both from the dataset info page. The functional tests will now provide output
of these on tool test failure. The functional tests can now use
tool_dependency_dir as well.
Add support for a single "import_module" to be passed to the new load_datatypes() method in the datatypes registry. This provides the ability to load a single class module from an installed tool shed repository along with a datatypes_conf.xml file included in the installed repository and pass them to the new load_datatypes() method. In the future, multiple imported modules may be allowed. The datatypes_conf.xml file included in the repository must conform to a slightly different definition than the same named file that comes with the distribution. This new definition will be documented in the Galaxy tool shed wiki.
We now have the ability to load new data types into the Galaxy server from an installed tool shed repository without restarting the Galaxy server.
This patch adds messages for the "purge histories" step:
1. A message is printed when processing a new history (so that the user can tell to which history the following dataset/hda messages belong).
2. in "info_only" mode, a message is printed about each deleted history
3. in "info_only" mode, a message is printed for each HDA that is checked
4. The message for HDA is changed to include the associated dataset id.
1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all.
2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed.
3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags.
4. The final summary message is slightly changed.
an environment variable "GALAXY_TEST_SAVE" if defined before running functional tests
If the environment variable is empty, all tests procede as usual and test outputs are deleted
without saving
* Extract "section" headers from the toolbox XML file, and put them into the tool XML;
prepare the tool XML for associating "tags" with the tool.
* Build a toolbox XML file based on augmented tool XML files with section identification.
2. Clean up the code that renders the jquery file browser plugin - things work much cleaner now. One remaining item is handing the issue where rsh / ssh keys are not set. Also clean up a lot of code related to manual file transfers in the requests_admin controller.
3. In addition to the new ManualDataTransferPlugin, add the Pacific Biosciences SMRTPortalPlugin that automatically transfers files produced by SMRT Portal to a Galaxy data library.
4. Add the external service type config for Pac Bio SMRT Portal version 1.1.0.
Nate Coraor