hapi-fhir/hapi-fhir-storage-cr/pom.xml

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Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
2024-07-16 12:43:14 -04:00
<version>7.5.0-SNAPSHOT</version>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-storage-cr</artifactId>
<packaging>jar</packaging>
<name>HAPI FHIR - Clinical Reasoning</name>
<properties>
<org.antlr-version>4.10.1</org.antlr-version>
<spring-security-core.version>5.7.8</spring-security-core.version>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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</properties>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>antlr4</artifactId>
<version>${org.antlr-version}</version>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>antlr4-runtime</artifactId>
<version>${org.antlr-version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4b</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>${project.version}</version>
</dependency>
Bulk export reducer step fix mergeback (#4606) * One more fix for #4467 * Enabling massIngestionMode causes incomplete resource deletion (#4476) * Adding initial test. * Adding fix and subsequent test. * Adding changelog. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Provide the capability to request that the name of the subscription matching channel be unqualified (#4464) * Adding initial test. * Adding initial solution implementation. * Adding change log and code clean up. * addressing comments from 1st code review. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Change visibility of migration method (#4471) * change migration visibility * add empty migration method for 640 --------- Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> * Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484) * First commit: Make SubscriptionValidatingInterceptor aware of which Pointcut is being called. In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED. Fix resulting compile errors in various unit tests. * Fix/enhance unit tests. Mark methods as deprecated instead of deleting them. Add proper error code. Complete changelog. * Remove erroneous TODOs and tweak the validation logic. * Enhance unit tests and fix changelog. * Reindex batch job fails when processing deleted resources. (#4482) * adding changelog. * Providing solution and adding changelog. * Adding new test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cleaning up checkstyle files (#4470) * cleaning up checkstyle files * One more fix for #4467 (#4469) * added exlusions for files at base project level so checkstyle doesn't error out * duplicate error code from merge * changing lifecycle goal for all module checkstyle check * moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code * wip * trying to figure out why pipeline cannot copy files * removing modules that don't actually need to be built. * I messed up the version --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * Bump core to 5.6.881 (#4496) * Bump core to 5.6.881-SNAPSHOT * Work on fixing tests * Work on fixing tests 2 * Bump to core release --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> * Issue 4486 mdm inconsistent possible match score values (#4487) * Extract method for readability * Save always normalized score values in POSSIBLE_MATCH links. * Avoid setting properties to null values. Adjust test. * Simplify fix * Fix test. Add RangeTestHelper. --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Revert "cleaning up checkstyle files (#4470)" This reverts commit efae3b5d5f397ab8fd92d7aaa82b484cfdfb3c33. * core version fix * Loosen rules for id helper * License * fix batch2 reduction step (#4499) * fix bug where FINALIZE jobs are not cancellable * moved reduction step to message hander * moving reduction step to queue * addingchangelog * cleaning up * review fixes * review fix' --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * Scheduled batch 2 bulk export job and binary delete (#4492) * First commit: Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted. * Refine solution and add a concrete unit test but still work to do. * Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline. * Unit tests complete. New Msg code for new IJobPersistence.fetchInstances() method. Cleanup TODOs and add others. * Finish final touches on implementation. * Add changelog. * Various cleanup. * Code review feedback. * Small tweak to changelog. * Last code review tweak. * Address more code review comments. * Reverse changes to consider work chunks. Add a constant for write-to-binary. * Change bulk import test for valueUri type (#4503) * change tests * suggested test change * CVE resolutions (#4513) * Bump Postgres for CVE * Bump jetty * Verison bump * Remove comments * Revrt bump * Add check in scanner (#4518) * 4516 create hapi fhir cli command to clear stale lock entries (#4517) * Initial implementation * better tests * Add changelog and docs * Forgotten files * Code review comments * Fix checkstyle * Unable to Expunge CodeSystem (#4507) * changes for GL-3943 * changes for GL-3943 --------- Co-authored-by: isaacwen <isaac.wen@smilecdr.com> * New line:: * Update to documentation regarding narrative generation; (#4521) Providing changelog; Co-authored-by: peartree <etienne.poirier@smilecdr.com> * changed what score is set for mdmlinks that created new golden resource (#4514) * changed what score is set for mdmlinks that created new golden resource * fix test --------- Co-authored-by: Long Ma <long@smilecdr.com> * REVERT: change to operationoutcome.html * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527) * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp * added change log --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * fix build (#4530) * Making narrative_generation.md reference an html snippet (#4531) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524) * fix + test * minor fix * Addressing suggestion * Minor changes * 4441 rel 6 4 bad references creation bug (#4519) * adding a test * fail in the case of ref enforce on type and on write and autocreate are all true * update to code * removing a line * cleanup * removing check on urn * changing just to trigger a build * adding a comment to the pom * updating test for better information --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * fixed channel import null pointer exception from null header (#4534) * retryCount 0 on null header + test + changelog * suggested changes * Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535) This reverts commit 53252b8d153f97f4a66a7d20751913911a71f098. * Better error handling for when channel type is not supported (#4538) Co-authored-by: kylejule <kyle.jule@smilecdr.com> * Avoid logging message payloads that contain sensitive data (#4537) Don't log payloads - they may contain sensitive data. * Bulk Export Bug With Many Resources and Low Max File Size (#4506) * failing test * fix + changelog * tweak * add method to IJobPersistence to use a Stream * tweak * tweak * decrease test time * clean up * code review comments * version bump * Increase timeout limit to match BulkExportUseCaseTest * shorten test * maintenance pass * add logging * Revert "add logging" This reverts commit b0453fd9538d6858e6bd212f402d4b04c6306136. * Revert "maintenance pass" This reverts commit bbc7418d519260c4b9827546a0bf822db1c78b1b. * test * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp * shorten tests * logging * move test location * fixes a regression caused my change in hapi-fhir * timeout * Revert "fixes a regression caused my change in hapi-fhir" This reverts commit 4b58013149836eededc568d295c5baf8fb3df989. * testing * Revert "testing" This reverts commit aafc95c2f36bf89ae935c6c342017ec300fe4289. --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * bump ver * License updates' * Downgrade dep' * Updating version to: 6.4.1 post release. * Add javadocs and sources to our serviceloaders * Reset version * Change parent * Remove bumped version * License fixes, new parent * Updating version to: 6.4.1 post release. * Fix bad creation of versionenum * Improve performance on bulk export * Add changelog * Start working on cleaned up reducer * Clean up batch calls * Work on issues * Build fixes * typedbundleprovider getallresources override (#4552) * typedbundleprovider getallresources override * added test to immunization tests that validates pagination does not result in null pointer if over default queryCount * moved HapiFhirDal test to its own test class * removed unused imports * Update to use JpaStorageSettings * adding changelog for issue 4551 * fix changelog spacing * changelog type to fix --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> * Add backport info * Upgrade core to 5.6.97, make adjustments in hapi-fhir, and ensure that all tests pass (#4579) * First commit: Create new branch from the release branch with changes from James' branch. This probably won't compile as the work is incomplete. * Second round of changes from integrating James' branch. * Mark most test failures with TODOs. * Add whitespace * Add changes to FhirPathR4 to set FHIRPathEngine to non-strict FP evaluation. * Fix CreatePackageCommandTest to assert null instead of empty string. Comments on tests that fail due to the double-quote encoding problem. * Downgrade to core 5.6.97. * Fix another test and remove TODOs. * Fix changelog. * Clean up some erroneous changes and TODOs. --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix up dal test * Address leftover code review feedback from the upgrade to core 5.6.97. (#4585) * Exclude pinned core deps * Force pin structs * Add model changes to IBaseCoding and related changes (#4587) * Add IbaseCoding changes, and tinder changes * Fix up tag definition * converter addition * Fix unit test and add changelog. * Add jira to changelog. --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix changelog * Tidy metadata * Test fixing * Test fixes * Work on progress * Add changelog * Build tweak * Fixes * Disable intermittently failing tests. (#4593) * rename tests to IT * Disable more intermittently failing tests (#4595) * Disable more intermittently failing tests. * Disable another intermittently failing tests. * ITify * Disable yet another intermittently failing tests. (#4596) * disable * disables * Fixes * disables * Fix compile * Test fixes * Updating version to: 6.4.2 post release. * Bump to 6.4.2-SNAPSHOT * Fix compile * fix version * Address review comments * Review comments * Version bump * Compile fix * Test fixes * Compile fixes * One more compile fix * Test fixes * Version bump * Resolve fixme --------- 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: nathaniel.doef <nathaniel.doef@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Mark Iantorno <markiantorno@gmail.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com> Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com> Co-authored-by: isaacwen <isaac.wen@smilecdr.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com> Co-authored-by: kylejule <kyle.jule@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-03-01 14:52:36 -05:00
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>com.icegreen</groupId>
<artifactId>greenmail</artifactId>
<version>1.6.4</version>
<scope>compile</scope>
<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
<exclusions>
<exclusion>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.simplejavamail</groupId>
<artifactId>simple-java-mail</artifactId>
<version>6.6.1</version>
<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
<exclusions>
<exclusion>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
</exclusion>
</exclusions>
</dependency>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
</dependencies>
</dependencyManagement>
<dependencies>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<dependency>
<groupId>com.fasterxml.jackson.module</groupId>
<artifactId>jackson-module-jakarta-xmlbind-annotations</artifactId>
</dependency>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-converter</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
5089 cr measure refactor (#5324) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * repository measure refactor * undo bundle edit, add config * embedded library true * undo post of bundle * clear library cache on test * fix sumbit-data test * missing packages from cql * fix test data and test cases for repository api * 3.0.0 clinical reasoning uplift * r4 cql execution provider and tests * fix submitdata provider config * wip cql tests * debugging cql op wip * wip debugging cql * update tests for $cql, fix class names * prep for Pre6 uplift * spotless checks and test fixes * bump to 3.0.0-PRE6 * cleanup * fix version * cleanup * fix exlusions in pom * add in cache invalidation config * search converter bug and test for repository * update searchconverter * version bump, add changelog * remove term config, move IDaoRegistryUser class * Break out dstu3 providers and move config to version folders * CVE-2023-26119 * remove * imports * code review updates --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com>
2023-09-22 19:51:36 -04:00
<artifactId>cqf-fhir-cr</artifactId>
<version>${clinical-reasoning.version}</version>
</dependency>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
<dependency>
5089 cr measure refactor (#5324) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * repository measure refactor * undo bundle edit, add config * embedded library true * undo post of bundle * clear library cache on test * fix sumbit-data test * missing packages from cql * fix test data and test cases for repository api * 3.0.0 clinical reasoning uplift * r4 cql execution provider and tests * fix submitdata provider config * wip cql tests * debugging cql op wip * wip debugging cql * update tests for $cql, fix class names * prep for Pre6 uplift * spotless checks and test fixes * bump to 3.0.0-PRE6 * cleanup * fix version * cleanup * fix exlusions in pom * add in cache invalidation config * search converter bug and test for repository * update searchconverter * version bump, add changelog * remove term config, move IDaoRegistryUser class * Break out dstu3 providers and move config to version folders * CVE-2023-26119 * remove * imports * code review updates --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com>
2023-09-22 19:51:36 -04:00
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-jackson</artifactId>
<version>${clinical-reasoning.version}</version>
5089 cr measure refactor (#5324) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * repository measure refactor * undo bundle edit, add config * embedded library true * undo post of bundle * clear library cache on test * fix sumbit-data test * missing packages from cql * fix test data and test cases for repository api * 3.0.0 clinical reasoning uplift * r4 cql execution provider and tests * fix submitdata provider config * wip cql tests * debugging cql op wip * wip debugging cql * update tests for $cql, fix class names * prep for Pre6 uplift * spotless checks and test fixes * bump to 3.0.0-PRE6 * cleanup * fix version * cleanup * fix exlusions in pom * add in cache invalidation config * search converter bug and test for repository * update searchconverter * version bump, add changelog * remove term config, move IDaoRegistryUser class * Break out dstu3 providers and move config to version folders * CVE-2023-26119 * remove * imports * code review updates --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com>
2023-09-22 19:51:36 -04:00
<type>pom</type>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-storage</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
</exclusion>
</exclusions>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
</dependency>
<!-- This is needed for the threaded execution -->
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-core</artifactId>
<version>${spring-security-core.version}</version>
</dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<!-- This is needed for the CqlExceptionHandlingInterceptor -->
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.servlet</groupId>
<artifactId>jakarta.servlet-api</artifactId>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
</dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<dependency>
Jakarta/Javax Servlet Migration (#5429) * Servlet migrsation changes * Apply spotless * Work on migration * Start working on JPA migration * Test fixes * Test fixes * Test fixes * Work * Work on servlet migration * Work on migration * Work on fixes * Imports fix * Work on tests * Test fix * All tests passing * Work on migration * Schema generator * Refactor ID strategy * Some test fixes * Test fixes * API additions * Work on websockets * Test fixe * Version bump * Work on migration * All tests have passed! * Work on test fixes * Fixes * Work on fixes * CDR fix * Work on migration * Fixes * Spotless * Disable onetoone ban * Adjust migratyions * Transaction service fix * Add tinyint to migrator * Work * Migration * Compile fix * Add license * Test fix * Test fix * Cleanup * Cleanup attempt * Test fix * Reslve fixmes * Remove legacy lastn implementation * Test cleanup * Cleanup * Remove dead import * Bad import setups * Review comments * Review fixes * Build fix * Test fix * Spotless * Account for CR changes * Compile fixes * Rollback one change * Test tweak * License header * Test fix * Test fix part 2: * Clean up tx isolation * Spotless * Spotless apply * Drop min SQL Server level * Attempted test fix * Test fix * Test fix * Test fix * Bump hibernate * Test fix * Test fixes * Test fixes * Test fixes * Test cleanup * One more test fix * Test fix * Try to fix test * Clean up expunge * Test fix * Remove unneeded task * Spotless * Bump compiler plugin * Spotless * Compile fix * Add license headers * License header * Test fixes * Bump animal sniffer * Spotless * Bump Jetty version * Test fix and version bump * Cleanup --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
</dependency>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
<!-- test -->
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>junit-jupiter</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.specto</groupId>
<artifactId>hoverfly-java-junit5</artifactId>
GM1 Mergeback (#5203) * version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * Rename file to force IT mode * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * wip * Fix API usage * wip * Version bump --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
2023-08-15 15:32:10 -04:00
<version>0.14.4</version>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-storage-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<profiles>
<profile>
<id>CI</id>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<executions>
<execution>
<id>enforce-no-snapshot-cr-dependencies</id>
<goals>
<goal>enforce</goal>
</goals>
<phase>verify</phase>
<configuration>
<rules>
<requireReleaseDeps>
<message>No Clinical Reasoning Snapshots Allowed!</message>
<excludes>
<exclude>*:*</exclude>
</excludes>
<includes>
<include>org.opencds.cqf:*</include>
<include>org.opencds.cqf.cql:*</include>
<include>org.opencds.cqf.fhir:*</include>
<include>info.cqframework:*</include>
</includes>
</requireReleaseDeps>
</rules>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
</profile>
</profiles>
Clinical reasoning module (#4347) * Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 14:49:57 -05:00
</project>