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Convert tool_form/tool_executed to mako (for performance)

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This commit is contained in:
James Taylor
2008-10-30 17:34:46 -04:00
parent 5be8fefaf5
commit 952c12bd60
4 changed files with 215 additions and 219 deletions
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lib/galaxy/tools/__init__.py
+5 -5
View File
@@ -676,7 +676,7 @@ class Tool:
# on the standard run form) or "URL" (a parameter provided by
# external data source tools).
if "runtool_btn" not in incoming and "URL" not in incoming:
return "tool_form.tmpl", dict( errors={}, tool_state=state, param_values={}, incoming={} )
return "tool_form.mako", dict( errors={}, tool_state=state, param_values={}, incoming={} )
# Process incoming data
if not( self.check_values ):
# If `self.check_values` is false we don't do any checking or
@@ -702,20 +702,20 @@ class Tool:
# error messages
if errors:
error_message = "One or more errors were found in the input you provided. The specific errors are marked below."
return "tool_form.tmpl", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message )
return "tool_form.mako", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message )
# If we've completed the last page we can execute the tool
elif state.page == self.last_page:
out_data = self.execute( trans, incoming=params )
return 'tool_executed.tmpl', dict( out_data=out_data )
return 'tool_executed.mako', dict( out_data=out_data )
# Otherwise move on to the next page
else:
state.page += 1
# Fill in the default values for the next page
self.fill_in_new_state( trans, self.inputs_by_page[ state.page ], state.inputs )
return 'tool_form.tmpl', dict( errors=errors, tool_state=state )
return 'tool_form.mako', dict( errors=errors, tool_state=state )
else:
# Just a refresh, render the form with updated state and errors.
return 'tool_form.tmpl', dict( errors=errors, tool_state=state )
return 'tool_form.mako', dict( errors=errors, tool_state=state )
def update_state( self, trans, inputs, state, incoming, prefix="", context=None,
update_only=False, old_errors={}, changed_dependencies={} ):
templates/tool_executed.tmpl → templates/tool_executed.mako
+16 -23
View File
@@ -4,37 +4,31 @@
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<link href="$h.url_for('/static/style/base.css')" rel="stylesheet" type="text/css" />
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
<script type="text/javascript">
var inside_galaxy_frameset = false;
if ( parent.frames && parent.frames.galaxy_history )
{
parent.frames.galaxy_history.location.href="$h.url_for( controller='root', action='history' )";
if ( parent.frames && parent.frames.galaxy_history ) {
parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' )}";
inside_galaxy_frameset = true;
}
if ( parent.handle_minwidth_hint )
{
if ( parent.handle_minwidth_hint ) {
parent.handle_minwidth_hint( -1 );
}
function main()
{
function main() {
// If called from outside the galaxy frameset, redirect there
#if $tool.options.refresh
if ( ! inside_galaxy_frameset )
{
%if tool.options.refresh:
if ( ! inside_galaxy_frameset ) {
setTimeout( "refresh()", 1000 );
document.getElementById( "refresh_message" ).style.display = "block";
}
#end if
%endif
}
function refresh()
{
top.location.href = '$request.base';
function refresh() {
top.location.href = '${request.base}';
}
</script>
@@ -43,14 +37,13 @@
<body onLoad="main()">
<div class="donemessage">
<p>The following job has been succesfully added to the queue:</p>
#for $data in $out_data.values
<div style="padding: 10px"><b> $data.hid: $data.name</b></div>
#end for
%for data in out_data.values():
<div style="padding: 10px"><b> ${data.hid}: ${data.name}</b></div>
%endfor
<p>
You can check the status of queued jobs and view the resulting
@@ -59,9 +52,9 @@ the status will change from 'running' to 'finished' if completed
succesfully or 'error' if problems were encountered.
</p>
#if $tool.options.refresh
<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="$request.base">Galaxy</a></div>
#end if
%if tool.options.refresh:
<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="${request.base}">Galaxy</a></div>
%endif
</div>
templates/tool_form.mako
+194
View File
@@ -0,0 +1,194 @@
<!-- -->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<%
from galaxy.util.expressions import ExpressionContext
%>
<html>
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
<script type='text/javascript' src="${h.url_for('/static/scripts/jquery.js')}"> </script>
<script type="text/javascript">
$( function() {
$( "select[@refresh_on_change='true']").change( function() {
$( "#tool_form" ).submit();
});
});
%if not add_frame.debug:
if( window.name != "galaxy_main" ) {
location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' );
}
%endif
</script>
</head>
<body>
<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )">
<% other_values = ExpressionContext( tool_state, other_values ) %>
%for input_index, input in enumerate( inputs.itervalues() ):
%if input.type == "repeat":
<div class="repeat-group">
<div class="form-title-row"><b>${input.title_plural}</b></div>
<% repeat_state = tool_state[input.name] %>
%for i in range( len( repeat_state ) ):
<div class="repeat-group-item">
<%
if input.name in errors:
rep_errors = errors[input.name][i]
else:
rep_errors = dict()
index = repeat_state[i]['__index__']
%>
<div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
</div>
%endfor
<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
</div>
%elif input.type == "conditional":
<%
group_state = tool_state[input.name]
group_errors = errors.get( input.name, {} )
current_case = group_state['__current_case__']
group_prefix = prefix + input.name + "|"
%>
${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )}
${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )}
%else:
${row_for_param( prefix, input, tool_state, errors, other_values )}
%endif
%endfor
</%def>
<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )">
<%
if parent_errors.has_key( param.name ):
cls = "form-row form-row-error"
else:
cls = "form-row"
%>
<div class="${cls}">
<% label = param.get_label() %>
%if label:
<label>
${label}:
</label>
%endif
<%
field = param.get_html_field( trans, parent_state[ param.name ], other_values )
field.refresh_on_change = param.refresh_on_change
%>
<div style="float: left; width: 250px; margin-right: 10px;">${field.get_html( prefix )}</div>
%if parent_errors.has_key( param.name ):
<div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">
<div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${parent_errors[param.name]}</span></div>
</div>
%endif
%if param.help:
<div class="toolParamHelp" style="clear: both;">
${param.help}
</div>
%endif
<div style="clear: both"></div>
</div>
</%def>
%if add_frame.from_noframe:
<div class="warningmessage">
<strong>Welcome to Galaxy</strong>
<hr/>
It appears that you found this tool from a link outside of Galaxy.
If you're not familiar with Galaxy, please consider visiting the
<a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>.
To learn more about what Galaxy is and what it can do for you, please visit
the <a href="$add_frame.wiki_url" target="_top">Galaxy wiki</a>.
</div>
<br/>
%endif
<div class="toolForm" id="$tool.id">
%if tool.has_multiple_pages:
<div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div>
%else:
<div class="toolFormTitle">${tool.name}</div>
%endif
<div class="toolFormBody">
<form id="tool_form" name="tool_form" action="${h.url_for( tool.action )}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}">
<input type="hidden" name="tool_id" value="${tool.id}">
<input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}">
%if tool.display_by_page[tool_state.page]:
${trans.fill_template_string( tool.display_by_page[tool_state.page], other_values=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )}
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
%else:
<div style="display: none;">
%if tool_state.page == tool.last_page:
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
%else:
<input type="submit" class="primary-button" name="runtool_btn" value="Next step">
%endif
</div>
${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )}
<div class="form-row">
%if tool_state.page == tool.last_page:
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
%else:
<input type="submit" class="primary-button" name="runtool_btn" value="Next step">
%endif
</div>
%endif
</form>
</div>
</div>
%if tool.help:
<div class="toolHelp">
<div class="toolHelpBody">
%if tool.has_multiple_pages:
${tool.help_by_page[tool_state.page]}
%else:
${tool.help}
%endif
</div>
</div>
%endif
</body>
<script type="text/javascript">
$( function() {
$( 'li > ul' ).each( function( i ) {
if ( $( this )[0].className == 'toolParameterExpandableCollapsable' )
{
var parent_li = $( this ).parent( 'li' );
var sub_ul = $( this ).remove();
parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() {
sub_ul.toggle();
$( this )[0].innerHTML = ( sub_ul[0].style.display=='none' ) ? '[+]' : '[-]';
});
parent_li.append( sub_ul );
}
});
$( 'ul ul' ).each( function(i) {
if ( $( this )[0].className == 'toolParameterExpandableCollapsable' && this.attributes.getNamedItem( 'default_state' ).value == 'collapsed' )
{
$( this ).hide();
}
});
});
</script>
</html>
templates/tool_form.tmpl
-191
View File
@@ -1,191 +0,0 @@
<!-- -->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
#from galaxy.util.expressions import ExpressionContext
<html>
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<link href="$h.url_for('/static/style/base.css')" rel="stylesheet" type="text/css" />
<script type='text/javascript' src="$h.url_for('/static/scripts/jquery.js')"> </script>
<script type="text/javascript">
jQuery( function() {
jQuery( "select[@refresh_on_change='true']").change( function() {
jQuery( "#tool_form" ).submit();
});
});
#if not $add_frame.debug
if( window.name != "galaxy_main" ) {
location.replace( '$h.url_for( controller='root', action='index', tool_id=$tool.id )' );
}
#end if
</script>
</head>
<body>
## #if $getVar( 'error_message', None )
## <div class="errormessagesmall">$error_message</div>
## <p></p>
## #end if
#def do_inputs( $inputs, $tool_state, $errors, $prefix, $context=None )
#set $context = ExpressionContext( $tool_state, $context )
#for $input_index, $input in enumerate( $inputs.itervalues() )
#if $input.type == "repeat"
<div class="repeat-group">
<div class="form-title-row"><b>${input.title_plural}</b></div>
#set repeat_state = $tool_state[$input.name]
#for i in range( len( $repeat_state ) ):
<div class="repeat-group-item">
#if $input.name in errors
#set rep_errors = $errors[$input.name][$i]
#else
#set rep_errors = dict()
#end if
#set index = $repeat_state[$i]['__index__']
<div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
$do_inputs( $input.inputs, $repeat_state[$i], $rep_errors, $prefix + $input.name + "_" + str($index) + "|", $context )
<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
</div>
#end for
<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
</div>
#elif $input.type == "conditional"
#set group_state = $tool_state[$input.name]
#set group_errors = $errors.get( $input.name, {} )
#set current_case = $group_state['__current_case__']
#set group_prefix = $prefix + $input.name + "|"
$row_for_param( $group_prefix, $input.test_param, $group_state, $group_errors, $context )
$do_inputs( $input.cases[$current_case].inputs, $group_state, $group_errors, $group_prefix, $context )
#else
$row_for_param( $prefix, $input, $tool_state, $errors, $context )
#end if
#end for
#end def
#def row_for_param( $prefix, $param, $parent_state, $parent_errors, $context )
#if $parent_errors.has_key( $param.name ):
#set cls = "form-row form-row-error"
#else
#set cls = "form-row"
#end if
<div class="$cls">
#set label = $param.get_label()
#if $label:
<label>
$label:
</label>
#end if
#set field = $param.get_html_field( $caller, $parent_state[ $param.name ], $context )
#set $field.refresh_on_change = $param.refresh_on_change
<div style="float: left; width: 250px; margin-right: 10px;">$field.get_html( $prefix )</div>
#if $parent_errors.has_key( $param.name ):
<div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">
<div style="width: 300px;"><img style="vertical-align: middle;" src="$h.url_for('/static/style/error_small.png')">&nbsp;<span style="vertical-align: middle;">$parent_errors[$param.name]</span></div>
</div>
#elif $param.help
##<div class="toolParamHelp" style="float: right;">$param.help</div>
#end if
#if $param.help
<div class="toolParamHelp" style="clear: both;">
$param.help
</div>
#end if
<div style="clear: both"></div>
</div>
#end def
#if $add_frame.from_noframe
<div class="warningmessage">
<strong>Welcome to Galaxy</strong>
<hr/>
It appears that you found this tool from a link outside of Galaxy. If you're not familiar with Galaxy, please consider visiting the <a href="$h.url_for( controller='root' )" target="_top">welcome page</a>. To learn more about what Galaxy is and what it can do for you, please visit the <a href="$add_frame.wiki_url" target="_top">Galaxy wiki</a>.
</div>
<br/>
#end if
<div class="toolForm" id="$tool.id">
#if $tool.has_multiple_pages
<div class="toolFormTitle">$tool.name (step #echo $tool_state.page+1 # of $tool.npages)</div>
#else
<div class="toolFormTitle">$tool.name</div>
#end if
<div class="toolFormBody">
<form id="tool_form" name="tool_form" action="$h.url_for( $tool.action )" enctype="$tool.enctype" target="$tool.target" method="$tool.method">
<input type="hidden" name="tool_id" value="$tool.id">
<input type="hidden" name="tool_state" value="$util.object_to_string( $tool_state.encode( $tool, $app ) )">
#if $tool.display_by_page[$tool_state.page]
$caller.fill_template_string( $tool.display_by_page[$tool_state.page], context=$tool.get_param_html_map( $caller, $tool_state.page, $tool_state.inputs ) )
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
#else
<div style="display: none;">
#if $tool_state.page == $tool.last_page
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
#else
<input type="submit" class="primary-button" name="runtool_btn" value="Next step">
#end if
</div>
$do_inputs( $tool.inputs_by_page[ $tool_state.page ], $tool_state.inputs, $errors, "" )
<div class="form-row">
#if $tool_state.page == $tool.last_page
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
#else
<input type="submit" class="primary-button" name="runtool_btn" value="Next step">
#end if
</div>
#end if
</form>
</div>
</div>
#if $tool.help
<div class="toolHelp">
<div class="toolHelpBody">
#if $tool.has_multiple_pages
$tool.help_by_page[$tool_state.page]
#else
$tool.help
#end if
</div>
</div>
#end if
</body>
<script type="text/javascript">
\$( function() {
\$( 'li > ul' ).each( function( i ) {
if ( \$( this )[0].className == 'toolParameterExpandableCollapsable' )
{
var parent_li = \$( this ).parent( 'li' );
var sub_ul = \$( this ).remove();
parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() {
sub_ul.toggle();
\$( this )[0].innerHTML = ( sub_ul[0].style.display=='none' ) ? '[+]' : '[-]';
});
parent_li.append( sub_ul );
}
});
\$( 'ul ul' ).each( function(i) {
if ( \$( this )[0].className == 'toolParameterExpandableCollapsable' && this.attributes.getNamedItem( 'default_state' ).value == 'collapsed' )
{
\$( this ).hide();
}
});
});
</script>
</html>