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* updated dockerfile to use root user before creating directory

* Updated hapi-fhir dependency version to 6.2.5 (#44)

* reverted dockerfile which was earlier modified to test build issue on jenkins

* Added newline in Dockerfile

* 6.4.0 (#47)

* registering ValueSetOperationProvider

* Upgrade to 5.7.0-PRE4-SNAPSHOT for testing

* Share elasticsearch configuration

* Fixed compile issues

* Fix misconfiguration

modelConfig is part of DaoConfig and should not have a separate lifecycle.

* Bump to 5.7.0-PRE8-SNAPSHOT

* Typo fix in README

* Add configuration flag to enable storing of resources in lucene index (#304)

* Add configuration flag to enable storing of resources in lucene index

* Fix build issue

* Fix code review suggestions

Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com>

* Add ES native aggregation builder for lastN

* Revert "Add ES native aggregation builder for lastN"

This reverts commit 5312f78b956d4ad4863580035972263586d616c3.

* bump version

* Update for 5.7.x changes

* Fix h2 dialect, replace mail dep

* Bump postgresql from 42.2.23 to 42.2.25

Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25.
- [Release notes](https://github.com/pgjdbc/pgjdbc/releases)
- [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md)
- [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25)

---
updated-dependencies:
- dependency-name: org.postgresql:postgresql
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* bump Hapi PRE version

* Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider.

* Version bump to 5.7.0 and a few other components now draw the version from parent

* Update application.yaml

Momentarily added `allow-circular-references: true`

* bump to real version

* Bump version

* Remove search coord thread pool

* Added instructions about removing Hibernate dialect

To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue.

* Bump HAPI-FHIR version

* Move to newlines

* fix to work with latest hapi-fhir

* Feature/update docker support (#319)

* Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305

* Added doc

* Added corrections according to comments

* Update Dockerfile

* Update build-images.yaml

Updated to default to distroless

* add dao_scheduling_enabled configuration property (#324)

* added reindexProvider to Config (#326)

* Update application.yaml

* Update application.yaml

Roll back - mistake from my side

* Bump hapi-fhir version to 'PRE5' (#329)

* Add actuator

* Bump to PRE8

* disable springboot actuator endpoints other than 'health' for security reasons (#338)

Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com>

* Bump to PRE9

* Update application.yaml (#345)

* add support for ms sql server (#347)

* Fix comments in Demo that lead to 404 (#348)

Co-authored-by: dotasek <david.otasek@smilecdr.com>

* updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346)

* Update application.yaml

Reverted to sane defaults

* Bump to PRE10

* Updated to HAPI FHIR version 5.7.2 (#349)

* Revert accidental default activation of experimental lucene indexing

* Add disclaimer for advanced_lucene_indexing

added warning to     advanced_lucene_indexing: false property

* Bump to hapi PRE11

* Expose Prometheus metrics (#355)

* Add: of-type modifier option in application.yaml (#363)

Co-authored-by: Alejandro Medina <amedina@cens.cl>

* Fix applying supported_resource_types option with list that already includes SearchParameter (#365)

* Bump pom and minimum java version

* Bump ES version

* hibernate search application properties updates.

* make lastN test pass

* Remove value set provider as it causes a boot failure without lucene

* Fix reindex provider

* Bump java version for test

* Bump to pre-01

* fix build

* Re-add valuesetoperation provider

* Disable lucene by default

* Re-add valueset operation provider

* adding smoke test files

* adding base documentation

* wip

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* bumping to non-snapshot version (#377)

* updated helm chart to use latest v6.0.1 version of the image (#382)

* updated helm chart to use latest v6.0.1 version of the image

* updated workflow to run against multiple k8s versions

* add BinaryAccessProvider to BaseJpaRestfulServer

* Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>

* Applying fix from upstream for h2 Binaries

This issue is already fixed upstream. Can be removed with next hapi version upgrade.
https://github.com/hapifhir/hapi-fhir/pull/3676

* removed wrong and duplicated config entry

`daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy`

* Added OpenTelemetry Java Agent JAR to container image (#391)

Closes #387

* changes to pom.xml to enable publishing

* fixed directory of the .war in tomcat-based image

* bulk data instrumentation included

* bulk data instrumentation turned off by default

* updated opentelemetry-java-instrumentation JAR to 1.16.0

* Better support for ARM

java17 regular doesn't have ARM, java17-debian11 does

* Updated Otel Java agent to 1.17.0

* Updated hapi-fhir to 6.1.0

* Minor Helm chart dependency updates and security improvements

* Don't run maven CI on changes to the helm chart

* updated helm chart to use version 6.1.0 of the image

* added appProperties.getInline_resource_storage_below_size() (#420)

* added appProperties.getInline_resource_storage_below_size()

* indentations

* Feat/restructuring (#422)

* Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean

* Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library

* Disabled default validation enabled

* Extract IG loading (#426)

* added back lost config entry: allowed_bundle_types (#427)

* added back lost config entry

* disabled entry

* Bump snakeyaml from 1.30 to 1.31

Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31.
- [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30)

---
updated-dependencies:
- dependency-name: org.yaml:snakeyaml
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* fix: configuration of cors

Refs: #430

* Proper close DB connection after dialect was resolved (#435)

* removed duplicated and wrong subscription code (#440)

* fixed SubscriptionDebugLogInterceptor adding logic

* switch to postgres db (#444)

* revering to H2 (#449)

* Tracking Hapi 6.2-PRE releases (#408)

* Tracking branch for 6.1 pre-releases.

* Update to 6.1.0-PRE3-SNAPSHOT

* Adjust for hapi-fhir namespace changes and version

* Adjust version to include new hapi-fhir HSearch fast path feature

* Bump hapi PRE

* Update to PRE16

* Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation.
Add commented out sample properties for lucene and elastic.
Move batch.job.enabled property under spring: prefix to have it considered.

* Adjust enumeration renaming

* Repoint FHIR 6.2.0-PRE1-SNAPSHOT

* Add missing Bean to starter configuration

* Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT

* Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod.

* Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT

* Update dep

* Bump version fix failures

* Remove dead import

* Fix up

* remove batch refs

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Added hibernate.dialect for Postgress to Readme (#451)

* fixes for support of R4B / 6.2.0 (#455)

* upping hapi version to 6.2.1

* Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458)

* Bumped version (#462)

* allow interceptors to be registered via properties

* Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT.  This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)

* Update pom.xml to reference hapi-fhir 6.3.4-SNAPSHOT.  This also involves renaming websocket dependencies whose names have changed since 6.2.2 (ex websocket-api to websocket-jetty-api).

* Update pom to reference logback 1.2.10 explicitly to resolve the missing StaticLoggerBinder errors.

* Fix logback issue by pulling the same logback version as hapi-fhir and setting the following system property at boot: org.springframework.boot.logging.LoggingSystem=none.   Also, fix the hapi-fhir-jpaserver-base dependency error by setting this in application.yaml: allow-bean-definition-overriding: true

* Set allow-bean-definition-overriding: true on test application.yaml as well.

* Remove lines in ExampleServerR4BIT that causes an implementation guide version error.

* Upgrade to 6.3.6-SNAPSHOT and once again disable allow-bean-definition-overriding.  Also remove the Bean for IMdmLinkDoa from StartJpaConfig and the Bean for ITermCodeSystemStorageSvc in FhirServerConfigDstu2.

* Explicitly use logback 1.2.10 for both logback-classic and logback-core to resolve StaticBinderLogger not found errors.  Also, remove explici logger disabling code in Application.java.

* Restore Application.java as well as both application.yaml files to the same as master.

* Feature/static files (#456)

* Added mapping

* Added documentation

* Remove old junit4 usage.

* Revert "Update pom.xml to reference hapi-fhir 6.3.6-SNAPSHOT.  This hapi-fhir release contains a fix for POSTing an XML resource with comments results in a fhir_comments error (#465)" (#476)

This reverts commit 9a513cd1845723c630565ac2b124d74e56491006.

* Restore rolled back changes to ExampleServerR4BIT that pass unnecessary properties that will cause problems when using hapi-fhir 6.3.6-SNAPSHOT. (#479)

* First commit to restore hapi-fhir 6.3.6-SNAPSHOT changes.  Add static code blocks to Application.java as well as all tests to System.setProperty("org.springframework.boot.logging.LoggingSystem", "none");

* Feature/index default (#475)

* Added default

* Refactored the default resolution

* Updated Helm chart to use hapi fhir image 6.2.2 (#472)

* Implement a new solution:  Instead of static code blocks disabling logging, rollback slf4j-api, logback-classic, and logback-core to older versions.   It's the addition of the rollback for slf4j-api that seems to restore logging.

* Fix tests for websocket

* Update pipeline to run integration tests.

* Initial IPS + Cql to Cr migration

* Allow Enabling IPS via config

* typo

* CQL to CR

* HAPI FHIR bump

* docs: Updated README.md. Discontinue mysql

* removed mysql-connector-java dependency since no longer supported and due to CVE-2022-3171 in transitive dependency on protobuf-java-3.19.4

* docs: Fix postgresql typo in docker-compose

* docs: Explicitly set hibnerate.search.enabled to false if database is postgresql

* refactor: Separate unrelated settings and documentation

* docs: Explicitly set hibernate.search.enabled to false if database is postgress in docker-compose instructions

* docs: Revert dislaimer in postgres

* Bump Hapi

* Fix Application error regarding multiple beans

* Add optional explicit ip config for smoke tests

* Revert "Add optional explicit ip config for smoke tests"

This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe.

* Dev (#45)

* updated dockerfile to use root user before creating directory

* Updated hapi-fhir dependency version to 6.2.5 (#44)

* reverted dockerfile which was earlier modified to test build issue on jenkins

* Added newline in Dockerfile

* Changes how the capability statement is implemented (#46)

* Added custom property file

* SAP-1596 Updated custom property file to read values from env

* SAP-1687 Updated code to allow metadata request for server healthcheck (#7)

Co-authored-by: Shubham Parikh

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com>
Co-authored-by: jvi <jvi@trifork.com>
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Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>

* Updated docker compose file with required env variables

* SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4)

Co-authored-by: Shubham Parikh <sparikh@heaptrace.com>

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com>
Co-authored-by: jvi <jvi@trifork.com>
Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>

* Updated code to read url pattern from environment. (#10)

* BT-96 Added OAuth support

* BT-96 Fixed indentation

* BT-96 Fixed spacing

* BT-96 Removed unwanted filed

* Changes in code as per PR suggestions

* added rest security extension in metadata

* Updated PR as per suggestions

* Updated README.md file to run the app with custom property file & env variables

* Updated PR as per suggestions

* Added user role validation in Oauth

* code refactor

* Updated code for using single oauth user role

* Updated code as per PR suggestions

* Updated code as pr PR siggestions

* Added suppoet of delete operation to admin only

* Refactored code

* Added custom search narrowing filter

* Updated code to work with oauth disabled

* Updated code to get claim name from environment

* change claim name env varible to proper name

* Updated code to use hard-coded claim name

* Changed custom mapper claim name to patient from subject

* Added rule builder to filter resources

* code refactor

* Update CustomAuthorizationInterceptor.java

* updated code to support operations on bundle resources

* Added consent rule to allow patch request

* Added oauth support for task resource

* Updated code to make refrence check generic method

* Updated method names

* Updated code as per PR suggestions

* Update code as per PR suggestion

* Updated code as per PR

* Added verification of clientId from token

* Added basic authentication

* Code refactor

* Added username/password check while checking is basic auth enabled

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com>
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Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>

* Updated docker compose file with required env variables

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com>
Co-authored-by: jvi <jvi@trifork.com>
Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>

* BT-80 Updated code to allow header x-api-key

* BT-140 set legacy sql builder based on hibernate to true

* BT-96 Fixed spacing

* BT-96 Removed unwanted filed

* Changes in code as per PR suggestions

* Added user role validation in Oauth

* code refactor

* Updated code for using single oauth user role

* Updated code as per PR suggestions

* Updated code as pr PR siggestions

* Added custom search narrowing filter

* Updated code to get claim name from environment

* Added rule builder to filter resources

* code refactor

* Added basic authentication

* Added hibernate physical_naming_strategy to use proper table names.

* updated code to use url mapping from environment

* Removed client id validation from oauth token

* fixed indentation

* PT-669 Updated dockerfile to use user dir path for build

* Sync 6.1.0 (#38)

* Bump dep version

* Remove javamail and replace with simple-java-mail

* WIP

* Remove print

* Remove bean override

* Bump version

* Add broken test

* Update for new style of container bean

* Bump for new version

* Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index

* Disable default flyway processing

* Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal()

* Added OpenAPI / Swagger option

* Upgraded to 5.6.0
Subscription tests fail ...

* Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90

* Update application.yaml

See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292

* documented use of Values.extraEnv

* added options for specifying a PodDisruptionBudget

* simplified chart release workflow

the Ubuntu runner base image already includes Helm 3.7.0

* Support HTTPS

* Use default application.yaml

* registering ValueSetOperationProvider

* Upgrade to 5.7.0-PRE4-SNAPSHOT for testing

* Share elasticsearch configuration

* Fixed compile issues

* Fix misconfiguration

modelConfig is part of DaoConfig and should not have a separate lifecycle.

* Bump to 5.7.0-PRE8-SNAPSHOT

* Typo fix in README

* Add configuration flag to enable storing of resources in lucene index (#304)

* Add configuration flag to enable storing of resources in lucene index

* Fix build issue

* Fix code review suggestions

Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com>

* Add ES native aggregation builder for lastN

* Revert "Add ES native aggregation builder for lastN"

This reverts commit 5312f78b956d4ad4863580035972263586d616c3.

* bump version

* Update for 5.7.x changes

* Fix h2 dialect, replace mail dep

* Bump postgresql from 42.2.23 to 42.2.25

Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25.
- [Release notes](https://github.com/pgjdbc/pgjdbc/releases)
- [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md)
- [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25)

---
updated-dependencies:
- dependency-name: org.postgresql:postgresql
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* bump Hapi PRE version

* Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider.

* Version bump to 5.7.0 and a few other components now draw the version from parent

* Update application.yaml

Momentarily added `allow-circular-references: true`

* bump to real version

* Bump version

* Remove search coord thread pool

* Added instructions about removing Hibernate dialect

To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue.

* Bump HAPI-FHIR version

* Move to newlines

* fix to work with latest hapi-fhir

* Feature/update docker support (#319)

* Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305

* Added doc

* Added corrections according to comments

* Update Dockerfile

* Update build-images.yaml

Updated to default to distroless

* add dao_scheduling_enabled configuration property (#324)

* added reindexProvider to Config (#326)

* Update application.yaml

* Update application.yaml

Roll back - mistake from my side

* Bump hapi-fhir version to 'PRE5' (#329)

* Add actuator

* Bump to PRE8

* disable springboot actuator endpoints other than 'health' for security reasons (#338)

Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com>

* Bump to PRE9

* Update application.yaml (#345)

* add support for ms sql server (#347)

* Fix comments in Demo that lead to 404 (#348)

Co-authored-by: dotasek <david.otasek@smilecdr.com>

* updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346)

* Update application.yaml

Reverted to sane defaults

* Bump to PRE10

* Updated to HAPI FHIR version 5.7.2 (#349)

* Revert accidental default activation of experimental lucene indexing

* Add disclaimer for advanced_lucene_indexing

added warning to     advanced_lucene_indexing: false property

* Bump to hapi PRE11

* Expose Prometheus metrics (#355)

* Add: of-type modifier option in application.yaml (#363)

Co-authored-by: Alejandro Medina <amedina@cens.cl>

* Fix applying supported_resource_types option with list that already includes SearchParameter (#365)

* Bump pom and minimum java version

* Bump ES version

* hibernate search application properties updates.

* make lastN test pass

* Remove value set provider as it causes a boot failure without lucene

* Fix reindex provider

* Bump java version for test

* Bump to pre-01

* fix build

* Re-add valuesetoperation provider

* Disable lucene by default

* Re-add valueset operation provider

* adding smoke test files

* adding base documentation

* wip

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* bumping to non-snapshot version (#377)

* updated helm chart to use latest v6.0.1 version of the image (#382)

* updated helm chart to use latest v6.0.1 version of the image

* updated workflow to run against multiple k8s versions

* Tracking branch for 6.1 pre-releases.

* add BinaryAccessProvider to BaseJpaRestfulServer

* Update to 6.1.0-PRE3-SNAPSHOT

* Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>

* Adjust for hapi-fhir namespace changes and version

* Adjust version to include new hapi-fhir HSearch fast path feature

* Bump hapi PRE

* Update to PRE16

* Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation.
Add commented out sample properties for lucene and elastic.
Move batch.job.enabled property under spring: prefix to have it considered.

* Bump to release

* Add missing bean

* Added custom property file

* SAP-1596 Updated custom property file to read values from env

* SAP-1687 Updated code to allow metadata request for server healthcheck (#7)

Co-authored-by: Shubham Parikh

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
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* BT-80 Updated code to allow header x-api-key

* Updated docker compose file with required env variables

* SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4)

Co-authored-by: Shubham Parikh <sparikh@heaptrace.com>

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
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* Updated code to read url pattern from environment. (#10)

* BT-140 set legacy sql builder based on hibernate to true

* BT-96 Added OAuth support

* BT-96 Fixed indentation

* BT-96 Fixed spacing

* BT-96 Removed unwanted filed

* Changes in code as per PR suggestions

* added rest security extension in metadata

* code refactor

* Updated PR as per suggestions

* Updated README.md file to run the app with custom property file & env variables

* Updated PR as per suggestions

* Added user role validation in Oauth

* code refactor

* Updated code for using single oauth user role

* Updated code as per PR suggestions

* Updated code as pr PR siggestions

* Added suppoet of delete operation to admin only

* Refactored code

* Added custom search narrowing filter

* Updated code to work with oauth disabled

* Updated code to get claim name from environment

* change claim name env varible to proper name

* Updated code to use hard-coded claim name

* Changed custom mapper claim name to patient from subject

* Added rule builder to filter resources

* code refactor

* Update CustomAuthorizationInterceptor.java

* updated code to support operations on bundle resources

* Added consent rule to allow patch request

* Added oauth support for task resource

* Updated code to make refrence check generic method

* Updated method names

* Updated code as per PR suggestions

* Update code as per PR suggestion

* Updated code as per PR

* Added verification of clientId from token

* Added basic authentication

* Code refactor

* Added username/password check while checking is basic auth enabled

* Added custom property file

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com>
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* Updated docker compose file with required env variables

* Update docker-compose.yml

Updated file as per suggestions

* Added custom property file

* SAP-1596 Updated custom property file to read values from env

* SAP-1667 Added interceptor for authorization (#5)

* SAP-1667 Added interceptor for authorization

* SAP-1667 Removed unused space.

* SAP-1667 Added newline at the end of the file.

Co-authored-by: Shubham Parikh <>

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
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* BT-96 Fixed spacing

* BT-96 Removed unwanted filed

* added rest security extension in metadata

* code refactor

* Update JpaRestfulServer.java

* Updated PR as per suggestions

* Added user role validation in Oauth

* code refactor

* Updated code for using single oauth user role

* Updated code as per PR suggestions

* Updated code as pr PR siggestions

* Added custom search narrowing filter

* Updated code to get claim name from environment

* Added rule builder to filter resources

* code refactor

* Added oauth support for task resource

* Added verification of clientId from token

* Added hibernate physical_naming_strategy to use proper table names.

* updated code to use url mapping from environment

* Removed client id validation from oauth token

* fixed indentation

* Updated fork with upstream

* Removed unwanted files

* removed unwanted imports and files merged during rebase 6.1.0

* removed unwanted imports and files merged during rebase 6.1.0

* removed unwanted imports and files merged during rebase 6.1.0

* removed unwanted imports and files merged during rebase 6.1.0

* Updated application-custom.yaml

* commented allow-bean-definition-overriding

* Sync application-custom.yaml

* commented unused hibernate settings

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* Updated docker file to use /user/app dir (#39)

* PT-689 split url (#40)

* PT-689 splitting the URL of datasource

* PT-689 splitting the URL of datasource

* PT-689 adding an easier ability to switch to another DB server

* PT-689 standardizing variable names

Co-authored-by: Vadim Dribinsky <ddribinsky@elimu.io>

* Sync 6.2.2 (#41)

* Bump dep version

* Remove javamail and replace with simple-java-mail

* WIP

* Remove print

* Remove bean override

* Bump version

* Add broken test

* Update for new style of container bean

* Bump for new version

* Update to 5.6.0-PRE7_NIH-SNAPSHOT and activate advanced index

* Disable default flyway processing

* Add local_base_urls configuration to feed DaoConfig.setTreatBaseUrlsAsLocal()

* Added OpenAPI / Swagger option

* Upgraded to 5.6.0
Subscription tests fail ...

* Bumped version of Spring Boot in order to fix same issue as https://github.com/Haulmont/jmix-security/issues/90

* Update application.yaml

See https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/292

* documented use of Values.extraEnv

* added options for specifying a PodDisruptionBudget

* simplified chart release workflow

the Ubuntu runner base image already includes Helm 3.7.0

* Support HTTPS

* Use default application.yaml

* registering ValueSetOperationProvider

* Upgrade to 5.7.0-PRE4-SNAPSHOT for testing

* Share elasticsearch configuration

* Fixed compile issues

* Fix misconfiguration

modelConfig is part of DaoConfig and should not have a separate lifecycle.

* Bump to 5.7.0-PRE8-SNAPSHOT

* Typo fix in README

* Add configuration flag to enable storing of resources in lucene index (#304)

* Add configuration flag to enable storing of resources in lucene index

* Fix build issue

* Fix code review suggestions

Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com>

* Add ES native aggregation builder for lastN

* Revert "Add ES native aggregation builder for lastN"

This reverts commit 5312f78b956d4ad4863580035972263586d616c3.

* bump version

* Update for 5.7.x changes

* Fix h2 dialect, replace mail dep

* Bump postgresql from 42.2.23 to 42.2.25

Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25.
- [Release notes](https://github.com/pgjdbc/pgjdbc/releases)
- [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md)
- [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25)

---
updated-dependencies:
- dependency-name: org.postgresql:postgresql
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* bump Hapi PRE version

* Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider.

* Version bump to 5.7.0 and a few other components now draw the version from parent

* Update application.yaml

Momentarily added `allow-circular-references: true`

* bump to real version

* Bump version

* Remove search coord thread pool

* Added instructions about removing Hibernate dialect

To fix the problem raised in [this](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/318) issue.

* Bump HAPI-FHIR version

* Move to newlines

* fix to work with latest hapi-fhir

* Feature/update docker support (#319)

* Updated docker image according to discussion on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/pull/305

* Added doc

* Added corrections according to comments

* Update Dockerfile

* Update build-images.yaml

Updated to default to distroless

* add dao_scheduling_enabled configuration property (#324)

* added reindexProvider to Config (#326)

* Update application.yaml

* Update application.yaml

Roll back - mistake from my side

* Bump hapi-fhir version to 'PRE5' (#329)

* Add actuator

* Bump to PRE8

* disable springboot actuator endpoints other than 'health' for security reasons (#338)

Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com>

* Bump to PRE9

* Update application.yaml (#345)

* add support for ms sql server (#347)

* Fix comments in Demo that lead to 404 (#348)

Co-authored-by: dotasek <david.otasek@smilecdr.com>

* updated helm chart to use v5.7.0 and latest PostgreSQL sub-chart (#346)

* Update application.yaml

Reverted to sane defaults

* Bump to PRE10

* Updated to HAPI FHIR version 5.7.2 (#349)

* Revert accidental default activation of experimental lucene indexing

* Add disclaimer for advanced_lucene_indexing

added warning to     advanced_lucene_indexing: false property

* Bump to hapi PRE11

* Expose Prometheus metrics (#355)

* Add: of-type modifier option in application.yaml (#363)

Co-authored-by: Alejandro Medina <amedina@cens.cl>

* Fix applying supported_resource_types option with list that already includes SearchParameter (#365)

* Bump pom and minimum java version

* Bump ES version

* hibernate search application properties updates.

* make lastN test pass

* Remove value set provider as it causes a boot failure without lucene

* Fix reindex provider

* Bump java version for test

* Bump to pre-01

* fix build

* Re-add valuesetoperation provider

* Disable lucene by default

* Re-add valueset operation provider

* adding smoke test files

* adding base documentation

* wip

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* bumping to non-snapshot version (#377)

* updated helm chart to use latest v6.0.1 version of the image (#382)

* updated helm chart to use latest v6.0.1 version of the image

* updated workflow to run against multiple k8s versions

* add BinaryAccessProvider to BaseJpaRestfulServer

* Update src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>

* Applying fix from upstream for h2 Binaries

This issue is already fixed upstream. Can be removed with next hapi version upgrade.
https://github.com/hapifhir/hapi-fhir/pull/3676

* removed wrong and duplicated config entry

`daoconfig_client_id_strategy`does not resolve and is a duplicate of `client_id_strategy`

* Added OpenTelemetry Java Agent JAR to container image (#391)

Closes #387

* changes to pom.xml to enable publishing

* fixed directory of the .war in tomcat-based image

* bulk data instrumentation included

* bulk data instrumentation turned off by default

* updated opentelemetry-java-instrumentation JAR to 1.16.0

* Better support for ARM

java17 regular doesn't have ARM, java17-debian11 does

* Updated Otel Java agent to 1.17.0

* Updated hapi-fhir to 6.1.0

* Minor Helm chart dependency updates and security improvements

* Don't run maven CI on changes to the helm chart

* updated helm chart to use version 6.1.0 of the image

* added appProperties.getInline_resource_storage_below_size() (#420)

* added appProperties.getInline_resource_storage_below_size()

* indentations

* Feat/restructuring (#422)

* Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean

* Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library

* Disabled default validation enabled

* Extract IG loading (#426)

* added back lost config entry: allowed_bundle_types (#427)

* added back lost config entry

* disabled entry

* Bump snakeyaml from 1.30 to 1.31

Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.30 to 1.31.
- [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-1.31..snakeyaml-1.30)

---
updated-dependencies:
- dependency-name: org.yaml:snakeyaml
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* fix: configuration of cors

Refs: #430

* Proper close DB connection after dialect was resolved (#435)

* removed duplicated and wrong subscription code (#440)

* fixed SubscriptionDebugLogInterceptor adding logic

* switch to postgres db (#444)

* revering to H2 (#449)

* Tracking Hapi 6.2-PRE releases (#408)

* Tracking branch for 6.1 pre-releases.

* Update to 6.1.0-PRE3-SNAPSHOT

* Adjust for hapi-fhir namespace changes and version

* Adjust version to include new hapi-fhir HSearch fast path feature

* Bump hapi PRE

* Update to PRE16

* Adjust configuration class name to HAPI-FHIR HSearch namespace consolidation.
Add commented out sample properties for lucene and elastic.
Move batch.job.enabled property under spring: prefix to have it considered.

* Adjust enumeration renaming

* Repoint FHIR 6.2.0-PRE1-SNAPSHOT

* Add missing Bean to starter configuration

* Update to hapi-fhir 6.2.0-PRE2-SNAPSHOT

* Update application-integrationtest.yaml and rename it as application.yaml to make test configuration independent of prod.

* Update to hapi-fhir 6.2.0-PRE5-SNAPSHOT

* Update dep

* Bump version fix failures

* Remove dead import

* Fix up

* remove batch refs

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Added hibernate.dialect for Postgress to Readme (#451)

* fixes for support of R4B / 6.2.0 (#455)

* upping hapi version to 6.2.1

* Updated Helm chart to use image 6.2.1 and latest PostgreSQL (#458)

* Bumped version (#462)

* Added custom property file

* SAP-1596 Updated custom property file to read values from env

* SAP-1687 Updated code to allow metadata request for server healthcheck (#7)

Co-authored-by: Shubham Parikh

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com>
Co-authored-by: jvi <jvi@trifork.com>
Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>

* Updated docker compose file with required env variables

* SAP-1656 Added enabled parameter for webservlet to enable/disable webapp (#4)

Co-authored-by: Shubham Parikh <sparikh@heaptrace.com>

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi properties with env ones

* Start Release branch for 5.1.0

* Add property for multitenancy

* Get test passing

* Add repo

* Bump to current release

* Rework the JPA server class a bit

* Updating Dockerfile to use context code instead of re-cloning the hapi-fhir-jpaserver-starter project. Still re-builds the base hapi libraries, though.

* Adding .dockerignore file to improve the efficiency of docker builds

* Added support for configurable client ID strategy

* Bump mysql-connector-java from 8.0.11 to 8.0.16

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.11 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.11...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

* Resolve some compile errors

* Fix EMPI rules json

* Have EmpiSettings actually return an EmpiSettings bean

* Update readme

* Remove dead space

* Update property

* Update README to include Docker info

* Prepare for release

* Merge master

* Removing commands from Dockerfile that clone and build the core hapi-fhir libraries since it is not required for building hapi-fhir-jpaserver-starter; it pulls the core libraries from the maven repo regardless.

* Combining base Dockerfile with main dockerfile so that there is a single image related to hapi-jpaserver-starter

* Update Dockerfile

Added caching of maven dependency resolving

* Fix #122 - EMPI error on startup when EMPI not enabled

Co-authored-by: Peter Micuch <peter.micuch@siemens-healthineers.com>
Co-authored-by: Vladimir Nemergut <vladimir.nemergut@siemens-healthineers.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
Co-authored-by: Sean McIlvenna <sean.mcilvenna@lantanagroup.com>
Co-authored-by: jvi <jvi@trifork.com>
Co-authored-by: Sean McIlvenna <seanmcilvenna@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>

* Updated code to read url pattern from environment. (#10)

* BT-96 Added OAuth support

* BT-96 Fixed indentation

* BT-96 Fixed spacing

* BT-96 Removed unwanted filed

* Changes in code as per PR suggestions

* added rest security extension in metadata

* Updated PR as per suggestions

* Updated README.md file to run the app with custom property file & env variables

* Updated PR as per suggestions

* Added user role validation in Oauth

* code refactor

* Updated code for using single oauth user role

* Updated code as per PR suggestions

* Updated code as pr PR siggestions

* Added suppoet of delete operation to admin only

* Refactored code

* Added custom search narrowing filter

* Updated code to work with oauth disabled

* Updated code to get claim name from environment

* change claim name env varible to proper name

* Updated code to use hard-coded claim name

* Changed custom mapper claim name to patient from subject

* Added rule builder to filter resources

* code refactor

* Update CustomAuthorizationInterceptor.java

* updated code to support operations on bundle resources

* Added consent rule to allow patch request

* Added oauth support for task resource

* Updated code to make refrence check generic method

* Updated method names

* Updated code as per PR suggestions

* Update code as per PR suggestion

* Updated code as per PR

* Added verification of clientId from token

* Added basic authentication

* Code refactor

* Added username/password check while checking is basic auth enabled

* DEV-769: Update from upstream branch (#9)

* Adding environment variables to override hapi properties file settings

* Only override existing hapi pro…

* removed duplicate variable

* Logging changes (#50)

* Updated the logging when auth fail to show in warn level

* added newline

* updated dockerfile to use root user before creating directory

* reverted dockerfile which was earlier modified to test build issue on jenkins

* Added newline in Dockerfile

* 6.4.0 (#47)

* registering ValueSetOperationProvider

* Upgrade to 5.7.0-PRE4-SNAPSHOT for testing

* Share elasticsearch configuration

* Fixed compile issues

* Fix misconfiguration

modelConfig is part of DaoConfig and should not have a separate lifecycle.

* Bump to 5.7.0-PRE8-SNAPSHOT

* Typo fix in README

* Add configuration flag to enable storing of resources in lucene index (#304)

* Add configuration flag to enable storing of resources in lucene index

* Fix build issue

* Fix code review suggestions

Co-authored-by: Jaison B <jaison.baskaran@smilecdr.com>

* Add ES native aggregation builder for lastN

* Revert "Add ES native aggregation builder for lastN"

This reverts commit 5312f78b956d4ad4863580035972263586d616c3.

* bump version

* Update for 5.7.x changes

* Fix h2 dialect, replace mail dep

* Bump postgresql from 42.2.23 to 42.2.25

Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.2.23 to 42.2.25.
- [Release notes](https://github.com/pgjdbc/pgjdbc/releases)
- [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md)
- [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.2.23...REL42.2.25)

---
updated-dependencies:
- dependency-name: org.postgresql:postgresql
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* bump Hapi PRE version

* Bump to Hapi 6.0-SNAPSHOT and register the ValueSet provider.

* Version bump to 5.7.0 and a few other components now draw the version from parent

* Update application.yaml

Momentarily added `allow-circular-references: true`

* bump to real version

* Bump version

* Remove search coord thread pool

* Added instructions about removing Hibernate dialect

To fix the problem raised in [this](htt…
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51 people committed Jun 14, 2023
1 parent 89ddec5 commit d23fce6
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions src/main/java/ca/uhn/fhir/jpa/starter/CustomAuthorizationInterceptor.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ public List<IAuthRule> buildRuleList(RequestDetails theRequest) {
return authorizeBasicAuth(theRequest);
}
} catch (Exception e) {
logger.info("Unexpected authorization error", e);
logger.warn("Unexpected authorization error :{}", e.getMessage());
return denyAll();
}

Expand All @@ -87,13 +87,13 @@ private List<IAuthRule> allowAll() {

private List<IAuthRule> authorizeOAuth(RequestDetails theRequest) throws Exception {
String token = theRequest.getHeader(HttpHeaders.AUTHORIZATION);
if (StringUtils.isEmpty(token)) {
logger.info("Authorization failure - missing authorization header");
if (ObjectUtils.isEmpty(token)) {
logger.warn("Authorization failure - missing authorization header");
return denyAll();
}

if (!token.toUpperCase().startsWith(OAUTH_TOKEN_PREFIX)) {
logger.info("Authorization failure - invalid authorization header");
logger.warn("Authorization failure - invalid authorization header");
return denyAll();
}

Expand All @@ -118,12 +118,12 @@ private List<IAuthRule> authorizeOAuth(RequestDetails theRequest) throws Excepti
return ObjectUtils.isEmpty(patientId) ? allowAll() : allowForClaimResourceId(theRequest,patientId);
}
} catch (TokenExpiredException e) {
logger.info("Authorization failure - token has expired");
logger.warn("Authorization failure - token has expired");
} catch (Exception e) {
logger.info("Unexpected exception verifying token", e);
logger.warn("Unexpected exception verifying token: {}", e.getMessage());
}

logger.info("Authentication failure");
logger.warn("Authentication failure");
return denyAll();
}
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