Change Log

* 5.8.2

    Update base docker image

* 5.8.1

    Update docker-compose examples to cater for Postgres image changes

    Add support for the 'definition' property in $lookup

    Ensure required properties 'name' and 'display' are returned by $lookup

    Allow an RF2 SNAPSHOT .zip to be POSTed to `[base]/CodeSystem/$x-upload-external` to create a SNOMED CT index.

    Fix preformance bug with internal search caching

* 5.8.0

    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)

* 5.7.3

    Work-arounds for changes in HAPI 4.1.0

* 5.7.2

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

* 5.7.1

    Fix bug regarding handling of preload and syndicated indexes

* 5.7.0

    Add support for validating using "remote" profiles

    Added support for "publisher" and "status" search parameters on ValueSet, CodeSystem, ConceptMap and StructureDefinition resources

    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

* 5.6.2

    Adjusted ranking scores where synonyms are best matches

    Fixed bug in recorded index version of SNOMED CT binary indexes

    Badly formatted count and offset parameters for $expand will now result in a 400 instead of a 500

    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

* 5.6.1

    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

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

    Bug fixes related to fetching Bundle resources from syndication

* 5.6.0

    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

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

* 5.5.2

    Documentation improvements, especially for Authorization configuration to support RBAC

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

* 5.5.1

    Fix syndication bug resulting in excessive redundant downloading of resources

* 5.5.0

    Add support for [base]/$convert

    Produce much more compact OperationOutcome Issue lists from $validate

    Fix bug with paged _search results and ETags

    Fix bugs with support for authorization using RS256 keys 

* 5.4.0

    Support SNOMED Edition URIs in version parameters (for $lookup etc)

    Include Provenance resource for SNOMED CT CodeSystems

    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

    Support default filters parent EQUALS and child EQUALS for SNOMED CT

    X-Correlation-Id and X-Request-Id support

    Fix bug with automap and stemmed words that are not also prefixes

    Fix bug with ValueSet filter on the 'inactive' property for FHIR CodeSystems

    Support version:text in _search for terminology resources

    Support distribution format changes for Loinc 2.65

    Fix syndication bug whereby StructureDefinition syndication entries would have the wrong category

    Improve robustness of syndication client when encountering unrecognized categories

* 5.3.1

    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

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

    Add support for .well-known and .well-known/logo.png in particular

* 5.3.0

    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

* 5.2.3

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

* 5.2.2

    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 bug with overly permissive parsing of RF2 syndication feed entries

    Fixed bug related to $translate using implicit ConceptMaps in reverse

    Fixed bug where ECL expressions with certain unicode characters were incorrectly escaped

    Fixed bug that would block ConceptMap create/update when source or target ValueSets were ambiguous

* 5.2.1

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

* 5.2.0

    Upgraded 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 axis properties and filters (PROPERTY, COMPONENT, SYSTEM, TIME_ASPCT, METHOD_TYP and SCALE_TYP) now correctly use codes instead of display strings

    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

    Fixed bug in $expand of ValueSets using LOINC and 'exists' filters

    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 concept's CodeSystem 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 bug triggered by empty property parameter to $lookup operations on SNOMED-CT

* 5.1.1

    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

    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

    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

    Fix race condition loading default and built-in profiles on startup

* 5.1.0

    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 SCRUD operations on Bundle resources. 

    Ontoserver now SCRUD operations on StructureDefinition resources. Stored StructureDefinitions can be used for validation of terminology resources

    $validate methods now support the profile parameter

* 5.0.10

    Stricter parsing checks for JSON and XML Resources

    Support CTV3 implicit map

    Improve handling of inactive rows in the MDRS when building SNOMED indexes

    Fixed problem where, in rare cases, inactive concepts would have missing display text

    Certain resource validation errors that were not previously being reported are now being reported

    Fixed bug where deleted ValueSets could cause $expand to fail in rare cases

* 5.0.9

    Added support for Edition-specific language-reference-sets in config

    Added explicit handling of OutOfMemory exceptions to allow Ontoserver to shutdown

    Added optimisations for ECL-based ValueSets with expensive match criteria

    Fixed bug handling malformed ValueSets with incompletely specified filters

    Fixed recall performance in "automap" algorithms associated with automated spelling correction

    Fixed bug in scoring algorithm that was failing to weight the score of preferred terms properly

    Check codes are valid during $subsumes

* 5.0.8

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

    Fixed a bug where ValueSet.compose.inactive=false was being ignored.

* 5.0.7

    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.
    Previously an Ontoserver-specific extension was used for this.  It is now deprecated and is scheduled for removal in the 5.1.0 release.

    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

* 5.0.6

    Fixed a bug where inactive map entries were appearing in SNOMED implicit concept maps

    Improved error reporting for malformed ValueSet filters

    Improved metadata for LOINC CodeSystem and implicit ValueSets

* 5.0.5

    Fixed a 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.

    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)

    Improved cleanup of files when an index is deleted

* 5.0.4

    Support Concrete Domains in ECL and use flatter DL representation of AMT Concrete Domains information ready for integration with SNOMED International drug model changes.

    Fixed performance problem with batch requests.

    Minor improvements to error reporting for $subsumes requests, and LOINC implicit ValueSets

* 5.0.3

    Added 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

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

* 5.0.2

    Improved performance of batch operations by allowing concurrent execution

    Added JSON-style logging for api/syndication methods

    Fixed bug with batch operations when Ontoserver RBAC security is enabled

    Updated NCTS profiles for ValueSet, CodeSystem and ConceptMap

    Fixed bug for $subsumes requests that use codings rather than codes

    $validate requests using the unsupported profile parameter will now result in 400-code responses.

* 5.0.1

    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'

    Fixed bug in SNOMED CT indexer that affected some ECL cardinality constraints inside role groups

    Fixed bug in ECL compiler that affected cardinality constraints on grouped relationships

    Fixed some problems arising when publishing older binary indexes for syndication

    Fixed a bug related to indexing extra columns in RF2 refsets, which affected the SNOMED International release

    AuditEvent reporting is now turned off by default. Consult config documentation to enable and configure endpoint/s.

    Some improvements to robustness of syndication.

* 5.0.0

    Migrate to STU3 version of FHIR

    Support inactive = true/false filter for SNOMED CT

    Http/2 support added

    Added support for explicit properties and filters on FHIR code systems

    Added support for implicit filters on FHIR code systems: concept =/is-a/is-not-a/in/not-in, parent =/in/not-in

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

    CodeSystems created/updated with content=not-present will now not list concepts in a read (concepts are still accessible through expand, lookup, etc)

    Added support for lang.X values in the property parameter of $lookup requests

    Updated properties and filters for LOINC CodeSystems including support for CLASS, CONSUMER_NAME, CLASSTYPE, ORDER_OBS and DOCUMENT_SECTION

    Added 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

    Added 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

    Updated 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 

* 4.1.18

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

* 4.1.17

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

* 4.1.16

    Fix bug related to SNOMED codes without descriptions

* 4.1.15

    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)

* 4.1.14

    Bumped SNOMED Binary Index version to 1.3.2 for following five fixes/improvements:
      1. Fix bug where | symbols in RF2 files would confuse the CSV parser during an addRf2 call
      2. Fix bug where multiple language reference sets referring to the same description id would result in multiple designations
      3. 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.
      4. Make description IDs searchable terms
      5. Ensure that FSNs are always acceptable synonyms

* 4.1.13

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

* 4.1.12

    Revert flyway change that broke database migration

* 4.1.11

    $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

    Changed syndication OAuth2 endpoint in line with NCTS change

    Fixed bug related to incorrect formats reported in Conformance resource

    Fixed bug related to international RF2 release package structure

* 4.1.10

    Fixed (benign) bug where LOINC and FHIR index versions were not incremented with change to support index version compatibility

    Fixed bug where some existing compatible indexes were not being detected in the file system, which triggered unnecessary updating of SNOMED indexes

* 4.1.9

    Fixed a limitation that prevented support for type-level $translate without a source CodeSystem / value set and only display text in a Coding/CodeableConcept

    Fixed a bug that prevented expansion of multi-version ValueSets with exclude criteria from working

    Improve $translate's automap precision

    Updated SNOMED CT binary index file format to 1.3.1 and implemented support for semantic versioning of binary indexes with forward and backward compatibility

    Fixed a bug related to empty codes in batch validate-code requests

    ValueSets that come back from $expand requests will now include the originating ValueSet's identifier and version elements (if any)

    Fixed a bug that prevented including all of a LOINC code system in a ValueSet

* 4.1.8

    Improved 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

    Improved log format to facilitate automated log processing

    Improved transactional behaviour to avoid race conditions during creates/updates/deletes

    Updated HL7 Sharable ValueSet Profile from 1.0.2 to 1.4.0

    Fixed bug in $closure where incorrect subsumptions could be computed

    Added support for the Prefer: return=representation Header

    Fixed bug in $expand that made it impossible to use count/offset to retrieve concepts beyond the maxResults threshold

* 4.1.7

    Updated IHTSDO ECL implementation to match v1.1.1

    Fix implementation of cardinality constraints in SNOMED CT 'expression' filters

    Significant speed increase for the 'automap' flavour of $translate

    Performance improvement for loading SNOMED CT's RF2 data

    Fix a bug where republished entries would not all have source links

    Fix a bug regarding incorrect diagnosis of snomed/loinc index version mismatch on startup

* 4.1.6

    Fixed handling of valueSet parameter on $validate-code

    Batch requests will now permit String values for Code-typed parameters

    Made $validate-code less dogmatic about matching the version parameter

    Fixed handling of type-level $validate requests that do not provide a resource parameter

    Allow the parameters 'valueSet' and 'source' to be used as alternatives on $translate

    Allow CORS requests from Origin file://

    Fixed bug in $closure where #additional edges > maxResults limit (default 10,000)

* 4.1.5

    Include Vary and HTML Content-Type headers for exception responses

    Improve handling of batch/transaction requests, especially regarding error handling

    Added /api/mode endpoint for querying security mode

    Support "property" parameter in batch GET $lookup

* 4.1.4

    Include Vary header with Accept and Accept-Encoding to avoid caching problems

    Include comment in Conformance to indicate which operations are supported in batch

    Fix error code for unsupported conditional deletes

    Customise CodeSystem.publisher for known editions of SNOMED (SCT-AU, AMT)

* 4.1.3

    Return a 422 error when invoking operations with ambiguous resource references (URLs)

    Include the HTTP 'Prefer' header as an acceptable CORS header

    Fix incorrect behaviour of id:present and id:missing search modifiers

    Added version search parameter for ValueSet, CodeSystem and ConceptMap

    Added system search parameter for CodeSystem

    Fixed bug with validation of multi-typed properties, e.g. ConceptMap.sourceUri

* 4.1.2

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

    Fixed bug that was causing Ontoserver to not log to file.

* 4.1.1

    Ontoserver no longer includes headers to disable caching

    $closure operation now supports arbitrary CodeSystems (with hierarchy), not just SNOMED CT

    Fixes for $closure table bug relating to the order of the added codes

    Updated to Spring-Boot 1.3.6

    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