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‎.dockerignore

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data/
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!data/projects/knoweng/demo_files/
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!data/projects/knoweng/pipeline_readmes/
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docker/
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!docker/flask_entrypoint.sh
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ci_scripts/
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.git
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.gitignore
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client-debug.log

‎.gitignore

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data/db/*
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data/userfiles/*
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!data/userfiles/.gitkeep
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# created by data/projects/knoweng/populate.sh
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data/src
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data/gene_annotations
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data/logs
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data/networks
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data/projects/knoweng/demo_files
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data/projects/knoweng/networks
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data/projects/knoweng/pipeline_readmes
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data/projects/mmbdb/*
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data/projects/hello_world/*
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‎Dockerfile.flask

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FROM tiangolo/uwsgi-nginx-flask:python2.7
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# Install package dependencies
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RUN apt-get -qq update && \
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apt-get -qq install --no-install-recommends \
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build-essential \
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curl \
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netcat \
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libpq-dev \
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python-dev \
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sudo && \
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curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - && \
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apt-get -qq update && \
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apt-get -qq install nodejs && \
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apt-get -qq clean all && \
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apt-get -qq autoclean && \
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apt-get -qq autoremove && \
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rm -rf /var/lib/apt/lists/*
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RUN npm install -g [email protected]
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# Configure/clear flask working directory
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ENV BASEDIR="/code_live"
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WORKDIR $BASEDIR/
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# Install Python dependencies
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RUN pip --no-cache-dir install -q setuptools==33.1.1
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ADD ./requirements/ $BASEDIR/requirements
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RUN pip --no-cache-dir install -q -r requirements/nest_flask.txt
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RUN rm -rf /app
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# Copy in our app source and config files
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#COPY data/projects/knoweng/demo_files/*.txt /demo_files/
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COPY nest_flask_etc/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini
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COPY nest_flask_etc/nginx/ /etc/nginx/
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COPY nest_flask_etc/supervisor/ /etc/supervisor/
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COPY client $BASEDIR/client
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# Build UI from source
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WORKDIR $BASEDIR/client/
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RUN npm install && \
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gulp dist
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# Copy in demo files, publication data, and pipeline readmes
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WORKDIR /
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RUN git clone https://github.com/KnowEnG/quickstart-demos && \
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cp -r quickstart-demos/demo_files / && \
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cp -r quickstart-demos/publication_data /demo_files/ && \
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find /demo_files -type f -name \*.bz2 | xargs bzip2 -d && \
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cp -r quickstart-demos/pipeline_readmes / && \
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rm -rf /quickstart-demos
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WORKDIR $BASEDIR/
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COPY . .
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RUN cp $BASEDIR/docker/flask_entrypoint.sh $BASEDIR/entrypoint.sh
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# Set runtime environment options
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ENV PROJECT_ENV="knoweng" \
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NEST_RUNLEVEL="development" \
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PYTHONPATH="$BASEDIR"
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# We need to override the entrypoint from the base image, because it clobbers our config
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# Note the k8s yamls override the entrypoint *again*
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ENTRYPOINT [ "./entrypoint.sh" ]

‎Dockerfile.jobs

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FROM python:2.7
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# Install package dependencies for jobs
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RUN apt-get -qq update && \
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apt-get -qq install --no-install-recommends \
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pkg-config \
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libpng-dev \
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libfreetype6-dev \
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libblas-dev \
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liblapack-dev \
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gfortran \
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netcat \
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libatlas-base-dev \
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libhdf5-dev \
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python-tk \
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r-base \
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r-base-dev \
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libffi-dev \
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libssl-dev && \
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apt-get -qq clean all && \
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apt-get -qq autoclean && \
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apt-get -qq autoremove && \
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rm -rf /var/lib/apt/lists/*
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# Configure our app's expected working directory
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ENV BASEDIR="/app" \
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PYTHONPATH="$BASEDIR"
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WORKDIR $BASEDIR/
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# Install Python dependencies for jobs (1/2)
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# force setuptools v33; newer versions will fail https://github.com/pypa/setuptools/issues/937
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# alternative is to update pip, but that requires updating python (otherwise we
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# hit security errors), and that's complicated, because ubuntu 14.04 locks in
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# 2.7.6
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COPY requirements $BASEDIR/requirements/
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RUN pip --no-cache-dir install -q setuptools==33.1.1
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RUN pip --no-cache-dir install -q numpy==1.11.3
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RUN pip --no-cache-dir install -q -r requirements/nest_jobs.txt
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# Install Python dependencies for jobs (2/2)
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# The following pip packages do not declare their dependencies properly, and
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# therefore cannot reliably be installed from the requirements txt files.
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# (pip does not install in the order declared in the file, but rather
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# an ordering based on installing the order to resolve dependencies)
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RUN pip --no-cache-dir install -q biom-format==2.1.5
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RUN pip --no-cache-dir install -q h5py==2.5.0 && \
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python -c "import skbio" #this prevents a "caching fonts" message on every command
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# Copy in demo files, publication data, and pipeline readmes
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WORKDIR /
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RUN git clone https://github.com/KnowEnG/quickstart-demos && \
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cp -r quickstart-demos/demo_files / && \
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cp -r quickstart-demos/publication_data /demo_files/ && \
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find /demo_files -type f -name \*.bz2 | xargs bzip2 -d && \
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cp -r quickstart-demos/pipeline_readmes / && \
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rm -rf /quickstart-demos
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WORKDIR $BASEDIR/
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COPY . .
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# Define our jobs worker entrypoint
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ENTRYPOINT ["python","-m","nest_py.knoweng.jobs.worker_app"]

‎README.rst

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===============================
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Platform
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Nest
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===============================
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This repository contains the codebase implementing the KnowEnG platform's
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web services and client.
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This repository contains the codebase implementing both the Mayo Microbiome
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Database project and the KnowEnG frontend.
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To Install Docker

‎client/css/knoweng/style.css

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text-align: center;
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margin-left: auto;
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margin-right: auto;
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margin-top: 80px;
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padding-top: 80px;
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font-size: 16pt;
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z-index: -1;
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}
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.brand-text {
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color: #1D609E;
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}
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}
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/* Start of ngx-bootstrap popover customization */
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.popover.customClass {
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margin-top: -22px;
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margin-left: 66px;
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}
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.popover.customClass>.arrow, .popover.customClass>.arrow:after {
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border-style: none;
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}
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.popover.customClass>.popover-content {
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padding: 0;
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background-color: #EBF2F2;
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}
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.popover.infoClass {
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padding: 0px;
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color: #000000;
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font-family: Lato;
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font-size: 14px;
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line-height: 17px;
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max-width: 100%;
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margin-left: 10px;
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margin-top: 10px;
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}
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.popover.infoClass>.popover-title {
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background-color: #35516A;
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}
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.popover.infoClass>.arrow:before, .popover.infoClass>.arrow:after {
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border-bottom-color: #35516A;
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}
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.popover.infoClass>.popover-content .popover-content-blue {
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color: #1D609E;
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}
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.popover.infoClass>.popover-content .help-info-popover {
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width: 292px;
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padding-bottom: 10px;
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}
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.popover.infoClass>.popover-content h5 {
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font-weight: 700;
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}
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.popover.gradientPickerClass {
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margin-top: 3px;
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margin-left: 20px;
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}
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.popover.gradientPickerClass>.arrow, .popover.gradientPickerClass>.arrow:after {
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border-style: none;
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}
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.popover.gradientPickerClass>.popover-content {
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padding: 0px;
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}
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/* End of ngx-bootstrap popover customization */
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.ng-draggable {
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cursor: move;
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}
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‎client/data/demofiles.json

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{
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"gene_prioritization": {
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"features": {
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"filename": "demo_GP.genomic.txt",
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"url": "https://raw.githubusercontent.com/KnowEnG/quickstart-demos/master/demo_files/demo_GP.genomic.txt"
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},
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"response": {
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"filename": "demo_GP.phenotypic.txt",
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"url": "https://raw.githubusercontent.com/KnowEnG/quickstart-demos/master/demo_files/demo_GP.phenotypic.txt"
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}
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"feature_prioritization": {
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"features_file": [{
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"filename": "demo_FP.genomic.txt"
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}],
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"response_file": [{
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"filename": "demo_FP.phenotypic.txt"
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}]
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},
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"gene_set_characterization": {
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"features": {
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"filename": "demo_GSC.spreadsheet.txt",
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"url": "https://raw.githubusercontent.com/KnowEnG/quickstart-demos/master/demo_files/demo_GSC.spreadsheet.txt"
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}
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"gene_set_file": [{
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"filename": "demo_GSC.spreadsheet.txt"
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}]
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},
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"sample_clustering": {
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"features": {
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"filename": "demo_SC.genomic.txt",
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"url": "https://raw.githubusercontent.com/KnowEnG/quickstart-demos/master/demo_files/demo_SC.genomic.txt"
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},
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"response": {
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"filename": "demo_SC.phenotypic.txt",
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"url": "https://raw.githubusercontent.com/KnowEnG/quickstart-demos/master/demo_files/demo_SC.phenotypic.txt"
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}
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"features_file": [{
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"filename": "demo_SC.genomic.txt"
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}],
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"response_file": [{
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"filename": "demo_SC.phenotypic.txt"
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}]
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},
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"signature_analysis": {
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"query_file": [{
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"filename": "demo_SA.samples.txt"
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}],
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"signatures_file": [{
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"filename": "demo_SA.signatures.mapped.txt"
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}]
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},
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"spreadsheet_visualization": {
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"spreadsheets": [
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{
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"filename": "demo_SSV.genomic.txt"
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}, {
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"filename": "demo_SSV.phenotypic.txt"
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}
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]
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}
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}

‎client/data/manuscripts.json

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{
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"manuscripts": [
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{
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"title": "Knowledge-guided analysis of \"omics\" data using the KnowEnG cloud platform",
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"authors": "Charles Blatti III, Amin Emad, Matthew J. Berry, Lisa Gatzke, Milt Epstein, Daniel Lanier, Pramod Rizal, Jing Ge, Xiaoxia Liao, Omar Sobh, Mike Lambert, Corey S. Post, Jinfeng Xiao, Peter Groves, Aidan T. Epstein, Xi Chen, Subhashini Srinivasan, Erik Lehnert, Krishna R. Kalari, Liewei Wang, Richard M. Weinshilboum, Jun S. Song, C. Victor Jongeneel, Jiawei Han, Umberto Ravaioli, Nahil Sobh, Colleen B. Bushell, Saurabh Sinha",
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"link": {
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"text": "bioRxiv",
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"url": "https://www.biorxiv.org/content/10.1101/642124v1"
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},
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"abstract_sections": [
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{
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"title": "Abstract",
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"text": "We present KnowEnG, a free-to-use computational system for analysis of genomics data sets, designed to accelerate biomedical discovery. It includes tools for popular bioinformatics tasks such as gene prioritization, sample clustering, gene set analysis and expression signature analysis. The system offers \"knowledge-guided\" data-mining and machine learning algorithms, where user-provided data are analyzed in light of prior information about genes, aggregated from numerous knowledge-bases and encoded in a massive \"Knowledge Network.\" KnowEnG adheres to \"FAIR\" principles: its tools are easily portable to diverse computing environments, run on the cloud for scalable and cost-effective execution of compute-intensive and data-intensive algorithms, and are interoperable with other computing platforms. They are made available through multiple access modes including a web-portal, and include specialized visualization modules. We present use cases and re-analysis of published cancer data sets using KnowEnG tools and demonstrate its potential value in democratization of advanced tools for the modern genomics era."
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}
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],
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"data_files_directory": "publication_data/blatti_et_al_2019/spreadsheets/",
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"data_files": [
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"in1_SC_pancanClinical",
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"in1_SC_pancanMutations",
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"in2_SC_pancanClinical",
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"in2_SC_pancanMultiomicsClusters",
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"in3_SC_metabricClinical",
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"in3_SC_metabricExpression",
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"in4_FP_pancanDiseaseType",
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"in4_FP_pancanExpression",
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"in5_GSC_diseaseGenes_out4",
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"in6_SA_esccExpression",
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"in6_SA_luscSignatures",
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"in7_FP_esccBestSignature_out6",
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"in7_FP_esccExpression",
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"in8_GSC_signatSpecificGenes_out7",
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"out1_SC_pancanMutationClusters",
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"out2_SC_cocaClusters",
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"out3_SC_metabricClusters",
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"out5_GSC_diseaseGeneOntology",
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"out8_GSC_pathwayEnrichments"
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],
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"data_readme_url": "https://github.com/KnowEnG/quickstart-demos/blob/master/publication_data/blatti_et_al_2019/README.md"
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}
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]
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}

‎client/data/youtube.json

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[
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"nAZzN100B3w",
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"Vp76-Oz-Yuc",
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"mQJ7Y0jh5xM"
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"nP4wtVZOY3E"
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]

‎client/gulpfile.js

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var gulp = require('gulp');
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var git = require('git-rev');
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var fs = require('fs');
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var del = require('del');
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});
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gulp.task('dist', [ /*'css', 'img',*/ 'ts', 'html', 'cachebuster:js', 'cachebuster:html' , 'cachebuster:css' ], function () {
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// git-rev expose long or short SHA
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git.long(function (sha) {
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// TODO: Add more fields to this, as necessary / helpful
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var status = {
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sha: sha,
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runlevel: process.env.NEST_RUNLEVEL || 'development',
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hzHost: process.env.HUBZERO_APPLICATION_HOST || '',
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maxUploadSize: process.env.MAX_CONTENT_LENGTH || ''
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};
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fs.writeFileSync('dist/status.json', JSON.stringify(status));
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console.log('Status Written:', status);
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});
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});
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//run tests once and exit, suitable for testing in build environment like Jenkins

‎client/img/knoweng/linen.png

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