[hg] galaxy 1590: Convert tool_form/tool_executed to mako (for p...

1 Nov 2008

details:   http://www.bx.psu.edu/hg/galaxy/rev/7e94f40ee9e8
changeset: 1590:7e94f40ee9e8
user:      James Taylor <james@jamestaylor.org>
date:      Thu Oct 30 17:34:46 2008 -0400
description:
Convert tool_form/tool_executed to mako (for performance)

5 file(s) affected in this change:

lib/galaxy/tools/__init__.py
templates/tool_executed.mako
templates/tool_executed.tmpl
templates/tool_form.mako
templates/tool_form.tmpl

diffs (573 lines):

diff -r 1d113c5386da -r 7e94f40ee9e8 lib/galaxy/tools/__init__.py

--- a/lib/galaxy/tools/__init__.py	Thu Oct 30 16:17:46 2008 -0400
+++ b/lib/galaxy/tools/__init__.py	Thu Oct 30 17:34:46 2008 -0400
@@ -676,7 +676,7 @@
             # 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 @@
             # 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={} ):
diff -r 1d113c5386da -r 7e94f40ee9e8 templates/tool_executed.mako
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/tool_executed.mako	Thu Oct 30 17:34:46 2008 -0400
@@ -0,0 +1,63 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+
+<head>
+<title>Galaxy</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
+<script type="text/javascript">
+  var inside_galaxy_frameset = false;
+
+  if ( parent.frames && parent.frames.galaxy_history ) {
+      parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' )}";
+      inside_galaxy_frameset = true;
+  }
+  
+  if ( parent.handle_minwidth_hint ) {
+      parent.handle_minwidth_hint( -1 );
+  }
+
+  function main() {
+    // If called from outside the galaxy frameset, redirect there
+    %if tool.options.refresh:
+      if ( ! inside_galaxy_frameset ) {
+        setTimeout( "refresh()", 1000 );
+        document.getElementById( "refresh_message" ).style.display = "block";
+      }
+    %endif
+  }
+
+  function refresh() {
+    top.location.href = '${request.base}';
+  }
+
+</script>
+
+</head>
+
+<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}: ${data.name}</b></div>
+%endfor
+
+<p>
+You can check the status of queued jobs and view the resulting 
+data by refreshing the <b>History</b> pane. When the job has been run
+the status will change from 'running' to 'finished' if completed 
+succesfully or 'error' if problems were encountered.
+</p>
+
+%if tool.options.refresh:
+<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="${request.base}">Galaxy</a></div>
+%endif
+
+</div>
+
+</body>
+
+</html>
\ No newline at end of file
diff -r 1d113c5386da -r 7e94f40ee9e8 templates/tool_executed.tmpl
--- a/templates/tool_executed.tmpl	Thu Oct 30 16:17:46 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-
-<head>
-<title>Galaxy</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-<link href="$h.url_for('/static/style/base.css')" rel="stylesheet" type="text/css" />
-<script type="text/javascript">
-  var inside_galaxy_frameset = false;
-
-  if ( parent.frames && parent.frames.galaxy_history )
-  {
-      parent.frames.galaxy_history.location.href="$h.url_for( controller='root', action='history' )";
-    
-      inside_galaxy_frameset = true;
-  }
-  
-  if ( parent.handle_minwidth_hint )
-  {
-      parent.handle_minwidth_hint( -1 );
-  }
-
-  function main()
-  {
-    // If called from outside the galaxy frameset, redirect there
-    #if $tool.options.refresh
-      if ( ! inside_galaxy_frameset )
-      {
-        setTimeout( "refresh()", 1000 );
-        document.getElementById( "refresh_message" ).style.display = "block";
-      }
-    #end if
-  }
-
-  function refresh()
-  {
-    top.location.href = '$request.base';
-  }
-
-</script>
-
-</head>
-
-<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
-
-<p>
-You can check the status of queued jobs and view the resulting 
-data by refreshing the <b>History</b> pane. When the job has been run
-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
-
-</div>
-
-</body>
-
-</html>
\ No newline at end of file
diff -r 1d113c5386da -r 7e94f40ee9e8 templates/tool_form.mako
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/tool_form.mako	Thu Oct 30 17:34:46 2008 -0400
@@ -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="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${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' )
+           {
+               $( this ).hide();
+           }
+       });
+   });
+</script>
+
+</html>
diff -r 1d113c5386da -r 7e94f40ee9e8 templates/tool_form.tmpl
--- a/templates/tool_form.tmpl	Thu Oct 30 16:17:46 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,191 +0,0 @@
-<!-- -->
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-
-#from galaxy.util.expressions import ExpressionContext 
-
-<html>
-
-<head>
-<title>Galaxy</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-<link href="$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')"> <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>

    

Greg Von Kuster

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