viditvarshney/distro

Docker distribution of camicroscope and all its components

caMicroscope Distribution

caMicroscope 3.X distribution

run with docker-compose -f caMicroscope.yml up

this will build all services and run in the foreground. Use docker-compose -f caMicroscope.yml build to rebuild the services.

Once everything is up, go to :4010/ to see the landing page.

SSL

To enable ssl, mount the private key and certificate files to the security service in /root/src/ssl/privatekey.pem and /root/src/ssl/certificate.pem respectively. HTTPS mode will only be enabled if both of these files are present.

Component Services

mongo - vanilla mongo container

idxMongo - ephemeral container to index mongo (that is, this container is expected to exit once it's done its job)

bindaas - api service for mongo (see https://github.com/sharmalab/bindaas)

iip - slide tile server (see https://github.com/camicroscope/iipImage)

viewer - hosts the viewer files and builds packages ( see https://github.com/camicroscope/caMicroscope)

loader - extracts metadata needed for image loading (see https://github.com/camicroscope/SlideLoader)

security - security proxy (see https://github.com/camicroscope/Security)

Configuration

Logging - Container Logging is, for HIPAA reasons, disabled. Feel free to use a different logging engine if desired, especially for development.

Security and Routes - This is handled by the security container. By default routes go the viewer, unless a specific pattern in routes.json is matched. If security is enabled, supply the SECRET (pub key or secret of JWT) for verification, otherwise set DISABLE_SEC to true.

Image Volume - This is, by default, the images directory in this directory. If this is changed, please make the same change across all impacted services.

Packages - Packages are built in the viewer service using parcel, mount a different directory with packages.js to the package directory to overwrite or add functionality.

PathDB

To use PathDB, use quip-pathdb.yml instead of caMicroscope.yml. This deployment does not include the auth and loader as separate services, as this PathDB provides that functionality.

Running QuIP with PathDB (https://github.com/SBU-BMI/PathDB):

0. place yourself in quip_distro folder.
   
1. copy config/httpd.conf.template to config/httpd.conf
   
2. copy config/pathdb_routes.json to config/routes.json (this will overwrite an existing routes.json file)
   
3. configure httpd.conf with your certificates to enable https.
   
4. build with, "docker-compose -f quip-pathdb.yml build"
   
5. run with, "docker-compose -f quip-pathdb.yml up -d"

Support

Feel free to add any support inquiry as a github issue to this repository. Other feedback can be given via this form.