Update best_practice_search() for changes in galaxy-tool-util#1224
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mvdbeek merged 7 commits intogalaxyproject:masterfrom Apr 20, 2022
Merged
Update best_practice_search() for changes in galaxy-tool-util#1224mvdbeek merged 7 commits intogalaxyproject:masterfrom
best_practice_search() for changes in galaxy-tool-util#1224mvdbeek merged 7 commits intogalaxyproject:masterfrom
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Fix issue found when testing planemo in galaxyproject/planemo#1224 (comment) : ``` 2022-04-01T14:44:05.3964452Z [2022-04-01 14:41:23 +0000] [6904] [WARNING] Invalid HTTP request received. 2022-04-01T14:44:05.3964583Z Traceback (most recent call last): 2022-04-01T14:44:05.3965087Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/uvicorn/protocols/http/h11_impl.py", line 136, in handle_events 2022-04-01T14:44:05.3965218Z event = self.conn.next_event() 2022-04-01T14:44:05.3965652Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 443, in next_event 2022-04-01T14:44:05.3965801Z exc._reraise_as_remote_protocol_error() 2022-04-01T14:44:05.3966277Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_util.py", line 76, in _reraise_as_remote_protocol_error 2022-04-01T14:44:05.3966383Z raise self 2022-04-01T14:44:05.3966831Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 425, in next_event 2022-04-01T14:44:05.3966977Z event = self._extract_next_receive_event() 2022-04-01T14:44:05.3967445Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 367, in _extract_next_receive_event 2022-04-01T14:44:05.3967588Z event = self._reader(self._receive_buffer) 2022-04-01T14:44:05.3968049Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_readers.py", line 73, in maybe_read_from_IDLE_client 2022-04-01T14:44:05.3968225Z request_line_re, lines[0], "illegal request line: {!r}", lines[0] 2022-04-01T14:44:05.3968629Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_util.py", line 88, in validate 2022-04-01T14:44:05.3968781Z raise LocalProtocolError(msg) 2022-04-01T14:44:05.3969215Z h11._util.RemoteProtocolError: illegal request line: bytearray(b'--a250a2c0546542508998e4e0ac8f1001') 2022-04-01T14:44:05.3969497Z [2022-04-01 14:41:23 +0000] [6904] [WARNING] Invalid HTTP request received. 2022-04-01T14:44:05.3969623Z Traceback (most recent call last): 2022-04-01T14:44:05.3970105Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/uvicorn/protocols/http/h11_impl.py", line 136, in handle_events 2022-04-01T14:44:05.3970231Z event = self.conn.next_event() 2022-04-01T14:44:05.3970655Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 423, in next_event 2022-04-01T14:44:05.3971003Z raise RemoteProtocolError("Can't receive data when peer state is ERROR") 2022-04-01T14:44:05.3971287Z h11._util.RemoteProtocolError: Can't receive data when peer state is ERROR ```
5 tasks
nsoranzo
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Apr 4, 2022
Fix issue found when testing planemo in galaxyproject/planemo#1224 (comment) : ``` 2022-04-01T14:44:05.3964452Z [2022-04-01 14:41:23 +0000] [6904] [WARNING] Invalid HTTP request received. 2022-04-01T14:44:05.3964583Z Traceback (most recent call last): 2022-04-01T14:44:05.3965087Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/uvicorn/protocols/http/h11_impl.py", line 136, in handle_events 2022-04-01T14:44:05.3965218Z event = self.conn.next_event() 2022-04-01T14:44:05.3965652Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 443, in next_event 2022-04-01T14:44:05.3965801Z exc._reraise_as_remote_protocol_error() 2022-04-01T14:44:05.3966277Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_util.py", line 76, in _reraise_as_remote_protocol_error 2022-04-01T14:44:05.3966383Z raise self 2022-04-01T14:44:05.3966831Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 425, in next_event 2022-04-01T14:44:05.3966977Z event = self._extract_next_receive_event() 2022-04-01T14:44:05.3967445Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 367, in _extract_next_receive_event 2022-04-01T14:44:05.3967588Z event = self._reader(self._receive_buffer) 2022-04-01T14:44:05.3968049Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_readers.py", line 73, in maybe_read_from_IDLE_client 2022-04-01T14:44:05.3968225Z request_line_re, lines[0], "illegal request line: {!r}", lines[0] 2022-04-01T14:44:05.3968629Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_util.py", line 88, in validate 2022-04-01T14:44:05.3968781Z raise LocalProtocolError(msg) 2022-04-01T14:44:05.3969215Z h11._util.RemoteProtocolError: illegal request line: bytearray(b'--a250a2c0546542508998e4e0ac8f1001') 2022-04-01T14:44:05.3969497Z [2022-04-01 14:41:23 +0000] [6904] [WARNING] Invalid HTTP request received. 2022-04-01T14:44:05.3969623Z Traceback (most recent call last): 2022-04-01T14:44:05.3970105Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/uvicorn/protocols/http/h11_impl.py", line 136, in handle_events 2022-04-01T14:44:05.3970231Z event = self.conn.next_event() 2022-04-01T14:44:05.3970655Z File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 423, in next_event 2022-04-01T14:44:05.3971003Z raise RemoteProtocolError("Can't receive data when peer state is ERROR") 2022-04-01T14:44:05.3971287Z h11._util.RemoteProtocolError: Can't receive data when peer state is ERROR ```
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The unit-quick and unit-nonredundant-noclientbuild-noshed test builds now pass, but they don't complete properly until they time out after 90'. Maybe a Galaxy process that doesn't stop? |
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In galaxyproject/galaxy#13532 I've removed the `channels_override` parameter from the `best_search_result()` method in galaxy-tool-util.
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Found the issue with tests not terminating! |
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- Remove unused `skip_unless_python_2_7()` function. - Do not use mutable data structures for argument defaults. - Sync ``modify_environ()`` with Galaxy version, with fixes.
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Thank you so much @nsoranzo ! |
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In galaxyproject/galaxy#13532 I've removed the
channels_overrideparameter from thebest_search_result()method in galaxy-tool-util.