... in other words to note where index in the resulting tuple is not actually used. Doing this to enable hiding this implementation detail (index) from components in subsequent commits.
May seem sort of like Tool Shed specific stuff - but I think it can be reused elsewhere down the road. Regardless of this however as of this commit no external components directly access ToolBox.tool_panel or ToolBox.integrated_tool_panel - which I think is important - these should be internal details of the ToolBox (or newer modules it leverages).
Start a gradual process of referring to these as dynamic tool confs instead of shed tool confs. I would like like to make them more generally Galaxy-managed tool configurations and distinguish them from deployer-managed configurations - rather then having overtly ToolShed-only logic in ToolBox.
Create one public method load_item on ToolBox that should be used externally instead of load_tool_tag_set, load_section_tag_set, etc.... This reduces the duplication within the toolbox and between the toolbox and the Tool Shed's ToolPanelManager. Probably more importantly it also is another step down the road toward hiding implementation details such as toolbox.tool_panel and toolbox.intergrated_tool_panel from the ToolPanelManager.
Already had unit test coverage for ToolPanelManager stuff here - but added test coverage for loading labels, workflows, and tool directories.
... objects (directly anyway). I would like to refactor all the tool shed components to not deal directly with ToolSection objects but instead just pass around IDs.
Instead of reloading upload actions at this level and exposing tools_by_id - move this logic into the ToolBox in a new method called handle_datatypes_changed().
Big conditional in remove_guids switched on sectioned versus un-sectioned with very little difference in what was actually being done. This reduces the cyclomatic complexity of that method from 35 down to 26 (though it is still the most 'complex' method in that file by a wide margin).
Now with unit test. Part of broader effort to make ToolBox interface more explicit, tested, and hide implementation details from other parts of code (such as ToolPanelManager).
Also reworked the code to now build up and re-parse XML structures - just use a dictionary - thanks to 34b3e1c.
Hides some details of writing out integrated tool panel, reindexing, etc... from tool shed install code and reduces duplicatation in tool shed's tool_panel_manager.
Add unit tests.
John Chilton