# HG changeset patch --
Bitbucket.org
# Project galaxy-dist
# URL
http://bitbucket.org/galaxy/galaxy-dist/overview
# User Dannon Baker <dannon.baker(a)emory.edu>
# Date 1278796427 14400
# Node ID e65936a1fa4923925a7a5c3848c9ced7c1ad883f
# Parent 19e07ef6eb25ea4bd1531ba42c2187f3f5d384d6
# Parent 2d046444998edb1c4a5126897990bddd25de69f5
Merge
--- a/templates/admin/requests/show_request.mako
+++ /dev/null
@@ -1,528 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/requests/sample_state.mako"
import="render_sample_state" />
-<%namespace file="/requests/sample_datasets.mako"
import="render_sample_datasets" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem(
'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ','
);
- var last_selected_value = $( this )[0].attributes.getNamedItem(
'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || (
last_selected_value && last_selected_value.value == refresh_on_change_values[i] )
){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#show_request" ).submit();
- }
- });
-});
-</script>
-
-
-<script type="text/javascript">
-$(document).ready(function(){
- //hide the all of the element with class msg_body
- $(".msg_body").hide();
- //toggle the componenet with class msg_body
- $(".msg_head").click(function(){
- $(this).next(".msg_body").slideToggle(450);
- });
-});
-</script>
-
-<script type="text/javascript">
- // Looks for changes in sample states using an async request. Keeps
- // calling itself (via setTimeout) until all samples are in a terminal
- // state.
- var updater = function ( sample_states ) {
- // Check if there are any items left to track
- var empty = true;
- for ( i in sample_states ) {
- empty = false;
- break;
- }
- if ( ! empty ) {
- setTimeout( function() { updater_callback( sample_states ) }, 1000 );
- }
- };
- var updater_callback = function ( sample_states ) {
- // Build request data
- var ids = []
- var states = []
- $.each( sample_states, function ( id, state ) {
- ids.push( id );
- states.push( state );
- });
- // Make ajax call
- $.ajax( {
- type: "POST",
- url: "${h.url_for( controller='requests_admin',
action='sample_state_updates' )}",
- dataType: "json",
- data: { ids: ids.join( "," ), states: states.join( "," )
},
- success : function ( data ) {
- $.each( data, function( id, val ) {
- // Replace HTML
- var cell1 = $("#sampleState-" + id);
- cell1.html( val.html_state );
- var cell2 = $("#sampleDatasets-" + id);
- cell2.html( val.html_datasets );
- sample_states[ parseInt(id) ] = val.state;
- });
- updater( sample_states );
- },
- error: function() {
- // Just retry, like the old method, should try to be smarter
- updater( sample_states );
- }
- });
- };
-</script>
-
-<style type="text/css">
-.msg_head {
- padding: 0px 0px;
- cursor: pointer;
-}
-</style>
-
-<script type="text/javascript">
- function stopRKey(evt) {
- var evt = (evt) ? evt : ((event) ? event : null);
- var node = (evt.target) ? evt.target : ((evt.srcElement) ? evt.srcElement : null);
- if ((evt.keyCode == 13) && (node.type=="text")) {return false;}
- }
- document.onkeypress = stopRKey
-</script>
-
-%if request.submitted():
- <% samples_not_ready = request.sequence_run_ready() %>
- %if samples_not_ready:
- ${render_msg( "Select a target library and folder for all the samples before
starting the sequence run", "warning" )}
- %endif
-%endif
-
-%if request.rejected():
- ${render_msg( "Reason for rejection: "+request.last_comment(),
"warning" )}
-%endif
-
-<div class="grid-header">
- <h2>Sequencing Request "${request.name}"</h2>
-</div>
-
-<ul class="manage-table-actions">
-
- %if request.unsubmitted() and request.samples:
- <li>
- <a class="action-button" confirm="More samples cannot be
added to this request once it is submitted. Click OK to submit."
href="${h.url_for( controller='requests_admin', action='list',
operation='Submit', id=trans.security.encode_id(request.id) )}">
- <span>Submit request</span></a>
- </li>
- %endif
- %if request.submitted():
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list', operation='Reject',
id=trans.security.encode_id(request.id))}">
- <span>Reject request</span></a>
- </li>
- %endif
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list', operation='events',
id=trans.security.encode_id(request.id) )}">
- <span>History</span></a>
- </li>
-
-
-</ul>
-
-<%def name="show_basic_info_form( sample_index, sample, info )">
- <td>
- <input type="text" name=sample_${sample_index}_name
value="${info['name']}" size="10"/>
- <div class="toolParamHelp" style="clear: both;">
- <i>${' (required)' }</i>
- </div>
- </td>
- %if sample:
- %if sample.request.unsubmitted():
- <td></td>
- %else:
- <td><input type="text" name=sample_${sample_index}_barcode
value="${info['barcode']}" size="10"/></td>
- %endif
- %else:
- <td></td>
- %endif
- %if sample:
- %if sample.request.unsubmitted():
- <td>Unsubmitted</td>
- %else:
- <td><a href="${h.url_for( controller='requests_admin',
action='show_events',
sample_id=sample.id)}">${sample.current_state().name}</a></td>
- %endif
- %else:
- <td></td>
- %endif
- <td>${info['lib_widget'].get_html()}</td>
- <td>${info['folder_widget'].get_html()}</td>
- %if request.submitted() or request.complete():
- %if sample:
- <td><a href="${h.url_for( controller='requests_admin',
action='show_datatx_page', sample_id=trans.security.encode_id(sample.id)
)}">${len(sample.dataset_files)}</a></td>
- %else:
- <td><a href="${h.url_for( controller='requests_admin',
action='show_datatx_page', sample_id=trans.security.encode_id(sample.id)
)}">Add</a></td>
- %endif
- %endif
-</%def>
-
-## This function displays the "Basic Information" grid
-<%def name="render_basic_info_grid()">
- <h4>Sample Information</h4>
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- <th>Barcode</th>
- <th>State</th>
- <th>Data Library</th>
- <th>Folder</th>
- %if request.submitted() or request.complete():
- <th>Dataset(s) Transferred</th>
- %endif
- <th></th>
- </tr>
- <thead>
- <tbody>
- <%
- trans.sa_session.refresh( request )
- %>
- %for sample_index, info in enumerate(current_samples):
- <%
- if sample_index in range(len(request.samples)):
- sample = request.samples[sample_index]
- else:
- sample = None
- %>
- %if edit_mode == 'True':
- <tr>
- ${show_basic_info_form( sample_index, sample, info )}
- </tr>
- %else:
- <tr>
- %if sample_index in range(len(request.samples)):
- <td>${info['name']}</td>
- <td>${info['barcode']}</td>
- %if sample.request.unsubmitted():
- <td>Unsubmitted</td>
- %else:
- <td
id="sampleState-${sample.id}">${render_sample_state( sample )}</td>
- %endif
-
-## <td>
-## %if sample:
-## %if sample.request.unsubmitted():
-## Unsubmitted
-## %else:
-## <a href="${h.url_for(
controller='requests_admin', action='show_events',
sample_id=sample.id)}">${sample.current_state().name}</a>
-## %endif
-## %endif
-## </td>
- %if info['library']:
- <td><a href="${h.url_for(
controller='library_common', action='browse_library',
cntrller='library', id=trans.security.encode_id( info['library'].id )
)}">${info['library'].name}</a></td>
- %else:
- <td></td>
- %endif
- %if info['folder']:
- <td>${info['folder'].name}</td>
- %else:
- <td></td>
- %endif
- %if request.submitted() or request.complete():
- <td id="sampleDatasets-${sample.id}">
- ${render_sample_datasets( sample )}
-## <a href="${h.url_for(
controller='requests_admin', action='show_datatx_page',
sample_id=trans.security.encode_id(sample.id)
)}">${len(sample.dataset_files)}</a>
- </td>
- %endif
-
-
- %else:
- ${show_basic_info_form( sample_index, sample, info )}
- %endif
- %if request.unsubmitted() or request.rejected():
- <td>
- %if sample:
- %if sample.request.unsubmitted():
- <a class="action-button"
href="${h.url_for( controller='requests_admin',
action='delete_sample', request_id=request.id, sample_id=sample_index
)}">
- <img
src="${h.url_for('/static/images/delete_icon.png')}" />
- <span></span></a>
- %endif
- %endif
- </td>
- %endif
- </tr>
- %endif
- %endfor
- </tbody>
- </table>
-</%def>
-
-<%def name="render_sample_form( index, sample_name, sample_values, fields_dict
)">
- <td>
- ${sample_name}
- </td>
- %for field_index, field in fields_dict.items():
- <td>
- %if field['type'] == 'TextField':
- <input type="text"
name="sample_${index}_field_${field_index}"
value="${sample_values[field_index]}" size="7"/>
- %elif field['type'] == 'SelectField':
- <select name="sample_${index}_field_${field_index}"
last_selected_value="2">
- %for option_index, option in enumerate(field['selectlist']):
- %if option == sample_values[field_index]:
- <option value="${option}"
selected>${option}</option>
- %else:
- <option
value="${option}">${option}</option>
- %endif
- %endfor
- </select>
- %elif field['type'] == 'WorkflowField':
- <select name="sample_${index}_field_${field_index}">
- %if str(sample_values[field_index]) == 'none':
- <option value="none" selected>Select
one</option>
- %else:
- <option value="none">Select one</option>
- %endif
- %for option_index, option in
enumerate(request.user.stored_workflows):
- %if not option.deleted:
- %if str(option.id) == str(sample_values[field_index]):
- <option value="${option.id}"
selected>${option.name}</option>
- %else:
- <option
value="${option.id}">${option.name}</option>
- %endif
- %endif
- %endfor
- </select>
- %elif field['type'] == 'CheckboxField':
- <input type="checkbox"
name="sample_${index}_field_${field_index}" value="Yes"/>
- %endif
- <div class="toolParamHelp" style="clear: both;">
- <i>${'('+field['required']+')' }</i>
- </div>
- </td>
- %endfor
-</%def>
-
-<%def name="render_sample( index, sample_name, sample_values, fields_dict
)">
- <td>
- ${sample_name}
- </td>
- %for field_index, field in fields_dict.items():
- <td>
- %if sample_values[field_index]:
- %if field['type'] == 'WorkflowField':
- %if str(sample_values[field_index]) != 'none':
- <% workflow = trans.sa_session.query(
trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %>
- <a href="${h.url_for( controller='workflow',
action='run', id=trans.security.encode_id(workflow.id)
)}">${workflow.name}</a>
- %endif
- %else:
- ${sample_values[field_index]}
- %endif
- %else:
- <i>None</i>
- %endif
- </td>
- %endfor
-</%def>
-
-<div class="toolForm">
- <div class="form-row">
- <div class="msg_list">
- <h4 class="msg_head"><u>Request
Information</u></h4>
- <div class="msg_body">
- %for index, rd in enumerate(request_details):
- <div class="form-row">
- <label>${rd['label']}</label>
- %if not rd['value']:
- <i>None</i>
- %else:
- %if rd['label'] == 'State':
- <a href="${h.url_for(
controller='requests_admin', action='list', operation='events',
id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
- %else:
- ${rd['value']}
- %endif
- %endif
- </div>
- <div style="clear: both"></div>
- %endfor
- <div class="form-row">
- <ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list', operation='Edit',
id=trans.security.encode_id(request.id))}">
- <span>Edit request details</span></a>
- </li>
- </ul>
- </div>
- </div>
- </div>
- </div>
-</div>
-
-<br/>
-
-
-<%def name="render_grid( grid_index, grid_name, fields_dict )">
- <br/>
- <div class="msg_list">
- %if grid_name:
- <h4 class="msg_head"><u>${grid_name}</u></h4>
- %else:
- <h4>Grid ${grid_index}</h4>
- %endif
- %if edit_mode == 'False' or len(current_samples) <= len(request.samples):
- <div class="msg_body">
- %else:
- <div class="msg_body2">
- %endif
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- %for index, field in fields_dict.items():
- <th>
- ${field['label']}
- <div class="toolParamHelp" style="clear:
both;">
- <i>${field['helptext']}</i>
- </div>
- </th>
- %endfor
- <th></th>
- </tr>
- <thead>
- <tbody>
- <%
- trans.sa_session.refresh( request )
- %>
- %for sample_index, sample in enumerate(current_samples):
- %if edit_mode == 'True':
- <tr>
- ${render_sample_form( sample_index, sample['name'],
sample['field_values'], fields_dict)}
- </tr>
- %else:
- <tr>
- %if sample_index in range(len(request.samples)):
- ${render_sample( sample_index, sample['name'],
sample['field_values'], fields_dict )}
- %else:
- ${render_sample_form( sample_index, sample['name'],
sample['field_values'], fields_dict)}
- %endif
- </tr>
- %endif
- %endfor
- </tbody>
- </table>
- </div>
- </div>
-</%def>
-
-<div class="toolForm">
- ##<div class="toolFormTitle">Samples
(${len(request.samples)})</div>
- <form id="show_request" name="show_request"
action="${h.url_for( controller='requests_admin',
action='show_request', edit_mode=edit_mode )}"
enctype="multipart/form-data" method="post" >
- <div class="form-row">
- %if current_samples:
- ## first render the basic info grid
- ${render_basic_info_grid()}
- ## then render the other grid(s)
- <% trans.sa_session.refresh( request.type.sample_form ) %>
- %for grid_index, grid_name in
enumerate(request.type.sample_form.layout):
- ${render_grid( grid_index, grid_name,
request.type.sample_form.fields_of_grid( grid_index ) )}
- <br/>
- %endfor
- %else:
- <label>There are no samples.</label>
- %endif
- </div>
- %if request.samples and request.submitted():
- <script type="text/javascript">
- // Updater
- updater({${ ",".join( [ '"%s" :
"%s"' % ( s.id, s.current_state().name ) for s in request.samples ] ) }});
- </script>
- %endif
-
- %if edit_mode == 'False':
- <table class="grid">
- <tbody>
- <tr>
- <div class="form-row">
-
- %if request.unsubmitted():
- <td>
- %if current_samples:
- <label>Copy </label>
- <input type="integer"
name="num_sample_to_copy" value="1" size="3"/>
- <label>sample(s) from sample</label>
- ${sample_copy.get_html()}
- %endif
- <input type="submit"
name="add_sample_button" value="Add New"/>
- </td>
- %endif
- <td>
- %if len(current_samples) and len(current_samples) <=
len(request.samples):
- <input type="submit"
name="edit_samples_button" value="Edit samples"/>
- %endif
- </td>
- </div>
- </tr>
- </tbody>
- </table>
- %endif
- %if request.samples or current_samples:
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right:
10px;">
- <input type="hidden" name="refresh"
value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- %if edit_mode == 'True':
- <div class="form-row">
- <input type="submit"
name="save_samples_button" value="Save"/>
- <input type="submit"
name="cancel_changes_button" value="Cancel"/>
- </div>
- %elif request.unsubmitted():
- <div class="form-row">
- <input type="submit"
name="save_samples_button" value="Save"/>
- </div>
- %endif
-
- %endif
- <input type="hidden" name="request_id"
value="${request.id}" />
- </form>
-</div>
-
-<br/>
-
-%if request.unsubmitted():
-<div class="toolForm">
- <form id="show_request" name="show_request"
action="${h.url_for( controller='requests_admin',
action='show_request', edit_mode=edit_mode )}"
enctype="multipart/form-data" method="post" >
- <div class="form-row">
- <div class="msg_list">
- <h4 class="msg_head"><u>Import samples from csv
file</u></h4>
- <div class="msg_body">
- <input type="file" name="file_data" />
- <input type="submit"
name="import_samples_button" value="Import samples"/>
- <br/>
- <div class="toolParamHelp" style="clear:
both;">
- The csv file must be in the following format:<br/>
-
SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
- </div>
- </div>
- </div>
- </div>
- <input type="hidden" name="request_id"
value="${request.id}" />
- </form>
-</div>
-%endif
-
--- a/templates/admin/samples/events.mako
+++ /dev/null
@@ -1,63 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<%def name="title()">Events for Sample ${sample.name}</%def>
-
-<h2>Events for Sample "${sample.name}"</h2>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list',
operation='show_request', id=trans.security.encode_id(sample.request.id)
)}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-<h3>User: ${sample.request.user.email}</h3>
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <table class="grid">
- <thead>
- <tr>
- <th>State</th>
- <th>Description</th>
- <th>Last Update</th>
- <th>Comments</th>
- </tr>
- </thead>
- <tbody>
- %for state, desc, updated, comments in events_list:
- <tr class="libraryRow libraryOrFolderRow"
id="libraryRow">
- <td><b><a>${state}</a></b></td>
- <td><a>${desc}</a></td>
- <td><a>${updated}</a></td>
- <td><a>${comments}</a></td>
- </tr>
- %endfor
- </tbody>
- </table>
-</div>
-<div class="toolForm">
- <div class="toolFormTitle">Change current state</div>
- <div class="toolFormBody">
- <form name="event" action="${h.url_for(
controller='requests_admin', action='save_state', new=True,
sample_id=sample.id)}" method="post" >
- %for w in widgets:
- <div class="form-row">
- <label>
- ${w[0]}
- </label>
- ${w[1].get_html()}
- %if w[0] == 'Comments':
- <div class="toolParamHelp" style="clear:
both;">
- Optional
- </div>
- %endif
- </div>
- %endfor
- <div class="form-row">
- <input type="submit" name="add_event_button"
value="Save"/>
- </div>
- </form>
- </div>
-</div>
--- a/tool-data/shared/bx/bx_build_sites.txt
+++ /dev/null
@@ -1,1 +0,0 @@
-main
http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks? hg18,hg19,mm8,mm9 bx-main
--- a/static/trackster.css
+++ /dev/null
@@ -1,132 +0,0 @@
-#content {
- width: 100%;
-}
-
-#center {
- overflow: auto;
-}
-
-#nav-container {
- position: fixed;
- left: 0;
- bottom: 0;
-}
-
-/*canvas{
- border-left: 1px solid green;
- border-right: 1px solid red; } /* debugging */
-#nav {
- padding: 0 0;
- color:#333;font-weight:bold;
-}
-
-#nav-controls {
- text-align: center;
- background:#cccccc;
- background-image:url(style/panel_header_bg.png);
- background-position:top center;
- background-repeat:repeat-x;
- padding-bottom: 5px;
-}
-
-#nav-controls a {
- padding: 5px 0.4em;
-}
-
-#overview {
- width: 100%;
- margin: 0px;
- color: white;
- margin-top: -6px;
- margin-bottom: -4px;
-}
-
-#overview-viewport {
- position: relative;
- height: 14px;
-/* border-top: solid #666 1px;*/
-/* border-bottom: solid #aaa 1px;*/
- background: white;
- border-top: solid gray 1px;
- border-bottom: solid gray 1px;
- margin: 5px 0;
-}
-#overview-box {
- position: absolute;
- margin-top: 0px;
- height: 14px;
- background: #ddd url(images/visualization/draggable_horizontal.png) center center
no-repeat;
- /*border-style: outset;*/
-}
-
-#viewport {
-/* overflow-x: hidden;*/
- background-color: #fff;
-/* overflow: scroll;*/
-/* border-bottom: 2px solid black;*/
-}
-
-#viewport-canvas {
- width: 100%;
- height: 100px;
-}
-
-.yaxislabel {
- color: #777;
-}
-/* Line track needs borders to show range */
-.line-track .track-content {
- border-top: 1px solid #ddd;
- border-bottom: 1px solid #ddd;
-}
-
-.track {
- /* border-top: solid #DDDDDD 1px; */
- /* border-bottom: solid #DDDDDD 1px; */
- background: white;
-}
-
-.track-header {
- text-align: center;
- padding: 4px;
- color: #666;
-}
-
-.track-content {
- overflow: hidden;
- text-align: center;
-}
-
-.track.error {
- background-color: #ECB4AF;
-}
-.track.nodata {
- background-color: #ddd;
-}
-
-.loading {
- min-height: 100px;
-}
-
-.label-track {
- /* font-weight: bold; */
- /* font-size: 10px; */
-}
-.label-track .label {
- border-left: solid #999 1px;
- padding: 1px;
- display: inline-block;
-}
-.right-float {
- float: right;
- margin-left: 5px;
-}
-
-#top-labeltrack {
- border-bottom: solid #999 1px;
-}
-
-#nav-labeltrack {
- border-top: solid #999 1px;
- border-bottom: solid #999 1px;
-}
--- a/templates/requests/sample_state.mako
+++ /dev/null
@@ -1,5 +0,0 @@
-<%def name="render_sample_state( sample )">
- <a href="${h.url_for( controller='requests_admin',
action='show_events',
sample_id=sample.id)}">${sample.current_state().name}</a>
-</%def>
-
-${render_sample_state( sample )}
--- a/templates/admin/samples/bar_codes.mako
+++ /dev/null
@@ -1,46 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-
-<h2>Bar codes for Samples of Request "${request.name}"</h2>
-<h3>User: ${user.email}</h3>
-
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list',
operation='show_request', id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <form name="bar_codes" action="${h.url_for(
controller='requests_admin', action='save_bar_codes',
request_id=request.id)}" method="post" >
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- <th>Description</th>
- <th>Bar code</th>
- </tr>
- </thead>
- <tbody>
- %for index, sample in enumerate(samples_list):
- <tr class="libraryRow libraryOrFolderRow"
id="libraryRow">
-
<td><b><a>${sample.name}</a></b></td>
- <td><a>${sample.desc}</a></td>
- <td>
- ${widgets[index].get_html()}
- </td>
- </tr>
- %endfor
- </tbody>
- </table>
- <div class="form-row">
- <input type="submit" name="save_bar_codes"
value="Save"/>
- </div>
- </form>
-</div>
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -1251,7 +1251,9 @@ class Admin( object ):
# sort filter instead of this class's.
kwargs[ 'user_id' ] = kwargs[ 'id' ]
kwargs[ 'sort' ] = 'name'
- return self.browse_tools( trans, **kwargs )
+ return trans.response.send_redirect( web.url_for(
controller='admin',
+
action='browse_tools',
+ **kwargs ) )
# Render the list view
return self.user_list_grid( trans, **kwargs )
@web.expose
--- a/templates/requests/edit_request.mako
+++ /dev/null
@@ -1,84 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem(
'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ','
);
- var last_selected_value = $( this )[0].attributes.getNamedItem(
'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || (
last_selected_value && last_selected_value.value == refresh_on_change_values[i] )
){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#edit_request" ).submit();
- }
- });
-});
-</script>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <div class="toolFormTitle">Edit request
"${request.name}"</div>
- %if len(select_request_type.options) == 1:
- There are no request types created for a new request.
- %else:
- <div class="toolFormBody">
- <form name="edit_request" id="edit_request"
action="${h.url_for( controller='requests', action='edit',
request_id=request.id)}" method="post" >
- <div class="form-row">
- <label>
- Select Request Type:
- </label>
- ${select_request_type.get_html()}
- </div>
-
- %if select_request_type.get_selected() != ('Select one',
'none'):
- %for i, field in enumerate(widgets):
- <div class="form-row">
- <label>${field['label']}</label>
- ${field['widget'].get_html()}
- %if field['label'] == 'Data library' and
new_library:
- ${new_library.get_html()}
- %endif
- <div class="toolParamHelp" style="clear:
both;">
- ${field['helptext']}
- </div>
- <div style="clear: both"></div>
- </div>
- %endfor
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right:
10px;">
- <input type="hidden" name="refresh"
value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit"
name="save_changes_request_button" value="Save changes"/>
- ##<input type="submit"
name="edit_samples_button" value="Edit samples"/>
- </div>
- %endif
- </form>
- </div>
-</div>
-%endif
--- a/templates/root/index.mako
+++ b/templates/root/index.mako
@@ -43,9 +43,9 @@
"Show structure": function() {
galaxy_main.location = "${h.url_for( controller='history',
action='display_structured' )}";
},
- "Export to File": function() {
- galaxy_main.location = "${h.url_for( controller='history',
action='export_archive' )}";
- },
+ ##"Export to File": function() {
+ ## galaxy_main.location = "${h.url_for( controller='history',
action='export_archive' )}";
+ ##},
"Delete": function()
{
if ( confirm( "Really delete the current history?" ) )
@@ -53,10 +53,10 @@
galaxy_main.location = "${h.url_for(
controller='history', action='delete_current' )}";
}
},
- "Other Actions": null,
- "Import from File": function() {
- galaxy_main.location = "${h.url_for( controller='history',
action='import_archive' )}";
- }
+ ##"Other Actions": null,
+ ##"Import from File": function() {
+ ## galaxy_main.location = "${h.url_for( controller='history',
action='import_archive' )}";
+ ##}
});
// Init tool options.
--- a/templates/requests/new_request.mako
+++ /dev/null
@@ -1,94 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem(
'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ','
);
- var last_selected_value = $( this )[0].attributes.getNamedItem(
'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || (
last_selected_value && last_selected_value.value == refresh_on_change_values[i] )
){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#new_request" ).submit();
- }
- });
-});
-</script>
-
-<%def name="javascripts()">
- ${parent.javascripts()}
- ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
-</%def>
-
-<%def name="stylesheets()">
- ${parent.stylesheets()}
- ${h.css( "autocomplete_tagging" )}
-</%def>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <div class="toolFormTitle">Add a new request</div>
- %if len(select_request_type.options) == 1:
- There are no request types created for a new request.
- %else:
- <div class="toolFormBody">
- <form name="new_request" id="new_request"
action="${h.url_for( controller='requests', action='new', create=True
)}" method="post" >
- <div class="form-row">
- <label>
- Select Request Type:
- </label>
- ${select_request_type.get_html()}
- </div>
-
- %if select_request_type.get_selected() != ('Select one',
'none'):
- %for i, field in enumerate(widgets):
- <div class="form-row">
- <label>${field['label']}</label>
- ${field['widget'].get_html()}
- ##%if field['label'] == 'Data library' and
new_library:
- ## ${new_library.get_html()}
- ##%endif
- <div class="toolParamHelp" style="clear:
both;">
- ${field['helptext']}
- </div>
- <div style="clear: both"></div>
- </div>
- %endfor
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right:
10px;">
- <input type="hidden" name="refresh"
value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit"
name="create_request_button" value="Save"/>
- <input type="submit"
name="create_request_samples_button" value="Add samples"/>
- </div>
- %endif
- </form>
- </div>
-</div>
-%endif
--- a/lib/galaxy/util/memory_usage.py
+++ /dev/null
@@ -1,44 +0,0 @@
-import os, platform, logging
-from galaxy.datatypes.data import nice_size
-
-log = logging.getLogger( __name__ )
-
-_proc_status = '/proc/%d/status' % os.getpid()
-
-_scale = { 'kB': 1024.0, 'mB': 1024.0*1024.0, 'KB': 1024.0,
'MB': 1024.0*1024.0 }
-
-def _VmB( VmKey ):
- '''Private.
- '''
- global _proc_status, _scale
- # get pseudo file /proc/<pid>/status
- try:
- t = open( _proc_status )
- v = t.read()
- t.close()
- except:
- log.debug("memory_usage is currently supported only on Linux, your platform
is %s %s" % ( platform.system(), platform.release() ) )
- return 0.0 # non-Linux?
- # get VmKey line e.g. 'VmRSS: 9999 kB\n ...'
- i = v.index( VmKey )
- v = v[ i: ].split( None, 3 ) # whitespace
- if len( v ) < 3:
- return 0.0 # invalid format?
- # convert Vm value to bytes
- return float( v[ 1 ] ) * _scale[ v[ 2 ] ]
-def memory( since=0.0, pretty=False ):
- '''Return memory usage in bytes.
- '''
- size = _VmB( 'VmSize:' ) - since
- if pretty:
- return nice_size( size )
- else:
- return size
-def resident( since=0.0 ):
- '''Return resident memory usage in bytes.
- '''
- return _VmB( 'VmRSS:' ) - since
-def stacksize( since=0.0 ):
- '''Return stack size in bytes.
- '''
- return _VmB( 'VmStk:' ) - since
--- a/templates/sample/index.mako
+++ /dev/null
@@ -1,16 +0,0 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
-
-<%def name="init()">
-<%
- self.has_left_panel=False
- self.has_right_panel=False
- self.active_view="requests"
-
-%>
-</%def>
-
-<%def name="center_panel()">
-
- <iframe name="galaxy_main" id="galaxy_main"
frameborder="0" style="position: absolute; width: 100%; height: 100%;"
src="${h.url_for( controller="sample", action="list",
request_id=request_id )}"></iframe>
-
-</%def>
--- a/templates/requests/show_request.mako
+++ /dev/null
@@ -1,430 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem(
'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ','
);
- var last_selected_value = $( this )[0].attributes.getNamedItem(
'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || (
last_selected_value && last_selected_value.value == refresh_on_change_values[i] )
){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#show_request" ).submit();
- }
- });
-});
-</script>
-
-
-<script type="text/javascript">
-$(document).ready(function(){
- //hide the all of the element with class msg_body
- $(".msg_body").hide();
- //toggle the componenet with class msg_body
- $(".msg_head").click(function(){
- $(this).next(".msg_body").slideToggle(450);
- });
-});
-</script>
-<style type="text/css">
-.msg_head {
- padding: 0px 0px;
- cursor: pointer;
-}
-
-}
-</style>
-
-%if request.rejected():
- ${render_msg( "Reason for rejection: "+request.last_comment(),
"warning" )}
-%endif
-
-<div class="grid-header">
- <h2>Sequencing Request "${request.name}"</h2>
-</div>
-
-<ul class="manage-table-actions">
- %if request.unsubmitted() and request.samples:
- <li>
- <a class="action-button" confirm="More samples cannot be
added to this request once it is submitted. Click OK to submit."
href="${h.url_for( controller='requests', action='list',
operation='Submit', id=trans.security.encode_id(request.id) )}">
- <span>Submit request</span></a>
- </li>
- %endif
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='list', operation='events',
id=trans.security.encode_id(request.id) )}">
- <span>History</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<%def name="show_basic_info_form( sample_index, sample, info )">
- <td>
- <input type="text" name=sample_${sample_index}_name
value="${info['name']}" size="10"/>
- <div class="toolParamHelp" style="clear: both;">
- <i>${' (required)' }</i>
- </div>
- </td>
- %if sample:
- %if sample.request.unsubmitted():
- <td></td>
- %else:
- <td><input type="text" name=sample_${sample_index}_barcode
value="${info['barcode']}" size="10"/></td>
- %endif
- %else:
- <td></td>
- %endif
- %if sample:
- %if not sample.current_state():
- <td>Unsubmitted</td>
- %else:
- <td><a href="${h.url_for( controller='requests_admin',
action='show_events',
sample_id=sample.id)}">${sample.current_state().name}</a></td>
- %endif
- %else:
- <td></td>
- %endif
- <td>${info['lib_widget'].get_html()}</td>
- <td>${info['folder_widget'].get_html()}</td>
- %if request.submitted() or request.complete():
- %if sample:
- <td><a href="${h.url_for( controller='requests_admin',
action='show_datatx_page', sample_id=trans.security.encode_id(sample.id)
)}">${len(sample.dataset_files)}</a></td>
- %else:
- <td><a href="${h.url_for( controller='requests_admin',
action='show_datatx_page', sample_id=trans.security.encode_id(sample.id)
)}">Add</a></td>
- %endif
- %endif
-</%def>
-
-## This function displays the "Basic Information" grid
-<%def name="render_basic_info_grid()">
- <h4>Sample Information</h4>
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- <th>Barcode</th>
- <th>State</th>
- <th>Data Library</th>
- <th>Folder</th>
- %if request.submitted() or request.complete():
- <th>Dataset(s) Transferred</th>
- %endif
- <th></th>
- </tr>
- <thead>
- <tbody>
- <%
- trans.sa_session.refresh( request )
- %>
- %for sample_index, info in enumerate(current_samples):
- <%
- if sample_index in range(len(request.samples)):
- sample = request.samples[sample_index]
- else:
- sample = None
- %>
- %if edit_mode == 'True':
- <tr>
- ${show_basic_info_form( sample_index, sample, info )}
- </tr>
- %else:
- <tr>
- %if sample_index in range(len(request.samples)):
- <td>${info['name']}</td>
- <td>${info['barcode']}</td>
- <td>
- %if sample.current_state():
- <a href="${h.url_for(
controller='requests', action='show_events',
sample_id=sample.id)}">${sample.current_state().name}</a>
- %else:
- Unsubmitted
- %endif
- </td>
- %if info['library']:
- <td><a href="${h.url_for(
controller='library_common', action='browse_library',
cntrller='library', id=trans.security.encode_id( info['library'].id )
)}">${info['library'].name}</a></td>
- %else:
- <td></td>
- %endif
- %if info['folder']:
- <td>${info['folder'].name}</td>
- %else:
- <td></td>
- %endif
- %if request.submitted() or request.complete():
- <td>
- <a href="${h.url_for(
controller='requests', action='show_datatx_page',
sample_id=trans.security.encode_id(sample.id)
)}">${len(sample.dataset_files)}</a>
- </td>
- %endif
-
-
- %else:
- ${show_basic_info_form( sample_index, sample, info )}
- %endif
- %if request.unsubmitted() or request.rejected():
- <td>
- %if sample:
- %if sample.request.unsubmitted():
- <a class="action-button"
href="${h.url_for( controller='requests_admin',
action='delete_sample', request_id=request.id, sample_id=sample_index
)}">
- <img
src="${h.url_for('/static/images/delete_icon.png')}" />
- <span></span></a>
- %endif
- %endif
- </td>
- %endif
- </tr>
- %endif
- %endfor
- </tbody>
- </table>
-</%def>
-
-<%def name="render_sample_form( index, sample_name, sample_values, fields_dict
)">
- <td>
- ${sample_name}
- </td>
- %for field_index, field in fields_dict.items():
- <td>
- %if field['type'] == 'TextField':
- <input type="text"
name="sample_${index}_field_${field_index}"
value="${sample_values[field_index]}" size="7"/>
- %elif field['type'] == 'SelectField':
- <select name="sample_${index}_field_${field_index}"
last_selected_value="2">
- %for option_index, option in enumerate(field['selectlist']):
- %if option == sample_values[field_index]:
- <option value="${option}"
selected>${option}</option>
- %else:
- <option
value="${option}">${option}</option>
- %endif
- %endfor
- </select>
- %elif field['type'] == 'WorkflowField':
- <select name="sample_${index}_field_${field_index}">
- %if str(sample_values[field_index]) == 'none':
- <option value="none" selected>Select
one</option>
- %else:
- <option value="none">Select one</option>
- %endif
- %for option_index, option in
enumerate(request.user.stored_workflows):
- %if not option.deleted:
- %if str(option.id) == str(sample_values[field_index]):
- <option value="${option.id}"
selected>${option.name}</option>
- %else:
- <option
value="${option.id}">${option.name}</option>
- %endif
- %endif
- %endfor
- </select>
- %elif field['type'] == 'CheckboxField':
- <input type="checkbox"
name="sample_${index}_field_${field_index}" value="Yes"/>
- %endif
- <div class="toolParamHelp" style="clear: both;">
- <i>${'('+field['required']+')' }</i>
- </div>
- </td>
- %endfor
-</%def>
-
-<%def name="render_sample( index, sample_name, sample_values, fields_dict
)">
- <td>
- ${sample_name}
- </td>
- %for field_index, field in fields_dict.items():
- <td>
- %if sample_values[field_index]:
- %if field['type'] == 'WorkflowField':
- %if str(sample_values[field_index]) != 'none':
- <% workflow = trans.sa_session.query(
trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %>
- <a href="${h.url_for( controller='workflow',
action='run', id=trans.security.encode_id(workflow.id)
)}">${workflow.name}</a>
- %endif
- %else:
- ${sample_values[field_index]}
- %endif
- %else:
- <i>None</i>
- %endif
-
- </td>
- %endfor
-</%def>
-
-<%def name="render_grid( grid_index, grid_name, fields_dict )">
- <br/>
- <div class="msg_list">
- %if grid_name:
- <h4 class="msg_head"><u>${grid_name}</u></h4>
- %else:
- <h4>Grid ${grid_index}</h4>
- %endif
- %if edit_mode == 'False' or len(current_samples) <= len(request.samples):
- <div class="msg_body">
- %else:
- <div class="msg_body2">
- %endif
- <table class="grid">
- <thead>
- <tr>
- <th>Name</th>
- %for index, field in fields_dict.items():
- <th>
- ${field['label']}
- <div class="toolParamHelp" style="clear:
both;">
- <i>${field['helptext']}</i>
- </div>
- </th>
- %endfor
- <th></th>
- </tr>
- <thead>
- <tbody>
- <%
- trans.sa_session.refresh( request )
- %>
- %for sample_index, sample in enumerate(current_samples):
- %if edit_mode == 'True':
- <tr>
- ${render_sample_form( sample_index, sample['name'],
sample['field_values'], fields_dict)}
- </tr>
- %else:
- <tr>
- %if sample_index in range(len(request.samples)):
- ${render_sample( sample_index, sample['name'],
sample['field_values'], fields_dict )}
- %else:
- ${render_sample_form( sample_index, sample['name'],
sample['field_values'], fields_dict)}
- %endif
- </tr>
- %endif
- %endfor
- </tbody>
- </table>
- </div>
- </div>
-</%def>
-
-<div class="toolForm">
- <form id="request_details" name="request_details" >
- <div class="form-row">
- <div class="msg_list">
- <h4 class="msg_head"><u>Request
Information</u></h4>
- <div class="msg_body">
- %for index, rd in enumerate(request_details):
- <div class="form-row">
- <label>${rd['label']}</label>
- %if not rd['value']:
- <i>None</i>
- %else:
- %if rd['label'] == 'State':
- <a href="${h.url_for(
controller='requests_admin', action='list', operation='events',
id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
- %else:
- ${rd['value']}
- %endif
- %endif
- </div>
- <div style="clear: both"></div>
- %endfor
- <div class="form-row">
- <ul class="manage-table-actions">
- <li>
- <a class="action-button"
href="${h.url_for( controller='requests_admin', action='list',
operation='Edit', id=trans.security.encode_id(request.id))}">
- <span>Edit request details</span></a>
- </li>
- </ul>
- </div>
- </div>
- </div>
- </div>
- </form>
- <form id="show_request" name="show_request"
action="${h.url_for( controller='requests', action='show_request',
edit_mode=edit_mode )}" enctype="multipart/form-data"
method="post" >
- <div class="form-row">
- %if current_samples:
- ## first render the basic info grid
- ${render_basic_info_grid()}
- ## then render the other grid(s)
- <% trans.sa_session.refresh( request.type.sample_form ) %>
- %for grid_index, grid_name in
enumerate(request.type.sample_form.layout):
- ${render_grid( grid_index, grid_name,
request.type.sample_form.fields_of_grid( grid_index ) )}
- <br/>
- %endfor
- %else:
- <label>There are no samples.</label>
- %endif
- </div>
- %if request.unsubmitted() and edit_mode == 'False':
- <table class="grid">
- <tbody>
- <tr>
- <div class="form-row">
- <td>
- %if current_samples:
- <label>Copy </label>
- <input type="integer"
name="num_sample_to_copy" value="1" size="3"/>
- <label>sample(s) from sample</label>
- ${sample_copy.get_html()}
- %endif
- <input type="submit"
name="add_sample_button" value="Add New"/>
- </td>
- <td>
- %if len(current_samples) and len(current_samples) <=
len(request.samples):
- <input type="submit"
name="edit_samples_button" value="Edit samples"/>
- %endif
- </td>
- </div>
- </tr>
- </tbody>
- </table>
- %endif
- %if request.unsubmitted() and (request.samples or current_samples):
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right:
10px;">
- <input type="hidden" name="refresh"
value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="save_samples_button"
value="Save"/>
- %if edit_mode == 'True':
- <input type="submit"
name="cancel_changes_button" value="Cancel"/>
- %endif
- </div>
- %endif
- <input type="hidden" name="request_id"
value="${request.id}" />
- </form>
-</div>
-
-
-<br/>
-%if request.unsubmitted():
-<div class="toolForm">
- <form id="show_request" name="show_request"
action="${h.url_for( controller='requests', action='show_request',
edit_mode=edit_mode )}" enctype="multipart/form-data"
method="post" >
- <div class="form-row">
- <div class="msg_list">
- <h4 class="msg_head"><u>Import samples from csv
file</u></h4>
- <div class="msg_body">
- <input type="file" name="file_data" />
- <input type="submit"
name="import_samples_button" value="Import samples"/>
- <br/>
- <div class="toolParamHelp" style="clear:
both;">
- The csv file must be in the following format:<br/>
-
SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
- </div>
- </div>
- </div>
- </div>
- <input type="hidden" name="request_id"
value="${request.id}" />
- </form>
-</div>
-%endif
--- a/templates/admin/requests/get_data.mako
+++ /dev/null
@@ -1,227 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$(document).ready(function(){
- //hide the all of the element with class msg_body
- $(".msg_body").hide();
- //toggle the componenet with class msg_body
- $(".msg_head").click(function(){
- $(this).next(".msg_body").slideToggle(450);
- });
-});
-
-
-
-
-</script>
-
-<script type="text/javascript">
- function display_file_details(sample_id, folder_path)
- {
- var w = document.get_data.files_list.selectedIndex;
- var selected_value = document.get_data.files_list.options[w].value;
- var cell = $("#file_details");
- if(selected_value.charAt(selected_value.length-1) != '/')
- {
- // Make ajax call
- $.ajax( {
- type: "POST",
- url: "${h.url_for( controller='requests_admin',
action='get_file_details' )}",
- dataType: "json",
- data: { id: sample_id, folder_path:
document.get_data.folder_path.value+selected_value },
- success : function ( data ) {
- cell.html( '<label>'+data+'</label>' )
- }
- });
- }
- else
- {
- cell.html( '' )
- }
-
-
- }
-</script>
-
-<script type="text/javascript">
- function open_folder1(sample_id, folder_path)
- {
- var w = document.get_data.files_list.selectedIndex;
- var selected_value = document.get_data.files_list.options[w].value;
- var cell = $("#file_details");
- if(selected_value.charAt(selected_value.length-1) == '/')
- {
- document.get_data.folder_path.value =
document.get_data.folder_path.value+selected_value
- // Make ajax call
- $.ajax( {
- type: "POST",
- url: "${h.url_for( controller='requests_admin',
action='open_folder' )}",
- dataType: "json",
- data: { id: sample_id, folder_path: document.get_data.folder_path.value
},
- success : function ( data ) {
- document.get_data.files_list.options.length = 0
- for(i=0; i<data.length; i++)
- {
- var newOpt = new Option(data[i], data[i]);
- document.get_data.files_list.options[i] = newOpt;
- }
- //cell.html( '<label>'+data+'</label>' )
-
- }
- });
- }
- else
- {
- cell.html( '' )
- }
- }
-</script>
-
-
-<style type="text/css">
-.msg_head {
- padding: 0px 0px;
- cursor: pointer;
-}
-
-}
-</style>
-
-
-<h2>Data transfer from Sequencer</h2>
-<h3>Sample "${sample.name}" of Request
"${sample.request.name}"</h3>
-<br/>
-<br/>
-
-<ul class="manage-table-actions">
- %if sample.request.submitted() and sample.inprogress_dataset_files():
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='show_datatx_page',
sample_id=trans.security.encode_id(sample.id) )}">
- <span>Refresh this page</span></a>
- </li>
- %endif
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='manage_request_types',
operation='view', id=trans.security.encode_id(sample.request.type.id)
)}">
- <span>Sequencer information</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for(
controller='library_common', action='browse_library',
cntrller='library_admin', id=trans.security.encode_id( sample.library.id )
)}">
- <span>${sample.library.name} Data Library</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list',
operation='show_request', id=trans.security.encode_id(sample.request.id)
)}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- %if len(dataset_files):
-## <form name="get_data" action="${h.url_for(
controller='requests_admin', action='get_data',
sample_id=sample.id)}" method="post" >
- <div class="form-row">
- <h4>Sample Dataset(s)</h4>
- %if sample.untransferred_dataset_files():
- <div class="form-row">
- <ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='get_data',
start_transfer_button=True, sample_id=sample.id )}">
- <span>Start transfer</span></a>
- </li>
- </ul>
- </div>
- %endif
- <div class="form-row">
- <table class="grid">
- <thead>
- <tr>
- <th>Dataset File</th>
- <th>Transfer Status</th>
- <th></th>
- </tr>
- <thead>
- <tbody>
- %for dataset_index, dataset_file in enumerate(dataset_files):
- ${sample_dataset_files( dataset_index,
dataset_file['name'], dataset_file['status'] )}
- %endfor
- </tbody>
- </table>
- </div>
- </div>
-
-## </form>
-##</div>
-
-
-<br/>
-<br/>
-%endif
-
-##<div class="toolForm">
- <form name="get_data" id="get_data" action="${h.url_for(
controller='requests_admin', action='get_data',
sample_id=sample.id)}" method="post" >
- <div class="form-row">
- ##<div class="toolFormTitle">Select files for
transfer</div>
- <h4>Select files for transfer</h4>
- <div style="width: 60%;">
- <div class="form-row">
- <label>Folder path on the sequencer:</label>
- <input type="text" name="folder_path"
value="${folder_path}" size="100"/>
- <input type="submit" name="browse_button"
value="List contents"/>
- ##<input type="submit" name="open_folder"
value="Open folder"/>
- <input type="submit" name="folder_up"
value="Up"/>
- </div>
- <div class="form-row">
- <select name="files_list" id="files_list"
style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;"
ondblclick="open_folder1(${sample.id}, '${folder_path}')"
onChange="display_file_details(${sample.id}, '${folder_path}')"
multiple>
- %for index, f in enumerate(files):
- <option value="${f}">${f}</option>
- %endfor
- </select>
- <br/>
- <div id="file_details" class="toolParamHelp"
style="clear: both;">
-
- </div>
- </div>
- <div class="form-row">
- <div class="toolParamHelp" style="clear:
both;">
- After selecting dataset(s), be sure to click on the
<b>Start transfer</b> button.
- Once the transfer is complete the dataset(s) will show up on this
page.
- </div>
- <input type="submit"
name="select_files_button" value="Select"/>
- </div>
- </div>
- </div>
- </form>
-</div>
-
-<%def name="sample_dataset_files( dataset_index, dataset_name, status
)">
- <tr>
- <td>
- <label class="msg_head"><a href="${h.url_for(
controller='requests_admin', action='dataset_details',
sample_id=trans.security.encode_id(sample.id), dataset_index=dataset_index
)}">${dataset_name}</a></label>
-## <div
class="msg_head"><u>${dataset_file.split('/')[-1]}</u></div>
-## <div class="msg_body">
-## ${dataset_file}
-## </div>
- </td>
- <td>
- %if status not in [sample.transfer_status.NOT_STARTED,
sample.transfer_status.COMPLETE]:
- <i>${status}</i>
- %else:
- ${status}
- %endif
- </td>
- ##<td></td>
- %if status == sample.transfer_status.NOT_STARTED:
- <td>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='get_data', sample_id=sample.id,
remove_dataset_button=True, dataset_index=dataset_index )}">
- <img
src="${h.url_for('/static/images/delete_icon.png')}" />
- <span></span></a>
- </td>
- %else:
- <td></td>
- %endif
- </tr>
-</%def>
--- a/templates/admin/requests/add_states.mako
+++ /dev/null
@@ -1,26 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <div class="toolFormTitle">Create ${num_states} states for the
'${request_type_name}' request type</div>
- <form name="new_form_fields" action="${h.url_for(
controller='requests_admin', action='request_type',
name=request_type_name, description=desc, num_states=num_states,
request_form_id=request_form_id, sample_form_id=sample_form_id)}"
method="post" >
- <div class="toolFormBody">
- %for element_count in range( num_states ):
- <div class="form-row">
- <label>${1+element_count}) State name:</label>
- <input type="text"
name="state_name_${element_count}" value="" size="40"/>
- <label>State help text (optional):</label>
- <input type="text"
name="state_desc_${element_count}" value="" size="40"/>
- </div>
- <div style="clear: both"></div>
- %endfor
- </div>
- <div class="form-row">
- <input type="submit" name="save_request_type"
value="Save"/>
- </div>
- </form>
-</div>
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -115,6 +115,7 @@ class Job( object ):
self.job_runner_name = None
self.job_runner_external_id = None
self.post_job_actions = None
+ self.imported = False
def add_parameter( self, name, value ):
self.parameters.append( JobParameter( name, value ) )
@@ -964,16 +965,16 @@ class LibraryFolder( object ):
intermed.sort()
return map( operator.getitem, intermed, ( -1, ) * len( intermed ) )
# This needs to be a list
- active_library_datasets = [ ld for ld in self.datasets if not
ld.library_dataset_dataset_association.deleted ]
+ active_library_datasets = [ ld for ld in self.datasets if
ld.library_dataset_dataset_association and not
ld.library_dataset_dataset_association.deleted ]
return sort_by_attr( [ ld for ld in active_library_datasets ], 'name' )
@property
def activatable_library_datasets( self ):
# This needs to be a list
- return [ ld for ld in self.datasets if not
ld.library_dataset_dataset_association.dataset.deleted ]
+ return [ ld for ld in self.datasets if ld.library_dataset_dataset_association and
not ld.library_dataset_dataset_association.dataset.deleted ]
@property
def active_datasets( self ):
# This needs to be a list
- return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets
if not ld.library_dataset_dataset_association.deleted ]
+ return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets
if ld.library_dataset_dataset_association and not
ld.library_dataset_dataset_association.deleted ]
def get_display_name( self ):
# Library folder name can be either a string or a unicode object. If string,
# convert to unicode object assuming 'utf-8' format.
@@ -1558,6 +1559,7 @@ class RequestEvent( object ):
class RequestType( object ):
rename_dataset_options = Bunch( NO = 'Do not rename',
SAMPLE_NAME = 'Preprend sample name',
+ EXPERIMENT_NAME = 'Prepend experiment name',
EXPERIMENT_AND_SAMPLE_NAME = 'Prepend experiment
and sample name')
permitted_actions = get_permitted_actions( filter='REQUEST_TYPE' )
def __init__(self, name=None, desc=None, request_form=None, sample_form=None,
--- a/templates/admin/requests/edit_request.mako
+++ /dev/null
@@ -1,88 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem(
'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ','
);
- var last_selected_value = $( this )[0].attributes.getNamedItem(
'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || (
last_selected_value && last_selected_value.value == refresh_on_change_values[i] )
){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#edit_request" ).submit();
- }
- });
-});
-</script>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list',
operation='show_request', id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <div class="toolFormTitle">Edit request "${request.name}"
from ${request.user.email}</div>
- %if len(select_request_type.options) == 1:
- There are no request types created for a new request.
- %else:
- <div class="toolFormBody">
- <form name="edit_request" id="edit_request"
action="${h.url_for( controller='requests_admin', action='edit',
request_id=request.id)}" method="post" >
- <div class="form-row">
- <label>
- Select Request Type:
- </label>
- ${select_request_type.get_html()}
- </div>
-
- %if select_request_type.get_selected() != ('Select one',
'none'):
- %for i, field in enumerate(widgets):
- <div class="form-row">
- <label>${field['label']}</label>
- ${field['widget'].get_html()}
- %if field['label'] == 'Library' and
new_library:
- ${new_library.get_html()}
- %endif
- <div class="toolParamHelp" style="clear:
both;">
- ${field['helptext']}
- </div>
- <div style="clear: both"></div>
- </div>
- %endfor
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right:
10px;">
- <input type="hidden" name="refresh"
value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit"
name="save_changes_request_button" value="Save changes"/>
- ##<input type="submit"
name="edit_samples_button" value="Edit samples"/>
- </div>
- %endif
- </form>
- </div>
-</div>
-%endif
--- a/static/about.html
+++ /dev/null
@@ -1,78 +0,0 @@
-<?xml version="1.0" encoding="utf-8" ?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html
xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"
lang="en">
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8"
/>
-<meta name="generator" content="Docutils 0.3.9:
http://docutils.sourceforge.net/" />
-<title>ABOUT GALAXY</title>
-<link rel="stylesheet" href="/static/style/base.css"
type="text/css" />
-<link rel="stylesheet" href="/static/style/help.css"
type="text/css" />
-</head>
-<body>
-<div class="document" id="about-galaxy">
-<h1 class="title">ABOUT GALAXY</h1>
-<div class="section" id="people">
-<h2><a name="people">People:</a></h2>
-<ul class="simple">
-<li>Istvan Albert - <em>Co-PI</em></li>
-<li>Daniel Blankenberg - <em>Graduate student</em></li>
-<li>Richard Burhans - <em>Sysadmin</em></li>
-<li>Laura Elnitski - <em>Co-PI</em></li>
-<li>Belinda Giardine - <em>Programmer</em></li>
-<li>Ross Hardison - <em>Co-PI</em></li>
-<li>Jim Kent - <em>Co-PI</em></li>
-<li>David King - <em>Graduate student</em></li>
-<li>Webb Miller - <em>Co-PI</em></li>
-<li>Anton Nekrutenko - <em>PI</em></li>
-<li>Cathy Riemer - <em>Programmer</em></li>
-<li>Prachi Shah - <em>Programmer</em></li>
-<li>Ian Schenck - <em>Undergraduate student</em></li>
-<li>James Taylor - <em>Graduate student</em></li>
-<li>Yi Zhang - <em>Programmer</em></li>
-</ul>
-</div>
-<hr class="docutils" />
-<div class="section" id="development">
-<h2><a name="development">Development:</a></h2>
-<p><strong>Galaxy core</strong> - <em>Istvan Albert</em>
and <em>James Taylor</em></p>
-<p><strong>Interface</strong> - <em>James Taylor</em>,
<em>Istvan Albert</em>, <em>Anton Nekrutenko</em></p>
-<p><strong>Tools</strong> -</p>
-<ul class="simple">
-<li>Data sources - <em>Istvan Albert</em></li>
-<li>EMBOSS, Phylip, mafs - <em>Daniel Blankenberg</em></li>
-<li>Text Tools, Sequence Extractors - <em>Richard Burhans</em>,
<em>Anton Nekrutenko</em>, <em>Ian Schenck</em></li>
-<li>Operations - <em>James Taylor</em>, <em>Yi
Zhang</em></li>
-<li>Statistics, Graphs - <em>Istvan Albert</em>, <em>David
King</em></li>
-</ul>
-<p><strong>Project management</strong> - <em>Anton
Nekrutenko</em></p>
-<p>Current version of Galaxy uses many ideas developed by <em>Laura
Elnitski</em>, <em>Belinda Giardine</em>, and <em>Cathy
Riemer</em> in Galaxy1 and GALA.</p>
-</div>
-<hr class="docutils" />
-<div class="section" id="special-thanks-to">
-<h2><a name="special-thanks-to">Special thanks
to:</a></h2>
-<ul class="simple">
-<li>David Haussler</li>
-<li>Ewan Birney</li>
-<li>Hiram Clawson</li>
-<li>Angie Hinrichs</li>
-<li>Darin London</li>
-<li>Members of Hardison, Makova, Miller, and Nekrutenko Labs</li>
-</ul>
-</div>
-<hr class="docutils" />
-<div class="section" id="technology">
-<h2><a name="technology">Technology:</a></h2>
-<p>Galaxy core is written entirely in Python. It uses the following open source
technologies:</p>
-<ul class="simple">
-<li>web-server <a class="reference"
href="http://www.cherrypy.org/">CherryPy</a></li>
-<li>database <a class="reference"
href="http://www.sleepycat.com/products/db.shtml">BerkelyDB&...
-<li>XML library <a class="reference"
href="http://effbot.org/zone/element-index.htm">ElementTree&...
-<li>HTML templating library <a class="reference"
href="http://www.cheetahtemplate.org/">Cheetah</a><...
-</ul>
-<p>Galaxy API generated from source code can be found <a
class="reference"
href="http://www.bx.psu.edu/trac/local/docs/index.html">here...
-<hr class="docutils" />
-<p><a class="reference" href="http://www.bx.psu.edu">The
Center for Comparative Genomics and Bioinformatics</a> at <a
class="reference" href="http://www.psu.edu">Penn State</a> |
2005</p>
-</div>
-</div>
-</body>
-</html>
--- a/templates/requests/sample_datasets.mako
+++ /dev/null
@@ -1,7 +0,0 @@
-<%def name="render_sample_datasets( sample )">
- <a href="${h.url_for(controller='requests_admin',
action='show_datatx_page',
sample_id=trans.security.encode_id(sample.id))}">${sample.transferred_dataset_files()}/${len(sample.dataset_files)}</a>
-</%def>
-
-
-
-${render_sample_datasets( sample )}
--- a/static/about.rst
+++ /dev/null
@@ -1,82 +0,0 @@
-ABOUT GALAXY
-============
-
-People:
--------
-
-* Istvan Albert - *Co-PI*
-* Daniel Blankenberg - *Graduate student*
-* Richard Burhans - *Sysadmin*
-* Laura Elnitski - *Co-PI*
-* Belinda Giardine - *Programmer*
-* Ross Hardison - *Co-PI*
-* Jim Kent - *Co-PI*
-* David King - *Graduate student*
-* Webb Miller - *Co-PI*
-* Anton Nekrutenko - *PI*
-* Cathy Riemer - *Programmer*
-* Prachi Shah - *Programmer*
-* Ian Schenck - *Undergraduate student*
-* James Taylor - *Graduate student*
-* Yi Zhang - *Programmer*
-
------
-
-Development:
-------------
-
-**Galaxy core** - *Istvan Albert* and *James Taylor*
-
-**Interface** - *James Taylor*, *Istvan Albert*, *Anton Nekrutenko*
-
-**Tools** -
-
-* Data sources - *Istvan Albert*
-* EMBOSS, Phylip, mafs - *Daniel Blankenberg*
-* Text Tools, Sequence Extractors - *Richard Burhans*, *Anton Nekrutenko*, *Ian Schenck*
-* Operations - *James Taylor*, *Yi Zhang*
-* Statistics, Graphs - *Istvan Albert*, *David King*
-
-**Project management** - *Anton Nekrutenko*
-
-Current version of Galaxy uses many ideas developed by *Laura Elnitski*, *Belinda
Giardine*, and *Cathy Riemer* in Galaxy1 and GALA.
-
------
-
-Special thanks to:
-------------------
-
-* David Haussler
-* Ewan Birney
-* Hiram Clawson
-* Angie Hinrichs
-* Darin London
-* Members of Hardison, Makova, Miller, and Nekrutenko Labs
-
------
-
-Technology:
------------
-
-Galaxy core is written entirely in Python. It uses the following open source
technologies:
-
-* web-server `CherryPy`__
-* database `BerkelyDB`__
-* XML library `ElementTree`__
-* HTML templating library `Cheetah`__
-
-Galaxy API generated from source code can be found `here`__
-
-.. __:
http://www.cherrypy.org/
-.. __:
http://www.sleepycat.com/products/db.shtml
-.. __:
http://effbot.org/zone/element-index.htm
-.. __:
http://www.cheetahtemplate.org/
-.. __:
http://www.bx.psu.edu/trac/local/docs/index.html
-
------
-
-`The Center for Comparative Genomics and Bioinformatics`__ at `Penn State`__ | 2005
-
-.. __:
http://www.bx.psu.edu
-.. __:
http://www.psu.edu
-
--- a/templates/admin/requests/new_request.mako
+++ /dev/null
@@ -1,94 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- var refresh = false;
- var refresh_on_change_values = $( this )[0].attributes.getNamedItem(
'refresh_on_change_values' )
- if ( refresh_on_change_values ) {
- refresh_on_change_values = refresh_on_change_values.value.split( ','
);
- var last_selected_value = $( this )[0].attributes.getNamedItem(
'last_selected_value' );
- for( i= 0; i < refresh_on_change_values.length; i++ ) {
- if ( $( this )[0].value == refresh_on_change_values[i] || (
last_selected_value && last_selected_value.value == refresh_on_change_values[i] )
){
- refresh = true;
- break;
- }
- }
- }
- else {
- refresh = true;
- }
- if ( refresh ){
- $( "#new_request" ).submit();
- }
- });
-});
-</script>
-
-<%def name="javascripts()">
- ${parent.javascripts()}
- ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
-</%def>
-
-<%def name="stylesheets()">
- ${parent.stylesheets()}
- ${h.css( "autocomplete_tagging" )}
-</%def>
-
-<br/>
-<br/>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <div class="toolFormTitle">Add a new request</div>
- %if len(select_request_type.options) == 1:
- There are no request types created for a new request.
- %else:
- <div class="toolFormBody">
- <form name="new_request" id="new_request"
action="${h.url_for( controller='requests_admin', action='new',
create=True )}" method="post" >
- <div class="form-row">
- <label>
- Select Request Type
- </label>
- ${select_request_type.get_html()}
- </div>
-
- %if select_request_type.get_selected() != ('Select one',
'none'):
- %for i, field in enumerate(widgets):
- <div class="form-row">
- <label>${field['label']}</label>
- ${field['widget'].get_html()}
- %if field['label'] == 'Library' and
new_library:
- ${new_library.get_html()}
- %endif
- <div class="toolParamHelp" style="clear:
both;">
- ${field['helptext']}
- </div>
- <div style="clear: both"></div>
- </div>
- %endfor
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right:
10px;">
- <input type="hidden" name="refresh"
value="true" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit"
name="create_request_button" value="Save"/>
- <input type="submit"
name="create_request_samples_button" value="Add samples"/>
- </div>
- %endif
- </form>
- </div>
-</div>
-%endif
--- a/templates/sample/sample_events.mako
+++ /dev/null
@@ -1,45 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<%def name="title()">Events for Sample ${sample_name}</%def>
-
-
-<h2>Events for Sample "${sample_name}"</h2>
-
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='list', operation='show_request',
id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <table class="grid">
- <thead>
- <tr>
- <th>State</th>
- <th>Description</th>
- <th>Updated</th>
- <th>Comments</th>
- </tr>
- </thead>
- <tbody>
- %for state, desc, updated, comments in events_list:
- <tr class="libraryRow libraryOrFolderRow"
id="libraryRow">
- <td><b><a>${state}</a></b></td>
- <td><a>${desc}</a></td>
- <td><a>${updated}</a></td>
- <td><a>${comments}</a></td>
- </tr>
- %endfor
- </tbody>
- </table>
-</div>
Binary file test-data/1.scf.zip has changed
--- a/templates/requests/show_data.mako
+++ /dev/null
@@ -1,86 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<script type="text/javascript">
-$(document).ready(function(){
- //hide the all of the element with class msg_body
- $(".msg_body").hide();
- //toggle the componenet with class msg_body
- $(".msg_head").click(function(){
- $(this).next(".msg_body").slideToggle(450);
- });
-});
-</script>
-<style type="text/css">
-.msg_head {
- padding: 0px 0px;
- cursor: pointer;
-}
-
-}
-</style>
-
-
-<h2>Data transfer from Sequencer</h2>
-<h3>Sample "${sample.name}" of Request
"${sample.request.name}"</h3>
-
-<ul class="manage-table-actions">
- %if sample.request.submitted() and sample.inprogress_dataset_files():
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='show_datatx_page',
sample_id=trans.security.encode_id(sample.id) )}">
- <span>Refresh this page</span></a>
- </li>
- %endif
- %if sample.library:
- <li>
- <a class="action-button" href="${h.url_for(
controller='library_common', action='browse_library',
cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">
- <span>${sample.library.name} Data Library</span></a>
- </li>
- %endif
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='list', operation='show_request',
id=trans.security.encode_id(sample.request.id) )}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <form name="get_data" action="${h.url_for(
controller='requests_admin', action='get_data',
sample_id=sample.id)}" method="post" >
- <div class="form-row">
- %if len(dataset_files):
- <table class="grid">
- <thead>
- <tr>
- <th>Dataset File</th>
- <th>Transfer Status</th>
- </tr>
- <thead>
- <tbody>
- %for dataset_index, dataset_file in enumerate(dataset_files):
- ${sample_dataset_files( dataset_index, dataset_file[0],
dataset_file[1] )}
- %endfor
- </tbody>
- </table>
- %else:
- There are no dataset files.
- %endif
- </div>
- </form>
-</div>
-
-<%def name="sample_dataset_files( dataset_index, dataset_file, status
)">
- <tr>
- <td>${dataset_file.split('/')[-1]}</td>
- <td>
- %if status == sample.transfer_status.IN_PROGRESS:
- <i>${status}</i>
- %else:
- ${status}
- %endif
- </td>
- </tr>
-</%def>
--- a/templates/requests/events.mako
+++ /dev/null
@@ -1,39 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<h2>History of Sequencing Request "${request.name}"</h2>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='list', operation='show_request',
id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests', action='list')}">
- <span>Browse all requests</span></a>
- </li>
-</ul>
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <table class="grid">
- <thead>
- <tr>
- <th>State</th>
- <th>Last Update</th>
- <th>Comments</th>
- </tr>
- </thead>
- <tbody>
- %for state, updated, comments in events_list:
- <tr class="libraryRow libraryOrFolderRow"
id="libraryRow">
- <td><b><a>${state}</a></b></td>
- <td><a>${updated}</a></td>
- <td><a>${comments}</a></td>
- </tr>
- %endfor
- </tbody>
- </table>
-</div>
--- a/templates/admin/requests/events.mako
+++ /dev/null
@@ -1,36 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<h2>History of Sequencing Request "${request.name}"</h2>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for(
controller='requests_admin', action='list',
operation='show_request', id=trans.security.encode_id(request.id) )}">
- <span>Browse this request</span></a>
- </li>
-</ul>
-<h3>User: ${request.user.email}</h3>
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="toolForm">
- <table class="grid">
- <thead>
- <tr>
- <th>State</th>
- <th>Last Update</th>
- <th>Comments</th>
- </tr>
- </thead>
- <tbody>
- %for state, updated, comments in events_list:
- <tr class="libraryRow libraryOrFolderRow"
id="libraryRow">
- <td><b><a>${state}</a></b></td>
- <td><a>${updated}</a></td>
- <td><a>${comments}</a></td>
- </tr>
- %endfor
- </tbody>
- </table>
-</div>