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fixed batch jobs on Postgres (#5022) 

* fixed issue

* fixed pipeline issue

* review changes

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
This commit is contained in:
StevenXLi 2023-06-23 09:06:38 -04:00 committed by GitHub
parent 1f44ac1092
commit 73d6997d21
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 37 additions and 7 deletions
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4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5021-unable-to-run-batch-jobs-on-postgres.yaml Normal file
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@ -0,0 +1,4 @@
---
type: fix
issue: 5021
title: "Previously, running batch jobs with postgresql as the db will result in SQL error. This has now been fixed."

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Batch2JobInstanceEntity.java
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@ -42,6 +42,7 @@ import java.util.Date;
import static ca.uhn.fhir.batch2.model.JobDefinition.ID_MAX_LENGTH;
import static ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity.ERROR_MSG_MAX_LENGTH;
import static ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity.WARNING_MSG_MAX_LENGTH;
import static org.apache.commons.lang3.StringUtils.left;
@Entity
@ -113,8 +114,7 @@ public class Batch2JobInstanceEntity implements Serializable {
private String myEstimatedTimeRemaining;
@Column(name = "CUR_GATED_STEP_ID", length = ID_MAX_LENGTH, nullable = true)
private String myCurrentGatedStepId;
@Lob
@Column(name = "WARNING_MSG", nullable = true)
@Column(name = "WARNING_MSG", length = WARNING_MSG_MAX_LENGTH, nullable = true)
private String myWarningMessages;
/**

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Batch2WorkChunkEntity.java
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@ -53,6 +53,7 @@ import static org.apache.commons.lang3.StringUtils.left;
public class Batch2WorkChunkEntity implements Serializable {
public static final int ERROR_MSG_MAX_LENGTH = 500;
public static final int WARNING_MSG_MAX_LENGTH = 4000;
private static final long serialVersionUID = -6202771941965780558L;
@Id
@Column(name = "ID", length = ID_MAX_LENGTH)
@ -96,8 +97,7 @@ public class Batch2WorkChunkEntity implements Serializable {
private String myErrorMessage;
@Column(name = "ERROR_COUNT", nullable = false)
private int myErrorCount;
@Lob
@Column(name = "WARNING_MSG", nullable = true)
@Column(name = "WARNING_MSG", length = WARNING_MSG_MAX_LENGTH, nullable = true)
private String myWarningMessage;
/**

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
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@ -162,13 +162,15 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.onTable("BT2_WORK_CHUNK")
.addColumn("20230524.1", "WARNING_MSG")
.nullable()
.type(ColumnTypeEnum.CLOB);
.type(ColumnTypeEnum.CLOB)
.doNothing(); // the migration below is the better implementation
version
.onTable("BT2_JOB_INSTANCE")
.addColumn("20230524.2", "WARNING_MSG")
.nullable()
.type(ColumnTypeEnum.CLOB);
.type(ColumnTypeEnum.CLOB)
.doNothing(); // the migration below is the better implementation
// adding indexes to foreign keys
// this makes our table scans more efficient,
@ -277,6 +279,29 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.unique(false)
.withColumns("CONCEPT_MAP_GRP_ELM_PID")
.onlyAppliesToPlatforms(NON_AUTOMATIC_FK_INDEX_PLATFORMS);
// add warning message to batch job instance using limited varchar column to store
version
.onTable("BT2_WORK_CHUNK")
.dropColumn("20230622.1", "WARNING_MSG")
.failureAllowed();
version
.onTable("BT2_WORK_CHUNK")
.addColumn("20230622.2", "WARNING_MSG")
.nullable()
.type(ColumnTypeEnum.STRING, 4000);
version
.onTable("BT2_JOB_INSTANCE")
.dropColumn("20230622.3", "WARNING_MSG")
.failureAllowed();
version
.onTable("BT2_JOB_INSTANCE")
.addColumn("20230622.4", "WARNING_MSG")
.nullable()
.type(ColumnTypeEnum.STRING, 4000);
}
protected void init660() {

3
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/progress/InstanceProgress.java
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@ -25,6 +25,7 @@ import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.batch2.model.WorkChunkStatusEnum;
import ca.uhn.fhir.util.Logs;
import ca.uhn.fhir.util.StopWatch;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.slf4j.Logger;
@ -125,7 +126,7 @@ public class InstanceProgress {
public void updateInstance(JobInstance theInstance) {
updateInstance(theInstance, false);
String newWarningMessage = String.join("\n", myWarningMessages);
String newWarningMessage = StringUtils.right(String.join("\n", myWarningMessages), 4000);
theInstance.setWarningMessages(newWarningMessage);
}