From a0cb7edd08de00ceaeadcd665b02278a00d9dd0e Mon Sep 17 00:00:00 2001 From: James Agnew Date: Sat, 22 Dec 2018 20:13:03 -0500 Subject: [PATCH] Version bump a few dependencies --- hapi-deployable-pom/pom.xml | 4 + hapi-fhir-base/pom.xml | 6 ++ hapi-fhir-cli/hapi-fhir-cli-api/pom.xml | 16 +-- hapi-fhir-jpaserver-base/pom.xml | 63 ++++++------ .../ca/uhn/fhir/jpa/migrate/JdbcUtils.java | 97 ++++++++++++++++--- .../BaseSubscriptionChannelDstu3Test.java | 2 +- hapi-fhir-structures-dstu2.1/pom.xml | 20 ++-- hapi-fhir-structures-dstu2/pom.xml | 20 ++-- hapi-fhir-structures-dstu3/pom.xml | 20 ++-- hapi-fhir-structures-hl7org-dstu2/pom.xml | 20 ++-- hapi-fhir-structures-r4/pom.xml | 20 ++-- hapi-fhir-testpage-overlay/pom.xml | 5 + hapi-fhir-validation/pom.xml | 20 ++-- pom.xml | 38 +++++--- src/changes/changes.xml | 7 ++ 15 files changed, 238 insertions(+), 120 deletions(-) diff --git a/hapi-deployable-pom/pom.xml b/hapi-deployable-pom/pom.xml index 054dde91604..84ec5a98714 100644 --- a/hapi-deployable-pom/pom.xml +++ b/hapi-deployable-pom/pom.xml @@ -99,6 +99,10 @@ javax.mail javax.mail-api + + javax.activation + javax.activation-api + com.helger ph-schematron diff --git a/hapi-fhir-base/pom.xml b/hapi-fhir-base/pom.xml index bd368198eff..04014775ce1 100644 --- a/hapi-fhir-base/pom.xml +++ b/hapi-fhir-base/pom.xml @@ -48,6 +48,12 @@ com.helger ph-schematron true + + + org.glassfish.jaxb + jaxb-core + + com.helger diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml index 1ffeda550f2..92f20af6b75 100644 --- a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml +++ b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml @@ -218,13 +218,17 @@ javax.xml.bind jaxb-api + + + + + + + + - com.sun.xml.bind - jaxb-core - - - com.sun.xml.bind - jaxb-impl + org.glassfish.jaxb + jaxb-runtime diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml index 6f662773851..d0662b73e4a 100644 --- a/hapi-fhir-jpaserver-base/pom.xml +++ b/hapi-fhir-jpaserver-base/pom.xml @@ -231,14 +231,14 @@ javax.xml.bind jaxb-api - + @@ -360,18 +360,10 @@ xml-apis xml-apis - - org.jboss.spec.javax.transaction - jboss-transaction-api_1.2_spec - - - javax.activation - activation - - - javax.activation - javax.activation-api - + + + + @@ -409,9 +401,14 @@ - javax.transaction - javax.transaction-api + com.sun.activation + javax.activation + 1.2.0 + + + + javax.mail javax.mail-api @@ -428,10 +425,10 @@ - - com.sun.activation - javax.activation - + + + + - javax.xml.bind - jaxb-api - ${jaxb_api_version} - - - com.sun.xml.bind - jaxb-core - ${jaxb_core_version} - - - com.sun.xml.bind - jaxb-impl - ${jaxb_core_version} + org.glassfish.jaxb + jaxb-runtime + ${jaxb_runtime_version} + + + + + + + + + + diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java index 5f65b2b108b..c8b659e1da3 100644 --- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java +++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java @@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate; * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * + * * http://www.apache.org/licenses/LICENSE-2.0 - * + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. @@ -22,10 +22,19 @@ package ca.uhn.fhir.jpa.migrate; import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableColumnTypeTask; import ca.uhn.fhir.rest.server.exceptions.InternalErrorException; +import org.hibernate.boot.model.naming.Identifier; import org.hibernate.dialect.Dialect; import org.hibernate.engine.jdbc.dialect.internal.StandardDialectResolver; import org.hibernate.engine.jdbc.dialect.spi.DatabaseMetaDataDialectResolutionInfoAdapter; import org.hibernate.engine.jdbc.dialect.spi.DialectResolver; +import org.hibernate.engine.jdbc.env.internal.NormalizingIdentifierHelperImpl; +import org.hibernate.engine.jdbc.env.spi.*; +import org.hibernate.engine.jdbc.spi.SqlExceptionHelper; +import org.hibernate.engine.jdbc.spi.TypeInfo; +import org.hibernate.service.ServiceRegistry; +import org.hibernate.tool.schema.extract.spi.ExtractionContext; +import org.hibernate.tool.schema.extract.spi.SequenceInformation; +import org.hibernate.tool.schema.extract.spi.SequenceInformationExtractor; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.jdbc.core.ColumnMapRowMapper; @@ -233,24 +242,80 @@ public class JdbcUtils { Set sequenceNames = new HashSet<>(); if (dialect.supportsSequences()) { - String sql = dialect.getQuerySequencesString(); - if (sql != null) { - Statement statement = null; - ResultSet rs = null; - try { - statement = connection.createStatement(); - rs = statement.executeQuery(sql); - - while (rs.next()) { - sequenceNames.add(rs.getString(1).toUpperCase()); - } - } finally { - if (rs != null) rs.close(); - if (statement != null) statement.close(); + // Use Hibernate to get a list of current sequences + SequenceInformationExtractor sequenceInformationExtractor = dialect.getSequenceInformationExtractor(); + ExtractionContext extractionContext = new ExtractionContext.EmptyExtractionContext() { + @Override + public Connection getJdbcConnection() { + return connection; } + @Override + public ServiceRegistry getServiceRegistry() { + return super.getServiceRegistry(); + } + + @Override + public JdbcEnvironment getJdbcEnvironment() { + return new JdbcEnvironment() { + @Override + public Dialect getDialect() { + return dialect; + } + + @Override + public ExtractedDatabaseMetaData getExtractedDatabaseMetaData() { + return null; + } + + @Override + public Identifier getCurrentCatalog() { + return null; + } + + @Override + public Identifier getCurrentSchema() { + return null; + } + + @Override + public QualifiedObjectNameFormatter getQualifiedObjectNameFormatter() { + return null; + } + + @Override + public IdentifierHelper getIdentifierHelper() { + return new NormalizingIdentifierHelperImpl(this, null, true, true, true, null, null, null); + } + + @Override + public NameQualifierSupport getNameQualifierSupport() { + return null; + } + + @Override + public SqlExceptionHelper getSqlExceptionHelper() { + return null; + } + + @Override + public LobCreatorBuilder getLobCreatorBuilder() { + return null; + } + + @Override + public TypeInfo getTypeInfoForJdbcCode(int jdbcTypeCode) { + return null; + } + }; + } + }; + Iterable sequences = sequenceInformationExtractor.extractMetadata(extractionContext); + for (SequenceInformation next : sequences) { + sequenceNames.add(next.getSequenceName().getSequenceName().getText()); } + } return sequenceNames; } catch (SQLException e) { diff --git a/hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/standalone/BaseSubscriptionChannelDstu3Test.java b/hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/standalone/BaseSubscriptionChannelDstu3Test.java index 0c4555ef824..1c8ba0b36c0 100644 --- a/hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/standalone/BaseSubscriptionChannelDstu3Test.java +++ b/hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/standalone/BaseSubscriptionChannelDstu3Test.java @@ -164,8 +164,8 @@ public abstract class BaseSubscriptionChannelDstu3Test extends BaseSubscriptionD @Update public MethodOutcome update(@ResourceParam Observation theObservation, HttpServletRequest theRequest) { - ourUpdatedObservations.add(theObservation); ourContentTypes.add(theRequest.getHeader(Constants.HEADER_CONTENT_TYPE).replaceAll(";.*", "")); + ourUpdatedObservations.add(theObservation); ourLog.info("Received Listener Update (now have {} updates)", ourUpdatedObservations.size()); return new MethodOutcome(new IdType("Observation/1"), false); } diff --git a/hapi-fhir-structures-dstu2.1/pom.xml b/hapi-fhir-structures-dstu2.1/pom.xml index 5e0d5a2c16f..cba39f3228a 100644 --- a/hapi-fhir-structures-dstu2.1/pom.xml +++ b/hapi-fhir-structures-dstu2.1/pom.xml @@ -214,15 +214,19 @@ jaxb-api test + + + + + + + + + + - com.sun.xml.bind - jaxb-core - test - - - com.sun.xml.bind - jaxb-impl - test + org.glassfish.jaxb + jaxb-runtime diff --git a/hapi-fhir-structures-dstu2/pom.xml b/hapi-fhir-structures-dstu2/pom.xml index 26ff214acf0..b0d20486c60 100644 --- a/hapi-fhir-structures-dstu2/pom.xml +++ b/hapi-fhir-structures-dstu2/pom.xml @@ -119,15 +119,19 @@ jaxb-api test + + + + + + + + + + - com.sun.xml.bind - jaxb-core - test - - - com.sun.xml.bind - jaxb-impl - test + org.glassfish.jaxb + jaxb-runtime diff --git a/hapi-fhir-structures-dstu3/pom.xml b/hapi-fhir-structures-dstu3/pom.xml index 9d6604bca4c..7e4c703fbf7 100644 --- a/hapi-fhir-structures-dstu3/pom.xml +++ b/hapi-fhir-structures-dstu3/pom.xml @@ -245,15 +245,19 @@ jaxb-api test + + + + + + + + + + - com.sun.xml.bind - jaxb-core - test - - - com.sun.xml.bind - jaxb-impl - test + org.glassfish.jaxb + jaxb-runtime diff --git a/hapi-fhir-structures-hl7org-dstu2/pom.xml b/hapi-fhir-structures-hl7org-dstu2/pom.xml index 296ee6048c5..d2c626d7014 100644 --- a/hapi-fhir-structures-hl7org-dstu2/pom.xml +++ b/hapi-fhir-structures-hl7org-dstu2/pom.xml @@ -143,15 +143,19 @@ jaxb-api test + + + + + + + + + + - com.sun.xml.bind - jaxb-core - test - - - com.sun.xml.bind - jaxb-impl - test + org.glassfish.jaxb + jaxb-runtime diff --git a/hapi-fhir-structures-r4/pom.xml b/hapi-fhir-structures-r4/pom.xml index 47f0aa435ee..1d6909efc5c 100644 --- a/hapi-fhir-structures-r4/pom.xml +++ b/hapi-fhir-structures-r4/pom.xml @@ -153,15 +153,19 @@ jaxb-api test + + + + + + + + + + - com.sun.xml.bind - jaxb-core - test - - - com.sun.xml.bind - jaxb-impl - test + org.glassfish.jaxb + jaxb-runtime diff --git a/hapi-fhir-testpage-overlay/pom.xml b/hapi-fhir-testpage-overlay/pom.xml index d377521707b..2e3849b44e4 100644 --- a/hapi-fhir-testpage-overlay/pom.xml +++ b/hapi-fhir-testpage-overlay/pom.xml @@ -75,6 +75,11 @@ provided + + javax.annotation + javax.annotation-api + + ch.qos.logback logback-classic diff --git a/hapi-fhir-validation/pom.xml b/hapi-fhir-validation/pom.xml index 6723bc84d70..8d72b9ebeea 100644 --- a/hapi-fhir-validation/pom.xml +++ b/hapi-fhir-validation/pom.xml @@ -189,15 +189,19 @@ jaxb-api test + + + + + + + + + + - com.sun.xml.bind - jaxb-core - test - - - com.sun.xml.bind - jaxb-impl - test + org.glassfish.jaxb + jaxb-runtime diff --git a/pom.xml b/pom.xml index 68c40130438..e09431cbca6 100644 --- a/pom.xml +++ b/pom.xml @@ -510,28 +510,29 @@ 1.0.10 2.6.2 1.11 - 1.4 + 1.6 2.6 - 3.8 + 3.8.1 10.14.2.0 2.0.18 25.0-jre 2.8.5 2.2.11_1 - 2.3.0 - 2.3.0 + 2.3.1 + 2.3.0.1 + 2.3.1 2.25.1 9.4.14.v20181114 3.0.2 - 5.3.6.Final - 5.10.3.Final - 5.4.1.Final + 5.4.0.Final + 5.11.0.Final + 5.5.5 + 5.4.1.Final 4.4.6 4.5.3 2.9.7 - 5.5.5 2.5.3 1.8 4.0.0.Beta3 @@ -541,12 +542,12 @@ 9.5.1-5_1 1.2_5 1.7.25 - 5.0.8.RELEASE - 2.0.7.RELEASE + 5.1.3.RELEASE + 2.1.3.RELEASE 1.5.6.RELEASE 3.1.4 - 3.0.9.RELEASE + 3.0.11.RELEASE 4.4.1 @@ -663,6 +664,11 @@ javax.activation 1.2.0 + + com.sun.activation + jakarta.activation + 1.2.1 + com.sun.mail javax.mail @@ -755,6 +761,7 @@ mssql-jdbc 6.2.2.jre8 + javax.mail javax.mail-api @@ -1064,13 +1072,11 @@ javax.json 1.0.4 - org.glassfish.jersey.core jersey-server @@ -1154,7 +1160,7 @@ org.mockito mockito-core - 2.18.3 + 2.23.4 org.postgresql @@ -1323,7 +1329,7 @@ org.basepom.maven duplicate-finder-maven-plugin - 1.2.1 + 1.3.0 de.jpdigital @@ -1485,7 +1491,7 @@ org.codehaus.mojo versions-maven-plugin - 2.6 + 2.7 false diff --git a/src/changes/changes.xml b/src/changes/changes.xml index 132d1297618..98e511ef6bb 100644 --- a/src/changes/changes.xml +++ b/src/changes/changes.xml @@ -12,7 +12,14 @@ latest versions (dependent HAPI modules listed in brackets): +
  • Spring (JPA): 5.0.8.RELEASE -> 5.1.3.RELEASE
    • +
  • Spring-Data (JPA): 2.0.7.RELEASE -> 2.1.3.RELEASE
    • +
  • Hibernate-Core (JPA): 5.3.6.FINAL -> 5.4.0.FINAL
    • +
  • Hibernate-Search (JPA): 5.10.3.FINAL -> 5.11.0.FINAL
    • +
  • Thymeleaf (JPA): 3.0.9.RELEASE -> 3.0.11.RELEASE
  • thymeleaf-spring4 (Testpage Overlay) has been replaced with thymeleaf-spring5
    • +
  • Commons-Lang3: 3.8 -> 3.8.1
    • +
  • Commons-Text: 1.4 -> 1.4
    • ]]>