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Rework valueset index for MySQL (#2269) 

* Rework valueset index for MySQL

* Add changelog
This commit is contained in:
James Agnew 2021-01-05 10:03:33 -05:00 committed by GitHub
parent 14fc8f2598
commit d943260927
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4 changed files with 89 additions and 7 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_0/2269-rework-valueset-index.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 2269
title: "A database index in the JPA server was added in HAPI FHIR 5.2.0 and Smile CDR 2020.11 that
exceeded the maximum index length in MySQL, preventing server upgrades on that database platform.
This has been corrected."

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConcept.java
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@ -36,11 +36,11 @@ import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
/*
* DM 2019-08-01 - Do not use IDX_VALUESET_CONCEPT_CS_CD; this was previously used as an index so reusing the name will
* DM 2019-08-01 - Do not use IDX_VALUESET_CONCEPT_CS_CD or IDX_VALUESET_CONCEPT_CS_CODE; this was previously used as an index so reusing the name will
* bork up migration tasks.
*/
@Table(name = "TRM_VALUESET_CONCEPT", uniqueConstraints = {
@UniqueConstraint(name = "IDX_VS_CONCEPT_CS_CODE", columnNames = {"VALUESET_PID", "SYSTEM_URL", "SYSTEM_VER", "CODEVAL"}),
@UniqueConstraint(name = "IDX_VS_CONCEPT_CSCD", columnNames = {"VALUESET_PID", "SYSTEM_URL", "CODEVAL"}),
@UniqueConstraint(name = "IDX_VS_CONCEPT_ORDER", columnNames = {"VALUESET_PID", "VALUESET_ORDER"})
})
@Entity()

68
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java
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@ -33,7 +33,21 @@ import org.hibernate.validator.constraints.Length;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.InstantType;
import javax.persistence.*;
import javax.persistence.Column;
import javax.persistence.Embedded;
import javax.persistence.EmbeddedId;
import javax.persistence.Entity;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.Index;
import javax.persistence.JoinColumn;
import javax.persistence.Lob;
import javax.persistence.OneToMany;
import javax.persistence.OneToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;
import javax.validation.constraints.Size;
import java.io.IOException;
import java.io.InputStream;
@ -43,7 +57,9 @@ import java.lang.reflect.Modifier;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
@ -99,6 +115,41 @@ public class TestUtil {
}
private static void scanClass(Set<String> theNames, Class<?> theClazz, boolean theIsSuperClass) {
Map<String, Integer> columnNameToLength = new HashMap<>();
scanClassOrSuperclass(theNames, theClazz, theIsSuperClass, columnNameToLength);
Table table = theClazz.getAnnotation(Table.class);
if (table != null) {
// This is the length for MySQL per https://dev.mysql.com/doc/refman/8.0/en/innodb-limits.html
// No idea why 3072.. what a weird limit but I'm sure they have their reason.
int maxIndexLength = 3072;
for (UniqueConstraint nextIndex : table.uniqueConstraints()) {
int indexLength = calculateIndexLength(nextIndex.columnNames(), columnNameToLength, theClazz, nextIndex.name());
if (indexLength > maxIndexLength) {
throw new IllegalStateException("Index '" + nextIndex.name() + "' is too long. Length is " + indexLength + " and must not exceed " + maxIndexLength + " which is the maximum MySQL length");
}
}
}
}
private static int calculateIndexLength(String[] theColumnNames, Map<String, Integer> theColumnNameToLength, Class<?> theClazz, String theIndexName) {
int retVal = 0;
for (String nextName : theColumnNames) {
Integer nextLength = theColumnNameToLength.get(nextName);
if (nextLength == null) {
throw new IllegalStateException("Index '" + theIndexName + "' references unknown column: " + nextName);
}
retVal += nextLength;
}
return retVal;
}
private static void scanClassOrSuperclass(Set<String> theNames, Class<?> theClazz, boolean theIsSuperClass, Map<String, Integer> columnNameToLength) {
ourLog.info("Scanning: {}", theClazz.getSimpleName());
Subselect subselect = theClazz.getAnnotation(Subselect.class);
@ -140,6 +191,19 @@ public class TestUtil {
isOtherSideOfOneToOneMapping ||
hasEmbeddedId ||
isField, "Non-transient has no @Column or @JoinColumn or @EmbeddedId: " + nextField);
if (hasColumn) {
String columnName = nextField.getAnnotation(Column.class).name();
int columnLength = nextField.getAnnotation(Column.class).length();
if (nextField.getType().isAssignableFrom(String.class)) {
columnLength = columnLength * 4;
} else {
columnLength = 16;
}
columnNameToLength.put(columnName, columnLength);
}
}
@ -149,7 +213,7 @@ public class TestUtil {
return;
}
scanClass(theNames, theClazz.getSuperclass(), true);
scanClassOrSuperclass(theNames, theClazz.getSuperclass(), true, columnNameToLength);
}
private static void scan(AnnotatedElement theAnnotatedElement, Set<String> theNames, boolean theIsSuperClass, boolean theIsView) {

16
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
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@ -70,7 +70,19 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
init500(); // 20200218 - 20200513
init501(); // 20200514 - 20200515
init510(); // 20200516 - 20201028
init520(); // 20201029 - Present
init520(); // 20201029 -
init530();
}
private void init530() {
Builder version = forVersion(VersionEnum.V5_3_0);
version
.onTable("TRM_VALUESET_CONCEPT")
.dropIndex("20210104.1", "IDX_VS_CONCEPT_CS_CODE");
version
.onTable("TRM_VALUESET_CONCEPT")
.addIndex("20210104.2", "IDX_VS_CONCEPT_CSCD").unique(true).withColumns("VALUESET_PID", "SYSTEM_URL", "CODEVAL").doNothing();
}
protected void init520() {
@ -174,7 +186,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
Builder.BuilderWithTableName trmValueSetComp = version.onTable("TRM_VALUESET_CONCEPT");
trmValueSetComp.addColumn("20201028.1", "SYSTEM_VER").nullable().type(ColumnTypeEnum.STRING, 200);
trmValueSetComp.dropIndex("20201028.2", "IDX_VS_CONCEPT_CS_CD");
trmValueSetComp.addIndex("20201028.3", "IDX_VS_CONCEPT_CS_CODE").unique(true).withColumns("VALUESET_PID", "SYSTEM_URL", "SYSTEM_VER", "CODEVAL");
trmValueSetComp.addIndex("20201028.3", "IDX_VS_CONCEPT_CS_CODE").unique(true).withColumns("VALUESET_PID", "SYSTEM_URL", "SYSTEM_VER", "CODEVAL").doNothing();
}
protected void init510_20200725() {