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CaronLab / MhcVizPipe

A reporting pipeline for visualization of immunopeptidomics MS data.
MIT License
9 stars 6 forks source link

Javascript error: Missing jQuery #3

Closed courcelm closed 4 years ago

courcelm commented 4 years ago

Chrome complains about this on page load.

Uncaught TypeError: Bootstrap's JavaScript requires jQuery. jQuery must be included before Bootstrap's JavaScript. at Object.jQueryDetection (bootstrap_4.5.0.min.js?m=1600089067.789378:6) at bootstrap_4.5.0.min.js?m=1600089067.789378:6 at bootstrap_4.5.0.min.js?m=1600089067.789378:6 at bootstrap_4.5.0.min.js?m=1600089067.789378:6

kevinkovalchik commented 4 years ago

Strange, it was tested in Chrome. I'll reorder the references.

On Mon, Sep 14, 2020, 10:02 AM courcelm, notifications@github.com wrote:

Chrome complains about this on page load.

Uncaught TypeError: Bootstrap's JavaScript requires jQuery. jQuery must be included before Bootstrap's JavaScript. at Object.jQueryDetection (bootstrap_4.5.0.min.js?m=1600089067.789378:6) at bootstrap_4.5.0.min.js?m=1600089067.789378:6 at bootstrap_4.5.0.min.js?m=1600089067.789378:6 at bootstrap_4.5.0.min.js?m=1600089067.789378:6

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kevinkovalchik commented 4 years ago

Does this happen when the GUI first loads or when generating a report?

courcelm commented 4 years ago

On page load

kevinkovalchik commented 4 years ago

Ah, I see the error now.

I believe the issue is coming from Dash Bootstrap Components. The only time I am explicitly doing anything with bootstrap.js and jquery is in the reports, and there I am already including jquery before bootstrap.

I explicitly told the app to load jquery, and this seems to be getting it in there before bootstrap. This is in v0.4.7b1 if you want to check it out, or in the master branch.

courcelm commented 4 years ago

Install is now broken with this release. See bold parts below:

(base) mathieu@protub1-iric:~/mvp$ ./MhcVizPipe_install.sh

MhcVizPipe Installation Utility

This utility will help you install and set up MhcVizPipe on your Mac or Linux computer.

Installation Options

The default installation directory for MhcVizPipe is: /home/mathieu/MhcVizPipe

To install into the default directory, enter y. To specify a different location, enter n.

Default directory selected.

Would you like to add MhcVizPipe to your PATH? This will make it much easier to start the program in the future.

Would you like to add NetMHCpan, NetMHCIIpan and GibbsCluster to your PATH? This will make it easier to use these programs in the future. If you have existing installations of these programs, enter n.

MhcVizPipe will be installed with the following options:

Installation directory: /home/mathieu/MhcVizPipe Add MhcVizPipe to PATH: true Add NetMHCpan, NetMHCIIpan and GibbsCluster to PATH: true NetMHCpan version: 4.0

Procced? y/n:y

Downloading Python bundle

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 689 100 689 0 0 1701 0 --:--:-- --:--:-- --:--:-- 1701 100 58.4M 100 58.4M 0 0 14.3M 0 0:00:04 0:00:04 --:--:-- 18.1M exit_on_error $? curl -L -o ./temp/python.tar.gz "$URL"

Done!
Extracting Python bundle

exit_on_error $? tar -xf ./temp/python.tar.gz --directory "$INSTALL_DIR"

Done!

./MhcVizPipe_install.sh: line 175: !.: event not found

Installing MhcVizPipe

Collecting wheel Using cached wheel-0.35.1-py2.py3-none-any.whl (33 kB) Installing collected packages: wheel Successfully installed wheel-0.35.1 exit_on_error $? "$INSTALL_DIR"/python/install/bin/python3 -m pip install wheel Collecting MhcVizPipe Using cached MhcVizPipe-0.4.6-py3-none-any.whl (198 kB) Processing /home/mathieu/.cache/pip/wheels/cc/68/3c/dc8c9aa36930f5380cf58f261513212e36f8fa759b63585f7c/dash-1.16.0-py3-none-any.whl Collecting pandas Using cached pandas-1.1.2-cp37-cp37m-manylinux1_x86_64.whl (10.5 MB) Collecting plotly Using cached plotly-4.10.0-py2.py3-none-any.whl (13.0 MB) Collecting numpy Using cached numpy-1.19.2-cp37-cp37m-manylinux2010_x86_64.whl (14.5 MB) Processing /home/mathieu/.cache/pip/wheels/fa/fa/75/2549bb389f10788afb69643e8bc42cd1516104b2a58a4c1fe8/UpSetPlot-0.4.1-py3-none-any.whl Collecting waitress Using cached waitress-1.4.4-py2.py3-none-any.whl (58 kB) Collecting dash-bootstrap-components Using cached dash_bootstrap_components-0.10.6-py2.py3-none-any.whl (185 kB) Collecting plotly-logo Using cached plotly_logo-0.0.2-py3-none-any.whl (10 kB) Collecting seaborn Using cached seaborn-0.11.0-py3-none-any.whl (283 kB) Collecting dominate Using cached dominate-2.5.2-py2.py3-none-any.whl (29 kB) Collecting Flask>=1.0.2 Using cached Flask-1.1.2-py2.py3-none-any.whl (94 kB) Processing /home/mathieu/.cache/pip/wheels/da/e6/d9/9c2ef00bab380df9224bcafb26f7ba565e784cacc7e9e68157/dash_core_components-1.12.0-py3-none-any.whl Processing /home/mathieu/.cache/pip/wheels/40/b5/64/09141cef39aecc7bce0436e12cc5b4ff1698da43fa1e5decdb/dash_renderer-1.8.0-py3-none-any.whl Processing /home/mathieu/.cache/pip/wheels/c8/a8/46/2900a0845e7992a317eca9ba18e55d47c03ccc4e80d6a37e73/dash_html_components-1.1.1-py3-none-any.whl Processing /home/mathieu/.cache/pip/wheels/d6/9f/c9/4bf2abf65cceaa8d19423bc34b88443b3b063f167d2082c212/Flask_Compress-1.5.0-py3-none-any.whl Processing /home/mathieu/.cache/pip/wheels/9b/89/a5/cfba33913363625344b4b3b63a51d958038c8e7b83139e702c/dash_table-4.10.1-py3-none-any.whl Processing /home/mathieu/.cache/pip/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0/future-0.18.2-py3-none-any.whl Collecting python-dateutil>=2.7.3 Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting pytz>=2017.2 Using cached pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting six Using cached six-1.15.0-py2.py3-none-any.whl (10 kB) Processing /home/mathieu/.cache/pip/wheels/f9/8d/8d/f6af3f7f9eea3553bc2fe6d53e4b287dad18b06a861ac56ddf/retrying-1.3.3-py3-none-any.whl Collecting matplotlib>=2.0 Downloading matplotlib-3.3.2-cp37-cp37m-manylinux1_x86_64.whl (11.6 MB) |████████████████████████████████| 11.6 MB 677 kB/s Collecting scipy>=1.0 Using cached scipy-1.5.2-cp37-cp37m-manylinux1_x86_64.whl (25.9 MB) Collecting Werkzeug>=0.15 Using cached Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB) Collecting itsdangerous>=0.24 Using cached itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB) Collecting click>=5.1 Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Collecting Jinja2>=2.10.1 Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting brotli Using cached Brotli-1.0.9-cp37-cp37m-manylinux1_x86_64.whl (357 kB) Collecting pillow>=6.2.0 Using cached Pillow-7.2.0-cp37-cp37m-manylinux1_x86_64.whl (2.2 MB) Collecting certifi>=2020.06.20 Using cached certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting cycler>=0.10 Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting kiwisolver>=1.0.1 Using cached kiwisolver-1.2.0-cp37-cp37m-manylinux1_x86_64.whl (88 kB) Collecting MarkupSafe>=0.23 Using cached MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Installing collected packages: Werkzeug, itsdangerous, click, MarkupSafe, Jinja2, Flask, six, retrying, plotly, dash-core-components, dash-renderer, dash-html-components, brotli, flask-compress, dash-table, future, dash, python-dateutil, pytz, numpy, pandas, pillow, certifi, cycler, pyparsing, kiwisolver, matplotlib, upsetplot, waitress, dash-bootstrap-components, plotly-logo, scipy, seaborn, dominate, MhcVizPipe ^[[B^[[A^[[A^[[ASuccessfully installed Flask-1.1.2 Jinja2-2.11.2 MarkupSafe-1.1.1 MhcVizPipe-0.4.6 Werkzeug-1.0.1 brotli-1.0.9 certifi-2020.6.20 click-7.1.2 cycler-0.10.0 dash-1.16.0 dash-bootstrap-components-0.10.6 dash-core-components-1.12.0 dash-html-components-1.1.1 dash-renderer-1.8.0 dash-table-4.10.1 dominate-2.5.2 flask-compress-1.5.0 future-0.18.2 itsdangerous-1.1.0 kiwisolver-1.2.0 matplotlib-3.3.2 numpy-1.19.2 pandas-1.1.2 pillow-7.2.0 plotly-4.10.0 plotly-logo-0.0.2 pyparsing-2.4.7 python-dateutil-2.8.1 pytz-2020.1 retrying-1.3.3 scipy-1.5.2 seaborn-0.11.0 six-1.15.0 upsetplot-0.4.1 waitress-1.4.4 exit_on_error $? "$INSTALL_DIR"/python/install/bin/python3 -m pip install MhcVizPipe

Done!
Installing and configuring third-party tools

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 151 100 151 0 0 364 0 --:--:-- --:--:-- --:--:-- 363 100 1702 100 1702 0 0 2586 0 --:--:-- --:--:-- --:--:-- 2586 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 152 100 152 0 0 392 0 --:--:-- --:--:-- --:--:-- 392 100 1498 100 1498 0 0 1413 0 0:00:01 0:00:01 --:--:-- 2587 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 152 100 152 0 0 426 0 --:--:-- --:--:-- --:--:-- 426 100 1457 100 1457 0 0 906 0 0:00:01 0:00:01 --:--:-- 1206

Downloading data files for netMHCIIpan

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 49.7M 100 49.7M 0 0 5332k 0 0:00:09 0:00:09 --:--:-- 10.0M

Extracting archive... done

Downloading data files for netMHCpan4.0

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 24.1M 100 24.1M 0 0 4252k 0 0:00:05 0:00:05 --:--:-- 6132k

Extracting archive... done exit_on_error $? "$INSTALL_DIR/python/install/bin/python3" -m MhcVizPipe.Tools.install_tools "$INSTALL_DIR/tools"

Done!

### ./MhcVizPipe_install.sh: line 195: !/bin/bash\n: event not found chmod: cannot access '/home/mathieu/MhcVizPipe/MhcVizPipe.sh': No such file or directory grep: !=: No such file or directory grep: 0: No such file or directory grep: !=: No such file or directory grep: 0: No such file or directory exit_on_error $? if [[ "$MHCVIZPIPE_TO_PATH" == "true" ]]; then cp "$INSTALL_DIR"/MhcVizPipe.sh "$INSTALL_DIR"/bin/MhcVizPipe ./MhcVizPipe_install.sh: line 237: syntax error near unexpected token then' ./MhcVizPipe_install.sh: line 237: exit_on_error $? if [[ "$MHCVIZPIPE_TO_PATH" == "true" ]]; then cp "$INSTALL_DIR"/MhcVizPipe.sh "$INSTALL_DIR"/bin/MhcVizPipe'

kevinkovalchik commented 4 years ago

Oops, sorry. I forgot to push some changes to the installation script. Try it now.

courcelm commented 4 years ago

Installation script fixed but still no jquery loaded....

courcelm commented 4 years ago

gui.py not updated during the install

courcelm commented 4 years ago

Jquery ok after manualy fixing the file.

kevinkovalchik commented 4 years ago

Oh, I see that it installed 0.4.6 in your console output above. Because the release is tagged as beta Pip won't use it as the most recent version. If you modify line 174 of the installation script to include pip install MhcVizPipe==0.4.7b1 it should work the same as when you manually fixed the file.