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OsHCuellarOsHCuellar
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Merge pull request #5 from lcmd-epfl/dev
cell2mol as dependency, cif2cell as input, update visualization and instructions added
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‎Dockerfile

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FROM materialscloud/tools-barebone:1.3.0
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LABEL maintainer="Developer Name <developer.email@xxx.yy>"
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LABEL maintainer="Osvaldo Hernandez-Cuellar <osvaldo.hernandezcuellar@epfl.ch>, Liam O. Marsh <liam.marsh@epfl.ch>, and Ruben Laplaza <ruben.laplazasolanas@epfl.ch>"
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# Python requirements
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COPY ./requirements.txt /home/app/code/requirements.txt
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COPY ./cell2mol/requirements.txt /home/app/code/compute-requirements.txt
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# Run this as sudo to replace the version of pip
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RUN pip3 install -U 'pip>=10' setuptools wheel
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# install packages as normal user (app, provided by passenger)
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WORKDIR /home/app/code
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# Install pinned versions of packages
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COPY ./requirements.txt /home/app/code/requirements.txt
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COPY ./cell2mol/requirements.txt /home/app/code/compute-requirements.txt
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RUN pip3 install --user -r requirements.txt
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RUN pip3 install --user -r compute-requirements.txt
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# Go back to root.
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# Also, it should remain as user root for startup
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COPY ./config.yaml /home/app/code/webservice/static/config.yaml
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COPY ./user_templates/ /home/app/code/webservice/templates/user_templates/
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COPY ./user_static/ /home/app/code/webservice/user_static/
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COPY ./cell2mol/ /home/app/code/webservice/cell2mol/
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COPY ./compute/ /home/app/code/webservice/compute/
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#Needed to allow only .cif file formats in the upload_structure_block
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COPY ./web_module.py /home/app/code/webservice/
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COPY ./base.html /home/app/code/webservice/templates/
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COPY ./base_templates/* /home/app/code/webservice/templates/
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# If you put any static file (CSS, JS, images),
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#create this folder and put them here
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# COPY ./user_static/ /home/app/code/webservice/user_static/
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###
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# Copy any additional files needed into /home/app/code/webservice/
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# Set proper permissions on files just copied
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RUN chown -R app:app /home/app/code/webservice/
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USER app
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WORKDIR /home/app/code/webservice/cell2mol/
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RUN python3 ./setup.py build
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USER root
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‎base.html renamed to ‎base_templates/base.html

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<div id='container'>
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<div id='maintitle'>
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{% block pagetitle %}
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<h1 style="text-align: center;">{{ config["page_title"] }}</h1>

‎base_templates/visualizer_select_structure.html

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<h2><a name="tool"></a>Upload your structure</h2>
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<div style="margin-left: 20px; margin-right: 20px">
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<form action="compute/process_structure/" enctype="multipart/form-data" method="post">
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<div class='alert alert-info'>
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<div class='row'>
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<div class='col-xs-12 col-sm-6'>
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<label for="file">Upload a crystal structure:</label>
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</div>
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<div class="col-xs-12 col-sm-6">
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<input type="file" name="structurefile" size="100">
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</div>
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</div>
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<div class='row'>
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<div class='col-sm-6'>
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<label for="fileformatSelect">Select here the file format:</label>
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</div>
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<div class='col-sm-6'>
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<select name="fileformat" id="fileformatSelect" onchange="formatInfo();" autocomplete="off">
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<option disabled selected value> -- select an option -- </option>
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{# First put the formats the user specified, if existing #}
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{% for parser_name in config.get('upload_structure_block_order', []) %}
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{% if parser_name in upload_structure_block_known_formats %}
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<option value="{{ parser_name }}">{{ upload_structure_block_known_formats[parser_name] }}</option>
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{% endif %}
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{% endfor %}
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{# Then put any remaining format #}
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{% for parser_name in upload_structure_block_known_formats %}
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{% if parser_name not in config.get('upload_structure_block_order', []) %}
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<option value="{{ parser_name }}">{{ upload_structure_block_known_formats[parser_name] }}</option>
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{% endif %}
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{% endfor %}
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</select>
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</div>
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</div>
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<div class="row col-sm-12" style="margin-top:10px; margin-bottom:-10px;">
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<div id="cifImportantInfo" class="alert alert-warning" hidden>
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<i> <ul style="padding-left: 10px;">
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<li>
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cell2mol web interface incorporates cif2cell v2.0.0 instead of v1.2.10
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</li>
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<li>
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To reproduce results reported on
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<a href="https://doi.org/10.1038/s41524-022-00874-9 " target="_blank">doi: 10.1038/s41524-022-00874-9 </a>,
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please use the cif2cell v1.2.10 output as input file with the <i>.info</i> extension.
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</li>
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</i></ul>
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</div>
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<div id="infoImportantInfo" class="alert alert-warning" hidden>
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<i> <ul style="padding-left: 10px;">
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<li>
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Please use use the flag <code>--cartesian</code> when generating the input file with cif2cell, and make sure
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it has the <i>.info</i> file extension.
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</li>
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<li>
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To reproduce results reported on
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<a href="https://doi.org/10.1038/s41524-022-00874-9 " target="_blank">doi: 10.1038/s41524-022-00874-9 </a>,
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please use cif2cell v1.2.10
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</li>
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</i></ul>
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</div>
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</div>
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<div id="xyzFormatFields" class="row" style="display: none">
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<div class='col-sm-6'>Cell vectors (&#x212B;)</div>
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<div class='col-sm-6'>
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<div class='row'>
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<div class='col-xs-2'>A</div>
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<div class='col-xs-3'><input type="number" step="any" class="form-control" name="xyzCellVecAx"></div>
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<div class='col-xs-3'><input type="number" step="any" class="form-control" name="xyzCellVecAy"></div>
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<div class='col-xs-3'><input type="number" step="any" class="form-control" name="xyzCellVecAz"></div>
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</div>
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<div class='row'>
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<div class='col-xs-2'>B</div>
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<div class='col-xs-3'><input type="number" step="any" class="form-control" name="xyzCellVecBx"></div>
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<div class='col-xs-3'><input type="number" step="any" class="form-control" name="xyzCellVecBy"></div>
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<div class='col-xs-3'><input type="number" step="any" class="form-control" name="xyzCellVecBz"></div>
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</div>
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<div class='row'>
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<div class='col-xs-2'>C</div>
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<div class='col-xs-3'><input type="number" step="any" class="form-control" name="xyzCellVecCx"></div>
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<div class='col-xs-3'><input type="number" step="any" class="form-control" name="xyzCellVecCy"></div>
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<div class='col-xs-3'><input type="number" step="any" class="form-control" name="xyzCellVecCz"></div>
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</div>
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</div>
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</div>
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{% if include_pages['upload_structure_additional_content'] is not none %}
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{% include include_pages['upload_structure_additional_content'] %}
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{% endif %}
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{% block structure_additional_content %}{% endblock %}
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<div class='row' style="text-align:center">
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<br/>
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<input type="submit" value="Calculate my structure" class="btn btn-default">
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</div>
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</div>
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</form>
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</div>
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<script>
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function formatInfo() {
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var inputFileFormat = document.getElementById("fileformatSelect").value;
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if (inputFileFormat == "cif") {
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document.getElementById("cifImportantInfo").style.display="block";
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document.getElementById("infoImportantInfo").style.display="none";
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} else if (inputFileFormat == "info") {
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document.getElementById("cifImportantInfo").style.display="none";
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document.getElementById("infoImportantInfo").style.display="block";
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} else {
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document.getElementById("cifImportantInfo").style.display="none";
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document.getElementById("infoImportantInfo").style.display="none";
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}
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}
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</script>

‎cell2mol/.docker/Dockerfile

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