[CHR-1152] - fix pom structure #525
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.