Jenkins_Console_pytests.txt

Started by user Nour Mahfel
[Pipeline] Start of Pipeline
[Pipeline] node
Running on Jenkins in C:\data\jenkins_home\workspace\panelgenemapper
[Pipeline] {
[Pipeline] withEnv
[Pipeline] {
[Pipeline] stage
[Pipeline] { (Checkout Code)
[Pipeline] echo
Checking out the source code from GitHub...
[Pipeline] git
The recommended git tool is: NONE
No credentials specified
 > git.exe rev-parse --resolve-git-dir C:\data\jenkins_home\workspace\panelgenemapper\.git # timeout=10
Fetching changes from the remote Git repository
 > git.exe config remote.origin.url https://github.com/Miladeb77/Y2_Genepanel_project.git # timeout=10
Fetching upstream changes from https://github.com/Miladeb77/Y2_Genepanel_project.git
 > git.exe --version # timeout=10
 > git --version # 'git version 2.47.1.windows.1'
 > git.exe fetch --tags --force --progress -- https://github.com/Miladeb77/Y2_Genepanel_project.git +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git.exe rev-parse "refs/remotes/origin/development^{commit}" # timeout=10
Checking out Revision 881c8a2570f37c738f584608e002e7d2a1fd65db (refs/remotes/origin/development)
 > git.exe config core.sparsecheckout # timeout=10
 > git.exe checkout -f 881c8a2570f37c738f584608e002e7d2a1fd65db # timeout=10
 > git.exe branch -a -v --no-abbrev # timeout=10
 > git.exe branch -D development # timeout=10
 > git.exe checkout -b development 881c8a2570f37c738f584608e002e7d2a1fd65db # timeout=10
Commit message: "Added documentation"
 > git.exe rev-list --no-walk 937455ba66a197a69e6779b1370f899e97264eb1 # timeout=10
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Build Docker Image)
[Pipeline] script
[Pipeline] {
[Pipeline] echo
Building the Docker image...
[Pipeline] bat

C:\data\jenkins_home\workspace\panelgenemapper>docker build -t genepanel-app . 
#0 building with "default" instance using docker driver

#1 [internal] load build definition from Dockerfile
#1 transferring dockerfile: 1.17kB done
#1 DONE 0.0s

#2 [internal] load metadata for docker.io/library/python:3.9
#2 DONE 1.5s

#3 [internal] load .dockerignore
#3 transferring context: 2B done
#3 DONE 0.0s

#4 [ 1/10] FROM docker.io/library/python:3.9@sha256:eeb155c46fdd3f03ff0e5efc8cac0c475b31eb4ea92c4b85231280b663a6f9a0
#4 DONE 0.0s

#5 [internal] load build context
#5 transferring context: 45.46MB 1.2s done
#5 DONE 1.2s

#6 [ 2/10] WORKDIR /app
#6 CACHED

#7 [ 3/10] COPY . /app
#7 DONE 0.2s

#8 [ 4/10] RUN mkdir -p /usr/local/share/logs
#8 DONE 0.3s

#9 [ 5/10] RUN apt update && apt -y install     git     sqlite3     libsqlite3-dev     gzip
#9 0.385 
#9 0.385 WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
#9 0.385 
#9 0.768 Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB]
#9 2.026 Get:2 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB]
#9 2.194 Get:3 http://deb.debian.org/debian-security bookworm-security InRelease [48.0 kB]
#9 2.299 Get:4 http://deb.debian.org/debian bookworm/main amd64 Packages [8789 kB]
#9 10.93 Get:5 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [8856 B]
#9 11.02 Get:6 http://deb.debian.org/debian-security bookworm-security/main amd64 Packages [240 kB]
#9 11.85 Fetched 9292 kB in 11s (813 kB/s)
#9 11.85 Reading package lists...
#9 12.21 Building dependency tree...
#9 12.31 Reading state information...
#9 12.32 All packages are up to date.
#9 12.32 
#9 12.32 WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
#9 12.32 
#9 12.32 Reading package lists...
#9 12.65 Building dependency tree...
#9 12.74 Reading state information...
#9 12.84 git is already the newest version (1:2.39.5-0+deb12u1).
#9 12.84 libsqlite3-dev is already the newest version (3.40.1-2+deb12u1).
#9 12.84 gzip is already the newest version (1.12-1).
#9 12.84 gzip set to manually installed.
#9 12.84 Suggested packages:
#9 12.84   sqlite3-doc
#9 12.86 The following NEW packages will be installed:
#9 12.86   sqlite3
#9 13.16 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
#9 13.16 Need to get 353 kB of archives.
#9 13.16 After this operation, 546 kB of additional disk space will be used.
#9 13.16 Get:1 http://deb.debian.org/debian bookworm/main amd64 sqlite3 amd64 3.40.1-2+deb12u1 [353 kB]
#9 13.49 debconf: delaying package configuration, since apt-utils is not installed
#9 13.52 Fetched 353 kB in 1s (687 kB/s)
#9 13.54 Selecting previously unselected package sqlite3.
#9 13.54 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 23969 files and directories currently installed.)
#9 13.61 Preparing to unpack .../sqlite3_3.40.1-2+deb12u1_amd64.deb ...
#9 13.61 Unpacking sqlite3 (3.40.1-2+deb12u1) ...
#9 13.66 Setting up sqlite3 (3.40.1-2+deb12u1) ...
#9 DONE 13.7s

#10 [ 6/10] RUN pip install --upgrade pip
#10 1.548 Requirement already satisfied: pip in /usr/local/lib/python3.9/site-packages (23.0.1)
#10 1.948 Collecting pip
#10 2.334   Downloading pip-24.3.1-py3-none-any.whl (1.8 MB)
#10 2.761      ���������������������������������������� 1.8/1.8 MB 4.4 MB/s eta 0:00:00
#10 2.795 Installing collected packages: pip
#10 2.795   Attempting uninstall: pip
#10 2.795     Found existing installation: pip 23.0.1
#10 2.876     Uninstalling pip-23.0.1:
#10 3.088       Successfully uninstalled pip-23.0.1
#10 3.653 Successfully installed pip-24.3.1
#10 3.653 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
#10 DONE 4.2s

#11 [ 7/10] RUN pip install -r requirements.txt
#11 0.790 Collecting anyio==4.6.2.post1 (from -r requirements.txt (line 1))
#11 1.013   Downloading anyio-4.6.2.post1-py3-none-any.whl.metadata (4.7 kB)
#11 1.248 Collecting argon2-cffi==23.1.0 (from -r requirements.txt (line 2))
#11 1.367   Downloading argon2_cffi-23.1.0-py3-none-any.whl.metadata (5.2 kB)
#11 1.536 Collecting argon2-cffi-bindings==21.2.0 (from -r requirements.txt (line 3))
#11 1.667   Downloading argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB)
#11 1.883 Collecting arrow==1.3.0 (from -r requirements.txt (line 4))
#11 2.019   Downloading arrow-1.3.0-py3-none-any.whl.metadata (7.5 kB)
#11 2.277 Collecting asttokens==3.0.0 (from -r requirements.txt (line 5))
#11 2.390   Downloading asttokens-3.0.0-py3-none-any.whl.metadata (4.7 kB)
#11 2.556 Collecting async-lru==2.0.4 (from -r requirements.txt (line 6))
#11 2.622   Downloading async_lru-2.0.4-py3-none-any.whl.metadata (4.5 kB)
#11 2.737 Collecting attrs==24.2.0 (from -r requirements.txt (line 7))
#11 2.787   Downloading attrs-24.2.0-py3-none-any.whl.metadata (11 kB)
#11 2.929 Collecting babel==2.16.0 (from -r requirements.txt (line 8))
#11 3.017   Downloading babel-2.16.0-py3-none-any.whl.metadata (1.5 kB)
#11 3.097 Collecting beautifulsoup4==4.12.3 (from -r requirements.txt (line 9))
#11 3.177   Downloading beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB)
#11 3.431 Collecting biopython==1.84 (from -r requirements.txt (line 10))
#11 3.573   Downloading biopython-1.84-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
#11 3.727 Collecting bleach==6.2.0 (from -r requirements.txt (line 11))
#11 3.834   Downloading bleach-6.2.0-py3-none-any.whl.metadata (30 kB)
#11 3.996 Collecting Brotli==1.1.0 (from -r requirements.txt (line 12))
#11 4.193   Downloading Brotli-1.1.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (5.5 kB)
#11 4.277 Collecting cached-property==1.5.2 (from -r requirements.txt (line 13))
#11 4.362   Downloading cached_property-1.5.2-py2.py3-none-any.whl.metadata (11 kB)
#11 4.470 Collecting certifi==2024.8.30 (from -r requirements.txt (line 14))
#11 4.539   Downloading certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
#11 4.927 Collecting cffi==1.17.1 (from -r requirements.txt (line 15))
#11 5.040   Downloading cffi-1.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB)
#11 5.726 Collecting charset-normalizer==3.4.0 (from -r requirements.txt (line 16))
#11 5.784   Downloading charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (34 kB)
#11 5.920 Collecting colorama==0.4.6 (from -r requirements.txt (line 17))
#11 5.978   Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)
#11 6.122 Collecting comm==0.2.2 (from -r requirements.txt (line 18))
#11 6.238   Downloading comm-0.2.2-py3-none-any.whl.metadata (3.7 kB)
#11 6.405 Collecting contourpy==1.3.0 (from -r requirements.txt (line 19))
#11 6.477   Downloading contourpy-1.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.4 kB)
#11 6.540 Collecting cycler==0.12.1 (from -r requirements.txt (line 20))
#11 6.640   Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
#11 6.863 Collecting debugpy==1.8.9 (from -r requirements.txt (line 21))
#11 6.978   Downloading debugpy-1.8.9-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.1 kB)
#11 7.177 Collecting decorator==5.1.1 (from -r requirements.txt (line 22))
#11 7.299   Downloading decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
#11 7.427 Collecting defusedxml==0.7.1 (from -r requirements.txt (line 23))
#11 7.491   Downloading defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB)
#11 7.617 Collecting entrypoints==0.4 (from -r requirements.txt (line 24))
#11 7.685   Downloading entrypoints-0.4-py3-none-any.whl.metadata (2.6 kB)
#11 7.790 Collecting exceptiongroup==1.2.2 (from -r requirements.txt (line 25))
#11 7.879   Downloading exceptiongroup-1.2.2-py3-none-any.whl.metadata (6.6 kB)
#11 7.982 Collecting executing==2.1.0 (from -r requirements.txt (line 26))
#11 8.059   Downloading executing-2.1.0-py2.py3-none-any.whl.metadata (8.9 kB)
#11 8.175 Collecting fastjsonschema==2.21.0 (from -r requirements.txt (line 27))
#11 8.228   Downloading fastjsonschema-2.21.0-py3-none-any.whl.metadata (2.2 kB)
#11 8.399 Collecting flake8==7.1.1 (from -r requirements.txt (line 28))
#11 8.506   Downloading flake8-7.1.1-py2.py3-none-any.whl.metadata (3.8 kB)
#11 9.099 Collecting fonttools==4.55.0 (from -r requirements.txt (line 29))
#11 9.200   Downloading fonttools-4.55.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (164 kB)
#11 9.562 Collecting fqdn==1.5.1 (from -r requirements.txt (line 30))
#11 9.644   Downloading fqdn-1.5.1-py3-none-any.whl.metadata (1.4 kB)
#11 10.07 Collecting greenlet==3.1.1 (from -r requirements.txt (line 31))
#11 10.18   Downloading greenlet-3.1.1-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.8 kB)
#11 10.30 Collecting h11==0.14.0 (from -r requirements.txt (line 32))
#11 10.45   Downloading h11-0.14.0-py3-none-any.whl.metadata (8.2 kB)
#11 10.68 Collecting h2==4.1.0 (from -r requirements.txt (line 33))
#11 10.78   Downloading h2-4.1.0-py3-none-any.whl.metadata (3.6 kB)
#11 10.98 Collecting hpack==4.0.0 (from -r requirements.txt (line 34))
#11 11.08   Downloading hpack-4.0.0-py3-none-any.whl.metadata (2.5 kB)
#11 11.22 Collecting httpcore==1.0.7 (from -r requirements.txt (line 35))
#11 11.29   Downloading httpcore-1.0.7-py3-none-any.whl.metadata (21 kB)
#11 11.43 Collecting httpx==0.28.0 (from -r requirements.txt (line 36))
#11 11.50   Downloading httpx-0.28.0-py3-none-any.whl.metadata (7.1 kB)
#11 11.65 Collecting hyperframe==6.0.1 (from -r requirements.txt (line 37))
#11 11.89   Downloading hyperframe-6.0.1-py3-none-any.whl.metadata (2.7 kB)
#11 12.06 Collecting idna==3.10 (from -r requirements.txt (line 38))
#11 12.17   Downloading idna-3.10-py3-none-any.whl.metadata (10 kB)
#11 12.34 Collecting importlib-metadata==8.5.0 (from -r requirements.txt (line 39))
#11 12.46   Downloading importlib_metadata-8.5.0-py3-none-any.whl.metadata (4.8 kB)
#11 12.66 Collecting importlib-resources==6.4.5 (from -r requirements.txt (line 40))
#11 12.76   Downloading importlib_resources-6.4.5-py3-none-any.whl.metadata (4.0 kB)
#11 12.85 Collecting iniconfig==2.0.0 (from -r requirements.txt (line 41))
#11 13.02   Downloading iniconfig-2.0.0-py3-none-any.whl.metadata (2.6 kB)
#11 13.33 Collecting ipykernel==6.29.5 (from -r requirements.txt (line 42))
#11 13.50   Downloading ipykernel-6.29.5-py3-none-any.whl.metadata (6.3 kB)
#11 13.71 Collecting ipython==8.18.1 (from -r requirements.txt (line 43))
#11 13.78   Downloading ipython-8.18.1-py3-none-any.whl.metadata (6.0 kB)
#11 13.90 Collecting ipython-genutils==0.2.0 (from -r requirements.txt (line 44))
#11 13.97   Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl.metadata (755 bytes)
#11 14.13 Collecting ipywidgets==8.1.5 (from -r requirements.txt (line 45))
#11 14.21   Downloading ipywidgets-8.1.5-py3-none-any.whl.metadata (2.3 kB)
#11 14.37 Collecting isoduration==20.11.0 (from -r requirements.txt (line 46))
#11 14.47   Downloading isoduration-20.11.0-py3-none-any.whl.metadata (5.7 kB)
#11 14.58 Collecting jedi==0.19.2 (from -r requirements.txt (line 47))
#11 14.63   Downloading jedi-0.19.2-py2.py3-none-any.whl.metadata (22 kB)
#11 14.78 Collecting Jinja2==3.1.4 (from -r requirements.txt (line 48))
#11 14.86   Downloading jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
#11 14.96 Collecting json5==0.10.0 (from -r requirements.txt (line 49))
#11 15.02   Downloading json5-0.10.0-py3-none-any.whl.metadata (34 kB)
#11 15.18 Collecting jsonpointer==3.0.0 (from -r requirements.txt (line 50))
#11 15.25   Downloading jsonpointer-3.0.0-py2.py3-none-any.whl.metadata (2.3 kB)
#11 15.37 Collecting jsonschema==4.23.0 (from -r requirements.txt (line 51))
#11 15.46   Downloading jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB)
#11 15.54 Collecting jsonschema-specifications==2024.10.1 (from -r requirements.txt (line 52))
#11 15.64   Downloading jsonschema_specifications-2024.10.1-py3-none-any.whl.metadata (3.0 kB)
#11 16.31 Collecting kiwisolver==1.4.7 (from -r requirements.txt (line 53))
#11 16.38   Downloading kiwisolver-1.4.7-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.3 kB)
#11 16.71 Collecting MarkupSafe==3.0.2 (from -r requirements.txt (line 54))
#11 16.82   Downloading MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
#11 17.17 Collecting matplotlib==3.9.3 (from -r requirements.txt (line 55))
#11 17.29   Downloading matplotlib-3.9.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
#11 17.40 Collecting matplotlib-inline==0.1.7 (from -r requirements.txt (line 56))
#11 17.49   Downloading matplotlib_inline-0.1.7-py3-none-any.whl.metadata (3.9 kB)
#11 17.60 Collecting mistune==3.0.2 (from -r requirements.txt (line 57))
#11 17.70   Downloading mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB)
#11 17.87 Collecting munkres==1.1.4 (from -r requirements.txt (line 58))
#11 17.99   Downloading munkres-1.1.4-py2.py3-none-any.whl.metadata (980 bytes)
#11 18.20 Collecting mysql-connector-python==9.1.0 (from -r requirements.txt (line 59))
#11 18.29   Downloading mysql_connector_python-9.1.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (6.0 kB)
#11 18.53 Collecting nbclassic==1.1.0 (from -r requirements.txt (line 60))
#11 18.62   Downloading nbclassic-1.1.0-py3-none-any.whl.metadata (3.6 kB)
#11 18.72 Collecting nbclient==0.10.1 (from -r requirements.txt (line 61))
#11 18.79   Downloading nbclient-0.10.1-py3-none-any.whl.metadata (8.2 kB)
#11 18.94 Collecting nbconvert==7.16.4 (from -r requirements.txt (line 62))
#11 19.06   Downloading nbconvert-7.16.4-py3-none-any.whl.metadata (8.5 kB)
#11 19.25 Collecting nbformat==5.10.4 (from -r requirements.txt (line 63))
#11 19.36   Downloading nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)
#11 19.53 Collecting nest-asyncio==1.6.0 (from -r requirements.txt (line 64))
#11 19.70   Downloading nest_asyncio-1.6.0-py3-none-any.whl.metadata (2.8 kB)
#11 19.91 Collecting notebook==6.5.7 (from -r requirements.txt (line 65))
#11 19.99   Downloading notebook-6.5.7-py3-none-any.whl.metadata (2.5 kB)
#11 20.13 Collecting notebook-shim==0.2.4 (from -r requirements.txt (line 66))
#11 20.26   Downloading notebook_shim-0.2.4-py3-none-any.whl.metadata (4.0 kB)
#11 20.65 Collecting numpy==2.0.2 (from -r requirements.txt (line 67))
#11 20.76   Downloading numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
#11 20.90 Collecting overrides==7.7.0 (from -r requirements.txt (line 68))
#11 20.95   Downloading overrides-7.7.0-py3-none-any.whl.metadata (5.8 kB)
#11 21.29 Collecting packaging==24.2 (from -r requirements.txt (line 69))
#11 21.40   Downloading packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
#11 21.87 Collecting pandas==2.2.3 (from -r requirements.txt (line 70))
#11 21.94   Downloading pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
#11 22.07 Collecting pandocfilters==1.5.0 (from -r requirements.txt (line 71))
#11 22.13   Downloading pandocfilters-1.5.0-py2.py3-none-any.whl.metadata (9.0 kB)
#11 22.22 Collecting parso==0.8.4 (from -r requirements.txt (line 72))
#11 22.27   Downloading parso-0.8.4-py2.py3-none-any.whl.metadata (7.7 kB)
#11 22.39 Collecting patsy==1.0.1 (from -r requirements.txt (line 73))
#11 22.45   Downloading patsy-1.0.1-py2.py3-none-any.whl.metadata (3.3 kB)
#11 22.54 Collecting pickleshare==0.7.5 (from -r requirements.txt (line 74))
#11 22.61   Downloading pickleshare-0.7.5-py2.py3-none-any.whl.metadata (1.5 kB)
#11 23.04 Collecting pillow==11.0.0 (from -r requirements.txt (line 75))
#11 23.16   Downloading pillow-11.0.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
#11 23.17 Requirement already satisfied: pip==24.3.1 in /usr/local/lib/python3.9/site-packages (from -r requirements.txt (line 76)) (24.3.1)
#11 23.27 Collecting pkgutil-resolve-name==1.3.10 (from -r requirements.txt (line 77))
#11 23.34   Downloading pkgutil_resolve_name-1.3.10-py3-none-any.whl.metadata (624 bytes)
#11 23.41 Collecting platformdirs==4.3.6 (from -r requirements.txt (line 78))
#11 23.50   Downloading platformdirs-4.3.6-py3-none-any.whl.metadata (11 kB)
#11 23.69 Collecting pluggy==1.5.0 (from -r requirements.txt (line 79))
#11 23.80   Downloading pluggy-1.5.0-py3-none-any.whl.metadata (4.8 kB)
#11 23.93 Collecting prometheus-client==0.21.0 (from -r requirements.txt (line 80))
#11 24.06   Downloading prometheus_client-0.21.0-py3-none-any.whl.metadata (1.8 kB)
#11 24.20 Collecting prompt-toolkit==3.0.48 (from -r requirements.txt (line 81))
#11 24.28   Downloading prompt_toolkit-3.0.48-py3-none-any.whl.metadata (6.4 kB)
#11 24.47 Collecting psutil==6.1.0 (from -r requirements.txt (line 82))
#11 24.58   Downloading psutil-6.1.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (22 kB)
#11 24.77 Collecting pure-eval==0.2.3 (from -r requirements.txt (line 83))
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#11 29.27 Collecting rfc3339-validator==0.1.4 (from -r requirements.txt (line 98))
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#11 264.8 Installing collected packages: win-inet-pton, webencodings, wcwidth, unicodedata2, pytz, pure-eval, ptyprocess, pickleshare, munkres, ipython-genutils, fastjsonschema, cached-property, Brotli, zstandard, zipp, widgetsnbextension, websocket-client, webcolors, urllib3, uri-template, tzdata, typing-utils, typing-extensions, types-python-dateutil, traitlets, tornado, tomli, tinycss2, soupsieve, sniffio, six, shiboken6, setuptools, Send2Trash, rpds-py, rfc3986-validator, pyzmq, PyYAML, python-json-logger, PySocks, pyparsing, Pygments, pyflakes, pycparser, pycodestyle, psutil, prompt-toolkit, prometheus-client, pluggy, platformdirs, pkgutil-resolve-name, pillow, pexpect, parso, pandocfilters, packaging, overrides, numpy, nest-asyncio, mysql-connector-python, mistune, mccabe, MarkupSafe, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, json5, iniconfig, idna, hyperframe, hpack, h11, greenlet, fqdn, fonttools, executing, exceptiongroup, entrypoints, defusedxml, decorator, debugpy, cycler, colorama, charset-normalizer, certifi, bleach, babel, attrs, asttokens, terminado, stack-data, SQLAlchemy, scipy, rfc3339-validator, requests, referencing, python-dateutil, pytest, PySide6-Essentials, patsy, matplotlib-inline, jupyter-core, Jinja2, jedi, importlib-resources, importlib-metadata, httpcore, h2, flake8, contourpy, comm, cffi, biopython, beautifulsoup4, async-lru, anyio, python-crontab, PySide6-Addons, pandas, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, ipython, httpx, arrow, argon2-cffi-bindings, statsmodels, seaborn, PySide6, jsonschema, isoduration, ipywidgets, ipykernel, argon2-cffi, nbformat, nbclient, jupyter-events, nbconvert, jupyter-server, notebook-shim, nbclassic, notebook
#11 266.0   Attempting uninstall: setuptools
#11 266.0     Found existing installation: setuptools 58.1.0
#11 266.0     Uninstalling setuptools-58.1.0:
#11 266.2       Successfully uninstalled setuptools-58.1.0
#11 286.9 Successfully installed Brotli-1.1.0 Jinja2-3.1.4 MarkupSafe-3.0.2 PySide6-6.8.0.2 PySide6-Addons-6.8.0.2 PySide6-Essentials-6.8.0.2 PySocks-1.7.1 PyYAML-6.0.2 Pygments-2.18.0 SQLAlchemy-2.0.36 Send2Trash-1.8.3 anyio-4.6.2.post1 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-3.0.0 async-lru-2.0.4 attrs-24.2.0 babel-2.16.0 beautifulsoup4-4.12.3 biopython-1.84 bleach-6.2.0 cached-property-1.5.2 certifi-2024.8.30 cffi-1.17.1 charset-normalizer-3.4.0 colorama-0.4.6 comm-0.2.2 contourpy-1.3.0 cycler-0.12.1 debugpy-1.8.9 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 exceptiongroup-1.2.2 executing-2.1.0 fastjsonschema-2.21.0 flake8-7.1.1 fonttools-4.55.0 fqdn-1.5.1 greenlet-3.1.1 h11-0.14.0 h2-4.1.0 hpack-4.0.0 httpcore-1.0.7 httpx-0.28.0 hyperframe-6.0.1 idna-3.10 importlib-metadata-8.5.0 importlib-resources-6.4.5 iniconfig-2.0.0 ipykernel-6.29.5 ipython-8.18.1 ipython-genutils-0.2.0 ipywidgets-8.1.5 isoduration-20.11.0 jedi-0.19.2 json5-0.10.0 jsonpointer-3.0.0 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-client-7.4.9 jupyter-core-5.7.2 jupyter-events-0.11.0 jupyter-server-2.15.0 jupyter-server-terminals-0.5.3 jupyterlab-pygments-0.3.0 jupyterlab-widgets-3.0.13 kiwisolver-1.4.7 matplotlib-3.9.3 matplotlib-inline-0.1.7 mccabe-0.7.0 mistune-3.0.2 munkres-1.1.4 mysql-connector-python-9.1.0 nbclassic-1.1.0 nbclient-0.10.1 nbconvert-7.16.4 nbformat-5.10.4 nest-asyncio-1.6.0 notebook-6.5.7 notebook-shim-0.2.4 numpy-2.0.2 overrides-7.7.0 packaging-24.2 pandas-2.2.3 pandocfilters-1.5.0 parso-0.8.4 patsy-1.0.1 pexpect-4.9.0 pickleshare-0.7.5 pillow-11.0.0 pkgutil-resolve-name-1.3.10 platformdirs-4.3.6 pluggy-1.5.0 prometheus-client-0.21.0 prompt-toolkit-3.0.48 psutil-6.1.0 ptyprocess-0.7.0 pure-eval-0.2.3 pycodestyle-2.12.1 pycparser-2.22 pyflakes-3.2.0 pyparsing-3.2.0 pytest-8.3.4 python-crontab-3.2.0 python-dateutil-2.9.0.post0 python-json-logger-2.0.7 pytz-2024.1 pyzmq-26.2.0 referencing-0.35.1 requests-2.32.3 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.22.0 scipy-1.13.1 seaborn-0.13.2 setuptools-75.6.0 shiboken6-6.8.0.2 six-1.16.0 sniffio-1.3.1 soupsieve-2.5 stack-data-0.6.2 statsmodels-0.14.4 terminado-0.18.1 tinycss2-1.4.0 tomli-2.2.1 tornado-6.4.2 traitlets-5.14.3 types-python-dateutil-2.9.0.20241003 typing-extensions-4.12.2 typing-utils-0.1.0 tzdata-2024.2 unicodedata2-15.1.0 uri-template-1.3.0 urllib3-2.2.3 wcwidth-0.2.13 webcolors-24.8.0 webencodings-0.5.1 websocket-client-1.8.0 widgetsnbextension-4.0.13 win-inet-pton-1.1.0 zipp-3.21.0 zstandard-0.23.0
#11 286.9 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
#11 DONE 289.3s

#12 [ 8/10] COPY configuration/build_panelApp_database_config.json /root/.genepanel_config
#12 DONE 0.0s

#13 [ 9/10] RUN mkdir -p /app/databases /app/archive_databases /app/output
#13 DONE 0.2s

#14 [10/10] WORKDIR /app
#14 DONE 0.1s

#15 exporting to image
#15 exporting layers
#15 exporting layers 3.7s done
#15 writing image sha256:9bbf736a25bcd8612d24793055d5ee09c7e36b9dac0b5a9210bff7bcd2a97342 done
#15 naming to docker.io/library/genepanel-app done
#15 DONE 3.8s
[Pipeline] }
[Pipeline] // script
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Run Unit Tests in Docker Container)
[Pipeline] script
[Pipeline] {
[Pipeline] echo
Running tests in the Docker container...
[Pipeline] bat

C:\data\jenkins_home\workspace\panelgenemapper>docker run --rm --name genepanel-container                         -v C:\data\jenkins_home\workspace\panelgenemapper\output/test-results:/app/output                         genepanel-app pytest /app/tests --junitxml=/app/output/test-results.xml 
============================= test session starts ==============================
platform linux -- Python 3.9.21, pytest-8.3.4, pluggy-1.5.0
rootdir: /app
plugins: anyio-4.6.2.post1
collected 15 items

tests/test_build_panelApp_database.py .....                              [ 33%]
tests/test_build_patient_database.py ...                                 [ 53%]
tests/test_check_panel_updates.py .                                      [ 60%]
tests/test_custom_logging.py .                                           [ 66%]
tests/test_patient_db_lookup_add.py ...                                  [ 86%]
tests/test_retrieve_gene_local_db.py ..                                  [100%]

--------------- generated xml file: /app/output/test-results.xml ---------------
============================== 15 passed in 0.40s ==============================
[Pipeline] }
[Pipeline] // script
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Archive Test Results)
[Pipeline] echo
Archiving test results...
[Pipeline] junit
Recording test results
[Checks API] No suitable checks publisher found.
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Lint and Static Code Analysis)
[Pipeline] script
[Pipeline] {
[Pipeline] echo
Running flake8 for linting...
[Pipeline] bat

C:\data\jenkins_home\workspace\panelgenemapper>docker run --rm --name genepanel-container                         genepanel-app flake8 PanelGeneMapper/   1>lint-results.txt  || true
'true' is not recognized as an internal or external command,
operable program or batch file.
[Pipeline] }
[Pipeline] // script
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Generate Documentation)
Stage "Generate Documentation" skipped due to earlier failure(s)
[Pipeline] getContext
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Declarative: Post Actions)
[Pipeline] script
[Pipeline] {
[Pipeline] echo
Cleaning up Docker resources...
[Pipeline] bat

C:\data\jenkins_home\workspace\panelgenemapper>docker system prune --all --volumes --force   || true
Deleted Images:
deleted: sha256:e264cb954fff18b1234bcf99ee098404cd04d0500c3ac6c7cb2c5886f4234e2b
untagged: genepanel-app:latest
deleted: sha256:9bbf736a25bcd8612d24793055d5ee09c7e36b9dac0b5a9210bff7bcd2a97342

Deleted build cache objects:
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49pl7zqmzep54hg9wy44bfpo4
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ueliiicflxxi8jpq5vyk49bk8
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okbpd7hla45a9g8htki6s97eu
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malis2z1kawrga0z0tiydrjvf
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xz6uclucaf9qpodaa3jv1cpkq
koc7t0et1iv0zcxnh0h913wc8
unx5piuqthbi16zv9ipnb9jbt
9zp6v8mly7x0n1fbjfk0q7mzg
jq18o5wehkx7qizjzwkidauh3
ktvqvmkf4s20ciqwtthlvynpl
76fmha8lvmairgdn5a921jsu5
19qtrz5vriv7recssspzteqfv
yiur4ou8hd83qtuls82r3s38h
3ju7165ou1vw0whxmitrvuuui
jtaxrz3cr8ol4lyyl0y4adgyn
y48qq2mackwevc8mggvzvbgqg

Total reclaimed space: 3.872GB
[Pipeline] }
[Pipeline] // script
[Pipeline] echo
Pipeline failed. Check logs for details.
[Pipeline] }
[Pipeline] // stage
[Pipeline] }
[Pipeline] // withEnv
[Pipeline] }
[Pipeline] // node
[Pipeline] End of Pipeline
ERROR: script returned exit code 1
Finished: FAILURE