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Development

Hermes consists of two distinct subprojects:

  1. A command-line tool
  2. A library

The command-line tool provides a mechanism to download, import and index SNOMED CT, as well as run a terminology server. Source code can be found in /cmd.

The library is used by the command-line tool, but can be used by other applications to embed SNOMED CT into other applications. Source code can be found in /src.

Hermes generates a file-based 'database' consisting of three sub-databases:

  • core component store : keys and values, and indexes (LMDB)
  • description index : a search index for descriptions (Apache Lucene)
  • members index : a search index for refset members (Apache Lucene)

LMDB is a very fast memory-mapped key value store. See https://www.symas.com/lmdb.

Apache Lucene provides very fast indexing and search. See https://lucene.apache.org.

Hermes is essentially a very thin wrapper around these two highly-optimised and well engineered backends.

Namespace organisation

The library provides a single unified API com.eldrix.hermes.core. This can be used from Java or Clojure clients directly.

The other top-level namespaces comprise:

  • com.eldrix.hermes.graph: Graph-API using multiple discrete resolvers via Pathom.
  • com.eldrix.hermes.download: API to download SNOMED distributions
  • com.eldrix.hermes.importer: API to examine and consume SNOMED distributions
  • com.eldrix.hermes.rf2: Specifications for SNOMED RF2 to enable validation and runtime synthetic distribution generation
  • com.eldrix.hermes.snomed: Core SNOMED model data types and well known identifiers
  • com.eldrix.hermes.verhoeff: Implementation of the Verhoeff check digit algorithm

Overview of namespaces

Namespaces in com.eldrix.hermes.impl should be regarded as private and subject to change.

  • com.eldrix.hermes.impl.ser : Low-level serialization of SNOMED data types
  • com.eldrix.hermes.impl.lmdb : Low-level LMDB implementation
  • com.eldrix.hermes.impl.store : An abstract 'store' for SNOMED data
  • com.eldrix.hermes.impl.lucene : Low-level Lucene utility functions
  • com.eldrix.hermes.impl.search : Search index for descriptions
  • com.eldrix.hermes.impl.members : Search index for refset members
  • com.eldrix.hermes.impl.language : Language and Locale matching
  • com.eldrix.hermes.impl.ecl : Implementation of the SNOMED expression constraint language
  • com.eldrix.hermes.impl.scg : A partial implementation of compositional grammar

The LMDB implementation was deliberately not designed to be a generic key value store, but instead optimised for the domain, and therefore speed of access. That decision could be changed in the future.

How to build from source code

Run compilation checks (optional)

clj -M:check

Run unit tests and linters (optional)

By default, testing includes tests against a real local SNOMED CT datafile named 'snomed.db' in the local directory. This is ideal for development.

However, for automation purposes, you can exclude those tests and rely on tests using synthetic data instead.

clj -M:test                # Run all tests
clj -M:test -e :live       # Run tests but exclude those needing a real local SNOMED distribution

Additional test coverage reports and linting are also available:

clj -M:test/cloverage
clj -M:lint/kondo
clj -M:lint/eastwood

View outdated dependencies

clj -M:outdated

You can view a complete list of dependencies; try:

clj -X:deps tree

Building uberjar

Build the uberjar:

clojure -T:build uber

To release the uberjar to GitHub, if you have the right credentials:

clojure -T:build release

For this to work you need to set an environment variable named GITHUB_TOKEN with your personal access token. You can create the token on github.com under your profile: Settings -> Developer settings -> Personal access tokens.

Building library jar

A library jar contains only hermes-code, and none of the bundled dependencies.

clojure -T:build jar

Or you can install hermes into your local maven repository:

clojure -T:build install

To deploy the library jar to clojars, if you have the right credentials

clojure -T:build deploy

For this to work, you need to set the environment variables CLOJARS_USERNAME and CLOJARS_PASSWORD. These can be downloaded from www.clojars.org on the "Deploy Tokens" page after logging in.