mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Nicola Soranzo
d159d26764
twill 3.2 replaced `requests` with `httpx`, and `httpx` has a default
timeout of 5 s on a request, while `requests` didn't enforce a timeout by
default.
Fix errors like the following in ToolShed tests, where resetting
repository metadata takes longer than 5 s:
```
self = <tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures object at 0x7f28f99197c0>
def test_0090_verify_repository_metadata(self):
"""Verify that resetting the metadata does not change it."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
> self.verify_unchanged_repository_metadata(repository)
lib/tool_shed/test/functional/test_0000_basic_repository_features.py:264:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/tool_shed/test/base/twilltestcase.py:2073: in verify_unchanged_repository_metadata
self.reset_repository_metadata(repository)
lib/tool_shed/test/base/twilltestcase.py:1774: in reset_repository_metadata
self.visit_url("/repository/reset_all_metadata", params=params)
lib/tool_shed/test/base/twilltestcase.py:845: in visit_url
return self._browser.visit_url(url, allowed_codes=allowed_codes)
lib/tool_shed/test/base/twillbrowser.py:35: in visit_url
return visit_url(url, allowed_codes=allowed_codes)
lib/tool_shed/test/base/twillbrowser.py:20: in visit_url
new_url = tc.go(url)
.venv/lib/python3.8/site-packages/twill/commands.py:120: in go
browser.go(url)
.venv/lib/python3.8/site-packages/twill/browser.py:192: in go
self._journey("open", try_url)
.venv/lib/python3.8/site-packages/twill/browser.py:677: in _journey
result = self._client.get(url)
.venv/lib/python3.8/site-packages/httpx/_client.py:1041: in get
return self.request(
.venv/lib/python3.8/site-packages/httpx/_client.py:814: in request
return self.send(request, auth=auth, follow_redirects=follow_redirects)
.venv/lib/python3.8/site-packages/httpx/_client.py:901: in send
response = self._send_handling_auth(
.venv/lib/python3.8/site-packages/httpx/_client.py:929: in _send_handling_auth
response = self._send_handling_redirects(
.venv/lib/python3.8/site-packages/httpx/_client.py:966: in _send_handling_redirects
response = self._send_single_request(request)
.venv/lib/python3.8/site-packages/httpx/_client.py:1002: in _send_single_request
response = transport.handle_request(request)
.venv/lib/python3.8/site-packages/httpx/_transports/default.py:228: in handle_request
resp = self._pool.handle_request(req)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/contextlib.py:131: in __exit__
self.gen.throw(type, value, traceback)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
@contextlib.contextmanager
def map_httpcore_exceptions() -> typing.Iterator[None]:
try:
yield
except Exception as exc:
mapped_exc = None
for from_exc, to_exc in HTTPCORE_EXC_MAP.items():
if not isinstance(exc, from_exc):
continue
# We want to map to the most specific exception we can find.
# Eg if `exc` is an `httpcore.ReadTimeout`, we want to map to
# `httpx.ReadTimeout`, not just `httpx.TimeoutException`.
if mapped_exc is None or issubclass(to_exc, mapped_exc):
mapped_exc = to_exc
if mapped_exc is None: # pragma: no cover
raise
message = str(exc)
> raise mapped_exc(message) from exc
E httpx.ReadTimeout: timed out
.venv/lib/python3.8/site-packages/httpx/_transports/default.py:83: ReadTimeout
```
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
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:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
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:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
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:target: https://docs.galaxyproject.org/en/master/
:alt: Release Documentation
.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
:target: https://travis-ci.org/galaxyproject/galaxy
:alt: Inspect the test results
Galaxy Quickstart
=================
Galaxy requires Python 3.8 . To check your Python version, run:
.. code:: console
$ python -V
Python 3.8.18
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>`_ .