Changed behavior of history import and added BioMart test instance.

lib/galaxy/interfaces/root.py

@@ -357,7 +357,7 @@ class Universe(common.Root):
             if not user_history.datasets:
                 trans.set_history( new_history )
             trans.log_event( "History imported, id: %s, name: '%s': " % (str(new_history.id) , new_history.name ) )
-            return trans.show_message( "History has been imported", refresh_frames=['history'])
+            return trans.fill_template("history_imported.tmpl", history=new_history)
         elif not user_history.datasets or confirm:
             new_history = self.copy_history(import_history)
             new_history.name = "imported: "+new_history.name
@@ -366,7 +366,7 @@ class Universe(common.Root):
             new_history.flush()
             trans.set_history( new_history )
             trans.log_event( "History imported, id: %s, name: '%s': " % (str(new_history.id) , new_history.name ) )
-            return trans.show_message( "History has been imported", refresh_frames=['history'])
+            return trans.fill_template("history_imported.tmpl", history=new_history)
         return trans.fill_template("history_import.tmpl", history=import_history)
 
     @web.expose

templates/history_imported.tmpl

@@ -0,0 +1,16 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<title> History Imported </title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<link href="/static/style/base.css" rel="stylesheet" type="text/css">
+<script language="JavaScript" type="text/javascript" src="/static/universe.js"></script>
+</head>
+<body>
+ 	<div class="toolForm">
+    <div class="toolFormTitle">History Imported</div>
+	<div class="infomessage">
+	History "$history.name" has been imported. Click <a href="/index">here</a> to begin.
+	</div>
+</body>
+</html>

tool_conf.xml.sample

@@ -9,6 +9,7 @@
     <tool file="data_source/ucsc_archaea.xml" />
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
+    <tool file="data_source/biomart_test.xml" />
     <tool file="data_source/encode_db.xml" />
     <tool file="data_source/hbvar.xml" />
     <tool file="validation/fix_errors.xml" />

tools/data_source/biomart.xml

@@ -5,7 +5,7 @@
 	
 	<command/>
 	
-	<inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
+	<inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
 		<display>go to BioMart Central $GALAXY_URL</display>
 		<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
 	</inputs>

tools/data_source/biomart_filter.py

@@ -1,4 +1,5 @@
 #TODO: Set dbkey to proper UCSC build, if known
+# Greg Von Kuster
 import urllib
 
 from galaxy import datatypes, config

tools/data_source/biomart_test.xml

@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool name="BioMart" id="biomart">
+	
+	<description>Test server</description>
+	
+	<command/>
+	
+	<inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
+		<display>go to BioMart Central $GALAXY_URL</display>
+		<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
+	</inputs>
+	
+	<code file="biomart_filter.py"/>
+	
+	<outputs>
+		<data name="output" format="text" />
+	</outputs>
+	
+	<options sanitize="False" refresh="True"/>
+
+</tool>
+