updating from original

* [CHR-1066]

* [CHR-1066]

* [CHR-1066]

* [CHR-1066]

* [CHR-1066]

* [CHR-1066]

* [CHR-1066]

* [CHR-1066]

* [CHR-1066]

* [CHR-1066]

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* CHR-1066

* chr-1066 - add cache and test if javadoc in path

* chr-1066 - print out some debug info

* chr-1066 -fix copy/paste mistake

* chr-1066 - print debug info

* chr-1066 - print debug info

* chr-1066 - yet another print debug info

* chr-1066 - yet another print debug info

* chr-1066 - extract var to control use of local artifacts

* chr-1066 - extract var to control use of local artifacts

* chr-1066 - extract var to control use of local artifacts

* chr-1066 - print stuff

* chr-1066 - change npm config, errors and skips next lines

* chr-1066 - nes

* chr-1066 - ..

* chr-1066 - remove debug

* chr-1066 - put env vars in docker and in the bash env

* chr-1066 - put env vars in job as well, print debug

* chr-1066 - yet another try to change path.. print debug

* chr-1066 - yet another try to change path.. print debug

* chr-1066 - I am doing stupid things now...fixing copy/paste error

* chr-1066 - still not set...their documentation lies ...

* chr-1066 - still not set completely...

* chr-1066 - remove the debug echoed info

Co-authored-by: Matteo Casu <[email protected]>

* [releng] prepare 6.24.0-SNAPSHOT

* SO-3845: Handle ECL expressions in attributes' concept set ...

... definitions in MRCM validation rules

* Revert "[releng] prepare 6.24.0-SNAPSHOT"

This reverts commit 8cbd3f8.

* [releng] prepare 6.23.1-SNAPSHOT

* [releng] release 6.23.1

* [releng] prepare 6.24.0-SNAPSHOT

* [snomed.import] Set code system shortname in import details

* Added VALUE_SET, MAPPING_SET as allowed  values for supportedRefSetType

* Exposed the supportedRefSetType XML attribute values.

* SO-3853: Register ValueSet and MappingSet to contribute

* SO-3864: change cardinality of ValueSet.compose to 0..1

As of https://www.hl7.org/fhir/valueset-definitions.html#ValueSet.compose

* SO-3864: return object ID from TransactionContext.add method

* SO-3864: set clearResources to true by default in SnowOwlAppRule

* [index] Allow setting boost on all ES QueryBuilder instances

* [index] Log the number of pending cluster tasks; don't repeat messages

* SO-3864: extract common repository APIs to core.rest module

* SO-3864: extract common Resource search props to ResourceRestSearch

Introduce SnomedReferenceSetRestSearch and `POST /:path/refsets/search`
endpoint.

* SO-3864: remove unused classes from snomed.core.rest plugin

* SO-3864: support dynamic loading of available API docs

* SO-3821 Enabled search by mapPriority.

* SO-3864: extract common branch aware test infrastructure to test.commons

* SO-3864: minor changes to test.commons MANIFEST.MF

* SO-3864: expose Elasticsearch Base64 UUID generator as IDs.base64UUID()

* SO-3864: expose core.id package

* SO-3881: Remove semantic engine projects including previous ...

... implementation of SCG

https://snowowl.atlassian.net/browse/SO-3881

* SO-3864: rename ChangeRequest types

`core.rest.codesystem.ChangeRequest` to
`core.rest.domain.ResourceRequest`.
`snomed.core.rest.domain.ChangeRequest` to
`snomed.core.rest.domain.SnomedResourceRequest`.

* SO-3864: pull up getResourceLocationURI to AbstractRestService

* SO-3864: pull up comma joiner and JSON_UTF8 constants to RestExtensions

* SO-3864: fix failed SNOMED CT FHIR ValueSet API tests

* SO-3881: Implement grammar, parser and tests for SCG v2.3.1

- tests cover all available examples @
https://github.com/IHTSDO/SNOMEDCT-Languages

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Add scg modules to parent pom

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Add missing pom

https://snowowl.atlassian.net/browse/SO-3881

* SO-3864: minor API improvements

* SO-3864: minor API improvements

* SO-3864: add RestExtensions.assertCreated helper

* SO-3881: Update ECL parsing tests

- ECL v1.3 Brief Syntax examples as of today from
https://github.com/IHTSDO/SNOMEDCT-Languages

https://snowowl.atlassian.net/browse/SO-3881

* SO-3892: Change member status to active if refset already contains ...

...the inactive concept, do not duplicate members.

* SO-3881: Regenerate ECL grammar

- renamed the following rules to be in sync with the specification and
to avoid collision when ECL is mixed with other grammars:
  - Refinement -> EclRefinement
  - FocusConcept -> EclFocusConcept
  - ConceptReference -> EclConceptReference
  - AttributeGroup -> EclAttributeGroup
  - AttributeSet -> EclAttributeSet

- removed unused terminal '!'

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Regenerate QL grammar due to ECL changes

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Share basic parser tests for Query Language

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Remove unused files

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Regenerate SCG grammar to synchronize terminal names ...

among existing grammar definitions

- removed Xtend stubs

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Replace AND, OR, MINUS and COMMA with grammar terminals

- this is necessary to avoid collision with other derived language
terminals

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Replace AND, OR, MINUS and COMMA with grammar terminals

- add 'Filter' suffix to Conjunction, Disjunction and Exclusion grammar
rules to distinguish rules and terminals

* SO-3881: Share initial Xtext definition of ETL

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Share parser tests for ETL

https://snowowl.atlassian.net/browse/SO-3881

* SO-3892: Handle MemberChangeKind.CHANGE as added

* SO-3881: Prefer upper case version of AND / OR / MINUS in case of ...

ECL serialization

- generated extendable Xtext serializer classes
- added parsing tests

https://snowowl.atlassian.net/browse/SO-3881

* [core] Allow customization of component adjustment during publication

* SO-3881: Fix various issues in ETL grammar definition

- allow slot name to be unquoted with certain restrictions
- fix whitespace in TokenReplacementSlot
- introduce custom cardinality rule compared to Ecl.Cardinality
- make exclusive terminals optional in integer and decimal ranges

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Add ETL parsing tests to parent pom

https://snowowl.atlassian.net/browse/SO-3881

* [history] Ignore many-valued features altogether in HistoryInfoProvider

Copy scalar fields to an "empty" CDO revision instead of cloning the
original and unsetting the many-valued properties (which can cause an
exception, if uninitialized EAttribute lists are present on the
revision).

* SO-3864: report method not allowed errors properly

* SO-3881: Fix issues in ETL grammar definition

- rename concept replacement slots for better readability
- fix slot integer and slot decimal types
- simplify StringReplacementSlot values

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Implement detailed ETL parser tests

- added all IHTSDO templates as well

https://snowowl.atlassian.net/browse/SO-3881

* [tests] add more specific concept reactivation test cases

* SO-3893 #resolve

Fix incorrect parentage values when reactivating concept's relationships
first then the concept in two different commits.

* [export] Create general ExportResult class (filename, UUID pair)

* [releng] update changelog with 6.24.0 changes

* SO-3881: Remove xtend generated files

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Prevent xtend generated files to be committed

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Share current ABNF syntax for ECL, SCG and ETL

https://snowowl.atlassian.net/browse/SO-3881

* [snomed] accept all SctId statuses when publishing them

* [releng] update changelog with 6.24.0 changes

* SO-3858: Allow specifying namespace in random id generation

* [releng] release 6.24.0

* [releng] prepare 6.25.0-SNAPSHOT

* SO-3858: Fix generic validation rules, tests, test setup

* SO-3858: Extract language member function variable to helper method

* [cis] fix config file name of CIS product

* [core] support unprotected routes/requests

* [snomed] Update remaining references to Rf2ExportResult

* SO-3893: Relocate fix for issue to Taxonomies class (7.x, partial).

Stated OWL axiom handling is still missing.

* [tests] add more specific concept reactivation test cases (7.x)

* SO-3853: Register ValueSet and MappingSet to contribute (7.x)

* [snomed.import] Set code system shortname in import details (7.x)

* [validation] Add reference set type to OWL axiom members in... (7.x)

...GenericValidationRuleTest

* [export] Wrap reads into an IndexReadRequest in SnomedRf2ExportRequest

* [core] allow multiple unprotected requests to execute in bulk

* [core] always include responseTime metric in request log entries

* SO-3881: add ETL and SCG core bundles to snomed.core.feature

* SO-3864: set clearResources to true by default in SnowOwlAppRule

* [core] merge IndexReadRequest functionality into RepositoryRequest

* [mrcm] Remove remaining checked in source files from mrcm.model project

* [documentation] Remove non-existent project references from MANIFEST.MF

* [releng] update changelog with 7.3.0 changes

* [releng] release 7.3.0

* [releng] release 7.3.0

* [releng] update README.md with 7.3.0 release links

* [releng] prepare 7.4.0-SNAPSHOT

* [core] Ensure that all TerminologyRepositoryPlugin subclasses provide...

...a terminology repository initializer instance (used for initializing
a default code system entry for each tooling).

* [core] Fix AccessControl subclass on RepositoryClearRequest, move...

...factory method of request builder to RepositoryRequests

* [core] Implement RepositoryTransactionContext#clearContents

The implementation calls stageRemove on all instances of Revision and
subclasses that are visible on the context branch using a matchAll
query, at the time of method invocation.

* [snomed] convert NumberFormatException to BadRequestException

* [oomph] Add preference settings for .* package and static imports

* [snomed] add support for module() expand

* [api] change type of SnomedConcept.definitionStatus to SnomedConcept

Support expansion of definition status concept via definitionStatus()
expand parameter.
Remove DefinitionStatus enum literal.

* Update core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/id/IDs.java

Co-Authored-By: András Péteri <[email protected]>

* [core] update javadoc suggested in #472

b2ihealthcare/snow-owl#472 (comment)

* [api] add `id` filter to `commits` API

Related to #473.

* [api] support `affectedComponentId` details() expand parameter

Related to #473.

* Cast to distinguish from Map parameter.

* [snomed] remove unnecessary definitionStatusId field from SnomedConcept

* [snomed] fix possible definitionStatus NPE when using field selection

* SO-3123: Add support for "complex map with map block" type reference sets (#474)

- Add SnomedRefSetType enum literal for complex block map
- Handle complex block maps in SnomedRefSetUtil methods
- Add new "map block" field and refset header to SnomedRf2Headers
- Specify supported referenced component type for complex block maps in class RefSetSupport
- Add support for complex block map import; update index format
- Extend refset member create and update requests with complex block map support; ensure that class cast exceptions are translated to bad requests when inspecting member properties.
- Add support for exporting complex block maps to RF2
- Add SnomedDsvExportItemType literal for "map block" field
- Add SCTID of complex block map identifier parent concept
- Add complex block map type test cases to SNOMED e2e tests
- Update FHIR's SnomedConceptMapApiProvider
- Update FHIR concept map test cases

* Exchanged descriptions.

* [core] remove IComponent.ID_FUNCTION

* [snomed] fix definitionStatus() expansion issues

* [snomed] add acceptabilities() expansion to /descriptions API

* [snomed] remove CaseSignificance enum literals

* [snomed] support caseSignificance() expansion on descriptions

* [core] fix unauthorized issue when executing console commands

* SO-3123: Convert mapBlock field to an Integer when importing

* SO-3858: Add support for nested, and reverse nested aggregation

* [snomed] remove CharacteristicType enum literals

* [snomed] remove RelationshipModifier enum literals

* [snomed] support characteristicType() and modifier() expansion...

...on relationships

* [qa] fix lgtm issue https://lgtm.com/rules/1511220334423/

* Revert "[qa] fix lgtm issue https://lgtm.com/rules/1511220334423/"

This reverts commit 628bad4.

* [snomed] run effective time restore only in non-import scenarios

* [qa] suppress lgtm warning https://lgtm.com/rules/1511220334423/

* Upgrade to Elasticsearch 7.x (#478)

* [index] bump version to Elasticsearch 7.5.2
* [index] fix tokenizer/analyzer compile errors
* [index] use indices level when fetching cluster health
* [index] fix EsNode initialization
* [index] fix client compile errors
* Fix type and other warnings printed by ES API.
* [index] add CMS GC config to index tests
* Fixes [parent] data too large issues during tests.
* [rf2] reduce RF2 exporter scroll timeout to 1m
* [tests] fix negative scores in SortIndexTest
* [api] remove scrollId and scrollKeepAlive from Java API
* Use searchAfter + branch@timestamp for efficient data snapshot paging/scrolling.
* [core] remove scrollId from core models and API
* [snomed] remove scrollId from snomed models and API
* [rest] remove scrollId from core REST API
* [snomed] remove scrollId from snomed REST API
* [rf2] use branch@timestamp for RF2 exports
* [build] add CMS GC settings to all tycho surefire executions
* [launch] add CMS GC settings to all test launch configs
* [qa] fix lgtm issues https://lgtm.com/rules/2049510531/
* [index] use bool query with should clauses for term filters with more than the configured index.max_terms_count.
* Also make it possible to configure both maxTermsCount and resultWindow values from snowowl.yml (repository.index config).
* [index] fix some of the type_removal warnings reported by ES
* The remaining warnings thrown by the Mapping API, but we cannot remove it yet, due to our dependency to the TCP client infrastructure. Those warnings will be eliminated once ES 8 is out and we decide to upgrade to that (which will remove the TCP client functionality entirely).
Fix some java compile warnings as well. And also add some serialVersionUIDs.
* [index] fix nested field name in terms queries. Also fix decimal value conversion when number of terms is less than the
max_terms_count.
* [index] searches should always track total hits accurately
* [core] update comments in SearchResourceRequestIterator
* [index] aggregations should always track total hits accurately
* [index] fix typo

* [docker] bump elasticsearch-oss image version to 7.5.2

* [index] prevent unnecessary mapping updates during startup

* [qa] fix lgtm issue https://lgtm.com/rules/1930000368/

* [qa] fix lgtm issue https://lgtm.com/rules/9990077/

* [qa] fix lgtm issue https://lgtm.com/rules/11000068/

* [qa] fix lgtm issue https://lgtm.com/rules/9990077/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] ignore lgtm issue https://lgtm.com/rules/1954750296/ in Base64

* [qa] ignore lgtm issue https://lgtm.com/rules/1954750296/ (JavaBinCodec)

* [qa] fix lgtm issue https://lgtm.com/rules/1507082716110/

* [snomed] remove InactivationIndicator and AssociationType enum literals

Use new InactivationProperties object to specify indicator and
association target values during component inactivation.
Make processInactivation method generic in SnomedComponentUpdateRequest.

* [index] Reorder classpath entries, remove source attachment paths

* [dev] fix launch configurations

Co-authored-by: Gábor Nagy <[email protected]>
Co-authored-by: AAAlinaaa <[email protected]>
Co-authored-by: Mark Czotter <[email protected]>
Co-authored-by: Balazs Banfai <[email protected]>
Co-authored-by: Gabriella Deak <[email protected]>
Co-authored-by: András Péteri <[email protected]>

* chr-1516 - customize snowowl.yml, Dockerfile, create Makefile, adjust circleCi config

* chr-1516 - for testing make circleCi run on all branches but the master

* chr-1516 - for testing change circleCi

* chr-1516 - fix inentation

* chr-1516 -install maven

* chr-1516 - install maven...

* chr-1516 - install maven again

* chr-1516 - install maven again ???

* chr-1516 - use wrapper...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - ..

* chr-1516 - split builds... why is file not found?!?!

* chr-1516 - split builds... why is file not found?!?!

* chr-1516 - push docker

* chr-1516 - test if this will move the docs files where they have to be

* chr-1516 - test build in circle ci

* chr-1516 - test build in circle ci

* chr-1516 - test build in circle ci

* chr-1516 - test build in circle ci again

* chr-1516 - test build in circle ci again2

* chr-1516 - print  debug

* chr-1516 - print other debug info, not so detailed

* chr-1516 - print other debug info, not so detailed

* chr-1516 - replace mvn plugin

* chr-1516 - replace mvn plugin

* chr-1516 - try stable node version

* chr-1516 - try stable node version without sudo

* chr-1516 - try stable node version without sudo

* chr-1516 - try updating node stuff

* chr-1516 - try updating node stuff more

* chr-1516 - try updating docker image

* chr-1516 - try updating make..

* chr-1516 - install npm

* chr-1516 - install npm

* chr-1516 - release libs on merge to master, release docker on tag

* chr-1516 - release to dev on master merge, release to staging on tag

* chr-1516 - code review changes

* chr-1516 - fix staging deploy step

* chr-1516 - fix staging deploy step

* chr-1516 - fix staging deploy step

* chr-1516 - fix deployment - install curl + debug it

* chr-1516 - fix release version

* chr-1516 - get rid of unnecessary env var

* chr-1516 - add langs again

* chr-1516 - revert debug config

* SO-3892: Change member status to active if refset already contains ...

...the inactive concept, do not duplicate members.

* SO-3881: Regenerate ECL grammar

- renamed the following rules to be in sync with the specification and
to avoid collision when ECL is mixed with other grammars:
  - Refinement -> EclRefinement
  - FocusConcept -> EclFocusConcept
  - ConceptReference -> EclConceptReference
  - AttributeGroup -> EclAttributeGroup
  - AttributeSet -> EclAttributeSet

- removed unused terminal '!'

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Regenerate QL grammar due to ECL changes

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Share basic parser tests for Query Language

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Remove unused files

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Regenerate SCG grammar to synchronize terminal names ...

among existing grammar definitions

- removed Xtend stubs

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Replace AND, OR, MINUS and COMMA with grammar terminals

- this is necessary to avoid collision with other derived language
terminals

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Replace AND, OR, MINUS and COMMA with grammar terminals

- add 'Filter' suffix to Conjunction, Disjunction and Exclusion grammar
rules to distinguish rules and terminals

* SO-3881: Share initial Xtext definition of ETL

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Share parser tests for ETL

https://snowowl.atlassian.net/browse/SO-3881

* SO-3892: Handle MemberChangeKind.CHANGE as added

* SO-3881: Prefer upper case version of AND / OR / MINUS in case of ...

ECL serialization

- generated extendable Xtext serializer classes
- added parsing tests

https://snowowl.atlassian.net/browse/SO-3881

* [core] Allow customization of component adjustment during publication

* SO-3881: Fix various issues in ETL grammar definition

- allow slot name to be unquoted with certain restrictions
- fix whitespace in TokenReplacementSlot
- introduce custom cardinality rule compared to Ecl.Cardinality
- make exclusive terminals optional in integer and decimal ranges

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Add ETL parsing tests to parent pom

https://snowowl.atlassian.net/browse/SO-3881

* [history] Ignore many-valued features altogether in HistoryInfoProvider

Copy scalar fields to an "empty" CDO revision instead of cloning the
original and unsetting the many-valued properties (which can cause an
exception, if uninitialized EAttribute lists are present on the
revision).

* SO-3864: report method not allowed errors properly

* SO-3881: Fix issues in ETL grammar definition

- rename concept replacement slots for better readability
- fix slot integer and slot decimal types
- simplify StringReplacementSlot values

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Implement detailed ETL parser tests

- added all IHTSDO templates as well

https://snowowl.atlassian.net/browse/SO-3881

* [tests] add more specific concept reactivation test cases

* SO-3893 #resolve

Fix incorrect parentage values when reactivating concept's relationships
first then the concept in two different commits.

* [export] Create general ExportResult class (filename, UUID pair)

* [releng] update changelog with 6.24.0 changes

* SO-3881: Remove xtend generated files

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Prevent xtend generated files to be committed

https://snowowl.atlassian.net/browse/SO-3881

* SO-3881: Share current ABNF syntax for ECL, SCG and ETL

https://snowowl.atlassian.net/browse/SO-3881

* [snomed] accept all SctId statuses when publishing them

* [releng] update changelog with 6.24.0 changes

* SO-3858: Allow specifying namespace in random id generation

* [releng] release 6.24.0

* [releng] prepare 6.25.0-SNAPSHOT

* SO-3858: Fix generic validation rules, tests, test setup

* SO-3858: Extract language member function variable to helper method

* [cis] fix config file name of CIS product

* [core] support unprotected routes/requests

* [snomed] Update remaining references to Rf2ExportResult

* SO-3893: Relocate fix for issue to Taxonomies class (7.x, partial).

Stated OWL axiom handling is still missing.

* [tests] add more specific concept reactivation test cases (7.x)

* SO-3853: Register ValueSet and MappingSet to contribute (7.x)

* [snomed.import] Set code system shortname in import details (7.x)

* [validation] Add reference set type to OWL axiom members in... (7.x)

...GenericValidationRuleTest

* [export] Wrap reads into an IndexReadRequest in SnomedRf2ExportRequest

* [core] allow multiple unprotected requests to execute in bulk

* [core] always include responseTime metric in request log entries

* SO-3881: add ETL and SCG core bundles to snomed.core.feature

* SO-3864: set clearResources to true by default in SnowOwlAppRule

* [core] merge IndexReadRequest functionality into RepositoryRequest

* [mrcm] Remove remaining checked in source files from mrcm.model project

* [documentation] Remove non-existent project references from MANIFEST.MF

* [releng] update changelog with 7.3.0 changes

* [releng] release 7.3.0

* [releng] release 7.3.0

* [releng] update README.md with 7.3.0 release links

* [releng] prepare 7.4.0-SNAPSHOT

* [core] Ensure that all TerminologyRepositoryPlugin subclasses provide...

...a terminology repository initializer instance (used for initializing
a default code system entry for each tooling).

* [core] Fix AccessControl subclass on RepositoryClearRequest, move...

...factory method of request builder to RepositoryRequests

* [core] Implement RepositoryTransactionContext#clearContents

The implementation calls stageRemove on all instances of Revision and
subclasses that are visible on the context branch using a matchAll
query, at the time of method invocation.

* [snomed] convert NumberFormatException to BadRequestException

* [oomph] Add preference settings for .* package and static imports

* SO-3882: Add ability to define additional component deletion policies...

... in implementations of TerminologyRepositoryConfigurers

https://snowowl.atlassian.net/browse/SO-3882

* SO-3882: Fix license header

https://snowowl.atlassian.net/browse/SO-3882

* SO-3882: Fix invalid type in deletion policy rule

https://snowowl.atlassian.net/browse/SO-3882

* [snomed] add support for module() expand

* [api] change type of SnomedConcept.definitionStatus to SnomedConcept

Support expansion of definition status concept via definitionStatus()
expand parameter.
Remove DefinitionStatus enum literal.

* Update core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/id/IDs.java

Co-Authored-By: András Péteri <[email protected]>

* [core] update javadoc suggested in #472

b2ihealthcare/snow-owl#472 (comment)

* [api] add `id` filter to `commits` API

Related to #473.

* [api] support `affectedComponentId` details() expand parameter

Related to #473.

* Cast to distinguish from Map parameter.

* SO-3889: Move Charmatcher for invalid file name characters to FileUtils

https://snowowl.atlassian.net/browse/SO-3889

* [snomed] remove unnecessary definitionStatusId field from SnomedConcept

* [snomed] fix possible definitionStatus NPE when using field selection

* SO-3123: Add support for "complex map with map block" type reference sets (#474)

- Add SnomedRefSetType enum literal for complex block map
- Handle complex block maps in SnomedRefSetUtil methods
- Add new "map block" field and refset header to SnomedRf2Headers
- Specify supported referenced component type for complex block maps in class RefSetSupport
- Add support for complex block map import; update index format
- Extend refset member create and update requests with complex block map support; ensure that class cast exceptions are translated to bad requests when inspecting member properties.
- Add support for exporting complex block maps to RF2
- Add SnomedDsvExportItemType literal for "map block" field
- Add SCTID of complex block map identifier parent concept
- Add complex block map type test cases to SNOMED e2e tests
- Update FHIR's SnomedConceptMapApiProvider
- Update FHIR concept map test cases

* Exchanged descriptions.

* [core] remove IComponent.ID_FUNCTION

* [snomed] fix definitionStatus() expansion issues

* [snomed] add acceptabilities() expansion to /descriptions API

* [snomed] remove CaseSignificance enum literals

* [snomed] support caseSignificance() expansion on descriptions

* [core] fix unauthorized issue when executing console commands

* SO-3123: Convert mapBlock field to an Integer when importing

* SO-3858: Add support for nested, and reverse nested aggregation

* [snomed] remove CharacteristicType enum literals

* [snomed] remove RelationshipModifier enum literals

* [snomed] support characteristicType() and modifier() expansion...

...on relationships

* [qa] fix lgtm issue https://lgtm.com/rules/1511220334423/

* Revert "[qa] fix lgtm issue https://lgtm.com/rules/1511220334423/"

This reverts commit 628bad4.

* [snomed] run effective time restore only in non-import scenarios

* [qa] suppress lgtm warning https://lgtm.com/rules/1511220334423/

* Upgrade to Elasticsearch 7.x (#478)

* [index] bump version to Elasticsearch 7.5.2
* [index] fix tokenizer/analyzer compile errors
* [index] use indices level when fetching cluster health
* [index] fix EsNode initialization
* [index] fix client compile errors
* Fix type and other warnings printed by ES API.
* [index] add CMS GC config to index tests
* Fixes [parent] data too large issues during tests.
* [rf2] reduce RF2 exporter scroll timeout to 1m
* [tests] fix negative scores in SortIndexTest
* [api] remove scrollId and scrollKeepAlive from Java API
* Use searchAfter + branch@timestamp for efficient data snapshot paging/scrolling.
* [core] remove scrollId from core models and API
* [snomed] remove scrollId from snomed models and API
* [rest] remove scrollId from core REST API
* [snomed] remove scrollId from snomed REST API
* [rf2] use branch@timestamp for RF2 exports
* [build] add CMS GC settings to all tycho surefire executions
* [launch] add CMS GC settings to all test launch configs
* [qa] fix lgtm issues https://lgtm.com/rules/2049510531/
* [index] use bool query with should clauses for term filters with more than the configured index.max_terms_count.
* Also make it possible to configure both maxTermsCount and resultWindow values from snowowl.yml (repository.index config).
* [index] fix some of the type_removal warnings reported by ES
* The remaining warnings thrown by the Mapping API, but we cannot remove it yet, due to our dependency to the TCP client infrastructure. Those warnings will be eliminated once ES 8 is out and we decide to upgrade to that (which will remove the TCP client functionality entirely).
Fix some java compile warnings as well. And also add some serialVersionUIDs.
* [index] fix nested field name in terms queries. Also fix decimal value conversion when number of terms is less than the
max_terms_count.
* [index] searches should always track total hits accurately
* [core] update comments in SearchResourceRequestIterator
* [index] aggregations should always track total hits accurately
* [index] fix typo

* [docker] bump elasticsearch-oss image version to 7.5.2

* [index] prevent unnecessary mapping updates during startup

* [qa] fix lgtm issue https://lgtm.com/rules/1930000368/

* [qa] fix lgtm issue https://lgtm.com/rules/9990077/

* [qa] fix lgtm issue https://lgtm.com/rules/11000068/

* [qa] fix lgtm issue https://lgtm.com/rules/9990077/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] ignore lgtm issue https://lgtm.com/rules/1954750296/ in Base64

* [qa] ignore lgtm issue https://lgtm.com/rules/1954750296/ (JavaBinCodec)

* [qa] fix lgtm issue https://lgtm.com/rules/1507082716110/

* [snomed] remove InactivationIndicator and AssociationType enum literals

Use new InactivationProperties object to specify indicator and
association target values during component inactivation.
Make processInactivation method generic in SnomedComponentUpdateRequest.

* [index] Reorder classpath entries, remove source attachment paths

* [dev] fix launch configurations

* [ecl] add a handy `Ecl.or(expressions)` helper method

* [build] fix snomed.validation.snomed build.properties

* [api] fix incorrect conversion of null values to empty filter values...

...in refset API (refSetType, referencedComponentType and
mapTargetComponentType filters).

Fixes #482.

* [validation] fix setScrollId call in rule666

* [tests] add missing scripting.groovy fragment

* [auth] support pre-7.x LDAP permissions

* [snomed] Fix permission level of SNOMED component create requests

* [core] Make CLI-authorized IEventBus accessible to console scripts

* [validation] use index bulk delete in ValidationIssueDeleteRequest

* [snomed] Unset effective time for members inactivated by...

...ComponentInactivationChangeProcessor (activated by the inactivation
of referenced core components and containing reference sets).

* [snomed] Add filter to inactivate currently active components only

* [validation] use dash characters to separate relationships label parts

* [commons] Re-introduce JDBC helper class and H2 library

* [api] support unpublished effectiveTime filter in REST API (fixes #485)

* [snomed] restrict http-core lib to 4.5.3,4.5.4

* [snomed] do not report unauthorized and forbidden errors in the log

* [tests] reduce extra tp requirement redundancy in test plugins

* [qa] remove unused, deprecated, obsolete classes and functionality

* [api] allow descriptions to be created without any lang refset members

* [snomed] Don't inactivate referring members which have staged changes

This causes problems for eg. existing inactivation indicator members.

* SO-3917: Create CIS status update bash script

* [index] fix calculation of RevisionCompare added/changed/removed numbers

* [cis] fix API endpoint call in change_id_status script

* [tests] disable snomed validation tests in TRAVIS env

* [commons] Fix potential ResultSet resource leak in JdbcUtils

* [validation.snomed] Skip Travis CI tests using a profile

* [core] rename numberOfWorkers configuration key to maxThreads

Change its default value to `200`.
Change EventBus thread pool configuration to be not fixed, keep
Runtime.availableProcessor() or maxThreads (at least 1) as core threads,
and the configured maxThreads as maximum number of allowed event bus
threads.
Deprecate getNumberOfWorkers() and setNumberOfWorkers(), keeping it for
compatibility reasons.

* [cis] use Assigned for the -a option

* [core] keep excess threads available for 1 minute before terminating

* [tests] reduce maxThreads to 8 in snomed.core.rest.tests

* [build] enable travis-ci profile in .travis.yml

* [docs] upgrade api-docs dependencies to latest version

* [tests] disable EclSerializerTest temporarily

* [api] fix incorrect paramType value for nested query parameters

Fixes #441

* [eventbus] remove unnecessary finalize method (unsupported from java9)

* [snomed] use Promise chaining in SnomedEclRefinementEvaluator

* [tests] enable EclSerializerTest

* [api] make sure we time out from ECL evaluations after 3 minutes

* [core] change default REST API timeout to 2 minutes in most of the...

...endpoints

Add timeout values to server side Promise.getSync calls.

* [snomed] fix OWL expression conversion issue

* [build] skip validation test execution via skip xml node

* [tests] increase max number of threads in snomed tests

* [core] constrain concurrency level to the 1-4 range

* [ci] setup maven GitHub action workflow

* [ci] add Java CI GitHub action badge to README

* [doc] replace Travis shield badge...

...with GitHub workflow badge

* [ci] add .m2 cache step

* [core] use custom queue implementation and rejection policy...

...to properly scale eventbus worker thread pool to the configured
maxThreads.

Additional info:
https://stackoverflow.com/questions/15485840/threadpoolexecutor-with-unbounded-queue-not-creating-new-threads

* [ci] run mvn clean verify in GH workflow

* [ci] cache core.rest/api-docs npm dependencies

* [tests] use default-test execution instead of custom execution...

...in validation.snomed module tests.

Fixes build failures in Travis and GH Workflow.

* [test] remove unnecessary maxThreads configuration key from snomed tests

* [ci] add back snomed.core.rest.tests module

* [core] Add ApiError JSON object to errored out remote jobs where the...

...source is not an instance of ApiException

* [snomed] Allow filtering reference set members by complex map block

* [ci] add missing project to dist project

Reports code coverage from tests ql.tests, etl.tests, scg.tests modules.

* [ci] remove unnecessary travis-ci profile from script

* [request] Remove unnecessary method override

* SO-3885: Allow SnomedBulkRequest instantiation outside of package

https://snowowl.atlassian.net/browse/SO-3885

* SO-3916 #resolve

Set definitionStatusId to primitive when inactivating concept.
Also, support definitionStatusId declaration when creating concept.

* [index] use list instead of treeset in mergeSources COMMIT script param

* [compare] Avoid counting versioning among new compnents

* [commons] Extend constructor to find resources relative to class ...

... in case the test bundle is a fragment

* [datastore] Clean up CompositeComponentDeletionPolicy

* Test plugins optional.

* [snomed] Allow external configuration of namespace-module assigners

* SO-3882: Refactor CompositeComponentDeletionPolicy

- use ComponentDeletionPolicy instead of Predicate
- add mergeWith method to combine multiple composite policies

https://snowowl.atlassian.net/browse/SO-3882

* [config] remove unnecessary systemUser configuration key

* [api] fix bug details() expansion affectedComponentId filtering

Fixes #473.

* [core] fix RevisionSegment.withEnd(newEnd) logic

Do not extend the segment to later timestamps than the currently set end
value. Fixes branch@timestamp scenarios where multiple parent branches
are participating in the search.

* [index] increase embedded Elasticsearch max_buckets to 1.500.000...

...temporarily

A proper fix for large aggregations using composite agg is planned for
v7.5.0.

* Revert "[core] fix RevisionSegment.withEnd(newEnd) logic"

This reverts commit 7db86ac.

* [core] use new RevisionSegment.restrictEnd(restrictTo) method...

...to restrict segments to certain timestamp value.

Fixes branch@timestamp scenarios where multiple parent branches with
shorter segments are participating in the search.

* [core] remove diagnostic code statement

* [cis] allow ID registration of already published IDs

* [cis] remove unnecessary validation of incoming ID status changes

Changing ID status should work in a best effort manner and it should not
fail and report back any IDs that cannot be transitioned to the desired
state.

* [tests] fix failed DefaultSnomedIdentifierServiceTest case

* [releng] update changelog with 7.4.0 changes

* Bump netty.version from 4.1.43.Final to 4.1.45.Final

Bumps `netty.version` from 4.1.43.Final to 4.1.45.Final.

Updates `netty-buffer` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-codec` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-codec-http` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-common` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-handler` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-resolver` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-transport` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Signed-off-by: dependabot[bot] <[email protected]>

* [ci] add codecov upload step to maven workflow

* Update maven.yml

* [ci] trigger the build workflow on pull request

* [ci] trigger build only when...

...push, pr changes against the 7.x branch

* [commons] Make set of invalid resource characters visible

* [config] remove deprecated `snomed.ids` configuration key

* [classify] refactor namespace and module assignment logic

Require module and namespace to be specified in SaveJobRequests.
Remove defaultModule and defaultNamespace from snowowl.yml configuratio
file.
Allow multiple assigner instances from the same type, fixes parallel
classification issues in different extension branches.
Add mandatory `module` and `namespace` parameters to classification save
endpoint.

* [classify] add NotEmpty annotation to ClassificationRunRestUpdate

* [classify] remove 'default' assigner type from classification run update

* [releng] change commons.logging require-bundle directives to...

...import-package statements

* [releng] add commons-logging jar dependency to core.rest module

* [releng] release 7.4.0

* [core] Remove SNAPSHOT suffix from logback.config

* [releng] release 7.4.0 (update links)

* [releng] prepare 7.5.0-SNAPSHOT

* [docs] add from-6x migration guide

* [scripts] remove db related scripts from assembly

* [docs] add backup guide

* [docs] update JDK links

* [api] fix malformed Location header values

Fixes #500

* [api] fix possible NPE when not supplying any acceptability values

* revert package-lock.json

* regenerate lock

* chr-1516- get rid of the github config, duplicate of circleCi or unnecessary

Co-authored-by: Gabriella Deak <[email protected]>
Co-authored-by: Gábor Nagy <[email protected]>
Co-authored-by: Mark Czotter <[email protected]>
Co-authored-by: András Péteri <[email protected]>
Co-authored-by: AAAlinaaa <[email protected]>
Co-authored-by: Balazs Banfai <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* chr-1516- revert accidentally overridden pom bit

* chr-1516- change lang config

* [cis] fix config file name of CIS product

* [core] support unprotected routes/requests

* [snomed] Update remaining references to Rf2ExportResult

* SO-3893: Relocate fix for issue to Taxonomies class (7.x, partial).

Stated OWL axiom handling is still missing.

* [tests] add more specific concept reactivation test cases (7.x)

* SO-3853: Register ValueSet and MappingSet to contribute (7.x)

* [snomed.import] Set code system shortname in import details (7.x)

* [validation] Add reference set type to OWL axiom members in... (7.x)

...GenericValidationRuleTest

* [export] Wrap reads into an IndexReadRequest in SnomedRf2ExportRequest

* [core] allow multiple unprotected requests to execute in bulk

* [core] always include responseTime metric in request log entries

* SO-3881: add ETL and SCG core bundles to snomed.core.feature

* SO-3864: set clearResources to true by default in SnowOwlAppRule

* [core] merge IndexReadRequest functionality into RepositoryRequest

* [mrcm] Remove remaining checked in source files from mrcm.model project

* [documentation] Remove non-existent project references from MANIFEST.MF

* [releng] update changelog with 7.3.0 changes

* [releng] release 7.3.0

* [releng] release 7.3.0

* [releng] update README.md with 7.3.0 release links

* [releng] prepare 7.4.0-SNAPSHOT

* [core] Ensure that all TerminologyRepositoryPlugin subclasses provide...

...a terminology repository initializer instance (used for initializing
a default code system entry for each tooling).

* [core] Fix AccessControl subclass on RepositoryClearRequest, move...

...factory method of request builder to RepositoryRequests

* [core] Implement RepositoryTransactionContext#clearContents

The implementation calls stageRemove on all instances of Revision and
subclasses that are visible on the context branch using a matchAll
query, at the time of method invocation.

* [snomed] convert NumberFormatException to BadRequestException

* [oomph] Add preference settings for .* package and static imports

* SO-3882: Add ability to define additional component deletion policies...

... in implementations of TerminologyRepositoryConfigurers

https://snowowl.atlassian.net/browse/SO-3882

* SO-3882: Fix license header

https://snowowl.atlassian.net/browse/SO-3882

* SO-3882: Fix invalid type in deletion policy rule

https://snowowl.atlassian.net/browse/SO-3882

* [snomed] add support for module() expand

* [api] change type of SnomedConcept.definitionStatus to SnomedConcept

Support expansion of definition status concept via definitionStatus()
expand parameter.
Remove DefinitionStatus enum literal.

* Update core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/id/IDs.java

Co-Authored-By: András Péteri <[email protected]>

* [core] update javadoc suggested in #472

b2ihealthcare/snow-owl#472 (comment)

* [api] add `id` filter to `commits` API

Related to #473.

* [api] support `affectedComponentId` details() expand parameter

Related to #473.

* Cast to distinguish from Map parameter.

* SO-3889: Move Charmatcher for invalid file name characters to FileUtils

https://snowowl.atlassian.net/browse/SO-3889

* [snomed] remove unnecessary definitionStatusId field from SnomedConcept

* [snomed] fix possible definitionStatus NPE when using field selection

* SO-3123: Add support for "complex map with map block" type reference sets (#474)

- Add SnomedRefSetType enum literal for complex block map
- Handle complex block maps in SnomedRefSetUtil methods
- Add new "map block" field and refset header to SnomedRf2Headers
- Specify supported referenced component type for complex block maps in class RefSetSupport
- Add support for complex block map import; update index format
- Extend refset member create and update requests with complex block map support; ensure that class cast exceptions are translated to bad requests when inspecting member properties.
- Add support for exporting complex block maps to RF2
- Add SnomedDsvExportItemType literal for "map block" field
- Add SCTID of complex block map identifier parent concept
- Add complex block map type test cases to SNOMED e2e tests
- Update FHIR's SnomedConceptMapApiProvider
- Update FHIR concept map test cases

* Exchanged descriptions.

* [core] remove IComponent.ID_FUNCTION

* [snomed] fix definitionStatus() expansion issues

* [snomed] add acceptabilities() expansion to /descriptions API

* [snomed] remove CaseSignificance enum literals

* [snomed] support caseSignificance() expansion on descriptions

* [core] fix unauthorized issue when executing console commands

* SO-3123: Convert mapBlock field to an Integer when importing

* SO-3858: Add support for nested, and reverse nested aggregation

* [snomed] remove CharacteristicType enum literals

* [snomed] remove RelationshipModifier enum literals

* [snomed] support characteristicType() and modifier() expansion...

...on relationships

* [qa] fix lgtm issue https://lgtm.com/rules/1511220334423/

* Revert "[qa] fix lgtm issue https://lgtm.com/rules/1511220334423/"

This reverts commit 628bad4.

* [snomed] run effective time restore only in non-import scenarios

* [qa] suppress lgtm warning https://lgtm.com/rules/1511220334423/

* Upgrade to Elasticsearch 7.x (#478)

* [index] bump version to Elasticsearch 7.5.2
* [index] fix tokenizer/analyzer compile errors
* [index] use indices level when fetching cluster health
* [index] fix EsNode initialization
* [index] fix client compile errors
* Fix type and other warnings printed by ES API.
* [index] add CMS GC config to index tests
* Fixes [parent] data too large issues during tests.
* [rf2] reduce RF2 exporter scroll timeout to 1m
* [tests] fix negative scores in SortIndexTest
* [api] remove scrollId and scrollKeepAlive from Java API
* Use searchAfter + branch@timestamp for efficient data snapshot paging/scrolling.
* [core] remove scrollId from core models and API
* [snomed] remove scrollId from snomed models and API
* [rest] remove scrollId from core REST API
* [snomed] remove scrollId from snomed REST API
* [rf2] use branch@timestamp for RF2 exports
* [build] add CMS GC settings to all tycho surefire executions
* [launch] add CMS GC settings to all test launch configs
* [qa] fix lgtm issues https://lgtm.com/rules/2049510531/
* [index] use bool query with should clauses for term filters with more than the configured index.max_terms_count.
* Also make it possible to configure both maxTermsCount and resultWindow values from snowowl.yml (repository.index config).
* [index] fix some of the type_removal warnings reported by ES
* The remaining warnings thrown by the Mapping API, but we cannot remove it yet, due to our dependency to the TCP client infrastructure. Those warnings will be eliminated once ES 8 is out and we decide to upgrade to that (which will remove the TCP client functionality entirely).
Fix some java compile warnings as well. And also add some serialVersionUIDs.
* [index] fix nested field name in terms queries. Also fix decimal value conversion when number of terms is less than the
max_terms_count.
* [index] searches should always track total hits accurately
* [core] update comments in SearchResourceRequestIterator
* [index] aggregations should always track total hits accurately
* [index] fix typo

* [docker] bump elasticsearch-oss image version to 7.5.2

* [index] prevent unnecessary mapping updates during startup

* [qa] fix lgtm issue https://lgtm.com/rules/1930000368/

* [qa] fix lgtm issue https://lgtm.com/rules/9990077/

* [qa] fix lgtm issue https://lgtm.com/rules/11000068/

* [qa] fix lgtm issue https://lgtm.com/rules/9990077/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] fix lgtm issue https://lgtm.com/rules/2049510531/

* [qa] ignore lgtm issue https://lgtm.com/rules/1954750296/ in Base64

* [qa] ignore lgtm issue https://lgtm.com/rules/1954750296/ (JavaBinCodec)

* [qa] fix lgtm issue https://lgtm.com/rules/1507082716110/

* [snomed] remove InactivationIndicator and AssociationType enum literals

Use new InactivationProperties object to specify indicator and
association target values during component inactivation.
Make processInactivation method generic in SnomedComponentUpdateRequest.

* [index] Reorder classpath entries, remove source attachment paths

* [dev] fix launch configurations

* [ecl] add a handy `Ecl.or(expressions)` helper method

* [build] fix snomed.validation.snomed build.properties

* [api] fix incorrect conversion of null values to empty filter values...

...in refset API (refSetType, referencedComponentType and
mapTargetComponentType filters).

Fixes #482.

* [validation] fix setScrollId call in rule666

* [tests] add missing scripting.groovy fragment

* [auth] support pre-7.x LDAP permissions

* [snomed] Fix permission level of SNOMED component create requests

* [core] Make CLI-authorized IEventBus accessible to console scripts

* [validation] use index bulk delete in ValidationIssueDeleteRequest

* [snomed] Unset effective time for members inactivated by...

...ComponentInactivationChangeProcessor (activated by the inactivation
of referenced core components and containing reference sets).

* [snomed] Add filter to inactivate currently active components only

* [validation] use dash characters to separate relationships label parts

* [commons] Re-introduce JDBC helper class and H2 library

* [api] support unpublished effectiveTime filter in REST API (fixes #485)

* [snomed] restrict http-core lib to 4.5.3,4.5.4

* [snomed] do not report unauthorized and forbidden errors in the log

* [tests] reduce extra tp requirement redundancy in test plugins

* [qa] remove unused, deprecated, obsolete classes and functionality

* [api] allow descriptions to be created without any lang refset members

* [snomed] Don't inactivate referring members which have staged changes

This causes problems for eg. existing inactivation indicator members.

* SO-3917: Create CIS status update bash script

* [index] fix calculation of RevisionCompare added/changed/removed numbers

* [cis] fix API endpoint call in change_id_status script

* [tests] disable snomed validation tests in TRAVIS env

* [commons] Fix potential ResultSet resource leak in JdbcUtils

* [validation.snomed] Skip Travis CI tests using a profile

* [core] rename numberOfWorkers configuration key to maxThreads

Change its default value to `200`.
Change EventBus thread pool configuration to be not fixed, keep
Runtime.availableProcessor() or maxThreads (at least 1) as core threads,
and the configured maxThreads as maximum number of allowed event bus
threads.
Deprecate getNumberOfWorkers() and setNumberOfWorkers(), keeping it for
compatibility reasons.

* [cis] use Assigned for the -a option

* [core] keep excess threads available for 1 minute before terminating

* [tests] reduce maxThreads to 8 in snomed.core.rest.tests

* [build] enable travis-ci profile in .travis.yml

* [docs] upgrade api-docs dependencies to latest version

* [tests] disable EclSerializerTest temporarily

* [api] fix incorrect paramType value for nested query parameters

Fixes #441

* [eventbus] remove unnecessary finalize method (unsupported from java9)

* [snomed] use Promise chaining in SnomedEclRefinementEvaluator

* [tests] enable EclSerializerTest

* [api] make sure we time out from ECL evaluations after 3 minutes

* [core] change default REST API timeout to 2 minutes in most of the...

...endpoints

Add timeout values to server side Promise.getSync calls.

* [snomed] fix OWL expression conversion issue

* [build] skip validation test execution via skip xml node

* [tests] increase max number of threads in snomed tests

* [core] constrain concurrency level to the 1-4 range

* [ci] setup maven GitHub action workflow

* [ci] add Java CI GitHub action badge to README

* [doc] replace Travis shield badge...

...with GitHub workflow badge

* [ci] add .m2 cache step

* [core] use custom queue implementation and rejection policy...

...to properly scale eventbus worker thread pool to the configured
maxThreads.

Additional info:
https://stackoverflow.com/questions/15485840/threadpoolexecutor-with-unbounded-queue-not-creating-new-threads

* [ci] run mvn clean verify in GH workflow

* [ci] cache core.rest/api-docs npm dependencies

* [tests] use default-test execution instead of custom execution...

...in validation.snomed module tests.

Fixes build failures in Travis and GH Workflow.

* [test] remove unnecessary maxThreads configuration key from snomed tests

* [ci] add back snomed.core.rest.tests module

* [core] Add ApiError JSON object to errored out remote jobs where the...

...source is not an instance of ApiException

* [snomed] Allow filtering reference set members by complex map block

* [ci] add missing project to dist project

Reports code coverage from tests ql.tests, etl.tests, scg.tests modules.

* [ci] remove unnecessary travis-ci profile from script

* [request] Remove unnecessary method override

* SO-3885: Allow SnomedBulkRequest instantiation outside of package

https://snowowl.atlassian.net/browse/SO-3885

* SO-3916 #resolve

Set definitionStatusId to primitive when inactivating concept.
Also, support definitionStatusId declaration when creating concept.

* [index] use list instead of treeset in mergeSources COMMIT script param

* [compare] Avoid counting versioning among new compnents

* [commons] Extend constructor to find resources relative to class ...

... in case the test bundle is a fragment

* [datastore] Clean up CompositeComponentDeletionPolicy

* Test plugins optional.

* [snomed] Allow external configuration of namespace-module assigners

* SO-3882: Refactor CompositeComponentDeletionPolicy

- use ComponentDeletionPolicy instead of Predicate
- add mergeWith method to combine multiple composite policies

https://snowowl.atlassian.net/browse/SO-3882

* [config] remove unnecessary systemUser configuration key

* [api] fix bug details() expansion affectedComponentId filtering

Fixes #473.

* [core] fix RevisionSegment.withEnd(newEnd) logic

Do not extend the segment to later timestamps than the currently set end
value. Fixes branch@timestamp scenarios where multiple parent branches
are participating in the search.

* [index] increase embedded Elasticsearch max_buckets to 1.500.000...

...temporarily

A proper fix for large aggregations using composite agg is planned for
v7.5.0.

* Revert "[core] fix RevisionSegment.withEnd(newEnd) logic"

This reverts commit 7db86ac.

* [core] use new RevisionSegment.restrictEnd(restrictTo) method...

...to restrict segments to certain timestamp value.

Fixes branch@timestamp scenarios where multiple parent branches with
shorter segments are participating in the search.

* [core] remove diagnostic code statement

* [cis] allow ID registration of already published IDs

* [cis] remove unnecessary validation of incoming ID status changes

Changing ID status should work in a best effort manner and it should not
fail and report back any IDs that cannot be transitioned to the desired
state.

* [tests] fix failed DefaultSnomedIdentifierServiceTest case

* [releng] update changelog with 7.4.0 changes

* Bump netty.version from 4.1.43.Final to 4.1.45.Final

Bumps `netty.version` from 4.1.43.Final to 4.1.45.Final.

Updates `netty-buffer` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-codec` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-codec-http` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-common` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-handler` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-resolver` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Updates `netty-transport` from 4.1.43.Final to 4.1.45.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.43.Final...netty-4.1.45.Final)

Signed-off-by: dependabot[bot] <[email protected]>

* [ci] add codecov upload step to maven workflow

* Update maven.yml

* [ci] trigger the build workflow on pull request

* [ci] trigger build only when...

...push, pr changes against the 7.x branch

* [commons] Make set of invalid resource characters visible

* [config] remove deprecated `snomed.ids` configuration key

* [classify] refactor namespace and module assignment logic

Require module and namespace to be specified in SaveJobRequests.
Remove defaultModule and defaultNamespace from snowowl.yml configuratio
file.
Allow multiple assigner instances from the same type, fixes parallel
classification issues in different extension branches.
Add mandatory `module` and `namespace` parameters to classification save
endpoint.

* [classify] add NotEmpty annotation to ClassificationRunRestUpdate

* [classify] remove 'default' assigner type from classification run update

* [releng] change commons.logging require-bundle directives to...

...import-package statements

* [releng] add commons-logging jar dependency to core.rest module

* [releng] release 7.4.0

* [core] Remove SNAPSHOT suffix from logback.config

* [releng] release 7.4.0 (update links)

* [releng] prepare 7.5.0-SNAPSHOT

* [docs] add from-6x migration guide

* [scripts] remove db related scripts from assembly

* [docs] add backup guide

* [docs] update JDK links

* [api] fix malformed Location header values

Fixes #500

* [api] fix possible NPE when not supplying any acceptability values

* [api] introduce CodeSystemURI and CodeSystemResourceRequest

Support `build(uri)` request builder method on selected SNOMED CT APIs.
This allows clients to call the API with a CodeSystemURI String
representation instead of specifying the repositoryId and branch to
delegate the request to.
CodeSystemURI represents a String in format of `<CODESYSTEM>[/<PATH>]`,
where:
- `<CODESYSTEM>` is the shortName ID of a Code System
- `<PATH>` is one of the following values:
  * `LATEST` - special value that represents the latest released version
of the codesystem. This is the default value if PATH is omitted.
Examples: `SNOMEDCT` (implicit latest) or `SNOMEDCT/LATEST` (explicit
latest).
  * `HEAD` - special value that represents the latest development
version of the codesystem. Examples: `SNOMEDCT/HEAD`
  * `<versionId>` - an explicit `versionId` that matches one existing
version of the Code System. Examples: `SNOMEDCT/2019-01-31` or
`SNOMEDCT-UK/2019-10-31`
  * `<branch_path>` - any other path value will be treated as relative
path to the CodeSystem's current working branch
(`CodeSystem.branchPath`). Examples: `SNOMEDCT/a/b`.

This new feature is available in all endpoints that require a `/:path`
parameter.

* [api] fix failed ECL test cases

* [api] minor PR changes related to CodeSystemURI API feature

* [api] use health checking request properly in new CodeSystemRequests...

...helper methods

* SO-3929: Clean up Permissions to allow removal of Eclipse contributions

https://snowowl.atlassian.net/browse/SO-3929

* Bump jackson-databind from 2.9.10.1 to 2.9.10.3

Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.9.10.1 to 2.9.10.3.
- [Release notes](https://github.com/FasterXML/jackson/releases)
- [Commits](https://github.com/FasterXML/jackson/commits)

Signed-off-by: dependabot[bot] <[email protected]>

* [api] add Enum keyed accessor methods to Options

* [api] add generic Concept model and ConceptSearchRequest and its Builder

* [core] refactor TerminologyRepositoryPlugin initialization

Remove type specific builder methods from RepositoryBuilder.
Add generic bind(type, instance) method to bind any service to the
repository context.

* [api] initial version of SNOMED CT specific search request evaluator

* [tests] add generic access test to SNOMED CT api tests

* [api] add filterByQuery test and fix remaining issues with filters

* Update javadoc

Thanks @apeteri!

Co-Authored-By: András Péteri <[email protected]>

* [api] add javadoc to MUST_NOT_QUERY optionkey

* [commons] remove existing mapping if the new value is null (Options)

* [ldap] make LDAP identity provider more customizable

Support customization of user and role object classes (defaults are
`inetOrgPerson` and `groupOfUniqueNames`).
Support customization of permission and member properties (defaults are
`description` and `uniqueMember`).

* [api] fix potential NPE when using sortBy with null value

* [api] add prepareCommit to RepositoryRequests

* [api] fix potential NPE when using filterById() with null value

* [api] support term filter in SnomedConceptSearchRequestEvaluator

* [api] set the codeSystem URI and the terminologyComponentId...

...in Concepts returned by the generic concept request API

* [core] add two more rules to CodeSystemURI

* [api] return timestamp as String in CommitInfo

* Utility method added to check without exception.

* [api] expose timestampFrom and timestampTo filters

* [api] add getTimestampString property to CommitInfo JSON representation

Timestamp field will remain a 64bit number (long), a with the newest
BigInt JavaScript support it is supported in the browsers as well.

* Registered converter for string-to enums as well as validators.

* [api] fix missing brackets when evaluating multiple OR'd clauses

* [api] fix MAIN/LATEST branch not found exception when...

...no codesystem version is present.

* [api] extract IndexResourceRequest from ResourceRequest

This allows Request implementations to subclass from ResourceRequest and
use locales and generic arguments without depending on Index/Document
specific `fields` and `expand`.

* [api] support Accept-Language header parsing on Java API level

Remove deprecated `acceptability` filter option from SNOMED CT
Description API. Use `acceptableIn`, `preferredIn` or `languageRefSet`
alternatives instead.

* Template authoring support (#515)

- Allow extending repositories with additional components
- Add fields in SnomedTerminologyComponentConstants for templates
- Add missing terminologyComponentId conversion cases in SnomedTerminologyComponentConstants utility methods
- Trim nested property paths in RevisionDiff#diff

Co-authored-by: Gabor Nagy <[email protected]>
Co-authored-by: aalaswadi <[email protected]>

* [api] remove unnecessary class

* remove file

Co-authored-by: Mark Czotter <[email protected]>
Co-authored-by: András Péteri <[email protected]>
Co-authored-by: Gabor Nagy <[email protected]>
Co-authored-by: Balazs Banfai <[email protected]>
Co-authored-by: aalaswadi <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

This reverts commit 3943dd4.

* test adding new plugin

* renaming

* renaming to extend

* change plugin creation

* add MonitoringRestService

* add MonitoringRestService

* fixes

* change build.properties

* rename rest

* fix rest

* change config spring

* final adjustment

* enable local

* change baseUrl

* chr-1152 - fix pom

* chr-1152 - fix pom

chr-1152 - deploy test

* update cis

* update commons

* update md files

* update tests

* update snomed

* update releng

* update net4j

* update fhir

* update docs

* update dist

* update core

* update main pom

* update documentation

* revert mistakenly overriden pom

* revert mistakenly overridden files

* update bbl module

* update bbl module

* update bbl module

* fix swagger for bbl

* update cis

* update cis

* update commons

* update tests

* update snomed

* update snomed

* update releng

* update net4j

* update fhir

* update docker

* update core

* update md files

* adjust custom files

* add some update doc

* fix overridden pom....

* add file to look out for in the md

…(kube...) to write

CHR-2065 - relax restriction to configuration folder for other users …

…nfig-folder

CHR-2065 attempt fix custom linux permission for password

CHR-2065 relaxing file permission snowowl conf

CHR-2065 symlink trick attempt to allow kubernetes to write mount file

CHR-2065 revert change with symlink

* [core] do NOT perform empty commit when staging area is not dirty

* [commons] Update changed component reporting in StagingArea (WIP)

* Revert "[commons] Update changed component reporting in StagingArea (WIP)"

This reverts commit e126b95.

* [core] add all objects as changed to the commit notification

* [core] make UpdateRequest context customizable

* [core] replace `BranchContextProvider` with openBranch method

Also, replace TransactionContextProvider with openTransaction methods.

* [core] bind the User to the job execution context

* [locks] add new Locks API to build a lock context

Migrate all existing Lock contexts to the new API.

* [snomed] add a lock context around RF2 import

* [core] throw NotFoundException from CodeSystemRequests.getCodeSystem().

...instead of BadRequestException

* [snomed] Add missing reference set type in SnomedVersioningRequest

* [core.tests] Add IdentityProvider.NOOP to JobRequestsTest context

* [core] use generic context in UpdateRequestBuilder

* [releng] add missing Bundle-Vendor header

* [build] install/deploy at the end of the maven build

* [build] use https for all p2 sites

* [build] disable Jenkins artifactPublisher

* [snomed] rename method importJobId to importJobKey

* [core] support async execution of CodeSystemVersionCreateRequests

* Revert "[build] disable Jenkins artifactPublisher"

This reverts commit c362c62.

* Revert "[build] install/deploy at the end of the maven build"

This reverts commit 5fe4eb0.

* [export] Allow exporting members with inactive referenced components

* [core] allow deleted version branches to be reused for versioning

* [core] require each terminology repository plugin to implement...

...a ConceptSearchRequestEvaluator.

* [index] add commented out disk threshold configs

* [index] add the current revision if we mark it as revised

* [index] fix waitUntilValue implementation

Let the memoizer decide whether it needs to check the value again or not
without enforcing it with a 0 reset value.

* [index] fix waitUntilValue implementation

Check the value first and then waitUntil the value becames acceptable.

* [core] generate unique ID for code system version documents

* [releng] update changelog with 7.5.0 changes

* [releng] release 7.5.0

* [releng] update release links

* [releng] update release links

* [releng] prepare 7.5.1-SNAPSHOT

* [releng] prepare 7.5.1-SNAPSHOT (logback)

* [api] allow any path under the specified apiBaseUrl...

...to be part of the docs

* Revert "Revert "[build] install/deploy at the end of the maven build""

This reverts commit 033b9c4.

* Revert "Revert "[build] disable Jenkins artifactPublisher""

This reverts commit 8d6702f.

* SO-3965: Add lock context to non-SNOMEDCT import requests

* [build] create the p2 site as main maven module artifact...

...as opposed to additional attached artifact

The previous state prevented installation and deployment of additional
artifacts produced by the `server.update` module because there were no
main artifact(s) attached to this build.
This fixes installAtEnd and deployAtEnd issue and allows the usage of
the maven-deployer-extension.

* [build] remove custom p2 site filename

* [build] append oss suffix to packageFiles

* [build] append oss suffix to packageFiles parent folder

* Refactored branch-isolated support, provided core API equivalent.

* Added utility method to find the concept-type component ID.

* [docs] initial version of SNOMED CT Extension Guides

* GitBook: [7.x] 95 pages modified

* Revert "GitBook: [7.x] 95 pages modified"

This reverts commit eede338.

* [docs] remove old documentation project

* [docs] add basic international and extension...

...commit graph renders

* [docs] add extension from scratch image

* [docs] add basic edition structure image

Add images to single edition page.

* [docs] add multi extension scenario

* [docs] add deep extension images

* [docs] add extension development and release docs

* SO-3998: Change extensionOf property type to CodeSystemURI

* SO-3998: Decrease visibility of FHIR CodeSystem constructor

* Minor non-substantive cleanup

* Minor non-substantive cleanup

* Minor non-substantive cleanup

* Minor non-substantive cleanup

* DNF->NNF

* DNF->NNF

* Minor non-substantive cleanup

* Minor non-substantive cleanup

* Minor non-substantive cleanup

* [docs] remove unfinished sentence

* SO-3998: Add "additionalProperties" property to code systems

* [docs] initial version of Extension Upgrade

* [docs] minor non-substantive cleanup

* [docs] corrected hyperlink

* [docs] clarified SNOMED QL

* [core] add sortBy() method to SearchResourceRequest to access sort param

* [core] support ContextConfigurer in TerminologyRepositoryPlugins

* [snomed] configure the Synonyms cache for each BranchContext

* [commons] fix variable name in HashMapOptions

* [core] support custom sort keys in SearchIndexResourceRequest

Move custom termSort script sort to SnomedConceptSearchRequest.
Add SnomedConceptSearchRequestBuilder.TERM_SORT to reference the script
sort as a field sort.

* [core] support sorting in generic ConceptSearchRequest

* [index] bump Elasticsearch to the latest 7.6.2 release

Release notes:
https://www.elastic.co/guide/en/elasticsearch/reference/current/release-notes-7.6.0.html
https://www.elastic.co/guide/en/elasticsearch/reference/current/release-notes-7.6.1.html
https://www.elastic.co/guide/en/elasticsearch/reference/current/release-notes-7.6.2.html

Breaking changes that affect Snow Owl:
* Tokenizer `edgeNgram` has been renamed to `edge_ngram` (applied to
analysis.json)
* Sorting on `_id` field is deprecated and should be migrated before
removed completely (reported as SO-4008)

* [index] bump asm libraries to 7.2

* [build] use elasticsearch-oss:7.6.2 in docker-compose.yml

* Add license scan report and status

Signed-off-by: fossabot <[email protected]>

* SO-4007: support additional predicate when checking for running jobs

* SO-4007: rename RF2ReleaseType field `type` due to collision with...

...`Request.getType()` method.

* SO-4007 #resolve

Run effectiveTime restore process during RF2 Delta imports.

* SO-4007: use parametersPredicate instead of jobPredicate in...

...ServiceProvider.isJobRunning() method

* Update core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/ServiceProvider.java

Co-Authored-By: András Péteri <[email protected]>

* Update core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/ServiceProvider.java

Co-Authored-By: András Péteri <[email protected]>

* Update core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/ServiceProvider.java

Co-Authored-By: András Péteri <[email protected]>

* SO-3998: Add "locales" property to code systems

* [core] fix registration of additional TerminologyComponent types in...

...TerminologyRegistry.

* SO-3998: Update locale list on code system in SnomedRf2ImportRequest

* SO-3965: Make parent lock context configurable

* SO-3965: Make import parent lock context configurable

* [core] fix incorrect path expression propagated to revision search...

...from BranchContext.

`BranchContext.branchPath()` method has been replaced with a `path()`
method to reflect that the value returned is a path, but might not be
exactly the same as the current branch's path.
Added relevant assertions to verify the behavior to
BranchCompareRequestTest test case (using the `branch^` expression).

* SO-3965: Let import lock context wrap subsequent lock operations

* [core] remove duplicate ExportResult object

Use Attachment instead.

* SO-3965: Convert import request to generic lock request

* SO-3965: Change visibility of LockRequest constructors

* SO-3998: Add support for determining code system path from...

...the short name (and extensionOf attribute, if set)

* [tests] add syserr calls to trace RF2 export test failures...

...on Travis and Github Actions

* Update LockRequest.java

* SO-3998: Fix extension working branch in API test constants

* [export] trigger another build by adding more systrace

* [tests] add assertions to verify that RF2 package does exist...

...before verifying its contents

* [api] add degree-of-interest scoring to REST API

* SO-4007: make sure we keep the released flag on its original value

* SO-4007: add missing released flag set for refset members

* SO-4007: organize builder() methods

Convert primitive fields to object, so we can properly select them via
`com.b2international.snowowl.core.request.IndexResourceRequest.fields`.

* SO-4007 #resolve

Set the released flag to its proper value during import so effective
time restore functionality can run properly.

* SO-3927 #resolve

* SO-4007: fix NPE when getting refset without maptarget type

* [core] lock branch for commit with the currently executing user...

...and not with the author of the commit.

* [build] add log silencer to validation.snomed module

* SO-4006: Update SNOMED CT auto RF2 export script (#536)

Co-authored-by: András Péteri <[email protected]>

* Fix typo

* [core] support special search expressions in certain search option keys

`@field(value)` style special search expression values can be used in
selected option keys (currently in SNOMED CT Concept `term` filters
only) to search content via the other options but using a single option
key as source.

Examples:
`term=@ECL(<408739003)` used on the `GET /:path/concepts` API will
return concepts that match the given ECL.
`term=@Active(true)` used on the `GET /:path/concepts` API will return
active concepts only.
`term=@moduleId(900000000000207008)` used on the `GET /:path/concepts`
API will return concepts with the specified module.

* [releng] update changelog with 7.5.1 changes

* [releng] release 7.5.1

* [releng] release 7.5.1 (update links)

* [releng] prepare 7.6.0-SNAPSHOT

* SO-3998: Use CodeSystem instead of CodeSystemEntry in requests

* Add issue templates

* [fossa] remove unused jetty-annotations

This transitively removes javax.annotations-api as well and eliminates
one of the reported OSS licensing issues.

* [releng] remove unused dependencies from pom.xml

* [fossa] upgrade ua-parser-js to latest 0.7.21

The new version is licensed under the MIT license without any GPL-2.0-only parts.

* [releng] add bug_report template suggestions

NOTE about exposing credentials.
Some additional bullet points to the useful things to include section.

* SO-4039: remove duplicate RandomSnomedIdentiferGenerator class

* SO-4039: initial implementation of query labeler request

* INFRA-42: Shrink size of Snow Owl OSS docker images

- use prebuilt CentOS 7 image as a base. The image comes with daily
package updates and AdoptOpenJDK11 pre-installed
- use multistage build to get rid of install layers
- use simple tar.gz artifact to extract and install Snow Owl
- set explicit user and group ID
- removed enforced ownership mutation in case of bind-mounts. It is now
the responsibility of the user to setup necessary permissions for log,
data and configuration dirs.


https://snowowl.atlassian.net/browse/INFRA-42

* SO-3998: Implement "available upgrades" property expansion

* SO-4039: add a TermStringConverter to strip off pipes from concept terms

* SO-4039: fix remaining test failures

* SO-4039: add javadoc to...

...SnomedQueryLabelerRequestBuilder.setDescriptionType

* SO-4039: fix failed ETL parsing test cases

* INFRA-40: Remove OSS docker image build for private registry

https://snowowl.atlassian.net/browse/INFRA-40

* SO-3947: add commons-fileupload to snowowl.core.rest dependencies

* SO-3947: remove java configured properties

* SO-3947: add new fields to read by ApiConfig bootstrap

* SO-3947: add class to store file upload configuration properties

* SO-3947: configure MultipartResolver with the new registered properties

* SO-4044 #resolve

* SO-4045 #resolve

Prevent duplicate language refset IDs when converting a list of
ExtendedLocales to list of language refset ids.
Bug: The value is present twice in the `Accept-Language` header as
`en-x-<langRefSetId>` and as a replacement for an `en-gb` locale due to
the setting in `snomed.languages` configuration key.

* INFRA-30: Make product name and repo url configurable during docker ...

... build

https://snowowl.atlassian.net/browse/INFRA-30

* INFRA-30: Rename version argument to 'tag'

https://snowowl.atlassian.net/browse/INFRA-30

* INFRA-30: Move docker image build to separate Jenkins job

https://snowowl.atlassian.net/browse/INFRA-30

* [dev] make sure we have proper GC settings in all launch configs

* SO-3998: Implement "available upgrades" expansion in REST service

* SO-3998: Remove STORAGE_KEY constant from CodeSystemEntry.Fields

* SO-3998: Add support for "extensionOf" updates in CS update request

* SO-3998: Add happy-path test case for "extensionOf" code system update

* SO-3998: Update core-e2e-tests launch configuration format

* [docs] update security realm guide and configurations

Update File realm configuration.
Update LDAP realm configuration.

* Update docs/setup/security/index.md

Co-Authored-By: András Péteri <[email protected]>

* Update docs/setup/security/index.md

Co-Authored-By: András Péteri <[email protected]>

* Update docs/setup/security/index.md

Co-Authored-By: András Péteri <[email protected]>

* Update docs/setup/security/index.md

Co-Authored-By: András Péteri <[email protected]>

* Update docs/setup/security/index.md

Co-Authored-By: András Péteri <[email protected]>

* Update docs/setup/security/index.md

Co-Authored-By: András Péteri <[email protected]>

* Update docs/setup/security/ldap.md

Co-Authored-By: András Péteri <[email protected]>

* SO-3947 #resolve

Final changes to upload file size configuration.
Increase max allowed upload file size to `1gb`.
Configure it through the `api.http.maxFileSize` and
`api.http.maxRequestSize` configuration settings.

* SO-3947: add NotEmpty annotations to HttpConfig fields

* Update docs/setup/security/index.md

Co-Authored-By: Gábor Nagy <[email protected]>

* Update docs/setup/security/ldap.md

Co-Authored-By: Gábor Nagy <[email protected]>

* Update docs/setup/security/ldap.md

Co-Authored-By: Gábor Nagy <[email protected]>

* [docs] update ldap.md Authentication section

* SO-4058: Support setting start/end effective times in RF2 export script

* [core] fix spurious javadoc

* SO-3998: Remove ResponseBody annotation from REST controller methods

* SO-3998: Change repositoryUuid to repositoryId on CodeSystem

* [snomed] make sure we return the version in descending effective time...

...order when calculating exportable versions.

Also, make sure cut off base time calculation does not lead to
occasional branch not found exceptions.

* SO-3998: Change repositoryUuid to repositoryId on CodeSystemEntry...

...and CodeSystemCreateRequest

* SO-3998: Add precondition check to CodeSystemRestService#searchByGet

* SO-3998: Add missing since tag to CodeSystemConverter

* SO-3998: Implement Serializable in CodeSystem

* SO-3998: Revert import statement changes in SnomedRf2ExportRequest

* SO-3998: Update request body parameters in core.rest.tests

* SO-3998: Update request body parameters in snomed.core.rest.tests

* [core] make pre-7.6.0 datasets compatible with 7.6.0

* [index] skip transient fields when creating index mapping

Map types with `JsonValue` annotated, `String` return value methods as
`keyword`s in the mapping.

* SO-4039: support list of expressions in SnomedQueryLabelerRequest

* [launch] fix launch configurations

* [api] add missing Swagger Docs alternate type rules

CodeSystemURI -> String
ExtendedLocale -> String
List<CodeSystemURI> -> List<String>
List<ExtendedLocale> -> List<String>

* [mrcm] Fix authorization issue with MRCM import/export

* [ldap] Fetch users from a single LDAP group

* [core] extract SNOMED CT specific additional properties to...

...SnomedTerminologyComponentConstants

* [ldap] support custom user and role filters in LdapIdentityProvider

Support `roleBaseDn` to fetch roles from a different baseDn node.
Replace `rootDn` and `rootDnPassword` with `bindDn` and `bindDnPassword`
configuration keys.

* [core] add getNestedRequests implementation to TransactionalRequest

Fixes authorization issue when performing commits/edits.

* [core] add JsonIgnore to TransactionalRequest.getNestedRequests

* [ldap] log LDAP naming/bind/search errors

* [ldap] use {baseDn} template for the default `roleBaseDn` value

* [docs] update LDAP guide with latest configuration changes

* [ldap] log the configuration settings during boot

* [migration] remove 6.x specific migration stuff from OSS 7.x product

* [docs] add curator based snapshot/restore backup example

* [releng] update changelog with 7.6.0 changes

* [releng] release 7.6.0

* [CHR-1066] - snowowlFork to Artifactory (#2)

* chr-1066 - add cache and test if javadoc in path

* chr-1066 - print out some debug info

* chr-1066 -fix copy/paste mistake

* chr-1066 - print debug info

* chr-1066 - print debug info

* chr-1066 - yet another print debug info

* chr-1066 - yet another print debug info

* chr-1066 - extract var to control use of local artifacts

* chr-1066 - extract var to control use of local artifacts

* chr-1066 - extract var to control use of local artifacts

* chr-1066 - print stuff

* chr-1066 - change npm config, errors and skips next lines

* chr-1066 - nes

* chr-1066 - ..

* chr-1066 - remove debug

* chr-1066 - put env vars in docker and in the bash env

* chr-1066 - put env vars in job as well, print debug

* chr-1066 - yet another try to change path.. print debug

* chr-1066 - yet another try to change path.. print debug

* chr-1066 - I am doing stupid things now...fixing copy/paste error

* chr-1066 - still not set...their documentation lies ...

* chr-1066 - still not set completely...

* chr-1066 - remove the debug echoed info

Co-authored-by: Matteo Casu <[email protected]>

* [CHR-1516] - dockerizing and adding languages and ES config

* chr-1516 - customize snowowl.yml, Dockerfile, create Makefile, adjust circleCi config

* chr-1516 - for testing make circleCi run on all branches but the master

* chr-1516 - for testing change circleCi

* chr-1516 - fix inentation

* chr-1516 -install maven

* chr-1516 - install maven...

* chr-1516 - install maven again

* chr-1516 - install maven again ???

* chr-1516 - use wrapper...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - use wrapper and fix error...

* chr-1516 - ..

* chr-1516 - split builds... why is file not found?!?!

* chr-1516 - split builds... why is file not found?!?!

* chr-1516 - push docker

* chr-1516 - test if this will move the docs files where they have to be

* chr-1516 - test build in circle ci

* chr-1516 - test build in circle ci

* chr-1516 - test build in circle ci

* chr-1516 - test build in circle ci again

* chr-1516 - test build in circle ci again2

* chr-1516 - print  debug

* chr-1516 - print other debug info, not so detailed

* chr-1516 - print other debug info, not so detailed

* chr-1516 - replace mvn plugin

* chr-1516 - replace mvn plugin

* chr-1516 - try stable node version

* chr-1516 - try stable node version without sudo

* chr-1516 - try stable node version without sudo

* chr-1516 - try updating node stuff

* chr-1516 - try updating node stuff more

* chr-1516 - try updating docker image

* chr-1516 - try updating make..

* chr-1516 - install npm

* chr-1516 - install npm

* chr-1516 - release libs on merge to master, release docker on tag

* chr-1516 - release to dev on master merge, release to staging on tag

* chr-1516 - code review changes

* chr-1516 - fix staging deploy step

* chr-1516 - fix staging deploy step

* chr-1516 - fix staging deploy step

* [CHR-1516] - add curl (#6)

* chr-1516 - fix deployment - install curl + debug it

* chr-1516 - fix release version

* chr-1516 - get rid of unnecessary env var

* chr-1516 - add langs again

* chr-1516 - revert debug config

* [CHR-1516]- revert deploy pom bit, change lang hierarchy (#9)

* chr-1516- revert accidentally overridden pom bit

* chr-1516- change lang config

* chr-1516 - fix versioning (#10)

* chr-1152 - expose metrics add custom plugin bit

* test adding new plugin

* renaming

* renaming to extend

* change plugin creation

* add MonitoringRestService

* add MonitoringRestService

* fixes

* change build.properties

* rename rest

* fix rest

* change config spring

* final adjustment

* enable local

* change baseUrl

* [CHR-1152] - fix pom structure (#15)

* chr-1152 - fix pom

* chr-1152 - fix pom

* chr-1152 - change the deployment - rename

* update bbl (#26)

* update dist (#27)

* [CHR-1848] - fix overridden pom.... (#28)

* fix overridden pom....

* add file to look out for in the md

* Merge remote-tracking branch 'remotes/origin/7.x' into update

# Conflicts:
#	CHANGELOG.md
#	Jenkinsfile
#	Makefile
#	README.md
#	SUMMARY.md
#	babylonhealth/.project
#	babylonhealth/com.babylonhealth.snowowl.rest.feature/.project
#	babylonhealth/com.babylonhealth.snowowl.rest.feature/feature.xml
#	babylonhealth/com.babylonhealth.snowowl.rest.feature/pom.xml
#	babylonhealth/com.babylonhealth.snowowl.rest/.project
#	babylonhealth/com.babylonhealth.snowowl.rest/META-INF/MANIFEST.MF
#	babylonhealth/com.babylonhealth.snowowl.rest/pom.xml
#	babylonhealth/com.babylonhealth.snowowl.rest/src/com/b2international/snowowl/core/rest/BblApiConfig.java
#	babylonhealth/pom.xml
#	cis/com.b2international.snowowl.snomed.cis.feature/feature.xml
#	cis/com.b2international.snowowl.snomed.cis.feature/pom.xml
#	cis/com.b2international.snowowl.snomed.cis.product/pom.xml
#	cis/com.b2international.snowowl.snomed.cis.product/snow-owl-cis.product
#	cis/com.b2international.snowowl.snomed.cis.rest/META-INF/MANIFEST.MF
#	cis/com.b2international.snowowl.snomed.cis.rest/pom.xml
#	cis/com.b2international.snowowl.snomed.cis/META-INF/MANIFEST.MF
#	cis/com.b2international.snowowl.snomed.cis/pom.xml
#	cis/pom.xml
#	commons/com.b2international.collections.api/META-INF/MANIFEST.MF
#	commons/com.b2international.collections.api/pom.xml
#	commons/com.b2international.collections.fastutil/META-INF/MANIFEST.MF
#	commons/com.b2international.collections.fastutil/pom.xml
#	commons/com.b2international.collections.jackson/META-INF/MANIFEST.MF
#	commons/com.b2international.collections.jackson/pom.xml
#	commons/com.b2international.commons.base/META-INF/MANIFEST.MF
#	commons/com.b2international.commons.base/pom.xml
#	commons/com.b2international.commons.test/META-INF/MANIFEST.MF
#	commons/com.b2international.commons.test/pom.xml
#	commons/com.b2international.commons/META-INF/MANIFEST.MF
#	commons/com.b2international.commons/pom.xml
#	commons/com.b2international.index.tests.tools/META-INF/MANIFEST.MF
#	commons/com.b2international.index.tests.tools/pom.xml
#	commons/com.b2international.index.tests/META-INF/MANIFEST.MF
#	commons/com.b2international.index.tests/pom.xml
#	commons/com.b2international.index/META-INF/MANIFEST.MF
#	commons/com.b2international.index/pom.xml
#	commons/com.b2international.mapdb/pom.xml
#	commons/com.b2international.scripting.api/.project
#	commons/com.b2international.scripting.groovy/.project
#	commons/com.b2international.scripting.groovy/build.properties
#	commons/pom.xml
#	core/com.b2international.snowowl.core.dependencies.feature/feature.xml
#	core/com.b2international.snowowl.core.dependencies.feature/pom.xml
#	core/com.b2international.snowowl.core.feature/feature.xml
#	core/com.b2international.snowowl.core.feature/pom.xml
#	core/com.b2international.snowowl.core.rest.feature/feature.xml
#	core/com.b2international.snowowl.core.rest.feature/pom.xml
#	core/com.b2international.snowowl.core.rest.tests/.launch/core-e2e-tests.launch
#	core/com.b2international.snowowl.core.rest.tests/META-INF/MANIFEST.MF
#	core/com.b2international.snowowl.core.rest.tests/pom.xml
#	core/com.b2international.snowowl.core.rest/META-INF/MANIFEST.MF
#	core/com.b2international.snowowl.core.rest/pom.xml
#	core/com.b2international.snowowl.core.rest/snow-owl-api-docs/package-lock.json
#	core/com.b2international.snowowl.core.rest/snow-owl-api-docs/package.json
#	core/com.b2international.snowowl.core.rest/src/com/b2international/snowowl/core/rest/ControllerExceptionMapper.java
#	core/com.b2international.snowowl.core.rest/src/com/b2international/snowowl/core/rest/SnowOwlApiConfig.java
#	core/com.b2international.snowowl.core.rest/src/com/b2international/snowowl/core/rest/codesystem/CodeSystemRestSearch.java
#	core/com.b2international.snowowl.core.rest/src/com/b2international/snowowl/core/rest/codesystem/CodeSystemRestService.java
#	core/com.b2international.snowowl.core.rest/src/com/b2international/snowowl/core/rest/codesystem/CodeSystemService.java
#	core/com.b2international.snowowl.core.tests/.launch/core-unit-tests.launch
#	core/com.b2international.snowowl.core.tests/META-INF/MANIFEST.MF
#	core/com.b2international.snowowl.core.tests/pom.xml
#	core/com.b2international.snowowl.core/META-INF/MANIFEST.MF
#	core/com.b2international.snowowl.core/pom.xml
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/attachments/Attachment.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystem.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystemCreateRequest.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystemCreateRequestBuilder.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystemEntry.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystemGetRequestBuilder.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystemRequests.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystemSearchRequest.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystemUpdateRequest.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystemUpdateRequestBuilder.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/CodeSystems.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/codesystem/version/CodeSystemVersionCreateRequest.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/console/CodeSystemsCommand.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/domain/BranchContextProvider.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/domain/ExportResult.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/repository/RepositoryCodeSystemProvider.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/repository/TerminologyRepositoryInitializer.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/repository/TerminologyRepositoryPlugin.java
#	core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/request/CodeSystemResourceRequest.java
#	core/com.b2international.snowowl.datastore.server.tests/.classpath
#	core/com.b2international.snowowl.datastore.server.tests/.project
#	core/com.b2international.snowowl.datastore.server.tests/build.properties
#	core/com.b2international.snowowl.datastore/.project
#	core/com.b2international.snowowl.identity.ldap/META-INF/MANIFEST.MF
#	core/com.b2international.snowowl.identity.ldap/pom.xml
#	core/com.b2international.snowowl.identity.ldap/src/com/b2international/snowowl/identity/ldap/LdapIdentityPlugin.java
#	core/com.b2international.snowowl.identity.ldap/src/com/b2international/snowowl/identity/ldap/LdapIdentityProvider.java
#	core/com.b2international.snowowl.identity.ldap/src/com/b2international/snowowl/identity/ldap/LdapIdentityProviderConfig.java
#	core/com.b2international.snowowl.logback.config/META-INF/MANIFEST.MF
#	core/com.b2international.snowowl.logback.config/pom.xml
#	core/com.b2international.snowowl.server.product.feature/feature.xml
#	core/com.b2international.snowowl.server.product.feature/pom.xml
#	core/com.b2international.snowowl.server.product/META-INF/MANIFEST.MF
#	core/com.b2international.snowowl.server.product/pom.xml
#	core/pom.xml
#	dist/pom.xml
#	docker/Dockerfile
#	docker/config/snowowl.yml
#	docs/backup/index.md
#	fhir/com.b2international.snowowl.fhir.core/META-INF/MANIFEST.MF
#	fhir/com.b2international.snowowl.fhir.core/pom.xml
#	fhir/com.b2international.snowowl.fhir.core/src/com/b2international/snowowl/fhir/core/provider/CodeSystemApiProvider.java
#	fhir/com.b2international.snowowl.fhir.core/src/com/b2international/snowowl/fhir/core/provider/FhirCodeSystemApiProvider.java
#	fhir/com.b2international.snowowl.fhir.rest.feature/feature.xml
#	fhir/com.b2international.snowowl.fhir.rest.feature/pom.xml
#	fhir/com.b2international.snowowl.fhir.rest.tests/.launch/fhir-api-tests.launch
#	fhir/com.b2international.snowowl.fhir.rest.tests/META-INF/MANIFEST.MF
#	fhir/com.b2international.snowowl.fhir.rest.tests/pom.xml
#	fhir/com.b2international.snowowl.fhir.rest/META-INF/MANIFEST.MF
#	fhir/com.b2international.snowowl.fhir.rest/pom.xml
#	fhir/pom.xml
#	net4j/com.b2international.snowowl.eventbus.tests/META-INF/MANIFEST.MF
#	net4j/com.b2international.snowowl.eventbus.tests/pom.xml
#	net4j/com.b2international.snowowl.eventbus/META-INF/MANIFEST.MF
#	net4j/com.b2international.snowowl.eventbus/pom.xml
#	net4j/com.b2international.snowowl.rpc.test/META-INF/MANIFEST.MF
#	net4j/com.b2international.snowowl.rpc.test/pom.xml
#	net4j/com.b2international.snowowl.rpc/META-INF/MANIFEST.MF
#	net4j/com.b2international.snowowl.rpc/pom.xml
#	net4j/pom.xml
#	pom.xml
#	releng/com.b2international.snowowl.server.update/.launch/snow-owl-oss.launch
#	releng/com.b2international.snowowl.server.update/assembly/common/configuration/snowowl.yml
#	releng/com.b2international.snowowl.server.update/assembly/common/scripts/snowowl_export.sh
#	releng/com.b2international.snowowl.server.update/category.xml
#	releng/com.b2international.snowowl.server.update/pom.xml
#	releng/com.b2international.snowowl.server.update/snow-owl-oss.product
#	releng/pom.xml
#	releng/target-platform/pom.xml
#	snomed/com.b2international.snowowl.snomed.common/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.common/pom.xml
#	snomed/com.b2international.snowowl.snomed.common/src/com/b2international/snowowl/snomed/common/SnomedTerminologyComponentConstants.java
#	snomed/com.b2international.snowowl.snomed.core.feature/feature.xml
#	snomed/com.b2international.snowowl.snomed.core.feature/pom.xml
#	snomed/com.b2international.snowowl.snomed.core.rest.feature/feature.xml
#	snomed/com.b2international.snowowl.snomed.core.rest.feature/pom.xml
#	snomed/com.b2international.snowowl.snomed.core.rest.tests/.launch/snomed-e2e-tests.launch
#	snomed/com.b2international.snowowl.snomed.core.rest.tests/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.core.rest.tests/pom.xml
#	snomed/com.b2international.snowowl.snomed.core.rest.tests/src/com/b2international/snowowl/snomed/core/rest/SnomedApiTestConstants.java
#	snomed/com.b2international.snowowl.snomed.core.rest.tests/src/com/b2international/snowowl/snomed/core/rest/io/SnomedExportApiTest.java
#	snomed/com.b2international.snowowl.snomed.core.rest/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.core.rest/pom.xml
#	snomed/com.b2international.snowowl.snomed.core.rest/src/com/b2international/snowowl/snomed/core/rest/SnomedExportRestService.java
#	snomed/com.b2international.snowowl.snomed.core.rest/src/com/b2international/snowowl/snomed/core/rest/SnomedRf2ExportRestService.java
#	snomed/com.b2international.snowowl.snomed.core.rest/src/com/b2international/snowowl/snomed/core/rest/domain/SnomedIdentifierResponse.java
#	snomed/com.b2international.snowowl.snomed.datastore.tests/.launch/snomed-core-unit-tests.launch
#	snomed/com.b2international.snowowl.snomed.datastore.tests/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.datastore.tests/pom.xml
#	snomed/com.b2international.snowowl.snomed.datastore.tests/src/com/b2international/snowowl/snomed/datastore/index/entry/SnomedRelationshipIndexEntrySerializationTest.java
#	snomed/com.b2international.snowowl.snomed.datastore/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.datastore/pom.xml
#	snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/core/ql/Expressions.java
#	snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/datastore/index/change/ComponentEffectiveTimeRestoreChangeProcessor.java
#	snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/datastore/index/change/SnomedRepositoryPreCommitHook.java
#	snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/datastore/internal/SnomedRepositoryInitializer.java
#	snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/datastore/request/rf2/SnomedRf2ExportRequest.java
#	snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/datastore/request/rf2/SnomedRf2ExportRequestBuilder.java
#	snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/datastore/request/rf2/SnomedRf2ImportRequest.java
#	snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/datastore/request/rf2/importer/Rf2EffectiveTimeSlice.java
#	snomed/com.b2international.snowowl.snomed.dsl/src/com/b2international/snowowl/snomed/dsl/query/queryast/AttributeClauseGroup.java
#	snomed/com.b2international.snowowl.snomed.dsl/src/com/b2international/snowowl/snomed/dsl/query/queryast/NotClause.java
#	snomed/com.b2international.snowowl.snomed.ecl.tests/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.ecl.tests/pom.xml
#	snomed/com.b2international.snowowl.snomed.ecl/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.ecl/pom.xml
#	snomed/com.b2international.snowowl.snomed.etl.tests/.project
#	snomed/com.b2international.snowowl.snomed.etl.tests/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.etl.tests/pom.xml
#	snomed/com.b2international.snowowl.snomed.etl.tests/src/com/b2international/snowowl/snomed/etl/tests/EtlParsingTest.xtend
#	snomed/com.b2international.snowowl.snomed.etl/.classpath
#	snomed/com.b2international.snowowl.snomed.etl/.project
#	snomed/com.b2international.snowowl.snomed.etl/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.etl/pom.xml
#	snomed/com.b2international.snowowl.snomed.etl/src-gen/com/b2international/snowowl/snomed/etl/etl/ConceptIdReplacementSlot.java
#	snomed/com.b2international.snowowl.snomed.etl/src-gen/com/b2international/snowowl/snomed/etl/etl/ExpressionReplacementSlot.java
#	snomed/com.b2international.snowowl.snomed.etl/src-gen/com/b2international/snowowl/snomed/etl/validation/AbstractEtlValidator.java
#	snomed/com.b2international.snowowl.snomed.etl/src/com/b2international/snowowl/snomed/etl/EtlStandaloneSetup.java
#	snomed/com.b2international.snowowl.snomed.etl/src/com/b2international/snowowl/snomed/etl/scoping/EtlScopeProvider.java
#	snomed/com.b2international.snowowl.snomed.fhir/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.fhir/pom.xml
#	snomed/com.b2international.snowowl.snomed.fhir/src/com/b2international/snowowl/snomed/fhir/SnomedCodeSystemApiProvider.java
#	snomed/com.b2international.snowowl.snomed.fhir/src/com/b2international/snowowl/snomed/fhir/SnomedConceptMapApiProvider.java
#	snomed/com.b2international.snowowl.snomed.icons/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.icons/pom.xml
#	snomed/com.b2international.snowowl.snomed.ql.tests/.project
#	snomed/com.b2international.snowowl.snomed.ql.tests/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.ql.tests/pom.xml
#	snomed/com.b2international.snowowl.snomed.ql/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.ql/pom.xml
#	snomed/com.b2international.snowowl.snomed.reasoner.tests/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.reasoner.tests/pom.xml
#	snomed/com.b2international.snowowl.snomed.reasoner/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.reasoner/pom.xml
#	snomed/com.b2international.snowowl.snomed.scg.tests/.project
#	snomed/com.b2international.snowowl.snomed.scg.tests/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.scg.tests/pom.xml
#	snomed/com.b2international.snowowl.snomed.scg/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.snomed.scg/pom.xml
#	snomed/com.b2international.snowowl.snomed.scg/src-gen/com/b2international/snowowl/dsl/validation/AbstractSCGJavaValidator.java
#	snomed/com.b2international.snowowl.snomed.scg/src-gen/com/b2international/snowowl/snomed/scg/validation/AbstractScgValidator.java
#	snomed/com.b2international.snowowl.snomed.scg/src/com/b2international/snowowl/dsl/ParseException.java
#	snomed/com.b2international.snowowl.snomed.scg/src/com/b2international/snowowl/snomed/scg/ScgStandaloneSetup.java
#	snomed/com.b2international.snowowl.snomed.semanticengine.simpleast.test/.classpath
#	snomed/com.b2international.snowowl.validation.snomed/.launch/validation-snomed-tests.launch
#	snomed/com.b2international.snowowl.validation.snomed/META-INF/MANIFEST.MF
#	snomed/com.b2international.snowowl.validation.snomed/pom.xml
#	snomed/pom.xml
#	tests/com.b2international.restassured-all/pom.xml
#	tests/com.b2international.snowowl.test.commons/META-INF/MANIFEST.MF
#	tests/com.b2international.snowowl.test.commons/pom.xml
#	tests/com.b2international.snowowl.test.commons/src/com/b2international/snowowl/test/commons/SnomedContentRule.java
#	tests/com.b2international.snowowl.test.dependencies/META-INF/MANIFEST.MF
#	tests/com.b2international.snowowl.test.dependencies/pom.xml
#	tests/com.b2international.snowowl.test.feature/feature.xml
#	tests/com.b2international.snowowl.test.feature/pom.xml
#	tests/pom.xml

* fix errored files on merge..........

* fix errored files on merge.....

* remove unnecessary files

* remove unnecessary files and update the md file

* fix error by merge...

* fix error by merge...

* just for test, to revert!!!

* fix config - change env var in circle ci as well

* fix config - change env var in circle ci as well, again

* facepalm

* revert test config

Co-authored-by: Mark Czotter <[email protected]>
Co-authored-by: András Péteri <[email protected]>
Co-authored-by: aalaswadi <[email protected]>
Co-authored-by: Gábor Nagy <[email protected]>
Co-authored-by: Balazs Banfai <[email protected]>
Co-authored-by: Brandon Ulrich <[email protected]>
Co-authored-by: fossabot <[email protected]>
Co-authored-by: Kovacs Tamas <[email protected]>
Co-authored-by: Matteo Casu <[email protected]>

[CHR-2065] change config folder

…em prop java

…er-2

[CHR-2065] add debug in java, and experiment force usage of conf syst…

…er-2

[CHR-2065] allow logs in static methods here

…er-3-fix-NPE

[CHR-2065] fix NPE blind attempt

Chr 2262

[CHR-2262] forgot IndexConfiguration file to add nb replicas there too

[CHR-2262] tentative mimic of shards

[CHR-2262] string integer mismatch conf replica

Update

* chr-2112 - remove check to test intl snapshot import

* chr-2112 - add comment

* SO-4029: Generate worklist for mappings

* Revert "SO-4029: Generate worklist for mappings"

This reverts commit 6d08ec3.

* SO-4029: Generate work list for mappings

* SO-4028: Support exclusions from merge operation

* SO-4028: Use passed in exclusion id set in StagingArea

* SO-4028: Add exclusion merge revision branch index test case

* SO-4028: Avoid concurrent map modification

* SO-4101: Add generic terminology query optimization request

An initial implementation for SNOMED CT is also included that always
suggests adding the same (single) expression to the list of inclusions.

* SO-4103: add new validation rule for inactive members

* SO-4101: Implement direct descendant compacting optimization...

...for SNOMED CT query expressions

If the following single concept inclusions exist:
=c1, =c2, =c3, ... =cn

And a common ancestor concept c4 exists where the following expression
is true:
<c4 === [c1, c2, c3, ..., cn]

Then suggest removing the original "n" single concept references and
adding <c4 to the inclusions.

* SO-4029: Create generic member domain, search

* SO-4028: Track excluded objects without removing from staged objects

* SO-4029: Test the generic member search API from the SNOMEDCT side

* [icons] Include additional icon hierarchies based on semantic tags (#582)

* SO-4028: Rename, overload exclude method

* SO-4103: remove sysout

* SO-4103: change order of equation

* SO-4101: Add "since" tag to QueryOptimizeRequest

* SO-4094: Add ComponentURI support to snowowl.core

* SO-4028: Create merge exclude tests for changed, remvoed, new revisions

* SO-4028: Use varargs, defensive copy in merge operation exclude setters

* SO-4100:Check if description already exists...

...in Description Inactivation Indicator refset to not create duplicate
members

* SO-4028: Create private method to get filtered staged objects

* SO-4094: Refactor ComponentURI constructors

* SO-4094: Remove semicolons from the end of method bodies

* SO-4094: Reverse check argument logic, fix typo

* SO-4028: Remove unnecessary check

* SO-4028: Use ImmutableSet in defensive copy

* SO-4100: Use multimap for refSetMembers

* SO-4100: Filter for active members and members...

...with Concept non-current inactivation indicator

* [tests] fix ComponentURI related compile error

* [core] add URI to generic Concept model

* SO-4113 Minor Permission class changes.

* SO-4029: Fix hardcoded codesystem uri

* SO-4029: Make request, builder classes final

* SO-4029: Add locales support to member search request evaluator

* SO-4029: Refactor SetMemberSearch API

* Use new ComponentURI to store referenced component
* Add json deserialization annotiations to SetMember
* Fix method name typo
* Add sort by option to member evaluation request
* Return all members in SNOMED CT member search if no set id is
specified
* Extend SNOMED CT set member evaluation to other component types
besides concepts

* SO-4029: Use fsn expand to obtain set member terms

* SO-4103: fix rule

* SO-4029: Fix ComponentURI initialization errors

* SO-4103: add test for rule 671

* SO-4029: Add JSON deserialization annotations to collection resource

* [core] omit -1 and ROOT concepts when optimizing queries

* SO-4029: Remove BaseComponent as SetMember superclass, make all ...

...fields final, add equals, hashcode toString methods

* SO-4029: Use a weak interner to cache ComponentURI instances

* SO-4113 Enabled file-style wildcards (*,?) for permission resources.

* SO-4029: Use MoreObjects.toStringHelper

* SO-4029: Shift jackson annotation to factory method, use obj references

* SO-4094: Fix ComponentURI initialization

https://snowowl.atlassian.net/browse/SO-4094

* SO-4029: Add support for multi-valued filtering by Set ID

* SO-4091: Add known semantic tags as icons, to be used in icon ID...

...computation

* SO-4091: Collapse multiple '_' separators in IconIdUpdater

* SO-4100: Add filter for description type...

...referenced component

* SO-4100: Remove filter

* SO-4091: Use hierarchical iconId computation on metadata concepts

* SO-4100: Add filter by referencedComponentIds

* SO-4103: add new cases for testing rule 671

* SO-4103: change filtering logic

* [owl axiom] Update owl axiom member expressions on member update

* SO-4103: fix test

* SO-4103: refactor script

* SO-4100: extract inactivation/reactivation test cases to another class

* SO-4100: add description status/indicator checks to inactivation tests

* SO-4100 #resolve

* [snomed] calculate class/gci axiomRelationships for OWL members...

...regardless of their status

Rename AbstractSnomedOWLExpressionMemberCreateDelegate to
SnomedOWLExpressionMemberCreateDelegate.
Remove SnomedOWLAxiomMemberCreateDelegate and
SnomedOWLOntologyMemberCreateDelegate.

* SO-4103: rename variable

* [owl axioms] Add owl axiom relationship update test

* [owl axioms] Uncomment junit test annotations

* [tests] update mini RF2 from 2018-01-31 to 2020-01-31

* [snomed] prevent creating Class/GCI OWL Axiom members...

...with inconsistent referencedComponentIds/focusConceptIds.
Fix `owlExpression` member field update test.

* [fhir] fix failed tests after bumping RF2 test data to 20200131

* [core] support `.` and `~` characters in branch names

* [core] support `CodeSystemEntry` and `CodeSystemVersionEntry`...

...in `TransactionContext.delete(Object, boolean)`

* [core] fix unrecognized object error messages

* SO-4029: change codeSystem field type to CodeSystemURI

* SO-4029: add CodeSystemURI alternative ctor and request build method

* SO-4029: fix RF2 import content vs release type validation

* [vs] support query evaluation in non SNOMED terminologies

* [vs] fix getIds()

* SO-3387: Use curator, index snapshot config from farmyard environments

* SO-3387: Add last 10 snapshot keeping action, example crontab entry...

...to curator.md

* [owl authoring] check if there is at least one axiom or relationship

* [core] Add helper method to retrieve authorized system bus

* [validation] connect filtering with toolingId

* [core] make TransactionContexts reusable for subsequent commits

Support CodeSystemURI in all branch path based requests
Deprecate old repositoryId + branch request build methods.
Add throws declaration to LockRequest.doExecute(C).

* [core] index read request wrapping in RepositoryCommitRequestBuilder

Fix nested request validation in DelegatingRequest.

* [core] support extracting ids from ID|TERM| like query strings

* [core] fix multiple tooling ID filter issues

* [validation] use toolingIDs to filter details by corresponding tooling..

...specific queries only

* [api] allow creating SNOMED CT Concepts without any relationship/axiom

* [api] move upload method to Attachment class

AttachmentRegistry uses proxy method invocation to call server side
upload method, but it proxies the defaults methods as well, which makes
it impossible to have those methods on this interface.

* [core] add support for ID|TERM| like concept String format ser/deser

* [core] add CodeSystemURI.branch helper method

* [core] Allow all terminology components to be used as map target types (#599)

* [core] add Collections3.equals method

* [core] Use single boolean property in TerminologyComponent annotation...

...to determine whether a component is allowed to participate in a
SNOMED CT map type reference member as the map target.

* [core] Use single boolean property in TerminologyComponent annotation... (#601)

...to determine whether a component is allowed to participate in a
SNOMED CT map type reference member as the map target.

* [core] add javadoc to Concept.fromConceptString and toConceptString

* Constants extracted.

* [snomed] add allowed active component attribute values to refset util

* [core] add generic DescendantsExpander base class

Extract SNOMED CT Concept descendants expand to
SnomedDescendantsExpander.
Require `direct` parameter to be specified to follow API best practices.

* move Files.lines() into try with resources block

* [snomed] Fix option key for extended locales in search request evaluator

* [validation] override tooling ruleIds with the user specified ruleIds

* [releng] update changelog with 7.7.0 changes

* [releng] release 7.7.0

* bbl plugin update

* rename file

* CHR-2455

Co-authored-by: aalaswadi <[email protected]>
Co-authored-by: András Péteri <[email protected]>
Co-authored-by: Laura Molnár <[email protected]>
Co-authored-by: Gabriella Deak <[email protected]>
Co-authored-by: Mark Czotter <[email protected]>
Co-authored-by: Balazs Banfai <[email protected]>
Co-authored-by: Gabor Nagy <[email protected]>
Co-authored-by: Kovacs Tamas <[email protected]>

CHR-2610 introduce variable log level

[CHR-2610] configure log level by variable on the 2nd xml file

[CHR-2610] - try 3rd file blindly

[CHR-2610] hardcode log WARN

[CHR-2610] trial and error logging conf

* version with build params

* edit mk file and circle ci to deploy diff docker

* override user

* change version

* change cirleci

* revert change

* try combination

* try combination

* move env in the yml file

* copy over the other config files

* copy over the other config files

* try moving with the copy command

* try moving with after owner changed

* try to use prev hack

* try to simplify a bit

* test logging

* revert log config

* revert circleci

* clean up comments

* revert previous logging changes

* add log level

* SO-4094: Reverse check argument logic, fix typo

* SO-4028: Remove unnecessary check

* SO-4028: Use ImmutableSet in defensive copy

* SO-4100: Use multimap for refSetMembers

* SO-4100: Filter for active members and members...

...with Concept non-current inactivation indicator

* [tests] fix ComponentURI related compile error

* [core] add URI to generic Concept model

* SO-4113 Minor Permission class changes.

* SO-4029: Fix hardcoded codesystem uri

* SO-4029: Make request, builder classes final

* SO-4029: Add locales support to member search request evaluator

* SO-4029: Refactor SetMemberSearch API

* Use new ComponentURI to store referenced component
* Add json deserialization annotiations to SetMember
* Fix method name typo
* Add sort by option to member evaluation request
* Return all members in SNOMED CT member search if no set id is
specified
* Extend SNOMED CT set member evaluation to other component types
besides concepts

* SO-4029: Use fsn expand to obtain set member terms

* SO-4103: fix rule

* SO-4029: Fix ComponentURI initialization errors

* SO-4103: add test for rule 671

* SO-4029: Add JSON deserialization annotations to collection resource

* [core] omit -1 and ROOT concepts when optimizing queries

* SO-4029: Remove BaseComponent as SetMember superclass, make all ...

...fields final, add equals, hashcode toString methods

* SO-4029: Use a weak interner to cache ComponentURI instances

* SO-4113 Enabled file-style wildcards (*,?) for permission resources.

* SO-4029: Use MoreObjects.toStringHelper

* SO-4029: Shift jackson annotation to factory method, use obj references

* SO-4094: Fix ComponentURI initialization

https://snowowl.atlassian.net/browse/SO-4094

* SO-4029: Add support for multi-valued filtering by Set ID

* SO-4091: Add known semantic tags as icons, to be used in icon ID...

...computation

* SO-4091: Collapse multiple '_' separators in IconIdUpdater

* SO-4100: Add filter for description type...

...referenced component

* SO-4100: Remove filter

* SO-4091: Use hierarchical iconId computation on metadata concepts

* SO-4100: Add filter by referencedComponentIds

* SO-4103: add new cases for testing rule 671

* SO-4103: change filtering logic

* [owl axiom] Update owl axiom member expressions on member update

* SO-4103: fix test

* SO-4103: refactor script

* SO-4100: extract inactivation/reactivation test cases to another class

* SO-4100: add description status/indicator checks to inactivation tests

* SO-4100 #resolve

* [snomed] calculate class/gci axiomRelationships for OWL members...

...regardless of their status

Rename AbstractSnomedOWLExpressionMemberCreateDelegate to
SnomedOWLExpressionMemberCreateDelegate.
Remove SnomedOWLAxiomMemberCreateDelegate and
SnomedOWLOntologyMemberCreateDelegate.

* SO-4103: rename variable

* [owl axioms] Add owl axiom relationship update test

* [owl axioms] Uncomment junit test annotations

* [tests] update mini RF2 from 2018-01-31 to 2020-01-31

* [snomed] prevent creating Class/GCI OWL Axiom members...

...with inconsistent referencedComponentIds/focusConceptIds.
Fix `owlExpression` member field update test.

* [fhir] fix failed tests after bumping RF2 test data to 20200131

* [core] support `.` and `~` characters in branch names

* [core] support `CodeSystemEntry` and `CodeSystemVersionEntry`...

...in `TransactionContext.delete(Object, boolean)`

* [core] fix unrecognized object error messages

* SO-4029: change codeSystem field type to CodeSystemURI

* SO-4029: add CodeSystemURI alternative ctor and request build method

* SO-4029: fix RF2 import content vs release type validation

* [vs] support query evaluation in non SNOMED terminologies

* [vs] fix getIds()

* SO-3387: Use curator, index snapshot config from farmyard environments

* SO-3387: Add last 10 snapshot keeping action, example crontab entry...

...to curator.md

* [owl authoring] check if there is at least one axiom or relationship

* [core] Add helper method to retrieve authorized system bus

* [validation] connect filtering with toolingId

* [core] make TransactionContexts reusable for subsequent commits

Support CodeSystemURI in all branch path based requests
Deprecate old repositoryId + branch request build methods.
Add throws declaration to LockRequest.doExecute(C).

* [core] index read request wrapping in RepositoryCommitRequestBuilder

Fix nested request validation in DelegatingRequest.

* [core] support extracting ids from ID|TERM| like query strings

* [core] fix multiple tooling ID filter issues

* [validation] use toolingIDs to filter details by corresponding tooling..

...specific queries only

* [api] allow creating SNOMED CT Concepts without any relationship/axiom

* [api] move upload method to Attachment class

AttachmentRegistry uses proxy method invocation to call server side
upload method, but it proxies the defaults methods as well, which makes
it impossible to have those methods on this interface.

* [core] add support for ID|TERM| like concept String format ser/deser

* [core] add CodeSystemURI.branch helper method

* [core] Allow all terminology components to be used as map target types (#599)

* [core] add Collections3.equals method

* [core] Use single boolean property in TerminologyComponent annotation...

...to determine whether a component is allowed to participate in a
SNOMED CT map type reference member as the map target.

* [core] Use single boolean property in TerminologyComponent annotation... (#601)

...to determine whether a component is allowed to participate in a
SNOMED CT map type reference member as the map target.

* [core] add javadoc to Concept.fromConceptString and toConceptString

* Constants extracted.

* [snomed] add allowed active component attribute values to refset util

* [core] add generic DescendantsExpander base class

Extract SNOMED CT Concept descendants expand to
SnomedDescendantsExpander.
Require `direct` parameter to be specified to follow API best practices.

* move Files.lines() into try with resources block

* [snomed] Fix option key for extended locales in search request evaluator

* [validation] override tooling ruleIds with the user specified ruleIds

* [releng] update changelog with 7.7.0 changes

* [releng] release 7.7.0

* Bump netty.version from 4.1.45.Final to 4.1.50.Final

Bumps `netty.version` from 4.1.45.Final to 4.1.50.Final.

Updates `netty-buffer` from 4.1.45.Final to 4.1.50.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.45.Final...netty-4.1.50.Final)

Updates `netty-codec` from 4.1.45.Final to 4.1.50.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.45.Final...netty-4.1.50.Final)

Updates `netty-codec-http` from 4.1.45.Final to 4.1.50.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.45.Final...netty-4.1.50.Final)

Updates `netty-common` from 4.1.45.Final to 4.1.50.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.45.Final...netty-4.1.50.Final)

Updates `netty-handler` from 4.1.45.Final to 4.1.50.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.45.Final...netty-4.1.50.Final)

Updates `netty-resolver` from 4.1.45.Final to 4.1.50.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.45.Final...netty-4.1.50.Final)

Updates `netty-transport` from 4.1.45.Final to 4.1.50.Final
- [Release notes](https://github.com/netty/netty/releases)
- [Commits](netty/netty@netty-4.1.45.Final...netty-4.1.50.Final)

Signed-off-by: dependabot[bot] <[email protected]>

* [releng] prepare 7.8.0-SNAPSHOT

* [setMembers] fix typo

* Revert "[setMembers] fix typo"

This reverts commit 635a4d3.

* [setMember] remove JSON annotations

* [setMember] implement Serializable

* [setMember] add toString()

* SO-4025: add set compare logic

* SO-4025: implement set compare for simple map type reference sets

* SO-4131 Support for generic mappings.

* SO-4025: count as changed when only the source is equal

* SO-4025: support search by map target type

* SO-4025: support to compare any type of sets

* Revert "SO-4025: support to compare any type of sets"

This reverts commit 7d31911.

* SO-4025: support to compare any type of sets

* SO-4131 Generic mapping domain object updated.

* SO-4131 Correlation support added.

* SO-4131 Builder added.

* SO-4131: add request that finds every code system in every repository

* SO-4131: add test cases for the new all code system searcher request

* Added repository to the printed info.

* SO-4142 Refset update request added.

* SO-4142 Convenience method added.

* SO-4142 Serial ID added.

* SO-4142 Error handling added for incorrect arguments.

* SO-4142 TargetComponentType as tracked change.

* SO-4142 Guard for not setting mapTargetType for incorrect refset types.

* SO-4142 Allow unspecified to be propagated to the domain object.

* SO-4131: add map group and priority field

* SO-4131: add map rule and advice fields

* SO-4142 MapGroup added.

* SO-4025: add number for compare result

* SO-4025: export compare budle

* SO-4111: Move rule 110 to generic snomed validation rules

* Revert "SO-4111: Add OWL axiom support to rule 663"

This reverts commit 57c2daf.

* SO-4111: Detect invalid sources too in rule 668

* SO-4025: correct license

* SO-4025: rename class

* SO-4151: When finding unpublished duplicate FSNS, ensure they are ...

... compared to every other FSN and not only other unpublished FSNs

* SO-4142 Added missing properties.

* SO-4025: move concept map compare tests to core

* SO-4025: add request for concept map compare

* SO-4025: fix filter by map target component type request

* SO-4131: remove unnecessary print lines

* SO-4151: Use EffectiveTimes helper method

* SO-4025: use unspecified number for component URI

* SO-4025: fix generic compare request

* SO-4025: add simple type reference set compare request tests

* [tests] add low and high level test case to verify functionality...

...described in #594

* [index] upgrade Elasticsearch to 7.8.0

* [docker] upgrade Elasticsearch to 7.8.0

* [index] commit progress on fixing branch state computation issue

* SO-4025: remove deleted package from MANIFEST

* SO-4025: rename classes

* SO-4025: rename method

* SO-4025: rename class

* SO-4025: rename class

* SO-4025: rename method

* SO-4025: rename variables

* SO-4025: rename method

* SO-4025: add correct license

* SO-4025: rename class

* SO-4025: rename class

* SO-4025: rename method

* SO-4025: rename method

* SO-4025: make class final and package private

* SO-4025: set limit to all results

* SO-4025: make class final

* SO-4025: use public final instead of final public

* SO-4025: make Builder final

* SO-4025: rename field

* SO-4025: make fields final

* SO-4025: rename method

* SO-4025: use assertThat instead of assertEquals

* SO-4025: use assertThat instead of assertEquals

* SO-4142: Fix update of map target component value

- allow updating map target component value even if it is already set

https://snowowl.atlassian.net/browse/SO-4142

* SO-4025: remove abstract class

* SO-4025: make class final and methods private

* SO-4025: fix indentation

* SO-4025: create method to get the map type refset types

* SO-4025: use the static method to get the map type refset types

* SO-4025: search for simple and description type refsets as well

* [index] remove unused, obsolete branch doc replace script

* [index] fix bug in RevisionBranchRef.difference method

Empty segments should not be returned.

* [index] commit progress on fixing rebase missing document issue

* SO-4183: Ensure rule only returns owl refset members

* [index] fix branch synchronization issue

Properly calculate the state of a branch compared to another branch even
if the branch has been synchronized with the other branch a couple of
times. Take actual commits into account before deciding whether a branch
is in forward or behind state.
After applying changes to the index writer double check whether it has
any actual changes in it, if not, do not create an empty commit object
Empty, non-merge commits incorrectly modify the branch state, which
require unnecessary compare and merge operations between the branches.

* SO-4188: Fix Boolean compare in status update check

* SO-4181: Add default id filter evaluation to generic concept search ...

... interface

https://snowowl.atlassian.net/browse/SO-4181

* [tests] add missing getTypes method to RevisionBranchingTest

* SO-4192: Incorrect codesystemURI created on task branch

* SO-4188 #resolve

Add test case to verify incorrect deserialization behaviour in Java
ser/deser.
Boolean values are deserialized into new objects instead of using the
constant `Boolean.TRUE/FALSE` values.
Changing the `!=` check to `Objects.equals` fixes the issue.

* SO-4192 #resolve

* [core] fix issue with CodeSystemURI calculation on CodeSystem type

* [core] fix incorrect evaluation of generic concept search ID filter

* [core] expand mapTarget term from the first CodeSystem in the available

...members

Multiple CodeSystems in Map type reference sets are not supported yet.

* Revert "SO-4151: When finding unpublished duplicate FSNS, ensure they are ..."

* [releng] update changelog with 7.8.0 changes

* [releng] release 7.8.0

* [releng] prepare 7.9.0-SNAPSHOT

* [validation] fix missing limit setting when collecting attributes...

...in rule110.
Also, report members and relationships individually instead of reporting
just the containing concepts.

* [validation] do NOT report non-class, non-gci axioms in rule110

* [validation] change rule to support any OWL AXIOM refset

* [validation] rename variable

* [scripts] Refactor validate script to be compatible with 7.x

* [index] do NOT perform authoring related change processing...

...during merge commits

* [index] remove fast forward commit timestamp functionality

Each commit has a unique timestamp from now on.

* [index] remove shouldSetRevisedOnMergeBranch() method

* [index] fix issue in ComponentInactivationChangeProcessor

Inactivate active relationships only.
Set the effective time to unpublished on inactivated components.

* [releng] update changelog with 7.8.1 changes

* [releng] release 7.8.1

* update updates.md

* chr-2717 - update docker version

* chr-2717 - update md file

* chr-2717 - revert Dockerfile to b2is version, now using custom one

* chr-2717 - revert other custom changes

* chr-2717 - test build in circleci

* chr-2717 - revert test change

Co-authored-by: aalaswadi <[email protected]>
Co-authored-by: Mark Czotter <[email protected]>
Co-authored-by: Gabriella Deak <[email protected]>
Co-authored-by: Balazs Banfai <[email protected]>
Co-authored-by: Laura Molnár <[email protected]>
Co-authored-by: Gabor Nagy <[email protected]>
Co-authored-by: András Péteri <[email protected]>
Co-authored-by: Kovacs Tamas <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Chr 2724

Snow Owl v7.8.4