From 08b4fbf7ca10a057253a39562247f1c1ce69af89 Mon Sep 17 00:00:00 2001
From: yunfangjuan <yunfang@chanzuckerberg.com>
Date: Fri, 6 Oct 2017 14:29:06 -0700
Subject: [PATCH 1/9] put pipeline runs back

---
 app/controllers/samples_controller.rb    |  5 ++-
 app/views/samples/_samples.html.erb      |  2 +-
 app/views/samples/pipeline_runs.html.erb | 55 ++++++++++++++++++++++++
 config/routes.rb                         |  1 +
 4 files changed, 61 insertions(+), 2 deletions(-)
 create mode 100644 app/views/samples/pipeline_runs.html.erb

diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
index 50b9396145..a22036d1d9 100644
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@@ -1,6 +1,6 @@
 class SamplesController < ApplicationController
   before_action :login_required, only: [:new, :update, :destroy]
-  before_action :set_sample, only: [:show, :edit, :update, :destroy, :reupload_source, :kickoff_pipeline]
+  before_action :set_sample, only: [:show, :edit, :update, :destroy, :reupload_source, :kickoff_pipeline, :pipeline_runs]
   acts_as_token_authentication_handler_for User, only: [:create], fallback: :devise
   protect_from_forgery unless: -> { request.format.json? }
 
@@ -92,6 +92,9 @@ def kickoff_pipeline
     end
   end
 
+  def pipeline_runs
+  end
+
   private
 
   # Use callbacks to share common setup or constraints between actions.
diff --git a/app/views/samples/_samples.html.erb b/app/views/samples/_samples.html.erb
index a00d759a8e..057b8c094e 100644
--- a/app/views/samples/_samples.html.erb
+++ b/app/views/samples/_samples.html.erb
@@ -40,7 +40,7 @@
             <% end %>
           </td>
           <td><%= sample.created_at %></td>
-          <td><%= link_to 'Show', sample %></td>
+          <td><%= link_to 'Runs', pipeline_runs_sample_path(sample) %></td>
           <td><%= link_to 'Edit', edit_sample_path(sample) %></td>
           <!--
           <td><%= link_to 'Destroy', sample, method: :delete, data: { confirm: 'Are you sure?' } %></td>
diff --git a/app/views/samples/pipeline_runs.html.erb b/app/views/samples/pipeline_runs.html.erb
new file mode 100644
index 0000000000..ea8b72ef29
--- /dev/null
+++ b/app/views/samples/pipeline_runs.html.erb
@@ -0,0 +1,55 @@
+<p>
+  <strong>Name:</strong>
+  <%= @sample.name %>
+</p>
+
+<p>
+  <strong>Project:</strong>
+  <%= link_to @sample.project.name, @sample.project %>
+</p>
+
+<p>
+  <strong>Date created:</strong>
+  <%= @sample.created_at %>
+</p>
+
+<p>
+  <strong>Pipeline runs:</strong>
+</p>
+
+<table class="table table-condensed">
+      <thead>
+        <tr>
+          <th> Job Status </th>
+          <th> Job Id </th>
+          <th> Job Log </th>
+          <th>Remaining reads</th>
+          <th>Job Started</th>
+          <th>Output Created</th>
+          <th> Pipeline Output&nbsp; </th>
+        </tr>
+      </thead>
+      <tbody>
+        <% @sample.pipeline_runs.each do |pipeline_run| %>
+          <tr>
+            <td> <%= pipeline_run.job_status %>
+            <td> <%= pipeline_run.job_id %>
+            <td> <%= link_to 'Logs', pipeline_run.log_url %>
+            <td><%= pipeline_run.pipeline_output.remaining_reads if pipeline_run.pipeline_output%> &nbsp;</td>
+            <td><%= pipeline_run.created_at %></td>
+            <td><%= pipeline_run.pipeline_output.created_at if pipeline_run.pipeline_output %></td>
+            <td>
+              <% if pipeline_run.pipeline_output %>
+                <%= link_to 'Show', pipeline_run.pipeline_output %>
+              <% else %>
+                 Pending
+              <% end %>
+            </td>
+          </tr>
+        <% end %>
+      </tbody>
+</table>
+
+<p>
+<%= link_to 'See all samples', samples_path %> |
+</p>
diff --git a/config/routes.rb b/config/routes.rb
index 1e4387bf0f..ecc32b3c2a 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -8,6 +8,7 @@
   resources :samples do
     put :reupload_source, on: :member
     put :kickoff_pipeline, on: :member
+    get :pipeline_runs, on: :member
   end
   resources :projects
   resources :users

From 5095f29e8c95c4e5272af69c2d7c48f942f29fdd Mon Sep 17 00:00:00 2001
From: yunfangjuan <yunfang@chanzuckerberg.com>
Date: Fri, 6 Oct 2017 16:52:01 -0700
Subject: [PATCH 2/9] users clean up

---
 app/controllers/application_controller.rb     |  6 +-
 app/controllers/backgrounds_controller.rb     |  1 +
 .../pipeline_outputs_controller.rb            | 68 +------------------
 app/controllers/projects_controller.rb        |  1 +
 app/controllers/reports_controller.rb         |  1 +
 app/controllers/samples_controller.rb         |  2 +-
 app/controllers/users_controller.rb           |  5 --
 app/views/layouts/_page_header.html.erb       |  7 ++
 app/views/layouts/application.html.erb        |  1 +
 app/views/projects/index.html.erb             |  6 +-
 app/views/users/index.html.erb                |  3 +-
 config/routes.rb                              |  4 +-
 12 files changed, 24 insertions(+), 81 deletions(-)
 create mode 100644 app/views/layouts/_page_header.html.erb

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 98664b65d2..f654d62357 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -1,8 +1,12 @@
 class ApplicationController < ActionController::Base
   protect_from_forgery with: :exception
+  before_action :set_user
 
   def login_required
     redirect_to '/users/sign_in' unless current_user
-    @user = current_user
+  end
+
+  def set_user
+    @user = current_user if current_user and current_user.id
   end
 end
diff --git a/app/controllers/backgrounds_controller.rb b/app/controllers/backgrounds_controller.rb
index 6155606ec6..ec5497435d 100644
--- a/app/controllers/backgrounds_controller.rb
+++ b/app/controllers/backgrounds_controller.rb
@@ -1,4 +1,5 @@
 class BackgroundsController < ApplicationController
+  before_action :login_required, only: [:new, :edit, :update, :destroy, :create]
   before_action :set_background, only: [:show, :edit, :update, :destroy]
 
   # GET /backgrounds
diff --git a/app/controllers/pipeline_outputs_controller.rb b/app/controllers/pipeline_outputs_controller.rb
index 6ba44aa921..3c959473b1 100644
--- a/app/controllers/pipeline_outputs_controller.rb
+++ b/app/controllers/pipeline_outputs_controller.rb
@@ -1,6 +1,6 @@
 class PipelineOutputsController < ApplicationController
   include ReportHelper
-  before_action :set_pipeline_output, only: [:show, :edit, :update, :destroy]
+  before_action :set_pipeline_output, only: [:show]
   protect_from_forgery unless: -> { request.format.json? }
 
   # GET /pipeline_outputs
@@ -24,66 +24,6 @@ def show
     end
   end
 
-  # GET /pipeline_outputs/new
-  def new
-    @pipeline_output = PipelineOutput.new
-  end
-
-  # GET /pipeline_outputs/1/edit
-  def edit
-  end
-
-  # POST /pipeline_outputs
-  # POST /pipeline_outputs.json
-  def create
-    project_name = params[:pipeline_output].delete(:project_name)
-    sample_name = params[:pipeline_output].delete(:sample_name)
-    project = Project.find_by(name: project_name)
-    @sample = Sample.find_by(name: sample_name, project: project) || Sample.new(name: sample_name, project: project)
-    @sample.save
-
-    @pipeline_output = PipelineOutput.new(pipeline_output_params)
-    @pipeline_output.sample = @sample
-
-    # params.require(:job_id)
-    fake_job_id = (0...8).map { (65 + rand(26)).chr }. join
-    @pipeline_output.pipeline_run = PipelineRun.create(sample: @sample, job_id: fake_job_id)
-
-    respond_to do |format|
-      if @pipeline_output.save
-        format.html { redirect_to @pipeline_output, notice: 'Pipeline output was successfully created.' }
-        format.json { render :show, status: :created, location: @pipeline_output }
-      else
-        format.html { render :new }
-        format.json { render json: @pipeline_output.errors, status: :unprocessable_entity }
-      end
-    end
-  end
-
-  # PATCH/PUT /pipeline_outputs/1
-  # PATCH/PUT /pipeline_outputs/1.json
-  def update
-    respond_to do |format|
-      if @pipeline_output.update(pipeline_output_params)
-        format.html { redirect_to @pipeline_output, notice: 'Pipeline output was successfully updated.' }
-        format.json { render :show, status: :ok, location: @pipeline_output }
-      else
-        format.html { render :edit }
-        format.json { render json: @pipeline_output.errors, status: :unprocessable_entity }
-      end
-    end
-  end
-
-  # DELETE /pipeline_outputs/1
-  # DELETE /pipeline_outputs/1.json
-  def destroy
-    @pipeline_output.destroy
-    respond_to do |format|
-      format.html { redirect_to pipeline_outputs_url, notice: 'Pipeline output was successfully destroyed.' }
-      format.json { head :no_content }
-    end
-  end
-
   private
 
   # Use callbacks to share common setup or constraints between actions.
@@ -91,10 +31,4 @@ def set_pipeline_output
     @pipeline_output = PipelineOutput.find(params[:id])
   end
 
-  # Never trust parameters from the scary internet, only allow the white list through.
-  def pipeline_output_params
-    params.require(:pipeline_output).permit(:sample_id, :name, :total_reads, :remaining_reads,
-                                            taxon_counts_attributes: [:tax_id, :tax_level, :count, :name, :count_type],
-                                            job_stats_attributes: [:task, :reads_before, :reads_after])
-  end
 end
diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb
index 609f6863cb..d4ca528e65 100644
--- a/app/controllers/projects_controller.rb
+++ b/app/controllers/projects_controller.rb
@@ -1,5 +1,6 @@
 class ProjectsController < ApplicationController
   before_action :set_project, only: [:show, :edit, :update, :destroy]
+  before_action :login_required, only: [:new, :edit, :create, :update, :destroy]
 
   # GET /projects
   # GET /projects.json
diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index f9a62d8848..5bd1e23a3e 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -1,4 +1,5 @@
 class ReportsController < ApplicationController
+  before_action :login_required, only: [:new, :edit, :update, :destroy, :create]
   before_action :set_report, only: [:show, :edit, :update, :destroy]
   include ReportHelper
   # GET /reports
diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
index a22036d1d9..f308155b67 100644
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@@ -1,5 +1,5 @@
 class SamplesController < ApplicationController
-  before_action :login_required, only: [:new, :update, :destroy]
+  before_action :login_required, only: [:new, :update, :destroy, :edit, :reupload_source, :kickoff_pipeline]
   before_action :set_sample, only: [:show, :edit, :update, :destroy, :reupload_source, :kickoff_pipeline, :pipeline_runs]
   acts_as_token_authentication_handler_for User, only: [:create], fallback: :devise
   protect_from_forgery unless: -> { request.format.json? }
diff --git a/app/controllers/users_controller.rb b/app/controllers/users_controller.rb
index 813b50bf7d..b4030037a0 100644
--- a/app/controllers/users_controller.rb
+++ b/app/controllers/users_controller.rb
@@ -8,11 +8,6 @@ def index
     @users = User.all
   end
 
-  # GET /users/1
-  # GET /users/1.json
-  def show
-  end
-
   # GET /users/new
   def new
     @user = User.new
diff --git a/app/views/layouts/_page_header.html.erb b/app/views/layouts/_page_header.html.erb
new file mode 100644
index 0000000000..9ed7427070
--- /dev/null
+++ b/app/views/layouts/_page_header.html.erb
@@ -0,0 +1,7 @@
+<div class="right header-right-nav">
+  <% if @user && @user.id %>
+    <%= button_to 'Sign Out', destroy_user_session_path, method: :delete %>
+  <% else %>
+    <%= button_to 'Sign In', new_user_session_path %>
+  <% end %>
+</div>
diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index 64d49cef47..f10917169d 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -9,6 +9,7 @@
   </head>
 
   <body>
+    <%= render "layouts/page_header" %>
     <%= yield %>
   </body>
 </html>
diff --git a/app/views/projects/index.html.erb b/app/views/projects/index.html.erb
index 940908e40a..59043c79ee 100644
--- a/app/views/projects/index.html.erb
+++ b/app/views/projects/index.html.erb
@@ -24,9 +24,9 @@
         </td>
         <td><%= project.samples.count %></td>
         <td><%= project.created_at %></td>
-        <td><%= link_to 'Show', project %></td>
-        <td><%= link_to 'Edit', edit_project_path(project) %></td>
-        <td><%= link_to 'Destroy', project, method: :delete, data: { confirm: 'Are you sure?' } %></td>
+        <td><%= button_to 'Show', project %></td>
+        <td><%= button_to 'Edit', edit_project_path(project) %></td>
+        <td><%= button_to 'Destroy', project, method: :delete, data: { confirm: 'Are you sure?' } %></td>
       </tr>
     <% end %>
   </tbody>
diff --git a/app/views/users/index.html.erb b/app/views/users/index.html.erb
index d3fe17daba..431c492af7 100644
--- a/app/views/users/index.html.erb
+++ b/app/views/users/index.html.erb
@@ -19,12 +19,11 @@
         <td><%= user.email %></td>
         <td><%= link_to user.name, user if user.name %></td>
         <td><% user.projects[0...-1].each do |p| %>
-              <%= link_to p.name, p if p %>, 
+              <%= link_to p.name, p if p %>,
             <% end %>
             <%= link_to user.projects.last.name, user.projects.last if user.projects.last %>
         </td>
         <td><%= user.created_at %></td>
-        <td><%= link_to 'Show', user %></td>
         <td><%= link_to 'Edit', edit_user_path(user) %></td>
         <td><%= link_to 'Destroy', user, method: :delete, data: { confirm: 'Are you sure?' } %></td>
       </tr>
diff --git a/config/routes.rb b/config/routes.rb
index ecc32b3c2a..bd1b1cc7b0 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -3,7 +3,7 @@
 Rails.application.routes.draw do
   resources :backgrounds
   resources :reports
-  resources :pipeline_outputs
+  resources :pipeline_outputs, only: [:index, :show]
   devise_for :users
   resources :samples do
     put :reupload_source, on: :member
@@ -11,7 +11,7 @@
     get :pipeline_runs, on: :member
   end
   resources :projects
-  resources :users
+  resources :users, only: [:create, :new, :edit, :update, :destroy, :index]
   mount Resque::Server.new, at: '/resque'
   # For details on the DSL available within this file, see http://guides.rubyonrails.org/routing.html
   root to: 'home#home'

From bce44ef86c7ed669e8d37e1847f9143f61bd3449 Mon Sep 17 00:00:00 2001
From: yunfangjuan <yunfang@chanzuckerberg.com>
Date: Tue, 10 Oct 2017 11:48:05 -0700
Subject: [PATCH 3/9] fix all the failures

---
 app/views/pipeline_outputs/index.html.erb     |  3 --
 app/views/pipeline_outputs/show.html.erb      |  1 -
 .../backgrounds_controller_test.rb            |  2 ++
 .../pipeline_outputs_controller_test.rb       | 32 -------------------
 test/controllers/projects_controller_test.rb  |  7 ++++
 test/controllers/reports_controller_test.rb   |  7 ++++
 test/controllers/users_controller_test.rb     |  5 ---
 7 files changed, 16 insertions(+), 41 deletions(-)

diff --git a/app/views/pipeline_outputs/index.html.erb b/app/views/pipeline_outputs/index.html.erb
index dc0d8fbb3b..bd22964dcb 100644
--- a/app/views/pipeline_outputs/index.html.erb
+++ b/app/views/pipeline_outputs/index.html.erb
@@ -27,14 +27,11 @@
         <td><%= pipeline_output.reports.count %></td>
         <td><%= pipeline_output.created_at %></td>
         <td><%= link_to 'Show', pipeline_output %></td>
-        <td><%= link_to 'Edit', edit_pipeline_output_path(pipeline_output) %></td>
-        <td><%= link_to 'Destroy', pipeline_output, method: :delete, data: { confirm: 'Are you sure?' } %></td>
       </tr>
     <% end %>
   </tbody>
 </table>
 
 <p>
-<%= link_to 'New Pipeline Output', new_pipeline_output_path %> |
 <%= link_to 'Front portal', root_path %>
 </p>
diff --git a/app/views/pipeline_outputs/show.html.erb b/app/views/pipeline_outputs/show.html.erb
index 8e2ec48350..8bb1725af7 100644
--- a/app/views/pipeline_outputs/show.html.erb
+++ b/app/views/pipeline_outputs/show.html.erb
@@ -90,7 +90,6 @@
 </table>
 
 <p>
-<%= link_to 'Edit', edit_pipeline_output_path(@pipeline_output) %> |
 <%= link_to 'See all pipeline runs', pipeline_outputs_path %> |
 <%= link_to 'Front portal', root_path %>
 </p>
diff --git a/test/controllers/backgrounds_controller_test.rb b/test/controllers/backgrounds_controller_test.rb
index b2b676fae5..d16a078337 100644
--- a/test/controllers/backgrounds_controller_test.rb
+++ b/test/controllers/backgrounds_controller_test.rb
@@ -3,6 +3,8 @@
 class BackgroundsControllerTest < ActionDispatch::IntegrationTest
   setup do
     @background = backgrounds(:one)
+    @user = users(:one)
+    post user_session_path, params: { 'user[email]' => @user.email, 'user[password]' => 'password' }
   end
 
   test "should get index" do
diff --git a/test/controllers/pipeline_outputs_controller_test.rb b/test/controllers/pipeline_outputs_controller_test.rb
index 85a65a00b7..0eac9f4ee7 100644
--- a/test/controllers/pipeline_outputs_controller_test.rb
+++ b/test/controllers/pipeline_outputs_controller_test.rb
@@ -11,40 +11,8 @@ class PipelineOutputsControllerTest < ActionDispatch::IntegrationTest
     assert_response :success
   end
 
-  test 'should get new' do
-    get new_pipeline_output_url
-    assert_response :success
-  end
-
-  test 'should create pipeline_output' do
-    assert_difference('PipelineOutput.count') do
-      parameters = { pipeline_output: { project_name: @pipeline_output.sample.project.name, sample_name: @pipeline_output.sample.name, remaining_reads: @pipeline_output.remaining_reads, sample_id: @pipeline_output.sample_id, total_reads: @pipeline_output.total_reads }, job_id: @pipeline_run.job_id }
-      post pipeline_outputs_url, params: parameters
-    end
-
-    assert_redirected_to pipeline_output_url(PipelineOutput.last)
-  end
-
   test 'should show pipeline_output' do
     get pipeline_output_url(@pipeline_output)
     assert_response :success
   end
-
-  test 'should get edit' do
-    get edit_pipeline_output_url(@pipeline_output)
-    assert_response :success
-  end
-
-  test 'should update pipeline_output' do
-    patch pipeline_output_url(@pipeline_output), params: { pipeline_output: { remaining_reads: @pipeline_output.remaining_reads, sample_id: @pipeline_output.sample_id, total_reads: @pipeline_output.total_reads } }
-    assert_redirected_to pipeline_output_url(@pipeline_output)
-  end
-
-  test 'should destroy pipeline_output' do
-    assert_difference('PipelineOutput.count', -1) do
-      delete pipeline_output_url(@pipeline_output)
-    end
-
-    assert_redirected_to pipeline_outputs_url
-  end
 end
diff --git a/test/controllers/projects_controller_test.rb b/test/controllers/projects_controller_test.rb
index bad57ec2be..1fa76f098a 100644
--- a/test/controllers/projects_controller_test.rb
+++ b/test/controllers/projects_controller_test.rb
@@ -3,6 +3,8 @@
 class ProjectsControllerTest < ActionDispatch::IntegrationTest
   setup do
     @project = projects(:one)
+    @user = users(:one)
+    @user_params = { 'user[email]' => @user.email, 'user[password]' => 'password' }
   end
 
   test 'should get index' do
@@ -11,11 +13,13 @@ class ProjectsControllerTest < ActionDispatch::IntegrationTest
   end
 
   test 'should get new' do
+    post user_session_path, params: @user_params
     get new_project_url
     assert_response :success
   end
 
   test 'should create project' do
+    post user_session_path, params: @user_params
     assert_difference('Project.count') do
       post projects_url, params: { project: { name: 'New Project' } }
     end
@@ -29,16 +33,19 @@ class ProjectsControllerTest < ActionDispatch::IntegrationTest
   end
 
   test 'should get edit' do
+    post user_session_path, params: @user_params
     get edit_project_url(@project)
     assert_response :success
   end
 
   test 'should update project' do
+    post user_session_path, params: @user_params
     patch project_url(@project), params: { project: { name: @project.name } }
     assert_redirected_to project_url(@project)
   end
 
   test 'should destroy project' do
+    post user_session_path, params: @user_params
     assert_difference('Project.count', -1) do
       delete project_url(@project)
     end
diff --git a/test/controllers/reports_controller_test.rb b/test/controllers/reports_controller_test.rb
index 8e895b9990..4154bae29c 100644
--- a/test/controllers/reports_controller_test.rb
+++ b/test/controllers/reports_controller_test.rb
@@ -3,6 +3,8 @@
 class ReportsControllerTest < ActionDispatch::IntegrationTest
   setup do
     @report = reports(:one)
+    @user = users(:one)
+    @user_params = { 'user[email]' => @user.email, 'user[password]' => 'password' }
   end
 
   test "should get index" do
@@ -11,11 +13,13 @@ class ReportsControllerTest < ActionDispatch::IntegrationTest
   end
 
   test "should get new" do
+    post user_session_path, params: @user_params
     get new_report_url
     assert_response :success
   end
 
   test "should create report" do
+    post user_session_path, params: @user_params
     assert_difference('Report.count') do
       post reports_url, params: { report: { name: @report.name, pipeline_output_id: @report.pipeline_output_id, background_id: @report.background_id } }
     end
@@ -29,16 +33,19 @@ class ReportsControllerTest < ActionDispatch::IntegrationTest
   end
 
   test "should get edit" do
+    post user_session_path, params: @user_params
     get edit_report_url(@report)
     assert_response :success
   end
 
   test "should update report" do
+    post user_session_path, params: @user_params
     patch report_url(@report), params: { report: { name: @report.name, pipeline_output_id: @report.pipeline_output_id } }
     assert_redirected_to report_url(@report)
   end
 
   test "should destroy report" do
+    post user_session_path, params: @user_params
     assert_difference('Report.count', -1) do
       delete report_url(@report)
     end
diff --git a/test/controllers/users_controller_test.rb b/test/controllers/users_controller_test.rb
index 555e349da5..738220df1d 100644
--- a/test/controllers/users_controller_test.rb
+++ b/test/controllers/users_controller_test.rb
@@ -16,11 +16,6 @@ class UsersControllerTest < ActionDispatch::IntegrationTest
     assert_response :success
   end
 
-  test 'should show user' do
-    get user_url(@user)
-    assert_response :success
-  end
-
   test 'should get edit' do
     get edit_user_url(@user)
     assert_response :success

From 1d6b83df954e76338e35e622abce34f3d864fc71 Mon Sep 17 00:00:00 2001
From: yunfangjuan <yunfang@chanzuckerberg.com>
Date: Tue, 10 Oct 2017 14:23:05 -0700
Subject: [PATCH 4/9] add more tests

---
 .../application_controller_test.rb            | 29 +++++++++
 test/controllers/samples_controller_test.rb   | 63 ++++++++++++++++++-
 2 files changed, 91 insertions(+), 1 deletion(-)
 create mode 100644 test/controllers/application_controller_test.rb

diff --git a/test/controllers/application_controller_test.rb b/test/controllers/application_controller_test.rb
new file mode 100644
index 0000000000..a90fae0188
--- /dev/null
+++ b/test/controllers/application_controller_test.rb
@@ -0,0 +1,29 @@
+require 'test_helper'
+
+class ProjectsControllerTest < ActionDispatch::IntegrationTest
+  setup do
+    @user = users(:one)
+    @user_params = { 'user[email]' => @user.email, 'user[password]' => 'password' }
+  end
+
+  test 'should log in' do
+    post user_session_path, params: @user_params
+    assert_redirected_to root_url
+
+  end
+
+  test 'should log out' do
+    post user_session_path, params: @user_params
+    delete destroy_user_session_url
+    post projects_url, params: { project: { name: 'New Project' } }
+    assert_redirected_to new_user_session_url
+
+  end
+
+  test 'log in should fail' do
+    post user_session_path, params: { 'user[email]' => @user.email, 'user[password]' => 'badpass' }
+    assert_equal flash[:alert], 'Invalid Email or password.'
+
+  end
+
+end
diff --git a/test/controllers/samples_controller_test.rb b/test/controllers/samples_controller_test.rb
index 4dee82f5fb..b4e13be723 100644
--- a/test/controllers/samples_controller_test.rb
+++ b/test/controllers/samples_controller_test.rb
@@ -7,7 +7,7 @@ class SamplesControllerTest < ActionDispatch::IntegrationTest
     @user = users(:one)
     @user.authentication_token = 'sdfsdfsdff'
     @user.save
-    post user_session_path, params: { 'user[email]' => @user.email, 'user[password]' => 'password' }
+    @user_params = { 'user[email]' => @user.email, 'user[password]' => 'password' }
   end
 
   test 'should get index' do
@@ -16,6 +16,7 @@ class SamplesControllerTest < ActionDispatch::IntegrationTest
   end
 
   test 'should get new' do
+    post user_session_path, params: @user_params
     get new_sample_url
     assert_response :success
   end
@@ -36,23 +37,83 @@ class SamplesControllerTest < ActionDispatch::IntegrationTest
     assert_redirected_to sample_url(Sample.last)
   end
 
+  test 'should redirect ' do
+    input_files = [{ source: "RR004_water_2_S23_R1_001.fastq.gz",
+                     name: "RR004_water_2_S23_R1_001.fastq.gz",
+                     source_type: "local" },
+                   { source: "RR004_water_2_S23_R2_001.fastq.gz",
+                     name: "RR004_water_2_S23_R2_001.fastq.gz",
+                     source_type: "local" }]
+    assert_difference('Sample.count', 0) do
+      post samples_url, params: { sample: { name: 'new sample', project_name: @project.name, input_files_attributes: input_files } }
+    end
+
+    assert_redirected_to new_user_session_url
+  end
+
+  test 'pipeline_runs' do
+    get pipeline_runs_sample_url(@sample)
+    assert :success
+  end
+
+  test 'reupload source' do
+    post user_session_path, params: @user_params
+    put reupload_source_sample_url(@sample)
+    assert :success
+  end
+
+  test 'reupload source 2' do
+    put reupload_source_sample_url(@sample)
+    assert_redirected_to new_user_session_url
+  end
+
+  test 'kick off pipeline' do
+    post user_session_path, params: @user_params
+    put kickoff_pipeline_sample_url(@sample)
+    assert :success
+  end
+
+  test 'kick off pipeline redirect' do
+    put kickoff_pipeline_sample_url(@sample)
+    assert_redirected_to new_user_session_url
+  end
+
+  test 'should create sample through web' do
+    post user_session_path, params: @user_params
+    input_files = [{ source: "RR004_water_2_S23_R1_001.fastq.gz",
+                     name: "RR004_water_2_S23_R1_001.fastq.gz",
+                     source_type: "local" },
+                   { source: "RR004_water_2_S23_R2_001.fastq.gz",
+                     name: "RR004_water_2_S23_R2_001.fastq.gz",
+                     source_type: "local" }]
+    assert_difference('Sample.count') do
+      post samples_url, params: { sample: { name: 'new sample', project_name: @project.name, input_files_attributes: input_files } }
+    end
+
+    assert_redirected_to sample_url(Sample.last)
+  end
+
   test 'should show sample' do
+    post user_session_path, params: @user_params
     get sample_url(@sample)
     assert_response :success
   end
 
   test 'should get edit' do
+    post user_session_path, params: @user_params
     get edit_sample_url(@sample)
     assert_response :success
   end
 
   test 'should update sample' do
+    post user_session_path, params: @user_params
     assert @sample.valid?
     patch sample_url(@sample), params: { sample: { name: @sample.name + ' asdf' } }
     assert_redirected_to sample_url(@sample)
   end
 
   test 'should destroy sample' do
+    post user_session_path, params: @user_params
     assert_difference('Sample.count', -1) do
       delete sample_url(@sample)
     end

From 6f4204a320642cc8657eba888e6dfe97f3ac237e Mon Sep 17 00:00:00 2001
From: yunfangjuan <yunfang@chanzuckerberg.com>
Date: Tue, 10 Oct 2017 14:29:56 -0700
Subject: [PATCH 5/9] more tests

---
 app/controllers/application_controller.rb       | 2 +-
 test/controllers/application_controller_test.rb | 6 +-----
 test/controllers/samples_controller_test.rb     | 5 -----
 3 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index f654d62357..aece0f25b9 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -7,6 +7,6 @@ def login_required
   end
 
   def set_user
-    @user = current_user if current_user and current_user.id
+    @user = current_user if current_user && current_user.id
   end
 end
diff --git a/test/controllers/application_controller_test.rb b/test/controllers/application_controller_test.rb
index a90fae0188..b5c3c359f2 100644
--- a/test/controllers/application_controller_test.rb
+++ b/test/controllers/application_controller_test.rb
@@ -1,6 +1,6 @@
 require 'test_helper'
 
-class ProjectsControllerTest < ActionDispatch::IntegrationTest
+class ApplicationControllerTest < ActionDispatch::IntegrationTest
   setup do
     @user = users(:one)
     @user_params = { 'user[email]' => @user.email, 'user[password]' => 'password' }
@@ -9,7 +9,6 @@ class ProjectsControllerTest < ActionDispatch::IntegrationTest
   test 'should log in' do
     post user_session_path, params: @user_params
     assert_redirected_to root_url
-
   end
 
   test 'should log out' do
@@ -17,13 +16,10 @@ class ProjectsControllerTest < ActionDispatch::IntegrationTest
     delete destroy_user_session_url
     post projects_url, params: { project: { name: 'New Project' } }
     assert_redirected_to new_user_session_url
-
   end
 
   test 'log in should fail' do
     post user_session_path, params: { 'user[email]' => @user.email, 'user[password]' => 'badpass' }
     assert_equal flash[:alert], 'Invalid Email or password.'
-
   end
-
 end
diff --git a/test/controllers/samples_controller_test.rb b/test/controllers/samples_controller_test.rb
index b4e13be723..8ede54c338 100644
--- a/test/controllers/samples_controller_test.rb
+++ b/test/controllers/samples_controller_test.rb
@@ -33,7 +33,6 @@ class SamplesControllerTest < ActionDispatch::IntegrationTest
     assert_difference('Sample.count') do
       post samples_url, params: { sample: { name: 'new sample', project_name: @project.name, input_files_attributes: input_files } }, headers: req_headers
     end
-
     assert_redirected_to sample_url(Sample.last)
   end
 
@@ -47,7 +46,6 @@ class SamplesControllerTest < ActionDispatch::IntegrationTest
     assert_difference('Sample.count', 0) do
       post samples_url, params: { sample: { name: 'new sample', project_name: @project.name, input_files_attributes: input_files } }
     end
-
     assert_redirected_to new_user_session_url
   end
 
@@ -89,12 +87,10 @@ class SamplesControllerTest < ActionDispatch::IntegrationTest
     assert_difference('Sample.count') do
       post samples_url, params: { sample: { name: 'new sample', project_name: @project.name, input_files_attributes: input_files } }
     end
-
     assert_redirected_to sample_url(Sample.last)
   end
 
   test 'should show sample' do
-    post user_session_path, params: @user_params
     get sample_url(@sample)
     assert_response :success
   end
@@ -117,7 +113,6 @@ class SamplesControllerTest < ActionDispatch::IntegrationTest
     assert_difference('Sample.count', -1) do
       delete sample_url(@sample)
     end
-
     assert_redirected_to samples_url
   end
 end

From f8d71352b27743d82f8742648301ec2d34e1ebc0 Mon Sep 17 00:00:00 2001
From: yunfangjuan <yunfang@chanzuckerberg.com>
Date: Tue, 10 Oct 2017 17:30:35 -0700
Subject: [PATCH 6/9] fix the right section for samples

---
 .../components/PipelineSampleReads.jsx        | 27 +++++++++++++------
 app/controllers/reports_controller.rb         |  2 +-
 app/models/sample.rb                          |  8 ++++++
 3 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/app/assets/javascripts/components/PipelineSampleReads.jsx b/app/assets/javascripts/components/PipelineSampleReads.jsx
index ff49c4242d..9cc2255534 100644
--- a/app/assets/javascripts/components/PipelineSampleReads.jsx
+++ b/app/assets/javascripts/components/PipelineSampleReads.jsx
@@ -45,6 +45,7 @@ class PipelineSampleReads extends React.Component {
     }
 
     let pipeline_run = null;
+    let down_load_section = null;
     if (this.pipelineOutput) {
       pipeline_run = (
         <div className="data">
@@ -80,7 +81,22 @@ class PipelineSampleReads extends React.Component {
             </div>
           </div>
         </div>
-      )
+    );
+
+    download_section = (
+      <div>
+        <a className="custom-button" href= { this.sampleInfo.sample_annotated_fasta_url }>
+          <i className="fa fa-cloud-download left"></i> DOWNLOAD NON HUMAN READS
+        </a>
+        <a className="custom-button" href= { this.sampleInfo.sample_output_folder_url }>
+          <i className="fa fa-cloud-download left"></i> GO TO RESULTS FOLDER
+        </a>
+        <a className="custom-button" href= { '/reports/new?report[pipeline_output_id]=' + this.pipelineOutput.id }>
+          <i className="fa fa-file-text-o left"></i> GENERATE REPORT
+        </a>
+      </div>
+    );
+
     } else {
       pipeline_run = (
         <div className="center">
@@ -192,16 +208,11 @@ class PipelineSampleReads extends React.Component {
               </div>
 
               <div className="col s3 download-area">
-                <a className="custom-button">
+                <a className="custom-button" href={ this.sampleInfo.sample_input_folder_url }>
                   <i className="fa fa-cloud-download left"></i> DOWNLOAD ALL READS
                 </a>
+                { download_section }
 
-                <a className="custom-button">
-                  <i className="fa fa-user-times left"></i> DOWNLOAD NON HUMAN READS
-                </a>
-                <a onClick={this.gotoReport}  className="custom-button">
-                  <i className="fa fa-file-text-o left"></i> GENERATE REPORT
-                </a>
               </div>
 
             </div>
diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index c93f893534..c15a285265 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -20,7 +20,7 @@ def show
 
   # GET /reports/new
   def new
-    @report = Report.new
+    @report = Report.new(report_params)
   end
 
   # GET /reports/1/edit
diff --git a/app/models/sample.rb b/app/models/sample.rb
index 373f3edeef..e6c01cf31b 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -79,6 +79,14 @@ def sample_output_folder_url
     "https://s3.console.aws.amazon.com/s3/object/#{SAMPLES_BUCKET_NAME}/#{sample_path}/results/"
   end
 
+  def sample_input_folder_url
+    "https://s3.console.aws.amazon.com/s3/object/#{SAMPLES_BUCKET_NAME}/#{sample_path}/fastqs/"
+  end
+
+  def as_json(options={})
+    super(methods: [:sample_input_folder_url, :sample_output_folder_url, :sample_annotated_fasta_url])
+  end
+
   def pipeline_command
     script_name = File.basename(IdSeqPipeline::S3_SCRIPT_LOC)
     batch_command_env_variables = "INPUT_BUCKET=#{sample_input_s3_path} OUTPUT_BUCKET=#{sample_output_s3_path} " \

From 4ead9b749c98cc8cf6f8fd1e9a8c2213f35dc61a Mon Sep 17 00:00:00 2001
From: yunfangjuan <yunfang@chanzuckerberg.com>
Date: Tue, 10 Oct 2017 17:33:48 -0700
Subject: [PATCH 7/9] fix a typo

---
 app/assets/javascripts/components/PipelineSampleReads.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/assets/javascripts/components/PipelineSampleReads.jsx b/app/assets/javascripts/components/PipelineSampleReads.jsx
index 9cc2255534..cf423944e1 100644
--- a/app/assets/javascripts/components/PipelineSampleReads.jsx
+++ b/app/assets/javascripts/components/PipelineSampleReads.jsx
@@ -45,7 +45,7 @@ class PipelineSampleReads extends React.Component {
     }
 
     let pipeline_run = null;
-    let down_load_section = null;
+    let download_section = null;
     if (this.pipelineOutput) {
       pipeline_run = (
         <div className="data">

From 40ac0d642f2c3850d280621cc56abb3138aef009 Mon Sep 17 00:00:00 2001
From: yunfangjuan <yunfang@chanzuckerberg.com>
Date: Tue, 10 Oct 2017 17:35:26 -0700
Subject: [PATCH 8/9] fix rubocop

---
 app/models/sample.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/sample.rb b/app/models/sample.rb
index e6c01cf31b..9d150c9a7e 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -83,7 +83,7 @@ def sample_input_folder_url
     "https://s3.console.aws.amazon.com/s3/object/#{SAMPLES_BUCKET_NAME}/#{sample_path}/fastqs/"
   end
 
-  def as_json(options={})
+  def as_json(_options = {})
     super(methods: [:sample_input_folder_url, :sample_output_folder_url, :sample_annotated_fasta_url])
   end
 

From d6458519b56811ce84b64fd8e35178ba63714b21 Mon Sep 17 00:00:00 2001
From: yunfangjuan <yunfang@chanzuckerberg.com>
Date: Tue, 10 Oct 2017 17:45:50 -0700
Subject: [PATCH 9/9] fix rubocop

---
 app/controllers/reports_controller.rb | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index c15a285265..7101a57170 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -20,7 +20,11 @@ def show
 
   # GET /reports/new
   def new
-    @report = Report.new(report_params)
+    @report = if params[:report]
+                Report.new(params.require(:report).permit(:pipeline_output_id))
+              else
+                Report.new
+              end
   end
 
   # GET /reports/1/edit