Change Log

Fixed

• Fixed $validate-code bug where inferSystem was used with case-insensitive CodeSystems

Security

• The following CVE has been withdrawn
  • CVE-2024-31033

Fixed

• Fixed bugs with actuator endpoints including health when operating in secure mode
• Removed bogus warnings about an “Unsupported authentication class”

Security

• Updated library versions to mitigate CVEs:
  • CVE-2016-1000027
  • CVE-2024-22257
  • CVE-2024-22259
  • CVE-2024-24549
  • CVE-2023-52428
• Known CVEs:
  • CVE-2024-31033 (disputed, medium severity)

Changed

• The ontoserver.search.summary configuration parameter can be used to control whether search requests default to summary or complete resources.
• Cached internal syndication feed entries for significant performance improvement

Fixed

• Avoid considering CodeSystems with content = example / missing for operations like $lookup, $subsumes, and validation
• Work around possible case of missing id in persisted JSON blobs

Security

• Removed unused h2 jar to resolve warnings regarding CVE-2022-45868
• Updated library versions to mitigate CVEs:
  • CVE-2024-25710
  • CVE-2024-26308
  • CVE-2024-1597
  • CVE-2024-22243

Changed

• Added support for the content-mode search parameter on CodeSystem
• Added support for context, context-type and context-type-value search parameters for CodeSystem, ConceptMap, NamingSystem, StructureDefinition and ValueSet resources
• Broadened support for filter operators on some of the FHIR specification's Defined Concept Properties

Fixed

• Fix bug affecting identifier:missing queries
• Improved some validation messages for post-coordinated expressions
• Fixed bug where failures to fetch a Syndication feed were cached indefinitely
• Fixed performance issues with SEARCH and the reference parameter. e.g., [base]/ValueSet?reference=http://loinc.org
• Fixed bug where certain incorrect SNOMED CT versions were allowed in a ValueSet definition
• Fixed bug where ValueSet-specified display text would be ignored when SNOMED CT Editions were used in a ValueSet definition
• Improved handling of an invalid displayLangauge parameter
• Fix bug with regex and case-insensitive code systems
• Fix bugs affecting _id search parameters
• Fix bug where SNOMED designations with use display could have incorrect language

Fixed

• Fixed bug with pre-existing LOINC indexes and case-sensitivity

Security

• Updated library versions to mitigate CVEs:
  • None

Changed

• Add support for delete-history interactions (e.g., DELETE {Resource}/{id}/_history) from R6
• Improved support for case-insensitive CodeSystems. This includes an index format change for FHIR CodeSystems (migration is performed automatically)

Fixed

• Fixed resolution of implicit ValueSets for CodeSystems provided via the tx-resource parameter.
• Fixed bug processing CodeSystems without an id provided via the tx-resource parameter.
• Fixed bug handling a valid coding in CodeableConcept that is not also in the ValueSet.

Fixed

• Fixed regression with $expand, the property parameter, and implicit SNOMED reference sets.

Security

False positives:

• CVE-2024-22233 affects specific Spring Boot 3 versions. Ontoserver currently uses Spring Boot 2. The CVE explicitly states these older versions are not affected.

• Updated library versions to mitigate CVEs:

  • CVE-2023-5072
  • CVE-2024-20918
  • CVE-2024-20932
  • CVE-2024-20952
  • CVE-2024-20919
  • CVE-2024-20921
  • CVE-2024-20926
  • CVE-2024-20945
  • CVE-2024-20955
  • CVE-2023-33201

Fixed

• Add support for caseInsensitive CodeSystem in $validate-code
• Fixed healthcheck.sh -l semantics to only look at startup preload, and add -L to look for any preload (eg including redoPreload)
• Fixed bug where failing HEAD requests on syndication feeds would not trigger authorisation token renewal
• Fixed bug where SNOMED FSN's were mis-characterised during validation

Changed

• Tolerate CodeSystems that attempt to re-define the URIs for standard properties like parent and child.

Fixed

• Fixed ValueSet resolution bug where tx-resource supplied ValueSets could conflict with persisted ValueSets.
• Work around Infinispan change that affects Search results when running in a scaled deployment mode.

Security

• Updated library versions to mitigate CVEs:
  • CVE-2023-6378
  • CVE-2023-6481
  • CVE-2023-46589

Changed

• Improved handling and validation of default CodeSystem properties like status
• Enabled R5 support for the $convert operation
• Added support for contained CodeSystems. For example, a ValueSet may contain a CodeSystem (or supplements) that are then used in operations on the ValueSet.
• Added support for the useSupplement parameter, pre-adopted from R5.
• Added support for ValueSet.expansion.property (via Extensions) pre-adopted from R5.
• Added support for various SDC extensions:
  • http://hl7.org/fhir/StructureDefinition/codesystem-conceptOrder
  • http://hl7.org/fhir/StructureDefinition/codesystem-label
  • http://hl7.org/fhir/StructureDefinition/itemWeight
  • http://hl7.org/fhir/StructureDefinition/rendering-style
  • http://hl7.org/fhir/StructureDefinition/rendering-xhtml
  • http://hl7.org/fhir/StructureDefinition/valueset-concept-definition
  • http://hl7.org/fhir/StructureDefinition/valueset-deprecated
  • http://hl7.org/fhir/StructureDefinition/valueset-label
  • http://hl7.org/fhir/StructureDefinition/valueset-conceptOrder
• MANY additional changes to support using Ontoserver with the FHIR Validator or IG Publisher as described here and to align with the tx tests in https://github.com/FHIR/fhir-test-cases
  • Improved consistency and detail in $validate-code messages
  • Additional machine-readable output for $validate-code
  • Eliminated redundant designations for use="display" translations
  • …
• Added support for the Extension http://hl7.org/fhir/tools/StructureDefinion/valueset-expansion-param
• Added spell-correction support to ValueSet/$expand?filter=...
• Added the atom.syndication.republishUpstreamFeeds configuration parameter, which specifies the upstream feeds whose entries should be republished.
• Added support for prometheus endpoint (disabled and not exposed by default) at /actuator/prometheus.
• Exclude CodeSystems with content=example or content=not-present from use with $validate-code.

Fixed

• Improved consistency in CodeSystem version resolution within a ValueSet.compose when performing an $expand or $validate-code.
• Fixed bug with ECL cardinality constraints on role-grouped attributes.
• Fixed bug in PATCH interactions that used delete with where conditions
• Improved consistency in CodeSystem version resolution within a ValueSet.compose when performing an $expand or $validate-code.
• Fixed bug with ECL cardinality constraints on role-grouped attributes.
• Fixed bug with ECL cardinality constraints of the form [0..n] not matching concepts with no (non-IS A) relationships.

Changed

• Added caching for TerminologyCapabilites to improve performance for large sets of CodeSystems.
• Added support for SNOMED International's new Edition dependency element in a syndication feed.
• Optional support ValueSet.identifier matching when resolving ValueSet uri in $expand.
• Allow for inactive concepts to have an inactive FSN.

Fixed

• Fixed bug resolving appropriate CodeSystem version for the LOINC all-codes implicit ValueSet.
• Fixed bug storing compressed JSON form of very large resources.

Security

• Updated library versions to mitigate CVEs:
• CVE-2023-38286

Fixed

• Fixed bug where certain hash collisions could cause incorrect $expand, $validate-code, or $validate behaviour. This was extremely rare except in cases where two ValueSet compose clauses differed in only a single concept from a very large CodeSystem.
• SNOMED Binary Index format changed to 2.0.10; Fixed bug with handling of ECL wildcard and regular expression term matches containing whitespace.
• Fixed bug where ValueSet.expansion.offset was not being set when paging.
• Cleaned up unused default Spring Boot user management.

Changed

• NCTS Composed ValueSet profile updated to 4.1.0 (relaxes cardinality of ValueSet.purpose)

Fixed

• Handle case where SNOMED CT RF2 files contain logically duplicate language reference set entries.
• Fixed bug in PATCH support where code-typed elements with bindings were not properly handled.
• Fixed bug where an empty search parameter could trigger an IndexOutOfBoundsException.

Fixed

• Based on change in 20220228, updated default type config for reference set: 1193544002

Security

• Updated library versions to mitigate CVEs:
• CVE-2023-35945

Changed

• Added support for concept-typed fields in ECL reference set membership filters.

Security

• Updated library versions to mitigate CVEs:
• CVE-2023-2650

Fixed

• Fixed regression where alpha-sorted designation without a “use” could be mis-identified as the display value.
• Improved error message for ambiguous SNOMED editions

Security

• Updated library versions to mitigate CVEs:
• CVE-2023-20862
• CVE-2023-20873
• CVE-2023-20883
• CVE-2023-21930
• CVE-2023-29491

Changed

• Added caching layer to speed up $validate
• Changes to support using Ontoserver with the FHIR Validator or IG Publisher as described here
  • Add support for valuesetMode and implySystem parameters to ValueSet/$validate-code.
  • Add support for excludeNested parameter to ValueSet/$expand.
  • The ValueSet expansion.parameter element may now include more parameters that affect expansion.
  • The Parameters resource resulting from a ValueSet/$validate-code can now include issues.
  • Only specific extensions that affect $expand are propagated to expanded ValueSets.

Fixed

• Fixed bug where id field value of search result Bundles was non-conformant.

Security

• Updated library versions to mitigate CVEs:
• CVE-2023-1370

Changed

• Reduce space consumption when storing very large resources.
• Specific ValueSet expansions now include extension content from concepts in ValueSet definition into expansion result. This is important for, for example, the ordinalValue extension and Questionnaires.
• ValueSet expansions now include ValueSet-specified display/designations from nested ValueSet includes.
• Added support for PATCH operation (FHIRPath Patch only)
• Added support $diff operation
• Improved validation of CodeSystem.count element value, if present.
• The FHIR base URL (which otherwise has no content) now redirects to OntoCommand by default for an improved user experience.
• Added support for inequality matching for numbers and dateTimes in ValueSet filters as per https://jira.hl7.org/browse/FHIR-38171 The syntax mirrors that used in the FHIR search syntax using prefixes, e.g., releaseDate = ge2021-01-01.
• FHIR index version has been incremented to 2.4.0 to support the above change.

Fixed

• Fixed matching for the dependency parameter in $translate. Note that this can only be used in a POST request.
• ETags now generated by default for read and vread operations.
• Fixed bug with caching of expansion-only ValueSet expansion results.
• Certain ECL errors will no longer be reported as 5xx but instead as 4xx.
• Fixed bug where cached expansion queries would ignore supplement content.

Fixed

• Fixed bug where re-validation of selected FHIR_* resources in syndication feeds would still happen even if disabled.

Fixed

• Fixed regression where $find-matches failed to establish a transaction.

Security

• Updated library versions to mitigate CVEs:
• CVE-2021-46848 – libtasn1: Out-of-bound access in ETYPE_OK
• CVE-2022-43551 – curl: HSTS bypass via IDN
• CVE-2022-45143 – The JsonErrorReportValve in Apache Tomcat 8.5.83, 9.0.40 to …
• CVE-2023-0286 – There is a type confusion vulnerability relating to X.400 address proc …

Changed

• Added explicit configuration flags for readonly and scaled (readonly) deployment mode.
• Added support for $closure and search result paging when in scaled (readonly) deployment mode.
• Added support for skipping re-validation of selected FHIR_* resources in syndication feeds.

Fixed

• Fixed bug in filtering syndication feeds by fhirVersion where BINARY indexes would never match.
• Fixed bug expanding some CodeSystem supplements.
• Fixed bug where Lucene indexes were not being deleted after CodeSystem deletion.
• Fixed bug where onto/* style scopes would be ignored.
• Fixed bug where experimental versions of SNOMED would be treated as newer than non-experimental versions.
• Fixed bug where a malformed fullUrl in a Bundle could result in a Resource with a blank id.
• Fixed bug where synd/getBinaryIndexZip failed due to a missing transaction context.
• Fixed bug where Loinc indexing might use the wrong part link file.
• Fixed bug where SNOMED CT string-valued concrete domains had their last character truncated.

Fixed

• Fixed bug validating security tag syntax.

Security

• Updated library versions to mitigate CVEs:
• CVE-2022-31690
• CVE-2022-31692
• CVE-2022-40153
• CVE-2022-42889

Changed

• Added MRCM Attribute Domain checking support for validation of SNOMED CT post coordinated expressions.
• Updated /synd/redoPreload to return 201 status and associated jobId on success
• Additional validation of ECL in ValueSet.compose - check for inactive concepts
• Ontoserver will now detect malformed security permissions (those not ending in .read or .write)

Fixed

• Fixed bug where the display text supplied in a ValueSet would not override that from the CodeSystem.
• Fixed bug where stored expansion might be used inadvertently.
• Fixed bug where CodeSystem supplements were not being ignored when resolving CodeSystem references.
• Fixed bug where setting certain logging levels to less than INFO (eg WARN) caused failures
• Fixed bug where an explicit definition property was silently ignored.
• Fixed bug where the same version of both experimental and non-experimental Editions of SNOMED are loaded.
• Fixed bug whereby OperationOutcomes for some custom operations were not valid resources.

Fixed

• Fixed bug where /api/startupProbe required authentication.
• Fixed bug where empty search parameters were not being ignored.

Changed

• Added /api/startupProbe to support AGIC and similar.
• Add support for the dependency parameter to ConceptMap/$translate.

Fixed

• Fixed bugs that caused valueSetVersion to be ignored sometimes on $expand and $validate-code
• Fixed typo in displayLanguage parameter of CodeSystem/$validate-code and ValueSet/$validate-code
• Fixed bug importing Loinc 2.72
• Fixed race conditions in /api/getJobs

Changed

• LOINC index version has been incremented to 2.0.4
• Add support for LOINC Linguistic Variants

Fixed

• Fix import of LOINC from source via syndication
• Fix LOINC Hierarchy import (for LOINC 2.73 and above)
• Fix bug in $preferred-id where deleted resources were not ignored

Changed

• FHIR index version has been incremented to 2.3.0
• Support POST of application/tar+tgz to $x-load-package to allow adding the Ontoserver-compatible contents of a FHIR Package.
• Changed indexCodeSystemDebug message output, it now prints one argument per line so it's easier to see what was passed to the java application.

Fixed

• Significantly improved performance of ConceptMap update and delete.
• Fixed bug where $lookup of property that is a container of sub-properties would be ignored.
• Fixed bug where post coordinated expressions would fail to validate with respect to a suitable ValueSet.
• Fixed bug enforcing permissions on instance-level $find-matches
• Fixed bug reporting on permissions failure for instance-level $validate-code
• Fixed bug invoking $validate with a Parameters specifying the profile as a Canonical.
• Fixed bug where CodeSystem version would be omitted from tabular-formatted ValueSet/$expand responses.
• Fixed bug property.url values for standard “parent” and “child” semantics were being ignored.
• Fixed bug in logging of start_ms for batch request operations.
• Fixed bug where system-version and force-system-version would not be effective for implicit SNOMED ValueSets.
• Fix Docker image entry point where the passed command line argument with quotes was split at the whitespaces into separate arguments.

Changed

• Added indexCodeSystemDebug Indexer mode to display command line arguments passed to the Docker container's entry point.
• Added text/tab-separated-values as an addition valid Accept MIME type for ValueSet/$expand.

Fixed

• Fixed broken Indexer mode where classpath was pointing to non-existent ontoserver.jar file.

Fixed

• Fixed bug where a ValueSet with overlapping codes from different CodeSystems could be treated as equivalent.
• Fixed Bundle/Package add semantics to treat NamingSystem resources with same id and date values as related. If related, then only update the resource if the new one has a later date.
• Fix bug with _summary/_elements for NamingSystem and Bundle

Changed

• Docker image is now multi-architecture; includes ARM support
• Search requests can now provide multiple values for all search parameters, using AND semantics (e.g. ?name=Chronic&name:contains=Kidney) or OR semantics (e.g. ?name=Chronic,Recurrent)
• Include code, system, version in $validate-code and $lookup results by default, pre-adopted from R5
• If a ValueSet includes an existing expansion that is compatible with the $expand call, then use it directly
• Support csv, tsv, scsv as values for _format for $expand
• Improved logging of user/principal

Fixed

• Support equivalent codes (hierarchy cycles) in a CodeSystem
• Fix missing keywords ‘accept’ and ‘prefer’ in ECL parser
• $expand?property=... no longer causes all sub-properties to be automatically included

Changed

• Updated to Spring Boot 2.6.5
• Updated to Flyway 8.5.5
• Enhance algorithmic concept map results to respect Accept-Language header for display term.
• Minor enhancements to CapabilitiesStatement and explicit handling of date parameter for $expand

Fixed

• Fix incorrect ETags for implicit algorithmic $translate results.
• Fix incorrect sufficientlyDefined status for inactive SNOMED CT concepts.
• Add support for SNOMED ValueSet filters on: moduleId and effectiveTime.

Changed

• FHIR index version has been incremented to 2.2.2
• Add support for typed values in target.product and target.dependsOn, pre-adopted from R5
• Add support for concept subproperties specified in a CodeSystem using extensions (FHIR index version change).
• Add initial support for history supplements in ECL (from v2.0).
• Add initial support for member filters in ECL (from v2.0).
• Add initial support for description and concept filters in ECL (from v1.5, v.1.6). The concept filters: definitionStatus, moduleFilter, effectiveTimeFilter, and activeFilter are supported. The description filter: termFilter is supported.
• All resources now support the _lastUpdated search parameter, including the lt, gt, le, ge and eq prefixes, and also including multiple values (e.g. for searching for resources updated between two times)
• Update to HAPI 5.7.0 Changes
• Add support for “all known codes” implicit ValueSet: http://hl7.org/fhir/ValueSet/@all
• Add support for SNOMED CT attribute names as filter properties for operators = and in; all concept model attributes are concept properties and thus should support = and in as filter operators.
• metadata?mode=terminology now returns information on CodeSystem instances rather than generic capabilities.
• Add support for the conceptMapVersion parameter on the ConceptMap $translate operation.

Fixed

• Fix long-standing error in naming property parts in $lookup results; old names deprecated but are retained for backwards compatibility
• Fix handling of corrected/alternate spellings/stems in Automap
• Fix support for multi-valued Coding typed properties (FHIR index version change).
• Fix bug handling ValueSets with an empty ValueSet.compose

Fixed

• Fix transaction boundary error in validation leading to spurious rollback errors

Fixed

• Fix error handling fully declared status property when adding a CodeSystem
• Fix bug in $find-matches for SNOMED CT where some valid properties would be rejected
• When logging, treat clientId in token as alternative to client_id

Fixed

• Fix regression in calculation of length and sha256 values for syndication feed entries.

Changed

• Add simple support for /CodeSystem/$find-matches.
• Optimise Syndication feed generation for large Resources.
• New config (atom.syndication.excludeLength and atom.syndication.excludeXml, both defaulting to false) to further speed Syndication feed generation.

Fixed

• Fix bug in $expand where a search string involving repeated units could return additional concepts.

Changed

• SNOMED Binary Index format changed to 2.0.6; RF2 Concrete Domains and improved Language Reference Set support
• Designation use of preferredForLanguage can now be used to select preferred terms in languages other than the primary one, analogous to display.
• CodeSystem/$lookup now respects the Accept-Language header
• SNOMED CT Language Reference Sets are now handled through a BCP-47 language tag extension. This provides the capability for preferring a code's display on both language AND reference-set dimensions.
• Faster _search performance when large resources are involved.
• Generalised version sorting; relaxes the constraints around version strings for selecting the “latest version” of resources.
• Health status now checks for database connectivity.

Fixed

• Fix bug in $subsumes for post-coordinated expressions where order mattered checking for equivalence.
• Fix bug in $expand where R5 pre-adopted property support did not respect the type of property values.
• Fix bug in /synd/setSyndicationStatus where calling it for SNOMED or LOINC would fail to properly manage the binary index file.
• Fix bug where Ontoserver was performing too many URIdecode operations on URI-typed request parameters.

Fixed

• Fix bug where Indexer mode did not handle duplicates when processing multiple RF2 Zip files

Security

• Fix bug where security tag of *.read effectively disabled Resource-level protections for that Resource.

Changed

• Support :not modifier for the url search parameter.
• Ignore duplicates when processing multiple RF2 Zip files

Fixed

• Fix handling of uri-typed search parameters with modifiers.

Fixed

• Fix issue when TextDefinitions do not have language referenceset entries; SNOMED Binary Index format changed to 2.0.5

Changed

• The results of the $translate operation will now include any dependencies or products of the matches
• The Text Definition for a SNOMED CT concept is now used as its concept.definition; SNOMED Binary Index format changed to 2.0.4
• Updated to HAPI 5.4.0

Fixed

• Fix bug where string properties without a value can cause $expand?property=... to fail.
• Fix bug where codes with colons can be confused with SNOMED post coordinated expressions.
• Fix bug where ValueSet filter on property of Coding type failed for most values.
• Fix bug where ECL expressions containing only optional grouped relationships would fail.
• Fix potential concurrency bug when downloading binary indexes.
• Fix concurrency issue when repairing multiple SNOMED CT indexes.
• Fix bug where system-version or force-system-version were being ignored for implicit ValueSets.
• Fix syntax error in necessaryNormalForm property of SNOMED CT concepts (expressions contained extraneous + symbols)
• Fix bug where automap failed for CodeSystems other than SNOMED CT and LOINC

Fixed

• Fix bug in handling _summary=false parameter

Changed

• Add support for decimal-typed CodeSystem properties
• Add support for $expand?property=... pre-adopted from R5
• ValueSet regex filter has implied anchors; also allow for explicit ones (at start and end only).
• Ensure that searches for codes that look like quantities (e.g., 50L) still match the code.
• Properly support multiple CodeSystems in $closure.
• When $closure is called with codes not known to belong to the specified CodeSystem, include in result as “unmapped” (previously these were silently ignored).
• Added a parameter -s to Ontoserver's healthcheck.sh script so an Ontoserver container can report as unhealthy unless and until it has successfully loaded all the content of a preload feed.
• Add support for atom.syndication.client.connectTimeout, atom.syndication.client.requestTimeout, and atom.syndication.client.socketTimeout configuration to allow overriding the 10 second default

Fixed

• Fix bug where passing both parameters _elements=*&_summary=true triggers 5xx instead of 4xx error.
• Fix bug where codes without display text can cause $expand to fail.
• Fix bug where last set of codes in ValueSet.expansion with same score were not alpha-sorted.

Changed

• Add extra validation of LOINC codes when indexing and handling implicit ValueSets.

Fixed

• Fix issue where concept.display has a translation. Results in additional designation for every concept corresponding to it's display(s).
  Both FHIR and Loinc patch-level index versions have been incremented due to this fix.
• Fix issue where ValueSet supplement extension references a non-supplement CodeSystem.
• Fix issue where a CodeSystem supplement specifies an implicit “all codes” ValueSet.

Fixed

• Fix issue preventing LOINC index creation using Ontoserver in start/finish “indexer mode”.

Fixed

• Fix enabling overriding security labels on FHIR resources imported from a syndication/preload feed using the feed entry's permissions extension.

Changed

• Support the Syndication Feed content-type FHIR_Package.
• Significantly enhanced validation support due to upgrade to HAPI 5 (5.2.0).

Changed

• Speed improvements for various operations, including translate with SNOMED implicit ConceptMaps
• Adjust the order of preload such that FHIR resources are scheduled first, then all SNOMED and LOINC indexes from newest to oldest.

Changed

• SNOMED Index version patch change to fix issue with preferredTerm selection and multiple languages.
• Updated directory layout for Lucene indexes to avoid possible location contention.
• Improved robustness of indexRepair.
• Added work-around for bug in FHIR Validator code.
• Now include logs for rejected FHIR requests following refactored request handling layer.
• More robust handling of errors during preload.

Changed

• Improved error messages relating to language reference sets when indexing SNOMED CT.
• Minor docker-packaging updates.

Fixed

• Fixed bug where fhirVersion was not being checked in syndication feed entries.
• Fixed bug when attempting to return history of Bundle resource.

Fixed

• Fixed typo in default configuration that would lead to a healthy ontoserver being reported as unhealthy when running in secure mode.

Changed

• Support SNOMED CT post-coordinated expressions with $subsumes, $closure, and $lookup
• Support SNOMED CT CodeSystem supplements referencing post-coordinated expressions
• Add support for $meta-add and $meta-delete
• meta.tag and meta.label are now associated with a resource instance, and not the resource instance version. This provides a better experience and more flexible model for managing per-resource permissions
• Surface Ontoserver resource permissions in syndication feed
• Support ;fhirVersion=3.0 in Content-Type header auto-convert STU3 inputs to R4
• Optionally redirect a request to the base to the Administration UI
• Expanded the list of parameters that can be used for sorting resource searches. These are now listed in the documentation.
• Individual FHIR resources can now be selected for publication in the downstream syndication feed by setting atom.syndication.publish.fhir.enabled=selected and calling /synd/setSyndicationStatus for the individual resources.
• Added the parameter atom.syndication.publish.index.enabled (default=selected) allowing 3 values for publication of binary indexes in the syndication feed - all, selected, or none
• Added ontoserver.well-known.openid-configuration config as redirect target for [base]/fhir/.well-known/smart-configuration to simplify OAuth2 config for SMART on FHIR.
• Support POST of multipart/form-data to $x-upload-external to allow for releases split over multiple RF2 zips.
• Support for adding a set of resources to the server by POSTing a Collection-typed Bundle to the FHIR base URL. This is conditionally enabled with the parameter ontoserver.fhir.batch.addBundle (default is false).
• Support additional hierarchy-based concept filter operators for LOINC.
• Add support for ‘title’ as a search/sort parameter for CodeSystem, ConceptMap, ValueSet and StructureDefinition
• The downstream syndication feed title can now be configured using atom.syndication.publish.feedTitle
• Search requests can now sort (but not yet search) using the _lastUpdated search parameter.
• Syndication status on a FHIR resource can now be used in search and sort criteria using the ‘x-syndication-status’ parameter.
• FHIR resources explicitly marked for syndication using setSyndicationStatus can be protected from modification using the atom.syndication.publish.fhir.secureSyndication config option.

Removed

• Remove support for internal RF2 caching including the (deprecated) APIs /api/sct/addRf2 and /api/sct/modules. Note, this also includes removal of support for RF2 in the /synd/fetchSyndicatedContentEntry API.

Fixed

• Fix potential issue with HTTP caching - added Authorization to the Vary header.
• Fix bug where old ConceptMap data would interfere with url-less type-level $translate
• Fix for FHIR syndication entry length calculation where resources contain multibyte UTF-8 characters, Atom specification is based on data length (octets) not characters https://tools.ietf.org/html/rfc4287#section-4.2.7.6
• Fixed syndication feed to contain a “self” rel type link and remove incorrect “alternate” type links for upstream feeds.

Changed

• Improved error messages when indexes on disk are missing and cannot be retrieved from upstream Atom feed(s).

Fixed

• Fix for SHA256 and length calculation for FHIR resources in the syndication feed, including accounting for multi-byte UTF8 characters in FHIR resource length.
• Fixed duplicated CodeSystem resource entries in the syndication feed.

Changed

• Updated NCTS profiles
• Added an API call to re-execute preload on a running server (see /synd/redoPreload), and a parameter to enabled scheduled re-execution of preload using cron expressions (see atom.preload.schedule.cron)

Fixed

• Some $validate requests were failing because of outdated snapshots in built-in profiles. These have been fixed.

Changed

• Syndication and preload feeds can now be filtered by category, content identifier, content version or FHIR version. More information on how to do this is provided in the Syndication Configuration page of the online documentation.
• Implement support for ConceptMap.group.unmapped
• Performance improvements for searches with _elements parameter(s)

Fixed

• Fix performance bug with internal caching of search results
• Fixed default syndication endpoints

Changed

• Update docker-compose examples to cater for Postgres image changes
• Add support for the ‘definition’ property in $lookup
• Add support for ‘display’ as a filter, including regex support (does not include designations)
• Ensure required properties ‘name’ and ‘display’ are returned by $lookup
• Initial support for Coding-typed properties in FHIR CodeSystem resources

Fixed

• Fix bug when passing ValueSet URI containing | as parameter to $expand

Changed

• Support FHIR R4. This brings major index version changes, across all index-types, which are not compatible with FHIR STU3 and Ontoserver 5.x
• Support CodeSystem.supplements
• Support /$versions operation
• Support for NamingSystem and $preferred-id
• Allow an RF2 SNAPSHOT .zip to be POSTed to [base]/CodeSystem/$x-upload-external to create a SNOMED CT index.
• FHIR Search requests now default to _summary=true for significant performance improvements
• Support reference parameter in ValueSet search
• More detailed validation of ValueSets; implicits and ECL filters are parsed for correctness
• A FHIR CodeSystem claiming to be http://snomed.info/sct (or http://loinc.org) can now be created directly as long as CodeSystem.content != complete. This is primarily to support the SNOMED CT GPS for users that are not SNOMED-licensed and therefore unable to load an RF2-backed instance.
• Tidy up JSON logging format - blank fields are omitted rather than the empty string
• Refactored indexing to reduce memory footprint
• Refactored index filesystem layout to support dynamic healing
• Migrate from Java 8 to Java 11
• Migrate from Lucene 6 to Lucene 8

Removed

• Remove support for FHIR STU3
• Remove support for legacy ‘identifier’ parameter to the ValueSet/$expand operation

Changed

• Add support for alternate negation syntax and childOrSelf (<<!) etc in ECL
• Less noisy (in logs) healthcheck mechanism using Spring Boot health endpoint on private port
• Update security model to use scope values in JWT token in preference to authorities. This also includes changes to the values - see documentation for details.
• SNOMED CT Long normal forms that get really long will now be shortened somewhat (but still conformantly)

Changed

• Work-arounds for changes in HAPI 4.1.0

Fixed

• Fix error where preload would attempt to import incompatible binary index versions

Fixed

• Fix bug regarding handling of preload and syndicated indexes

Changed

• Add support for validating using “remote” profiles
• Added support for “publisher” and “status” search parameters on ValueSet, CodeSystem, ConceptMap and StructureDefinition resources

Fixed

• Fix normalForm syntax to use RF2 syntax for numbers rather than scientific notation, correct grouping for concrete domain info, and nested relationships
• Fix bug in MML automap strategy where low-ranked matches were returned

Changed

• Adjusted ranking scores where synonyms are best matches
• Badly formatted count and offset parameters for $expand will now result in a 400 instead of a 500

Fixed

• Fixed bug in recorded index version of SNOMED CT binary indexes
• Fixed bug where some CodeSystem $validate-code requests would produce a 500 instead of a 400
• Fixed bug in syndication feed; ids must be absolute URIs

Changed

• Designations added to ValueSets should not be available using $expand with includeDesignations=true

Fixed

• Fixed bug in Ontoserver initialization that would cause problematic repair of CodeSystem indexes on startup
• Fixed bug where unrecognized syndication entry categories would break the ability to fetch upstream syndicated content
• Bug fixes related to fetching Bundle resources from syndication

Changed

• Support for preloading content into Ontoserver on startup using a Bundle resource or ATOM syndication feed/s.
• Support for indexing SNOMED CT releases based on the July 2019 international release
• The /synd/fetchSyndicatedContentEntry endpoint now supports ‘resourceType’, ‘url’ and ‘version’ parameters, as an alternative to fetching using the ATOM entry ID

Fixed

• Fix bug when generating syndication feed of FHIR resources; exclude SCT and LOINC

Changed

• Documentation improvements, especially for Authorization configuration to support RBAC

Fixed

• Fix bug where HTTP 500 rather than 404 would be returned when asking to index a non-existant code system

Fixed

• Fix syndication bug resulting in excessive redundant downloading of resources

Changed

• Add support for [base]/$convert
• Produce much more compact OperationOutcome Issue lists from $validate

Fixed

• Fix bug with paged _search results and ETags
• Fix bugs with support for authorization using RS256 keys

Changed

• Add support for experimental versions of SNOMED CT with special-case version URIs
• Support SNOMED Edition URIs in version parameters (for $lookup etc)
• Include Provenance resource for SNOMED CT CodeSystems
• Support default filters parent EQUALS and child EQUALS for SNOMED CT
• X-Correlation-Id and X-Request-Id support
• Support version:text in _search for terminology resources
• Support distribution format changes for Loinc 2.65
• Improve robustness of syndication client when encountering unrecognized categories

Fixed

• Fix bug where ECL cardinality constraints of [0..*] were incorrectly applied
• Fix bug where CodeSystem.system was usable as an implicit ValueSet.url under certain circumstances
• Fix bug with automap and stemmed words that are not also prefixes
• Fix bug with ValueSet filter on the ‘inactive’ property for FHIR CodeSystems
• Fix syndication bug whereby StructureDefinition syndication entries would have the wrong category

Deprecated

• Deprecate /api/sct/addRf2 and /api/sct/getModules

Changed

• Support human-friendly HTML rendering of FHIR responses
• Exception stack traces are now logged on a single line as a JSON array
• Add support for kind as a search parameter on StructureDefinition
• Add support for the _tag:not modifier
• Add support for .well-known and .well-known/logo.png in particular

Fixed

• Fix bug with $validate-code and multiple versions of the same CodeSystem

Fixed

• Fix index error to support ValueSets with cross-version CodeSystems This includes an index minor-version update and will trigger re-indexing of all (LOINC, SNOMED, and FHIR) CodeSystems
• Fix bug in ECL that allowed never-grouped attributes (eg laterality) to match inside groups
• Fix bug in language detection for designations without language

Fixed

• Fix bug where displayLanguage / Accept-Language support was ignoring the default display text

Changed

• Enable support for HTTP(S)_PROXY_HOST, HTTP(S)_PROXY_PORT and HTTP_NON_PROXY_HOSTS
• Support * as a property name in $lookup to represent all known properties
• Add support for language ranges (eg en-*) with displayLanguage parameter

Fixed

• Fix bug with overly permissive parsing of RF2 syndication feed entries
• Fix bug related to $translate using implicit ConceptMaps in reverse
• Fix bug where ECL expressions with certain unicode characters were incorrectly escaped
• Fix bug that would block ConceptMap create/update when source or target ValueSets were ambiguous

Fixed

• Fix bug where caching of ECL constraints with multiple relationship clauses could return incorrect results

Changed

• Upgrade LOINC importer and indexer to support more recent LOINC releases (2.59-2.64). Note: Because of this, the Binary Index Format for LOINC is now 1.6.0.
• The LOINC property/filter DOCUMENT_SECTION is no longer supported, as it has been removed from the LOINC distribution
• Greatly expanded the set of available LOINC Answer List and Part codes
• LOINC implicit ValueSet URIs now allow versions (e.g. http://loinc.org/2.64/vs), reflecting a likely upcoming normative change. Unversioned LOINC URIs are still valid, too
• The following additional code-typed LOINC CodeSystem properties are now available on LOINC Terms: CHALLENGE, COUNT, TIME MODIFIER, SUPER SYSTEM, DIVISORS, ADJUSTMENT
• Support context parameter for ValueSet/$expand and ValueSet/$validate-code
• Support displayLanguage parameter for $expand
• $validate-code now returns display text when code is valid
• Support CodeSystem/$validate-code and CodeSystem/[id]/$validate-code, pre-adopted from R4
• Support default = and in filters for all defined CodeSystem properties
• Type-level $translate with no url parameter no longer uses available ConceptMap instances rather than a term-based string matching algorithm
• $translate now includes match.source in most cases
• $translate now includes match.concept.display when the CodeSystem of the concept is available
• Add support for latest-version semantics when only a single Edition of SNOMED CT is available
• Return ETag on DELETE
• Support returning alternate display text in top-level ValueSet.compose.include
• Support instance-level and type-level _history operations with both _since and _at parameters
• Support type-level $validate for all Resource types
• Switch to using validator reference implementation
• Significantly reduce heap usage when obtaining syndicated content. Minimum required heap now documented as only 2GB

Fixed

• LOINC axis properties and filters (PROPERTY, COMPONENT, SYSTEM, TIME_ASPCT, METHOD_TYP and SCALE_TYP) now correctly use codes instead of display strings
• Fixed bug in $expand of ValueSets using LOINC and ‘exists’ filters
• Fixed bug triggered by empty property parameter to $lookup operations on SNOMED-CT

Changed

• Very slightly reduce scores for inactive concepts
• Allow (encoded) newlines in ECL Implicit ValueSet URIs
• Include request protocol in logs
• SNOMED Concept Inactivation Indicators are now available as an implicit concept map
• Support direct POST of Bundle to addBundle in addition to POST of multipart/form-data
• Add support for bundleInterpretation=collection in /synd/fetchSyndicatedContentEntry
• Relax constraints around acceptable display text when validating SNOMED codes; now also allows any acceptable synonym
• Report http://hl7.org/fhir/StructureDefinition/valueset-unclosed for expansion of certain SNOMED ValueSets
• Support additional FHIR code properties in LOINC: EXAMPLE_UCUM_UNITS and STATUS

Fixed

• Fix rare bug when automapping unversioned codes and other complex conditions satisfied
• Fix bug where CodeSystems with corrupt/missing index data could sometimes appear in search results
• Fix bug in addBundle where reported resource Identities were of the supplied Resources rather than the updated Resources
• Fix race condition loading default and built-in profiles on startup

Changed

• Pre-adopt the new SNOMED CT Implicit ValueSet URI pattern for the Expression Constraint Language, as defined for FHIR R4
• Support consumption of FHIR_Bundle artifact type in the syndication feed.
• Ontoserver now supports SCRUD operations on Bundle resources.
• Ontoserver now supports SCRUD operations on StructureDefinition resources. Stored StructureDefinitions can be used for validation of terminology resources
• $validate methods now support the profile parameter

Changed

• Stricter parsing checks for JSON and XML Resources
• Support CTV3 implicit map
• Improve handling of inactive rows in the MDRS when building SNOMED indexes
• Certain resource validation errors that were not previously being reported are now being reported

Fixed

• Fix problem where, in rare cases, inactive concepts would have missing display text
• Fix bug where deleted ValueSets could cause $expand to fail in rare cases

Changed

• Add support for Edition-specific language-reference-sets in config
• Add explicit handling of OutOfMemory exceptions to allow Ontoserver to shutdown
• Add optimisations for ECL-based ValueSets with expensive match criteria
• Check codes are valid during $subsumes

Fixed

• Fix bug handling malformed ValueSets with incompletely specified filters
• Fix recall performance in “automap” algorithms associated with automated spelling correction
• Fix bug in scoring algorithm that was failing to weight the score of preferred terms properly

Changed

• Document minimum Java heap size and likely need to set it explicitly in docker-compose configuration.

Fixed

• Fix bug where ValueSet.compose.inactive=false was being ignored.

Changed

• SNOMED Index version patch to 1.6.2
• Explicitly index SNOMED acronyms / abbreviations for better search behaviour
• Support “inactive” property for FHIR Code Systems (already supported for SNOMED CT)
• Use “inactive” property in ValueSet expansions to indicate whether an included code is inactive in the underlying code system.
• Support SNOMED CT relationship properties as per http://hl7.org/fhir/snomedct.html#props
• New buildLocal parameter for indexCodeSystem to avoid syndicated binary indexes
• Binary index versions are now included in the Ontoserver CapabilityStatement
• Avoid file copy when syndicating local content
• Improved ranking of searches involving FSN semantic tag matches

Deprecated

• Ontoserver-specific extension was used to indicate inactive concepts is now deprecated and is scheduled for removal in the 5.1.0 release.

Changed

• Improve error reporting for malformed ValueSet filters
• Improve metadata for LOINC CodeSystem and implicit ValueSets

Fixed

• Fix bug where inactive map entries were appearing in SNOMED implicit concept maps

Changed

• When syndicating from an upstream feed, Ontoserver will now be stricter about the presence of a SHA256 checksum attribute (either ‘sha256Hash’ or the deprecated ‘sha256’) on links. (If necessary, this can be disabled using the atom.syndication.disableChecksums configuration property)
• Improve cleanup of files when an index is deleted

Fixed

• Fix bug in syndication where downstream syndication entries were using an incorrectly named attribute for SHA256 checksums on download links (‘sha256’ instead of ‘sha256Hash’). Links will now have the correct attribute.

Changed

• Support Concrete Domains in ECL and use flatter DL representation of AMT Concrete Domains information ready for integration with SNOMED International drug model changes.
• Minor improvements to error reporting for $subsumes requests, and LOINC implicit ValueSets
• Improve performance of batch requests.

Changed

• Add support for version ordering. Resources whose versions are uniformly formatted using semantic versioning (x.y.z) or date versions (yyyymmdd) can now share a url, and will be resolved to the latest version if no specific version is provided.
• Certain ECL errors no longer result in a 500 series error, instead producing a 422

Fixed

• Fix syndication bug when local binary index exists as well as an upstream binary index of the same version

Changed

• Improve performance of batch operations by allowing concurrent execution
• Adde JSON-style logging for api/syndication methods
• Update NCTS profiles for ValueSet, CodeSystem and ConceptMap
• $validate requests using the unsupported profile parameter will now result in 400-code responses.

Fixed

• Fix bug with batch operations when Ontoserver RBAC security is enabled
• Fix bug for $subsumes requests that use codings rather than codes

Changed

• Instance-level $translate no longer returns an empty ‘source’ parameter
• $expand on an ambiguous ValueSet url will now result in a 422 error, not a 500 error
• SNOMED CT ECL parser now correctly recognizes ChildrenOf
• AuditEvent reporting is now turned off by default. Consult config documentation to enable and configure endpoint/s.
• Some improvements to robustness of syndication.

Fixed

• Fix bug in SNOMED CT indexer that affected some ECL cardinality constraints inside role groups
• Fix bug in ECL compiler that affected cardinality constraints on grouped relationships
• Fix problems arising when publishing older binary indexes for syndication
• Fix bug related to indexing extra columns in RF2 refsets, which affected the SNOMED International release

Changed

• Migrate to STU3 version of FHIR
• Support inactive = true/false filter for SNOMED CT
• HTTP/2 support added
• Add support for explicit properties and filters on FHIR code systems
• Add support for implicit filters on FHIR code systems: concept =/is-a/is-not-a/in/not-in, parent =/in/not-in
• CodeSystems created/updated with content=not-present will now not list concepts in a read (concepts are still accessible through expand, lookup, etc)
• Add support for lang.X values in the property parameter of $lookup requests
• Update properties and filters for LOINC CodeSystems including support for CLASS, CONSUMER_NAME, CLASSTYPE, ORDER_OBS and DOCUMENT_SECTION
• Add support for the $subsumes operation (including within batch requests) for testing subsumption/equivalence between concepts within a code system
• The ‘descendent-of’ filter is now available for the ‘concept’ property in both SNOMED and FHIR CodeSystems
• Add support for the includeDesignations and includeDefinition parameters on ValueSet $expand
• Support boosting in ValueSets via http://ontoserver.csiro.au/profiles/boost extension on ValueSet.compose.include
• Update properties and filters for SNOMED CT CodeSystems including support for sufficientlyDefined, effectiveTime, moduleId, normalForm, and normalFormTerse
• Support multiple Syndication feed sources
• Support implicit concept maps for SNOMED CT Historical Associations reference sets
• Support implicit concept maps URI http://ontoserver.csiro.au/profiles/automapstrategy/default as default Automap strategy
• Support the logging of code selection, through the creation of AuditEvent resources
• $validate-code requests for SNOMED codes now respect concept permanence
• Support for the _tag search parameter on all resources
• Support for the source-uri, target-uri, source-system, target-system, source-code and target-code search parameters on ConceptMap

Removed

• Remove support for DSTU2.1

Fixed

• Fixed a bug where filters longer than 20 characters would return no matches

Fixed

• Fix problem with syndicating newer binary indexes (from Ontoserver >= 5.0.0)

Fixed

• Fix long standing bug related to OWL generation from RF2 (SNOMED Binary Index version incremented to 1.3.4)

Fixed

• Fix bug related to SNOMED codes without descriptions

Fixed

• Fix bug in CodeSystem/$lookup
• Fix bug in SNOMED indexes where non-defining relationships were being treated as defining (SNOMED Binary Index version incremented to 1.3.3)

Changed

• Bump SNOMED Binary Index version to 1.3.2 for following five fixes/improvements
• Make description IDs searchable terms
• Ensure that FSNs are always acceptable synonyms

Fixed

• Fix bug where | symbols in RF2 files would confuse the CSV parser during an addRf2 call
• Fix bug where multiple language reference sets referring to the same description id would result in multiple designations
• Fix minor bug where “fall-through semantics” for language reference sets was not being applied. Note, these semantics are under-specified in the SNOMED CT TIG.

Fixed

• Fix bug where Vary response header was incorrect when Accept-Encoding did not include gzip

Fixed

• Revert flyway change that broke database migration

Changed

• $lookup now returns inactive status as a property (as per spec) rather than directly as an output parameter
• Adding RF2 content to the database has been significantly sped up (Postgres only)
• The If-None-Match request header (used to support caching) is now supported for read, vread and search operations on ValueSets, CodeSystems and ConceptMaps, as well as $lookup and instance-level $translate operations
• ETag headers (usable for caching) are now produced by GET-style $lookup and instance-level $translate operations, and by search requests on ValueSets, CodeSystems and ConceptMaps
• Change syndication OAuth2 endpoint in line with NCTS change

Fixed

• Fix bug related to incorrect formats reported in Conformance resource
• Fix bug related to international RF2 release package structure

Fixed

• Fix (benign) bug where LOINC and FHIR index versions were not incremented with change to support index version compatibility
• Fix bug where some existing compatible indexes were not being detected in the file system, which triggered unnecessary updating of SNOMED indexes

Changed

• Improve automap precision
• Update SNOMED CT binary index file format to 1.3.1 and implemented support for semantic versioning of binary indexes with forward and backward compatibility
• ValueSets that come back from $expand requests will now include the identifier and version elements (if any) of the originating ValueSet

Fixed

• Fix limitation that prevented support for type-level $translate without a source CodeSystem / value set and only display text in a Coding/CodeableConcept
• Fix bug that prevented expansion of multi-version ValueSets with exclude criteria from working
• Fix bug related to empty codes in batch validate-code requests
• Fix bug that prevented including all of a LOINC code system in a ValueSet

Changed

• Improve speed of SNOMED (RF2) indexing from source; if RF2 not in db then work directly from ZIP. To get RF2 in db, use /synd/fetchSyndicatedContentEntry or /api/sct/addRf2
• Improve log format to facilitate automated log processing
• Improve transactional behaviour to avoid race conditions during creates/updates/deletes
• Update HL7 Sharable ValueSet Profile from 1.0.2 to 1.4.0
• Add support for the Prefer: return=representation Header

Fixed

• Fix bug in $closure where incorrect subsumptions could be computed
• Fix bug in $expand that made it impossible to use count/offset to retrieve concepts beyond the maxResults threshold

Changed

• Update IHTSDO ECL implementation to match v1.1.1
• Significant speed increase for the ‘automap’ flavour of $translate
• Performance improvement for loading RF2 data of SNOMED CT

Fixed

• Fix implementation of cardinality constraints in SNOMED CT ‘expression’ filters
• Fix bug where republished entries would not all have source links
• Fix bug regarding incorrect diagnosis of snomed/loinc index version mismatch on startup

Changed

• Batch requests now permit String values for Code-typed parameters
• Make $validate-code less dogmatic about matching the version parameter
• Allow the parameters ‘valueSet’ and ‘source’ to be used as alternatives on $translate
• Allow CORS requests from Origin file://

Fixed

• Fix handling of valueSet parameter on $validate-code
• Fix handling of type-level $validate requests that do not provide a resource parameter
• Fix bug in $closure where #additional edges > maxResults limit (default 10,000)

Changed

• Include Vary and HTML Content-Type headers for exception responses
• Improve handling of batch/transaction requests, especially regarding error handling
• Add /api/mode endpoint for querying security mode
• Support “property” parameter in batch GET $lookup

Changed

• Include Vary header with Accept and Accept-Encoding to avoid caching problems
• Include comment in Conformance to indicate which operations are supported in batch
• Customise CodeSystem.publisher for known editions of SNOMED (SCT-AU, AMT)

Fixed

• Fix error code for unsupported conditional deletes

Changed

• Return a 422 error when invoking operations with ambiguous resource references (URLs)
• Include the HTTP ‘Prefer’ header as an acceptable CORS header
• Add version search parameter for ValueSet, CodeSystem and ConceptMap
• Add system search parameter for CodeSystem

Fixed

• Fix incorrect behaviour of id:present and id:missing search modifiers
• Fix bug with validation of multi-typed properties, e.g. ConceptMap.sourceUri

Changed

• Issue a 400 Bad Request for $translate requests that do not specify a target value set

Fixed

• Fix bug that was causing Ontoserver to not log to file.

Changed

• Ontoserver no longer includes headers to disable caching
• $closure operation now supports arbitrary CodeSystems (with hierarchy), not just SNOMED CT
• Updated to Spring-Boot 1.3.6

Fixed

• Fix $closure table bug relating to the order of the added codes
• Fix incorrect response code 5xx rather than 4xx when source/target URIs are omitted from a $translate request
• Fix CodeSystem validation to report all duplicate codes at once, rather than just the first one found