Rename columns in code mapping
This commit is contained in:
James Agnew
parent
6e20b53979
commit
2a6436af23
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@ -60,6 +60,7 @@ public class TermCodeSystemVersion implements Serializable {
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@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_CODESYSVER_CS_ID"))
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private TermCodeSystem myCodeSystem;
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@SuppressWarnings("unused")
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@OneToOne(mappedBy = "myCurrentVersion", optional = true)
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private TermCodeSystem myCodeSystemHavingThisVersionAsCurrentVersionIfAny;
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@ -56,8 +56,13 @@ public class TermConceptMapGroup implements Serializable {
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@OneToMany(mappedBy = "myConceptMapGroup")
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private List<TermConceptMapGroupElement> myConceptMapGroupElements;
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@Column(name= "CONCEPT_MAP_URL", length = 200, nullable = true)
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private String myConceptMapUrl;
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@Column(name= "SOURCE_VS", length = 200, nullable = true)
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private String mySourceValueSet;
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@Column(name= "TARGET_VS", length = 200, nullable = true)
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private String myTargetValueSet;
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public TermConceptMap getConceptMap() {
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@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.entity;
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* #L%
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*/
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import org.apache.commons.lang3.Validate;
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import org.apache.commons.lang3.builder.EqualsBuilder;
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import org.apache.commons.lang3.builder.HashCodeBuilder;
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import org.apache.commons.lang3.builder.ToStringBuilder;
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@ -54,9 +55,16 @@ public class TermConceptMapGroupElement implements Serializable {
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@OneToMany(mappedBy = "myConceptMapGroupElement")
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private List<TermConceptMapGroupElementTarget> myConceptMapGroupElementTargets;
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@Column(name = "CONCEPT_MAP_URL", length = 200)
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private String myConceptMapUrl;
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@Column(name = "SYSTEM_URL", length = 200)
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private String mySystem;
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@Column(name = "SYSTEM_VERSION", length = 200)
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private String mySystemVersion;
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@Column(name = "VALUESET_URL", length = 200)
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private String myValueSet;
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public String getCode() {
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@ -64,6 +72,7 @@ public class TermConceptMapGroupElement implements Serializable {
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}
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public void setCode(String theCode) {
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Validate.notBlank(theCode, "theCode must not be blank");
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myCode = theCode;
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}
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@ -54,9 +54,13 @@ public class TermConceptMapGroupElementTarget implements Serializable {
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@Column(name = "TARGET_EQUIVALENCE", length = 50)
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private ConceptMapEquivalence myEquivalence;
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@Column(name = "CONCEPT_MAP_URL", length = 200)
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private String myConceptMapUrl;
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@Column(name = "SYSTEM_URL", length = 200)
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private String mySystem;
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@Column(name = "SYSTEM_VERSION", length = 200)
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private String mySystemVersion;
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@Column(name = "VALUESET_URL", length = 200)
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private String myValueSet;
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public String getCode() {
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@ -1288,6 +1288,11 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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if (group.hasElement()) {
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TermConceptMapGroupElement termConceptMapGroupElement;
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for (ConceptMap.SourceElementComponent element : group.getElement()) {
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if (isBlank(element.getCode())) {
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// FIXME: JA - send this to an interceptor message so it can be
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// output
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continue;
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}
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termConceptMapGroupElement = new TermConceptMapGroupElement();
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termConceptMapGroupElement.setConceptMapGroup(termConceptMapGroup);
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termConceptMapGroupElement.setCode(element.getCode());
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@ -27,12 +27,12 @@ import com.google.common.reflect.ClassPath.ClassInfo;
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import org.apache.commons.lang3.Validate;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.InstantType;
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import org.hl7.fhir.r4.model.Patient;
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import javax.persistence.*;
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import java.io.IOException;
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import java.lang.reflect.AnnotatedElement;
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import java.lang.reflect.Field;
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import java.lang.reflect.Modifier;
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import java.util.Date;
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import java.util.HashSet;
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import java.util.Set;
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@ -54,6 +54,7 @@ public class TestUtil {
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/**
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* This is really only useful for unit tests, do not call otherwise
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*/
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@SuppressWarnings("UnstableApiUsage")
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public static void scanEntities(String packageName) throws IOException, ClassNotFoundException {
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ImmutableSet<ClassInfo> classes = ClassPath.from(TestUtil.class.getClassLoader()).getTopLevelClasses(packageName);
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Set<String> names = new HashSet<String>();
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@ -80,6 +81,10 @@ public class TestUtil {
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scan(theClazz, theNames, theIsSuperClass);
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for (Field nextField : theClazz.getDeclaredFields()) {
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if (Modifier.isStatic(nextField.getModifiers())) {
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continue;
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}
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ourLog.info(" * Scanning field: {}", nextField.getName());
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scan(nextField, theNames, theIsSuperClass);
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@ -90,6 +95,22 @@ public class TestUtil {
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}
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}
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boolean isTransient = nextField.getAnnotation(Transient.class) != null;
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if (!isTransient) {
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boolean hasColumn = nextField.getAnnotation(Column.class) != null;
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boolean hasJoinColumn = nextField.getAnnotation(JoinColumn.class) != null;
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OneToMany oneToMany = nextField.getAnnotation(OneToMany.class);
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OneToOne oneToOne = nextField.getAnnotation(OneToOne.class);
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boolean isOtherSideOfOneToManyMapping = oneToMany != null && isNotBlank(oneToMany.mappedBy());
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boolean isOtherSideOfOneToOneMapping = oneToOne != null && isNotBlank(oneToOne.mappedBy());
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Validate.isTrue(
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hasColumn ||
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hasJoinColumn ||
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isOtherSideOfOneToManyMapping ||
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isOtherSideOfOneToOneMapping, "Non-transient has no @Column or @JoinColumn: " + nextField);
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}
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}
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if (theClazz.getSuperclass().equals(Object.class)) {
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@ -3,10 +3,10 @@ package ca.uhn.fhir.jpa.config;
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import ca.uhn.fhir.jpa.util.TestUtil;
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import org.junit.Test;
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public class IdentifierLengthTest {
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public class JpaEntityTest {
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@Test
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public void testIdentifierLength() throws Exception {
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public void testEntitiesAreValid() throws Exception {
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TestUtil.scanEntities(ca.uhn.fhir.jpa.model.entity.ResourceTable.class.getPackage().getName());
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TestUtil.scanEntities(ca.uhn.fhir.jpa.entity.TermConcept.class.getPackage().getName());
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}
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@ -6,7 +6,6 @@ import ca.uhn.fhir.jpa.config.TestR4Config;
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import ca.uhn.fhir.jpa.dao.*;
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import ca.uhn.fhir.jpa.dao.data.*;
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import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
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import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
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import ca.uhn.fhir.jpa.interceptor.PerformanceTracingLoggingInterceptor;
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import ca.uhn.fhir.jpa.model.entity.ModelConfig;
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import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
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@ -34,6 +33,7 @@ import ca.uhn.fhir.util.TestUtil;
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import ca.uhn.fhir.util.UrlUtil;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.ValidationResult;
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import com.google.common.base.Charsets;
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import org.apache.commons.io.IOUtils;
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import org.hibernate.search.jpa.FullTextEntityManager;
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import org.hibernate.search.jpa.Search;
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@ -294,11 +294,13 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
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protected ICacheWarmingSvc myCacheWarmingSvc;
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@Autowired
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protected SubscriptionRegistry mySubscriptionRegistry;
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protected IServerInterceptor myInterceptor;
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@Autowired
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private JpaValidationSupportChainR4 myJpaValidationSupportChainR4;
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private PerformanceTracingLoggingInterceptor myPerformanceTracingLoggingInterceptor;
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private List<Object> mySystemInterceptors;
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protected IServerInterceptor myInterceptor;
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@Autowired
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private DaoRegistry myDaoRegistry;
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@After()
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public void afterCleanupDao() {
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@ -402,6 +404,19 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
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}
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}
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@SuppressWarnings("unchecked")
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protected void upload(String theClasspath) throws IOException {
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String resource = loadResource(theClasspath);
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IParser parser = EncodingEnum.detectEncoding(resource).newParser(myFhirCtx);
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IBaseResource resourceParsed = parser.parseResource(resource);
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IFhirResourceDao dao = myDaoRegistry.getResourceDao(resourceParsed.getIdElement().getResourceType());
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dao.update(resourceParsed);
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}
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protected String loadResource(String theClasspath) throws IOException {
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return IOUtils.toString(FhirResourceDaoR4ValidateTest.class.getResourceAsStream(theClasspath), Charsets.UTF_8);
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}
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@AfterClass
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public static void afterClassClearContextBaseJpaR4Test() {
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@ -3,12 +3,13 @@ package ca.uhn.fhir.jpa.dao.r4;
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import ca.uhn.fhir.jpa.term.TranslationMatch;
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import ca.uhn.fhir.jpa.term.TranslationRequest;
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import ca.uhn.fhir.jpa.term.TranslationResult;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
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import ca.uhn.fhir.util.TestUtil;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.ConceptMap;
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import org.hl7.fhir.r4.model.*;
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import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
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import org.hl7.fhir.r4.model.UriType;
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import org.junit.AfterClass;
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import org.junit.Before;
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import org.junit.Test;
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@ -19,6 +20,9 @@ import org.springframework.transaction.annotation.Transactional;
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import org.springframework.transaction.support.TransactionCallbackWithoutResult;
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import org.springframework.transaction.support.TransactionTemplate;
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import java.io.IOException;
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import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.*;
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public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
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@ -1037,6 +1041,24 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
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});
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}
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@Test
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public void testUploadAndApplyR4DemoConceptMap() throws IOException {
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upload("/r4/ConceptMap-icd-sct.xml");
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CodeableConcept sourceCode = new CodeableConcept();
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sourceCode.addCoding()
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.setSystem("http://snomed.info/sct")
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.setCode("263204007");
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TranslationRequest request = new TranslationRequest();
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request.setCodeableConcept(sourceCode);
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request.setTargetSystem(new UriType("http://hl7.org/fhir/sid/icd-10-us"));
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TranslationResult outcome = myConceptMapDao.translate(request, mySrd);
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assertEquals("S52.209A", outcome.getMatches().get(1).getConcept().getCode());
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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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@ -1,8 +1,6 @@
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package ca.uhn.fhir.jpa.dao.r4;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.ValidationModeEnum;
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@ -13,7 +11,6 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.StopWatch;
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import ca.uhn.fhir.util.TestUtil;
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import ca.uhn.fhir.validation.IValidatorModule;
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import com.google.common.base.Charsets;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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@ -417,21 +414,6 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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}
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}
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@SuppressWarnings("unchecked")
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private void upload(String theClasspath) throws IOException {
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String resource = loadResource(theClasspath);
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IBaseResource resourceParsed = myFhirCtx.newJsonParser().parseResource(resource);
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IFhirResourceDao dao = myDaoRegistry.getResourceDao(resourceParsed.getIdElement().getResourceType());
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dao.update(resourceParsed);
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}
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private String loadResource(String theClasspath) throws IOException {
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return IOUtils.toString(FhirResourceDaoR4ValidateTest.class.getResourceAsStream(theClasspath), Charsets.UTF_8);
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}
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@Autowired
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private DaoRegistry myDaoRegistry;
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private IBaseResource findResourceByIdInBundle(Bundle vss, String name) {
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IBaseResource retVal = null;
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for (BundleEntryComponent next : vss.getEntry()) {
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@ -0,0 +1,57 @@
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<ConceptMap xmlns="http://hl7.org/fhir">
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<id value="sct-icd"/>
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<url value="http://hl7.org/fhir/ConceptMap/103"/>
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<identifier>
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<system value="urn:ietf:rfc:3986"/>
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<value value="urn:uuid:53cd62ee-033e-414c-9f58-3ca97b5ffc3b"/>
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</identifier>
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<version value="4.0.0"/>
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<name value="SNOMED CT to ICD-10-CM mappings for fracture of ulna"/>
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<status value="draft"/>
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<experimental value="true"/>
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<date value="2012-06-13"/>
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<publisher value="HL7, Inc"/>
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<contact>
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<name value="FHIR project team (example)"/>
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<telecom>
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<system value="url"/>
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<value value="http://hl7.org/fhir"/>
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</telecom>
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</contact>
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<description value="Example rule-based mappings between SNOMED CT to ICD-10-CM for fracture of ulna"/>
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<jurisdiction>
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<coding>
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<system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
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<code value="840"/>
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<display value="United States of America"/>
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</coding>
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</jurisdiction>
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<purpose value="Show example rule based mappings"/>
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<copyright value="Creative Commons 0"/>
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<sourceCanonical value="http://snomed.info/id?fhir_vs"/>
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<targetCanonical value="http://hl7.org/fhir/sid/icd-10-us"/>
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<group>
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<source value="http://snomed.info/sct"/>
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<sourceVersion value="March 2015 US Edition"/>
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<target value="http://hl7.org/fhir/sid/icd-10-us"/>
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<targetVersion value="2015"/>
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<element>
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<code value="263204007"/>
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<target>
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<code value="S52.209A"/>
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<equivalence value="narrower"/>
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<comment value="The target mapping to ICD-10-CM is narrower, since additional patient data on the encounter
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(initial vs. subsequent) and fracture type is required for a valid ICD-10-CM mapping."/>
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</target>
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</element>
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<element>
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<target>
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<code value="S52.209D"/>
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<equivalence value="narrower"/>
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<comment value="The target mapping to ICD-10-CM is narrower, since additional patient data on the encounter
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(initial vs. subsequent), fracture type and healing (for subsequent encounter) is required
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for a valid ICD-10-CM mapping."/>
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</target>
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</element>
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</group>
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</ConceptMap>
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@ -30,6 +30,8 @@ import java.util.ArrayList;
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import java.util.List;
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import java.util.Objects;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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public class Migrator {
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private static final Logger ourLog = LoggerFactory.getLogger(Migrator.class);
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@ -83,7 +85,12 @@ public class Migrator {
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try {
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next.execute();
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} catch (SQLException e) {
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throw new InternalErrorException("Failure executing task \"" + next.getDescription() + "\", aborting! Cause: " + e.toString(), e);
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String description = next.getDescription();
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if (isBlank(description)) {
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description = next.getClass().getSimpleName();
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}
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String prefix = "Failure executing task \"" + description + "\", aborting! Cause: ";
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throw new InternalErrorException(prefix + e.toString(), e);
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}
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myChangesCount += next.getChangesCount();
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@ -30,6 +30,7 @@ public abstract class BaseTableTask<T extends BaseTableTask> extends BaseTask {
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}
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public T setTableName(String theTableName) {
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Validate.notBlank(theTableName);
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myTableName = theTableName;
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return (T) this;
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}
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@ -0,0 +1,67 @@
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package ca.uhn.fhir.jpa.migrate.taskdef;
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import ca.uhn.fhir.jpa.migrate.JdbcUtils;
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import org.apache.commons.lang3.Validate;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.sql.SQLException;
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import java.util.Set;
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public class RenameColumnTask extends BaseTableTask<RenameColumnTask> {
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private static final Logger ourLog = LoggerFactory.getLogger(RenameColumnTask.class);
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private String myOldName;
|
||||
private String myNewName;
|
||||
|
||||
public void setOldName(String theOldName) {
|
||||
Validate.notBlank(theOldName);
|
||||
myOldName = theOldName;
|
||||
}
|
||||
|
||||
public void setNewName(String theNewName) {
|
||||
Validate.notBlank(theNewName);
|
||||
myNewName = theNewName;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void execute() throws SQLException {
|
||||
Set<String> columnNames = JdbcUtils.getColumnNames(getConnectionProperties(), getTableName());
|
||||
boolean haveOldName = columnNames.contains(myOldName.toUpperCase());
|
||||
boolean haveNewName = columnNames.contains(myNewName.toUpperCase());
|
||||
if (haveOldName && haveNewName) {
|
||||
throw new SQLException("Can not rename " + getTableName() + "." + myOldName + " to " + myNewName + " because both columns exist!");
|
||||
}
|
||||
if (!haveOldName && !haveNewName) {
|
||||
throw new SQLException("Can not rename " + getTableName() + "." + myOldName + " to " + myNewName + " because neither column exists!");
|
||||
}
|
||||
if (haveNewName) {
|
||||
ourLog.info("Column {} already exists on table {} - No action performed", myNewName, getTableName());
|
||||
return;
|
||||
}
|
||||
|
||||
String sql = "";
|
||||
switch (getDriverType()) {
|
||||
case DERBY_EMBEDDED:
|
||||
sql = "RENAME COLUMN " + getTableName() + "." + myOldName + " TO " + myNewName;
|
||||
break;
|
||||
case MARIADB_10_1:
|
||||
case MYSQL_5_7:
|
||||
sql = "ALTER TABLE " + getTableName() + " CHANGE COLUMN " + myOldName + " TO " + myNewName;
|
||||
break;
|
||||
case POSTGRES_9_4:
|
||||
sql = "ALTER TABLE " + getTableName() + " RENAME COLUMN " + myOldName + " TO " + myNewName;
|
||||
break;
|
||||
case MSSQL_2012:
|
||||
sql = "sp_rename '" + getTableName() + "." + myOldName + "', '" + myNewName + "', 'COLUMN'";
|
||||
break;
|
||||
case ORACLE_12C:
|
||||
sql = "ALTER TABLE " + getTableName() + " RENAME COLUMN " + myOldName + " TO " + myNewName;
|
||||
break;
|
||||
}
|
||||
|
||||
ourLog.info("Renaming column {} on table {} to {}", myOldName, getTableName(), myNewName);
|
||||
executeSql(getTableName(), sql);
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate.tasks;
|
|||
* 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.
|
||||
|
|
@ -20,13 +20,13 @@ package ca.uhn.fhir.jpa.migrate.tasks;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.jpa.model.entity.*;
|
||||
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.AddColumnTask;
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.ArbitrarySqlTask;
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableColumnTypeTask;
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.CalculateHashesTask;
|
||||
import ca.uhn.fhir.jpa.migrate.tasks.api.BaseMigrationTasks;
|
||||
import ca.uhn.fhir.jpa.model.entity.*;
|
||||
import ca.uhn.fhir.util.VersionEnum;
|
||||
|
||||
import java.util.Arrays;
|
||||
|
|
@ -53,8 +53,29 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
|
|||
init340();
|
||||
init350();
|
||||
init360();
|
||||
init400();
|
||||
}
|
||||
|
||||
private void init400() {
|
||||
Builder version = forVersion(VersionEnum.V4_0_0);
|
||||
|
||||
version.onTable("TRM_CONCEPT_MAP_GROUP")
|
||||
.renameColumn("myConceptMapUrl", "CONCEPT_MAP_URL")
|
||||
.renameColumn("mySourceValueSet", "SOURCE_VS")
|
||||
.renameColumn("myTargetValueSet", "TARGET_VS");
|
||||
|
||||
version.onTable("TRM_CONCEPT_MAP_GRP_ELEMENT")
|
||||
.renameColumn("myConceptMapUrl", "CONCEPT_MAP_URL")
|
||||
.renameColumn("mySystem", "SYSTEM_URL")
|
||||
.renameColumn("mySystemVersion", "SYSTEM_VERSION")
|
||||
.renameColumn("myValueSet", "VALUESET_URL");
|
||||
|
||||
version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
|
||||
.renameColumn("myConceptMapUrl", "CONCEPT_MAP_URL")
|
||||
.renameColumn("mySystem", "SYSTEM_URL")
|
||||
.renameColumn("mySystemVersion", "SYSTEM_VERSION")
|
||||
.renameColumn("myValueSet", "VALUESET_URL");
|
||||
}
|
||||
|
||||
|
||||
private void init360() {
|
||||
|
|
|
|||
|
|
@ -167,6 +167,15 @@ public class BaseMigrationTasks<T extends Enum> {
|
|||
return new BuilderAddForeignKey(theForeignKeyName);
|
||||
}
|
||||
|
||||
public BuilderWithTableName renameColumn(String theOldName, String theNewName) {
|
||||
RenameColumnTask task = new RenameColumnTask();
|
||||
task.setTableName(myTableName);
|
||||
task.setOldName(theOldName);
|
||||
task.setNewName(theNewName);
|
||||
addTask(task);
|
||||
return this;
|
||||
}
|
||||
|
||||
public class BuilderAddIndexWithName {
|
||||
private final String myIndexName;
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,87 @@
|
|||
package ca.uhn.fhir.jpa.migrate.taskdef;
|
||||
|
||||
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import org.junit.Test;
|
||||
|
||||
import java.sql.SQLException;
|
||||
|
||||
import static org.hamcrest.Matchers.contains;
|
||||
import static org.hamcrest.Matchers.containsInAnyOrder;
|
||||
import static org.junit.Assert.*;
|
||||
|
||||
public class RenameColumnTaskTest extends BaseTest {
|
||||
|
||||
@Test
|
||||
public void testColumnAlreadyExists() throws SQLException {
|
||||
executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
|
||||
|
||||
RenameColumnTask task = new RenameColumnTask();
|
||||
task.setTableName("SOMETABLE");
|
||||
task.setDescription("Drop an index");
|
||||
task.setOldName("myTextCol");
|
||||
task.setNewName("TEXTCOL");
|
||||
getMigrator().addTask(task);
|
||||
|
||||
getMigrator().migrate();
|
||||
|
||||
assertThat(JdbcUtils.getColumnNames(getConnectionProperties(), "SOMETABLE"), containsInAnyOrder("PID", "TEXTCOL"));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testColumnDoesntAlreadyExist() throws SQLException {
|
||||
executeSql("create table SOMETABLE (PID bigint not null, myTextCol varchar(255))");
|
||||
|
||||
RenameColumnTask task = new RenameColumnTask();
|
||||
task.setTableName("SOMETABLE");
|
||||
task.setDescription("Drop an index");
|
||||
task.setOldName("myTextCol");
|
||||
task.setNewName("TEXTCOL");
|
||||
getMigrator().addTask(task);
|
||||
|
||||
getMigrator().migrate();
|
||||
|
||||
assertThat(JdbcUtils.getColumnNames(getConnectionProperties(), "SOMETABLE"), containsInAnyOrder("PID", "TEXTCOL"));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testNeitherColumnExists() throws SQLException {
|
||||
executeSql("create table SOMETABLE (PID bigint not null)");
|
||||
|
||||
RenameColumnTask task = new RenameColumnTask();
|
||||
task.setTableName("SOMETABLE");
|
||||
task.setOldName("myTextCol");
|
||||
task.setNewName("TEXTCOL");
|
||||
getMigrator().addTask(task);
|
||||
|
||||
try {
|
||||
getMigrator().migrate();
|
||||
fail();
|
||||
} catch (InternalErrorException e) {
|
||||
assertEquals("Failure executing task \"RenameColumnTask\", aborting! Cause: java.sql.SQLException: Can not rename SOMETABLE.myTextCol to TEXTCOL because neither column exists!", e.getMessage());
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBothColumnsExist() throws SQLException {
|
||||
executeSql("create table SOMETABLE (PID bigint not null, PID2 bigint)");
|
||||
|
||||
RenameColumnTask task = new RenameColumnTask();
|
||||
task.setTableName("SOMETABLE");
|
||||
task.setOldName("PID");
|
||||
task.setNewName("PID2");
|
||||
getMigrator().addTask(task);
|
||||
|
||||
try {
|
||||
getMigrator().migrate();
|
||||
fail();
|
||||
} catch (InternalErrorException e) {
|
||||
assertEquals("Failure executing task \"RenameColumnTask\", aborting! Cause: java.sql.SQLException: Can not rename SOMETABLE.PID to PID2 because both columns exist!", e.getMessage());
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -24,14 +24,20 @@ import ca.uhn.fhir.context.ConfigurationException;
|
|||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.RuntimeResourceDefinition;
|
||||
import ca.uhn.fhir.context.RuntimeSearchParam;
|
||||
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.model.entity.ModelConfig;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
|
||||
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
|
||||
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
|
||||
import ca.uhn.fhir.parser.DataFormatException;
|
||||
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.hl7.fhir.instance.model.api.*;
|
||||
import org.hl7.fhir.r4.model.CanonicalType;
|
||||
|
|
@ -58,6 +64,8 @@ public class ResourceLinkExtractor {
|
|||
private ISearchParamRegistry mySearchParamRegistry;
|
||||
@Autowired
|
||||
private ISearchParamExtractor mySearchParamExtractor;
|
||||
@Autowired
|
||||
private IInterceptorBroadcaster myInterceptorBroadcaster;
|
||||
|
||||
public void extractResourceLinks(ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, boolean theFailOnInvalidReference, RequestDetails theRequest) {
|
||||
String resourceType = theEntity.getResourceType();
|
||||
|
|
@ -111,7 +119,17 @@ public class ResourceLinkExtractor {
|
|||
}
|
||||
|
||||
if (nextObject instanceof CanonicalType) {
|
||||
nextObject = new Reference(((CanonicalType) nextObject).getValueAsString());
|
||||
StorageProcessingMessage msg = new StorageProcessingMessage();
|
||||
msg.setMessage("Ignoring canonical reference (indexing canonidcal is not yet supported): " + ((CanonicalType) nextObject).getValueAsString());
|
||||
HookParams params = new HookParams()
|
||||
.add(RequestDetails.class, theRequest)
|
||||
.addIfMatchesType(ServletRequestDetails.class, theRequest)
|
||||
.add(StorageProcessingMessage.class, msg);
|
||||
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.JPA_PERFTRACE_WARNING, params);
|
||||
|
||||
// nextObject = new Reference(((CanonicalType) nextObject).getValueAsString());
|
||||
// wasCanonical = true;
|
||||
return;
|
||||
}
|
||||
|
||||
IIdType nextId;
|
||||
|
|
|
|||
|
|
@ -225,6 +225,20 @@
|
|||
returned that includes the resource ID and the version ID for the deleted
|
||||
resource.
|
||||
</action>
|
||||
<action type="fix">
|
||||
A number of columns in the JPA Terminology Services ConceptMap tables were not
|
||||
explicitly annotated with @Column, so the DB columns that were generated had
|
||||
Java ugly field names as their SQL column names. These have been renamed, and
|
||||
entries in the JPA migrator tool have been added for anyone upgrading.
|
||||
</action>
|
||||
<action type="fix">
|
||||
Field values with a datatype of <![CDATA[<code>canonical</code>]]> were indexed as
|
||||
though they were explicit resource references by the JPA server. This led to
|
||||
errors about external references not being supported when uploading various
|
||||
resources (e.g. Questionnaires with HL7-defined ValueSet references). This has
|
||||
been corrected. Note that at this time, we do not index canonical references
|
||||
at all (as we were previously doing it incorrectly). This will be improved soon.
|
||||
</action>
|
||||
</release>
|
||||
<release version="3.8.0" date="2019-05-30" description="Hippo">
|
||||
<action type="fix">
|
||||
|
|
|
|||
Loading…
Reference in New Issue