hapi-fhir-storage-api (#3006)
* rename hapi-fhir-jpaserver-migrate to hapi-fhir-sql-migrate and move hapi-tasks into jpaserver-persistence * rename hapi-fhir-jpaserver-api to hapi-fhir-storage-api * move bulk import apis * create hapi-fhir-jpa * create hapi-fhir-jpa * move CircularQueueCaptureQueriesListener to japi-fhir-jpa * move mdm logs to storage-api * move gziputil to storage-api * move quartz scheduling to hapi-fhir-jpa * move default subscription channel factory to storage-api * consolidated batch constants * correct accidental Logs change * remove dependency of cdr-api on cdr-persistence * fix javadoc * pom descriptions * review feedback
This commit is contained in:
Ken Stevens
GitHub
parent
f1f9c672ad
commit
060791aeb4
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@ -4,7 +4,7 @@
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<parent>
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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir</artifactId>
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<artifactId>hapi-fhir</artifactId>
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<version>5.6.0-PRE5-SNAPSHOT</version>
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<version>5.6.0-PRE6-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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<relativePath>../pom.xml</relativePath>
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</parent>
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</parent>
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@ -5,7 +5,7 @@
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<parent>
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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-deployable-pom</artifactId>
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<artifactId>hapi-deployable-pom</artifactId>
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<version>5.6.0-PRE5-SNAPSHOT</version>
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<version>5.6.0-PRE6-SNAPSHOT</version>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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</parent>
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</parent>
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@ -5,7 +5,7 @@
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<parent>
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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-deployable-pom</artifactId>
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<artifactId>hapi-deployable-pom</artifactId>
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<version>5.6.0-PRE5-SNAPSHOT</version>
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<version>5.6.0-PRE6-SNAPSHOT</version>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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</parent>
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</parent>
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@ -18,6 +18,9 @@
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<dependencies>
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<dependencies>
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<!-- IMPORTANT NOTE: This pom is used by multiple platforms (including Android) so please avoid adding any new
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dependencies here. -->
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<!-- JSON -->
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<!-- JSON -->
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<dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.datatype</groupId>
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<groupId>com.fasterxml.jackson.datatype</groupId>
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@ -192,4 +192,26 @@ public class TestUtil {
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return stripReturns(theString).replace(" ", "");
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return stripReturns(theString).replace(" ", "");
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}
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}
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public static void sleepAtLeast(long theMillis) {
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sleepAtLeast(theMillis, true);
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}
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@SuppressWarnings("BusyWait")
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public static void sleepAtLeast(long theMillis, boolean theLogProgress) {
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long start = System.currentTimeMillis();
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while (System.currentTimeMillis() <= start + theMillis) {
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try {
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long timeSinceStarted = System.currentTimeMillis() - start;
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long timeToSleep = Math.max(0, theMillis - timeSinceStarted);
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if (theLogProgress) {
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ourLog.info("Sleeping for {}ms", timeToSleep);
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}
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Thread.sleep(timeToSleep);
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} catch (InterruptedException e) {
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Thread.currentThread().interrupt();
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ourLog.error("Interrupted", e);
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}
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}
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}
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}
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}
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@ -1,19 +1,22 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns="http://maven.apache.org/POM/4.0.0"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-deployable-pom</artifactId>
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<artifactId>hapi-deployable-pom</artifactId>
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<version>5.6.0-PRE5-SNAPSHOT</version>
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<version>5.6.0-PRE6-SNAPSHOT</version>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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</parent>
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</parent>
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<artifactId>hapi-fhir-jpaserver-batch</artifactId>
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<artifactId>hapi-fhir-batch</artifactId>
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<packaging>jar</packaging>
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<packaging>jar</packaging>
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<name>HAPI FHIR JPA Server - Batch Task Processor</name>
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<name>HAPI FHIR JPA Server - Batch Task Processor</name>
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<description>Default implementation of batch job submitter along with constants used by the different hapi-fhir batch
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jobs.
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</description>
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<dependencies>
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<dependencies>
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<dependency>
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<dependency>
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@ -24,10 +27,6 @@
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<groupId>org.springframework.batch</groupId>
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<groupId>org.springframework.batch</groupId>
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<artifactId>spring-batch-infrastructure</artifactId>
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<artifactId>spring-batch-infrastructure</artifactId>
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</dependency>
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</dependency>
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<dependency>
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<groupId>org.springframework.data</groupId>
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<artifactId>spring-data-jpa</artifactId>
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</dependency>
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<dependency>
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<dependency>
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<groupId>javax.annotation</groupId>
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<groupId>javax.annotation</groupId>
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<artifactId>javax.annotation-api</artifactId>
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<artifactId>javax.annotation-api</artifactId>
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@ -0,0 +1,81 @@
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package ca.uhn.fhir.jpa.batch.config;
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/*-
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* #%L
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* HAPI FHIR JPA Server - Batch Task Processor
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* %%
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* Copyright (C) 2014 - 2021 Smile CDR, Inc.
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.Set;
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public final class BatchConstants {
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public static final String JOB_PARAM_REQUEST_LIST = "url-list";
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public static final String JOB_PARAM_BATCH_SIZE = "batch-size";
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public static final String JOB_PARAM_START_TIME = "start-time";
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public static final String CURRENT_URL_INDEX = "current.url-index";
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public static final String CURRENT_THRESHOLD_HIGH = "current.threshold-high";
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public static final String JOB_UUID_PARAMETER = "jobUUID";
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public static final String JOB_LAUNCHING_TASK_EXECUTOR = "jobLaunchingTaskExecutor";
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public static final String BULK_EXPORT_JOB_NAME = "bulkExportJob";
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public static final String GROUP_BULK_EXPORT_JOB_NAME = "groupBulkExportJob";
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public static final String PATIENT_BULK_EXPORT_JOB_NAME = "patientBulkExportJob";
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public static final String BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP = "bulkExportGenerateResourceFilesStep";
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public static final String BULK_IMPORT_JOB_NAME = "bulkImportJob";
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public static final String BULK_IMPORT_PROCESSING_STEP = "bulkImportProcessingStep";
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/**
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* Delete Expunge
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*/
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public static final String DELETE_EXPUNGE_JOB_NAME = "deleteExpungeJob";
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/**
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* Reindex
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*/
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public static final String REINDEX_JOB_NAME = "reindexJob";
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/**
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* Reindex Everything
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*/
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public static final String REINDEX_EVERYTHING_JOB_NAME = "reindexEverythingJob";
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/**
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* MDM Clear
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*/
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public static final String MDM_CLEAR_JOB_NAME = "mdmClearJob";
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/**
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* This Set contains the step names across all job types that are appropriate for
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* someone to look at the write count for that given step in order to determine the
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* number of processed records.
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* <p>
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* This is provided since a job might have multiple steps that the same data passes
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* through, so you can't just sum up the total of all of them.
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* <p>
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* For any given batch job type, there should only be one step name in this set
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*/
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public static Set<String> RECORD_PROCESSING_STEP_NAMES;
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static {
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HashSet<String> recordProcessingStepNames = new HashSet<>();
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recordProcessingStepNames.add(BatchConstants.BULK_IMPORT_PROCESSING_STEP);
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recordProcessingStepNames.add(BatchConstants.BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP);
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BatchConstants.RECORD_PROCESSING_STEP_NAMES = Collections.unmodifiableSet(recordProcessingStepNames);
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}
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/**
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* v * Non instantiable
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*/
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private BatchConstants() {
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}
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}
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@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.batch.config;
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* #L%
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* #L%
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*/
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*/
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import ca.uhn.fhir.jpa.batch.BatchConstants;
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import org.springframework.batch.core.configuration.annotation.DefaultBatchConfigurer;
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import org.springframework.batch.core.configuration.annotation.DefaultBatchConfigurer;
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import org.springframework.batch.core.explore.JobExplorer;
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import org.springframework.batch.core.explore.JobExplorer;
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import org.springframework.batch.core.explore.support.MapJobExplorerFactoryBean;
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import org.springframework.batch.core.explore.support.MapJobExplorerFactoryBean;
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@ -22,7 +22,6 @@ public class BatchJobConfig {
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private StepBuilderFactory myStepBuilderFactory;
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private StepBuilderFactory myStepBuilderFactory;
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@Bean
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@Bean
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public Job testJob() {
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public Job testJob() {
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return myJobBuilderFactory.get("testJob")
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return myJobBuilderFactory.get("testJob")
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@ -28,6 +28,7 @@ public class TestBatchConfig {
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asyncTaskExecutor.initialize();
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asyncTaskExecutor.initialize();
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return asyncTaskExecutor;
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return asyncTaskExecutor;
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}
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}
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@Bean
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@Bean
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public BatchConfigurer batchConfigurer() {
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public BatchConfigurer batchConfigurer() {
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return new NonPersistedBatchConfigurer();
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return new NonPersistedBatchConfigurer();
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@ -8,7 +8,8 @@
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</encoder>
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</encoder>
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</appender>
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</appender>
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<logger name="org.springframework.web.socket.handler.ExceptionWebSocketHandlerDecorator" additivity="false" level="info">
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<logger name="org.springframework.web.socket.handler.ExceptionWebSocketHandlerDecorator" additivity="false"
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level="info">
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<appender-ref ref="STDOUT"/>
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<appender-ref ref="STDOUT"/>
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</logger>
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</logger>
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@ -48,7 +49,9 @@
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<appender-ref ref="STDOUT"/>
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<appender-ref ref="STDOUT"/>
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</logger>
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</logger>
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<appender name="BATCH_TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
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<appender name="BATCH_TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
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<filter class="ch.qos.logback.classic.filter.ThresholdFilter"><level>INFO</level></filter>
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<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
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<level>INFO</level>
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</filter>
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<file>${smile.basedir}/log/batch-troubleshooting.log</file>
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<file>${smile.basedir}/log/batch-troubleshooting.log</file>
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<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
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<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
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<fileNamePattern>${smile.basedir}/log/batch-troubleshooting.log.%i.gz</fileNamePattern>
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<fileNamePattern>${smile.basedir}/log/batch-troubleshooting.log.%i.gz</fileNamePattern>
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@ -59,7 +62,8 @@
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<maxFileSize>5MB</maxFileSize>
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<maxFileSize>5MB</maxFileSize>
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</triggeringPolicy>
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</triggeringPolicy>
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<encoder>
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<encoder>
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<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n${log.stackfilter.pattern}</pattern>
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<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n${log.stackfilter.pattern}
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|
</pattern>
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</encoder>
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</encoder>
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</appender>
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</appender>
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<logger name="ca.uhn.fhir.log.batch_troubleshooting" level="TRACE">
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<logger name="ca.uhn.fhir.log.batch_troubleshooting" level="TRACE">
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@ -3,14 +3,14 @@
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<modelVersion>4.0.0</modelVersion>
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<modelVersion>4.0.0</modelVersion>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<groupId>ca.uhn.hapi.fhir</groupId>
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||||||
<artifactId>hapi-fhir-bom</artifactId>
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<artifactId>hapi-fhir-bom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
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<packaging>pom</packaging>
|
<packaging>pom</packaging>
|
||||||
<name>HAPI FHIR BOM</name>
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<name>HAPI FHIR BOM</name>
|
||||||
|
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
@ -133,7 +133,7 @@
|
||||||
</dependency>
|
</dependency>
|
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<dependency>
|
<dependency>
|
||||||
<groupId>${project.groupId}</groupId>
|
<groupId>${project.groupId}</groupId>
|
||||||
<artifactId>hapi-fhir-jpaserver-migrate</artifactId>
|
<artifactId>hapi-fhir-sql-migrate</artifactId>
|
||||||
<version>${project.version}</version>
|
<version>${project.version}</version>
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
|
|
|
||||||
|
|
@ -4,7 +4,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
|
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
@ -35,7 +35,7 @@
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-fhir-jpaserver-migrate</artifactId>
|
<artifactId>hapi-fhir-sql-migrate</artifactId>
|
||||||
<version>${project.version}</version>
|
<version>${project.version}</version>
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
|
|
|
||||||
|
|
@ -6,7 +6,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-fhir-cli</artifactId>
|
<artifactId>hapi-fhir-cli</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../pom.xml</relativePath>
|
<relativePath>../pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -6,7 +6,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../../hapi-deployable-pom</relativePath>
|
<relativePath>../../hapi-deployable-pom</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -5,7 +5,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-fhir</artifactId>
|
<artifactId>hapi-fhir</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../pom.xml</relativePath>
|
<relativePath>../pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -4,7 +4,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -4,7 +4,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -5,7 +5,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -5,7 +5,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-fhir</artifactId>
|
<artifactId>hapi-fhir</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../pom.xml</relativePath>
|
<relativePath>../pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -5,7 +5,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,5 @@
|
||||||
---
|
---
|
||||||
type: change
|
type: change
|
||||||
issue: 2446
|
issue: 2446
|
||||||
title: "DaoConfig setting for [Populate Identifier In Auto Created Placeholder Reference Targets](https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(boolean))
|
title: "DaoConfig setting for [Populate Identifier In Auto Created Placeholder Reference Targets](https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(boolean))
|
||||||
now defaults to `true`."
|
now defaults to `true`."
|
||||||
|
|
|
||||||
|
|
@ -9,7 +9,7 @@ See the [Modules Page](/docs/getting_started/modules.html) for more information
|
||||||
* [Model API (R5)](/apidocs/hapi-fhir-structures-r5/) - hapi-fhir-structures-r5
|
* [Model API (R5)](/apidocs/hapi-fhir-structures-r5/) - hapi-fhir-structures-r5
|
||||||
* [Client API](/apidocs/hapi-fhir-client/) - hapi-fhir-client
|
* [Client API](/apidocs/hapi-fhir-client/) - hapi-fhir-client
|
||||||
* [Plain Server API](/apidocs/hapi-fhir-server/) - hapi-fhir-server
|
* [Plain Server API](/apidocs/hapi-fhir-server/) - hapi-fhir-server
|
||||||
* [JPA Server - API](/apidocs/hapi-fhir-jpaserver-api/) - hapi-fhir-jpaserver-api
|
* [JPA Server - API](/apidocs/hapi-fhir-storage-api/) - hapi-fhir-storage-api
|
||||||
* [JPA Server - Model](/apidocs/hapi-fhir-jpaserver-model/) - hapi-fhir-jpaserver-model
|
* [JPA Server - Model](/apidocs/hapi-fhir-jpaserver-model/) - hapi-fhir-jpaserver-model
|
||||||
* [JPA Server - Base](/apidocs/hapi-fhir-jpaserver-base/) - hapi-fhir-jpaserver-base
|
* [JPA Server - Base](/apidocs/hapi-fhir-jpaserver-base/) - hapi-fhir-jpaserver-base
|
||||||
* [Version Converter API](/apidocs/hapi-fhir-converter/) - hapi-fhir-converter
|
* [Version Converter API](/apidocs/hapi-fhir-converter/) - hapi-fhir-converter
|
||||||
|
|
|
||||||
|
|
@ -54,9 +54,15 @@ In some cases, you may have references which are <i>Logical References</i>,
|
||||||
which means that they act as an identifier and not necessarily as a literal
|
which means that they act as an identifier and not necessarily as a literal
|
||||||
web address.
|
web address.
|
||||||
|
|
||||||
A common use for logical references is in references to conformance resources, such as ValueSets, StructureDefinitions, etc. For example, you might refer to the ValueSet `http://hl7.org/fhir/ValueSet/quantity-comparator` from your own resources. In this case, you are not necessarily telling the server that this is a real address that it should resolve, but rather that this is an identifier for a ValueSet where `ValueSet.url` has the given URI/URL.
|
A common use for logical references is in references to conformance resources, such as ValueSets, StructureDefinitions,
|
||||||
|
etc. For example, you might refer to the ValueSet `http://hl7.org/fhir/ValueSet/quantity-comparator` from your own
|
||||||
|
resources. In this case, you are not necessarily telling the server that this is a real address that it should resolve,
|
||||||
|
but rather that this is an identifier for a ValueSet where `ValueSet.url` has the given URI/URL.
|
||||||
|
|
||||||
HAPI can be configured to treat certain URI/URL patterns as logical by using the DaoConfig#setTreatReferencesAsLogical property (see [JavaDoc](/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setTreatReferencesAsLogical(java.util.Set))).
|
HAPI can be configured to treat certain URI/URL patterns as logical by using the DaoConfig#setTreatReferencesAsLogical
|
||||||
|
property (
|
||||||
|
see [JavaDoc](/hapi-fhir/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setTreatReferencesAsLogical(java.util.Set)))
|
||||||
|
.
|
||||||
|
|
||||||
For example:
|
For example:
|
||||||
|
|
||||||
|
|
@ -131,5 +137,5 @@ X-Retry-On-Version-Conflict: retry; max-retries=100
|
||||||
|
|
||||||
Delete with expunge submits a job to delete and expunge the requested resources. This is done in batches. If the DELETE
|
Delete with expunge submits a job to delete and expunge the requested resources. This is done in batches. If the DELETE
|
||||||
?_expunge=true syntax is used to trigger the delete expunge, then the batch size will be determined by the value
|
?_expunge=true syntax is used to trigger the delete expunge, then the batch size will be determined by the value
|
||||||
of [Expunge Batch Size](/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#getExpungeBatchSize())
|
of [Expunge Batch Size](/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#getExpungeBatchSize())
|
||||||
property.
|
property.
|
||||||
|
|
|
||||||
|
|
@ -24,9 +24,13 @@ The grouping of Observation resources by `Observation.code` means that the `$las
|
||||||
|
|
||||||
# Deployment and Configuration
|
# Deployment and Configuration
|
||||||
|
|
||||||
The `$lastn` operation is disabled by default. The operation can be enabled by setting the DaoConfig#setLastNEnabled property (see [JavaDoc](/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setLastNEnabled(boolean))).
|
The `$lastn` operation is disabled by default. The operation can be enabled by setting the DaoConfig#setLastNEnabled
|
||||||
|
property (
|
||||||
|
see [JavaDoc](/hapi-fhir/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setLastNEnabled(boolean)))
|
||||||
|
.
|
||||||
|
|
||||||
In addition, the Elasticsearch client service, `ElasticsearchSvcImpl` will need to be instantiated with parameters specifying how to connect to the Elasticsearch server, for e.g.:
|
In addition, the Elasticsearch client service, `ElasticsearchSvcImpl` will need to be instantiated with parameters
|
||||||
|
specifying how to connect to the Elasticsearch server, for e.g.:
|
||||||
|
|
||||||
```java
|
```java
|
||||||
@Bean()
|
@Bean()
|
||||||
|
|
|
||||||
|
|
@ -240,9 +240,18 @@ The complete raw contents of the resource is stored in the `RES_TEXT` column, us
|
||||||
|
|
||||||
By default, the **HFJ_RESOURCE.RES_ID** column is used as the resource ID for all server-assigned IDs. For example, if a Patient resource is created in a completely empty database, it will be assigned the ID `Patient/1` by the server and RES_ID will have a value of 1.
|
By default, the **HFJ_RESOURCE.RES_ID** column is used as the resource ID for all server-assigned IDs. For example, if a Patient resource is created in a completely empty database, it will be assigned the ID `Patient/1` by the server and RES_ID will have a value of 1.
|
||||||
|
|
||||||
However, when client-assigned IDs are used, these may contain text values to allow a client to create an ID such as `Patient/ABC`. When a client-assigned ID is given to a resource, a row is created in the **HFJ_RESOURCE** table. When an **HFJ_FORCED_ID** row exists corresponding to the equivalent **HFJ_RESOURCE** row, the RES_ID value is no longer visible or usable by FHIR clients and it becomes purely an internal ID to the JPA server.
|
However, when client-assigned IDs are used, these may contain text values to allow a client to create an ID such
|
||||||
|
as `Patient/ABC`. When a client-assigned ID is given to a resource, a row is created in the **HFJ_RESOURCE** table. When
|
||||||
|
an **HFJ_FORCED_ID** row exists corresponding to the equivalent **HFJ_RESOURCE** row, the RES_ID value is no longer
|
||||||
|
visible or usable by FHIR clients and it becomes purely an internal ID to the JPA server.
|
||||||
|
|
||||||
If the server has been configured with a [Resource Server ID Strategy](/apidocs/hapi-fhir-jpaserver-api/undefined/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setResourceServerIdStrategy(ca.uhn.fhir.jpa.api.config.DaoConfig.IdStrategyEnum)) of [UUID](/apidocs/hapi-fhir-jpaserver-api/undefined/ca/uhn/fhir/jpa/api/config/DaoConfig.IdStrategyEnum.html#UUID), or the server has been configured with a [Resource Client ID Strategy](/apidocs/hapi-fhir-jpaserver-api/undefined/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setResourceClientIdStrategy(ca.uhn.fhir.jpa.api.config.DaoConfig.ClientIdStrategyEnum)) of [ANY](/apidocs/hapi-fhir-jpaserver-api/undefined/ca/uhn/fhir/jpa/api/config/DaoConfig.ClientIdStrategyEnum.html#ANY) the server will create a Forced ID for all resources (not only resources having textual IDs).
|
If the server has been configured with
|
||||||
|
a [Resource Server ID Strategy](/apidocs/hapi-fhir-storage-api/undefined/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setResourceServerIdStrategy(ca.uhn.fhir.jpa.api.config.DaoConfig.IdStrategyEnum))
|
||||||
|
of [UUID](/apidocs/hapi-fhir-storage-api/undefined/ca/uhn/fhir/jpa/api/config/DaoConfig.IdStrategyEnum.html#UUID), or
|
||||||
|
the server has been configured with
|
||||||
|
a [Resource Client ID Strategy](/apidocs/hapi-fhir-storage-api/undefined/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setResourceClientIdStrategy(ca.uhn.fhir.jpa.api.config.DaoConfig.ClientIdStrategyEnum))
|
||||||
|
of [ANY](/apidocs/hapi-fhir-storage-api/undefined/ca/uhn/fhir/jpa/api/config/DaoConfig.ClientIdStrategyEnum.html#ANY)
|
||||||
|
the server will create a Forced ID for all resources (not only resources having textual IDs).
|
||||||
|
|
||||||
## Columns
|
## Columns
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -25,7 +25,10 @@ One important caveat is that chaining is currently not supported when using this
|
||||||
|
|
||||||
## Enabling MDM Expansion
|
## Enabling MDM Expansion
|
||||||
|
|
||||||
On top of needing to instantiate an MDM module, you must enable this feature in the [DaoConfig](/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html) bean, using the [Allow MDM Expansion](/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setAllowMdmExpansion(boolean)) property.
|
On top of needing to instantiate an MDM module, you must enable this feature in
|
||||||
|
the [DaoConfig](/hapi-fhir/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html) bean, using
|
||||||
|
the [Allow MDM Expansion](/hapi-fhir/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setAllowMdmExpansion(boolean))
|
||||||
|
property.
|
||||||
|
|
||||||
<div class="helpWarningCalloutBox">
|
<div class="helpWarningCalloutBox">
|
||||||
It is important to note that enabling this functionality can lead to incorrect data being returned by a request, if your MDM links are incorrect. Use with caution.
|
It is important to note that enabling this functionality can lead to incorrect data being returned by a request, if your MDM links are incorrect. Use with caution.
|
||||||
|
|
|
||||||
|
|
@ -601,7 +601,7 @@ This operation takes two optional Parameters.
|
||||||
<td>0..1</td>
|
<td>0..1</td>
|
||||||
<td>
|
<td>
|
||||||
The number of links that should be deleted at a time. If ommitted, then the batch size will be determined by the value
|
The number of links that should be deleted at a time. If ommitted, then the batch size will be determined by the value
|
||||||
of [Expunge Batch Size](/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#getExpungeBatchSize())
|
of [Expunge Batch Size](/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#getExpungeBatchSize())
|
||||||
property.
|
property.
|
||||||
</td>
|
</td>
|
||||||
</tr>
|
</tr>
|
||||||
|
|
|
||||||
|
|
@ -53,9 +53,12 @@ In a partitioned repository, it is important to understand that only a single po
|
||||||
|
|
||||||
This fact can have security implications:
|
This fact can have security implications:
|
||||||
|
|
||||||
* A client might be blocked from creating `Patient/ABC` in the partition they have access to because this ID is already in use in another partition.
|
* A client might be blocked from creating `Patient/ABC` in the partition they have access to because this ID is already
|
||||||
|
in use in another partition.
|
||||||
|
|
||||||
* In a server using the default configuration of SEQUENTIAL_NUMERIC [Server ID Strategy](/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setResourceServerIdStrategy(ca.uhn.fhir.jpa.api.config.DaoConfig.IdStrategyEnum)) a client may be able to infer the IDs of resources in other partitions based on the ID they were assigned.
|
* In a server using the default configuration of
|
||||||
|
SEQUENTIAL_NUMERIC [Server ID Strategy](/hapi-fhir/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setResourceServerIdStrategy(ca.uhn.fhir.jpa.api.config.DaoConfig.IdStrategyEnum))
|
||||||
|
a client may be able to infer the IDs of resources in other partitions based on the ID they were assigned.
|
||||||
|
|
||||||
These considerations can be addressed by using UUID Server ID Strategy, and disallowing client-assigned IDs.
|
These considerations can be addressed by using UUID Server ID Strategy, and disallowing client-assigned IDs.
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -11,7 +11,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
@ -118,7 +118,7 @@
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-fhir-jpaserver-api</artifactId>
|
<artifactId>hapi-fhir-storage-api</artifactId>
|
||||||
<version>${project.version}</version>
|
<version>${project.version}</version>
|
||||||
</dependency>
|
</dependency>
|
||||||
</dependencies>
|
</dependencies>
|
||||||
|
|
|
||||||
|
|
@ -4,7 +4,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,119 @@
|
||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xmlns="http://maven.apache.org/POM/4.0.0"
|
||||||
|
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||||
|
<parent>
|
||||||
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
|
</parent>
|
||||||
|
<modelVersion>4.0.0</modelVersion>
|
||||||
|
|
||||||
|
<artifactId>hapi-fhir-jpa</artifactId>
|
||||||
|
<description>This project contains utility classes for working with spring-hibernate jpa and the Quartz Scheduler.
|
||||||
|
</description>
|
||||||
|
|
||||||
|
<dependencies>
|
||||||
|
<dependency>
|
||||||
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
|
<artifactId>hapi-fhir-base</artifactId>
|
||||||
|
<version>${project.version}</version>
|
||||||
|
</dependency>
|
||||||
|
|
||||||
|
<dependency>
|
||||||
|
<groupId>javax.annotation</groupId>
|
||||||
|
<artifactId>javax.annotation-api</artifactId>
|
||||||
|
</dependency>
|
||||||
|
<!-- for date logging -->
|
||||||
|
<dependency>
|
||||||
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
|
<artifactId>hapi-fhir-structures-r4</artifactId>
|
||||||
|
<version>${project.version}</version>
|
||||||
|
</dependency>
|
||||||
|
|
||||||
|
<!-- Hibernate -->
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.hibernate</groupId>
|
||||||
|
<artifactId>hibernate-entitymanager</artifactId>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.hibernate</groupId>
|
||||||
|
<artifactId>hibernate-java8</artifactId>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.hibernate</groupId>
|
||||||
|
<artifactId>hibernate-ehcache</artifactId>
|
||||||
|
<exclusions>
|
||||||
|
<exclusion>
|
||||||
|
<groupId>net.sf.ehcache</groupId>
|
||||||
|
<artifactId>ehcache-core</artifactId>
|
||||||
|
</exclusion>
|
||||||
|
</exclusions>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.hibernate.validator</groupId>
|
||||||
|
<artifactId>hibernate-validator</artifactId>
|
||||||
|
<exclusions>
|
||||||
|
<exclusion>
|
||||||
|
<groupId>com.fasterxml</groupId>
|
||||||
|
<artifactId>classmate</artifactId>
|
||||||
|
</exclusion>
|
||||||
|
<exclusion>
|
||||||
|
<groupId>org.jboss.logging</groupId>
|
||||||
|
<artifactId>jboss-logging</artifactId>
|
||||||
|
</exclusion>
|
||||||
|
</exclusions>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.hibernate.search</groupId>
|
||||||
|
<artifactId>hibernate-search-mapper-orm</artifactId>
|
||||||
|
<exclusions>
|
||||||
|
<exclusion>
|
||||||
|
<groupId>org.apache.logging.log4j</groupId>
|
||||||
|
<artifactId>log4j-api</artifactId>
|
||||||
|
</exclusion>
|
||||||
|
</exclusions>
|
||||||
|
</dependency>
|
||||||
|
<!-- Spring -->
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.springframework</groupId>
|
||||||
|
<artifactId>spring-beans</artifactId>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.springframework</groupId>
|
||||||
|
<artifactId>spring-orm</artifactId>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.springframework</groupId>
|
||||||
|
<artifactId>spring-context</artifactId>
|
||||||
|
<exclusions>
|
||||||
|
<exclusion>
|
||||||
|
<artifactId>xml-apis</artifactId>
|
||||||
|
<groupId>xml-apis</groupId>
|
||||||
|
</exclusion>
|
||||||
|
</exclusions>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.springframework</groupId>
|
||||||
|
<artifactId>spring-context-support</artifactId>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>net.ttddyy</groupId>
|
||||||
|
<artifactId>datasource-proxy</artifactId>
|
||||||
|
</dependency>
|
||||||
|
|
||||||
|
<!-- Quartz Scheduler -->
|
||||||
|
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.quartz-scheduler</groupId>
|
||||||
|
<artifactId>quartz</artifactId>
|
||||||
|
</dependency>
|
||||||
|
|
||||||
|
<!-- Apache -->
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.apache.commons</groupId>
|
||||||
|
<artifactId>commons-collections4</artifactId>
|
||||||
|
</dependency>
|
||||||
|
</dependencies>
|
||||||
|
</project>
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.config;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -23,7 +23,6 @@ package ca.uhn.fhir.jpa.config;
|
||||||
import org.hibernate.cfg.AvailableSettings;
|
import org.hibernate.cfg.AvailableSettings;
|
||||||
import org.hibernate.query.criteria.LiteralHandlingMode;
|
import org.hibernate.query.criteria.LiteralHandlingMode;
|
||||||
import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
|
import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
|
||||||
import org.springframework.beans.factory.annotation.Autowired;
|
|
||||||
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
|
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
|
||||||
import org.springframework.orm.hibernate5.SpringBeanContainer;
|
import org.springframework.orm.hibernate5.SpringBeanContainer;
|
||||||
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
|
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.model.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Model
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.model.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Model
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.model.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Model
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.model.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Model
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.model.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Model
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -20,8 +20,7 @@ package ca.uhn.fhir.jpa.sched;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import org.hl7.fhir.r5.model.InstantType;
|
import org.hl7.fhir.r4.model.InstantType;
|
||||||
import org.hl7.fhir.utilities.DateTimeUtil;
|
|
||||||
import org.quartz.JobKey;
|
import org.quartz.JobKey;
|
||||||
import org.quartz.spi.TriggerFiredBundle;
|
import org.quartz.spi.TriggerFiredBundle;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -27,7 +27,15 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||||
import com.google.common.annotations.VisibleForTesting;
|
import com.google.common.annotations.VisibleForTesting;
|
||||||
import com.google.common.collect.Sets;
|
import com.google.common.collect.Sets;
|
||||||
import org.apache.commons.lang3.Validate;
|
import org.apache.commons.lang3.Validate;
|
||||||
import org.quartz.*;
|
import org.quartz.JobDataMap;
|
||||||
|
import org.quartz.JobKey;
|
||||||
|
import org.quartz.ScheduleBuilder;
|
||||||
|
import org.quartz.Scheduler;
|
||||||
|
import org.quartz.SchedulerException;
|
||||||
|
import org.quartz.SimpleScheduleBuilder;
|
||||||
|
import org.quartz.Trigger;
|
||||||
|
import org.quartz.TriggerBuilder;
|
||||||
|
import org.quartz.TriggerKey;
|
||||||
import org.quartz.impl.JobDetailImpl;
|
import org.quartz.impl.JobDetailImpl;
|
||||||
import org.quartz.impl.StdSchedulerFactory;
|
import org.quartz.impl.StdSchedulerFactory;
|
||||||
import org.quartz.impl.matchers.GroupMatcher;
|
import org.quartz.impl.matchers.GroupMatcher;
|
||||||
|
|
@ -41,8 +49,6 @@ import java.util.Set;
|
||||||
import java.util.concurrent.atomic.AtomicInteger;
|
import java.util.concurrent.atomic.AtomicInteger;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import static org.quartz.impl.StdSchedulerFactory.PROP_SCHED_INSTANCE_NAME;
|
|
||||||
|
|
||||||
public abstract class BaseHapiScheduler implements IHapiScheduler {
|
public abstract class BaseHapiScheduler implements IHapiScheduler {
|
||||||
private static final Logger ourLog = LoggerFactory.getLogger(BaseHapiScheduler.class);
|
private static final Logger ourLog = LoggerFactory.getLogger(BaseHapiScheduler.class);
|
||||||
|
|
||||||
|
|
@ -96,7 +102,7 @@ public abstract class BaseHapiScheduler implements IHapiScheduler {
|
||||||
|
|
||||||
protected void setProperties() {
|
protected void setProperties() {
|
||||||
addProperty("org.quartz.threadPool.threadCount", "4");
|
addProperty("org.quartz.threadPool.threadCount", "4");
|
||||||
myProperties.setProperty(PROP_SCHED_INSTANCE_NAME, myInstanceName + "-" + nextSchedulerId());
|
myProperties.setProperty(StdSchedulerFactory.PROP_SCHED_INSTANCE_NAME, myInstanceName + "-" + nextSchedulerId());
|
||||||
addProperty("org.quartz.threadPool.threadNamePrefix", getThreadPrefix());
|
addProperty("org.quartz.threadPool.threadNamePrefix", getThreadPrefix());
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.sched;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.util;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.util;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -24,7 +24,7 @@ import ca.uhn.fhir.util.StopWatch;
|
||||||
import com.google.common.collect.Queues;
|
import com.google.common.collect.Queues;
|
||||||
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
|
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
|
||||||
import org.apache.commons.collections4.queue.CircularFifoQueue;
|
import org.apache.commons.collections4.queue.CircularFifoQueue;
|
||||||
import org.hl7.fhir.dstu3.model.InstantType;
|
import org.hl7.fhir.r4.model.InstantType;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.util;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.util;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.util;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.util;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.util;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* hapi-fhir-jpa
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.util;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
|
|
||||||
import ca.uhn.fhir.rest.api.Constants;
|
import ca.uhn.fhir.rest.api.Constants;
|
||||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||||
import com.google.common.collect.ImmutableSet;
|
import com.google.common.collect.ImmutableSet;
|
||||||
|
|
@ -347,16 +346,12 @@ public class TestUtil {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
public static void sleepAtLeast(long theMillis) {
|
|
||||||
HapiTransactionService.sleepAtLeast(theMillis, true);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static InstantType getTimestamp(IBaseResource resource) {
|
public static InstantType getTimestamp(IBaseResource resource) {
|
||||||
return new InstantType(new Date(resource.getMeta().getLastUpdated().getTime()));
|
return new InstantType(new Date(resource.getMeta().getLastUpdated().getTime()));
|
||||||
}
|
}
|
||||||
|
|
||||||
public static void sleepOneClick() {
|
public static void sleepOneClick() {
|
||||||
sleepAtLeast(1);
|
ca.uhn.fhir.util.TestUtil.sleepAtLeast(1);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -5,7 +5,7 @@
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-deployable-pom</artifactId>
|
<artifactId>hapi-deployable-pom</artifactId>
|
||||||
<version>5.6.0-PRE5-SNAPSHOT</version>
|
<version>5.6.0-PRE6-SNAPSHOT</version>
|
||||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
|
|
@ -90,6 +90,11 @@
|
||||||
<artifactId>hapi-fhir-jpaserver-searchparam</artifactId>
|
<artifactId>hapi-fhir-jpaserver-searchparam</artifactId>
|
||||||
<version>${project.version}</version>
|
<version>${project.version}</version>
|
||||||
</dependency>
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
|
<artifactId>hapi-fhir-sql-migrate</artifactId>
|
||||||
|
<version>${project.version}</version>
|
||||||
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-fhir-jpaserver-model</artifactId>
|
<artifactId>hapi-fhir-jpaserver-model</artifactId>
|
||||||
|
|
@ -147,13 +152,9 @@
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||||
<artifactId>hapi-fhir-jpaserver-batch</artifactId>
|
<artifactId>hapi-fhir-batch</artifactId>
|
||||||
<version>${project.version}</version>
|
<version>${project.version}</version>
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
|
||||||
<groupId>net.ttddyy</groupId>
|
|
||||||
<artifactId>datasource-proxy</artifactId>
|
|
||||||
</dependency>
|
|
||||||
|
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>ch.qos.logback</groupId>
|
<groupId>ch.qos.logback</groupId>
|
||||||
|
|
@ -307,12 +308,6 @@
|
||||||
<scope>provided</scope>
|
<scope>provided</scope>
|
||||||
</dependency>
|
</dependency>
|
||||||
|
|
||||||
<dependency>
|
|
||||||
<groupId>org.quartz-scheduler</groupId>
|
|
||||||
<artifactId>quartz</artifactId>
|
|
||||||
</dependency>
|
|
||||||
|
|
||||||
|
|
||||||
<!-- Spring -->
|
<!-- Spring -->
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.springframework</groupId>
|
<groupId>org.springframework</groupId>
|
||||||
|
|
@ -324,24 +319,6 @@
|
||||||
</exclusion>
|
</exclusion>
|
||||||
</exclusions>
|
</exclusions>
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
|
||||||
<groupId>org.springframework</groupId>
|
|
||||||
<artifactId>spring-orm</artifactId>
|
|
||||||
</dependency>
|
|
||||||
<dependency>
|
|
||||||
<groupId>org.springframework</groupId>
|
|
||||||
<artifactId>spring-context</artifactId>
|
|
||||||
<exclusions>
|
|
||||||
<exclusion>
|
|
||||||
<artifactId>xml-apis</artifactId>
|
|
||||||
<groupId>xml-apis</groupId>
|
|
||||||
</exclusion>
|
|
||||||
</exclusions>
|
|
||||||
</dependency>
|
|
||||||
<dependency>
|
|
||||||
<groupId>org.springframework</groupId>
|
|
||||||
<artifactId>spring-beans</artifactId>
|
|
||||||
</dependency>
|
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.springframework.data</groupId>
|
<groupId>org.springframework.data</groupId>
|
||||||
<artifactId>spring-data-jpa</artifactId>
|
<artifactId>spring-data-jpa</artifactId>
|
||||||
|
|
@ -376,40 +353,6 @@
|
||||||
<groupId>org.springframework</groupId>
|
<groupId>org.springframework</groupId>
|
||||||
<artifactId>spring-websocket</artifactId>
|
<artifactId>spring-websocket</artifactId>
|
||||||
</dependency>
|
</dependency>
|
||||||
|
|
||||||
<!-- Hibernate -->
|
|
||||||
<dependency>
|
|
||||||
<groupId>org.hibernate</groupId>
|
|
||||||
<artifactId>hibernate-entitymanager</artifactId>
|
|
||||||
</dependency>
|
|
||||||
<dependency>
|
|
||||||
<groupId>org.hibernate</groupId>
|
|
||||||
<artifactId>hibernate-java8</artifactId>
|
|
||||||
</dependency>
|
|
||||||
<dependency>
|
|
||||||
<groupId>org.hibernate</groupId>
|
|
||||||
<artifactId>hibernate-ehcache</artifactId>
|
|
||||||
<exclusions>
|
|
||||||
<exclusion>
|
|
||||||
<groupId>net.sf.ehcache</groupId>
|
|
||||||
<artifactId>ehcache-core</artifactId>
|
|
||||||
</exclusion>
|
|
||||||
</exclusions>
|
|
||||||
</dependency>
|
|
||||||
<dependency>
|
|
||||||
<groupId>org.hibernate.validator</groupId>
|
|
||||||
<artifactId>hibernate-validator</artifactId>
|
|
||||||
<exclusions>
|
|
||||||
<exclusion>
|
|
||||||
<groupId>com.fasterxml</groupId>
|
|
||||||
<artifactId>classmate</artifactId>
|
|
||||||
</exclusion>
|
|
||||||
<exclusion>
|
|
||||||
<groupId>org.jboss.logging</groupId>
|
|
||||||
<artifactId>jboss-logging</artifactId>
|
|
||||||
</exclusion>
|
|
||||||
</exclusions>
|
|
||||||
</dependency>
|
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>javax.el</groupId>
|
<groupId>javax.el</groupId>
|
||||||
<artifactId>javax.el-api</artifactId>
|
<artifactId>javax.el-api</artifactId>
|
||||||
|
|
@ -426,16 +369,6 @@
|
||||||
<artifactId>log4j-to-slf4j</artifactId>
|
<artifactId>log4j-to-slf4j</artifactId>
|
||||||
</dependency>
|
</dependency>
|
||||||
<!-- Hibernate Search -->
|
<!-- Hibernate Search -->
|
||||||
<dependency>
|
|
||||||
<groupId>org.hibernate.search</groupId>
|
|
||||||
<artifactId>hibernate-search-mapper-orm</artifactId>
|
|
||||||
<exclusions>
|
|
||||||
<exclusion>
|
|
||||||
<groupId>org.apache.logging.log4j</groupId>
|
|
||||||
<artifactId>log4j-api</artifactId>
|
|
||||||
</exclusion>
|
|
||||||
</exclusions>
|
|
||||||
</dependency>
|
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.elasticsearch.client</groupId>
|
<groupId>org.elasticsearch.client</groupId>
|
||||||
<artifactId>elasticsearch-rest-high-level-client</artifactId>
|
<artifactId>elasticsearch-rest-high-level-client</artifactId>
|
||||||
|
|
@ -467,10 +400,6 @@
|
||||||
<groupId>com.google.guava</groupId>
|
<groupId>com.google.guava</groupId>
|
||||||
<artifactId>guava</artifactId>
|
<artifactId>guava</artifactId>
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
|
||||||
<groupId>org.apache.commons</groupId>
|
|
||||||
<artifactId>commons-collections4</artifactId>
|
|
||||||
</dependency>
|
|
||||||
|
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.eclipse.jetty</groupId>
|
<groupId>org.eclipse.jetty</groupId>
|
||||||
|
|
|
||||||
|
|
@ -29,10 +29,6 @@ import ca.uhn.fhir.jpa.reindex.job.ReindexJobConfig;
|
||||||
import org.springframework.context.annotation.Configuration;
|
import org.springframework.context.annotation.Configuration;
|
||||||
import org.springframework.context.annotation.Import;
|
import org.springframework.context.annotation.Import;
|
||||||
|
|
||||||
import java.util.Collections;
|
|
||||||
import java.util.HashSet;
|
|
||||||
import java.util.Set;
|
|
||||||
|
|
||||||
@Configuration
|
@Configuration
|
||||||
//When you define a new batch job, add it here.
|
//When you define a new batch job, add it here.
|
||||||
@Import({
|
@Import({
|
||||||
|
|
@ -45,60 +41,4 @@ import java.util.Set;
|
||||||
MdmClearJobConfig.class
|
MdmClearJobConfig.class
|
||||||
})
|
})
|
||||||
public class BatchJobsConfig {
|
public class BatchJobsConfig {
|
||||||
|
|
||||||
/*
|
|
||||||
* Bulk Export
|
|
||||||
*/
|
|
||||||
|
|
||||||
public static final String BULK_EXPORT_JOB_NAME = "bulkExportJob";
|
|
||||||
public static final String GROUP_BULK_EXPORT_JOB_NAME = "groupBulkExportJob";
|
|
||||||
public static final String PATIENT_BULK_EXPORT_JOB_NAME = "patientBulkExportJob";
|
|
||||||
public static final String BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP = "bulkExportGenerateResourceFilesStep";
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Bulk Import
|
|
||||||
*/
|
|
||||||
|
|
||||||
public static final String BULK_IMPORT_JOB_NAME = "bulkImportJob";
|
|
||||||
public static final String BULK_IMPORT_PROCESSING_STEP = "bulkImportProcessingStep";
|
|
||||||
|
|
||||||
/**
|
|
||||||
* This Set contains the step names across all job types that are appropriate for
|
|
||||||
* someone to look at the write count for that given step in order to determine the
|
|
||||||
* number of processed records.
|
|
||||||
*
|
|
||||||
* This is provided since a job might have multiple steps that the same data passes
|
|
||||||
* through, so you can't just sum up the total of all of them.
|
|
||||||
*
|
|
||||||
* For any given batch job type, there should only be one step name in this set
|
|
||||||
*/
|
|
||||||
public static final Set<String> RECORD_PROCESSING_STEP_NAMES;
|
|
||||||
|
|
||||||
static {
|
|
||||||
HashSet<String> recordProcessingStepNames = new HashSet<>();
|
|
||||||
recordProcessingStepNames.add(BULK_IMPORT_PROCESSING_STEP);
|
|
||||||
recordProcessingStepNames.add(BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP);
|
|
||||||
RECORD_PROCESSING_STEP_NAMES = Collections.unmodifiableSet(recordProcessingStepNames);
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Delete Expunge
|
|
||||||
*/
|
|
||||||
public static final String DELETE_EXPUNGE_JOB_NAME = "deleteExpungeJob";
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Reindex
|
|
||||||
*/
|
|
||||||
public static final String REINDEX_JOB_NAME = "reindexJob";
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Reindex Everything
|
|
||||||
*/
|
|
||||||
public static final String REINDEX_EVERYTHING_JOB_NAME = "reindexEverythingJob";
|
|
||||||
|
|
||||||
/**
|
|
||||||
* MDM Clear
|
|
||||||
*/
|
|
||||||
public static final String MDM_CLEAR_JOB_NAME = "mdmClearJob";
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.batch.job;
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.job.model.PartitionedUrl;
|
import ca.uhn.fhir.jpa.batch.job.model.PartitionedUrl;
|
||||||
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
||||||
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
|
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
|
||||||
|
|
@ -29,8 +30,6 @@ import org.springframework.batch.core.JobParameters;
|
||||||
import org.springframework.batch.core.JobParametersInvalidException;
|
import org.springframework.batch.core.JobParametersInvalidException;
|
||||||
import org.springframework.batch.core.JobParametersValidator;
|
import org.springframework.batch.core.JobParametersValidator;
|
||||||
|
|
||||||
import static ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader.JOB_PARAM_REQUEST_LIST;
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* This class will prevent a job from running any of the provided URLs are not valid on this server.
|
* This class will prevent a job from running any of the provided URLs are not valid on this server.
|
||||||
*/
|
*/
|
||||||
|
|
@ -50,7 +49,7 @@ public class MultiUrlJobParameterValidator implements JobParametersValidator {
|
||||||
throw new JobParametersInvalidException("This job requires Parameters: [urlList]");
|
throw new JobParametersInvalidException("This job requires Parameters: [urlList]");
|
||||||
}
|
}
|
||||||
|
|
||||||
RequestListJson requestListJson = RequestListJson.fromJson(theJobParameters.getString(JOB_PARAM_REQUEST_LIST));
|
RequestListJson requestListJson = RequestListJson.fromJson(theJobParameters.getString(BatchConstants.JOB_PARAM_REQUEST_LIST));
|
||||||
for (PartitionedUrl partitionedUrl : requestListJson.getPartitionedUrls()) {
|
for (PartitionedUrl partitionedUrl : requestListJson.getPartitionedUrls()) {
|
||||||
String url = partitionedUrl.getUrl();
|
String url = partitionedUrl.getUrl();
|
||||||
try {
|
try {
|
||||||
|
|
@ -60,7 +59,7 @@ public class MultiUrlJobParameterValidator implements JobParametersValidator {
|
||||||
throw new JobParametersInvalidException("The resource type " + resourceName + " is not supported on this server.");
|
throw new JobParametersInvalidException("The resource type " + resourceName + " is not supported on this server.");
|
||||||
}
|
}
|
||||||
} catch (UnsupportedOperationException e) {
|
} catch (UnsupportedOperationException e) {
|
||||||
throw new JobParametersInvalidException("Failed to parse " + theJobParameters.getString(JOB_PARAM_OPERATION_NAME) + " " + JOB_PARAM_REQUEST_LIST + " item " + url + ": " + e.getMessage());
|
throw new JobParametersInvalidException("Failed to parse " + theJobParameters.getString(JOB_PARAM_OPERATION_NAME) + " " + BatchConstants.JOB_PARAM_REQUEST_LIST + " item " + url + ": " + e.getMessage());
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -24,8 +24,8 @@ import ca.uhn.fhir.interceptor.api.HookParams;
|
||||||
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
|
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
|
||||||
import ca.uhn.fhir.interceptor.api.Pointcut;
|
import ca.uhn.fhir.interceptor.api.Pointcut;
|
||||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
|
||||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
|
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
|
||||||
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
||||||
import ca.uhn.fhir.jpa.batch.mdm.job.ReverseCronologicalBatchMdmLinkPidReader;
|
import ca.uhn.fhir.jpa.batch.mdm.job.ReverseCronologicalBatchMdmLinkPidReader;
|
||||||
|
|
@ -55,7 +55,7 @@ public class MdmClearJobSubmitterImpl implements IMdmClearJobSubmitter {
|
||||||
@Autowired
|
@Autowired
|
||||||
private IBatchJobSubmitter myBatchJobSubmitter;
|
private IBatchJobSubmitter myBatchJobSubmitter;
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.MDM_CLEAR_JOB_NAME)
|
@Qualifier(BatchConstants.MDM_CLEAR_JOB_NAME)
|
||||||
private Job myMdmClearJob;
|
private Job myMdmClearJob;
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
|
|
|
||||||
|
|
@ -41,7 +41,7 @@ import org.springframework.context.annotation.Lazy;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.MDM_CLEAR_JOB_NAME;
|
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.MDM_CLEAR_JOB_NAME;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
||||||
|
|
|
||||||
|
|
@ -24,6 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
|
||||||
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
|
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
|
||||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||||
import ca.uhn.fhir.jpa.batch.CommonBatchJobConfig;
|
import ca.uhn.fhir.jpa.batch.CommonBatchJobConfig;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterValidator;
|
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterValidator;
|
||||||
import ca.uhn.fhir.jpa.batch.job.model.PartitionedUrl;
|
import ca.uhn.fhir.jpa.batch.job.model.PartitionedUrl;
|
||||||
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
||||||
|
|
@ -58,22 +59,17 @@ import java.util.function.Function;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* This Spring Batch reader takes 4 parameters:
|
* This Spring Batch reader takes 4 parameters:
|
||||||
* {@link #JOB_PARAM_REQUEST_LIST}: A list of URLs to search for along with the partitions those searches should be performed on
|
* {@link BatchConstants#JOB_PARAM_REQUEST_LIST}: A list of URLs to search for along with the partitions those searches should be performed on
|
||||||
* {@link #JOB_PARAM_BATCH_SIZE}: The number of resources to return with each search. If ommitted, {@link DaoConfig#getExpungeBatchSize} will be used.
|
* {@link BatchConstants#JOB_PARAM_BATCH_SIZE}: The number of resources to return with each search. If ommitted, {@link DaoConfig#getExpungeBatchSize} will be used.
|
||||||
* {@link #JOB_PARAM_START_TIME}: The latest timestamp of entities to search for
|
* {@link BatchConstants#JOB_PARAM_START_TIME}: The latest timestamp of entities to search for
|
||||||
* <p>
|
* <p>
|
||||||
* The reader will return at most {@link #JOB_PARAM_BATCH_SIZE} pids every time it is called, or null
|
* The reader will return at most {@link BatchConstants#JOB_PARAM_BATCH_SIZE} pids every time it is called, or null
|
||||||
* once no more matching entities are available. It returns the resources in reverse chronological order
|
* once no more matching entities are available. It returns the resources in reverse chronological order
|
||||||
* and stores where it's at in the Spring Batch execution context with the key {@link #CURRENT_THRESHOLD_HIGH}
|
* and stores where it's at in the Spring Batch execution context with the key {@link BatchConstants#CURRENT_THRESHOLD_HIGH}
|
||||||
* appended with "." and the index number of the url list item it has gotten up to. This is to permit
|
* appended with "." and the index number of the url list item it has gotten up to. This is to permit
|
||||||
* restarting jobs that use this reader so it can pick up where it left off.
|
* restarting jobs that use this reader so it can pick up where it left off.
|
||||||
*/
|
*/
|
||||||
public abstract class BaseReverseCronologicalBatchPidReader implements ItemReader<List<Long>>, ItemStream {
|
public abstract class BaseReverseCronologicalBatchPidReader implements ItemReader<List<Long>>, ItemStream {
|
||||||
public static final String JOB_PARAM_REQUEST_LIST = "url-list";
|
|
||||||
public static final String JOB_PARAM_BATCH_SIZE = "batch-size";
|
|
||||||
public static final String JOB_PARAM_START_TIME = "start-time";
|
|
||||||
public static final String CURRENT_URL_INDEX = "current.url-index";
|
|
||||||
public static final String CURRENT_THRESHOLD_HIGH = "current.threshold-high";
|
|
||||||
private static final Logger ourLog = LoggerFactory.getLogger(ReverseCronologicalBatchResourcePidReader.class);
|
private static final Logger ourLog = LoggerFactory.getLogger(ReverseCronologicalBatchResourcePidReader.class);
|
||||||
private final BatchDateThresholdUpdater myBatchDateThresholdUpdater = new BatchDateThresholdUpdater();
|
private final BatchDateThresholdUpdater myBatchDateThresholdUpdater = new BatchDateThresholdUpdater();
|
||||||
private final Map<Integer, Date> myThresholdHighByUrlIndex = new HashMap<>();
|
private final Map<Integer, Date> myThresholdHighByUrlIndex = new HashMap<>();
|
||||||
|
|
@ -88,30 +84,30 @@ public abstract class BaseReverseCronologicalBatchPidReader implements ItemReade
|
||||||
private Date myStartTime;
|
private Date myStartTime;
|
||||||
|
|
||||||
private static String highKey(int theIndex) {
|
private static String highKey(int theIndex) {
|
||||||
return CURRENT_THRESHOLD_HIGH + "." + theIndex;
|
return BatchConstants.CURRENT_THRESHOLD_HIGH + "." + theIndex;
|
||||||
}
|
}
|
||||||
|
|
||||||
@Nonnull
|
@Nonnull
|
||||||
public static JobParameters buildJobParameters(String theOperationName, Integer theBatchSize, RequestListJson theRequestListJson) {
|
public static JobParameters buildJobParameters(String theOperationName, Integer theBatchSize, RequestListJson theRequestListJson) {
|
||||||
Map<String, JobParameter> map = new HashMap<>();
|
Map<String, JobParameter> map = new HashMap<>();
|
||||||
map.put(MultiUrlJobParameterValidator.JOB_PARAM_OPERATION_NAME, new JobParameter(theOperationName));
|
map.put(MultiUrlJobParameterValidator.JOB_PARAM_OPERATION_NAME, new JobParameter(theOperationName));
|
||||||
map.put(ReverseCronologicalBatchResourcePidReader.JOB_PARAM_REQUEST_LIST, new JobParameter(theRequestListJson.toJson()));
|
map.put(BatchConstants.JOB_PARAM_REQUEST_LIST, new JobParameter(theRequestListJson.toJson()));
|
||||||
map.put(ReverseCronologicalBatchResourcePidReader.JOB_PARAM_START_TIME, new JobParameter(DateUtils.addMinutes(new Date(), CommonBatchJobConfig.MINUTES_IN_FUTURE_TO_PROCESS_FROM)));
|
map.put(BatchConstants.JOB_PARAM_START_TIME, new JobParameter(DateUtils.addMinutes(new Date(), CommonBatchJobConfig.MINUTES_IN_FUTURE_TO_PROCESS_FROM)));
|
||||||
if (theBatchSize != null) {
|
if (theBatchSize != null) {
|
||||||
map.put(ReverseCronologicalBatchResourcePidReader.JOB_PARAM_BATCH_SIZE, new JobParameter(theBatchSize.longValue()));
|
map.put(BatchConstants.JOB_PARAM_BATCH_SIZE, new JobParameter(theBatchSize.longValue()));
|
||||||
}
|
}
|
||||||
JobParameters parameters = new JobParameters(map);
|
JobParameters parameters = new JobParameters(map);
|
||||||
return parameters;
|
return parameters;
|
||||||
}
|
}
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
public void setRequestListJson(@Value("#{jobParameters['" + JOB_PARAM_REQUEST_LIST + "']}") String theRequestListJson) {
|
public void setRequestListJson(@Value("#{jobParameters['" + BatchConstants.JOB_PARAM_REQUEST_LIST + "']}") String theRequestListJson) {
|
||||||
RequestListJson requestListJson = RequestListJson.fromJson(theRequestListJson);
|
RequestListJson requestListJson = RequestListJson.fromJson(theRequestListJson);
|
||||||
myPartitionedUrls = requestListJson.getPartitionedUrls();
|
myPartitionedUrls = requestListJson.getPartitionedUrls();
|
||||||
}
|
}
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
public void setStartTime(@Value("#{jobParameters['" + JOB_PARAM_START_TIME + "']}") Date theStartTime) {
|
public void setStartTime(@Value("#{jobParameters['" + BatchConstants.JOB_PARAM_START_TIME + "']}") Date theStartTime) {
|
||||||
myStartTime = theStartTime;
|
myStartTime = theStartTime;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -166,8 +162,8 @@ public abstract class BaseReverseCronologicalBatchPidReader implements ItemReade
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public void open(ExecutionContext executionContext) throws ItemStreamException {
|
public void open(ExecutionContext executionContext) throws ItemStreamException {
|
||||||
if (executionContext.containsKey(CURRENT_URL_INDEX)) {
|
if (executionContext.containsKey(BatchConstants.CURRENT_URL_INDEX)) {
|
||||||
myUrlIndex = new Long(executionContext.getLong(CURRENT_URL_INDEX)).intValue();
|
myUrlIndex = new Long(executionContext.getLong(BatchConstants.CURRENT_URL_INDEX)).intValue();
|
||||||
}
|
}
|
||||||
for (int index = 0; index < myPartitionedUrls.size(); ++index) {
|
for (int index = 0; index < myPartitionedUrls.size(); ++index) {
|
||||||
String key = highKey(index);
|
String key = highKey(index);
|
||||||
|
|
@ -181,7 +177,7 @@ public abstract class BaseReverseCronologicalBatchPidReader implements ItemReade
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public void update(ExecutionContext executionContext) throws ItemStreamException {
|
public void update(ExecutionContext executionContext) throws ItemStreamException {
|
||||||
executionContext.putLong(CURRENT_URL_INDEX, myUrlIndex);
|
executionContext.putLong(BatchConstants.CURRENT_URL_INDEX, myUrlIndex);
|
||||||
for (int index = 0; index < myPartitionedUrls.size(); ++index) {
|
for (int index = 0; index < myPartitionedUrls.size(); ++index) {
|
||||||
Date date = myThresholdHighByUrlIndex.get(index);
|
Date date = myThresholdHighByUrlIndex.get(index);
|
||||||
if (date != null) {
|
if (date != null) {
|
||||||
|
|
@ -199,7 +195,7 @@ public abstract class BaseReverseCronologicalBatchPidReader implements ItemReade
|
||||||
}
|
}
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
public void setBatchSize(@Value("#{jobParameters['" + JOB_PARAM_BATCH_SIZE + "']}") Integer theBatchSize) {
|
public void setBatchSize(@Value("#{jobParameters['" + BatchConstants.JOB_PARAM_BATCH_SIZE + "']}") Integer theBatchSize) {
|
||||||
myBatchSize = theBatchSize;
|
myBatchSize = theBatchSize;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -25,6 +25,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
|
||||||
import ca.uhn.fhir.context.RuntimeSearchParam;
|
import ca.uhn.fhir.context.RuntimeSearchParam;
|
||||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
|
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.log.Logs;
|
import ca.uhn.fhir.jpa.batch.log.Logs;
|
||||||
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
|
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
|
||||||
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
|
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
|
||||||
|
|
@ -57,7 +58,7 @@ public abstract class BaseBulkItemReader implements ItemReader<List<ResourcePers
|
||||||
|
|
||||||
@Value("#{stepExecutionContext['resourceType']}")
|
@Value("#{stepExecutionContext['resourceType']}")
|
||||||
protected String myResourceType;
|
protected String myResourceType;
|
||||||
@Value("#{jobExecutionContext['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
|
@Value("#{jobExecutionContext['" + BatchConstants.JOB_UUID_PARAMETER + "']}")
|
||||||
protected String myJobUUID;
|
protected String myJobUUID;
|
||||||
@Value("#{jobParameters['" + BulkExportJobConfig.READ_CHUNK_PARAMETER + "']}")
|
@Value("#{jobParameters['" + BulkExportJobConfig.READ_CHUNK_PARAMETER + "']}")
|
||||||
protected Long myReadChunkSize;
|
protected Long myReadChunkSize;
|
||||||
|
|
|
||||||
|
|
@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.bulk.export.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
|
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
|
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
|
||||||
import org.springframework.batch.core.ExitStatus;
|
import org.springframework.batch.core.ExitStatus;
|
||||||
|
|
@ -49,9 +50,9 @@ public class BulkExportGenerateResourceFilesStepListener implements StepExecutio
|
||||||
public ExitStatus afterStep(StepExecution theStepExecution) {
|
public ExitStatus afterStep(StepExecution theStepExecution) {
|
||||||
if (theStepExecution.getExitStatus().getExitCode().equals(ExitStatus.FAILED.getExitCode())) {
|
if (theStepExecution.getExitStatus().getExitCode().equals(ExitStatus.FAILED.getExitCode())) {
|
||||||
//Try to fetch it from the parameters first, and if it doesn't exist, fetch it from the context.
|
//Try to fetch it from the parameters first, and if it doesn't exist, fetch it from the context.
|
||||||
String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
|
String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BatchConstants.JOB_UUID_PARAMETER);
|
||||||
if (jobUuid == null) {
|
if (jobUuid == null) {
|
||||||
jobUuid = theStepExecution.getJobExecution().getExecutionContext().getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
|
jobUuid = theStepExecution.getJobExecution().getExecutionContext().getString(BatchConstants.JOB_UUID_PARAMETER);
|
||||||
}
|
}
|
||||||
assert isNotBlank(jobUuid);
|
assert isNotBlank(jobUuid);
|
||||||
String exitDescription = theStepExecution.getExitStatus().getExitDescription();
|
String exitDescription = theStepExecution.getExitStatus().getExitDescription();
|
||||||
|
|
|
||||||
|
|
@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.export.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.processor.GoldenResourceAnnotatingProcessor;
|
import ca.uhn.fhir.jpa.batch.processor.GoldenResourceAnnotatingProcessor;
|
||||||
import ca.uhn.fhir.jpa.batch.processor.PidToIBaseResourceProcessor;
|
import ca.uhn.fhir.jpa.batch.processor.PidToIBaseResourceProcessor;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
|
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
|
||||||
|
|
@ -51,7 +51,6 @@ import java.util.List;
|
||||||
@Configuration
|
@Configuration
|
||||||
public class BulkExportJobConfig {
|
public class BulkExportJobConfig {
|
||||||
|
|
||||||
public static final String JOB_UUID_PARAMETER = "jobUUID";
|
|
||||||
public static final String READ_CHUNK_PARAMETER = "readChunkSize";
|
public static final String READ_CHUNK_PARAMETER = "readChunkSize";
|
||||||
public static final String EXPAND_MDM_PARAMETER = "expandMdm";
|
public static final String EXPAND_MDM_PARAMETER = "expandMdm";
|
||||||
public static final String GROUP_ID_PARAMETER = "groupId";
|
public static final String GROUP_ID_PARAMETER = "groupId";
|
||||||
|
|
@ -88,7 +87,7 @@ public class BulkExportJobConfig {
|
||||||
@Bean
|
@Bean
|
||||||
@Lazy
|
@Lazy
|
||||||
public Job bulkExportJob() {
|
public Job bulkExportJob() {
|
||||||
return myJobBuilderFactory.get(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
|
return myJobBuilderFactory.get(BatchConstants.BULK_EXPORT_JOB_NAME)
|
||||||
.validator(bulkExportJobParameterValidator())
|
.validator(bulkExportJobParameterValidator())
|
||||||
.start(createBulkExportEntityStep())
|
.start(createBulkExportEntityStep())
|
||||||
.next(bulkExportPartitionStep())
|
.next(bulkExportPartitionStep())
|
||||||
|
|
@ -111,7 +110,7 @@ public class BulkExportJobConfig {
|
||||||
@Bean
|
@Bean
|
||||||
@Lazy
|
@Lazy
|
||||||
public Job groupBulkExportJob() {
|
public Job groupBulkExportJob() {
|
||||||
return myJobBuilderFactory.get(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
|
return myJobBuilderFactory.get(BatchConstants.GROUP_BULK_EXPORT_JOB_NAME)
|
||||||
.validator(groupBulkJobParameterValidator())
|
.validator(groupBulkJobParameterValidator())
|
||||||
.validator(bulkExportJobParameterValidator())
|
.validator(bulkExportJobParameterValidator())
|
||||||
.start(createBulkExportEntityStep())
|
.start(createBulkExportEntityStep())
|
||||||
|
|
@ -123,7 +122,7 @@ public class BulkExportJobConfig {
|
||||||
@Bean
|
@Bean
|
||||||
@Lazy
|
@Lazy
|
||||||
public Job patientBulkExportJob() {
|
public Job patientBulkExportJob() {
|
||||||
return myJobBuilderFactory.get(BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME)
|
return myJobBuilderFactory.get(BatchConstants.PATIENT_BULK_EXPORT_JOB_NAME)
|
||||||
.validator(bulkExportJobParameterValidator())
|
.validator(bulkExportJobParameterValidator())
|
||||||
.start(createBulkExportEntityStep())
|
.start(createBulkExportEntityStep())
|
||||||
.next(patientPartitionStep())
|
.next(patientPartitionStep())
|
||||||
|
|
@ -169,7 +168,7 @@ public class BulkExportJobConfig {
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
public Step bulkExportGenerateResourceFilesStep() {
|
public Step bulkExportGenerateResourceFilesStep() {
|
||||||
return myStepBuilderFactory.get(BatchJobsConfig.BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP)
|
return myStepBuilderFactory.get(BatchConstants.BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP)
|
||||||
.<List<ResourcePersistentId>, List<IBaseResource>>chunk(CHUNK_SIZE) //1000 resources per generated file, as the reader returns 10 resources at a time.
|
.<List<ResourcePersistentId>, List<IBaseResource>>chunk(CHUNK_SIZE) //1000 resources per generated file, as the reader returns 10 resources at a time.
|
||||||
.reader(bulkItemReader())
|
.reader(bulkItemReader())
|
||||||
.processor(myPidToIBaseResourceProcessor)
|
.processor(myPidToIBaseResourceProcessor)
|
||||||
|
|
@ -217,7 +216,7 @@ public class BulkExportJobConfig {
|
||||||
@Bean
|
@Bean
|
||||||
public Step bulkExportPartitionStep() {
|
public Step bulkExportPartitionStep() {
|
||||||
return myStepBuilderFactory.get("partitionStep")
|
return myStepBuilderFactory.get("partitionStep")
|
||||||
.partitioner(BatchJobsConfig.BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP, bulkExportResourceTypePartitioner())
|
.partitioner(BatchConstants.BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP, bulkExportResourceTypePartitioner())
|
||||||
.step(bulkExportGenerateResourceFilesStep())
|
.step(bulkExportGenerateResourceFilesStep())
|
||||||
.build();
|
.build();
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.bulk.export.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
|
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
|
||||||
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
|
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
|
||||||
import ca.uhn.fhir.rest.api.Constants;
|
import ca.uhn.fhir.rest.api.Constants;
|
||||||
|
|
@ -34,8 +35,6 @@ import org.springframework.transaction.support.TransactionTemplate;
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
|
|
||||||
import static org.slf4j.LoggerFactory.getLogger;
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* This class will prevent a job from running if the UUID does not exist or is invalid.
|
* This class will prevent a job from running if the UUID does not exist or is invalid.
|
||||||
*/
|
*/
|
||||||
|
|
@ -59,7 +58,7 @@ public class BulkExportJobParameterValidator implements JobParametersValidator {
|
||||||
if (readChunkSize == null || readChunkSize < 1) {
|
if (readChunkSize == null || readChunkSize < 1) {
|
||||||
errorBuilder.append("There must be a valid number for readChunkSize, which is at least 1. ");
|
errorBuilder.append("There must be a valid number for readChunkSize, which is at least 1. ");
|
||||||
}
|
}
|
||||||
String jobUUID = theJobParameters.getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
|
String jobUUID = theJobParameters.getString(BatchConstants.JOB_UUID_PARAMETER);
|
||||||
Optional<BulkExportJobEntity> oJob = myBulkExportJobDao.findByJobId(jobUUID);
|
Optional<BulkExportJobEntity> oJob = myBulkExportJobDao.findByJobId(jobUUID);
|
||||||
if (!StringUtils.isBlank(jobUUID) && !oJob.isPresent()) {
|
if (!StringUtils.isBlank(jobUUID) && !oJob.isPresent()) {
|
||||||
errorBuilder.append("There is no persisted job that exists with UUID: " + jobUUID + ". ");
|
errorBuilder.append("There is no persisted job that exists with UUID: " + jobUUID + ". ");
|
||||||
|
|
|
||||||
|
|
@ -20,10 +20,11 @@ package ca.uhn.fhir.jpa.bulk.export.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
|
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
|
||||||
import ca.uhn.fhir.model.primitive.IdDt;
|
import ca.uhn.fhir.model.primitive.IdDt;
|
||||||
import ca.uhn.fhir.rest.api.Constants;
|
import ca.uhn.fhir.rest.api.Constants;
|
||||||
|
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
import org.springframework.batch.core.StepContribution;
|
import org.springframework.batch.core.StepContribution;
|
||||||
import org.springframework.batch.core.scope.context.ChunkContext;
|
import org.springframework.batch.core.scope.context.ChunkContext;
|
||||||
|
|
@ -42,13 +43,22 @@ public class CreateBulkExportEntityTasklet implements Tasklet {
|
||||||
@Autowired
|
@Autowired
|
||||||
private IBulkDataExportSvc myBulkDataExportSvc;
|
private IBulkDataExportSvc myBulkDataExportSvc;
|
||||||
|
|
||||||
|
public static void addUUIDToJobContext(ChunkContext theChunkContext, String theJobUUID) {
|
||||||
|
theChunkContext
|
||||||
|
.getStepContext()
|
||||||
|
.getStepExecution()
|
||||||
|
.getJobExecution()
|
||||||
|
.getExecutionContext()
|
||||||
|
.putString(BatchConstants.JOB_UUID_PARAMETER, theJobUUID);
|
||||||
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public RepeatStatus execute(StepContribution theStepContribution, ChunkContext theChunkContext) throws Exception {
|
public RepeatStatus execute(StepContribution theStepContribution, ChunkContext theChunkContext) throws Exception {
|
||||||
Map<String, Object> jobParameters = theChunkContext.getStepContext().getJobParameters();
|
Map<String, Object> jobParameters = theChunkContext.getStepContext().getJobParameters();
|
||||||
|
|
||||||
//We can leave early if they provided us with an existing job.
|
//We can leave early if they provided us with an existing job.
|
||||||
if (jobParameters.containsKey(BulkExportJobConfig.JOB_UUID_PARAMETER)) {
|
if (jobParameters.containsKey(BatchConstants.JOB_UUID_PARAMETER)) {
|
||||||
addUUIDToJobContext(theChunkContext, (String)jobParameters.get(BulkExportJobConfig.JOB_UUID_PARAMETER));
|
addUUIDToJobContext(theChunkContext, (String) jobParameters.get(BatchConstants.JOB_UUID_PARAMETER));
|
||||||
return RepeatStatus.FINISHED;
|
return RepeatStatus.FINISHED;
|
||||||
} else {
|
} else {
|
||||||
String resourceTypes = (String) jobParameters.get("resourceTypes");
|
String resourceTypes = (String) jobParameters.get("resourceTypes");
|
||||||
|
|
@ -86,13 +96,4 @@ public class CreateBulkExportEntityTasklet implements Tasklet {
|
||||||
return RepeatStatus.FINISHED;
|
return RepeatStatus.FINISHED;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
public static void addUUIDToJobContext(ChunkContext theChunkContext, String theJobUUID) {
|
|
||||||
theChunkContext
|
|
||||||
.getStepContext()
|
|
||||||
.getStepExecution()
|
|
||||||
.getJobExecution()
|
|
||||||
.getExecutionContext()
|
|
||||||
.putString(BulkExportJobConfig.JOB_UUID_PARAMETER, theJobUUID);
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.bulk.export.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
|
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.springframework.batch.core.partition.support.Partitioner;
|
import org.springframework.batch.core.partition.support.Partitioner;
|
||||||
|
|
@ -60,7 +61,7 @@ public class ResourceTypePartitioner implements Partitioner {
|
||||||
|
|
||||||
// The worker step needs to know which parent job it is processing for, and which collection entity it will be
|
// The worker step needs to know which parent job it is processing for, and which collection entity it will be
|
||||||
// attaching its results to.
|
// attaching its results to.
|
||||||
context.putString(BulkExportJobConfig.JOB_UUID_PARAMETER, myJobUUID);
|
context.putString(BatchConstants.JOB_UUID_PARAMETER, myJobUUID);
|
||||||
context.putLong("bulkExportCollectionEntityId", collectionEntityId);
|
context.putLong("bulkExportCollectionEntityId", collectionEntityId);
|
||||||
|
|
||||||
// Name the partition based on the resource type
|
// Name the partition based on the resource type
|
||||||
|
|
|
||||||
|
|
@ -30,9 +30,8 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
|
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
|
||||||
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
|
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
|
||||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||||
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
|
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
|
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
|
||||||
|
|
@ -49,6 +48,7 @@ import ca.uhn.fhir.jpa.model.util.JpaConstants;
|
||||||
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
|
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
|
||||||
import ca.uhn.fhir.rest.api.Constants;
|
import ca.uhn.fhir.rest.api.Constants;
|
||||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||||
|
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
|
||||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||||
|
|
@ -114,15 +114,15 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
|
||||||
private IBatchJobSubmitter myJobSubmitter;
|
private IBatchJobSubmitter myJobSubmitter;
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
|
@Qualifier(BatchConstants.BULK_EXPORT_JOB_NAME)
|
||||||
private org.springframework.batch.core.Job myBulkExportJob;
|
private org.springframework.batch.core.Job myBulkExportJob;
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
|
@Qualifier(BatchConstants.GROUP_BULK_EXPORT_JOB_NAME)
|
||||||
private org.springframework.batch.core.Job myGroupBulkExportJob;
|
private org.springframework.batch.core.Job myGroupBulkExportJob;
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME)
|
@Qualifier(BatchConstants.PATIENT_BULK_EXPORT_JOB_NAME)
|
||||||
private org.springframework.batch.core.Job myPatientBulkExportJob;
|
private org.springframework.batch.core.Job myPatientBulkExportJob;
|
||||||
|
|
||||||
private Set<String> myCompartmentResources;
|
private Set<String> myCompartmentResources;
|
||||||
|
|
@ -243,7 +243,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
|
||||||
private void processJob(BulkExportJobEntity theBulkExportJobEntity) {
|
private void processJob(BulkExportJobEntity theBulkExportJobEntity) {
|
||||||
String theJobUuid = theBulkExportJobEntity.getJobId();
|
String theJobUuid = theBulkExportJobEntity.getJobId();
|
||||||
JobParametersBuilder parameters = new JobParametersBuilder()
|
JobParametersBuilder parameters = new JobParametersBuilder()
|
||||||
.addString(BulkExportJobConfig.JOB_UUID_PARAMETER, theJobUuid)
|
.addString(BatchConstants.JOB_UUID_PARAMETER, theJobUuid)
|
||||||
.addLong(BulkExportJobConfig.READ_CHUNK_PARAMETER, READ_CHUNK_SIZE);
|
.addLong(BulkExportJobConfig.READ_CHUNK_PARAMETER, READ_CHUNK_SIZE);
|
||||||
|
|
||||||
ourLog.info("Submitting bulk export job {} to job scheduler", theJobUuid);
|
ourLog.info("Submitting bulk export job {} to job scheduler", theJobUuid);
|
||||||
|
|
|
||||||
|
|
@ -20,10 +20,9 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
|
||||||
import org.elasticsearch.client.enrich.ExecutePolicyResponse;
|
|
||||||
import org.springframework.batch.core.ExitStatus;
|
import org.springframework.batch.core.ExitStatus;
|
||||||
import org.springframework.batch.core.StepExecution;
|
import org.springframework.batch.core.StepExecution;
|
||||||
import org.springframework.batch.core.StepExecutionListener;
|
import org.springframework.batch.core.StepExecutionListener;
|
||||||
|
|
@ -39,7 +38,7 @@ public class ActivateBulkImportEntityStepListener implements StepExecutionListen
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public void beforeStep(StepExecution theStepExecution) {
|
public void beforeStep(StepExecution theStepExecution) {
|
||||||
String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
|
String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BatchConstants.JOB_UUID_PARAMETER);
|
||||||
if (jobUuid != null) {
|
if (jobUuid != null) {
|
||||||
myBulkImportDaoSvc.setJobToStatus(jobUuid, BulkImportJobStatusEnum.RUNNING);
|
myBulkImportDaoSvc.setJobToStatus(jobUuid, BulkImportJobStatusEnum.RUNNING);
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.context.FhirContext;
|
import ca.uhn.fhir.context.FhirContext;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.log.Logs;
|
import ca.uhn.fhir.jpa.batch.log.Logs;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
|
||||||
|
|
@ -42,7 +42,7 @@ public class BulkImportFileReader implements ItemReader<ParsedBulkImportRecord>
|
||||||
private IBulkDataImportSvc myBulkDataImportSvc;
|
private IBulkDataImportSvc myBulkDataImportSvc;
|
||||||
@Autowired
|
@Autowired
|
||||||
private FhirContext myFhirContext;
|
private FhirContext myFhirContext;
|
||||||
@Value("#{stepExecutionContext['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
|
@Value("#{stepExecutionContext['" + BatchConstants.JOB_UUID_PARAMETER + "']}")
|
||||||
private String myJobUuid;
|
private String myJobUuid;
|
||||||
@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
|
@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
|
||||||
private int myFileIndex;
|
private int myFileIndex;
|
||||||
|
|
|
||||||
|
|
@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||||
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
|
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.JobFileRowProcessingModeEnum;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.JobFileRowProcessingModeEnum;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
|
||||||
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
|
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
|
||||||
|
|
@ -39,7 +39,7 @@ import java.util.List;
|
||||||
public class BulkImportFileWriter implements ItemWriter<ParsedBulkImportRecord> {
|
public class BulkImportFileWriter implements ItemWriter<ParsedBulkImportRecord> {
|
||||||
|
|
||||||
private static final Logger ourLog = LoggerFactory.getLogger(BulkImportFileWriter.class);
|
private static final Logger ourLog = LoggerFactory.getLogger(BulkImportFileWriter.class);
|
||||||
@Value("#{stepExecutionContext['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
|
@Value("#{stepExecutionContext['" + BatchConstants.JOB_UUID_PARAMETER + "']}")
|
||||||
private String myJobUuid;
|
private String myJobUuid;
|
||||||
@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
|
@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
|
||||||
private int myFileIndex;
|
private int myFileIndex;
|
||||||
|
|
|
||||||
|
|
@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
|
||||||
import org.springframework.batch.core.BatchStatus;
|
import org.springframework.batch.core.BatchStatus;
|
||||||
|
|
@ -36,7 +36,7 @@ import org.springframework.beans.factory.annotation.Value;
|
||||||
*/
|
*/
|
||||||
public class BulkImportJobCloser implements Tasklet {
|
public class BulkImportJobCloser implements Tasklet {
|
||||||
|
|
||||||
@Value("#{jobParameters['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
|
@Value("#{jobParameters['" + BatchConstants.JOB_UUID_PARAMETER + "']}")
|
||||||
private String myJobUUID;
|
private String myJobUUID;
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
|
|
|
||||||
|
|
@ -21,14 +21,13 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||||
import ca.uhn.fhir.jpa.batch.BatchConstants;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
import org.springframework.batch.core.Job;
|
import org.springframework.batch.core.Job;
|
||||||
import org.springframework.batch.core.JobParametersValidator;
|
import org.springframework.batch.core.JobParametersValidator;
|
||||||
import org.springframework.batch.core.Step;
|
import org.springframework.batch.core.Step;
|
||||||
import org.springframework.batch.core.configuration.JobRegistry;
|
|
||||||
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
|
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
|
||||||
import org.springframework.batch.core.configuration.annotation.JobScope;
|
import org.springframework.batch.core.configuration.annotation.JobScope;
|
||||||
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
|
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
|
||||||
|
|
@ -50,8 +49,8 @@ import org.springframework.retry.policy.TimeoutRetryPolicy;
|
||||||
|
|
||||||
import javax.batch.api.chunk.listener.RetryProcessListener;
|
import javax.batch.api.chunk.listener.RetryProcessListener;
|
||||||
|
|
||||||
import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.BULK_IMPORT_JOB_NAME;
|
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.BULK_IMPORT_JOB_NAME;
|
||||||
import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.BULK_IMPORT_PROCESSING_STEP;
|
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.BULK_IMPORT_PROCESSING_STEP;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
||||||
|
|
|
||||||
|
|
@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.dao.data.IBulkImportJobDao;
|
import ca.uhn.fhir.jpa.dao.data.IBulkImportJobDao;
|
||||||
import ca.uhn.fhir.jpa.entity.BulkImportJobEntity;
|
import ca.uhn.fhir.jpa.entity.BulkImportJobEntity;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
|
@ -52,7 +52,7 @@ public class BulkImportJobParameterValidator implements JobParametersValidator {
|
||||||
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
|
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
|
||||||
String errorMessage = txTemplate.execute(tx -> {
|
String errorMessage = txTemplate.execute(tx -> {
|
||||||
StringBuilder errorBuilder = new StringBuilder();
|
StringBuilder errorBuilder = new StringBuilder();
|
||||||
String jobUUID = theJobParameters.getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
|
String jobUUID = theJobParameters.getString(BatchConstants.JOB_UUID_PARAMETER);
|
||||||
Optional<BulkImportJobEntity> oJob = myBulkImportJobDao.findByJobId(jobUUID);
|
Optional<BulkImportJobEntity> oJob = myBulkImportJobDao.findByJobId(jobUUID);
|
||||||
if (!StringUtils.isBlank(jobUUID) && !oJob.isPresent()) {
|
if (!StringUtils.isBlank(jobUUID) && !oJob.isPresent()) {
|
||||||
errorBuilder.append("There is no persisted job that exists with UUID: ");
|
errorBuilder.append("There is no persisted job that exists with UUID: ");
|
||||||
|
|
|
||||||
|
|
@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobJson;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobJson;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
|
|
@ -43,7 +43,7 @@ public class BulkImportPartitioner implements Partitioner {
|
||||||
|
|
||||||
private static final Logger ourLog = getLogger(BulkImportPartitioner.class);
|
private static final Logger ourLog = getLogger(BulkImportPartitioner.class);
|
||||||
|
|
||||||
@Value("#{jobParameters['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
|
@Value("#{jobParameters['" + BatchConstants.JOB_UUID_PARAMETER + "']}")
|
||||||
private String myJobUUID;
|
private String myJobUUID;
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
|
|
@ -61,7 +61,7 @@ public class BulkImportPartitioner implements Partitioner {
|
||||||
String fileDescription = myBulkDataImportSvc.getFileDescription(myJobUUID, i);
|
String fileDescription = myBulkDataImportSvc.getFileDescription(myJobUUID, i);
|
||||||
|
|
||||||
ExecutionContext context = new ExecutionContext();
|
ExecutionContext context = new ExecutionContext();
|
||||||
context.putString(BulkExportJobConfig.JOB_UUID_PARAMETER, myJobUUID);
|
context.putString(BatchConstants.JOB_UUID_PARAMETER, myJobUUID);
|
||||||
context.putInt(FILE_INDEX, i);
|
context.putInt(FILE_INDEX, i);
|
||||||
context.put(ROW_PROCESSING_MODE, job.getProcessingMode());
|
context.put(ROW_PROCESSING_MODE, job.getProcessingMode());
|
||||||
context.put(JOB_DESCRIPTION, job.getJobDescription());
|
context.put(JOB_DESCRIPTION, job.getJobDescription());
|
||||||
|
|
|
||||||
|
|
@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
|
||||||
import org.springframework.batch.core.ExitStatus;
|
import org.springframework.batch.core.ExitStatus;
|
||||||
|
|
@ -52,9 +52,9 @@ public class BulkImportStepListener implements StepExecutionListener, RetryListe
|
||||||
public ExitStatus afterStep(StepExecution theStepExecution) {
|
public ExitStatus afterStep(StepExecution theStepExecution) {
|
||||||
if (theStepExecution.getExitStatus().getExitCode().equals(ExitStatus.FAILED.getExitCode())) {
|
if (theStepExecution.getExitStatus().getExitCode().equals(ExitStatus.FAILED.getExitCode())) {
|
||||||
//Try to fetch it from the parameters first, and if it doesn't exist, fetch it from the context.
|
//Try to fetch it from the parameters first, and if it doesn't exist, fetch it from the context.
|
||||||
String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
|
String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BatchConstants.JOB_UUID_PARAMETER);
|
||||||
if (jobUuid == null) {
|
if (jobUuid == null) {
|
||||||
jobUuid = theStepExecution.getJobExecution().getExecutionContext().getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
|
jobUuid = theStepExecution.getJobExecution().getExecutionContext().getString(BatchConstants.JOB_UUID_PARAMETER);
|
||||||
}
|
}
|
||||||
assert isNotBlank(jobUuid);
|
assert isNotBlank(jobUuid);
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.CreateBulkExportEntityTasklet;
|
import ca.uhn.fhir.jpa.bulk.export.job.CreateBulkExportEntityTasklet;
|
||||||
import ca.uhn.fhir.util.ValidateUtil;
|
import ca.uhn.fhir.util.ValidateUtil;
|
||||||
import org.springframework.batch.core.StepContribution;
|
import org.springframework.batch.core.StepContribution;
|
||||||
|
|
@ -37,8 +37,8 @@ public class CreateBulkImportEntityTasklet implements Tasklet {
|
||||||
Map<String, Object> jobParameters = theChunkContext.getStepContext().getJobParameters();
|
Map<String, Object> jobParameters = theChunkContext.getStepContext().getJobParameters();
|
||||||
|
|
||||||
//We can leave early if they provided us with an existing job.
|
//We can leave early if they provided us with an existing job.
|
||||||
ValidateUtil.isTrueOrThrowInvalidRequest(jobParameters.containsKey(BulkExportJobConfig.JOB_UUID_PARAMETER), "Job doesn't have a UUID");
|
ValidateUtil.isTrueOrThrowInvalidRequest(jobParameters.containsKey(BatchConstants.JOB_UUID_PARAMETER), "Job doesn't have a UUID");
|
||||||
CreateBulkExportEntityTasklet.addUUIDToJobContext(theChunkContext, (String) jobParameters.get(BulkExportJobConfig.JOB_UUID_PARAMETER));
|
CreateBulkExportEntityTasklet.addUUIDToJobContext(theChunkContext, (String) jobParameters.get(BatchConstants.JOB_UUID_PARAMETER));
|
||||||
return RepeatStatus.FINISHED;
|
return RepeatStatus.FINISHED;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.bulk.imprt.svc;
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
|
||||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.log.Logs;
|
import ca.uhn.fhir.jpa.batch.log.Logs;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
||||||
|
|
@ -79,7 +79,7 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
|
||||||
@Autowired
|
@Autowired
|
||||||
private IBatchJobSubmitter myJobSubmitter;
|
private IBatchJobSubmitter myJobSubmitter;
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.BULK_IMPORT_JOB_NAME)
|
@Qualifier(BatchConstants.BULK_IMPORT_JOB_NAME)
|
||||||
private org.springframework.batch.core.Job myBulkImportJob;
|
private org.springframework.batch.core.Job myBulkImportJob;
|
||||||
@Autowired
|
@Autowired
|
||||||
private DaoConfig myDaoConfig;
|
private DaoConfig myDaoConfig;
|
||||||
|
|
@ -271,7 +271,7 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
|
||||||
ValidateUtil.isTrueOrThrowInvalidRequest(batchSize > 0, "Batch size must be positive");
|
ValidateUtil.isTrueOrThrowInvalidRequest(batchSize > 0, "Batch size must be positive");
|
||||||
|
|
||||||
JobParametersBuilder parameters = new JobParametersBuilder()
|
JobParametersBuilder parameters = new JobParametersBuilder()
|
||||||
.addString(BulkExportJobConfig.JOB_UUID_PARAMETER, jobId)
|
.addString(BatchConstants.JOB_UUID_PARAMETER, jobId)
|
||||||
.addLong(BulkImportJobConfig.JOB_PARAM_COMMIT_INTERVAL, (long) batchSize);
|
.addLong(BulkImportJobConfig.JOB_PARAM_COMMIT_INTERVAL, (long) batchSize);
|
||||||
|
|
||||||
if (isNotBlank(theBulkExportJobEntity.getJobDescription())) {
|
if (isNotBlank(theBulkExportJobEntity.getJobDescription())) {
|
||||||
|
|
|
||||||
|
|
@ -11,9 +11,9 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||||
import ca.uhn.fhir.jpa.api.dao.IDao;
|
import ca.uhn.fhir.jpa.api.dao.IDao;
|
||||||
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
|
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
|
||||||
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
|
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
|
||||||
import ca.uhn.fhir.jpa.batch.BatchConstants;
|
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
||||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
|
import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
|
||||||
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
|
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
|
||||||
import ca.uhn.fhir.jpa.batch.mdm.MdmBatchJobSubmitterFactoryImpl;
|
import ca.uhn.fhir.jpa.batch.mdm.MdmBatchJobSubmitterFactoryImpl;
|
||||||
|
|
|
||||||
|
|
@ -32,6 +32,7 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||||
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
|
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
|
||||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||||
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
|
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
|
||||||
|
import ca.uhn.fhir.util.TestUtil;
|
||||||
import com.google.common.annotations.VisibleForTesting;
|
import com.google.common.annotations.VisibleForTesting;
|
||||||
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
|
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
|
|
@ -118,7 +119,7 @@ public class HapiTransactionService {
|
||||||
theTransactionDetails.clearUserData(BaseHapiFhirDao.XACT_USERDATA_KEY_EXISTING_SEARCH_PARAMS);
|
theTransactionDetails.clearUserData(BaseHapiFhirDao.XACT_USERDATA_KEY_EXISTING_SEARCH_PARAMS);
|
||||||
double sleepAmount = (250.0d * i) * Math.random();
|
double sleepAmount = (250.0d * i) * Math.random();
|
||||||
long sleepAmountLong = (long) sleepAmount;
|
long sleepAmountLong = (long) sleepAmount;
|
||||||
sleepAtLeast(sleepAmountLong, false);
|
TestUtil.sleepAtLeast(sleepAmountLong, false);
|
||||||
|
|
||||||
ourLog.info("About to start a transaction retry due to conflict or constraint error. Sleeping {}ms first.", sleepAmountLong);
|
ourLog.info("About to start a transaction retry due to conflict or constraint error. Sleeping {}ms first.", sleepAmountLong);
|
||||||
continue;
|
continue;
|
||||||
|
|
@ -164,22 +165,4 @@ public class HapiTransactionService {
|
||||||
super(theThrowable);
|
super(theThrowable);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@SuppressWarnings("BusyWait")
|
|
||||||
public static void sleepAtLeast(long theMillis, boolean theLogProgress) {
|
|
||||||
long start = System.currentTimeMillis();
|
|
||||||
while (System.currentTimeMillis() <= start + theMillis) {
|
|
||||||
try {
|
|
||||||
long timeSinceStarted = System.currentTimeMillis() - start;
|
|
||||||
long timeToSleep = Math.max(0, theMillis - timeSinceStarted);
|
|
||||||
if (theLogProgress) {
|
|
||||||
ourLog.info("Sleeping for {}ms", timeToSleep);
|
|
||||||
}
|
|
||||||
Thread.sleep(timeToSleep);
|
|
||||||
} catch (InterruptedException e) {
|
|
||||||
Thread.currentThread().interrupt();
|
|
||||||
ourLog.error("Interrupted", e);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -25,8 +25,8 @@ import ca.uhn.fhir.interceptor.api.HookParams;
|
||||||
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
|
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
|
||||||
import ca.uhn.fhir.interceptor.api.Pointcut;
|
import ca.uhn.fhir.interceptor.api.Pointcut;
|
||||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
|
||||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
|
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
|
||||||
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
||||||
import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
|
import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
|
||||||
|
|
@ -52,7 +52,7 @@ public class DeleteExpungeJobSubmitterImpl implements IDeleteExpungeJobSubmitter
|
||||||
@Autowired
|
@Autowired
|
||||||
private IBatchJobSubmitter myBatchJobSubmitter;
|
private IBatchJobSubmitter myBatchJobSubmitter;
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME)
|
@Qualifier(BatchConstants.DELETE_EXPUNGE_JOB_NAME)
|
||||||
private Job myDeleteExpungeJob;
|
private Job myDeleteExpungeJob;
|
||||||
@Autowired
|
@Autowired
|
||||||
FhirContext myFhirContext;
|
FhirContext myFhirContext;
|
||||||
|
|
|
||||||
|
|
@ -20,12 +20,10 @@ package ca.uhn.fhir.jpa.delete.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
|
||||||
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterValidator;
|
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterValidator;
|
||||||
import ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener;
|
import ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener;
|
||||||
import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
|
import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
|
||||||
import ca.uhn.fhir.jpa.batch.writer.SqlExecutorWriter;
|
import ca.uhn.fhir.jpa.batch.writer.SqlExecutorWriter;
|
||||||
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
|
|
||||||
import org.springframework.batch.core.Job;
|
import org.springframework.batch.core.Job;
|
||||||
import org.springframework.batch.core.Step;
|
import org.springframework.batch.core.Step;
|
||||||
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
|
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
|
||||||
|
|
@ -39,7 +37,7 @@ import org.springframework.context.annotation.Lazy;
|
||||||
|
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME;
|
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.DELETE_EXPUNGE_JOB_NAME;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
||||||
|
|
|
||||||
|
|
@ -29,9 +29,7 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||||
import ca.uhn.fhir.mdm.log.Logs;
|
import ca.uhn.fhir.mdm.log.Logs;
|
||||||
import ca.uhn.fhir.model.api.IQueryParameterType;
|
import ca.uhn.fhir.model.api.IQueryParameterType;
|
||||||
import ca.uhn.fhir.model.primitive.IdDt;
|
import ca.uhn.fhir.model.primitive.IdDt;
|
||||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
|
||||||
import ca.uhn.fhir.rest.param.ReferenceParam;
|
import ca.uhn.fhir.rest.param.ReferenceParam;
|
||||||
import joptsimple.internal.Strings;
|
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.springframework.beans.factory.annotation.Autowired;
|
import org.springframework.beans.factory.annotation.Autowired;
|
||||||
|
|
||||||
|
|
@ -39,8 +37,6 @@ import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Set;
|
import java.util.Set;
|
||||||
|
|
||||||
import static org.slf4j.LoggerFactory.getLogger;
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* This interceptor replaces the auto-generated CapabilityStatement that is generated
|
* This interceptor replaces the auto-generated CapabilityStatement that is generated
|
||||||
* by the HAPI FHIR Server with a static hard-coded resource.
|
* by the HAPI FHIR Server with a static hard-coded resource.
|
||||||
|
|
|
||||||
|
|
@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.migrate.tasks;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server - Migration
|
* HAPI FHIR JPA Server
|
||||||
* %%
|
* %%
|
||||||
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
|
||||||
* %%
|
* %%
|
||||||
|
|
@ -50,13 +50,13 @@ public class BaseJpaSystemProvider<T, MT> extends BaseJpaProvider implements IJp
|
||||||
* @deprecated
|
* @deprecated
|
||||||
*/
|
*/
|
||||||
@Deprecated
|
@Deprecated
|
||||||
public static final String MARK_ALL_RESOURCES_FOR_REINDEXING = "$mark-all-resources-for-reindexing";
|
public static final String MARK_ALL_RESOURCES_FOR_REINDEXING = ProviderConstants.MARK_ALL_RESOURCES_FOR_REINDEXING;
|
||||||
/**
|
/**
|
||||||
* @see ProviderConstants#OPERATION_REINDEX
|
* @see ProviderConstants#OPERATION_REINDEX
|
||||||
* @deprecated
|
* @deprecated
|
||||||
*/
|
*/
|
||||||
@Deprecated
|
@Deprecated
|
||||||
public static final String PERFORM_REINDEXING_PASS = "$perform-reindexing-pass";
|
public static final String PERFORM_REINDEXING_PASS = ProviderConstants.PERFORM_REINDEXING_PASS;
|
||||||
|
|
||||||
private IFhirSystemDao<T, MT> myDao;
|
private IFhirSystemDao<T, MT> myDao;
|
||||||
@Autowired
|
@Autowired
|
||||||
|
|
|
||||||
|
|
@ -22,8 +22,8 @@ package ca.uhn.fhir.jpa.reindex;
|
||||||
|
|
||||||
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
|
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
|
||||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
|
||||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
|
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
|
||||||
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
|
||||||
import ca.uhn.fhir.jpa.batch.reader.CronologicalBatchAllResourcePidReader;
|
import ca.uhn.fhir.jpa.batch.reader.CronologicalBatchAllResourcePidReader;
|
||||||
|
|
@ -53,10 +53,10 @@ public class ReindexJobSubmitterImpl implements IReindexJobSubmitter {
|
||||||
@Autowired
|
@Autowired
|
||||||
private IBatchJobSubmitter myBatchJobSubmitter;
|
private IBatchJobSubmitter myBatchJobSubmitter;
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.REINDEX_JOB_NAME)
|
@Qualifier(BatchConstants.REINDEX_JOB_NAME)
|
||||||
private Job myReindexJob;
|
private Job myReindexJob;
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.REINDEX_EVERYTHING_JOB_NAME)
|
@Qualifier(BatchConstants.REINDEX_EVERYTHING_JOB_NAME)
|
||||||
private Job myReindexEverythingJob;
|
private Job myReindexEverythingJob;
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
|
|
|
||||||
|
|
@ -35,7 +35,7 @@ import org.springframework.context.annotation.Lazy;
|
||||||
|
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.REINDEX_EVERYTHING_JOB_NAME;
|
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.REINDEX_EVERYTHING_JOB_NAME;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
||||||
|
|
|
||||||
|
|
@ -20,18 +20,14 @@ package ca.uhn.fhir.jpa.reindex.job;
|
||||||
* #L%
|
* #L%
|
||||||
*/
|
*/
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
|
||||||
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterValidator;
|
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterValidator;
|
||||||
import ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener;
|
import ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener;
|
||||||
import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
|
import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
|
||||||
import ca.uhn.fhir.jpa.batch.writer.SqlExecutorWriter;
|
|
||||||
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
|
|
||||||
import org.springframework.batch.core.Job;
|
import org.springframework.batch.core.Job;
|
||||||
import org.springframework.batch.core.Step;
|
import org.springframework.batch.core.Step;
|
||||||
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
|
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
|
||||||
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
|
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
|
||||||
import org.springframework.batch.core.listener.ExecutionContextPromotionListener;
|
import org.springframework.batch.core.listener.ExecutionContextPromotionListener;
|
||||||
import org.springframework.batch.item.ItemReader;
|
|
||||||
import org.springframework.beans.factory.annotation.Autowired;
|
import org.springframework.beans.factory.annotation.Autowired;
|
||||||
import org.springframework.context.annotation.Bean;
|
import org.springframework.context.annotation.Bean;
|
||||||
import org.springframework.context.annotation.Configuration;
|
import org.springframework.context.annotation.Configuration;
|
||||||
|
|
@ -39,7 +35,7 @@ import org.springframework.context.annotation.Lazy;
|
||||||
|
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.REINDEX_JOB_NAME;
|
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.REINDEX_JOB_NAME;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
* Spring batch Job configuration file. Contains all necessary plumbing to run a
|
||||||
|
|
|
||||||
|
|
@ -6,8 +6,8 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
|
||||||
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
|
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
|
||||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||||
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
|
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
|
||||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
|
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobParametersBuilder;
|
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobParametersBuilder;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.GroupBulkExportJobParametersBuilder;
|
import ca.uhn.fhir.jpa.bulk.export.job.GroupBulkExportJobParametersBuilder;
|
||||||
|
|
@ -102,15 +102,15 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
||||||
private BatchJobHelper myBatchJobHelper;
|
private BatchJobHelper myBatchJobHelper;
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
|
@Qualifier(BatchConstants.BULK_EXPORT_JOB_NAME)
|
||||||
private Job myBulkJob;
|
private Job myBulkJob;
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
|
@Qualifier(BatchConstants.GROUP_BULK_EXPORT_JOB_NAME)
|
||||||
private Job myGroupBulkJob;
|
private Job myGroupBulkJob;
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME)
|
@Qualifier(BatchConstants.PATIENT_BULK_EXPORT_JOB_NAME)
|
||||||
private Job myPatientBulkJob;
|
private Job myPatientBulkJob;
|
||||||
|
|
||||||
private IIdType myPatientGroupId;
|
private IIdType myPatientGroupId;
|
||||||
|
|
@ -328,11 +328,11 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
||||||
|
|
||||||
private void awaitAllBulkJobCompletions() {
|
private void awaitAllBulkJobCompletions() {
|
||||||
myBatchJobHelper.awaitAllBulkJobCompletions(
|
myBatchJobHelper.awaitAllBulkJobCompletions(
|
||||||
BatchJobsConfig.BULK_EXPORT_JOB_NAME,
|
BatchConstants.BULK_EXPORT_JOB_NAME,
|
||||||
BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME,
|
BatchConstants.PATIENT_BULK_EXPORT_JOB_NAME,
|
||||||
BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME,
|
BatchConstants.GROUP_BULK_EXPORT_JOB_NAME,
|
||||||
BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME,
|
BatchConstants.DELETE_EXPUNGE_JOB_NAME,
|
||||||
BatchJobsConfig.MDM_CLEAR_JOB_NAME
|
BatchConstants.MDM_CLEAR_JOB_NAME
|
||||||
);
|
);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -5,7 +5,7 @@ import ca.uhn.fhir.interceptor.api.HookParams;
|
||||||
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
|
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
|
||||||
import ca.uhn.fhir.interceptor.api.Interceptor;
|
import ca.uhn.fhir.interceptor.api.Interceptor;
|
||||||
import ca.uhn.fhir.interceptor.api.Pointcut;
|
import ca.uhn.fhir.interceptor.api.Pointcut;
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
|
||||||
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
|
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
|
||||||
|
|
@ -44,7 +44,7 @@ import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.BULK_IMPORT_JOB_NAME;
|
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.BULK_IMPORT_JOB_NAME;
|
||||||
import static org.awaitility.Awaitility.await;
|
import static org.awaitility.Awaitility.await;
|
||||||
import static org.hamcrest.MatcherAssert.assertThat;
|
import static org.hamcrest.MatcherAssert.assertThat;
|
||||||
import static org.hamcrest.Matchers.containsInAnyOrder;
|
import static org.hamcrest.Matchers.containsInAnyOrder;
|
||||||
|
|
@ -212,7 +212,7 @@ public class BulkDataImportR4Test extends BaseJpaR4Test implements ITestDataBuil
|
||||||
}
|
}
|
||||||
|
|
||||||
protected List<JobExecution> awaitAllBulkImportJobCompletion() {
|
protected List<JobExecution> awaitAllBulkImportJobCompletion() {
|
||||||
return myBatchJobHelper.awaitAllBulkJobCompletions(BatchJobsConfig.BULK_IMPORT_JOB_NAME);
|
return myBatchJobHelper.awaitAllBulkJobCompletions(BatchConstants.BULK_IMPORT_JOB_NAME);
|
||||||
}
|
}
|
||||||
|
|
||||||
@Interceptor
|
@Interceptor
|
||||||
|
|
|
||||||
|
|
@ -1451,9 +1451,9 @@ public class FhirResourceDaoR4SearchNoHashesTest extends BaseJpaR4Test {
|
||||||
id1b = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
|
id1b = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
|
||||||
}
|
}
|
||||||
|
|
||||||
TestUtil.sleepAtLeast(1100);
|
ca.uhn.fhir.util.TestUtil.sleepAtLeast(1100);
|
||||||
DateTimeType beforeR2 = new DateTimeType(new Date(), TemporalPrecisionEnum.MILLI);
|
DateTimeType beforeR2 = new DateTimeType(new Date(), TemporalPrecisionEnum.MILLI);
|
||||||
TestUtil.sleepAtLeast(1100);
|
ca.uhn.fhir.util.TestUtil.sleepAtLeast(1100);
|
||||||
|
|
||||||
IIdType id2;
|
IIdType id2;
|
||||||
{
|
{
|
||||||
|
|
|
||||||
|
|
@ -6,11 +6,11 @@ import ca.uhn.fhir.jpa.entity.Search;
|
||||||
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
|
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
|
||||||
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
|
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
|
||||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||||
import ca.uhn.fhir.jpa.util.TestUtil;
|
|
||||||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||||
import ca.uhn.fhir.rest.param.StringParam;
|
import ca.uhn.fhir.rest.param.StringParam;
|
||||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||||
import ca.uhn.fhir.util.StopWatch;
|
import ca.uhn.fhir.util.StopWatch;
|
||||||
|
import ca.uhn.fhir.util.TestUtil;
|
||||||
import org.apache.commons.lang3.Validate;
|
import org.apache.commons.lang3.Validate;
|
||||||
import org.apache.commons.lang3.time.DateUtils;
|
import org.apache.commons.lang3.time.DateUtils;
|
||||||
import org.hl7.fhir.instance.model.api.IIdType;
|
import org.hl7.fhir.instance.model.api.IIdType;
|
||||||
|
|
@ -116,7 +116,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
|
||||||
}
|
}
|
||||||
assertEquals(searchUuid1, searchUuid2);
|
assertEquals(searchUuid1, searchUuid2);
|
||||||
|
|
||||||
TestUtil.sleepAtLeast(reuseCachedSearchResultsForMillis + 1);
|
ca.uhn.fhir.util.TestUtil.sleepAtLeast(reuseCachedSearchResultsForMillis + 1);
|
||||||
|
|
||||||
// We're now past reuseCachedSearchResultsForMillis so we shouldn't reuse the search
|
// We're now past reuseCachedSearchResultsForMillis so we shouldn't reuse the search
|
||||||
|
|
||||||
|
|
@ -291,7 +291,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
|
||||||
}
|
}
|
||||||
assertEquals(searchUuid1, searchUuid2);
|
assertEquals(searchUuid1, searchUuid2);
|
||||||
|
|
||||||
TestUtil.sleepAtLeast(reuseCachedSearchResultsForMillis + 1);
|
ca.uhn.fhir.util.TestUtil.sleepAtLeast(reuseCachedSearchResultsForMillis + 1);
|
||||||
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
|
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
|
||||||
|
|
||||||
// We're now past reuseCachedSearchResultsForMillis so we shouldn't reuse the search
|
// We're now past reuseCachedSearchResultsForMillis so we shouldn't reuse the search
|
||||||
|
|
@ -376,7 +376,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
|
||||||
}
|
}
|
||||||
});
|
});
|
||||||
if (search == null) {
|
if (search == null) {
|
||||||
TestUtil.sleepAtLeast(100);
|
ca.uhn.fhir.util.TestUtil.sleepAtLeast(100);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
assertNotNull(search, "Search " + bundleProvider.getUuid() + " not found on disk after 10 seconds");
|
assertNotNull(search, "Search " + bundleProvider.getUuid() + " not found on disk after 10 seconds");
|
||||||
|
|
|
||||||
|
|
@ -22,7 +22,7 @@ import java.util.concurrent.ExecutorService;
|
||||||
import java.util.concurrent.Executors;
|
import java.util.concurrent.Executors;
|
||||||
import java.util.concurrent.Future;
|
import java.util.concurrent.Future;
|
||||||
|
|
||||||
import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
|
import static ca.uhn.fhir.util.TestUtil.sleepAtLeast;
|
||||||
import static org.hamcrest.MatcherAssert.assertThat;
|
import static org.hamcrest.MatcherAssert.assertThat;
|
||||||
import static org.hamcrest.Matchers.containsString;
|
import static org.hamcrest.Matchers.containsString;
|
||||||
import static org.hamcrest.Matchers.not;
|
import static org.hamcrest.Matchers.not;
|
||||||
|
|
|
||||||
|
|
@ -72,7 +72,7 @@ import java.util.concurrent.atomic.AtomicInteger;
|
||||||
import java.util.function.Supplier;
|
import java.util.function.Supplier;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
|
import static ca.uhn.fhir.util.TestUtil.sleepAtLeast;
|
||||||
import static org.apache.commons.lang3.StringUtils.countMatches;
|
import static org.apache.commons.lang3.StringUtils.countMatches;
|
||||||
import static org.hamcrest.MatcherAssert.assertThat;
|
import static org.hamcrest.MatcherAssert.assertThat;
|
||||||
import static org.hamcrest.Matchers.contains;
|
import static org.hamcrest.Matchers.contains;
|
||||||
|
|
|
||||||
|
|
@ -1,7 +1,7 @@
|
||||||
package ca.uhn.fhir.jpa.delete.job;
|
package ca.uhn.fhir.jpa.delete.job;
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
|
||||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterUtil;
|
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterUtil;
|
||||||
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
|
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
|
||||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||||
|
|
@ -23,7 +23,7 @@ public class DeleteExpungeJobTest extends BaseJpaR4Test {
|
||||||
@Autowired
|
@Autowired
|
||||||
private IBatchJobSubmitter myBatchJobSubmitter;
|
private IBatchJobSubmitter myBatchJobSubmitter;
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME)
|
@Qualifier(BatchConstants.DELETE_EXPUNGE_JOB_NAME)
|
||||||
private Job myDeleteExpungeJob;
|
private Job myDeleteExpungeJob;
|
||||||
@Autowired
|
@Autowired
|
||||||
private BatchJobHelper myBatchJobHelper;
|
private BatchJobHelper myBatchJobHelper;
|
||||||
|
|
|
||||||
|
|
@ -1,8 +1,8 @@
|
||||||
package ca.uhn.fhir.jpa.delete.job;
|
package ca.uhn.fhir.jpa.delete.job;
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
|
|
||||||
import ca.uhn.fhir.jpa.batch.CommonBatchJobConfig;
|
import ca.uhn.fhir.jpa.batch.CommonBatchJobConfig;
|
||||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||||
|
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
|
||||||
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterUtil;
|
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterUtil;
|
||||||
import ca.uhn.fhir.jpa.batch.reader.CronologicalBatchAllResourcePidReader;
|
import ca.uhn.fhir.jpa.batch.reader.CronologicalBatchAllResourcePidReader;
|
||||||
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
|
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
|
||||||
|
|
@ -37,10 +37,10 @@ public class ReindexJobTest extends BaseJpaR4Test {
|
||||||
@Autowired
|
@Autowired
|
||||||
private IBatchJobSubmitter myBatchJobSubmitter;
|
private IBatchJobSubmitter myBatchJobSubmitter;
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.REINDEX_JOB_NAME)
|
@Qualifier(BatchConstants.REINDEX_JOB_NAME)
|
||||||
private Job myReindexJob;
|
private Job myReindexJob;
|
||||||
@Autowired
|
@Autowired
|
||||||
@Qualifier(BatchJobsConfig.REINDEX_EVERYTHING_JOB_NAME)
|
@Qualifier(BatchConstants.REINDEX_EVERYTHING_JOB_NAME)
|
||||||
private Job myReindexEverythingJob;
|
private Job myReindexEverythingJob;
|
||||||
@Autowired
|
@Autowired
|
||||||
private BatchJobHelper myBatchJobHelper;
|
private BatchJobHelper myBatchJobHelper;
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,161 @@
|
||||||
|
package ca.uhn.fhir.jpa.migrate.taskdef;
|
||||||
|
|
||||||
|
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
|
||||||
|
import ca.uhn.fhir.jpa.migrate.FlywayMigrator;
|
||||||
|
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
|
||||||
|
import ca.uhn.fhir.jpa.migrate.SchemaMigrator;
|
||||||
|
import org.apache.commons.dbcp2.BasicDataSource;
|
||||||
|
import org.intellij.lang.annotations.Language;
|
||||||
|
import org.junit.jupiter.api.AfterEach;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
import org.springframework.jdbc.core.ColumnMapRowMapper;
|
||||||
|
|
||||||
|
import java.sql.SQLException;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.Set;
|
||||||
|
import java.util.function.Supplier;
|
||||||
|
import java.util.stream.Stream;
|
||||||
|
|
||||||
|
// TODO KHS copied from hapi-fhir-sql-migrate
|
||||||
|
public abstract class BaseTest {
|
||||||
|
|
||||||
|
private static final String DATABASE_NAME = "DATABASE";
|
||||||
|
private static final Logger ourLog = LoggerFactory.getLogger(BaseTest.class);
|
||||||
|
private static int ourDatabaseUrl = 0;
|
||||||
|
private BasicDataSource myDataSource;
|
||||||
|
private String myUrl;
|
||||||
|
private FlywayMigrator myMigrator;
|
||||||
|
private DriverTypeEnum.ConnectionProperties myConnectionProperties;
|
||||||
|
|
||||||
|
public static Stream<Supplier<TestDatabaseDetails>> data() {
|
||||||
|
ourLog.info("H2: {}", org.h2.Driver.class.toString());
|
||||||
|
|
||||||
|
ArrayList<Supplier<TestDatabaseDetails>> retVal = new ArrayList<>();
|
||||||
|
|
||||||
|
// H2
|
||||||
|
retVal.add(new Supplier<TestDatabaseDetails>() {
|
||||||
|
@Override
|
||||||
|
public TestDatabaseDetails get() {
|
||||||
|
String url = "jdbc:h2:mem:" + DATABASE_NAME + ourDatabaseUrl++;
|
||||||
|
DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.H2_EMBEDDED.newConnectionProperties(url, "SA", "SA");
|
||||||
|
BasicDataSource dataSource = new BasicDataSource();
|
||||||
|
dataSource.setUrl(url);
|
||||||
|
dataSource.setUsername("SA");
|
||||||
|
dataSource.setPassword("SA");
|
||||||
|
dataSource.setDriverClassName(DriverTypeEnum.H2_EMBEDDED.getDriverClassName());
|
||||||
|
FlywayMigrator migrator = new FlywayMigrator(SchemaMigrator.HAPI_FHIR_MIGRATION_TABLENAME, dataSource, DriverTypeEnum.H2_EMBEDDED);
|
||||||
|
return new TestDatabaseDetails(url, connectionProperties, dataSource, migrator);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String toString() {
|
||||||
|
return "H2";
|
||||||
|
}
|
||||||
|
});
|
||||||
|
|
||||||
|
// Derby
|
||||||
|
retVal.add(new Supplier<TestDatabaseDetails>() {
|
||||||
|
@Override
|
||||||
|
public TestDatabaseDetails get() {
|
||||||
|
String url = "jdbc:derby:memory:" + DATABASE_NAME + ourDatabaseUrl++ + ";create=true";
|
||||||
|
DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.DERBY_EMBEDDED.newConnectionProperties(url, "SA", "SA");
|
||||||
|
BasicDataSource dataSource = new BasicDataSource();
|
||||||
|
dataSource.setUrl(url);
|
||||||
|
dataSource.setUsername("SA");
|
||||||
|
dataSource.setPassword("SA");
|
||||||
|
dataSource.setDriverClassName(DriverTypeEnum.DERBY_EMBEDDED.getDriverClassName());
|
||||||
|
FlywayMigrator migrator = new FlywayMigrator(SchemaMigrator.HAPI_FHIR_MIGRATION_TABLENAME, dataSource, DriverTypeEnum.DERBY_EMBEDDED);
|
||||||
|
return new TestDatabaseDetails(url, connectionProperties, dataSource, migrator);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String toString() {
|
||||||
|
return "Derby";
|
||||||
|
}
|
||||||
|
});
|
||||||
|
|
||||||
|
return retVal.stream();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void before(Supplier<TestDatabaseDetails> theTestDatabaseDetails) {
|
||||||
|
TestDatabaseDetails testDatabaseDetails = theTestDatabaseDetails.get();
|
||||||
|
myUrl = testDatabaseDetails.myUrl;
|
||||||
|
myConnectionProperties = testDatabaseDetails.myConnectionProperties;
|
||||||
|
myDataSource = testDatabaseDetails.myDataSource;
|
||||||
|
myMigrator = testDatabaseDetails.myMigrator;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getUrl() {
|
||||||
|
return myUrl;
|
||||||
|
}
|
||||||
|
|
||||||
|
public DriverTypeEnum.ConnectionProperties getConnectionProperties() {
|
||||||
|
return myConnectionProperties;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected BasicDataSource getDataSource() {
|
||||||
|
return myDataSource;
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterEach
|
||||||
|
public void resetMigrationVersion() throws SQLException {
|
||||||
|
if (getConnectionProperties() != null) {
|
||||||
|
Set<String> tableNames = JdbcUtils.getTableNames(getConnectionProperties());
|
||||||
|
if (tableNames.contains(SchemaMigrator.HAPI_FHIR_MIGRATION_TABLENAME)) {
|
||||||
|
executeSql("DELETE from " + SchemaMigrator.HAPI_FHIR_MIGRATION_TABLENAME + " where \"installed_rank\" > 0");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
protected void executeSql(@Language("SQL") String theSql, Object... theArgs) {
|
||||||
|
myConnectionProperties.getTxTemplate().execute(t -> {
|
||||||
|
myConnectionProperties.newJdbcTemplate().update(theSql, theArgs);
|
||||||
|
return null;
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
protected List<Map<String, Object>> executeQuery(@Language("SQL") String theSql, Object... theArgs) {
|
||||||
|
return myConnectionProperties.getTxTemplate().execute(t -> {
|
||||||
|
return myConnectionProperties.newJdbcTemplate().query(theSql, theArgs, new ColumnMapRowMapper());
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
public FlywayMigrator getMigrator() {
|
||||||
|
return myMigrator;
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterEach
|
||||||
|
public void after() {
|
||||||
|
if (myConnectionProperties != null) {
|
||||||
|
myConnectionProperties.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
protected DriverTypeEnum getDriverType() {
|
||||||
|
return myConnectionProperties.getDriverType();
|
||||||
|
}
|
||||||
|
|
||||||
|
public static class TestDatabaseDetails {
|
||||||
|
|
||||||
|
private final String myUrl;
|
||||||
|
private final DriverTypeEnum.ConnectionProperties myConnectionProperties;
|
||||||
|
private final BasicDataSource myDataSource;
|
||||||
|
private final FlywayMigrator myMigrator;
|
||||||
|
|
||||||
|
public TestDatabaseDetails(String theUrl, DriverTypeEnum.ConnectionProperties theConnectionProperties, BasicDataSource theDataSource, FlywayMigrator theMigrator) {
|
||||||
|
myUrl = theUrl;
|
||||||
|
myConnectionProperties = theConnectionProperties;
|
||||||
|
myDataSource = theDataSource;
|
||||||
|
myMigrator = theMigrator;
|
||||||
|
}
|
||||||
|
|
||||||
|
public DriverTypeEnum getDriverType() {
|
||||||
|
return myConnectionProperties.getDriverType();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue