2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fa8bdf1f6fc7/ Changeset: fa8bdf1f6fc7 Branch: stable User: inithello Date: 2014-02-14 21:59:35 Summary: Also check for tool config path when installing migrated tools and rewriting the tool_conf.xml. This resolves the issue described in pull request 324. Affected #: 1 file diff -r 75672e1cba2bd569b729156f3d8f8f1f994240f0 -r fa8bdf1f6fc7318d120a3420c50e4045dbdb1e8b lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -197,8 +197,7 @@ file_path = section_elem.get( 'file', None ) if file_path: file_name = suc.strip_path( file_path ) - - if file_name in tool_configs_to_filter: + if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter: elem.remove( section_elem ) persist_required = True if persist_required: @@ -223,7 +222,7 @@ # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' ) proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: + if tool_config == proprietary_name or tool_config == proprietary_tool_config: # The tool is loaded outside of any sections. tool_sections.append( None ) if not is_displayed: @@ -235,7 +234,7 @@ # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = section_elem.get( 'file' ) proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: + if tool_config == proprietary_name or tool_config == proprietary_tool_config: # The tool is loaded inside of the section_elem. tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) if not is_displayed: @@ -314,7 +313,7 @@ file_path = elem.get( 'file', None ) if file_path: name = suc.strip_path( file_path ) - if name in migrated_tool_configs: + if name in migrated_tool_configs or file_path in migrated_tool_configs: if elem not in tool_panel_elems: tool_panel_elems.append( elem ) elif elem.tag == 'section': @@ -324,7 +323,7 @@ file_path = section_elem.get( 'file', None ) if file_path: name = suc.strip_path( file_path ) - if name in migrated_tool_configs: + if name in migrated_tool_configs or file_path in migrated_tool_configs: # Append the section, not the tool. if elem not in tool_panel_elems: tool_panel_elems.append( elem ) https://bitbucket.org/galaxy/galaxy-central/commits/5079dae08441/ Changeset: 5079dae08441 User: inithello Date: 2014-02-14 22:00:00 Summary: Merge bugfix from stable. Affected #: 1 file diff -r 479b72075bc8a68ec602081987375ca1dfa20a2f -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -197,8 +197,7 @@ file_path = section_elem.get( 'file', None ) if file_path: file_name = suc.strip_path( file_path ) - - if file_name in tool_configs_to_filter: + if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter: elem.remove( section_elem ) persist_required = True if persist_required: @@ -223,7 +222,7 @@ # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' ) proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: + if tool_config == proprietary_name or tool_config == proprietary_tool_config: # The tool is loaded outside of any sections. tool_sections.append( None ) if not is_displayed: @@ -235,7 +234,7 @@ # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = section_elem.get( 'file' ) proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: + if tool_config == proprietary_name or tool_config == proprietary_tool_config: # The tool is loaded inside of the section_elem. tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) if not is_displayed: @@ -314,7 +313,7 @@ file_path = elem.get( 'file', None ) if file_path: name = suc.strip_path( file_path ) - if name in migrated_tool_configs: + if name in migrated_tool_configs or file_path in migrated_tool_configs: if elem not in tool_panel_elems: tool_panel_elems.append( elem ) elif elem.tag == 'section': @@ -324,7 +323,7 @@ file_path = section_elem.get( 'file', None ) if file_path: name = suc.strip_path( file_path ) - if name in migrated_tool_configs: + if name in migrated_tool_configs or file_path in migrated_tool_configs: # Append the section, not the tool. if elem not in tool_panel_elems: tool_panel_elems.append( elem ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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