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Luis Aleixo 2022-12-15 14:30:11 +00:00
parent d3a7fa5f2f
commit 37d699d483
16 changed files with 20 additions and 20 deletions
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2
.github/workflows/tests.yml vendored
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# This module is part of CAiMIRA. Please see the repository at # This module is part of CAiMIRA. Please see the repository at
# https://gitlab.cern.ch/cara/caimira for details of the license and terms of use. # https://gitlab.cern.ch/caimira/caimira for details of the license and terms of use.
name: CI name: CI
on: on:

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README.md
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@ -76,10 +76,10 @@ In no event shall the authors or copyright holders be liable for any claim, dama
## Running CAiMIRA locally ## Running CAiMIRA locally
The easiest way to run a version of CAiMIRA Calculator is to use docker. A pre-built The easiest way to run a version of CAiMIRA Calculator is to use docker. A pre-built
image of CAiMIRA is made available at https://gitlab.cern.ch/cara/caimira/container_registry. image of CAiMIRA is made available at https://gitlab.cern.ch/caimira/caimira/container_registry.
In order to run CAiMIRA locally with docker, run the following: In order to run CAiMIRA locally with docker, run the following:
$ docker run -it -p 8080:8080 gitlab-registry.cern.ch/cara/caimira/calculator $ docker run -it -p 8080:8080 gitlab-registry.cern.ch/caimira/caimira/calculator
This will start a local version of CAiMIRA, which can be visited at http://localhost:8080/. This will start a local version of CAiMIRA, which can be visited at http://localhost:8080/.

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app-config/caimira-public-docker-image/run_caimira.sh
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echo 'CAiMIRA is running on http://localhost:8080' echo 'CAiMIRA is running on http://localhost:8080'
echo 'Please see https://gitlab.cern.ch/cara/caimira for terms of use.' echo 'Please see https://gitlab.cern.ch/caimira/caimira for terms of use.'
# Run a proxy for the apps (listening on 8080). # Run a proxy for the apps (listening on 8080).
nginx -c /opt/caimira/nginx.conf nginx -c /opt/caimira/nginx.conf

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app-config/openshift/buildconfig.yaml
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parameters: parameters:
- name: GIT_REPO - name: GIT_REPO
description: The GIT repo URL description: The GIT repo URL
value: 'https://gitlab.cern.ch/cara/caimira.git' value: 'https://gitlab.cern.ch/caimira/caimira.git'
- name: GIT_BRANCH - name: GIT_BRANCH
description: The name of the GIT branch to use when building the app, e.g. `live/caimira-test` in TEST, `master` in prod description: The name of the GIT branch to use when building the app, e.g. `live/caimira-test` in TEST, `master` in prod
required: true required: true

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caimira/__init__.py
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# This module is part of CAiMIRA. Please see the repository at # This module is part of CAiMIRA. Please see the repository at
# https://gitlab.cern.ch/cara/caimira for details of the license and terms of use. # https://gitlab.cern.ch/caimira/caimira for details of the license and terms of use.
""" """
Documentation for the CAiMIRA package Documentation for the CAiMIRA package

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caimira/apps/calculator/__init__.py
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# This module is part of CAiMIRA. Please see the repository at # This module is part of CAiMIRA. Please see the repository at
# https://gitlab.cern.ch/cara/caimira for details of the license and terms of use. # https://gitlab.cern.ch/caimira/caimira for details of the license and terms of use.
import asyncio import asyncio
import concurrent.futures import concurrent.futures

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caimira/apps/templates/base/calculator.report.html.j2
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@ -363,7 +363,7 @@
{% elif form.virus_type == "SARS_CoV_2_DELTA" %} {% elif form.virus_type == "SARS_CoV_2_DELTA" %}
<a href="https://www.bmj.com/content/373/bmj.n1513">SARS-CoV-2 (Delta VOC)</a> <a href="https://www.bmj.com/content/373/bmj.n1513">SARS-CoV-2 (Delta VOC)</a>
{% elif form.virus_type == "SARS_CoV_2_OMICRON" %} {% elif form.virus_type == "SARS_CoV_2_OMICRON" %}
<a href="https://gitlab.cern.ch/cara/caimira/-/issues/226">SARS-CoV-2 (Omicron VOC)</a> <a href="https://gitlab.cern.ch/caimira/caimira/-/issues/226">SARS-CoV-2 (Omicron VOC)</a>
{% endif %} {% endif %}
</p></li> </p></li>
<li><p class="data_text">Room Volume: {{ model.concentration_model.room.volume }} m³</p></li> <li><p class="data_text">Room Volume: {{ model.concentration_model.room.volume }} m³</p></li>

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caimira/apps/templates/base/index.html.j2
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@ -23,7 +23,7 @@
Please see the <a href="/about">About</a> page for more details on the methodology, assumptions and limitations of CAiMIRA. Please see the <a href="/about">About</a> page for more details on the methodology, assumptions and limitations of CAiMIRA.
</p> </p>
<p> <p>
The full CAiMIRA source code can be accessed freely under an Apache 2.0 open source license from our <a href="https://gitlab.cern.ch/cara/caimira">code repository</a>. The full CAiMIRA source code can be accessed freely under an Apache 2.0 open source license from our <a href="https://gitlab.cern.ch/caimira/caimira">code repository</a>.
It includes detailed instructions on how to run your own version of this tool. It includes detailed instructions on how to run your own version of this tool.
</p> </p>
<br> <br>
@ -58,7 +58,7 @@
</div> </div>
<div class="w-25 mobile-sub-section"><hr width="95%"> <div class="w-25 mobile-sub-section"><hr width="95%">
<div class="d-flex m-2 align-items-center"><i class="bi bi-git" style="font-size: 25px"></i><div><p class="paragraph-title ml-2">Git</p></div></div> <div class="d-flex m-2 align-items-center"><i class="bi bi-git" style="font-size: 25px"></i><div><p class="paragraph-title ml-2">Git</p></div></div>
<div class="m-2">Official CAiMIRA GitLab <a href="https://gitlab.cern.ch/cara/caimira">repository</a>.<br></div> <div class="m-2">Official CAiMIRA GitLab <a href="https://gitlab.cern.ch/caimira/caimira">repository</a>.<br></div>
</div> </div>
</div> </div>
</div> </div>
@ -91,7 +91,7 @@
<a href="https://doi.org/10.5281/zenodo.6520431"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.6520431.svg" alt="DOI"></a><br> <a href="https://doi.org/10.5281/zenodo.6520431"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.6520431.svg" alt="DOI"></a><br>
© Copyright 2020-2021 CERN. All rights not expressly granted are reserved.<br> © Copyright 2020-2021 CERN. All rights not expressly granted are reserved.<br>
Licensed under the Apache License, Version 2.0<br> Licensed under the Apache License, Version 2.0<br>
<a href=https://gitlab.cern.ch/cara/caimira/-/blob/master/LICENSE><i>LICENSE</i></a> <a href=https://gitlab.cern.ch/caimira/caimira/-/blob/master/LICENSE><i>LICENSE</i></a>
</ul> </ul>
</p> </p>
</div> </div>

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caimira/apps/templates/base/layout.html.j2
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@ -92,9 +92,9 @@
policy issues. Any initiative is conducted on a best effort and as-is basis, without liability or policy issues. Any initiative is conducted on a best effort and as-is basis, without liability or
warranty.</em></span></p> warranty.</em></span></p>
<p style="font-size:10px;"> <p style="font-size:10px;">
CAiMIRA is <a href="https://gitlab.cern.ch/cara/caimira/-/blob/master/LICENSE" class="ext">Apache 2.0 licensed</a> open-source CAiMIRA is <a href="https://gitlab.cern.ch/caimira/caimira/-/blob/master/LICENSE" class="ext">Apache 2.0 licensed</a> open-source
software developed at CERN. software developed at CERN.
You can find the source code at <a href="https://gitlab.cern.ch/cara/caimira">https://gitlab.cern.ch/cara/caimira</a>, You can find the source code at <a href="https://gitlab.cern.ch/caimira/caimira">https://gitlab.cern.ch/caimira/caimira</a>,
where we welcome contributions, feature requests and issue reports. where we welcome contributions, feature requests and issue reports.
</p> </p>
</div> </div>

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caimira/apps/templates/base/userguide.html.j2
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@ -54,7 +54,7 @@ However, this value may be revised in the future as more studies of the Gamma VO
<h4>Vaccine effectiveness</h4> <h4>Vaccine effectiveness</h4>
<br> <br>
<p>The vaccination input corresponds to the vaccine type(s) administrated to the exposed population, assuming every exposed (or the occupant in question) has received the vaccine cocktail selected by the user. <p>The vaccination input corresponds to the vaccine type(s) administrated to the exposed population, assuming every exposed (or the occupant in question) has received the vaccine cocktail selected by the user.
The respective vaccine effectiveness values were extracted from data available in <a href="https://view-hub.org/resources">Results of COVID-19 Vaccine Effectiveness Studies: An Ongoing Systematic Review - Updated September 8, 2022</a>, using <a href="https://gitlab.cern.ch/cara/caimira/-/tree/master/caimira/scripts/data/vaccine_effectiveness.py">this script</a>.</p> The respective vaccine effectiveness values were extracted from data available in <a href="https://view-hub.org/resources">Results of COVID-19 Vaccine Effectiveness Studies: An Ongoing Systematic Review - Updated September 8, 2022</a>, using <a href="https://gitlab.cern.ch/caimira/caimira/-/tree/master/caimira/scripts/data/vaccine_effectiveness.py">this script</a>.</p>
<br> <br>
<h3>Room Data</h3> <h3>Room Data</h3>
<br> <br>

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caimira/models.py
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# This module is part of CAiMIRA. Please see the repository at # This module is part of CAiMIRA. Please see the repository at
# https://gitlab.cern.ch/cara/caimira for details of the license and terms of use. # https://gitlab.cern.ch/caimira/caimira for details of the license and terms of use.
""" """
This module implements the core CAiMIRA models. This module implements the core CAiMIRA models.

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caimira/scripts/themes/base/caimira_script.command
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cd Downloads cd Downloads
git clone https://gitlab.cern.ch/cara/caimira.git git clone https://gitlab.cern.ch/caimira/caimira.git
cd caimira cd caimira
if [[ `uname -m` == 'arm64' ]]; then if [[ `uname -m` == 'arm64' ]]; then
pip3 install scipy --index-url=https://pypi.anaconda.org/scipy-wheels-nightly/simple pip3 install scipy --index-url=https://pypi.anaconda.org/scipy-wheels-nightly/simple

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caimira/scripts/themes/base/caimira_script.sh
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git clone https://gitlab.cern.ch/cara/caimira.git git clone https://gitlab.cern.ch/caimira/caimira.git
cd caimira cd caimira
pip install -e . pip install -e .
echo "############################################" echo "############################################"

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caimira/scripts/themes/cern/caimira_script.command
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cd Downloads cd Downloads
git clone https://gitlab.cern.ch/cara/caimira.git git clone https://gitlab.cern.ch/caimira/caimira.git
cd caimira cd caimira
if [[ `uname -m` == 'arm64' ]]; then if [[ `uname -m` == 'arm64' ]]; then
pip3 install scipy --index-url=https://pypi.anaconda.org/scipy-wheels-nightly/simple pip3 install scipy --index-url=https://pypi.anaconda.org/scipy-wheels-nightly/simple

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caimira/scripts/themes/cern/caimira_script.sh
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git clone https://gitlab.cern.ch/cara/caimira.git git clone https://gitlab.cern.ch/caimira/caimira.git
cd caimira cd caimira
pip install -e . pip install -e .
echo "############################################" echo "############################################"

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setup.py
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# This module is part of CAiMIRA. Please see the repository at # This module is part of CAiMIRA. Please see the repository at
# https://gitlab.cern.ch/cara/caimira for details of the license and terms of use. # https://gitlab.cern.ch/caimira/caimira for details of the license and terms of use.
""" """
setup.py for CAiMIRA. setup.py for CAiMIRA.