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Last pushed: a year ago
Short Description
The data warehouse component of the Lens system.
Full Description

Please start at the Top-Level Lens Repo.

Lens Warehouse Service

The data warehouse service of the Lens system which is one of several backend
services. The data warehouse service holds the medical study data which can be
queried.

Usage with Leiningen

To start the service with leiningen, run the following command

lein with-profile production,datomic-free trampoline run -h

This prints a help of all command line options. You need to specify at least a
database URI. The database URI has to point to a Datomic Free Edition Database.
If you like to use the Pro Edition, you have to use the datomic-pro leiningen
profile instead of the datomic-free profile. An example database URI is:

datomic:free://localhost:4334/lens-warehouse

Usage on Heroku Compatible PaaS

This application uses the following environment vars:

  • PORT - the port to listen on
  • DB_URI - the Datomic database URI
  • CONTEXT_PATH - an optional context path under which the warehouse service
    runs. Has to be empty for root context or start with a slash but not ending with a slash.
  • DATOMIC_EDITION - one of free or pro with a default of free
  • SEARCH_HOST - hostname of the Elastic Search Cluster
  • SEARCH_PORT - port of the Elastic Search Cluster (defaults to 9200)
  • SEARCH_INDEX - index to use in the Elastic Search Cluster

If you have foreman installed you can create an .env file listing the
environment vars specified above and just type foreman start.

Usage through Docker Container

You have to start a database volume container, a database container and a
warehouse container linking them all together:

docker run --name lens-warehouse-db-vol akiel/lens-warehouse:db-latest
docker run -d --volumes-from lens-warehouse-db-vol -e ALT_HOST=lens-warehouse-db --name lens-warehouse-db akiel/datomic-free
docker run -d -p 8080:80 --link lens-warehouse-db:db --name lens-warehouse akiel/lens-warehouse

After starting all containers, a curl http://localhost:8080 should show the
service document of Lens Warehouse.

Development

First you need a running Datomic database. The easiest way to bring one up is
the following:

docker run -d --name lens-warehouse-db -p 4334-4336:4334-4336 akiel/datomic-free

after that, create an .env file in the project root with the following
content:

DB_URI=datomic:free://localhost:4334/lens-warehouse

now you can start a REPL with lein repl. After it is up, go into the user
namespace which is located under dev. There is a comment block
"Init Development". Just invoke the functions:

(startup)
(create-database)
(load-base-schema)

one after each other. You should be able to see the Warehouse service running
at port 8080. If you like to specify a different port, you can do it in the
.env file.

If you have already a database, a (startup) will be sufficient. If you make
changes, a (reset) will reload the code. In order to get rid of the database,
simply delete the Datomic container with docker rm -f datomic and start it
again.

If you use Intellij IDEA with Cursive, you can add a Datomic stub JAR
to your project dependencies as described here. The stub will provide
signatures and documentation for the Datomic API functions. I can't add the
stub dependency to the project.clj file because it is currently not available on
Clojars. I opened an issue here.

Using Datomic Pro

You need a license to be able to use the Pro Edition of Datomic. The Leiningen
project file contains two profiles, one for the Free Edition (datomic-free) and
one for the Pro Edition (datomic-pro).

Metadata Model

The metadata model used in Lens Warehouse is based on the CDISC ODM
standard. The goal is to implement a sufficent subset of the ODM concepts to be
able to import metadata from ODM files. Lens Warehouse will not directly contain
an ODM importer. Instead there will be a command line client called
lens-import which reads ODM files and uses the REST API of Lens Warehouse
to create metadata entities.

You can find more in the ODM Section of the documentation.

License

Copyright © 2015 Alexander Kiel

Distributed under the Eclipse Public License, the same as Clojure.

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