Merge pull request #1942 from jamesagnew/im_20200619_mariadb_expand_valueset_fix
Im 20200619 mariadb expand valueset fix
This commit is contained in:
commit
ceeff0ccf0
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@ -38,7 +38,7 @@ import java.io.Serializable;
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* Note about the CONCAT function below- We need a primary key (an @Id) column
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* because hibernate won't allow the view the function without it, but
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*/
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"SELECT CONCAT(vsc.PID, CONCAT(' ', vscd.PID)) AS PID, " +
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"SELECT CONCAT_WS(' ', vsc.PID, vscd.PID) AS PID, " +
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" vsc.PID AS CONCEPT_PID, " +
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" vsc.VALUESET_PID AS CONCEPT_VALUESET_PID, " +
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" vsc.VALUESET_ORDER AS CONCEPT_VALUESET_ORDER, " +
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@ -75,6 +75,10 @@ public class ElasticsearchHibernatePropertiesBuilder {
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theProperties.put("hibernate.search.default." + ElasticsearchEnvironment.INDEX_MANAGEMENT_WAIT_TIMEOUT, Long.toString(myIndexManagementWaitTimeoutMillis));
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theProperties.put("hibernate.search.default." + ElasticsearchEnvironment.REQUIRED_INDEX_STATUS, myRequiredIndexStatus.getElasticsearchString());
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// Need the mapping to be dynamic because of terminology indexes.
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theProperties.put("hibernate.search.default.elasticsearch.dynamic_mapping", "true");
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// Only for unit tests
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theProperties.put("hibernate.search.default." + ElasticsearchEnvironment.REFRESH_AFTER_WRITE, Boolean.toString(myDebugRefreshAfterWrite));
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theProperties.put("hibernate.search." + ElasticsearchEnvironment.LOG_JSON_PRETTY_PRINTING, Boolean.toString(myDebugPrettyPrintJsonLog));
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@ -51,7 +51,7 @@ public class ElasticsearchMappingProvider implements ElasticsearchAnalysisDefini
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builder.analyzer("standardAnalyzer").withTokenizer("standard").withTokenFilters("lowercase");
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builder.analyzer("exactAnalyzer").withTokenizer("standard");
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builder.analyzer("exactAnalyzer").withTokenizer("keyword");
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builder.analyzer("conceptParentPidsAnalyzer").withTokenizer("whitespace");
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@ -0,0 +1,157 @@
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package ca.uhn.fhir.jpa.dao.r4;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
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import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
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import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
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import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
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import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticSearch;
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import ca.uhn.fhir.jpa.dao.BaseJpaTest;
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import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
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import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
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import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
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import ca.uhn.fhir.util.TestUtil;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent;
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import org.mockito.Answers;
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import org.mockito.Mock;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.test.context.ContextConfiguration;
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import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
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import org.springframework.transaction.PlatformTransactionManager;
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import java.util.Set;
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import java.util.stream.Collectors;
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import static org.hamcrest.Matchers.containsInAnyOrder;
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import static org.junit.Assert.assertThat;
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@RunWith(SpringJUnit4ClassRunner.class)
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@ContextConfiguration(classes = {TestR4ConfigWithElasticSearch.class})
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public class FhirResourceDaoR4TerminologyElasticsearchIT extends BaseJpaTest {
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public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
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public static final String URL_MY_VALUE_SET = "http://example.com/my_value_set";
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4TerminologyElasticsearchIT.class);
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@Autowired
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protected DaoConfig myDaoConfig;
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@Autowired
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@Qualifier("myCodeSystemDaoR4")
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protected IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
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@Autowired
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protected IResourceTableDao myResourceTableDao;
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@Autowired
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protected ITermCodeSystemStorageSvc myTermCodeSystemStorageSvc;
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@Autowired
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@Qualifier("myValueSetDaoR4")
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protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
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@Autowired
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FhirContext myFhirContext;
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@Autowired
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PlatformTransactionManager myTxManager;
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@Autowired
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private IFhirSystemDao mySystemDao;
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@Autowired
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private IResourceReindexingSvc myResourceReindexingSvc;
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@Autowired
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private ISearchCoordinatorSvc mySearchCoordinatorSvc;
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@Autowired
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private ISearchParamRegistry mySearchParamRegistry;
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@Autowired
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private IBulkDataExportSvc myBulkDataExportSvc;
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@Mock(answer = Answers.RETURNS_DEEP_STUBS)
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protected ServletRequestDetails mySrd;
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@Test
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public void testExpandWithIncludeContainingDashesInInclude() {
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CodeSystem codeSystem = new CodeSystem();
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codeSystem.setUrl(URL_MY_CODE_SYSTEM);
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codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
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IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
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ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
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TermCodeSystemVersion cs = new TermCodeSystemVersion();
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cs.setResource(table);
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TermConcept concept;
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concept = new TermConcept(cs, "LA1111-2");
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cs.getConcepts().add(concept);
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concept = new TermConcept(cs, "LA2222-2");
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cs.getConcepts().add(concept);
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concept = new TermConcept(cs, "LA3333-2");
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cs.getConcepts().add(concept);
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concept = new TermConcept(cs, "LA1122-2");
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cs.getConcepts().add(concept);
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concept = new TermConcept(cs, "LA1133-2");
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cs.getConcepts().add(concept);
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concept = new TermConcept(cs, "LA4444-2");
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cs.getConcepts().add(concept);
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concept = new TermConcept(cs, "LA9999-7");
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cs.getConcepts().add(concept);
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myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
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ValueSet valueSet = new ValueSet();
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valueSet.setUrl(URL_MY_VALUE_SET);
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valueSet.getCompose()
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.addInclude()
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.setSystem(codeSystem.getUrl())
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.addConcept(new ConceptReferenceComponent().setCode("LA2222-2"))
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.addConcept(new ConceptReferenceComponent().setCode("LA1122-2"));
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IIdType vsId = myValueSetDao.create(valueSet, mySrd).getId().toUnqualifiedVersionless();
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ValueSet expansion = myValueSetDao.expand(vsId, null, null);
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Set<String> codes = expansion
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.getExpansion()
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.getContains()
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.stream()
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.map(ValueSet.ValueSetExpansionContainsComponent::getCode)
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.collect(Collectors.toSet());
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ourLog.info("Codes: {}", codes);
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assertThat(codes, containsInAnyOrder("LA2222-2", "LA1122-2"));
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}
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@Override
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protected FhirContext getContext() {
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return myFhirContext;
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}
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@Override
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protected PlatformTransactionManager getTxManager() {
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return myTxManager;
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}
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@After
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public void afterPurgeDatabase() {
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purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
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}
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@AfterClass
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public static void afterClassClearContext() {
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TestUtil.clearAllStaticFieldsForUnitTest();
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}
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}
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@ -0,0 +1,216 @@
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package ca.uhn.fhir.jpa.term;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
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import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
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import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
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import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
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import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticSearch;
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import ca.uhn.fhir.jpa.dao.BaseJpaTest;
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import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
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import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
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import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
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import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.junit.After;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import org.mockito.Answers;
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import org.mockito.Mock;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.test.context.ContextConfiguration;
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import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
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import org.springframework.transaction.PlatformTransactionManager;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.fail;
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import static org.mockito.ArgumentMatchers.anyCollection;
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import static org.mockito.ArgumentMatchers.anyString;
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import static org.mockito.ArgumentMatchers.nullable;
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import static org.mockito.Mockito.times;
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import static org.mockito.Mockito.verify;
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import static org.mockito.Mockito.when;
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@RunWith(SpringJUnit4ClassRunner.class)
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@ContextConfiguration(classes = {TestR4ConfigWithElasticSearch.class})
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public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest {
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@Autowired
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protected DaoConfig myDaoConfig;
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@Autowired
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@Qualifier("myCodeSystemDaoR4")
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protected IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
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@Autowired
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protected IResourceTableDao myResourceTableDao;
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@Autowired
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protected ITermCodeSystemStorageSvc myTermCodeSystemStorageSvc;
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@Autowired
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@Qualifier("myValueSetDaoR4")
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protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
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@Autowired
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protected ITermReadSvcR4 myTermSvc;
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@Autowired
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protected ITermDeferredStorageSvc myTerminologyDeferredStorageSvc;
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@Autowired
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FhirContext myFhirContext;
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@Autowired
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PlatformTransactionManager myTxManager;
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@Autowired
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private IFhirSystemDao mySystemDao;
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@Autowired
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private IResourceReindexingSvc myResourceReindexingSvc;
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@Autowired
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private ISearchCoordinatorSvc mySearchCoordinatorSvc;
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@Autowired
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private ISearchParamRegistry mySearchParamRegistry;
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@Autowired
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private IBulkDataExportSvc myBulkDataExportSvc;
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@Mock
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private IValueSetConceptAccumulator myValueSetCodeAccumulator;
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@Mock(answer = Answers.RETURNS_DEEP_STUBS)
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protected ServletRequestDetails mySrd;
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protected static final String CS_URL = "http://example.com/my_code_system";
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@After
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public void after() {
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myDaoConfig.setMaximumExpansionSize(DaoConfig.DEFAULT_MAX_EXPANSION_SIZE);
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}
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@After
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public void afterPurgeDatabase() {
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purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
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}
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void createCodeSystem() {
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CodeSystem codeSystem = new CodeSystem();
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codeSystem.setUrl(CS_URL);
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codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
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codeSystem.setName("SYSTEM NAME");
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codeSystem.setVersion("SYSTEM VERSION");
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IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
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ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
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TermCodeSystemVersion cs = new TermCodeSystemVersion();
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cs.setResource(table);
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TermConcept parent;
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parent = new TermConcept(cs, "ParentWithNoChildrenA");
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cs.getConcepts().add(parent);
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parent = new TermConcept(cs, "ParentWithNoChildrenB");
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cs.getConcepts().add(parent);
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parent = new TermConcept(cs, "ParentWithNoChildrenC");
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cs.getConcepts().add(parent);
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TermConcept parentA = new TermConcept(cs, "ParentA");
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cs.getConcepts().add(parentA);
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TermConcept childAA = new TermConcept(cs, "childAA");
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parentA.addChild(childAA, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
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TermConcept childAAA = new TermConcept(cs, "childAAA");
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childAAA.addPropertyString("propA", "valueAAA");
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childAAA.addPropertyString("propB", "foo");
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childAA.addChild(childAAA, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
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TermConcept childAAB = new TermConcept(cs, "childAAB");
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childAAB.addPropertyString("propA", "valueAAB");
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childAAB.addPropertyString("propB", "foo");
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childAAB.addDesignation()
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.setUseSystem("D1S")
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.setUseCode("D1C")
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.setUseDisplay("D1D")
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.setValue("D1V");
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childAA.addChild(childAAB, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
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TermConcept childAB = new TermConcept(cs, "childAB");
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parentA.addChild(childAB, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
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TermConcept parentB = new TermConcept(cs, "ParentB");
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cs.getConcepts().add(parentB);
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myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
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}
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@Test
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public void testExpandValueSetInMemoryRespectsMaxSize() {
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createCodeSystem();
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// Add lots more codes
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CustomTerminologySet additions = new CustomTerminologySet();
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for (int i = 0; i < 100; i++) {
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additions.addRootConcept("CODE" + i, "Display " + i);
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}
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myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd(CS_URL, additions);
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// Codes available exceeds the max
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myDaoConfig.setMaximumExpansionSize(50);
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ValueSet vs = new ValueSet();
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ValueSet.ConceptSetComponent include = vs.getCompose().addInclude();
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include.setSystem(CS_URL);
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try {
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myTermSvc.expandValueSet(null, vs);
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fail();
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} catch (InternalErrorException e) {
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assertEquals("Expansion of ValueSet produced too many codes (maximum 50) - Operation aborted!", e.getMessage());
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}
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// Increase the max so it won't exceed
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myDaoConfig.setMaximumExpansionSize(150);
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vs = new ValueSet();
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include = vs.getCompose().addInclude();
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include.setSystem(CS_URL);
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ValueSet outcome = myTermSvc.expandValueSet(null, vs);
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assertEquals(109, outcome.getExpansion().getContains().size());
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}
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@Test
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public void testExpandValueSetWithValueSetCodeAccumulator() {
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createCodeSystem();
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when(myValueSetCodeAccumulator.getCapacityRemaining()).thenReturn(100);
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ValueSet vs = new ValueSet();
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ValueSet.ConceptSetComponent include = vs.getCompose().addInclude();
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include.setSystem(CS_URL);
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myTermSvc.expandValueSet(null, vs, myValueSetCodeAccumulator);
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verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
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}
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@Override
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protected FhirContext getContext() {
|
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return myFhirContext;
|
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}
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||||
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@Override
|
||||
protected PlatformTransactionManager getTxManager() {
|
||||
return myTxManager;
|
||||
}
|
||||
}
|
|
@ -54,11 +54,11 @@ public class AddColumnTask extends BaseTableColumnTypeTask {
|
|||
String sql;
|
||||
switch (getDriverType()) {
|
||||
case MYSQL_5_7:
|
||||
case MARIADB_10_1:
|
||||
// Quote the column name as "SYSTEM" is a reserved word in MySQL
|
||||
sql = "alter table " + getTableName() + " add column `" + getColumnName() + "` " + typeStatement;
|
||||
break;
|
||||
case DERBY_EMBEDDED:
|
||||
case MARIADB_10_1:
|
||||
case POSTGRES_9_4:
|
||||
sql = "alter table " + getTableName() + " add column " + getColumnName() + " " + typeStatement;
|
||||
break;
|
||||
|
|
|
@ -26,6 +26,7 @@ import org.intellij.lang.annotations.Language;
|
|||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.sql.Driver;
|
||||
import java.sql.SQLException;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
|
@ -52,8 +53,8 @@ public class DropColumnTask extends BaseTableColumnTask {
|
|||
return;
|
||||
}
|
||||
|
||||
if(getDriverType().equals(DriverTypeEnum.MYSQL_5_7)) {
|
||||
// Some DBs such as MYSQL require that foreign keys depending on the column be dropped before the column itself is dropped.
|
||||
if(getDriverType().equals(DriverTypeEnum.MYSQL_5_7) || getDriverType().equals(DriverTypeEnum.MARIADB_10_1)) {
|
||||
// Some DBs such as MYSQL and Maria DB require that foreign keys depending on the column be dropped before the column itself is dropped.
|
||||
logInfo(ourLog, "Dropping any foreign keys on table {} depending on column {}", getTableName(), getColumnName());
|
||||
Set<String> foreignKeys = JdbcUtils.getForeignKeysForColumn(getConnectionProperties(), getColumnName(), getTableName());
|
||||
if(foreignKeys != null) {
|
||||
|
|
|
@ -101,10 +101,10 @@ public class DropForeignKeyTask extends BaseTableTask {
|
|||
List<String> sqls = new ArrayList<>();
|
||||
switch (theDriverType) {
|
||||
case MYSQL_5_7:
|
||||
case MARIADB_10_1:
|
||||
// Lousy MYQL....
|
||||
sqls.add("alter table " + theTableName + " drop foreign key " + theConstraintName);
|
||||
break;
|
||||
case MARIADB_10_1:
|
||||
case POSTGRES_9_4:
|
||||
case DERBY_EMBEDDED:
|
||||
case H2_EMBEDDED:
|
||||
|
|
|
@ -107,12 +107,10 @@ public class DropIndexTask extends BaseTableTask {
|
|||
// Drop constraint
|
||||
switch (theDriverType) {
|
||||
case MYSQL_5_7:
|
||||
case MARIADB_10_1:
|
||||
// Need to quote the index name as the word "PRIMARY" is reserved in MySQL
|
||||
sql.add("alter table " + theTableName + " drop index `" + theIndexName + "`");
|
||||
break;
|
||||
case MARIADB_10_1:
|
||||
sql.add("alter table " + theTableName + " drop index " + theIndexName);
|
||||
break;
|
||||
case H2_EMBEDDED:
|
||||
sql.add("drop index " + theIndexName);
|
||||
break;
|
||||
|
|
|
@ -139,10 +139,8 @@ public class RenameColumnTask extends BaseTableTask {
|
|||
case DERBY_EMBEDDED:
|
||||
sql = "RENAME COLUMN " + getTableName() + "." + myOldName + " TO " + myNewName;
|
||||
break;
|
||||
case MARIADB_10_1:
|
||||
sql = "ALTER TABLE " + getTableName() + " CHANGE COLUMN " + myOldName + " TO " + myNewName;
|
||||
break;
|
||||
case MYSQL_5_7:
|
||||
case MARIADB_10_1:
|
||||
// Quote the column names as "SYSTEM" is a reserved word in MySQL
|
||||
sql = "ALTER TABLE " + getTableName() + " CHANGE COLUMN `" + myOldName + "` `" + myNewName + "` " + theExistingType + " " + theExistingNotNull;
|
||||
break;
|
||||
|
|
|
@ -110,10 +110,10 @@ public class RenameIndexTask extends BaseTableTask {
|
|||
// Drop constraint
|
||||
switch (theDriverType) {
|
||||
case MYSQL_5_7:
|
||||
case MARIADB_10_1:
|
||||
// Quote the index names as "PRIMARY" is a reserved word in MySQL
|
||||
sql.add("rename index `" + theOldIndexName + "` to `" + theNewIndexName + "`");
|
||||
break;
|
||||
case MARIADB_10_1:
|
||||
case DERBY_EMBEDDED:
|
||||
sql.add("rename index " + theOldIndexName + " to " + theNewIndexName);
|
||||
break;
|
||||
|
|
|
@ -27,7 +27,7 @@ public class RenameColumnTaskDbSpecificTest {
|
|||
|
||||
@Test
|
||||
public void testBuildSqlStatementForMariaDB() {
|
||||
assertEquals("ALTER TABLE SOMETABLE CHANGE COLUMN myTextCol TO TEXTCOL", createRenameColumnSql(DriverTypeEnum.MARIADB_10_1));
|
||||
assertEquals("ALTER TABLE SOMETABLE CHANGE COLUMN `myTextCol` `TEXTCOL` integer null", createRenameColumnSql(DriverTypeEnum.MARIADB_10_1));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
Loading…
Reference in New Issue