Add ability to have a directory of files associated with an individual dataset. Relative links in html work.

Put all desired files in the directory specified in a tool XML as $output.files_path.
Example:
<command interpreter="python">script.py $input $output $output.files_path</command>
becomes:
python ./tools/filters/script.py ./database/files/dataset_1.dat ./database/files/dataset_2.dat ./database/tmp/dataset_2_files
Any file put in ./database/tmp/dataset_2_files will be accessable to html files using a relative link.

Directories are moved to a more permanent location only if they contain files.

lib/galaxy/jobs/__init__.py

@@ -286,6 +286,8 @@ class JobWrapper( object ):
         out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
         param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         param_dict = self.tool.params_from_strings( param_dict, self.app )
+        # Check for and move associated_files
+        self.tool.collect_associated_files(out_data)
         # Create generated output children and primary datasets and add to param_dict
         collected_datasets = {'children':self.tool.collect_child_datasets(out_data),'primary':self.tool.collect_primary_datasets(out_data)}
         param_dict.update({'__collected_datasets__':collected_datasets})

lib/galaxy/model/__init__.py

@@ -278,6 +278,8 @@ class Dataset( object ):
         self.purged = True
         try: os.unlink(self.file_name)
         except: pass
+        try: os.unlink(os.path.join(self.file_path, "dataset_%d_files" % (self.id)))
+        except: pass
     def get_converter_types(self):
         return self.datatype.get_converter_types( self, datatypes_registry)
     def add_validation_error( self, validation_error ):

lib/galaxy/tools/__init__.py

@@ -778,6 +778,8 @@ class Tool:
                 param_dict[ key ] = DatasetFilenameWrapper( child )
         for name, data in output_datasets.items():
             param_dict[name] = DatasetFilenameWrapper( data )
+            # Provide access to a path to store additional files
+            param_dict[name].files_path = os.path.join(self.app.config.new_file_path, "dataset_%s_files" % (data.id) )
             for child_association in data.children:
                 child = child_association.child
                 key = "_CHILD___%s___%s" % ( name, child.designation ) 
@@ -860,8 +862,18 @@ class Tool:
                 return code( *args, **kwargs )
         except Exception, e:
             e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ) )
-            raise 
-        
+            raise
+    
+    def collect_associated_files( self, output):
+        for name, outdata in output.items():
+            temp_file_path = os.path.join(self.app.config.new_file_path, "dataset_%s_files" % (outdata.id) )
+            try:
+                if len(os.listdir(temp_file_path)) > 0:
+                    store_file_path = os.path.join(self.app.config.file_path, "dataset_%s_files" % (outdata.id) )
+                    shutil.move(temp_file_path, store_file_path)
+            except:
+                continue
+    
     def collect_child_datasets( self, output):
         children = {}
         #Loop through output file names, looking for generated children in form of 'child_parentId_designation_visibility_extension'

lib/galaxy/web/buildapp.py

@@ -47,6 +47,7 @@ def app_factory( global_conf, **kwargs ):
     webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None )
     webapp.add_route( '/:controller/:action', action='index' )
     webapp.add_route( '/:action', controller='root', action='index' )
+    webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None)
     webapp.finalize_config()
     # Wrap the webapp in some useful middleware
     if kwargs.get( 'middleware', True ):

lib/galaxy/web/controllers/dataset.py

@@ -10,6 +10,10 @@ from cgi import escape, FieldStorage
 import smtplib
 from email.MIMEText import MIMEText
 
+import pkg_resources; 
+pkg_resources.require( "Paste" )
+import paste.httpexceptions
+
 log = logging.getLogger( __name__ )
 
 error_report_template = """
@@ -82,4 +86,34 @@ class DatasetInterface( BaseController ):
             s.close()
             return trans.show_ok_message( "Your error report has been sent" )
         except:
-            return trans.show_error_message( "An error occurred sending the report by email" )
+            return trans.show_error_message( "An error occurred sending the report by email" )
+    
+    @web.expose
+    def default(self, trans, dataset_id=None, **kwd):
+        return 'This link may not be followed from within Galaxy.'
+    
+    @web.expose
+    def display(self, trans, dataset_id=None, filename=None, **kwd):
+        """Catches the dataset id and displays file contents as directed"""
+        if filename is None or filename.lower() == "index":
+            try:
+                data = trans.app.model.Dataset.get( dataset_id )
+                if data:
+                    mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() )
+                    trans.response.set_content_type(mime)
+                    trans.log_event( "Display dataset id: %s" % str(dataset_id) )
+                    try:
+                        return open( data.file_name )
+                    except: 
+                        return "This item contains no content"
+            except:
+                pass
+            return "Invalid dataset specified"
+        else:
+            #display files from directory here
+            try:
+                file_path = os.path.join(trans.app.config.file_path, "dataset_%s_files" % (dataset_id))
+                file_path = os.path.join(file_path, filename)
+                return open(file_path)
+            except:
+                raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % (filename) )

templates/dataset_code.tmpl

@@ -111,7 +111,7 @@
                 </td>
                 <td>
                     <div>
-                        <div style="float: right;"><a href="$h.url_for( 'display', id=data.id )" target="_top"><img src="$h.url_for('/static/images/eye_icon.png')" rollover="$h.url_for('/static/images/eye_icon_dark.png')" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a>
+                        <div style="float: right;"><a href="/datasets/$data.id/display/index" target="_top"><img src="$h.url_for('/static/images/eye_icon.png')" rollover="$h.url_for('/static/images/eye_icon_dark.png')" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a>
                         <a href="edit?id=$data.id" target="galaxy_main"><img src="$h.url_for('/static/images/pencil_icon.png')" rollover="$h.url_for('/static/images/pencil_icon_dark.png')" width='16' height='16' alt='edit attributes' title='edit attributes' class='editButton' border='0'></a>
                         <a href="delete?id=$data.id" class="historyItemDelete" id="historyItemDelter-${data.id}"><img src="$h.url_for('/static/images/delete_icon.png')" rollover="$h.url_for('/static/images/delete_icon_dark.png')" width='16' height='16' alt='delete' class='deleteButton' border='0'></a>
                         <!--

templates/history.tmpl

@@ -179,7 +179,7 @@ div#footer {
                 </td>
                 <td>
                     <div>
-                        <div style="float: right;"><a href="$h.url_for( 'display', id=data.id )" target="_top"><img src="$h.url_for('/static/images/eye_icon.png')" rollover="$h.url_for('/static/images/eye_icon_dark.png')" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a>
+                        <div style="float: right;"><a href="/datasets/$data.id/display/index" target="_top"><img src="$h.url_for('/static/images/eye_icon.png')" rollover="$h.url_for('/static/images/eye_icon_dark.png')" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a>
                         <a href="edit?id=$data.id" target="galaxy_main"><img src="$h.url_for('/static/images/pencil_icon.png')" rollover="$h.url_for('/static/images/pencil_icon_dark.png')" width='16' height='16' alt='edit attributes' title='edit attributes' class='editButton' border='0'></a>
                         <a href="delete?id=$data.id" class="historyItemDelete" id="historyItemDelter-${data.id}"><img src="$h.url_for('/static/images/delete_icon.png')" rollover="$h.url_for('/static/images/delete_icon_dark.png')" width='16' height='16' alt='delete' class='deleteButton' border='0'></a>
                         <!--