mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +08:00
Nicola Soranzo
02da697c79
Follow-up on commit 18891f3791 .
Fix tracebacks on CWL conformance tests like:
```
> self.cwl_populator.run_conformance_test("""v1.0""", """Testing Any type compatibility in outputSource""")
lib/galaxy_test/api/cwl/test_cwl_conformance_v1_0.py:535:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy_test/base/populators.py:482: in run_conformance_test
run = self.run_cwl_job(artifact, job_path=job_path)
lib/galaxy_test/base/populators.py:467: in run_cwl_job
run_object.wait()
lib/galaxy_test/base/populators.py:343: in wait
self.workflow_populator.wait_for_invocation_and_jobs(self.history_id, self.workflow_id, self.invocation_id)
lib/galaxy_test/base/populators.py:1629: in wait_for_invocation_and_jobs
state = self.wait_for_invocation(workflow_id, invocation_id)
lib/galaxy_test/base/populators.py:1301: in wait_for_invocation
return wait_on_state(workflow_state, desc="workflow invocation state", timeout=timeout, assert_ok=assert_ok)
lib/galaxy_test/base/populators.py:2379: in wait_on_state
return wait_on(get_state, desc=desc, timeout=timeout)
lib/galaxy_test/base/populators.py:2465: in wait_on
return tool_util_wait_on(function, desc, timeout)
lib/galaxy/tool_util/verify/wait.py:38: in wait_on
value = function()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
def get_state():
response = state_func()
> assert response.status_code == 200, f"Failed to fetch state update while waiting. [{response.content}]"
E AssertionError: Failed to fetch state update while waiting. [b'{"err_msg": "Wrong id ( <Response [200]> ) specified, unable to decode.", "err_code": 400009}']
```
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:alt: Galaxy Logo
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Galaxy Quickstart
=================
Galaxy requires Python 3.7 . To check your Python version, run:
.. code:: console
$ python -V
Python 3.7.6
Start Galaxy:
.. code:: console
$ sh run.sh
Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080
For more installation details please see: https://getgalaxy.org/
Documentation is available at: https://docs.galaxyproject.org/
Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
Tools
=====
Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.
Issues and Galaxy Development
=============================
Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .