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rename pipeline to pipeline template. refs #1416
author
Tom Clegg <tom@clinicalfuture.com>
Tue, 19 Mar 2013 20:05:17 +0000
(13:05 -0700)
committer
Tom Clegg <tom@clinicalfuture.com>
Tue, 19 Mar 2013 20:07:31 +0000
(13:07 -0700)
18 files changed:
app/assets/javascripts/pipeline_templates.js.coffee
[moved from
app/assets/javascripts/pipelines.js.coffee
with 100% similarity]
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app/assets/stylesheets/pipeline_templates.css.scss
[moved from
app/assets/stylesheets/pipelines.css.scss
with 60% similarity]
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app/controllers/pipeline_templates_controller.rb
[new file with mode: 0644]
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app/controllers/pipelines_controller.rb
[deleted file]
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app/helpers/pipeline_templates_helper.rb
[new file with mode: 0644]
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app/helpers/pipelines_helper.rb
[deleted file]
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app/helpers/vcf_pipeline_helper.rb
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app/models/orvos_base.rb
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app/models/pipeline.rb
[deleted file]
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app/models/pipeline_instance.rb
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app/models/pipeline_template.rb
[new file with mode: 0644]
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app/views/pipeline_templates/show.html.erb
[moved from
app/views/pipelines/show.html.erb
with 100% similarity]
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config/routes.rb
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test/fixtures/pipeline_templates.yml
[moved from
test/fixtures/pipelines.yml
with 100% similarity]
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test/functional/pipeline_templates_controller_test.rb
[moved from
test/functional/pipelines_controller_test.rb
with 53% similarity]
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test/unit/helpers/pipeline_templates_helper_test.rb
[new file with mode: 0644]
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test/unit/helpers/pipelines_helper_test.rb
[deleted file]
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test/unit/pipeline_template_test.rb
[moved from
test/unit/pipeline_test.rb
with 59% similarity]
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diff --git
a/app/assets/javascripts/pipelines.js.coffee
b/app/assets/javascripts/pipeline_templates.js.coffee
similarity index 100%
rename from
app/assets/javascripts/pipelines.js.coffee
rename to
app/assets/javascripts/pipeline_templates.js.coffee
diff --git
a/app/assets/stylesheets/pipelines.css.scss
b/app/assets/stylesheets/pipeline_templates.css.scss
similarity index 60%
rename from
app/assets/stylesheets/pipelines.css.scss
rename to
app/assets/stylesheets/pipeline_templates.css.scss
index fa5d69a15d0e83838fe660a4ee3e9075c7a7677e..35d2946bb0e4868dad2694945bc5ab0970158eb2 100644
(file)
--- a/
app/assets/stylesheets/pipelines.css.scss
+++ b/
app/assets/stylesheets/pipeline_templates.css.scss
@@
-1,3
+1,3
@@
-// Place all the styles related to the Pipelines controller here.
+// Place all the styles related to the Pipeline
Template
s controller here.
// They will automatically be included in application.css.
// You can use Sass (SCSS) here: http://sass-lang.com/
// They will automatically be included in application.css.
// You can use Sass (SCSS) here: http://sass-lang.com/
diff --git a/app/controllers/pipeline_templates_controller.rb
b/app/controllers/pipeline_templates_controller.rb
new file mode 100644
(file)
index 0000000..
cff5893
--- /dev/null
+++ b/
app/controllers/pipeline_templates_controller.rb
@@ -0,0
+1,3
@@
+class PipelineTemplatesController < ApplicationController
+ before_filter :ensure_current_user_is_admin
+end
diff --git
a/app/controllers/pipelines_controller.rb
b/app/controllers/pipelines_controller.rb
deleted file mode 100644
(file)
index
2af4d42
..0000000
--- a/
app/controllers/pipelines_controller.rb
+++ /dev/null
@@
-1,3
+0,0 @@
-class PipelinesController < ApplicationController
- before_filter :ensure_current_user_is_admin
-end
diff --git a/app/helpers/pipeline_templates_helper.rb
b/app/helpers/pipeline_templates_helper.rb
new file mode 100644
(file)
index 0000000..
be82878
--- /dev/null
+++ b/
app/helpers/pipeline_templates_helper.rb
@@ -0,0
+1,2
@@
+module PipelineTemplatesHelper
+end
diff --git
a/app/helpers/pipelines_helper.rb
b/app/helpers/pipelines_helper.rb
deleted file mode 100644
(file)
index
6837cde
..0000000
--- a/
app/helpers/pipelines_helper.rb
+++ /dev/null
@@
-1,2
+0,0 @@
-module PipelinesHelper
-end
diff --git
a/app/helpers/vcf_pipeline_helper.rb
b/app/helpers/vcf_pipeline_helper.rb
index 255c6524acc90b3d687243605b59f8d861d63964..9a3d6e730b240a8d186997bca98a068ca3d4f8f1 100644
(file)
--- a/
app/helpers/vcf_pipeline_helper.rb
+++ b/
app/helpers/vcf_pipeline_helper.rb
@@
-14,7
+14,7
@@
module VcfPipelineHelper
'STAND_EMIT_CONF' => '4.0',
"bwa/INPUT" => input_manifest
}
'STAND_EMIT_CONF' => '4.0',
"bwa/INPUT" => input_manifest
}
- pi.components = Pipeline.find(pi.pipeline_uuid).components
+ pi.components = Pipeline
Template
.find(pi.pipeline_uuid).components
pi.update_job_parameters(params)
pi.active = true
pi.success = nil
pi.update_job_parameters(params)
pi.active = true
pi.success = nil
diff --git
a/app/models/orvos_base.rb
b/app/models/orvos_base.rb
index 4478e60a17166f99625765f6c6bf52fc1402d018..fa5ed002afdf6da015235d623308df4e9fecf0a6 100644
(file)
--- a/
app/models/orvos_base.rb
+++ b/
app/models/orvos_base.rb
@@
-10,7
+10,8
@@
class OrvosBase < ActiveRecord::Base
'8i9sb' => 'orvos#job',
'57u5n' => 'orvos#log',
'j58dm' => 'orvos#specimen',
'8i9sb' => 'orvos#job',
'57u5n' => 'orvos#log',
'j58dm' => 'orvos#specimen',
- 'mxsvm' => 'orvos#pipeline',
+ 'p5p6p' => 'orvos#pipeline_template',
+ 'mxsvm' => 'orvos#pipeline_template', # legacy Pipeline objects
'd1hrv' => 'orvos#pipeline_instance',
'uo14g' => 'orvos#pipeline_instance', # legacy PipelineInstance objects
'j7d0g' => 'orvos#group',
'd1hrv' => 'orvos#pipeline_instance',
'uo14g' => 'orvos#pipeline_instance', # legacy PipelineInstance objects
'j7d0g' => 'orvos#group',
diff --git
a/app/models/pipeline.rb
b/app/models/pipeline.rb
deleted file mode 100644
(file)
index
1edeb60
..0000000
--- a/
app/models/pipeline.rb
+++ /dev/null
@@
-1,2
+0,0 @@
-class Pipeline < OrvosBase
-end
diff --git
a/app/models/pipeline_instance.rb
b/app/models/pipeline_instance.rb
index 6ba897d18dc0184bc3018cf7a766cd1ef4d3e34a..7fe88c62a8b0a28b02664d0aa2984dcf96d7b328 100644
(file)
--- a/
app/models/pipeline_instance.rb
+++ b/
app/models/pipeline_instance.rb
@@
-1,5
+1,5
@@
class PipelineInstance < OrvosBase
class PipelineInstance < OrvosBase
- attr_accessor :pipeline
+ attr_accessor :pipeline
_template
def update_job_parameters(new_params)
self.components[:steps].each_with_index do |step, i|
def update_job_parameters(new_params)
self.components[:steps].each_with_index do |step, i|
diff --git a/app/models/pipeline_template.rb
b/app/models/pipeline_template.rb
new file mode 100644
(file)
index 0000000..
b68aa57
--- /dev/null
+++ b/
app/models/pipeline_template.rb
@@ -0,0
+1,2
@@
+class PipelineTemplate < OrvosBase
+end
diff --git
a/app/views/pipelines/show.html.erb
b/app/views/pipeline_templates/show.html.erb
similarity index 100%
rename from
app/views/pipelines/show.html.erb
rename to
app/views/pipeline_templates/show.html.erb
diff --git
a/config/routes.rb
b/config/routes.rb
index bb5e60414fd3ec7e6e6a4f31e6e693fd7ec17e51..5002398306de3fbe23e0478f4a78343286107901 100644
(file)
--- a/
config/routes.rb
+++ b/
config/routes.rb
@@
-28,7
+28,7
@@
Vcffarm::Application.routes.draw do
resources :specimens
resources :specimens
- resources :pipelines
+ resources :pipeline
_template
s
resources :pipeline_instances
resources :pipeline_instances
diff --git
a/test/fixtures/pipelines.yml
b/test/fixtures/pipeline_templates.yml
similarity index 100%
rename from
test/fixtures/pipelines.yml
rename to
test/fixtures/pipeline_templates.yml
diff --git
a/test/functional/pipelines_controller_test.rb
b/test/functional/pipeline_templates_controller_test.rb
similarity index 53%
rename from
test/functional/pipelines_controller_test.rb
rename to
test/functional/pipeline_templates_controller_test.rb
index 468bf6a067906895b3329717c6cb619800ccaa62..41588151a5badee247f6c03476a5882bb3a8314b 100644
(file)
--- a/
test/functional/pipelines_controller_test.rb
+++ b/
test/functional/pipeline_templates_controller_test.rb
@@
-1,6
+1,6
@@
require 'test_helper'
require 'test_helper'
-class PipelinesControllerTest < ActionController::TestCase
+class Pipeline
Template
sControllerTest < ActionController::TestCase
# test "the truth" do
# assert true
# end
# test "the truth" do
# assert true
# end
diff --git a/test/unit/helpers/pipeline_templates_helper_test.rb
b/test/unit/helpers/pipeline_templates_helper_test.rb
new file mode 100644
(file)
index 0000000..
fb54368
--- /dev/null
+++ b/
test/unit/helpers/pipeline_templates_helper_test.rb
@@ -0,0
+1,4
@@
+require 'test_helper'
+
+class PipelineTemplatesHelperTest < ActionView::TestCase
+end
diff --git
a/test/unit/helpers/pipelines_helper_test.rb
b/test/unit/helpers/pipelines_helper_test.rb
deleted file mode 100644
(file)
index
2c4030a
..0000000
--- a/
test/unit/helpers/pipelines_helper_test.rb
+++ /dev/null
@@
-1,4
+0,0 @@
-require 'test_helper'
-
-class PipelinesHelperTest < ActionView::TestCase
-end
diff --git
a/test/unit/pipeline_test.rb
b/test/unit/pipeline_template_test.rb
similarity index 59%
rename from
test/unit/pipeline_test.rb
rename to
test/unit/pipeline_template_test.rb
index ab21010f974364c5e6e665b08a4bc539c3b9c6c9..a28a2c98405212d058cf22190e371bd2611ba182 100644
(file)
--- a/
test/unit/pipeline_test.rb
+++ b/
test/unit/pipeline_template_test.rb
@@
-1,6
+1,6
@@
require 'test_helper'
require 'test_helper'
-class PipelineTest < ActiveSupport::TestCase
+class PipelineTe
mplateTe
st < ActiveSupport::TestCase
# test "the truth" do
# assert true
# end
# test "the truth" do
# assert true
# end