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Changes

This log documents significant changes for each release.

[1.0.792] - 2022-11-14

  • Add get description and relationship to code API
  • Add polymorphic get component via graph API
  • Add additional reference set item resolution via graph API
  • Address miscellaneous code linting (removal unused imports and requires, avoid shadowing vars, improved comments / docstrings)

[1.0.772] - 2022-11-08

  • Tweak indexing so that reference set items are indexed in a separate pass as an interim step during import, for refset reification, and then re-indexed in the formal 'index' step.
  • Update documentation to recommend compaction should be run after indexing, now that the core datastore is updated during indexing.

[1.0.770] - 2022-11-07

  • Fix #42 in which relationship indices could be incorrect if more than one relationship in a distribution relates to the same source-target-type tuple.
  • Add 'intersect-ecl' to core library to intersect a set of concept identifiers with an ECL expression.

[1.0.764] - 2022-10-23

  • Add recognised installed locales into status report
  • Harmonise parameter style for HTTP REST server endpoints

[1.0.754] - 2022-10-22

  • Upgrade dependencies (including netty-buffer,logback-classic and tools.cli)
  • Add automated release to GitHub for uberjar, to supplement automation to clojars for library jar

[1.0.734] - 2022-10-15

  • Add support to automatically remove duplicates during search, when term and conceptId match.
  • Add ability to explicitly include or exclude inactive concepts and descriptions from HTTP API

[1.0.712] - 2022-08-14

  • Tweak logging during import
  • Refine handling of distribution metadata
  • Remove unused code
  • Fix graph resolution of a concept's membership of reference sets (via properties /refsetIds and /refsetItems).
  • Upgrade dependencies (Lucene 9.3, netty buffers 4.1.79)

[0.12.684] - 2022-06-12

  • Add ability to download a specific release by date, for UK users.

[0.12.681] - 2022-06-08

  • Improve logging of metadata when importing distribution(s)
  • For uberjar, fully ahead-of-time (AOT) compile, elide some metadata and use direct-linking
  • Reduce logging during build process

[0.12.664] - 2022-06-02

  • More deterministic build for uberjars
  • Reduce build product sizes by reducing dependencies
  • Simplify usage when used as a library by java clients, with an externally defined java API.
  • Avoid ahead-of-time compilation when used as a library
  • Improve logging for distribution import
  • Upgrade dependencies (Lucene v9.2, trud v1.0.80,

[0.12.644] - 2022-05-17

  • Improve download provider parameters so can optionally use explicit assignment e.g. api-key=../trud/api-key.txt

[0.12.640] - 2022-05-10

  • Switch to new lmdb storage backend, version 'lmdb/15'
  • Speed improvements and optional compaction step to reduce database size

[0.11.604] - 2022-05-06

  • Bump file-based database to 0.11
  • Improve refset extended attribute support
  • Add new search index 'members.db' for search of reference set members
  • Partial ECL v2.0 support including +HISTORY and member filters
  • Add support for lucene v8 usage when required (e.g. for java 8 compatibility)

[0.10.533] - 2022-04-11

  • New two-phase import permitting reification of refset items on import.
  • Return refset items with extended attributes by default in graph and HTTP APIs.

[0.10.519] - 2022-04-09

  • Improve speed and error handling in import
  • Revise approach to extended fields in reference set items
  • Bump to version 0.7 of the file-based database given changes in schema. This means this version will refuse to read databases created in prior versions.
  • Add runtime reification of refset items for those not reified during import.

[0.9.486] - 2022-04-03

  • Add specifications for all supported SNOMED CT entities
  • Add generative tests for parsing and unparsing SNOMED data files
  • Add synth_test.clj to export and then re-import generated synthetic data
  • Bump to Clojure 1.11.0
  • Speed up import and indexing

[0.9.458] - 2022-03-27

  • Upgrade to Lucene 9.1
  • Add and improve graph API resolvers
  • Improve synthetic and live test suite
  • Fix extended reference set import pattern matching

[0.9.408] - 2022-03-21

  • Add synthetic SNOMED data generation
  • Much more complete automated testing using synthetic data
  • Add greater instrumentation when in development or testing
  • Add import of OWL reference set types
  • Fix accept-language parsing and fallback in http server

[0.9.369] - 2022-02-17

  • Bump to Lucene 9.0 - hermes now requires JDK 11 or newer.
  • Switch to using clojure.data.json for JSON export.
  • Bump other minor outdated dependencies (logback, trud).

[0.9.362] - 2022-02-15

  • Support for mapping concepts into a defined subset of concepts.
  • Add get-synonyms convenience function
  • Expose get-all-children at top-level API

[0.8.341] - 2022-01-22

  • Bump to Apache Lucene 8.11.0 - no API or index changes, but simply bug fixes
  • Add --allowed-origins option to server to enable configuration of CORS, if required
  • Add build via tools.build
  • Add deployment to clojars.

[0.8.3] - 2021-11-04

  • More complete UK language refset priority list
  • Fail fast if there are any issues caught during processing (e.g. broken data such as invalid dates)
  • Optimise import, parsing and storage flow. Better handling of errors during import.
  • Fix import of simple reference sets, including when 'Simple' not in summary field of filename
  • Tidy status output when importing data if no metadata found.
  • Add support for simple reference set extensions with flexible fields based on 's' 'c' or 'i' in filename for local customisation

[0.8.2] - 2021-10-31

  • Status command now prints installed reference sets, and optionally counts of SNOMED data
  • Add -v --verbose flag to increase verbosity for commands, although they're pretty verbose already
  • Better error reporting during import

[0.8.1] - 2021-10-30

  • Add explicit choice of locale at time of index creation for preferred concept cache. Hermes supports multiple languages but for convenience caches the preferred synonym for a given locale (or set of reference sets) in the search index.
  • Fallback to en-US if chosen locale, or system default locale, does not have a known set of 'best' language reference sets

[0.8.0] - 2021-10-24

  • Add fuzzy and fallback-fuzzy search to graph API.
  • Add get-all-parents, and parent-relationships to core API
  • Permit configuration of with-historical to allow choice of association refset types
  • Add ECL membership check
  • Add reverse cross-map prefix search (useful for ICD-10 and Read)
  • Optimisations

[0.7.5] - 2021-09-13

  • Fix handling of '<<' in expressions.
  • Improve validation of HTTP parameters
  • Backend paths-to-root and some-indexed for dimensionality reduction work

[0.7.4] - 2021-07-27

  • Make JSON default for HTTP server
  • Add refsets HTTP endpoint

[0.7.3] - 2021-07-27

  • Add reverse index specifically for association reference set items
  • Add expand API endpoint to HTTP server, including historical if requested

[0.7.2] - 2021-07-20

  • Bind address specified at command line now actually used.

[0.7.1] - 2021-06-04

  • Add support for new SNOMED filename naming system used by UK since May 21
  • Force UTF-8 encoding to ensure works on platforms with different default character encoding.

[0.7.0] - 2021-05-31

  • New graph API using declarative approach permitting clients to ask for exactly what they need
  • Expose fuzzy search in REST API.
  • Restructuring - separate library code from cli commands / server
  • Add rudimentary GitHub Actions tests, but not yet using live db
  • Add historical associations reference set support
  • Update database version to v0.6 given new indexes.
  • Better query re-writing for when single must-not clauses used alone.

[0.6.2] - 2021-04-20

  • Permit prefix search to run with one character or more, rather than minimum of three, for better autocompletion functionality.

[0.6.1] - 2021-04-19

  • Upgrade dependencies
  • Temporarily bind to 0.0.0.0 pending more complete server configuration options

[0.6.0] - 2021-03-31

  • Support for unlimited results when used as a library, and when processing expressions
  • Harmonise web service key names to use camel case and not mix in kebab-case.
  • Expose library API call to get installed reference sets
  • Expose support for 'Accept-Language' using BCP 47 language tags in REST server, with additional support for specific language reference set extension of form en-gb-x-XXXX where XXXX is preferred language refset.
  • Release information included in log files

[0.5.0] - 2021-03-09

  • Minor fixes

[0.4.0] - 2021-03-08

  • Major change to backend store with new custom serialization resulting in enormous speed-up and size benefits.
  • UK dictionary of medicines and devices (dm+d) custom code extracted to another repository
  • Add support for transitive synonyms

[0.3.0] - 2021-01-27

  • Add special custom extension for UK dictionary of medicines and devices (dm+d) to bring in non-SNOMED BSA data
  • SNOMED ECL (expression constraint language) support
  • SNOMED CG (compositional grammar) support
  • Major improvements to server and backend. Unified terminology service abstracting underlying implementations.

[0.2.0] - 2020-11-18

  • Add search and autocompletion using Apache Lucene

[0.1.0] - 2020-11-12

  • Basic SNOMED service (store/retrieval/inference)

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