Changes

This log documents significant changes for each release.

[1.4.xxxx] - Not yet released

• Upgrade to Apache Lucene 9.8
• Automatically generate CITATION.cff file for GitHub during build

[1.4.1296] - 2023-09-20

• #60 When not explicitly set, derive database default fallback locale on the basis of installed reference sets rather than the system default locale

[1.4.1292] - 2023-09-19

• #59 Improve error reporting if installed reference sets do not support the requested, or default fallback locale

[1.4.1278] - 2023-09-15

• #58 In case of an aborted compact, delete intermediary files prior to another attempt
• #58 Close store after copying datafiles and before moving to new location during compact

[1.4.1265] - 2023-09-09

• Always use normalized search and normalized index (Fixes #56)

This version breaks compatibility with previously indexed databases.

[1.3.1262] - 2023-09-07

• Use 'Accept-Language' header in HTTP server to select preferred terms
• Better logging during indexing
• Fail fast rather than trying to continue when there is a critical error during import (e.g. running out of disk space)
• Add term folding / normalization to improve search in content with diacritics (Fixes #55)

This version updates the index to add a search field for normalized (folded) text, particularly helpful in international deployments in which release centres do not include synonyms with and without non-semantically meaningful diacritics. This does not break compatibility with older indexes, but search using the folded index will obviously not work with indexes created by prior versions; as such, this release will show a warning to say that index is missing. This can be safely ignored if you do not need search against a folded index.

[1.3.1232] - 2023-07-14

• Change to search index structure to better handle runtime, dynamic results
  based on requested locale. This version is therefore incompatible with databases created by previous versions. Hermes always permitted getting a preferred term given localisation preferences, but the search index, for convenience, cached a preferred term at the time of index creation. Instead, v1.3 series caches all preferred terms so that search can return locale-specific results without requiring further round-trips.
• Remove --locale as an option during index creation given now unnecessary
• Add options :accept-language :language-refset-ids to core search API

[1.2.1244] - 2023-07-07

• Add language preferences to synonyms in core (Clojure), graph (Pathom) and Java APIs
• For graph API, expect service to be under key :com.eldrix/hermes in environment

[1.2.1218] - 2023-06-26

• Fix build of library jar

[1.2.1214] - 2023-06-25

• Unmerge Java source files and resume using hermes-api as an internal dependency
• Upgrade dependencies, include Lucene 9.7.0 and Pedestal 0.6.0, with performance benefits, particularly on modern Java.

[1.2.1208] - 2023-06-03

• Explicitly define Java 11 as the compilation target for Java source code files, as otherwise whatever is installed on build server is used.

[1.2.1204] - 2023-05-29

• Add expand-ecl* to core API for human-readable results optimising fetch of preferred synonym for each result (and add expandEclPreferred for Java API clients)
• Merge Java API wrapper ('hermes-api') into the main source repository
• Add build steps to compile Java source code as part of 'prep-lib' and build of jar/uberjar artefacts thus deprecating code in https://github.com/wardle/hermes-api. That repository will now be archived.

[1.2.1190] - 2023-05-18

• Add search-concept-ids to facilitate pre-populating search results in pick lists
• When streaming concepts from store, abort if channel is closed rather than continuing to send to a closed channel
• Better reporting of errors when installing directly from MLDS

[1.2.1172] - 2023-05-02

• Make mrcm-domains public in library API
• Add /v1/snomed/mrcm-domains to HTTP API
• More uniform error reporting when parsing SNOMED ECL
• More comprehensive unit testing for SNOMED ECL
• Update instructions for use under different architectures and operating systems

[1.2.1150] - 2023-04-23

• HTTP 404 for concept/properties if concept not found, rather than HTTP 200 response with empty data
• Upgrade to latest version of trud

[1.2.1142] - 2023-04-18

• Make properties public in top-level library API
• Add match-locale to top-level library API for when consumers need to parse the same language preferences for a number of separate calls
• Add /v1/snomed/concepts/:concept-id/properties endpoint to HTTP API with configuration options for pretty printing for human users, and expand for machine users
• Improve handling of invalid parameters in HTTP API
• Improve documentation, including links to live examples

[1.2.1115] - 2023-04-15

• Return HTTP 200 and empty collection instead of HTTP 404 when search gives no results
• Add trace logging for all HTTP requests although default configuration logs only at the INFO level. This means this can be configured at deployment.
• Add concrete values to 'status' and 'statistics' reports

[1.2.1108] - 2023-04-13

• Avoid HTTP 500 errors for bad client input in HTTP server.
• More consistent responses for HTTP server (result vs. empty result vs. not found).
• Automated testing of HTTP server responses

[1.2.1102] - 2023-04-12

• Show progress reporting when downloading from the UK's 'TRUD'
• Avoid unnecessary network calls for distribution metadata
• Fix import of concrete values when updating in place
• Add valid-ecl? and isValidEcl() to top-level Clojure and Java APIs respectively.

[1.2.1088] - 2023-04-07

• Add support for the MLDS (Member Licensing and Distribution Service) for automated downloads and install of a number of distributions across the World.

[1.2.1080] - 2023-04-06

• Add support for the MRCM (Machine Readable Concept Model)
• Use MRCM to return concept properties according to cardinality rules

[1.2.1060] - 2023-04-04

• Add support for concrete values for store, indexing and search
• Improve server error handling and reporting
• Improve cardinality queries in ECL parsing/expansion
• Improve wildcard attribute search

[1.2.1040] - 2023-04-03

• Improve cardinality constraints during ECL processing

[1.2.1032] - 2023-04-01

• Optimise handling wildcard value for attribute in an ECL refinement; the prior implementation had no special handling for this, and so expanded the value to all concepts, impacting performance.
• Fix handling of cardinality in expressions with a minimum of '0' (e.g. [0..1] or [0..0]).

[1.2.1026] - 2023-03-29

• Significant but backwards-compatible change in top-level API with improved, and shortened function names (e.g. concept rather than get-concept for Clojure-based library clients)
• Miscellaneous code style and performance improvements
• Internal (private) API changes
• Improve tests
• More deterministic derivation of 'replace by' in graph API.
• Remove unnecessary dependencies when building uberjar, improving start-up performance

[1.1.1000] - 2023-03-23

• Update to version 1.1 series given drop in support for Lucene 8.x series and therefore Java 1.8
• Upgrade dependencies (e.g. netty-buffer 4.1.90)
• Add ability to stream search results asynchronously
• Miscellaneous performance improvements
• Miscellaneous code style improvements

[1.0.960] - 2023-02-15

• Drop support for Lucene 8.x series and therefore Java 1.8 (latter out of support from 31 March 2022, and Lucene 9.x requires at least Java 11).
• Improve Java API
• Add ability to stream all concepts to top level API
• Use new Lucene 9.5 'storedFields' in favour of deprecated document field access
• Add new benchmark test suite
• Optimisations

[1.0.946] - 2023-02-06

• Add thin wrapper API for use by Java and other JVM languages when used as a library
• Upgrade internal dependencies (Lucene 9.5, lmdbjava 0.8.3)

[1.0.938] - 2023-01-31

• Add support to give multiple commands in one invocation via command-line interface
• Improve speed of import through tweaking memory map synchronisation
• Improve speed of indexing through more efficient calculation of transitive closure tables for relationships

[1.0.914] - 2023-01-23

• Improve speed and efficiency of import. Use a single thread for LMDB writes.
• Improve error handling (e.g. for automated install of distributions when a national distribution site is offline) and messages (e.g. when a database is not found on filesystem).

[1.0.895] - 2023-01-15

• Significant update to command-line operation, while maintaining backwards-compatibility
• Status reports now record count data in a nested map with a choice of formatting in the CLI.

[1.0.875] - 2023-01-07

• Fix and speed-up `get-refset-members'
• More complete unit testing
• Add support for module dependency reference set items
• Flag any module dependency problems on indexing and serve
• Report size of search indices in status report
• Use language preferences for fully specified name

[1.0.822] - 2022-12-24

• Enable native support for Apple Silicon, rather than needing to use an x86-64 JDK. (To add native aarm64 support, you will need to manually build lmdb binary - see README).
• Log detailed system information on server startup, including architecture.

[1.0.815] - 2022-12-22

• Upgrade to netty-buffer 4.1.86
• Improve namespace stratification by factoring out common Lucene functions shared by the two indices (descriptions and refset members).
• Move ECL and CG implementations into com.eldrix.hermes.impl as they contain no public-facing API.
• Explicitly use an opaque handle for core API to represent encapsulated runtime state. The prior public but undocumented Service is now deprecated in favour of a private Svc with hermes/open returning Closeable.

[1.0.804] - 2022-11-27

• Upgrade to Lucene 9.4.2 (and Lucene 8.11.2 when Java 8 compatibility required)
• Improve namespace layering structure by ensuring graph API only uses top-level APIs

[1.0.792] - 2022-11-14

• Add get-description and get-relationship to top-level 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 get-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 identifier.
• 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)