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Load empty tool sections into the in-memory tool_panel dictionary, just don't display them in the tool panel. Also include a fix for reactivating or unintallting a tool shed repository that includes tools - ToolVersion ovjects cannot be marked deleted.

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This commit is contained in:
Greg Von Kuster
2012-02-06 10:19:43 -05:00
parent 89072cd220
commit ca87cfd82a
3 changed files with 21 additions and 27 deletions
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lib/galaxy/tools/__init__.py
+1 -1
View File
@@ -295,7 +295,7 @@ class ToolBox( object ):
self.load_workflow_tag_set( sub_elem, elems )
elif sub_elem.tag == 'label':
self.load_label_tag_set( sub_elem, elems )
if key not in panel_dict and section.elems:
if key not in panel_dict:
panel_dict[ key ] = section
def load_tool( self, config_file, guid=None ):
"""
lib/galaxy/web/controllers/admin_toolshed.py
+2 -11
View File
@@ -499,18 +499,9 @@ class AdminToolshed( AdminGalaxy ):
metadata = repository.metadata
repository_tools_tups = get_repository_tools_tups( trans.app, metadata )
guids_to_activate = [ repository_tool_tup[1] for repository_tool_tup in repository_tools_tups ]
# Undelete the tool_version for each guid.
# Make sure we have a tool_version for each guid.
for guid_to_activate in guids_to_activate:
tool_version = get_tool_version( trans.app, guid_to_activate )
if tool_version:
if tool_version.deleted:
# This should not happen as we are currently not marking tool versions as deleted
# upon deactivation. We may decide to eliminate the tool_version.deleted column
# at some point, but we'll keep it for now in case we decide its useful.
tool_version.deleted = False
trans.sa_session.add( tool_version )
trans.sa_session.flush()
else:
if not get_tool_version( trans.app, guid_to_activate ):
# We're somehow missing a tool_version, so create a new one.
tool_version = trans.model.ToolVersion( tool_id=guid_to_activate, tool_shed_repository=repository )
trans.sa_session.add( tool_version )
templates/root/tool_menu.mako
+18 -15
View File
@@ -365,22 +365,25 @@
${render_workflow( key, val, False )}
%elif key.startswith( 'section' ):
<% section = val %>
<div class="toolSectionTitle" id="title_${section.id}">
<span>${section.name}</span>
</div>
<div id="${section.id}" class="toolSectionBody">
<div class="toolSectionBg">
%for section_key, section_val in section.elems.items():
%if section_key.startswith( 'tool' ):
${render_tool( section_val, True )}
%elif section_key.startswith( 'workflow' ):
${render_workflow( section_key, section_val, True )}
%elif section_key.startswith( 'label' ):
${render_label( section_val )}
%endif
%endfor
## Render the section only if it is not empty.
%if section.elems:
<div class="toolSectionTitle" id="title_${section.id}">
<span>${section.name}</span>
</div>
</div>
<div id="${section.id}" class="toolSectionBody">
<div class="toolSectionBg">
%for section_key, section_val in section.elems.items():
%if section_key.startswith( 'tool' ):
${render_tool( section_val, True )}
%elif section_key.startswith( 'workflow' ):
${render_workflow( section_key, section_val, True )}
%elif section_key.startswith( 'label' ):
${render_label( section_val )}
%endif
%endfor
</div>
</div>
%endif
%elif key.startswith( 'label' ):
${render_label( val )}
%endif