Started by timer
Running as SYSTEM
Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/SPARC-API-DEV
[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-DEV # 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 44e28f2f0c3b9474cef7c1d33f7e79e77e1a763e (refs/remotes/origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f 44e28f2f0c3b9474cef7c1d33f7e79e77e1a763e # timeout=10
Commit message: "Merge pull request #203 from nih-sparc/update-osparc-services-default-limit"
> git rev-list --no-walk 8a628a1a088723fb80f32e4728544ca0d3abb9fd # timeout=10
[SPARC-API-DEV] $ /usr/bin/python3.9 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenv.py:1041: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
Using base prefix '/usr'
New python executable in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/bin/python3.9
Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/bin/python
Installing setuptools, pip, wheel...done.
[SPARC-API-DEV] $ /bin/sh -xe /tmp/shiningpanda7964342749773104698.sh
+ pwd
+ export PYTHONPATH=/home/cmiss/Jenkins/workspace/SPARC-API-DEV
+ export SCICRUNCH_HOST=https://scicrunch.org/api/1/elastic/SPARC_PortalDatasets_dev
+ export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python
+ pip install -r requirements.txt
Collecting api==0.0.7 (from -r requirements.txt (line 1))
Using cached api-0.0.7-py3-none-any.whl
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Using cached public-2019.4.13-py3-none-any.whl
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Collecting urllib3==1.26.4 (from -r requirements.txt (line 33))
Downloading urllib3-1.26.4-py2.py3-none-any.whl.metadata (43 kB)
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Collecting psycopg2-binary==2.9.5 (from -r requirements.txt (line 35))
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Downloading APScheduler-3.7.0-py2.py3-none-any.whl.metadata (5.7 kB)
Collecting google-api-python-client==2.52.0 (from -r requirements.txt (line 37))
Downloading google_api_python_client-2.52.0-py2.py3-none-any.whl.metadata (6.6 kB)
Collecting oauth2client==4.1.3 (from -r requirements.txt (line 38))
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Downloading Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)
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Downloading protobuf-5.26.1-cp37-abi3-manylinux2014_x86_64.whl.metadata (592 bytes)
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Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Requirement already satisfied: setuptools>=3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gunicorn==20.0.4->-r requirements.txt (line 12)) (69.2.0)
Collecting python-http-client>=3.2.1 (from sendgrid==6.9.7->-r requirements.txt (line 30))
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Collecting httplib2<1dev,>=0.15.0 (from google-api-python-client==2.52.0->-r requirements.txt (line 37))
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Collecting google-auth<3.0.0dev,>=1.19.0 (from google-api-python-client==2.52.0->-r requirements.txt (line 37))
Downloading google_auth-2.29.0-py2.py3-none-any.whl.metadata (4.7 kB)
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Collecting googleapis-common-protos<2.0.dev0,>=1.56.2 (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))
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Installing collected packages: starkbank-ecdsa, pytz, python-dotenv, nose, jmespath, futures, docopt, chardet, certifi, wrapt, Werkzeug, websocket-client, urllib3, uritemplate, tzlocal, tomli, SQLAlchemy, six, semver, python-http-client, pyparsing, pymongo, pyasn1, public, psycopg2-binary, psutil, protobuf, pluggy, pillow, packaging, marshmallow, MarkupSafe, itsdangerous, iniconfig, idna, gunicorn, future, exceptiongroup, docutils, configparser, Click, cachetools, sendgrid, rsa, requests, query-string, python-dateutil, pytest, pyasn1-modules, proto-plus, Jinja2, httplib2, googleapis-common-protos, ecdsa, deprecated, APScheduler, python-jose, osparc, oauth2client, google-auth, Flask, contentful_management, contentful, botocore, api, algoliasearch, s3transfer, google-auth-httplib2, google-api-core, flask-marshmallow, flask-cors, google-api-python-client, boto3, pennsieve
Successfully installed APScheduler-3.7.0 Click-7.1.2 Flask-1.1.1 Jinja2-2.11.3 MarkupSafe-1.1.1 SQLAlchemy-1.3.20 Werkzeug-0.16.0 algoliasearch-2.6.2 api-0.0.7 boto3-1.17.67 botocore-1.20.67 cachetools-5.3.3 certifi-2019.11.28 chardet-3.0.4 configparser-6.0.1 contentful-1.13.1 contentful_management-2.11.0 deprecated-1.2.14 docopt-0.6.2 docutils-0.15.2 ecdsa-0.14.1 exceptiongroup-1.2.0 flask-cors-3.0.8 flask-marshmallow-0.10.1 future-1.0.0 futures-3.0.5 google-api-core-2.18.0 google-api-python-client-2.52.0 google-auth-2.29.0 google-auth-httplib2-0.2.0 googleapis-common-protos-1.63.0 gunicorn-20.0.4 httplib2-0.22.0 idna-2.8 iniconfig-2.0.0 itsdangerous-1.1.0 jmespath-0.9.4 marshmallow-3.2.2 nose-1.3.7 oauth2client-4.1.3 osparc-0.4.3 packaging-24.0 pennsieve-6.1.1 pillow-10.3.0 pluggy-1.4.0 proto-plus-1.23.0 protobuf-4.25.3 psutil-5.9.8 psycopg2-binary-2.9.5 public-2019.4.13 pyasn1-0.6.0 pyasn1-modules-0.4.0 pymongo-3.8.0 pyparsing-3.1.2 pytest-8.1.1 python-dateutil-2.8.0 python-dotenv-0.10.3 python-http-client-3.3.7 python-jose-3.2.0 pytz-2024.1 query-string-2019.4.13 requests-2.25.1 rsa-4.0 s3transfer-0.4.2 semver-3.0.2 sendgrid-6.9.7 six-1.13.0 starkbank-ecdsa-2.2.0 tomli-2.0.1 tzlocal-2.1 uritemplate-4.1.1 urllib3-1.26.4 websocket-client-1.7.0 wrapt-1.16.0
+ pip install -r requirements-dev.txt
Collecting pytest==5.4.3 (from -r requirements-dev.txt (line 1))
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Installing collected packages: wcwidth, typing-extensions, py, pluggy, platformdirs, pathspec, mypy-extensions, more-itertools, isort, click, attrs, pytest, black
Attempting uninstall: pluggy
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Attempting uninstall: click
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Attempting uninstall: pytest
Found existing installation: pytest 8.1.1
Uninstalling pytest-8.1.1:
Successfully uninstalled pytest-8.1.1
Successfully installed attrs-23.2.0 black-24.3.0 click-8.1.7 isort-5.13.2 more-itertools-10.2.0 mypy-extensions-1.0.0 pathspec-0.12.1 platformdirs-4.2.0 pluggy-0.13.1 py-1.11.0 pytest-5.4.3 typing-extensions-4.11.0 wcwidth-0.2.13
+ pytest
============================= test session starts ==============================
platform linux -- Python 3.9.19, pytest-5.4.3, py-1.11.0, pluggy-0.13.1
rootdir: /home/cmiss/Jenkins/workspace/SPARC-API-DEV
collected 101 items
tests/test_api.py ................... [ 18%]
tests/test_biolucida.py ............. [ 31%]
tests/test_dataset_info.py .s..ss..... [ 42%]
tests/test_health.py . [ 43%]
tests/test_monthly_stats.py ...... [ 49%]
tests/test_osparc.py .............. [ 63%]
tests/test_pmr.py ..... [ 68%]
tests/test_scicrunch.py ................s......... [ 94%]
tests/test_segmentation_info.py .. [ 96%]
tests/test_thumbnails.py ... [ 99%]
tests/test_update_contentful_entries.py . [100%]
=============================== warnings summary ===============================
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/__init__.py:1
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/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/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/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/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/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/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:19
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/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/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:36
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/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/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:53
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/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/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:70
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/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/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:29
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/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(
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/nose/importer.py:12
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
from imp import find_module, load_module, acquire_lock, release_lock
tests/test_health.py::test_request_response
/home/cmiss/Jenkins/workspace/SPARC-API-DEV/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
============ 97 passed, 4 skipped, 10 warnings in 349.44s (0:05:49) ============
[Slack Notifications] found #859 as previous completed, non-aborted build
[Slack Notifications] will send OnBackToNormalNotification because build matches and user preferences allow it
Finished: SUCCESS