- Library dataset LDDAs can now be implicitly converted to another format. For this to happen, an HDA is created by copying the LDDA info, and the HDA is then used as the tool input parameter. The implicitly converted dataset table will map the LDDA to the resulting converted output HDA.
- Added set_output_history optional param to tool.execute to specify whether output dataset is added to the current (or specified) history. Defaults to true but is set to false for implicitly converted datasets so that it does not show up as a hidden history item, which show up in features like "extract workflow from history".
Initial pass at UI for adding data library datasets to trackster using the "Select Library, then Select Datasets" paradigm currently also used for adding history datasets. Currently uses browse_library.mako code but this will need to be enhanced for trackster's purposes.
The offending nodes are marked as having an error state, and the workflow cannot be saved.
This will enable users to at least look at and try to recover a workflow by removing (and potentially replacing) the offending steps, as well as providing a better view of what's actually wrong with the workflow.
Important: these changes only guarantee that use_panels is appended to page requests when necessary. It does not guarantee that controller methods work with use_panels or that methods behave correctly with and without panels.
- Fix track preferences not being applied
- Fix chroms not being selectable when a new track browser is created
- Fix ReferenceTrack not working with filters
- Fix visual analytics error when tool configuration has changed
Basic steps are:
-create subset of input data
-run tool with input data subset
-convert new output for display in trackster
-display in trackster
Although framework is applicable to any tool, only cufflinks wrapper has been augmented to work in visual analytics framework. Specifically, min and max values have been added to cufflinks' numerical parameters.
Currently, when a tool is run in trackster, all of a tool's input and output datasets are associated with the original dataset's history, though they are hidden.
Enhancements that were made to support visual analytics include:
-add UI for setting tool parameters in trackster;
-add tool_data method to trackster controller that reruns a tool and produce;
-refactoring of GFFReaderWrapper code for efficiency;
-enabling a tool's output datasets to be directed to a particular history rather than only the current history;
-optional 'min' and 'max' attributes for tool integer and float parameters;
-enable trackster data providers to write a region of data--defined by chrom, start, and end--to a file;
-styles for tool parameters and dynamic filters.
Remove the creation of a background element that closes the active menu clicked. Instead, bind an event to close active menus to the document object of current and all other framesets. Tested in IE.
Update Tool Search/Recently Used code to reflect new changes.
Made some small tweaks to pass JSlint
This resolves the issue with multiple HideDatasetActions being created.
Existing workflows displaying multiple HideDatasetActions per step on the Run Workflow screen will persist.
These extra HideDatasetActions are harmless, but a simple edit workflow -> save will remove them.
Kanwei Li