In practice we use ParsedFiler.filter_type to discriminate
the different filter types. Filters that require the correct
model class for a specific query are now functions that take
a model_class and generate the correct filter.
Report if empty inputs were used or if the same input was used more than once, these were identified as common sources of potential errors across many tools. Neither of these are definite problems, but both could be depending on the tool and both happen frequently. Outline a few more ideas as TODOs in the code.
The included script takes in an object store definition to write to, model store output target (e.g. tar file or directory or bagit file/directory format matching the new history exports added in 7367), and a bunch of files in defined via an upload-2.0-style YAML - and writes the physical files into the object store and writes persisted metadata into the model store. The supplied script describes the input format as do the new unit tests in test_model_discover.py.
Right now datasets for a history and whole libraries (including recursive folders and library datasets) can be described this way. These concepts have been extended to collections in #7058 but only in the context of discovering job outputs and writing them to an export model store current.
This script was created mostly by refactoring stuff out of output_collect.py that is used to create datasets during output discovery (i.e. parsing the same data out of galaxy.json files).
If the user is not an admin.
Fixes https://github.com/galaxyproject/galaxy/issues/7710
An alternative would be to skip Accessibility / Ownership
exceptions, but given that we can just restrict the query
this seems like the better approach to me.
I want to be able to make more integration tests like test_pulsar_embedded.py, where we just define a configuration and then some tool tests to run. In particular this will be useful for extended metadata testing of the most interesting tools.
Setup forcing export of format2 workflows by default in next release. There should be a least one release between enabling them to be imported by default and exporting them by default anyway I think - so 19.09 workflows can still be used on slightly older Galaxy instances.
John Chilton