docker_galaxy engine broken in latest release #1160
Description
Running Planemo with the docker_galaxy engine leads to:
AttributeError: 'DockerGalaxyConfig' object has no attribute 'log_file'
This affects release 0.74.3, but not 0.74.2.
The problem is still present in the current master.
Steps to reproduce (Docker 20.10.5 on Ubuntu 18.0):
planemo test --engine docker_galaxy --docker_galaxy_image bgruening/galaxy-stable:20.09 --extra_tools tests/data/repos/single_tool/cat.xml tests/data/wf2.ga
Full error:
Traceback (most recent call last):
File "/home/simleo/repos/planemo/venv/bin/planemo", line 11, in <module>
load_entry_point('planemo==0.74.4', 'console_scripts', 'planemo')()
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/click/decorators.py", line 73, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/cli.py", line 98, in handle_blended_options
return f(*args, **kwds)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/commands/cmd_test.py", line 82, in cli
return_value = test_runnables(ctx, runnables, original_paths=uris, **kwds)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/engine/test.py", line 25, in test_runnables
test_data = engine.test(runnables)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/engine/interface.py", line 80, in test
test_results = self._collect_test_results(test_cases)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/engine/interface.py", line 99, in _collect_test_results
run_response = self._run_test_case(test_case)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/engine/galaxy.py", line 50, in _run_test_case
return super(GalaxyEngine, self)._run_test_case(test_case)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/engine/interface.py", line 126, in _run_test_case
run_response = self._run(runnable, job_path)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/engine/galaxy.py", line 35, in _run
with self.ensure_runnables_served([runnable]) as config:
File "/usr/lib/python3.6/contextlib.py", line 81, in __enter__
return next(self.gen)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/engine/galaxy.py", line 104, in ensure_runnables_served
with serve_daemon(self._ctx, runnables, **self._serve_kwds()) as config:
File "/usr/lib/python3.6/contextlib.py", line 81, in __enter__
return next(self.gen)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/galaxy/serve.py", line 109, in serve_daemon
config = serve(ctx, runnables, **kwds)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/galaxy/serve.py", line 25, in serve
return _serve(ctx, runnables, **kwds)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/galaxy/serve.py", line 45, in _serve
with galaxy_config(ctx, runnables, **kwds) as config:
File "/usr/lib/python3.6/contextlib.py", line 81, in __enter__
return next(self.gen)
File "/home/simleo/repos/planemo/venv/lib/python3.6/site-packages/planemo-0.74.4-py3.6.egg/planemo/galaxy/config.py", line 220, in galaxy_config
log_thread = threading.Thread(target=read_log, args=(ctx, config.log_file))
AttributeError: 'DockerGalaxyConfig' object has no attribute 'log_file'
With Planemo 0.74.2, instead, the above command runs fine.