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 01/20] 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 02/20] 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 03/20] 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 04/20] 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 05/20] 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 06/20] 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 07/20] 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 08/20] 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 09/20] 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 10/20] 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 11/20] 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 12/20] 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 13/20] 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 14/20] 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 15/20] 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 16/20] 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 17/20] 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 18/20] 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 19/20] 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 20/20] 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')