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Static content redirect - error (too many redirects) when the path has trailing slash #485

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costateixeira opened this issue Jan 12, 2023 · 1 comment
Closed

Static content redirect - error (too many redirects) when the path has trailing slash #485

costateixeira opened this issue Jan 12, 2023 · 1 comment
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@jkiddo

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@costateixeira
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when using the static content hosting feature,

hapi:
  fhir:
    staticLocation: file:/apps

provides the correct behaviour.
However, when there is a trailing slash, e.g.

hapi:
  fhir:
    staticLocation: file:/apps/

The redirect doesn't work -
http://localhost:8080/static/index.html - ends up at
`http://localhost:8080/static//index.html and the browser gives up after too many redirects
@jkiddo jkiddo self-assigned this Jan 13, 2023
jkiddo added a commit to trifork/hapi-fhir-jpaserver-starter that referenced this issue Jun 9, 2023
@jkiddo
Addressing hapifhir#486 and hapifhir#485
afaec85
bstewartlg added a commit to HL7-DaVinci/pdex-server that referenced this issue Dec 21, 2023
@bstewartlg
Squashed commit of the following:
e9cda9c 
commit 9c557e2c80e597b92b5fb855e611ec39e021bb14
Author: Jens Kristian Villadsen <[email protected]>
Date:   Tue Dec 5 19:56:31 2023 +0100

    Cleaned up for running boot as default (#620)

commit 0be636c169344523b44587ebc94645523edf1823
Author: Levi <[email protected]>
Date:   Tue Dec 5 03:10:21 2023 +0700

    Affected Issue(s): #606 (#612)

    What this commit has achieved:
    1. Externalized location of "mdm-rules.json" in the `AppProperties`
    2. More info about the `ResourceLoader` interface is available at
    https://docs.spring.io/spring-framework/reference/core/resources.html#resources-resourceloader

commit 41a537efb206e3ff2ffb7588fc6376ac1e6c6da6
Author: Levi <[email protected]>
Date:   Tue Dec 5 03:07:51 2023 +0700

    Affected Issue(s): #611 (#617)

    * Affected Issue(s): #611

    What this commit has achieved:
    1. MDM requires an implementation of `INicknameSvc`, it was instantiated
    in `NicknameServiceConfig`
    The error message regarding this was:
    ```
    APPLICATION FAILED TO START

    Description:

    Parameter 2 of method matcherFactory in
    ca.uhn.fhir.jpa.mdm.config.MdmCommonConfig required a bean of type
    'ca.uhn.fhir.jpa.nickname.INicknameSvc' that could not be found.

    Action:

    Consider defining a bean of type 'ca.uhn.fhir.jpa.nickname.INicknameSvc'
    in your configuration.
    ```
    2. MDM requires the subscription of type message
    The error message regarding this was:
    ```
    2023-12-01 11:34:03
    org.springframework.beans.factory.BeanCreationException: Error creating
    bean with name 'mdmSubmitterInterceptorLoader': Invocation of init
    method failed; nested exception is
    ca.uhn.fhir.context.ConfigurationException: HAPI-2421: MDM requires
    Message Subscriptions to be enabled in the Storage Settings
    ```

    * Affected Issue(s): #611

    What this commit has achieved:
    1. Added Integration Test for future-proof

commit 31f9f0b00ba9a88d5cd17b6c24fe8f7ab6bc4c38
Author: dotasek <[email protected]>
Date:   Mon Dec 4 15:04:08 2023 -0500

    Bump github actions used in docker build workflow (#619)

commit b578ee39f605700e9175622a3b9f22348c830043
Merge: f147c83 d1c6b06
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Tue Nov 28 13:30:18 2023 -0500

    Merge pull request #610 from hapifhir/cr-6.9.6-snapshot

    6.10.0 release merge with Clinical Reasoning config

commit d1c6b0661de071f4f77144355e500e1cc90d517f
Author: Justin McKelvy <[email protected]>
Date:   Tue Nov 28 11:08:59 2023 -0700

    new ide formatting

commit 79f631acf4e40f0cbb42f1b605023e11ba12ffaa
Author: Justin McKelvy <[email protected]>
Date:   Tue Nov 28 11:00:38 2023 -0700

    indent reformat

commit 1715ee5aaf058be5a9cb9f772f00a8c023d30c72
Author: Justin McKelvy <[email protected]>
Date:   Tue Nov 28 10:57:56 2023 -0700

    remove indents

commit 82f100747860459f3f4c711f4035f5e9ed4131fc
Author: Justin McKelvy <[email protected]>
Date:   Tue Nov 28 10:52:58 2023 -0700

    reformatting indents

commit a490d1a6938dbce0b8416e3ee6b737abe2c29000
Author: Justin McKelvy <[email protected]>
Date:   Tue Nov 28 10:19:29 2023 -0700

    update margins

commit efe11069699dcfcd74f8973c00f0328969201934
Author: Justin McKelvy <[email protected]>
Date:   Tue Nov 28 10:16:56 2023 -0700

    reset appProperties

commit 0aa001b6f61afbbf20c8ffc781467770113281f7
Author: Justin McKelvy <[email protected]>
Date:   Tue Nov 28 07:19:13 2023 -0700

    spotless apply formatting

commit 8c18c7dbc72926cc4e16e69d0157cb8927094fd0
Author: Justin McKelvy <[email protected]>
Date:   Mon Nov 27 08:42:56 2023 -0700

    fix redundant variables from merge

commit e2f49e3090e8cc739f7cbf465779ddcb3c6d0091
Merge: 8a0e947 f147c83
Author: Justin McKelvy <[email protected]>
Date:   Mon Nov 27 08:40:31 2023 -0700

    Merge branch 'master' into cr-6.9.6-snapshot

commit f147c8315ec51afde2dacec52a6804e4705457cd
Author: dotasek <[email protected]>
Date:   Fri Nov 24 16:11:12 2023 -0500

    Bump setup-java and checkout versions in github actions (#613)

    * Bump setup-java and checkout versions

    * Set java distribution

commit 8a0e947d3e38a4027f74b5d6d7b8ae3d1e019743
Author: Justin McKelvy <[email protected]>
Date:   Fri Nov 24 12:25:43 2023 -0700

    fix missing patient ref in unit test

commit 3303cb2bbb16d0a3d530930ab10cf82d1773cb41
Author: Justin McKelvy <[email protected]>
Date:   Wed Nov 22 09:36:27 2023 -0700

    match master appProperties

commit 1f7d25c5e57b1901fb8290151dc41a3d238933bf
Author: Jens Kristian Villadsen <[email protected]>
Date:   Thu Nov 23 22:25:32 2023 +0100

    Feat/ig install (#601)

    * Added IG operation providers for run time installation of IG's

    * Refactored conditions for enabling the provider

    * Refactoring

    * Disable it by default in config as well

    * document package install feature

    ---------

    Co-authored-by: Jose Costa Teixeira <[email protected]>

commit 23ef1d3c3272cb547db648145ce978404db3ceb3
Merge: c0b8980 b0ae4f2
Author: Justin McKelvy <[email protected]>
Date:   Wed Nov 22 12:39:19 2023 -0700

    Merge branch 'master' into cr-6.9.6-snapshot

commit c0b89800f1cd6a0312972d0df96cc7d4d5fb60dd
Author: c-schuler <[email protected]>
Date:   Wed Nov 22 12:37:04 2023 -0700

    Added fix for HAPI CDS Hooks request extensions element json parsing error

commit b0ae4f292dca653002d8a54c85892d7edcdba0b1
Merge: 21d51be 4bfa537
Author: dotasek <[email protected]>
Date:   Wed Nov 22 13:52:59 2023 -0500

    Merge pull request #598 from hapifhir/rel_6_9_tracking

    Bump HAPI version

commit 4bfa53789fdd407efab4b04fb96238533e072616
Merge: d55aa31 21d51be
Author: dotasek <[email protected]>
Date:   Wed Nov 22 13:24:39 2023 -0500

    Merge remote-tracking branch 'origin/master' into rel_6_9_tracking

commit d55aa31145bb67f51cc9f47418458af3a90fc333
Author: dotasek <[email protected]>
Date:   Wed Nov 22 13:24:28 2023 -0500

    Bump parent pom to version 6.10.0

commit aaa8a1f8cc0fa596b630dea641d70e24c8a21406
Merge: 0cf1ec8 21d51be
Author: Justin McKelvy <[email protected]>
Date:   Wed Nov 22 09:44:51 2023 -0700

    Merge branch 'master' into cr-6.9.6-snapshot

commit 0cf1ec8a7e4b4062848d1b6ae99945c72edeb6fa
Author: Justin McKelvy <[email protected]>
Date:   Tue Nov 21 15:30:44 2023 -0700

    removed basecr config due to spring errors

commit 21d51be45118303206bfd6ec5bd462cdab205738
Author: craig mcclendon <[email protected]>
Date:   Tue Nov 21 11:47:02 2023 -0600

    remove redundant/unused reload-existing-ig property (#607)

commit 5ae8349fbff85bbe692a75aa8b506d533a423fe2
Merge: 49c3db2 3640bd0
Author: dotasek <[email protected]>
Date:   Wed Nov 8 09:45:56 2023 -0500

    Merge remote-tracking branch 'origin/master' into rel_6_9_tracking

commit 3640bd03a2f885dc07e3ca61116bb178697f08a3
Author: chgl <[email protected]>
Date:   Sat Oct 28 15:14:02 2023 +0200

    Updated helm chart to use image v6.8.0 and some minor improvements (#600)

commit 49c3db27d6c606021433360f742431e59d36db90
Merge: afce59e d2b421a
Author: dotasek <[email protected]>
Date:   Tue Oct 24 14:41:13 2023 -0400

    Merge remote-tracking branch 'origin/master' into rel_6_9_tracking

commit afce59e5ad14701923bd32ee9b926ec9ff93aaf4
Author: dotasek <[email protected]>
Date:   Tue Oct 24 14:40:59 2023 -0400

    Bump to 6.9.10-SNAPSHOT

commit 408da72cf4e7bdbd89ead2946817f78b71b46520
Author: Brenin Rhodes <[email protected]>
Date:   Thu Oct 19 06:50:29 2023 -0600

    Add settings for CDS Hooks and use latest hapi-fhir-cr configs

commit d2b421a58ba88629f8da4aedcc3e24fbb7085309
Merge: 55d9973 5dade56
Author: dotasek <[email protected]>
Date:   Fri Oct 13 15:25:19 2023 -0400

    Merge pull request #594 from hapifhir/jkiddo-patch-1

    Update application.yaml

commit 0afe6ae0509d6d70279e4d29df2a5b6df7e03f13
Author: dotasek <[email protected]>
Date:   Thu Oct 12 16:01:12 2023 -0400

    Fix formatting

commit 735a6bd588caea9b60af82347317ff1c14ca4c0f
Merge: bd8dc63 55d9973
Author: dotasek <[email protected]>
Date:   Thu Oct 12 14:22:15 2023 -0400

    Merge branch 'master' into rel_6_9_tracking

commit 55d997301e34e5d18ebbf2cf82b905e2e266021c
Merge: 7cad4f3 252219d
Author: dotasek <[email protected]>
Date:   Thu Oct 12 11:41:44 2023 -0400

    Merge pull request #597 from hapifhir/do-20231011-6_8_x

    Bump HAPI version to 6.8.3

commit bd8dc63138f6dc694667afdc334e4d29cb8a1c44
Merge: ce0d7d4 7cad4f3
Author: dotasek <[email protected]>
Date:   Thu Oct 12 10:59:40 2023 -0400

    Merge remote-tracking branch 'origin/master' into rel_6_9_tracking

commit ce0d7d43d27f25f4513e9d43a4303389f51c8abc
Author: dotasek <[email protected]>
Date:   Thu Oct 12 10:53:46 2023 -0400

    Fix ExampleServerR4IT, restrict config to specific tests

commit bcd10350fe2656b468e07e489de75f425652645a
Author: dotasek <[email protected]>
Date:   Thu Oct 12 10:27:27 2023 -0400

    Formatting

commit 6b8c702f2a8ca21b1d550bea4cda2d63b5b16ad7
Author: dotasek <[email protected]>
Date:   Thu Oct 12 10:03:49 2023 -0400

    Bump HAPI version to 6.9.9-SNAPSHOT

commit 4f6f3162f18c2fb37ff8b9cff435482e77665895
Author: dotasek <[email protected]>
Date:   Thu Oct 12 10:03:16 2023 -0400

    Fix ExampleServerDstu3IT

commit 6d10c0badecb4d45cd4e3dbcadd4c17dc43081f4
Author: Justin McKelvy <[email protected]>
Date:   Wed Oct 11 15:16:17 2023 -0600

    add valueset cache and cache invalidation listeners

commit 252219d6c72e81fbe6d4c8553a8ae9b9333c14db
Author: dotasek <[email protected]>
Date:   Wed Oct 11 13:31:01 2023 -0400

    Bump HAPI version to 6.8.3

commit 7cad4f3d5d6feb7523837672f9a58e6ccb1b2c46
Merge: f93ea20 aeabf62
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Wed Oct 11 11:53:32 2023 -0400

    Merge pull request #593 from jkiddo/master

    Fixing null beans

commit 5dade564f187baf8dd5e7926234aad53ef6ac0ad
Author: Jens Kristian Villadsen <[email protected]>
Date:   Wed Oct 11 12:09:04 2023 +0200

    Update application.yaml

commit aeabf621e8c7d664c6bfafb30234b148cda203c8
Merge: 2307413 f93ea20
Author: Jens Kristian Villadsen <[email protected]>
Date:   Tue Oct 10 23:11:48 2023 +0200

    Merge branch 'master' of github.com:jkiddo/hapi-fhir-jpaserver-starter

commit 2307413a45b9a5a18cb445aaec6ce83d598b01bd
Author: Jens Kristian Villadsen <[email protected]>
Date:   Tue Oct 10 23:09:04 2023 +0200

    Fixing null beans as mentioned on https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/591

commit 3a0b42b2658bc641fc963dcbedea3fb3b810b419
Author: c-schuler <[email protected]>
Date:   Tue Oct 10 15:02:16 2023 -0600

    Fixed cds-services discovery response

commit 3b79897ff98a7f67e8720cc7cfd8804072fffd87
Author: Brenin Rhodes <[email protected]>
Date:   Tue Oct 3 12:28:56 2023 -0600

    Use hapi object mapper

commit f33dd6f09323d1b7f1340f022aa64884d1d79b78
Author: Brenin Rhodes <[email protected]>
Date:   Tue Oct 3 11:07:19 2023 -0600

    Add error handling for cds hooks servlet

commit f93ea209925bb6c1a51897aeb65369bde51358df
Merge: bfa85ce 39fba77
Author: James Agnew <[email protected]>
Date:   Mon Oct 2 16:35:13 2023 -0400

    Merge pull request #581 from Thopap/master

    Fix #580 Build artifact contain certain unused (but declared) dependencies

commit 3d51876a8d9724aa331cc23fa7babf467f843048
Author: Brenin Rhodes <[email protected]>
Date:   Thu Sep 28 20:15:28 2023 -0600

    Update to 6.9.8

commit 68b83d0c8ece7a5191bdb3041a29526506361e2e
Author: Brenin Rhodes <[email protected]>
Date:   Thu Sep 28 20:10:20 2023 -0600

    Add CdsHooksServlet

commit 6379e8ae609118fa6dc60273394fce7416c2ed20
Author: Justin McKelvy <[email protected]>
Date:   Mon Sep 25 14:16:39 2023 -0600

    conditional bean change

commit db9ed84d74a5b0062106506a90f4c8307129bbfd
Author: Justin McKelvy <[email protected]>
Date:   Mon Sep 25 13:35:08 2023 -0600

    add config for postinit provider loading

commit d5457fd688f66ada20c452c964b271950f7ead1f
Author: Justin McKelvy <[email protected]>
Date:   Thu Sep 21 14:20:22 2023 -0600

    remove * imports

commit 66940645c28533d0c7d304762a5bebdab8ec66be
Author: Justin McKelvy <[email protected]>
Date:   Thu Sep 21 12:52:35 2023 -0600

    update configs and hapi-version

commit 4ac5f03a0de3e690d9648f2441a0b8da705e830c
Merge: 1bb6e9e bfa85ce
Author: Justin McKelvy <[email protected]>
Date:   Mon Sep 18 18:41:34 2023 -0600

    merge master

commit 1bb6e9e6104b98192faf88e7e4ea9acce9c90dc1
Author: Justin McKelvy <[email protected]>
Date:   Mon Sep 18 16:53:32 2023 -0600

    updating to latest hapi, fixing cr tests

commit bfa85ceec9a1dc97930ffcb2d250c85b1606358b
Merge: 37a9317 0255d37
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Tue Sep 5 08:06:19 2023 -0400

    Merge pull request #582 from HussamNujaim/master

    Fixing some typos in README.md

commit 0255d373cb08f0b264a2e601884bf27cefe6f910
Merge: 37a9317 63c4825
Author: Husam Nujaim <[email protected]>
Date:   Sun Sep 3 01:15:59 2023 +0200

    Merge pull request #1 from HussamNujaim/typos-readme

    Fixing some typos in README.md

commit 63c4825d569b070ae2f47b8fb5cb96a647c2391a
Author: Husam Nujaim <[email protected]>
Date:   Sun Sep 3 01:15:10 2023 +0200

    Fixing some typos in README.md

commit 2fead63542e1023ee794ea362a490e2eb9d1f9b1
Author: Michael Buckley <[email protected]>
Date:   Thu Aug 31 10:47:55 2023 -0400

    Start tracking 6.9.x-SNAPSHOT

commit 39fba77e11bce1b68a4485cb6cc58d936c253e6f
Author: Thomas Papke <[email protected]>
Date:   Thu Aug 31 11:27:19 2023 +0200

    #580 Build artifact contain certain unused (but declared) dependencies

commit 37a9317355a96fb438d6d9ba027bd34ada3d9db6
Author: Jens Kristian Villadsen <[email protected]>
Date:   Tue Aug 22 20:14:43 2023 +0200

    Feature/using package installer spec (#577)

    * Adjusting to HAPI core classes

    * Added example as default

    * Commented the example IG out again

commit d6e9abad8cf3892e4f516c5adf42423921a7e0a8
Merge: 0252fa4 0a91a2d
Author: Patrick Werner <[email protected]>
Date:   Tue Aug 22 10:40:32 2023 +0200

    Merge pull request #546 from trifork/feat/static-hosting-additions

    Feat/static hosting additions

commit 0252fa4856ccf5327aa2b51b7739a08e19328a68
Merge: 8b0623d b4232e7
Author: Patrick Werner <[email protected]>
Date:   Tue Aug 22 10:39:30 2023 +0200

    Merge pull request #556 from trifork/feature/tester-configurable

    Feature/tester configurable

commit 8b0623d393e20ba932074b5bb10f326825046712
Merge: 8ef5083 b88ffda
Author: dotasek <[email protected]>
Date:   Thu Aug 17 13:42:37 2023 -0400

    Merge pull request #572 from hapifhir/do-20230731-bump-to-hapi-6-8-0

    Bump to HAPI 6.8.0

commit b88ffdada00cb16d19e9dad68289cd07d1473f88
Author: dotasek <[email protected]>
Date:   Thu Aug 17 13:02:02 2023 -0400

    Fix breakages due to https://github.com/hapifhir/hapi-fhir/pull/5180

commit 69ff8c4d0675ba88521b6050e0975634381de7f4
Author: dotasek <[email protected]>
Date:   Thu Aug 17 09:54:46 2023 -0400

    Bump to HAPI 6.8.0

commit 7265b115dd83664d972235f677d898e89a1d3c48
Author: dotasek <[email protected]>
Date:   Thu Aug 10 12:55:30 2023 -0400

    Leave comment in case of updates

commit 1907536d28ec527cc57a6f9536f1742af0fa6e60
Author: dotasek <[email protected]>
Date:   Thu Aug 10 12:51:34 2023 -0400

    Fix one more failing IT config

commit bdf593f151e9210d0c7736f022fa4fe9ae7ab335
Author: dotasek <[email protected]>
Date:   Thu Aug 10 12:34:45 2023 -0400

    Clean up code

commit f7853f5e19afd1f16854c3fd352fe1fc423ef04e
Author: Tadgh <[email protected]>
Date:   Thu Aug 10 09:30:01 2023 -0700

    Fix up test

commit 3c395e9dbe23ee7de43869f3e2ad8dfc3ad06521
Author: dotasek <[email protected]>
Date:   Thu Aug 10 12:08:57 2023 -0400

    WIP try to expand default max_result_window

commit bf7698bf0bfb8ce64a9641cb6234d0e6579a41ee
Merge: aafd4fa 8ef5083
Author: dotasek <[email protected]>
Date:   Mon Jul 31 15:23:57 2023 -0400

    Merge remote-tracking branch 'origin/master' into do-20230731-bump-to-hapi-6-8-0

commit aafd4fa0d9484214ffd49f6e68ef665551ccc117
Author: dotasek <[email protected]>
Date:   Mon Jul 31 14:43:58 2023 -0400

    Switch to new ca.uhn.fhir.batch2.jobs.export to fix StarterJpaConfig

commit e9f29af1aac64f9a0453bd95b602e6b019a7388f
Author: dotasek <[email protected]>
Date:   Mon Jul 31 14:34:47 2023 -0400

    Bump to hapi 6.8.0-SNAPSHOT

commit 8ef50832d3459d4eb35ecb4f116c580475acb59d
Author: chgl <[email protected]>
Date:   Fri Jul 21 16:26:10 2023 +0200

    Updated helm chart with additional config settings (#566)

commit 5bd43b29c9a5f807626c708e72bcb92f3dfd8dbb
Merge: 484aa9d 98165e8
Author: Patrick Werner <[email protected]>
Date:   Tue Jul 18 14:34:42 2023 +0200

    Merge pull request #564 from winne42/feature/add_configuration_for_auto_version_references

    #563 Add configuration for auto-versioning references

commit 8566f7f8ed4b0b52282fa94609a0963f143d7260
Author: justin.mckelvy <[email protected]>
Date:   Mon Jul 17 11:07:32 2023 -0600

    updating to 6.7.14-snapshot

commit 98165e848ff9cfba415d8d8098efdeaf7302664a
Author: Gerlach, Winfried <[email protected]>
Date:   Thu Jul 13 09:06:42 2023 +0200

    #563 fix indentation

commit 9d8fc4d2e59d7af4166113325f3e663d77024a09
Author: Gerlach, Winfried <[email protected]>
Date:   Wed Jul 12 17:53:58 2023 +0200

    #563 Add configuration for auto-versioning references

commit 484aa9deb5c184ef47569b8bb1d2c523b2a969ea
Author: winne42 <[email protected]>
Date:   Tue Jul 11 23:53:18 2023 +0200

    Boyscouting (#558)

    * Boyscouting: Docker conventions

    * Boyscouting: JUnit 5 conventions ("It is generally recommended to omit the public modifier for test classes, test methods, and lifecycle methods unless there is a technical reason for doing so)"

    * Boyscouting: typo in RepositoryValidationInterceptorFactoryDstu3

    * Boyscouting: use List.of instead of Guava; use StandardCharsets instead of Guava; remove unused imports

    ---------

    Co-authored-by: Gerlach, Winfried <[email protected]>

commit f92c2041183bb0eab9a11421347f5a5f0355cde6
Author: justin.mckelvy <[email protected]>
Date:   Fri Jun 30 15:15:53 2023 -0600

    update pom

commit 26662c24768db835487c478c5aa841fd91e6ca19
Author: justin.mckelvy <[email protected]>
Date:   Fri Jun 30 14:53:51 2023 -0600

    configure caregaps operation and properties

commit 29580e550156c6da7e432af48860022398fce8cb
Author: justin.mckelvy <[email protected]>
Date:   Mon Jun 26 16:37:13 2023 -0600

    6.6.1 with clinical reasoning fixes

commit fdcd021e6614bd995dc8a70e31bd9edc1d4857e9
Author: chgl <[email protected]>
Date:   Sun Jun 25 23:59:09 2023 +0200

    Updated helm chart and dockerfile dependencies (#540)

    * Updated Helm chart to use hapi fhir image v6.6.0

    * Updated maven base image due to openjdk deprecation

    * Removed superfluous app/main.war in entrypoint

    * Update curlimages/curl to 8.1.2

commit b4232e712755d53d3fae0a97ffe6f9552f177d30
Merge: 776afde a06c0b9
Author: Jens Kristian Villadsen <[email protected]>
Date:   Sun Jun 25 23:56:30 2023 +0200

    Merge branch 'hapifhir:master' into feature/tester-configurable

commit 776afdee5606c19458bebd47baf27bd471055842
Author: Jens Kristian Villadsen <[email protected]>
Date:   Sun Jun 25 23:55:48 2023 +0200

    no message

commit d6c152c524a84d63af509303371e7357cfdb14b8
Author: Jonathan Percival <[email protected]>
Date:   Fri Jun 16 10:36:52 2023 -0600

    Add empty map for tester

commit 300a21fcb4d23aabaece19deadc61deca01d06f2
Author: justin.mckelvy <[email protected]>
Date:   Fri Jun 16 09:15:54 2023 -0600

    add cqlconfigbeans

commit 6fe8784860993cfed55982daa21c5673fa6d771f
Author: justin.mckelvy <[email protected]>
Date:   Thu Jun 15 13:14:48 2023 -0600

    add cql translator options

commit af4a5f9d6bbbba00b064dd0f91609de823dc4b1a
Author: Jonathan Percival <[email protected]>
Date:   Wed Jun 14 10:38:14 2023 -0600

    Post init provider registerer

commit 291ccc4a266b47bb96bd59902ec8f37065b08ad2
Author: Jonathan Percival <[email protected]>
Date:   Tue Jun 13 16:42:25 2023 -0600

    Renaming operations

commit 3bff25ec54ddbaa958f985ce3099ca370f94d901
Author: justin.mckelvy <[email protected]>
Date:   Tue Jun 13 11:59:48 2023 -0600

    remove annotation and repositoryfactory

commit 283c16db0f70dbdedc99f959f592ea13015f7105
Author: justin.mckelvy <[email protected]>
Date:   Tue Jun 13 11:02:37 2023 -0600

    rename classes

commit a9158f7e6b6d4f28d85d7cb0a4b78044397144b1
Author: justin.mckelvy <[email protected]>
Date:   Tue Jun 13 09:38:47 2023 -0600

    remove unused imports, update config

commit f7a4d24ab278d0736940628ea4a86dceea5055a1
Author: justin.mckelvy <[email protected]>
Date:   Tue Jun 13 09:14:37 2023 -0600

    complete config for cr

commit 27e250f9302dba5a18c850e3a3974960f9fa3419
Author: justin.mckelvy <[email protected]>
Date:   Mon Jun 12 16:36:11 2023 -0600

    add factory loader

commit 77c0e896682302dbf4e4a362685eff3f9f6b155d
Author: Jonathan Percival <[email protected]>
Date:   Mon Jun 12 14:57:31 2023 -0600

    Revert provider loader

commit e97788dab381c2fa1db504270948702adaec1788
Author: justin.mckelvy <[email protected]>
Date:   Sun Jun 11 14:20:30 2023 -0600

    update integration tests and appproperties

commit eaaf27b5d0d17627af0555664cf00b0c4815442c
Author: justin.mckelvy <[email protected]>
Date:   Sat Jun 10 22:42:05 2023 -0600

    add factories for cr

commit f59ecd961ab820d283018f8177b2a27eccbde59a
Author: justin.mckelvy <[email protected]>
Date:   Sat Jun 10 22:29:25 2023 -0600

    adding factories and beans for cr

commit b5351ae237892e051824fec52008290edefb6b0e
Author: justin.mckelvy <[email protected]>
Date:   Fri Jun 9 16:24:08 2023 -0600

    add cr operation loader

commit 0a91a2d23cb5a2cacea322c4317fc5aa4b951747
Merge: afaec85 a06c0b9
Author: Jens Kristian Villadsen <[email protected]>
Date:   Fri Jun 9 11:40:30 2023 +0200

    Merge branch 'hapifhir:master' into feat/static-hosting-additions

commit afaec85653197db5516f8495eff71a46314e24cf
Author: Jens Kristian Villadsen <[email protected]>
Date:   Fri Jun 9 11:39:54 2023 +0200

    Addressing https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/486 and https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/485

commit 51615ac005758d74ecbda1ac0659a369e3584f9d
Author: justin.mckelvy <[email protected]>
Date:   Thu Jun 8 07:46:14 2023 -0600

    remove unused imports

commit a06c0b9ce47a05f0719edeaba2a325ff5bef8cce
Merge: 53a958a 2899060
Author: jmarchionatto <[email protected]>
Date:   Wed May 31 08:48:29 2023 -0400

    Merge pull request #541 from hapifhir/501_fix_cr_enabled

    Add fix to enable the CR module.

commit 2899060de07868e07693143d40a5592893896ce3
Author: Chalma Maadaadi <[email protected]>
Date:   Tue May 30 19:20:19 2023 -0400

    Addressed comment to for cr_enabled flag.

commit 9e9c08bafe5c3533e5e2b149fae141be402c32ba
Author: Chalma Maadaadi <[email protected]>
Date:   Tue May 30 15:28:55 2023 -0400

    Add fix to enable the CR module.

commit 53a958ac664231c4d17b25fcb2337ffdc1236cde
Author: dotasek <[email protected]>
Date:   Mon May 29 14:33:45 2023 -0400

    Bump HAPI to release 6.6.0 (#539)

    * Start tracking 6.5

    * Use JpaStorageSettings and StorageSettings

    * Bump parent pom version + add deps for jaxb

    * Bump HAPI

    * Fix Subscription/Topic resource creation

    * fix subscription topic beans

    * Change to rel_6_6 hapi-fhir SNAPSHOT

    * Fix emailSender config

    * Split method calls by line.

    * Merge pull request #524 from hapifhir/do-20230509-smoke-test-ci

    Create smoke-tests.yml

    * Bump core to release 6.6.0

    ---------

    Co-authored-by: Michael Buckley <[email protected]>
    Co-authored-by: Kevin Dougan SmileCDR <[email protected]>
    Co-authored-by: Ken Stevens <[email protected]>
    Co-authored-by: Mark Iantorno <[email protected]>

commit eb65ec68cca73f294bcbe7a4adcf221998d1efe0
Merge: b4ab761 a2cf95a
Author: Mark Iantorno <[email protected]>
Date:   Tue May 23 07:33:20 2023 -0700

    Merge pull request #535 from hapifhir/do-20230519-use-docker-for-smoke-tests

    Use docker for HTTP client

commit a2cf95ae5e4fe43951aeed3307b008b9cf13be8f
Author: dotasek <[email protected]>
Date:   Fri May 19 16:35:48 2023 -0400

    Restore reasonable sleep time

commit 8bf9dfd1cf4de7967684f0452812109a1691ac62
Author: dotasek <[email protected]>
Date:   Fri May 19 16:31:42 2023 -0400

    Intentional failure

commit 9a18b23a26214fcd5512a79967fbe95f73fcb3c6
Author: dotasek <[email protected]>
Date:   Fri May 19 16:26:23 2023 -0400

    Additional param for linux localhost

commit f54088efab6bc745f7a99ae9c1dbc166f5bf9fea
Author: dotasek <[email protected]>
Date:   Fri May 19 16:17:54 2023 -0400

    Sleep a little longer...

commit 8b7c35c9dc44cc3340634386b68d5a90d1ff0b93
Author: dotasek <[email protected]>
Date:   Fri May 19 16:13:49 2023 -0400

    Try fixing TTY issue

commit 3eab2fcf9efe7f50b2cc438d4e925d5c2fecad5a
Author: dotasek <[email protected]>
Date:   Fri May 19 16:06:11 2023 -0400

    Use docker for HTTP client

commit b4ab7610eea7acb906095375e5da67befd01a2e5
Merge: 4077cf5 ec64299
Author: Mark Iantorno <[email protected]>
Date:   Wed May 17 11:09:11 2023 -0400

    Merge pull request #524 from hapifhir/do-20230509-smoke-test-ci

    Create smoke-tests.yml

commit ec64299976a9d1b3bc9c03ed88d68ce945f56bf1
Author: dotasek <[email protected]>
Date:   Tue May 9 16:41:42 2023 -0400

    Update smoke-tests.yml

    Wait longer just in case

    Maybe don't kill the jetty server?

commit dbd6ff0eddf28bdc661b7f3fc499553b7279e5ba
Author: dotasek <[email protected]>
Date:   Tue May 9 16:34:55 2023 -0400

    Update smoke-tests.yml

    Skip maven tests
    Wait longer for server

commit f1765a314f197a9234966ffb72c27aa93e29a886
Author: dotasek <[email protected]>
Date:   Tue May 9 16:26:31 2023 -0400

    Rename plain_server.rest to plain_server.http

commit d47d048a4f3bb31f1fead85eb0ae851f7dbee3a4
Author: dotasek <[email protected]>
Date:   Tue May 9 16:25:55 2023 -0400

    Update smoke-tests.yml

    Don't do integration tests.

    Start server
    Run smoke tests
    Stop Server

commit e8d19311997f924c3c7adfcff2322f4f0ab0d8fe
Author: dotasek <[email protected]>
Date:   Tue May 9 16:08:13 2023 -0400

    Create smoke-tests.yml

commit 4077cf58404afccd7597978fc5e19851d4ff22fe
Merge: d96c90c 75e0e68
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Fri May 5 14:41:11 2023 -0400

    Merge pull request #522 from hapifhir/497-set-bundle-batch-max-pool-size

    497 - Fix typo on property setter

commit 75e0e681045bc0cdc1665f8f58db792954db90f8
Author: Kevin Dougan <[email protected]>
Date:   Fri May 5 10:49:13 2023 -0400

    497 - Fix typo on property setter.

commit d96c90c18f984d4b9db7502ed089ceda5e2d69af
Author: Jens Kristian Villadsen <[email protected]>
Date:   Thu Mar 30 10:25:13 2023 +0200

    Update pom.xml

commit a1bdba589038aba0614c356fe16951af01abff00
Author: Jens Kristian Villadsen <[email protected]>
Date:   Fri Mar 3 19:51:08 2023 +0100

    Update pom.xml

commit c73c5808239f9fcd26fa4c2f5ca6d81a53f602ff
Author: Jens Kristian Villadsen <[email protected]>
Date:   Mon Feb 27 20:46:39 2023 +0100

    Update pom.xml

    Update to 6.4.1

commit 7e0fb80dac478dee882ecf23e9590aff557acb4d
Author: Bert Roos <[email protected]>
Date:   Fri Mar 31 12:17:33 2023 +0200

    Simplify using an interceptor with Docker

    Now it is possible to mount a folder with extra classes that are loaded
    by HAPI. This makes it easy to load an interceptor JAR while using the
    standard Docker image. The README explains how to use it.

    Spring by default uses the WarLauncher. Now the ENTRYPOINT uses the
    PropertiesLauncher, configured in such a way that it is compatible with
    the WarLauncher, but adding the folder /app/extra-classes to the
    loader.path.

commit 43890a4b9db8c8a5aec48de64382238c8697b18b
Author: Kevin Dougan <[email protected]>
Date:   Fri Mar 31 12:54:27 2023 -0400

    Removed explicit inclusion of snakeyaml and allow spring-boot-starter-actuator to pull it in as a needed dependency.

commit 600f3fe692c6c55b49eb8e9cd581f1108c428c3d
Author: Bert Roos <[email protected]>
Date:   Wed Feb 22 20:05:27 2023 +0100

    Update docker-compose sample with small application.properties

    When running from Docker Hub, it is not convenient to have to copy the full application.yaml as a starting point. Based on Spring's property initialization order, it's possible to mount a small version of application.yaml in the config folder in the run directory.

commit c83e324692f337f3405b18dbd69f2c1cfc0236b4
Author: Craig McClendon <[email protected]>
Date:   Thu Mar 23 14:54:20 2023 -0500

    configuration option to not reload IG resources that are already loaded

commit cb4f560413a1afb83efaf86a2a0c7f2ae5e82b72
Merge: 9cabe35 236c1e8
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Wed Mar 1 08:43:57 2023 -0500

    Merge pull request #505 from psavva/patch-4

    Spelling error in Application.yaml

commit 236c1e82bac4749a14f05a7b9d509f0bdee67f5e
Author: Panayiotis Savva <[email protected]>
Date:   Wed Mar 1 14:04:42 2023 +0200

    Spelling error in Application.yaml

    Fix spelling error in comments section

commit 9cabe35c40c18a27944eb90f75f4715980b35353
Merge: 35d09cc 20ed5d9
Author: Tadgh <[email protected]>
Date:   Fri Feb 17 10:56:27 2023 -0800

    Merge pull request #498 from hapifhir/rel_6_4

    Bump HAPI to 6.4.0

commit 20ed5d90ab6330617b6c64e832bde0c20af0d561
Author: dotasek <[email protected]>
Date:   Tue Feb 14 14:52:26 2023 -0500

    Revert "Add optional explicit ip config for smoke tests"

    This reverts commit afcd2fc13138c5f105d81932a473d9afbf2398fe.

commit afcd2fc13138c5f105d81932a473d9afbf2398fe
Author: dotasek <[email protected]>
Date:   Tue Feb 14 14:52:26 2023 -0500

    Add optional explicit ip config for smoke tests

commit 9d126a4f563f60e05f29dd34a926fc5ccfe73627
Author: dotasek <[email protected]>
Date:   Tue Feb 14 14:52:03 2023 -0500

    Fix Application error regarding multiple beans

commit 19988c505d8b341d7dee0a838d643d141d992525
Author: dotasek <[email protected]>
Date:   Tue Feb 14 12:47:32 2023 -0500

    Bump Hapi

commit 35d09cce16c6585a86102d9a224319812ab5f4b5
Author: Juvar Abrera <[email protected]>
Date:   Sun Feb 5 21:10:34 2023 +0800

    docs: Revert dislaimer in postgres

commit 7f7ea920d0e7c39873b2b30f4e8329d7aae270bc
Author: Juvar Abrera <[email protected]>
Date:   Sun Feb 5 20:57:34 2023 +0800

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

commit 74be71351588aee7a69e221cc71da52dbe6d77e5
Author: Juvar Abrera <[email protected]>
Date:   Sun Feb 5 20:48:24 2023 +0800

    refactor: Separate unrelated settings and documentation

commit b6c1b9f47c17b468e68edc4dd605ad0660f58ce3
Author: Juvar Abrera <[email protected]>
Date:   Sun Feb 5 20:47:08 2023 +0800

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

commit c88d26d2e5657cf2fa8f18e686413805715495fd
Author: Juvar Abrera <[email protected]>
Date:   Sun Feb 5 09:50:41 2023 +0800

    docs: Fix postgresql typo in docker-compose

commit 7dd16193698ac81569ec38c790b4b8e36f44a3d8
Merge: 9847d82 c9bc40c
Author: James Agnew <[email protected]>
Date:   Thu Feb 9 09:51:08 2023 -0500

    Merge pull request #495 from XcrigX/remove-mysql-dependency

    removed mysql-connector-java dependency since no longer supported and…

commit c9bc40c10aeb76120b1d28cb53c2db03b3404d9f
Author: Craig McClendon <[email protected]>
Date:   Wed Feb 8 16:46:15 2023 -0600

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

commit 9847d82257dc4a135bfc46f1839e1c0d9ac0e35b
Merge: 64b497e 3f66973
Author: James Agnew <[email protected]>
Date:   Sat Feb 4 15:04:18 2023 -0500

    Merge pull request #491 from juvarabrera/update-readme

    docs: Updated README.md. Discontinue mysql

commit 3f669739528303c940601b9a024a4917193848fb
Author: Juvar Abrera <[email protected]>
Date:   Sat Feb 4 21:20:37 2023 +0800

    docs: Updated README.md. Discontinue mysql

commit 64b497e4e9b17f38c77b83a3b7085fc06a994604
Author: James Agnew <[email protected]>
Date:   Tue Jan 24 13:30:09 2023 -0500

    HAPI FHIR bump

commit e905da77338dc7bb8f5d08b18d7a953b8206223f
Author: Panayiotis Savva <[email protected]>
Date:   Mon Jan 16 03:38:17 2023 +0200

    CQL to CR

commit 99ea176a9cd11c53c5b30662a62ef2ac50cfd38e
Author: Panayiotis Savva <[email protected]>
Date:   Mon Jan 16 03:35:30 2023 +0200

    typo

commit c7ee984b301d1bd1aa8d41c47f6dd9f27b8fbc24
Author: Panayiotis Savva <[email protected]>
Date:   Mon Jan 16 03:32:58 2023 +0200

    Allow Enabling IPS via config

commit 7c89addbefe20a44534197434e04e02b511c6cf8
Author: Panayiotis Savva <[email protected]>
Date:   Mon Jan 16 02:27:33 2023 +0200

    Initial IPS + Cql to Cr migration

commit c7962b69798f320f6f46904255fead7f3a9e4d83
Merge: cd6a876 5b42944
Author: Mark Iantorno <[email protected]>
Date:   Fri Jan 13 13:28:05 2023 -0500

    Merge pull request #482 from hapifhir/ld-20230110-hapi-fhir-6-3-6-snapshot-with-logs-working-downgrade-logback-solution

    Upgrade to hapi-fhir 6.3.6-SNAPSHOT:  Alternative solution.

commit 5b4294421b524289f50fedf65510c9ab49508de8
Merge: ea3d858 cd6a876
Author: Luke deGruchy <[email protected]>
Date:   Thu Jan 12 09:27:05 2023 -0500

    Merge remote-tracking branch 'origin/master' into ld-20230110-hapi-fhir-6-3-6-snapshot-with-logs-working-downgrade-logback-solution

commit cd6a8761bb166bddc2b78522843c154055f1b3ea
Merge: ef8c487 8f528db
Author: Mark Iantorno <[email protected]>
Date:   Thu Jan 12 09:25:09 2023 -0500

    Merge pull request #483 from hapifhir/ld-20230111-pipeline-maven-verify

    Update pipeline to run integration tests.

commit 8f528dbddbb62c2849bdba33bd75ce44b4cea4be
Author: Luke deGruchy <[email protected]>
Date:   Wed Jan 11 17:09:38 2023 -0500

    Update pipeline to run integration tests.

commit ea3d858563e97b5e6cd617ecd1c4e0ece6e08dcc
Author: James Agnew <[email protected]>
Date:   Wed Jan 11 16:30:12 2023 -0500

    Fix tests for websocket

commit 38ed00a84b1b7ff70771b5367e85ca41f7301251
Author: Luke deGruchy <[email protected]>
Date:   Tue Jan 10 16:53:57 2023 -0500

    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.

commit d9f5e5c7da8ac316ba8c9904dc3acfe95af3adbf
Merge: 76650df ef8c487
Author: Luke deGruchy <[email protected]>
Date:   Tue Jan 10 14:53:11 2023 -0500

    Merge remote-tracking branch 'origin/master' into ld-20230110-hapi-fhir-6-3-6-snapshot-with-logs-working

commit ef8c487da43cfe6bb43d1dd2cadc004194ccd126
Author: chgl <[email protected]>
Date:   Tue Jan 10 20:52:16 2023 +0100

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

commit 07d9a193d2d9add9ae561839477ed9593f690484
Author: Jens Kristian Villadsen <[email protected]>
Date:   Tue Jan 10 20:51:47 2023 +0100

    Feature/index default (#475)

    * Added default

    * Refactored the default resolution

commit 76650df4dcd0bf6944b9a80ddd1d0070ffc41422
Author: Luke deGruchy <[email protected]>
Date:   Tue Jan 10 14:51:32 2023 -0500

    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");

commit f3493c7026a545c2be7a35455bd285f384f1642d
Author: Luke deGruchy <[email protected]>
Date:   Tue Jan 10 14:51:31 2023 -0500

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

commit 0c7e48cb4da3e00742ea975636fefed55cdb9eae
Author: Luke deGruchy <[email protected]>
Date:   Tue Jan 10 14:14:52 2023 -0500

    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.

commit f8c69bf3e1126fa30662d339e883693c2e9d107f
Merge: 96ff27f d903ab9
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Tue Jan 10 08:18:51 2023 -0500

    Merge pull request #474 from inspector-cochise/junit-dep-remove

    Remove old junit4 usage.

commit d903ab9661d148a8f6777c5f30122bc580638df1
Author: isims <[email protected]>
Date:   Tue Jan 10 11:21:21 2023 +0100

    Remove old junit4 usage.

commit 96ff27f173143aaf7c3f88d1e563809603fc23b5
Author: Jens Kristian Villadsen <[email protected]>
Date:   Thu Jan 5 23:26:09 2023 +0100

    Feature/static files (#456)

    * Added mapping

    * Added documentation

commit 9a513cd1845723c630565ac2b124d74e56491006
Author: Luke deGruchy <[email protected]>
Date:   Thu Jan 5 16:56:01 2023 -0500

    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.

commit 194358968238db8d98a0896b5f789f329a0a8e7d
Merge: 19c68e7 ba58a71
Author: James Agnew <[email protected]>
Date:   Wed Dec 21 09:27:51 2022 -0500

    Merge pull request #467 from XcrigX/feature/interceptor-discovery

    allow interceptors to be registered via properties

commit ba58a71624c6fc5669394848ce0614af152225dd
Author: Craig McClendon <[email protected]>
Date:   Tue Dec 20 20:07:18 2022 -0600

    allow interceptors to be registered via properties

commit 19c68e7cfcbb0eec064da8b4c9b5a43dc1879e83
Author: Jens Kristian Villadsen <[email protected]>
Date:   Sat Dec 3 14:43:37 2022 +0100

    Bumped version (#462)

commit 05d76c78ad8508dfe9bfa7d6ddaa3968804dd631
Author: chgl <[email protected]>
Date:   Thu Nov 24 23:09:24 2022 +0100

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

commit daea3916caa4717c42de9557df6f62d94d88357c
Merge: 2e1f5f5 4fb2558
Author: Mark Iantorno <[email protected]>
Date:   Thu Nov 17 11:12:19 2022 -0500

    Merge pull request #457 from hapifhir/update_HAPI_version

    upping hapi version to 6.2.1

commit 4fb2558d7ce123a4c8187bba5d4788525f8e4bf3
Author: markiantorno <[email protected]>
Date:   Thu Nov 17 10:07:25 2022 -0500

    upping hapi version to 6.2.1

commit 2e1f5f52769cf5f38883f3ac27e20f1fe1bdd84a
Author: Jens Kristian Villadsen <[email protected]>
Date:   Sat Nov 12 18:39:38 2022 +0100

    fixes for support of R4B / 6.2.0 (#455)

commit 64aeb9b2fe250ce843e47a60763d5012dee19016
Author: Kai-W <[email protected]>
Date:   Sat Nov 12 16:43:56 2022 +0100

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

commit f8d749ae28dbccc173a18a28269456e87b1ea6a4
Author: jmarchionatto <[email protected]>
Date:   Sat Nov 12 08:16:38 2022 -0500

    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 <[email protected]>
    Co-authored-by: michaelabuckley <[email protected]>
    Co-authored-by: juan.marchionatto <[email protected]>
    Co-authored-by: Tadgh <[email protected]>

commit a1e2ca3ae13d24e7f66b856ac251c39de02d3eb5
Author: Jens Kristian Villadsen <[email protected]>
Date:   Thu Oct 27 08:21:08 2022 +0200

    revering to H2 (#449)

commit d61c8a5f96aca475b6b5ccc8aedef64614127f7b
Author: rti <[email protected]>
Date:   Tue Oct 11 20:02:45 2022 +0200

    switch to postgres db (#444)

commit a95c40dd05af40434a86a7b03c475e4142dd3743
Author: patrick-werner <[email protected]>
Date:   Thu Oct 6 16:34:29 2022 +0200

    fixed SubscriptionDebugLogInterceptor adding logic

commit 7a72c86a637548d3bb1fb7ee69fe7c5d7884c8c8
Author: Patrick Werner <[email protected]>
Date:   Thu Oct 6 14:26:43 2022 +0200

    removed duplicated and wrong subscription code (#440)

commit 531d2557820b5ecbe725a9142dd231413a6dd716
Author: Thomas Papke <[email protected]>
Date:   Sat Oct 1 17:19:01 2022 +0200

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

commit f3b9ffed4d314190b22b85b805c99f0623cb5b31
Merge: cd1a2e1 3d03cd0
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Fri Sep 30 08:46:48 2022 -0400

    Merge pull request #434 from jkiddo/feat/fix-cors

    fix: configuration of cors

commit 3d03cd00c56f48a1115adce5b266fe9c3f157109
Author: Jens Kristian Villadsen <[email protected]>
Date:   Wed Sep 28 22:51:57 2022 +0200

    fix: configuration of cors

    Refs: #430

commit cd1a2e1687cd164c1bc3823025f50e5b19b2d5bb
Merge: 38f37e4 5c1f99b
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Tue Sep 27 09:54:09 2022 -0400

    Merge pull request #432 from hapifhir/dependabot/maven/org.yaml-snakeyaml-1.31

    Bump snakeyaml from 1.30 to 1.31

commit 5c1f99bf188de68dcf3dfc7beb3f38b58be75995
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Sep 27 13:25:21 2022 +0000

    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] <[email protected]>

commit 38f37e4db04d3790432f70b1ccf4fb1329c74b36
Author: Patrick Werner <[email protected]>
Date:   Thu Sep 15 13:10:22 2022 +0200

    added back lost config entry: allowed_bundle_types (#427)

    * added back lost config entry

    * disabled entry

commit 43d50a0c71bb5c3194c05a17db74386773c518f2
Author: Jens Kristian Villadsen <[email protected]>
Date:   Tue Sep 13 18:54:14 2022 +0200

    Extract IG loading (#426)

commit d660d5f76d63ad4697148f9d612aedd29640efe9
Author: Jens Kristian Villadsen <[email protected]>
Date:   Sat Sep 10 21:14:01 2022 +0200

    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

commit c5e460dab02c32714fbe05f44b514ef8bdf273b8
Author: Patrick Werner <[email protected]>
Date:   Sat Sep 3 20:04:59 2022 +0200

    added appProperties.getInline_resource_storage_below_size() (#420)

    * added appProperties.getInline_resource_storage_below_size()

    * indentations

commit bdc621e535a15eacca3891abd94f1bfc6a8fa333
Author: chgl <[email protected]>
Date:   Thu Aug 25 23:21:19 2022 +0200

    updated helm chart to use version 6.1.0 of the image

commit 4790c4372f28a21cd76e29169a1827095aa555ef
Author: chgl <[email protected]>
Date:   Thu Aug 25 02:46:13 2022 +0200

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

commit 68e64f2f33757a33cb0183be35730f303b90e1ad
Author: chgl <[email protected]>
Date:   Thu Aug 25 02:34:02 2022 +0200

    Minor Helm chart dependency updates and security improvements

commit 001bc9c57a95ab04ef439f1081a800b9e387df5a
Merge: ac5364c d059954
Author: Mark Iantorno <[email protected]>
Date:   Tue Aug 23 11:42:46 2022 -0400

    Merge pull request #415 from chgl/updated-to-hapi-6.1.0

    Updated to hapi 6.1.0

commit ac5364c786a32a000e98081b93dd8ef546b35152
Merge: 4978f32 ee74116
Author: Patrick Werner <[email protected]>
Date:   Tue Aug 23 09:53:31 2022 +0200

    Merge pull request #413 from hapifhir/jkiddo-patch-1

    Better support for ARM

commit d059954c5f40d59bc0553539e678fdc892526ddb
Author: chgl <[email protected]>
Date:   Mon Aug 22 18:16:24 2022 +0200

    Updated hapi-fhir to 6.1.0

commit 956cfb171dd8562d60ac49623e05338420d32264
Author: chgl <[email protected]>
Date:   Mon Aug 22 18:15:34 2022 +0200

    Updated Otel Java agent to 1.17.0

commit ee74116e6b4b73b84da374eca01892d30fb410ef
Author: Jens Kristian Villadsen <[email protected]>
Date:   Thu Aug 18 21:05:36 2022 +0200

    Better support for ARM

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

commit 4978f32e320da49317ba490db11712d83834c8c6
Merge: 427a147 1753272
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Mon Aug 15 07:57:39 2022 -0400

    Merge pull request #411 from chgl/patch-1

    updated opentelemetry-java-instrumentation JAR to 1.16.0

commit 1753272122665df6b2b25dc99944be44f275abdb
Author: chgl <[email protected]>
Date:   Mon Aug 15 01:20:49 2022 +0200

    updated opentelemetry-java-instrumentation JAR to 1.16.0

commit 427a1473e957d1a34e1e4feb2d40784f817c3631
Merge: 5c102f7 c617f4e
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Wed Aug 10 13:35:47 2022 -0400

    Merge pull request #410 from amuslim-fn/master

    Inclusion of bulk data instrumentation

commit c617f4e395957b72c4eba9cbfe58843436705307
Author: Arbaaz Muslim <[email protected]>
Date:   Tue Aug 9 16:48:22 2022 -0700

    bulk data instrumentation turned off by default

commit d148f458e0e07dad1ee2ce55c79b07bc3f612aad
Author: Arbaaz Muslim <[email protected]>
Date:   Tue Aug 9 16:31:49 2022 -0700

    bulk data instrumentation included

commit 5c102f76fc133846ee9a1154e94ca60a453a2442
Merge: 014dd14 c9dd605
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Tue Jul 12 08:06:08 2022 -0400

    Merge pull request #400 from chgl/fixed-tomcat-wrong-war-dir

    fixed directory of the .war in tomcat-based image

commit c9dd6054fa253d3769859942e3f3ac4e71463f20
Author: chgl <[email protected]>
Date:   Fri Jul 8 00:18:49 2022 +0200

    fixed directory of the .war in tomcat-based image

commit 014dd149b63a66a88155cebda5122763954541bb
Merge: cd8b06b 6ad2989
Author: Mark Iantorno <[email protected]>
Date:   Tue Jul 5 14:44:12 2022 -0400

    Merge pull request #398 from hapifhir/oss_publishing_update

    changes to pom.xml to enable publishing

commit 6ad29890f0e85e240e207a6c7183c8109fd4fe87
Author: markiantorno <[email protected]>
Date:   Tue Jul 5 14:27:05 2022 -0400

    changes to pom.xml to enable publishing

commit cd8b06b263a9d18ca820fb09860e51a6029e16eb
Author: chgl <[email protected]>
Date:   Mon Jul 4 19:44:20 2022 +0200

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

    Closes #387

commit 8a5d2f8aa563036e988644a11acedc18ba6c846c
Merge: 82d1b35 bea4d47
Author: Patrick Werner <[email protected]>
Date:   Mon Jul 4 14:57:31 2022 +0200

    Merge pull request #397 from hapifhir/patrick-werner-remove-config-duplicate

    removed wrong and duplicated config entry

commit bea4d471aaa1d4370ed79bb3615054c2be5b18c3
Author: Patrick Werner <[email protected]>
Date:   Mon Jul 4 14:54:49 2022 +0200

    removed wrong and duplicated config entry

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

commit 82d1b357f7fef7ac5edb7589e3eca7041f7501e2
Merge: aa56061 d6b5bc3
Author: Patrick Werner <[email protected]>
Date:   Mon Jul 4 14:48:39 2022 +0200

    Merge pull request #396 from hapifhir/patrick-werner-fix-h2

    Applying fix from upstream for h2 Binaries

commit d6b5bc3cd22c018f283a2699ab77ec643cd1ccba
Author: Patrick Werner <[email protected]>
Date:   Mon Jul 4 14:46:15 2022 +0200

    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

commit aa5606158a291e1431d25ec4e9ec9f6249229d78
Merge: 67caa88 a026b1f
Author: Kevin Dougan SmileCDR <[email protected]>
Date:   Mon Jun 27 10:25:08 2022 -0400

    Merge pull request #386 from ehealth-co-id/fix-binary

    add BinaryAccessProvider to BaseJpaRestfulServer when binary_storage_enabled is true

commit a026b1f390ab5c4cefc00ccd22cd5928206924ff
Author: Ibrohim Kholilul Islam <[email protected]>
Date:   Thu Jun 23 12:00:55 2022 +0700

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

    Co-authored-by: Kevin Dougan SmileCDR <[email protected]>

commit 41ba07a5e5fcdbcee05b23f4d58c3c1d115b2052
Author: Ibrohim Kholilul Islam <[email protected]>
Date:   Fri Jun 17 18:15:58 2022 +0000

    add BinaryAccessProvider to BaseJpaRestfulServer

commit 67caa88e06cf79df9f52db95ea9b2da03b00af6c
Author: chgl <[email protected]>
Date:   Sat Jun 4 14:24:28 2022 +0200

    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

commit 2daf365bdf0c6826bb0ebd3cbe12110877584dad
Merge: 73d7ee1 e9ff226
Author: Mark Iantorno <[email protected]>
Date:   Sun May 29 09:28:43 2022 -0400

    Merge pull request #376 from hapifhir/smoke_tests

    Smoke tests

commit 73d7ee185771a10e9156d7b2d97fe7e5af6ae20f
Author: Mark Iantorno <[email protected]>
Date:   Thu May 26 15:00:07 2022 -0400

    bumping to non-snapshot version (#377)

commit e9ff226750d5ac335d46bbddad1bdaa6a3baa935
Author: Mark Iantorno <[email protected]>
Date:   Wed May 25 12:55:41 2022 -0400

    Update src/test/smoketest/SMOKE_TEST.md

    Co-authored-by: Ken Stevens <[email protected]>

commit 788015f467b91c9fb5dfaf043a7a4edd21553f94
Author: Mark Iantorno <[email protected]>
Date:   Wed May 25 12:55:22 2022 -0400

    Update src/test/smoketest/SMOKE_TEST.md

    Co-authored-by: Ken Stevens <[email protected]>

commit b71880e39ea06392a0a9aefdf40bc2621831dbef
Author: Mark Iantorno <[email protected]>
Date:   Wed May 25 12:55:16 2022 -0400

    Update src/test/smoketest/SMOKE_TEST.md

    Co-authored-by: Ken Stevens <[email protected]>

commit 8d6247bfe8357f0769ff7478e3533ed765006bae
Author: markiantorno <[email protected]>
Date:   Tue May 24 19:20:13 2022 -0400

    wip

commit 067c7f16c4f450599e088b7a30f4cb50475495ad
Author: markiantorno <[email protected]>
Date:   Tue May 24 19:18:07 2022 -0400

    adding base documentation

commit 9882a1cd58065bf90f2d9ef011d99ffe7acbb779
Author: markiantorno <[email protected]>
Date:   Tue May 24 17:37:45 2022 -0400

    adding smoke test files

commit d660dc137004d8bbe2c635fe6b7ae31701f286c0
Author: Tadgh <[email protected]>
Date:   Sat May 21 10:31:49 2022 -0700

    Re-add valueset operation provider

commit f39393ca976db25e0dda588bb67451683af074e6
Author: Tadgh <[email protected]>
Date:   Sat May 21 10:10:20 2022 -0700

    Disable lucene by default

commit 4dacf6ae904fa45a04c38a7bb9622cdff9115247
Author: Tadgh <[email protected]>
Date:   Sat May 21 09:54:50 2022 -0700

    Re-add valuesetoperation provider

commit 8ac32ddf7f65d2ef16250a3a9d79f725792bd9c1
Merge: 6ad499c e5b0fc7
Author: Tadgh <[email protected]>
Date:   Fri May 20 12:28:39 2022 -0700

    Merge pull request #373 from hapifhir/20200520-test-failure

    fix build

commit e5b0fc721621eaece1291bbdacc72a4caabf67a2
Author: Ken Stevens <[email protected]>
Date:   Fri May 20 15:24:17 2022 -0400

    fix build

commit 6ad499cecb82c3bc1c76b50aa58d46ea6b95a91b
Author: Tadgh <[email protected]>
Date:   Thu May 19 14:45:42 2022 -0700

    Bump to pre-01

commit 7cfbac89561c6ce5c831ea04f6d5926540a4a016
Merge: 244113b d4bc6fe
Author: Tadgh <[email protected]>
Date:   Thu May 19 14:44:36 2022 -0700

    Merge pull request #372 from hapifhir/rel_6_0_0_mergeback

    Rel 6 0 0 mergeback

commit d4bc6febb39d5fdd240bb3dee9c381d5003507bf
Author: Tadgh <[email protected]>
Date:   Thu May 19 13:34:29 2022 -0700

    Bump java version for test

commit af842619b0f9de2684a633c49e9078416b231d5a
Author: Tadgh <[email protected]>
Date:   Thu May 19 12:59:22 2022 -0700

    Fix reindex provider

commit 5942823f17f6cdf0e6c0888b16db0dcac9908db4
Author: Tadgh <[email protected]>
Date:   Thu May 19 11:56:14 2022 -0700

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

commit 2a71578516a35db18951331e764dd23602a9bcb0
Merge: 12ea07b 244113b
Author: Tadgh <[email protected]>
Date:   Thu May 19 10:43:51 2022 -0700

    Merge branch 'master' into rel_6_0_0_mergeback

commit 12ea07b460bdf71dbf92e4d198a1869e6dbc75e5
Author: Tadgh <[email protected]>
Date:   Mon May 16 15:45:49 2022 -0700

    make lastN test pass

commit 87585ec7cc3d17c2bc4b51cc148f2537031244c2
Author: Jaison Baskaran <[email protected]>
Date:   Mon May 16 16:18:30 2022 -0600

    hibernate search application properties updates.

commit ffd0cb1a4f8a662f01058ce5bf7a5101c5298241
Author: Tadgh <[email protected]>
Date:   Mon May 16 14:26:52 2022 -0700

    Bump ES version

commit cd0b8d7392ceaef13a68aa9f56fb038489f0152f
Author: Tadgh <[email protected]>
Date:   Mon May 16 09:57:30 2022 -0700

    Bump pom and minimum java version

commit 244113ba67d99b414f2c1bba6379145c16b922dd
Author: Dennis Verspuij <[email protected]>
Date:   Mon May 9 21:39:56 2022 +0200

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

commit 91e4105fd8c0c900e552633fbe02d436564b8675
Author: Alejandro Medina <[email protected]>
Date:   Fri May 6 12:25:51 2022 -0400

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

    Co-authored-by: Alejandro Medina <[email protected]>

commit fdfa6fd711f411c58b9175223c05141cea0598fe
Author: chgl <[email protected]>
Date:   Sun May 1 21:48:18 2022 +0200

    Expose Prometheus metrics (#355)

commit f736b6d8e63bd6bf802eeec57614fd768629a116
Author: Michael Buckley <[email protected]>
Date:   Fri Apr 29 08:57:37 2022 -0400

    Bump to hapi PRE11

commit 51cf27a4f9a6385bd47895a88dd6d1482d9a6768
Merge: 3a880ee 1a52897
Author: Patrick Werner <[email protected]>
Date:   Wed Apr 20 20:00:00 2022 +0200

    Merge pull request #321 from MacL3an/patch-3

    Added instructions about removing Hibernate dialect

commit 3a880ee42cd6f9c0a7e193acf5c76b804e84febc
Merge: c607a98 c8da589
Author: michaelabuckley <[email protected]>
Date:   Wed Apr 20 13:19:01 2022 -0400

    Merge pull request #353 from hapifhir/advanced-lucene-disclaimer

    Add disclaimer for advanced_lucene_indexing

commit b589542519a06a04c1e739b35ec3ff2b7f32ae5c
Merge: ae724f4 f1e18d2
Author: michaelabuckley <[email protected]>
Date:   Wed Apr 20 12:35:04 2022 -0400

    Merge pull request #352 from hapifhir/mb-turn-off-lucene

    Revert accidental default activation of experimental lucene indexing

commit c8da589636ca510445310efb36692806cb8b8a7b
Author: Patrick Werner <[email protected]>
Date:   Wed Apr 20 18:31:37 2022 +0200

    Add disclaimer for advanced_lucene_indexing

    added warning to     advanced_lucene_indexing: false property

commit f1e18d200a2656db37a81dd355909bf1fd9b587b
Author: Michael Buckley <[email protected]>
Date:   Wed Apr 20 12:23:10 2022 -0400

    Revert accidental default activation of experimental lucene indexing

commit c607a98728b2eb79bf73b266e3457bbab7f44e3c
Author: chgl <[email protected]>
Date:   Fri Apr 15 19:28:53 2022 +0200

    Updated to HAPI FHIR version 5.7.2 (#349)

commit ae724f417224c41fb6ab6eb527b1e5f9d522a86e
Author: Jaison Baskaran <[email protected]>
Date:   Wed Apr 13 08:54:11 2022 -0600

    Bump to PRE10

commit 21165ccfaa82748e22cde939cdee8e98437c1ce2
Merge: bf51c22 da319e8
Author: Patrick Werner <[email protected]>
Date:   Wed Apr 13 13:52:06 2022 +0200

    Merge pull request #337 from hapifhir/feature/spring-boot-actuator

    Add actuator

commit bf51c2263af48f1a5927363d45c136068c78bd21
Author: Jens Kristian Villadsen <[email protected]>
Date:   Mon Apr 11 20:00:06 2022 +0200

    Update application.yaml

    Reverted to sane defaults

commit 4bed69fedfd1f3021c1ecdae388dfee9067073e2
Author: chgl <[email protected]>
Date:   Mon Apr 11 17:56:32 2022 +0200

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

commit bb21ccfe90e5e40b86587bcf9b04cda08114b878
Author: dotasek <[email protected]>
Date:   Mon Apr 11 11:47:09 2022 -0400

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

    Co-authored-by: dotasek <[email protected]>

commit cdda71b25320afa83538c2c6d88e097bedbfaa70
Author: craig mcclendon <[email protected]>
Date:   Sat Apr 9 12:19:44 2022 -0500

    add support for ms sql server (#347)

commit 6b3f57cf12a1f264a9ef9ce9bcd885de0a67d269
Author: Jens Kristian Villadsen <[email protected]>
Date:   Thu Apr 7 22:32:38 2022 +0200

    Update application.yaml (#345)

commit 49401c0d3dbd52c9a5b8ac3c9c4407fcb973a367
Author: Jaison Baskaran <[email protected]>
Date:   Tue Mar 29 15:16:08 2022 -0600

    Bump to PRE9

commit da319e8761ed2ef017ed5e9dcbde489a99489123
Author: craig mcclendon <[email protected]>
Date:   Wed Mar 23 14:12:48 2022 -0500

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

    Co-authored-by: Craig McClendon <[email protected]>

commit 403b87573d6381e85186f8d3c1f4226052fdae98
Author: Michael Buckley <[email protected]>
Date:   Wed Mar 23 10:34:42 2022 -0400

    Bump to PRE8

commit aeef4b176c0a48065c6190f6b56d27a45a62db33
Author: jkv <[email protected]>
Date:   Sun Mar 20 21:22:36 2022 +0100

    Add actuator

commit 146b9f68ac92ae62da878de36450bd7619d016ff
Author: Jaison Baskaran <[email protected]>
Date:   Wed Mar 9 09:03:10 2022 -0700

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

commit 929a3535fa93d33b24cef06ed4158ae2fcb9f6a2
Author: Jens Kristian Villadsen <[email protected]>
Date:   Tue Mar 8 10:44:13 2022 +0100

    Update application.yaml

    Roll back - mistake from my side

commit 0483db9195057326a574b29af654f8da0b1cfee1
Author: Jens Kristian Villadsen <[email protected]>
Date:   Tue Mar 8 10:42:52 2022 +0100

    Update application.yaml

commit 40d7b9ce27355fedb3fb70fcd79a09d7bd8290bb
Author: Patrick Werner <[email protected]>
Date:   Mon Mar 7 13:20:06 2022 +0100

    added reindexProvider to Config (#326)

commit 7db15103fe4790817588e74a099126e8008b620f
Author: Joel Schneider (NMDP) <[email protected]>
Date:   Fri Mar 4 04:38:16 2022 -0600

    add dao_scheduling_enabled configuration property (#324)

commit 24a20a7e973aef9674204bbce202cac860d9a472
Author: Jens Kristian Villadsen <[email protected]>
Date:   Wed Mar 2 16:39:13 2022 +0100

    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

commit 31ed166ab97adef2eebbfe137d82078fcadd961c
Merge: 810b090 28e86bd
Author: Michael Buckley <[email protected]>
Date:   Mon Feb 28 14:41:03 2022 -0500

    Merge branch 'nih-testing' into rel_6_0_0

    * nih-testing:
     register the ValueSet provider.

commit 810b090846d6c2365d709ed119745cd3d293778d
Author: Ken Stevens <[email protected]>
Date:   Wed Feb 23 17:24:21 2022 -0500

    fix to work with latest hapi-fhir

commit f2ba86d7db3780b3be0028c04cb0d0be8f7b0105
Author: Tadgh <[email protected]>
Date:   Wed Feb 23 09:29:22 2022 -0800

    Move to newlines

commit 28e86bdb8ddb10fb0cb3d906a6b8a25cb8c12d47
Author: Jaison Baskaran <[email protected]>
Date:   Wed Feb 23 09:38:42 2022 -0700

    Bump HAPI-FHIR version

commit 1a528978b87bc8c78420fac4281cc1e01d7a3b21
Author: Håkan MacLean <[email protected]>
Date:   Tue Feb 22 09:36:41 2022 +0100

    Added instructions about removing Hibernate dialect

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

commit 0e4926e59bd3aaef09a424fc709f1077cc05dd8c
Author: Tadgh <[email protected]>
Date:   Mon Feb 21 16:24:08 2022 -0800

    Remove search coord thread pool

commit 94f47f4736df7293c44336462139ed17dee947d4
Author: Tadgh <[email protected]>
Date:   Mon Feb 21 16:13:35 2022 -0800

    Bump version

commit deefd595dd0189efe9f1945a7aac7757a04f3cba
Merge: 3fd8803 a6abfb9
Author: Tadgh <[email protected]>
Date:   Mon Feb 21 14:27:49 2022 -0800

    Merge pull request #316 from hapifhir/rel_5_7

    Rel 5 7

commit a6abfb9e24e291391f6b1d0d6cd9bcaeef1dac36
Merge: fa8999b 3fd8803
Author: Tadgh <[email protected]>
Date:   Thu Feb 17 17:5…
hankwallace added a commit to elimuinformatics/hapi-fhir-jpaserver-starter that referenced this issue Feb 26, 2024
@hankwallace @fil512
@tadgh @markiantorno @chgl @ibrohimislam @KevinDougan @patrick-werner @amuslim-fn @jkiddo @dependabot @Thopap @rti @jmarchionatto @michaelabuckley @Kai-W @XcrigX @jamesagnew @lukedegruchy @inspector-cochise @psavva @juvarabrera @dotasek @Bert-R @Capt-Mac @JPercival @shubhamparikh927 @janol77 @dennisverspuij @ashaban @vadi2 @jaison-b @MacL3an @jschneid-nmdp @shubham927-ht @petermicuch @vladonemo @seanmcilvenna @jvitrifork @ShubhamParikh9 @ZuSe @dimon37 @vsinghht @winne42 @winfriedgerlach @HussamNujaim @barhodes @c-schuler @semicolin @costateixeira
Updates the dev branch from master (#83)
4da798f 
* 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 <[email protected]>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <[email protected]>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <[email protected]>

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: michaelabuckley <[email protected]>
Co-authored-by: juan.marchionatto <[email protected]>
Co-authored-by: Tadgh <[email protected]>

* 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.

* Spelling error in Application.yaml

Fix spelling error in comments section

* configuration option to not reload IG resources that are already loaded

* Update docker-compose sample with small application.properties

When running from Docker Hub, it is not convenient to have to copy the full application.yaml as a starting point. Based on Spring's property initialization order, it's possible to mount a small version of application.yaml in the config folder in the run directory.

* Removed explicit inclusion of snakeyaml and allow spring-boot-starter-actuator to pull it in as a needed dependency.

* Simplify using an interceptor with Docker

Now it is possible to mount a folder with extra classes that are loaded
by HAPI. This makes it easy to load an interceptor JAR while using the
standard Docker image. The README explains how to use it.

Spring by default uses the WarLauncher. Now the ENTRYPOINT uses the
PropertiesLauncher, configured in such a way that it is compatible with
the WarLauncher, but adding the folder /app/extra-classes to the
loader.path.

* Update pom.xml

Update to 6.4.1

* Update pom.xml

* Update pom.xml

* 497 - Fix typo on property setter.

* Create smoke-tests.yml

* Update smoke-tests.yml

Don't do integration tests.

Start server
Run smoke tests
Stop Server

* Rename plain_server.rest to plain_server.http

* Update smoke-tests.yml

Skip maven tests
Wait longer for server

* Update smoke-tests.yml

Wait longer just in case

Maybe don't kill the jetty server?

* Use docker for HTTP client

* Try fixing TTY issue

* Sleep a little longer...

* Additional param for linux localhost

* Intentional failure

* Restore reasonable sleep time

* Bump HAPI to release 6.6.0 (#539)

* Start tracking 6.5

* Use JpaStorageSettings and StorageSettings

* Bump parent pom version + add deps for jaxb

* Bump HAPI

* Fix Subscription/Topic resource creation

* fix subscription topic beans

* Change to rel_6_6 hapi-fhir SNAPSHOT

* Fix emailSender config

* Split method calls by line.

* Merge pull request #524 from hapifhir/do-20230509-smoke-test-ci

Create smoke-tests.yml

* Bump core to release 6.6.0

---------

Co-authored-by: Michael Buckley <[email protected]>
Co-authored-by: Kevin Dougan SmileCDR <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
Co-authored-by: Mark Iantorno <[email protected]>

* Add fix to enable the CR module.

* Addressed comment to for cr_enabled flag.

* remove unused imports

* Addressing https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/486 and https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/485

* add cr operation loader

* adding factories and beans for cr

* add factories for cr

* update integration tests and appproperties

* Revert provider loader

* add factory loader

* complete config for cr

* remove unused imports, update config

* rename classes

* remove annotation and repositoryfactory

* Renaming operations

* Post init provider registerer

* Spring boot banner is updated to use log instead of console. (#57)

* add cql translator options

* add cqlconfigbeans

* Add empty map for tester

* Updates our fork to v6.6.0 from the upstream repo (#59)

* Bump to PRE8

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

Co-authored-by: Craig McClendon <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <[email protected]>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <[email protected]>

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: michaelabuckley <[email protected]>
Co-authored-by: juan.marchionatto <[email protected]>
Co-authored-by: Tadgh <[email protected]>

* 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

* updated dockerfile to use root user before creating directory

* 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.

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

* Spelling error in Application.yaml

Fix spelling error in comments section

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <[email protected]>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <[email protected]>

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: michaelabuckley <[email protected]>
Co-authored-by: juan.marchionatto <[email protected]>
Co-authored-by: Tadgh <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Vladimir Nemergut <[email protected]>
Co-authored-by: jamesagnew <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: jvi <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
Co-authored-by: Jens Kristian Villadsen <[email protected]>

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Vladimir Nemergut <[email protected]>
Co-authored-by: jamesagnew <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: jvi <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
Co-authored-by: Jens Kristian Villadsen <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Vladimir Nemergut <[email protected]>
Co-authored-by: jamesagnew <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: jvi <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
Co-authored-by: Jens Kristian Villadsen <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Vladimir Nemergut <[email protected]>
Co-authored-by: jamesagnew <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: jvi <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
Co-authored-by: Jens Kristian Villadsen <[email protected]>

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <[email protected]>

* Update src/test/smoketest/SMOKE_TEST.md

Co-authored-by: Ken Stevens <[email protected]>

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Vladimir Nemergut <[email protected]>
Co-authored-by: jamesagnew <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: jvi <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
Co-authored-by: Jens Kristian Villadsen <[email protected]>

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Vladimir Nemergut <[email protected]>
Co-authored-by: jamesagnew <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: jvi <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
Co-authored-by: Jens Kristian Villadsen <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Vladimir Nemergut <[email protected]>
Co-authored-by: jamesagnew <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: jvi <[email protected]>
Co-authored-by: Sean McIlvenna <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
Co-authored-by: Jens Kristian Villadsen <[email protected]>

* 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] <[email protected]>

* 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

* …
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jkiddo commented Apr 17, 2024

Fixed in #605

@jkiddo jkiddo closed this as completed Apr 17, 2024
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