Merge.

lib/galaxy/objectstore/__init__.py

@@ -223,7 +223,7 @@ class DiskObjectStore(ObjectStore):
         if not os.path.exists(path):
             return self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name)
     
-    def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, **kwargs):
         """ Construct the expected absolute path for accessing the object
             identified by `obj`.id.
         

lib/galaxy/tools/__init__.py

@@ -2181,7 +2181,7 @@ class Tool:
                                                                           sa_session=self.sa_session )
                 self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset )
                 # Move data from temp location to dataset location
-                self.app.object_store.update_from_file(child_dataset.dataset, filename, create=True)
+                self.app.object_store.update_from_file(child_dataset.dataset, file_name=filename, create=True)
                 self.sa_session.add( child_dataset )
                 self.sa_session.flush()
                 child_dataset.set_size()
@@ -2248,7 +2248,7 @@ class Tool:
                 self.sa_session.add( primary_data )
                 self.sa_session.flush()
                 # Move data from temp location to dataset location
-                self.app.object_store.update_from_file(primary_data.dataset, filename, create=True)
+                self.app.object_store.update_from_file(primary_data.dataset, file_name=filename, create=True)
                 primary_data.set_size()
                 primary_data.name = "%s (%s)" % ( outdata.name, designation )
                 primary_data.info = outdata.info

lib/galaxy/web/controllers/admin_toolshed.py

@@ -367,6 +367,22 @@ class AdminToolshed( AdminGalaxy ):
             shed_tool_conf = shed_tool_conf.replace( './', '', 1 )
             shed_tool_conf_select_field = None
         tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
+        if includes_tools:
+            # If we're installing a single repository that contains a readme file, get it's contents to display.
+            decoded_repo_info_dict = tool_shed_decode( repo_info_dict )
+            if len( decoded_repo_info_dict ) == 1:
+                name = decoded_repo_info_dict.keys()[ 0 ]
+                repo_info_tuple = decoded_repo_info_dict[ name ]
+                description, repository_clone_url, changeset_revision = repo_info_tuple
+                owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
+                url = '%s/repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( tool_shed_url, name, owner, changeset_revision )
+                response = urllib2.urlopen( url )
+                readme_text = response.read()
+                response.close()
+            else:
+                readme_text = '' 
+        else:
+            readme_text = ''
         return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
                                     tool_shed_url=tool_shed_url,
                                     repo_info_dict=repo_info_dict,
@@ -375,6 +391,7 @@ class AdminToolshed( AdminGalaxy ):
                                     shed_tool_conf_select_field=shed_tool_conf_select_field,
                                     tool_panel_section_select_field=tool_panel_section_select_field,
                                     new_tool_panel_section=new_tool_panel_section,
+                                    readme_text=readme_text,
                                     message=message,
                                     status=status )
     @web.expose

lib/galaxy/webapps/community/config.py

@@ -86,6 +86,7 @@ class Configuration( object ):
         self.cloud_controller_instance = False
         self.server_name = ''
         self.job_manager = ''
+        self.default_job_handlers = []
         self.job_handlers = []
         self.tool_handlers = []
         self.tool_runners = []

lib/galaxy/webapps/community/controllers/repository.py

@@ -773,6 +773,25 @@ class RepositoryController( BaseUIController, ItemRatings ):
             ( galaxy_url, url_for( '/', qualified=True ), encoded_repo_info_dict, str( includes_tools ) )
         return trans.response.send_redirect( url )
     @web.expose
+    def get_readme( self, trans, **kwd ):
+        """
+        If the received changeset_revision includes a file named readme (case ignored), return it's contents.
+        """
+        name = kwd[ 'name' ]
+        owner = kwd[ 'owner' ]
+        changeset_revision = kwd[ 'changeset_revision' ]
+        repository = get_repository_by_name_and_owner( trans, name, owner )
+        repo_dir = repository.repo_path
+        repo = hg.repository( get_configured_ui(), repo_dir )
+        for root, dirs, files in os.walk( repo_dir ):
+            for name in files:
+                if name.lower() in [ 'readme', 'read_me' ]:
+                    f = open( os.path.join( root, name ), 'r' )
+                    text = f.read()
+                    f.close()
+                    return str( text )
+        return ''
+    @web.expose
     def get_tool_versions( self, trans, **kwd ):
         """
         For each valid /downloadable change set (up to the received changeset_revision) in the

templates/admin/tool_shed_repository/select_tool_panel_section.mako

@@ -62,3 +62,13 @@
         </form>
     </div>
 </div>
+%if readme_text:
+    <div class="toolForm">
+        <div class="toolFormTitle">Repository README file (may contain important installation or license information)</div>
+        <div class="toolFormBody">
+            <div class="form-row">
+                <pre>${readme_text}</pre>
+            </div>
+        </div>
+    </div>
+%endif