Started by timer
Running as SYSTEM
Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/12-Labours-API
[WS-CLEANUP] Deleting project workspace...
[WS-CLEANUP] Deferred wipeout is used...
[WS-CLEANUP] Done
The recommended git tool is: NONE
No credentials specified
Cloning the remote Git repository
Cloning repository https://github.com/ABI-Software/12-labours-api.git
> git init /home/cmiss/Jenkins/workspace/12-Labours-API # timeout=10
Fetching upstream changes from https://github.com/ABI-Software/12-labours-api.git
> git --version # timeout=10
> git --version # 'git version 2.25.1'
> git fetch --tags --force --progress -- https://github.com/ABI-Software/12-labours-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10
> git config remote.origin.url https://github.com/ABI-Software/12-labours-api.git # timeout=10
> git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
> git rev-parse refs/remotes/origin/dev^{commit} # timeout=10
Checking out Revision fed7495860d0492a0d83f51077693f3de98e748d (refs/remotes/origin/dev)
> git config core.sparsecheckout # timeout=10
> git checkout -f fed7495860d0492a0d83f51077693f3de98e748d # timeout=10
Commit message: "Merge pull request #43 from ddjnw1yu/access-control"
> git rev-list --no-walk fed7495860d0492a0d83f51077693f3de98e748d # timeout=10
[12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda12481048079190294476.sh
+ pwd
+ export PYTHONPATH=/home/cmiss/Jenkins/workspace/12-Labours-API
+ pip install -r requirements.txt
Requirement already satisfied: fastapi==0.80.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.80.0)
Requirement already satisfied: fastapi-utils==0.2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (0.2.1)
Requirement already satisfied: gen3==4.19.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (4.19.1)
Requirement already satisfied: gunicorn==20.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (20.1.0)
Requirement already satisfied: PyJWT==2.7.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (2.7.0)
Requirement already satisfied: pyorthanc==1.11.5 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (1.11.5)
Requirement already satisfied: python-dotenv==0.20.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (0.20.0)
Requirement already satisfied: python-irodsclient==1.1.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (1.1.8)
Requirement already satisfied: sgqlc==16.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 9)) (16.3)
Requirement already satisfied: uvicorn==0.18.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (0.18.2)
Requirement already satisfied: starlette==0.19.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from fastapi==0.80.0->-r requirements.txt (line 1)) (0.19.1)
Requirement already satisfied: pydantic!=1.7,!=1.7.1,!=1.7.2,!=1.7.3,!=1.8,!=1.8.1,<2.0.0,>=1.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from fastapi==0.80.0->-r requirements.txt (line 1)) (1.10.15)
Requirement already satisfied: sqlalchemy<2.0.0,>=1.3.12 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from fastapi-utils==0.2.1->-r requirements.txt (line 2)) (1.4.52)
Requirement already satisfied: aiofiles<0.9.0,>=0.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.8.0)
Requirement already satisfied: aiohttp in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (3.9.5)
Requirement already satisfied: backoff in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (1.11.1)
Requirement already satisfied: cdislogging<2.0.0,>=1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (1.1.1)
Requirement already satisfied: click in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (8.1.7)
Requirement already satisfied: dataclasses-json in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.6.4)
Requirement already satisfied: drsclient<0.3.0,>=0.2.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.2.3)
Requirement already satisfied: httpx in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.23.3)
Requirement already satisfied: humanfriendly in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (10.0)
Requirement already satisfied: indexclient in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (2.2.1)
Requirement already satisfied: jsonschema in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (3.2.0)
Requirement already satisfied: pandas<2.0.0,>=1.4.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (1.5.3)
Requirement already satisfied: pypfb<1.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.5.29)
Requirement already satisfied: python-dateutil in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (2.9.0.post0)
Requirement already satisfied: requests in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (2.31.0)
Requirement already satisfied: tqdm<5.0.0,>=4.61.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (4.66.2)
Requirement already satisfied: urllib3<2.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (1.26.18)
Requirement already satisfied: xmltodict<0.14.0,>=0.13.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.13.0)
Requirement already satisfied: setuptools>=3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gunicorn==20.1.0->-r requirements.txt (line 4)) (69.5.1)
Requirement already satisfied: pydicom<3.0.0,>=2.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pyorthanc==1.11.5->-r requirements.txt (line 6)) (2.4.4)
Requirement already satisfied: PrettyTable>=0.7.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) (3.10.0)
Requirement already satisfied: defusedxml in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) (0.7.1)
Requirement already satisfied: six>=1.10.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) (1.16.0)
Requirement already satisfied: graphql-core<4.0.0,>=3.1.7 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sgqlc==16.3->-r requirements.txt (line 9)) (3.2.3)
Requirement already satisfied: h11>=0.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from uvicorn==0.18.2->-r requirements.txt (line 10)) (0.14.0)
Requirement already satisfied: anyio<5,>=3.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 1)) (3.6.2)
Requirement already satisfied: typing-extensions>=3.10.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 1)) (4.11.0)
Requirement already satisfied: asyncio<4.0.0,>=3.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from drsclient<0.3.0,>=0.2.2->gen3==4.19.1->-r requirements.txt (line 3)) (3.4.3)
Requirement already satisfied: certifi in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 3)) (2024.2.2)
Requirement already satisfied: httpcore<0.17.0,>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 3)) (0.16.3)
Requirement already satisfied: rfc3986<2,>=1.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from rfc3986[idna2008]<2,>=1.3->httpx->gen3==4.19.1->-r requirements.txt (line 3)) (1.5.0)
Requirement already satisfied: sniffio in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 3)) (1.3.1)
Requirement already satisfied: pytz>=2020.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pandas<2.0.0,>=1.4.2->gen3==4.19.1->-r requirements.txt (line 3)) (2024.1)
Requirement already satisfied: numpy>=1.20.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pandas<2.0.0,>=1.4.2->gen3==4.19.1->-r requirements.txt (line 3)) (1.26.4)
Requirement already satisfied: wcwidth in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from PrettyTable>=0.7.2->python-irodsclient==1.1.8->-r requirements.txt (line 8)) (0.2.13)
Requirement already satisfied: PyYAML<7.0.0,>=6.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (6.0.1)
Requirement already satisfied: dictionaryutils<4.0.0,>=3.4.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (3.4.10)
Requirement already satisfied: fastavro<1.9.0,>=1.8.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (1.8.4)
Requirement already satisfied: gen3dictionary>=2.0.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (2.0.3)
Requirement already satisfied: python-json-logger<0.2.0,>=0.1.11 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (0.1.11)
Requirement already satisfied: aiosignal>=1.1.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (1.3.1)
Requirement already satisfied: attrs>=17.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (23.2.0)
Requirement already satisfied: frozenlist>=1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (1.4.1)
Requirement already satisfied: multidict<7.0,>=4.5 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (6.0.5)
Requirement already satisfied: yarl<2.0,>=1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (1.9.4)
Requirement already satisfied: async-timeout<5.0,>=4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (4.0.3)
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Requirement already satisfied: idna<4,>=2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests->gen3==4.19.1->-r requirements.txt (line 3)) (3.7)
Requirement already satisfied: greenlet!=0.4.17 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sqlalchemy<2.0.0,>=1.3.12->fastapi-utils==0.2.1->-r requirements.txt (line 2)) (3.0.3)
Requirement already satisfied: marshmallow<4.0.0,>=3.18.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) (3.21.1)
Requirement already satisfied: typing-inspect<1,>=0.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) (0.9.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from jsonschema->gen3==4.19.1->-r requirements.txt (line 3)) (0.20.0)
Requirement already satisfied: packaging>=17.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from marshmallow<4.0.0,>=3.18.0->dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) (24.0)
Requirement already satisfied: mypy-extensions>=0.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from typing-inspect<1,>=0.4.0->dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) (1.0.0)
[notice] A new release of pip is available: 24.0 -> 24.2
[notice] To update, run: pip install --upgrade pip
+ pip install -r requirements-dev.txt
Requirement already satisfied: pytest==7.1.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 1)) (7.1.2)
Requirement already satisfied: pytest-timeout==2.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 2)) (2.1.0)
Requirement already satisfied: anyio==3.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 3)) (3.6.2)
Requirement already satisfied: attrs>=19.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (23.2.0)
Requirement already satisfied: iniconfig in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (2.0.0)
Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (24.0)
Requirement already satisfied: pluggy<2.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (1.5.0)
Requirement already satisfied: py>=1.8.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (1.11.0)
Requirement already satisfied: tomli>=1.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (2.0.1)
Requirement already satisfied: idna>=2.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from anyio==3.6.2->-r requirements-dev.txt (line 3)) (3.7)
Requirement already satisfied: sniffio>=1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from anyio==3.6.2->-r requirements-dev.txt (line 3)) (1.3.1)
[notice] A new release of pip is available: 24.0 -> 24.2
[notice] To update, run: pip install --upgrade pip
+ pytest
============================= test session starts ==============================
platform linux -- Python 3.9.19, pytest-7.1.2, pluggy-1.5.0
rootdir: /home/cmiss/Jenkins/workspace/12-Labours-API
plugins: anyio-3.6.2, timeout-2.1.0
collected 39 items
tests/test_api/test_access_api.py ... [ 7%]
tests/test_api/test_gen3_api.py FFF. [ 17%]
tests/test_api/test_irods_api.py FF [ 23%]
tests/test_api/test_orthanc_api.py .. [ 28%]
tests/test_data/test_gen3_data.py FFFF [ 38%]
tests/test_data/test_irods_data.py F [ 41%]
tests/test_function/test_filter/test_filter_editor.py .. [ 46%]
tests/test_function/test_filter/test_filter_formatter.py .... [ 56%]
tests/test_function/test_filter/test_filter_generator.py ... [ 64%]
tests/test_function/test_filter/test_filter_logic.py ... [ 71%]
tests/test_function/test_pagination/test_pagination_formatter.py . [ 74%]
tests/test_function/test_query/test_query_formatter.py ...... [ 89%]
tests/test_function/test_search/test_search_logic.py .... [100%]
=================================== FAILURES ===================================
_____________________________ test_get_gen3_record _____________________________
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e45803c40>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
> httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:715:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e45803c40>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e457a3ac0>
method = 'POST', url = '/user/credentials/cdis/access_token'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwd...p, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
def _make_request(
self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw
):
"""
Perform a request on a given urllib connection object taken from our
pool.
:param conn:
a connection from one of our connection pools
:param timeout:
Socket timeout in seconds for the request. This can be a
float or integer, which will set the same timeout value for
the socket connect and the socket read, or an instance of
:class:`urllib3.util.Timeout`, which gives you more fine-grained
control over your timeouts.
"""
self.num_requests += 1
timeout_obj = self._get_timeout(timeout)
timeout_obj.start_connect()
conn.timeout = Timeout.resolve_default_timeout(timeout_obj.connect_timeout)
# Trigger any extra validation we need to do.
try:
> self._validate_conn(conn)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:404:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e45803c40>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e457a3ac0>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1058:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f8e457a3ac0>
def connect(self):
# Add certificate verification
self.sock = conn = self._new_conn()
hostname = self.host
tls_in_tls = False
if self._is_using_tunnel():
if self.tls_in_tls_required:
self.sock = conn = self._connect_tls_proxy(hostname, conn)
tls_in_tls = True
# Calls self._set_hostport(), so self.host is
# self._tunnel_host below.
self._tunnel()
# Mark this connection as not reusable
self.auto_open = 0
# Override the host with the one we're requesting data from.
hostname = self._tunnel_host
server_hostname = hostname
if self.server_hostname is not None:
server_hostname = self.server_hostname
is_time_off = datetime.date.today() < RECENT_DATE
if is_time_off:
warnings.warn(
(
"System time is way off (before {0}). This will probably "
"lead to SSL verification errors"
).format(RECENT_DATE),
SystemTimeWarning,
)
# Wrap socket using verification with the root certs in
# trusted_root_certs
default_ssl_context = False
if self.ssl_context is None:
default_ssl_context = True
self.ssl_context = create_urllib3_context(
ssl_version=resolve_ssl_version(self.ssl_version),
cert_reqs=resolve_cert_reqs(self.cert_reqs),
)
context = self.ssl_context
context.verify_mode = resolve_cert_reqs(self.cert_reqs)
# Try to load OS default certs if none are given.
# Works well on Windows (requires Python3.4+)
if (
not self.ca_certs
and not self.ca_cert_dir
and not self.ca_cert_data
and default_ssl_context
and hasattr(context, "load_default_certs")
):
context.load_default_certs()
> self.sock = ssl_wrap_socket(
sock=conn,
keyfile=self.key_file,
certfile=self.cert_file,
key_password=self.key_password,
ca_certs=self.ca_certs,
ca_cert_dir=self.ca_cert_dir,
ca_cert_data=self.ca_cert_data,
server_hostname=server_hostname,
ssl_context=context,
tls_in_tls=tls_in_tls,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:419:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
keyfile = None, certfile = None, cert_reqs = None
ca_certs = '/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/certifi/cacert.pem'
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', ssl_version = None
ciphers = None, ssl_context = <ssl.SSLContext object at 0x7f8e4579e740>
ca_cert_dir = None, key_password = None, ca_cert_data = None, tls_in_tls = False
def ssl_wrap_socket(
sock,
keyfile=None,
certfile=None,
cert_reqs=None,
ca_certs=None,
server_hostname=None,
ssl_version=None,
ciphers=None,
ssl_context=None,
ca_cert_dir=None,
key_password=None,
ca_cert_data=None,
tls_in_tls=False,
):
"""
All arguments except for server_hostname, ssl_context, and ca_cert_dir have
the same meaning as they do when using :func:`ssl.wrap_socket`.
:param server_hostname:
When SNI is supported, the expected hostname of the certificate
:param ssl_context:
A pre-made :class:`SSLContext` object. If none is provided, one will
be created using :func:`create_urllib3_context`.
:param ciphers:
A string of ciphers we wish the client to support.
:param ca_cert_dir:
A directory containing CA certificates in multiple separate files, as
supported by OpenSSL's -CApath flag or the capath argument to
SSLContext.load_verify_locations().
:param key_password:
Optional password if the keyfile is encrypted.
:param ca_cert_data:
Optional string containing CA certificates in PEM format suitable for
passing as the cadata parameter to SSLContext.load_verify_locations()
:param tls_in_tls:
Use SSLTransport to wrap the existing socket.
"""
context = ssl_context
if context is None:
# Note: This branch of code and all the variables in it are no longer
# used by urllib3 itself. We should consider deprecating and removing
# this code.
context = create_urllib3_context(ssl_version, cert_reqs, ciphers=ciphers)
if ca_certs or ca_cert_dir or ca_cert_data:
try:
context.load_verify_locations(ca_certs, ca_cert_dir, ca_cert_data)
except (IOError, OSError) as e:
raise SSLError(e)
elif ssl_context is None and hasattr(context, "load_default_certs"):
# try to load OS default certs; works well on Windows (require Python3.4+)
context.load_default_certs()
# Attempt to detect if we get the goofy behavior of the
# keyfile being encrypted and OpenSSL asking for the
# passphrase via the terminal and instead error out.
if keyfile and key_password is None and _is_key_file_encrypted(keyfile):
raise SSLError("Client private key is encrypted, password is required")
if certfile:
if key_password is None:
context.load_cert_chain(certfile, keyfile)
else:
context.load_cert_chain(certfile, keyfile, key_password)
try:
if hasattr(context, "set_alpn_protocols"):
context.set_alpn_protocols(ALPN_PROTOCOLS)
except NotImplementedError: # Defensive: in CI, we always have set_alpn_protocols
pass
# If we detect server_hostname is an IP address then the SNI
# extension should not be used according to RFC3546 Section 3.1
use_sni_hostname = server_hostname and not is_ipaddress(server_hostname)
# SecureTransport uses server_hostname in certificate verification.
send_sni = (use_sni_hostname and HAS_SNI) or (
IS_SECURETRANSPORT and server_hostname
)
# Do not warn the user if server_hostname is an invalid SNI hostname.
if not HAS_SNI and use_sni_hostname:
warnings.warn(
"An HTTPS request has been made, but the SNI (Server Name "
"Indication) extension to TLS is not available on this platform. "
"This may cause the server to present an incorrect TLS "
"certificate, which can cause validation failures. You can upgrade to "
"a newer version of Python to solve this. For more information, see "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#ssl-warnings",
SNIMissingWarning,
)
if send_sni:
> ssl_sock = _ssl_wrap_socket_impl(
sock, context, tls_in_tls, server_hostname=server_hostname
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:449:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
ssl_context = <ssl.SSLContext object at 0x7f8e4579e740>, tls_in_tls = False
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
def _ssl_wrap_socket_impl(sock, ssl_context, tls_in_tls, server_hostname=None):
if tls_in_tls:
if not SSLTransport:
# Import error, ssl is not available.
raise ProxySchemeUnsupported(
"TLS in TLS requires support for the 'ssl' module"
)
SSLTransport._validate_ssl_context_for_tls_in_tls(ssl_context)
return SSLTransport(sock, ssl_context, server_hostname)
if server_hostname:
> return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:493:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLContext object at 0x7f8e4579e740>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', session = None
def wrap_socket(self, sock, server_side=False,
do_handshake_on_connect=True,
suppress_ragged_eofs=True,
server_hostname=None, session=None):
# SSLSocket class handles server_hostname encoding before it calls
# ctx._wrap_socket()
> return self.sslsocket_class._create(
sock=sock,
server_side=server_side,
do_handshake_on_connect=do_handshake_on_connect,
suppress_ragged_eofs=suppress_ragged_eofs,
server_hostname=server_hostname,
context=self,
session=session
)
/usr/lib/python3.9/ssl.py:501:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'ssl.SSLSocket'>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
context = <ssl.SSLContext object at 0x7f8e4579e740>, session = None
@classmethod
def _create(cls, sock, server_side=False, do_handshake_on_connect=True,
suppress_ragged_eofs=True, server_hostname=None,
context=None, session=None):
if sock.getsockopt(SOL_SOCKET, SO_TYPE) != SOCK_STREAM:
raise NotImplementedError("only stream sockets are supported")
if server_side:
if server_hostname:
raise ValueError("server_hostname can only be specified "
"in client mode")
if session is not None:
raise ValueError("session can only be specified in "
"client mode")
if context.check_hostname and not server_hostname:
raise ValueError("check_hostname requires server_hostname")
kwargs = dict(
family=sock.family, type=sock.type, proto=sock.proto,
fileno=sock.fileno()
)
self = cls.__new__(cls, **kwargs)
super(SSLSocket, self).__init__(**kwargs)
sock_timeout = sock.gettimeout()
sock.detach()
self._context = context
self._session = session
self._closed = False
self._sslobj = None
self.server_side = server_side
self.server_hostname = context._encode_hostname(server_hostname)
self.do_handshake_on_connect = do_handshake_on_connect
self.suppress_ragged_eofs = suppress_ragged_eofs
# See if we are connected
try:
self.getpeername()
except OSError as e:
if e.errno != errno.ENOTCONN:
raise
connected = False
blocking = self.getblocking()
self.setblocking(False)
try:
# We are not connected so this is not supposed to block, but
# testing revealed otherwise on macOS and Windows so we do
# the non-blocking dance regardless. Our raise when any data
# is found means consuming the data is harmless.
notconn_pre_handshake_data = self.recv(1)
except OSError as e:
# EINVAL occurs for recv(1) on non-connected on unix sockets.
if e.errno not in (errno.ENOTCONN, errno.EINVAL):
raise
notconn_pre_handshake_data = b''
self.setblocking(blocking)
if notconn_pre_handshake_data:
# This prevents pending data sent to the socket before it was
# closed from escaping to the caller who could otherwise
# presume it came through a successful TLS connection.
reason = "Closed before TLS handshake with data in recv buffer."
notconn_pre_handshake_data_error = SSLError(e.errno, reason)
# Add the SSLError attributes that _ssl.c always adds.
notconn_pre_handshake_data_error.reason = reason
notconn_pre_handshake_data_error.library = None
try:
self.close()
except OSError:
pass
try:
raise notconn_pre_handshake_data_error
finally:
# Explicitly break the reference cycle.
notconn_pre_handshake_data_error = None
else:
connected = True
self.settimeout(sock_timeout) # Must come after setblocking() calls.
self._connected = connected
if connected:
# create the SSL object
try:
self._sslobj = self._context._wrap_socket(
self, server_side, self.server_hostname,
owner=self, session=self._session,
)
if do_handshake_on_connect:
timeout = self.gettimeout()
if timeout == 0.0:
# non-blocking
raise ValueError("do_handshake_on_connect should not be specified for non-blocking sockets")
> self.do_handshake()
/usr/lib/python3.9/ssl.py:1074:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLSocket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
block = False
@_sslcopydoc
def do_handshake(self, block=False):
self._check_connected()
timeout = self.gettimeout()
try:
if timeout == 0.0 and block:
self.settimeout(None)
> self._sslobj.do_handshake()
E ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)
/usr/lib/python3.9/ssl.py:1343: SSLCertVerificationError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f8e45803640>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e45803c40>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
# If we're going to release the connection in ``finally:``, then
# the response doesn't need to know about the connection. Otherwise
# it will also try to release it and we'll have a double-release
# mess.
response_conn = conn if not release_conn else None
# Pass method to Response for length checking
response_kw["request_method"] = method
# Import httplib's response into our own wrapper object
response = self.ResponseCls.from_httplib(
httplib_response,
pool=self,
connection=response_conn,
retries=retries,
**response_kw
)
# Everything went great!
clean_exit = True
except EmptyPoolError:
# Didn't get a connection from the pool, no need to clean up
clean_exit = True
release_this_conn = False
raise
except (
TimeoutError,
HTTPException,
SocketError,
ProtocolError,
BaseSSLError,
SSLError,
CertificateError,
) as e:
# Discard the connection for these exceptions. It will be
# replaced during the next _get_conn() call.
clean_exit = False
def _is_ssl_error_message_from_http_proxy(ssl_error):
# We're trying to detect the message 'WRONG_VERSION_NUMBER' but
# SSLErrors are kinda all over the place when it comes to the message,
# so we try to cover our bases here!
message = " ".join(re.split("[^a-z]", str(ssl_error).lower()))
return (
"wrong version number" in message or "unknown protocol" in message
)
# Try to detect a common user error with proxies which is to
# set an HTTP proxy to be HTTPS when it should be 'http://'
# (ie {'http': 'http://proxy', 'https': 'https://proxy'})
# Instead we add a nice error message and point to a URL.
if (
isinstance(e, BaseSSLError)
and self.proxy
and _is_ssl_error_message_from_http_proxy(e)
and conn.proxy
and conn.proxy.scheme == "https"
):
e = ProxyError(
"Your proxy appears to only use HTTP and not HTTPS, "
"try changing your proxy URL to be HTTP. See: "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#https-proxy-error-http-proxy",
SSLError(e),
)
elif isinstance(e, (BaseSSLError, CertificateError)):
e = SSLError(e)
elif isinstance(e, (SocketError, NewConnectionError)) and self.proxy:
e = ProxyError("Cannot connect to proxy.", e)
elif isinstance(e, (SocketError, HTTPException)):
e = ProtocolError("Connection aborted.", e)
> retries = retries.increment(
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:799:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST', url = '/user/credentials/cdis/access_token', response = None
error = SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)'))
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e45803c40>
_stacktrace = <traceback object at 0x7f8e45801d80>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py:592: MaxRetryError
During handling of the above exception, another exception occurred:
client = <starlette.testclient.TestClient object at 0x7f8e458ef280>
token = {'access_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsInNjb3BlIjpbImRlbW8xLTEyTCJdLCJleHBpcmUiOiJOb25lIn0.doEgWg8P2u6dGhajC1CBwJHS3TtbJh4L_vhMfK75uJQ'}
def test_get_gen3_record(client, token):
UUID = "5b9ae1bd-e780-4869-a458-b3422084c480"
> response = client.get(
f"/record/{UUID}",
headers={"Authorization": f"Bearer {token['access_token']}"},
)
tests/test_api/test_gen3_api.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:602: in get
return self.request("GET", url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:476: in request
return super().request(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:270: in send
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:267: in send
portal.call(self.app, scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:283: in call
return cast(T_Retval, self.start_task_soon(func, *args).result())
/usr/lib/python3.9/concurrent/futures/_base.py:446: in result
return self.__get_result()
/usr/lib/python3.9/concurrent/futures/_base.py:391: in __get_result
raise self._exception
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:219: in _call_func
retval = await retval
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/applications.py:269: in __call__
await super().__call__(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/applications.py:124: in __call__
await self.middleware_stack(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:184: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:162: in __call__
await self.app(scope, receive, _send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/cors.py:84: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:93: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:82: in __call__
await self.app(scope, receive, sender)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:21: in __call__
raise e
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:18: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:670: in __call__
await route.handle(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:266: in handle
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:65: in app
response = await func(request)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:227: in app
raw_response = await run_endpoint_function(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:160: in run_endpoint_function
return await dependant.call(**values)
app/main.py:318: in get_gen3_record
record = connection["gen3"].export_record(program, project, uuid, "json")
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:348: in export_record
output = requests.get(api_url, auth=self._auth_provider).text
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:73: in get
return request("get", url, params=params, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:575: in request
prep = self.prepare_request(req)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:486: in prepare_request
p.prepare(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:372: in prepare
self.prepare_auth(auth, url)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:603: in prepare_auth
r = auth(self)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:325: in __call__
request.headers["Authorization"] = self._get_auth_value()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:446: in _get_auth_value
return "bearer " + self.get_access_token()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:433: in get_access_token
return self.refresh_access_token(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:367: in refresh_access_token
self._access_token = get_access_token_with_key(self._refresh_token)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:75: in get_access_token_with_key
resp = requests.post(auth_url, json=api_key)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f8e45803640>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
> raise SSLError(e, request=request)
E requests.exceptions.SSLError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:517: SSLError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
_________________________ test_get_gen3_graphql_query __________________________
client = <starlette.testclient.TestClient object at 0x7f8e37c1bc40>
token = {'access_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsInNjb3BlIjpbImRlbW8xLTEyTCJdLCJleHBpcmUiOiJOb25lIn0.doEgWg8P2u6dGhajC1CBwJHS3TtbJh4L_vhMfK75uJQ'}
def test_get_gen3_graphql_query(client, token):
DATASET_ID = "dataset-217-version-2"
pass_case = {
"node": "experiment_query",
"filter": {"submitter_id": [DATASET_ID]},
"search": "",
}
> response = client.post(
"/graphql/query?mode=data",
json=pass_case,
headers={"Authorization": f"Bearer {token['access_token']}"},
)
tests/test_api/test_gen3_api.py:54:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:637: in post
return self.request("POST", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:476: in request
return super().request(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:270: in send
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:267: in send
portal.call(self.app, scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:283: in call
return cast(T_Retval, self.start_task_soon(func, *args).result())
/usr/lib/python3.9/concurrent/futures/_base.py:446: in result
return self.__get_result()
/usr/lib/python3.9/concurrent/futures/_base.py:391: in __get_result
raise self._exception
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:219: in _call_func
retval = await retval
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/applications.py:269: in __call__
await super().__call__(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/applications.py:124: in __call__
await self.middleware_stack(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:184: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:162: in __call__
await self.app(scope, receive, _send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/cors.py:84: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:93: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:82: in __call__
await self.app(scope, receive, sender)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:21: in __call__
raise e
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:18: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:670: in __call__
await route.handle(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:266: in handle
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:65: in app
response = await func(request)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:227: in app
raw_response = await run_endpoint_function(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:160: in run_endpoint_function
return await dependant.call(**values)
app/main.py:416: in get_gen3_graphql_query
query_result = QL.get_query_data(item)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <app.function.query.query_logic.QueryLogic object at 0x7f8e459ce610>
item = GraphQLQueryItem(node='experiment_query', page=None, limit=None, filter={'submitter_id': ['dataset-217-version-2']}, search='', access=['demo1-12L'], asc=None, desc=None)
def get_query_data(self, item):
"""
Handler for fetching data based on query item
"""
items = self._process_query_item(item)
# Assume there will have maximum two datasets have same submitter id at current stage
# One for public, another one for private
# Show private dataset by default if user has the authority
fetch_result = self._handle_thread_fetch(items)
if "private" in fetch_result and fetch_result["private"] != []:
return fetch_result["private"]
> return fetch_result["public"]
E KeyError: 'public'
app/function/query/query_logic.py:69: KeyError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
_______________________ test_get_gen3_graphql_pagination _______________________
client = <starlette.testclient.TestClient object at 0x7f8e44080640>
token = {'access_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsInNjb3BlIjpbImRlbW8xLTEyTCJdLCJleHBpcmUiOiJOb25lIn0.doEgWg8P2u6dGhajC1CBwJHS3TtbJh4L_vhMfK75uJQ'}
def test_get_gen3_graphql_pagination(client, token):
filter_pass_case = {
"filter": {
"dataset_description_filter>study_organ_system": ["Stomach", "Vagus nerve"],
"manifest_filter>additional_types": ["Plot"],
"case_filter>species": ["Rat"],
"case_filter>sex": ["Male"],
}
}
response = client.post(
"/graphql/pagination",
json=filter_pass_case,
headers={"Authorization": f"Bearer {token['access_token']}"},
)
result = response.json()
> assert response.status_code == 200
E assert 400 == 200
E + where 400 = <Response [400]>.status_code
tests/test_api/test_gen3_api.py:167: AssertionError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
__________________________ test_get_irods_collection ___________________________
client = <starlette.testclient.TestClient object at 0x7f8e457ea370>
token = {'access_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsInNjb3BlIjpbImRlbW8xLTEyTCJdLCJleHBpcmUiOiJOb25lIn0.doEgWg8P2u6dGhajC1CBwJHS3TtbJh4L_vhMfK75uJQ'}
def test_get_irods_collection(client, token):
pass_case_root = {}
response = client.post(
"/collection",
json=pass_case_root,
headers={"Authorization": f"Bearer {token['access_token']}"},
)
result = response.json()
> assert response.status_code == 200
E assert 404 == 200
E + where 404 = <Response [404]>.status_code
tests/test_api/test_irods_api.py:41: AssertionError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
___________________________ test_get_irods_data_file ___________________________
client = <starlette.testclient.TestClient object at 0x7f8e37fde6a0>
one_off_token = {'one_off_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsImV4cCI6MTcyNTU2MzgwNn0.H7uIePQP6zztWMio2XO6yylNvwcSdZtYjujx0HaJo5Y'}
def test_get_irods_data_file(client, one_off_token):
ACTION = "preview"
FILEPATH = "dataset-217-version-2/derivative/scaffold_context_info.json"
response = client.get(
f"/data/{ACTION}/{FILEPATH}?token={one_off_token['one_off_token']}"
)
result = response.json()
> assert response.status_code == 200
E assert 404 == 200
E + where 404 = <Response [404]>.status_code
tests/test_api/test_irods_api.py:92: AssertionError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
_____________________________ test_experiment_node _____________________________
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e444e3a30>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
> httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:715:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e444e3a30>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e444e33a0>
method = 'POST', url = '/user/credentials/cdis/access_token'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwd...p, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
def _make_request(
self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw
):
"""
Perform a request on a given urllib connection object taken from our
pool.
:param conn:
a connection from one of our connection pools
:param timeout:
Socket timeout in seconds for the request. This can be a
float or integer, which will set the same timeout value for
the socket connect and the socket read, or an instance of
:class:`urllib3.util.Timeout`, which gives you more fine-grained
control over your timeouts.
"""
self.num_requests += 1
timeout_obj = self._get_timeout(timeout)
timeout_obj.start_connect()
conn.timeout = Timeout.resolve_default_timeout(timeout_obj.connect_timeout)
# Trigger any extra validation we need to do.
try:
> self._validate_conn(conn)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:404:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e444e3a30>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e444e33a0>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1058:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f8e444e33a0>
def connect(self):
# Add certificate verification
self.sock = conn = self._new_conn()
hostname = self.host
tls_in_tls = False
if self._is_using_tunnel():
if self.tls_in_tls_required:
self.sock = conn = self._connect_tls_proxy(hostname, conn)
tls_in_tls = True
# Calls self._set_hostport(), so self.host is
# self._tunnel_host below.
self._tunnel()
# Mark this connection as not reusable
self.auto_open = 0
# Override the host with the one we're requesting data from.
hostname = self._tunnel_host
server_hostname = hostname
if self.server_hostname is not None:
server_hostname = self.server_hostname
is_time_off = datetime.date.today() < RECENT_DATE
if is_time_off:
warnings.warn(
(
"System time is way off (before {0}). This will probably "
"lead to SSL verification errors"
).format(RECENT_DATE),
SystemTimeWarning,
)
# Wrap socket using verification with the root certs in
# trusted_root_certs
default_ssl_context = False
if self.ssl_context is None:
default_ssl_context = True
self.ssl_context = create_urllib3_context(
ssl_version=resolve_ssl_version(self.ssl_version),
cert_reqs=resolve_cert_reqs(self.cert_reqs),
)
context = self.ssl_context
context.verify_mode = resolve_cert_reqs(self.cert_reqs)
# Try to load OS default certs if none are given.
# Works well on Windows (requires Python3.4+)
if (
not self.ca_certs
and not self.ca_cert_dir
and not self.ca_cert_data
and default_ssl_context
and hasattr(context, "load_default_certs")
):
context.load_default_certs()
> self.sock = ssl_wrap_socket(
sock=conn,
keyfile=self.key_file,
certfile=self.cert_file,
key_password=self.key_password,
ca_certs=self.ca_certs,
ca_cert_dir=self.ca_cert_dir,
ca_cert_data=self.ca_cert_data,
server_hostname=server_hostname,
ssl_context=context,
tls_in_tls=tls_in_tls,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:419:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
keyfile = None, certfile = None, cert_reqs = None
ca_certs = '/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/certifi/cacert.pem'
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', ssl_version = None
ciphers = None, ssl_context = <ssl.SSLContext object at 0x7f8e446c5c40>
ca_cert_dir = None, key_password = None, ca_cert_data = None, tls_in_tls = False
def ssl_wrap_socket(
sock,
keyfile=None,
certfile=None,
cert_reqs=None,
ca_certs=None,
server_hostname=None,
ssl_version=None,
ciphers=None,
ssl_context=None,
ca_cert_dir=None,
key_password=None,
ca_cert_data=None,
tls_in_tls=False,
):
"""
All arguments except for server_hostname, ssl_context, and ca_cert_dir have
the same meaning as they do when using :func:`ssl.wrap_socket`.
:param server_hostname:
When SNI is supported, the expected hostname of the certificate
:param ssl_context:
A pre-made :class:`SSLContext` object. If none is provided, one will
be created using :func:`create_urllib3_context`.
:param ciphers:
A string of ciphers we wish the client to support.
:param ca_cert_dir:
A directory containing CA certificates in multiple separate files, as
supported by OpenSSL's -CApath flag or the capath argument to
SSLContext.load_verify_locations().
:param key_password:
Optional password if the keyfile is encrypted.
:param ca_cert_data:
Optional string containing CA certificates in PEM format suitable for
passing as the cadata parameter to SSLContext.load_verify_locations()
:param tls_in_tls:
Use SSLTransport to wrap the existing socket.
"""
context = ssl_context
if context is None:
# Note: This branch of code and all the variables in it are no longer
# used by urllib3 itself. We should consider deprecating and removing
# this code.
context = create_urllib3_context(ssl_version, cert_reqs, ciphers=ciphers)
if ca_certs or ca_cert_dir or ca_cert_data:
try:
context.load_verify_locations(ca_certs, ca_cert_dir, ca_cert_data)
except (IOError, OSError) as e:
raise SSLError(e)
elif ssl_context is None and hasattr(context, "load_default_certs"):
# try to load OS default certs; works well on Windows (require Python3.4+)
context.load_default_certs()
# Attempt to detect if we get the goofy behavior of the
# keyfile being encrypted and OpenSSL asking for the
# passphrase via the terminal and instead error out.
if keyfile and key_password is None and _is_key_file_encrypted(keyfile):
raise SSLError("Client private key is encrypted, password is required")
if certfile:
if key_password is None:
context.load_cert_chain(certfile, keyfile)
else:
context.load_cert_chain(certfile, keyfile, key_password)
try:
if hasattr(context, "set_alpn_protocols"):
context.set_alpn_protocols(ALPN_PROTOCOLS)
except NotImplementedError: # Defensive: in CI, we always have set_alpn_protocols
pass
# If we detect server_hostname is an IP address then the SNI
# extension should not be used according to RFC3546 Section 3.1
use_sni_hostname = server_hostname and not is_ipaddress(server_hostname)
# SecureTransport uses server_hostname in certificate verification.
send_sni = (use_sni_hostname and HAS_SNI) or (
IS_SECURETRANSPORT and server_hostname
)
# Do not warn the user if server_hostname is an invalid SNI hostname.
if not HAS_SNI and use_sni_hostname:
warnings.warn(
"An HTTPS request has been made, but the SNI (Server Name "
"Indication) extension to TLS is not available on this platform. "
"This may cause the server to present an incorrect TLS "
"certificate, which can cause validation failures. You can upgrade to "
"a newer version of Python to solve this. For more information, see "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#ssl-warnings",
SNIMissingWarning,
)
if send_sni:
> ssl_sock = _ssl_wrap_socket_impl(
sock, context, tls_in_tls, server_hostname=server_hostname
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:449:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
ssl_context = <ssl.SSLContext object at 0x7f8e446c5c40>, tls_in_tls = False
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
def _ssl_wrap_socket_impl(sock, ssl_context, tls_in_tls, server_hostname=None):
if tls_in_tls:
if not SSLTransport:
# Import error, ssl is not available.
raise ProxySchemeUnsupported(
"TLS in TLS requires support for the 'ssl' module"
)
SSLTransport._validate_ssl_context_for_tls_in_tls(ssl_context)
return SSLTransport(sock, ssl_context, server_hostname)
if server_hostname:
> return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:493:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLContext object at 0x7f8e446c5c40>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', session = None
def wrap_socket(self, sock, server_side=False,
do_handshake_on_connect=True,
suppress_ragged_eofs=True,
server_hostname=None, session=None):
# SSLSocket class handles server_hostname encoding before it calls
# ctx._wrap_socket()
> return self.sslsocket_class._create(
sock=sock,
server_side=server_side,
do_handshake_on_connect=do_handshake_on_connect,
suppress_ragged_eofs=suppress_ragged_eofs,
server_hostname=server_hostname,
context=self,
session=session
)
/usr/lib/python3.9/ssl.py:501:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'ssl.SSLSocket'>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
context = <ssl.SSLContext object at 0x7f8e446c5c40>, session = None
@classmethod
def _create(cls, sock, server_side=False, do_handshake_on_connect=True,
suppress_ragged_eofs=True, server_hostname=None,
context=None, session=None):
if sock.getsockopt(SOL_SOCKET, SO_TYPE) != SOCK_STREAM:
raise NotImplementedError("only stream sockets are supported")
if server_side:
if server_hostname:
raise ValueError("server_hostname can only be specified "
"in client mode")
if session is not None:
raise ValueError("session can only be specified in "
"client mode")
if context.check_hostname and not server_hostname:
raise ValueError("check_hostname requires server_hostname")
kwargs = dict(
family=sock.family, type=sock.type, proto=sock.proto,
fileno=sock.fileno()
)
self = cls.__new__(cls, **kwargs)
super(SSLSocket, self).__init__(**kwargs)
sock_timeout = sock.gettimeout()
sock.detach()
self._context = context
self._session = session
self._closed = False
self._sslobj = None
self.server_side = server_side
self.server_hostname = context._encode_hostname(server_hostname)
self.do_handshake_on_connect = do_handshake_on_connect
self.suppress_ragged_eofs = suppress_ragged_eofs
# See if we are connected
try:
self.getpeername()
except OSError as e:
if e.errno != errno.ENOTCONN:
raise
connected = False
blocking = self.getblocking()
self.setblocking(False)
try:
# We are not connected so this is not supposed to block, but
# testing revealed otherwise on macOS and Windows so we do
# the non-blocking dance regardless. Our raise when any data
# is found means consuming the data is harmless.
notconn_pre_handshake_data = self.recv(1)
except OSError as e:
# EINVAL occurs for recv(1) on non-connected on unix sockets.
if e.errno not in (errno.ENOTCONN, errno.EINVAL):
raise
notconn_pre_handshake_data = b''
self.setblocking(blocking)
if notconn_pre_handshake_data:
# This prevents pending data sent to the socket before it was
# closed from escaping to the caller who could otherwise
# presume it came through a successful TLS connection.
reason = "Closed before TLS handshake with data in recv buffer."
notconn_pre_handshake_data_error = SSLError(e.errno, reason)
# Add the SSLError attributes that _ssl.c always adds.
notconn_pre_handshake_data_error.reason = reason
notconn_pre_handshake_data_error.library = None
try:
self.close()
except OSError:
pass
try:
raise notconn_pre_handshake_data_error
finally:
# Explicitly break the reference cycle.
notconn_pre_handshake_data_error = None
else:
connected = True
self.settimeout(sock_timeout) # Must come after setblocking() calls.
self._connected = connected
if connected:
# create the SSL object
try:
self._sslobj = self._context._wrap_socket(
self, server_side, self.server_hostname,
owner=self, session=self._session,
)
if do_handshake_on_connect:
timeout = self.gettimeout()
if timeout == 0.0:
# non-blocking
raise ValueError("do_handshake_on_connect should not be specified for non-blocking sockets")
> self.do_handshake()
/usr/lib/python3.9/ssl.py:1074:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLSocket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
block = False
@_sslcopydoc
def do_handshake(self, block=False):
self._check_connected()
timeout = self.gettimeout()
try:
if timeout == 0.0 and block:
self.settimeout(None)
> self._sslobj.do_handshake()
E ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)
/usr/lib/python3.9/ssl.py:1343: SSLCertVerificationError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f8e444e3190>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e444e3a30>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
# If we're going to release the connection in ``finally:``, then
# the response doesn't need to know about the connection. Otherwise
# it will also try to release it and we'll have a double-release
# mess.
response_conn = conn if not release_conn else None
# Pass method to Response for length checking
response_kw["request_method"] = method
# Import httplib's response into our own wrapper object
response = self.ResponseCls.from_httplib(
httplib_response,
pool=self,
connection=response_conn,
retries=retries,
**response_kw
)
# Everything went great!
clean_exit = True
except EmptyPoolError:
# Didn't get a connection from the pool, no need to clean up
clean_exit = True
release_this_conn = False
raise
except (
TimeoutError,
HTTPException,
SocketError,
ProtocolError,
BaseSSLError,
SSLError,
CertificateError,
) as e:
# Discard the connection for these exceptions. It will be
# replaced during the next _get_conn() call.
clean_exit = False
def _is_ssl_error_message_from_http_proxy(ssl_error):
# We're trying to detect the message 'WRONG_VERSION_NUMBER' but
# SSLErrors are kinda all over the place when it comes to the message,
# so we try to cover our bases here!
message = " ".join(re.split("[^a-z]", str(ssl_error).lower()))
return (
"wrong version number" in message or "unknown protocol" in message
)
# Try to detect a common user error with proxies which is to
# set an HTTP proxy to be HTTPS when it should be 'http://'
# (ie {'http': 'http://proxy', 'https': 'https://proxy'})
# Instead we add a nice error message and point to a URL.
if (
isinstance(e, BaseSSLError)
and self.proxy
and _is_ssl_error_message_from_http_proxy(e)
and conn.proxy
and conn.proxy.scheme == "https"
):
e = ProxyError(
"Your proxy appears to only use HTTP and not HTTPS, "
"try changing your proxy URL to be HTTP. See: "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#https-proxy-error-http-proxy",
SSLError(e),
)
elif isinstance(e, (BaseSSLError, CertificateError)):
e = SSLError(e)
elif isinstance(e, (SocketError, NewConnectionError)) and self.proxy:
e = ProxyError("Cannot connect to proxy.", e)
elif isinstance(e, (SocketError, HTTPException)):
e = ProtocolError("Connection aborted.", e)
> retries = retries.increment(
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:799:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST', url = '/user/credentials/cdis/access_token', response = None
error = SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)'))
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e444e3a30>
_stacktrace = <traceback object at 0x7f8e457ae500>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py:592: MaxRetryError
During handling of the above exception, another exception occurred:
client = <starlette.testclient.TestClient object at 0x7f8e45839940>
token = {'access_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsInNjb3BlIjpbImRlbW8xLTEyTCJdLCJleHBpcmUiOiJOb25lIn0.doEgWg8P2u6dGhajC1CBwJHS3TtbJh4L_vhMfK75uJQ'}
def test_experiment_node(client, token):
UUID = "22c4459b-5f4f-4e62-abd2-2aa205fe838b"
> response = client.get(
f"/record/{UUID}",
headers={"Authorization": f"Bearer {token['access_token']}"},
)
tests/test_data/test_gen3_data.py:31:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:602: in get
return self.request("GET", url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:476: in request
return super().request(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:270: in send
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:267: in send
portal.call(self.app, scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:283: in call
return cast(T_Retval, self.start_task_soon(func, *args).result())
/usr/lib/python3.9/concurrent/futures/_base.py:446: in result
return self.__get_result()
/usr/lib/python3.9/concurrent/futures/_base.py:391: in __get_result
raise self._exception
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:219: in _call_func
retval = await retval
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/applications.py:269: in __call__
await super().__call__(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/applications.py:124: in __call__
await self.middleware_stack(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:184: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:162: in __call__
await self.app(scope, receive, _send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/cors.py:84: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:93: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:82: in __call__
await self.app(scope, receive, sender)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:21: in __call__
raise e
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:18: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:670: in __call__
await route.handle(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:266: in handle
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:65: in app
response = await func(request)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:227: in app
raw_response = await run_endpoint_function(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:160: in run_endpoint_function
return await dependant.call(**values)
app/main.py:318: in get_gen3_record
record = connection["gen3"].export_record(program, project, uuid, "json")
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:348: in export_record
output = requests.get(api_url, auth=self._auth_provider).text
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:73: in get
return request("get", url, params=params, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:575: in request
prep = self.prepare_request(req)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:486: in prepare_request
p.prepare(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:372: in prepare
self.prepare_auth(auth, url)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:603: in prepare_auth
r = auth(self)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:325: in __call__
request.headers["Authorization"] = self._get_auth_value()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:446: in _get_auth_value
return "bearer " + self.get_access_token()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:433: in get_access_token
return self.refresh_access_token(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:367: in refresh_access_token
self._access_token = get_access_token_with_key(self._refresh_token)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:75: in get_access_token_with_key
resp = requests.post(auth_url, json=api_key)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f8e444e3190>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
> raise SSLError(e, request=request)
E requests.exceptions.SSLError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:517: SSLError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
________________________ test_dataset_description_node _________________________
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e44080640>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
> httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:715:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e44080640>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e44080a60>
method = 'POST', url = '/user/credentials/cdis/access_token'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwd...p, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
def _make_request(
self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw
):
"""
Perform a request on a given urllib connection object taken from our
pool.
:param conn:
a connection from one of our connection pools
:param timeout:
Socket timeout in seconds for the request. This can be a
float or integer, which will set the same timeout value for
the socket connect and the socket read, or an instance of
:class:`urllib3.util.Timeout`, which gives you more fine-grained
control over your timeouts.
"""
self.num_requests += 1
timeout_obj = self._get_timeout(timeout)
timeout_obj.start_connect()
conn.timeout = Timeout.resolve_default_timeout(timeout_obj.connect_timeout)
# Trigger any extra validation we need to do.
try:
> self._validate_conn(conn)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:404:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e44080640>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e44080a60>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1058:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f8e44080a60>
def connect(self):
# Add certificate verification
self.sock = conn = self._new_conn()
hostname = self.host
tls_in_tls = False
if self._is_using_tunnel():
if self.tls_in_tls_required:
self.sock = conn = self._connect_tls_proxy(hostname, conn)
tls_in_tls = True
# Calls self._set_hostport(), so self.host is
# self._tunnel_host below.
self._tunnel()
# Mark this connection as not reusable
self.auto_open = 0
# Override the host with the one we're requesting data from.
hostname = self._tunnel_host
server_hostname = hostname
if self.server_hostname is not None:
server_hostname = self.server_hostname
is_time_off = datetime.date.today() < RECENT_DATE
if is_time_off:
warnings.warn(
(
"System time is way off (before {0}). This will probably "
"lead to SSL verification errors"
).format(RECENT_DATE),
SystemTimeWarning,
)
# Wrap socket using verification with the root certs in
# trusted_root_certs
default_ssl_context = False
if self.ssl_context is None:
default_ssl_context = True
self.ssl_context = create_urllib3_context(
ssl_version=resolve_ssl_version(self.ssl_version),
cert_reqs=resolve_cert_reqs(self.cert_reqs),
)
context = self.ssl_context
context.verify_mode = resolve_cert_reqs(self.cert_reqs)
# Try to load OS default certs if none are given.
# Works well on Windows (requires Python3.4+)
if (
not self.ca_certs
and not self.ca_cert_dir
and not self.ca_cert_data
and default_ssl_context
and hasattr(context, "load_default_certs")
):
context.load_default_certs()
> self.sock = ssl_wrap_socket(
sock=conn,
keyfile=self.key_file,
certfile=self.cert_file,
key_password=self.key_password,
ca_certs=self.ca_certs,
ca_cert_dir=self.ca_cert_dir,
ca_cert_data=self.ca_cert_data,
server_hostname=server_hostname,
ssl_context=context,
tls_in_tls=tls_in_tls,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:419:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
keyfile = None, certfile = None, cert_reqs = None
ca_certs = '/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/certifi/cacert.pem'
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', ssl_version = None
ciphers = None, ssl_context = <ssl.SSLContext object at 0x7f8e44482440>
ca_cert_dir = None, key_password = None, ca_cert_data = None, tls_in_tls = False
def ssl_wrap_socket(
sock,
keyfile=None,
certfile=None,
cert_reqs=None,
ca_certs=None,
server_hostname=None,
ssl_version=None,
ciphers=None,
ssl_context=None,
ca_cert_dir=None,
key_password=None,
ca_cert_data=None,
tls_in_tls=False,
):
"""
All arguments except for server_hostname, ssl_context, and ca_cert_dir have
the same meaning as they do when using :func:`ssl.wrap_socket`.
:param server_hostname:
When SNI is supported, the expected hostname of the certificate
:param ssl_context:
A pre-made :class:`SSLContext` object. If none is provided, one will
be created using :func:`create_urllib3_context`.
:param ciphers:
A string of ciphers we wish the client to support.
:param ca_cert_dir:
A directory containing CA certificates in multiple separate files, as
supported by OpenSSL's -CApath flag or the capath argument to
SSLContext.load_verify_locations().
:param key_password:
Optional password if the keyfile is encrypted.
:param ca_cert_data:
Optional string containing CA certificates in PEM format suitable for
passing as the cadata parameter to SSLContext.load_verify_locations()
:param tls_in_tls:
Use SSLTransport to wrap the existing socket.
"""
context = ssl_context
if context is None:
# Note: This branch of code and all the variables in it are no longer
# used by urllib3 itself. We should consider deprecating and removing
# this code.
context = create_urllib3_context(ssl_version, cert_reqs, ciphers=ciphers)
if ca_certs or ca_cert_dir or ca_cert_data:
try:
context.load_verify_locations(ca_certs, ca_cert_dir, ca_cert_data)
except (IOError, OSError) as e:
raise SSLError(e)
elif ssl_context is None and hasattr(context, "load_default_certs"):
# try to load OS default certs; works well on Windows (require Python3.4+)
context.load_default_certs()
# Attempt to detect if we get the goofy behavior of the
# keyfile being encrypted and OpenSSL asking for the
# passphrase via the terminal and instead error out.
if keyfile and key_password is None and _is_key_file_encrypted(keyfile):
raise SSLError("Client private key is encrypted, password is required")
if certfile:
if key_password is None:
context.load_cert_chain(certfile, keyfile)
else:
context.load_cert_chain(certfile, keyfile, key_password)
try:
if hasattr(context, "set_alpn_protocols"):
context.set_alpn_protocols(ALPN_PROTOCOLS)
except NotImplementedError: # Defensive: in CI, we always have set_alpn_protocols
pass
# If we detect server_hostname is an IP address then the SNI
# extension should not be used according to RFC3546 Section 3.1
use_sni_hostname = server_hostname and not is_ipaddress(server_hostname)
# SecureTransport uses server_hostname in certificate verification.
send_sni = (use_sni_hostname and HAS_SNI) or (
IS_SECURETRANSPORT and server_hostname
)
# Do not warn the user if server_hostname is an invalid SNI hostname.
if not HAS_SNI and use_sni_hostname:
warnings.warn(
"An HTTPS request has been made, but the SNI (Server Name "
"Indication) extension to TLS is not available on this platform. "
"This may cause the server to present an incorrect TLS "
"certificate, which can cause validation failures. You can upgrade to "
"a newer version of Python to solve this. For more information, see "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#ssl-warnings",
SNIMissingWarning,
)
if send_sni:
> ssl_sock = _ssl_wrap_socket_impl(
sock, context, tls_in_tls, server_hostname=server_hostname
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:449:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
ssl_context = <ssl.SSLContext object at 0x7f8e44482440>, tls_in_tls = False
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
def _ssl_wrap_socket_impl(sock, ssl_context, tls_in_tls, server_hostname=None):
if tls_in_tls:
if not SSLTransport:
# Import error, ssl is not available.
raise ProxySchemeUnsupported(
"TLS in TLS requires support for the 'ssl' module"
)
SSLTransport._validate_ssl_context_for_tls_in_tls(ssl_context)
return SSLTransport(sock, ssl_context, server_hostname)
if server_hostname:
> return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:493:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLContext object at 0x7f8e44482440>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', session = None
def wrap_socket(self, sock, server_side=False,
do_handshake_on_connect=True,
suppress_ragged_eofs=True,
server_hostname=None, session=None):
# SSLSocket class handles server_hostname encoding before it calls
# ctx._wrap_socket()
> return self.sslsocket_class._create(
sock=sock,
server_side=server_side,
do_handshake_on_connect=do_handshake_on_connect,
suppress_ragged_eofs=suppress_ragged_eofs,
server_hostname=server_hostname,
context=self,
session=session
)
/usr/lib/python3.9/ssl.py:501:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'ssl.SSLSocket'>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
context = <ssl.SSLContext object at 0x7f8e44482440>, session = None
@classmethod
def _create(cls, sock, server_side=False, do_handshake_on_connect=True,
suppress_ragged_eofs=True, server_hostname=None,
context=None, session=None):
if sock.getsockopt(SOL_SOCKET, SO_TYPE) != SOCK_STREAM:
raise NotImplementedError("only stream sockets are supported")
if server_side:
if server_hostname:
raise ValueError("server_hostname can only be specified "
"in client mode")
if session is not None:
raise ValueError("session can only be specified in "
"client mode")
if context.check_hostname and not server_hostname:
raise ValueError("check_hostname requires server_hostname")
kwargs = dict(
family=sock.family, type=sock.type, proto=sock.proto,
fileno=sock.fileno()
)
self = cls.__new__(cls, **kwargs)
super(SSLSocket, self).__init__(**kwargs)
sock_timeout = sock.gettimeout()
sock.detach()
self._context = context
self._session = session
self._closed = False
self._sslobj = None
self.server_side = server_side
self.server_hostname = context._encode_hostname(server_hostname)
self.do_handshake_on_connect = do_handshake_on_connect
self.suppress_ragged_eofs = suppress_ragged_eofs
# See if we are connected
try:
self.getpeername()
except OSError as e:
if e.errno != errno.ENOTCONN:
raise
connected = False
blocking = self.getblocking()
self.setblocking(False)
try:
# We are not connected so this is not supposed to block, but
# testing revealed otherwise on macOS and Windows so we do
# the non-blocking dance regardless. Our raise when any data
# is found means consuming the data is harmless.
notconn_pre_handshake_data = self.recv(1)
except OSError as e:
# EINVAL occurs for recv(1) on non-connected on unix sockets.
if e.errno not in (errno.ENOTCONN, errno.EINVAL):
raise
notconn_pre_handshake_data = b''
self.setblocking(blocking)
if notconn_pre_handshake_data:
# This prevents pending data sent to the socket before it was
# closed from escaping to the caller who could otherwise
# presume it came through a successful TLS connection.
reason = "Closed before TLS handshake with data in recv buffer."
notconn_pre_handshake_data_error = SSLError(e.errno, reason)
# Add the SSLError attributes that _ssl.c always adds.
notconn_pre_handshake_data_error.reason = reason
notconn_pre_handshake_data_error.library = None
try:
self.close()
except OSError:
pass
try:
raise notconn_pre_handshake_data_error
finally:
# Explicitly break the reference cycle.
notconn_pre_handshake_data_error = None
else:
connected = True
self.settimeout(sock_timeout) # Must come after setblocking() calls.
self._connected = connected
if connected:
# create the SSL object
try:
self._sslobj = self._context._wrap_socket(
self, server_side, self.server_hostname,
owner=self, session=self._session,
)
if do_handshake_on_connect:
timeout = self.gettimeout()
if timeout == 0.0:
# non-blocking
raise ValueError("do_handshake_on_connect should not be specified for non-blocking sockets")
> self.do_handshake()
/usr/lib/python3.9/ssl.py:1074:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLSocket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
block = False
@_sslcopydoc
def do_handshake(self, block=False):
self._check_connected()
timeout = self.gettimeout()
try:
if timeout == 0.0 and block:
self.settimeout(None)
> self._sslobj.do_handshake()
E ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)
/usr/lib/python3.9/ssl.py:1343: SSLCertVerificationError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f8e443a56d0>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e44080640>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
# If we're going to release the connection in ``finally:``, then
# the response doesn't need to know about the connection. Otherwise
# it will also try to release it and we'll have a double-release
# mess.
response_conn = conn if not release_conn else None
# Pass method to Response for length checking
response_kw["request_method"] = method
# Import httplib's response into our own wrapper object
response = self.ResponseCls.from_httplib(
httplib_response,
pool=self,
connection=response_conn,
retries=retries,
**response_kw
)
# Everything went great!
clean_exit = True
except EmptyPoolError:
# Didn't get a connection from the pool, no need to clean up
clean_exit = True
release_this_conn = False
raise
except (
TimeoutError,
HTTPException,
SocketError,
ProtocolError,
BaseSSLError,
SSLError,
CertificateError,
) as e:
# Discard the connection for these exceptions. It will be
# replaced during the next _get_conn() call.
clean_exit = False
def _is_ssl_error_message_from_http_proxy(ssl_error):
# We're trying to detect the message 'WRONG_VERSION_NUMBER' but
# SSLErrors are kinda all over the place when it comes to the message,
# so we try to cover our bases here!
message = " ".join(re.split("[^a-z]", str(ssl_error).lower()))
return (
"wrong version number" in message or "unknown protocol" in message
)
# Try to detect a common user error with proxies which is to
# set an HTTP proxy to be HTTPS when it should be 'http://'
# (ie {'http': 'http://proxy', 'https': 'https://proxy'})
# Instead we add a nice error message and point to a URL.
if (
isinstance(e, BaseSSLError)
and self.proxy
and _is_ssl_error_message_from_http_proxy(e)
and conn.proxy
and conn.proxy.scheme == "https"
):
e = ProxyError(
"Your proxy appears to only use HTTP and not HTTPS, "
"try changing your proxy URL to be HTTP. See: "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#https-proxy-error-http-proxy",
SSLError(e),
)
elif isinstance(e, (BaseSSLError, CertificateError)):
e = SSLError(e)
elif isinstance(e, (SocketError, NewConnectionError)) and self.proxy:
e = ProxyError("Cannot connect to proxy.", e)
elif isinstance(e, (SocketError, HTTPException)):
e = ProtocolError("Connection aborted.", e)
> retries = retries.increment(
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:799:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST', url = '/user/credentials/cdis/access_token', response = None
error = SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)'))
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e44080640>
_stacktrace = <traceback object at 0x7f8e37c954c0>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py:592: MaxRetryError
During handling of the above exception, another exception occurred:
client = <starlette.testclient.TestClient object at 0x7f8e443c96d0>
token = {'access_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsInNjb3BlIjpbImRlbW8xLTEyTCJdLCJleHBpcmUiOiJOb25lIn0.doEgWg8P2u6dGhajC1CBwJHS3TtbJh4L_vhMfK75uJQ'}
def test_dataset_description_node(client, token):
UUID = "5b9ae1bd-e780-4869-a458-b3422084c480"
> response = client.get(
f"/record/{UUID}",
headers={"Authorization": f"Bearer {token['access_token']}"},
)
tests/test_data/test_gen3_data.py:72:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:602: in get
return self.request("GET", url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:476: in request
return super().request(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:270: in send
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:267: in send
portal.call(self.app, scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:283: in call
return cast(T_Retval, self.start_task_soon(func, *args).result())
/usr/lib/python3.9/concurrent/futures/_base.py:446: in result
return self.__get_result()
/usr/lib/python3.9/concurrent/futures/_base.py:391: in __get_result
raise self._exception
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:219: in _call_func
retval = await retval
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/applications.py:269: in __call__
await super().__call__(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/applications.py:124: in __call__
await self.middleware_stack(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:184: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:162: in __call__
await self.app(scope, receive, _send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/cors.py:84: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:93: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:82: in __call__
await self.app(scope, receive, sender)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:21: in __call__
raise e
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:18: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:670: in __call__
await route.handle(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:266: in handle
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:65: in app
response = await func(request)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:227: in app
raw_response = await run_endpoint_function(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:160: in run_endpoint_function
return await dependant.call(**values)
app/main.py:318: in get_gen3_record
record = connection["gen3"].export_record(program, project, uuid, "json")
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:348: in export_record
output = requests.get(api_url, auth=self._auth_provider).text
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:73: in get
return request("get", url, params=params, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:575: in request
prep = self.prepare_request(req)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:486: in prepare_request
p.prepare(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:372: in prepare
self.prepare_auth(auth, url)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:603: in prepare_auth
r = auth(self)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:325: in __call__
request.headers["Authorization"] = self._get_auth_value()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:446: in _get_auth_value
return "bearer " + self.get_access_token()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:433: in get_access_token
return self.refresh_access_token(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:367: in refresh_access_token
self._access_token = get_access_token_with_key(self._refresh_token)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:75: in get_access_token_with_key
resp = requests.post(auth_url, json=api_key)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f8e443a56d0>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
> raise SSLError(e, request=request)
E requests.exceptions.SSLError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:517: SSLError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
______________________________ test_manifest_node ______________________________
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37f5bb80>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
> httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:715:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37f5bb80>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e37f5beb0>
method = 'POST', url = '/user/credentials/cdis/access_token'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwd...p, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
def _make_request(
self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw
):
"""
Perform a request on a given urllib connection object taken from our
pool.
:param conn:
a connection from one of our connection pools
:param timeout:
Socket timeout in seconds for the request. This can be a
float or integer, which will set the same timeout value for
the socket connect and the socket read, or an instance of
:class:`urllib3.util.Timeout`, which gives you more fine-grained
control over your timeouts.
"""
self.num_requests += 1
timeout_obj = self._get_timeout(timeout)
timeout_obj.start_connect()
conn.timeout = Timeout.resolve_default_timeout(timeout_obj.connect_timeout)
# Trigger any extra validation we need to do.
try:
> self._validate_conn(conn)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:404:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37f5bb80>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e37f5beb0>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1058:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f8e37f5beb0>
def connect(self):
# Add certificate verification
self.sock = conn = self._new_conn()
hostname = self.host
tls_in_tls = False
if self._is_using_tunnel():
if self.tls_in_tls_required:
self.sock = conn = self._connect_tls_proxy(hostname, conn)
tls_in_tls = True
# Calls self._set_hostport(), so self.host is
# self._tunnel_host below.
self._tunnel()
# Mark this connection as not reusable
self.auto_open = 0
# Override the host with the one we're requesting data from.
hostname = self._tunnel_host
server_hostname = hostname
if self.server_hostname is not None:
server_hostname = self.server_hostname
is_time_off = datetime.date.today() < RECENT_DATE
if is_time_off:
warnings.warn(
(
"System time is way off (before {0}). This will probably "
"lead to SSL verification errors"
).format(RECENT_DATE),
SystemTimeWarning,
)
# Wrap socket using verification with the root certs in
# trusted_root_certs
default_ssl_context = False
if self.ssl_context is None:
default_ssl_context = True
self.ssl_context = create_urllib3_context(
ssl_version=resolve_ssl_version(self.ssl_version),
cert_reqs=resolve_cert_reqs(self.cert_reqs),
)
context = self.ssl_context
context.verify_mode = resolve_cert_reqs(self.cert_reqs)
# Try to load OS default certs if none are given.
# Works well on Windows (requires Python3.4+)
if (
not self.ca_certs
and not self.ca_cert_dir
and not self.ca_cert_data
and default_ssl_context
and hasattr(context, "load_default_certs")
):
context.load_default_certs()
> self.sock = ssl_wrap_socket(
sock=conn,
keyfile=self.key_file,
certfile=self.cert_file,
key_password=self.key_password,
ca_certs=self.ca_certs,
ca_cert_dir=self.ca_cert_dir,
ca_cert_data=self.ca_cert_data,
server_hostname=server_hostname,
ssl_context=context,
tls_in_tls=tls_in_tls,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:419:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
keyfile = None, certfile = None, cert_reqs = None
ca_certs = '/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/certifi/cacert.pem'
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', ssl_version = None
ciphers = None, ssl_context = <ssl.SSLContext object at 0x7f8e440cc640>
ca_cert_dir = None, key_password = None, ca_cert_data = None, tls_in_tls = False
def ssl_wrap_socket(
sock,
keyfile=None,
certfile=None,
cert_reqs=None,
ca_certs=None,
server_hostname=None,
ssl_version=None,
ciphers=None,
ssl_context=None,
ca_cert_dir=None,
key_password=None,
ca_cert_data=None,
tls_in_tls=False,
):
"""
All arguments except for server_hostname, ssl_context, and ca_cert_dir have
the same meaning as they do when using :func:`ssl.wrap_socket`.
:param server_hostname:
When SNI is supported, the expected hostname of the certificate
:param ssl_context:
A pre-made :class:`SSLContext` object. If none is provided, one will
be created using :func:`create_urllib3_context`.
:param ciphers:
A string of ciphers we wish the client to support.
:param ca_cert_dir:
A directory containing CA certificates in multiple separate files, as
supported by OpenSSL's -CApath flag or the capath argument to
SSLContext.load_verify_locations().
:param key_password:
Optional password if the keyfile is encrypted.
:param ca_cert_data:
Optional string containing CA certificates in PEM format suitable for
passing as the cadata parameter to SSLContext.load_verify_locations()
:param tls_in_tls:
Use SSLTransport to wrap the existing socket.
"""
context = ssl_context
if context is None:
# Note: This branch of code and all the variables in it are no longer
# used by urllib3 itself. We should consider deprecating and removing
# this code.
context = create_urllib3_context(ssl_version, cert_reqs, ciphers=ciphers)
if ca_certs or ca_cert_dir or ca_cert_data:
try:
context.load_verify_locations(ca_certs, ca_cert_dir, ca_cert_data)
except (IOError, OSError) as e:
raise SSLError(e)
elif ssl_context is None and hasattr(context, "load_default_certs"):
# try to load OS default certs; works well on Windows (require Python3.4+)
context.load_default_certs()
# Attempt to detect if we get the goofy behavior of the
# keyfile being encrypted and OpenSSL asking for the
# passphrase via the terminal and instead error out.
if keyfile and key_password is None and _is_key_file_encrypted(keyfile):
raise SSLError("Client private key is encrypted, password is required")
if certfile:
if key_password is None:
context.load_cert_chain(certfile, keyfile)
else:
context.load_cert_chain(certfile, keyfile, key_password)
try:
if hasattr(context, "set_alpn_protocols"):
context.set_alpn_protocols(ALPN_PROTOCOLS)
except NotImplementedError: # Defensive: in CI, we always have set_alpn_protocols
pass
# If we detect server_hostname is an IP address then the SNI
# extension should not be used according to RFC3546 Section 3.1
use_sni_hostname = server_hostname and not is_ipaddress(server_hostname)
# SecureTransport uses server_hostname in certificate verification.
send_sni = (use_sni_hostname and HAS_SNI) or (
IS_SECURETRANSPORT and server_hostname
)
# Do not warn the user if server_hostname is an invalid SNI hostname.
if not HAS_SNI and use_sni_hostname:
warnings.warn(
"An HTTPS request has been made, but the SNI (Server Name "
"Indication) extension to TLS is not available on this platform. "
"This may cause the server to present an incorrect TLS "
"certificate, which can cause validation failures. You can upgrade to "
"a newer version of Python to solve this. For more information, see "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#ssl-warnings",
SNIMissingWarning,
)
if send_sni:
> ssl_sock = _ssl_wrap_socket_impl(
sock, context, tls_in_tls, server_hostname=server_hostname
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:449:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
ssl_context = <ssl.SSLContext object at 0x7f8e440cc640>, tls_in_tls = False
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
def _ssl_wrap_socket_impl(sock, ssl_context, tls_in_tls, server_hostname=None):
if tls_in_tls:
if not SSLTransport:
# Import error, ssl is not available.
raise ProxySchemeUnsupported(
"TLS in TLS requires support for the 'ssl' module"
)
SSLTransport._validate_ssl_context_for_tls_in_tls(ssl_context)
return SSLTransport(sock, ssl_context, server_hostname)
if server_hostname:
> return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:493:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLContext object at 0x7f8e440cc640>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', session = None
def wrap_socket(self, sock, server_side=False,
do_handshake_on_connect=True,
suppress_ragged_eofs=True,
server_hostname=None, session=None):
# SSLSocket class handles server_hostname encoding before it calls
# ctx._wrap_socket()
> return self.sslsocket_class._create(
sock=sock,
server_side=server_side,
do_handshake_on_connect=do_handshake_on_connect,
suppress_ragged_eofs=suppress_ragged_eofs,
server_hostname=server_hostname,
context=self,
session=session
)
/usr/lib/python3.9/ssl.py:501:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'ssl.SSLSocket'>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
context = <ssl.SSLContext object at 0x7f8e440cc640>, session = None
@classmethod
def _create(cls, sock, server_side=False, do_handshake_on_connect=True,
suppress_ragged_eofs=True, server_hostname=None,
context=None, session=None):
if sock.getsockopt(SOL_SOCKET, SO_TYPE) != SOCK_STREAM:
raise NotImplementedError("only stream sockets are supported")
if server_side:
if server_hostname:
raise ValueError("server_hostname can only be specified "
"in client mode")
if session is not None:
raise ValueError("session can only be specified in "
"client mode")
if context.check_hostname and not server_hostname:
raise ValueError("check_hostname requires server_hostname")
kwargs = dict(
family=sock.family, type=sock.type, proto=sock.proto,
fileno=sock.fileno()
)
self = cls.__new__(cls, **kwargs)
super(SSLSocket, self).__init__(**kwargs)
sock_timeout = sock.gettimeout()
sock.detach()
self._context = context
self._session = session
self._closed = False
self._sslobj = None
self.server_side = server_side
self.server_hostname = context._encode_hostname(server_hostname)
self.do_handshake_on_connect = do_handshake_on_connect
self.suppress_ragged_eofs = suppress_ragged_eofs
# See if we are connected
try:
self.getpeername()
except OSError as e:
if e.errno != errno.ENOTCONN:
raise
connected = False
blocking = self.getblocking()
self.setblocking(False)
try:
# We are not connected so this is not supposed to block, but
# testing revealed otherwise on macOS and Windows so we do
# the non-blocking dance regardless. Our raise when any data
# is found means consuming the data is harmless.
notconn_pre_handshake_data = self.recv(1)
except OSError as e:
# EINVAL occurs for recv(1) on non-connected on unix sockets.
if e.errno not in (errno.ENOTCONN, errno.EINVAL):
raise
notconn_pre_handshake_data = b''
self.setblocking(blocking)
if notconn_pre_handshake_data:
# This prevents pending data sent to the socket before it was
# closed from escaping to the caller who could otherwise
# presume it came through a successful TLS connection.
reason = "Closed before TLS handshake with data in recv buffer."
notconn_pre_handshake_data_error = SSLError(e.errno, reason)
# Add the SSLError attributes that _ssl.c always adds.
notconn_pre_handshake_data_error.reason = reason
notconn_pre_handshake_data_error.library = None
try:
self.close()
except OSError:
pass
try:
raise notconn_pre_handshake_data_error
finally:
# Explicitly break the reference cycle.
notconn_pre_handshake_data_error = None
else:
connected = True
self.settimeout(sock_timeout) # Must come after setblocking() calls.
self._connected = connected
if connected:
# create the SSL object
try:
self._sslobj = self._context._wrap_socket(
self, server_side, self.server_hostname,
owner=self, session=self._session,
)
if do_handshake_on_connect:
timeout = self.gettimeout()
if timeout == 0.0:
# non-blocking
raise ValueError("do_handshake_on_connect should not be specified for non-blocking sockets")
> self.do_handshake()
/usr/lib/python3.9/ssl.py:1074:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLSocket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
block = False
@_sslcopydoc
def do_handshake(self, block=False):
self._check_connected()
timeout = self.gettimeout()
try:
if timeout == 0.0 and block:
self.settimeout(None)
> self._sslobj.do_handshake()
E ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)
/usr/lib/python3.9/ssl.py:1343: SSLCertVerificationError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f8e37f40e50>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37f5bb80>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
# If we're going to release the connection in ``finally:``, then
# the response doesn't need to know about the connection. Otherwise
# it will also try to release it and we'll have a double-release
# mess.
response_conn = conn if not release_conn else None
# Pass method to Response for length checking
response_kw["request_method"] = method
# Import httplib's response into our own wrapper object
response = self.ResponseCls.from_httplib(
httplib_response,
pool=self,
connection=response_conn,
retries=retries,
**response_kw
)
# Everything went great!
clean_exit = True
except EmptyPoolError:
# Didn't get a connection from the pool, no need to clean up
clean_exit = True
release_this_conn = False
raise
except (
TimeoutError,
HTTPException,
SocketError,
ProtocolError,
BaseSSLError,
SSLError,
CertificateError,
) as e:
# Discard the connection for these exceptions. It will be
# replaced during the next _get_conn() call.
clean_exit = False
def _is_ssl_error_message_from_http_proxy(ssl_error):
# We're trying to detect the message 'WRONG_VERSION_NUMBER' but
# SSLErrors are kinda all over the place when it comes to the message,
# so we try to cover our bases here!
message = " ".join(re.split("[^a-z]", str(ssl_error).lower()))
return (
"wrong version number" in message or "unknown protocol" in message
)
# Try to detect a common user error with proxies which is to
# set an HTTP proxy to be HTTPS when it should be 'http://'
# (ie {'http': 'http://proxy', 'https': 'https://proxy'})
# Instead we add a nice error message and point to a URL.
if (
isinstance(e, BaseSSLError)
and self.proxy
and _is_ssl_error_message_from_http_proxy(e)
and conn.proxy
and conn.proxy.scheme == "https"
):
e = ProxyError(
"Your proxy appears to only use HTTP and not HTTPS, "
"try changing your proxy URL to be HTTP. See: "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#https-proxy-error-http-proxy",
SSLError(e),
)
elif isinstance(e, (BaseSSLError, CertificateError)):
e = SSLError(e)
elif isinstance(e, (SocketError, NewConnectionError)) and self.proxy:
e = ProxyError("Cannot connect to proxy.", e)
elif isinstance(e, (SocketError, HTTPException)):
e = ProtocolError("Connection aborted.", e)
> retries = retries.increment(
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:799:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST', url = '/user/credentials/cdis/access_token', response = None
error = SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)'))
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37f5bb80>
_stacktrace = <traceback object at 0x7f8e37e27680>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py:592: MaxRetryError
During handling of the above exception, another exception occurred:
client = <starlette.testclient.TestClient object at 0x7f8e37b9dbe0>
token = {'access_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsInNjb3BlIjpbImRlbW8xLTEyTCJdLCJleHBpcmUiOiJOb25lIn0.doEgWg8P2u6dGhajC1CBwJHS3TtbJh4L_vhMfK75uJQ'}
def test_manifest_node(client, token):
UUID = "fd65a93f-ff62-45e4-b7b6-96419ef4f749"
> response = client.get(
f"/record/{UUID}",
headers={"Authorization": f"Bearer {token['access_token']}"},
)
tests/test_data/test_gen3_data.py:173:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:602: in get
return self.request("GET", url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:476: in request
return super().request(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:270: in send
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:267: in send
portal.call(self.app, scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:283: in call
return cast(T_Retval, self.start_task_soon(func, *args).result())
/usr/lib/python3.9/concurrent/futures/_base.py:446: in result
return self.__get_result()
/usr/lib/python3.9/concurrent/futures/_base.py:391: in __get_result
raise self._exception
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:219: in _call_func
retval = await retval
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/applications.py:269: in __call__
await super().__call__(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/applications.py:124: in __call__
await self.middleware_stack(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:184: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:162: in __call__
await self.app(scope, receive, _send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/cors.py:84: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:93: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:82: in __call__
await self.app(scope, receive, sender)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:21: in __call__
raise e
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:18: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:670: in __call__
await route.handle(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:266: in handle
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:65: in app
response = await func(request)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:227: in app
raw_response = await run_endpoint_function(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:160: in run_endpoint_function
return await dependant.call(**values)
app/main.py:318: in get_gen3_record
record = connection["gen3"].export_record(program, project, uuid, "json")
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:348: in export_record
output = requests.get(api_url, auth=self._auth_provider).text
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:73: in get
return request("get", url, params=params, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:575: in request
prep = self.prepare_request(req)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:486: in prepare_request
p.prepare(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:372: in prepare
self.prepare_auth(auth, url)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:603: in prepare_auth
r = auth(self)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:325: in __call__
request.headers["Authorization"] = self._get_auth_value()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:446: in _get_auth_value
return "bearer " + self.get_access_token()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:433: in get_access_token
return self.refresh_access_token(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:367: in refresh_access_token
self._access_token = get_access_token_with_key(self._refresh_token)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:75: in get_access_token_with_key
resp = requests.post(auth_url, json=api_key)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f8e37f40e50>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
> raise SSLError(e, request=request)
E requests.exceptions.SSLError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:517: SSLError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
________________________________ test_case_node ________________________________
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37eb38e0>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
> httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:715:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37eb38e0>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e37eb3f70>
method = 'POST', url = '/user/credentials/cdis/access_token'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwd...p, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
def _make_request(
self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw
):
"""
Perform a request on a given urllib connection object taken from our
pool.
:param conn:
a connection from one of our connection pools
:param timeout:
Socket timeout in seconds for the request. This can be a
float or integer, which will set the same timeout value for
the socket connect and the socket read, or an instance of
:class:`urllib3.util.Timeout`, which gives you more fine-grained
control over your timeouts.
"""
self.num_requests += 1
timeout_obj = self._get_timeout(timeout)
timeout_obj.start_connect()
conn.timeout = Timeout.resolve_default_timeout(timeout_obj.connect_timeout)
# Trigger any extra validation we need to do.
try:
> self._validate_conn(conn)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:404:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37eb38e0>
conn = <urllib3.connection.HTTPSConnection object at 0x7f8e37eb3f70>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1058:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f8e37eb3f70>
def connect(self):
# Add certificate verification
self.sock = conn = self._new_conn()
hostname = self.host
tls_in_tls = False
if self._is_using_tunnel():
if self.tls_in_tls_required:
self.sock = conn = self._connect_tls_proxy(hostname, conn)
tls_in_tls = True
# Calls self._set_hostport(), so self.host is
# self._tunnel_host below.
self._tunnel()
# Mark this connection as not reusable
self.auto_open = 0
# Override the host with the one we're requesting data from.
hostname = self._tunnel_host
server_hostname = hostname
if self.server_hostname is not None:
server_hostname = self.server_hostname
is_time_off = datetime.date.today() < RECENT_DATE
if is_time_off:
warnings.warn(
(
"System time is way off (before {0}). This will probably "
"lead to SSL verification errors"
).format(RECENT_DATE),
SystemTimeWarning,
)
# Wrap socket using verification with the root certs in
# trusted_root_certs
default_ssl_context = False
if self.ssl_context is None:
default_ssl_context = True
self.ssl_context = create_urllib3_context(
ssl_version=resolve_ssl_version(self.ssl_version),
cert_reqs=resolve_cert_reqs(self.cert_reqs),
)
context = self.ssl_context
context.verify_mode = resolve_cert_reqs(self.cert_reqs)
# Try to load OS default certs if none are given.
# Works well on Windows (requires Python3.4+)
if (
not self.ca_certs
and not self.ca_cert_dir
and not self.ca_cert_data
and default_ssl_context
and hasattr(context, "load_default_certs")
):
context.load_default_certs()
> self.sock = ssl_wrap_socket(
sock=conn,
keyfile=self.key_file,
certfile=self.cert_file,
key_password=self.key_password,
ca_certs=self.ca_certs,
ca_cert_dir=self.ca_cert_dir,
ca_cert_data=self.ca_cert_data,
server_hostname=server_hostname,
ssl_context=context,
tls_in_tls=tls_in_tls,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:419:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
keyfile = None, certfile = None, cert_reqs = None
ca_certs = '/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/certifi/cacert.pem'
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', ssl_version = None
ciphers = None, ssl_context = <ssl.SSLContext object at 0x7f8e446c8c40>
ca_cert_dir = None, key_password = None, ca_cert_data = None, tls_in_tls = False
def ssl_wrap_socket(
sock,
keyfile=None,
certfile=None,
cert_reqs=None,
ca_certs=None,
server_hostname=None,
ssl_version=None,
ciphers=None,
ssl_context=None,
ca_cert_dir=None,
key_password=None,
ca_cert_data=None,
tls_in_tls=False,
):
"""
All arguments except for server_hostname, ssl_context, and ca_cert_dir have
the same meaning as they do when using :func:`ssl.wrap_socket`.
:param server_hostname:
When SNI is supported, the expected hostname of the certificate
:param ssl_context:
A pre-made :class:`SSLContext` object. If none is provided, one will
be created using :func:`create_urllib3_context`.
:param ciphers:
A string of ciphers we wish the client to support.
:param ca_cert_dir:
A directory containing CA certificates in multiple separate files, as
supported by OpenSSL's -CApath flag or the capath argument to
SSLContext.load_verify_locations().
:param key_password:
Optional password if the keyfile is encrypted.
:param ca_cert_data:
Optional string containing CA certificates in PEM format suitable for
passing as the cadata parameter to SSLContext.load_verify_locations()
:param tls_in_tls:
Use SSLTransport to wrap the existing socket.
"""
context = ssl_context
if context is None:
# Note: This branch of code and all the variables in it are no longer
# used by urllib3 itself. We should consider deprecating and removing
# this code.
context = create_urllib3_context(ssl_version, cert_reqs, ciphers=ciphers)
if ca_certs or ca_cert_dir or ca_cert_data:
try:
context.load_verify_locations(ca_certs, ca_cert_dir, ca_cert_data)
except (IOError, OSError) as e:
raise SSLError(e)
elif ssl_context is None and hasattr(context, "load_default_certs"):
# try to load OS default certs; works well on Windows (require Python3.4+)
context.load_default_certs()
# Attempt to detect if we get the goofy behavior of the
# keyfile being encrypted and OpenSSL asking for the
# passphrase via the terminal and instead error out.
if keyfile and key_password is None and _is_key_file_encrypted(keyfile):
raise SSLError("Client private key is encrypted, password is required")
if certfile:
if key_password is None:
context.load_cert_chain(certfile, keyfile)
else:
context.load_cert_chain(certfile, keyfile, key_password)
try:
if hasattr(context, "set_alpn_protocols"):
context.set_alpn_protocols(ALPN_PROTOCOLS)
except NotImplementedError: # Defensive: in CI, we always have set_alpn_protocols
pass
# If we detect server_hostname is an IP address then the SNI
# extension should not be used according to RFC3546 Section 3.1
use_sni_hostname = server_hostname and not is_ipaddress(server_hostname)
# SecureTransport uses server_hostname in certificate verification.
send_sni = (use_sni_hostname and HAS_SNI) or (
IS_SECURETRANSPORT and server_hostname
)
# Do not warn the user if server_hostname is an invalid SNI hostname.
if not HAS_SNI and use_sni_hostname:
warnings.warn(
"An HTTPS request has been made, but the SNI (Server Name "
"Indication) extension to TLS is not available on this platform. "
"This may cause the server to present an incorrect TLS "
"certificate, which can cause validation failures. You can upgrade to "
"a newer version of Python to solve this. For more information, see "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#ssl-warnings",
SNIMissingWarning,
)
if send_sni:
> ssl_sock = _ssl_wrap_socket_impl(
sock, context, tls_in_tls, server_hostname=server_hostname
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:449:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
ssl_context = <ssl.SSLContext object at 0x7f8e446c8c40>, tls_in_tls = False
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
def _ssl_wrap_socket_impl(sock, ssl_context, tls_in_tls, server_hostname=None):
if tls_in_tls:
if not SSLTransport:
# Import error, ssl is not available.
raise ProxySchemeUnsupported(
"TLS in TLS requires support for the 'ssl' module"
)
SSLTransport._validate_ssl_context_for_tls_in_tls(ssl_context)
return SSLTransport(sock, ssl_context, server_hostname)
if server_hostname:
> return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:493:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLContext object at 0x7f8e446c8c40>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au', session = None
def wrap_socket(self, sock, server_side=False,
do_handshake_on_connect=True,
suppress_ragged_eofs=True,
server_hostname=None, session=None):
# SSLSocket class handles server_hostname encoding before it calls
# ctx._wrap_socket()
> return self.sslsocket_class._create(
sock=sock,
server_side=server_side,
do_handshake_on_connect=do_handshake_on_connect,
suppress_ragged_eofs=suppress_ragged_eofs,
server_hostname=server_hostname,
context=self,
session=session
)
/usr/lib/python3.9/ssl.py:501:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'ssl.SSLSocket'>
sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
server_side = False, do_handshake_on_connect = True, suppress_ragged_eofs = True
server_hostname = 'gen3.abi-ctt-ctp.cloud.edu.au'
context = <ssl.SSLContext object at 0x7f8e446c8c40>, session = None
@classmethod
def _create(cls, sock, server_side=False, do_handshake_on_connect=True,
suppress_ragged_eofs=True, server_hostname=None,
context=None, session=None):
if sock.getsockopt(SOL_SOCKET, SO_TYPE) != SOCK_STREAM:
raise NotImplementedError("only stream sockets are supported")
if server_side:
if server_hostname:
raise ValueError("server_hostname can only be specified "
"in client mode")
if session is not None:
raise ValueError("session can only be specified in "
"client mode")
if context.check_hostname and not server_hostname:
raise ValueError("check_hostname requires server_hostname")
kwargs = dict(
family=sock.family, type=sock.type, proto=sock.proto,
fileno=sock.fileno()
)
self = cls.__new__(cls, **kwargs)
super(SSLSocket, self).__init__(**kwargs)
sock_timeout = sock.gettimeout()
sock.detach()
self._context = context
self._session = session
self._closed = False
self._sslobj = None
self.server_side = server_side
self.server_hostname = context._encode_hostname(server_hostname)
self.do_handshake_on_connect = do_handshake_on_connect
self.suppress_ragged_eofs = suppress_ragged_eofs
# See if we are connected
try:
self.getpeername()
except OSError as e:
if e.errno != errno.ENOTCONN:
raise
connected = False
blocking = self.getblocking()
self.setblocking(False)
try:
# We are not connected so this is not supposed to block, but
# testing revealed otherwise on macOS and Windows so we do
# the non-blocking dance regardless. Our raise when any data
# is found means consuming the data is harmless.
notconn_pre_handshake_data = self.recv(1)
except OSError as e:
# EINVAL occurs for recv(1) on non-connected on unix sockets.
if e.errno not in (errno.ENOTCONN, errno.EINVAL):
raise
notconn_pre_handshake_data = b''
self.setblocking(blocking)
if notconn_pre_handshake_data:
# This prevents pending data sent to the socket before it was
# closed from escaping to the caller who could otherwise
# presume it came through a successful TLS connection.
reason = "Closed before TLS handshake with data in recv buffer."
notconn_pre_handshake_data_error = SSLError(e.errno, reason)
# Add the SSLError attributes that _ssl.c always adds.
notconn_pre_handshake_data_error.reason = reason
notconn_pre_handshake_data_error.library = None
try:
self.close()
except OSError:
pass
try:
raise notconn_pre_handshake_data_error
finally:
# Explicitly break the reference cycle.
notconn_pre_handshake_data_error = None
else:
connected = True
self.settimeout(sock_timeout) # Must come after setblocking() calls.
self._connected = connected
if connected:
# create the SSL object
try:
self._sslobj = self._context._wrap_socket(
self, server_side, self.server_hostname,
owner=self, session=self._session,
)
if do_handshake_on_connect:
timeout = self.gettimeout()
if timeout == 0.0:
# non-blocking
raise ValueError("do_handshake_on_connect should not be specified for non-blocking sockets")
> self.do_handshake()
/usr/lib/python3.9/ssl.py:1074:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLSocket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
block = False
@_sslcopydoc
def do_handshake(self, block=False):
self._check_connected()
timeout = self.gettimeout()
try:
if timeout == 0.0 and block:
self.settimeout(None)
> self._sslobj.do_handshake()
E ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)
/usr/lib/python3.9/ssl.py:1343: SSLCertVerificationError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f8e37eb3940>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37eb38e0>
method = 'POST', url = '/user/credentials/cdis/access_token'
body = b'{"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIyLTA4LTIzVDE5OjI4OjM0WiJ9.eyJwdXIiOiJhcG...NPva0i6TdvsONgWYV1N3mET3cX78Px5n6SH84sTMCLqWr5EOzw4ImhcQ2kOYfMOqKA", "key_id": "92c93027-24d6-4240-825c-30b9395d78cf"}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '771', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/user/credentials/cdis/access_token', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
# If we're going to release the connection in ``finally:``, then
# the response doesn't need to know about the connection. Otherwise
# it will also try to release it and we'll have a double-release
# mess.
response_conn = conn if not release_conn else None
# Pass method to Response for length checking
response_kw["request_method"] = method
# Import httplib's response into our own wrapper object
response = self.ResponseCls.from_httplib(
httplib_response,
pool=self,
connection=response_conn,
retries=retries,
**response_kw
)
# Everything went great!
clean_exit = True
except EmptyPoolError:
# Didn't get a connection from the pool, no need to clean up
clean_exit = True
release_this_conn = False
raise
except (
TimeoutError,
HTTPException,
SocketError,
ProtocolError,
BaseSSLError,
SSLError,
CertificateError,
) as e:
# Discard the connection for these exceptions. It will be
# replaced during the next _get_conn() call.
clean_exit = False
def _is_ssl_error_message_from_http_proxy(ssl_error):
# We're trying to detect the message 'WRONG_VERSION_NUMBER' but
# SSLErrors are kinda all over the place when it comes to the message,
# so we try to cover our bases here!
message = " ".join(re.split("[^a-z]", str(ssl_error).lower()))
return (
"wrong version number" in message or "unknown protocol" in message
)
# Try to detect a common user error with proxies which is to
# set an HTTP proxy to be HTTPS when it should be 'http://'
# (ie {'http': 'http://proxy', 'https': 'https://proxy'})
# Instead we add a nice error message and point to a URL.
if (
isinstance(e, BaseSSLError)
and self.proxy
and _is_ssl_error_message_from_http_proxy(e)
and conn.proxy
and conn.proxy.scheme == "https"
):
e = ProxyError(
"Your proxy appears to only use HTTP and not HTTPS, "
"try changing your proxy URL to be HTTP. See: "
"https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html"
"#https-proxy-error-http-proxy",
SSLError(e),
)
elif isinstance(e, (BaseSSLError, CertificateError)):
e = SSLError(e)
elif isinstance(e, (SocketError, NewConnectionError)) and self.proxy:
e = ProxyError("Cannot connect to proxy.", e)
elif isinstance(e, (SocketError, HTTPException)):
e = ProtocolError("Connection aborted.", e)
> retries = retries.increment(
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:799:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST', url = '/user/credentials/cdis/access_token', response = None
error = SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)'))
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f8e37eb38e0>
_stacktrace = <traceback object at 0x7f8e445557c0>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py:592: MaxRetryError
During handling of the above exception, another exception occurred:
client = <starlette.testclient.TestClient object at 0x7f8e37949a00>
token = {'access_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsInNjb3BlIjpbImRlbW8xLTEyTCJdLCJleHBpcmUiOiJOb25lIn0.doEgWg8P2u6dGhajC1CBwJHS3TtbJh4L_vhMfK75uJQ'}
def test_case_node(client, token):
UUID = "c58ab983-6cf9-4174-a7a9-20cdf1d6bc33"
> response = client.get(
f"/record/{UUID}",
headers={"Authorization": f"Bearer {token['access_token']}"},
)
tests/test_data/test_gen3_data.py:227:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:602: in get
return self.request("GET", url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:476: in request
return super().request(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:270: in send
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:267: in send
portal.call(self.app, scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:283: in call
return cast(T_Retval, self.start_task_soon(func, *args).result())
/usr/lib/python3.9/concurrent/futures/_base.py:446: in result
return self.__get_result()
/usr/lib/python3.9/concurrent/futures/_base.py:391: in __get_result
raise self._exception
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:219: in _call_func
retval = await retval
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/applications.py:269: in __call__
await super().__call__(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/applications.py:124: in __call__
await self.middleware_stack(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:184: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:162: in __call__
await self.app(scope, receive, _send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/cors.py:84: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:93: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:82: in __call__
await self.app(scope, receive, sender)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:21: in __call__
raise e
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:18: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:670: in __call__
await route.handle(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:266: in handle
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:65: in app
response = await func(request)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:227: in app
raw_response = await run_endpoint_function(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:160: in run_endpoint_function
return await dependant.call(**values)
app/main.py:318: in get_gen3_record
record = connection["gen3"].export_record(program, project, uuid, "json")
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:348: in export_record
output = requests.get(api_url, auth=self._auth_provider).text
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:73: in get
return request("get", url, params=params, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:575: in request
prep = self.prepare_request(req)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:486: in prepare_request
p.prepare(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:372: in prepare
self.prepare_auth(auth, url)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:603: in prepare_auth
r = auth(self)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:325: in __call__
request.headers["Authorization"] = self._get_auth_value()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:446: in _get_auth_value
return "bearer " + self.get_access_token()
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:433: in get_access_token
return self.refresh_access_token(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:367: in refresh_access_token
self._access_token = get_access_token_with_key(self._refresh_token)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:75: in get_access_token_with_key
resp = requests.post(auth_url, json=api_key)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f8e37eb3940>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
> raise SSLError(e, request=request)
E requests.exceptions.SSLError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:517: SSLError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
____________________________ test_irods_collection _____________________________
client = <starlette.testclient.TestClient object at 0x7f8e37cbaa00>
token = {'access_token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6InB1YmxpYyIsInNjb3BlIjpbImRlbW8xLTEyTCJdLCJleHBpcmUiOiJOb25lIn0.doEgWg8P2u6dGhajC1CBwJHS3TtbJh4L_vhMfK75uJQ'}
def test_irods_collection(client, token):
payload1 = {"path": "/dataset-217-version-2"}
response = client.post(
"/collection",
json=payload1,
headers={"Authorization": f"Bearer {token['access_token']}"},
)
result = response.json()
> assert result["folders"] == [
{"name": "derivative", "path": "/dataset-217-version-2/derivative"},
{"name": "primary", "path": "/dataset-217-version-2/primary"},
]
E KeyError: 'folders'
tests/test_data/test_irods_data.py:32: KeyError
------------------------------ Captured log setup ------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
INFO app.main:main.py:166 {'gen3': False, 'irods': True, 'orthanc': True}
WARNING app.main:main.py:185 Failed to update default filter.
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
------------------------------ Captured log call -------------------------------
ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission.
=============================== warnings summary ===============================
tests/test_api/test_gen3_api.py::test_get_gen3_graphql_query
/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/threadexception.py:73: PytestUnhandledThreadExceptionWarning: Exception in thread Thread-1
Traceback (most recent call last):
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 715, in urlopen
httplib_response = self._make_request(
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 404, in _make_request
self._validate_conn(conn)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1058, in _validate_conn
conn.connect()
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 419, in connect
self.sock = ssl_wrap_socket(
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
File "/usr/lib/python3.9/ssl.py", line 501, in wrap_socket
return self.sslsocket_class._create(
File "/usr/lib/python3.9/ssl.py", line 1074, in _create
self.do_handshake()
File "/usr/lib/python3.9/ssl.py", line 1343, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py", line 486, in send
resp = conn.urlopen(
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 799, in urlopen
retries = retries.increment(
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/cmiss/Jenkins/workspace/12-Labours-API/services/gen3/gen3_service.py", line 43, in process_graphql_query
query_result = self.__submission.query(query_code)["data"][item.node]
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py", line 423, in query
output = requests.post(api_url, auth=self._auth_provider, json=query).text
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 115, in post
return request("post", url, data=data, json=json, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 575, in request
prep = self.prepare_request(req)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 486, in prepare_request
p.prepare(
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py", line 372, in prepare
self.prepare_auth(auth, url)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py", line 603, in prepare_auth
r = auth(self)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py", line 325, in __call__
request.headers["Authorization"] = self._get_auth_value()
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py", line 446, in _get_auth_value
return "bearer " + self.get_access_token()
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py", line 433, in get_access_token
return self.refresh_access_token(
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py", line 367, in refresh_access_token
self._access_token = get_access_token_with_key(self._refresh_token)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py", line 75, in get_access_token_with_key
resp = requests.post(auth_url, json=api_key)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 115, in post
return request("post", url, data=data, json=json, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py", line 517, in send
raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='gen3.abi-ctt-ctp.cloud.edu.au', port=443): Max retries exceeded with url: /user/credentials/cdis/access_token (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1133)')))
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/python3.9/threading.py", line 980, in _bootstrap_inner
self.run()
File "/usr/lib/python3.9/threading.py", line 917, in run
self._target(*self._args, **self._kwargs)
File "/home/cmiss/Jenkins/workspace/12-Labours-API/services/gen3/gen3_service.py", line 48, in process_graphql_query
raise HTTPException(
fastapi.exceptions.HTTPException
warnings.warn(pytest.PytestUnhandledThreadExceptionWarning(msg))
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_api/test_gen3_api.py::test_get_gen3_record - requests.excep...
FAILED tests/test_api/test_gen3_api.py::test_get_gen3_graphql_query - KeyErro...
FAILED tests/test_api/test_gen3_api.py::test_get_gen3_graphql_pagination - as...
FAILED tests/test_api/test_irods_api.py::test_get_irods_collection - assert 4...
FAILED tests/test_api/test_irods_api.py::test_get_irods_data_file - assert 40...
FAILED tests/test_data/test_gen3_data.py::test_experiment_node - requests.exc...
FAILED tests/test_data/test_gen3_data.py::test_dataset_description_node - req...
FAILED tests/test_data/test_gen3_data.py::test_manifest_node - requests.excep...
FAILED tests/test_data/test_gen3_data.py::test_case_node - requests.exception...
FAILED tests/test_data/test_irods_data.py::test_irods_collection - KeyError: ...
============= 10 failed, 29 passed, 1 warning in 166.47s (0:02:46) =============
Build step 'Virtualenv Builder' marked build as failure
[Slack Notifications] found #2653 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE