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Delete dead code now that Hapi has merged. (#4946)

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michaelabuckley 2023-06-01 20:27:14 -04:00 committed by GitHub
parent 83411e585b
commit 9838f8a19a
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3 changed files with 23 additions and 75 deletions
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3
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/TagDefinition.java
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@ -38,7 +38,6 @@ import javax.persistence.OneToMany;
import javax.persistence.SequenceGenerator; import javax.persistence.SequenceGenerator;
import javax.persistence.Table; import javax.persistence.Table;
import javax.persistence.Transient; import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;
import java.io.Serializable; import java.io.Serializable;
import java.util.Collection; import java.util.Collection;
@ -159,7 +158,7 @@ public class TagDefinition implements Serializable {
/** /**
* Warning - this is nullable, while IBaseCoding getUserSelected isn't. * Warning - this is nullable, while IBaseCoding getUserSelected isn't.
* wipmb maybe rename? * todo maybe rename?
*/ */
public Boolean getUserSelected() { public Boolean getUserSelected() {
return myUserSelected; return myUserSelected;

44
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4MetaTest.java
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@ -9,7 +9,6 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails; import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.param.TokenParam; import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.system.HapiTestSystemProperties; import ca.uhn.fhir.system.HapiTestSystemProperties;
import ch.qos.logback.classic.Level;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle; import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Coding; import org.hl7.fhir.r4.model.Coding;
@ -30,10 +29,10 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService; import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors; import java.util.concurrent.Executors;
import java.util.concurrent.Future; import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import static ca.uhn.fhir.rest.api.Constants.PARAM_TAG; import static ca.uhn.fhir.rest.api.Constants.PARAM_TAG;
@ -69,9 +68,9 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
Patient patient = new Patient(); Patient patient = new Patient();
patient.setActive(true); patient.setActive(true);
patient.getMeta().addExtension("http://foo", new StringType("hello")); patient.getMeta().addExtension("http://foo", new StringType("hello"));
IIdType id = myPatientDao.create(patient).getId(); IIdType id = myPatientDao.create(patient, mySrd).getId();
patient = myPatientDao.read(id); patient = myPatientDao.read(id, mySrd);
assertTrue(patient.getActive()); assertTrue(patient.getActive());
assertEquals(1, patient.getMeta().getExtensionsByUrl("http://foo").size()); assertEquals(1, patient.getMeta().getExtensionsByUrl("http://foo").size());
assertEquals("hello", patient.getMeta().getExtensionByUrl("http://foo").getValueAsPrimitive().getValueAsString()); assertEquals("hello", patient.getMeta().getExtensionByUrl("http://foo").getValueAsPrimitive().getValueAsString());
@ -94,9 +93,9 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
Bundle bundle = new Bundle(); Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.COLLECTION); bundle.setType(Bundle.BundleType.COLLECTION);
bundle.addEntry().setResource(patient); bundle.addEntry().setResource(patient);
IIdType id = myBundleDao.create(bundle).getId(); IIdType id = myBundleDao.create(bundle, mySrd).getId();
bundle = myBundleDao.read(id); bundle = myBundleDao.read(id, mySrd);
ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle)); ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
patient = (Patient) bundle.getEntryFirstRep().getResource(); patient = (Patient) bundle.getEntryFirstRep().getResource();
assertTrue(patient.getActive()); assertTrue(patient.getActive());
@ -116,7 +115,7 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
patient.getMeta().addProfile("http://foo"); patient.getMeta().addProfile("http://foo");
patient.getMeta().addTag("http://tag", "value", "the tag"); patient.getMeta().addTag("http://tag", "value", "the tag");
patient.getMeta().addSecurity("http://tag", "security", "the tag"); patient.getMeta().addSecurity("http://tag", "security", "the tag");
IIdType id = myPatientDao.create(patient).getId(); IIdType id = myPatientDao.create(patient, mySrd).getId();
Meta meta = new Meta(); Meta meta = new Meta();
meta.addProfile("http://foo"); meta.addProfile("http://foo");
@ -124,7 +123,7 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
meta.addSecurity("http://tag", "security", "the tag"); meta.addSecurity("http://tag", "security", "the tag");
myPatientDao.metaDeleteOperation(id, meta, mySrd); myPatientDao.metaDeleteOperation(id, meta, mySrd);
patient = myPatientDao.read(id); patient = myPatientDao.read(id, mySrd);
assertThat(patient.getMeta().getProfile(), empty()); assertThat(patient.getMeta().getProfile(), empty());
assertThat(patient.getMeta().getTag(), empty()); assertThat(patient.getMeta().getTag(), empty());
assertThat(patient.getMeta().getSecurity(), empty()); assertThat(patient.getMeta().getSecurity(), empty());
@ -136,20 +135,20 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
Patient patient1 = new Patient(); Patient patient1 = new Patient();
patient1.getMeta().addTag().setSystem("http://foo").setCode("bar"); patient1.getMeta().addTag().setSystem("http://foo").setCode("bar");
patient1.setActive(true); patient1.setActive(true);
IIdType pid1 = myPatientDao.create(patient1).getId(); IIdType pid1 = myPatientDao.create(patient1, mySrd).getId();
Patient patient2 = new Patient(); Patient patient2 = new Patient();
patient2.getMeta().addSecurity().setSystem("http://foo").setCode("bar"); patient2.getMeta().addSecurity().setSystem("http://foo").setCode("bar");
patient2.setActive(true); patient2.setActive(true);
IIdType pid2 = myPatientDao.create(patient2).getId(); IIdType pid2 = myPatientDao.create(patient2, mySrd).getId();
patient1 = myPatientDao.read(pid1); patient1 = myPatientDao.read(pid1, mySrd);
assertEquals(1, patient1.getMeta().getTag().size()); assertEquals(1, patient1.getMeta().getTag().size());
assertEquals(0, patient1.getMeta().getSecurity().size()); assertEquals(0, patient1.getMeta().getSecurity().size());
assertEquals("http://foo", patient1.getMeta().getTagFirstRep().getSystem()); assertEquals("http://foo", patient1.getMeta().getTagFirstRep().getSystem());
assertEquals("bar", patient1.getMeta().getTagFirstRep().getCode()); assertEquals("bar", patient1.getMeta().getTagFirstRep().getCode());
patient2 = myPatientDao.read(pid2); patient2 = myPatientDao.read(pid2, mySrd);
assertEquals(0, patient2.getMeta().getTag().size()); assertEquals(0, patient2.getMeta().getTag().size());
assertEquals(1, patient2.getMeta().getSecurity().size()); assertEquals(1, patient2.getMeta().getSecurity().size());
assertEquals("http://foo", patient2.getMeta().getSecurityFirstRep().getSystem()); assertEquals("http://foo", patient2.getMeta().getSecurityFirstRep().getSystem());
@ -158,7 +157,6 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
/** /**
* Make sure round-trips with tags don't add a userSelected property. * Make sure round-trips with tags don't add a userSelected property.
* wipmb tag userSelected test
* Verify https://github.com/hapifhir/hapi-fhir/issues/4819 * Verify https://github.com/hapifhir/hapi-fhir/issues/4819
*/ */
@Test @Test
@ -167,10 +165,10 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
Patient patient1 = new Patient(); Patient patient1 = new Patient();
patient1.getMeta().addTag().setSystem("http://foo").setCode("bar"); patient1.getMeta().addTag().setSystem("http://foo").setCode("bar");
patient1.setActive(true); patient1.setActive(true);
IIdType pid1 = myPatientDao.create(patient1).getId(); IIdType pid1 = myPatientDao.create(patient1, mySrd).getId();
// when // when
var patientReadback = myPatientDao.read(pid1); var patientReadback = myPatientDao.read(pid1, mySrd);
ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patientReadback)); ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patientReadback));
// then // then
@ -339,9 +337,9 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
} }
@Disabled // TODO JA: This test fails regularly, need to get a dedicated connection pool for tag creation @Disabled("This test fails regularly, need to get a dedicated connection pool for tag creation") // TODO JA:
@Test @Test
public void testConcurrentAddTag() throws ExecutionException, InterruptedException { public void testConcurrentAddTag() {
ExecutorService pool = Executors.newFixedThreadPool(10); ExecutorService pool = Executors.newFixedThreadPool(10);
@ -353,7 +351,7 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
patient.getMeta().addTag().setSystem("http://foo").setCode("bar"); patient.getMeta().addTag().setSystem("http://foo").setCode("bar");
patient.setActive(true); patient.setActive(true);
ourLog.info("creating patient {}", index); ourLog.info("creating patient {}", index);
myPatientDao.create(patient); myPatientDao.create(patient, mySrd);
}; };
ourLog.info("Submitting task {}...", index); ourLog.info("Submitting task {}...", index);
Future<?> future = pool.submit(task); Future<?> future = pool.submit(task);
@ -366,20 +364,18 @@ public class FhirResourceDaoR4MetaTest extends BaseJpaR4Test {
for (Future<?> next : futures) { for (Future<?> next : futures) {
try { try {
ourLog.info("Getting future {}", count); ourLog.info("Getting future {}", count);
next.get(); next.get(5, TimeUnit.SECONDS);
} catch (Exception e) { } catch (Exception e) {
ourLog.error("Failure", e); ourLog.error("Failure", e);
fail(e.toString()); fail(e.toString());
} }
} }
runInTransaction(() -> { runInTransaction(() -> ourLog.info("Tag definitions:\n * {}", myTagDefinitionDao.findAll().stream().map(TagDefinition::toString).collect(Collectors.joining("\n * "))));
ourLog.info("Tag definitions:\n * {}", myTagDefinitionDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
});
IBundleProvider bundle = myPatientDao.search(SearchParameterMap.newSynchronous()); IBundleProvider bundle = myPatientDao.search(SearchParameterMap.newSynchronous(), mySrd);
assertEquals(10, bundle.sizeOrThrowNpe()); assertEquals(10, bundle.sizeOrThrowNpe());
IBundleProvider tagBundle = myPatientDao.search(SearchParameterMap.newSynchronous(PARAM_TAG, new TokenParam("http://foo", "bar"))); IBundleProvider tagBundle = myPatientDao.search(SearchParameterMap.newSynchronous(PARAM_TAG, new TokenParam("http://foo", "bar")), mySrd);
assertEquals(10, tagBundle.sizeOrThrowNpe()); assertEquals(10, tagBundle.sizeOrThrowNpe());
} }

51
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobPersistence.java
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@ -26,7 +26,6 @@ import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.batch2.model.WorkChunk; import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.batch2.model.WorkChunkCreateEvent; import ca.uhn.fhir.batch2.model.WorkChunkCreateEvent;
import ca.uhn.fhir.batch2.models.JobInstanceFetchRequest; import ca.uhn.fhir.batch2.models.JobInstanceFetchRequest;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.ToStringBuilder; import org.apache.commons.lang3.builder.ToStringBuilder;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
@ -115,21 +114,6 @@ public interface IJobPersistence extends IWorkChunkPersistence {
// on implementations @Transactional(propagation = Propagation.REQUIRES_NEW) // on implementations @Transactional(propagation = Propagation.REQUIRES_NEW)
boolean canAdvanceInstanceToNextStep(String theInstanceId, String theCurrentStepId); boolean canAdvanceInstanceToNextStep(String theInstanceId, String theCurrentStepId);
/**
* Fetches all chunks for a given instance, without loading the data
*
* TODO MB this seems to only be used by tests. Can we use the iterator instead?
* @param theInstanceId The instance ID
* @param thePageSize The page size
* @param thePageIndex The page index
*/
default List<WorkChunk> fetchWorkChunksWithoutData(String theInstanceId, int thePageSize, int thePageIndex) {
// for back-compat
// wipmb delete after merge.
Validate.isTrue(false, "Dead path");
return null;
}
/** /**
* Fetch all chunks for a given instance. * Fetch all chunks for a given instance.
* *
@ -137,24 +121,14 @@ public interface IJobPersistence extends IWorkChunkPersistence {
* @param theWithData - whether or not to include the data * @param theWithData - whether or not to include the data
* @return - an iterator for fetching work chunks * @return - an iterator for fetching work chunks
*/ */
default Iterator<WorkChunk> fetchAllWorkChunksIterator(String theInstanceId, boolean theWithData) { Iterator<WorkChunk> fetchAllWorkChunksIterator(String theInstanceId, boolean theWithData);
// for back-compat
// wipmb delete after merge.
Validate.isTrue(false, "Dead path");
return null;
}
/** /**
* Fetch all chunks with data for a given instance for a given step id - read-only. * Fetch all chunks with data for a given instance for a given step id - read-only.
* *
* @return - a stream for fetching work chunks * @return - a stream for fetching work chunks
*/ */
default Stream<WorkChunk> fetchAllWorkChunksForStepStream(String theInstanceId, String theStepId) { Stream<WorkChunk> fetchAllWorkChunksForStepStream(String theInstanceId, String theStepId);
// for back-compat
// wipmb delete after merge.
Validate.isTrue(false, "Dead path");
return null;
}
/** /**
* Callback to update a JobInstance within a locked transaction. * Callback to update a JobInstance within a locked transaction.
@ -201,27 +175,6 @@ public interface IJobPersistence extends IWorkChunkPersistence {
// on implementations @Transactional(propagation = Propagation.REQUIRES_NEW) // on implementations @Transactional(propagation = Propagation.REQUIRES_NEW)
void deleteChunksAndMarkInstanceAsChunksPurged(String theInstanceId); void deleteChunksAndMarkInstanceAsChunksPurged(String theInstanceId);
/**
* Marks an instance as being complete
*
* @param theInstanceId The instance ID
* @return true if the instance status changed
*/
default boolean markInstanceAsCompleted(String theInstanceId) {
// for back-compat
// wipmb delete after merge.
Validate.isTrue(false, "Dead path");
return false;
}
default boolean markInstanceAsStatus(String theInstance, StatusEnum theStatusEnum) {
// wipmb delete after merge.
// for back-compat
Validate.isTrue(false, "Dead path");
return false;
}
@Transactional(propagation = Propagation.MANDATORY) @Transactional(propagation = Propagation.MANDATORY)
boolean markInstanceAsStatusWhenStatusIn(String theInstance, StatusEnum theStatusEnum, Set<StatusEnum> thePriorStates); boolean markInstanceAsStatusWhenStatusIn(String theInstance, StatusEnum theStatusEnum, Set<StatusEnum> thePriorStates);