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Implement FHIR Types in Java #2989

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@alexanderkiel alexanderkiel commented Sep 30, 2025

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@alexanderkiel alexanderkiel marked this pull request as draft September 30, 2025 14:56
@alexanderkiel alexanderkiel self-assigned this Sep 30, 2025
@alexanderkiel alexanderkiel force-pushed the fhir-types-java branch 5 times, most recently from 0c03fa1 to ab2c3e8 Compare October 1, 2025 10:08
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codecov bot commented Oct 1, 2025 •
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Codecov Report

❌ Patch coverage is 96.79144% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 95.86%. Comparing base (f6ead9f) to head (db0a0cd).

Files with missing lines Patch % Lines
...les/db/src/blaze/db/impl/search_param/quantity.clj 88.23% 2 Missing ⚠️
modules/fhir-path/src/blaze/fhir_path.clj 94.11% 1 Missing and 1 partial ⚠️
...dules/cql/src/blaze/elm/compiler/reusing_logic.clj 95.00% 0 Missing and 1 partial ⚠️
modules/db/src/blaze/db/node/resource_indexer.clj 75.00% 0 Missing and 1 partial ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #2989      +/-   ##
==========================================
+ Coverage   95.50%   95.86%   +0.35%     
==========================================
  Files         401      397       -4     
  Lines       25430    24679     -751     
  Branches      714      633      -81     
==========================================
- Hits        24288    23659     -629     
+ Misses        539      499      -40     
+ Partials      603      521      -82
Files with missing lines Coverage Δ
modules/admin-api/src/blaze/admin_api.clj 97.05% <100.00%> (ø)
...dules/cql/src/blaze/elm/compiler/external_data.clj 88.80% <100.00%> (+1.39%) ⬆️
...s/cql/src/blaze/elm/compiler/structured_values.clj 89.36% <100.00%> (-1.71%) ⬇️
...ules/cql/src/blaze/elm/compiler/type_operators.clj 88.23% <100.00%> (ø)
modules/cql/src/blaze/elm/ts_util.clj 100.00% <100.00%> (ø)
modules/db/src/blaze/db/impl/search_param.clj 98.88% <100.00%> (-0.02%) ⬇️
modules/db/src/blaze/db/impl/search_param/date.clj 98.25% <100.00%> (ø)
modules/db/src/blaze/db/impl/search_param/near.clj 100.00% <100.00%> (ø)
...dules/db/src/blaze/db/impl/search_param/number.clj 100.00% <100.00%> (ø)
...dules/db/src/blaze/db/impl/search_param/string.clj 98.33% <100.00%> (+1.66%) ⬆️
... and 65 more

... and 20 files with indirect coverage changes

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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
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@alexanderkiel alexanderkiel force-pushed the fhir-types-java branch 14 times, most recently from ceed128 to 80f43dd Compare October 6, 2025 10:34
@alexanderkiel alexanderkiel force-pushed the fhir-types-java branch 8 times, most recently from b7c7c6f to cd4e8ff Compare October 12, 2025 07:59
@alexanderkiel alexanderkiel force-pushed the fhir-types-java branch 2 times, most recently from 74c9d6e to 5e07af8 Compare December 14, 2025 19:53
@alexanderkiel alexanderkiel mentioned this pull request Dec 15, 2025
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@alexanderkiel alexanderkiel force-pushed the fhir-types-java branch 4 times, most recently from 4dcf4ed to fbc30a4 Compare December 28, 2025 14:44
@alexanderkiel alexanderkiel force-pushed the fhir-types-java branch 4 times, most recently from 1bc29fc to 0d55bd9 Compare December 30, 2025 13:55
@alexanderkiel alexanderkiel force-pushed the fhir-types-java branch 4 times, most recently from a0f9726 to b6255ca Compare January 9, 2026 11:37
@alexanderkiel alexanderkiel requested a review from knoppiks January 9, 2026 11:37
@alexanderkiel alexanderkiel marked this pull request as ready for review January 9, 2026 11:37
@alexanderkiel alexanderkiel force-pushed the fhir-types-java branch 4 times, most recently from d106b2e to ffe9fe2 Compare January 9, 2026 18:54
knoppiks
knoppiks requested changes Jan 12, 2026
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docs/deployment/environment-variables.md
**Default:** 128

#### `DB_RESOURCE_CACHE_SIZE` <Badge type="warning" text="Since 0.8"/>
#### `DB_RESOURCE_CACHE_SIZE` <Badge type="warning" text="Since 0.8"/> <Badge type="danger" text="unreleased"/>
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@knoppiks knoppiks Jan 9, 2026

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Unreleased AND deprecated? For those who used the development versions?

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@alexanderkiel alexanderkiel Jan 13, 2026

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yes the deprecation is unreleased

Dockerfile Outdated
@@ -1,4 +1,4 @@
FROM eclipse-temurin:21.0.9_10-jre-noble@sha256:67fc762eabacb56e5444b367889e04ce8c839b8f4b3d8ef3e459c5579fbefd8a
FROM eclipse-temurin:25-jre-noble
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@knoppiks knoppiks Jan 12, 2026

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eclipse-temurin:25 no longer ships curl. This will probably break docker compose health checks.

modules/fhir-structure/java/blaze/fhir/spec/type/Base.java Outdated
Keyword FHIR_TYPE_BUNDLE_ENTRY = RT.keyword("fhir.Bundle", "entry");

int MEM_SIZE_OBJECT_HEADER = 8;
int MEM_SIZE_PERSISTENT_VECTOR_OBJECT = 40;
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@knoppiks knoppiks Jan 12, 2026

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Looks like magic numbers, can we document them?

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@alexanderkiel alexanderkiel Jan 13, 2026

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done

modules/fhir-structure/java/blaze/fhir/spec/type/Base.java Outdated
hashIntoMap(m, sink);
break;
case List<?> l:
sink.putByte((byte) 36);
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@knoppiks knoppiks Jan 12, 2026

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another HASH_MARKER?

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@alexanderkiel alexanderkiel Jan 13, 2026

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done

@alexanderkiel alexanderkiel force-pushed the fhir-types-java branch 4 times, most recently from 685e90e to 540b697 Compare January 13, 2026 17:08
@alexanderkiel alexanderkiel marked this pull request as draft January 14, 2026 09:15
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