If slurm decided the job is in error. There are configurations of slurm
that error out when cancelling the job monitor script, and others that
don't do this.
defintion.
Fixes
```
2022-02-03 12:40:03,491 ERROR [galaxy.web.framework.decorators] Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/web/framework/decorators.py", line 320, in decorator
rval = func(self, trans, *args, **kwargs)
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/webapps/galaxy/api/tools.py", line 563, in create
return self._create(trans, payload, **kwd)
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/webapps/galaxy/api/tools.py", line 631, in _create
vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job, input_format=input_format)
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/tools/__init__.py", line 1767, in handle_input
all_params, all_errors, rerun_remap_job_id, collection_info = self.expand_incoming(trans=trans, incoming=incoming, request_context=request_context, input_format=input_format)
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/tools/__init__.py", line 1747, in expand_incoming
populate_state(request_context, self.inputs, expanded_incoming, params, errors, simple_errors=False, input_format=input_format)
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 348, in populate_state
_populate_state_legacy(request_context, inputs, incoming, state, errors=errors, context=context, check=check, simple_errors=simple_errors)
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 408, in _populate_state_legacy
state[input.name] = input.get_initial_value(request_context, context)
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/tools/parameters/basic.py", line 1001, in get_initial_value
options = list(self.get_options(trans, other_values))
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/tools/parameters/basic.py", line 890, in get_options
return self.options.get_options(trans, other_values)
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/tools/parameters/dynamic_options.py", line 763, in get_options
rval = filter.filter_options(rval, trans, other_values)
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/tools/parameters/dynamic_options.py", line 207, in filter_options
if not r.metadata.element_is_set(self.key):
File "/tmp/tmp778b108w/galaxy-dev/lib/galaxy/model/metadata.py", line 175, in element_is_set
meta_spec = self.parent.metadata.spec[name]
KeyError: 'groups'
```
which happens when forcing a tabular dataset into a more specialized
input https://github.com/galaxyproject/tools-iuc/blob/e22821f51ae326b3696a9456cbc44f9982512a52/tools/mothur/homova.xml#L48
Arguably this is a tool issue, but we already log a KeyError above and
it seems more of a linting issue than something that should cause a test
failure.
```
Traceback (most recent call last):
File "lib/galaxy/jobs/runners/__init__.py", line 707, in monitor
self.check_watched_items()
File "lib/galaxy/jobs/runners/drmaa.py", line 338, in check_watched_items
if self._complete_terminal_job(ajs, drmaa_state=state) is not None:
File "lib/galaxy/jobs/runners/univa.py", line 85, in _complete_terminal_job
time_granted, mem_granted = _parse_native_specs(ajs.job_id, native_spec)
File "lib/galaxy/jobs/runners/univa.py", line 572, in _parse_native_specs
m = re.search(r"rt=([0-9:]+)[\s,]*", native_spec)
File "/pool/spare/galaxy/galaxy/.venv/lib64/python3.6/re.py", line 182, in search
return _compile(pattern, flags).search(string)
TypeError: expected string or bytes-like object
```
See https://github.com/galaxyproject/galaxy/issues/13297 reported by @ajs6f fix from @mvdbeek
with:
```
find packages/ -name '*.py' | xargs black
```
The `packages/` directory is currently excluded in the `[tool.black]`
section of `pyproject.toml` because black follows symlinks.
sweeping changes. To use this locally just do:
`git config blame.ignoreRevsFile .git-blame-ignore-revs`
And your git blame will now skip revisions indicated in the file.
Now that we have gitignore-ignore-revs, we might as well use it for the big prettier passes
Add isort application to .git-blame-ignore-revs
There used to be a long-standing bug in setting up the MetadataValidator
if default values were used. We fixed this in
https://github.com/galaxyproject/galaxy/pull/13139/commits/e194ef97e49c4947711ad1d20873ddc0aa686a66,
but that means we're now checking for all non-optional values before
running a tool. We have a ton of non-optional MetadatElement items
in datatypes that should maybe be optional (an indication might be if
`default` and `no_value` are specified and set to the same value ... but
I'm not sure that's a 100% thing). So I think that reviewing this
requires domain knowledge of the datatypes and what elements are really required,
and I'm not sure we can do this in a timely fashion, and not break
something that used to work.
So my suggestion is that we add `check_required_metadata=True`
on datatypes for which we have checked that non-optional metadata
elements are really non-optional. For those metadata elements
for which this is not the case we skip the validation as we would
do prior to
https://github.com/galaxyproject/galaxy/pull/13139/commits/e194ef97e49c4947711ad1d20873ddc0aa686a66.
As an example I have marked RDS and RData with check_required_metadata
and added a test for check_required_metadata.
Nicola Soranzo