mirror of
https://github.com/hapifhir/hapi-fhir.git
synced 2025-02-22 05:35:45 +00:00
Work on loinc mapping
This commit is contained in:
James Agnew
parent
611ee457cb
commit
5a653aeb20
@ -1,4 +1,22 @@
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Database migration:
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update table TRM_CODESYSTEM_VER drop column RES_VERSION_ID;
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TODO:
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In answer lists, figure out what to do with externally defined lists
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Comments for Loinc:
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Answer Lists
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- Per the notes, there is no way in FHIR currently to map answer lists to
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codes based on context. For this reason, I am ignoring any entries in
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LoincAnswerListLink_Beta_1.csv where the "ApplicableContext" context is
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not empty. Is this correct?
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Parts
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- Only parts with a status of "ACTIVE" are being imported, any others are
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ignored.
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- The PartTypeName (e.g. "ADJUSTMENT") is ignored as there is no corresponding
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property in loinc.xml
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- PartDisplayName is not mapped
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@ -91,7 +91,7 @@ ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number pr
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ca.uhn.fhir.jpa.provider.BaseJpaProvider.cantCombintAtAndSince=Unable to combine _at and _since parameters for history operation
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ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}
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ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
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ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
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ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}
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ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
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ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
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@ -110,12 +110,7 @@ public class BaseDstu3Config extends BaseConfig {
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}
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@Bean(autowire = Autowire.BY_TYPE)
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public IHapiTerminologySvc terminologyService() {
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return new HapiTerminologySvcImpl();
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}
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@Bean(autowire = Autowire.BY_TYPE)
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public IHapiTerminologySvcDstu3 terminologyServiceDstu3() {
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public IHapiTerminologySvcDstu3 terminologyService() {
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return new HapiTerminologySvcDstu3();
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}
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@ -65,6 +65,18 @@ public class BaseR4Config extends BaseConfig {
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return retVal;
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}
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@Bean(name = "myGraphQLProvider")
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@Lazy
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public GraphQLProvider graphQLProvider() {
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return new GraphQLProvider(fhirContextR4(), validationSupportChainR4(), graphqlStorageServices());
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}
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@Bean
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@Lazy
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public GraphQLEngine.IGraphQLStorageServices graphqlStorageServices() {
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return new JpaStorageServices();
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}
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@Bean(name = "myInstanceValidatorR4")
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@Lazy
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public IValidatorModule instanceValidatorR4() {
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@ -86,12 +98,6 @@ public class BaseR4Config extends BaseConfig {
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return searchDao;
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}
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@Bean(name = "myGraphQLProvider")
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@Lazy
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public GraphQLProvider graphQLProvider() {
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return new GraphQLProvider(fhirContextR4(), validationSupportChainR4(), graphqlStorageServices());
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}
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@Bean(autowire = Autowire.BY_TYPE)
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public SearchParamExtractorR4 searchParamExtractor() {
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return new SearchParamExtractorR4();
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@ -122,7 +128,7 @@ public class BaseR4Config extends BaseConfig {
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}
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@Bean(autowire = Autowire.BY_TYPE)
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public IHapiTerminologySvcR4 terminologyServiceR4() {
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public IHapiTerminologySvcR4 terminologyService() {
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return new HapiTerminologySvcR4();
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}
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@ -139,10 +145,4 @@ public class BaseR4Config extends BaseConfig {
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return new JpaValidationSupportChainR4();
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}
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@Bean
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@Lazy
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public GraphQLEngine.IGraphQLStorageServices graphqlStorageServices() {
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return new JpaStorageServices();
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}
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}
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@ -229,6 +229,16 @@ public class TermConcept implements Serializable {
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return null;
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}
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public List<String> getProperties(String thePropertyName) {
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List<String> retVal = new ArrayList<>();
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for (TermConceptProperty next : getProperties()) {
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if (thePropertyName.equals(next.getKey())) {
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retVal.add(next.getValue());
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}
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}
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return retVal;
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}
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@Override
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public int hashCode() {
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HashCodeBuilder b = new HashCodeBuilder();
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@ -20,7 +20,8 @@ package ca.uhn.fhir.jpa.entity;
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* #L%
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*/
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import org.hibernate.search.annotations.Field;
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import org.apache.commons.lang3.builder.ToStringBuilder;
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import org.apache.commons.lang3.builder.ToStringStyle;
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import org.hibernate.validator.constraints.NotBlank;
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import javax.persistence.*;
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@ -37,38 +38,43 @@ public class TermConceptProperty implements Serializable {
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@ManyToOne
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@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CONCEPT"))
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private TermConcept myConcept;
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@Id()
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@SequenceGenerator(name = "SEQ_CONCEPT_PROP_PID", sequenceName = "SEQ_CONCEPT_PROP_PID")
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@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PROP_PID")
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@Column(name = "PID")
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private Long myId;
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@Column(name="PROP_KEY", length=200, nullable=false)
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@Column(name = "PROP_KEY", length = 200, nullable = false)
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@NotBlank
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private String myKey;
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@Column(name="PROP_VAL", length=200, nullable=true)
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@Column(name = "PROP_VAL", length = 200, nullable = true)
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private String myValue;
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public String getKey() {
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return myKey;
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}
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public String getValue() {
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return myValue;
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}
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public void setConcept(TermConcept theConcept) {
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myConcept = theConcept;
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}
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public void setKey(String theKey) {
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myKey = theKey;
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}
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public String getValue() {
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return myValue;
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}
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public void setValue(String theValue) {
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myValue = theValue;
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}
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public void setConcept(TermConcept theConcept) {
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myConcept = theConcept;
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}
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@Override
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public String toString() {
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return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
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.append("key", myKey)
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.append("value", myValue)
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.toString();
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}
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}
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@ -23,12 +23,14 @@ 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.dao.BaseHapiFhirDao;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
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import ca.uhn.fhir.jpa.entity.*;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.ObjectUtil;
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@ -44,6 +46,8 @@ import org.hibernate.search.jpa.FullTextEntityManager;
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import org.hibernate.search.jpa.FullTextQuery;
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import org.hibernate.search.query.dsl.BooleanJunction;
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import org.hibernate.search.query.dsl.QueryBuilder;
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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.ValueSet;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.data.domain.Page;
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@ -65,8 +69,8 @@ import java.util.concurrent.TimeUnit;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public class HapiTerminologySvcImpl implements IHapiTerminologySvc {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HapiTerminologySvcImpl.class);
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public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiTerminologySvcImpl.class);
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private static final Object PLACEHOLDER_OBJECT = new Object();
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private static boolean ourForceSaveDeferredAlwaysForUnitTest;
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@Autowired
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@ -93,7 +97,7 @@ public class HapiTerminologySvcImpl implements IHapiTerminologySvc {
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@Autowired
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private PlatformTransactionManager myTransactionMgr;
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@Autowired
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private IVersionSpecificValidationSupport myVersionSpecificValidationSupport;
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private IFhirResourceDaoCodeSystem<?, ?, ?> myCodeSystemResourceDao;
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private void addCodeIfNotAlreadyAdded(String system, ValueSet.ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
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if (addedCodes.add(nextConcept.getCode())) {
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@ -124,13 +128,17 @@ public class HapiTerminologySvcImpl implements IHapiTerminologySvc {
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boolean retVal = theSetToPopulate.add(theConcept);
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if (retVal) {
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if (theSetToPopulate.size() >= myDaoConfig.getMaximumExpansionSize()) {
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String msg = myContext.getLocalizer().getMessage(HapiTerminologySvcImpl.class, "expansionTooLarge", myDaoConfig.getMaximumExpansionSize());
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String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "expansionTooLarge", myDaoConfig.getMaximumExpansionSize());
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throw new InvalidRequestException(msg);
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}
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}
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return retVal;
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}
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protected abstract IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource, RequestDetails theRequestDetails);
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abstract void createOrUpdateValueSet(ValueSet theValueSet, RequestDetails theRequestDetails);
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@Override
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public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
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ourLog.info(" * Deleting code system {}", theCodeSystem.getPid());
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@ -241,7 +249,7 @@ public class HapiTerminologySvcImpl implements IHapiTerminologySvc {
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} else {
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// bool.must(qb.keyword().onField("myProperties").matching(nextFilter.getProperty()+"="+nextFilter.getValue()).createQuery());
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bool.must(qb.phrase().onField("myProperties").sentence(nextFilter.getProperty()+"="+nextFilter.getValue()).createQuery());
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bool.must(qb.phrase().onField("myProperties").sentence(nextFilter.getProperty() + "=" + nextFilter.getValue()).createQuery());
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}
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}
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@ -340,7 +348,7 @@ public class HapiTerminologySvcImpl implements IHapiTerminologySvc {
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public List<VersionIndependentConcept> findCodesAbove(String theSystem, String theCode) {
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TermCodeSystem cs = getCodeSystem(theSystem);
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if (cs == null) {
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return myVersionSpecificValidationSupport.findCodesAboveUsingBuiltInSystems(theSystem, theCode);
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return findCodesAboveUsingBuiltInSystems(theSystem, theCode);
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}
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TermCodeSystemVersion csv = cs.getCurrentVersion();
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@ -372,7 +380,7 @@ public class HapiTerminologySvcImpl implements IHapiTerminologySvc {
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public List<VersionIndependentConcept> findCodesBelow(String theSystem, String theCode) {
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TermCodeSystem cs = getCodeSystem(theSystem);
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if (cs == null) {
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return myVersionSpecificValidationSupport.findCodesBelowUsingBuiltInSystems(theSystem, theCode);
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return findCodesBelowUsingBuiltInSystems(theSystem, theCode);
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}
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TermCodeSystemVersion csv = cs.getCurrentVersion();
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@ -651,7 +659,7 @@ public class HapiTerminologySvcImpl implements IHapiTerminologySvc {
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myCodeSystemDao.save(codeSystem);
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} else {
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if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemVersion.getResource().getId())) {
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String msg = myContext.getLocalizer().getMessage(HapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri,
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String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri,
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codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
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throw new UnprocessableEntityException(msg);
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}
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@ -701,6 +709,27 @@ public class HapiTerminologySvcImpl implements IHapiTerminologySvc {
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}
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}
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@Override
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@Transactional(propagation = Propagation.REQUIRED)
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public void storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets) {
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Validate.notBlank(theCodeSystemResource.getUrl(), "theCodeSystemResource must have a URL");
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IIdType csId = createOrUpdateCodeSystem(theCodeSystemResource, theRequestDetails);
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ResourceTable resource = (ResourceTable) myCodeSystemResourceDao.readEntity(csId);
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Long codeSystemResourcePid = resource.getId();
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ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
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theCodeSystemVersion.setResource(resource);
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storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemVersion);
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for (ValueSet nextValueSet : theValueSets) {
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createOrUpdateValueSet(nextValueSet, theRequestDetails);
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}
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}
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@Override
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public boolean supportsSystem(String theSystem) {
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TermCodeSystem cs = getCodeSystem(theSystem);
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@ -20,23 +20,107 @@ package ca.uhn.fhir.jpa.term;
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* #L%
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*/
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
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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.ValueSet;
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import org.springframework.beans.factory.annotation.Autowired;
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import java.util.ArrayList;
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import java.util.List;
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public class HapiTerminologySvcDstu2 extends HapiTerminologySvcImpl {
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
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@Autowired
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private IValidationSupport myValidationSupport;
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private void addAllChildren(String theSystemString, org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent theCode, List<VersionIndependentConcept> theListToPopulate) {
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if (isNotBlank(theCode.getCode())) {
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theListToPopulate.add(new VersionIndependentConcept(theSystemString, theCode.getCode()));
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}
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for (org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent nextChild : theCode.getConcept()) {
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addAllChildren(theSystemString, nextChild, theListToPopulate);
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}
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}
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private boolean addTreeIfItContainsCode(String theSystemString, org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent theNext, String theCode, List<VersionIndependentConcept> theListToPopulate) {
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boolean foundCodeInChild = false;
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for (org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent nextChild : theNext.getConcept()) {
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foundCodeInChild |= addTreeIfItContainsCode(theSystemString, nextChild, theCode, theListToPopulate);
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}
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if (theCode.equals(theNext.getCode()) || foundCodeInChild) {
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theListToPopulate.add(new VersionIndependentConcept(theSystemString, theNext.getCode()));
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return true;
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}
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return false;
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}
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@Override
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protected IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource, RequestDetails theRequestDetails) {
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throw new UnsupportedOperationException();
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}
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@Override
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public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
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throw new UnsupportedOperationException();
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}
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private void findCodesAbove(org.hl7.fhir.instance.model.ValueSet theSystem, String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate) {
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List<org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent> conceptList = theSystem.getCodeSystem().getConcept();
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for (org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent next : conceptList) {
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addTreeIfItContainsCode(theSystemString, next, theCode, theListToPopulate);
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}
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}
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@Override
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public List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
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ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
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org.hl7.fhir.instance.model.ValueSet system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
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if (system != null) {
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findCodesAbove(system, theSystem, theCode, retVal);
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}
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return retVal;
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}
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private void findCodesBelow(org.hl7.fhir.instance.model.ValueSet theSystem, String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate) {
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List<org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent> conceptList = theSystem.getCodeSystem().getConcept();
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findCodesBelow(theSystemString, theCode, theListToPopulate, conceptList);
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}
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private void findCodesBelow(String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate, List<org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent> conceptList) {
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for (org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent next : conceptList) {
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if (theCode.equals(next.getCode())) {
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addAllChildren(theSystemString, next, theListToPopulate);
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} else {
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findCodesBelow(theSystemString, theCode, theListToPopulate, next.getConcept());
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||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
|
||||
ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
|
||||
org.hl7.fhir.instance.model.ValueSet system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
|
||||
if (system != null) {
|
||||
findCodesBelow(system, theSystem, theCode, retVal);
|
||||
}
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets) {
|
||||
throw new UnsupportedOperationException();
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void createOrUpdateValueSet(ValueSet theValueSet, RequestDetails theRequestDetails) {
|
||||
throw new UnsupportedOperationException();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@ -1,44 +1,34 @@
|
||||
package ca.uhn.fhir.jpa.term;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
|
||||
import ca.uhn.fhir.jpa.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.util.CoverageIgnore;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import org.apache.lucene.search.Query;
|
||||
import org.hibernate.search.jpa.FullTextEntityManager;
|
||||
import org.hibernate.search.jpa.FullTextQuery;
|
||||
import org.hibernate.search.query.dsl.BooleanJunction;
|
||||
import org.hibernate.search.query.dsl.QueryBuilder;
|
||||
import org.hl7.fhir.convertors.VersionConvertor_30_40;
|
||||
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
|
||||
import org.hl7.fhir.dstu3.model.CodeSystem;
|
||||
import org.hl7.fhir.dstu3.model.*;
|
||||
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
|
||||
import org.hl7.fhir.dstu3.model.CodeableConcept;
|
||||
import org.hl7.fhir.dstu3.model.Coding;
|
||||
import org.hl7.fhir.dstu3.model.StructureDefinition;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet.*;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.transaction.annotation.Propagation;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
|
||||
import javax.persistence.EntityManager;
|
||||
import javax.persistence.PersistenceContext;
|
||||
import javax.persistence.PersistenceContextType;
|
||||
import java.util.*;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
||||
/*
|
||||
@ -61,9 +51,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
* #L%
|
||||
*/
|
||||
|
||||
public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTerminologySvcDstu3 {
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HapiTerminologySvcDstu3.class);
|
||||
private final VersionConvertor_30_40 myConverter;
|
||||
public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implements IValidationSupport, IHapiTerminologySvcDstu3 {
|
||||
|
||||
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
|
||||
protected EntityManager myEntityManager;
|
||||
@ -71,10 +59,11 @@ public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTermino
|
||||
protected FhirContext myContext;
|
||||
@Autowired
|
||||
protected ITermCodeSystemDao myCodeSystemDao;
|
||||
|
||||
@Autowired
|
||||
@Qualifier("myValueSetDaoDstu3")
|
||||
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
|
||||
@Autowired
|
||||
private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemResourceDao;
|
||||
|
||||
@Autowired
|
||||
private IValidationSupport myValidationSupport;
|
||||
@Autowired
|
||||
@ -84,19 +73,22 @@ public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTermino
|
||||
* Constructor
|
||||
*/
|
||||
public HapiTerminologySvcDstu3() {
|
||||
myConverter = new VersionConvertor_30_40();
|
||||
super();
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
|
||||
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
|
||||
CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
|
||||
if (system != null) {
|
||||
findCodesBelow(system, theSystem, theCode, retVal);
|
||||
protected void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet, RequestDetails theRequestDetails) {
|
||||
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
|
||||
ValueSet valueSetDstu3;
|
||||
try {
|
||||
valueSetDstu3 = VersionConvertor_30_40.convertValueSet(theValueSet);
|
||||
} catch (FHIRException e) {
|
||||
throw new InternalErrorException(e);
|
||||
}
|
||||
return retVal;
|
||||
myValueSetResourceDao.update(valueSetDstu3, matchUrl, theRequestDetails);
|
||||
}
|
||||
|
||||
|
||||
private void addAllChildren(String theSystemString, ConceptDefinitionComponent theCode, List<VersionIndependentConcept> theListToPopulate) {
|
||||
if (isNotBlank(theCode.getCode())) {
|
||||
theListToPopulate.add(new VersionIndependentConcept(theSystemString, theCode.getCode()));
|
||||
@ -106,31 +98,6 @@ public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTermino
|
||||
}
|
||||
}
|
||||
|
||||
private void addCodeIfNotAlreadyAdded(String system, ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
|
||||
if (addedCodes.add(nextConcept.getCode())) {
|
||||
ValueSetExpansionContainsComponent contains = retVal.addContains();
|
||||
contains.setCode(nextConcept.getCode());
|
||||
contains.setSystem(system);
|
||||
contains.setDisplay(nextConcept.getDisplay());
|
||||
}
|
||||
}
|
||||
|
||||
private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
|
||||
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
|
||||
}
|
||||
|
||||
private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
|
||||
Query textQuery = qb
|
||||
.phrase()
|
||||
.withSlop(2)
|
||||
.onField("myDisplay").boostedTo(4.0f)
|
||||
.andField("myDisplayEdgeNGram").boostedTo(2.0f)
|
||||
// .andField("myDisplayNGram").boostedTo(1.0f)
|
||||
// .andField("myDisplayPhonetic").boostedTo(0.5f)
|
||||
.sentence(nextFilter.getValue().toLowerCase()).createQuery();
|
||||
bool.must(textQuery);
|
||||
}
|
||||
|
||||
private boolean addTreeIfItContainsCode(String theSystemString, ConceptDefinitionComponent theNext, String theCode, List<VersionIndependentConcept> theListToPopulate) {
|
||||
boolean foundCodeInChild = false;
|
||||
for (ConceptDefinitionComponent nextChild : theNext.getConcept()) {
|
||||
@ -146,116 +113,31 @@ public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTermino
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
|
||||
ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
|
||||
CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
|
||||
if (system != null) {
|
||||
findCodesAbove(system, theSystem, theCode, retVal);
|
||||
protected IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, RequestDetails theRequestDetails) {
|
||||
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
|
||||
CodeSystem resourceToStore;
|
||||
try {
|
||||
resourceToStore = VersionConvertor_30_40.convertCodeSystem(theCodeSystemResource);
|
||||
} catch (FHIRException e) {
|
||||
throw new InternalErrorException(e);
|
||||
}
|
||||
return retVal;
|
||||
return myCodeSystemResourceDao.update(resourceToStore, matchUrl, theRequestDetails).getId();
|
||||
}
|
||||
|
||||
@Override
|
||||
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
|
||||
String system = theInclude.getSystem();
|
||||
ourLog.info("Starting expansion around code system: {}", system);
|
||||
ValueSet valueSetToExpand = new ValueSet();
|
||||
valueSetToExpand.getCompose().addInclude(theInclude);
|
||||
|
||||
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
|
||||
TermCodeSystemVersion csv = cs.getCurrentVersion();
|
||||
|
||||
ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
|
||||
Set<String> addedCodes = new HashSet<>();
|
||||
boolean haveIncludeCriteria = false;
|
||||
|
||||
/*
|
||||
* Include Concepts
|
||||
*/
|
||||
for (ConceptReferenceComponent next : theInclude.getConcept()) {
|
||||
String nextCode = next.getCode();
|
||||
if (isNotBlank(nextCode) && !addedCodes.contains(nextCode)) {
|
||||
haveIncludeCriteria = true;
|
||||
TermConcept code = myTerminologySvc.findCode(system, nextCode);
|
||||
if (code != null) {
|
||||
addedCodes.add(nextCode);
|
||||
ValueSetExpansionContainsComponent contains = retVal.addContains();
|
||||
contains.setCode(nextCode);
|
||||
contains.setSystem(system);
|
||||
contains.setDisplay(code.getDisplay());
|
||||
try {
|
||||
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
|
||||
valueSetToExpandR4 = VersionConvertor_30_40.convertValueSet(valueSetToExpand);
|
||||
org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent expandedR4 = super.expandValueSet(valueSetToExpandR4).getExpansion();
|
||||
return VersionConvertor_30_40.convertValueSetExpansionComponent(expandedR4);
|
||||
} catch (FHIRException e) {
|
||||
throw new InternalErrorException(e);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* Filters
|
||||
*/
|
||||
|
||||
if (theInclude.getFilter().size() > 0) {
|
||||
haveIncludeCriteria = true;
|
||||
|
||||
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
|
||||
QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(TermConcept.class).get();
|
||||
BooleanJunction<?> bool = qb.bool();
|
||||
|
||||
bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
|
||||
|
||||
for (ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
|
||||
if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
|
||||
continue;
|
||||
}
|
||||
|
||||
if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
|
||||
throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
|
||||
}
|
||||
|
||||
|
||||
if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == FilterOperator.EQUAL) {
|
||||
addDisplayFilterExact(qb, bool, nextFilter);
|
||||
} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == FilterOperator.EQUAL) {
|
||||
if (nextFilter.getValue().trim().contains(" ")) {
|
||||
addDisplayFilterExact(qb, bool, nextFilter);
|
||||
} else {
|
||||
addDisplayFilterInexact(qb, bool, nextFilter);
|
||||
}
|
||||
} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == FilterOperator.ISA) {
|
||||
TermConcept code = myTerminologySvc.findCode(system, nextFilter.getValue());
|
||||
if (code == null) {
|
||||
throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
|
||||
}
|
||||
|
||||
ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
|
||||
bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
|
||||
} else {
|
||||
throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
|
||||
}
|
||||
}
|
||||
|
||||
Query luceneQuery = bool.createQuery();
|
||||
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
|
||||
jpaQuery.setMaxResults(1000);
|
||||
|
||||
StopWatch sw = new StopWatch();
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
List<TermConcept> result = jpaQuery.getResultList();
|
||||
|
||||
ourLog.info("Expansion completed in {}ms", sw.getMillis());
|
||||
|
||||
for (TermConcept nextConcept : result) {
|
||||
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
|
||||
}
|
||||
|
||||
retVal.setTotal(jpaQuery.getResultSize());
|
||||
}
|
||||
|
||||
if (!haveIncludeCriteria) {
|
||||
List<TermConcept> allCodes = myTerminologySvc.findCodes(system);
|
||||
for (TermConcept nextConcept : allCodes) {
|
||||
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
|
||||
}
|
||||
}
|
||||
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
|
||||
@ -278,29 +160,6 @@ public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTermino
|
||||
return null;
|
||||
}
|
||||
|
||||
// @Override
|
||||
// public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
|
||||
// ValueSet source = new ValueSet();
|
||||
// source.getCompose().addInclude().addValueSet(theValueSet);
|
||||
// try {
|
||||
// ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
|
||||
//
|
||||
// HapiWorkerContext worker = new HapiWorkerContext(myContext, myValidationSupport);
|
||||
// ValueSetExpansionOutcome outcome = worker.expand(source, null);
|
||||
// for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
|
||||
// retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
|
||||
// }
|
||||
//
|
||||
// return retVal;
|
||||
//
|
||||
// } catch (BaseServerResponseException e) {
|
||||
// throw e;
|
||||
// } catch (Exception e) {
|
||||
// throw new InternalErrorException(e);
|
||||
// }
|
||||
//
|
||||
// }
|
||||
|
||||
@CoverageIgnore
|
||||
@Override
|
||||
public StructureDefinition fetchStructureDefinition(FhirContext theCtx, String theUrl) {
|
||||
@ -314,6 +173,16 @@ public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTermino
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
|
||||
ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
|
||||
CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
|
||||
if (system != null) {
|
||||
findCodesAbove(system, theSystem, theCode, retVal);
|
||||
}
|
||||
return retVal;
|
||||
}
|
||||
|
||||
private void findCodesBelow(CodeSystem theSystem, String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate) {
|
||||
List<ConceptDefinitionComponent> conceptList = theSystem.getConcept();
|
||||
findCodesBelow(theSystemString, theCode, theListToPopulate, conceptList);
|
||||
@ -330,34 +199,18 @@ public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTermino
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
|
||||
return myTerminologySvc.supportsSystem(theSystem);
|
||||
public List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
|
||||
ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
|
||||
CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
|
||||
if (system != null) {
|
||||
findCodesBelow(system, theSystem, theCode, retVal);
|
||||
}
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Override
|
||||
@org.springframework.transaction.annotation.Transactional(propagation = Propagation.REQUIRED)
|
||||
public void storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets) {
|
||||
CodeSystem cs = new org.hl7.fhir.dstu3.model.CodeSystem();
|
||||
cs.setUrl(theCodeSystemResource.getUrl());
|
||||
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
|
||||
DaoMethodOutcome createOutcome = myCodeSystemResourceDao.create(cs, "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl()), theRequestDetails);
|
||||
IIdType csId = createOutcome.getId().toUnqualifiedVersionless();
|
||||
if (createOutcome.getCreated() != Boolean.TRUE) {
|
||||
CodeSystem existing = myCodeSystemResourceDao.read(csId, theRequestDetails);
|
||||
csId = myCodeSystemResourceDao.update(existing, null, false, true, theRequestDetails).getId();
|
||||
|
||||
ourLog.info("Created new version of CodeSystem, got ID: {}", csId.toUnqualified().getValue());
|
||||
}
|
||||
|
||||
ResourceTable resource = (ResourceTable) myCodeSystemResourceDao.readEntity(csId);
|
||||
Long codeSystemResourcePid = resource.getId();
|
||||
|
||||
ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
|
||||
|
||||
theCodeSystemVersion.setResource(resource);
|
||||
myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemVersion);
|
||||
|
||||
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
|
||||
return myTerminologySvc.supportsSystem(theSystem);
|
||||
}
|
||||
|
||||
@CoverageIgnore
|
||||
@ -371,7 +224,8 @@ public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTermino
|
||||
return new CodeValidationResult(def);
|
||||
}
|
||||
|
||||
return new CodeValidationResult(IssueSeverity.ERROR, "Unkonwn code {" + theCodeSystem + "}" + theCode);
|
||||
return new CodeValidationResult(IssueSeverity.ERROR, "Unknown code {" + theCodeSystem + "}" + theCode);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
@ -3,21 +3,10 @@ package ca.uhn.fhir.jpa.term;
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
|
||||
import ca.uhn.fhir.jpa.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.util.CoverageIgnore;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
import org.apache.lucene.search.Query;
|
||||
import org.hibernate.search.jpa.FullTextEntityManager;
|
||||
import org.hibernate.search.jpa.FullTextQuery;
|
||||
import org.hibernate.search.query.dsl.BooleanJunction;
|
||||
import org.hibernate.search.query.dsl.QueryBuilder;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
|
||||
@ -25,19 +14,19 @@ import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
|
||||
import org.hl7.fhir.r4.model.StructureDefinition;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.hl7.fhir.r4.model.ValueSet.*;
|
||||
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
|
||||
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
import org.springframework.transaction.annotation.Propagation;
|
||||
import org.springframework.transaction.annotation.Transactional;
|
||||
|
||||
import javax.persistence.EntityManager;
|
||||
import javax.persistence.PersistenceContext;
|
||||
import javax.persistence.PersistenceContextType;
|
||||
import java.util.*;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
||||
/*
|
||||
@ -60,8 +49,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
* #L%
|
||||
*/
|
||||
|
||||
public class HapiTerminologySvcR4 implements IHapiTerminologySvcR4 {
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HapiTerminologySvcR4.class);
|
||||
public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements IHapiTerminologySvcR4 {
|
||||
@Autowired
|
||||
protected ITermCodeSystemDao myCodeSystemDao;
|
||||
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
|
||||
@ -70,6 +58,9 @@ public class HapiTerminologySvcR4 implements IHapiTerminologySvcR4 {
|
||||
@Qualifier("myCodeSystemDaoR4")
|
||||
private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
|
||||
@Autowired
|
||||
@Qualifier("myValueSetDaoR4")
|
||||
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
|
||||
@Autowired
|
||||
private IValidationSupport myValidationSupport;
|
||||
@Autowired
|
||||
private IHapiTerminologySvc myTerminologySvc;
|
||||
@ -85,30 +76,6 @@ public class HapiTerminologySvcR4 implements IHapiTerminologySvcR4 {
|
||||
}
|
||||
}
|
||||
|
||||
private void addCodeIfNotAlreadyAdded(String system, ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
|
||||
if (addedCodes.add(nextConcept.getCode())) {
|
||||
ValueSetExpansionContainsComponent contains = retVal.addContains();
|
||||
contains.setCode(nextConcept.getCode());
|
||||
contains.setSystem(system);
|
||||
contains.setDisplay(nextConcept.getDisplay());
|
||||
}
|
||||
}
|
||||
|
||||
private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
|
||||
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
|
||||
}
|
||||
|
||||
private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
|
||||
Query textQuery = qb
|
||||
.phrase()
|
||||
.withSlop(2)
|
||||
.onField("myDisplay").boostedTo(4.0f)
|
||||
.andField("myDisplayEdgeNGram").boostedTo(2.0f)
|
||||
// .andField("myDisplayNGram").boostedTo(1.0f)
|
||||
// .andField("myDisplayPhonetic").boostedTo(0.5f)
|
||||
.sentence(nextFilter.getValue().toLowerCase()).createQuery();
|
||||
bool.must(textQuery);
|
||||
}
|
||||
|
||||
private boolean addTreeIfItContainsCode(String theSystemString, ConceptDefinitionComponent theNext, String theCode, List<VersionIndependentConcept> theListToPopulate) {
|
||||
boolean foundCodeInChild = false;
|
||||
@ -124,130 +91,24 @@ public class HapiTerminologySvcR4 implements IHapiTerminologySvcR4 {
|
||||
return false;
|
||||
}
|
||||
|
||||
@Override
|
||||
protected IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource, RequestDetails theRequestDetails) {
|
||||
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
|
||||
return myCodeSystemResourceDao.update(theCodeSystemResource, matchUrl, theRequestDetails).getId();
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void createOrUpdateValueSet(ValueSet theValueSet, RequestDetails theRequestDetails) {
|
||||
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
|
||||
myValueSetResourceDao.update(theValueSet, matchUrl, theRequestDetails);
|
||||
}
|
||||
|
||||
@Override
|
||||
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
|
||||
String system = theInclude.getSystem();
|
||||
ourLog.info("Starting expansion around code system: {}", system);
|
||||
|
||||
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
|
||||
TermCodeSystemVersion csv = cs.getCurrentVersion();
|
||||
|
||||
ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
|
||||
Set<String> addedCodes = new HashSet<>();
|
||||
boolean haveIncludeCriteria = false;
|
||||
|
||||
/*
|
||||
* Include Concepts
|
||||
*/
|
||||
for (ConceptReferenceComponent next : theInclude.getConcept()) {
|
||||
String nextCode = next.getCode();
|
||||
if (isNotBlank(nextCode) && !addedCodes.contains(nextCode)) {
|
||||
haveIncludeCriteria = true;
|
||||
TermConcept code = myTerminologySvc.findCode(system, nextCode);
|
||||
if (code != null) {
|
||||
addedCodes.add(nextCode);
|
||||
ValueSetExpansionContainsComponent contains = retVal.addContains();
|
||||
contains.setCode(nextCode);
|
||||
contains.setSystem(system);
|
||||
contains.setDisplay(code.getDisplay());
|
||||
ValueSet valueSetToExpand = new ValueSet();
|
||||
valueSetToExpand.getCompose().addInclude(theInclude);
|
||||
return super.expandValueSet(valueSetToExpand).getExpansion();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* Filters
|
||||
*/
|
||||
|
||||
if (theInclude.getFilter().size() > 0) {
|
||||
haveIncludeCriteria = true;
|
||||
|
||||
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
|
||||
QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(TermConcept.class).get();
|
||||
BooleanJunction<?> bool = qb.bool();
|
||||
|
||||
bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
|
||||
|
||||
for (ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
|
||||
if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
|
||||
continue;
|
||||
}
|
||||
|
||||
if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
|
||||
throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
|
||||
}
|
||||
|
||||
|
||||
if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == FilterOperator.EQUAL) {
|
||||
addDisplayFilterExact(qb, bool, nextFilter);
|
||||
} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == FilterOperator.EQUAL) {
|
||||
if (nextFilter.getValue().trim().contains(" ")) {
|
||||
addDisplayFilterExact(qb, bool, nextFilter);
|
||||
} else {
|
||||
addDisplayFilterInexact(qb, bool, nextFilter);
|
||||
}
|
||||
} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == FilterOperator.ISA) {
|
||||
TermConcept code = myTerminologySvc.findCode(system, nextFilter.getValue());
|
||||
if (code == null) {
|
||||
throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
|
||||
}
|
||||
|
||||
ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
|
||||
bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
|
||||
} else {
|
||||
throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
|
||||
}
|
||||
}
|
||||
|
||||
Query luceneQuery = bool.createQuery();
|
||||
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
|
||||
jpaQuery.setMaxResults(1000);
|
||||
|
||||
StopWatch sw = new StopWatch();
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
List<TermConcept> result = jpaQuery.getResultList();
|
||||
|
||||
ourLog.info("Expansion completed in {}ms", sw.getMillis());
|
||||
|
||||
for (TermConcept nextConcept : result) {
|
||||
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
|
||||
}
|
||||
|
||||
retVal.setTotal(jpaQuery.getResultSize());
|
||||
}
|
||||
|
||||
if (!haveIncludeCriteria) {
|
||||
List<TermConcept> allCodes = myTerminologySvc.findCodes(system);
|
||||
for (TermConcept nextConcept : allCodes) {
|
||||
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
|
||||
}
|
||||
}
|
||||
|
||||
return retVal;
|
||||
}
|
||||
|
||||
// @Override
|
||||
// public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
|
||||
// ValueSet source = new ValueSet();
|
||||
// source.getCompose().addInclude().addValueSet(theValueSet);
|
||||
// try {
|
||||
// ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
|
||||
//
|
||||
// HapiWorkerContext worker = new HapiWorkerContext(myContext, myValidationSupport);
|
||||
// ValueSetExpansionOutcome outcome = worker.expand(source, null);
|
||||
// for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
|
||||
// retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
|
||||
// }
|
||||
//
|
||||
// return retVal;
|
||||
//
|
||||
// } catch (BaseServerResponseException e) {
|
||||
// throw e;
|
||||
// } catch (Exception e) {
|
||||
// throw new InternalErrorException(e);
|
||||
// }
|
||||
//
|
||||
// }
|
||||
|
||||
@Override
|
||||
public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
|
||||
@ -323,23 +184,6 @@ public class HapiTerminologySvcR4 implements IHapiTerminologySvcR4 {
|
||||
return myTerminologySvc.supportsSystem(theSystem);
|
||||
}
|
||||
|
||||
@Override
|
||||
@Transactional(propagation = Propagation.REQUIRED)
|
||||
public void storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets) {
|
||||
Validate.notBlank(theCodeSystemResource.getUrl(), "theCodeSystemResource must have a URL");
|
||||
|
||||
IIdType csId = myCodeSystemResourceDao.update(theCodeSystemResource, "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl()), theRequestDetails).getId();
|
||||
|
||||
ResourceTable resource = (ResourceTable) myCodeSystemResourceDao.readEntity(csId);
|
||||
Long codeSystemResourcePid = resource.getId();
|
||||
|
||||
ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
|
||||
|
||||
theCodeSystemVersion.setResource(resource);
|
||||
myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemVersion);
|
||||
|
||||
}
|
||||
|
||||
@CoverageIgnore
|
||||
@Override
|
||||
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
|
||||
|
||||
@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.term;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
|
||||
import java.util.List;
|
||||
@ -60,4 +61,10 @@ public interface IHapiTerminologySvc {
|
||||
|
||||
boolean supportsSystem(String theCodeSystem);
|
||||
|
||||
}
|
||||
List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode);
|
||||
|
||||
List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode);
|
||||
|
||||
void storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<org.hl7.fhir.r4.model.ValueSet> theValueSets);
|
||||
|
||||
}
|
||||
|
||||
@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
|
||||
|
||||
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
|
||||
|
||||
public interface IHapiTerminologySvcDstu3 extends IValidationSupport, IVersionSpecificValidationSupport {
|
||||
|
||||
public interface IHapiTerminologySvcDstu3 extends IHapiTerminologySvc, IValidationSupport {
|
||||
// nothing
|
||||
}
|
||||
|
||||
@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
|
||||
|
||||
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
|
||||
|
||||
public interface IHapiTerminologySvcR4 extends IValidationSupport {
|
||||
|
||||
public interface IHapiTerminologySvcR4 extends IHapiTerminologySvc, IValidationSupport {
|
||||
// nothing
|
||||
}
|
||||
|
||||
@ -1,18 +0,0 @@
|
||||
package ca.uhn.fhir.jpa.term;
|
||||
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
public interface IVersionSpecificValidationSupport {
|
||||
|
||||
List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode);
|
||||
|
||||
List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode);
|
||||
|
||||
void storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets);
|
||||
|
||||
}
|
||||
@ -4,9 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListHandler;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincHandler;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincHierarchyHandler;
|
||||
import ca.uhn.fhir.jpa.term.loinc.*;
|
||||
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerConcept;
|
||||
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerDescription;
|
||||
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerRelationship;
|
||||
@ -62,6 +60,9 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
|
||||
public static final String LOINC_HIERARCHY_FILE = "MULTI-AXIAL_HIERARCHY.CSV";
|
||||
public static final String LOINC_ANSWERLIST_FILE = "AnswerList_Beta_1.csv";
|
||||
public static final String LOINC_ANSWERLIST_LINK_FILE = "LoincAnswerListLink_Beta_1.csv";
|
||||
public static final String LOINC_PART_FILE = "Part_Beta_1.csv";
|
||||
public static final String LOINC_PART_LINK_FILE = "LoincPartLink_Beta_1.csv";
|
||||
public static final String LOINC_PART_RELATED_CODE_MAPPING_FILE = "PartRelatedCodeMapping_Beta_1.csv";
|
||||
public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
|
||||
public static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
|
||||
public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
|
||||
@ -193,7 +194,7 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
|
||||
|
||||
CodeSystem loincCs;
|
||||
try {
|
||||
String loincCsString = IOUtils.toString(HapiTerminologySvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/loinc/loinc.xml"), Charsets.UTF_8);
|
||||
String loincCsString = IOUtils.toString(BaseHapiTerminologySvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/loinc/loinc.xml"), Charsets.UTF_8);
|
||||
loincCs = FhirContext.forR4().newXmlParser().parseResource(CodeSystem.class, loincCsString);
|
||||
} catch (IOException e) {
|
||||
throw new InternalErrorException("Failed to load loinc.xml", e);
|
||||
@ -220,6 +221,18 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
|
||||
handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, propertyNames, valueSets);
|
||||
iterateOverZipFile(theZipBytes, LOINC_ANSWERLIST_FILE, handler, ',', QuoteMode.NON_NUMERIC);
|
||||
|
||||
// Answer list links (connects loinc observation codes to answerlist codes)
|
||||
handler = new LoincAnswerListLinkHandler(code2concept, valueSets);
|
||||
iterateOverZipFile(theZipBytes, LOINC_ANSWERLIST_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC);
|
||||
|
||||
// Part file
|
||||
handler = new LoincPartHandler(codeSystemVersion, code2concept);
|
||||
iterateOverZipFile(theZipBytes, LOINC_PART_FILE, handler, ',', QuoteMode.NON_NUMERIC);
|
||||
|
||||
// Part link file
|
||||
handler = new LoincPartLinkHandler(codeSystemVersion, code2concept);
|
||||
iterateOverZipFile(theZipBytes, LOINC_PART_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC);
|
||||
|
||||
theZipBytes.clear();
|
||||
|
||||
for (Entry<String, TermConcept> next : code2concept.entrySet()) {
|
||||
|
||||
@ -0,0 +1,72 @@
|
||||
package ca.uhn.fhir.jpa.term.loinc;
|
||||
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
|
||||
import ca.uhn.fhir.jpa.term.IRecordHandler;
|
||||
import org.apache.commons.csv.CSVRecord;
|
||||
import org.hl7.fhir.r4.model.Enumerations;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.trim;
|
||||
|
||||
public class LoincAnswerListLinkHandler implements IRecordHandler {
|
||||
|
||||
private final Map<String, TermConcept> myCode2Concept;
|
||||
private final Map<String, ValueSet> myIdToValueSet = new HashMap<>();
|
||||
|
||||
public LoincAnswerListLinkHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets) {
|
||||
myCode2Concept = theCode2concept;
|
||||
for (ValueSet next : theValueSets) {
|
||||
myIdToValueSet.put(next.getId(), next);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void accept(CSVRecord theRecord) {
|
||||
String applicableContext = trim(theRecord.get("ApplicableContext"));
|
||||
|
||||
/*
|
||||
* Per Dan V's Notes:
|
||||
*
|
||||
* Note: in our current format, we support binding of the same
|
||||
* LOINC term to different answer lists depending on the panel
|
||||
* context. I don’t believe there’s a way to handle that in
|
||||
* the current FHIR spec, so I might suggest we discuss either
|
||||
* only binding the “default” (non-context specific) list or
|
||||
* if multiple bindings could be supported.
|
||||
*/
|
||||
if (isNotBlank(applicableContext)) {
|
||||
return;
|
||||
}
|
||||
|
||||
String answerListId = trim(theRecord.get("AnswerListId"));
|
||||
if (isBlank(answerListId)) {
|
||||
return;
|
||||
}
|
||||
|
||||
String loincNumber = trim(theRecord.get("LoincNumber"));
|
||||
if (isBlank(loincNumber)) {
|
||||
return;
|
||||
}
|
||||
|
||||
TermConcept loincCode = myCode2Concept.get(loincNumber);
|
||||
if (loincCode != null) {
|
||||
loincCode.addProperty("answer-list", answerListId);
|
||||
}
|
||||
|
||||
TermConcept answerListCode = myCode2Concept.get(answerListId);
|
||||
if (answerListCode != null) {
|
||||
answerListCode.addProperty("answers-for", loincNumber);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,45 @@
|
||||
package ca.uhn.fhir.jpa.term.loinc;
|
||||
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.term.IRecordHandler;
|
||||
import org.apache.commons.csv.CSVRecord;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.trim;
|
||||
|
||||
public class LoincPartHandler implements IRecordHandler {
|
||||
|
||||
private final Map<String, TermConcept> myCode2Concept;
|
||||
private final TermCodeSystemVersion myCodeSystemVersion;
|
||||
private final Map<String, ValueSet> myIdToValueSet = new HashMap<>();
|
||||
|
||||
public LoincPartHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept) {
|
||||
myCodeSystemVersion = theCodeSystemVersion;
|
||||
myCode2Concept = theCode2concept;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void accept(CSVRecord theRecord) {
|
||||
|
||||
// this is the code for the list (will repeat)
|
||||
String partNumber = trim(theRecord.get("PartNumber"));
|
||||
String partTypeName = trim(theRecord.get("PartTypeName"));
|
||||
String partName = trim(theRecord.get("PartName"));
|
||||
String partDisplayName = trim(theRecord.get("PartDisplayName"));
|
||||
String status = trim(theRecord.get("Status"));
|
||||
|
||||
if (!"ACTIVE".equals(status)) {
|
||||
return;
|
||||
}
|
||||
|
||||
TermConcept concept = new TermConcept(myCodeSystemVersion, partNumber);
|
||||
concept.setDisplay(partName);
|
||||
|
||||
myCode2Concept.put(partDisplayName, concept);
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,51 @@
|
||||
package ca.uhn.fhir.jpa.term.loinc;
|
||||
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.term.IRecordHandler;
|
||||
import org.apache.commons.csv.CSVRecord;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.trim;
|
||||
|
||||
public class LoincPartLinkHandler implements IRecordHandler {
|
||||
|
||||
private final Map<String, TermConcept> myCode2Concept;
|
||||
private final TermCodeSystemVersion myCodeSystemVersion;
|
||||
|
||||
public LoincPartLinkHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept) {
|
||||
myCodeSystemVersion = theCodeSystemVersion;
|
||||
myCode2Concept = theCode2concept;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void accept(CSVRecord theRecord) {
|
||||
|
||||
String loincNumber = trim(theRecord.get("LoincNumber"));
|
||||
String longCommonName = trim(theRecord.get("LongCommonName"));
|
||||
String partNumber = trim(theRecord.get("PartNumber"));
|
||||
String partDisplayName = trim(theRecord.get("PartDisplayName"));
|
||||
String status = trim(theRecord.get("Status"));
|
||||
|
||||
TermConcept loincConcept = myCode2Concept.get(loincNumber);
|
||||
TermConcept partConcept = myCode2Concept.get(partNumber);
|
||||
|
||||
if (loincConcept==null) {
|
||||
ourLog.warn("No loinc code: {}", loincNumber);
|
||||
return;
|
||||
}
|
||||
if (partConcept==null) {
|
||||
ourLog.warn("No part code: {}", partNumber);
|
||||
return;
|
||||
}
|
||||
|
||||
partConcept.addProperty();
|
||||
|
||||
}
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(LoincPartLinkHandler.class);
|
||||
}
|
||||
@ -4,7 +4,7 @@ import static org.junit.Assert.assertNotEquals;
|
||||
|
||||
import java.nio.charset.StandardCharsets;
|
||||
|
||||
import ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.hl7.fhir.dstu3.model.CodeSystem;
|
||||
import org.junit.AfterClass;
|
||||
@ -18,13 +18,13 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
|
||||
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testIndexContained() throws Exception {
|
||||
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
|
||||
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
|
||||
|
||||
String input = IOUtils.toString(getClass().getResource("/dstu3_codesystem_complete.json"), StandardCharsets.UTF_8);
|
||||
CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);
|
||||
|
||||
@ -9,7 +9,7 @@ import static org.junit.Assert.fail;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
import ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
|
||||
import org.hl7.fhir.dstu3.model.*;
|
||||
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
|
||||
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
|
||||
@ -48,7 +48,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
|
||||
public void after() {
|
||||
myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
|
||||
|
||||
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
|
||||
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
|
||||
}
|
||||
|
||||
@Before
|
||||
@ -483,7 +483,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
|
||||
|
||||
@Test
|
||||
public void testExpandWithIsAInExternalValueSetReindex() {
|
||||
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
|
||||
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
|
||||
|
||||
createExternalCsAndLocalVs();
|
||||
|
||||
|
||||
@ -4,12 +4,12 @@ import static org.junit.Assert.assertNotEquals;
|
||||
|
||||
import java.nio.charset.StandardCharsets;
|
||||
|
||||
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.Test;
|
||||
|
||||
import ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
|
||||
public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
|
||||
@ -18,13 +18,13 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
|
||||
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testIndexContained() throws Exception {
|
||||
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
|
||||
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
|
||||
|
||||
String input = IOUtils.toString(getClass().getResource("/r4/codesystem_complete.json"), StandardCharsets.UTF_8);
|
||||
CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);
|
||||
|
||||
@ -9,7 +9,7 @@ import static org.junit.Assert.fail;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
import ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceCategory;
|
||||
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
|
||||
@ -48,7 +48,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
||||
public void after() {
|
||||
myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
|
||||
|
||||
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
|
||||
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
|
||||
}
|
||||
|
||||
@Before
|
||||
@ -483,7 +483,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
||||
|
||||
@Test
|
||||
public void testExpandWithIsAInExternalValueSetReindex() {
|
||||
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
|
||||
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
|
||||
|
||||
createExternalCsAndLocalVs();
|
||||
|
||||
|
||||
@ -28,6 +28,7 @@ import java.util.Map;
|
||||
import java.util.zip.ZipEntry;
|
||||
import java.util.zip.ZipOutputStream;
|
||||
|
||||
import static org.hamcrest.Matchers.contains;
|
||||
import static org.junit.Assert.*;
|
||||
import static org.mockito.Matchers.any;
|
||||
import static org.mockito.Matchers.anyListOf;
|
||||
@ -88,6 +89,7 @@ public class TerminologyLoaderSvcLoincTest {
|
||||
addFile("/loinc/", "loinc.csv", TerminologyLoaderSvc.LOINC_FILE);
|
||||
addFile("/loinc/", "hierarchy.csv", TerminologyLoaderSvc.LOINC_HIERARCHY_FILE);
|
||||
addFile("/loinc/", "AnswerList_Beta_1.csv", TerminologyLoaderSvc.LOINC_ANSWERLIST_FILE);
|
||||
addFile("/loinc/", "LoincAnswerListLink_Beta_1.csv", TerminologyLoaderSvc.LOINC_ANSWERLIST_LINK_FILE);
|
||||
|
||||
// Actually do the load
|
||||
mySvc.loadLoinc(myFiles, details);
|
||||
@ -108,6 +110,10 @@ public class TerminologyLoaderSvcLoincTest {
|
||||
assertEquals("Pt", code.getProperty("TIME_ASPCT"));
|
||||
assertEquals("R' wave amplitude in lead I", code.getDisplay());
|
||||
|
||||
// Loinc code with answer
|
||||
code = concepts.get("61438-8");
|
||||
assertThat(code.getProperties("answer-list"), contains("LL1000-0"));
|
||||
|
||||
// Answer list
|
||||
code = concepts.get("LL1001-8");
|
||||
assertEquals("LL1001-8", code.getCode());
|
||||
@ -119,6 +125,11 @@ public class TerminologyLoaderSvcLoincTest {
|
||||
assertEquals("1-2 times per week", code.getDisplay());
|
||||
assertEquals(3, code.getSequence().intValue());
|
||||
|
||||
// Answer list code with link to answers-for
|
||||
code = concepts.get("LL1000-0");
|
||||
assertThat(code.getProperties("answers-for"), contains("61438-8"));
|
||||
|
||||
|
||||
// AnswerList valueSet
|
||||
Map<String, ValueSet> valueSets = new HashMap<>();
|
||||
for (ValueSet next : myValueSetsCaptor.getValue()) {
|
||||
@ -130,11 +141,16 @@ public class TerminologyLoaderSvcLoincTest {
|
||||
assertEquals("PhenX05_14_30D freq amts", vs.getName());
|
||||
assertEquals("urn:oid:1.3.6.1.4.1.12009.10.1.166", vs.getUrl());
|
||||
assertEquals(1, vs.getCompose().getInclude().size());
|
||||
assertEquals(6, vs.getCompose().getInclude().get(0).getConcept().size());
|
||||
assertEquals(7, vs.getCompose().getInclude().get(0).getConcept().size());
|
||||
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URL, vs.getCompose().getInclude().get(0).getSystem());
|
||||
assertEquals("LA6270-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
|
||||
assertEquals("Never", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
|
||||
|
||||
// Part
|
||||
code = concepts.get("LP101394-7");
|
||||
assertEquals("LP101394-7", code.getCode());
|
||||
assertEquals("adjusted for maternal weight", code.getDisplay());
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
"AnswerListId","AnswerListName" ,"AnswerListOID" ,"ExtDefinedYN","ExtDefinedAnswerListCodeSystem","ExtDefinedAnswerListLink","AnswerStringId","LocalAnswerCode","LocalAnswerCodeSystem","SequenceNumber","DisplayText" ,"ExtCodeId","ExtCodeDisplayName","ExtCodeSystem","ExtCodeSystemVersion","ExtCodeSystemCopyrightNotice","SubsequentTextPrompt","Description","Score"
|
||||
"AnswerListId","AnswerListName" ,"AnswerListOID" ,"ExtDefinedYN","ExtDefinedAnswerListCodeSystem","ExtDefinedAnswerListLink","AnswerStringId","LocalAnswerCode","LocalAnswerCodeSystem","SequenceNumber","DisplayText" ,"ExtCodeId","ExtCodeDisplayName" ,"ExtCodeSystem" ,"ExtCodeSystemVersion" ,"ExtCodeSystemCopyrightNotice" ,"SubsequentTextPrompt","Description","Score"
|
||||
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165","N" , , ,"LA13825-7" ,"1" , ,1 ,"1 slice or 1 dinner roll" , , , , , , , ,
|
||||
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165","N" , , ,"LA13838-0" ,"2" , ,2 ,"2 slices or 2 dinner rolls" , , , , , , , ,
|
||||
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165","N" , , ,"LA13892-7" ,"3" , ,3 ,"More than 2 slices or 2 dinner rolls", , , , , , , ,
|
||||
@ -8,3 +8,4 @@
|
||||
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13853-9" ,"03" , ,4 ,"3-4 times per week" , , , , , , , ,
|
||||
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13860-4" ,"04" , ,5 ,"5-6 times per week" , , , , , , , ,
|
||||
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13827-3" ,"05" , ,6 ,"1 time per day" , , , , , , , ,
|
||||
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA4389-8" ,"97" , ,11 ,"Refused" ,"443390004","Refused (qualifier value)","http://snomed.info/sct","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College", , ,
|
||||
|
||||
|
Can't render this file because it contains an unexpected character in line 1 and column 31.
|
@ -1,4 +1,5 @@
|
||||
"LoincNumber","LongCommonName" ,"AnswerListId","AnswerListName" ,"AnswerListLinkType","ApplicableContext"
|
||||
"61438-8" ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days [PhenX]","LL1000-0" ,"PhenX05_13_30D bread amt","NORMATIVE" ,
|
||||
"10061-0" ,"S' wave amplitude in lead I" ,"LL1311-1" ,"PhenX12_44" ,"EXAMPLE" ,
|
||||
"10331-7" ,"Rh [Type] in Blood" ,"LL360-9" ,"Pos|Neg" ,"EXAMPLE" ,
|
||||
"10389-5" ,"Blood product.other [Type]" ,"LL2413-4" ,"Othr bld prod" ,"EXAMPLE" ,
|
||||
@ -8,4 +9,3 @@
|
||||
"10401-8" ,"Immune serum globulin given [Type]" ,"LL2421-7" ,"IM/IV" ,"EXAMPLE" ,
|
||||
"10410-9" ,"Plasma given [Type]" ,"LL2417-5" ,"Plasma type" ,"EXAMPLE" ,
|
||||
"10568-4" ,"Clarity of Semen" ,"LL2427-4" ,"Clear/Opales/Milky" ,"EXAMPLE" ,
|
||||
"61438-8" ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days [PhenX]","LL1000-0" ,"PhenX05_13_30D bread amt","NORMATIVE" ,
|
||||
|
||||
|
Can't render this file because it contains an unexpected character in line 1 and column 30.
|
@ -0,0 +1,10 @@
|
||||
"LoincNumber","LongCommonName","PartNumber","PartName","PartTypeName","LinkTypeName"
|
||||
"10000-8","R wave duration in lead AVR","LP31088-5","R wave duration.lead AVR","COMPONENT","Primary"
|
||||
"10000-8","R wave duration in lead AVR","LP6244-0","EKG","METHOD","Primary"
|
||||
"10000-8","R wave duration in lead AVR","LP6879-3","Time","PROPERTY","Primary"
|
||||
"10000-8","R wave duration in lead AVR","LP6960-1","Pt","TIME","Primary"
|
||||
"10000-8","R wave duration in lead AVR","LP7289-4","Heart","SYSTEM","Primary"
|
||||
"10000-8","R wave duration in lead AVR","LP7753-9","Qn","SCALE","Primary"
|
||||
"10000-8","R wave duration in lead AVR","LP7795-0","EKG.MEAS","CLASS","Primary"
|
||||
"10000-8","R wave duration in lead AVR","LP14259-3","Lead","COMPONENT","Search"
|
||||
"10000-8","R wave duration in lead AVR","LP14744-4","Duration","COMPONENT","Search"
|
||||
|
@ -0,0 +1,9 @@
|
||||
"PartNumber","PartTypeName","PartName","PartDisplayName","Status"
|
||||
"LP101394-7","ADJUSTMENT","adjusted for maternal weight","adjusted for maternal weight","ACTIVE"
|
||||
"LP101907-6","ADJUSTMENT","corrected for age","corrected for age","ACTIVE"
|
||||
"LP115711-6","ADJUSTMENT","corrected for background","corrected for background","ACTIVE"
|
||||
"LP147359-6","ADJUSTMENT","adjusted for body weight","adjusted for body weight","ACTIVE"
|
||||
"LP173482-3","ADJUSTMENT","1st specimen","1st specimen","DEPRECATED"
|
||||
"LP173483-1","ADJUSTMENT","post cyanocobalamin",,"ACTIVE"
|
||||
"LP173484-9","ADJUSTMENT","W hyperextension)",,"ACTIVE"
|
||||
"LP6244-0","METHOD","EKG","Electrocardiogram (EKG)","ACTIVE"
|
||||
|
@ -9,3 +9,4 @@
|
||||
"10019-8" ,"R' wave amplitude.lead V4" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V4; R wave Amp L-V4; Random; Right; Voltage" ,"R' wave Amp L-V4" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V4" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
|
||||
"10020-6" ,"R' wave amplitude.lead V5" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V5; R wave Amp L-V5; Random; Right; Voltage" ,"R' wave Amp L-V5" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V5" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
|
||||
"61438-8" ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30D","Find" ,"Pt" ,"^Patient" ,"Ord" ,"PhenX" ,"PHENX" ,"PhenX" ,"2.44" ,"MIN" , ,"TRIAL" , ,2 , , , ,"Each time you eat bread, toast or dinner rolls, how much do you usually eat?","PhenX.050201100100","N" , ,"Finding; Findings; How much bread in 30D; Last; Ordinal; Point in time; QL; Qual; Qualitative; Random; Screen" ,"How much bread in 30D PhenX", , , , , ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days [PhenX]", , , , , , , ,0 ,0 ,0 , , , , ,
|
||||
"10000-8" ,"R wave duration.lead AVR" ,"Time" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; Durat; ECG; EKG.MEASUREMENTS; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave dur L-AVR; R wave dur L-AVR; Random; Right" ,"R wave dur L-AVR" ,"Observation", , , ,"s" ,"R wave duration in lead AVR" , , ,"s" , , , , ,0 ,0 ,0 , , , , ,
|
||||
|
||||
|
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Reference in New Issue
Block a user