From e1c2d6c00dd1343a8193f4c113bc10ee7a7f897f Mon Sep 17 00:00:00 2001 From: Michele Adduci Date: Wed, 6 Nov 2024 15:15:39 +0100 Subject: [PATCH 01/10] Updated dependencies, bumped SpringBoot to 3.3.5 --- pom.xml | 77 ++++++++++++++++++++++++++++++--------------------------- 1 file changed, 41 insertions(+), 36 deletions(-) diff --git a/pom.xml b/pom.xml index cc6e2894400..fd50c6c7ee0 100644 --- a/pom.xml +++ b/pom.xml @@ -957,6 +957,11 @@ Ibrahim Trifork A/S + + madduci + Michele Adduci + gematik GmbH + @@ -1017,49 +1022,49 @@ 3.0.2 5.10.1 0.64.8 - 9.4.0 - 6.4.1.Final - 1.4.14 + 10.20.1 + 6.6.1.Final + 1.5.12 - 7.0.0.Final + 7.2.1.Final - 9.8.0 + 9.12.0 2.2 8.0.0.Final - 4.4.13 - 4.5.13 - 2.17.1 - 2.17.1 + 4.4.16 + 4.5.14 + 2.18.1 + 2.18.1 3.3.0 1.8 4.12.0 - 2.8.0 + 2.9.0 4.1.2 1.4 - 6.2.9.Final + 6.2.10.Final 7.1.2 9.5.4 2.13.0 0.9.11 9.8.0-15 1.2_5 - 2.2.22 - 2.0.13 - 2.19.0 - 6.1.8 - 2023.1.6 + 2.2.25 + 2.0.16 + 2.24.1 + 6.1.14 + 2024.0.5 4.3.10 - 3.2.6 - 2.0.6 + 3.3.5 + 2.0.10 2.9.0 3.1.4 - 1.19.3 + 1.20.3 3.1.2.RELEASE 4.4.1 UTF-8 1.0.1 - 1.44.0 - 8.14.3 + 1.52.0 + 8.15.3 1.0.8 @@ -1167,18 +1172,18 @@ com.googlecode.owasp-java-html-sanitizer owasp-java-html-sanitizer - 20211018.2 + 20240325.1 com.graphql-java graphql-java - 21.5 + 22.3 org.simplejavamail simple-java-mail - 8.11.2 + 8.12.2 com.github.bbottema @@ -1277,14 +1282,14 @@ com.squareup.okio okio-jvm - 3.4.0 + 3.9.1 com.tngtech.archunit archunit-junit5 - 1.0.1 + 1.3.0 test @@ -1310,7 +1315,7 @@ commons-cli commons-cli - 1.5.0 + 1.9.0 commons-codec @@ -1355,7 +1360,7 @@ org.jetbrains annotations - 23.0.0 + 26.0.1 commons-io @@ -1486,12 +1491,12 @@ com.mysql mysql-connector-j - 8.2.0 + 9.1.0 org.springdoc springdoc-openapi-starter-webmvc-ui - 2.2.0 + 2.6.0 net.sf.json-lib @@ -2167,17 +2172,17 @@ org.webjars.npm ace-builds - 1.22.0 + 1.36.3 org.webjars.npm bootstrap - 4.5.2 + 4.6.2 org.webjars Eonasdan-bootstrap-datetimepicker - 4.17.47 + 4.17.49 * @@ -2188,7 +2193,7 @@ org.webjars font-awesome - 5.8.2 + 5.15.4 org.webjars.bower @@ -2229,12 +2234,12 @@ org.webjars swagger-ui - 4.1.3 + 4.19.1 org.xmlunit xmlunit-core - 2.4.0 + 2.10.0 org.testcontainers From e11ba49685644ccac9573c5dc6235097a817e73c Mon Sep 17 00:00:00 2001 From: Michele Adduci Date: Thu, 7 Nov 2024 05:53:20 +0100 Subject: [PATCH 02/10] Fixing compilation issues, added changelog --- .../hapi/fhir/changelog/7_8_0/changes.yaml | 33 +++++++++++++++++++ .../uhn/fhir/jpa/dao/search/PathContext.java | 24 ++++++++++++++ .../ResourceIndexedSearchParamCoords.java | 2 -- .../ResourceIndexedSearchParamDate.java | 2 -- .../ResourceIndexedSearchParamNumber.java | 2 -- .../ResourceIndexedSearchParamQuantity.java | 2 -- ...eIndexedSearchParamQuantityNormalized.java | 2 -- .../ResourceIndexedSearchParamString.java | 2 -- .../ResourceIndexedSearchParamToken.java | 2 -- .../entity/ResourceIndexedSearchParamUri.java | 2 -- 10 files changed, 57 insertions(+), 16 deletions(-) diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml index 0331ee9c487..98c799e5d04 100644 --- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml @@ -5,4 +5,37 @@ (dependent HAPI modules listed in brackets):
  • org.hl7.fhir.core (Base): 6.3.25 -> 6.4.0
    • +
  • spring-boot-bom (Base): 3.2.6 -> 3.3.5
    • +
  • spring-retry (Base): 2.0.6 -> 2.0.10
    • +
  • spring-data-bom (Base): 2023.1.6 -> 2024.0.5
    • +
  • spring (Base): 6.1.8 -> 6.1.14
    • +
  • slf4j-api (Base): 2.0.13 -> 2.0.16
    • +
  • log4j-to-slf4j (Base): 2.19.0 -> 2.24.1
    • +
  • jackson (Base): 2.17.1 -> 2.18.1
    • +
  • jackson-databind (Base): 2.17.1 -> 2.18.1
    • +
  • opentelemetry-instrumentation-bom (Base): 2.8.0 -> 2.9.0
    • +
  • resteasy (Base): 6.2.9.Final -> 6.2.10.Final
    • +
  • flyway (Base): 9.4.0 -> 10.20.1
    • +
  • hibernate (Base): 6.4.1.Final -> 6.6.1.Final
    • +
  • hibernate-search (Base): 7.0.0.Final -> 7.2.1.Final
    • +
  • logback-classic (Base): 1.4.14 -> 1.5.12
    • +
  • owasp-java-html-sanitizer (Base): 20211018.2 -> 20240325.1
    • +
  • graphql-java (Base): 21.5 -> 22.3
    • +
  • simple-java-mail (Base): 8.11.2 -> 8.12.2
    • +
  • okio-jvm (Base): 3.4.0 -> 3.9.1
    • +
  • commons-cli (Base): 1.5.0 -> 1.9.0
    • +
  • org.jetbrains.annotations (Base): 23.0.0 -> 26.0.1
    • +
  • mysql-connector-j (Base): 8.2.0 -> 9.1.0
    • +
  • springdoc-openapi-starter-webmvc-ui (Base): 2.2.0 -> 2.6.0
    • +
  • ace-builds (Base): 1.22.0 -> 1.36.3
    • +
  • bootstrap (Base): 4.5.2 -> 4.6.2
    • +
  • Eonasdan-bootstrap-datetimepicker (Base): 4.17.47 -> 4.17.49
    • +
  • font-awesome (Base): 5.8.2 -> 5.15.4
    • +
  • swagger-ui (Base): 4.1.3 -> 4.19.1
    • +
  • xmlunit-core (Base): 2.4.0 -> 2.10.0
    • +
  • elastic-apm (Base): 1.44.0 -> 1.52.0
    • +
  • elastic-search (Base): 8.14.3 -> 8.15.3
    • +
  • lucene (Base): 9.8.0 -> 9.12.0
    • +
  • httpcore (Base): 4.4.13 -> 4.4.16
    • +
  • httpclient (Base): 4.5.13 -> 4.5.14
" diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/PathContext.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/PathContext.java index 3576e9b7908..0aee74c4411 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/PathContext.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/PathContext.java @@ -20,9 +20,11 @@ package ca.uhn.fhir.jpa.dao.search; import jakarta.annotation.Nonnull; +import org.hibernate.search.engine.search.common.NamedValues; import org.hibernate.search.engine.search.predicate.SearchPredicate; import org.hibernate.search.engine.search.predicate.dsl.BooleanPredicateClausesStep; import org.hibernate.search.engine.search.predicate.dsl.ExistsPredicateFieldStep; +import org.hibernate.search.engine.search.predicate.dsl.KnnPredicateFieldStep; import org.hibernate.search.engine.search.predicate.dsl.MatchAllPredicateOptionsStep; import org.hibernate.search.engine.search.predicate.dsl.MatchIdPredicateMatchingStep; import org.hibernate.search.engine.search.predicate.dsl.MatchNonePredicateFinalStep; @@ -34,6 +36,8 @@ import org.hibernate.search.engine.search.predicate.dsl.NestedPredicateOptionsSt import org.hibernate.search.engine.search.predicate.dsl.NotPredicateFinalStep; import org.hibernate.search.engine.search.predicate.dsl.PhrasePredicateFieldStep; import org.hibernate.search.engine.search.predicate.dsl.PredicateFinalStep; +import org.hibernate.search.engine.search.predicate.dsl.PrefixPredicateFieldStep; +import org.hibernate.search.engine.search.predicate.dsl.QueryStringPredicateFieldStep; import org.hibernate.search.engine.search.predicate.dsl.RangePredicateFieldStep; import org.hibernate.search.engine.search.predicate.dsl.RegexpPredicateFieldStep; import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory; @@ -221,6 +225,11 @@ class PathContext implements SearchPredicateFactory { return myPredicateFactory.wildcard(); } + @Override + public PrefixPredicateFieldStep prefix() { + return myPredicateFactory.prefix(); + } + @Override public RegexpPredicateFieldStep regexp() { return myPredicateFactory.regexp(); @@ -246,6 +255,11 @@ class PathContext implements SearchPredicateFactory { return myPredicateFactory.simpleQueryString(); } + @Override + public QueryStringPredicateFieldStep queryString() { + return myPredicateFactory.queryString(); + } + @Override public ExistsPredicateFieldStep exists() { return myPredicateFactory.exists(); @@ -262,6 +276,16 @@ class PathContext implements SearchPredicateFactory { return myPredicateFactory.named(path); } + @Override + public KnnPredicateFieldStep knn(int i) { + return myPredicateFactory.knn(i); + } + + @Override + public PredicateFinalStep withParameters(Function function) { + return myPredicateFactory.withParameters(function); + } + @Override public T extension(SearchPredicateFactoryExtension extension) { return myPredicateFactory.extension(extension); diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamCoords.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamCoords.java index 647490860ab..a0c210d1bef 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamCoords.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamCoords.java @@ -24,7 +24,6 @@ import ca.uhn.fhir.jpa.model.listener.IndexStorageOptimizationListener; import ca.uhn.fhir.model.api.IQueryParameterType; import jakarta.annotation.Nullable; import jakarta.persistence.Column; -import jakarta.persistence.Embeddable; import jakarta.persistence.Entity; import jakarta.persistence.EntityListeners; import jakarta.persistence.FetchType; @@ -42,7 +41,6 @@ import org.apache.commons.lang3.builder.ToStringBuilder; import org.apache.commons.lang3.builder.ToStringStyle; import org.hibernate.annotations.GenericGenerator; -@Embeddable @EntityListeners(IndexStorageOptimizationListener.class) @Entity @Table( diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamDate.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamDate.java index 3a98bc66dfe..ed6de776b5f 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamDate.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamDate.java @@ -28,7 +28,6 @@ import ca.uhn.fhir.rest.param.DateParam; import ca.uhn.fhir.rest.param.DateRangeParam; import ca.uhn.fhir.util.DateUtils; import jakarta.persistence.Column; -import jakarta.persistence.Embeddable; import jakarta.persistence.Entity; import jakarta.persistence.EntityListeners; import jakarta.persistence.FetchType; @@ -56,7 +55,6 @@ import java.text.ParseException; import java.text.SimpleDateFormat; import java.util.Date; -@Embeddable @EntityListeners(IndexStorageOptimizationListener.class) @Entity @Table( diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamNumber.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamNumber.java index 393ab64d60e..8a6a8417d0b 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamNumber.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamNumber.java @@ -24,7 +24,6 @@ import ca.uhn.fhir.jpa.model.listener.IndexStorageOptimizationListener; import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.rest.param.NumberParam; import jakarta.persistence.Column; -import jakarta.persistence.Embeddable; import jakarta.persistence.Entity; import jakarta.persistence.EntityListeners; import jakarta.persistence.FetchType; @@ -48,7 +47,6 @@ import org.hibernate.type.SqlTypes; import java.math.BigDecimal; import java.util.Objects; -@Embeddable @EntityListeners(IndexStorageOptimizationListener.class) @Entity @Table( diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java index 02129a99600..4ec11e41f3c 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java @@ -24,7 +24,6 @@ import ca.uhn.fhir.jpa.model.listener.IndexStorageOptimizationListener; import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.rest.param.QuantityParam; import jakarta.persistence.Column; -import jakarta.persistence.Embeddable; import jakarta.persistence.Entity; import jakarta.persistence.EntityListeners; import jakarta.persistence.FetchType; @@ -50,7 +49,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString; import static org.apache.commons.lang3.StringUtils.isBlank; // @formatter:off -@Embeddable @EntityListeners(IndexStorageOptimizationListener.class) @Entity @Table( diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java index 86ec8a7d9bd..8666cff8171 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java @@ -25,7 +25,6 @@ import ca.uhn.fhir.jpa.model.util.UcumServiceUtil; import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.rest.param.QuantityParam; import jakarta.persistence.Column; -import jakarta.persistence.Embeddable; import jakarta.persistence.Entity; import jakarta.persistence.EntityListeners; import jakarta.persistence.FetchType; @@ -52,7 +51,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString; import static org.apache.commons.lang3.StringUtils.isBlank; // @formatter:off -@Embeddable @EntityListeners(IndexStorageOptimizationListener.class) @Entity @Table( diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamString.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamString.java index 5d5466291c6..c1e5240bf8b 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamString.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamString.java @@ -27,7 +27,6 @@ import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.rest.param.StringParam; import ca.uhn.fhir.util.StringUtil; import jakarta.persistence.Column; -import jakarta.persistence.Embeddable; import jakarta.persistence.Entity; import jakarta.persistence.EntityListeners; import jakarta.persistence.ForeignKey; @@ -48,7 +47,6 @@ import static ca.uhn.fhir.jpa.model.util.SearchParamHash.hashSearchParam; import static org.apache.commons.lang3.StringUtils.defaultString; // @formatter:off -@Embeddable @EntityListeners(IndexStorageOptimizationListener.class) @Entity @Table( diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamToken.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamToken.java index 50cd671dcb4..3f93d696974 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamToken.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamToken.java @@ -26,7 +26,6 @@ import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.rest.api.Constants; import ca.uhn.fhir.rest.param.TokenParam; import jakarta.persistence.Column; -import jakarta.persistence.Embeddable; import jakarta.persistence.Entity; import jakarta.persistence.EntityListeners; import jakarta.persistence.FetchType; @@ -52,7 +51,6 @@ import static ca.uhn.fhir.jpa.model.util.SearchParamHash.hashSearchParam; import static org.apache.commons.lang3.StringUtils.defaultString; import static org.apache.commons.lang3.StringUtils.trim; -@Embeddable @EntityListeners(IndexStorageOptimizationListener.class) @Entity @Table( diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamUri.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamUri.java index 0db8b2ad2b3..95329046bc8 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamUri.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamUri.java @@ -25,7 +25,6 @@ import ca.uhn.fhir.jpa.model.listener.IndexStorageOptimizationListener; import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.rest.param.UriParam; import jakarta.persistence.Column; -import jakarta.persistence.Embeddable; import jakarta.persistence.Entity; import jakarta.persistence.EntityListeners; import jakarta.persistence.FetchType; @@ -47,7 +46,6 @@ import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextFi import static ca.uhn.fhir.jpa.model.util.SearchParamHash.hashSearchParam; import static org.apache.commons.lang3.StringUtils.defaultString; -@Embeddable @EntityListeners(IndexStorageOptimizationListener.class) @Entity @Table( From d8be4eb07372962b3208f9698a9bd71039346704 Mon Sep 17 00:00:00 2001 From: Michele Adduci Date: Thu, 7 Nov 2024 05:59:31 +0100 Subject: [PATCH 03/10] Fixing compilation issues, updated changelog, Postgres and Oracle drivers --- .../uhn/hapi/fhir/changelog/7_8_0/changes.yaml | 16 +++++++++------- .../jpa/model/entity/ResourceHistoryTag.java | 1 - pom.xml | 4 ++-- 3 files changed, 11 insertions(+), 10 deletions(-) diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml index 98c799e5d04..a1bc47cb8c7 100644 --- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml @@ -15,9 +15,6 @@
  • jackson-databind (Base): 2.17.1 -> 2.18.1
  • opentelemetry-instrumentation-bom (Base): 2.8.0 -> 2.9.0
  • resteasy (Base): 6.2.9.Final -> 6.2.10.Final
    • -
  • flyway (Base): 9.4.0 -> 10.20.1
    • -
  • hibernate (Base): 6.4.1.Final -> 6.6.1.Final
    • -
  • hibernate-search (Base): 7.0.0.Final -> 7.2.1.Final
  • logback-classic (Base): 1.4.14 -> 1.5.12
  • owasp-java-html-sanitizer (Base): 20211018.2 -> 20240325.1
  • graphql-java (Base): 21.5 -> 22.3
    • @@ -25,7 +22,6 @@
  • okio-jvm (Base): 3.4.0 -> 3.9.1
  • commons-cli (Base): 1.5.0 -> 1.9.0
  • org.jetbrains.annotations (Base): 23.0.0 -> 26.0.1
    • -
  • mysql-connector-j (Base): 8.2.0 -> 9.1.0
  • springdoc-openapi-starter-webmvc-ui (Base): 2.2.0 -> 2.6.0
  • ace-builds (Base): 1.22.0 -> 1.36.3
  • bootstrap (Base): 4.5.2 -> 4.6.2
    • @@ -33,9 +29,15 @@
  • font-awesome (Base): 5.8.2 -> 5.15.4
  • swagger-ui (Base): 4.1.3 -> 4.19.1
  • xmlunit-core (Base): 2.4.0 -> 2.10.0
    • -
  • elastic-apm (Base): 1.44.0 -> 1.52.0
    • -
  • elastic-search (Base): 8.14.3 -> 8.15.3
    • -
  • lucene (Base): 9.8.0 -> 9.12.0
  • httpcore (Base): 4.4.13 -> 4.4.16
  • httpclient (Base): 4.5.13 -> 4.5.14
    • +
  • flyway (JPA): 9.4.0 -> 10.20.1
    • +
  • hibernate (JPA): 6.4.1.Final -> 6.6.1.Final
    • +
  • hibernate-search (JPA): 7.0.0.Final -> 7.2.1.Final
    • +
  • elastic-apm (JPA): 1.44.0 -> 1.52.0
    • +
  • elastic-search (JPA): 8.14.3 -> 8.15.3
    • +
  • lucene (JPA): 9.8.0 -> 9.12.0
    • +
  • postgresql (JPA): 42.7.3 -> 42.7.4
    • +
  • mysql-connector-j (JPA): 8.2.0 -> 9.1.0
    • +
  • ojdbc11 (JPA): 23.3.0.23.09 -> 23.6.0.24.10
    • " diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java index c78e68a4a90..4dfb3d1cda6 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java @@ -35,7 +35,6 @@ import org.hibernate.annotations.GenericGenerator; import java.io.Serializable; -@Embeddable @Entity @Table( name = "HFJ_HISTORY_TAG", diff --git a/pom.xml b/pom.xml index fd50c6c7ee0..7bb68739634 100644 --- a/pom.xml +++ b/pom.xml @@ -2028,12 +2028,12 @@ org.postgresql postgresql - 42.7.3 + 42.7.4 com.oracle.database.jdbc ojdbc11 - 23.3.0.23.09 + 23.6.0.24.10 org.quartz-scheduler From 1e95fee9935c2b4d76836cb568174f56a9f7c788 Mon Sep 17 00:00:00 2001 From: Michele Adduci Date: Thu, 7 Nov 2024 08:32:45 +0100 Subject: [PATCH 04/10] Fixing version conflicts for jboss-logging, fixing tests --- .../uhn/hapi/fhir/changelog/7_8_0/changes.yaml | 17 +++++++++-------- .../ca/uhn/hapi/fhir/changelog/7_8_0/upgrade.md | 3 +++ .../jpa/model/entity/ResourceHistoryTag.java | 1 - hapi-fhir-sql-migrate/pom.xml | 12 ++---------- pom.xml | 6 ++++++ 5 files changed, 20 insertions(+), 19 deletions(-) diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml index a1bc47cb8c7..456db673005 100644 --- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml @@ -22,15 +22,16 @@
  • okio-jvm (Base): 3.4.0 -> 3.9.1
  • commons-cli (Base): 1.5.0 -> 1.9.0
  • org.jetbrains.annotations (Base): 23.0.0 -> 26.0.1
    • -
  • springdoc-openapi-starter-webmvc-ui (Base): 2.2.0 -> 2.6.0
    • -
  • ace-builds (Base): 1.22.0 -> 1.36.3
    • -
  • bootstrap (Base): 4.5.2 -> 4.6.2
    • -
  • Eonasdan-bootstrap-datetimepicker (Base): 4.17.47 -> 4.17.49
    • -
  • font-awesome (Base): 5.8.2 -> 5.15.4
    • -
  • swagger-ui (Base): 4.1.3 -> 4.19.1
  • xmlunit-core (Base): 2.4.0 -> 2.10.0
    • -
  • httpcore (Base): 4.4.13 -> 4.4.16
    • -
  • httpclient (Base): 4.5.13 -> 4.5.14
    • +
  • jboss-logging (Tinder): 3.4.2.Final -> 3.6.1.Final
    • +
  • springdoc-openapi-starter-webmvc-ui (Server): 2.2.0 -> 2.6.0
    • +
  • ace-builds (Server): 1.22.0 -> 1.36.3
    • +
  • bootstrap (Server): 4.5.2 -> 4.6.2
    • +
  • Eonasdan-bootstrap-datetimepicker (Server): 4.17.47 -> 4.17.49
    • +
  • font-awesome (Server): 5.8.2 -> 5.15.4
    • +
  • swagger-ui (Server): 4.1.3 -> 4.19.1
    • +
  • httpcore (Client): 4.4.13 -> 4.4.16
    • +
  • httpclient (Client): 4.5.13 -> 4.5.14
  • flyway (JPA): 9.4.0 -> 10.20.1
  • hibernate (JPA): 6.4.1.Final -> 6.6.1.Final
  • hibernate-search (JPA): 7.0.0.Final -> 7.2.1.Final
    • diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/upgrade.md b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/upgrade.md index e69de29bb2d..d4b0609fbdd 100644 --- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/upgrade.md +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/upgrade.md @@ -0,0 +1,3 @@ +## Entities annotations + +The `@Embedded` Annotation is no longer allowed, in presences of the `@Entity` one. diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java index 4dfb3d1cda6..25ac724a1a6 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java @@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.model.entity; import jakarta.persistence.Column; -import jakarta.persistence.Embeddable; import jakarta.persistence.Entity; import jakarta.persistence.ForeignKey; import jakarta.persistence.GeneratedValue; diff --git a/hapi-fhir-sql-migrate/pom.xml b/hapi-fhir-sql-migrate/pom.xml index 01295205e79..fd8e441f1f5 100644 --- a/hapi-fhir-sql-migrate/pom.xml +++ b/hapi-fhir-sql-migrate/pom.xml @@ -54,13 +54,13 @@ org.apache.derby derby test - 10.16.1.1 + 10.17.1.0     org.apache.derby derbytools test - 10.16.1.1 + 10.17.1.0 org.postgresql @@ -80,13 +80,6 @@ logback-classic test - - - ca.uhn.hapi.fhir - hapi-fhir-test-utilities - ${project.version} - test - org.testcontainers junit-jupiter @@ -131,7 +124,6 @@ - ca.uhn.hapi.fhir hapi-fhir-test-utilities diff --git a/pom.xml b/pom.xml index 7bb68739634..52cea8506b2 100644 --- a/pom.xml +++ b/pom.xml @@ -1057,6 +1057,7 @@ 3.3.5 2.0.10 2.9.0 + 3.6.1.Final 3.1.4 1.20.3 3.1.2.RELEASE @@ -1119,6 +1120,11 @@ logback-core ${logback_version} + + org.jboss.logging + jboss-logging + ${jboss_logging_version} + com.atlassian.commonmark commonmark From ab768795f6ea54aa6a08d8b2168d0ff96d72621a Mon Sep 17 00:00:00 2001 From: Michele Adduci Date: Thu, 7 Nov 2024 09:34:29 +0100 Subject: [PATCH 05/10] Fixed query due to new hibernate validation --- .../ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java index e9611614e45..47f22ea85a9 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java @@ -150,6 +150,6 @@ public interface IBatch2WorkChunkRepository @Param("status") WorkChunkStatusEnum theStatus); @Query( - "SELECT new ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO(e.myTargetStepId, e.myStatus, min(e.myStartTime), max(e.myEndTime), avg(e.myEndTime - e.myStartTime), count(*)) FROM Batch2WorkChunkEntity e WHERE e.myInstanceId=:instanceId GROUP BY e.myTargetStepId, e.myStatus") + "SELECT new ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO(e.myTargetStepId, e.myStatus, min(e.myStartTime), max(e.myEndTime), avg(DATEDIFF(e.myEndTime - e.myStartTime) * 86400000), count(*)) FROM Batch2WorkChunkEntity e WHERE e.myInstanceId=:instanceId GROUP BY e.myTargetStepId, e.myStatus") List fetchWorkChunkStatusForInstance(@Param("instanceId") String theInstanceId); } From 001e928ca0ae40badd99bbc5c24715386f3e1846 Mon Sep 17 00:00:00 2001 From: Michele Adduci Date: Thu, 7 Nov 2024 10:12:54 +0100 Subject: [PATCH 06/10] Fixed broken Query for IBatch2WorkChunkRepository --- .../ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java index 47f22ea85a9..2be10b9f8b9 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java @@ -150,6 +150,6 @@ public interface IBatch2WorkChunkRepository @Param("status") WorkChunkStatusEnum theStatus); @Query( - "SELECT new ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO(e.myTargetStepId, e.myStatus, min(e.myStartTime), max(e.myEndTime), avg(DATEDIFF(e.myEndTime - e.myStartTime) * 86400000), count(*)) FROM Batch2WorkChunkEntity e WHERE e.myInstanceId=:instanceId GROUP BY e.myTargetStepId, e.myStatus") + "SELECT new ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO(e.myTargetStepId, e.myStatus, min(e.myStartTime), max(e.myEndTime), avg(timestampdiff(SECOND, e.myStartTime, e.myEndTime) * 1000), count(*)) FROM Batch2WorkChunkEntity e WHERE e.myInstanceId=:instanceId GROUP BY e.myTargetStepId, e.myStatus") List fetchWorkChunkStatusForInstance(@Param("instanceId") String theInstanceId); } From 3ecd417bcb47fb26f51ca676a0410dae6fa914da Mon Sep 17 00:00:00 2001 From: James Agnew Date: Thu, 7 Nov 2024 09:04:18 -0500 Subject: [PATCH 07/10] Test fix --- .../graphql/GraphQLProviderWithIntrospection.java | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java index 1d08ddbc41d..0e7006065f1 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java @@ -33,6 +33,10 @@ import ca.uhn.fhir.util.StringUtil; import ca.uhn.fhir.util.VersionUtil; import com.google.gson.Gson; import com.google.gson.GsonBuilder; +import com.google.gson.JsonArray; +import com.google.gson.JsonElement; +import com.google.gson.JsonSerializationContext; +import com.google.gson.JsonSerializer; import graphql.ExecutionResult; import graphql.GraphQL; import graphql.language.InterfaceTypeDefinition; @@ -62,6 +66,7 @@ import org.slf4j.LoggerFactory; import java.io.IOException; import java.io.Writer; +import java.lang.reflect.Type; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; @@ -80,6 +85,7 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider { private final ISearchParamRegistry mySearchParamRegistry; private final VersionSpecificWorkerContextWrapper myContext; private final IDaoRegistry myDaoRegistry; + private final Gson myGson; /** * Constructor @@ -97,6 +103,10 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider { myContext = VersionSpecificWorkerContextWrapper.newVersionSpecificWorkerContextWrapper(theValidationSupport); myGenerator = new GraphQLSchemaGenerator(myContext, VersionUtil.getVersion()); + + GsonBuilder gsonBuilder = new GsonBuilder(); + gsonBuilder.registerTypeAdapter(Collections.emptyList().getClass(), (JsonSerializer) (src, typeOfSrc, context) -> new JsonArray()); + myGson = gsonBuilder.create(); } @Override @@ -250,8 +260,7 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider { ExecutionResult executionResult = build.execute(theQueryBody); Map data = executionResult.toSpecification(); - Gson gson = new GsonBuilder().create(); - return gson.toJson(data); + return myGson.toJson(data); } @Nonnull From 86e1eadbca7d983d21fba24b5333d8de91b8d3e0 Mon Sep 17 00:00:00 2001 From: jamesagnew Date: Thu, 7 Nov 2024 09:27:44 -0500 Subject: [PATCH 08/10] Spotless --- .../fhir/jpa/graphql/GraphQLProviderWithIntrospection.java | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java index 0e7006065f1..cb34cc222ff 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java @@ -34,8 +34,6 @@ import ca.uhn.fhir.util.VersionUtil; import com.google.gson.Gson; import com.google.gson.GsonBuilder; import com.google.gson.JsonArray; -import com.google.gson.JsonElement; -import com.google.gson.JsonSerializationContext; import com.google.gson.JsonSerializer; import graphql.ExecutionResult; import graphql.GraphQL; @@ -66,7 +64,6 @@ import org.slf4j.LoggerFactory; import java.io.IOException; import java.io.Writer; -import java.lang.reflect.Type; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; @@ -105,7 +102,8 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider { myGenerator = new GraphQLSchemaGenerator(myContext, VersionUtil.getVersion()); GsonBuilder gsonBuilder = new GsonBuilder(); - gsonBuilder.registerTypeAdapter(Collections.emptyList().getClass(), (JsonSerializer) (src, typeOfSrc, context) -> new JsonArray()); + gsonBuilder.registerTypeAdapter(Collections.emptyList().getClass(), (JsonSerializer) + (src, typeOfSrc, context) -> new JsonArray()); myGson = gsonBuilder.create(); } From c69c50830dcfb763d2a93aff80f0434f4f0352de Mon Sep 17 00:00:00 2001 From: James Agnew Date: Thu, 7 Nov 2024 14:03:49 -0500 Subject: [PATCH 09/10] Add bumps --- .../resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml | 2 +- pom.xml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml index 456db673005..4c86813da8e 100644 --- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml @@ -33,7 +33,7 @@
  • httpcore (Client): 4.4.13 -> 4.4.16
  • httpclient (Client): 4.5.13 -> 4.5.14
  • flyway (JPA): 9.4.0 -> 10.20.1
    • -
  • hibernate (JPA): 6.4.1.Final -> 6.6.1.Final
    • +
  • hibernate (JPA): 6.4.1.Final -> 6.6.2.Final
  • hibernate-search (JPA): 7.0.0.Final -> 7.2.1.Final
  • elastic-apm (JPA): 1.44.0 -> 1.52.0
  • elastic-search (JPA): 8.14.3 -> 8.15.3
    • diff --git a/pom.xml b/pom.xml index 52cea8506b2..830826f7a78 100644 --- a/pom.xml +++ b/pom.xml @@ -1018,12 +1018,12 @@ 4.0.4 4.9.0 3.0.3 - 12.0.9 + 12.0.15 3.0.2 5.10.1 0.64.8 10.20.1 - 6.6.1.Final + 6.6.2.Final 1.5.12 7.2.1.Final From eb1704e1a332ed841e4abd4041f222d7760f62c8 Mon Sep 17 00:00:00 2001 From: Michele Adduci Date: Fri, 8 Nov 2024 05:24:35 +0100 Subject: [PATCH 10/10] Using a JPQL compliant query in IBatch2WorkChunckRepository class --- .../ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java index 2be10b9f8b9..2b646207295 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java @@ -150,6 +150,6 @@ public interface IBatch2WorkChunkRepository @Param("status") WorkChunkStatusEnum theStatus); @Query( - "SELECT new ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO(e.myTargetStepId, e.myStatus, min(e.myStartTime), max(e.myEndTime), avg(timestampdiff(SECOND, e.myStartTime, e.myEndTime) * 1000), count(*)) FROM Batch2WorkChunkEntity e WHERE e.myInstanceId=:instanceId GROUP BY e.myTargetStepId, e.myStatus") + "SELECT new ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO(e.myTargetStepId, e.myStatus, min(e.myStartTime), max(e.myEndTime), avg(cast((e.myEndTime - e.myStartTime) as long)), count(*)) FROM Batch2WorkChunkEntity e WHERE e.myInstanceId=:instanceId GROUP BY e.myTargetStepId, e.myStatus") List fetchWorkChunkStatusForInstance(@Param("instanceId") String theInstanceId); }