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422 Commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
James Agnew
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744a0d7096
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Database partition mode Part 2 (#6409)
* First pass at segmenting out changes * Test fixes * Test fixes * Test fix * Work on tests * Fix test * Test fix * Test fix * Fixes * Test fixes * Test fix * License headers * Test fix * Add changelog * Address review comments * Review comments * Fixes * Work on tests * Address review comments * Fix * Add tests * Cleanup * Rename JpaPidValueTuples * Add changelog * Spotless * Resolve compile issues * Fix signature issue * Test fix * Add header * Spotless * Test cleanup * Work on merge * Work on tests |
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TipzCM
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c9c8371a98
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6478 conditional updates should batch resourcesearchurl deletes (#6479)
* minor perf fix for transaction bundles * spotless * removing uneeded classes * review fixes - adding jira to changelog * code review points * supporting single transaction processing --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> |
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James Agnew
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ea1d179b9a
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Caching cleanup (#6522)
* Tests passing * Cleanup * Cleanupo * Test fixes * Test fix * Cleanup * Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java Co-authored-by: Ken Stevens <khstevens@gmail.com> * Account for review comments * Spotless * Compile fix * Test fixes * Test cleanup * Test cleanup * Test fixes * Resolve fixme * Test fix * Test fixes * Test fixes * Test fixes * Fix * Test fix * Test fixes * Test fixes * Cache cleanup * Work on caches * Add changelog * Compile fix * Spotless * Test fix * Fix * Cache cleanup * Trying to figure out why Lucene tests are failing * Test fix * More cleanuo * Test fix * Test fix * Address some review comments * HAPI FHIR version bump * Test fixes * Cleanup * Add assert * Add check * Test fixes * Bulk export fix * Test fixes * Add some test logging * Cleanup * Cleanup * Test cleanup * Add test logging * Attemped test fix * Add testing method * FIx build * Attempted test fix * Try to fix tests * Restore fixme * Spotless * Test fix --------- Co-authored-by: Ken Stevens <khstevens@gmail.com> |
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TipzCM
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d145e2a4bb
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6404 lucene search fulltext fix (#6517) | ||
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James Agnew
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362dc095ac
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Streamline ValidationSupportChain (#6508)
* Tests passing * Cleanup * Cleanupo * Test fixes * Test fix * Cleanup * Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java Co-authored-by: Ken Stevens <khstevens@gmail.com> * Account for review comments * Spotless * Compile fix * Test fixes * Test cleanup * Test cleanup * Test fixes * Resolve fixme * Test fix * Test fixes * Test fixes * Test fixes * Fix * Test fix * Test fixes * Test fixes * HAPI version bump * Try to address intermittent --------- Co-authored-by: Ken Stevens <khstevens@gmail.com> |
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James Agnew
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061390d76b
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Add composite interceptor registry (#6511)
* Composite interceptor improvements * Add composite interceptor registry * Add changelog * Composite Interceptor Broadcaster Improvements * Fix compile error * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6511-rework-composite-interceptor-broadcaster.yaml Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Address review comments * Test fixes * Test fix * Test fix --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> |
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Tadgh
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86c2c13e0f
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7.6.0 Mergeback (#6494)
* 6323 resource creation deadlock (#6324) * make map reads concurrent * change log * CUstom version number for guaranteed build determinism * licenses * Expand translation cache (#6341) * Expand translation cache * Add changelog * Correction to #6341 (#6342) * Contained bug (#6402) * Contained bug * more tests * changelog, tests, implementation * code review * backwards logic * Fix Questionnaire doc (#6400) * fix reindex optimizeStorage=ALL_VERSIONS (#6421) * fixing broken rename of last step of reindex (#6429) * Fixes for the translation of parameter issues as part of the output for $validate-code operation. (#6438) * Move the validation providers to the test utilities package such that they can be reused. * Update IValidationSupport.CodeValidationIssue structure such that it meets the FHIR specification. Update RemoteTerminologyServiceValidationSupport and VersionSpecificWorkerContextWrapper translation for issues. * New tests for issue translation. Move test class to a different package so that we can add another test class. * Some simplification in the issue API to simplify building of issues. * Fix compilation errors. * Update providers to allow multiple responses and add support for the fetchCodeSystem call through method find. * Setup the first test for resource validation with remote terminology providers. * Fix NullPointerException * avoid calling validateCode for CodeSystem where system is null * Keep old public API methods (and class name) in IValidationSupport and mark them as deprecated to avoid breaking dependencies. * Revert local change to debug for duplicate errors. * Add more test cases for resource validation. Throw exception to signal missing test setup to make it obvious. * Simplify test setup. * Add some more javadoc * Add javadoc for the new test class * Add more tests * Address code review comments in IValidationSupport. * Add changelog * Change Repository search interface from Map to Multimap (#6445) Change Map to Multimap to support multiple and clauses. * licenses * fix interceptor hooks from requestDetails not getting called for STORAGE_PRECHECK_FOR_CACHED_SEARCH (#6436) * fix interceptor hooks from requestDetails not getting called for STORAGE_PRECHECK_FOR_CACHED_SEARCH * added unit tests and updated changelog * added one more test case * Add Adapter api (#6450) Lightweight implementation of the adapter pattern. * Bulk Import job status not changed after activation - failing test, fix, changelog (#6452) * Update CR to 3.13.1 (#6433) * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 (#6439) * Rel 7 6 CVE (#6446) * Bump commons io * Bump HS and Lucene, and hibernate * Jetty bump for CVE * Resolve CVES * Bump with mismatch lucene * Bump velocity template engine * Revert bom bump * wip * Version bump * move changelog, fix cve * Bump commons-lang * Replace imports * wip * fix HQL break * remove dead code * Fix changelog entry * Bump org.hl7.fhir.core to 6.4.0 (#6454) * Bump HAPI version + org.hl7.fhir.core to 6.4.0 * Apply spotless * Correct a bug with duplicate parser IDs being assigned. (#6456) * Fix changelog entry * wip * compilation problem * Correct tests * changelog * Update hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Correct a bug with duplicate parser IDs being assigned - test fixes * Correct a bug with duplicate parser IDs being assigned - spotless * Correct a bug with duplicate parser IDs being assigned - added test-utilities dependency to fhir-structures poms * Correct a bug with duplicate parser IDs being assigned - test fixes * Contained resources without assigned IDs are now assigned GUIDs - address comments --------- Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com> * licenses * ValueSet expansion fails if Hibernate Search configured to use Lucene - fixed incompatibility between Hibernate Search and Lucene versions (#6468) * Change the migrator to avoid table locks when adding an index. (#6489) * version bump * Updating version to: 7.6.1 post release. * Bump to 7.7.7. * deadsapce * Profile reference param (#6501) * updated QueryStack to not throw error with _profile as a ReferenceParam * update QueryStack * remove warnings * cleanup cast * cleanup test * add changelog * cleanup imports * updates per review feedback * updates per review feedback --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> * move changelog --------- Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Gary Graham <garygraham@smiledigitalhealth.com> Co-authored-by: Taha <TahaAttari@users.noreply.github.com> Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> |
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James Agnew
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d4f1766ca5
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Optimize transaction writes (#6460)
* Optimize transaction writes * Cleanup * Work on tests * Work on fixes * Fixes * Fixes * Test fixes * Cleanup * Cleanup * Work on tests * Work on tests * Test fixes * Test fixes * Remove redundant test * Test fixes * Test fix * Test fixes * Test fixes * Test fixes * Add changelog * Checkstyle fixes * Test fixes * Spotless * Test cleanup * Spotless * Test fix * Work on review comments * Address review comments * Test fixes * Ongoing test cleanup work * Work on tests * Query count tests passing * Test fixes * Test fixes * Rmove fixme * Test cleanup * Test fix * Remove default method * Service celanup * Test fix * version bump * Test cleanup |
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James Agnew
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dea9706652
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MDM Virtualization Interceptor (#6464)
* Work on virtualization * Fixes * Cleanup * Fixes * MDM virtualization * Remove fixme * Test cleanup * Cleanup * Version bump * Fixes * Cleanup * Fixes * WIP * Test cleanup * Spotless * Checkstyle * Spotless * Address review comments * Test fix * Test fix * Address review comments * Version bump * Version bump * License header |
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volodymyr-korzh
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e182694608
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Excessive Hibernate warnings when processing conditional create and delete operations on referenced resources in a transaction bundle (#6477)
* Excessive Hibernate warnings when processing conditional create and delete operations on referenced resources in a transaction bundle - failing test * Excessive Hibernate warnings when processing conditional create and delete operations on referenced resources in a transaction bundle - fix * Excessive Hibernate warnings when processing conditional create and delete operations on referenced resources in a transaction bundle - changelog |
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VK-SMILECDR
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cbbba75d9a
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6472 move cds hooks related classes to hapi fhir server package (#6473)
* moving CDS Hooks Json files * spotless |
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jmarchionatto
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cdb0a9c480
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Add tinder plugin to pluginManagement to allow to run generate-ddl from parent (#6192)
* Add tinder to parent project's pluginManagement * Use specific version to avoid inheriting projects to replace by theirs * Move dialects down to executing project because appendFile included in postgres dialect precludes to define it at the parent level * Improve logging * Use temporary project version * Revert "Use temporary project version" This reverts commit 24f5e648ed3aecf057fd90cf4398e339f4dc4a6e. * Increment version * Increment missed version * Added headers * Document new command --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> |
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dotasek
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ef78b46621
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Bump org.hl7.fhir.core to 6.4.0 (#6410)
* Add missing implementations + update changed classnames * Fix breaking test due to new validation rules * Add changes.yaml * Bump to HAPI version 7.7.1-SNAPSHOT * Copyright autogen ***NO_CI*** * Bump to HAPI 7.7.2-SNAPSHOT |
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James Agnew
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96e1c2a5db
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Add extension for disabling search params (#6107)
* Combo permutations * Work on combo * Add tests * Add changelog * Spotless * Test fix * Drop label * Add tests * Spotles * Work on disable code * Cleanup * CLeanup * Cleanup * Add changelog * Test cleanup * Review comments * Spotless * Compile fix * Version bump * Test fix * Test fixes |
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Tadgh
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9365ad9509
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Revert "Fixes for the translation of parameter issues as part of the output f…" (#6441)
This reverts commit fca3ea444593175b5187525ec33cbb56142d1383. |
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Martha Mitran
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fca3ea4445
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Fixes for the translation of parameter issues as part of the output for $validate-code operation. (#6423)
* Move the validation providers to the test utilities package such that they can be reused. * Update IValidationSupport.CodeValidationIssue structure such that it meets the FHIR specification. Update RemoteTerminologyServiceValidationSupport and VersionSpecificWorkerContextWrapper translation for issues. * New tests for issue translation. Move test class to a different package so that we can add another test class. * Some simplification in the issue API to simplify building of issues. * Fix compilation errors. * Update providers to allow multiple responses and add support for the fetchCodeSystem call through method find. * Setup the first test for resource validation with remote terminology providers. * Fix NullPointerException * avoid calling validateCode for CodeSystem where system is null * Keep old public API methods (and class name) in IValidationSupport and mark them as deprecated to avoid breaking dependencies. * Revert local change to debug for duplicate errors. * Add more test cases for resource validation. Throw exception to signal missing test setup to make it obvious. * Simplify test setup. * Add some more javadoc * Add javadoc for the new test class * Add more tests * Address code review comments in IValidationSupport. * Add changelog |
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James Agnew
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f17e5fbb4e
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Second attempt at improving auth handling (#6382)
* Revert "Revert "Improve auth interceptor operation handling (#6278)" (#6381)" This reverts commit 422d4f0741502aec0a2a617fbbc1fda6a85d77d5. * Move changelog |
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Ibrahim
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e43c140a24
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Refactor BaseHapiFhirDao.getOrCreateTag method to run in a separate thread for XA transaction compatibility (#6224)
* Fix typo in docs.
* Refactor the use of ConcurrentTaskScheduler to use the non-deprecated constructor.
* Refactor getOrCreateTag method to prevent transaction suspension for XA transaction compatibility
The getOrCreateTag method previously used a propagation behavior that caused issues with
XA transactions when using the PostgreSQL JDBC driver. The PGXAConnection does not support
transaction suspend/resume, which made it incompatible with the existing propagation strategy
'PROPAGATION_REQUIRES_NEW'.
This refactor changes the getOrCreateTag logic to perform a lookup/write in a new transaction
as before, but running in a separate thread, such that the main transaction is not suspended.
The result is retrieved through a future.
This change aims to improve compatibility and prevent transaction-related issues when using HAPI-FHIR with
XA transactions and PostgreSQL.
Closes #3412
* Refactor tag creation logic and handle concurrent access:
- Simplified tag creation by removing unnecessary transaction complexity, since we allow duplicate tags in hfj_tag_def from #4813
- Removed redundant retry logic based on updated DB constraints
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James Agnew
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71cb097aa6
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Add author searchin to NPM package search (#6398)
* Add author searchin to NPM package search * Add changelog * License header * Address review comments |
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Tadgh
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443b59a78b
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Bump For February Release (#6392)
* Bump Version * new versions, new folder |
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Tadgh
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60ed1fd225
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Rel 7 4 mb 20241018 (#6385)
* use SearchParamater validator in package installer (#6112) * Ensure ' ' is treated as '+' in timezones with offsets. (#6115) * Use lockless mode when adding index on Azure Sql server (#6100) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT (#6127) * fix hfj search migration task (#6143) * fix migration task * changelog * changelog * code review * spotless --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> * Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive (#6135) * MSSQL: Migrate HFJ_RESOURCE.FHIR_ID to new collation: SQL_Latin1_General_CP1_CS_AS * Spotless. * Enhance test. Fix case in ResourceSearchView to defend against future migration to case insensitive collation. * Remove TODOs. Add comment to ResourceSearchView explaining why all columns are uppercase. Changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml Code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Common API for FHIR Data Access (#6141) * Add initial interface for common FHIR API * Fix formatting * Update javadocs * Address code review comments * Add path value to _id search parameter and other missing search param… (#6128) * Add path value to _id search parameter and other missing search parameters to IAnyResource. * Adjust tests and remove now unnecessary addition of meta parameters which are now provided by IAnyResource * Revert unneeded change * _security param is not token but uri * Add tests for new defined resource-level standard parameters * Adjust test --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * update to online (#6157) * SEARCH_UUID should be non-null (#6165) Avoid using constants in migrations because it creates false history. * Handle 400 and 404 codes returned by remote terminology operation. (#6151) * Handle 400 and 404 codes returned by remote terminology operation. * Some simplification * Adjust changelog * Add a comment to explain alternate solution which can be reused. * fix concepts with no display element for $apply-codesystem-delta-add and $apply-codesystem-delta-remove (#6164) * allow transaction with update conditional urls (#6155) * Revert "Add path value to _id search parameter and other missing search param…" (#6171) This reverts commit 2275eba1a0f379b6ccb2d1b467fa22bd9febcf54. * 7 2 2 mb (#6160) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * 6051 bulk export security errors (#5915) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * refactor bulk export rule, add concept of appliestoallpatients, fix tests * spotless * Cahgnelog, tests * more tests * refactor style checks --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> * Convert a few nulls to aggressive denies * Change chain sort syntax for MS SQL (#5917) * Change sort type on chains * Change sort type on chains * Test for MS SQL * Comments * Version bump * Updating version to: 7.2.1 post release. * Fix queries with chained sort with Lucene by checking supported SortSpecs (#5958) * First commit with very rough solution. * Solidify solutions for both requirements. Add new tests. Enhance others. * Spotless. * Add new chained sort spec algorithm. Add new Msg.codes. Finalize tests. Update docs. Add changelog. * pom remove the snapshot * Updating version to: 7.2.2 post release. * cherry-picked pr 6051 * changelog fix * cherry-picked 6027 * docs and changelog * merge fix for issue with infinite cache refresh loop * Use lockless mode when adding index on Azure Sql server (#6100) (#6129) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * added fix for 6133 * failing Test * Add fix * spotless * Remove useless file * Fix claeaner * cleanup * Remove dead class * Changelog * test description * Add test. Fix broken logic. * fix quantity search parameter test to pass * reverted test testDirectPathWholeResourceNotIndexedWorks in FhirResourceDaoR4SearchWithElasticSearchIT * spotless * cleanup mistake during merge * added missing imports * fix more mergeback oopsies * bump to 7.3.13-snapshot --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> * Patient validate operation with remote terminology service enabled returns 400 bad request (#6124) * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - failing test * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - implementation * - Changing method accessibility from default to public to allow method overwriting. (#6172) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying Taha Attari's fix on branch merging to rel_7_4 (#6177) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Automated Migration Testing (HAPI-FHIR) V7_4_0 (#6170) * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_2_0 * To provide the target resource partitionId and partitionDate in the resourceLinlk (#6149) * initial POC. * addressing comments from first code review * Adding tests * adding changelog and spotless * fixing tests * spotless --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying patch (#6190) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cve for 08 release (#6197) Co-authored-by: Long Ma <long@smilecdr.com> * Search param path missing for _id param (#6175) * Add path tp _id search param and definitions for _lastUpdated _tag, _profile and _security * Add tests and changelog * Increase snapshot version * Irrelevant change to force new build --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Reverting to core fhir-test-cases 1.1.14; (#6194) re-enabling FhirPatchCoreTest Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Fix $reindex job with custom partition interceptor based on resource type. Update reindex job to always run with urls. (#6185) * Refactor logic to bring together partition related logic in batch2 jobs using IJobPartitionProvider. Update logic such that reindex job without urls will attempt to create urls for all supported resource types. * Small changes and fix of pipeline error. * Small change to enable mdm-submit to use PartitionedUrl in the job parameters * Revert logback change. Fix dependency version generating errors in the pipeline. * Spotless fix. Add test dependency back without version. * Upgrade test dependency to another version * Add javadoc for PartitionedUrl. Other small fixes and refactoring in tests. * Spotless fix. * Change to JobParameters to fix some of the tests. * Small changes for code review in test * Address code review comments. * Revert change from bad merge. * Address remaining code review comments * 6188 subscription not marked as a cross partition subscription matches operation on resources in other partitions (#6191) * initial failing test * WIP * fixing/adding tests * added changelog * spotless * fixing tests * Cleaning up tests * addressing commetns from first code review. * no-op to get pipelines going --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Resolve 6173 - Log unhandled Exceptions in RestfulServer (#6176) (#6205) * 6173 - Log unhandled Exceptions in RestfulServer. * Use placeholder for failed streams. * Starting test for server handling. * Got test working. * Fixed use of synchronized keyword. * Applied mvn spotless. --------- Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Partition aware transactions (#6167) * Partition aware transactions * Address review comments * Test fixes * Remove dead issue field * Test fixes --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Add license header * Attempt fix for npe (#6213) * wip * wip * wip * remove whitespace * Add test * changelog * Version bump * Updating version to: 7.4.1 post release. * Backport for 7.4.2 (#6303) * version bumps and change log * cherry pick 6420 * various updates to changelogs * build formatting changes --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> * Updating version to: 7.4.3 post release. * Backport for 7.4.3 (#6322) * Composite unique search parameter with dateTime component does not reject resource duplication (#6318) * Composite Unique Search Parameter with dateTime component does not reject resource duplication - failing tests * Composite Unique Search Parameter with dateTime component does not reject resource duplication - implementation * Composite Unique Search Parameter with dateTime component does not reject resource duplication - changelog and test fixes * 2024.08.R03 backport - version bump * merge conflicts * conflicts * Updating version to: 7.4.4 post release. * bumping fhir core version (#6364) * bumping fhir core version * default methods * adding changelog * fixes * remove commented out code * version bump and some minor test fixes * version bump * changelog * review fixes --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * Fix up folders, rewrite changelog * Add support for response parameter issues for `validate-code` operation (#6360) * Add support for response parameter issues for validate-code operation. Implement workaround for missing error for invalid codes by adding an issue when it is absent. * address minor code review comments * revert functionality of adding original code from remote validate-code call to the CodeValidationResult * revert change to FhirInstanceValidatorR4Test * Revert some of the code review addressal after responding. * Remove populating message in success scenarios. * Fix compilation failure in test after reverting method rename. * Revert change to populate the code from the response again as it implies more refactoring. --------- Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> * Backport info * resolution * bad merge * wip * spotless * duplicate changelog * bad merges * Fix NPE * Test failure * wip --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: JP <jonathan.i.percival@gmail.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: Martha Mitran <marthamitran@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com> Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> |
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James Agnew
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422d4f0741
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Revert "Improve auth interceptor operation handling (#6278)" (#6381)
This reverts commit 2b3858572d5831de2dff41574ae65e3884b527d7. |
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James Agnew
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2b3858572d
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Improve auth interceptor operation handling (#6278)
* Fix #6258 - Improve auth interceptor operation handling * Cleanup |
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TipzCM
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5b23e1bbec
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fixing bug with fulltext and jpa search filters (#6374) | ||
Brenin Rhodes
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161a077f2a
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Update Clinical Reasoning to 3.13.0 (#6358)
* Update Clinical Reasoning to 3.12.0 * Update to 3.13.0 * add stub for new not document parameter * Add new client Timezone header and enhance JsonUtil to handle ZonedDateTime. * Add StringTimePeriodHandler and test. Add new code to DateUtils and new test class. Inject StringTimePeriodHandler into MeasureOperationsProvider and CareGapsOperationProvider. Change CareGapsOperationProvider to take String params instead of IPrimitiveType<Date>. * Remove old LibraryEvaluationOperationProvider * Fix test * Fix tests * Add $data-requirement parameters to docs * Update docs for new measures timezone header. * Add prefetchData parameter to $apply doc * Add changelog * Fix test * Update snapshot version * Add new $extract parameters to docs * Remove old test * fix test and properties for care-gaps * Fix dstu3 config * remove property for fhirserverurl * update upgrade.md doc * fix formatting of upgrade doc * comment on measureidentifier param * nonDocument parameter inclusion * java doc on care-gaps * No longer dead code. * Spotless. * Change CareGapsOperationProvider to R4 BooleanType. * Update to release * change log update * change log edit * cleanup * Use existing bean * spotless * Ensure CollectDataOperationProvider uses StringTimePeriodHandler to convert periods. * Spotless. * Add tests for id * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md Co-authored-by: Tadgh <garygrantgraham@gmail.com> * cleanup and comments * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md Implement code reviewer suggestion on timezone docs Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md Implement code reviewer suggestion on timezone docs Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md Implement code reviewer suggestion on timezone docs Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md Implement code reviewer suggestion on timezone docs Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Code review feedback: Add logging for StringTimePeriodHandler. * Spotless. * cleanup * Code review feedback: measures.md style changes. Change code 2560 to 2561. * Change error code. --------- Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> |
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Nathan Doef
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8f52f1c769
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Fix Regression (#6376)
* failing test * fix |
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James Agnew
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4ab958a58f
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Add hash identity token mode (#6375)
* Add hash identity token mode * Spotless * Test fix |
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Michael Buckley
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d4227baf2a
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Add partition_id to search joins (#6325)
* Failing test * cleanup * revert partition in group by clause * test update for new joins * Give up on nullable join :not joins require sub-selects and the nullability can't support an in(select ) clause. Bring in flag, and set based on partition settings * spotless * changelog * cleanup * cleanup * fixmes * partitioned sql test * get sort tested * revert tests expecting nullable partition joins * Fix result set parsing when coord-sort is present. * Cleanup sql test * Change to default select partition_id Add sort test cases. * Fix everything sql * Fix everything sql * Fix group-by on offset path * More sql test fixups * More sql test fixups * Test case for cache key * review feedback * Revert to HFJ_RES_VER_PROV until we get the migration * fix for everything from james * fixme * Revert column name * Cleanup * Test fix --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> |
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Martha Mitran
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7581920a15
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Add support for response parameter issues for validate-code operation (#6360)
* Add support for response parameter issues for validate-code operation. Implement workaround for missing error for invalid codes by adding an issue when it is absent. * address minor code review comments * revert functionality of adding original code from remote validate-code call to the CodeValidationResult * revert change to FhirInstanceValidatorR4Test * Revert some of the code review addressal after responding. * Remove populating message in success scenarios. * Fix compilation failure in test after reverting method rename. * Revert change to populate the code from the response again as it implies more refactoring. --------- Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> |
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TipzCM
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eadd8c6f0d
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improved performance of date searching (#6353) | ||
jdar8
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96cc20dc0d
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add delete partition pointcut (#6314)
Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> |
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Ken Stevens
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6f94e228b0
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batch2 new svc methods (#6310)
* started work on adding new methods * started work on adding new methods * review feedback. move dto from api to model * checkstyle |
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dotasek
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43e28da0c5
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Bump org.hl7.fhir.core to 6.3.25 (#6293)
* org.hl7.fhir.core bump 6.3.25 * Add setting for UnknownCodeSystemsCauseErrors + fix tests * Spotless * Don't expose unknownCodeSystemsCausesErrors for now. Use a constant. |
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TipzCM
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62fa7ec787
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value set expansion (#6286) | ||
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volodymyr-korzh
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fb7571185a
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Composite unique search parameter with dateTime component does not reject resource duplication (#6318)
* Composite Unique Search Parameter with dateTime component does not reject resource duplication - failing tests * Composite Unique Search Parameter with dateTime component does not reject resource duplication - implementation * Composite Unique Search Parameter with dateTime component does not reject resource duplication - changelog and test fixes |
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Martha Mitran
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20d3e6bb25
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Fix missing qualifier search for reference search parameters (#6306)
* Fix missing qualifier search for reference search parameter. Reuse tests and run them for both indexing enabled and disabled. * Fix edge case where the search parameter has multiple paths. Add a test. Fix some of the compile warnings in a test class. * Fix test setup. |
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Aditya Dave
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1fad912193
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6262 cds hooks returns 400 when extension passed in the cdsservicerequestjson (#6274)
* fail test * potential fix * spotless * alternative fix * spotless * remove the new method and replace usage for the old one * spotless * fix issue with context failing deserialization * add validation for context, hook and hook instance * spotless * add message codes * spotless * changelog * cleanup * spotless * bump version to 7.5.1-SNAPSHOT |
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jmarchionatto
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ab2ba05fb5
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Narrow version check scope to fix intermittency produced because argu… (#6279)
* Narrow version check scope to fix intermittency produced because argument was present in CodeSystem field different from version * Remove duplication * Remove code duplication * fix comment syntax --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> |
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jdar8
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12765ac397
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Disabling enforce referential integrity on write still checks references (#6219)
* fix * tests, changelog, spotless * document tests better * address review comments * reset settings so other tests don't fail * unused import --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> |
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Ken Stevens
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1e2d8b123e
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improve match error (#6260)
* improve error message * improve error message * fix tests |
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Etienne Poirier
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5e48e38b1d
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6203 subscriptionvalidatinginterceptor allows invalid url for rest hook endpoint (#6225)
* use SearchParamater validator in package installer (#6112) * Ensure ' ' is treated as '+' in timezones with offsets. (#6115) * Use lockless mode when adding index on Azure Sql server (#6100) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT (#6127) * fix hfj search migration task (#6143) * fix migration task * changelog * changelog * code review * spotless --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> * Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive (#6135) * MSSQL: Migrate HFJ_RESOURCE.FHIR_ID to new collation: SQL_Latin1_General_CP1_CS_AS * Spotless. * Enhance test. Fix case in ResourceSearchView to defend against future migration to case insensitive collation. * Remove TODOs. Add comment to ResourceSearchView explaining why all columns are uppercase. Changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml Code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Common API for FHIR Data Access (#6141) * Add initial interface for common FHIR API * Fix formatting * Update javadocs * Address code review comments * Add path value to _id search parameter and other missing search param… (#6128) * Add path value to _id search parameter and other missing search parameters to IAnyResource. * Adjust tests and remove now unnecessary addition of meta parameters which are now provided by IAnyResource * Revert unneeded change * _security param is not token but uri * Add tests for new defined resource-level standard parameters * Adjust test --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * update to online (#6157) * SEARCH_UUID should be non-null (#6165) Avoid using constants in migrations because it creates false history. * Handle 400 and 404 codes returned by remote terminology operation. (#6151) * Handle 400 and 404 codes returned by remote terminology operation. * Some simplification * Adjust changelog * Add a comment to explain alternate solution which can be reused. * fix concepts with no display element for $apply-codesystem-delta-add and $apply-codesystem-delta-remove (#6164) * allow transaction with update conditional urls (#6155) * Revert "Add path value to _id search parameter and other missing search param…" (#6171) This reverts commit 2275eba1a0f379b6ccb2d1b467fa22bd9febcf54. * 7 2 2 mb (#6160) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * 6051 bulk export security errors (#5915) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * refactor bulk export rule, add concept of appliestoallpatients, fix tests * spotless * Cahgnelog, tests * more tests * refactor style checks --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> * Convert a few nulls to aggressive denies * Change chain sort syntax for MS SQL (#5917) * Change sort type on chains * Change sort type on chains * Test for MS SQL * Comments * Version bump * Updating version to: 7.2.1 post release. * Fix queries with chained sort with Lucene by checking supported SortSpecs (#5958) * First commit with very rough solution. * Solidify solutions for both requirements. Add new tests. Enhance others. * Spotless. * Add new chained sort spec algorithm. Add new Msg.codes. Finalize tests. Update docs. Add changelog. * pom remove the snapshot * Updating version to: 7.2.2 post release. * cherry-picked pr 6051 * changelog fix * cherry-picked 6027 * docs and changelog * merge fix for issue with infinite cache refresh loop * Use lockless mode when adding index on Azure Sql server (#6100) (#6129) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * added fix for 6133 * failing Test * Add fix * spotless * Remove useless file * Fix claeaner * cleanup * Remove dead class * Changelog * test description * Add test. Fix broken logic. * fix quantity search parameter test to pass * reverted test testDirectPathWholeResourceNotIndexedWorks in FhirResourceDaoR4SearchWithElasticSearchIT * spotless * cleanup mistake during merge * added missing imports * fix more mergeback oopsies * bump to 7.3.13-snapshot --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> * Patient validate operation with remote terminology service enabled returns 400 bad request (#6124) * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - failing test * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - implementation * - Changing method accessibility from default to public to allow method overwriting. (#6172) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying Taha Attari's fix on branch merging to rel_7_4 (#6177) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Automated Migration Testing (HAPI-FHIR) V7_4_0 (#6170) * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_2_0 * To provide the target resource partitionId and partitionDate in the resourceLinlk (#6149) * initial POC. * addressing comments from first code review * Adding tests * adding changelog and spotless * fixing tests * spotless --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying patch (#6190) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cve for 08 release (#6197) Co-authored-by: Long Ma <long@smilecdr.com> * Search param path missing for _id param (#6175) * Add path tp _id search param and definitions for _lastUpdated _tag, _profile and _security * Add tests and changelog * Increase snapshot version * Irrelevant change to force new build --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Reverting to core fhir-test-cases 1.1.14; (#6194) re-enabling FhirPatchCoreTest Co-authored-by: peartree <etienne.poirier@smilecdr.com> * initial failing test * providing capability to tailor resthook endpoint url validation through supplied regex * adding necessary import. * conformance with spotless * adding tests * adding test for payload * spotless * adding changelogs * passing all tests * passing all tests * no-op commit to kickstart the pipeline. * - slight modification to the solution; - spotless; * pre-code review submission. * moving validator instantiation to the submitter configuration so it is create along side the subscriptionValidatorInterceptor * last min tweeking before submission for review. * fixing spotless post merging in master --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: JP <jonathan.i.percival@gmail.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: Martha Mitran <marthamitran@gmail.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> |
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Ken Stevens
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48d8fac6ea
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fix patientId interceptor partition selection (#6236)
* fixed * fixed * detect uuid references earlier in the PatientIdPartitionInterceptor * TODO |
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Tadgh
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947291e7f5
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Final Mergeback of 7.4.0 (#6223)
* use SearchParamater validator in package installer (#6112) * Ensure ' ' is treated as '+' in timezones with offsets. (#6115) * Use lockless mode when adding index on Azure Sql server (#6100) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT (#6127) * fix hfj search migration task (#6143) * fix migration task * changelog * changelog * code review * spotless --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> * Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive (#6135) * MSSQL: Migrate HFJ_RESOURCE.FHIR_ID to new collation: SQL_Latin1_General_CP1_CS_AS * Spotless. * Enhance test. Fix case in ResourceSearchView to defend against future migration to case insensitive collation. * Remove TODOs. Add comment to ResourceSearchView explaining why all columns are uppercase. Changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml Code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Common API for FHIR Data Access (#6141) * Add initial interface for common FHIR API * Fix formatting * Update javadocs * Address code review comments * Add path value to _id search parameter and other missing search param… (#6128) * Add path value to _id search parameter and other missing search parameters to IAnyResource. * Adjust tests and remove now unnecessary addition of meta parameters which are now provided by IAnyResource * Revert unneeded change * _security param is not token but uri * Add tests for new defined resource-level standard parameters * Adjust test --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * update to online (#6157) * SEARCH_UUID should be non-null (#6165) Avoid using constants in migrations because it creates false history. * Handle 400 and 404 codes returned by remote terminology operation. (#6151) * Handle 400 and 404 codes returned by remote terminology operation. * Some simplification * Adjust changelog * Add a comment to explain alternate solution which can be reused. * fix concepts with no display element for $apply-codesystem-delta-add and $apply-codesystem-delta-remove (#6164) * allow transaction with update conditional urls (#6155) * Revert "Add path value to _id search parameter and other missing search param…" (#6171) This reverts commit 2275eba1a0f379b6ccb2d1b467fa22bd9febcf54. * 7 2 2 mb (#6160) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * 6051 bulk export security errors (#5915) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * refactor bulk export rule, add concept of appliestoallpatients, fix tests * spotless * Cahgnelog, tests * more tests * refactor style checks --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> * Convert a few nulls to aggressive denies * Change chain sort syntax for MS SQL (#5917) * Change sort type on chains * Change sort type on chains * Test for MS SQL * Comments * Version bump * Updating version to: 7.2.1 post release. * Fix queries with chained sort with Lucene by checking supported SortSpecs (#5958) * First commit with very rough solution. * Solidify solutions for both requirements. Add new tests. Enhance others. * Spotless. * Add new chained sort spec algorithm. Add new Msg.codes. Finalize tests. Update docs. Add changelog. * pom remove the snapshot * Updating version to: 7.2.2 post release. * cherry-picked pr 6051 * changelog fix * cherry-picked 6027 * docs and changelog * merge fix for issue with infinite cache refresh loop * Use lockless mode when adding index on Azure Sql server (#6100) (#6129) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * added fix for 6133 * failing Test * Add fix * spotless * Remove useless file * Fix claeaner * cleanup * Remove dead class * Changelog * test description * Add test. Fix broken logic. * fix quantity search parameter test to pass * reverted test testDirectPathWholeResourceNotIndexedWorks in FhirResourceDaoR4SearchWithElasticSearchIT * spotless * cleanup mistake during merge * added missing imports * fix more mergeback oopsies * bump to 7.3.13-snapshot --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> * Patient validate operation with remote terminology service enabled returns 400 bad request (#6124) * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - failing test * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - implementation * - Changing method accessibility from default to public to allow method overwriting. (#6172) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying Taha Attari's fix on branch merging to rel_7_4 (#6177) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Automated Migration Testing (HAPI-FHIR) V7_4_0 (#6170) * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_2_0 * To provide the target resource partitionId and partitionDate in the resourceLinlk (#6149) * initial POC. * addressing comments from first code review * Adding tests * adding changelog and spotless * fixing tests * spotless --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying patch (#6190) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cve for 08 release (#6197) Co-authored-by: Long Ma <long@smilecdr.com> * Search param path missing for _id param (#6175) * Add path tp _id search param and definitions for _lastUpdated _tag, _profile and _security * Add tests and changelog * Increase snapshot version * Irrelevant change to force new build --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Reverting to core fhir-test-cases 1.1.14; (#6194) re-enabling FhirPatchCoreTest Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Fix $reindex job with custom partition interceptor based on resource type. Update reindex job to always run with urls. (#6185) * Refactor logic to bring together partition related logic in batch2 jobs using IJobPartitionProvider. Update logic such that reindex job without urls will attempt to create urls for all supported resource types. * Small changes and fix of pipeline error. * Small change to enable mdm-submit to use PartitionedUrl in the job parameters * Revert logback change. Fix dependency version generating errors in the pipeline. * Spotless fix. Add test dependency back without version. * Upgrade test dependency to another version * Add javadoc for PartitionedUrl. Other small fixes and refactoring in tests. * Spotless fix. * Change to JobParameters to fix some of the tests. * Small changes for code review in test * Address code review comments. * Revert change from bad merge. * Address remaining code review comments * 6188 subscription not marked as a cross partition subscription matches operation on resources in other partitions (#6191) * initial failing test * WIP * fixing/adding tests * added changelog * spotless * fixing tests * Cleaning up tests * addressing commetns from first code review. * no-op to get pipelines going --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Resolve 6173 - Log unhandled Exceptions in RestfulServer (#6176) (#6205) * 6173 - Log unhandled Exceptions in RestfulServer. * Use placeholder for failed streams. * Starting test for server handling. * Got test working. * Fixed use of synchronized keyword. * Applied mvn spotless. --------- Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Partition aware transactions (#6167) * Partition aware transactions * Address review comments * Test fixes * Remove dead issue field * Test fixes --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Add license header * rel_7_4 mergeback * Attempt fix for npe (#6213) * wip * wip * wip * remove whitespace * Add test * changelog * Version bump --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: JP <jonathan.i.percival@gmail.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: Martha Mitran <marthamitran@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com> Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com> |
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Etienne Poirier
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3e2d84d0f7
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Query with FullText searching (_text) does not return expected result (#6217)
* sketch of scroll solution * implementation of a scrolled search to handle Lucene large resultset. * legacy code clean up * adding changelog * addressing comments from first code review * adding more test * correcting implementation after failing test * no-op change to trigger pipeline * no-op change to trigger pipeline again --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> |
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Michael Buckley
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3dd576bc86
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Extend default batch2 test deadline (#6221)
Extend default batch2 test deadline 10s is very quick on slow runners. Fix bad test. |
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volodymyr-korzh
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568c6d20db
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rel_7_4 Merge-back (#6212)
* use SearchParamater validator in package installer (#6112) * Ensure ' ' is treated as '+' in timezones with offsets. (#6115) * Use lockless mode when adding index on Azure Sql server (#6100) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT (#6127) * fix hfj search migration task (#6143) * fix migration task * changelog * changelog * code review * spotless --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> * Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive (#6135) * MSSQL: Migrate HFJ_RESOURCE.FHIR_ID to new collation: SQL_Latin1_General_CP1_CS_AS * Spotless. * Enhance test. Fix case in ResourceSearchView to defend against future migration to case insensitive collation. * Remove TODOs. Add comment to ResourceSearchView explaining why all columns are uppercase. Changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml Code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Common API for FHIR Data Access (#6141) * Add initial interface for common FHIR API * Fix formatting * Update javadocs * Address code review comments * Add path value to _id search parameter and other missing search param… (#6128) * Add path value to _id search parameter and other missing search parameters to IAnyResource. * Adjust tests and remove now unnecessary addition of meta parameters which are now provided by IAnyResource * Revert unneeded change * _security param is not token but uri * Add tests for new defined resource-level standard parameters * Adjust test --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * update to online (#6157) * SEARCH_UUID should be non-null (#6165) Avoid using constants in migrations because it creates false history. * Handle 400 and 404 codes returned by remote terminology operation. (#6151) * Handle 400 and 404 codes returned by remote terminology operation. * Some simplification * Adjust changelog * Add a comment to explain alternate solution which can be reused. * fix concepts with no display element for $apply-codesystem-delta-add and $apply-codesystem-delta-remove (#6164) * allow transaction with update conditional urls (#6155) * Revert "Add path value to _id search parameter and other missing search param…" (#6171) This reverts commit 2275eba1a0f379b6ccb2d1b467fa22bd9febcf54. * 7 2 2 mb (#6160) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * 6051 bulk export security errors (#5915) * Enhance RuleBuilder code to support multiple instances (#5852) * Overhaul bulk export permissions. * Overhaul bulk export permissions. * Small tweak to rule builder. * Cleanup validation. * Cleanup validation. * Code review feedback. * Postgres terminology service hard coded column names migration (#5866) * updating parent pids column name * updating name of the fullTestField Search * updating name of the fullTestField Search * fixing typo. * failing test. * - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity; - reverting the name of the FullTextField entity to its previous name of 'myParentPids'; - reverting the name of the lucene index to search on in the terminology service. - updating the changelog; * making spotless happy --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881) * initial failing test. * solution * adding changelog * spotless * moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811) * Expose BaseRequestPartitionHelperSvc validate and normalize methods * Compilation errors * change mock test to jpa test * change mock test to jpa test * validateAndNormalizePartitionIds * validateAndNormalizePartitionNames * validateAndNormalizePartitionIds validation + bug fix * validateAndNormalizePartitionNames validation * fix test * version bump * Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883) * Add failing test as well as commented out potential solution. * Fix for NumberFormatException. * Add conditional test for survivorship rules. * Spotless. * Add changelog. * Code review feedback. * updating documentation (#5889) * Ensure temp file ends with "." and then suffix. (#5894) * bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892) Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Enhance mdm interceptor (#5899) * Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened. * Added javadoc * Cahngelog * spotless --------- Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> * Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896) * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything. * Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug. * Add changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml Commit code reviewer suggestion. Co-authored-by: Tadgh <garygrantgraham@gmail.com> --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix query chained on sort bug where we over-filter results (#5903) * Failing test. * Ensure test cleanup doesn't fail by deleting Patients before Practitioners. * Implement fix. * Spotless. * Clean up unit test and add changelog. Fix unit test. * Fix changelog file. * Apply suggestions from code review Apply code review suggestions. Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Spotless --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve fix (#5906) Co-authored-by: Long Ma <long@smilecdr.com> * Fixing issues with postgres LOB migration. (#5895) * Fixing issues with postgres LOB migration. * addressing code review comments for audit/transaction logs. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for BinaryStorageEntity migration post code review. * test and implementation for TermConcept migration post code review. * applying spotless * test and implementation for TermConceptProperty migration post code review. * test and implementation for TermValueSetConcept migration post code review. * fixing migration version * fixing migration task * changelog * fixing changelog * Minor renames * addressing comments and suggestions from second code review. * passing tests * fixing more tests --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * refactor bulk export rule, add concept of appliestoallpatients, fix tests * spotless * Cahgnelog, tests * more tests * refactor style checks --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> * Convert a few nulls to aggressive denies * Change chain sort syntax for MS SQL (#5917) * Change sort type on chains * Change sort type on chains * Test for MS SQL * Comments * Version bump * Updating version to: 7.2.1 post release. * Fix queries with chained sort with Lucene by checking supported SortSpecs (#5958) * First commit with very rough solution. * Solidify solutions for both requirements. Add new tests. Enhance others. * Spotless. * Add new chained sort spec algorithm. Add new Msg.codes. Finalize tests. Update docs. Add changelog. * pom remove the snapshot * Updating version to: 7.2.2 post release. * cherry-picked pr 6051 * changelog fix * cherry-picked 6027 * docs and changelog * merge fix for issue with infinite cache refresh loop * Use lockless mode when adding index on Azure Sql server (#6100) (#6129) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * added fix for 6133 * failing Test * Add fix * spotless * Remove useless file * Fix claeaner * cleanup * Remove dead class * Changelog * test description * Add test. Fix broken logic. * fix quantity search parameter test to pass * reverted test testDirectPathWholeResourceNotIndexedWorks in FhirResourceDaoR4SearchWithElasticSearchIT * spotless * cleanup mistake during merge * added missing imports * fix more mergeback oopsies * bump to 7.3.13-snapshot --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> * Patient validate operation with remote terminology service enabled returns 400 bad request (#6124) * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - failing test * Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - implementation * - Changing method accessibility from default to public to allow method overwriting. (#6172) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying Taha Attari's fix on branch merging to rel_7_4 (#6177) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Automated Migration Testing (HAPI-FHIR) V7_4_0 (#6170) * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_2_0 * To provide the target resource partitionId and partitionDate in the resourceLinlk (#6149) * initial POC. * addressing comments from first code review * Adding tests * adding changelog and spotless * fixing tests * spotless --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying patch (#6190) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cve for 08 release (#6197) Co-authored-by: Long Ma <long@smilecdr.com> * Search param path missing for _id param (#6175) * Add path tp _id search param and definitions for _lastUpdated _tag, _profile and _security * Add tests and changelog * Increase snapshot version * Irrelevant change to force new build --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Reverting to core fhir-test-cases 1.1.14; (#6194) re-enabling FhirPatchCoreTest Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Fix $reindex job with custom partition interceptor based on resource type. Update reindex job to always run with urls. (#6185) * Refactor logic to bring together partition related logic in batch2 jobs using IJobPartitionProvider. Update logic such that reindex job without urls will attempt to create urls for all supported resource types. * Small changes and fix of pipeline error. * Small change to enable mdm-submit to use PartitionedUrl in the job parameters * Revert logback change. Fix dependency version generating errors in the pipeline. * Spotless fix. Add test dependency back without version. * Upgrade test dependency to another version * Add javadoc for PartitionedUrl. Other small fixes and refactoring in tests. * Spotless fix. * Change to JobParameters to fix some of the tests. * Small changes for code review in test * Address code review comments. * Revert change from bad merge. * Address remaining code review comments * 6188 subscription not marked as a cross partition subscription matches operation on resources in other partitions (#6191) * initial failing test * WIP * fixing/adding tests * added changelog * spotless * fixing tests * Cleaning up tests * addressing commetns from first code review. * no-op to get pipelines going --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Resolve 6173 - Log unhandled Exceptions in RestfulServer (#6176) (#6205) * 6173 - Log unhandled Exceptions in RestfulServer. * Use placeholder for failed streams. * Starting test for server handling. * Got test working. * Fixed use of synchronized keyword. * Applied mvn spotless. --------- Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Partition aware transactions (#6167) * Partition aware transactions * Address review comments * Test fixes * Remove dead issue field * Test fixes --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Add license header * rel_7_4 mergeback --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: JP <jonathan.i.percival@gmail.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: Martha Mitran <marthamitran@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com> Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> |
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Michael Buckley
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cd43523afe
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Mergeback 7_4 (#6158)
* use SearchParamater validator in package installer (#6112) * Ensure ' ' is treated as '+' in timezones with offsets. (#6115) * Use lockless mode when adding index on Azure Sql server (#6100) * Use lockless mode when adding index on Azure Sql server Use try-catch for Online add-index on Sql Server. This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support. Warnings in docs, and cleanups * make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT (#6127) * fix hfj search migration task (#6143) * fix migration task * changelog * changelog * code review * spotless --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> * Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive (#6135) * MSSQL: Migrate HFJ_RESOURCE.FHIR_ID to new collation: SQL_Latin1_General_CP1_CS_AS * Spotless. * Enhance test. Fix case in ResourceSearchView to defend against future migration to case insensitive collation. * Remove TODOs. Add comment to ResourceSearchView explaining why all columns are uppercase. Changelog. * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml Code reviewer suggestion Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone. --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Common API for FHIR Data Access (#6141) * Add initial interface for common FHIR API * Fix formatting * Update javadocs * Address code review comments --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com> Co-authored-by: JP <jonathan.i.percival@gmail.com> |
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dotasek
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d68a71abb4
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Bump to core 6.3.18 (#6121)
* Bump to core 6.3.18 * Fix test failures due to new validation messages |
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Long Ma
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406db339ce | bump to 7.5.0-snapshot | ||
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Long Ma
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0e8f474b51 | revert 6e208f16ecdf60859ca581d089c1ff448787bdb2 |