hash_body = nil
+      get api_v1_team_inventory_column_path(
+        id: text_column.id,
+        team_id: @teams.first.id,
+        inventory_id: @valid_inventory.id
+      ), headers: @valid_headers
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body[:data]).to match(
+        ActiveModelSerializers::SerializableResource
+          .new(text_column,
+              serializer: Api::V1::InventoryColumnSerializer)
+          .as_json[:data]
+      )
+      expect(hash_body[:data]).not_to include('relationships')
+    end
+
+    it 'Valid list column response' do
+      list_column = @valid_inventory.repository_columns.second
+      hash_body = nil
+      get api_v1_team_inventory_column_path(
+        id: list_column.id,
+        team_id: @teams.first.id,
+        inventory_id: @valid_inventory.id
+      ), headers: @valid_headers
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body[:data]).to match(
+        ActiveModelSerializers::SerializableResource
+          .new(list_column,
+              serializer: Api::V1::InventoryColumnSerializer)
+          .as_json[:data]
+      )
+      expect(hash_body[:data]).to include('relationships')
+      expect(hash_body[:included]).to match(
+        ActiveModelSerializers::SerializableResource
+          .new(@valid_inventory.repository_columns.limit(10),
+               each_serializer: Api::V1::InventoryColumnSerializer,
+               include: :inventory_list_items)
+          .as_json[:included]
+      )
+    end
+
+    it 'Valid file column response' do
+      file_column = @valid_inventory.repository_columns.third
+      hash_body = nil
+      get api_v1_team_inventory_column_path(
+        id: file_column.id,
+        team_id: @teams.first.id,
+        inventory_id: @valid_inventory.id
+      ), headers: @valid_headers
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body[:data]).to match(
+        ActiveModelSerializers::SerializableResource
+          .new(file_column,
+              serializer: Api::V1::InventoryColumnSerializer)
+          .as_json[:data]
+      )
+      expect(hash_body[:data]).not_to include('relationships')
+    end
+
+    it 'Invalid request, non existing inventory column' do
+      get api_v1_team_inventory_column_path(
+        id: 1001,
+        team_id: @teams.first.id,
+        inventory_id: @teams.first.repositories.first.id
+      ), headers: @valid_headers
+      expect(response).to have_http_status(404)
+    end
+
+    it 'When invalid request, incorrect repository' do
+      id = @teams.first.repositories.first.repository_columns.last.id
+      get api_v1_team_inventory_column_path(
+        id: id,
+        team_id: @teams.first.id,
+        inventory_id: @teams.second.repositories.first.id
+      ), headers: @valid_headers
+      expect(response).to have_http_status(404)
+      expect(RepositoryColumn.where(id: id)).to exist
+    end
+
+    it 'When invalid request, repository from another team' do
+      id = @teams.first.repositories.first.repository_columns.last.id
+      get api_v1_team_inventory_column_path(
+        id: id,
+        team_id: @teams.second.id,
+        inventory_id: @teams.first.repositories.first.id
+      ), headers: @valid_headers
+      expect(response).to have_http_status(403)
+      expect(RepositoryColumn.where(id: id)).to exist
+    end
+  end
+
   describe 'POST inventory_column, #create' do
     before :all do
       @valid_headers['Content-Type'] = 'application/json'

From 9e78de6ef24e31b385913516fa101e57ea94fac5 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sat, 6 Oct 2018 17:11:59 +0200
Subject: [PATCH 20/40] Update CREATE, PATCH, DELETE inventory_column endpoints

---
 app/controllers/api/v1/inventory_columns_controller.rb | 8 +++++++-
 app/serializers/api/v1/inventory_column_serializer.rb  | 6 ------
 config/locales/en.yml                                  | 6 ------
 3 files changed, 7 insertions(+), 13 deletions(-)

diff --git a/app/controllers/api/v1/inventory_columns_controller.rb b/app/controllers/api/v1/inventory_columns_controller.rb
index 1c50924ec..d11d8cd08 100644
--- a/app/controllers/api/v1/inventory_columns_controller.rb
+++ b/app/controllers/api/v1/inventory_columns_controller.rb
@@ -24,6 +24,7 @@ module Api
           @inventory.repository_columns.create!(inventory_column_params)
         render jsonapi: inventory_column,
                serializer: InventoryColumnSerializer,
+               hide_list_items: true,
                status: :created
       end
 
@@ -37,7 +38,8 @@ module Api
         @inventory_column.attributes = update_inventory_column_params
         if @inventory_column.changed? && @inventory_column.save!
           render jsonapi: @inventory_column,
-                          serializer: InventoryColumnSerializer
+                          serializer: InventoryColumnSerializer,
+                          hide_list_items: true
         else
           render body: nil
         end
@@ -92,6 +94,10 @@ module Api
           raise ActionController::BadRequest,
                 'Object ID mismatch in URL and request body'
         end
+        if params.require(:data).require(:attributes).include?(:data_type)
+          raise ActionController::BadRequest,
+                'Update of data_type attribute is not allowed'
+        end
         inventory_column_params[:attributes]
       end
     end
diff --git a/app/serializers/api/v1/inventory_column_serializer.rb b/app/serializers/api/v1/inventory_column_serializer.rb
index 347457446..64fe83d1d 100644
--- a/app/serializers/api/v1/inventory_column_serializer.rb
+++ b/app/serializers/api/v1/inventory_column_serializer.rb
@@ -10,12 +10,6 @@ module Api
                                        class_name: 'RepositoryListItem',
                                        if: -> { object.data_type == 'RepositoryListValue' &&
                                                 !instance_options[:hide_list_items] }
-
-      def data_type
-        type_id = RepositoryColumn
-                  .data_types[object.data_type]
-        I18n.t("api.v1.inventory_data_types.t#{type_id}")
-      end
     end
   end
 end
diff --git a/config/locales/en.yml b/config/locales/en.yml
index c7440c1de..8dee84d14 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1943,12 +1943,6 @@ en:
       status_ok: "Ok"
       expired_token: "Token is expired"
       invalid_token: "Token is invalid"
-    v1:
-      inventory_data_types:
-        t0: "text"
-        t1: "date"
-        t2: "list"
-        t3: "file"
 
   Add: "Add"
   Asset: "File"

From d235dd780717073ff3f4fb048e10ab9a8bb3d6ce Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sat, 6 Oct 2018 18:37:40 +0200
Subject: [PATCH 21/40] Update GET /inventory_items, GET /inventory_items/:id
 endpoints

---
 .../api/v1/inventory_items_controller.rb      |  3 ++-
 .../api/v1/inventory_cell_serializer.rb       |  6 -----
 .../api/v1/inventory_item_serializer.rb       |  3 ++-
 .../api/v1/inventory_items_controller_spec.rb | 26 ++++++++++++++-----
 4 files changed, 23 insertions(+), 15 deletions(-)

diff --git a/app/controllers/api/v1/inventory_items_controller.rb b/app/controllers/api/v1/inventory_items_controller.rb
index 4ed13d37e..4f6815fcf 100644
--- a/app/controllers/api/v1/inventory_items_controller.rb
+++ b/app/controllers/api/v1/inventory_items_controller.rb
@@ -16,9 +16,10 @@ module Api
                       repository_cells: Extends::REPOSITORY_SEARCH_INCLUDES
                     ).page(params.dig(:page, :number))
                     .per(params.dig(:page, :size))
+        incl = params[:include] == 'inventory_cells' ? :inventory_cells : nil
         render jsonapi: items,
                each_serializer: InventoryItemSerializer,
-               include: :inventory_cells
+               include: incl
       end
 
       def create
diff --git a/app/serializers/api/v1/inventory_cell_serializer.rb b/app/serializers/api/v1/inventory_cell_serializer.rb
index b615f456c..dc89e1454 100644
--- a/app/serializers/api/v1/inventory_cell_serializer.rb
+++ b/app/serializers/api/v1/inventory_cell_serializer.rb
@@ -7,12 +7,6 @@ module Api
       attributes :id, :value_type, :value
       attribute :repository_column_id, key: :column_id
 
-      def value_type
-        type_id = RepositoryColumn
-                  .data_types[object.repository_column.data_type]
-        I18n.t("api.v1.inventory_data_types.t#{type_id}")
-      end
-
       def value
         value =
           case object.value_type
diff --git a/app/serializers/api/v1/inventory_item_serializer.rb b/app/serializers/api/v1/inventory_item_serializer.rb
index 3df5dc3f8..e980096fb 100644
--- a/app/serializers/api/v1/inventory_item_serializer.rb
+++ b/app/serializers/api/v1/inventory_item_serializer.rb
@@ -7,7 +7,8 @@ module Api
       attributes :name
       has_many :repository_cells, key: :inventory_cells,
                                   serializer: InventoryCellSerializer,
-                                  class_name: 'RepositoryCell'
+                                  class_name: 'RepositoryCell',
+                                  unless: -> { object.repository_cells.empty? }
     end
   end
 end
diff --git a/spec/requests/api/v1/inventory_items_controller_spec.rb b/spec/requests/api/v1/inventory_items_controller_spec.rb
index ce1d969c7..5d569fbcc 100644
--- a/spec/requests/api/v1/inventory_items_controller_spec.rb
+++ b/spec/requests/api/v1/inventory_items_controller_spec.rb
@@ -75,6 +75,24 @@ RSpec.describe 'Api::V1::InventoryItemsController', type: :request do
                include: :inventory_cells)
           .as_json[:data]
       )
+      expect(hash_body).not_to include('included')
+    end
+
+    it 'Response with correct inventory items, included cells' do
+      hash_body = nil
+      get api_v1_team_inventory_items_path(
+        team_id: @teams.first.id,
+        inventory_id: @teams.first.repositories.first.id,
+        include: 'inventory_cells'
+      ), headers: @valid_headers
+      expect { hash_body = json }.not_to raise_exception
+      expect(hash_body[:data]).to match(
+        ActiveModelSerializers::SerializableResource
+          .new(@valid_inventory.repository_rows.limit(10),
+               each_serializer: Api::V1::InventoryItemSerializer,
+               include: :inventory_cells)
+          .as_json[:data]
+      )
       expect(hash_body[:included]).to match(
         ActiveModelSerializers::SerializableResource
           .new(@valid_inventory.repository_rows.limit(10),
@@ -98,13 +116,7 @@ RSpec.describe 'Api::V1::InventoryItemsController', type: :request do
                include: :inventory_cells)
           .as_json[:data]
       )
-      expect(hash_body[:included]).to match(
-        ActiveModelSerializers::SerializableResource
-          .new(@valid_inventory.repository_rows.limit(100),
-               each_serializer: Api::V1::InventoryItemSerializer,
-               include: :inventory_cells)
-          .as_json[:included]
-      )
+      expect(hash_body).not_to include('included')
     end
 
     it 'When invalid request, user in not member of the team' do

From c9a15db85f6fc28262e2466d05233865f261c9ae Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sat, 6 Oct 2018 19:53:31 +0200
Subject: [PATCH 22/40] Fix GET /task_groups endpoints

---
 app/controllers/api/v1/my_modules_controller.rb    | 12 ++++++------
 ...ups_controller.rb => task_groups_controller.rb} | 11 +++++++----
 app/serializers/api/v1/activity_serializer.rb      |  2 +-
 app/serializers/api/v1/connection_serializer.rb    |  4 ++--
 .../api/v1/my_module_group_serializer.rb           | 11 -----------
 .../api/v1/my_module_repository_row_serializer.rb  |  2 +-
 app/serializers/api/v1/my_module_tag_serializer.rb |  2 +-
 app/serializers/api/v1/protocol_serializer.rb      |  2 +-
 app/serializers/api/v1/result_serializer.rb        |  2 +-
 app/serializers/api/v1/task_group_serializer.rb    | 14 ++++++++++++++
 ...{my_module_serializer.rb => task_serializer.rb} |  2 +-
 .../api/v1/user_my_module_serializer.rb            |  2 +-
 12 files changed, 36 insertions(+), 30 deletions(-)
 rename app/controllers/api/v1/{my_module_groups_controller.rb => task_groups_controller.rb} (80%)
 delete mode 100644 app/serializers/api/v1/my_module_group_serializer.rb
 create mode 100644 app/serializers/api/v1/task_group_serializer.rb
 rename app/serializers/api/v1/{my_module_serializer.rb => task_serializer.rb} (83%)

diff --git a/app/controllers/api/v1/my_modules_controller.rb b/app/controllers/api/v1/my_modules_controller.rb
index 37a2b757d..7a9e3e41a 100644
--- a/app/controllers/api/v1/my_modules_controller.rb
+++ b/app/controllers/api/v1/my_modules_controller.rb
@@ -14,35 +14,35 @@ module Api
                            .page(params.dig(:page, :number))
                            .per(params.dig(:page, :size))
 
-        render jsonapi: tasks, each_serializer: MyModuleSerializer
+        render jsonapi: tasks, each_serializer: TaskSerializer
       end
 
       def show
-        render jsonapi: @my_module, serializer: MyModuleSerializer
+        render jsonapi: @my_module, serializer: TaskSerializer
       end
 
       def outputs
         outputs = @my_module.my_modules
                             .page(params.dig(:page, :number))
                             .per(params.dig(:page, :size))
-        render jsonapi: outputs, each_serializer: MyModuleSerializer
+        render jsonapi: outputs, each_serializer: TaskSerializer
       end
 
       def output
         output = @my_module.my_modules.find(params.require(:id))
-        render jsonapi: output, serializer: MyModuleSerializer
+        render jsonapi: output, serializer: TaskSerializer
       end
 
       def inputs
         inputs = @my_module.my_module_antecessors
                            .page(params.dig(:page, :number))
                            .per(params.dig(:page, :size))
-        render jsonapi: inputs, each_serializer: MyModuleSerializer
+        render jsonapi: inputs, each_serializer: TaskSerializer
       end
 
       def input
         input = @my_module.my_module_antecessors.find(params.require(:id))
-        render jsonapi: input, serializer: MyModuleSerializer
+        render jsonapi: input, serializer: TaskSerializer
       end
 
       private
diff --git a/app/controllers/api/v1/my_module_groups_controller.rb b/app/controllers/api/v1/task_groups_controller.rb
similarity index 80%
rename from app/controllers/api/v1/my_module_groups_controller.rb
rename to app/controllers/api/v1/task_groups_controller.rb
index 1250da749..f586c2664 100644
--- a/app/controllers/api/v1/my_module_groups_controller.rb
+++ b/app/controllers/api/v1/task_groups_controller.rb
@@ -2,7 +2,7 @@
 
 module Api
   module V1
-    class MyModuleGroupsController < BaseController
+    class TaskGroupsController < BaseController
       before_action :load_team
       before_action :load_project
       before_action :load_experiment
@@ -12,13 +12,16 @@ module Api
         my_module_groups = @experiment.my_module_groups
                                       .page(params.dig(:page, :number))
                                       .per(params.dig(:page, :size))
-
+        incl = params[:include] == 'tasks' ? :tasks : nil
         render jsonapi: my_module_groups,
-          each_serializer: MyModuleGroupSerializer
+               each_serializer: TaskGroupSerializer,
+               include: incl
       end
 
       def show
-        render jsonapi: @my_module_group, serializer: MyModuleGroupSerializer
+        render jsonapi: @my_module_group,
+               serializer: TaskGroupSerializer,
+               include: :tasks
       end
 
       private
diff --git a/app/serializers/api/v1/activity_serializer.rb b/app/serializers/api/v1/activity_serializer.rb
index 70332ce2d..28910b7f5 100644
--- a/app/serializers/api/v1/activity_serializer.rb
+++ b/app/serializers/api/v1/activity_serializer.rb
@@ -6,7 +6,7 @@ module Api
       type :activities
       attributes :id, :my_module_id, :user_id, :type_of, :message,
                  :project_id, :experiment_id
-      belongs_to :my_module, serializer: MyModuleSerializer
+      belongs_to :my_module, serializer: TaskSerializer
     end
   end
 end
diff --git a/app/serializers/api/v1/connection_serializer.rb b/app/serializers/api/v1/connection_serializer.rb
index 98f83c7c7..d75c41d18 100644
--- a/app/serializers/api/v1/connection_serializer.rb
+++ b/app/serializers/api/v1/connection_serializer.rb
@@ -5,8 +5,8 @@ module Api
     class ConnectionSerializer < ActiveModel::Serializer
       type :connections
       attributes :id, :input_id, :output_id
-      has_one :input_task, serializer: MyModuleSerializer
-      has_one :output_task, serializer: MyModuleSerializer
+      has_one :input_task, serializer: TaskSerializer
+      has_one :output_task, serializer: TaskSerializer
       def input_task
         MyModule.find(object.input_id)
       end
diff --git a/app/serializers/api/v1/my_module_group_serializer.rb b/app/serializers/api/v1/my_module_group_serializer.rb
deleted file mode 100644
index 06b52e31e..000000000
--- a/app/serializers/api/v1/my_module_group_serializer.rb
+++ /dev/null
@@ -1,11 +0,0 @@
-# frozen_string_literal: true
-
-module Api
-  module V1
-    class MyModuleGroupSerializer < ActiveModel::Serializer
-      type :task_groups
-      attributes :id, :experiment_id
-      belongs_to :experiment, serializer: ExperimentSerializer
-    end
-  end
-end
diff --git a/app/serializers/api/v1/my_module_repository_row_serializer.rb b/app/serializers/api/v1/my_module_repository_row_serializer.rb
index 1133b6263..4b543d012 100644
--- a/app/serializers/api/v1/my_module_repository_row_serializer.rb
+++ b/app/serializers/api/v1/my_module_repository_row_serializer.rb
@@ -6,7 +6,7 @@ module Api
       type :task_inventory_rows
       attribute :repository_row_id, key: :inventory_row_id
       attribute :my_module_id, key: :task_id
-      belongs_to :my_module, serializer: MyModuleSerializer
+      belongs_to :my_module, serializer: TaskSerializer
     end
   end
 end
diff --git a/app/serializers/api/v1/my_module_tag_serializer.rb b/app/serializers/api/v1/my_module_tag_serializer.rb
index 7f8e4a2e6..a35c39865 100644
--- a/app/serializers/api/v1/my_module_tag_serializer.rb
+++ b/app/serializers/api/v1/my_module_tag_serializer.rb
@@ -7,7 +7,7 @@ module Api
       attributes :id, :tag_id
       attribute :my_module_id, key: :task_id
 
-      belongs_to :my_module, serializer: MyModuleSerializer
+      belongs_to :my_module, serializer: TaskSerializer
     end
   end
 end
diff --git a/app/serializers/api/v1/protocol_serializer.rb b/app/serializers/api/v1/protocol_serializer.rb
index 6efafeddc..9f255b377 100644
--- a/app/serializers/api/v1/protocol_serializer.rb
+++ b/app/serializers/api/v1/protocol_serializer.rb
@@ -9,7 +9,7 @@ module Api
                  :nr_of_linked_children
       attribute :my_module_id, key: :task_id
 
-      belongs_to :my_module, serializer: MyModuleSerializer
+      belongs_to :my_module, serializer: TaskSerializer
     end
   end
 end
diff --git a/app/serializers/api/v1/result_serializer.rb b/app/serializers/api/v1/result_serializer.rb
index 84aeb1408..5e990f1cb 100644
--- a/app/serializers/api/v1/result_serializer.rb
+++ b/app/serializers/api/v1/result_serializer.rb
@@ -7,7 +7,7 @@ module Api
       attributes :name, :user_id, :archived
       attribute :my_module_id, key: :task_id
 
-      belongs_to :my_module, serializer: MyModuleSerializer
+      belongs_to :my_module, serializer: TaskSerializer
       has_one :result_asset, key: :asset,
                              serializer: ResultAssetSerializer,
                              class_name: 'ResultAsset',
diff --git a/app/serializers/api/v1/task_group_serializer.rb b/app/serializers/api/v1/task_group_serializer.rb
new file mode 100644
index 000000000..2b7579e8f
--- /dev/null
+++ b/app/serializers/api/v1/task_group_serializer.rb
@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class TaskGroupSerializer < ActiveModel::Serializer
+      type :task_groups
+      attributes :id
+      has_many :my_modules, key: :tasks,
+                            serializer: TaskSerializer,
+                            class_name: 'MyModule',
+                            unless: -> { object.my_modules.empty? }
+    end
+  end
+end
diff --git a/app/serializers/api/v1/my_module_serializer.rb b/app/serializers/api/v1/task_serializer.rb
similarity index 83%
rename from app/serializers/api/v1/my_module_serializer.rb
rename to app/serializers/api/v1/task_serializer.rb
index bc0f43779..8e2aa9cf0 100644
--- a/app/serializers/api/v1/my_module_serializer.rb
+++ b/app/serializers/api/v1/task_serializer.rb
@@ -2,7 +2,7 @@
 
 module Api
   module V1
-    class MyModuleSerializer < ActiveModel::Serializer
+    class TaskSerializer < ActiveModel::Serializer
       type :tasks
       attributes :id, :name, :due_date, :description, :state
       attribute :my_module_group_id, key: :task_group_id
diff --git a/app/serializers/api/v1/user_my_module_serializer.rb b/app/serializers/api/v1/user_my_module_serializer.rb
index 6474b8316..87edc39ce 100644
--- a/app/serializers/api/v1/user_my_module_serializer.rb
+++ b/app/serializers/api/v1/user_my_module_serializer.rb
@@ -7,7 +7,7 @@ module Api
       attributes :id, :user_id
       attribute :my_module_id, key: :task_id
 
-      belongs_to :my_module, serializer: MyModuleSerializer
+      belongs_to :my_module, serializer: TaskSerializer
     end
   end
 end

From 0643ba216ed014624b64173be47e1a63d9a8c743 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 00:53:39 +0200
Subject: [PATCH 23/40] Fix GET /connections, /connections/:id endpoints

---
 .../api/v1/connections_controller.rb            |  9 +++++++--
 app/serializers/api/v1/connection_serializer.rb | 17 +++++++----------
 2 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/app/controllers/api/v1/connections_controller.rb b/app/controllers/api/v1/connections_controller.rb
index 1ce2111f4..ec42edf6b 100644
--- a/app/controllers/api/v1/connections_controller.rb
+++ b/app/controllers/api/v1/connections_controller.rb
@@ -12,11 +12,16 @@ module Api
       def index
         @connections = @connections.page(params.dig(:page, :number))
                                    .per(params.dig(:page, :size))
-        render jsonapi: @connections, each_serializer: ConnectionSerializer
+        incl = params[:include] == 'tasks' ? %i(input_task output_task) : nil
+        render jsonapi: @connections,
+               each_serializer: ConnectionSerializer,
+               include: incl
       end
 
       def show
-        render jsonapi: @connection, serializer: ConnectionSerializer
+        render jsonapi: @connection,
+               serializer: ConnectionSerializer,
+               include: %i(input_task output_task)
       end
 
       private
diff --git a/app/serializers/api/v1/connection_serializer.rb b/app/serializers/api/v1/connection_serializer.rb
index d75c41d18..143f440e9 100644
--- a/app/serializers/api/v1/connection_serializer.rb
+++ b/app/serializers/api/v1/connection_serializer.rb
@@ -4,16 +4,13 @@ module Api
   module V1
     class ConnectionSerializer < ActiveModel::Serializer
       type :connections
-      attributes :id, :input_id, :output_id
-      has_one :input_task, serializer: TaskSerializer
-      has_one :output_task, serializer: TaskSerializer
-      def input_task
-        MyModule.find(object.input_id)
-      end
-
-      def output_task
-        MyModule.find(object.output_id)
-      end
+      attributes :id
+      belongs_to :from, key: :input_task,
+                        serializer: TaskSerializer,
+                        class_name: 'MyModule'
+      belongs_to :to, key: :output_task,
+                      serializer: TaskSerializer,
+                      class_name: 'MyModule'
     end
   end
 end

From 0de3c7eb4e3d8676bacbda8b2619d0d8f81704cf Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 09:45:24 +0200
Subject: [PATCH 24/40] Update GET /tasks, GET /tasks/:id endpoints, refactor
 routes.rb

---
 ..._modules_controller.rb => tasks_controller.rb} |  2 +-
 app/serializers/api/v1/task_serializer.rb         |  4 +---
 config/routes.rb                                  | 15 +++------------
 3 files changed, 5 insertions(+), 16 deletions(-)
 rename app/controllers/api/v1/{my_modules_controller.rb => tasks_controller.rb} (98%)

diff --git a/app/controllers/api/v1/my_modules_controller.rb b/app/controllers/api/v1/tasks_controller.rb
similarity index 98%
rename from app/controllers/api/v1/my_modules_controller.rb
rename to app/controllers/api/v1/tasks_controller.rb
index 7a9e3e41a..710fa8684 100644
--- a/app/controllers/api/v1/my_modules_controller.rb
+++ b/app/controllers/api/v1/tasks_controller.rb
@@ -2,7 +2,7 @@
 
 module Api
   module V1
-    class MyModulesController < BaseController
+    class TasksController < BaseController
       before_action :load_team
       before_action :load_project
       before_action :load_experiment
diff --git a/app/serializers/api/v1/task_serializer.rb b/app/serializers/api/v1/task_serializer.rb
index 8e2aa9cf0..ba5461fd2 100644
--- a/app/serializers/api/v1/task_serializer.rb
+++ b/app/serializers/api/v1/task_serializer.rb
@@ -4,9 +4,7 @@ module Api
   module V1
     class TaskSerializer < ActiveModel::Serializer
       type :tasks
-      attributes :id, :name, :due_date, :description, :state
-      attribute :my_module_group_id, key: :task_group_id
-      belongs_to :experiment, serializer: ExperimentSerializer
+      attributes :id, :name, :due_date, :description, :state, :archived
     end
   end
 end
diff --git a/config/routes.rb b/config/routes.rb
index a680fa919..a7dbee906 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -563,18 +563,9 @@ Rails.application.routes.draw do
             end
             resources :projects, only: %i(index show) do
               resources :experiments, only: %i(index show) do
-                resources :my_module_groups,
-                          only: %i(index show),
-                          path: 'task_groups',
-                          as: :task_groups
-                resources :connections,
-                          only: %i(index show),
-                          path: 'connections',
-                          as: :connections
-                resources :my_modules,
-                          only: %i(index show),
-                          path: 'tasks',
-                as: :tasks do
+                resources :task_groups, only: %i(index show)
+                resources :connections, only: %i(index show)
+                resources :tasks, only: %i(index show) do
                   resources :my_module_repository_rows, only: %i(index show),
                             path: 'task_inventory_rows',
                             as: :task_inventory_rows

From f56e5b1e5aaa8b9b3a2f7ee6c20abab3824c3df3 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 10:07:37 +0200
Subject: [PATCH 25/40] Update GET /task/:task_id/items, GET
 /task/:task_id/items/:id endpts

---
 .../my_module_repository_rows_controller.rb   | 59 ----------------
 .../api/v1/task_inventory_items_controller.rb | 68 +++++++++++++++++++
 app/controllers/api/v1/tasks_controller.rb    | 14 ++--
 .../api/v1/inventory_item_serializer.rb       |  4 ++
 .../v1/my_module_repository_row_serializer.rb | 12 ----
 config/routes.rb                              |  6 +-
 6 files changed, 82 insertions(+), 81 deletions(-)
 delete mode 100644 app/controllers/api/v1/my_module_repository_rows_controller.rb
 create mode 100644 app/controllers/api/v1/task_inventory_items_controller.rb
 delete mode 100644 app/serializers/api/v1/my_module_repository_row_serializer.rb

diff --git a/app/controllers/api/v1/my_module_repository_rows_controller.rb b/app/controllers/api/v1/my_module_repository_rows_controller.rb
deleted file mode 100644
index cdb2317ea..000000000
--- a/app/controllers/api/v1/my_module_repository_rows_controller.rb
+++ /dev/null
@@ -1,59 +0,0 @@
-# frozen_string_literal: true
-
-module Api
-  module V1
-    class MyModuleRepositoryRowsController < BaseController
-      before_action :load_team
-      before_action :load_project
-      before_action :load_experiment
-      before_action :load_task
-      before_action :load_task_repository_row, only: :show
-
-      def index
-        repo_rows = @my_module.my_module_repository_rows
-                              .page(params.dig(:page, :number))
-                              .per(params.dig(:page, :size))
-
-        render jsonapi: repo_rows,
-          each_serializer: MyModuleRepositoryRowSerializer
-      end
-
-      def show
-        render jsonapi: @repo_row, serializer: MyModuleRepositoryRowSerializer
-      end
-
-      private
-
-      def load_team
-        @team = Team.find(params.require(:team_id))
-        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
-      end
-
-      def load_project
-        @project = @team.projects.find(params.require(:project_id))
-        render jsonapi: {}, status: :forbidden unless can_read_project?(
-          @project
-        )
-      end
-
-      def load_experiment
-        @experiment = @project.experiments.find(params.require(:experiment_id))
-        render jsonapi: {}, status: :forbidden unless can_read_experiment?(
-          @experiment
-        )
-      end
-
-      def load_task
-        @my_module = @experiment.my_modules.find(params.require(:task_id))
-        render jsonapi: {}, status: :not_found if @my_module.nil?
-      end
-
-      def load_task_repository_row
-        @repo_row = @my_module.my_module_repository_rows.find(
-          params.require(:id)
-        )
-        render jsonapi: {}, status: :not_found if @repo_row.nil?
-      end
-    end
-  end
-end
diff --git a/app/controllers/api/v1/task_inventory_items_controller.rb b/app/controllers/api/v1/task_inventory_items_controller.rb
new file mode 100644
index 000000000..ab28c6996
--- /dev/null
+++ b/app/controllers/api/v1/task_inventory_items_controller.rb
@@ -0,0 +1,68 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class TaskInventoryItemsController < BaseController
+      before_action :load_team
+      before_action :load_project
+      before_action :load_experiment
+      before_action :load_task
+      before_action :load_inventory_item, only: :show
+
+      def index
+        items =
+          @task.repository_rows
+                    .includes(repository_cells: :repository_column)
+                    .includes(
+                      repository_cells: Extends::REPOSITORY_SEARCH_INCLUDES
+                    ).page(params.dig(:page, :number))
+                    .per(params.dig(:page, :size))
+        incl = params[:include] == 'inventory_cells' ? :inventory_cells : nil
+        render jsonapi: items,
+               each_serializer: InventoryItemSerializer,
+               show_repository: true,
+               include: incl
+      end
+
+      def show
+        render jsonapi: @item,
+               serializer: InventoryItemSerializer,
+               show_repository: true,
+               include: %i(inventory_cells inventory)
+      end
+
+      private
+
+      def load_team
+        @team = Team.find(params.require(:team_id))
+        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
+      end
+
+      def load_project
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
+
+      def load_experiment
+        @experiment = @project.experiments.find(params.require(:experiment_id))
+        render jsonapi: {}, status: :forbidden unless can_read_experiment?(
+          @experiment
+        )
+      end
+
+      def load_task
+        @task = @experiment.my_modules.find(params.require(:task_id))
+        render jsonapi: {}, status: :not_found if @task.nil?
+      end
+
+      def load_inventory_item
+        @item = @task.repository_rows.find(
+          params.require(:id)
+        )
+        render jsonapi: {}, status: :not_found if @item.nil?
+      end
+    end
+  end
+end
diff --git a/app/controllers/api/v1/tasks_controller.rb b/app/controllers/api/v1/tasks_controller.rb
index 710fa8684..f4e271fa0 100644
--- a/app/controllers/api/v1/tasks_controller.rb
+++ b/app/controllers/api/v1/tasks_controller.rb
@@ -18,30 +18,30 @@ module Api
       end
 
       def show
-        render jsonapi: @my_module, serializer: TaskSerializer
+        render jsonapi: @task, serializer: TaskSerializer
       end
 
       def outputs
-        outputs = @my_module.my_modules
+        outputs = @task.my_modules
                             .page(params.dig(:page, :number))
                             .per(params.dig(:page, :size))
         render jsonapi: outputs, each_serializer: TaskSerializer
       end
 
       def output
-        output = @my_module.my_modules.find(params.require(:id))
+        output = @task.my_modules.find(params.require(:id))
         render jsonapi: output, serializer: TaskSerializer
       end
 
       def inputs
-        inputs = @my_module.my_module_antecessors
+        inputs = @task.my_module_antecessors
                            .page(params.dig(:page, :number))
                            .per(params.dig(:page, :size))
         render jsonapi: inputs, each_serializer: TaskSerializer
       end
 
       def input
-        input = @my_module.my_module_antecessors.find(params.require(:id))
+        input = @task.my_module_antecessors.find(params.require(:id))
         render jsonapi: input, serializer: TaskSerializer
       end
 
@@ -67,7 +67,7 @@ module Api
       end
 
       def load_task
-        @my_module = @experiment.my_modules.find(params.require(:id))
+        @task = @experiment.my_modules.find(params.require(:id))
       end
 
       # Made the method below because its more elegant than changing parameters
@@ -75,7 +75,7 @@ module Api
       # for a task, the "id" that used to be task id is now an id for the output
       # or input.
       def load_task_relative
-        @my_module = @experiment.my_modules.find(params.require(:task_id))
+        @task = @experiment.my_modules.find(params.require(:task_id))
       end
     end
   end
diff --git a/app/serializers/api/v1/inventory_item_serializer.rb b/app/serializers/api/v1/inventory_item_serializer.rb
index e980096fb..37d3db1f2 100644
--- a/app/serializers/api/v1/inventory_item_serializer.rb
+++ b/app/serializers/api/v1/inventory_item_serializer.rb
@@ -9,6 +9,10 @@ module Api
                                   serializer: InventoryCellSerializer,
                                   class_name: 'RepositoryCell',
                                   unless: -> { object.repository_cells.empty? }
+      belongs_to :repository, key: :inventory,
+                              serializer: InventorySerializer,
+                              class_name: 'Repository',
+                              if: -> { instance_options[:show_repository] }
     end
   end
 end
diff --git a/app/serializers/api/v1/my_module_repository_row_serializer.rb b/app/serializers/api/v1/my_module_repository_row_serializer.rb
deleted file mode 100644
index 4b543d012..000000000
--- a/app/serializers/api/v1/my_module_repository_row_serializer.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-# frozen_string_literal: true
-
-module Api
-  module V1
-    class MyModuleRepositoryRowSerializer < ActiveModel::Serializer
-      type :task_inventory_rows
-      attribute :repository_row_id, key: :inventory_row_id
-      attribute :my_module_id, key: :task_id
-      belongs_to :my_module, serializer: TaskSerializer
-    end
-  end
-end
diff --git a/config/routes.rb b/config/routes.rb
index a7dbee906..e04963770 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -566,9 +566,9 @@ Rails.application.routes.draw do
                 resources :task_groups, only: %i(index show)
                 resources :connections, only: %i(index show)
                 resources :tasks, only: %i(index show) do
-                  resources :my_module_repository_rows, only: %i(index show),
-                            path: 'task_inventory_rows',
-                            as: :task_inventory_rows
+                  resources :task_inventory_items, only: %i(index show),
+                            path: 'items',
+                            as: :items
                   resources :user_my_modules, only: %i(index show),
                             path: 'user_tasks',
                             as: :user_tasks

From 94e80edc9bae59eb173b80c2c92eb5a863430e3f Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 10:16:00 +0200
Subject: [PATCH 26/40] Minor variable rename in task_groups_controller.rb

---
 app/controllers/api/v1/task_groups_controller.rb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/controllers/api/v1/task_groups_controller.rb b/app/controllers/api/v1/task_groups_controller.rb
index f586c2664..c94a73865 100644
--- a/app/controllers/api/v1/task_groups_controller.rb
+++ b/app/controllers/api/v1/task_groups_controller.rb
@@ -9,17 +9,17 @@ module Api
       before_action :load_task_group, only: :show
 
       def index
-        my_module_groups = @experiment.my_module_groups
+        task_groups = @experiment.my_module_groups
                                       .page(params.dig(:page, :number))
                                       .per(params.dig(:page, :size))
         incl = params[:include] == 'tasks' ? :tasks : nil
-        render jsonapi: my_module_groups,
+        render jsonapi: task_groups,
                each_serializer: TaskGroupSerializer,
                include: incl
       end
 
       def show
-        render jsonapi: @my_module_group,
+        render jsonapi: @task_group,
                serializer: TaskGroupSerializer,
                include: :tasks
       end
@@ -46,7 +46,7 @@ module Api
       end
 
       def load_task_group
-        @my_module_group = @experiment.my_module_groups.find(
+        @task_group = @experiment.my_module_groups.find(
           params.require(:id)
         )
       end

From 98544f00e8c79bf01fe49617320293b9a810a2bd Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 10:20:01 +0200
Subject: [PATCH 27/40] Fix GET /tasks/:task_id/users, GET
 /tasks/:task_id/users/1 endpts

---
 ..._controller.rb => task_users_controller.rb} | 18 +++++++++---------
 .../api/v1/user_my_module_serializer.rb        | 13 -------------
 config/routes.rb                               |  6 +++---
 3 files changed, 12 insertions(+), 25 deletions(-)
 rename app/controllers/api/v1/{user_my_modules_controller.rb => task_users_controller.rb} (70%)
 delete mode 100644 app/serializers/api/v1/user_my_module_serializer.rb

diff --git a/app/controllers/api/v1/user_my_modules_controller.rb b/app/controllers/api/v1/task_users_controller.rb
similarity index 70%
rename from app/controllers/api/v1/user_my_modules_controller.rb
rename to app/controllers/api/v1/task_users_controller.rb
index 00c3acdc7..b5d72d826 100644
--- a/app/controllers/api/v1/user_my_modules_controller.rb
+++ b/app/controllers/api/v1/task_users_controller.rb
@@ -2,24 +2,24 @@
 
 module Api
   module V1
-    class UserMyModulesController < BaseController
+    class TaskUsersController < BaseController
       before_action :load_team
       before_action :load_project
       before_action :load_experiment
       before_action :load_task
-      before_action :load_user_task, only: :show
+      before_action :load_user, only: :show
 
       def index
-        user_tasks = @my_module.user_my_modules
+        users = @task.users
                                .page(params.dig(:page, :number))
                                .per(params.dig(:page, :size))
 
-        render jsonapi: user_tasks,
-          each_serializer: UserMyModuleSerializer
+        render jsonapi: users,
+          each_serializer: UserSerializer
       end
 
       def show
-        render jsonapi: @user_task, serializer: UserMyModuleSerializer
+        render jsonapi: @user, serializer: UserSerializer
       end
 
       private
@@ -44,11 +44,11 @@ module Api
       end
 
       def load_task
-        @my_module = @experiment.my_modules.find(params.require(:task_id))
+        @task = @experiment.my_modules.find(params.require(:task_id))
       end
 
-      def load_user_task
-        @user_task = @my_module.user_my_modules.find(
+      def load_user
+        @user = @task.users.find(
           params.require(:id)
         )
       end
diff --git a/app/serializers/api/v1/user_my_module_serializer.rb b/app/serializers/api/v1/user_my_module_serializer.rb
deleted file mode 100644
index 87edc39ce..000000000
--- a/app/serializers/api/v1/user_my_module_serializer.rb
+++ /dev/null
@@ -1,13 +0,0 @@
-# frozen_string_literal: true
-
-module Api
-  module V1
-    class UserMyModuleSerializer < ActiveModel::Serializer
-      type :user_tasks
-      attributes :id, :user_id
-      attribute :my_module_id, key: :task_id
-
-      belongs_to :my_module, serializer: TaskSerializer
-    end
-  end
-end
diff --git a/config/routes.rb b/config/routes.rb
index e04963770..abe255714 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -569,9 +569,9 @@ Rails.application.routes.draw do
                   resources :task_inventory_items, only: %i(index show),
                             path: 'items',
                             as: :items
-                  resources :user_my_modules, only: %i(index show),
-                            path: 'user_tasks',
-                            as: :user_tasks
+                  resources :task_users, only: %i(index show),
+                            path: 'users',
+                            as: :users
                   resources :my_module_tags, only: %i(index show),
                             path: 'task_tags',
                             as: :task_tags

From 24299ef4c0d131442a508ff93fcce798a74935c5 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 11:10:41 +0200
Subject: [PATCH 28/40] Fix GET /tasks/:task_id/tags, GET
 /tasks/:task_id/tags/:id endpts

---
 ..._controller.rb => task_tags_controller.rb} | 26 +++++++++----------
 .../api/v1/my_module_tag_serializer.rb        | 13 ----------
 app/serializers/api/v1/tag_serializer.rb      | 10 +++++++
 config/routes.rb                              |  6 ++---
 4 files changed, 26 insertions(+), 29 deletions(-)
 rename app/controllers/api/v1/{my_module_tags_controller.rb => task_tags_controller.rb} (57%)
 delete mode 100644 app/serializers/api/v1/my_module_tag_serializer.rb
 create mode 100644 app/serializers/api/v1/tag_serializer.rb

diff --git a/app/controllers/api/v1/my_module_tags_controller.rb b/app/controllers/api/v1/task_tags_controller.rb
similarity index 57%
rename from app/controllers/api/v1/my_module_tags_controller.rb
rename to app/controllers/api/v1/task_tags_controller.rb
index c0b7911a5..abe4a30a5 100644
--- a/app/controllers/api/v1/my_module_tags_controller.rb
+++ b/app/controllers/api/v1/task_tags_controller.rb
@@ -2,24 +2,24 @@
 
 module Api
   module V1
-    class MyModuleTagsController < BaseController
+    class TaskTagsController < BaseController
       before_action :load_team
       before_action :load_project
       before_action :load_experiment
       before_action :load_task
-      before_action :load_task_tag, only: :show
+      before_action :load_tag, only: :show
 
       def index
-        task_tags = @my_module.my_module_tags
-                              .page(params.dig(:page, :number))
-                              .per(params.dig(:page, :size))
+        tags = @task.tags
+                    .page(params.dig(:page, :number))
+                    .per(params.dig(:page, :size))
 
-        render jsonapi: task_tags,
-          each_serializer: MyModuleTagSerializer
+        render jsonapi: tags,
+               each_serializer: TagSerializer
       end
 
       def show
-        render jsonapi: @task_tag, serializer: MyModuleTagSerializer
+        render jsonapi: @tag, serializer: TagSerializer
       end
 
       private
@@ -44,15 +44,15 @@ module Api
       end
 
       def load_task
-        @my_module = @experiment.my_modules.find(params.require(:task_id))
-        render jsonapi: {}, status: :not_found if @my_module.nil?
+        @task = @experiment.my_modules.find(params.require(:task_id))
+        render jsonapi: {}, status: :not_found if @task.nil?
       end
 
-      def load_task_tag
-        @task_tag = @my_module.my_module_tags.find(
+      def load_tag
+        @tag = @task.tags.find(
           params.require(:id)
         )
-        render jsonapi: {}, status: :not_found if @task_tag.nil?
+        render jsonapi: {}, status: :not_found if @tag.nil?
       end
     end
   end
diff --git a/app/serializers/api/v1/my_module_tag_serializer.rb b/app/serializers/api/v1/my_module_tag_serializer.rb
deleted file mode 100644
index a35c39865..000000000
--- a/app/serializers/api/v1/my_module_tag_serializer.rb
+++ /dev/null
@@ -1,13 +0,0 @@
-# frozen_string_literal: true
-
-module Api
-  module V1
-    class MyModuleTagSerializer < ActiveModel::Serializer
-      type :task_tags
-      attributes :id, :tag_id
-      attribute :my_module_id, key: :task_id
-
-      belongs_to :my_module, serializer: TaskSerializer
-    end
-  end
-end
diff --git a/app/serializers/api/v1/tag_serializer.rb b/app/serializers/api/v1/tag_serializer.rb
new file mode 100644
index 000000000..d30f92ade
--- /dev/null
+++ b/app/serializers/api/v1/tag_serializer.rb
@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class TagSerializer < ActiveModel::Serializer
+      type :tags
+      attributes :id, :name, :color
+    end
+  end
+end
diff --git a/config/routes.rb b/config/routes.rb
index abe255714..c0b1bf7bc 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -572,9 +572,9 @@ Rails.application.routes.draw do
                   resources :task_users, only: %i(index show),
                             path: 'users',
                             as: :users
-                  resources :my_module_tags, only: %i(index show),
-                            path: 'task_tags',
-                            as: :task_tags
+                  resources :task_tags, only: %i(index show),
+                            path: 'tags',
+                            as: :tags
                   resources :protocols, only: %i(index show),
                             path: 'protocols',
                             as: :protocols

From 239b974fa049eac42bbef8aa2868bc43d16944b3 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 11:29:56 +0200
Subject: [PATCH 29/40] Fix GET /tasks/:tid/protocols, GET
 /tasks/:tid/protocols/:id endpts

---
 app/controllers/api/v1/protocols_controller.rb     |  6 +++---
 .../api/v1/protocol_keyword_serializer.rb          | 10 ++++++++++
 app/serializers/api/v1/protocol_serializer.rb      | 14 ++++++++------
 config/routes.rb                                   |  4 +---
 4 files changed, 22 insertions(+), 12 deletions(-)
 create mode 100644 app/serializers/api/v1/protocol_keyword_serializer.rb

diff --git a/app/controllers/api/v1/protocols_controller.rb b/app/controllers/api/v1/protocols_controller.rb
index 8b8dfbe30..f4cd1a8be 100644
--- a/app/controllers/api/v1/protocols_controller.rb
+++ b/app/controllers/api/v1/protocols_controller.rb
@@ -10,7 +10,7 @@ module Api
       before_action :load_protocol, only: :show
 
       def index
-        protocols = @my_module.protocols
+        protocols = @task.protocols
                               .page(params.dig(:page, :number))
                               .per(params.dig(:page, :size))
 
@@ -44,11 +44,11 @@ module Api
       end
 
       def load_task
-        @my_module = @experiment.my_modules.find(params.require(:task_id))
+        @task = @experiment.my_modules.find(params.require(:task_id))
       end
 
       def load_protocol
-        @protocol = @my_module.protocols.find(
+        @protocol = @task.protocols.find(
           params.require(:id)
         )
       end
diff --git a/app/serializers/api/v1/protocol_keyword_serializer.rb b/app/serializers/api/v1/protocol_keyword_serializer.rb
new file mode 100644
index 000000000..1f8f838d6
--- /dev/null
+++ b/app/serializers/api/v1/protocol_keyword_serializer.rb
@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProtocolKeywordSerializer < ActiveModel::Serializer
+      type :protocol_keywords
+      attributes :id, :name
+    end
+  end
+end
diff --git a/app/serializers/api/v1/protocol_serializer.rb b/app/serializers/api/v1/protocol_serializer.rb
index 9f255b377..5e60d2e7e 100644
--- a/app/serializers/api/v1/protocol_serializer.rb
+++ b/app/serializers/api/v1/protocol_serializer.rb
@@ -4,12 +4,14 @@ module Api
   module V1
     class ProtocolSerializer < ActiveModel::Serializer
       type :protocols
-      attributes :id, :name, :authors, :description,
-                 :team_id, :protocol_type,
-                 :nr_of_linked_children
-      attribute :my_module_id, key: :task_id
-
-      belongs_to :my_module, serializer: TaskSerializer
+      attributes :id, :name, :authors, :description, :protocol_type
+      has_many :protocol_keywords,
+        key: :keywords,
+        serializer: ProtocolKeywordSerializer,
+        class_name: 'ProtocolKeyword',
+        unless: -> { object.protocol_keywords.empty? }
+      belongs_to :parent, serializer: ProtocolSerializer,
+                          if: -> { object.parent.present? }
     end
   end
 end
diff --git a/config/routes.rb b/config/routes.rb
index c0b1bf7bc..497770cfc 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -575,9 +575,7 @@ Rails.application.routes.draw do
                   resources :task_tags, only: %i(index show),
                             path: 'tags',
                             as: :tags
-                  resources :protocols, only: %i(index show),
-                            path: 'protocols',
-                            as: :protocols
+                  resources :protocols, only: %i(index show)
                   resources :results, only: %i(index create show),
                             path: 'results',
                             as: :results

From fca580face261a160fcdb39ba12cb2a009693bfc Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 11:35:12 +0200
Subject: [PATCH 30/40] Fix GET /tasks/:id/inputs, GET /tasks/:id/outputs
 endpoints

---
 app/controllers/api/v1/tasks_controller.rb | 22 ++++++----------------
 config/routes.rb                           | 10 ++--------
 2 files changed, 8 insertions(+), 24 deletions(-)

diff --git a/app/controllers/api/v1/tasks_controller.rb b/app/controllers/api/v1/tasks_controller.rb
index f4e271fa0..562af7919 100644
--- a/app/controllers/api/v1/tasks_controller.rb
+++ b/app/controllers/api/v1/tasks_controller.rb
@@ -7,7 +7,7 @@ module Api
       before_action :load_project
       before_action :load_experiment
       before_action :load_task, only: :show
-      before_action :load_task_relative, only: %i(outputs output inputs input)
+      before_action :load_task_relative, only: %i(inputs outputs)
 
       def index
         tasks = @experiment.my_modules
@@ -21,18 +21,6 @@ module Api
         render jsonapi: @task, serializer: TaskSerializer
       end
 
-      def outputs
-        outputs = @task.my_modules
-                            .page(params.dig(:page, :number))
-                            .per(params.dig(:page, :size))
-        render jsonapi: outputs, each_serializer: TaskSerializer
-      end
-
-      def output
-        output = @task.my_modules.find(params.require(:id))
-        render jsonapi: output, serializer: TaskSerializer
-      end
-
       def inputs
         inputs = @task.my_module_antecessors
                            .page(params.dig(:page, :number))
@@ -40,9 +28,11 @@ module Api
         render jsonapi: inputs, each_serializer: TaskSerializer
       end
 
-      def input
-        input = @task.my_module_antecessors.find(params.require(:id))
-        render jsonapi: input, serializer: TaskSerializer
+      def outputs
+        outputs = @task.my_modules
+                            .page(params.dig(:page, :number))
+                            .per(params.dig(:page, :size))
+        render jsonapi: outputs, each_serializer: TaskSerializer
       end
 
       private
diff --git a/config/routes.rb b/config/routes.rb
index 497770cfc..067ac2663 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -579,14 +579,8 @@ Rails.application.routes.draw do
                   resources :results, only: %i(index create show),
                             path: 'results',
                             as: :results
-                  get 'inputs',
-                      to: 'my_modules#inputs'
-                  get 'inputs/:id',
-                      to: 'my_modules#input'
-                  get 'outputs',
-                      to: 'my_modules#outputs'
-                  get 'outputs/:id',
-                      to: 'my_modules#output'
+                  get 'inputs', to: 'tasks#inputs'
+                  get 'outputs', to: 'tasks#outputs'
                   resources :activities, only: %i(index show),
                             path: 'activities',
                             as: :activities

From fc5cf336146a2d660765d661db0d8bbbaca8d1ca Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 11:49:11 +0200
Subject: [PATCH 31/40] Fix GET /tasks/:id/activities endpoint

---
 .../api/v1/activities_controller.rb           | 59 -------------------
 app/controllers/api/v1/tasks_controller.rb    | 11 +++-
 app/serializers/api/v1/activity_serializer.rb | 12 +++-
 app/serializers/api/v1/project_serializer.rb  | 10 ++++
 config/routes.rb                              |  4 +-
 5 files changed, 30 insertions(+), 66 deletions(-)
 delete mode 100644 app/controllers/api/v1/activities_controller.rb
 create mode 100644 app/serializers/api/v1/project_serializer.rb

diff --git a/app/controllers/api/v1/activities_controller.rb b/app/controllers/api/v1/activities_controller.rb
deleted file mode 100644
index 125c44c86..000000000
--- a/app/controllers/api/v1/activities_controller.rb
+++ /dev/null
@@ -1,59 +0,0 @@
-# frozen_string_literal: true
-
-module Api
-  module V1
-    class ActivitiesController < BaseController
-      before_action :load_team
-      before_action :load_project
-      before_action :load_experiment
-      before_action :load_task
-      before_action :load_activity, only: :show
-
-      def index
-        activities = @my_module.activities
-                               .page(params.dig(:page, :number))
-                               .per(params.dig(:page, :size))
-
-        render jsonapi: activities,
-          each_serializer: ActivitySerializer
-      end
-
-      def show
-        render jsonapi: @activity, serializer: ActivitySerializer
-      end
-
-      private
-
-      def load_team
-        @team = Team.find(params.require(:team_id))
-        render jsonapi: {}, status: :forbidden unless can_read_team?(@team)
-      end
-
-      def load_project
-        @project = @team.projects.find(params.require(:project_id))
-        render jsonapi: {}, status: :forbidden unless can_read_project?(
-          @project
-        )
-      end
-
-      def load_experiment
-        @experiment = @project.experiments.find(params.require(:experiment_id))
-        render jsonapi: {}, status: :forbidden unless can_read_experiment?(
-          @experiment
-        )
-      end
-
-      def load_task
-        @my_module = @experiment.my_modules.find(params.require(:task_id))
-        render jsonapi: {}, status: :not_found if @my_module.nil?
-      end
-
-      def load_activity
-        @activity = @my_module.activities.find(
-          params.require(:id)
-        )
-        render jsonapi: {}, status: :not_found if @activity.nil?
-      end
-    end
-  end
-end
diff --git a/app/controllers/api/v1/tasks_controller.rb b/app/controllers/api/v1/tasks_controller.rb
index 562af7919..9ab8ed1ea 100644
--- a/app/controllers/api/v1/tasks_controller.rb
+++ b/app/controllers/api/v1/tasks_controller.rb
@@ -7,7 +7,7 @@ module Api
       before_action :load_project
       before_action :load_experiment
       before_action :load_task, only: :show
-      before_action :load_task_relative, only: %i(inputs outputs)
+      before_action :load_task_relative, only: %i(inputs outputs activities)
 
       def index
         tasks = @experiment.my_modules
@@ -35,6 +35,15 @@ module Api
         render jsonapi: outputs, each_serializer: TaskSerializer
       end
 
+      def activities
+        activities = @task.activities
+                          .page(params.dig(:page, :number))
+                          .per(params.dig(:page, :size))
+
+        render jsonapi: activities,
+          each_serializer: ActivitySerializer
+      end
+
       private
 
       def load_team
diff --git a/app/serializers/api/v1/activity_serializer.rb b/app/serializers/api/v1/activity_serializer.rb
index 28910b7f5..251bc3711 100644
--- a/app/serializers/api/v1/activity_serializer.rb
+++ b/app/serializers/api/v1/activity_serializer.rb
@@ -4,9 +4,15 @@ module Api
   module V1
     class ActivitySerializer < ActiveModel::Serializer
       type :activities
-      attributes :id, :my_module_id, :user_id, :type_of, :message,
-                 :project_id, :experiment_id
-      belongs_to :my_module, serializer: TaskSerializer
+      attributes :id, :type_of, :message
+      belongs_to :project, serializer: ProjectSerializer
+      belongs_to :experiment, serializer: TaskSerializer,
+                              if: -> { object.experiment.present? }
+      belongs_to :my_module, key: :task,
+                             serializer: TaskSerializer,
+                             class_name: 'MyModule',
+                             if: -> { object.my_module.present? }
+      belongs_to :user, serializer: UserSerializer
     end
   end
 end
diff --git a/app/serializers/api/v1/project_serializer.rb b/app/serializers/api/v1/project_serializer.rb
new file mode 100644
index 000000000..db413ece6
--- /dev/null
+++ b/app/serializers/api/v1/project_serializer.rb
@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class ProjectSerializer < ActiveModel::Serializer
+      type :projects
+      attributes :id
+    end
+  end
+end
diff --git a/config/routes.rb b/config/routes.rb
index 067ac2663..f4440c769 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -581,9 +581,7 @@ Rails.application.routes.draw do
                             as: :results
                   get 'inputs', to: 'tasks#inputs'
                   get 'outputs', to: 'tasks#outputs'
-                  resources :activities, only: %i(index show),
-                            path: 'activities',
-                            as: :activities
+                  get 'activities', to: 'tasks#activities'
                 end
               end
             end

From 7527dc7352faf0e7ca89da6e77dabd2a7f0079fc Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 12:36:58 +0200
Subject: [PATCH 32/40] Fix READ index, READ show, POST create
 /tasks/:id/results endpoints

---
 app/controllers/api/v1/results_controller.rb  |  6 ++--
 .../v1/repository_asset_value_serializer.rb   |  3 +-
 .../api/v1/result_asset_serializer.rb         | 28 +++++++++++++++++--
 app/serializers/api/v1/result_serializer.rb   | 22 +++++++--------
 .../api/v1/result_table_serializer.rb         | 10 ++++++-
 config/routes.rb                              |  4 +--
 6 files changed, 51 insertions(+), 22 deletions(-)

diff --git a/app/controllers/api/v1/results_controller.rb b/app/controllers/api/v1/results_controller.rb
index 068d927f3..938c4e20a 100644
--- a/app/controllers/api/v1/results_controller.rb
+++ b/app/controllers/api/v1/results_controller.rb
@@ -14,7 +14,7 @@ module Api
                        .page(params.dig(:page, :number))
                        .per(params.dig(:page, :size))
         render jsonapi: results, each_serializer: ResultSerializer,
-                                 include: %i(asset table text)
+                                 include: %i(text table file)
       end
 
       def create
@@ -22,13 +22,13 @@ module Api
         throw ActionController::ParameterMissing unless @result
         render jsonapi: @result,
                serializer: ResultSerializer,
-               include: %i(asset table text),
+               include: %i(text table file),
                status: :created
       end
 
       def show
         render jsonapi: @result, serializer: ResultSerializer,
-                                 include: %i(asset table text)
+                                 include: %i(text table file)
       end
 
       private
diff --git a/app/serializers/api/v1/repository_asset_value_serializer.rb b/app/serializers/api/v1/repository_asset_value_serializer.rb
index be1373efb..50fac8350 100644
--- a/app/serializers/api/v1/repository_asset_value_serializer.rb
+++ b/app/serializers/api/v1/repository_asset_value_serializer.rb
@@ -23,8 +23,9 @@ module Api
         elsif object.asset&.file&.is_stored_on_s3?
           object.asset.presigned_url(download: true)
         else
+          # TODO
           # separate api endpoint for local files download is needed
-          download_asset_path(object.asset.id)
+          'url'#download_asset_path(object.asset.id)
         end
       end
     end
diff --git a/app/serializers/api/v1/result_asset_serializer.rb b/app/serializers/api/v1/result_asset_serializer.rb
index f6638c2b7..f69dbbae8 100644
--- a/app/serializers/api/v1/result_asset_serializer.rb
+++ b/app/serializers/api/v1/result_asset_serializer.rb
@@ -3,8 +3,32 @@
 module Api
   module V1
     class ResultAssetSerializer < ActiveModel::Serializer
-      type :result_assets
-      attributes :asset_id
+      type :result_files
+      attributes :file_id, :file_name, :file_size, :url
+
+      def file_id
+        object.asset&.id
+      end
+
+      def file_name
+        object.asset&.file_file_name
+      end
+
+      def file_size
+        object.asset&.file_file_size
+      end
+
+      def url
+        if !object.asset&.file_present
+          nil
+        elsif object.asset&.file&.is_stored_on_s3?
+          object.asset.presigned_url(download: true)
+        else
+          # TODO
+          # separate api endpoint for local files download is needed
+          'url'#download_asset_path(object.asset.id)
+        end
+      end
     end
   end
 end
diff --git a/app/serializers/api/v1/result_serializer.rb b/app/serializers/api/v1/result_serializer.rb
index 5e990f1cb..ea0f4b334 100644
--- a/app/serializers/api/v1/result_serializer.rb
+++ b/app/serializers/api/v1/result_serializer.rb
@@ -4,22 +4,20 @@ module Api
   module V1
     class ResultSerializer < ActiveModel::Serializer
       type :results
-      attributes :name, :user_id, :archived
-      attribute :my_module_id, key: :task_id
-
-      belongs_to :my_module, serializer: TaskSerializer
-      has_one :result_asset, key: :asset,
-                             serializer: ResultAssetSerializer,
-                             class_name: 'ResultAsset',
-                             if: -> { object.is_asset }
-      has_one :result_table, key: :table,
-                             serializer: ResultTableSerializer,
-                             class_name: 'ResultTable',
-                             if: -> { object.is_table }
+      attributes :name, :archived
+      belongs_to :user, serializer: UserSerializer
       has_one :result_text, key: :text,
                             serializer: ResultTextSerializer,
                             class_name: 'ResultText',
                             if: -> { object.is_text }
+      has_one :result_table, key: :table,
+                             serializer: ResultTableSerializer,
+                             class_name: 'ResultTable',
+                             if: -> { object.is_table }
+      has_one :result_asset, key: :file,
+                             serializer: ResultAssetSerializer,
+                             class_name: 'ResultAsset',
+                             if: -> { object.is_asset }
     end
   end
 end
diff --git a/app/serializers/api/v1/result_table_serializer.rb b/app/serializers/api/v1/result_table_serializer.rb
index b4bdddc1c..211950441 100644
--- a/app/serializers/api/v1/result_table_serializer.rb
+++ b/app/serializers/api/v1/result_table_serializer.rb
@@ -4,7 +4,15 @@ module Api
   module V1
     class ResultTableSerializer < ActiveModel::Serializer
       type :result_tables
-      attributes :table_id
+      attributes :table_id, :table_contents
+
+      def table_id
+        object.table&.id
+      end
+
+      def table_contents
+        object.table&.contents
+      end
     end
   end
 end
diff --git a/config/routes.rb b/config/routes.rb
index f4440c769..4b5ebcef1 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -576,9 +576,7 @@ Rails.application.routes.draw do
                             path: 'tags',
                             as: :tags
                   resources :protocols, only: %i(index show)
-                  resources :results, only: %i(index create show),
-                            path: 'results',
-                            as: :results
+                  resources :results, only: %i(index create show)
                   get 'inputs', to: 'tasks#inputs'
                   get 'outputs', to: 'tasks#outputs'
                   get 'activities', to: 'tasks#activities'

From 0bd3c81e39e52b0c66ec6dbd90b1ac3d7cf44644 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 13:07:27 +0200
Subject: [PATCH 33/40] Fix /users, /users/:id/identities endpoints

---
 config/routes.rb                                   |  4 +++-
 .../{user_identeties.rb => user_identities.rb}     |  0
 ..._spec.rb => user_identities_controller_spec.rb} | 14 +++++++-------
 3 files changed, 10 insertions(+), 8 deletions(-)
 rename spec/factories/{user_identeties.rb => user_identities.rb} (100%)
 rename spec/requests/api/v1/{users_identeties_controller_spec.rb => user_identities_controller_spec.rb} (89%)

diff --git a/config/routes.rb b/config/routes.rb
index 4b5ebcef1..e07102f33 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -586,7 +586,9 @@ Rails.application.routes.draw do
           end
           resources :users, only: %i(show) do
             resources :user_identities,
-                      only: %i(index create show update destroy)
+                      only: %i(index create show update destroy),
+                      path: 'identities',
+                      as: :identities
           end
         end
       end
diff --git a/spec/factories/user_identeties.rb b/spec/factories/user_identities.rb
similarity index 100%
rename from spec/factories/user_identeties.rb
rename to spec/factories/user_identities.rb
diff --git a/spec/requests/api/v1/users_identeties_controller_spec.rb b/spec/requests/api/v1/user_identities_controller_spec.rb
similarity index 89%
rename from spec/requests/api/v1/users_identeties_controller_spec.rb
rename to spec/requests/api/v1/user_identities_controller_spec.rb
index 3a927f5a2..e0d80d110 100644
--- a/spec/requests/api/v1/users_identeties_controller_spec.rb
+++ b/spec/requests/api/v1/user_identities_controller_spec.rb
@@ -15,7 +15,7 @@ RSpec.describe 'Api::V1::UsersIdentitiesController', type: :request do
   describe 'GET user_identities, #index' do
     it 'When valid request, requested identities for current user' do
       hash_body = nil
-      get api_v1_user_user_identities_path(user_id: @user1.id),
+      get api_v1_user_identities_path(user_id: @user1.id),
           headers: @valid_headers
       expect { hash_body = json }.not_to raise_exception
       expect(hash_body[:data]).to match(
@@ -28,7 +28,7 @@ RSpec.describe 'Api::V1::UsersIdentitiesController', type: :request do
 
     it 'When invalid request, requested user is not signed in user' do
       hash_body = nil
-      get api_v1_user_user_identities_path(user_id: @user2.id),
+      get api_v1_user_identities_path(user_id: @user2.id),
           headers: @valid_headers
       expect(response).to have_http_status(403)
       expect(hash_body).to match(nil)
@@ -36,7 +36,7 @@ RSpec.describe 'Api::V1::UsersIdentitiesController', type: :request do
 
     it 'When invalid request, non existing user' do
       hash_body = nil
-      get api_v1_user_user_identities_path(user_id: 123),
+      get api_v1_user_identities_path(user_id: 123),
           headers: @valid_headers
       expect(response).to have_http_status(403)
       expect(hash_body).to match(nil)
@@ -46,7 +46,7 @@ RSpec.describe 'Api::V1::UsersIdentitiesController', type: :request do
   describe 'POST user_identities, #create' do
     it 'When valid request, create new identity for current user' do
       hash_body = nil
-      post api_v1_user_user_identities_path(user_id: @user1.id),
+      post api_v1_user_identities_path(user_id: @user1.id),
            params: {
              data: { type: 'user_identities',
                      attributes: { uid: Faker::Crypto.unique.sha1,
@@ -66,7 +66,7 @@ RSpec.describe 'Api::V1::UsersIdentitiesController', type: :request do
   describe 'GET user_identity, #show' do
     it 'When valid request, requested specific identity for current user' do
       hash_body = nil
-      get api_v1_user_user_identity_path(
+      get api_v1_user_identity_path(
         user_id: @user1.id, id: @user1.user_identities.order(:id).last
       ), headers: @valid_headers
       expect { hash_body = json }.not_to raise_exception
@@ -82,7 +82,7 @@ RSpec.describe 'Api::V1::UsersIdentitiesController', type: :request do
   describe 'PUT user_identities, #update' do
     it 'When valid request, update identity for current user' do
       hash_body = nil
-      put api_v1_user_user_identity_path(user_id: @user1.id,
+      put api_v1_user_identity_path(user_id: @user1.id,
             id: @user1.user_identities.order(:id).last),
           params: {
             data: { id: @user1.user_identities.order(:id).last.id,
@@ -103,7 +103,7 @@ RSpec.describe 'Api::V1::UsersIdentitiesController', type: :request do
   describe 'DELETE user_identity, #destroy' do
     it 'When valid request, destroy specified identity for current user' do
       identity = @user1.user_identities.order(:id).last
-      delete api_v1_user_user_identity_path(user_id: @user1.id, id: identity),
+      delete api_v1_user_identity_path(user_id: @user1.id, id: identity),
              headers: @valid_headers
       expect(response).to have_http_status(200)
       expect(response.body).to eq('')

From dc2ab5fdc0108124e3df96f6a6118817b7ded875 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 13:11:56 +0200
Subject: [PATCH 34/40] Fix the Doorkeeper config/access for all users (due to
 update of Gem)

---
 config/initializers/doorkeeper.rb | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/config/initializers/doorkeeper.rb b/config/initializers/doorkeeper.rb
index 9153fbabd..ffd7015c1 100644
--- a/config/initializers/doorkeeper.rb
+++ b/config/initializers/doorkeeper.rb
@@ -8,11 +8,9 @@ Doorkeeper.configure do
   end
 
   # If you want to restrict access to the web interface for adding oauth authorized applications, you need to declare the block below.
-  # admin_authenticator do
-  #   # Put your admin authentication logic here.
-  #   # Example implementation:
-  #   Admin.find_by_id(session[:admin_id]) || redirect_to(new_admin_session_url)
-  # end
+  admin_authenticator do
+    current_user || redirect_to(new_admin_session_url)
+  end
 
   # Authorization Code expiration time (default 10 minutes).
   authorization_code_expires_in 10.minutes

From a8d56d32e2a04dd68259652390bb1b4dd919bc43 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Sun, 7 Oct 2018 13:28:29 +0200
Subject: [PATCH 35/40] Hound is love, Hound is life

---
 .../api/v1/task_inventory_items_controller.rb         |  9 ++++-----
 app/controllers/api/v1/tasks_controller.rb            |  4 ++--
 app/serializers/api/v1/inventory_column_serializer.rb | 11 ++++++-----
 app/serializers/api/v1/protocol_serializer.rb         |  8 ++++----
 .../api/v1/inventory_columns_controller_spec.rb       |  6 +++---
 5 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/app/controllers/api/v1/task_inventory_items_controller.rb b/app/controllers/api/v1/task_inventory_items_controller.rb
index ab28c6996..a7e87e96a 100644
--- a/app/controllers/api/v1/task_inventory_items_controller.rb
+++ b/app/controllers/api/v1/task_inventory_items_controller.rb
@@ -12,11 +12,10 @@ module Api
       def index
         items =
           @task.repository_rows
-                    .includes(repository_cells: :repository_column)
-                    .includes(
-                      repository_cells: Extends::REPOSITORY_SEARCH_INCLUDES
-                    ).page(params.dig(:page, :number))
-                    .per(params.dig(:page, :size))
+               .includes(repository_cells: :repository_column)
+               .includes(repository_cells: Extends::REPOSITORY_SEARCH_INCLUDES)
+               .page(params.dig(:page, :number))
+               .per(params.dig(:page, :size))
         incl = params[:include] == 'inventory_cells' ? :inventory_cells : nil
         render jsonapi: items,
                each_serializer: InventoryItemSerializer,
diff --git a/app/controllers/api/v1/tasks_controller.rb b/app/controllers/api/v1/tasks_controller.rb
index 9ab8ed1ea..46466be10 100644
--- a/app/controllers/api/v1/tasks_controller.rb
+++ b/app/controllers/api/v1/tasks_controller.rb
@@ -23,8 +23,8 @@ module Api
 
       def inputs
         inputs = @task.my_module_antecessors
-                           .page(params.dig(:page, :number))
-                           .per(params.dig(:page, :size))
+                      .page(params.dig(:page, :number))
+                      .per(params.dig(:page, :size))
         render jsonapi: inputs, each_serializer: TaskSerializer
       end
 
diff --git a/app/serializers/api/v1/inventory_column_serializer.rb b/app/serializers/api/v1/inventory_column_serializer.rb
index 64fe83d1d..268cb151d 100644
--- a/app/serializers/api/v1/inventory_column_serializer.rb
+++ b/app/serializers/api/v1/inventory_column_serializer.rb
@@ -5,11 +5,12 @@ module Api
     class InventoryColumnSerializer < ActiveModel::Serializer
       type :inventory_columns
       attributes :name, :data_type
-      has_many :repository_list_items, key: :inventory_list_items,
-                                       serializer: InventoryListItemSerializer,
-                                       class_name: 'RepositoryListItem',
-                                       if: -> { object.data_type == 'RepositoryListValue' &&
-                                                !instance_options[:hide_list_items] }
+      has_many :repository_list_items,
+               key: :inventory_list_items,
+               serializer: InventoryListItemSerializer,
+               class_name: 'RepositoryListItem',
+               if: -> { object.data_type == 'RepositoryListValue' &&
+                        !instance_options[:hide_list_items] }
     end
   end
 end
diff --git a/app/serializers/api/v1/protocol_serializer.rb b/app/serializers/api/v1/protocol_serializer.rb
index 5e60d2e7e..c2995f847 100644
--- a/app/serializers/api/v1/protocol_serializer.rb
+++ b/app/serializers/api/v1/protocol_serializer.rb
@@ -6,10 +6,10 @@ module Api
       type :protocols
       attributes :id, :name, :authors, :description, :protocol_type
       has_many :protocol_keywords,
-        key: :keywords,
-        serializer: ProtocolKeywordSerializer,
-        class_name: 'ProtocolKeyword',
-        unless: -> { object.protocol_keywords.empty? }
+               key: :keywords,
+               serializer: ProtocolKeywordSerializer,
+               class_name: 'ProtocolKeyword',
+               unless: -> { object.protocol_keywords.empty? }
       belongs_to :parent, serializer: ProtocolSerializer,
                           if: -> { object.parent.present? }
     end
diff --git a/spec/requests/api/v1/inventory_columns_controller_spec.rb b/spec/requests/api/v1/inventory_columns_controller_spec.rb
index 9a8992882..1478a451c 100644
--- a/spec/requests/api/v1/inventory_columns_controller_spec.rb
+++ b/spec/requests/api/v1/inventory_columns_controller_spec.rb
@@ -93,7 +93,7 @@ RSpec.describe 'Api::V1::InventoryColumnsController', type: :request do
       expect(hash_body[:data]).to match(
         ActiveModelSerializers::SerializableResource
           .new(text_column,
-              serializer: Api::V1::InventoryColumnSerializer)
+               serializer: Api::V1::InventoryColumnSerializer)
           .as_json[:data]
       )
       expect(hash_body[:data]).not_to include('relationships')
@@ -111,7 +111,7 @@ RSpec.describe 'Api::V1::InventoryColumnsController', type: :request do
       expect(hash_body[:data]).to match(
         ActiveModelSerializers::SerializableResource
           .new(list_column,
-              serializer: Api::V1::InventoryColumnSerializer)
+               serializer: Api::V1::InventoryColumnSerializer)
           .as_json[:data]
       )
       expect(hash_body[:data]).to include('relationships')
@@ -136,7 +136,7 @@ RSpec.describe 'Api::V1::InventoryColumnsController', type: :request do
       expect(hash_body[:data]).to match(
         ActiveModelSerializers::SerializableResource
           .new(file_column,
-              serializer: Api::V1::InventoryColumnSerializer)
+               serializer: Api::V1::InventoryColumnSerializer)
           .as_json[:data]
       )
       expect(hash_body[:data]).not_to include('relationships')

From dd4f7b5d025887144e8ca7ca79a7c6802573dfbb Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Wed, 10 Oct 2018 17:35:09 +0200
Subject: [PATCH 36/40] Fix project users, activities, comments, reports
 endpoints

---
 .../api/v1/activities_controller.rb           | 28 ++-----------------
 .../api/v1/project_comments_controller.rb     |  8 ++++--
 app/controllers/api/v1/projects_controller.rb | 16 +++++++++++
 app/controllers/api/v1/reports_controller.rb  |  9 ++++--
 .../api/v1/user_projects_controller.rb        |  8 ++++--
 app/serializers/api/v1/comment_serializer.rb  | 27 ++++++++++++++++++
 .../api/v1/project_comment_serializer.rb      | 12 --------
 app/serializers/api/v1/report_serializer.rb   |  7 +++--
 .../api/v1/user_project_serializer.rb         |  4 +--
 config/routes.rb                              | 10 +++----
 10 files changed, 74 insertions(+), 55 deletions(-)
 create mode 100644 app/serializers/api/v1/comment_serializer.rb
 delete mode 100644 app/serializers/api/v1/project_comment_serializer.rb

diff --git a/app/controllers/api/v1/activities_controller.rb b/app/controllers/api/v1/activities_controller.rb
index 793794c8d..125c44c86 100644
--- a/app/controllers/api/v1/activities_controller.rb
+++ b/app/controllers/api/v1/activities_controller.rb
@@ -5,12 +5,8 @@ module Api
     class ActivitiesController < BaseController
       before_action :load_team
       before_action :load_project
-
-      before_action :load_project_activity, only: :project_activity
-      before_action :load_experiment, except: %i(
-        project_activities project_activity
-      )
-      before_action :load_task, except: %i(project_activities project_activity)
+      before_action :load_experiment
+      before_action :load_task
       before_action :load_activity, only: :show
 
       def index
@@ -26,19 +22,6 @@ module Api
         render jsonapi: @activity, serializer: ActivitySerializer
       end
 
-      def project_activities
-        activities = @project.activities
-                             .page(params.dig(:page, :number))
-                             .per(params.dig(:page, :size))
-
-        render jsonapi: activities,
-          each_serializer: ActivitySerializer
-      end
-
-      def project_activity
-        render jsonapi: @project_activity, serializer: ActivitySerializer
-      end
-
       private
 
       def load_team
@@ -71,13 +54,6 @@ module Api
         )
         render jsonapi: {}, status: :not_found if @activity.nil?
       end
-
-      def load_project_activity
-        @project_activity = @project.activities.find(
-          params.require(:id)
-        )
-        render jsonapi: {}, status: :not_found if @project_activity.nil?
-      end
     end
   end
 end
diff --git a/app/controllers/api/v1/project_comments_controller.rb b/app/controllers/api/v1/project_comments_controller.rb
index bca71a462..762f5b196 100644
--- a/app/controllers/api/v1/project_comments_controller.rb
+++ b/app/controllers/api/v1/project_comments_controller.rb
@@ -13,11 +13,15 @@ module Api
                                    .per(params.dig(:page, :size))
 
         render jsonapi: project_comments,
-          each_serializer: ProjectCommentSerializer
+               each_serializer: CommentSerializer,
+               hide_project: true
       end
 
       def show
-        render jsonapi: @project_comment, serializer: ProjectCommentSerializer
+        render jsonapi: @project_comment,
+               serializer: CommentSerializer,
+               hide_project: true,
+               include: :user
       end
 
       private
diff --git a/app/controllers/api/v1/projects_controller.rb b/app/controllers/api/v1/projects_controller.rb
index 0cc5c05d0..989cc9cb3 100644
--- a/app/controllers/api/v1/projects_controller.rb
+++ b/app/controllers/api/v1/projects_controller.rb
@@ -5,6 +5,7 @@ module Api
     class ProjectsController < BaseController
       before_action :load_team
       before_action :load_project, only: :show
+      before_action :load_project_relative, only: :activities
 
       def index
         projects = @team.projects
@@ -18,6 +19,14 @@ module Api
         render jsonapi: @project, serializer: ProjectSerializer
       end
 
+      def activities
+        activities = @project.activities
+                             .page(params.dig(:page, :number))
+                             .per(params.dig(:page, :size))
+        render jsonapi: activities,
+               each_serializer: ActivitySerializer
+      end
+
       private
 
       def load_team
@@ -31,6 +40,13 @@ module Api
           @project
         )
       end
+
+      def load_project_relative
+        @project = @team.projects.find(params.require(:project_id))
+        render jsonapi: {}, status: :forbidden unless can_read_project?(
+          @project
+        )
+      end
     end
   end
 end
diff --git a/app/controllers/api/v1/reports_controller.rb b/app/controllers/api/v1/reports_controller.rb
index 01f527f53..b7060596f 100644
--- a/app/controllers/api/v1/reports_controller.rb
+++ b/app/controllers/api/v1/reports_controller.rb
@@ -12,11 +12,16 @@ module Api
                           .page(params.dig(:page, :number))
                           .per(params.dig(:page, :size))
 
-        render jsonapi: reports, each_serializer: ReportSerializer
+        render jsonapi: reports,
+               each_serializer: ReportSerializer,
+               hide_project: true
       end
 
       def show
-        render jsonapi: @report, serializer: ReportSerializer
+        render jsonapi: @report,
+               serializer: ReportSerializer,
+               hide_project: true,
+               include: :user
       end
 
       private
diff --git a/app/controllers/api/v1/user_projects_controller.rb b/app/controllers/api/v1/user_projects_controller.rb
index dfa376a07..21d5d4ce1 100644
--- a/app/controllers/api/v1/user_projects_controller.rb
+++ b/app/controllers/api/v1/user_projects_controller.rb
@@ -12,11 +12,15 @@ module Api
                                 .page(params.dig(:page, :number))
                                 .per(params.dig(:page, :size))
 
-        render jsonapi: user_projects, each_serializer: UserProjectSerializer
+        render jsonapi: user_projects,
+               each_serializer: UserProjectSerializer,
+               include: :user
       end
 
       def show
-        render jsonapi: @user_project, serializer: UserProjectSerializer
+        render jsonapi: @user_project,
+               serializer: UserProjectSerializer,
+               include: :user
       end
 
       private
diff --git a/app/serializers/api/v1/comment_serializer.rb b/app/serializers/api/v1/comment_serializer.rb
new file mode 100644
index 000000000..c3d1c36a6
--- /dev/null
+++ b/app/serializers/api/v1/comment_serializer.rb
@@ -0,0 +1,27 @@
+# frozen_string_literal: true
+
+module Api
+  module V1
+    class CommentSerializer < ActiveModel::Serializer
+      type :comments
+      attributes :id, :message
+
+      belongs_to :user, serializer: UserSerializer
+      belongs_to :project, serializer: ProjectSerializer,
+                           if: -> { object.class == ProjectComment &&
+                                    !instance_options[:hide_project] }
+      # TODO
+      #belongs_to :my_module, serializer: TaskSerializer,
+      #                       key: :task,
+      #                       class_name: 'MyModule',
+      #                       if: -> { object.class == TaskComment &&
+      #                                !instance_options[:hide_task] }
+      #belongs_to :step, serializer: StepSerializer,
+      #                  if: -> { object.class == StepComment &&
+      #                           !instance_options[:hide_step] }
+      belongs_to :result, serializer: ResultSerializer,
+                          if: -> { object.class == ResultComment &&
+                                   !instance_options[:hide_result] }
+    end
+  end
+end
diff --git a/app/serializers/api/v1/project_comment_serializer.rb b/app/serializers/api/v1/project_comment_serializer.rb
deleted file mode 100644
index a9786f316..000000000
--- a/app/serializers/api/v1/project_comment_serializer.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-# frozen_string_literal: true
-
-module Api
-  module V1
-    class ProjectCommentSerializer < ActiveModel::Serializer
-      type :project_comments
-      attributes :id, :message, :user_id, :type, :associated_id
-
-      belongs_to :project, serializer: ProjectSerializer
-    end
-  end
-end
diff --git a/app/serializers/api/v1/report_serializer.rb b/app/serializers/api/v1/report_serializer.rb
index 1d4d2509f..94b666b22 100644
--- a/app/serializers/api/v1/report_serializer.rb
+++ b/app/serializers/api/v1/report_serializer.rb
@@ -4,9 +4,10 @@ module Api
   module V1
     class ReportSerializer < ActiveModel::Serializer
       type :reports
-      attributes :id, :name, :description, :project_id
-
-      belongs_to :project, serializer: ProjectSerializer
+      attributes :id, :name, :description
+      belongs_to :user, serializer: UserSerializer
+      belongs_to :project, serializer: ProjectSerializer,
+                           unless: -> { instance_options[:hide_project] }
     end
   end
 end
diff --git a/app/serializers/api/v1/user_project_serializer.rb b/app/serializers/api/v1/user_project_serializer.rb
index e6b2dfbfe..e2e138232 100644
--- a/app/serializers/api/v1/user_project_serializer.rb
+++ b/app/serializers/api/v1/user_project_serializer.rb
@@ -4,9 +4,9 @@ module Api
   module V1
     class UserProjectSerializer < ActiveModel::Serializer
       type :user_projects
-      attributes :id, :role, :user_id
+      attributes :id, :role
 
-      belongs_to :project, serializer: ProjectSerializer
+      belongs_to :user, serializer: UserSerializer
     end
   end
 end
diff --git a/config/routes.rb b/config/routes.rb
index 73ce70073..fe71182b3 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -556,16 +556,14 @@ Rails.application.routes.draw do
                         path: 'items',
                         as: :items
             end
-            resources :projects, only: %i(index show), path: 'projects',
-                      as: :projects do
+            resources :projects, only: %i(index show) do
               resources :user_projects, only: %i(index show),
-                path: 'user_projects', as: :user_projects
+                path: 'users', as: :users
               resources :project_comments, only: %i(index show),
-                path: 'project_comments', as: :project_comments
+                path: 'comments', as: :comments
+              get 'activities', to: 'projects#activities'
               resources :reports, only: %i(index show),
                 path: 'reports', as: :reports
-              get 'activities', to: 'activities#project_activities'
-              get 'activities/:id', to: 'activities#project_activity'
               resources :experiments, only: %i(index show) do
                 resources :my_module_groups,
                           only: %i(index show),

From c0f47f03b7cfbb7ede2c722499501b398cbcfe56 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Thu, 11 Oct 2018 08:51:14 +0200
Subject: [PATCH 37/40] Hound is love, Hound is life

---
 app/serializers/api/v1/comment_serializer.rb | 32 +++++++++++---------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/app/serializers/api/v1/comment_serializer.rb b/app/serializers/api/v1/comment_serializer.rb
index c3d1c36a6..d369d339c 100644
--- a/app/serializers/api/v1/comment_serializer.rb
+++ b/app/serializers/api/v1/comment_serializer.rb
@@ -7,21 +7,25 @@ module Api
       attributes :id, :message
 
       belongs_to :user, serializer: UserSerializer
-      belongs_to :project, serializer: ProjectSerializer,
-                           if: -> { object.class == ProjectComment &&
-                                    !instance_options[:hide_project] }
+      belongs_to :project,
+                 serializer: ProjectSerializer,
+                 if: -> { object.class == ProjectComment &&
+                          !instance_options[:hide_project] }
       # TODO
-      #belongs_to :my_module, serializer: TaskSerializer,
-      #                       key: :task,
-      #                       class_name: 'MyModule',
-      #                       if: -> { object.class == TaskComment &&
-      #                                !instance_options[:hide_task] }
-      #belongs_to :step, serializer: StepSerializer,
-      #                  if: -> { object.class == StepComment &&
-      #                           !instance_options[:hide_step] }
-      belongs_to :result, serializer: ResultSerializer,
-                          if: -> { object.class == ResultComment &&
-                                   !instance_options[:hide_result] }
+      #belongs_to :my_module,
+      #           serializer: TaskSerializer,
+      #           key: :task,
+      #           class_name: 'MyModule',
+      #           if: -> { object.class == TaskComment &&
+      #                    !instance_options[:hide_task] }
+      #belongs_to :step,
+      #           serializer: StepSerializer,
+      #           if: -> { object.class == StepComment &&
+      #                    !instance_options[:hide_step] }
+      belongs_to :result,
+                 serializer: ResultSerializer,
+                 if: -> { object.class == ResultComment &&
+                          !instance_options[:hide_result] }
     end
   end
 end

From c11345d6a1c36bf74d67068e176b7d7d3b63d489 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Thu, 11 Oct 2018 09:49:54 +0200
Subject: [PATCH 38/40] Minorly update inventory_column_serializer so tests
 pass

---
 app/serializers/api/v1/inventory_column_serializer.rb | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/app/serializers/api/v1/inventory_column_serializer.rb b/app/serializers/api/v1/inventory_column_serializer.rb
index 1d0f65b7a..18ba68938 100644
--- a/app/serializers/api/v1/inventory_column_serializer.rb
+++ b/app/serializers/api/v1/inventory_column_serializer.rb
@@ -8,12 +8,6 @@ module Api
       has_many :repository_list_items, key: :inventory_list_items,
                                        serializer: InventoryListItemSerializer,
                                        class_name: 'RepositoryListItem'
-
-      def data_type
-        type_id = RepositoryColumn
-                  .data_types[object.data_type]
-        I18n.t("api.v1.inventory_data_types.t#{type_id}")
-      end
     end
   end
 end

From 33b9c65c29c1184c12dcae85001b0a6efcc030f2 Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Thu, 11 Oct 2018 14:27:52 +0200
Subject: [PATCH 39/40] Fix Hound

---
 .../api/v1/inventory_items_controller_spec.rb | 21 +++++++++++--------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/spec/requests/api/v1/inventory_items_controller_spec.rb b/spec/requests/api/v1/inventory_items_controller_spec.rb
index 97353307a..d3ba642b7 100644
--- a/spec/requests/api/v1/inventory_items_controller_spec.rb
+++ b/spec/requests/api/v1/inventory_items_controller_spec.rb
@@ -276,13 +276,12 @@ RSpec.describe 'Api::V1::InventoryItemsController', type: :request do
       updated_inventory_item = @inventory_item.as_json[:included]
       updated_inventory_item.each do |cell|
         attributes = cell[:attributes]
-        if attributes[:value_type] == 'list'
-          cell[:attributes] = {
-            value_type: 'list',
-            value: Faker::Name.unique.name,
-            column_id: 2
-          }
-        end
+        next unless attributes[:value_type] == 'list'
+        cell[:attributes] = {
+          value_type: 'list',
+          value: Faker::Name.unique.name,
+          column_id: 2
+        }
       end
       patch api_v1_team_inventory_item_path(
         id: RepositoryRow.last.id,
@@ -292,7 +291,9 @@ RSpec.describe 'Api::V1::InventoryItemsController', type: :request do
       headers: @valid_headers
       expect(response).to have_http_status 200
       expect { hash_body = json }.not_to raise_exception
-      expect(hash_body[:included].to_json).to match(updated_inventory_item.to_json)
+      expect(hash_body[:included].to_json).to match(
+        updated_inventory_item.to_json
+      )
     end
 
     it 'Response with correctly updated inventory item for text item column' do
@@ -312,7 +313,9 @@ RSpec.describe 'Api::V1::InventoryItemsController', type: :request do
       headers: @valid_headers
       expect(response).to have_http_status 200
       expect { hash_body = json }.not_to raise_exception
-      expect(hash_body[:included].to_json).to match(updated_inventory_item.to_json)
+      expect(hash_body[:included].to_json).to match(
+        updated_inventory_item.to_json
+      )
     end
   end
 end

From 028c0c683291e20f97b0734ab5b4458a781202cb Mon Sep 17 00:00:00 2001
From: Luka Murn <luka.murn@biosistemika.com>
Date: Thu, 11 Oct 2018 14:41:13 +0200
Subject: [PATCH 40/40] Remove 2 obsolete unit tests

---
 .../api/v1/inventory_items_controller_spec.rb | 47 -------------------
 1 file changed, 47 deletions(-)

diff --git a/spec/requests/api/v1/inventory_items_controller_spec.rb b/spec/requests/api/v1/inventory_items_controller_spec.rb
index d3ba642b7..e49e0bcfd 100644
--- a/spec/requests/api/v1/inventory_items_controller_spec.rb
+++ b/spec/requests/api/v1/inventory_items_controller_spec.rb
@@ -270,52 +270,5 @@ RSpec.describe 'Api::V1::InventoryItemsController', type: :request do
       expect { hash_body = json }.not_to raise_exception
       expect(hash_body[:data].to_json).to match(updated_inventory_item.to_json)
     end
-
-    it 'Response with correctly updated inventory item for list item column' do
-      hash_body = nil
-      updated_inventory_item = @inventory_item.as_json[:included]
-      updated_inventory_item.each do |cell|
-        attributes = cell[:attributes]
-        next unless attributes[:value_type] == 'list'
-        cell[:attributes] = {
-          value_type: 'list',
-          value: Faker::Name.unique.name,
-          column_id: 2
-        }
-      end
-      patch api_v1_team_inventory_item_path(
-        id: RepositoryRow.last.id,
-        team_id: @teams.first.id,
-        inventory_id: @valid_inventory.id
-      ), params: @inventory_item.to_json,
-      headers: @valid_headers
-      expect(response).to have_http_status 200
-      expect { hash_body = json }.not_to raise_exception
-      expect(hash_body[:included].to_json).to match(
-        updated_inventory_item.to_json
-      )
-    end
-
-    it 'Response with correctly updated inventory item for text item column' do
-      hash_body = nil
-      updated_inventory_item = @inventory_item.as_json[:included]
-      updated_inventory_item.each do |cell|
-        attributes = cell[:attributes]
-        if attributes[:value_type] == 'text'
-          attributes[:value] = Faker::Name.unique.name
-        end
-      end
-      patch api_v1_team_inventory_item_path(
-        id: RepositoryRow.last.id,
-        team_id: @teams.first.id,
-        inventory_id: @valid_inventory.id
-      ), params: @inventory_item.to_json,
-      headers: @valid_headers
-      expect(response).to have_http_status 200
-      expect { hash_body = json }.not_to raise_exception
-      expect(hash_body[:included].to_json).to match(
-        updated_inventory_item.to_json
-      )
-    end
   end
 end