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";
-
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/job/MultiUrlJobParameterValidator.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/job/MultiUrlJobParameterValidator.java
index 57b77ea52ac..69774c7ac70 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/job/MultiUrlJobParameterValidator.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/job/MultiUrlJobParameterValidator.java
@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.batch.job;
*/
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.RequestListJson;
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.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.
*/
@@ -50,7 +49,7 @@ public class MultiUrlJobParameterValidator implements JobParametersValidator {
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()) {
String url = partitionedUrl.getUrl();
try {
@@ -60,7 +59,7 @@ public class MultiUrlJobParameterValidator implements JobParametersValidator {
throw new JobParametersInvalidException("The resource type " + resourceName + " is not supported on this server.");
}
} 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());
}
}
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/MdmClearJobSubmitterImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/MdmClearJobSubmitterImpl.java
index 90bee86b963..246bebac7c4 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/MdmClearJobSubmitterImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/MdmClearJobSubmitterImpl.java
@@ -24,8 +24,8 @@ import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
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.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
import ca.uhn.fhir.jpa.batch.mdm.job.ReverseCronologicalBatchMdmLinkPidReader;
@@ -55,7 +55,7 @@ public class MdmClearJobSubmitterImpl implements IMdmClearJobSubmitter {
@Autowired
private IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
- @Qualifier(BatchJobsConfig.MDM_CLEAR_JOB_NAME)
+ @Qualifier(BatchConstants.MDM_CLEAR_JOB_NAME)
private Job myMdmClearJob;
@Override
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/job/MdmClearJobConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/job/MdmClearJobConfig.java
index b2786f7cc84..9f8f339191b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/job/MdmClearJobConfig.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/job/MdmClearJobConfig.java
@@ -41,7 +41,7 @@ import org.springframework.context.annotation.Lazy;
import java.util.ArrayList;
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
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/reader/BaseReverseCronologicalBatchPidReader.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/reader/BaseReverseCronologicalBatchPidReader.java
index 46c5e91c22f..d32a3c6cae3 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/reader/BaseReverseCronologicalBatchPidReader.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/reader/BaseReverseCronologicalBatchPidReader.java
@@ -24,6 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
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.model.PartitionedUrl;
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:
- * {@link #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 #JOB_PARAM_START_TIME}: The latest timestamp of entities to search for
+ * {@link BatchConstants#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_BATCH_SIZE}: The number of resources to return with each search. If ommitted, {@link DaoConfig#getExpungeBatchSize} will be used.
+ * {@link BatchConstants#JOB_PARAM_START_TIME}: The latest timestamp of entities to search for
*
- * 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
- * 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
* restarting jobs that use this reader so it can pick up where it left off.
*/
public abstract class BaseReverseCronologicalBatchPidReader implements ItemReader>, 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 final BatchDateThresholdUpdater myBatchDateThresholdUpdater = new BatchDateThresholdUpdater();
private final Map myThresholdHighByUrlIndex = new HashMap<>();
@@ -88,30 +84,30 @@ public abstract class BaseReverseCronologicalBatchPidReader implements ItemReade
private Date myStartTime;
private static String highKey(int theIndex) {
- return CURRENT_THRESHOLD_HIGH + "." + theIndex;
+ return BatchConstants.CURRENT_THRESHOLD_HIGH + "." + theIndex;
}
@Nonnull
public static JobParameters buildJobParameters(String theOperationName, Integer theBatchSize, RequestListJson theRequestListJson) {
Map map = new HashMap<>();
map.put(MultiUrlJobParameterValidator.JOB_PARAM_OPERATION_NAME, new JobParameter(theOperationName));
- map.put(ReverseCronologicalBatchResourcePidReader.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_REQUEST_LIST, new JobParameter(theRequestListJson.toJson()));
+ map.put(BatchConstants.JOB_PARAM_START_TIME, new JobParameter(DateUtils.addMinutes(new Date(), CommonBatchJobConfig.MINUTES_IN_FUTURE_TO_PROCESS_FROM)));
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);
return parameters;
}
@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);
myPartitionedUrls = requestListJson.getPartitionedUrls();
}
@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;
}
@@ -166,8 +162,8 @@ public abstract class BaseReverseCronologicalBatchPidReader implements ItemReade
@Override
public void open(ExecutionContext executionContext) throws ItemStreamException {
- if (executionContext.containsKey(CURRENT_URL_INDEX)) {
- myUrlIndex = new Long(executionContext.getLong(CURRENT_URL_INDEX)).intValue();
+ if (executionContext.containsKey(BatchConstants.CURRENT_URL_INDEX)) {
+ myUrlIndex = new Long(executionContext.getLong(BatchConstants.CURRENT_URL_INDEX)).intValue();
}
for (int index = 0; index < myPartitionedUrls.size(); ++index) {
String key = highKey(index);
@@ -181,7 +177,7 @@ public abstract class BaseReverseCronologicalBatchPidReader implements ItemReade
@Override
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) {
Date date = myThresholdHighByUrlIndex.get(index);
if (date != null) {
@@ -199,7 +195,7 @@ public abstract class BaseReverseCronologicalBatchPidReader implements ItemReade
}
@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;
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BaseBulkItemReader.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BaseBulkItemReader.java
index 7f934cfb248..6f647bd0e58 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BaseBulkItemReader.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BaseBulkItemReader.java
@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
@@ -57,7 +58,7 @@ public abstract class BaseBulkItemReader implements ItemReader, List>chunk(CHUNK_SIZE) //1000 resources per generated file, as the reader returns 10 resources at a time.
.reader(bulkItemReader())
.processor(myPidToIBaseResourceProcessor)
@@ -217,7 +216,7 @@ public class BulkExportJobConfig {
@Bean
public Step bulkExportPartitionStep() {
return myStepBuilderFactory.get("partitionStep")
- .partitioner(BatchJobsConfig.BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP, bulkExportResourceTypePartitioner())
+ .partitioner(BatchConstants.BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP, bulkExportResourceTypePartitioner())
.step(bulkExportGenerateResourceFilesStep())
.build();
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobParameterValidator.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobParameterValidator.java
index 64d06052d43..300a26c8c1f 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobParameterValidator.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobParameterValidator.java
@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.bulk.export.job;
* #L%
*/
+import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
import ca.uhn.fhir.rest.api.Constants;
@@ -34,8 +35,6 @@ import org.springframework.transaction.support.TransactionTemplate;
import java.util.Arrays;
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.
*/
@@ -59,7 +58,7 @@ public class BulkExportJobParameterValidator implements JobParametersValidator {
if (readChunkSize == null || readChunkSize < 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 oJob = myBulkExportJobDao.findByJobId(jobUUID);
if (!StringUtils.isBlank(jobUUID) && !oJob.isPresent()) {
errorBuilder.append("There is no persisted job that exists with UUID: " + jobUUID + ". ");
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/CreateBulkExportEntityTasklet.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/CreateBulkExportEntityTasklet.java
index 9c10bcecba8..8be17cb3b4d 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/CreateBulkExportEntityTasklet.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/CreateBulkExportEntityTasklet.java
@@ -20,10 +20,11 @@ package ca.uhn.fhir.jpa.bulk.export.job;
* #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.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
import org.apache.commons.lang3.StringUtils;
import org.springframework.batch.core.StepContribution;
import org.springframework.batch.core.scope.context.ChunkContext;
@@ -42,18 +43,27 @@ public class CreateBulkExportEntityTasklet implements Tasklet {
@Autowired
private IBulkDataExportSvc myBulkDataExportSvc;
+ public static void addUUIDToJobContext(ChunkContext theChunkContext, String theJobUUID) {
+ theChunkContext
+ .getStepContext()
+ .getStepExecution()
+ .getJobExecution()
+ .getExecutionContext()
+ .putString(BatchConstants.JOB_UUID_PARAMETER, theJobUUID);
+ }
+
@Override
public RepeatStatus execute(StepContribution theStepContribution, ChunkContext theChunkContext) throws Exception {
Map jobParameters = theChunkContext.getStepContext().getJobParameters();
//We can leave early if they provided us with an existing job.
- if (jobParameters.containsKey(BulkExportJobConfig.JOB_UUID_PARAMETER)) {
- addUUIDToJobContext(theChunkContext, (String)jobParameters.get(BulkExportJobConfig.JOB_UUID_PARAMETER));
+ if (jobParameters.containsKey(BatchConstants.JOB_UUID_PARAMETER)) {
+ addUUIDToJobContext(theChunkContext, (String) jobParameters.get(BatchConstants.JOB_UUID_PARAMETER));
return RepeatStatus.FINISHED;
} else {
- String resourceTypes = (String)jobParameters.get("resourceTypes");
- Date since = (Date)jobParameters.get("since");
- String filters = (String)jobParameters.get("filters");
+ String resourceTypes = (String) jobParameters.get("resourceTypes");
+ Date since = (Date) jobParameters.get("since");
+ String filters = (String) jobParameters.get("filters");
Set filterSet;
if (StringUtils.isBlank(filters)) {
filterSet = null;
@@ -86,13 +96,4 @@ public class CreateBulkExportEntityTasklet implements Tasklet {
return RepeatStatus.FINISHED;
}
}
-
- public static void addUUIDToJobContext(ChunkContext theChunkContext, String theJobUUID) {
- theChunkContext
- .getStepContext()
- .getStepExecution()
- .getJobExecution()
- .getExecutionContext()
- .putString(BulkExportJobConfig.JOB_UUID_PARAMETER, theJobUUID);
- }
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/ResourceTypePartitioner.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/ResourceTypePartitioner.java
index 7eb612d2211..f341d25ffdc 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/ResourceTypePartitioner.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/ResourceTypePartitioner.java
@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.bulk.export.job;
* #L%
*/
+import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
import org.slf4j.Logger;
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
// attaching its results to.
- context.putString(BulkExportJobConfig.JOB_UUID_PARAMETER, myJobUUID);
+ context.putString(BatchConstants.JOB_UUID_PARAMETER, myJobUUID);
context.putLong("bulkExportCollectionEntityId", collectionEntityId);
// Name the partition based on the resource type
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportSvcImpl.java
index ab862ce44f2..2caa72135bc 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportSvcImpl.java
@@ -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.IFhirResourceDao;
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.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.job.BulkExportJobConfig;
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.rest.api.Constants;
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.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@@ -114,15 +114,15 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
private IBatchJobSubmitter myJobSubmitter;
@Autowired
- @Qualifier(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
+ @Qualifier(BatchConstants.BULK_EXPORT_JOB_NAME)
private org.springframework.batch.core.Job myBulkExportJob;
@Autowired
- @Qualifier(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
+ @Qualifier(BatchConstants.GROUP_BULK_EXPORT_JOB_NAME)
private org.springframework.batch.core.Job myGroupBulkExportJob;
@Autowired
- @Qualifier(BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME)
+ @Qualifier(BatchConstants.PATIENT_BULK_EXPORT_JOB_NAME)
private org.springframework.batch.core.Job myPatientBulkExportJob;
private Set myCompartmentResources;
@@ -243,7 +243,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
private void processJob(BulkExportJobEntity theBulkExportJobEntity) {
String theJobUuid = theBulkExportJobEntity.getJobId();
JobParametersBuilder parameters = new JobParametersBuilder()
- .addString(BulkExportJobConfig.JOB_UUID_PARAMETER, theJobUuid)
+ .addString(BatchConstants.JOB_UUID_PARAMETER, theJobUuid)
.addLong(BulkExportJobConfig.READ_CHUNK_PARAMETER, READ_CHUNK_SIZE);
ourLog.info("Submitting bulk export job {} to job scheduler", theJobUuid);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/ActivateBulkImportEntityStepListener.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/ActivateBulkImportEntityStepListener.java
index 52520edf6b3..994aea3796e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/ActivateBulkImportEntityStepListener.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/ActivateBulkImportEntityStepListener.java
@@ -20,10 +20,9 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
* #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.model.BulkImportJobStatusEnum;
-import org.elasticsearch.client.enrich.ExecutePolicyResponse;
import org.springframework.batch.core.ExitStatus;
import org.springframework.batch.core.StepExecution;
import org.springframework.batch.core.StepExecutionListener;
@@ -39,7 +38,7 @@ public class ActivateBulkImportEntityStepListener implements StepExecutionListen
@Override
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) {
myBulkImportDaoSvc.setJobToStatus(jobUuid, BulkImportJobStatusEnum.RUNNING);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileReader.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileReader.java
index c16e7c3f67c..c1e4bec40fd 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileReader.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileReader.java
@@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
*/
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.bulk.export.job.BulkExportJobConfig;
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.ParsedBulkImportRecord;
@@ -42,7 +42,7 @@ public class BulkImportFileReader implements ItemReader
private IBulkDataImportSvc myBulkDataImportSvc;
@Autowired
private FhirContext myFhirContext;
- @Value("#{stepExecutionContext['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
+ @Value("#{stepExecutionContext['" + BatchConstants.JOB_UUID_PARAMETER + "']}")
private String myJobUuid;
@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
private int myFileIndex;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileWriter.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileWriter.java
index 37a49ca2a95..5edc7ef9e23 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileWriter.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileWriter.java
@@ -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.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.ParsedBulkImportRecord;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
@@ -39,7 +39,7 @@ import java.util.List;
public class BulkImportFileWriter implements ItemWriter {
private static final Logger ourLog = LoggerFactory.getLogger(BulkImportFileWriter.class);
- @Value("#{stepExecutionContext['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
+ @Value("#{stepExecutionContext['" + BatchConstants.JOB_UUID_PARAMETER + "']}")
private String myJobUuid;
@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
private int myFileIndex;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobCloser.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobCloser.java
index 504874e327d..3866829bf16 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobCloser.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobCloser.java
@@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
* #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.model.BulkImportJobStatusEnum;
import org.springframework.batch.core.BatchStatus;
@@ -36,7 +36,7 @@ import org.springframework.beans.factory.annotation.Value;
*/
public class BulkImportJobCloser implements Tasklet {
- @Value("#{jobParameters['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
+ @Value("#{jobParameters['" + BatchConstants.JOB_UUID_PARAMETER + "']}")
private String myJobUUID;
@Autowired
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobConfig.java
index b235c81ea2b..019b5db8ed1 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobConfig.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobConfig.java
@@ -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.batch.BatchConstants;
+import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobParametersValidator;
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.JobScope;
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 static ca.uhn.fhir.jpa.batch.BatchJobsConfig.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_JOB_NAME;
+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
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobParameterValidator.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobParameterValidator.java
index a46405fec31..c26673665ed 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobParameterValidator.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobParameterValidator.java
@@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
* #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.entity.BulkImportJobEntity;
import org.apache.commons.lang3.StringUtils;
@@ -52,7 +52,7 @@ public class BulkImportJobParameterValidator implements JobParametersValidator {
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
String errorMessage = txTemplate.execute(tx -> {
StringBuilder errorBuilder = new StringBuilder();
- String jobUUID = theJobParameters.getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
+ String jobUUID = theJobParameters.getString(BatchConstants.JOB_UUID_PARAMETER);
Optional oJob = myBulkImportJobDao.findByJobId(jobUUID);
if (!StringUtils.isBlank(jobUUID) && !oJob.isPresent()) {
errorBuilder.append("There is no persisted job that exists with UUID: ");
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportPartitioner.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportPartitioner.java
index 6a88cfbecab..6df34a9571d 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportPartitioner.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportPartitioner.java
@@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
* #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.model.BulkImportJobJson;
import org.slf4j.Logger;
@@ -43,7 +43,7 @@ public class BulkImportPartitioner implements Partitioner {
private static final Logger ourLog = getLogger(BulkImportPartitioner.class);
- @Value("#{jobParameters['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
+ @Value("#{jobParameters['" + BatchConstants.JOB_UUID_PARAMETER + "']}")
private String myJobUUID;
@Autowired
@@ -61,7 +61,7 @@ public class BulkImportPartitioner implements Partitioner {
String fileDescription = myBulkDataImportSvc.getFileDescription(myJobUUID, i);
ExecutionContext context = new ExecutionContext();
- context.putString(BulkExportJobConfig.JOB_UUID_PARAMETER, myJobUUID);
+ context.putString(BatchConstants.JOB_UUID_PARAMETER, myJobUUID);
context.putInt(FILE_INDEX, i);
context.put(ROW_PROCESSING_MODE, job.getProcessingMode());
context.put(JOB_DESCRIPTION, job.getJobDescription());
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportStepListener.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportStepListener.java
index 2861780a4ff..014ec74a92b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportStepListener.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportStepListener.java
@@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
* #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.model.BulkImportJobStatusEnum;
import org.springframework.batch.core.ExitStatus;
@@ -52,9 +52,9 @@ public class BulkImportStepListener implements StepExecutionListener, RetryListe
public ExitStatus afterStep(StepExecution theStepExecution) {
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.
- String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
+ String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BatchConstants.JOB_UUID_PARAMETER);
if (jobUuid == null) {
- jobUuid = theStepExecution.getJobExecution().getExecutionContext().getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
+ jobUuid = theStepExecution.getJobExecution().getExecutionContext().getString(BatchConstants.JOB_UUID_PARAMETER);
}
assert isNotBlank(jobUuid);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/CreateBulkImportEntityTasklet.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/CreateBulkImportEntityTasklet.java
index c543ba4961f..2d93b98c98f 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/CreateBulkImportEntityTasklet.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/CreateBulkImportEntityTasklet.java
@@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.imprt.job;
* #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.util.ValidateUtil;
import org.springframework.batch.core.StepContribution;
@@ -37,8 +37,8 @@ public class CreateBulkImportEntityTasklet implements Tasklet {
Map jobParameters = theChunkContext.getStepContext().getJobParameters();
//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");
- CreateBulkExportEntityTasklet.addUUIDToJobContext(theChunkContext, (String) jobParameters.get(BulkExportJobConfig.JOB_UUID_PARAMETER));
+ ValidateUtil.isTrueOrThrowInvalidRequest(jobParameters.containsKey(BatchConstants.JOB_UUID_PARAMETER), "Job doesn't have a UUID");
+ CreateBulkExportEntityTasklet.addUUIDToJobContext(theChunkContext, (String) jobParameters.get(BatchConstants.JOB_UUID_PARAMETER));
return RepeatStatus.FINISHED;
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImpl.java
index 7c162ea8aca..3124eb43dbf 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImpl.java
@@ -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.batch.BatchJobsConfig;
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.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
@@ -79,7 +79,7 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
@Autowired
private IBatchJobSubmitter myJobSubmitter;
@Autowired
- @Qualifier(BatchJobsConfig.BULK_IMPORT_JOB_NAME)
+ @Qualifier(BatchConstants.BULK_IMPORT_JOB_NAME)
private org.springframework.batch.core.Job myBulkImportJob;
@Autowired
private DaoConfig myDaoConfig;
@@ -271,7 +271,7 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
ValidateUtil.isTrueOrThrowInvalidRequest(batchSize > 0, "Batch size must be positive");
JobParametersBuilder parameters = new JobParametersBuilder()
- .addString(BulkExportJobConfig.JOB_UUID_PARAMETER, jobId)
+ .addString(BatchConstants.JOB_UUID_PARAMETER, jobId)
.addLong(BulkImportJobConfig.JOB_PARAM_COMMIT_INTERVAL, (long) batchSize);
if (isNotBlank(theBulkExportJobEntity.getJobDescription())) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
index 717e5c3aa0e..f2a6ccfe046 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
@@ -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.model.ExpungeOptions;
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.api.IBatchJobSubmitter;
+import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
import ca.uhn.fhir.jpa.batch.mdm.MdmBatchJobSubmitterFactoryImpl;
@@ -380,17 +380,6 @@ public abstract class BaseConfig {
return new TermConceptMappingSvcImpl();
}
- @Bean
- public ThreadPoolTaskExecutor searchCoordinatorThreadFactory() {
- final ThreadPoolTaskExecutor threadPoolTaskExecutor = new ThreadPoolTaskExecutor();
- threadPoolTaskExecutor.setThreadNamePrefix("search_coord_");
- threadPoolTaskExecutor.setCorePoolSize(searchCoordCorePoolSize);
- threadPoolTaskExecutor.setMaxPoolSize(searchCoordMaxPoolSize);
- threadPoolTaskExecutor.setQueueCapacity(searchCoordQueueCapacity);
- threadPoolTaskExecutor.initialize();
- return threadPoolTaskExecutor;
- }
-
@Bean
public TaskScheduler taskScheduler() {
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
@@ -851,8 +840,8 @@ public abstract class BaseConfig {
}
@Bean
- public ISearchCoordinatorSvc searchCoordinatorSvc(ThreadPoolTaskExecutor searchCoordinatorThreadFactory) {
- return new SearchCoordinatorSvcImpl(searchCoordinatorThreadFactory);
+ public ISearchCoordinatorSvc searchCoordinatorSvc() {
+ return new SearchCoordinatorSvcImpl();
}
@Bean
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
index d40d555a8de..a5830be5107 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
@@ -35,6 +35,7 @@ import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.model.DeleteConflict;
import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
+import ca.uhn.fhir.jpa.api.model.LazyDaoMethodOutcome;
import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
import ca.uhn.fhir.jpa.cache.ResourcePersistentIdMap;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
@@ -44,7 +45,9 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
+import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryMatchResult;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
+import ca.uhn.fhir.jpa.searchparam.matcher.SearchParamMatcher;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.parser.DataFormatException;
@@ -64,6 +67,7 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
import ca.uhn.fhir.rest.server.exceptions.PayloadTooLargeException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
import ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding;
@@ -80,6 +84,7 @@ import ca.uhn.fhir.util.UrlUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
+import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.exceptions.FHIRException;
@@ -156,6 +161,8 @@ public abstract class BaseTransactionProcessor {
private ModelConfig myModelConfig;
@Autowired
private InMemoryResourceMatcher myInMemoryResourceMatcher;
+ @Autowired
+ private SearchParamMatcher mySearchParamMatcher;
private TaskExecutor myExecutor ;
@@ -274,7 +281,9 @@ public abstract class BaseTransactionProcessor {
idSubstitutions.put(id, newId);
}
}
- idToPersistedOutcome.put(newId, outcome);
+
+ populateIdToPersistedOutcomeMap(idToPersistedOutcome, newId, outcome);
+
if (outcome.getCreated()) {
myVersionAdapter.setResponseStatus(newEntry, toStatusString(Constants.STATUS_HTTP_201_CREATED));
} else {
@@ -298,6 +307,21 @@ public abstract class BaseTransactionProcessor {
}
+ /** Method which populates entry in idToPersistedOutcome.
+ * Will store whatever outcome is sent, unless the key already exists, then we only replace an instance if we find that the instance
+ * we are replacing with is non-lazy. This allows us to evaluate later more easily, as we _know_ we need access to these.
+ */
+ private void populateIdToPersistedOutcomeMap(Map idToPersistedOutcome, IIdType newId, DaoMethodOutcome outcome) {
+ //Prefer real method outcomes over lazy ones.
+ if (idToPersistedOutcome.containsKey(newId)) {
+ if (!(outcome instanceof LazyDaoMethodOutcome)) {
+ idToPersistedOutcome.put(newId, outcome);
+ }
+ } else {
+ idToPersistedOutcome.put(newId, outcome);
+ }
+ }
+
private Date getLastModified(IBaseResource theRes) {
return theRes.getMeta().getLastUpdated();
}
@@ -481,7 +505,7 @@ public abstract class BaseTransactionProcessor {
entries.sort(new TransactionSorter(placeholderIds));
// perform all writes
- doTransactionWriteOperations(theRequestDetails, theActionName,
+ prepareThenExecuteTransactionWriteOperations(theRequestDetails, theActionName,
transactionDetails, transactionStopWatch,
response, originalRequestOrder, entries);
@@ -584,38 +608,15 @@ public abstract class BaseTransactionProcessor {
* heavy load with lots of concurrent transactions using all available
* database connections.
*/
- private void doTransactionWriteOperations(RequestDetails theRequestDetails, String theActionName,
- TransactionDetails theTransactionDetails, StopWatch theTransactionStopWatch,
- IBaseBundle theResponse, IdentityHashMap theOriginalRequestOrder,
- List theEntries) {
+ private void prepareThenExecuteTransactionWriteOperations(RequestDetails theRequestDetails, String theActionName,
+ TransactionDetails theTransactionDetails, StopWatch theTransactionStopWatch,
+ IBaseBundle theResponse, IdentityHashMap theOriginalRequestOrder,
+ List theEntries) {
+
TransactionWriteOperationsDetails writeOperationsDetails = null;
- if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, myInterceptorBroadcaster, theRequestDetails) ||
- CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_POST, myInterceptorBroadcaster, theRequestDetails)) {
-
- List updateRequestUrls = new ArrayList<>();
- List conditionalCreateRequestUrls = new ArrayList<>();
- for (IBase nextEntry : theEntries) {
- String method = myVersionAdapter.getEntryRequestVerb(myContext, nextEntry);
- if ("PUT".equals(method)) {
- String requestUrl = myVersionAdapter.getEntryRequestUrl(nextEntry);
- if (isNotBlank(requestUrl)) {
- updateRequestUrls.add(requestUrl);
- }
- } else if ("POST".equals(method)) {
- String requestUrl = myVersionAdapter.getEntryRequestIfNoneExist(nextEntry);
- if (isNotBlank(requestUrl) && requestUrl.contains("?")) {
- conditionalCreateRequestUrls.add(requestUrl);
- }
- }
- }
-
- writeOperationsDetails = new TransactionWriteOperationsDetails();
- writeOperationsDetails.setUpdateRequestUrls(updateRequestUrls);
- writeOperationsDetails.setConditionalCreateRequestUrls(conditionalCreateRequestUrls);
- HookParams params = new HookParams()
- .add(TransactionDetails.class, theTransactionDetails)
- .add(TransactionWriteOperationsDetails.class, writeOperationsDetails);
- CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, params);
+ if (haveWriteOperationsHooks(theRequestDetails)) {
+ writeOperationsDetails = buildWriteOperationsDetails(theEntries);
+ callWriteOperationsHook(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, theRequestDetails, theTransactionDetails, writeOperationsDetails);
}
TransactionCallback> txCallback = status -> {
@@ -636,13 +637,9 @@ public abstract class BaseTransactionProcessor {
try {
entriesToProcess = myHapiTransactionService.execute(theRequestDetails, theTransactionDetails, txCallback);
- }
- finally {
- if (writeOperationsDetails != null) {
- HookParams params = new HookParams()
- .add(TransactionDetails.class, theTransactionDetails)
- .add(TransactionWriteOperationsDetails.class, writeOperationsDetails);
- CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_POST, params);
+ } finally {
+ if (haveWriteOperationsHooks(theRequestDetails)) {
+ callWriteOperationsHook(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_POST, theRequestDetails, theTransactionDetails, writeOperationsDetails);
}
}
@@ -656,6 +653,45 @@ public abstract class BaseTransactionProcessor {
}
}
+ private boolean haveWriteOperationsHooks(RequestDetails theRequestDetails) {
+ return CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, myInterceptorBroadcaster, theRequestDetails) ||
+ CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_POST, myInterceptorBroadcaster, theRequestDetails);
+ }
+
+ private void callWriteOperationsHook(Pointcut thePointcut, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails, TransactionWriteOperationsDetails theWriteOperationsDetails) {
+ HookParams params = new HookParams()
+ .add(TransactionDetails.class, theTransactionDetails)
+ .add(TransactionWriteOperationsDetails.class, theWriteOperationsDetails);
+ CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, thePointcut, params);
+ }
+
+
+ private TransactionWriteOperationsDetails buildWriteOperationsDetails(List theEntries) {
+ TransactionWriteOperationsDetails writeOperationsDetails;
+ List updateRequestUrls = new ArrayList<>();
+ List conditionalCreateRequestUrls = new ArrayList<>();
+ //Extract
+ for (IBase nextEntry : theEntries) {
+ String method = myVersionAdapter.getEntryRequestVerb(myContext, nextEntry);
+ if ("PUT".equals(method)) {
+ String requestUrl = myVersionAdapter.getEntryRequestUrl(nextEntry);
+ if (isNotBlank(requestUrl)) {
+ updateRequestUrls.add(requestUrl);
+ }
+ } else if ("POST".equals(method)) {
+ String requestUrl = myVersionAdapter.getEntryRequestIfNoneExist(nextEntry);
+ if (isNotBlank(requestUrl) && requestUrl.contains("?")) {
+ conditionalCreateRequestUrls.add(requestUrl);
+ }
+ }
+ }
+
+ writeOperationsDetails = new TransactionWriteOperationsDetails();
+ writeOperationsDetails.setUpdateRequestUrls(updateRequestUrls);
+ writeOperationsDetails.setConditionalCreateRequestUrls(conditionalCreateRequestUrls);
+ return writeOperationsDetails;
+ }
+
private boolean isValidVerb(String theVerb) {
try {
return org.hl7.fhir.r4.model.Bundle.HTTPVerb.fromCode(theVerb) != null;
@@ -704,7 +740,7 @@ public abstract class BaseTransactionProcessor {
IBaseResource resource = myVersionAdapter.getResource(nextReqEntry);
if (resource != null) {
String verb = myVersionAdapter.getEntryRequestVerb(myContext, nextReqEntry);
- String entryUrl = myVersionAdapter.getFullUrl(nextReqEntry);
+ String entryFullUrl = myVersionAdapter.getFullUrl(nextReqEntry);
String requestUrl = myVersionAdapter.getEntryRequestUrl(nextReqEntry);
String ifNoneExist = myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry);
String key = verb + "|" + requestUrl + "|" + ifNoneExist;
@@ -712,7 +748,7 @@ public abstract class BaseTransactionProcessor {
// Conditional UPDATE
boolean consolidateEntry = false;
if ("PUT".equals(verb)) {
- if (isNotBlank(entryUrl) && isNotBlank(requestUrl)) {
+ if (isNotBlank(entryFullUrl) && isNotBlank(requestUrl)) {
int questionMarkIndex = requestUrl.indexOf('?');
if (questionMarkIndex >= 0 && requestUrl.length() > (questionMarkIndex + 1)) {
consolidateEntry = true;
@@ -722,8 +758,8 @@ public abstract class BaseTransactionProcessor {
// Conditional CREATE
if ("POST".equals(verb)) {
- if (isNotBlank(entryUrl) && isNotBlank(requestUrl) && isNotBlank(ifNoneExist)) {
- if (!entryUrl.equals(requestUrl)) {
+ if (isNotBlank(entryFullUrl) && isNotBlank(requestUrl) && isNotBlank(ifNoneExist)) {
+ if (!entryFullUrl.equals(requestUrl)) {
consolidateEntry = true;
}
}
@@ -731,33 +767,41 @@ public abstract class BaseTransactionProcessor {
if (consolidateEntry) {
if (!keyToUuid.containsKey(key)) {
- keyToUuid.put(key, entryUrl);
+ keyToUuid.put(key, entryFullUrl);
} else {
ourLog.info("Discarding transaction bundle entry {} as it contained a duplicate conditional {}", originalIndex, verb);
theEntries.remove(index);
index--;
String existingUuid = keyToUuid.get(key);
- for (IBase nextEntry : theEntries) {
- IBaseResource nextResource = myVersionAdapter.getResource(nextEntry);
- for (IBaseReference nextReference : myContext.newTerser().getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class)) {
- // We're interested in any references directly to the placeholder ID, but also
- // references that have a resource target that has the placeholder ID.
- String nextReferenceId = nextReference.getReferenceElement().getValue();
- if (isBlank(nextReferenceId) && nextReference.getResource() != null) {
- nextReferenceId = nextReference.getResource().getIdElement().getValue();
- }
- if (entryUrl.equals(nextReferenceId)) {
- nextReference.setReference(existingUuid);
- nextReference.setResource(null);
- }
- }
- }
+ replaceReferencesInEntriesWithConsolidatedUUID(theEntries, entryFullUrl, existingUuid);
}
}
}
}
}
+ /**
+ * Iterates over all entries, and if it finds any which have references which match the fullUrl of the entry that was consolidated out
+ * replace them with our new consolidated UUID
+ */
+ private void replaceReferencesInEntriesWithConsolidatedUUID(List theEntries, String theEntryFullUrl, String existingUuid) {
+ for (IBase nextEntry : theEntries) {
+ IBaseResource nextResource = myVersionAdapter.getResource(nextEntry);
+ for (IBaseReference nextReference : myContext.newTerser().getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class)) {
+ // We're interested in any references directly to the placeholder ID, but also
+ // references that have a resource target that has the placeholder ID.
+ String nextReferenceId = nextReference.getReferenceElement().getValue();
+ if (isBlank(nextReferenceId) && nextReference.getResource() != null) {
+ nextReferenceId = nextReference.getResource().getIdElement().getValue();
+ }
+ if (theEntryFullUrl.equals(nextReferenceId)) {
+ nextReference.setReference(existingUuid);
+ nextReference.setResource(null);
+ }
+ }
+ }
+ }
+
/**
* Retrieves the next resource id (IIdType) from the base resource and next request entry.
* @param theBaseResource - base resource
@@ -810,12 +854,16 @@ public abstract class BaseTransactionProcessor {
return nextResourceId;
}
+ /** After pre-hooks have been called
+ *
+ */
protected Map doTransactionWriteOperations(final RequestDetails theRequest, String theActionName,
TransactionDetails theTransactionDetails, Set theAllIds,
Map theIdSubstitutions, Map theIdToPersistedOutcome,
IBaseBundle theResponse, IdentityHashMap theOriginalRequestOrder,
List theEntries, StopWatch theTransactionStopWatch) {
+ // During a transaction, we don't execute hooks, instead, we execute them all post-transaction.
theTransactionDetails.beginAcceptingDeferredInterceptorBroadcasts(
Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED,
Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED,
@@ -827,6 +875,7 @@ public abstract class BaseTransactionProcessor {
Map entriesToProcess = new IdentityHashMap<>();
Set nonUpdatedEntities = new HashSet<>();
Set updatedEntities = new HashSet<>();
+ Map conditionalUrlToIdMap = new HashMap<>();
List updatedResources = new ArrayList<>();
Map> conditionalRequestUrls = new HashMap<>();
@@ -866,7 +915,8 @@ public abstract class BaseTransactionProcessor {
String matchUrl = myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry);
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
outcome = resourceDao.create(res, matchUrl, false, theTransactionDetails, theRequest);
- res.setId(outcome.getId());
+ setConditionalUrlToBeValidatedLater(conditionalUrlToIdMap, matchUrl, outcome.getId());
+ res.setId(outcome.getId());
if (nextResourceId != null) {
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequest);
}
@@ -900,6 +950,7 @@ public abstract class BaseTransactionProcessor {
String matchUrl = parts.getResourceType() + '?' + parts.getParams();
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
DeleteMethodOutcome deleteOutcome = dao.deleteByUrl(matchUrl, deleteConflicts, theRequest);
+ setConditionalUrlToBeValidatedLater(conditionalUrlToIdMap, matchUrl, deleteOutcome.getId());
List allDeleted = deleteOutcome.getDeletedEntities();
for (ResourceTable deleted : allDeleted) {
deletedResources.add(deleted.getIdDt().toUnqualifiedVersionless().getValueAsString());
@@ -942,6 +993,7 @@ public abstract class BaseTransactionProcessor {
}
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
outcome = resourceDao.update(res, matchUrl, false, false, theRequest, theTransactionDetails);
+ setConditionalUrlToBeValidatedLater(conditionalUrlToIdMap, matchUrl, outcome.getId());
if (Boolean.TRUE.equals(outcome.getCreated())) {
conditionalRequestUrls.put(matchUrl, res.getClass());
}
@@ -1000,6 +1052,7 @@ public abstract class BaseTransactionProcessor {
IFhirResourceDao dao = toDao(parts, verb, url);
IIdType patchId = myContext.getVersion().newIdType().setValue(parts.getResourceId());
DaoMethodOutcome outcome = dao.patch(patchId, matchUrl, patchType, patchBody, patchBodyParameters, theRequest);
+ setConditionalUrlToBeValidatedLater(conditionalUrlToIdMap, matchUrl, outcome.getId());
updatedEntities.add(outcome.getEntity());
if (outcome.getResource() != null) {
updatedResources.add(outcome.getResource());
@@ -1056,6 +1109,15 @@ public abstract class BaseTransactionProcessor {
if (!myDaoConfig.isMassIngestionMode()) {
validateNoDuplicates(theRequest, theActionName, conditionalRequestUrls, theIdToPersistedOutcome.values());
}
+
+ theTransactionStopWatch.endCurrentTask();
+ if (conditionalUrlToIdMap.size() > 0) {
+ theTransactionStopWatch.startTask("Check that all conditionally created/updated entities actually match their conditionals.");
+ }
+
+ if (!myDaoConfig.isMassIngestionMode()) {
+ validateAllInsertsMatchTheirConditionalUrls(theIdToPersistedOutcome, conditionalUrlToIdMap, theRequest);
+ }
theTransactionStopWatch.endCurrentTask();
for (IIdType next : theAllIds) {
@@ -1094,6 +1156,39 @@ public abstract class BaseTransactionProcessor {
}
}
+ private void setConditionalUrlToBeValidatedLater(Map theConditionalUrlToIdMap, String theMatchUrl, IIdType theId) {
+ if (!StringUtils.isBlank(theMatchUrl)) {
+ theConditionalUrlToIdMap.put(theMatchUrl, theId);
+ }
+ }
+
+ /**
+ * After transaction processing and resolution of indexes and references, we want to validate that the resources that were stored _actually_
+ * match the conditional URLs that they were brought in on.
+ * @param theIdToPersistedOutcome
+ * @param conditionalUrlToIdMap
+ */
+ private void validateAllInsertsMatchTheirConditionalUrls(Map theIdToPersistedOutcome, Map conditionalUrlToIdMap, RequestDetails theRequest) {
+ conditionalUrlToIdMap.entrySet().stream()
+ .filter(entry -> entry.getKey() != null)
+ .forEach(entry -> {
+ String matchUrl = entry.getKey();
+ IIdType value = entry.getValue();
+ DaoMethodOutcome daoMethodOutcome = theIdToPersistedOutcome.get(value);
+ if (daoMethodOutcome != null && !daoMethodOutcome.isNop() && daoMethodOutcome.getResource() != null) {
+ InMemoryMatchResult match = mySearchParamMatcher.match(matchUrl, daoMethodOutcome.getResource(), theRequest);
+ if (ourLog.isDebugEnabled()) {
+ ourLog.debug("Checking conditional URL [{}] against resource with ID [{}]: Supported?:[{}], Matched?:[{}]", matchUrl, value, match.supported(), match.matched());
+ }
+ if (match.supported()) {
+ if (!match.matched()) {
+ throw new PreconditionFailedException("Invalid conditional URL \"" + matchUrl + "\". The given resource is not matched by this URL.");
+ };
+ }
+ }
+ });
+ }
+
/**
* Checks for any delete conflicts.
* @param theDeleteConflicts - set of delete conflicts
@@ -1384,7 +1479,7 @@ public abstract class BaseTransactionProcessor {
thePersistedOutcomes
.stream()
.filter(t -> !t.isNop())
- .filter(t -> t.getEntity() instanceof ResourceTable)
+ .filter(t -> t.getEntity() instanceof ResourceTable)//N.B. GGG: This validation never occurs for mongo, as nothing is a ResourceTable.
.filter(t -> t.getEntity().getDeleted() == null)
.filter(t -> t.getResource() != null)
.forEach(t -> resourceToIndexedParams.put(t.getResource(), new ResourceIndexedSearchParams((ResourceTable) t.getEntity())));
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java
index 4a9c94376c8..200ac7a6861 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java
@@ -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.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
+import ca.uhn.fhir.util.TestUtil;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.slf4j.Logger;
@@ -118,7 +119,7 @@ public class HapiTransactionService {
theTransactionDetails.clearUserData(BaseHapiFhirDao.XACT_USERDATA_KEY_EXISTING_SEARCH_PARAMS);
double sleepAmount = (250.0d * i) * Math.random();
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);
continue;
@@ -164,22 +165,4 @@ public class HapiTransactionService {
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);
- }
- }
- }
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteExpungeJobSubmitterImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteExpungeJobSubmitterImpl.java
index 73e561d1dd1..deb926ab426 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteExpungeJobSubmitterImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteExpungeJobSubmitterImpl.java
@@ -25,8 +25,8 @@ import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
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.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
@@ -52,7 +52,7 @@ public class DeleteExpungeJobSubmitterImpl implements IDeleteExpungeJobSubmitter
@Autowired
private IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
- @Qualifier(BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME)
+ @Qualifier(BatchConstants.DELETE_EXPUNGE_JOB_NAME)
private Job myDeleteExpungeJob;
@Autowired
FhirContext myFhirContext;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobConfig.java
index 756aab743e4..4ab6c91bea4 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobConfig.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobConfig.java
@@ -20,12 +20,10 @@ package ca.uhn.fhir.jpa.delete.job;
* #L%
*/
-import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterValidator;
import ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener;
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.Step;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
@@ -39,7 +37,7 @@ import org.springframework.context.annotation.Lazy;
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
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/MdmLink.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/MdmLink.java
index cd8cbff422d..4892ed8c1f9 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/MdmLink.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/MdmLink.java
@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
+import ca.uhn.fhir.mdm.api.IMdmLink;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -47,7 +48,7 @@ import java.util.Date;
@Table(name = "MPI_LINK", uniqueConstraints = {
@UniqueConstraint(name = "IDX_EMPI_PERSON_TGT", columnNames = {"PERSON_PID", "TARGET_PID"}),
})
-public class MdmLink {
+public class MdmLink implements IMdmLink {
public static final int VERSION_LENGTH = 16;
private static final int MATCH_RESULT_LENGTH = 16;
private static final int LINK_SOURCE_LENGTH = 16;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java
index 1ec7b3593c9..5eb66b5aab2 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java
@@ -29,9 +29,7 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.ReferenceParam;
-import joptsimple.internal.Strings;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
@@ -39,8 +37,6 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Set;
-import static org.slf4j.LoggerFactory.getLogger;
-
/**
* This interceptor replaces the auto-generated CapabilityStatement that is generated
* by the HAPI FHIR Server with a static hard-coded resource.
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingRuleBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingRuleBuilder.java
index aff7afb1677..f1d2241eec3 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingRuleBuilder.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingRuleBuilder.java
@@ -305,6 +305,15 @@ public final class RepositoryValidatingRuleBuilder implements IRuleRoot {
return this;
}
+ /**
+ * Configure the validator to reject unknown extensions
+ */
+ @Nonnull
+ public FinalizedRequireValidationRule rejectUnknownExtensions() {
+ myRule.getValidator().setAnyExtensionsAllowed(false);
+ return this;
+ }
+
/**
* Configure the validator to not perform terminology validation
*/
diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
similarity index 99%
rename from hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
rename to hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
index 5cd1eb78135..2229c43cb64 100644
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
@@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.migrate.tasks;
/*-
* #%L
- * HAPI FHIR JPA Server - Migration
+ * HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java
index 05c695f6b47..876bae329fe 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java
@@ -50,13 +50,13 @@ public class BaseJpaSystemProvider extends BaseJpaProvider implements IJp
* @deprecated
*/
@Deprecated
- public static final String MARK_ALL_RESOURCES_FOR_REINDEXING = "$mark-all-resources-for-reindexing";
+ public static final String MARK_ALL_RESOURCES_FOR_REINDEXING = ProviderConstants.MARK_ALL_RESOURCES_FOR_REINDEXING;
/**
* @see ProviderConstants#OPERATION_REINDEX
* @deprecated
*/
@Deprecated
- public static final String PERFORM_REINDEXING_PASS = "$perform-reindexing-pass";
+ public static final String PERFORM_REINDEXING_PASS = ProviderConstants.PERFORM_REINDEXING_PASS;
private IFhirSystemDao myDao;
@Autowired
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/ReindexJobSubmitterImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/ReindexJobSubmitterImpl.java
index 582eba93e23..572d2f5e409 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/ReindexJobSubmitterImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/ReindexJobSubmitterImpl.java
@@ -22,8 +22,8 @@ package ca.uhn.fhir.jpa.reindex;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
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.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
import ca.uhn.fhir.jpa.batch.job.model.RequestListJson;
import ca.uhn.fhir.jpa.batch.reader.CronologicalBatchAllResourcePidReader;
@@ -53,10 +53,10 @@ public class ReindexJobSubmitterImpl implements IReindexJobSubmitter {
@Autowired
private IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
- @Qualifier(BatchJobsConfig.REINDEX_JOB_NAME)
+ @Qualifier(BatchConstants.REINDEX_JOB_NAME)
private Job myReindexJob;
@Autowired
- @Qualifier(BatchJobsConfig.REINDEX_EVERYTHING_JOB_NAME)
+ @Qualifier(BatchConstants.REINDEX_EVERYTHING_JOB_NAME)
private Job myReindexEverythingJob;
@Override
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexEverythingJobConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexEverythingJobConfig.java
index 33fdfaf8ece..48b9c3683c0 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexEverythingJobConfig.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexEverythingJobConfig.java
@@ -35,7 +35,7 @@ import org.springframework.context.annotation.Lazy;
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
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexJobConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexJobConfig.java
index c5465ec3533..d3aa68c8fda 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexJobConfig.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexJobConfig.java
@@ -20,18 +20,14 @@ package ca.uhn.fhir.jpa.reindex.job;
* #L%
*/
-import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterValidator;
import ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener;
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.Step;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.listener.ExecutionContextPromotionListener;
-import org.springframework.batch.item.ItemReader;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@@ -39,7 +35,7 @@ import org.springframework.context.annotation.Lazy;
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
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
index aa67d53c597..a64ba464246 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
@@ -82,7 +82,6 @@ import org.springframework.data.domain.Sort;
import org.springframework.orm.jpa.JpaDialect;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
-import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.stereotype.Component;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
@@ -111,7 +110,6 @@ import java.util.UUID;
import java.util.concurrent.Callable;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.CountDownLatch;
-import java.util.concurrent.ExecutorService;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
@@ -123,7 +121,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
public static final Integer INTEGER_0 = 0;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchCoordinatorSvcImpl.class);
private final ConcurrentHashMap myIdToSearchTask = new ConcurrentHashMap<>();
- private final ExecutorService myExecutor;
@Autowired
private FhirContext myContext;
@Autowired
@@ -162,8 +159,13 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
* Constructor
*/
@Autowired
- public SearchCoordinatorSvcImpl(ThreadPoolTaskExecutor searchCoordinatorThreadFactory) {
- myExecutor = searchCoordinatorThreadFactory.getThreadPoolExecutor();
+ public SearchCoordinatorSvcImpl() {
+ super();
+ }
+
+ @VisibleForTesting
+ Set getActiveSearchIds() {
+ return myIdToSearchTask.keySet();
}
@VisibleForTesting
@@ -274,7 +276,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(theRequestDetails, resourceType, params, null);
SearchContinuationTask task = new SearchContinuationTask(search, resourceDao, params, resourceType, theRequestDetails, requestPartitionId);
myIdToSearchTask.put(search.getUuid(), task);
- myExecutor.submit(task);
+ task.call();
}
}
@@ -406,7 +408,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
SearchTask task = new SearchTask(theSearch, theCallingDao, theParams, theResourceType, theRequestDetails, theRequestPartitionId);
myIdToSearchTask.put(theSearch.getUuid(), task);
- myExecutor.submit(task);
+ task.call();
PersistedJpaSearchFirstPageBundleProvider retVal = myPersistedJpaBundleProviderFactory.newInstanceFirstPage(theRequestDetails, theSearch, task, theSb);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
index 60f2952754c..be31eb190c3 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
@@ -723,7 +723,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
retVal.setPublisher("Regenstrief Institute, Inc.");
retVal.setDescription("A value set that includes all LOINC codes");
retVal.setCopyright("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/");
- retVal.getCompose().addInclude().setSystem(ITermLoaderSvc.LOINC_URI);
+ retVal.getCompose().addInclude().setSystem(ITermLoaderSvc.LOINC_URI).setVersion(codeSystemVersionId);
return retVal;
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
index cba3609fa8b..7cd49e97c45 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IZipContentsHandlerCsv;
+import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ContactPoint;
import org.hl7.fhir.r4.model.Enumerations;
@@ -74,6 +75,9 @@ public abstract class BaseLoincHandler implements IZipContentsHandlerCsv {
if (include == null) {
include = theVs.getCompose().addInclude();
include.setSystem(theCodeSystemUrl);
+ if (StringUtils.isNotBlank(theVs.getVersion())) {
+ include.setVersion(theVs.getVersion());
+ }
}
boolean found = false;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
index cdb97ca48d8..037a2fb0e6b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
@@ -104,6 +104,7 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
.getCompose()
.getIncludeFirstRep()
.setSystem(ITermLoaderSvc.LOINC_URI)
+ .setVersion(codeSystemVersionId)
.addConcept()
.setCode(answerString)
.setDisplay(displayText);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java
index d0b03f0acc9..d81466f5380 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java
@@ -120,6 +120,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IZipCo
.getCompose()
.getIncludeFirstRep()
.setSystem(ITermLoaderSvc.LOINC_URI)
+ .setVersion(codeSystemVersionId)
.addConcept()
.setCode(loincNumber)
.setDisplay(longCommonName);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
index 019e799e760..2aea7021f12 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
@@ -6,8 +6,8 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
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.config.BatchConstants;
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.GroupBulkExportJobParametersBuilder;
@@ -102,15 +102,15 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
private BatchJobHelper myBatchJobHelper;
@Autowired
- @Qualifier(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
+ @Qualifier(BatchConstants.BULK_EXPORT_JOB_NAME)
private Job myBulkJob;
@Autowired
- @Qualifier(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
+ @Qualifier(BatchConstants.GROUP_BULK_EXPORT_JOB_NAME)
private Job myGroupBulkJob;
@Autowired
- @Qualifier(BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME)
+ @Qualifier(BatchConstants.PATIENT_BULK_EXPORT_JOB_NAME)
private Job myPatientBulkJob;
private IIdType myPatientGroupId;
@@ -328,11 +328,11 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
private void awaitAllBulkJobCompletions() {
myBatchJobHelper.awaitAllBulkJobCompletions(
- BatchJobsConfig.BULK_EXPORT_JOB_NAME,
- BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME,
- BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME,
- BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME,
- BatchJobsConfig.MDM_CLEAR_JOB_NAME
+ BatchConstants.BULK_EXPORT_JOB_NAME,
+ BatchConstants.PATIENT_BULK_EXPORT_JOB_NAME,
+ BatchConstants.GROUP_BULK_EXPORT_JOB_NAME,
+ BatchConstants.DELETE_EXPUNGE_JOB_NAME,
+ BatchConstants.MDM_CLEAR_JOB_NAME
);
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportR4Test.java
index e34f63b3985..3eeb2fbea3c 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportR4Test.java
@@ -5,7 +5,7 @@ import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Interceptor;
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.imprt.api.IBulkDataImportSvc;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
@@ -44,7 +44,7 @@ import java.util.ArrayList;
import java.util.List;
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.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
@@ -212,7 +212,7 @@ public class BulkDataImportR4Test extends BaseJpaR4Test implements ITestDataBuil
}
protected List awaitAllBulkImportJobCompletion() {
- return myBatchJobHelper.awaitAllBulkJobCompletions(BatchJobsConfig.BULK_IMPORT_JOB_NAME);
+ return myBatchJobHelper.awaitAllBulkJobCompletions(BatchConstants.BULK_IMPORT_JOB_NAME);
}
@Interceptor
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java
index f48b4ede91f..02a797f60f6 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java
@@ -13,6 +13,7 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
+import ca.uhn.fhir.jpa.searchparam.matcher.SearchParamMatcher;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hibernate.Session;
import org.hibernate.internal.SessionImpl;
@@ -72,6 +73,8 @@ public class TransactionProcessorTest {
private IRequestPartitionHelperSvc myRequestPartitionHelperSvc;
@MockBean
private IResourceVersionSvc myResourceVersionSvc;
+ @MockBean
+ private SearchParamMatcher mySearchParamMatcher;
@MockBean(answer = Answers.RETURNS_DEEP_STUBS)
private SessionImpl mySession;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java
index 5366efa789c..5c33c51e5ab 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java
@@ -929,7 +929,7 @@ public class FhirResourceDaoR4LegacySearchBuilderTest extends BaseJpaR4Test {
List actual = toUnqualifiedVersionlessIds(resp);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(actual, containsInAnyOrder(orgId, medId, patId, moId, patId2));
- assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
+ assertEquals(8, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
// Specific patient ID with linked stuff
request = mock(HttpServletRequest.class);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNAsyncIT.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNAsyncIT.java
index 5ff05cac158..37661610e44 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNAsyncIT.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNAsyncIT.java
@@ -13,6 +13,8 @@ import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.junit.jupiter.SpringExtension;
@@ -30,6 +32,7 @@ import static org.mockito.Mockito.when;
@ExtendWith(SpringExtension.class)
public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
+ private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4SearchLastNAsyncIT.class);
@Autowired
protected DaoConfig myDaoConfig;
private List originalPreFetchThresholds;
@@ -108,8 +111,11 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
.map(t -> t.getSql(true, false))
.collect(Collectors.toList());
+ ourLog.info("Queries:\n * " + String.join("\n * ", queries));
+
+ // 3 queries to actually perform the search
// 1 query to lookup up Search from cache, and 2 chunked queries to retrieve resources by PID.
- assertEquals(3, queries.size());
+ assertEquals(6, queries.size());
// The first chunked query should have a full complement of PIDs
StringBuilder firstQueryPattern = new StringBuilder(".*RES_ID in \\('[0-9]+'");
@@ -117,7 +123,7 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
firstQueryPattern.append(" , '[0-9]+'");
}
firstQueryPattern.append("\\).*");
- assertThat(queries.get(1), matchesPattern(firstQueryPattern.toString()));
+ assertThat(queries.get(4), matchesPattern(firstQueryPattern.toString()));
// the second chunked query should be padded with "-1".
StringBuilder secondQueryPattern = new StringBuilder(".*RES_ID in \\('[0-9]+'");
@@ -128,7 +134,7 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
secondQueryPattern.append(" , '-1'");
}
secondQueryPattern.append("\\).*");
- assertThat(queries.get(2), matchesPattern(secondQueryPattern.toString()));
+ assertThat(queries.get(5), matchesPattern(secondQueryPattern.toString()));
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
index 5ee19c00c8e..2757b30ee0d 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
@@ -781,7 +781,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
List actual = toUnqualifiedVersionlessIds(resp);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(actual, containsInAnyOrder(orgId, medId, patId, moId, patId2));
- assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
+ assertEquals(7, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
// Specific patient ID with linked stuff
request = mock(HttpServletRequest.class);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoHashesTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoHashesTest.java
index 86220f8281d..23a9385d684 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoHashesTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoHashesTest.java
@@ -1451,9 +1451,9 @@ public class FhirResourceDaoR4SearchNoHashesTest extends BaseJpaR4Test {
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);
- TestUtil.sleepAtLeast(1100);
+ ca.uhn.fhir.util.TestUtil.sleepAtLeast(1100);
IIdType id2;
{
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
index e726c5254da..a9a9352b66d 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
@@ -1177,9 +1177,9 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
assertEquals(1, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
- assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
- assertEquals(0, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
- assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
+ assertEquals(4, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+ assertEquals(9, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
+ assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchPageExpiryTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchPageExpiryTest.java
index 2ea2fac62a0..64c22c667d6 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchPageExpiryTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchPageExpiryTest.java
@@ -6,11 +6,11 @@ import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
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.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IIdType;
@@ -116,7 +116,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
}
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
@@ -291,7 +291,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
}
assertEquals(searchUuid1, searchUuid2);
- TestUtil.sleepAtLeast(reuseCachedSearchResultsForMillis + 1);
+ ca.uhn.fhir.util.TestUtil.sleepAtLeast(reuseCachedSearchResultsForMillis + 1);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
// We're now past reuseCachedSearchResultsForMillis so we shouldn't reuse the search
@@ -376,7 +376,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
}
});
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");
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java
index 0c85f54f0a0..0975df2548e 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java
@@ -11,6 +11,7 @@ import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.util.BundleBuilder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.Encounter;
@@ -467,7 +468,8 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
Patient patient = new Patient();
patient.setId(IdType.newRandomUuid());
- patient.setActive(true);
+ patient.setDeceased(new BooleanType(true));
+ patient.setActive(false);
builder
.addTransactionUpdateEntry(patient)
.conditional("Patient?active=false");
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
index 88a0987be86..fd513807f31 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
@@ -51,7 +51,9 @@ import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.EpisodeOfCare;
+import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Medication;
import org.hl7.fhir.r4.model.MedicationRequest;
import org.hl7.fhir.r4.model.Meta;
@@ -83,6 +85,7 @@ import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.math.BigDecimal;
import java.nio.charset.StandardCharsets;
+import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@@ -96,7 +99,9 @@ import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.emptyString;
import static org.hamcrest.Matchers.endsWith;
+import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.greaterThan;
+import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.matchesPattern;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.startsWith;
@@ -1161,6 +1166,78 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
validate(outcome);
}
+ @Test
+ public void testConditionalUpdate_forObservationWithNonExistentPatientSubject_shouldCreateLinkedResources() {
+ Bundle transactionBundle = new Bundle().setType(BundleType.TRANSACTION);
+
+ // Patient
+ HumanName patientName = new HumanName().setFamily("TEST_LAST_NAME").addGiven("TEST_FIRST_NAME");
+ Identifier patientIdentifier = new Identifier().setSystem("http://example.com/mrns").setValue("U1234567890");
+ Patient patient = new Patient()
+ .setName(Arrays.asList(patientName))
+ .setIdentifier(Arrays.asList(patientIdentifier));
+ patient.setId(IdType.newRandomUuid());
+
+ transactionBundle
+ .addEntry()
+ .setFullUrl(patient.getId())
+ .setResource(patient)
+ .getRequest()
+ .setMethod(Bundle.HTTPVerb.PUT)
+ .setUrl("/Patient?identifier=" + patientIdentifier.getSystem() + "|" + patientIdentifier.getValue());
+
+ // Observation
+ Observation observation = new Observation();
+ observation.setId(IdType.newRandomUuid());
+ observation.getSubject().setReference(patient.getIdElement().toUnqualifiedVersionless().toString());
+
+ transactionBundle
+ .addEntry()
+ .setFullUrl(observation.getId())
+ .setResource(observation)
+ .getRequest()
+ .setMethod(Bundle.HTTPVerb.PUT)
+ .setUrl("/Observation?subject=" + patient.getIdElement().toUnqualifiedVersionless().toString());
+
+ ourLog.info("Patient TEMP UUID: {}", patient.getId());
+ String s = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(transactionBundle);
+ System.out.println(s);
+ Bundle outcome= mySystemDao.transaction(null, transactionBundle);
+ String patientLocation = outcome.getEntry().get(0).getResponse().getLocation();
+ assertThat(patientLocation, matchesPattern("Patient/[a-z0-9-]+/_history/1"));
+ String observationLocation = outcome.getEntry().get(1).getResponse().getLocation();
+ assertThat(observationLocation, matchesPattern("Observation/[a-z0-9-]+/_history/1"));
+ }
+
+ @Test
+ public void testConditionalUrlWhichDoesNotMatchResource() {
+ Bundle transactionBundle = new Bundle().setType(BundleType.TRANSACTION);
+
+ String storedIdentifierValue = "woop";
+ String conditionalUrlIdentifierValue = "zoop";
+ // Patient
+ HumanName patientName = new HumanName().setFamily("TEST_LAST_NAME").addGiven("TEST_FIRST_NAME");
+ Identifier patientIdentifier = new Identifier().setSystem("http://example.com/mrns").setValue(storedIdentifierValue);
+ Patient patient = new Patient()
+ .setName(Arrays.asList(patientName))
+ .setIdentifier(Arrays.asList(patientIdentifier));
+ patient.setId(IdType.newRandomUuid());
+
+ transactionBundle
+ .addEntry()
+ .setFullUrl(patient.getId())
+ .setResource(patient)
+ .getRequest()
+ .setMethod(Bundle.HTTPVerb.PUT)
+ .setUrl("/Patient?identifier=" + patientIdentifier.getSystem() + "|" + conditionalUrlIdentifierValue);
+
+ try {
+ mySystemDao.transaction(null, transactionBundle);
+ fail();
+ } catch (PreconditionFailedException e) {
+ assertThat(e.getMessage(), is(equalTo("Invalid conditional URL \"Patient?identifier=http://example.com/mrns|" + conditionalUrlIdentifierValue +"\". The given resource is not matched by this URL.")));
+ }
+ }
@Test
public void testTransactionCreateInlineMatchUrlWithOneMatch() {
@@ -1195,6 +1272,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
}
+
@Test
public void testTransactionUpdateTwoResourcesWithSameId() {
Bundle request = new Bundle();
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/JpaHistoryR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/JpaHistoryR4Test.java
index 8c9ec09fda1..096e37a461b 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/JpaHistoryR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/JpaHistoryR4Test.java
@@ -22,7 +22,7 @@ import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
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.Matchers.containsString;
import static org.hamcrest.Matchers.not;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java
index 150e795a5be..24bb7903c64 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java
@@ -72,7 +72,7 @@ import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Supplier;
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.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobTest.java
index 442102c0973..3931f4abb62 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobTest.java
@@ -1,7 +1,7 @@
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.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterUtil;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -23,7 +23,7 @@ public class DeleteExpungeJobTest extends BaseJpaR4Test {
@Autowired
private IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
- @Qualifier(BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME)
+ @Qualifier(BatchConstants.DELETE_EXPUNGE_JOB_NAME)
private Job myDeleteExpungeJob;
@Autowired
private BatchJobHelper myBatchJobHelper;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
index 61018ef82b1..8df82b52b93 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
@@ -1,8 +1,8 @@
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.api.IBatchJobSubmitter;
+import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.job.MultiUrlJobParameterUtil;
import ca.uhn.fhir.jpa.batch.reader.CronologicalBatchAllResourcePidReader;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
@@ -37,10 +37,10 @@ public class ReindexJobTest extends BaseJpaR4Test {
@Autowired
private IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
- @Qualifier(BatchJobsConfig.REINDEX_JOB_NAME)
+ @Qualifier(BatchConstants.REINDEX_JOB_NAME)
private Job myReindexJob;
@Autowired
- @Qualifier(BatchJobsConfig.REINDEX_EVERYTHING_JOB_NAME)
+ @Qualifier(BatchConstants.REINDEX_EVERYTHING_JOB_NAME)
private Job myReindexEverythingJob;
@Autowired
private BatchJobHelper myBatchJobHelper;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorR4Test.java
index d48e9cbe61f..ca49294dcda 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorR4Test.java
@@ -291,6 +291,33 @@ public class RepositoryValidatingInterceptorR4Test extends BaseJpaR4Test {
}
}
+ @Test
+ public void testRequireValidation_AdditionalOptions_Reject_UnKnown_Extensions() {
+ List rules = newRuleBuilder()
+ .forResourcesOfType("Observation")
+ .requireValidationToDeclaredProfiles()
+ .withBestPracticeWarningLevel("IGNORE")
+ .rejectUnknownExtensions()
+ .disableTerminologyChecks()
+ .errorOnUnknownProfiles()
+ .suppressNoBindingMessage()
+ .suppressWarningForExtensibleValueSetValidation()
+ .build();
+
+ myValInterceptor.setRules(rules);
+
+ Observation obs = new Observation();
+ obs.getCode().addCoding().setSystem("http://foo").setCode("123").setDisplay("help im a bug");
+ obs.setStatus(Observation.ObservationStatus.AMENDED);
+ try {
+ IIdType id = myObservationDao.create(obs).getId();
+ assertEquals("1", id.getVersionIdPart());
+ } catch (PreconditionFailedException e) {
+ // should not happen
+ fail(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
+ }
+ }
+
@Test
public void testRequireValidation_FailNoRejectAndTag() {
List rules = newRuleBuilder()
diff --git a/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTaskTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTaskTest.java
similarity index 100%
rename from hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTaskTest.java
rename to hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTaskTest.java
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTest.java
new file mode 100644
index 00000000000..878cc32cdbf
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTest.java
@@ -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> data() {
+ ourLog.info("H2: {}", org.h2.Driver.class.toString());
+
+ ArrayList> retVal = new ArrayList<>();
+
+ // H2
+ retVal.add(new Supplier() {
+ @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() {
+ @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 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 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> 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();
+ }
+
+ }
+
+}
diff --git a/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTest.java
similarity index 100%
rename from hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTest.java
rename to hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTest.java
diff --git a/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/HashTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/HashTest.java
similarity index 100%
rename from hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/HashTest.java
rename to hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/HashTest.java
diff --git a/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java
similarity index 100%
rename from hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java
rename to hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java
index 98e72802634..a961eafc12f 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java
@@ -1627,9 +1627,6 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
.execute();
assertEquals(10, response.getEntry().size());
- if (ourConnectionPoolSize > 1) {
- assertEquals(null, response.getTotalElement().getValueAsString(), "Total should be null but was " + response.getTotalElement().getValueAsString() + " in " + sw.toString());
- }
assertThat(response.getLink("next").getUrl(), not(emptyString()));
// Load page 2
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
index 6081f5019a5..760542e197f 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
@@ -179,9 +179,12 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
myFhirCtx.getRestfulClientFactory().setSocketTimeout(400000);
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+ connectionManager.setMaxTotal(10);
+ connectionManager.setDefaultMaxPerRoute(10);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
builder.setMaxConnPerRoute(99);
+
ourHttpClient = builder.build();
ourServer = server;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java
index 652ceff7947..2ce148054ac 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java
@@ -7,7 +7,7 @@ import ca.uhn.fhir.interceptor.api.IPointcut;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
+import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.delete.job.ReindexTestHelper;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -91,7 +91,7 @@ public class MultitenantBatchOperationR4Test extends BaseMultitenantResourceProv
.execute();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(response));
- myBatchJobHelper.awaitAllBulkJobCompletions(BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME);
+ myBatchJobHelper.awaitAllBulkJobCompletions(BatchConstants.DELETE_EXPUNGE_JOB_NAME);
assertThat(interceptor.requestPartitionIds, hasSize(1));
RequestPartitionId partitionId = interceptor.requestPartitionIds.get(0);
assertEquals(TENANT_B_ID, partitionId.getFirstPartitionIdOrNull());
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderConcurrencyR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderConcurrencyR4Test.java
new file mode 100644
index 00000000000..9b0ca550c62
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderConcurrencyR4Test.java
@@ -0,0 +1,202 @@
+package ca.uhn.fhir.jpa.provider.r4;
+
+import ca.uhn.fhir.interceptor.api.Hook;
+import ca.uhn.fhir.interceptor.api.Interceptor;
+import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import static org.awaitility.Awaitility.await;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.equalTo;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+@SuppressWarnings("Duplicates")
+public class ResourceProviderConcurrencyR4Test extends BaseResourceProviderR4Test {
+
+ private static final Logger ourLog = LoggerFactory.getLogger(ResourceProviderConcurrencyR4Test.class);
+ private ExecutorService myExecutor;
+ private List myReceivedNames = Collections.synchronizedList(new ArrayList<>());
+ private List myExceptions = Collections.synchronizedList(new ArrayList<>());
+
+ @Override
+ @BeforeEach
+ public void before() throws Exception {
+ super.before();
+
+ myExecutor = Executors.newFixedThreadPool(10);
+ myReceivedNames.clear();
+ myExceptions.clear();
+ }
+
+ @Override
+ @AfterEach
+ public void after() throws Exception {
+ super.after();
+
+ myInterceptorRegistry.unregisterInterceptorsIf(t -> t instanceof SearchBlockingInterceptor);
+ myExecutor.shutdown();
+
+ assertThat(myExceptions, empty());
+ }
+
+ /**
+ * This test is intended to verify that we are in fact executing searches in parallel
+ * when two different searches come in.
+ *
+ * We execute two identical searches (which should result in only one actual
+ * execution that will be reused by both) and one other search. We use an
+ * interceptor to artifically delay the execution of the first search in order
+ * to verify that the last search completes before the first one can finish.
+ */
+ @Test
+ public void testSearchesExecuteConcurrently() {
+ createPatient(withFamily("FAMILY1"));
+ createPatient(withFamily("FAMILY2"));
+ createPatient(withFamily("FAMILY3"));
+
+ SearchBlockingInterceptor searchBlockingInterceptorFamily1 = new SearchBlockingInterceptor("FAMILY1");
+ myInterceptorRegistry.registerInterceptor(searchBlockingInterceptorFamily1);
+
+ // Submit search 1 (should block because of interceptor semaphore)
+ {
+ String uri = ourServerBase + "/Patient?_format=json&family=FAMILY1";
+ ourLog.info("Submitting GET " + uri);
+ HttpGet get = new HttpGet(uri);
+ myExecutor.submit(() -> {
+ try (CloseableHttpResponse outcome = ourHttpClient.execute(get)) {
+ assertEquals(200, outcome.getStatusLine().getStatusCode());
+ String outcomeString = IOUtils.toString(outcome.getEntity().getContent(), StandardCharsets.UTF_8);
+ Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, outcomeString);
+ assertEquals(1, bundle.getEntry().size());
+ Patient pt = (Patient) bundle.getEntry().get(0).getResource();
+ String family = pt.getNameFirstRep().getFamily();
+ ourLog.info("Received response with family name: {}", family);
+ myReceivedNames.add(family);
+ } catch (Exception e) {
+ ourLog.error("Client failure", e);
+ myExceptions.add(e);
+ }
+ });
+ }
+
+ await().until(() -> searchBlockingInterceptorFamily1.getHits(), equalTo(1));
+
+ // Submit search 2 (should also block because it will reuse the first search - same name being searched)
+ {
+ String uri = ourServerBase + "/Patient?_format=json&family=FAMILY1";
+ HttpGet get = new HttpGet(uri);
+ myExecutor.submit(() -> {
+ ourLog.info("Submitting GET " + uri);
+ try (CloseableHttpResponse outcome = ourHttpClient.execute(get)) {
+ assertEquals(200, outcome.getStatusLine().getStatusCode());
+ String outcomeString = IOUtils.toString(outcome.getEntity().getContent(), StandardCharsets.UTF_8);
+ Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, outcomeString);
+ assertEquals(1, bundle.getEntry().size());
+ Patient pt = (Patient) bundle.getEntry().get(0).getResource();
+ String family = pt.getNameFirstRep().getFamily();
+ ourLog.info("Received response with family name: {}", family);
+ myReceivedNames.add(family);
+ } catch (Exception e) {
+ ourLog.error("Client failure", e);
+ myExceptions.add(e);
+ }
+ });
+ }
+
+ // Submit search 3 (should not block - different name being searched, so it should actually finish first)
+ {
+ String uri = ourServerBase + "/Patient?_format=json&family=FAMILY3";
+ HttpGet get = new HttpGet(uri);
+ myExecutor.submit(() -> {
+ ourLog.info("Submitting GET " + uri);
+ try (CloseableHttpResponse outcome = ourHttpClient.execute(get)) {
+ assertEquals(200, outcome.getStatusLine().getStatusCode());
+ String outcomeString = IOUtils.toString(outcome.getEntity().getContent(), StandardCharsets.UTF_8);
+ Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, outcomeString);
+ assertEquals(1, bundle.getEntry().size());
+ Patient pt = (Patient) bundle.getEntry().get(0).getResource();
+ String family = pt.getNameFirstRep().getFamily();
+ ourLog.info("Received response with family name: {}", family);
+ myReceivedNames.add(family);
+ } catch (Exception e) {
+ ourLog.error("Client failure", e);
+ myExceptions.add(e);
+ }
+ });
+ }
+
+ ourLog.info("About to wait for FAMILY3 to complete");
+ await().until(() -> myReceivedNames, contains("FAMILY3"));
+ ourLog.info("Got FAMILY3");
+
+ searchBlockingInterceptorFamily1.getLatch().countDown();
+
+ ourLog.info("About to wait for FAMILY1 to complete");
+ await().until(() -> myReceivedNames, contains("FAMILY3", "FAMILY1", "FAMILY1"));
+ ourLog.info("Got FAMILY1");
+
+ assertEquals(1, searchBlockingInterceptorFamily1.getHits());
+ }
+
+
+ @Interceptor
+ public static class SearchBlockingInterceptor {
+
+ private final CountDownLatch myLatch = new CountDownLatch(1);
+ private final String myFamily;
+ private AtomicInteger myHits = new AtomicInteger(0);
+
+ SearchBlockingInterceptor(String theFamily) {
+ myFamily = theFamily;
+ }
+
+ @Hook(Pointcut.JPA_PERFTRACE_SEARCH_FIRST_RESULT_LOADED)
+ public void firstResultLoaded(RequestDetails theRequestDetails) {
+ String family = theRequestDetails.getParameters().get("family")[0];
+ ourLog.info("See a hit for: {}", family);
+ if (family.equals(myFamily)) {
+ try {
+ myHits.incrementAndGet();
+ if (!myLatch.await(1, TimeUnit.MINUTES)) {
+ throw new InternalErrorException("Timed out waiting for " + Pointcut.JPA_PERFTRACE_SEARCH_FIRST_RESULT_LOADED);
+ }
+ } catch (InterruptedException e) {
+ throw new InternalErrorException(e);
+ }
+ }
+ }
+
+ public Integer getHits() {
+ return myHits.get();
+ }
+
+ public CountDownLatch getLatch() {
+ return myLatch;
+ }
+ }
+
+
+}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
index b939c4b1536..98fbd540de1 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
@@ -1,56 +1,47 @@
package ca.uhn.fhir.jpa.provider.r4;
-import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
-import static ca.uhn.fhir.jpa.util.TestUtil.sleepOneClick;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.contains;
-import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.hamcrest.Matchers.containsInRelativeOrder;
-import static org.hamcrest.Matchers.containsString;
-import static org.hamcrest.Matchers.empty;
-import static org.hamcrest.Matchers.emptyString;
-import static org.hamcrest.Matchers.endsWith;
-import static org.hamcrest.Matchers.greaterThan;
-import static org.hamcrest.Matchers.hasItem;
-import static org.hamcrest.Matchers.hasItems;
-import static org.hamcrest.Matchers.hasSize;
-import static org.hamcrest.Matchers.in;
-import static org.hamcrest.Matchers.lessThan;
-import static org.hamcrest.Matchers.lessThanOrEqualTo;
-import static org.hamcrest.Matchers.matchesPattern;
-import static org.hamcrest.Matchers.not;
-import static org.hamcrest.Matchers.startsWith;
-import static org.hamcrest.Matchers.stringContainsInOrder;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertNotEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-import static org.junit.jupiter.api.Assertions.fail;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.math.BigDecimal;
-import java.net.InetSocketAddress;
-import java.net.Socket;
-import java.net.SocketTimeoutException;
-import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.TreeSet;
-import java.util.stream.Collectors;
-
-import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.config.TestR4Config;
+import ca.uhn.fhir.jpa.dao.data.ISearchDao;
+import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
-import ca.uhn.fhir.util.BundleBuilder;
+import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
+import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
+import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.primitive.UriDt;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.parser.StrictErrorHandler;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
+import ca.uhn.fhir.rest.api.SummaryEnum;
+import ca.uhn.fhir.rest.client.apache.ResourceEntity;
+import ca.uhn.fhir.rest.client.api.IClientInterceptor;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.api.IHttpRequest;
+import ca.uhn.fhir.rest.client.api.IHttpResponse;
+import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
+import ca.uhn.fhir.rest.gclient.StringClientParam;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.NumberParam;
+import ca.uhn.fhir.rest.param.ParamPrefixEnum;
+import ca.uhn.fhir.rest.param.StringAndListParam;
+import ca.uhn.fhir.rest.param.StringOrListParam;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.util.UrlUtil;
+import com.google.common.base.Charsets;
+import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
@@ -151,49 +142,52 @@ import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
-import com.google.common.base.Charsets;
-import com.google.common.collect.Lists;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.math.BigDecimal;
+import java.net.InetSocketAddress;
+import java.net.Socket;
+import java.net.SocketTimeoutException;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.stream.Collectors;
-import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.config.TestR4Config;
-import ca.uhn.fhir.jpa.dao.data.ISearchDao;
-import ca.uhn.fhir.jpa.entity.Search;
-import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
-import ca.uhn.fhir.jpa.model.util.JpaConstants;
-import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
-import ca.uhn.fhir.jpa.util.SqlQuery;
-import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
-import ca.uhn.fhir.model.primitive.InstantDt;
-import ca.uhn.fhir.model.primitive.UriDt;
-import ca.uhn.fhir.parser.IParser;
-import ca.uhn.fhir.parser.StrictErrorHandler;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
-import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
-import ca.uhn.fhir.rest.api.SummaryEnum;
-import ca.uhn.fhir.rest.client.apache.ResourceEntity;
-import ca.uhn.fhir.rest.client.api.IClientInterceptor;
-import ca.uhn.fhir.rest.client.api.IGenericClient;
-import ca.uhn.fhir.rest.client.api.IHttpRequest;
-import ca.uhn.fhir.rest.client.api.IHttpResponse;
-import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
-import ca.uhn.fhir.rest.gclient.StringClientParam;
-import ca.uhn.fhir.rest.param.DateRangeParam;
-import ca.uhn.fhir.rest.param.NumberParam;
-import ca.uhn.fhir.rest.param.ParamPrefixEnum;
-import ca.uhn.fhir.rest.param.StringAndListParam;
-import ca.uhn.fhir.rest.param.StringOrListParam;
-import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
-import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
-import ca.uhn.fhir.util.StopWatch;
-import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
-import ca.uhn.fhir.util.UrlUtil;
+import static ca.uhn.fhir.jpa.util.TestUtil.sleepOneClick;
+import static ca.uhn.fhir.util.TestUtil.sleepAtLeast;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.containsInRelativeOrder;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.emptyString;
+import static org.hamcrest.Matchers.endsWith;
+import static org.hamcrest.Matchers.greaterThan;
+import static org.hamcrest.Matchers.hasItem;
+import static org.hamcrest.Matchers.hasItems;
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.lessThan;
+import static org.hamcrest.Matchers.lessThanOrEqualTo;
+import static org.hamcrest.Matchers.matchesPattern;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.startsWith;
+import static org.hamcrest.Matchers.stringContainsInOrder;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
@SuppressWarnings("Duplicates")
public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
@@ -4808,6 +4802,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
@Test
+ @Disabled("Not useful with the search coordinator thread pool removed")
public void testSearchWithCountNotSet() {
mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(1);
mySearchCoordinatorSvcRaw.setLoadingThrottleForUnitTests(200);
@@ -4876,6 +4871,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
@Test
+ @Disabled("Not useful with the search coordinator thread pool removed")
public void testSearchWithCountSearchResultsUpTo5() {
mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(1);
mySearchCoordinatorSvcRaw.setLoadingThrottleForUnitTests(200);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/StaleSearchDeletingSvcR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/StaleSearchDeletingSvcR4Test.java
index 56cabaf802b..9ef68d4c799 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/StaleSearchDeletingSvcR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/StaleSearchDeletingSvcR4Test.java
@@ -26,7 +26,7 @@ import org.springframework.test.util.AopTestUtils;
import java.util.Date;
import java.util.UUID;
-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.Matchers.blankOrNullString;
import static org.hamcrest.Matchers.containsString;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java
index 750953a8818..521397b0aab 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java
@@ -4,7 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
+import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
import ca.uhn.fhir.jpa.rp.r4.BinaryResourceProvider;
@@ -815,7 +815,7 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
.execute();
ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(response));
- myBatchJobHelper.awaitAllBulkJobCompletions(BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME);
+ myBatchJobHelper.awaitAllBulkJobCompletions(BatchConstants.DELETE_EXPUNGE_JOB_NAME);
Long jobId = BatchHelperR4.jobIdFromParameters(response);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/sched/SchedulerServiceImplTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/sched/SchedulerServiceImplTest.java
index 323b20ec1a6..fd1bef5a951 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/sched/SchedulerServiceImplTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/sched/SchedulerServiceImplTest.java
@@ -25,7 +25,7 @@ import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.test.util.AopTestUtils;
-import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
+import static ca.uhn.fhir.util.TestUtil.sleepAtLeast;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.greaterThan;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
index 830f77ba0f5..0e7d607bccb 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
@@ -6,7 +6,6 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
-import ca.uhn.fhir.jpa.config.dstu3.BaseDstu3Config;
import ca.uhn.fhir.jpa.dao.IResultIterator;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
@@ -29,6 +28,7 @@ import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import com.google.common.collect.Lists;
+import org.hamcrest.Matchers;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
@@ -57,7 +57,7 @@ import java.util.concurrent.CountDownLatch;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
-import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
+import static ca.uhn.fhir.util.TestUtil.sleepAtLeast;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
@@ -126,7 +126,7 @@ public class SearchCoordinatorSvcImplTest {
myCurrentSearch = null;
- mySvc = new SearchCoordinatorSvcImpl(new BaseDstu3Config().searchCoordinatorThreadFactory());
+ mySvc = new SearchCoordinatorSvcImpl();
mySvc.setEntityManagerForUnitTest(myEntityManager);
mySvc.setTransactionManagerForUnitTest(myTxManager);
mySvc.setContextForUnitTest(ourCtx);
@@ -174,12 +174,8 @@ public class SearchCoordinatorSvcImplTest {
IResultIterator iter = new FailAfterNIterator(new SlowIterator(pids.iterator(), 2), 300);
when(mySearchBuilder.createQuery(same(params), any(), any(), nullable(RequestPartitionId.class))).thenReturn(iter);
- IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null, RequestPartitionId.allPartitions());
- assertNotNull(result.getUuid());
- assertEquals(null, result.size());
-
try {
- result.getResources(0, 100000);
+ mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null, RequestPartitionId.allPartitions());
} catch (InternalErrorException e) {
assertThat(e.getMessage(), containsString("FAILED"));
assertThat(e.getMessage(), containsString("at ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImplTest"));
@@ -220,7 +216,7 @@ public class SearchCoordinatorSvcImplTest {
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null, RequestPartitionId.allPartitions());
assertNotNull(result.getUuid());
- assertEquals(null, result.size());
+ assertEquals(790, result.size());
List resources = result.getResources(0, 100000);
assertEquals(790, resources.size());
@@ -297,7 +293,7 @@ public class SearchCoordinatorSvcImplTest {
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null, RequestPartitionId.allPartitions());
assertNotNull(result.getUuid());
- assertEquals(null, result.size());
+ assertEquals(790, result.size());
List resources;
@@ -337,16 +333,19 @@ public class SearchCoordinatorSvcImplTest {
SlowIterator iter = new SlowIterator(pids.iterator(), 500);
when(mySearchBuilder.createQuery(same(params), any(), any(), nullable(RequestPartitionId.class))).thenReturn(iter);
- IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null, RequestPartitionId.allPartitions());
- assertNotNull(result.getUuid());
+ ourLog.info("Registering the first search");
+ new Thread(() -> mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null, RequestPartitionId.allPartitions())).start();
+ await().until(()->iter.getCountReturned(), Matchers.greaterThan(0));
+ String searchId = mySvc.getActiveSearchIds().iterator().next();
CountDownLatch completionLatch = new CountDownLatch(1);
Runnable taskStarter = () -> {
try {
+ assertNotNull(searchId);
ourLog.info("About to pull the first resource");
- List resources = result.getResources(0, 1);
+ List resources = mySvc.getResources(searchId, 0, 1, null);
ourLog.info("Done pulling the first resource");
- assertEquals(1, resources.size());
+ assertEquals(1, resources.size());
} finally {
completionLatch.countDown();
}
@@ -360,10 +359,9 @@ public class SearchCoordinatorSvcImplTest {
ourLog.info("Done cancelling all searches");
try {
- result.getResources(10, 20);
- } catch (InternalErrorException e) {
- assertThat(e.getMessage(), containsString("Abort has been requested"));
- assertThat(e.getMessage(), containsString("at ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl"));
+ mySvc.getResources(searchId, 0, 1, null);
+ } catch (ResourceGoneException e) {
+ // good
}
completionLatch.await(10, TimeUnit.SECONDS);
@@ -391,7 +389,7 @@ public class SearchCoordinatorSvcImplTest {
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null, RequestPartitionId.allPartitions());
assertNotNull(result.getUuid());
- assertEquals(null, result.size());
+ assertEquals(790, result.size());
ArgumentCaptor searchCaptor = ArgumentCaptor.forClass(Search.class);
verify(mySearchCacheSvc, atLeast(1)).save(searchCaptor.capture());
@@ -402,23 +400,11 @@ public class SearchCoordinatorSvcImplTest {
PersistedJpaBundleProvider provider;
resources = result.getResources(0, 10);
- assertNull(result.size());
+ assertEquals(790, result.size());
assertEquals(10, resources.size());
assertEquals("10", resources.get(0).getIdElement().getValueAsString());
assertEquals("19", resources.get(9).getIdElement().getValueAsString());
- when(mySearchCacheSvc.fetchByUuid(eq(result.getUuid()))).thenReturn(Optional.of(search));
-
- /*
- * Now call from a new bundle provider. This simulates a separate HTTP
- * client request coming in.
- */
- provider = newPersistedJpaBundleProvider(result.getUuid());
- resources = provider.getResources(10, 20);
- assertEquals(10, resources.size());
- assertEquals("20", resources.get(0).getIdElement().getValueAsString());
- assertEquals("29", resources.get(9).getIdElement().getValueAsString());
-
myExpectedNumberOfSearchBuildersCreated = 4;
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandlerTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandlerTest.java
new file mode 100644
index 00000000000..9a304b33bbb
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandlerTest.java
@@ -0,0 +1,304 @@
+package ca.uhn.fhir.jpa.term.loinc;
+
+import com.google.common.collect.Maps;
+import org.apache.commons.compress.utils.Lists;
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVParser;
+import org.apache.commons.csv.CSVRecord;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.jupiter.api.Nested;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Answers;
+import org.mockito.Mock;
+import org.mockito.Mockito;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import java.io.StringReader;
+import java.util.Map;
+import java.util.Properties;
+
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.never;
+import static org.mockito.Mockito.spy;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+class BaseLoincHandlerTest {
+
+ public static final String LOINC_NUMBER = "test-loinc-number";
+ public static final String DISPLAY_NAME = "test-display-name";
+ public static final String TEST_VERSION = "2.69";
+
+ @Mock(answer = Answers.RETURNS_DEEP_STUBS)
+ private ValueSet myValueSet;
+
+ @Mock
+ private ValueSet.ConceptSetComponent myInclude;
+
+ @Mock
+ private ValueSet.ConceptReferenceComponent myConceptReferenceComponent;
+
+ private Map headerMap;
+ private CSVRecord recordWithHeader;
+
+
+ /**
+ * Need to setup a real parser because we can't mock final classes (without PowerMockito)
+ */
+ private void setupCSVParser(Map headerValues) throws Exception {
+ final String[] headers = headerValues.keySet().toArray(new String[0]);
+ final String[] values = headerValues.values().toArray(new String[0]);
+ final String rowData = StringUtils.join(values, ',');
+
+ try (final CSVParser parser = CSVFormat.DEFAULT.parse(new StringReader(rowData))) {
+ parser.iterator().next();
+ }
+ try (final CSVParser parser = CSVFormat.DEFAULT.withHeader(headers).parse(new StringReader(rowData))) {
+ recordWithHeader = parser.iterator().next();
+ headerMap = parser.getHeaderMap();
+ }
+ }
+
+
+ @Nested
+ public class WithVersion {
+
+ @Test
+ void Top2000LabResultsHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LOINC #", "test-loinc-number");
+ recordDataMap.put("Long Common Name", "test-Long-Common-Names");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new BaseLoincTop2000LabResultsHandler(
+ null, Lists.newArrayList(), null, null, null, Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude).setVersion(Mockito.notNull());
+ }
+
+ @Test
+ void LoincDocumentOntologyHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LoincNumber", "test-LoincNumber");
+ recordDataMap.put("PartNumber", "test-PartNumber");
+ recordDataMap.put("PartTypeName", "Document.Role");
+ recordDataMap.put("PartSequenceOrder", "test-PartSequenceOrder");
+ recordDataMap.put("PartName", "test-PartName");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new LoincDocumentOntologyHandler(
+ Maps.newHashMap(), null, Lists.newArrayList(), Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude).setVersion(Mockito.notNull());
+ }
+
+
+ @Test
+ void LoincGroupTermsFileHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LoincNumber", "test-LoincNumber");
+ recordDataMap.put("GroupId", "test-GroupId");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new LoincGroupTermsFileHandler(
+ Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude).setVersion(Mockito.notNull());
+ }
+
+
+ @Test
+ void LoincImagingDocumentCodeHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LOINC_NUM", "test-loinc-number");
+ recordDataMap.put("LONG_COMMON_NAME", "test-Long-Common-Names");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new LoincImagingDocumentCodeHandler(
+ Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude).setVersion(Mockito.notNull());
+ }
+
+
+ @Test
+ void LoincUniversalOrderSetHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LOINC_NUM", "test-loinc-number");
+ recordDataMap.put("LONG_COMMON_NAME", "test-Long-Common-Names");
+ recordDataMap.put("ORDER_OBS", "test-ORDER_OBS");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new LoincUniversalOrderSetHandler(
+ Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude).setVersion(Mockito.notNull());
+ } }
+
+ @Nested
+ public class WithoutVersion {
+
+ @Test
+ void Top2000LabResultsHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LOINC #", "test-loinc-number");
+ recordDataMap.put("Long Common Name", "test-Long-Common-Names");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new BaseLoincTop2000LabResultsHandler(
+ Maps.newHashMap(), Lists.newArrayList(), null, null, null, Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude, never()).setVersion(any());
+ }
+
+ @Test
+ void LoincDocumentOntologyHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LoincNumber", "test-LoincNumber");
+ recordDataMap.put("PartNumber", "test-PartNumber");
+ recordDataMap.put("PartTypeName", "Document.Role");
+ recordDataMap.put("PartSequenceOrder", "test-PartSequenceOrder");
+ recordDataMap.put("PartName", "test-PartName");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new LoincDocumentOntologyHandler(
+ Maps.newHashMap(), null, Lists.newArrayList(), Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude, never()).setVersion(any());
+ }
+
+ @Test
+ void LoincGroupTermsFileHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LoincNumber", "test-LoincNumber");
+ recordDataMap.put("GroupId", "test-GroupId");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new LoincGroupTermsFileHandler(
+ Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude, never()).setVersion(any());
+ }
+
+
+ @Test
+ void LoincImagingDocumentCodeHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LOINC_NUM", "test-loinc-number");
+ recordDataMap.put("LONG_COMMON_NAME", "test-Long-Common-Names");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new LoincImagingDocumentCodeHandler(
+ Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude, never()).setVersion(any());
+ }
+
+
+ @Test
+ void LoincUniversalOrderSetHandlerTest() throws Exception {
+ Map recordDataMap = Maps.newHashMap();
+ recordDataMap.put("LOINC_NUM", "test-loinc-number");
+ recordDataMap.put("LONG_COMMON_NAME", "test-Long-Common-Names");
+ recordDataMap.put("ORDER_OBS", "test-ORDER_OBS");
+ setupCSVParser(recordDataMap);
+
+ BaseLoincHandler loincHandler = new LoincUniversalOrderSetHandler(
+ Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
+ BaseLoincHandler spiedLoincHandler = spy(loincHandler);
+
+ when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
+ when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
+ when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
+ when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
+
+ spiedLoincHandler.accept(recordWithHeader);
+
+ Mockito.verify(myInclude, never()).setVersion(any());
+ }
+
+ }
+
+
+
+
+}
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/cdr-bundle.json b/hapi-fhir-jpaserver-base/src/test/resources/cdr-bundle.json
index 2e8644593a5..9afb12a7cc8 100644
--- a/hapi-fhir-jpaserver-base/src/test/resources/cdr-bundle.json
+++ b/hapi-fhir-jpaserver-base/src/test/resources/cdr-bundle.json
@@ -44,7 +44,7 @@
},
"request": {
"method": "PUT",
- "url": "/Practitioner?identifier=http%253A%252F%252Facme.org%252Fclinicians%257C777"
+ "url": "/Practitioner?identifier=http%3A%2F%2Facme.org%2Fclinicians%7C777"
}
},
{
@@ -125,7 +125,7 @@
},
"request": {
"method": "PUT",
- "url": "/Patient?identifier=http%253A%252F%252Facme.org%252Fmrns%257C7000135"
+ "url": "/Patient?identifier=http%3A%2F%2Facme.org%2Fmrns%7C7000135"
}
},
{
@@ -203,7 +203,7 @@
},
"request": {
"method": "PUT",
- "url": "/Encounter?identifier=http%253A%252F%252Facme.org%252FvisitNumbers%257C4736455"
+ "url": "/Encounter?identifier=http%3A%2F%2Facme.org%2FvisitNumbers%7C4736455"
}
},
{
@@ -267,7 +267,7 @@
},
"request": {
"method": "PUT",
- "url": "/Practitioner?identifier=http%253A%252F%252Facme.org%252Fclinicians%257C3622"
+ "url": "/Practitioner?identifier=http%3A%2F%2Facme.org%2Fclinicians%7C3622"
}
},
{
@@ -312,8 +312,8 @@
},
"request": {
"method": "PUT",
- "url": "/Practitioner?identifier=http%253A%252F%252Facme.org%252Fclinicians%257C7452"
+ "url": "/Practitioner?identifier=http%3A%2F%2Facme.org%2Fclinicians%7C7452"
}
}
]
-}
\ No newline at end of file
+}
diff --git a/hapi-fhir-jpaserver-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/InMemoryJobRepositoryBatchConfig.java b/hapi-fhir-jpaserver-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/InMemoryJobRepositoryBatchConfig.java
deleted file mode 100644
index 57c28702fec..00000000000
--- a/hapi-fhir-jpaserver-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/InMemoryJobRepositoryBatchConfig.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package ca.uhn.fhir.jpa.batch.config;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server - Batch Task Processor
- * %%
- * Copyright (C) 2014 - 2021 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
-import org.springframework.batch.core.explore.JobExplorer;
-import org.springframework.batch.core.explore.support.MapJobExplorerFactoryBean;
-import org.springframework.batch.core.launch.JobLauncher;
-import org.springframework.batch.core.launch.support.SimpleJobLauncher;
-import org.springframework.batch.core.repository.JobRepository;
-import org.springframework.batch.core.repository.support.MapJobRepositoryFactoryBean;
-import org.springframework.batch.support.transaction.ResourcelessTransactionManager;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.stereotype.Component;
-import org.springframework.transaction.PlatformTransactionManager;
-
-import javax.annotation.PostConstruct;
-
-@Component
-@Configuration
-public class InMemoryJobRepositoryBatchConfig implements BatchConfigurer {
-
- private PlatformTransactionManager myPlatformTransactionManager;
- private JobLauncher myJobLauncher;
- private JobRepository myJobRepository;
- private JobExplorer myJobExplorer;
-
-
- @Override
- public PlatformTransactionManager getTransactionManager() {
- return myPlatformTransactionManager;
- }
-
- @Override
- public JobRepository getJobRepository() {
- return myJobRepository;
- }
-
- @Override
- public JobLauncher getJobLauncher() {
- return myJobLauncher;
- }
-
- @Override
- public JobExplorer getJobExplorer() {
- return myJobExplorer;
- }
-
- @PostConstruct
- public void setup() throws Exception{
- if (myPlatformTransactionManager == null) {
- myPlatformTransactionManager = new ResourcelessTransactionManager();
- }
- MapJobRepositoryFactoryBean jobRepositoryFactoryBean = new MapJobRepositoryFactoryBean(myPlatformTransactionManager);
- jobRepositoryFactoryBean.afterPropertiesSet();
- myJobRepository = jobRepositoryFactoryBean.getObject();
-
- MapJobExplorerFactoryBean jobExplorerFactoryBean = new MapJobExplorerFactoryBean(jobRepositoryFactoryBean);
- jobExplorerFactoryBean.afterPropertiesSet();
- myJobExplorer = jobExplorerFactoryBean.getObject();
-
- SimpleJobLauncher jobLauncher = new SimpleJobLauncher();
- jobLauncher.setJobRepository(myJobRepository);
- jobLauncher.afterPropertiesSet();
- myJobLauncher = jobLauncher;
- }
-}
diff --git a/hapi-fhir-jpaserver-cql/pom.xml b/hapi-fhir-jpaserver-cql/pom.xml
index d08c19cfdca..79b0f8682a9 100644
--- a/hapi-fhir-jpaserver-cql/pom.xml
+++ b/hapi-fhir-jpaserver-cql/pom.xml
@@ -7,7 +7,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE5-SNAPSHOT
+ 5.6.0-PRE6-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-jpaserver-mdm/pom.xml b/hapi-fhir-jpaserver-mdm/pom.xml
index 0ebb48c99dd..22fa4dceb98 100644
--- a/hapi-fhir-jpaserver-mdm/pom.xml
+++ b/hapi-fhir-jpaserver-mdm/pom.xml
@@ -6,7 +6,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE5-SNAPSHOT
+ 5.6.0-PRE6-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmMessageHandler.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmMessageHandler.java
index 3a84eebb083..360aae8af76 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmMessageHandler.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmMessageHandler.java
@@ -24,18 +24,23 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
+import ca.uhn.fhir.jpa.mdm.svc.IMdmModelConverterSvc;
import ca.uhn.fhir.jpa.mdm.svc.MdmMatchLinkSvc;
import ca.uhn.fhir.jpa.mdm.svc.MdmResourceFilteringSvc;
import ca.uhn.fhir.jpa.mdm.svc.candidate.TooManyCandidatesException;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import ca.uhn.fhir.mdm.api.IMdmSettings;
+import ca.uhn.fhir.mdm.api.MdmLinkEvent;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.rest.server.TransactionLogMessages;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage;
import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.messaging.Message;
@@ -45,9 +50,11 @@ import org.springframework.stereotype.Service;
@Service
public class MdmMessageHandler implements MessageHandler {
-
+
private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
+ @Autowired
+ private MdmLinkDaoSvc myMdmLinkDaoSvc;
@Autowired
private MdmMatchLinkSvc myMdmMatchLinkSvc;
@Autowired
@@ -58,6 +65,8 @@ public class MdmMessageHandler implements MessageHandler {
private MdmResourceFilteringSvc myMdmResourceFilteringSvc;
@Autowired
private IMdmSettings myMdmSettings;
+ @Autowired
+ private IMdmModelConverterSvc myModelConverter;
@Override
public void handleMessage(Message theMessage) throws MessagingException {
@@ -85,32 +94,41 @@ public class MdmMessageHandler implements MessageHandler {
private void matchMdmAndUpdateLinks(ResourceModifiedMessage theMsg) {
String resourceType = theMsg.getId(myFhirContext).getResourceType();
validateResourceType(resourceType);
- MdmTransactionContext mdmContext = createMdmContext(theMsg, resourceType);
+ MdmTransactionContext mdmContext = createMdmContext(theMsg, resourceType);
try {
switch (theMsg.getOperationType()) {
case CREATE:
- handleCreatePatientOrPractitioner(theMsg, mdmContext);
+ handleCreateResource(theMsg, mdmContext);
break;
case UPDATE:
case MANUALLY_TRIGGERED:
- handleUpdatePatientOrPractitioner(theMsg, mdmContext);
+ handleUpdateResource(theMsg, mdmContext);
break;
case DELETE:
default:
ourLog.trace("Not processing modified message for {}", theMsg.getOperationType());
}
- }catch (Exception e) {
+ } catch (Exception e) {
log(mdmContext, "Failure during MDM processing: " + e.getMessage(), e);
mdmContext.addTransactionLogMessage(e.getMessage());
} finally {
-
// Interceptor call: MDM_AFTER_PERSISTED_RESOURCE_CHECKED
- ResourceOperationMessage outgoingMsg = new ResourceOperationMessage(myFhirContext, theMsg.getPayload(myFhirContext), theMsg.getOperationType());
+ IBaseResource targetResource = theMsg.getPayload(myFhirContext);
+ ResourceOperationMessage outgoingMsg = new ResourceOperationMessage(myFhirContext, targetResource, theMsg.getOperationType());
outgoingMsg.setTransactionId(theMsg.getTransactionId());
+ MdmLinkEvent linkChangeEvent = new MdmLinkEvent();
+ mdmContext.getMdmLinks()
+ .stream()
+ .forEach(l -> {
+ linkChangeEvent.addMdmLink(myModelConverter.toJson((MdmLink) l));
+ });
+
HookParams params = new HookParams()
.add(ResourceOperationMessage.class, outgoingMsg)
- .add(TransactionLogMessages.class, mdmContext.getTransactionLogMessages());
+ .add(TransactionLogMessages.class, mdmContext.getTransactionLogMessages())
+ .add(MdmLinkEvent.class, linkChangeEvent);
+
myInterceptorBroadcaster.callHooks(Pointcut.MDM_AFTER_PERSISTED_RESOURCE_CHECKED, params);
}
}
@@ -142,7 +160,7 @@ public class MdmMessageHandler implements MessageHandler {
}
}
- private void handleCreatePatientOrPractitioner(ResourceModifiedMessage theMsg, MdmTransactionContext theMdmTransactionContext) {
+ private void handleCreateResource(ResourceModifiedMessage theMsg, MdmTransactionContext theMdmTransactionContext) {
myMdmMatchLinkSvc.updateMdmLinksForMdmSource(getResourceFromPayload(theMsg), theMdmTransactionContext);
}
@@ -150,7 +168,7 @@ public class MdmMessageHandler implements MessageHandler {
return (IAnyResource) theMsg.getNewPayload(myFhirContext);
}
- private void handleUpdatePatientOrPractitioner(ResourceModifiedMessage theMsg, MdmTransactionContext theMdmTransactionContext) {
+ private void handleUpdateResource(ResourceModifiedMessage theMsg, MdmTransactionContext theMdmTransactionContext) {
myMdmMatchLinkSvc.updateMdmLinksForMdmSource(getResourceFromPayload(theMsg), theMdmTransactionContext);
}
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmQueueConsumerLoader.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmQueueConsumerLoader.java
index 385d8265392..90e7b5ef065 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmQueueConsumerLoader.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmQueueConsumerLoader.java
@@ -1,11 +1,11 @@
package ca.uhn.fhir.jpa.mdm.broker;
-import ca.uhn.fhir.mdm.api.IMdmSettings;
-import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.jpa.subscription.channel.api.ChannelConsumerSettings;
import ca.uhn.fhir.jpa.subscription.channel.api.IChannelFactory;
import ca.uhn.fhir.jpa.subscription.channel.api.IChannelReceiver;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
+import ca.uhn.fhir.mdm.api.IMdmSettings;
+import ca.uhn.fhir.mdm.log.Logs;
import com.google.common.annotations.VisibleForTesting;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmConsumerConfig.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmConsumerConfig.java
index 3005c2d5735..e1b65abffc0 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmConsumerConfig.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmConsumerConfig.java
@@ -32,13 +32,15 @@ import ca.uhn.fhir.jpa.mdm.dao.MdmLinkFactory;
import ca.uhn.fhir.jpa.mdm.interceptor.IMdmStorageInterceptor;
import ca.uhn.fhir.jpa.mdm.interceptor.MdmStorageInterceptor;
import ca.uhn.fhir.jpa.mdm.svc.GoldenResourceMergerSvcImpl;
+import ca.uhn.fhir.jpa.mdm.svc.IMdmModelConverterSvc;
import ca.uhn.fhir.jpa.mdm.svc.MdmControllerSvcImpl;
import ca.uhn.fhir.jpa.mdm.svc.MdmEidUpdateService;
-import ca.uhn.fhir.jpa.mdm.svc.MdmLinkQuerySvcImpl;
+import ca.uhn.fhir.jpa.mdm.svc.MdmLinkQuerySvcImplSvc;
import ca.uhn.fhir.jpa.mdm.svc.MdmLinkSvcImpl;
import ca.uhn.fhir.jpa.mdm.svc.MdmLinkUpdaterSvcImpl;
import ca.uhn.fhir.jpa.mdm.svc.MdmMatchFinderSvcImpl;
import ca.uhn.fhir.jpa.mdm.svc.MdmMatchLinkSvc;
+import ca.uhn.fhir.jpa.mdm.svc.MdmModelConverterSvcImpl;
import ca.uhn.fhir.jpa.mdm.svc.MdmResourceDaoSvc;
import ca.uhn.fhir.jpa.mdm.svc.MdmResourceFilteringSvc;
import ca.uhn.fhir.jpa.mdm.svc.MdmSearchParamSvc;
@@ -178,7 +180,12 @@ public class MdmConsumerConfig {
@Bean
IMdmLinkQuerySvc mdmLinkQuerySvc() {
- return new MdmLinkQuerySvcImpl();
+ return new MdmLinkQuerySvcImplSvc();
+ }
+
+ @Bean
+ IMdmModelConverterSvc mdmModelConverterSvc() {
+ return new MdmModelConverterSvcImpl();
}
@Bean
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmSubmitterInterceptorLoader.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmSubmitterInterceptorLoader.java
index 912d39331ea..29ee64e5733 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmSubmitterInterceptorLoader.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmSubmitterInterceptorLoader.java
@@ -20,12 +20,12 @@ package ca.uhn.fhir.jpa.mdm.interceptor;
* #L%
*/
-import ca.uhn.fhir.jpa.interceptor.MdmSearchExpandingInterceptor;
-import ca.uhn.fhir.mdm.api.IMdmSettings;
-import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.interceptor.MdmSearchExpandingInterceptor;
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionSubmitInterceptorLoader;
+import ca.uhn.fhir.mdm.api.IMdmSettings;
+import ca.uhn.fhir.mdm.log.Logs;
import org.hl7.fhir.dstu2.model.Subscription;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/IMdmModelConverterSvc.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/IMdmModelConverterSvc.java
new file mode 100644
index 00000000000..67c534a9489
--- /dev/null
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/IMdmModelConverterSvc.java
@@ -0,0 +1,39 @@
+package ca.uhn.fhir.jpa.mdm.svc;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Master Data Management
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.mdm.api.MdmLinkJson;
+
+/**
+ * Contract for decoupling API dependency from the base / JPA modules.
+ */
+public interface IMdmModelConverterSvc {
+
+ /**
+ * Creates JSON representation of the provided MDM link
+ *
+ * @param theLink Link to convert
+ * @return Returns the converted link
+ */
+ public MdmLinkJson toJson(MdmLink theLink);
+
+}
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkQuerySvcImpl.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkQuerySvcImplSvc.java
similarity index 73%
rename from hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkQuerySvcImpl.java
rename to hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkQuerySvcImplSvc.java
index ea00e81ec4d..996dbe8e5cc 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkQuerySvcImpl.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkQuerySvcImplSvc.java
@@ -36,20 +36,24 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Example;
import org.springframework.data.domain.Page;
-public class MdmLinkQuerySvcImpl implements IMdmLinkQuerySvc {
+public class MdmLinkQuerySvcImplSvc implements IMdmLinkQuerySvc {
- private static final Logger ourLog = LoggerFactory.getLogger(MdmLinkQuerySvcImpl.class);
+ private static final Logger ourLog = LoggerFactory.getLogger(MdmLinkQuerySvcImplSvc.class);
+
+ @Autowired
+ MdmLinkDaoSvc myMdmLinkDaoSvc;
@Autowired
IdHelperService myIdHelperService;
+
@Autowired
- MdmLinkDaoSvc myMdmLinkDaoSvc;
+ IMdmModelConverterSvc myMdmModelConverterSvc;
@Override
public Page queryLinks(IIdType theGoldenResourceId, IIdType theSourceResourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmContext, MdmPageRequest thePageRequest) {
Example exampleLink = exampleLinkFromParameters(theGoldenResourceId, theSourceResourceId, theMatchResult, theLinkSource);
Page mdmLinkByExample = myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink, thePageRequest);
- Page map = mdmLinkByExample.map(this::toJson);
+ Page map = mdmLinkByExample.map(myMdmModelConverterSvc::toJson);
return map;
}
@@ -57,28 +61,10 @@ public class MdmLinkQuerySvcImpl implements IMdmLinkQuerySvc {
public Page getDuplicateGoldenResources(MdmTransactionContext theMdmContext, MdmPageRequest thePageRequest) {
Example exampleLink = exampleLinkFromParameters(null, null, MdmMatchResultEnum.POSSIBLE_DUPLICATE, null);
Page mdmLinkPage = myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink, thePageRequest);
- Page map = mdmLinkPage.map(this::toJson);
+ Page map = mdmLinkPage.map(myMdmModelConverterSvc::toJson);
return map;
}
- private MdmLinkJson toJson(MdmLink theLink) {
- MdmLinkJson retval = new MdmLinkJson();
- String sourceId = myIdHelperService.resourceIdFromPidOrThrowException(theLink.getSourcePid()).toVersionless().getValue();
- retval.setSourceId(sourceId);
- String goldenResourceId = myIdHelperService.resourceIdFromPidOrThrowException(theLink.getGoldenResourcePid()).toVersionless().getValue();
- retval.setGoldenResourceId(goldenResourceId);
- retval.setCreated(theLink.getCreated());
- retval.setEidMatch(theLink.getEidMatch());
- retval.setLinkSource(theLink.getLinkSource());
- retval.setMatchResult(theLink.getMatchResult());
- retval.setLinkCreatedNewResource(theLink.getHadToCreateNewGoldenResource());
- retval.setScore(theLink.getScore());
- retval.setUpdated(theLink.getUpdated());
- retval.setVector(theLink.getVector());
- retval.setVersion(theLink.getVersion());
- return retval;
- }
-
private Example exampleLinkFromParameters(IIdType theGoldenResourceId, IIdType theSourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource) {
MdmLink mdmLink = myMdmLinkDaoSvc.newMdmLink();
if (theGoldenResourceId != null) {
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java
index 3d744f43d11..7e4b95dad0c 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java
@@ -53,6 +53,8 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc {
private MdmLinkDaoSvc myMdmLinkDaoSvc;
@Autowired
private IdHelperService myIdHelperService;
+ @Autowired
+ private IMdmModelConverterSvc myMdmModelConverterSvc;
@Override
@Transactional
@@ -69,7 +71,8 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc {
validateRequestIsLegal(theGoldenResource, theSourceResource, matchResultEnum, theLinkSource);
myMdmResourceDaoSvc.upsertGoldenResource(theGoldenResource, theMdmTransactionContext.getResourceType());
- createOrUpdateLinkEntity(theGoldenResource, theSourceResource, theMatchOutcome, theLinkSource, theMdmTransactionContext);
+ MdmLink link = createOrUpdateLinkEntity(theGoldenResource, theSourceResource, theMatchOutcome, theLinkSource, theMdmTransactionContext);
+ theMdmTransactionContext.addMdmLink(link);
}
private boolean goldenResourceLinkedAsNoMatch(IAnyResource theGoldenResource, IAnyResource theSourceResource) {
@@ -87,6 +90,7 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc {
MdmLink mdmLink = optionalMdmLink.get();
log(theMdmTransactionContext, "Deleting MdmLink [" + theGoldenResource.getIdElement().toVersionless() + " -> " + theSourceResource.getIdElement().toVersionless() + "] with result: " + mdmLink.getMatchResult());
myMdmLinkDaoSvc.deleteLink(mdmLink);
+ theMdmTransactionContext.addMdmLink(mdmLink);
}
}
@@ -129,8 +133,8 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc {
}
}
- private void createOrUpdateLinkEntity(IBaseResource theGoldenResource, IBaseResource theSourceResource, MdmMatchOutcome theMatchOutcome, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmTransactionContext) {
- myMdmLinkDaoSvc.createOrUpdateLinkEntity(theGoldenResource, theSourceResource, theMatchOutcome, theLinkSource, theMdmTransactionContext);
+ private MdmLink createOrUpdateLinkEntity(IBaseResource theGoldenResource, IBaseResource theSourceResource, MdmMatchOutcome theMatchOutcome, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmTransactionContext) {
+ return myMdmLinkDaoSvc.createOrUpdateLinkEntity(theGoldenResource, theSourceResource, theMatchOutcome, theLinkSource, theMdmTransactionContext);
}
private void log(MdmTransactionContext theMdmTransactionContext, String theMessage) {
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java
index fdd04914646..8eda5742dd2 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java
@@ -99,6 +99,7 @@ public class MdmMatchLinkSvc {
handleMdmWithSingleCandidate(theResource, firstMatch, theMdmTransactionContext);
} else {
log(theMdmTransactionContext, "MDM received multiple match candidates, that were linked to different Golden Resources. Setting POSSIBLE_DUPLICATES and POSSIBLE_MATCHES.");
+
//Set them all as POSSIBLE_MATCH
List goldenResources = new ArrayList<>();
for (MatchedGoldenResourceCandidate matchedGoldenResourceCandidate : theCandidateList.getCandidates()) {
@@ -112,6 +113,7 @@ public class MdmMatchLinkSvc {
//Set all GoldenResources as POSSIBLE_DUPLICATE of the last GoldenResource.
IAnyResource firstGoldenResource = goldenResources.get(0);
+
goldenResources.subList(1, goldenResources.size())
.forEach(possibleDuplicateGoldenResource -> {
MdmMatchOutcome outcome = MdmMatchOutcome.POSSIBLE_DUPLICATE;
@@ -138,6 +140,7 @@ public class MdmMatchLinkSvc {
if (myGoldenResourceHelper.isPotentialDuplicate(goldenResource, theTargetResource)) {
log(theMdmTransactionContext, "Duplicate detected based on the fact that both resources have different external EIDs.");
IAnyResource newGoldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(theTargetResource, theMdmTransactionContext);
+
myMdmLinkSvc.updateLink(newGoldenResource, theTargetResource, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
myMdmLinkSvc.updateLink(newGoldenResource, goldenResource, MdmMatchOutcome.POSSIBLE_DUPLICATE, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
} else {
@@ -145,6 +148,7 @@ public class MdmMatchLinkSvc {
myGoldenResourceHelper.handleExternalEidAddition(goldenResource, theTargetResource, theMdmTransactionContext);
myEidUpdateService.applySurvivorshipRulesAndSaveGoldenResource(theTargetResource, goldenResource, theMdmTransactionContext);
}
+
myMdmLinkSvc.updateLink(goldenResource, theTargetResource, theGoldenResourceCandidate.getMatchResult(), MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
}
}
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmModelConverterSvcImpl.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmModelConverterSvcImpl.java
new file mode 100644
index 00000000000..89a8ae5c34e
--- /dev/null
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmModelConverterSvcImpl.java
@@ -0,0 +1,52 @@
+package ca.uhn.fhir.jpa.mdm.svc;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Master Data Management
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
+import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.mdm.api.MdmLinkJson;
+import org.springframework.beans.factory.annotation.Autowired;
+
+public class MdmModelConverterSvcImpl implements IMdmModelConverterSvc {
+
+ @Autowired
+ IdHelperService myIdHelperService;
+
+ public MdmLinkJson toJson(MdmLink theLink) {
+ MdmLinkJson retVal = new MdmLinkJson();
+ String sourceId = myIdHelperService.resourceIdFromPidOrThrowException(theLink.getSourcePid()).toVersionless().getValue();
+ retVal.setSourceId(sourceId);
+ String goldenResourceId = myIdHelperService.resourceIdFromPidOrThrowException(theLink.getGoldenResourcePid()).toVersionless().getValue();
+ retVal.setGoldenResourceId(goldenResourceId);
+ retVal.setCreated(theLink.getCreated());
+ retVal.setEidMatch(theLink.getEidMatch());
+ retVal.setLinkSource(theLink.getLinkSource());
+ retVal.setMatchResult(theLink.getMatchResult());
+ retVal.setLinkCreatedNewResource(theLink.getHadToCreateNewGoldenResource());
+ retVal.setScore(theLink.getScore());
+ retVal.setUpdated(theLink.getUpdated());
+ retVal.setVector(theLink.getVector());
+ retVal.setVersion(theLink.getVersion());
+ retVal.setRuleCount(theLink.getRuleCount());
+ return retVal;
+ }
+
+}
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByExampleSvc.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByExampleSvc.java
index 43606a95818..fe360c39e9f 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByExampleSvc.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByExampleSvc.java
@@ -21,13 +21,13 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
*/
import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
+import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
import ca.uhn.fhir.mdm.api.MatchedTarget;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.log.Logs;
-import ca.uhn.fhir.jpa.dao.index.IdHelperService;
-import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
-import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -54,9 +54,9 @@ public class FindCandidateByExampleSvc extends BaseCandidateFinder {
private IMdmMatchFinderSvc myMdmMatchFinderSvc;
/**
- * Attempt to find matching Golden Resources by resolving them from similar Matching target resources, where target resource
- * can be either Patient or Practitioner. Runs MDM logic over the existing target resources, then finds their
- * entries in the MdmLink table, and returns all the matches found therein.
+ * Attempt to find matching Golden Resources by resolving them from similar Matching target resources. Runs MDM logic
+ * over the existing target resources, then finds their entries in the MdmLink table, and returns all the matches
+ * found therein.
*
* @param theTarget the {@link IBaseResource} which we want to find candidate Golden Resources for.
* @return an Optional list of {@link MatchedGoldenResourceCandidate} indicating matches.
@@ -69,8 +69,8 @@ public class FindCandidateByExampleSvc extends BaseCandidateFinder {
List matchedCandidates = myMdmMatchFinderSvc.getMatchedTargets(myFhirContext.getResourceType(theTarget), theTarget);
- //Convert all possible match targets to their equivalent Golden Resources by looking up in the MdmLink table,
- //while ensuring that the matches aren't in our NO_MATCH list.
+ // Convert all possible match targets to their equivalent Golden Resources by looking up in the MdmLink table,
+ // while ensuring that the matches aren't in our NO_MATCH list.
// The data flow is as follows ->
// MatchedTargetCandidate -> Golden Resource -> MdmLink -> MatchedGoldenResourceCandidate
matchedCandidates = matchedCandidates.stream().filter(mc -> mc.isMatch() || mc.isPossibleMatch()).collect(Collectors.toList());
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByLinkSvc.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByLinkSvc.java
index 7214508d224..1e56299289c 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByLinkSvc.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByLinkSvc.java
@@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
* #L%
*/
-import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.slf4j.Logger;
diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmGoldenResourceFindingSvc.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmGoldenResourceFindingSvc.java
index d430525ee36..821b87712e9 100644
--- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmGoldenResourceFindingSvc.java
+++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmGoldenResourceFindingSvc.java
@@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
* #L%
*/
-import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.jpa.mdm.svc.MdmResourceDaoSvc;
+import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
diff --git a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java
index 96115a95bf2..6ef1ccb6284 100644
--- a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java
+++ b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java
@@ -61,7 +61,6 @@ import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Reference;
-import org.jetbrains.annotations.NotNull;
import javax.annotation.Nullable;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
@@ -326,14 +325,14 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
assertEquals(theExpectedCount, myMdmLinkDao.count());
}
- protected IAnyResource getGoldenResourceFromTargetResource(IAnyResource theBaseResource) {
+ protected T getGoldenResourceFromTargetResource(T theBaseResource) {
String resourceType = theBaseResource.getIdElement().getResourceType();
IFhirResourceDao relevantDao = myDaoRegistry.getResourceDao(resourceType);
Optional matchedLinkForTargetPid = myMdmLinkDaoSvc.getMatchedLinkForSourcePid(myIdHelperService.getPidOrNull(theBaseResource));
if (matchedLinkForTargetPid.isPresent()) {
Long goldenResourcePid = matchedLinkForTargetPid.get().getGoldenResourcePid();
- return (IAnyResource) relevantDao.readByPid(new ResourcePersistentId(goldenResourcePid));
+ return (T) relevantDao.readByPid(new ResourcePersistentId(goldenResourcePid));
} else {
return null;
}
diff --git a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/helper/BaseMdmHelper.java b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/helper/BaseMdmHelper.java
index 1389c4c5ea1..601b3ce2920 100644
--- a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/helper/BaseMdmHelper.java
+++ b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/helper/BaseMdmHelper.java
@@ -106,5 +106,8 @@ public abstract class BaseMdmHelper implements BeforeEachCallback, AfterEachCall
return channel.getQueueSizeForUnitTest();
}
+ public PointcutLatch getAfterMdmLatch() {
+ return myAfterMdmLatch;
+ }
}
diff --git a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmEventIT.java b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmEventIT.java
new file mode 100644
index 00000000000..cafbdebbff2
--- /dev/null
+++ b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmEventIT.java
@@ -0,0 +1,142 @@
+package ca.uhn.fhir.jpa.mdm.interceptor;
+
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
+import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
+import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
+import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
+import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
+import ca.uhn.fhir.mdm.api.IMdmLink;
+import ca.uhn.fhir.mdm.api.MdmLinkEvent;
+import ca.uhn.fhir.mdm.api.MdmLinkJson;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import ca.uhn.fhir.mdm.model.MdmTransactionContext;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage;
+import org.hibernate.dialect.H2Dialect;
+import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
+import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
+import org.hibernate.search.engine.cfg.BackendSettings;
+import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Practitioner;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
+import org.slf4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Primary;
+import org.springframework.data.domain.Example;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.TestPropertySource;
+
+import java.util.List;
+import java.util.Properties;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.slf4j.LoggerFactory.getLogger;
+
+@TestPropertySource(properties = {
+ "mdm.prevent_multiple_eids=false"
+})
+@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
+@ContextConfiguration(classes = {MdmHelperConfig.class})
+public class MdmEventIT extends BaseMdmR4Test {
+
+ private static final Logger ourLog = getLogger(MdmEventIT.class);
+
+ @RegisterExtension
+ @Autowired
+ public MdmHelperR4 myMdmHelper;
+ @Autowired
+ private IdHelperService myIdHelperService;
+
+ @Test
+ public void testDuplicateLinkChangeEvent() throws InterruptedException {
+ Patient patient1 = buildJanePatient();
+ addExternalEID(patient1, "eid-1");
+ addExternalEID(patient1, "eid-11");
+ myMdmHelper.createWithLatch(patient1);
+
+ Patient patient2 = buildPaulPatient();
+ addExternalEID(patient2, "eid-2");
+ addExternalEID(patient2, "eid-22");
+ myMdmHelper.createWithLatch(patient2);
+
+ Patient patient3 = buildPaulPatient();
+ addExternalEID(patient3, "eid-22");
+ myMdmHelper.createWithLatch(patient3);
+
+ patient2.getIdentifier().clear();
+ addExternalEID(patient2, "eid-11");
+ addExternalEID(patient2, "eid-22");
+
+ myMdmHelper.updateWithLatch(patient2);
+
+ MdmLinkEvent linkChangeEvent = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(MdmLinkEvent.class);
+ assertNotNull(linkChangeEvent);
+
+ ourLog.info("Got event: {}", linkChangeEvent);
+
+ long expectTwoPossibleMatchesForPatientTwo = linkChangeEvent.getMdmLinks()
+ .stream()
+ .filter(l -> l.getSourceId().equals(patient2.getIdElement().toVersionless().getValueAsString()) && l.getMatchResult() == MdmMatchResultEnum.POSSIBLE_MATCH)
+ .count();
+ assertEquals(2, expectTwoPossibleMatchesForPatientTwo);
+
+ long expectOnePossibleDuplicate = linkChangeEvent.getMdmLinks()
+ .stream()
+ .filter(l -> l.getMatchResult() == MdmMatchResultEnum.POSSIBLE_DUPLICATE)
+ .count();
+ assertEquals(1, expectOnePossibleDuplicate);
+
+ List mdmLinkEvent = linkChangeEvent.getMdmLinks();
+ assertEquals(3, mdmLinkEvent.size());
+ }
+
+ @Test
+ public void testCreateLinkChangeEvent() throws InterruptedException {
+ Practitioner pr = buildPractitionerWithNameAndId("Young", "AC-DC");
+ myMdmHelper.createWithLatch(pr);
+
+ ResourceOperationMessage resourceOperationMessage = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(ResourceOperationMessage.class);
+ assertNotNull(resourceOperationMessage);
+ assertEquals(pr.getId(), resourceOperationMessage.getId());
+
+ MdmLink link = getLinkByTargetId(pr);
+
+ MdmLinkEvent linkChangeEvent = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(MdmLinkEvent.class);
+ assertNotNull(linkChangeEvent);
+
+ assertEquals(1, linkChangeEvent.getMdmLinks().size());
+ MdmLinkJson l = linkChangeEvent.getMdmLinks().get(0);
+ assertEquals(link.getGoldenResourcePid(), new IdDt(l.getGoldenResourceId()).getIdPartAsLong());
+ assertEquals(link.getSourcePid(), new IdDt(l.getSourceId()).getIdPartAsLong());
+ }
+
+ private MdmLink getLinkByTargetId(IBaseResource theResource) {
+ MdmLink example = new MdmLink();
+ example.setSourcePid(theResource.getIdElement().getIdPartAsLong());
+ return myMdmLinkDao.findAll(Example.of(example)).get(0);
+ }
+
+ @Test
+ public void testUpdateLinkChangeEvent() throws InterruptedException {
+ Patient patient1 = addExternalEID(buildJanePatient(), "eid-1");
+ myMdmHelper.createWithLatch(patient1);
+
+ MdmLinkEvent linkChangeEvent = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(MdmLinkEvent.class);
+ assertNotNull(linkChangeEvent);
+ assertEquals(1, linkChangeEvent.getMdmLinks().size());
+
+ MdmLinkJson link = linkChangeEvent.getMdmLinks().get(0);
+ assertEquals(patient1.getIdElement().toVersionless().getValueAsString(), link.getSourceId());
+ assertEquals(getLinkByTargetId(patient1).getGoldenResourcePid(), new IdDt(link.getGoldenResourceId()).getIdPartAsLong());
+ assertEquals(MdmMatchResultEnum.MATCH, link.getMatchResult());
+ }
+
+}
diff --git a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmStorageInterceptorIT.java b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmStorageInterceptorIT.java
index c722b23dab2..4509b9052da 100644
--- a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmStorageInterceptorIT.java
+++ b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmStorageInterceptorIT.java
@@ -8,7 +8,9 @@ import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.model.CanonicalEID;
+import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
+import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.ReferenceParam;
@@ -26,6 +28,7 @@ import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Example;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
@@ -67,6 +70,12 @@ public class MdmStorageInterceptorIT extends BaseMdmR4Test {
assertLinkCount(1);
}
+ private MdmLink getLinkByTargetId(IBaseResource theResource) {
+ MdmLink example = new MdmLink();
+ example.setSourcePid(theResource.getIdElement().getIdPartAsLong());
+ return myMdmLinkDao.findAll(Example.of(example)).get(0);
+ }
+
@Test
public void testSearchExpandingInterceptorWorks() {
SearchParameterMap subject = new SearchParameterMap("subject", new ReferenceParam("Patient/123").setMdmExpand(true)).setLoadSynchronous(true);
diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeToDriverTypeToSqlType.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeToDriverTypeToSqlType.java
deleted file mode 100644
index 0523592f4d2..00000000000
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeToDriverTypeToSqlType.java
+++ /dev/null
@@ -1,124 +0,0 @@
-package ca.uhn.fhir.jpa.migrate.taskdef;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server - Migration
- * %%
- * Copyright (C) 2014 - 2021 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
-
-import java.util.HashMap;
-import java.util.Map;
-
-public class ColumnTypeToDriverTypeToSqlType {
- Map> myColumnTypeToDriverTypeToSqlType = new HashMap<>();
-
- public Map> getColumnTypeToDriverTypeToSqlType() {
- return myColumnTypeToDriverTypeToSqlType;
- }
-
- public ColumnTypeToDriverTypeToSqlType() {
- setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.H2_EMBEDDED, "integer");
- setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.DERBY_EMBEDDED, "integer");
- setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.MARIADB_10_1, "integer");
- setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.MYSQL_5_7, "integer");
- setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.MSSQL_2012, "int");
- setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.ORACLE_12C, "number(10,0)");
- setColumnType(ColumnTypeEnum.INT, DriverTypeEnum.POSTGRES_9_4, "int4");
-
- setColumnType(ColumnTypeEnum.FLOAT, DriverTypeEnum.H2_EMBEDDED, "float");
- setColumnType(ColumnTypeEnum.FLOAT, DriverTypeEnum.DERBY_EMBEDDED, "float");
- setColumnType(ColumnTypeEnum.FLOAT, DriverTypeEnum.MARIADB_10_1, "float");
- setColumnType(ColumnTypeEnum.FLOAT, DriverTypeEnum.MYSQL_5_7, "float");
- setColumnType(ColumnTypeEnum.FLOAT, DriverTypeEnum.MSSQL_2012, "float");
- setColumnType(ColumnTypeEnum.FLOAT, DriverTypeEnum.ORACLE_12C, "float");
- setColumnType(ColumnTypeEnum.FLOAT, DriverTypeEnum.POSTGRES_9_4, "float");
-
- setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.H2_EMBEDDED, "double");
- setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.DERBY_EMBEDDED, "double");
- setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.MARIADB_10_1, "double precision");
- setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.MYSQL_5_7, "double precision");
- setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.MSSQL_2012, "double precision");
- setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.ORACLE_12C, "double precision");
- setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.POSTGRES_9_4, "float8");
-
- setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.H2_EMBEDDED, "bigint");
- setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.DERBY_EMBEDDED, "bigint");
- setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MARIADB_10_1, "bigint");
- setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MYSQL_5_7, "bigint");
- setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MSSQL_2012, "bigint");
- setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.ORACLE_12C, "number(19,0)");
- setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.POSTGRES_9_4, "int8");
-
- setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.H2_EMBEDDED, "varchar(?)");
- setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.DERBY_EMBEDDED, "varchar(?)");
- setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.MARIADB_10_1, "varchar(?)");
- setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.MYSQL_5_7, "varchar(?)");
- setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.MSSQL_2012, "varchar(?)");
- setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.ORACLE_12C, "varchar2(?)");
- setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.POSTGRES_9_4, "varchar(?)");
-
- setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.H2_EMBEDDED, "timestamp");
- setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.DERBY_EMBEDDED, "timestamp");
- setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.MARIADB_10_1, "datetime(6)");
- setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.MYSQL_5_7, "datetime(6)");
- setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.MSSQL_2012, "datetime2");
- setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.ORACLE_12C, "timestamp");
- setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.POSTGRES_9_4, "timestamp");
-
- setColumnType(ColumnTypeEnum.DATE_ONLY, DriverTypeEnum.H2_EMBEDDED, "date");
- setColumnType(ColumnTypeEnum.DATE_ONLY, DriverTypeEnum.DERBY_EMBEDDED, "date");
- setColumnType(ColumnTypeEnum.DATE_ONLY, DriverTypeEnum.MARIADB_10_1, "date");
- setColumnType(ColumnTypeEnum.DATE_ONLY, DriverTypeEnum.MYSQL_5_7, "date");
- setColumnType(ColumnTypeEnum.DATE_ONLY, DriverTypeEnum.MSSQL_2012, "date");
- setColumnType(ColumnTypeEnum.DATE_ONLY, DriverTypeEnum.ORACLE_12C, "date");
- setColumnType(ColumnTypeEnum.DATE_ONLY, DriverTypeEnum.POSTGRES_9_4, "date");
-
- setColumnType(ColumnTypeEnum.BOOLEAN, DriverTypeEnum.H2_EMBEDDED, "boolean");
- setColumnType(ColumnTypeEnum.BOOLEAN, DriverTypeEnum.DERBY_EMBEDDED, "boolean");
- setColumnType(ColumnTypeEnum.BOOLEAN, DriverTypeEnum.MSSQL_2012, "bit");
- setColumnType(ColumnTypeEnum.BOOLEAN, DriverTypeEnum.MARIADB_10_1, "bit");
- setColumnType(ColumnTypeEnum.BOOLEAN, DriverTypeEnum.ORACLE_12C, "number(1,0)");
- setColumnType(ColumnTypeEnum.BOOLEAN, DriverTypeEnum.POSTGRES_9_4, "boolean");
- setColumnType(ColumnTypeEnum.BOOLEAN, DriverTypeEnum.MYSQL_5_7, "bit");
-
- setColumnType(ColumnTypeEnum.BLOB, DriverTypeEnum.H2_EMBEDDED, "blob");
- setColumnType(ColumnTypeEnum.BLOB, DriverTypeEnum.DERBY_EMBEDDED, "blob");
- setColumnType(ColumnTypeEnum.BLOB, DriverTypeEnum.MARIADB_10_1, "longblob");
- setColumnType(ColumnTypeEnum.BLOB, DriverTypeEnum.MYSQL_5_7, "longblob");
- setColumnType(ColumnTypeEnum.BLOB, DriverTypeEnum.ORACLE_12C, "blob");
- setColumnType(ColumnTypeEnum.BLOB, DriverTypeEnum.POSTGRES_9_4, "oid");
- setColumnType(ColumnTypeEnum.BLOB, DriverTypeEnum.MSSQL_2012, "varbinary(MAX)");
-
- setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.H2_EMBEDDED, "clob");
- setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.DERBY_EMBEDDED, "clob(100000)");
- setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.MARIADB_10_1, "longtext");
- setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.MYSQL_5_7, "longtext");
- setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.ORACLE_12C, "clob");
- setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.POSTGRES_9_4, "text");
- setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.MSSQL_2012, "varchar(MAX)");
- }
-
- private void setColumnType(ColumnTypeEnum theColumnType, DriverTypeEnum theDriverType, String theColumnTypeSql) {
- Map columnSqlType = myColumnTypeToDriverTypeToSqlType.computeIfAbsent(theColumnType, k -> new HashMap<>());
- if (columnSqlType.containsKey(theDriverType)) {
- throw new IllegalStateException("Duplicate key: " + theDriverType);
- }
- columnSqlType.put(theDriverType, theColumnTypeSql);
- }
-}
diff --git a/hapi-fhir-jpaserver-model/pom.xml b/hapi-fhir-jpaserver-model/pom.xml
index d37223e4c57..075066b6827 100644
--- a/hapi-fhir-jpaserver-model/pom.xml
+++ b/hapi-fhir-jpaserver-model/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE5-SNAPSHOT
+ 5.6.0-PRE6-SNAPSHOT
../hapi-deployable-pom/pom.xml
@@ -33,6 +33,11 @@