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modifications for "parameters" and "languages" #15

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modifications for "parameters" and "languages" #15

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274b992
changes for parameters group
bdc-ehealth Jan 17, 2025
72a6b10
changes for the language group
bdc-ehealth Jan 21, 2025
dd3c81a
fix valueset language bug
bdc-ehealth Jan 21, 2025
5837c28
Merge pull request #17 from IHTSDO/fhir-tests
bdc-ehealth Jan 27, 2025
6e6b615
Merge branch 'issue-15' into master
bdc-ehealth Jan 27, 2025
adbc0ac
Merge pull request #18 from ehealthplatformstandards/master
bdc-ehealth Jan 27, 2025
9d3b22d
Merge pull request #19 from ehealthplatformstandards/issue-15
bdc-ehealth Jan 27, 2025
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38 changes: 36 additions & 2 deletions src/main/java/org/snomed/snowstorm/fhir/domain/FHIRCodeSystemVersion.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import com.fasterxml.jackson.annotation.JsonIgnore;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Extension;
import org.joda.time.DateTime;
import org.joda.time.format.DateTimeFormat;
import org.joda.time.format.DateTimeFormatter;
Expand All @@ -16,6 +17,7 @@
import org.springframework.data.elasticsearch.annotations.*;

import java.util.Date;
import java.util.List;

import static org.snomed.snowstorm.fhir.config.FHIRConstants.*;

Expand All @@ -31,6 +33,9 @@ public class FHIRCodeSystemVersion {
@Field(type = FieldType.Keyword)
private String version;

@Field(type = FieldType.Keyword)
private String language;

@Field(type = FieldType.Date, format = DateFormat.date_time)
private Date date;

Expand All @@ -55,6 +60,9 @@ public class FHIRCodeSystemVersion {
@Field(type = FieldType.Keyword)
private String content;

@Field(type = FieldType.Nested)
private List<Extension> extensions;

@Transient
private String snomedBranch;

Expand Down Expand Up @@ -84,6 +92,7 @@ public FHIRCodeSystemVersion(CodeSystem codeSystem) {
version = codeSystem.getVersion();
date = codeSystem.getDate();
title = codeSystem.getTitle();
language = codeSystem.getLanguage();
if (title != null) {
title = title.replace(" Code System", "");
}
Expand All @@ -96,6 +105,7 @@ public FHIRCodeSystemVersion(CodeSystem codeSystem) {
compositional = codeSystem.getCompositional();
CodeSystem.CodeSystemContentMode codeSystemContent = codeSystem.getContent();
content = codeSystemContent != null ? codeSystemContent.toCode() : null;
extensions = codeSystem.getExtension();
}

public FHIRCodeSystemVersion(CodeSystemVersion snomedVersion) {
Expand Down Expand Up @@ -144,9 +154,13 @@ public FHIRCodeSystemVersion(org.snomed.snowstorm.core.data.domain.CodeSystem sn

public CodeSystem toHapiCodeSystem() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setExtension(extensions);
codeSystem.setId(id);
codeSystem.setUrl(url);
codeSystem.setVersion(version);
if(!"0".equals(version)) {
codeSystem.setVersion(version);
}
codeSystem.setLanguage(language);
codeSystem.setDate(date);
codeSystem.setName(name);
codeSystem.setTitle(title);
Expand Down Expand Up @@ -181,7 +195,11 @@ public boolean isVersionMatch(String requestedVersion) {
}

public String getCanonical() {
return url + "|" + version;
if ("0".equals(version)){
return url;
} else {
return url + "|" + version;
}
}

public String getId() {
Expand Down Expand Up @@ -248,6 +266,14 @@ public void setPublisher(String publisher) {
this.publisher = publisher;
}

public List<Extension> getExtensions() {
return extensions;
}

public void setExtensions(List<Extension> extensions) {
this.extensions = extensions;
}

public String getHierarchyMeaning() {
return hierarchyMeaning;
}
Expand Down Expand Up @@ -291,4 +317,12 @@ public CodeSystemVersion getSnomedCodeSystemVersion() {
public String toString() {
return getId();
}

public String getLanguage() {
return language;
}

public void setLanguage(String language) {
this.language = language;
}
}
53 changes: 50 additions & 3 deletions src/main/java/org/snomed/snowstorm/fhir/domain/FHIRConcept.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.*;
import org.snomed.snowstorm.core.data.domain.ConceptMini;
import org.snomed.snowstorm.core.data.domain.Description;
import org.snomed.snowstorm.core.pojo.LanguageDialect;
Expand All @@ -24,6 +24,8 @@
@Document(indexName = "#{@indexNameProvider.indexName('fhir-concept')}", createIndex = false)
public class FHIRConcept implements FHIRGraphNode {

public static final String EXTENSION_MARKER = "://";

public interface Fields {

String CODE_SYSTEM_VERSION = "codeSystemVersion";
Expand All @@ -33,6 +35,7 @@ public interface Fields {
String PARENTS = "parents";
String ANCESTORS = "ancestors";
String PROPERTIES = "properties";
String EXTENSIONS = "extensions";
}
@Id
// Internal ID
Expand Down Expand Up @@ -62,6 +65,8 @@ public interface Fields {

private Map<String, List<FHIRProperty>> properties;

private Map<String, List<FHIRProperty>> extensions;

public FHIRConcept() {
active = true;
}
Expand All @@ -80,11 +85,17 @@ public FHIRConcept(TermConcept termConcept, FHIRCodeSystemVersion codeSystemVers
}

properties = new HashMap<>();
for (TermConceptProperty property : termConcept.getProperties()) {
for (TermConceptProperty property : termConcept.getProperties().stream().filter(p -> !p.getKey().contains(EXTENSION_MARKER)).toList()) {
properties.computeIfAbsent(property.getKey(), (i) -> new ArrayList<>())
.add(new FHIRProperty(property));
}

extensions = new HashMap<>();
for (TermConceptProperty extension : termConcept.getProperties().stream().filter(p -> p.getKey().contains(EXTENSION_MARKER)).toList()) {
extensions.computeIfAbsent(extension.getKey(), (i) -> new ArrayList<>())
.add(new FHIRProperty(extension));
}

parents = new HashSet<>();
for (TermConceptParentChildLink parent : termConcept.getParents()) {
parents.add(parent.getParent().getCode());
Expand All @@ -109,9 +120,37 @@ public FHIRConcept(CodeSystem.ConceptDefinitionComponent definitionConcept, FHIR
Optional.ofNullable(definitionConcept.getDefinition()).ifPresent(x -> properties.put("definition",Collections.singletonList(new FHIRProperty("definition",null,x,FHIRProperty.STRING))));
definitionConcept.getProperty().stream().filter(x-> x.getCode().equals("status") && x.getValueCodeType().getCode().equals("retired") ).findFirst().ifPresentOrElse(x -> active= false, ()->active =true);
properties.put("inactive",Collections.singletonList(new FHIRProperty("inactive",null,Boolean.toString(!isActive()),FHIRProperty.BOOLEAN)));
extensions = new HashMap<>();
definitionConcept.getExtension().forEach(
e ->{
Optional.ofNullable(extensions.get(e.getUrl())).ifPresentOrElse(list ->{
list.add(new FHIRProperty(e.getUrl(), null,e.getValue().primitiveValue(), FHIRProperty.typeToFHIRPropertyType(e.getValue())));

}, ()->{
List<FHIRProperty> list = new ArrayList<>();
list.add(new FHIRProperty(e.getUrl(), null,e.getValue().primitiveValue(), FHIRProperty.typeToFHIRPropertyType(e.getValue())));
extensions.put(e.getUrl(), list);
});

}
);
parents = new HashSet<>();
for (CodeSystem.ConceptPropertyComponent propertyComponent : definitionConcept.getProperty()) {
properties.computeIfAbsent(propertyComponent.getCode(), k -> new ArrayList<>()).add(new FHIRProperty(propertyComponent));
if (properties.get(propertyComponent.getCode())==null && !propertyComponent.getCode().contains(EXTENSION_MARKER)){
properties.put(propertyComponent.getCode(),new ArrayList<>());
}
try{
if(!propertyComponent.getCode().contains(EXTENSION_MARKER)){
properties.get(propertyComponent.getCode()).add(new FHIRProperty(propertyComponent));
}
} catch( UnsupportedOperationException e){
List<FHIRProperty> unmodifiableList = properties.get(propertyComponent.getCode());
List<FHIRProperty> modifiableList = new ArrayList<>();
modifiableList.addAll(unmodifiableList);
properties.put(propertyComponent.getCode(), modifiableList);
properties.get(propertyComponent.getCode()).add(new FHIRProperty(propertyComponent));
}

if (propertyComponent.getCode().equals("parent") || propertyComponent.getCode().equals("subsumedBy")) {
parents.add(propertyComponent.hasValueCoding() ? propertyComponent.getValueCoding().getCode() : propertyComponent.getValue().toString());
}
Expand Down Expand Up @@ -228,4 +267,12 @@ public Map<String, List<FHIRProperty>> getProperties() {
public void setProperties(Map<String, List<FHIRProperty>> properties) {
this.properties = properties;
}

public Map<String, List<FHIRProperty>> getExtensions() {
return extensions;
}

public void setExtensions(Map<String, List<FHIRProperty>> extensions) {
this.extensions = extensions;
}
}
54 changes: 53 additions & 1 deletion src/main/java/org/snomed/snowstorm/fhir/domain/FHIRDesignation.java
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Original file line number Diff line number Diff line change
@@ -1,10 +1,17 @@
package org.snomed.snowstorm.fhir.domain;

import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ValueSet;
import org.snomed.snowstorm.core.data.domain.Description;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Optional;

import static org.snomed.snowstorm.fhir.config.FHIRConstants.SNOMED_URI;

public class FHIRDesignation {
Expand All @@ -13,6 +20,10 @@ public class FHIRDesignation {
private String use;
private String value;



private List<FHIRExtension> extensions;

public FHIRDesignation() {
}

Expand Down Expand Up @@ -43,14 +54,36 @@ public FHIRDesignation(CodeSystem.ConceptDefinitionDesignationComponent designat
language = designation.getLanguage();
value = designation.getValue();
setUse(designation.getUse());
designation.getExtension().forEach( ext -> {
if (extensions == null){
extensions = new ArrayList<>();
}
extensions.add(new FHIRExtension(ext));
});
}

public FHIRDesignation(ValueSet.ConceptReferenceDesignationComponent designation) {
language = designation.getLanguage();
value = designation.getValue();
setUse(designation.getUse());
designation.getExtension().forEach( ext -> {
if (extensions == null){
extensions = new ArrayList<>();
}
extensions.add(new FHIRExtension(ext));
});
}

public void setUse(Coding useCoding) {
setUse(useCoding.getSystem(), useCoding.getCode());
}

public void setUse(String useSystem, String useCode) {
use = useSystem + "|" + useCode;
if(useSystem == null && useCode == null){
use = null;
} else {
use = useSystem + "|" + useCode;
}
}

public Coding getUseCoding() {
Expand All @@ -65,6 +98,17 @@ public Coding getUseCoding() {
return null;
}

public ValueSet.ConceptReferenceDesignationComponent getHapi() {
ValueSet.ConceptReferenceDesignationComponent hapiConceptReferenceDesignationComponent = new ValueSet.ConceptReferenceDesignationComponent();
hapiConceptReferenceDesignationComponent.setLanguage(language);
hapiConceptReferenceDesignationComponent.setValue(value);
if (StringUtils.isNotEmpty(use)) {
hapiConceptReferenceDesignationComponent.setUse(this.getUseCoding());
}
hapiConceptReferenceDesignationComponent.setExtension(Optional.ofNullable(extensions).orElse(Collections.emptyList()).stream().map(d->d.getHapi()).toList());
return hapiConceptReferenceDesignationComponent;
}

private static Coding addKnownDisplays(Coding coding) {
if (coding != null) {
if (SNOMED_URI.equals(coding.getSystem())) {
Expand Down Expand Up @@ -107,4 +151,12 @@ public String getValue() {
public void setValue(String value) {
this.value = value;
}

public List<FHIRExtension> getExtensions() {
return extensions;
}

public void setExtensions(List<FHIRExtension> extensions) {
this.extensions = extensions;
}
}
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