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Started by timer Running as SYSTEM Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/SPARC-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/nih-sparc/sparc-api.git > git init /home/cmiss/Jenkins/workspace/SPARC-API # timeout=10 Fetching upstream changes from https://github.com/nih-sparc/sparc-api.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/nih-sparc/sparc-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/nih-sparc/sparc-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/master^{commit} # timeout=10 Checking out Revision 14ea83adacb50ddd7b3072646c019df401c9d3d8 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 14ea83adacb50ddd7b3072646c019df401c9d3d8 # timeout=10 Commit message: "Merge pull request #183 from Tehsurfer/s3-path-fix" > git rev-list --no-walk 14ea83adacb50ddd7b3072646c019df401c9d3d8 # timeout=10 [SPARC-API] $ /bin/sh -xe /tmp/shiningpanda5677058813867334880.sh + pwd + export PYTHONPATH=/home/cmiss/Jenkins/workspace/SPARC-API + export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python + pip install -r requirements.txt Requirement already satisfied: api==0.0.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.0.7) Requirement already satisfied: pennsieve==6.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (6.1.1) Requirement already satisfied: boto3==1.17.67 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.17.67) Requirement already satisfied: botocore==1.20.67 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.20.67) Requirement already satisfied: certifi==2019.11.28 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (2019.11.28) Requirement already satisfied: chardet==3.0.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.0.4) Collecting Click==7.1.2 (from -r requirements.txt (line 7)) Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Requirement already satisfied: docutils==0.15.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.15.2) Requirement already satisfied: Flask==1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 9)) (1.1.1) Requirement already satisfied: flask-marshmallow==0.10.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (0.10.1) Requirement already satisfied: flask-cors==3.0.8 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 11)) (3.0.8) Requirement already satisfied: gunicorn==20.0.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 12)) (20.0.4) Requirement already satisfied: idna==2.8 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 13)) (2.8) Requirement already satisfied: itsdangerous==1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 14)) (1.1.0) Requirement already satisfied: Jinja2==2.11.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 15)) (2.11.3) Requirement already satisfied: jmespath==0.9.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 16)) (0.9.4) Requirement already satisfied: MarkupSafe==1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 17)) (1.1.1) Requirement already satisfied: marshmallow==3.2.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 18)) (3.2.2) Requirement already satisfied: nose==1.3.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 19)) (1.3.7) Requirement already satisfied: osparc==0.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 20)) (0.4.3) Requirement already satisfied: pillow in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 21)) (10.0.0) Requirement already satisfied: public==2019.4.13 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 22)) (2019.4.13) Requirement already satisfied: pytest in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 23)) (5.4.3) Requirement already satisfied: pymongo==3.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 24)) (3.8.0) Requirement already satisfied: python-dateutil==2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 25)) (2.8.0) Requirement already satisfied: python-dotenv==0.10.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 26)) (0.10.3) Requirement already satisfied: query-string==2019.4.13 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 27)) (2019.4.13) Requirement already satisfied: requests==2.25.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 28)) (2.25.1) Requirement already satisfied: s3transfer==0.4.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 29)) (0.4.2) Requirement already satisfied: sendgrid==6.9.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 30)) (6.9.7) Requirement already satisfied: six==1.13.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 31)) (1.13.0) Requirement already satisfied: SQLAlchemy==1.3.20 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 32)) (1.3.20) Requirement already satisfied: urllib3==1.26.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 33)) (1.26.4) Requirement already satisfied: Werkzeug==0.16.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 34)) (0.16.0) Requirement already satisfied: psycopg2-binary==2.9.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 35)) (2.9.5) Requirement already satisfied: APScheduler==3.7.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 36)) (3.7.0) Requirement already satisfied: google-api-python-client==2.52.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 37)) (2.52.0) Requirement already satisfied: oauth2client==4.1.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 38)) (4.1.3) Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 39)) (2.6.2) Requirement already satisfied: contentful==1.13.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 40)) (1.13.1) Requirement already satisfied: contentful_management==2.11.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 41)) (2.11.0) Requirement already satisfied: configparser>=3.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (6.0.0) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (1.2.14) Requirement already satisfied: future>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (0.18.3) Requirement already satisfied: futures in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (3.0.5) Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (4.24.2) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (3.2.0) Requirement already satisfied: pytz>=2016 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (2023.3.post1) Requirement already satisfied: rsa==4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (4.0) Requirement already satisfied: semver>=2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (3.0.1) Requirement already satisfied: websocket-client>=0.57.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (1.6.2) Requirement already satisfied: docopt>=0.6 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (0.6.2) Requirement already satisfied: psutil>=5.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (5.9.5) Requirement already satisfied: setuptools>=3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gunicorn==20.0.4->-r requirements.txt (line 12)) (68.1.2) Requirement already satisfied: python-http-client>=3.2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 30)) (3.3.7) Requirement already satisfied: starkbank-ecdsa>=2.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 30)) (2.2.0) Requirement already satisfied: tzlocal~=2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 36)) (2.1) Requirement already satisfied: httplib2<1dev,>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (0.22.0) Requirement already satisfied: google-auth<3.0.0dev,>=1.19.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (2.22.0) Requirement already satisfied: google-auth-httplib2>=0.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (0.1.0) Requirement already satisfied: google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (2.11.1) Requirement already satisfied: uritemplate<5,>=3.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (4.1.1) Requirement already satisfied: pyasn1>=0.1.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 38)) (0.5.0) Requirement already satisfied: pyasn1-modules>=0.0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 38)) (0.3.0) Requirement already satisfied: ecdsa<0.15 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements.txt (line 2)) (0.14.1) Requirement already satisfied: py>=1.5.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (1.11.0) Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (23.1) Requirement already satisfied: attrs>=17.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (23.1.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (10.1.0) Requirement already satisfied: pluggy<1.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (0.13.1) Requirement already satisfied: wcwidth in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (0.2.6) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from deprecated>=1.2.0->pennsieve==6.1.1->-r requirements.txt (line 2)) (1.15.0) Requirement already satisfied: googleapis-common-protos<2.0.dev0,>=1.56.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 37)) (1.60.0) Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-auth<3.0.0dev,>=1.19.0->google-api-python-client==2.52.0->-r requirements.txt (line 37)) (5.3.1) Requirement already satisfied: pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httplib2<1dev,>=0.15.0->google-api-python-client==2.52.0->-r requirements.txt (line 37)) (3.1.1) Installing collected packages: Click Attempting uninstall: Click Found existing installation: click 8.1.7 Uninstalling click-8.1.7: Successfully uninstalled click-8.1.7 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. black 23.7.0 requires click>=8.0.0, but you have click 7.1.2 which is incompatible. Successfully installed Click-7.1.2 + pip install -r requirements-dev.txt Requirement already satisfied: pytest==5.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 1)) (5.4.3) Requirement already satisfied: pennsieve==6.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 2)) (6.1.1) Requirement already satisfied: black in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 3)) (23.7.0) Requirement already satisfied: isort in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 4)) (5.12.0) Requirement already satisfied: nose in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 5)) (1.3.7) Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 6)) (23.1) Requirement already satisfied: py>=1.5.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (1.11.0) Requirement already satisfied: attrs>=17.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (23.1.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (10.1.0) Requirement already satisfied: pluggy<1.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (0.13.1) Requirement already satisfied: wcwidth in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (0.2.6) Requirement already satisfied: boto3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.17.67) Requirement already satisfied: configparser>=3.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (6.0.0) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.2.14) Requirement already satisfied: future>=0.15.0 in 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3.9.18, pytest-5.4.3, py-1.11.0, pluggy-0.13.1 rootdir: /home/cmiss/Jenkins/workspace/SPARC-API collected 100 items tests/test_api.py ................... 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[100%] =================================== FAILURES =================================== __________________________ test_neurolucida_thumbnail __________________________ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb6afdf70> method = 'GET' url = '/thumbnail?datasetId=37&version=3&path=files%2Fderivative%2Fsub-54-5%2FTJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml' body = None headers = {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} 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='/thumbnail', query='datasetId=37&version=3&path=files%2Fderivative%2Fsub-54-5%2FTJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml', 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb6afdf70> conn = <urllib3.connection.HTTPSConnection object at 0x7fdbb433d370> method = 'GET' url = '/thumbnail?datasetId=37&version=3&path=files%2Fderivative%2Fsub-54-5%2FTJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml' timeout = Timeout(connect=None, read=None, total=None), chunked = False httplib_request_kw = {'body': None, 'headers': {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'}} 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_obj.connect_timeout # Trigger any extra validation we need to do. try: > self._validate_conn(conn) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb6afdf70> conn = <urllib3.connection.HTTPSConnection object at 0x7fdbb433d370> 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7fdbb433d370> def connect(self): # Add certificate verification conn = self._new_conn() hostname = self.host tls_in_tls = False if self._is_using_tunnel(): if self.tls_in_tls_required: conn = self._connect_tls_proxy(hostname, conn) tls_in_tls = True self.sock = conn # 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:411: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/certifi/cacert.pem' server_hostname = 'sparc.biolucida.net', ssl_version = None, ciphers = None ssl_context = <ssl.SSLContext object at 0x7fdbb685b440>, 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: 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/latest/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:428: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6> ssl_context = <ssl.SSLContext object at 0x7fdbb685b440>, tls_in_tls = False server_hostname = 'sparc.biolucida.net' 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:472: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <ssl.SSLContext object at 0x7fdbb685b440> 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 = 'sparc.biolucida.net', 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 = 'sparc.biolucida.net' context = <ssl.SSLContext object at 0x7fdbb685b440>, 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 ConnectionResetError: [Errno 104] Connection reset by peer /usr/lib/python3.9/ssl.py:1343: ConnectionResetError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7fdbb6ac3bb0> request = <PreparedRequest [GET]>, 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 as e: # this may raise a string formatting error. err = ("Invalid timeout {}. Pass a (connect, read) " "timeout tuple, or a single float to set " "both timeouts to the same value".format(timeout)) raise ValueError(err) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: if not chunked: > 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 ) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:439: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb6afdf70> method = 'GET' url = '/thumbnail?datasetId=37&version=3&path=files%2Fderivative%2Fsub-54-5%2FTJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml' body = None headers = {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} 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='/thumbnail', query='datasetId=37&version=3&path=files%2Fderivative%2Fsub-54-5%2FTJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml', 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 if 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:755: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'GET' url = '/thumbnail?datasetId=37&version=3&path=files%2Fderivative%2Fsub-54-5%2FTJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml' response = None error = ProtocolError('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb6afdf70> _stacktrace = <traceback object at 0x7fdbbc2864c0> 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) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py:532: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tp = <class 'urllib3.exceptions.ProtocolError'>, value = None, tb = None def reraise(tp, value, tb=None): try: if value is None: value = tp() if value.__traceback__ is not tb: > raise value.with_traceback(tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/packages/six.py:734: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb6afdf70> method = 'GET' url = '/thumbnail?datasetId=37&version=3&path=files%2Fderivative%2Fsub-54-5%2FTJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml' body = None headers = {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} 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='/thumbnail', query='datasetId=37&version=3&path=files%2Fderivative%2Fsub-54-5%2FTJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml', 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb6afdf70> conn = <urllib3.connection.HTTPSConnection object at 0x7fdbb433d370> method = 'GET' url = '/thumbnail?datasetId=37&version=3&path=files%2Fderivative%2Fsub-54-5%2FTJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml' timeout = Timeout(connect=None, read=None, total=None), chunked = False httplib_request_kw = {'body': None, 'headers': {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'}} 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_obj.connect_timeout # Trigger any extra validation we need to do. try: > self._validate_conn(conn) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb6afdf70> conn = <urllib3.connection.HTTPSConnection object at 0x7fdbb433d370> 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7fdbb433d370> def connect(self): # Add certificate verification conn = self._new_conn() hostname = self.host tls_in_tls = False if self._is_using_tunnel(): if self.tls_in_tls_required: conn = self._connect_tls_proxy(hostname, conn) tls_in_tls = True self.sock = conn # 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:411: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/certifi/cacert.pem' server_hostname = 'sparc.biolucida.net', ssl_version = None, ciphers = None ssl_context = <ssl.SSLContext object at 0x7fdbb685b440>, 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: 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/latest/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:428: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6> ssl_context = <ssl.SSLContext object at 0x7fdbb685b440>, tls_in_tls = False server_hostname = 'sparc.biolucida.net' 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:472: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <ssl.SSLContext object at 0x7fdbb685b440> 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 = 'sparc.biolucida.net', 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 = 'sparc.biolucida.net' context = <ssl.SSLContext object at 0x7fdbb685b440>, 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 urllib3.exceptions.ProtocolError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) /usr/lib/python3.9/ssl.py:1343: ProtocolError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_neurolucida_thumbnail(client): query_string = {'datasetId': 37, 'version': 3, 'path': 'files/derivative/sub-54-5/TJU_3Scan_ratheart54-5_updated_06_11_19_Fiducials.xml'} > r = client.get('/thumbnail/neurolucida', query_string=query_string) tests/test_thumbnails.py:20: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:306: in thumbnail_from_neurolucida_file response = requests.get(url, params=query_args) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:76: in get return request('get', url, params=params, **kwargs) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:61: in request return session.request(method=method, url=url, **kwargs) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:542: in request resp = self.send(prep, **send_kwargs) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:655: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7fdbb6ac3bb0> request = <PreparedRequest [GET]>, 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 as e: # this may raise a string formatting error. err = ("Invalid timeout {}. Pass a (connect, read) " "timeout tuple, or a single float to set " "both timeouts to the same value".format(timeout)) raise ValueError(err) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: if not chunked: 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 ) # Send the request. else: if hasattr(conn, 'proxy_pool'): conn = conn.proxy_pool low_conn = conn._get_conn(timeout=DEFAULT_POOL_TIMEOUT) try: low_conn.putrequest(request.method, url, skip_accept_encoding=True) for header, value in request.headers.items(): low_conn.putheader(header, value) low_conn.endheaders() for i in request.body: low_conn.send(hex(len(i))[2:].encode('utf-8')) low_conn.send(b'\r\n') low_conn.send(i) low_conn.send(b'\r\n') low_conn.send(b'0\r\n\r\n') # Receive the response from the server try: # For Python 2.7, use buffering of HTTP responses r = low_conn.getresponse(buffering=True) except TypeError: # For compatibility with Python 3.3+ r = low_conn.getresponse() resp = HTTPResponse.from_httplib( r, pool=conn, connection=low_conn, preload_content=False, decode_content=False ) except: # If we hit any problems here, clean up the connection. # Then, reraise so that we can handle the actual exception. low_conn.close() raise except (ProtocolError, socket.error) as err: > raise ConnectionError(err, request=request) E requests.exceptions.ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:498: ConnectionError ____________________ test_neurolucida_thumbnail_dataset_221 ____________________ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb4852100> method = 'GET' url = '/thumbnail?datasetId=221&version=3&path=files%2Fderivative%2Fsub-M168%2Fdigital-traces%2FpCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml' body = None headers = {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} 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='/thumbnail', query='datasetId=221&version=3&path=files%2Fderivative%2Fsub-M168%2Fdigital-traces%2FpCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml', 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb4852100> conn = <urllib3.connection.HTTPSConnection object at 0x7fdbb5b47ee0> method = 'GET' url = '/thumbnail?datasetId=221&version=3&path=files%2Fderivative%2Fsub-M168%2Fdigital-traces%2FpCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml' timeout = Timeout(connect=None, read=None, total=None), chunked = False httplib_request_kw = {'body': None, 'headers': {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'}} 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_obj.connect_timeout # Trigger any extra validation we need to do. try: > self._validate_conn(conn) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb4852100> conn = <urllib3.connection.HTTPSConnection object at 0x7fdbb5b47ee0> 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7fdbb5b47ee0> def connect(self): # Add certificate verification conn = self._new_conn() hostname = self.host tls_in_tls = False if self._is_using_tunnel(): if self.tls_in_tls_required: conn = self._connect_tls_proxy(hostname, conn) tls_in_tls = True self.sock = conn # 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:411: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/certifi/cacert.pem' server_hostname = 'sparc.biolucida.net', ssl_version = None, ciphers = None ssl_context = <ssl.SSLContext object at 0x7fdbb4d06a40>, 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: 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/latest/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:428: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6> ssl_context = <ssl.SSLContext object at 0x7fdbb4d06a40>, tls_in_tls = False server_hostname = 'sparc.biolucida.net' 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:472: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <ssl.SSLContext object at 0x7fdbb4d06a40> 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 = 'sparc.biolucida.net', 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 = 'sparc.biolucida.net' context = <ssl.SSLContext object at 0x7fdbb4d06a40>, 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 ConnectionResetError: [Errno 104] Connection reset by peer /usr/lib/python3.9/ssl.py:1343: ConnectionResetError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7fdbb48524c0> request = <PreparedRequest [GET]>, 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 as e: # this may raise a string formatting error. err = ("Invalid timeout {}. Pass a (connect, read) " "timeout tuple, or a single float to set " "both timeouts to the same value".format(timeout)) raise ValueError(err) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: if not chunked: > 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 ) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:439: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb4852100> method = 'GET' url = '/thumbnail?datasetId=221&version=3&path=files%2Fderivative%2Fsub-M168%2Fdigital-traces%2FpCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml' body = None headers = {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} 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='/thumbnail', query='datasetId=221&version=3&path=files%2Fderivative%2Fsub-M168%2Fdigital-traces%2FpCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml', 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 if 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:755: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'GET' url = '/thumbnail?datasetId=221&version=3&path=files%2Fderivative%2Fsub-M168%2Fdigital-traces%2FpCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml' response = None error = ProtocolError('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb4852100> _stacktrace = <traceback object at 0x7fdbb55ca500> 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) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py:532: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tp = <class 'urllib3.exceptions.ProtocolError'>, value = None, tb = None def reraise(tp, value, tb=None): try: if value is None: value = tp() if value.__traceback__ is not tb: > raise value.with_traceback(tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/packages/six.py:734: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb4852100> method = 'GET' url = '/thumbnail?datasetId=221&version=3&path=files%2Fderivative%2Fsub-M168%2Fdigital-traces%2FpCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml' body = None headers = {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} 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='/thumbnail', query='datasetId=221&version=3&path=files%2Fderivative%2Fsub-M168%2Fdigital-traces%2FpCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml', 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb4852100> conn = <urllib3.connection.HTTPSConnection object at 0x7fdbb5b47ee0> method = 'GET' url = '/thumbnail?datasetId=221&version=3&path=files%2Fderivative%2Fsub-M168%2Fdigital-traces%2FpCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml' timeout = Timeout(connect=None, read=None, total=None), chunked = False httplib_request_kw = {'body': None, 'headers': {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'}} 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_obj.connect_timeout # Trigger any extra validation we need to do. try: > self._validate_conn(conn) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fdbb4852100> conn = <urllib3.connection.HTTPSConnection object at 0x7fdbb5b47ee0> 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7fdbb5b47ee0> def connect(self): # Add certificate verification conn = self._new_conn() hostname = self.host tls_in_tls = False if self._is_using_tunnel(): if self.tls_in_tls_required: conn = self._connect_tls_proxy(hostname, conn) tls_in_tls = True self.sock = conn # 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:411: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/certifi/cacert.pem' server_hostname = 'sparc.biolucida.net', ssl_version = None, ciphers = None ssl_context = <ssl.SSLContext object at 0x7fdbb4d06a40>, 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: 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/latest/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:428: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ sock = <socket.socket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6> ssl_context = <ssl.SSLContext object at 0x7fdbb4d06a40>, tls_in_tls = False server_hostname = 'sparc.biolucida.net' 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/ssl_.py:472: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <ssl.SSLContext object at 0x7fdbb4d06a40> 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 = 'sparc.biolucida.net', 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 = 'sparc.biolucida.net' context = <ssl.SSLContext object at 0x7fdbb4d06a40>, 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 urllib3.exceptions.ProtocolError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) /usr/lib/python3.9/ssl.py:1343: ProtocolError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_neurolucida_thumbnail_dataset_221(client): query_string = {'datasetId': 221, 'version': 3, 'path': 'files/derivative/sub-M168/digital-traces/pCm168_AAV_Z_20x_191211_S3B_lx_IGS.xml'} > r = client.get('/thumbnail/neurolucida', query_string=query_string) tests/test_thumbnails.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:306: in thumbnail_from_neurolucida_file response = requests.get(url, params=query_args) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:76: in get return request('get', url, params=params, **kwargs) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:61: in request return session.request(method=method, url=url, **kwargs) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:542: in request resp = self.send(prep, **send_kwargs) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:655: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7fdbb48524c0> request = <PreparedRequest [GET]>, 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 as e: # this may raise a string formatting error. err = ("Invalid timeout {}. Pass a (connect, read) " "timeout tuple, or a single float to set " "both timeouts to the same value".format(timeout)) raise ValueError(err) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: if not chunked: 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 ) # Send the request. else: if hasattr(conn, 'proxy_pool'): conn = conn.proxy_pool low_conn = conn._get_conn(timeout=DEFAULT_POOL_TIMEOUT) try: low_conn.putrequest(request.method, url, skip_accept_encoding=True) for header, value in request.headers.items(): low_conn.putheader(header, value) low_conn.endheaders() for i in request.body: low_conn.send(hex(len(i))[2:].encode('utf-8')) low_conn.send(b'\r\n') low_conn.send(i) low_conn.send(b'\r\n') low_conn.send(b'0\r\n\r\n') # Receive the response from the server try: # For Python 2.7, use buffering of HTTP responses r = low_conn.getresponse(buffering=True) except TypeError: # For compatibility with Python 3.3+ r = low_conn.getresponse() resp = HTTPResponse.from_httplib( r, pool=conn, connection=low_conn, preload_content=False, decode_content=False ) except: # If we hit any problems here, clean up the connection. # Then, reraise so that we can handle the actual exception. low_conn.close() raise except (ProtocolError, socket.error) as err: > raise ConnectionError(err, request=request) E requests.exceptions.ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:498: ConnectionError =============================== warnings summary =============================== /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/__init__.py:1 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import get_distribution, DistributionNotFound /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google')`. Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages declare_namespace(pkg) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google.logging')`. Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages declare_namespace(pkg) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2350 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google')`. Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages declare_namespace(parent) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/future/standard_library/__init__.py:65 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/future/standard_library/__init__.py:65: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:19 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:19: DeprecationWarning: Call to deprecated create function FileDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. DESCRIPTOR = _descriptor.FileDescriptor( /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:36 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:36: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:53 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:53: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:70 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:70: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:29 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:29: DeprecationWarning: Call to deprecated create function Descriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _CACHESEGMENT = _descriptor.Descriptor( tests/test_health.py::test_request_response /home/cmiss/Jenkins/workspace/SPARC-API/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead. assert_equals("healthy", json_response.get("status")) -- Docs: https://docs.pytest.org/en/latest/warnings.html =========================== short test summary info ============================ FAILED tests/test_thumbnails.py::test_neurolucida_thumbnail - requests.except... FAILED tests/test_thumbnails.py::test_neurolucida_thumbnail_dataset_221 - req... ======= 2 failed, 95 passed, 3 skipped, 14 warnings in 229.33s (0:03:49) ======= Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #842 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE