Continuation of work started by @nsoranzo here 92a152d89c. In addition to increasing the max timeout it will now print the timeout in the assertion error so we can see if it is being overridden and attempt to adjust timeouts too small.
For tools which dynamically discover datasets for an output collection, keep the collection yellow until the structure of the HDCA has been fully defined. HDCAs still have the problem that they will always be green even if datasets contained within are in error, running, or queued states - but at least the structure is now reflected in the color.
Runtime post job actions are post job actions inserted when the workflow is invoked instead of being part of the workflow object in the database. The bug noticed by @kellrott was that these actions were being appended to the original workflow post job actions instead of being transient things just attached to the jobs themselves.
This fixes that problem and adds a test to try to prevent regressions.
- Add example tool demonstrating/testing specifing format via conditional output actions.
- Add API test testing mapping collections over tools without output action formatting.
- Add API test testing more complex actions using the Cut1 tool.
- Add script to hit the API with workflows requests.
- Update testing Dockerfile to allow just booting up with a fixed master API key for this test to leverage.
- WIP: on updating test Dockerfile to work with slurm, multiple handlers, uwsgi, etc...
Going to use bioblend for performance testing instead of galaxy_interactor. This refactoring allows all of those helpers to be reused with bioblend backing the helpers instead of galaxy_interactor.
It would fail when being run with the rest of the suite and not on its own - because it was using the same id for the workflow id and invocation id - which is obviously wrong unless it is a completely fresh database :).
These aren't ideal tests - but it is some indication that things are working that the API will import the workflow and produce a representation. Should follow up at some point and verify the representation is in fact the correct one.
Tools may now use $input.element_identifier during tool evalution for input 'data' parameters with the following semantics:
- If the input was specified as a single dataset by the user - this just fallbacks to providing the $input.name.
- If the input was mapped over a collection (to produce many jobs) or if the input is a 'multiple="true"' input that was provided a collection - the $input.element_identifier will be the element identifier for the corresponding collection item (generally much more useful the dataset name - since if preserved throughout workflows).
'data_collection' parameters already can access this kind of information - but it is something of a best practice to use simple 'data' parameters since they are compatible with more traditional un-collected datasets.
This commit really needs more comments - but Philip Mabon has been patiently waiting for this functionality for a long time.
Normal selects seem to be prevented from execution with invalid parameter values, but not columns. Values are escaped properly so shell exploitation isn't the problem - but as a usability thing Galaxy should prevent execution and provide a warning message.
Models:
Track whether dataset collections have been populated yet.
Dataset collections are still effectively immutable once populated - but dynamic output collections require them to be sort of like `final` fields in Java (analogy courtesy of JJ) - allowing them to be declared before they are initialized or populated. This is tracked by the `populated_state` field.
Tools:
Output collections can now describe `discover_datasets` elements just like datasets - except in this case instead of dynamically populating new datasets in the history - they will comprise the collection. `designation` has been reused to serve as the element_identifier for the collection element corresponding to the dataset.
See Pull Request 356 for more information on the discover_datasets tag https://bitbucket.org/galaxy/galaxy-central/pull-request/356/enhancements-for-runtime-discovered.
Workflows:
Update workflow execution and recovery for dynamic output collections.
Galaxy workflow data flow before collections
* - * - * - * - * - *
Galaxy worfklow data flow after collections (iteration 1)
* - * - * \
* - * - *
* - * - * / \
* - * - *
* - * - * \ /
* - * - *
* - * - * /
Galaxy worfklow data flow after this commit
/ * - * \
* - * * - *
/ \ * - * / \
/ \
/ \
/ / * - * \ \
* - * -- * - * * - * -- * - *
\ \ * - * / /
\ /
\ /
\ / * - * \ /
* - * * - *
\ * - * /
By "static" I mean tools such as a FASTQ de-interlacer that would produce a "paired" collection with two datasets everytime. By "determinable" I mean tools that perform N->N operations within the same job - such as a tool that needs to normalize a bunch of datasets all at once and not in separate jobs. (For N->N collection operations that should or can be done in N separate jobs tool authors should just write tools that operate over a dataset and produce a dataset and let the end-user 'map over' that operation.)
There are still large classes of operations where the structure of the output collection cannot be pre-determined - such as splitting files (e.g. bam files by read group) - that are not implemented in this commit.
Model:
The models have been updated to do a more thorough job of tracking collection outputs. Jobs just producing HistoryDatasetCollectionAssociations works fine for simple jobs producing collections - but you don't want to map a list over a tool that produces a pair and produce a bunch of pairs HDCAs and a list:pair HDCA- you just want a bunch of pieces and the one list:pair at that the top.
Workflow:
Workflows containing such operations can be executed - but the workflow editor has not been updated to handle this complexity (and it will require a significant overhaul) so such tools are not available in the workflow editor.
Tool Testing:
This commit also introduces a new tool XML syntax for describing tests on output collections. See files test/functional/tools/collection_creates_list.xml and test/functional/tools/collection_creates_pair.xml for examples.
Tests:
Includes two tools to test this - one that uses explicit pair output names and one that iterates over the structure of input list to produce an output list.
Includes several new tools API tests that test the tools described above via the API and implicit mapping over such tools. Includes two new workflow API tests - one that verifies a simple workflow with output collections works and one that verifies mapping over workflow steps in collections works.
John Chilton