[galaxy-commits] commit/galaxy-central: kanwei: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well.

19 Jul 2011

1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/8553b02ce9ee/
changeset:   8553b02ce9ee
user:        kanwei
date:        2011-07-19 03:56:23
summary:     Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well.

Refactor tool_form.mako to use base_panels.mako instead of its own custom HTML.
affected #:  9 files (4.1 KB)

--- a/lib/galaxy/tools/__init__.py	Mon Jul 18 15:02:37 2011 -0400
+++ b/lib/galaxy/tools/__init__.py	Mon Jul 18 21:56:23 2011 -0400
@@ -1463,6 +1463,11 @@
                 elif isinstance( input, SelectToolParameter ):
                     input_values[ input.name ] = SelectToolParameterWrapper( 
                         input, input_values[ input.name ], self.app, other_values = param_dict )
+                        
+                elif isinstance( input, LibraryDatasetToolParameter ):
+                    input_values[ input.name ] = LibraryDatasetValueWrapper( 
+                        input, input_values[ input.name ], param_dict )
+                        
                 else:
                     input_values[ input.name ] = InputValueWrapper( 
                         input, input_values[ input.name ], param_dict )
@@ -2013,6 +2018,31 @@
     def __getattr__( self, key ):
         return getattr( self.obj, key )
 
+class LibraryDatasetValueWrapper( object ):
+    """
+    Wraps an input so that __str__ gives the "param_dict" representation.
+    """
+    def __init__( self, input, value, other_values={} ):
+        self.input = input
+        self.value = value
+        self._other_values = other_values
+    def __str__( self ):
+        return self.value.name
+    def templates( self ):
+        if not self.value:
+            return None
+        template_data = {}
+        for temp_info in self.value.info_association:
+            template = temp_info.template
+            content = temp_info.info.content
+            tmp_dict = {}
+            for field in template.fields:
+                tmp_dict[field['label']] = content[field['name']]
+            template_data[template.name] = tmp_dict
+        return template_data
+    def __getattr__( self, key ):
+        return getattr( self.value, key )
+        
 class InputValueWrapper( object ):
     """
     Wraps an input so that __str__ gives the "param_dict" representation.


--- a/lib/galaxy/tools/parameters/basic.py	Mon Jul 18 15:02:37 2011 -0400
+++ b/lib/galaxy/tools/parameters/basic.py	Mon Jul 18 21:56:23 2011 -0400
@@ -1272,7 +1272,7 @@
           displayed as radio buttons and multiple selects as a set of checkboxes
 
     TODO: The following must be fixed to test correctly for the new security_check tag in the DataToolParameter ( the last test below is broken )
-    Nate's next passs at the dataset security stuff will dramatically alter this anyway.
+    Nate's next pass at the dataset security stuff will dramatically alter this anyway.
     """
 
     def __init__( self, tool, elem ):
@@ -1522,6 +1522,38 @@
             ref = ref()
         return ref
 
+class LibraryDatasetToolParameter( ToolParameter ):
+    """
+    Parameter that lets users select a LDDA from a modal window, then use it within the wrapper.
+    """
+
+    def __init__( self, tool, elem ):
+        ToolParameter.__init__( self, tool, elem )
+        
+    def get_html_field( self, trans=None, value=None, other_values={} ):
+        return form_builder.LibraryField( self.name, value=value, trans=trans )
+        
+    def get_initial_value( self, trans, context ):
+        return None
+
+    def from_html( self, value, trans, other_values={} ):
+        if not value:
+            return None
+        elif isinstance( value, trans.app.model.LibraryDatasetDatasetAssociation ):
+            return value
+        else:
+            return trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( value ) )
+
+    def to_string( self, value, app ):
+        if not value:
+            return None
+        return value.id
+
+    def to_python( self, value, app ):
+        if not value:
+            return value
+        return app.model.context.query( app.model.LibraryDatasetDatasetAssociation ).get( value )
+
 # class RawToolParameter( ToolParameter ):
 #     """
 #     Completely nondescript parameter, HTML representation is provided as text
@@ -1570,19 +1602,20 @@
 #         self.html = form_builder.HiddenField( self.name, trans.history.id ).get_html()
 #         return self.html
 
-parameter_types = dict( text        = TextToolParameter,
-                        integer     = IntegerToolParameter,
-                        float       = FloatToolParameter,
-                        boolean     = BooleanToolParameter,
-                        genomebuild = GenomeBuildParameter,
-                        select      = SelectToolParameter,
-                        data_column = ColumnListParameter,
-                        hidden      = HiddenToolParameter,
-                        baseurl     = BaseURLToolParameter,
-                        file        = FileToolParameter,
-                        ftpfile     = FTPFileToolParameter,
-                        data        = DataToolParameter,
-                        drill_down = DrillDownSelectToolParameter )
+parameter_types = dict( text            = TextToolParameter,
+                        integer         = IntegerToolParameter,
+                        float           = FloatToolParameter,
+                        boolean         = BooleanToolParameter,
+                        genomebuild     = GenomeBuildParameter,
+                        select          = SelectToolParameter,
+                        data_column     = ColumnListParameter,
+                        hidden          = HiddenToolParameter,
+                        baseurl         = BaseURLToolParameter,
+                        file            = FileToolParameter,
+                        ftpfile         = FTPFileToolParameter,
+                        data            = DataToolParameter,
+                        library_data    = LibraryDatasetToolParameter,
+                        drill_down      = DrillDownSelectToolParameter )
 
 class UnvalidatedValue( object ):
     """


--- a/lib/galaxy/web/form_builder.py	Mon Jul 18 15:02:37 2011 -0400
+++ b/lib/galaxy/web/form_builder.py	Mon Jul 18 21:56:23 2011 -0400
@@ -652,6 +652,27 @@
             return self.value
         else:
             return '-'
+            
+class LibraryField( BaseField ):
+    def __init__( self, name, value=None, trans=None ):
+        self.name = name
+        self.ldda = value
+        self.trans = trans
+    def get_html( self, disabled=False ):
+        if not self.ldda:
+            ldda = ""
+            text = "Choose a library dataset"
+        else:
+            ldda = self.trans.security.encode_id(self.ldda.id)
+            text = self.ldda.name
+        return '<a href="javascript:void(0);" class="add-librarydataset">%s</a> \
+                <input type="hidden" name="%s" value="%s">' % ( text, self.name, escape( str(ldda), quote=True ) )
+
+    def get_display_text(self):
+        if self.ldda:
+            return self.ldda.name
+        else:
+            return 'None'
 
 def get_suite():
     """Get unittest suite for this module"""


--- a/static/scripts/galaxy.base.js	Mon Jul 18 15:02:37 2011 -0400
+++ b/static/scripts/galaxy.base.js	Mon Jul 18 21:56:23 2011 -0400
@@ -725,4 +725,5 @@
         }
         return anchor;
     });
+
 });


--- a/static/scripts/galaxy.panels.js	Mon Jul 18 15:02:37 2011 -0400
+++ b/static/scripts/galaxy.panels.js	Mon Jul 18 21:56:23 2011 -0400
@@ -214,7 +214,7 @@
         init_fn();
     }
 };
-    
+
 function show_in_overlay( options ) {
     var width = options.width || '600';
     var height = options.height || '400';
@@ -226,9 +226,9 @@
     show_modal( null, $( "<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='" + image_path + "/closebox.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) );
     $("#close_button").bind( "click", function() { hide_modal(); } );
 }
-    
+
 // Tab management
-	
+
 $(function() {
     $(".tab").each( function() {
         var submenu = $(this).children( ".submenu" );


--- a/templates/base.mako	Mon Jul 18 15:02:37 2011 -0400
+++ b/templates/base.mako	Mon Jul 18 21:56:23 2011 -0400
@@ -1,15 +1,13 @@
 <% _=n_ %><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"><html>
-
-<head>
-<title>${self.title()}</title>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-${self.metas()}
-${self.stylesheets()}
-${self.javascripts()}
-</head>
-
+    <head>
+        <title>${self.title()}</title>
+        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+        ${self.metas()}
+        ${self.stylesheets()}
+        ${self.javascripts()}
+    </head><body>
         ${next.body()}
     </body>


--- a/templates/base_panels.mako	Mon Jul 18 15:02:37 2011 -0400
+++ b/templates/base_panels.mako	Mon Jul 18 21:56:23 2011 -0400
@@ -155,13 +155,13 @@
     ## Override
 </%def>
 
-<%def name="overlay( title='', content='' )">
+<%def name="overlay( title='', content='', visible=False )"><%def name="title()"></%def><%def name="content()"></%def><div id="overlay"
-    %if not self.overlay_visible:
-    style="display: none;"
+    %if not visible:
+        style="display: none;"
     %endif
     >
     ##
@@ -169,21 +169,21 @@
     
     ## Need a table here for centering in IE6
     <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0"
-    %if not self.overlay_visible:
+    %if not visible:
         style="display: none;"
     %endif
     ><tr><td><div class="dialog-box-wrapper"><div class="dialog-box">
-        <div class="unified-panel-header">
-            <div class="unified-panel-header-inner"><span class='title'>${title}</span></div>
-        </div>
-        <div class="body">${content}</div>
-        <div>
-            <div class="buttons" style="display: none; float: right;"></div>
-            <div class="extra_buttons" style="display: none; padding: 5px;"></div>
-            <div style="clear: both;"></div>
-        </div>
+            <div class="unified-panel-header">
+                <div class="unified-panel-header-inner"><span class='title'>${title}</span></div>
+            </div>
+            <div class="body">${content}</div>
+            <div>
+                <div class="buttons" style="display: none; float: right;"></div>
+                <div class="extra_buttons" style="display: none; padding: 5px;"></div>
+                <div style="clear: both;"></div>
+            </div></div></div></td></tr></table>
@@ -198,45 +198,45 @@
 <html>
     ${self.init()}    
     <head>
-    <title>${self.title()}</title>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <meta name = "viewport" content = "maximum-scale=1.0">
-    ${self.stylesheets()}
-    ${self.javascripts()}
+        <title>${self.title()}</title>
+        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+        <meta name = "viewport" content = "maximum-scale=1.0">
+        ${self.stylesheets()}
+        ${self.javascripts()}
     </head><body scroll="no" class="${self.body_class}">
-	<div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;">
-        ## Background displays first
-        <div id="background"></div>
-        ## Layer iframes over backgrounds
-        <div id="masthead">
-            ${self.masthead()}
-        </div>
-        <div id="messagebox" class="panel-${self.message_box_class}-message">
-            %if self.message_box_visible:
-                ${self.message_box_content()}
+        <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;">
+            ## Background displays first
+            <div id="background"></div>
+            ## Layer iframes over backgrounds
+            <div id="masthead">
+                ${self.masthead()}
+            </div>
+            <div id="messagebox" class="panel-${self.message_box_class}-message">
+                %if self.message_box_visible:
+                    ${self.message_box_content()}
+                %endif
+            </div>
+            ${self.overlay(visible=self.overlay_visible)}
+            %if self.has_left_panel:
+                <div id="left">
+                    ${self.left_panel()}
+                </div>
+                <div id="left-border">
+                    <div id="left-border-inner" style="display: none;"></div>
+                </div>
+            %endif
+            <div id="center">
+                ${self.center_panel()}
+            </div>
+            %if self.has_right_panel:
+                <div id="right-border"><div id="right-border-inner" style="display: none;"></div></div>
+                <div id="right">
+                    ${self.right_panel()}
+                </div>
             %endif
         </div>
-    ${self.overlay()}
-        %if self.has_left_panel:
-            <div id="left">
-                ${self.left_panel()}
-            </div>
-            <div id="left-border">
-                <div id="left-border-inner" style="display: none;"></div>
-            </div>
-        %endif
-        <div id="center">
-            ${self.center_panel()}
-        </div>
-        %if self.has_right_panel:
-            <div id="right-border"><div id="right-border-inner" style="display: none;"></div></div>
-            <div id="right">
-                ${self.right_panel()}
-            </div>
-        %endif
-	</div>
         ## Allow other body level elements
     </body>
     ## Scripts can be loaded later since they progressively add features to


--- a/templates/root/index.mako	Mon Jul 18 15:02:37 2011 -0400
+++ b/templates/root/index.mako	Mon Jul 18 21:56:23 2011 -0400
@@ -174,14 +174,14 @@
 
 <%def name="init()"><%
-	if trans.app.config.cloud_controller_instance:
-		self.has_left_panel=False
-		self.has_right_panel=False
-		self.active_view="cloud"
-	else:
-		self.has_left_panel=True
-		self.has_right_panel=True
-		self.active_view="analysis"
+    if trans.app.config.cloud_controller_instance:
+        self.has_left_panel=False
+        self.has_right_panel=False
+        self.active_view="cloud"
+    else:
+        self.has_left_panel=True
+        self.has_right_panel=True
+        self.active_view="analysis"
 %>
 %if trans.app.config.require_login and not trans.user:
     <script type="text/javascript">
@@ -219,7 +219,7 @@
     elif m_c is not None:
         center_url = h.url_for( controller=m_c, action=m_a )
     elif trans.app.config.cloud_controller_instance:
-    	center_url = h.url_for( controller='cloud', action='list' )
+        center_url = h.url_for( controller='cloud', action='list' )
     else:
         center_url = h.url_for( '/static/welcome.html' )
     %>


--- a/templates/tool_form.mako	Mon Jul 18 15:02:37 2011 -0400
+++ b/templates/tool_form.mako	Mon Jul 18 21:56:23 2011 -0400
@@ -1,203 +1,230 @@
-<!-- -->
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<%inherit file="/base.mako"/>
+<%namespace file="/base_panels.mako" import="overlay" />
 
-<%
-from galaxy.util.expressions import ExpressionContext
-%>
+<%def name="stylesheets()">
+    ${h.css( "autocomplete_tagging", "panel_layout", "base", "library" )}
+</%def>
 
-<html>
+<%def name="javascripts()">
+    ${h.js( "jquery", "galaxy.panels", "galaxy.base", "jquery.autocomplete", "jstorage" )}
+    <script type="text/javascript">
+    $(function() {
+        $(window).bind("refresh_on_change", function() {
+            $(':file').each( function() {
+                var file = $(this);
+                var file_value = file.val();
+                if (file_value) {
+                    // disable file input, since we don't want to upload the file on refresh
+                    var file_name = $(this).attr("name");
+                    file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } );
+                    // create a new hidden field which stores the filename and has the original name of the file input
+                    var new_file_input = $(document.createElement('input'));
+                    new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } );
+                    file.after(new_file_input);
+                }
+            });
+        });
 
-<head>
-<title>Galaxy</title>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-${h.css( "base", "autocomplete_tagging" )}
-${h.js( "jquery", "galaxy.base", "jquery.autocomplete" )}
-<script type="text/javascript">
-$(function() {
-    $(window).bind("refresh_on_change", function() {
-        $(':file').each( function() {
-            var file = $(this);
-            var file_value = file.val();
-            if (file_value) {
-                // disable file input, since we don't want to upload the file on refresh
-                var file_name = $(this).attr("name");
-                file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } );
-                // create a new hidden field which stores the filename and has the original name of the file input
-                var new_file_input = $(document.createElement('input'));
-                new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } );
-                file.after(new_file_input);
+        // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements
+        $( 'li ul.toolParameterExpandableCollapsable' ).each( function() {
+            var el = $(this),
+                parent_li = el.parent('li'),
+                sub_ul = el.remove();
+
+            parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() {
+                sub_ul.toggle();
+                (this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' );
+            });
+            parent_li.append( sub_ul );
+        });
+
+        $( 'ul ul.toolParameterExpandableCollapsable' ).each( function(i) {
+            var el = $(this);
+            if (el.attr("default_state") === "collapsed") {
+                el.hide();
             }
         });
+
+        function checkUncheckAll( name, check ) {
+            $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check);
+        }
+
+        // Inserts the Select All / Unselect All buttons for checkboxes
+        $("div.checkUncheckAllPlaceholder").each( function() {
+            var check_name = $(this).attr("checkbox_name");
+            select_link = $("<a class='action-button'></a>").text("Select All").click(function() {
+               checkUncheckAll(check_name, true);
+            });
+            unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() {
+               checkUncheckAll(check_name, false);
+            });
+            $(this).append(select_link).append(" ").append(unselect_link);
+        });
+        
+        $(".add-librarydataset").live("click", function() {
+            var link = $(this);
+            $.ajax({
+                url: "/tracks/list_libraries",
+                error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); },
+                success: function(table_html) {
+                    show_modal(
+                        "Select Library Dataset",
+                        table_html, {
+                            "Cancel": function() {
+                                hide_modal();
+                            },
+                            "Select": function() {
+                                $('input[name=ldda_ids]:checked').each(function() {
+                                    var name = $.trim( $(this).siblings("div").find("a").text() );
+                                    var id = $(this).val();
+                                    link.text(name);
+                                    link.siblings("input[type=hidden]").val(id);
+                                });
+                                hide_modal();
+                            }
+                        }
+                    );
+                }
+            });
+        });
     });
-    
-    // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements
-    $( 'li ul.toolParameterExpandableCollapsable' ).each( function() {
-        var el = $(this),
-            parent_li = el.parent('li'),
-            sub_ul = el.remove();
-        
-        parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() {
-            sub_ul.toggle();
-            (this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' );
-        });
-        parent_li.append( sub_ul );
-    });
-    
-    $( 'ul ul.toolParameterExpandableCollapsable' ).each( function(i) {
-        var el = $(this);
-        if (el.attr("default_state") === "collapsed") {
-            el.hide();
+
+    %if not add_frame.debug:
+        if( window.name != "galaxy_main" ) {
+            location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' );
         }
-    });
-    
-    function checkUncheckAll( name, check ) {
-        $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check);
-    }
-    
-    // Inserts the Select All / Unselect All buttons for checkboxes
-    $("div.checkUncheckAllPlaceholder").each( function() {
-        var check_name = $(this).attr("checkbox_name");
-        select_link = $("<a class='action-button'></a>").text("Select All").click(function() {
-           checkUncheckAll(check_name, true);
-        });
-        unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() {
-           checkUncheckAll(check_name, false);
-        });
-        $(this).append(select_link).append(" ").append(unselect_link);
-    });
-});
+    %endif
 
-%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>
 
-</script>
-</head>
+</%def>
 
-<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 not input.visible:
-                <% pass %>
-            %elif 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} ${i+1}"></div>
-                    </div>
-                    %if rep_errors.has_key( '__index__' ):
-                        <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div>
-                    %endif
-                  %endfor
-                  <div class="form-row"><input type="submit" name="${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 + "|"
-                %>
-                %if input.value_ref_in_group:
-                    ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )}
-                %endif
-                ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )}
-            %elif input.type == "upload_dataset":
-                %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before
+<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )">
+    <%
+    from galaxy.util.expressions import ExpressionContext
+    other_values = ExpressionContext( tool_state, other_values )
+    %>
+    %for input_index, input in enumerate( inputs.itervalues() ):
+        %if not input.visible:
+            <% pass %>
+        %elif input.type == "repeat":
+          <div class="repeat-group">
+              <div class="form-title-row"><strong>${input.title_plural}</strong></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][0]
+                        rep_errors = errors[input.name][i]
                     else:
                         rep_errors = dict()
+                    index = repeat_state[i]['__index__']
                     %>
-                  ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )}
-                %else:
-                    <div class="repeat-group">
-                        <div class="form-title-row"><b>${input.group_title( other_values )}</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>File Contents for ${input.title_by_index( trans, i, other_values )}</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 ${input.title}"></div>
-                    </div>
+                    <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></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} ${i+1}"></div>
+                </div>
+                %if rep_errors.has_key( '__index__' ):
+                    <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div>
                 %endif
+              %endfor
+              <div class="form-row"><input type="submit" name="${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 + "|"
+            %>
+            %if input.value_ref_in_group:
+                ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )}
+            %endif
+            ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )}
+        %elif input.type == "upload_dataset":
+            %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before
+                <%
+                if input.name in errors:
+                    rep_errors = errors[input.name][0]
+                else:
+                    rep_errors = dict()
+                %>
+              ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )}
             %else:
-                ${row_for_param( prefix, input, tool_state, errors, other_values )}
-            %endif
-        %endfor  
-    </%def>
-    
-    <%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )">
-        <%
-        if parent_errors.has_key( param.name ):
-            cls = "form-row form-row-error"
-        else:
-            cls = "form-row"
-            
-        label = param.get_label()
-        
-        field = param.get_html_field( trans, parent_state[ param.name ], other_values )
-        field.refresh_on_change = param.refresh_on_change
-        
-        # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully.
-        field_html = field.get_html( prefix )
-        if type( field_html ) is not unicode:
-            field_html = unicode( field_html, 'utf-8' )
-        
-        if param.type == "hidden":
-            return field_html
-        %>
-        <div class="${cls}">
-            %if label:
-                <label for="${param.name}">${label}:</label>
-            %endif
-            <div class="form-row-input">${field_html}</div>
-            %if parent_errors.has_key( param.name ):
-                <div class="form-row-error-message">
-                    <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div>
+                <div class="repeat-group">
+                    <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></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"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></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>
             %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">
+        %else:
+            ${row_for_param( prefix, input, tool_state, errors, other_values )}
+        %endif
+    %endfor
+</%def>
+
+<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )">
+    <%
+    if parent_errors.has_key( param.name ):
+        cls = "form-row form-row-error"
+    else:
+        cls = "form-row"
+
+    label = param.get_label()
+
+    field = param.get_html_field( trans, parent_state[ param.name ], other_values )
+    field.refresh_on_change = param.refresh_on_change
+
+    # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully.
+    field_html = field.get_html( prefix )
+    if type( field_html ) is not unicode:
+        field_html = unicode( field_html, 'utf-8' )
+
+    if param.type == "hidden":
+        return field_html
+    %>
+    <div class="${cls}">
+        %if label:
+            <label for="${param.name}">${label}:</label>
+        %endif
+        <div class="form-row-input">${field_html}</div>
+        %if parent_errors.has_key( param.name ):
+            <div class="form-row-error-message">
+                <div><img style="vertical-align: middle;" src="${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;">
+                ${param.help}
+            </div>
+        %endif
+
+        <div style="clear: both;"></div>
+
+    </div>
+</%def>
+
+<% overlay(visible=False) %>
+
+%if add_frame.from_noframe:
+    <div class="warningmessage"><strong>Welcome to Galaxy</strong><hr/>
         It appears that you found this tool from a link outside of Galaxy.
@@ -205,60 +232,59 @@
         <a href="${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="$add_frame.wiki_url" target="_top">Galaxy wiki</a>.
-        </div>
-        <br/>
+    </div>
+    <br/>
+%endif
+
+## handle calculating the redict url for the special case where we have nginx proxy
+## upload and need to do url_for on the redirect portion of the tool action
+<%
+    try:
+        tool_url = h.url_for(tool.action)
+    except AttributeError:
+        assert len(tool.action) == 2
+        tool_url = tool.action[0] + h.url_for(tool.action[1])
+%>
+<div class="toolForm" id="${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
-    
-    ## handle calculating the redict url for the special case where we have nginx proxy
-    ## upload and need to do url_for on the redirect portion of the tool action
-    <%
-        try:   
-            tool_url = h.url_for(tool.action)
-        except AttributeError:
-            assert len(tool.action) == 2
-            tool_url = tool.action[0] + h.url_for(tool.action[1])
-    %><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="${tool_url}" enctype="${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], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )}
-                    <input type="submit" class="primary-button" name="runtool_btn" value="Execute">
-                %else:
-                    ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )}
-                    <div class="form-row">
-                        %if tool_state.page == tool.last_page:
-                            <input type="submit" class="primary-button" name="runtool_btn" value="Execute">
-                        %else:
-                            <input type="submit" class="primary-button" name="runtool_btn" value="Next step">
-                        %endif
-                    </div>
-                %endif    
-            </form>
+    <div class="toolFormBody">
+        <form id="tool_form" name="tool_form" action="${tool_url}" 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], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )}
+                <input type="submit" class="primary-button" name="runtool_btn" value="Execute">
+            %else:
+                ${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 = tool.help_by_page[tool_state.page]
+                else:
+                    tool_help = tool.help
+
+                # Convert to unicode to display non-ascii characters.
+                if type( tool_help ) is not unicode:
+                    tool_help = unicode( tool_help, 'utf-8')
+            %>
+            ${tool_help}
         </div></div>
-    %if tool.help:
-        <div class="toolHelp">
-            <div class="toolHelpBody">
-                <%
-                    if tool.has_multiple_pages:
-                        tool_help = tool.help_by_page[tool_state.page]
-                    else:
-                        tool_help = tool.help
-                    
-                    # Convert to unicode to display non-ascii characters.
-                    if type( tool_help ) is not unicode:
-                        tool_help = unicode( tool_help, 'utf-8')
-                %>
-                ${tool_help}
-            </div>        
-        </div>
-    %endif
-</body>
-</html>
+%endif

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: kanwei: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well.

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