Snow Owl v8.6.0

Core

• Support negated filter values in owner and status filters in Resource API (006e44b, d9a0bb1)
• Support snomedFirst sort keyword in Resource API to display SNOMED CT resources before any other (#1061)

SNOMED CT

• Support ECL specification 2.1 (#1060)
• Support SNOMED CT Simple map to concept reference set types (#1043)
  • Complete read/write/export/import support for the new SNOMED CT Simple map to concept reference set

FHIR

• Support importing FHIR resources from FHIR JSON format (#1058)

Packaging

• Use Ubuntu 22.04 as base image instead of obsolete CentOS (#1052)

Bugs/Improvements

• [core] ecl labeling should handle Code System URI values (1103222)
• [ecl] throw HTTP 400 instead of HTTP 501 when encountering a not implemented ECL feature (6e2b411)
• [snomed] support knn vector search for SNOMED CT description documents (6cbe08f, 05fa3e8, f3ed8f7)
• [snomed] prevent NPE during computation of concept expand cache in SNOMED CT Concept API (cb2befe)
• [snomed] improve performance of query reference set evaluation (3de012a, 880e7e8)
• [snomed] improve performance of ECL query optimizer (670d8f0)
• [snomed] ensure that ECL query optimizer generates ECL expressions with FSN labels (d11fd38)
• [api] ensure that bulk suggest API responds even if one of the bulk item requests fails (f199e7c)

Snow Owl v8.5.2

Bugs/Improvements

• [api] fetch hit count only in resource update requests (9165d40)
• [api] add OID filter to GET /resources endpoint (f32391a)

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