- Admin are considered permitted when calling
** dataset_manager.permssions.access and
** dataset_manager.permissions.manage
- Update bad test
- Add admin test to other permission checks
Case made well by @erasche on #1746, fixes#1746.
To resolve this more correctly (and many other potential type problems) - the workflow editor should be significantly reworked to track the datatype (or a range of datatypes) on each terminal (the way it does for collection mapping information). The change would be a weeks worth of development effort and inappropriate to apply to a release branch.
Do the same relaxed thing we do for inputs of type 'input' as we do for outputs of this type. Someday we should have better tracking, but such a change is probably not wise for a release branch.
I was unable to reproduce #1531 in testing, but if the problem is something to do with stale state the following sledge hammer should fix it.
Runt the new test case with:
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_delete_intermediate_datasets_pja_1
I'm making more things configurable in case someday the BSD user wants to use Galaxy - the default shell for jobs can be configured at the galaxy or job destination level now.
Previously the job script underwent these checks and I had assumed since that got written later it would never be the case that tool_script.sh wouldn't be synchronized by the job script was - turns out file systems are more creative and less logical than one might expected.
Also increases the count for the number of syncs that will execute because 15 on rare occasion proved not to be enough as well as making both the count and sleep time configurable.
Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also.
Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem.
xref https://github.com/galaxyproject/tools-iuc/pull/412/files
Conflicts:
lib/galaxy/tools/actions/__init__.py
- Add monitor tag on toolbox root elements to force Galaxy to watch the toolbox for changes.
- Refactoring and test improvements for existing tool monitoring code.
- Implement toolbox shutdown process to ensure different watchers don't compete with each other.
- Set the default tool conf to be monitored.
- Add configuration option for overriding condarc location used by conda resolve commands.
- Default location of condarc to be in tool_dependency_dir.
- Delay updating the condarc to ensure channels until this would actually be needed (during package installation).
- Add configuration flag to allow Galaxy to *NOT* check the PATH for conda.
- Update unit test that verifies conda's installation to never use conda on PATH, since a precondition of this test is that certain packages haven't been installed previously.
- Change default behavior to not check the PATH for conda, everything else here I feel pretty good about - this I'm ambivalent about - it will reduce error reports and problems with network filesystems, but doesn't seem to be good Unix best practice.
Points 2 and 3 above should address this issue: https://github.com/galaxyproject/ansible-galaxy-extras/pull/33#issuecomment-168384555
This commit also addresses most of #1406.
- Drop version requirement per commends by @bgruening.
- Add examples for conditionals, repeats, sections, colors, and booleans specified truevalue/falsevalue.
- Various bug fixes unearthed by new test cases.
```
<configfiles>
<inputs name="inputs" format="json" version="1" />
</configfiles>
```
Version is specified as 1, because the Galaxy tool plumbing doesn't really distinguish between parameter is '', parameter was explicitly supplied as None, parameter was absent, etc... - everything is a just a string in some ways. This distinction may be more important with JSON and for instance the CWL will require more percision, so we may want to revise Galaxy's tool handling in a backward compatible way someday.
Guess here is that a flush is not occuring on that file because it is happening as part of garbage collection and not explictly as part of an explicit close.
carlfeberhard