introduced in https://github.com/galaxyproject/galaxy/pull/18003 .
In particular, when using requests in the tests to connect to Galaxy
or the ToolShed it's not needed to use the modified headers.
Also:
- Move some imports after conditional imports.
- Fix type annotations in `lib/tool_shed/test/base/populators.py`
- Fix typo bug in `test/unit/util/test_get_url.py`
so that the former always returns a `Response` object while the latter
returns the response content.
Also:
- In `CwlPopulator.run_cwl_job()` wait for the run only if `assert_ok`
is True; if the `wait()` call fails, summarize history also for
workflow runs.
That should make it significantly easier to debug issues when the
container monitor dies unexpectedly (which I sort of expect in the
future given that we parse output from the docker CLI).
Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
Instructions for setting up external goodies documented in docstring.
Small tweaks included:
- Allow serving proxies on ports different than Galaxy (so it can target external proxies without nginx/uwsgi).
- Fix up config options a bit.
Tested with Pulsar but not sure there is anything Pulsar specific about the implementation - simply set container_monitor_result on the job destination to 'callback' (instead of implicit default of 'file'). This causes the monitor.py script to hit a new job_ports API (that mirrors job_files API) and uses the same security mechanism (per-job keys that are only active while the job is active).
PR contains fixes for embedded Pulsar configuration handling, embedded Pulsar under uwsgi, and the introduction of new feature that allows dynamic expansion of ``$UWSGI_PORT`` inside of galaxy_infrastructure_url.
- enables docker destination for interactivetool tests
- fixes a wrong argument in entrypoint management
- fixes the test setup that targeted a previous iteration (which was
still called realtimetools)
- prevents deleting the working directory before python has a chance to
start the container monitor (that's the sleep command)
- fixes some odd interactive tool test assertions
- uses unicode arguments in key_type_token_mapping.py.
uwsgi arguments are always passed as bytestrings.
Split test/base into lib/galaxy_test/base and lib/galaxy_test/driver. Dividing things on whether they import galaxy-app code or not - with the goal of a galaxy-test-base package that doesn't depend on galaxy-app and a galaxy-test-driver package that does.
I've been refactoring around this division for a long time. Certain tests (namely the integration tests) always need to bootstrap Galaxy - but the API tests and the Selenium tests should be installable and runnable without Galaxy in the Python environment. So future galaxy-test-api and galaxy-test-selenium packages should have only an optional dependency on galaxy-test-driver.
Properly sturcturing these namespaces is a precursor for real packages on PyPI, clean separation of the tool shed testing code, and cleans up all the flake8 noqa hacks in test/.
Nicola Soranzo