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https://github.com/hapifhir/hapi-fhir.git
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2803 Commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
Luke deGruchy
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8fbbaef079
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Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient. (#5488)
* Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient. * Add FhirContext to ClientResponseContext. * Introduce a ModifiedStringApacheHttpResponse. Run spotless. * Remove TDOOs, add and update javadoc. * Spotless and copyright header. * Add changelog. * Unique error message code. * Only trigger the interceptor if the expected return type is a Bundle. * Fix spotless. * Code review feedback. * Spotless. * Bump to 6.11.3-SNAPSHOT |
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Martha Mitran
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ee414b73d9
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Pass properties through to Remote Terminology Service on CodeSystem lookup (#5477)
* Pass properties through to Remote Terminology Service on CodeSystem operation * Propagate list of property names throughout. Introduce a parameter object for the lookupCode method. Mark other lookupCode methods as deprecated. Add unit tests. * Update remote terminology service tests * Address code review comments * Fix unit tests * Address latest code review comments to update default methods * Address latest code review comments to update default methods - update fallback condition * Address latest code review comments to update default methods - update fallback condition |
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TynerGjs
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9f827a75c7
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Resolve 5480 Update member-match signature to match the spec (#5481)
* - Changed member-match function param names, and return value - modified existing tests to accomodate for the change * removed tests unsuitable for new return value * resolve code review comments * version bump |
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Tadgh
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f624cf75ad
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Rel 6 10 mb (#5474)
* Allow cached search with consent active when safe (#5387) Allow the search cache when using consent if safe * Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376) * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation * Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * first fix * tests and preliminary fixes * wip, commit before switching to release branch. * adding capability to handle _lastUpdated in reverse search (_has) * adding changelog * applying spotless. * addressing code review comments. --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> * Br 20231019 add cr settings for cds hooks (#5394) * Add settings used in CR CDS Services. Remove config dependency on Spring Boot. * Add changelog * Use String.format rather than concat strings * spotless apply * Add javadoc * Upgrade notes for the forced-id change (#5400) Add upgrade notes for forced-id * Clean stale search results more aggressively. (#5396) Use bulk DMA statements when cleaning the search cache. The cleaner job now works as long as possible until a deadline based on the scheduling frequency. * bump version of clinical reasoning (#5406) * Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added * removed unused alias from SQL query of mdm-clear (#5416) * Issue 5418 support Boolean class return type in BaseInterceptorService (#5421) * Enable child classes to use Boolean class return type * spotless --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420) * If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix * Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423) This reverts commit 4e295a59fb143a2ba54bc44305474096e2acd578. Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> * Use new FHIR_ID column for sorting (#5405) * Sort `_id` using new FHIR_ID column. * Fix old tests that put client-assigned ids first. * Better indexing for sort * Bump core to 6.1.2.2 (#5425) * Bump core to 6.1.2.1 Patch release that uses https for primary org.hl7.fhir.core package server * Bump core to 6.1.2.2 * Make sure to return always a value for Boolean class return type. (#5424) Implement change in a non-disruptive way for overriders Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428) Add a non-standard __pid SP. * Review changes for new _pid SP. (#5430) Change name to _pid to match our standard and add warning. * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432) * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition. * Fix spotless issue * CVEs for 6.10.0 (#5433) * Bump jetty * Bump okio-jvm * 8.2.0 mysql connector * Jena and elastic bumps * Fix test * 5412 post bundle on partition incorrect response.link shown (#5413) * Initial fix and unit test provided * spottless check * Made relevant changes to make solution version agnostic * relevant logic changes made * spotless changes made * New logic added to fix failing test cases * formatting * New logic to make the function more robust * spotless checks * Left a trailing slash in the tests * Made relevant test changes and changed logic * spotless changes * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml changing changelog Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Formatting requirements --------- Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414) * first fix * - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber - refactored code to reduce repeated code - cleaned unnecessary comments and reformatted files * Changed myResourceModifiedMessagePersistenceSvc to be autowired * removed unused import * added error handling when inflating the message to email and message subscriber * reformatted code * Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc * Changes by gary * Reformatted file * fixed failed tests * implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File. * - implemented IT - fixed logical error - added changelog * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * resolve code review comments * reformatted files * fixed tests * Fix for failing IT test in jpaserver-starter (#5435) Co-authored-by: dotasek <dotasek.dev@gmail.com> * wip * Bump jackson databind * Pin Version * Ignored duplicate classes * Updating version to: 6.10.1 post release. * Fix pom * Skip remorte nexus * make release faster * Updating version to: 6.10.1 post release. * remove skiptests --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: markiantorno <markiantorno@gmail.com> |
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Justin McKelvy
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86ea069437
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feature swap to non javax clinical reasoning (#5463)
* Update to a version of Clinical Reasoning/CQL that no longer includes javax dependencies * Rev to CR 3.0.0-PRE10 * version bump, pom changes for jakarta conflicts * undo exclusions from other modules * Rework exclusions * Fix type in dependency * new cr version, exclude conflicts in cr and cds-hooks * remove exclusions * pom update * Redo the exclusions * add retrieveSettings config * new CR retrieve settings and config * update config to new enums and parameters * update unit tests and config for new cql and terminology properties * bump CR to 3.0.0-PRE12 * spotless edits, update class path for CR config * missing dependencies * swap for jakarta * moving conflicting dependencies * Fix a couple code review items --------- Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> |
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Ken Stevens
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d5a1b0cdf3
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fix terserutil clear (#5473)
* fix test * review |
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Michael Buckley
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6abfed603e
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Use streams to avoid multiple queries during batch job id chunking. (#5444)
Use stream for chunking instead of repeated sorted query pages. |
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TynerGjs
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41d9abf6ac
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Resolve 5452-mdm-query-link-returns-scientific-notation-in-linkcreated-and-linkupdated (#5453)
* set the scale to 0 when transforming double to BigDecimal * - set negative scale to 0 when transforming double to BigDecimal - added test |
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Aditya Dave
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9dace159b4
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5426 enhance bundleutil (#5451)
* failing test * fix and more tests * cleanup * spotless * remove class paths * add changelog --------- Co-authored-by: aditya_dave <aditya@smilecdr.com> |
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Tadgh
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777859ad00
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Rel 6 10 mb (#5441)
* Allow cached search with consent active when safe (#5387) Allow the search cache when using consent if safe * Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376) * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation * Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * first fix * tests and preliminary fixes * wip, commit before switching to release branch. * adding capability to handle _lastUpdated in reverse search (_has) * adding changelog * applying spotless. * addressing code review comments. --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> * Br 20231019 add cr settings for cds hooks (#5394) * Add settings used in CR CDS Services. Remove config dependency on Spring Boot. * Add changelog * Use String.format rather than concat strings * spotless apply * Add javadoc * Upgrade notes for the forced-id change (#5400) Add upgrade notes for forced-id * Clean stale search results more aggressively. (#5396) Use bulk DMA statements when cleaning the search cache. The cleaner job now works as long as possible until a deadline based on the scheduling frequency. * bump version of clinical reasoning (#5406) * Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added * removed unused alias from SQL query of mdm-clear (#5416) * Issue 5418 support Boolean class return type in BaseInterceptorService (#5421) * Enable child classes to use Boolean class return type * spotless --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420) * If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix * Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423) This reverts commit 4e295a59fb143a2ba54bc44305474096e2acd578. Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> * Use new FHIR_ID column for sorting (#5405) * Sort `_id` using new FHIR_ID column. * Fix old tests that put client-assigned ids first. * Better indexing for sort * Bump core to 6.1.2.2 (#5425) * Bump core to 6.1.2.1 Patch release that uses https for primary org.hl7.fhir.core package server * Bump core to 6.1.2.2 * Make sure to return always a value for Boolean class return type. (#5424) Implement change in a non-disruptive way for overriders Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428) Add a non-standard __pid SP. * Review changes for new _pid SP. (#5430) Change name to _pid to match our standard and add warning. * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432) * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition. * Fix spotless issue * CVEs for 6.10.0 (#5433) * Bump jetty * Bump okio-jvm * 8.2.0 mysql connector * Jena and elastic bumps * Fix test * 5412 post bundle on partition incorrect response.link shown (#5413) * Initial fix and unit test provided * spottless check * Made relevant changes to make solution version agnostic * relevant logic changes made * spotless changes made * New logic added to fix failing test cases * formatting * New logic to make the function more robust * spotless checks * Left a trailing slash in the tests * Made relevant test changes and changed logic * spotless changes * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml changing changelog Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Formatting requirements --------- Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414) * first fix * - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber - refactored code to reduce repeated code - cleaned unnecessary comments and reformatted files * Changed myResourceModifiedMessagePersistenceSvc to be autowired * removed unused import * added error handling when inflating the message to email and message subscriber * reformatted code * Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc * Changes by gary * Reformatted file * fixed failed tests * implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File. * - implemented IT - fixed logical error - added changelog * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * resolve code review comments * reformatted files * fixed tests * Fix for failing IT test in jpaserver-starter (#5435) Co-authored-by: dotasek <dotasek.dev@gmail.com> * wip --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> |
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Ken Stevens
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3bba9fb1f2
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add terminology troubleshooting log (#5439)
* init rev * init rev * changelog and additional logging * changelog and additional logging * changelog and additional logging * spotless * review feedback |
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Ken Stevens
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a7a446903f
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5401 add terserutil clear by fhirpath (#5402)
* begin with failing test * test passes * test passes * changelog * moar testor |
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longma1
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84e3becf1c
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6 8 5 mb (#5399)
* version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * Fixing terminology upload with large file. (#5204) * create initial test * adding fix; adding changelog; * fixing format. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * up version to 6.8.0 from snapshot * fix up some duplicate deps for skipping * Force deployment of other projects * make dummy java class to pass sonatype checks * make dummy java class to pass sonatype checks * Cheeky test removal * Another test removal * Updating version to: 6.8.1 post release. * adding back in tests for release pipelines * Fix bad version insert * Bump to core library version 6.0.22.2 (#5261) * Bump to core library version 6.0.22.2 * Bump HAPI to 6.8.1-SNAPSHOT, core library version to 6.0.22.2 * up version to 6.8.1 * Prevent remote deployment * Updating version to: 6.8.2 post release. * Re-add deploy plugin skip * re-add version * Bump core library version to 6.0.22.2 * Bump HAPI to 6.8.2-SNAPSHOT * Fix up version enum * Version bump * Updating version to: 6.8.3 post release. * Make display name validation configurable (#5321) * Test fixes * Build cleanup * Initial test passing * Test fixes * Tests all seem to be working * Make display validation level configurable * Should be all working * Add changelog * Add to changelog --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * wip * wip * Fix conflicts * add backport info * Fix versioning * test fixes * disabled 1 test * backported 5271 to fix validation message tests * wip * Changelog * Fix tests * Fix backport * Add upgrade.md * Fix test * Fix key * Updating version to: 6.8.4 post release. * 5353 iterate on revincludes and includes does not return correct resources when used with non iterate revincludes (#5354) * added failing test * implemented solution * added doc generation * added changelog * fixed the order of includes and revincludes, based on what was implemented before * fixed formatting * fixed wording --------- Co-authored-by: Steven Li <steven@smilecdr.com> * added changelog * Updating version to: 6.8.5 post release. * merge back 5377 * changelog * undo unintended changes from mergeback --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: StevenXLi <stevenli_8118@hotmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> |
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Tadgh
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1776a8a395
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Bump version (#5386) | ||
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Tadgh
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25ce7d0b8f | fix broken version | ||
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Tadgh
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90bfe05b9d
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Fix version enum (#5352)
* Fix version enum * Add license |
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Justin McKelvy
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c832cf0507
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Hapi cr codecache (#5360)
* WIP code cache config * WIP test * Passing unit test * cachelistener IT * hardening cache listener tests * cache listener fixes & tests, measureService migration, add reporter parameter to r4 * fix ELMCache listener to match on version, update test, remove reporter parameter * edit inline notes * changelog, version bump, spotless apply --------- Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> |
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JasonRoberts-smile
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5411622dee
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add exclusions to terser reference method (#5343) | ||
TipzCM
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7e0fa9833c
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adding metrics (#5301)
* hapi metrics * step 1 * metrics service * adding metrics service * adding documentation * refactor * refactoring * cleanup * changing * adding changelog * some refactoring * format * review fixes part 1 * review points * review fixes * updates for code review * updates for code review * bumping versions --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> |
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Etienne Poirier
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6ee6031a5f
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CapabilityStatement doe not declare conformance to IG when a bulk data export provider is registered. (#5329)
* adding initial test * adding initial test * solution implementation * spotless apply * bumping to 6.9.8-SNAPSHOT * addressing comments from review and fixing typo * spotless --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> |
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TynerGjs
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bc0ee995a2
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Resolve MDM query links operation score field imprecise value (#5332)
* - Fixed precision error and rounded to 4 decimal places - Removed the vector field from the return value of mdmlink toJSON - modified tests for the above changes. * changed to use BigDecimal instead of Precision to round score * reformatted file |
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Justin McKelvy
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6a0b2794eb
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5089 cr measure refactor (#5324)
* version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * repository measure refactor * undo bundle edit, add config * embedded library true * undo post of bundle * clear library cache on test * fix sumbit-data test * missing packages from cql * fix test data and test cases for repository api * 3.0.0 clinical reasoning uplift * r4 cql execution provider and tests * fix submitdata provider config * wip cql tests * debugging cql op wip * wip debugging cql * update tests for $cql, fix class names * prep for Pre6 uplift * spotless checks and test fixes * bump to 3.0.0-PRE6 * cleanup * fix version * cleanup * fix exlusions in pom * add in cache invalidation config * search converter bug and test for repository * update searchconverter * version bump, add changelog * remove term config, move IDaoRegistryUser class * Break out dstu3 providers and move config to version folders * CVE-2023-26119 * remove * imports * code review updates --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> |
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James Agnew
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2b7ebbcb27
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Make display name validation configurable (#5321)
* Test fixes * Build cleanup * Initial test passing * Test fixes * Tests all seem to be working * Make display validation level configurable * Should be all working * Add changelog * Add to changelog --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> |
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Tadgh
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49a28efd53
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5290 - Feature Request - Implement toggle to prevent conditional updates from invalidating match criteria. (#5291)
* Test skeleton, TODO IMPLEMENTER added all over the place * Add test and TODO IMPLEMENTER * Add jpa storage property to allow preventing conditional updates to invalidate match criteria * spotless * Implement review suggestions --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> |
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longma1
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43e45db85a
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Rel 6 6 2 mb (#5315)
* Force Verify tests * fix ITs (#4809) * fix RestHookTestR5IT * fix intermittent --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> * Fix migrator error on Oracle (#4814) * Fix Oracle SQL error * Add changelog * Update clinical reasoning version (#4816) * Update clinical reasoning version * Update version * Update version * Clean-up and more wireup of evaluationSettings * Add changelog --------- Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> * Opening the care-gaps endpoint for GET. (#4823) Co-authored-by: Chalma Maadaadi <chalma@alphora.com> * added version to mdm golden resource tag (#4820) Co-authored-by: Long Ma <long@smilecdr.com> * Update the changelog for 4697 to be more descriptive (#4827) * Update the changelog for 4697 to be more descriptive * Futher tweaks of the changelog * Fixes a bug with tags. (#4813) * Test, fix * Drop constraint, add migration * Add changelog * Fix userSelected null vs false * Fix merge * Fix up checkstyle whining * One more failure * Fix test * wip * changelog clarity Co-authored-by: James Agnew <jamesagnew@gmail.com> * change index --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> * fix migration issue (#4830) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Create correct version enum * Remove superfluous migration * fixing test (#4835) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * email subscription, throw NullPointerException (#4790) * fix bug * Favoring constructor initialization to autowiring. * enhancing test. * Making class LoggingEmailSender available outside of the hapi-fhir-japserver-uhnfhirtest module. * Passing all tests. * adding changelog. * Bumping version to 6.5.20-SNAPSHOT * addressing code review comment. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Add docs for CR operations (#4855) * Add docs for CR operations * Correct changelog and javadoc for $package * Add documentation for $apply parameters * Add additional documentation for $package * Cleanup * Cleanup * Cleanup * Address review comments * Add documentation for $care-gaps operation. (#4862) * Add documentation for -gaps. * addressing the comments. --------- Co-authored-by: Chalma Maadaadi <chalma@alphora.com> * 4853 validation does not error when display is not the same as the display defined in the codesystem 2 (#4854) * added failing test * implemented the solution * changed test name * added change log * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4853-validation-does-not-error-when-display-is-not-the-same-as-the-display-defined-in-the-codesystem-2.yaml Co-authored-by: James Agnew <jamesagnew@gmail.com> --------- Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> * fixing patient everything operator (#4845) * fixing patient everything operator * review fix --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * fix link * Move image file * Bundle resources containing over 100 references to the same Organization will fail with HAPI-2207 (#4871) * Add failing unit test. * Fix JpaId Long equality comparison to use ! equals() instead of !=, which fails for different instances of the same Long value. * Add changelog. * added warn message and test (#4848) * added warn message and test * code review fixes --------- Co-authored-by: Long Ma <long@smilecdr.com> * Issue 4804 full table scan on mpi link during mdm clear (#4805) * version bump for next release (#4793) * version bump * Bump to correctnumber * Version Enum and folder * Remove interim from list * wip * Fix operation on nested type-choices in FhirPatch implementation (#4783) * Fix operation on nested type-choices in FhirPatch implementation * Add credit for #4783 --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * #4468 fix previous link offset no cache pagination (#4489) * #4468 Add test reproducing the issue * #4468 Fix previous link for no cache offset pagination * #4468 Use unchecked URI parsing * Credit for #4489 --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * Changelog and data generating test * Add MdmLink index * Avoid double link deletion * Use ThreadLocal safely --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Fix erroneous batch 2 $export 75% complete count when the job is COMPLETE (#4859) * Add failing unit test. * Add conditional logic to the InstanceProgress progress percentage to disregard the incomplete count if this is called from the reduction step. This is to get around a race condition in which a work chunk is QUEUED and not yet complete when the reduction step calculates the progress. * Add final. * Add changelog. * disable wars (#4877) Co-authored-by: Ken Stevens <ken@smilecdr.com> * 4868 fix paging hapi (#4870) * fixing some offset and adding a test * fixing the offset paging * Removing duplicate --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com> * 4875-binary-access-write-doest-trigger-STORAGE-BINARY-ASSIGN-BLOB-ID-PREFIX-pointcut (#4876) * Add failing test * Add failing test * Fix and changelog * Pass content type parameter * Back to auto wiring the context * Invoke interceptor only when getting blobId, not also when storing it * Avoid breaking implementers * Address review comment * Add new exception Msg code * Fix broken test --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Fix batch job (bulk export) processed record count (#4879) * Remove racy stats recalc. * Throw 404 when requesting $export of non-existent Group or Patient (#4890) * Remove default implementation intended only for interim backwards compatibility (#4894) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Rule apply patient export (#4893) * Test, fix, and changelog * Better partition resolution * Add checks based on rule applier * Fix ordering failure due to hash set * Allow empty auth interceptor * Fix up operation type on invocation * Add more tests, make hack implementation for patient instance level operation * Tighten test name * Changelog * Default method * remove dead method * Remove dead autowire --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve pom changes (#4898) Co-authored-by: Long Ma <long@smilecdr.com> * backport subscription topic bean cleanup (#4904) * 4891 bulk export do not recurse unasked for resources (#4895) * updating tests * fixing bulk export to not fetch resources not requested * cleanup * cleanup * more warning suppressing * adding error code * blah * fix test * review fixes --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * lowers log level to remove bootup noise (#4908) * CVE rel 6 6 (#4907) * cve pom changes * bump javax.el to jakarta.el --------- Co-authored-by: Long Ma <long@smilecdr.com> * Issue 4905 post binary failure invoking interceptor for pointcuts storage preshow resources (#4906) * Initial failing test * Avoid applying binary blob id prefix multiple times * Remove recently introduced method not needed anymore --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Enhance LogbackCaptureTestExtension (#4869) * repro bug with test, fix bug * ken informed me he resolved this bug on master, so i'm switching to use his solution * disable wars * review feedback * review feedback * review feedback again --------- Co-authored-by: josie <josie.vandewetering@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> * Resolve 4863 from release branch searchparametercanonicalizer does not account for search parameters for custom resources types when converting dstu23 into runtimesearchparam (#4887) * Modified canonicalizeSearchParameterDstu2 and 3, now correctly detect search parameters for custom resources * Canonicalizers now correctly handle search parameters for custom resources * created changelog * Modification based on comments: - remove Resource from target field when there are custom resource types - fixed changelog typo - removed unnecessary variable providesMembershipInCompartments * Added tests for the SearchParameterCanonicalizer to test if base and target of RuntimeSearchParam is set as expected for DSTU2, DSTU3, R4, R4B, and R5 resources * Fixed typo and removed commented code * re-ordered init methods * Update changelog Co-authored-by: Tadgh <garygrantgraham@gmail.com> * modifications following first code review. --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * License * Remove _lastUpdated filtering of _revincludes. (#4899) Remove _lastUpdated filtering of _revincludes. * 4910-dm-migration-error-for-oracle-19c (#4916) * Remove all_constraints references which break in oracle 19c * Add changelog --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * 4873 empty fhirid causes missing resource (#4874) * add check for empty fhirid string and add test * add test for populateid * changelog * version bump * version bump * reverse version bump * Back to 6.5.21-SNAPSHOT. --------- Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> * Fix include canonical url performance (#4919) Use hash_identity for canonical join * License * Version bump * Temp disable * Make this dependency provided * Updating version to: 6.6.1 post release. * Bump snakeyaml * Bump jackson to be compatible with new snakeyaml * Bump deps (#4926) * resolve CVEs, add new notes * Updating version to: 6.6.2 post release. * #5023 Unexpected usage of awssdk StringUtils in hapi 6.6 jpa migration (#5024) task Replace usage of awssdk * added docs * mssql test fixes * Updating version to: 6.6.3 post release. * fix up random errors when merging back * undisable test * remove mention of 6.6.3 which does not exist --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Sam Gunter <123124187+samguntersmilecdr@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: StevenXLi <stevenli_8118@hotmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com> Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Josie <80289977+pepsiofficial@users.noreply.github.com> Co-authored-by: josie <josie.vandewetering@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Thomas Papke <web@thopap.de> |
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michaelabuckley
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e20382c4c8
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Fix for userSelected and version. (#5310)
Fix `userSelected` and `version` in tags and security labels to DSTU2 and security labels in JPA storage. |
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longma1
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0c42229985
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Rel 6 8 2 mb (#5299)
* version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * Fixing terminology upload with large file. (#5204) * create initial test * adding fix; adding changelog; * fixing format. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * up version to 6.8.0 from snapshot * fix up some duplicate deps for skipping * Force deployment of other projects * make dummy java class to pass sonatype checks * make dummy java class to pass sonatype checks * Cheeky test removal * Another test removal * Updating version to: 6.8.1 post release. * adding back in tests for release pipelines * Fix bad version insert * Bump to core library version 6.0.22.2 (#5261) * Bump to core library version 6.0.22.2 * Bump HAPI to 6.8.1-SNAPSHOT, core library version to 6.0.22.2 * up version to 6.8.1 * Prevent remote deployment * Updating version to: 6.8.2 post release. * Re-add deploy plugin skip * re-add version * Bump core library version to 6.0.22.2 * Bump HAPI to 6.8.2-SNAPSHOT * Fix up version enum * Version bump * Updating version to: 6.8.3 post release. * mvn spotless:apply --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com> |
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TipzCM
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f97eadadc6
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rebuild golden resource from survivorship on link edit (#5250)
* adding rebuilding option for survivorship * rebuild survivorship resources * cleanup * configuring beans * fixing tests * cleanup * spotless * import fixing * cleaning up * fixing tests * fixing tests * version bump * undo change --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> |
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James Agnew
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2da8aafad0
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Add support for _lanugage SP (#5300)
* Add support for _lanugage SP * Add changelog * Formatting fix * Add to JPA * Add validator * Validate language SP * Assign new code * Fixes |
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James Agnew
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d4717a08d6
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Improve docs for NO-OP update pointcuts (#5294) | ||
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James Agnew
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5a88b505d0
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Upgrade Thymeleaf (#5239)
* Upgrade Thymeleaf * Apply spotless * Version bump * Test fix |
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James Agnew
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a676506fc5
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Improve terminology validation error messages (#5271)
* Improve terminology validation error messages * Changelog * Validation issues * Test fixes * Cleanup * Review comments * Fix |
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Nathan Doef
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cc283b7732
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Respect response status code set in MethodOutcome of a Resource provider (#5267)
* failing test * fix * extract response code modifying resource provider for testing * comment * remove TestResponseCodeModifyingPatientProvider |
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LalithE
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293f02ad7c
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Fix to Bulk Export Enabled Disrupts Custom Resource Addition (#5255)
* Required change to fix bug editing test case currently * Solution and unit test * Adding changelogs * adding coverage for registerCustomTypes * Fixing test cases, using same context for two tests messed it up |
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Etienne Poirier
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fb3e141c4d
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Messages submitted to the subscription pipeline are lost when submission fails. (#4733)
* One more fix for #4467 * Enabling massIngestionMode causes incomplete resource deletion (#4476) * Adding initial test. * Adding fix and subsequent test. * Adding changelog. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Provide the capability to request that the name of the subscription matching channel be unqualified (#4464) * Adding initial test. * Adding initial solution implementation. * Adding change log and code clean up. * addressing comments from 1st code review. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Change visibility of migration method (#4471) * change migration visibility * add empty migration method for 640 --------- Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> * Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484) * First commit: Make SubscriptionValidatingInterceptor aware of which Pointcut is being called. In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED. Fix resulting compile errors in various unit tests. * Fix/enhance unit tests. Mark methods as deprecated instead of deleting them. Add proper error code. Complete changelog. * Remove erroneous TODOs and tweak the validation logic. * Enhance unit tests and fix changelog. * Reindex batch job fails when processing deleted resources. (#4482) * adding changelog. * Providing solution and adding changelog. * Adding new test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cleaning up checkstyle files (#4470) * cleaning up checkstyle files * One more fix for #4467 (#4469) * added exlusions for files at base project level so checkstyle doesn't error out * duplicate error code from merge * changing lifecycle goal for all module checkstyle check * moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code * wip * trying to figure out why pipeline cannot copy files * removing modules that don't actually need to be built. * I messed up the version --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * Bump core to 5.6.881 (#4496) * Bump core to 5.6.881-SNAPSHOT * Work on fixing tests * Work on fixing tests 2 * Bump to core release --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> * Issue 4486 mdm inconsistent possible match score values (#4487) * Extract method for readability * Save always normalized score values in POSSIBLE_MATCH links. * Avoid setting properties to null values. Adjust test. * Simplify fix * Fix test. Add RangeTestHelper. --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Revert "cleaning up checkstyle files (#4470)" This reverts commit efae3b5d5f397ab8fd92d7aaa82b484cfdfb3c33. * core version fix * Loosen rules for id helper * initial test implementation/changes and solution wiring. * adding support for jpa/mongo abstraction. * refact completed. need to start implementing scheduling of subscription re-submission with the scheduler service. * post release, merging in master. * wip: commit before merging in branch master. * wip: resuming work on the issue. * wip: before merging in master. * wip: partial implementation of mongo support. * wip: more work to support partial implementation on mongo. * Test implementation * providing method getMessageKeyOrDefault(); * providing changelog * preping codereview. * wip: passing tests * wip: finally solving the Meta issue. * wip: adjusting interfaces * Adding IT and * IT test; fixing rollback issue. * removing non required logging * fixing merge conflict * Preparing for code review. * Preparing for code review. * Compiling code after merging in master. * Fixing checkstyle failure. * Modifications towards getting all tests to pass. * addressing comments from code review. * compiling code after switching target merge branch to rel_pub_2023_05 * compiling code after switching target merge branch to rel_6_6 * Addressing comments made in design meeting. wip. * Addressing comments made in design meeting. finally completed. and last 2 comments addressed. * removing non required override * reverting changes as they are not required. * Modified test and implementation. * implementation of a SynchronousSubscriptionMatcherInterceptor to submit modifiedResources to the subscription pipeline for testing only. * fix tests by modifying the matchingInterceptor to call pointcut when processing * fixing more tests. * WIP to pass all tests in jpaserer-4504-a-resource-submitted-to-the-subscription-pipeline-is-lost-when-the-pipeline-encounters-an-issue * fixing circular dependency * Adding import dependency to class TestSubscriptionSubmitterConfig to allow submission of messages with the SynchronousSubscriptionMatcherInterceptor. * bumping version 6.7.7-SNAPSHOT * bumping HAPI version to 6.7.7-SNAPSHOT * fixing tests failure caused by asynch deliver of resourceModifiedMsg to the processing pipeline. * passing all tests. * unbumping to 6.7.7 * compiling after merging in master. * creating a custom hapi version * providing an synchronous subscription matcher interceptor for testing. * updating pom version to generate artifacts. * fixing tests, WIP/0 * fixing tests, WIP/1 * fixing tests, WIP/2 * Matching entity annotation with migration task declarations. * Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage. * Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage. * Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc]. * Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc] again. * Removing creation of new transaction to inflate PersistedRresourceModifiedMessages since it is already executing in a transaction. * bumping to version 6.7.14-ASYNC-SNAPSHOT for pipeline. * bumping hapi version to 6.7.14-ASYNC-SNAPSHOT for pipeline. * Formatter changes. * add generic * add generic * Addressing code review comments. * Adding file asynch_subscription_610.md to docs/upgrades * changing poms to 6.9.2-SNAPSHOT before merging in master. * compiling after merging in master. * Lowering logging level to debug. * Bumping to 6.9.3-SNAPSHOT * Bumping hapi version to 6.9.4-SNAPSHOT * Adding update documentation. * Modifying update file following review. --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Mark Iantorno <markiantorno@gmail.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> |
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Ken Stevens
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deeffe2253
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fix some race conditions (#5220)
* fix memory leak * race condition fixes and change log * race condition fixes and change log |
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Tadgh
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a10856e091
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GM1 Mergeback (#5203)
* version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * Rename file to force IT mode * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * wip * Fix API usage * wip * Version bump --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> |
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TipzCM
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a48c602f71
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adding pointcuts for mdm operations (#5116)
* adding pointcuts for mdm operations * adding changelog * cleanup * cleaning up * formatting * review fixes * formatting * more cleanup * cleanup * moving changelog * fixing a bug * cleanup * formatting * version bump * fixing broken merge * fixing the version --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> |
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Tadgh
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5eda18f500
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Mergeback of rel_6_8 (#5146)
* version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * Rename file to force IT mode --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> |
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James Agnew
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2b91f0a232
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Version bump HAPI FHIR and a couple of deps (#5121)
* Version bumps * Version bump HAPI * Add enum for next release * Changelog update * HAPI version bump |
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Tadgh
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dcf3240191
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Proper version bump (#5135)
* Fix version * Fix version enum |
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Tadgh
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53ceb7cac4
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Bump to nov (#5120)
* bump version, make new folders * Fix typo in versionenum |
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James Agnew
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6d745b4f2d
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Initial HFQL SQL Implementation (#5083)
* FQL tests * Working so far * Tests working * Tests passing * Work on parser * Tests passing * Cleanup * Working * Work on parser * Work * Working * Work on tests * Work on driver * Work * Ongoing work * Rename SEARCH to WHERE * Work on fhirpath * Test fixes * Work on statements * Build fixes * Spotless application * Fix CI * Build fixes * Clean up changelogs * Remove redundant gitignore * Add docs * Add docs * Code cleanup * Build cleanup * Fix compile error * Test fixes * Test fix * Test fix * Work on integration * Work on design * Work on UI * Update hapi-fhir-jpaserver-hfql/src/main/java/ca/uhn/fhir/jpa/fql/jdbc/JdbcDriver.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Address review comments * Review comments * HFQL work * Cleanup * CLeanup * License headers * Test fixes * HAPI version bump * License header update * Changelog cleanup * Fixes * Test fix * Fix spotless issues --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> |
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Steve Corbett
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66f428d356
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5103 - Adjust our handling of space escape characters in URLs (#5104)
* 5103 - Adjust our handling of space escape characters in URLs * 5103 - Fix formatting * 5103 - Adjust URL escaping and update test expectations * 5103 - additional test for values with literal plus signs * 5103 add changelog for this issue * 5103 - documentation change to describe proper URL escaping * 5103 - Minor documentation addition |
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Kevin Dougan SmileCDR
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633a2d156d
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5097 - Fixed a couple of links in the javadocs for the IValidationSupport class. (#5098) | ||
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TipzCM
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906355dd65
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adding block list for mdm (#5059)
* using any/exact enum * bluck rule evaluation svc * adding blocklist * adding documentation * cleanup * adding mdm blocking service and code cleanup * review points * another review point * review points --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> |
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Ken Stevens
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c88662205d
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implement cds hooks (#5076)
* move json and interfaces to hapi * move serialization over * moar test move * move prefetch service * move service registry * moved everything we can. now just need to add a controller and controller test * controller done * IJ Warnings * Move test * licenses * mvn spotless:apply * checkstyle * spotless --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> |
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Luke deGruchy
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43694f378c
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Ensure FhirContext loads custom resources in the list of resource names (#5073)
* Fix bug by maintaining a separate list of resource types including the custom resources that will be used to validate the Bundle resources. * Add custom resource types to resource types list and add conditional logic in ValidationDataInitializerSvcImpl to ensure there is no Exception when parsing a custom resource type. * Add changelog. * Remove unnecessary change. * Address code review feedback. * Address code review feedback. * Add one more unit test. * Bump to 6.7.14-SNAPSHOT. |
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Tadgh
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52f3ef5992
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New formatting rules and pre-commit hooks (#5027)
* pre-apply spotless * New pre-format checkpoint * Once-over the repository * Add pre-commit hook * New github action * excludes * Revert "Once-over the repository" This reverts commit 89334ba8d107ce92c101ad11b0de2586d434e7c5. * Once-over the repo * do not inherit * Revert "Once-over the repo" This reverts commit 31ed8731ad7430d31388e2d942730c150f9edd91. * Add baisc license support to spotless * Move license * Fix inclusions * Fix inclusions * Fix licensing * license fixes * Remove dead file that is only a license * Remove dead class * remove dead file * Tighten licensing * Tighten licensing * Tighten licensing * Tighten licensing * Remove specific package * Make the precommit hook executable * Fix ordering * rollback license * wip * Add to deployable pom * remove file * Fix location * Remove dead comment * wipP * Fix ratchet * Fix up error * Add pre-commit * precommit fixes * wip * wip * Autoformat * remove dead pom parts * replace internal hook with pre-commit * Fix fetch-depth for checker action * Remove ratchet and filter * fix up * rename * Add comment check * rework message * First once-over of the repo * wip * format |
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Brenin Rhodes
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eb06b473b9
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Update version of the Clinical Reasoning module (#5045)
* Update version of the Clinical Reasoning module * cleanup * Add changelog * Update snapshot * Inc version |