Releases | Open Source Science

com.eldrix/hermes - v1.4.1474

Improve automated downloads for distributions using MLDS service - 'Member Licensing and Distribution Service'
Add GitHub Actions to test MLDS downloads for International, and Argentinian distributions and exclude some UK specific tests (localisation)

- Clojure
Published by wardle 7 months ago

com.eldrix/hermes - v1.4.1468

- Clojure
Published by wardle 7 months ago

com.eldrix/hermes - v1.4.1464

Add support for 'null' values in reference set fields (custom fields used by some distributions)

- Clojure
Published by wardle 7 months ago

com.eldrix/hermes - v1.4.1463

More lenient import of null/empty string reference set fields
Improved logging to help with automated pipelines and distribution files
Improve search for empty search strings

- Clojure
Published by wardle 7 months ago

com.eldrix/hermes - v1.4.1454

Fix #70 with handling unicode characters in ECL parsing
Fix #72 by forcing ordered choice to reduce ambiguity in parsing member filters
Fix #73 by updating ECL parser with newer 2.2 updates
Fix #75 with handling of unicode characters and normalization (folding) for search within ECL description term filter
Upgrade dependencies including lmdbjava 0.9.1

- Clojure
Published by wardle about 1 year ago

com.eldrix/hermes - v1.4.1433

Fix #69 by improving import of custom reference sets in which there are missing custom field values
Improve build process for uberjar to ensure backwards compatibility with JDK>=11
Update to latest trud library as the NHS TRUD service now supports SHA256 for integrity checks on downloaded files
Add intersect-ecl-fn to improve performance in data pipelines when an ECL expression may be re-used many times

- Clojure
Published by wardle about 1 year ago

com.eldrix/hermes - v1.4.1425

Updated to be compatible with JDK11 as v1.4.1424 was compiled with JDK21 and therefore required >=JDK21. See #69

- Clojure
Published by wardle over 1 year ago

com.eldrix/hermes - v1.4.1424

Improvements to ranked-search
Add support for Lucene 10 for testing and evaluation via a runtime switch (usable when run from source code, not from the released uberjar - a Lucene 10/Java>=21 version can be built or released on request).

- Clojure
Published by wardle over 1 year ago

com.eldrix/hermes - v1.4.1420

Add ranked search
Fix #68 and permit both additional custom query AND a constraint
Upgrade dependencies

- Clojure
Published by wardle over 1 year ago

com.eldrix/hermes - v1.4.1400

Add support for ECL v2.2, including the operators top and bottom

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1388...v1.4.1400

- Clojure
Published by wardle almost 2 years ago

[1.4.1388] - 2024-05-19

Avoid deprecated methods in Lucene 9.10 series (e.g. use CollectorManager and not Collector) - preparing for Lucene 10 release
Upgrade dependencies
Add more comprehensive tests for arbitrarily large descriptions (see #66) to prove Hermes will have no issues if maximum description length increases

What's Changed

Use CollectorManager instead of now deprecated Collector API in search by @wardle in https://github.com/wardle/hermes/pull/65

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1368...v1.4.1388

- Clojure
Published by wardle almost 2 years ago

com.eldrix/hermes - v1.4.1368

Upgrade dependencies - Clojure 1.11.2 and miscellaneous libraries
Improve GitHub actions to run tests after every release automatically

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1362...v1.4.1368

- Clojure
Published by wardle almost 2 years ago

com.eldrix/hermes - v1.4.1351

Upgrade to lmdbjava 0.9.0 - includes embedded lmdb binaries for multiple architectures and operating systems
Upgrade to Apache Lucene 9.9.1

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1346...v1.4.1351

- Clojure
Published by wardle almost 2 years ago

com.eldrix/hermes - v1.4.1362

Fix #64 such that integrity always maintained during updates-in-place and re-indexing
Upgrade to Apache Lucene 9.10.0

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1351...v1.4.1362

- Clojure
Published by wardle almost 2 years ago

com.eldrix/hermes - v1.4.1346

Fix #61 - attribute values defined by a subexpression that returns no results should not result in invalid expression error
Bump to pedestal v0.6.2 - fixes CVE-2023-36478
Fix resolution of relationship modifier in the graph API
Improve documentation and functional specifications

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1320...v1.4.1346

- Clojure
Published by wardle about 2 years ago

com.eldrix/hermes - v1.4.1320

Eclipse Public License v2.0
Include license in build products
Add support for automatically installing the new UK 'monolith' edition

Full Changelog: https://github.com/wardle/hermes/compare/v.1.4.1312...v1.4.1320

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.4.1312

Upgrade to Apache Lucene 9.8
Automatically generate CITATION.cff file for GitHub during build
Generated artifacts such as library jar now include improved metadata (pom.xml) *

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1296...v1.4.1312

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.4.1296

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1292...v1.4.1296

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.4.1292

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1278...v1.4.1292

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.4.1278

#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.

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1275...v1.4.1278

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.4.1275

#58 In case of an aborted compact, delete intermediary files prior to another attempt.

Full Changelog: https://github.com/wardle/hermes/compare/v1.4.1265...v1.4.1275

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.4.1265

Always use normalized search and normalized index

This version breaks compatibility with previously indexed databases. Either re-index or build a new database completely from latest release(s).

Full Changelog: https://github.com/wardle/hermes/compare/v1.3.1262...v1.4.1265

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.3.1262

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.

What's Changed

Term folding by @wardle in https://github.com/wardle/hermes/pull/56

Full Changelog: https://github.com/wardle/hermes/compare/v1.3.1232...v1.3.1262

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.3.1232

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1244...v1.3.1232

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.2.1224

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1218...v1.2.1224

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.2.1214

Java source files are no longer included in the main repository - resume using hermes-api as an internal dependency
Upgraded dependencies, include Lucene 9.7.0 and Pedestal 0.6.0, bringing performance benefits, particularly on modern Java.

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1208...v1.2.1214

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.2.1208

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1204...v1.2.1208

- Clojure
Published by wardle over 2 years ago

com.eldrix/hermes - v1.2.1204

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.

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1190...v1.2.1204

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1190

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1174...v1.2.1190

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1172

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1151...v1.2.1172

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1150

HTTP 404 for concept/properties if concept not found, rather than HTTP 200 response with empty data
Upgrade to latest version of trud (fixing automatic downloads stalling when used without progress printing)

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1142...v1.2.1150

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1142

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1115...v1.2.1142

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1115

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1108...v1.2.1115

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1108

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1102...v1.2.1108

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1102

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.

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1088...v1.2.1102

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1088

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

This uses a similar process to that already used for the UK release centre (TRUD), but I do not have permission to download distributions outside of the UK in order to fully test the whole process, either in automated tests, or manually. If there are issues, then please raise an issue and it is likely to be quite easy to fix.

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1080...v1.2.1088

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1080

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1060...v1.2.1080

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1060

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

This version does make a change to the backend file-based database. When this version is used against an older version of the database, a warning will be logged as that database will not support provided concrete value results. Any new databases created by this version of hermes will include concrete value support, but older versions of Hermes will ignore those indices. As such, this does not need to be regarded as a breaking change.

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1040...v1.2.1060

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1040

Improvements to cardinality constraints during ECL processing

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1032...v1.2.1040

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1032

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]).

Full Changelog: https://github.com/wardle/hermes/compare/v1.2.1026...v1.2.1032

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.2.1026

Backwards-compatible changes to core Clojure API with shortened function names (removal of redundant get- prefix)
Miscellaneous optimisations/speed-ups, including in building queries for ECL expansion
Internal (private API) changes
Improved, and more complete tests
More deterministic derivation of 'replaced by' relationship in the graph API
Remove unused dependencies from uberjar, speeding up startup

Full Changelog: https://github.com/wardle/hermes/compare/v1.1.1000...v1.2.1026

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.1.1000

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

Full Changelog: https://github.com/wardle/hermes/compare/v1.0.960...v1.1.1000

- Clojure
Published by wardle almost 3 years ago

com.eldrix/hermes - v1.0.960

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

- Clojure
Published by wardle about 3 years ago

com.eldrix/hermes - v1.0.938

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

- Clojure
Published by wardle about 3 years ago

com.eldrix/hermes - v1.0.921

Full Changelog: https://github.com/wardle/hermes/compare/v1.0.914...v1.0.921

- Clojure
Published by wardle about 3 years ago

com.eldrix/hermes - v1.0.914

- Clojure
Published by wardle about 3 years ago

com.eldrix/hermes - v1.0.910

This release has mainly internal changes compared to prior release. The only user-facing change is exposing status* as part of core API.

- Clojure
Published by wardle about 3 years ago

com.eldrix/hermes - v1.0.895

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.

Full Changelog: https://github.com/wardle/hermes/compare/v1.0.875...v1.0.895

- Clojure
Published by wardle about 3 years ago

com.eldrix/hermes - v1.0.875

- Clojure
Published by wardle about 3 years ago

com.eldrix/hermes - v1.0.822

Add native support for Apple Silicon, rather than needing to use an x86-64 JDK. Native aarm64 support currently dependent on manually building lmdb binary - see README.
Log detailed system information on server startup, including architecture.

Full Changelog: https://github.com/wardle/hermes/compare/v1.0.815...v1.0.822

- Clojure
Published by wardle about 3 years ago

com.eldrix/hermes - v1.0.815

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.

Full Changelog: https://github.com/wardle/hermes/compare/v1.0.804...v1.0.815

- Clojure
Published by wardle about 3 years ago