For instance, fixes#3859 restoring the correct ``element_identifier`` for reduces collections in conditionals. Add tests for combinations of repeats and conditionals.
It seems like the client is correctly setting the UUID to None, but the backend is treating the None as a UUID because it was (incorrectly IMO) making a distinction between ``uuid`` being absent and being set to ``None``.
Fixes#3845.
Currently the logs contain fairly uninformative step delayed messages that don't allow admins to understand why parts of the workflow are being delayed during scheduling.
Here are some examples of before and after.
When running the test:
```
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_pause
```
Before these lines would show up:
```
galaxy.workflow.run DEBUG 2017-03-30 09:23:47,327 Workflow step 2 of invocation 1 invoked (174.149 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:23:47,347 Workflow step 3 of invocation 1 invoked (19.355 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:23:47,364 Workflow step 4 of invocation 1 delayed (16.262 ms)
```
Now these same lines are as follows:
```
galaxy.workflow.run DEBUG 2017-03-30 09:19:28,601 Workflow step 2 of invocation 1 invoked (172.849 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:19:28,619 Marking step 3 outputs delayed (executing pause step)
galaxy.workflow.run DEBUG 2017-03-30 09:19:28,620 Workflow step 3 of invocation 1 invoked (17.999 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:19:28,633 Workflow step 4 of invocation 1 delayed (dependent step [3] delayed, so this step must be delayed) (13.398 ms)
```
Also, when running the test:
```
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections_3
```
Before these lines would be printed:
```
galaxy.workflow.run DEBUG 2017-03-30 09:25:35,910 Workflow step 4 of invocation 1 invoked (281.479 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:25:35,937 Workflow step 5 of invocation 1 delayed (25.904 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:25:35,970 Workflow step 6 of invocation 1 delayed (32.597 ms)
```
Now these same lines are as follows:
```
galaxy.workflow.run DEBUG 2017-03-30 09:27:54,270 Workflow step 4 of invocation 1 invoked (295.826 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:27:54,315 Workflow step 5 of invocation 1 delayed (dependent collection [1] not yet populated with datasets) (44.581 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:27:54,326 Workflow step 6 of invocation 1 delayed (dependent step [5] delayed, so this step must be delayed) (10.804 ms)
```
When running workflows with steps that depend explicitly on other steps (instead of implicitly between dataset connections), lines such as:
```
galaxy.workflow.run DEBUG 2017-03-30 09:33:52,966 Marking step 3 outputs delayed (workflow paused at this step waiting for review)
galaxy.workflow.run DEBUG 2017-03-30 09:33:53,001 Workflow step 4 of invocation 1 delayed (dependent step [3] delayed, so this step must be delayed) (0.157 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:33:53,001 Workflow step 5 of invocation 1 delayed (depends on step [4] but that step has not been invoked yet) (0.084 ms)
```
and
```
galaxy.workflow.run DEBUG 2017-03-30 09:33:57,090 Workflow step 5 of invocation 1 delayed (depends on step [4] but one or more jobs created from that step have not finished yet) (0.144 ms)
```
now may appear.
Lets revisit the problem that background scheduling workflows (as is the default UI behavior as of 16.10) makes it easier for histories to contain datasets interleaved from different workflow invocations under certain reasonable conditions (https://github.com/galaxyproject/galaxy/issues/3474).
Considering only a four year old workflow and tool feature set (no collection operations, no dynamic dataset discovery, only tool and input workflow modules), all workflows can and will fully schedule on the first scheduling iteration. Under those circumstances, this solution is functionally equivalent to history_local_serial_workflow_scheduling introduced #3520 - but should be more performant because all such workflows fully schedule in the first iteration and the double loop introduced here https://github.com/galaxyproject/galaxy/pull/3520/files#diff-d7e80a366f3965777de95cb0f5b13a4e is avoided for each workflow invocation for each iteration. This addresses both concerns I outlined [here](https://github.com/galaxyproject/galaxy/issues/3816#issuecomment-289323288).
For workflows that use certain classes of newer tools or newer workflow features - I'd argue this approach will not degrade as harshly as enabling history_local_serial_workflow_scheduling.
For instance, imagine a workflow with a dynamic dataset collection output step (such as used by IUC tools Deseq2, Trinity, Stacks, and various Mothur tools) half way through that takes 24 hour of queue time to reach. Now imagine a user running 5 such workflows at once.
- Without this and without history_local_serial_workflow_scheduling, the 5 workflows will each run as fast as possible and the UI will show as much of each workflow as can be scheduled but the order of the datsets may be shuffled. The workflows will be complete for the users in 48 hours.
- With history_local_serial_workflow_scheduling enabled, only 1 workflow will be scheduled only half way for the first 24 hours and the user will be given no visual indication for why the other workflows are not running for 1 day. The final workflow output will take nearly a week to be complete for the users.
- With this enabled - the new default in this commit - each workflow will be scheduled in two chunks but these chunks will be contingious and it should be fairly clear to the user what tool caused the discontinuity of the datasets in the history. So things are still mostly ordered, but the draw backs of history_local_serial_workflow_scheduling are avoided entirely. Namely, the other four workflows aren't hidden from the user without a UI indication and the workflows will still only take 48 hours to be complete and outputs ready for the user.
The only drawback of this new default behavior is that you could potentially see some performance improvements by scheduling multiple workflow invocations within one history - but this was never a design goal in my mind when implementing background scheduling and under typical Galaxy use cases I don't think this would be worth the UI problems. So, the older behavior can be re-enabled by setting parallelize_workflow_scheduling_within_histories to True in galaxy.ini but it won't be on by default or really recommended if the Galaxy UI is being used.
- When registering, put a little pause in after clicking to ensure the browser has a chance to submit the request before continuing to check if indeed the user is logged in.
- If the user doesn't appear to be logged in, dump the contents of the user menu out so we can see if a different user is logged in or if there is no log in.
- Attempt to be more robust about conditions being waited on when clicking history option menu - in case clicks were being fired during jQuery transitions or something.
xref #3838
Check frame column in Gff.sniff() and Gtf.sniff() .
Parse attributes column in Gff3.sniff() with a specific function to prevent
non-compliant GTF files being recognised as GFF3.
Björn Grüning