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RE: [myexperiment-hackers] [2295] trunk: workflow version api - handle u
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From: |
Don Cruickshank |
|
Subject: |
RE: [myexperiment-hackers] [2295] trunk: workflow version api - handle updating main record if last version changes |
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Date: |
Tue, 10 Nov 2009 16:40:37 -0000 |
Accidental commit - I'm aware but got called into a meeting.
-----Original Message-----
From: address@hidden [mailto:address@hidden On Behalf Of Jiten Bhagat
Sent: 10 November 2009 14:00
To: address@hidden
Subject: Re: [myexperiment-hackers] [2295] trunk: workflow version api - handle
updating main record if last version changes
Have you just classified all workflows on myExperiment as "Sequence Analysis"
and "Gene Prediction"? :-)
Jits
address@hidden wrote:
>
> Revision
> 2295
> Author
> dgc
> Date
> 2009-11-10 08:52:47 -0500 (Tue, 10 Nov 2009)
>
>
> Log Message
>
> workflow version api - handle updating main record if last version
> changes
>
>
> Modified Paths
>
> * trunk/app/views/workflows/show.rhtml
> <#trunkappviewsworkflowsshowrhtml>
> * trunk/lib/explicit_versioning.rb <#trunklibexplicit_versioningrb>
> * trunk/lib/rest.rb <#trunklibrestrb>
> * trunk/public/stylesheets/styles.css
> <#trunkpublicstylesheetsstylescss>
> * trunk/test/functional/workflows_controller_test.rb
> <#trunktestfunctionalworkflows_controller_testrb>
>
>
> Diff
>
>
> Modified: trunk/app/views/workflows/show.rhtml (2294 => 2295)
>
>
> --- trunk/app/views/workflows/show.rhtml 2009-11-09 15:50:47 UTC (rev
> 2294)
> +++ trunk/app/views/workflows/show.rhtml 2009-11-10 13:52:47 UTC (rev
> 2295)
> @@ -155,6 +155,16 @@
>
> <h3>
> <%= info_icon_with_tooltip("This section shows
> the preview of
> this version of the Workflow (click on the image to expand)") %>
> + Classification
> + </h3>
> +
> + <p>
> + <span class="classification">Sequence Analysis</span>
> + <span class="classification">Gene Prediction</span>
> + </p>
> +
> + <h3>
> + <%= info_icon_with_tooltip("This section shows
> the preview of
> +this version of the Workflow (click on the image to expand)") %>
> Preview
> </h3>
>
> @@ -210,8 +220,170 @@
>
> <br/>
>
> +
> <h3>
> <%= info_icon_with_tooltip("This section
> provides links to the
> different downloads for this version of the Workflow") %>
> + Inputs
> + </h3>
> +
> + <h4 style="text-align: left">Input 1: chromosome_name</h4>
> +
> + <table class="simple">
> + <tr>
> + <td>Name</td>
> + <td>chromosome_name</td>
> + </tr>
> + <tr>
> + <td>Type</td>
> + <td>Text</td>
> + </tr>
> + <tr>
> + <td>Description</td>
> + <td>A chromosome name or number.</td>
> + </tr>
> + <tr>
> + <td>Example 1</td>
> + <td>17</td>
> + </tr>
> + </table>
> + <br />
> + <br />
> +
> + <h4 style="text-align: left">Input 2: qtl_start_position</h4>
> +
> + <table class="simple">
> + <tr>
> + <td>Name</td>
> + <td>qtl_start_position</td>
> + </tr>
> + <tr>
> + <td>Type</td>
> + <td>Text</td>
> + </tr>
> + <tr>
> + <td>Description</td>
> + <td>QTL start base pair position</td>
> + </tr>
> + <tr>
> + <td>Example 1</td>
> + <td>28500000</td>
> + </tr>
> + </table>
> + <br />
> + <br />
> +
> + <h4 style="text-align: left">Input 3: qtl_end_position</h4>
> +
> + <table class="simple">
> + <tr>
> + <td>Name</td>
> + <td>qtl_end_position</td>
> + </tr>
> + <tr>
> + <td>Type</td>
> + <td>Text</td>
> + </tr>
> + <tr>
> + <td>Description</td>
> + <td>QTL end base pair position</td>
> + </tr>
> + <tr>
> + <td>Example 1</td>
> + <td>29500000</td>
> + </tr>
> + </table>
> + <br />
> + <br />
> +
> + <h3>
> + <%= info_icon_with_tooltip("This section
> provides links to the different downloads for this version of the Workflow")
> %>
> + Outputs
> + </h3>
> +
> + <h4 style="text-align: left">Output 1: chromosome_name</h4>
> +
> + <table class="simple">
> + <tr>
> + <td>Name</td>
> + <td>merged_pathways</td>
> + </tr>
> + <tr>
> + <td>Type</td>
> + <td><a href="">KEGG record</a></td>
> + </tr>
> + <tr>
> + <td>Description</td>
> + <td>The merged pathways</td>
> + </tr>
> + <tr>
> + <td>Example 1</td>
> + <td>17</td>
> + </tr>
> + </table>
> + <br />
> + <br />
> +
> +
> + <h3><%= info_icon_with_tooltip("This section provides
> links to the
> +different downloads for this version of the Workflow") %> Complete
> +examples</h3>
> +
> + <h4 style="text-align: left">Complete example 1: Example given
> + from the original description</h4>
> +
> + <table class="simple">
> + <tr>
> + <th>Input</th>
> + <th>Value</th>
> + </tr>
> + <tr>
> + <td>chromosome_name</td>
> + <td>17</td>
> + </tr>
> + <tr>
> + <td>qtl_start_position</td>
> + <td>28500000</td>
> + </tr>
> + <tr>
> + <td>qtl_end_position</td>
> + <td>29500000</td>
> + </tr>
> + </table>
> + <br />
> + <br />
> +
> + <table class="simple">
> + <tr>
> + <th>Output</th>
> + <th>Value</th>
> + </tr>
> + <tr>
> + <td>merged_pathways</td>
> + <td>Example output value.</td>
> + </tr>
> + </table>
> + <br />
> + <br />
> +
> +
> + <h3><%= info_icon_with_tooltip("This section provides
> links to the
> +different downloads for this version of the Workflow") %>
> +Dependencies</h3>
> +
> + <div class="dependencies">
> + <p>This workflow depends on the following:
> + <br />
> +
> + <ul>
> + <li>
> + <%= icon('blob', nil, nil, nil, '') %>
> + <a href="http://www.myexperiment.org/files/306";>KEGG Compounds
> to Inchi strings</a>
> + </li>
> + <li>
> + <span class="icon"><img src="/images/famfamfam_silk/link.png"
> /></span>
> + <a href="http://www.mathworks.com/products/matlab";>Matlab</a>
> + </li>
> + </ul>
> + </p>
> + </div>
> +
> + <h3>
> + <%= info_icon_with_tooltip("This section
> provides links to the
> +different downloads for this version of the Workflow") %>
> Download
> </h3>
>
> @@ -271,6 +443,23 @@
>
> <%= render :partial => "contributions/credits_attributions_box",
> :locals => { :contributable => @workflow, :edit_path =>
> edit_workflow_path(@workflow) } %>
>
> +<div class="contribution_section_box">
> + <p class="heading" style="margin-bottom: 0; padding-bottom: 0;">
> + <%= info_icon_with_tooltip("Which people/groups get the credit
> for this?") %>
> + Scope and Quality
> + </p>
> + <div style="font-size: 85%;">
> + <p>The scope and quality of this Workflow has been classified by
> +our curators as:</p>
> + </div>
> + <br />
> + <div class="quality"><a href="">Example</a></div>
> + <div class="quality"><a href="">Component</a></div>
> + <br />
> + <div style="font-size: 85%;">
> + <a href="">See breakdown</a>
> + </div>
> +</div>
> +
> <%= render :partial => "tags/tags_box", :locals => { :taggable =>
> @workflow,
>
>
> :owner_id =>
> ((@workflow.contribution.contributor_type == 'User') ?
> @workflow.contribution.contributor_id : nil),
>
>
> :add_path =>
> tag_workflow_path(@workflow),
>
>
> Modified: trunk/lib/explicit_versioning.rb (2294 => 2295)
>
>
> --- trunk/lib/explicit_versioning.rb 2009-11-09 15:50:47 UTC (rev 2294)
> +++ trunk/lib/explicit_versioning.rb 2009-11-10 13:52:47 UTC (rev 2295)
> @@ -47,6 +47,12 @@
> # create the dynamic versioned model
> const_set(versioned_class_name,
> Class.new(ActiveRecord::Base)).class_eval do
> def self.reloadable? ; false ; end
> +
> + after_update :sync_main_record
> +
> + def sync_main_record
> + # If this is the current version, update the main record with
> it
> + end
> end
>
> versioned_resource = self.to_s.demodulize.underscore.to_sym
>
>
> Modified: trunk/lib/rest.rb (2294 => 2295)
>
>
> --- trunk/lib/rest.rb 2009-11-09 15:50:47 UTC (rev 2294)
> +++ trunk/lib/rest.rb 2009-11-10 13:52:47 UTC (rev 2295)
> @@ -757,7 +757,11 @@
> return nil
> end
>
> - resource = resource.find_version(version) if version
> + if version
> + if resource.versions.last.version != version.to_i
> + resource = resource.find_version(version)
> + end
> + end
>
> if resource.nil?
> rest_response(404)
> @@ -956,9 +960,7 @@
> end
> end
>
> - if query['version']
> - ob = ob.versioned_resource
> - end
> + ob = ob.versioned_resource if ob.respond_to?("versioned_resource")
>
> rest_get_request(ob, "workflow", user,
> rest_resource_uri(ob), "workflow", { "id" => ob.id.to_s })
>
>
> Modified: trunk/public/stylesheets/styles.css (2294 => 2295)
>
>
> --- trunk/public/stylesheets/styles.css 2009-11-09 15:50:47 UTC (rev
> 2294)
> +++ trunk/public/stylesheets/styles.css 2009-11-10 13:52:47 UTC (rev
> 2295)
> @@ -1985,3 +1985,23 @@
> white-space: nowrap;
> }
>
> +.classification {
> + border: 1px SOLID gray;
> + padding: 3px;
> + padding-left: 6px;
> + padding-right: 6px;
> + background: #ffffd0;
> +}
> +
> +.quality {
> + width: 90%;
> + background: #EEA;
> + border: 1px solid #CCCCAA;
> + margin: 4px;
> + padding: 4px;
> +}
> +
> +.dependencies UL LI {
> + list-style-type: none;
> +}
> +
>
>
> Modified: trunk/test/functional/workflows_controller_test.rb
> (2294 => 2295)
>
>
> --- trunk/test/functional/workflows_controller_test.rb 2009-11-09
> 15:50:47 UTC (rev 2294)
> +++ trunk/test/functional/workflows_controller_test.rb 2009-11-10
> 13:52:47 UTC (rev 2295)
> @@ -5,6 +5,7 @@
>
> require File.dirname(__FILE__) + '/../test_helper'
> require 'workflows_controller'
> +require 'xml/libxml'
>
> # Re-raise errors caught by the controller.
> class WorkflowsController; def rescue_action(e) raise e end; end @@
> -80,4 +81,27 @@
> assert_equal old_count-1, Workflow.count
> assert_redirected_to workflows_path
> end
> +
> + def test_workflow_api
> + login_as(:john)
> +
> + content = LibXML::XML::Node.new("content") <<
> +
> + Base64.encode64(File.read('test/fixtures/files/workflow_dilbert.xml'
> + ))
> +
> + content["encoding"] = "base64"
> +
> + doc = LibXML::XML::Document.new
> + doc.root = LibXML::XML::Node.new("workflow")
> +
> + {
> + "title" => "Test title",
> + "description" => "Test description.",
> + "license-type" => "by-sa",
> + "content-type" => "application/vnd.taverna.scufl+xml",
> + "content" => content
> + }.each do |k, v|
> + doc.root << (LibXML::XML::Node.new(k) << v)
> + end
> +
> + end
> end
> ----------------------------------------------------------------------
> --
>
> _______________________________________________
> myexperiment-hackers mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/myexperiment-hackers
>
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