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Code Issues Packages Projects Releases Wiki Activity

Migrate CLOB columns to LOB (SMILE-3072) (#3016) 

* Migration finished

* Work on LOBS

* Add to ClobMigrated annotation

* Deal with lobs

* Work on new approach

* HAPI FHIR version bump

* Add changelog

* Add license header

* Fix intermittent

* CLeanup

* Cleanup
This commit is contained in:
James Agnew 2021-10-11 16:47:37 -04:00 committed by GitHub
parent 756b0fdc7b
commit 310a4cdb58
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
70 changed files with 201 additions and 86 deletions
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2
hapi-deployable-pom/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-batch/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-bom/pom.xml
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@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3016-fix-clob-column-type-on-postgres.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 3016
title: "A new customized Hibernate dialect is now used for HAPI FHIR JPA on Postgresql Database. This
dialect uses the PG `oid` datatype instead of `text` for CLOB columns, avoiding CLOBs being seen as
abandoned by the Postgresql VACUUMLO tool."

2
hapi-fhir-jacoco/pom.xml
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@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpa/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

6
hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java
View File

@ -264,10 +264,10 @@ public class TestUtil {
assertNotADuplicateName(columnName, null);
ForeignKey fk = joinColumn.foreignKey();
if (theIsSuperClass) {
Validate.isTrue(isBlank(fk.name()), "Foreign key on " + theAnnotatedElement.toString() + " has a name() and should not as it is a superclass");
Validate.isTrue(isBlank(fk.name()), "Foreign key on " + theAnnotatedElement + " has a name() and should not as it is a superclass");
} else {
Validate.notNull(fk);
Validate.isTrue(isNotBlank(fk.name()), "Foreign key on " + theAnnotatedElement.toString() + " has no name()");
Validate.isTrue(isNotBlank(fk.name()), "Foreign key on " + theAnnotatedElement + " has no name()");
Validate.isTrue(fk.name().startsWith("FK_"));
assertNotADuplicateName(fk.name(), theNames);
}
@ -279,7 +279,7 @@ public class TestUtil {
validateColumnName(columnName, theAnnotatedElement);
assertNotADuplicateName(columnName, null);
Validate.isTrue(column.unique() == false, "Should not use unique attribute on column (use named @UniqueConstraint instead) on " + theAnnotatedElement.toString());
Validate.isTrue(column.unique() == false, "Should not use unique attribute on column (use named @UniqueConstraint instead) on " + theAnnotatedElement);
boolean hasLob = theAnnotatedElement.getAnnotation(Lob.class) != null;
Field field = (Field) theAnnotatedElement;

11
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -575,12 +575,14 @@
<dialects>
<param>h2</param>
<param>derby_10_7</param>
<param>postgresql92</param>
<param>mysql57</param>
<param>mariadb</param>
<param>oracle12c</param>
<param>sqlserver2012</param>
</dialects>
<customDialects>
<customDialect>ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect</customDialect>
</customDialects>
<outputDirectory>${project.build.directory}/classes/ca/uhn/hapi/fhir/jpa/docs/database</outputDirectory>
<packages>
<param>ca.uhn.fhir.jpa.entity</param>
@ -605,6 +607,11 @@
<artifactId>jaxb-runtime</artifactId>
<version>${jaxb_runtime_version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-model</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</plugin>
<plugin>

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -132,6 +132,22 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.addColumn("20210915.1", "EXPANDED_AT")
.nullable()
.type(ColumnTypeEnum.DATE_TIMESTAMP);
/*
* Replace CLOB columns with BLOB columns
*/
// TRM_VALUESET_CONCEPT.SOURCE_DIRECT_PARENT_PIDS
version.onTable("TRM_VALUESET_CONCEPT")
.migratePostgresTextClobToBinaryClob("20211003.1", "SOURCE_DIRECT_PARENT_PIDS");
// TRM_CONCEPT.PARENT_PIDS
version.onTable("TRM_CONCEPT")
.migratePostgresTextClobToBinaryClob("20211003.2", "PARENT_PIDS");
// HFJ_SEARCH.SEARCH_QUERY_STRING
version.onTable("HFJ_SEARCH")
.migratePostgresTextClobToBinaryClob("20211003.3", "SEARCH_QUERY_STRING");
}
private void init540() {

2
hapi-fhir-jpaserver-cql/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-mdm/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-model/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

17
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirPostgres94Dialect.java Normal file
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@ -0,0 +1,17 @@
package ca.uhn.fhir.jpa.model.dialect;
import org.hibernate.dialect.PostgreSQL94Dialect;
import java.sql.Types;
/**
* This dialect is recommended when using HAPI FHIR JPA on Postgresql database.
*/
public class HapiFhirPostgres94Dialect extends PostgreSQL94Dialect {
public HapiFhirPostgres94Dialect() {
super();
registerColumnType( Types.CLOB, "oid" );
}
}

2
hapi-fhir-jpaserver-searchparam/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-subscription/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-utilities/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

3
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhirtest.config;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
@ -148,7 +149,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
if (CommonConfig.isLocalTestMode()) {
extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
} else {
extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");

3
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhirtest.config;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
@ -154,7 +155,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
if (CommonConfig.isLocalTestMode()) {
extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
} else {
extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");

7
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java
View File

@ -2,24 +2,21 @@ package ca.uhn.fhirtest.config;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
import ca.uhn.fhir.jpa.validation.ValidationSettings;
import ca.uhn.fhir.rest.client.interceptor.ThreadLocalCapturingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import org.apache.commons.lang3.time.DateUtils;
import org.hibernate.dialect.PostgreSQL94Dialect;
import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hl7.fhir.dstu2.model.Subscription;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.springframework.beans.factory.annotation.Autowire;
@ -147,7 +144,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
if (CommonConfig.isLocalTestMode()) {
extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
} else {
extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");

3
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR5Config.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhirtest.config;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.config.BaseJavaConfigR5;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
@ -147,7 +148,7 @@ public class TestR5Config extends BaseJavaConfigR5 {
if (CommonConfig.isLocalTestMode()) {
extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
} else {
extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");

2
hapi-fhir-server-mdm/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server-openapi/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

10
hapi-fhir-sql-migrate/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -53,6 +53,10 @@
<artifactId>derbytools</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
@ -68,6 +72,10 @@
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-commons</artifactId>
</dependency>
</dependencies>

3
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropColumnTask.java
View File

@ -34,6 +34,9 @@ public class DropColumnTask extends BaseTableColumnTask {
private static final Logger ourLog = LoggerFactory.getLogger(DropColumnTask.class);
/**
* Constructor
*/
public DropColumnTask(String theProductVersion, String theSchemaVersion) {
super(theProductVersion, theSchemaVersion);
}

46
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/MigratePostgresTextClobToBinaryClobTask.java Normal file
View File

@ -0,0 +1,46 @@
package ca.uhn.fhir.jpa.migrate.taskdef;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.sql.SQLException;
public class MigratePostgresTextClobToBinaryClobTask extends BaseTableColumnTask {
private static final Logger ourLog = LoggerFactory.getLogger(MigratePostgresTextClobToBinaryClobTask.class);
/**
* Constructor
*/
public MigratePostgresTextClobToBinaryClobTask(String theProductVersion, String theSchemaVersion) {
super(theProductVersion, theSchemaVersion);
}
@Override
public void validate() {
super.validate();
setDescription("Migrate text clob " + getColumnName() + " from table " + getTableName() + " (only affects Postgresql)");
}
@Override
protected void doExecute() throws SQLException {
if (getConnectionProperties().getDriverType() != DriverTypeEnum.POSTGRES_9_4) {
return;
}
JdbcUtils.ColumnType columnType = JdbcUtils.getColumnType(getConnectionProperties(), getTableName(), getColumnName());
if (columnType.getColumnTypeEnum() == ColumnTypeEnum.LONG) {
ourLog.info("Table {} column {} is already of type LONG, no migration needed", getTableName(), getColumnName());
return;
}
String tempColumnName = getColumnName() + "_m";
executeSql(getTableName(), "alter table ? add column ? oid", getTableName(), tempColumnName);
executeSql(getTableName(), "update ? set ? = cast(? as oid) where ? is not null", getTableName(), tempColumnName, getColumnName(), getColumnName());
executeSql(getTableName(), "alter table ? drop column ?", getTableName(), getColumnName());
executeSql(getTableName(), "alter table ? rename column ? to ?", getTableName(), tempColumnName, getColumnName());
}
}

8
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/Builder.java
View File

@ -37,6 +37,7 @@ import ca.uhn.fhir.jpa.migrate.taskdef.DropIndexTask;
import ca.uhn.fhir.jpa.migrate.taskdef.DropTableTask;
import ca.uhn.fhir.jpa.migrate.taskdef.ExecuteRawSqlTask;
import ca.uhn.fhir.jpa.migrate.taskdef.InitializeSchemaTask;
import ca.uhn.fhir.jpa.migrate.taskdef.MigratePostgresTextClobToBinaryClobTask;
import ca.uhn.fhir.jpa.migrate.taskdef.ModifyColumnTask;
import ca.uhn.fhir.jpa.migrate.taskdef.NopTask;
import ca.uhn.fhir.jpa.migrate.taskdef.RenameColumnTask;
@ -248,6 +249,13 @@ public class Builder {
addTask(task);
}
public void migratePostgresTextClobToBinaryClob(String theVersion, String theColumnName) {
MigratePostgresTextClobToBinaryClobTask task = new MigratePostgresTextClobToBinaryClobTask(myRelease, theVersion);
task.setTableName(getTableName());
task.setColumnName(theColumnName);
}
public class BuilderAddIndexWithName {
private final String myVersion;
private final String myIndexName;

5
hapi-fhir-sql-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/JdbcUtilsTest.java
View File

@ -5,6 +5,8 @@ import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.sql.DataSource;
import java.sql.Connection;
@ -23,6 +25,7 @@ import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class JdbcUtilsTest {
private static final Logger ourLog = LoggerFactory.getLogger(JdbcUtilsTest.class);
@Mock
DataSource myDataSource;
@Mock
@ -32,7 +35,6 @@ public class JdbcUtilsTest {
@Mock
ResultSet myResultSet;
@Test
public void testGetColumnType_verifyTypeMappings() throws SQLException {
testGetColumnType_verifyTypeMapping(Types.BIT, ColumnTypeEnum.BOOLEAN);
@ -65,6 +67,7 @@ public class JdbcUtilsTest {
when(myDataSource.getConnection()).thenReturn(myConnection);
DriverTypeEnum.ConnectionProperties myConnectionProperties = DriverTypeEnum.H2_EMBEDDED.newConnectionProperties(myDataSource);
JdbcUtils.ColumnType testColumnType = JdbcUtils.getColumnType(myConnectionProperties, "TEST_TABLE", "TEST_COLUMN");
ourLog.info("Column type: {}", testColumnType);
assertEquals(theExpectedColumnType, testColumnType.getColumnTypeEnum());
}

2
hapi-fhir-storage/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu2.1/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

13
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/InterceptorUserDataMapDstu2Test.java
View File

@ -51,7 +51,9 @@ import java.util.Set;
import java.util.concurrent.TimeUnit;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertSame;
@ -98,15 +100,16 @@ public class InterceptorUserDataMapDstu2Test {
public void testRead() throws Exception {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1");
try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
assertEquals(200, status.getStatusLine().getStatusCode());
String output = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.debug(output);
}
try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
String response = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
assertThat(response, containsString("\"id\":\"1\""));
await().until(() -> myMapCheckMethods, contains("incomingRequestPostProcessed", "incomingRequestPreHandled", "outgoingResponse", "processingCompletedNormally", "processingCompleted"));
}
}
private void updateMapUsing(Map<Object, Object> theUserData, String theMethod) {
assertNotNull(theUserData);
if (myMap == null) {

2
hapi-fhir-structures-dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-test-utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-testpage-overlay/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu2.1/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu3/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-r4/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-r5/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

16
hapi-tinder-plugin/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -58,37 +58,37 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.apache.velocity</groupId>

2
hapi-tinder-test/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

6
pom.xml
View File

@ -6,10 +6,7 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<packaging>pom</packaging>
<version>5.6.0-PRE7-SNAPSHOT</version>
<modules>
<module>hapi-fhir-jpa</module>
</modules>
<version>5.6.0-PRE8-SNAPSHOT</version>
<name>HAPI-FHIR</name>
<description>An open-source implementation of the FHIR specification in Java.</description>
<url>https://hapifhir.io</url>
@ -2777,6 +2774,7 @@
<module>hapi-fhir-validation-resources-r4</module>
<module>hapi-fhir-structures-r5</module>
<module>hapi-fhir-validation-resources-r5</module>
<module>hapi-fhir-jpa</module>
<module>hapi-fhir-storage</module>
<module>hapi-fhir-jpaserver-cql</module>
<module>hapi-fhir-jpaserver-model</module>

2
tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

2
tests/hapi-fhir-base-test-mindeps-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

2
tests/hapi-fhir-base-test-mindeps-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE7-SNAPSHOT</version>
<version>5.6.0-PRE8-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>