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.
e.g:
Exception exceptions.TypeError: TypeError('<galaxy.datatypes.metadata.MetadataTempFile object at 0x40d9a10> is not JSON serializable',) in <bound method MutableAttrInstanceState._cleanup of <sqlalchemy.orm.state.MutableAttrInstanceState object at 0x40d99d0>> ignored
Currently this is supported in the local runner (long running set_meta() can now be canceled the same as with jobs) and in the non-staging PBS runner.
There is a slight change to how new Metadata FileParameters are to be created in datatype.set_meta(), see the MAF datatype.
TODO:
Prevent editing of metadata on a running job when metadata is to be set externally.
Have datasets which were copied before job completion use the metadata from the original output dataset; currently .set_meta() is called locally on these.
Dannon Baker