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hapi-fhir
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Version bump a few dependencies

This commit is contained in:
James Agnew 2018-12-22 20:13:03 -05:00
parent 1311ef4157
commit a0cb7edd08
15 changed files with 238 additions and 120 deletions
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4
hapi-deployable-pom/pom.xml
View File

@ -99,6 +99,10 @@
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>javax.activation-api</artifactId>
</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>

6
hapi-fhir-base/pom.xml
View File

@ -48,6 +48,12 @@
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<optional>true</optional>
<exclusions>
<exclusion>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.helger</groupId>

16
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -218,13 +218,17 @@
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-core</artifactId>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-impl</artifactId>-->
<!--</dependency>-->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>

63
hapi-fhir-jpaserver-base/pom.xml
View File

@ -231,14 +231,14 @@
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<dependency>
<!--<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
</dependency>
</dependency>-->
<!-- Test Database -->
<dependency>
@ -360,18 +360,10 @@
<artifactId>xml-apis</artifactId>
<groupId>xml-apis</groupId>
</exclusion>
<exclusion>
<groupId>org.jboss.spec.javax.transaction</groupId>
<artifactId>jboss-transaction-api_1.2_spec</artifactId>
</exclusion>
<exclusion>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
</exclusion>
<exclusion>
<groupId>javax.activation</groupId>
<artifactId>javax.activation-api</artifactId>
</exclusion>
<!--<exclusion>-->
<!--<groupId>org.jboss.spec.javax.transaction</groupId>-->
<!--<artifactId>jboss-transaction-api_1.2_spec</artifactId>-->
<!--</exclusion>-->
</exclusions>
</dependency>
<dependency>
@ -409,9 +401,14 @@
</exclusions>
</dependency>
<dependency>
<groupId>javax.transaction</groupId>
<artifactId>javax.transaction-api</artifactId>
<groupId>com.sun.activation</groupId>
<artifactId>javax.activation</artifactId>
<version>1.2.0</version>
</dependency>
<!--<dependency>-->
<!--<groupId>javax.transaction</groupId>-->
<!--<artifactId>javax.transaction-api</artifactId>-->
<!--</dependency>-->
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
@ -428,10 +425,10 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.sun.activation</groupId>
<artifactId>javax.activation</artifactId>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.activation</groupId>-->
<!--<artifactId>javax.activation</artifactId>-->
<!--</dependency>-->
<!--<dependency>
<groupId>javax.validation</groupId>
<artifactId>validation-api</artifactId>
@ -596,20 +593,20 @@
as JDK9 no longer includes them by default
-->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>${jaxb_api_version}</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<version>${jaxb_core_version}</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>${jaxb_core_version}</version>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>${jaxb_runtime_version}</version>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-core</artifactId>-->
<!--<version>${jaxb_core_version}</version>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-impl</artifactId>-->
<!--<version>${jaxb_core_version}</version>-->
<!--</dependency>-->
</dependencies>
</plugin>
<plugin>

97
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java
View File

@ -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<String> 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<SequenceInformation> sequences = sequenceInformationExtractor.extractMetadata(extractionContext);
for (SequenceInformation next : sequences) {
sequenceNames.add(next.getSequenceName().getSequenceName().getText());
}
}
return sequenceNames;
} catch (SQLException e) {

2
hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/standalone/BaseSubscriptionChannelDstu3Test.java
View File

@ -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);
}

20
hapi-fhir-structures-dstu2.1/pom.xml
View File

@ -214,15 +214,19 @@
<artifactId>jaxb-api</artifactId>
<scope>test</scope>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-core</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-impl</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<scope>test</scope>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>
</dependencies>

20
hapi-fhir-structures-dstu2/pom.xml
View File

@ -119,15 +119,19 @@
<artifactId>jaxb-api</artifactId>
<scope>test</scope>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-core</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-impl</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<scope>test</scope>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>

20
hapi-fhir-structures-dstu3/pom.xml
View File

@ -245,15 +245,19 @@
<artifactId>jaxb-api</artifactId>
<scope>test</scope>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-core</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-impl</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<scope>test</scope>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>

20
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -143,15 +143,19 @@
<artifactId>jaxb-api</artifactId>
<scope>test</scope>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-core</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-impl</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<scope>test</scope>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>
<!-- UNIT TEST DEPENDENCIES -->

20
hapi-fhir-structures-r4/pom.xml
View File

@ -153,15 +153,19 @@
<artifactId>jaxb-api</artifactId>
<scope>test</scope>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-core</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-impl</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<scope>test</scope>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>
<!-- UNIT TEST DEPENDENCIES -->

5
hapi-fhir-testpage-overlay/pom.xml
View File

@ -75,6 +75,11 @@
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax.annotation</groupId>
<artifactId>javax.annotation-api</artifactId>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>

20
hapi-fhir-validation/pom.xml
View File

@ -189,15 +189,19 @@
<artifactId>jaxb-api</artifactId>
<scope>test</scope>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-core</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-impl</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<scope>test</scope>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>
<dependency>

38
pom.xml
View File

@ -510,28 +510,29 @@
<aries_spifly_version>1.0.10</aries_spifly_version>
<caffeine_version>2.6.2</caffeine_version>
<commons_codec_version>1.11</commons_codec_version>
<commons_text_version>1.4</commons_text_version>
<commons_text_version>1.6</commons_text_version>
<commons_io_version>2.6</commons_io_version>
<commons_lang3_version>3.8</commons_lang3_version>
<commons_lang3_version>3.8.1</commons_lang3_version>
<derby_version>10.14.2.0</derby_version>
<error_prone_annotations_version>2.0.18</error_prone_annotations_version>
<guava_version>25.0-jre</guava_version>
<gson_version>2.8.5</gson_version>
<jaxb_bundle_version>2.2.11_1</jaxb_bundle_version>
<jaxb_api_version>2.3.0</jaxb_api_version>
<jaxb_core_version>2.3.0</jaxb_core_version>
<jaxb_api_version>2.3.1</jaxb_api_version>
<jaxb_core_version>2.3.0.1</jaxb_core_version>
<jaxb_runtime_version>2.3.1</jaxb_runtime_version>
<jersey_version>2.25.1</jersey_version>
<jetty_version>9.4.14.v20181114</jetty_version>
<jsr305_version>3.0.2</jsr305_version>
<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
<hibernate_version>5.3.6.Final</hibernate_version>
<hibernate_search_version>5.10.3.Final</hibernate_search_version>
<hibernate_validator_version>5.4.1.Final</hibernate_validator_version>
<hibernate_version>5.4.0.Final</hibernate_version>
<!-- Update lucene version when you update hibernate-search version -->
<hibernate_search_version>5.11.0.Final</hibernate_search_version>
<lucene_version>5.5.5</lucene_version>
<hibernate_validator_version>5.4.1.Final</hibernate_validator_version>
<httpcore_version>4.4.6</httpcore_version>
<httpclient_version>4.5.3</httpclient_version>
<jackson_version>2.9.7</jackson_version>
<lucene_version>5.5.5</lucene_version>
<maven_assembly_plugin_version>2.5.3</maven_assembly_plugin_version>
<maven_license_plugin_version>1.8</maven_license_plugin_version>
<resteasy_version>4.0.0.Beta3</resteasy_version>
@ -541,12 +542,12 @@
<servicemix_saxon_version>9.5.1-5_1</servicemix_saxon_version>
<servicemix_xmlresolver_version>1.2_5</servicemix_xmlresolver_version>
<slf4j_version>1.7.25</slf4j_version>
<spring_version>5.0.8.RELEASE</spring_version>
<spring_data_version>2.0.7.RELEASE</spring_data_version>
<spring_version>5.1.3.RELEASE</spring_version>
<spring_data_version>2.1.3.RELEASE</spring_data_version>
<spring-boot.version>1.5.6.RELEASE</spring-boot.version>
<stax2_api_version>3.1.4</stax2_api_version>
<thymeleaf-version>3.0.9.RELEASE</thymeleaf-version>
<thymeleaf-version>3.0.11.RELEASE</thymeleaf-version>
<woodstox_core_asl_version>4.4.1</woodstox_core_asl_version>
<!-- We are aiming to still work on a very old version of SLF4j even though we depend on the newest, just to be nice to users of the API. This version is tested in the hapi-fhir-cobertura. -->
@ -663,6 +664,11 @@
<artifactId>javax.activation</artifactId>
<version>1.2.0</version>
</dependency>
<dependency>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>com.sun.mail</groupId>
<artifactId>javax.mail</artifactId>
@ -755,6 +761,7 @@
<artifactId>mssql-jdbc</artifactId>
<version>6.2.2.jre8</version>
</dependency>
<!--
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
@ -765,6 +772,7 @@
<artifactId>jaxb-impl</artifactId>
<version>${jaxb_core_version}</version>
</dependency>
-->
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
@ -1064,13 +1072,11 @@
<artifactId>javax.json</artifactId>
<version>1.0.4</version>
</dependency>
<!--
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>${jaxb_runtime_version}</version>
</dependency>
-->
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-server</artifactId>
@ -1154,7 +1160,7 @@
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>2.18.3</version>
<version>2.23.4</version>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
@ -1323,7 +1329,7 @@
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
<version>1.2.1</version>
<version>1.3.0</version>
</plugin>
<plugin>
<groupId>de.jpdigital</groupId>
@ -1485,7 +1491,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.6</version>
<version>2.7</version>
<configuration>
<processDependencyManagementTransitive>false</processDependencyManagementTransitive>
</configuration>

7
src/changes/changes.xml
View File

@ -12,7 +12,14 @@
latest versions (dependent HAPI modules listed in brackets):
<![CDATA[
<ul>
<li>Spring (JPA): 5.0.8.RELEASE -&gt; 5.1.3.RELEASE</li>
<li>Spring-Data (JPA): 2.0.7.RELEASE -&gt; 2.1.3.RELEASE</li>
<li>Hibernate-Core (JPA): 5.3.6.FINAL -&gt; 5.4.0.FINAL</li>
<li>Hibernate-Search (JPA): 5.10.3.FINAL -&gt; 5.11.0.FINAL</li>
<li>Thymeleaf (JPA): 3.0.9.RELEASE -&gt; 3.0.11.RELEASE</li>
<li>thymeleaf-spring4 (Testpage Overlay) has been replaced with thymeleaf-spring5</li>
<li>Commons-Lang3: 3.8 -&gt; 3.8.1</li>
<li>Commons-Text: 1.4 -&gt; 1.4</li>
</ul>
]]>
</action>