live-demo.md

Live Demo

The live demo of MedCo is available at https://medco-demo.epfl.ch. The profile test-local-3nodes with a custom configuration is used.

Update demo version

Connect with SSH to the machine, with the lca1 account. Ask Mickaël or Joao to set up your SSH public key there.

Get the latest version

Adapt the exported variables to the current versions.

export OLD_VER=0.2.1 NEW_VER=0.3.0

cd /home/lca1/medco-deployment/compose-profiles/test-local-3nodes
docker-compose down

cd /home/lca1
mv medco-deployment medco-deployment-${OLD_VER}
wget https://github.com/ldsec/medco-deployment/archive/v${NEW_VER}.tar.gz
tar xvzf v${NEW_VER}.tar.gz
mv medco-deployment-${NEW_VER} medco-deployment

Configuration update

Update the configuration according to the following examples. For the passwords, use the same as defined in the previous deployments.

{% code title="/home/lca1/medco-deployment/compose-profiles/test-local-3nodes/.env" %}

MEDCO_NODE_HOST=medco-demo.epfl.ch
MEDCO_NODE_HTTP_SCHEME=https
POSTGRES_PASSWORD=xxx
PGADMIN_PASSWORD=xxx
KEYCLOAK_PASSWORD=xxx
I2B2_WILDFLY_PASSWORD=xxx
I2B2_SERVICE_PASSWORD=xxx
I2B2_USER_PASSWORD=xxx

{% endcode %}

{% code title="/home/lca1/medco-deployment/compose-profiles/test-local-3nodes/docker-compose.yml" %}

  glowing-bear-medco:
    environment:
      - "GB_FOOTER_TEXT=Disclaimer: This demo complies with the EPFL regulations and guidelines regarding the storage and use of personal data: https://www.epfl.ch/about/overview/overview/regulations-and-guidelines/"

{% endcode %}

Copy the previously used certificate

cp /home/lca1/medco-deployment-${OLD_VER}/configuration-profiles/test-local-3nodes/certificate.* \
    /home/lca1/medco-deployment/configuration-profiles/test-local-3nodes/

Start deployment

cd medco-deployment/compose-profiles/test-local-3nodes
docker-compose up -d

Load v0 dataset (synthetic)

cd /home/lca1/medco-deployment/resources/data
bash download.sh

cd /home/lca1/medco-deployment/compose-profiles/test-local-3nodes
docker-compose -f docker-compose.tools.yml run medco-loader-srv0 v0 \
    --ont_clinical /data/genomic/tcga_cbio/clinical_data_fake.csv \
    --sen /data/genomic/sensitive.txt \
    --ont_genomic /data/genomic/tcga_cbio/mutation_data_fake.csv \
    --clinical /data/genomic/tcga_cbio/clinical_data_fake.csv \
    --genomic /data/genomic/tcga_cbio/mutation_data_fake.csv \
    --output /data/
docker-compose -f docker-compose.tools.yml run medco-loader-srv1 v0 \
    --ont_clinical /data/genomic/tcga_cbio/clinical_data_fake.csv \
    --sen /data/genomic/sensitive.txt \
    --ont_genomic /data/genomic/tcga_cbio/mutation_data_fake.csv \
    --clinical /data/genomic/tcga_cbio/clinical_data_fake.csv \
    --genomic /data/genomic/tcga_cbio/mutation_data_fake.csv \
    --output /data/
docker-compose -f docker-compose.tools.yml run medco-loader-srv2 v0 \
    --ont_clinical /data/genomic/tcga_cbio/clinical_data_fake.csv \
    --sen /data/genomic/sensitive.txt \
    --ont_genomic /data/genomic/tcga_cbio/mutation_data_fake.csv \
    --clinical /data/genomic/tcga_cbio/clinical_data_fake.csv \
    --genomic /data/genomic/tcga_cbio/mutation_data_fake.csv \
    --output /data/

Update certificate

The certificate is provided by Let's Encrypt and valid for a period of 3 months, it thus needs regular renewing. First ensure that the configuration located in /etc/letsencrypt/renewal/medco-demo.epfl.ch.conf is correct.

Then as the user root, renew the certificate:

certbot renew
cp /etc/letsencrypt/live/medco-demo.epfl.ch/fullchain.pem \
    /home/lca1/medco-deployment/configuration-profiles/test-local-3nodes/certificate.crt
cp /etc/letsencrypt/live/medco-demo.epfl.ch/privkey.pem \
    /home/lca1/medco-deployment/configuration-profiles/test-local-3nodes/certificate.key 

Finally as the user lca1 restart nginx:

cd /home/lca1/medco-deployment/compose-profiles/test-local-3nodes
docker-compose stop nginx
docker-compose up -d nginx