Workflow round five, workflows can now be constructed from histories. See

the history options page for "Construct workflow" link. It allows you to
select which steps from the current history you want to convert.

This is currently not very robust to changes in tool configuration, so old
histories may cause errors. This will be fixable to some extent, but we'll
probably need to go back and look at the past changes to tool configs and
define some migration rules.

lib/galaxy/model/__init__.py

@@ -67,6 +67,15 @@ class Job( object ):
         # For historical reasons state propogates down to datasets
         for da in self.output_datasets:
             da.dataset.state = state
+    def get_param_values( self, app ):
+        """
+        Read encoded parameter values from the database and turn back into a
+        dict of tool parameter values.
+        """
+        param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] )
+        tool = app.toolbox.tools_by_id[self.tool_id]
+        param_dict = tool.params_from_strings( param_dict, app )
+        return param_dict
                 
 class JobParameter( object ):
     def __init__( self, name, value ):

lib/galaxy/tools/__init__.py

@@ -280,6 +280,9 @@ class Tool:
                 log.exception( "Failed to parse tool tests" )
         else:
             self.tests = None
+        # Determine if this tool can be used in workflows
+        self.is_workflow_compatible = self.check_workflow_compatible()
+        
             
     def parse_inputs( self, root ):
         """
@@ -459,6 +462,19 @@ class Tool:
         for name in param.get_dependencies():
             context[ name ].refresh_on_change = True
         return param
+    
+    def check_workflow_compatible( self ):
+        # This is probably the best bet for detecting external web tools
+        # right now
+        if self.action != "/tool_runner/index":
+            return False
+        # HACK: upload is (as always) a special case becuase file parameters
+        #       can't be persisted.
+        if self.id == "upload1":
+            return False
+        # TODO: Anyway to capture tools that dynamically change their own
+        #       outputs?
+        return True
 
     def new_state( self, trans, all_pages=False ):
         """

lib/galaxy/tools/actions/__init__.py

@@ -44,7 +44,8 @@ class DefaultToolAction( object ):
         
         # FIXME: does this need to modify 'incoming' or should this be 
         #        moved into 'build_param_dict'? Is this just about getting the
-        #        metadata into the command line? 
+        #        metadata into the command line?
+        # NEED TO FIX THIS SOON.
         input_names = []
         input_ext = 'data'
         input_dbkey = incoming.get( "dbkey", "?" )

lib/galaxy/util/topsort.py

@@ -161,4 +161,49 @@ def topsort(pairlist):
             for x in numpreds.keys():
                 assert numpreds[x] > 0
         raise CycleError(answer, numpreds, successors)
-    return answer
+    return answer
+
+def topsort_levels(pairlist):
+    numpreds = {}   # elt -> # of predecessors
+    successors = {} # elt -> list of successors
+    for first, second in pairlist:
+        # make sure every elt is a key in numpreds
+        if not numpreds.has_key(first):
+            numpreds[first] = 0
+        if not numpreds.has_key(second):
+            numpreds[second] = 0
+
+        # if they're the same, there's no real dependence
+        if first == second:
+            continue
+
+        # since first < second, second gains a pred ...
+        numpreds[second] = numpreds[second] + 1
+
+        # ... and first gains a succ
+        if successors.has_key(first):
+            successors[first].append(second)
+        else:
+            successors[first] = [second]
+
+    answer = []
+    
+    while 1:
+        # Suck up everything without a predecessor.
+        levparents = [x for x in numpreds.keys() if numpreds[x] == 0]
+        if not levparents:
+            break
+        answer.append( levparents )
+        for levparent in levparents:
+            del numpreds[levparent]
+            if successors.has_key(levparent):
+                for levparentsucc in successors[levparent]:
+                    numpreds[levparentsucc] -= 1
+                del successors[levparent]
+        
+    if numpreds: 
+        # Everything in num_parents has at least one child -> 
+        # there's a cycle.
+        raise CycleError( answer, numpreds, successors )
+        
+    return answer

lib/galaxy/web/controllers/history.py

@@ -0,0 +1,158 @@
+from galaxy.web.base.controller import *
+
+from galaxy.tools.parameters import DataToolParameter
+from galaxy.tools import DefaultToolState
+from galaxy.tools.grouping import Repeat, Conditional
+from galaxy.datatypes.data import Data
+from galaxy.workflow import Workflow, WorkflowStep
+
+from galaxy.util.odict import odict
+
+import simplejson
+
+class HistoryController( BaseController ):
+    
+    def __get_job_dict( self, trans ):
+        """
+        Return a dictionary of Job -> [ Dataset ] mappings, for all finished
+        active Datasets in the current history and the jobs that created them.
+        """
+        history = trans.get_history()
+        # Get the jobs that created the datasets
+        warnings = set()
+        jobs = odict()
+        for dataset in history.active_datasets:
+            # FIXME: Create "Dataset.is_finished"
+            if dataset.state in ( 'new', 'running', 'queued' ):
+                warnings.add( "Some datasets still queued or running were ignored" )
+                continue
+            for assoc in dataset.creating_job_associations:
+                job = assoc.job
+                if job in jobs:
+                    jobs[ job ].append( ( assoc.name, dataset ) )
+                else:
+                    jobs[ job ] = [ ( assoc.name, dataset ) ]
+        return jobs, warnings    
+    
+    def __cleanup_param_values( self, inputs, values ):
+        """
+        Remove 'Data' values from `param_values` but track the associations
+        """
+        associations = []
+        names_to_clean = []
+        # dbkey is pushed in by the framework
+        if 'dbkey' in values:
+            del values['dbkey']
+        root_values = values
+        # Cleanup all data inputs
+        def cleanup( prefix, inputs, values ):
+            for key, input in inputs.items():
+                if isinstance( input, DataToolParameter ):
+                    tmp = values[key]
+                    values[key] = None
+                    # HACK: Nested associations are not yet working, but we
+                    #       still need to clean them up so we can serialize
+                    if not( prefix ):
+                        associations.append( ( tmp.hid, prefix + key ) )
+                    # Cleanup the other deprecated crap associated with datasets
+                    # as well. Worse, for nested datasets all the metadata is
+                    # being pushed into the root. FIXME: MUST REMOVE SOON
+                    key = prefix + key + "_"
+                    for k in root_values.keys():
+                        if k.startswith( key ):
+                            del root_values[k]            
+                elif isinstance( input, Repeat ):
+                    group_values = values[key]
+                    for i in range( len( group_values ) ):
+                        prefix = "%s_%d|" % ( key, i )
+                        cleanup( prefix, input.inputs, group_values[i] )
+                elif isinstance( input, Conditional ):
+                    group_values = values[input.name]
+                    current_case = group_values['__current_case__']
+                    prefix = "%s|" % ( key )
+                    cleanup( prefix, input.cases[current_case].inputs, group_values )
+        cleanup( "", inputs, values )
+        return associations
+    
+    @web.expose
+    def workflow_from_current_history( self, trans, job_ids=None, workflow_name=None ):
+        if trans.request.method == 'POST':
+            return self.workflow_from_current_history_post( trans, job_ids, workflow_name )
+        user = trans.get_user()
+        if not user:
+            return trans.show_error_message( "Must be logged in to create workflows" )
+        jobs, warnings = self.__get_job_dict( trans )
+        # Render
+        return trans.fill_template(
+                    "history/workflow_from_current_history.mako", 
+                    jobs=jobs,
+                    warnings=warnings )
+    
+    def workflow_from_current_history_post( self, trans, job_ids, workflow_name ):
+        user = trans.get_user()
+        if not user:
+            return trans.show_error_message( "Must be logged in to create workflows" )
+        # Ensure a list
+        if type( job_ids ) == str:
+            job_ids = [ job_ids ]
+        job_ids = [ int( id ) for id in job_ids ]
+        # Find each job, for security we (implicately) check that they are
+        # associated witha job in the current history. 
+        jobs, warnings = self.__get_job_dict( trans )
+        # Create a mapping from hid to ( job_id, output_name )
+        hid_to_output_pair = {}
+        for job, datasets in jobs.iteritems():
+            for assoc_name, data in datasets:
+                hid_to_output_pair[ data.hid ] = ( job.id, assoc_name )
+        # Mapping from job ids to workflow step ids (0, 1, 2, ...)
+        job_id_to_step_id = dict( ( job_id, i ) for ( i, job_id ) in enumerate( job_ids ) )
+        # Workflow to populate
+        workflow = Workflow()
+        # Back-translate each job
+        jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() )
+        for step_id, job_id in enumerate( job_ids ):
+            assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
+            job = jobs_by_id[ job_id ]
+            tool = trans.app.toolbox.tools_by_id[ job.tool_id ]
+            param_values = job.get_param_values( trans.app )
+            associations = self.__cleanup_param_values( tool.inputs, param_values )
+            step = WorkflowStep()
+            step.id = step_id
+            step.tool_id = job.tool_id
+            step.tool_inputs = param_values
+            for other_hid, input_name in associations:
+                other_job_id, other_name = hid_to_output_pair[ other_hid ]
+                # Only create association if the associated output dataset
+                # is being included in this workflow
+                if other_job_id in job_id_to_step_id:
+                    step.input_connections[input_name] = ( job_id_to_step_id[ other_job_id ], other_name )
+                else:
+                    step.input_connections[input_name] = None
+            workflow.steps[ step_id ] = step
+        # Try to order the nodes
+        workflow.order_nodes()
+        # And let's try to set up some reasonable locations
+        levorder = workflow.order_nodes_levels()
+        base_pos = 2510
+        for i, steps_at_level in enumerate( levorder ):
+            for j, step_id in enumerate( steps_at_level ):
+                step = workflow.steps[step_id]
+                step.position = dict( top = ( base_pos + 120 * j ),
+                                      left = ( base_pos + 220 * i ) )
+        # Store it
+        stored = model.StoredWorkflow.get_by( user = user, name = workflow_name )
+        if stored is None:
+            stored = model.StoredWorkflow()
+            stored.user = user
+            stored.name = workflow_name
+        stored.encoded_value = simplejson.dumps( workflow.to_simple() )
+        stored.flush()
+        # 
+        return trans.show_ok_message( "Workflow '%s' created.<br/><a target='_top' href='%s'>Click to load in workflow editor</a>"
+            % ( workflow_name, web.url_for( controller='workflow_editor', action=None, workflow_name=workflow_name ) ) )
+            
+            
+            
+        
+        
+        

lib/galaxy/web/controllers/workflow_editor.py

@@ -11,11 +11,12 @@ class WorkflowEditor( BaseController ):
     beta = True
     
     @web.expose
-    def index( self, trans ):
+    def index( self, trans, workflow_name=None ):
         user = trans.get_user()
         if not user:
             return trans.show_error_message( "Must be logged in to create or modify workflows" )
-        return trans.fill_template( "workflow_editor/index.mako" )
+        return trans.fill_template( "workflow_editor/index.mako",
+                                    workflow_name=workflow_name )
     
     @web.expose
     def canvas( self, trans ):
@@ -67,6 +68,7 @@ class WorkflowEditor( BaseController ):
             decode_state( node, trans.app )
         # Create workflow from json data
         workflow = Workflow.from_simple( data )
+        workflow.order_nodes()
         # Store it
         stored = model.StoredWorkflow.get_by( user = user, name = workflow_name )
         if stored is None:

lib/galaxy/workflow/__init__.py

@@ -1,5 +1,5 @@
 from galaxy.tools import DefaultToolState
-from galaxy.util.topsort import topsort, CycleError
+from galaxy.util.topsort import topsort, topsort_levels, CycleError
 
 class Workflow( object ):
  
@@ -21,7 +21,6 @@ class Workflow( object ):
             if step.has_errors:
                 workflow.has_errors = True
             workflow.steps[ id ] = step
-        workflow.node_order = workflow.order_nodes()
         return workflow
     
     def to_simple( self ):
@@ -35,27 +34,40 @@ class Workflow( object ):
                      has_cycles=self.has_cycles,
                      has_errors=self.has_errors )
 
+    def edge_list( self ):
+        edges = []
+        all_ids = set( self.steps.keys() )
+        for step in self.steps.values():
+            edges.append( ( step.id, step.id ) )
+            for name, conn in step.input_connections.iteritems():
+                if conn is not None:
+                    other_node_id, _ = conn
+                    edges.append( ( other_node_id, step.id ) )
+        return edges
+
     def order_nodes( self ):
         """
         Perform topological sort of the steps, return an ordered list of ids
         """
         self.has_cycles = False
-        edges = []
-        all_ids = set( self.steps.keys() )
-        for step in self.steps.values():
-            for name, conn in step.input_connections.iteritems():
-                if conn is not None:
-                    other_node_id, _ = conn
-                    edges.append( ( other_node_id, step.id ) )
+        edges = self.edge_list()
         try:
             node_order = topsort( edges )
-            node_order_set = set( node_order )
-            node_order.extend( [ id for id in all_ids if id not in node_order ] )
+            #node_order_set = set( node_order )
+            #node_order.extend( [ id for id in all_ids if id not in node_order ] )
             self.node_order = node_order
+            return self.node_order
         except CycleError:
             self.has_cycles = True
             self.node_order = None
-        return self.node_order
+            return None
+        
+    def order_nodes_levels( self ):
+        edges = self.edge_list()
+        try:
+            return topsort_levels( edges )
+        except CycleError:
+            return None
         
 class WorkflowStep( object ):
 

static/june_2007_style/base.css.tmpl

@@ -76,6 +76,15 @@ div.toolFormBody div.toolFormTitle
 	margin-bottom: 5px;
 }
 
+div.toolFormDisabled div.toolFormTitle {
+    background: ${layout_bg};
+    border-color: ${layout_border};
+}
+
+div.toolFormDisabled {
+    border-color: ${layout_border};
+}
+
 div.toolHelp
 { 
 }
@@ -86,6 +95,13 @@ div.toolHelpBody
 	overflow: auto;
 }
 
+div.titleRow {
+    font-weight: bold;
+    border-bottom: dotted gray 1px;
+    margin-bottom: 0.5em;
+    padding-bottom: 0.25em;
+}
+
 /* Forms */
 
 div.form-row 

static/june_2007_style/blue/base.css

@@ -76,6 +76,15 @@ div.toolFormBody div.toolFormTitle
 	margin-bottom: 5px;
 }
 
+div.toolFormDisabled div.toolFormTitle {
+    background: #eee;
+    border-color: #999;
+}
+
+div.toolFormDisabled {
+    border-color: #999;
+}
+
 div.toolHelp
 { 
 }
@@ -86,6 +95,13 @@ div.toolHelpBody
 	overflow: auto;
 }
 
+div.titleRow {
+    font-weight: bold;
+    border-bottom: dotted gray 1px;
+    margin-bottom: 0.5em;
+    padding-bottom: 0.25em;
+}
+
 /* Forms */
 
 div.form-row 
@@ -129,7 +145,7 @@ select, textarea, input[type="text"], input[type="file"]
 
 /* Messages */
 
-.errormessage, .warningmessage, .donemessage, .infomessage, .welcomeBlue, .welcomeRed
+.errormessage, .warningmessage, .donemessage, .infomessage, .welcomemessage
 {
     padding: 10px;
     padding-left: 52px;
@@ -162,20 +178,13 @@ select, textarea, input[type="text"], input[type="file"]
     background-color: #CCCCFF;
 }
 
-.welcomeBlue {
+.welcomemessage {
     padding-left: 10px;
     border-color: #6666AA;
     background-color: #CCCCFF;
     background-image: none;
 }
 
-.welcomeRed {
-    padding-left: 10px;
-    border-color: #AA6666;
-    background-color: #FFCCCC;
-    background-image: none;
-}
-
 .errormessagesmall, .warningmessagesmall, .donemessagesmall, .infomessagesmall 
 {
     padding: 5px;

templates/history/workflow_from_current_history.mako

@@ -0,0 +1,130 @@
+<!-- -->
+<!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="${h.url_for('/static/style/history.css')}" rel="stylesheet" type="text/css" />
+<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
+
+<style type="text/css">
+div.toolForm{
+    margin-top: 10px;
+    margin-bottom: 10px;
+}
+div.historyItem {
+    margin-right: 0;
+}
+th {
+    border-bottom: solid black 1px;
+}
+</style>
+
+<script type="text/javascript">
+## Always try to hide the history pane since it is redundant on this page
+if ( window.parent && window.parent.handle_minwidth_hint ) {
+    window.parent.handle_minwidth_hint( 10000 );
+}
+</script>
+
+</head>
+
+<body>
+
+<%def name="history_item( data )">
+    %if data.state in [ "no state", "", None ]:
+        <% data_state = "queued" %>
+    %else:
+        <% data_state = data.state %>
+    %endif
+    <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-$data.id">
+        <table cellpadding="0" cellspacing="0" border="0" width="100%">
+            <tr>
+                %if data_state != 'ok':
+                    <td style="width: 20px;">
+                        <div style='padding-right: 5px;'><img src="${h.url_for( '/static/style/data_%s.png' % data_state )}" border="0" align="middle"></div>
+                    </td>
+                %endif
+                <td>
+                    <div style="overflow: hidden;">
+                        <span class="historyItemTitle"><b>${data.hid}: ${data.display_name()}</b></span>
+                    </div>
+                </td>
+            </tr>
+        </table>
+    </div>
+</%def>
+
+<p>The following list contains each tool that was run to create the
+datasets in your current history. Please select those that you wish
+to include in the workflow.</p>
+
+<p>Tools which cannot be run interactively and thus cannot be incorporated
+into a workflow will be shown in gray.</p>
+
+%for warning in warnings:
+    <div class="warningmark">${warning}</div>
+%endfor
+
+<form method="post" action="${h.url_for()}">
+<div class='form-row'>
+    <label>Workflow name</label>
+    <input name="workflow_name" type="text" value="Unnamed workflow" />
+</div>
+<p><input type="submit" value="Create Workflow" /></p>
+
+<table border="0" cellspacing="0">
+    
+    <tr>
+        <th style="width: 47.5%">Tool</th>
+        <th style="width: 5%"></th>
+        <th style="width: 47.5%">History items created</th>
+    </tr>
+
+%for job, datasets in jobs.iteritems():
+
+    <%
+    tool = app.toolbox.tools_by_id[ job.tool_id ]
+    cls = "toolForm"
+    if not( tool.is_workflow_compatible ):
+        cls += " toolFormDisabled"
+        disabled = True
+    else:
+        disabled = False
+    %>
+    
+    <tr>
+        <td>
+            <div class="${cls}">
+
+                <div class="toolFormTitle">${tool.name}</div>
+                <div class="toolFormBody">
+                    %if disabled:
+                        <div style="font-style: italic; color: gray">This tool cannot be used in workflows</div>
+                    %else:
+                        <div><input type="checkbox" name="job_ids" value="${job.id}" checked="true" />Include "${tool.name}" in workflow</div>
+                    %endif
+                </div>
+            </div>
+        </td>
+        <td style="text-align: center;">
+            &#x25B6;
+        </td>
+        <td>
+            %for _, data in datasets:
+                <div>${history_item( data )}</div>     
+            %endfor
+        </td>
+    </tr>
+
+%endfor
+
+</table>
+
+</form>
+    
+</body>
+
+</html>

templates/history_options.tmpl

@@ -33,9 +33,12 @@ q( "a[@confirm]" ).click( function() {
     #if $len( $history.active_datasets ) > 0 and $history.user not in [ None , "" ]:
         <li><a href="$h.url_for('/history_new')">Create</a> a new empty history</li>
     #end if
+    #if $app.config.enable_beta_features
+    <li><a href="${h.url_for( controller='history', action='workflow_from_current_history' )}">Construct workflow</a> from the current history</li>
+    #end if
 #end if
-    <li><a href="$h.url_for('/history_share')" target="galaxy_main">share</a> current history</div>
-    <li><a href="$h.url_for('/history_delete', id=$history.id )" confirm="Are you sure you want to delete the current history?">delete</a> current history</div>
+    <li><a href="$h.url_for('/history_share')" target="galaxy_main">Share</a> current history</div>
+    <li><a href="$h.url_for('/history_delete', id=$history.id )" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div>
 </ul>
 
 </body>

templates/message.tmpl

@@ -19,6 +19,11 @@ if ( parent.frames && parent.frames.galaxy_history ) {
     parent.frames.galaxy_history.location.href="$h.url_for('/history')";
 }
 #end if
+
+if ( parent.handle_minwidth_hint )
+{
+    parent.handle_minwidth_hint( -1 );
+}
 </script>
 
 <body>

templates/workflow_editor/index.mako

@@ -11,6 +11,13 @@
 #center       { right: 309px; }
 #right-border { right: 300px; }
 #right        { width: 300px; }
+## /* Relative masthead size */
+## #masthead { height: 2.5em; }
+## #masthead div.title { font-size: 1.8em; }
+## #left, #left-border, #center, #right-border, #right {
+##     top: 2.5em;
+##     margin-top: 7px;
+## }
 </style>
 
 <script type='text/javascript' src="/static/scripts/jquery.js"> </script>
@@ -119,7 +126,25 @@ $( function() {
 });
 
 function notify() {
+    %if workflow_name:
+    $.ajax( {
+       url: "${h.url_for( action='load_workflow' )}",
+       data: { workflow_name: "${workflow_name}" },
+       dataType: 'json',
+       success: function( data ) {
+            window.frames.canvas.reset();
+            workflow.from_simple( data );
+            show_modal( "Workflow loaded", "Workflow loaded.", {
+                "Ok" : function () { hide_modal(); }
+            });
+        },
+        beforeSubmit: function( data ) {
+            show_modal( "Loading workflow", "progress" );
+        }
+    });
+    %else:
     hide_modal();
+    %endif
 };
 
 function show_form_for_tool( text, node ) {
@@ -149,6 +174,10 @@ function show_form_for_tool( text, node ) {
 
 var save_current_workflow = function () {
     var body = $("#save-dialog-form").clone();
+    if ( workflow.name ) {
+        body.find( "input[name='workflow_name']" ).get(0).value = workflow.name;
+    }
+    body.find( "input[name='workflow_name']" ).get(0).focus();
     var form = body.find( "form" ).ajaxForm( {
         dataType: 'json',
         success: function( data ) { 
@@ -261,6 +290,16 @@ div.toolTitle {
     display: list-item;
     list-style: square outside;
 }
+div.toolTitleDisabled {
+    padding-top: 5px;
+    padding-bottom: 5px;
+    margin-left: 16px;
+    margin-right: 10px;
+    display: list-item;
+    list-style: square outside;
+    font-style: italic;
+    color: gray;
+}
 div.toolFormRow {
     position: relative;
 }
@@ -279,13 +318,6 @@ div.toolFormRow {
     z-index: 50000;
 }
 
-div.titleRow {
-    font-weight: bold;
-    border-bottom: dotted gray 1px;
-    margin-bottom: 0.5em;
-    padding-bottom: 0.25em;
-}
-
 </style>
 
 </head>
@@ -334,22 +366,29 @@ div.titleRow {
                           <div class="toolSectionBg">
                              %for tool in section.tools:
                                 %if not tool.hidden:
-                                <div class="toolTitle">
-                                  ## #if $tool.input_required
-                                  ##    #set $link = $h.url_for( 'tool_runner', tool_id=$tool.id )
-                                  ## #else
-                                  ##    #set $link = $h.url_for( $tool.action, ** $tool.get_static_param_values( $t ) )
-                                  ## #end if
-                                  %if "[[" in tool.description and "]]" in tool.description:
-                                    ${tool.description.replace( '[[', '<a href="javascript:add_node_for_tool( ${tool.id} )">' % tool.id ).replace( "]]", "</a>" )}
-                                  %elif tool.name:
-                                    <a id="link-${tool.id}" href="javascript:add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description}
-                                  %else:
-                                    <a id="link-${tool.id}" href="javascript:add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a>
-                                  %endif
-                                </div>
+                                    %if tool.is_workflow_compatible:
+                                        <div class="toolTitle ">
+                                            %if "[[" in tool.description and "]]" in tool.description:
+                                                ${tool.description.replace( '[[', '<a id="link-${tool.id}" href="javascript:add_node_for_tool( ${tool.id} )">' % tool.id ).replace( "]]", "</a>" )}
+                                            %elif tool.name:
+                                                <a id="link-${tool.id}" href="javascript:add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description}
+                                            %else:
+                                                <a id="link-${tool.id}" href="javascript:add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a>
+                                            %endif
+                                        </div>
+                                    %else:
+                                        <div class="toolTitleDisabled">
+                                            %if "[[" in tool.description and "]]" in tool.description:
+                                                ${tool.description.replace( '[[', '' % tool.id ).replace( "]]", "" )}
+                                            %elif tool.name:
+                                                ${tool.name} ${tool.description}
+                                            %else:
+                                                ${tool.description}
+                                            %endif
+                                        </div>
+                                    %endif
                                 %endif
-                             %endfor
+                            %endfor
                           </div>
                        </div>
                     %endfor
@@ -378,7 +417,7 @@ div.titleRow {
                     <div class="center-block-inner">Details</div>
                 </div>
             </div>
-            <div class="unified-panel-body">
+            <div class="unified-panel-body" style="overflow: scroll;">
                 <div id="right-content"></div>
             </div>
         </div>