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.

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.

mongo - vanilla mongo container

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

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

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

back - security, data, and routing (see https://github.com/camicroscope/caracal)

back/viewer - within back, viewer files ( see https://github.com/camicroscope/caMicroscope)

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

See backend and security config notes (here)[https://github.com/camicroscope/caracal]

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.

When selecting, an identity provider, note that we expect it to provide a JWT, and to have a certificate/public key/secret which can be used to verify such JWTs.

The example given in the Distro within config/login.html is set up to use google as an identity provider. See this guide from google to set up your own project, which is necessary to enable login on your instance.

Add users as in ./config/add_users.js. This can be done either by editing this file before bringing up the stack, or by running similar code against the camic database in ca-mongo. Attributes can be added to deny access to routes (e.g. allow only some users to post and delete) and userFilters can be used to change visibility of particular documents.

The email field is the email field (or failing that, sub field) in that priority from the identity provider.

To use PathDB, use quip-pathdb.yml instead of caMicroscope.yml.

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"

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

We have a discussion mailing list! Stop by and discuss all things caMicroscope. https://groups.google.com/forum/#!forum/camicroscope