Snow Owl v8.5.1

Bugs/Improvements

• [index] properly catch and report bulk indexing failures during index commit (e93433c)
• [api] support field selection in SNOMED CT Concept expansions (661c774)
• [api] add update and delete resource REST API endpoints (b79a13c)
• [api] reduce execution time of bulk suggest requests by performing a single authorization check at the beginning (f507964)
• [api] support other resource URIs not just Code Systems in suggest API (64c5559)
• [docs] update rapidoc to latest 9.3.3 version (2dce6a6)
• [docs] minor changes to the Suggest API OpenAPI definition (f550166)
• [log] include auth/authz related execution time in request response metrics (1654004)

Snow Owl v8.5.0

Core

• Introducing the new Code System Concept Suggest API (#1049, 5aad00c)
  • Based on lexical and/or semantic information concepts can be retrieved for a given set of like and unlike texts or queries
  • Supports pluggable suggester implementations, currently available open-source suggesters are:
    • term suggester - based on the most frequent tokens in the given like/unlike corpus the implementation suggests concepts based on their terms using default Elasticsearch full-text queries (synonym support, ignore stopwords, fuzziness, min occurrence count configuration settings are available)
    • mlt suggester - based on the given most frequent tokens in the like/unlike corpus the implementation suggests concepts based on their terms using Elasticsearch More Like This query (MLT specific configuration values are available, works best for large number of like texts)
  • Add batchSize and batchSizeTimeout configuration parameters to POST /suggest/bulk API (05ae0ec)
• Support filtering resources by their settings key-value pairs (#1048, #1050)
• Support Elasticsearch 8 clusters and features via a dedicated high-level client (#1047)

Bugs/Improvements

• [docker] improve docker example (#1044)
• [index] add support for more-like-this Elasticsearch queries (#1049)
• [index] add support for knn Elasticsearch queries (#1049)
• [index] fix decimal value conversion issue (#1039)
• [index] allow configuration of number_of_shards and number_of_replicas in custom index specific configurations
• [index] ensure that local settings get updated even if there are no remote ES settings to update (5a8d165)
• [index] eliminate deprecation warning messages due to deprecated ignore_throttled query parameter in newer Elasticsearch versions (#1053)
• [index] increase default bulkActionSizeInMb setting value to 50 (da69def)
• [index] maintain order when merging term filters into a single filter array to ensure that the query is properly cached when requested (df0c594)
• [core] load only the default field selection in updatedAtCommit() expansion (baaf59a)
• [fhir] fix FHIR date parsing and formatting issue when timezone offset is specified (8e946e8)
• [api] support active and version parameters in content() expand in Resources API (0068a66)
• [core] allow querying draft resources with the special LATEST path using their current working branch (aka HEAD) (fa5898d)
• [core] add support for ECL query definition inside ResourceURI instances with the ?ecl= query part (1ded832, 79d112a)

Dependencies/Packaging

• Upgrade Jackson libraries to 2.12.7
• Upgrade Apache HTTP Core to 4.4.12
• Upgrade Apache HTTP Client to 4.5.10

Snow Owl v8.4.0

Core

• Introduce configurable authorization service (#1020, #1026)
  • External authorization systems can now be configured to provide list of accessible resource IDs and/or check whether a certain permission is present for a user or not
  • The default implementation performs the same evaluation as before based on either the incoming JWT's permissions claim or using information provided by the underlying identity provider
• Introduce a new GET /toolings endpoint (#1023)
  • Lists all supported tooling (aka schema) values from the current deployment
• Support querying resources by their url value (#1027)
• Support settings metadata on Bundle resource types (#1034)

FHIR

• Accept wider range of FHIR inputs based on official R4 and third-party CodeSystem sources (#1017)
  • Support SUPPLEMENT content mode
  • Support code extension type
  • Make div validator more lenient and accept opening tag without attributes
  • Support all FHIR-approved date formats in dateTime properties
  • Support FHIR contact property (1247e96)

Bugs/Improvements

• [index] fix incorrectly reduced "must" and "filter" clauses causing invalid search results in certain queries (#1015)
• [index] restrict the number of prefix values and prefix clauses that can be present in a request (eb6df3b)
• [transport] enable eventbus call stack tracing (#1021)
• [core] fix serialization of User object (#1022)
• [core] prevent creating resources with the reserved -1 identifier (#1036)
• [api] support X-Author header in Versioning API (#1018)
• [api] support X-Author header in RF2 Import API (#1031)
• [api] support X-Author header in FHIR CodeSystem API (#1031)
• [api] support filtering resources by owner field in Resources API (#1035)
• [api] respond with HTTP 401 properly when trying to authenticate with a Snow Owl without any identity provider configured (7f16e9f)
• [fhir] fix potential NPE during lookup property validation (#1019)
• [cli] allow commands to be executed when no JWT signing is configured (b0e81e8)
• [classification] add missing resourcePath parameter to classification jobs (#1025)
• [snomed] fix incorrect RF2 export component type when exporting refsets (#1028)

Dependencies/Packaging

• Upgrade snomed-ecl to 2.0.4 (76c464b)
• Upgrade bundled JDK to 17.0.3 (#1016)

Snow Owl v8.3.0

Core

• Secure connections are now by default enabled when using TCP connections to connect to the terminology server (#993, #1012)
  • New configuration values are available to configure SSL certificate (or let the server use a self-signed/generated certificate by default)
• Support Elasticsearch 8 via API compatibility mode (#1008)
  • Support running Elasticsearch in testcontainers
• Support externally customizable index type mappings via repository.index.<indexName>.mappings configuration key (#1010)
• Move ECL labeler API to core (#1009)

SNOMED CT

• Add batchSize configuration parameter to SNOMED CT RF2 import API (4109687)

Bugs/Improvements

• [index] backoff a bit when sending too much bulk requests to the connected Elasticsearch cluster on rejection errors, eg. high queue size (be85e38)
• [core] make toolingId/branch reflective access support a timestamp suffix (6df066f)
• [core] check bundleId before executing resource type specific logic (like automatic branch generation) to prevent creation of the corresponding branch as a side effect of an erroneous code system create request (c191ba3)
• [core] fetch extensionOf branch state from the code system's repository, not the one available from the context. The latter only stores resource metadata and no branches outside MAIN exist in it. (0d581a3)
• [core] add a generic implementation of ECL to use in other Code Systems and toolings when required (c5daa92, 76e353d, e6dbf9e)
• [snomed] do not kick off a concept map search in the SNOMED CT tooling if source tooling ID filtering is enabled, and snomed is not within the allowed list of tooling IDs. (b30d38d)
• [snomed] honor index.maxTermsCount when sending large queries to Elasticsearch during RF2 import (4a46daa)
• [snomed] reduce load of existing data from external Elasticsearch clusters when importing RF2 releases (cca6f87)
• [snomed] various performance optimizations when sending SNOMED CT commit requests sent to Elasticsearch (f52991a, 62101d6, 26d4a45)
• [suggest] avoid NPE when suggestion base concept does not have alternative terms (0364e6a)

Dependencies

• Bump Elasticsearch to 7.17.2 (87b4a22)
• Bump Spring to 5.3.19 (bfd162b)
• Add SQL, JSR223 (script engine) and date utility modules to Groovy wrapper (062cade, 8eb9486)

Snow Owl v8.2.1

Bugs/Improvements

• [core] reject versioning requests using reserved branch names (#1004)
• [core] make sure retired resources cannot be versioned or changed (#1007)

Dependencies

• Bump h2 dependency to 2.1.210

Snow Owl v8.2.0

Core

• Add new Base62 encoded UUID generator (93c1711)
  • Replace all uses of Base64 encoded UUID with Base62 encoded UUIDs (f345312)

SNOMED CT

• Support ECL 2.0 expressions to be parsed and evaluated, see official spec here (#997)
  • Support multi-valued string evaluation in concrete values
  • Support != operator in active and moduleId property filters
  • Support active/moduleId/effectiveTime property filters with member domain
  • Support member field property filters
  • Support history supplements
  • Selecting refsetFieldNames in memberOf expression is unsupported (anything that is not the referencedComponentId at the moment)
  • Support ignoring ECL specific validation warnings/errors when parsing expressions

Bugs/Improvements

• [core] add guards to prevent wrapping single collection values again in another collection in HashMapOptions (3acf6ec)
• [ecl] fix case when AND expression constraint has a single ID only (50e943d)
• [api] add support for explicit referencedComponentId filtering in SNOMED CT Member API prop filter (e10fff0)
• [api] properly set default values in resource create API even if properties exist with null values in the incoming JSON body (1dd0a54)
• [scripts] wrap groovy 3.0.9 jars into a bundle to avoid dependency issues in third party plug-ins (a3a5bd6)

Dependencies

• Bump snomed-ecl to 2.0.3
• Add uuid-creator 4.6.1

Snow Owl v8.1.1

Bugs/Improvements

• [packaging] add missing --add-opens JVM options (c3e57b0)
• [packaging] remove trailing whitespace from startup script (6a5a35a)
• [log] append user.sub information in each request log entry (92ccd7f)

Snow Owl v8.1.0

Breaking changes

The following changes in Snow Owl 8.1 might affect your applications and prevent them from operating normally. Before upgrading to 8.1, review these changes and take the described steps to mitigate the impact.

Java 17

Snow Owl 8.1 brings complete Java 17 support, both compile and runtime. This mostly affects users who manually install Snow Owl or use a development environment to develop plug-ins for it. Starting from 8.1.0, all Snow Owl release include the latest patch version of Eclipse Temurin JDK, which increases the package size slightly, but installation/deployment is simpler. See PR #963 for details.

Core

• Support retrieval of historical state for resources (#990)
• Support resourcePathSegments property and resourcePathLabels expansion on resources. This allows clients to get information about the placement of the resource in the bundle tree. (#961)
• Support expansion of commits() in Resource API (#966)
• Improved resource history information
  • Expose createdAt resource property (6a5a651)
  • Support expansion of updatedAtCommit in resource objects (e6c3edf)
  • Properly track createdAt and updatedAt values for Resource and Version documents (8d2d991)
• Support proper API doc navigation via query parameters (#980)
• Support pluggable resource expansion for third party plug-ins and features (#967)

SNOMED CT

Security

• OAuth 2.0 authorization token features (#937):
  • Support HS256, RS256 and RS512 algorithms (verification all, signing only HS256 and the existing HS512).
  • Support external JWKS URL for token verification
  • Support configuration of email and permissions JWT token claims to allow OIDC conformant JWT token verification. (claims have their own namespace, like https://example.com/email, https://example.com/permissions). Legacy token handling is still the default, where the email property is stored in the sub claim, while the permission list is stored in the permissions claim.
  • Support PKCS#8 signing and verification keys
  • Disable JWT token signing/verification if identity.jws is not configured.

Bugs/Improvements

• [index] optimize bool index queries as much as possible to prevent HTTP 400 errors because of deep nested queries (configurable in Elasticsearch via indices.query.bool.max_nested_depth) (#976)
• [index] filter out hidden indices to prevent issues when checking cluster health status (#958)
• [index] fix incorrectly detected read-only state when .index.blocks.read_only_allow_delete setting is set (3d829aa)
• [index] add support for immediate (partial) updates via scripts (#989)
• [monitor] add cluster health diagnosis message to cluster health errors (f1bc20c)
• [core] connect id filter in GET /versions endpoint (43c7992)
• [core] carry over parentage data to generic Concept model (#950)
• [core] make sure we track scores when filtering resources by title (299258a)
• [core] filter commit messages by the current user's permission list (#984)
• [core] include resource title in default delete commit message
• [core] add generic taxonomy change processor that calculates a transitive closure graph on each commit based on the changes (#981)
• [auth] prevent access to resources when permissions claim is empty for the current user or in the given JWT accessToken (#971)
• [fhir] allow filtering fhir resources by url in the id filter (01a6885)
• [fhir] make sure fields configured via _summary are returned even if user explicitly specifies additional fields via _elements (e75623e)
• [fhir] allow returning map targets for any target code systems (e14af6f)
• [fhir] support datetime type in concept properties (fd56483)
• [fhir] validate system URL against version given in subsumption requests (#982)
• [fhir] add abstractions that allow third party developers to implement FHIR Create/Update/Delete support (#968)
• [snomed] fixed an issue when getting namespace from concept with at least two different FSNs (translations) (e215814)
• [snomed] defer loading of expanded additional data to dedupe requests going to Elasticsearch and reduce load on both the ES cluster and the termserver (#948)
• [snomed] add missing expand and field selector to relationship GET by ID endpoint (#949)
• [security] mitigate CVE-2021-44228 vulnerability (a8127da)
• [security] mitigate CVE-2021-42550 vulnerability (69b710d)

Packaging

• Update bundled JDK to 17.0.2

Dependencies

• Bump Elasticsearch to 7.17.1
• Bump Groovy to 3.0.9
• Bump Xtend and Xtext to 2.25.0
• Bump MWE to 2.12.1
• Bump rapidoc to 9.2.0
• Bump typetools to 0.6.3
• Bump mockito to 3.11.2
• Bump jacoco to 0.8.7
• Bump rest-assured to 4.3.0
• Bump Tycho to 2.6.0

Snow Owl v8.0.0

Snow Owl's biggest release yet comes with fully customizable resource model and complete resource management functionality; the fastest RF2 importer and exporter in the world; externally configurable per resource access management; latest Expression Constraint Language 1.6 features and many many more.

Breaking changes

The following changes in Snow Owl 8.0 might affect your applications and prevent them from operating normally. Before upgrading to 8.0, review these changes and take the described steps to mitigate the impact.

RF2 index format changes

To support sorting, filtering and field selection on the official SNOMED CT RF2 property names, Snow Owl 8 comes with an updated index representation where each and every SNOMED CT component index has correct, officially supported RF2 column names. Migrating from Snow Owl 7.x to 8.0 requires a full re-import of all terminology resource content.

API routing changes

Snow Owl 8 changes the old /admin and /snomed-ct/v3 Core and SNOMED CT REST API base path segments to /core and /snomedct, respectively. Make sure you update your REST API clients when you start your migration process to the new version. See PR #893 for more details.

Update endpoint changes

Some of the old SNOMED CT Component endpoints were using a POST /:componentType/updates style instead of PUT /componentType. Snow Owl 8 migrated all API endpoints using the former pattern to the new one. Make sure you update your REST API clients to the new pattern, if you have used any of the SNOMED CT component update API endpoints. For more details, please see PR #866.

Configuration changes

• Snow Owl does not support node-level configuration of certain SNOMED CT specific settings. These all have been moved to Code System resource specific configuration keys and can be configured for each SNOMED CT specific Code System separately (eg. for each Extension). The affected configuration settings are:
  • RF2 Export API configuration settings (#842)
  • Language alias configuration (snomed.languages) (#869)
  • Other options, such as defaultReasonerId, defaultQueryTypeRefsetId, etc.

Removed custom MRCM model

To support variety of use cases and easier adoption of SNOMED CT MRCM constraints, Snow Owl from version 8 fully supports not just MRCM member access and authoring, but evaluation of official and custom (maintained by NRCs and Extensions) MRCM constraints in the fastest way possible. The old custom MRCM model and all related API functionality has been removed in favor of the official MRCM tooling. See PRs #917 and #930 for more details.

Removed scroll based paging

Scroll API in Elasticsearch has been marked as deprecated until complete removal in the upcoming Elasticsearch 8.0 release. Thus, Snow Owl is no longer offering low-level Java and index APIs to access the terminology content via scroll contexts. For more information see PR #903.

Core

• Introducing Resource Management (#821, #886)
  • Any type of resources (when the appropriate model and API is available, plug-ins can provide their own specific models if they so desire)
  • Supported resources are Code System, Bundle (and other resources such as Value Sets and Concept Maps are available in pro versions)
  • Full REST API support to access (get, search), author (create, update, delete) and maintain (versioning, configuration, history) resources
• New Core API features:
  • New concept suggest API (#878, #882, #884, #921)
  • Field selection support (#858)
    • Restricting the number of returned fields of a representation to a set of properties is now possible on read endpoints (e.g GET /snomedct/SNOMEDCT-UK-CL/concepts?field=id)
    • By default the system will always return all properties with a non-null value, but this can be altered using the field query parameter.
  • Support includeNull query parameter to allow API consumers to select whether they would like to get all properties (with any value, including null) or just the non-null ones (default setting) (#857)
  • Support pretty query parameter to pretty print the JSON output to make it human-readable (#857)
  • Support multi-value expand parameters on all search/get endpoints (#855, fixes #659)
  • Support filtering versions by createdAt and version (#874, cdae9ac)
  • Support Forwarded headers on incoming HTTP requests when needed (cc7c544)
  • Support deletion of Code Systems via DELETE /codesystems/:id (d416c1e)
  • Use yyyy-MM-dd effective time format when creating new versions (27e34ab)
  • Increase branch path segment max length to 100 characters from the previous 50 characters (2fe892e)
• New Index features:
  • Reduce the default number_of_shards to one as Elasticsearch offers the same default, number_of_replicas still defaults to 0 to support initial loading scenarios better (fdd10ce, 6b1d462)
  • Allow fully customizable indices settings in snowowl.yml configuration file via repository.index.[indexName] configuration objects (#929)
  • Customizable word equivalence (aka synonym) filtering (#863)
    • An SO_HOME/configuration/analysis/synonym.txt file can be configured to allow Snow Owl to use the defined set of synonym rules when performing full-text searches. In case of remote Elasticsearch cluster, it is required to deploy the synonyms.txt on all cluster nodes
  • Support index-level search request caching (#931)
    • Any kind of search can be cached and retrieved faster than ever before. Plug-in maintainers and new tool developers can configure their preference of how and when they'd like to cache the results of a search request. By default Snow Owl will cache all search requests that are executed on versioned state.
  • Support numeric script sorting in index searches (8e51c6b)
• Deprecated branch review API endpoints and services have been removed (b79c8e1)

SNOMED CT

• New SNOMED CT API features:
  • Support dedicated isActiveMemberOf filter which return concepts that has an active member in any of the given list of refsetIds (#879)
  • Support searching SNOMED CT components by namespaceConceptId not just namespace (#881, #920)
  • Support exporting Snapshot RF2 content at specific times via resourceId@timestamp format, Full and Delta are not supported (#887)
  • Support exporting RF2 content between specific branch path range, like comparing branches (#907)
  • Support nested expansion of inactivationIndicator() properties, like associationTarget(), referenceSet() (#914)
  • Support sorting when expanding descriptions(), relationships(), inboundRelationships() on Concept API (7e2516a)
  • Expose memberOf and activeMemberOf components document fields on component domain representations (5928462)
  • Support component type (concept, description, relationships, member) based filtering on RF2 export endpoint (c8662e4)
  • Support multi-value query parameters on a lot of filter query parameters (5e5fc2a)
  • Support module, active and effectiveTime filters on GET /refsets endpoint (5e5fc2a)
• RF2 import improvements (#918)
  • Support smart auto-generation of delta content when importing Full releases (the existing component-based effective time based filtering is still there, but this makes the import much faster and easier to understand)
  • Support importUntil effective time property to import only a portion from an RF2 release
  • Disallow importing RF2 releases with createVersions enabled when the target branch is a CodeSystem's main development branch and it has unpublished changes
  • Automatically configure known language dialect aliases after successful RF2 import (#876)
• Consolidate RF2 property names on index documents to allow sorting, filtering on them using official RF2 column names (#856)
• Update ECL to 1.6 features (#837, #915)
  • The Query Language Draft implementation has been removed and extra unofficial features of it have been merged entirely into the ECL syntax. The SNOMED CT Concept search REST API endpoint's query parameter has also been removed. If you had any query language specific expressions, you might need to migrate them to the new ECL 1.6 syntax which includes all previously supported QL features.
• Deprecated SNOMED CT /imports and /exports endpoints have been removed (82938f6)

Security

• Improved authorization options to allow/restrict access to server resources. Access tokens describe the necessary scopes to give access to certain resources, either by:
  • directly denoting the resource ID in the scope
  • denoting the containing bundle ID in the scope (supports direct and indirect parent bundles)
  • or by allowing access to all resources (*)
• rootDn and rootDnPassword support from ldap security realm configuration have been removed (6483870)

FHIR

• Support CodeSystem, ValueSet and ConceptMap filtering by _id, name, title, system, url, version and other useful FHIR properties that are supported in the underlying resource representation (#909)
• Support for CapabilityStatement and OperationDefinition resources (#899)
• Read-only Bundle API support (#867)
• Experimental Batch API support (#867)
• Revised and improved all existing FHIR API endpoints to resolve all outstanding issues, such as (#416, #426, #435, #494, #561)
• Support after cursor based paging when expanding Value Sets (e9431f9)

Documentation

• Update REST API documentation with generic and SNOMED CT concept specific information (#906) (more will come in future 8.x releases)
• Upgrade REST API documentation to Springdoc and OAS3 (#845)
• Use rapidoc instead of Swagger UI (0948ef4, b78b71d, fix...

Snow Owl v7.17.6

Bugs/Improvements

• [core] fix incorrectly backported duplicate revision fix (#913, f6e3c31)
• [cli] add duplicate revision checker cli tool, see snowowl snomed revision command for details (8d9d1e5)