Closed dhimmel closed 2 years ago
Just got another error on a scheduled job after fast forwarding my fork.
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/home/runner/work/bioregistry/bioregistry/src/bioregistry/__main__.py", line 8, in <module>
main()
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/click/core.py", line 1128, in __call__
return self.main(*args, **kwargs)
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/click/decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
File "/home/runner/work/bioregistry/bioregistry/src/bioregistry/cli.py", line [34](https://github.com/dhimmel/bioregistry/runs/5255581914?check_suite_focus=true#step:5:34), in update
ctx.invoke(align)
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/home/runner/work/bioregistry/bioregistry/src/bioregistry/align/cli.py", line 54, in align
aligner_cls.align()
File "/home/runner/work/bioregistry/bioregistry/src/bioregistry/align/utils.py", line 141, in align
instance = cls()
File "/home/runner/work/bioregistry/bioregistry/src/bioregistry/align/utils.py", line 58, in __init__
self.external_registry = self.__class__.getter(**kwargs)
File "/home/runner/work/bioregistry/bioregistry/src/bioregistry/external/bioportal.py", line 59, in get_bioportal
records = thread_map(_process, records, disable=True)
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/tqdm/contrib/concurrent.py", line 94, in thread_map
return _executor_map(ThreadPoolExecutor, fn, *iterables, **tqdm_kwargs)
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/tqdm/contrib/concurrent.py", line 76, in _executor_map
return list(tqdm_class(ex.map(fn, *iterables, **map_args), **kwargs))
File "/home/runner/work/bioregistry/bioregistry/.tox/update/lib/python3.9/site-packages/tqdm/std.py", line 1168, in __iter__
for obj in iterable:
File "/opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/concurrent/futures/_base.py", line 609, in result_iterator
yield fs.pop().result()
File "/opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/concurrent/futures/_base.py", line 4[39](https://github.com/dhimmel/bioregistry/runs/5255581914?check_suite_focus=true#step:5:39), in result
return self.__get_result()
File "/opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
raise self._exception
File "/opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/concurrent/futures/thread.py", line [58](https://github.com/dhimmel/bioregistry/runs/5255581914?check_suite_focus=true#step:5:58), in run
result = self.fn(*self.args, **self.kwargs)
File "/home/runner/work/bioregistry/bioregistry/src/bioregistry/external/bioportal.py", line [68](https://github.com/dhimmel/bioregistry/runs/5255581914?check_suite_focus=true#step:5:68), in _process
bioportal_key = entry["acronym"]
TypeError: string indices must be integers
ERROR: InvocationError for command /home/runner/work/bioregistry/bioregistry/.tox/update/bin/python -m bioregistry update (exited with code 1)
Perhaps schedules jobs should be disabled on forks. It currently is quite annoying to do this, see https://github.community/t/github-event-repository-fork-context-does-detect-forks-in-scheduled-jobs/185925/3
CI is failing on my fork: