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Initial support for JSON file-based Bundle only. Will expand to URL-based later.
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| Original file line number | Diff line number | Diff line change |
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| package edu.phema.elm_to_omop.io; | ||
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| import ca.uhn.fhir.context.FhirContext; | ||
| import ca.uhn.fhir.parser.IParser; | ||
| import edu.phema.elm_to_omop.phenotype.BundlePhenotype; | ||
| import edu.phema.elm_to_omop.phenotype.PhenotypeException; | ||
| import edu.phema.elm_to_omop.repository.IOmopRepositoryService; | ||
| import edu.phema.elm_to_omop.repository.OmopRepositoryException; | ||
| import edu.phema.elm_to_omop.vocabulary.FhirBundleConceptSetService; | ||
| import edu.phema.elm_to_omop.vocabulary.IValuesetService; | ||
| import edu.phema.elm_to_omop.vocabulary.ValuesetServiceException; | ||
| import edu.phema.elm_to_omop.vocabulary.phema.PhemaConceptSet; | ||
| import edu.phema.elm_to_omop.vocabulary.phema.PhemaValueSet; | ||
| import org.apache.poi.openxml4j.exceptions.InvalidFormatException; | ||
| import org.hl7.fhir.r4.model.Bundle; | ||
| import org.hl7.fhir.r4.model.Library; | ||
| import org.hl7.fhir.r4.model.ResourceType; | ||
| import org.hl7.fhir.r4.model.ValueSet; | ||
| import org.ohdsi.circe.vocabulary.Concept; | ||
| import org.ohdsi.circe.vocabulary.ConceptSetExpression; | ||
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|
||
| import java.io.File; | ||
| import java.io.FileReader; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.stream.Collectors; | ||
|
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| public class FhirReader { | ||
| // Initial file-based support will focus just on JSON files | ||
| public static final String BUNDLE_EXTENSION = ".json"; | ||
| private IOmopRepositoryService repository; | ||
| private static Map<String, String> codeSystemUriToOmopName = new HashMap<String, String>() {{ | ||
| // TODO Add more mappings as needed | ||
| put("http://www.ama-assn.org/go/cpt", "CPT4"); | ||
| put("http://hl7.org/fhir/sid/icd-9-cm", "ICD9CM"); | ||
| put("http://hl7.org/fhir/sid/icd-9-proc", "ICD9Proc"); | ||
| put("http://loinc.org", "LOINC"); | ||
| put("http://www.nlm.nih.gov/research/umls/rxnorm", "RxNorm"); | ||
| put("http://snomed.info/sct", "SNOMED"); | ||
| put("http://hl7.org/fhir/sid/icd-10", "ICD10"); | ||
| put("http://hl7.org/fhir/sid/icd-10-cm", "ICD10CM"); | ||
| put("http://www.icd10data.com/icd10pcs", "ICD10PCS"); | ||
| put("http://hl7.org/fhir/sid/icd-10-pcs", "ICD10PCS"); | ||
| put("http://hl7.org/fhir/sid/ndc", "NDC"); | ||
| put("http://hl7.org/fhir/ndfrt", "NDFRT"); | ||
| put("http://unitsofmeasure.org", "UCUM"); | ||
| put("http://www.whocc.no/atc", "ATC"); | ||
| put("http://terminology.hl7.org/CodeSystem/HCPCS", "HCPCS"); | ||
| }}; | ||
|
|
||
| public FhirReader(IOmopRepositoryService repository) { | ||
| this.repository = repository; | ||
| } | ||
|
|
||
| /** | ||
| * Given a FHIR Bundle stored as a JSON file, read all components (libraries, valuesets, etc.) | ||
| * and prepare it as a consolidated BundlePhenotype | ||
| * @param bundleFilePath The path to the Bundle JSON file | ||
| * @param omopService OMOP service to resolve concepts | ||
| * @return The consoldiated BundlePhenotype | ||
| * @throws PhenotypeException | ||
| */ | ||
| public static BundlePhenotype readBundleFromFile(String bundleFilePath, IOmopRepositoryService omopService) throws PhenotypeException { | ||
| File file = new File(bundleFilePath); | ||
| FhirContext ctx = FhirContext.forR4(); | ||
| IParser parser = ctx.newJsonParser(); | ||
| try { | ||
| Bundle bundle = parser.parseResource(Bundle.class, new FileReader(file)); | ||
| List<Bundle.BundleEntryComponent> entries = bundle.getEntry(); | ||
| // Load all of the libraries - this includes phenotype and supporting libraries | ||
| List<Library> libraryEntries = entries.stream() | ||
| .filter(x -> x.getResource().getResourceType() == ResourceType.Library) | ||
| .map(x -> (Library)x.getResource()) | ||
| .collect(Collectors.toList()); | ||
|
|
||
| List<ValueSet> valueSetEntries = entries.stream() | ||
| .filter(x -> x.getResource().getResourceType() == ResourceType.ValueSet) | ||
| .map(x -> (ValueSet)x.getResource()) | ||
| .collect(Collectors.toList()); | ||
|
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| IValuesetService service = new FhirBundleConceptSetService(valueSetEntries, omopService); | ||
| BundlePhenotype phenotype = new BundlePhenotype(); | ||
| phenotype.addLibraries(libraryEntries); | ||
| phenotype.setValuesetService(service); | ||
| return phenotype; | ||
| } catch (Exception e) { | ||
| throw new PhenotypeException("Error reading phenotype bundle", e); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Convert FHIR ValueSet resources to the PhemaConceptSet representation | ||
| * @param valueSets List of FHIR ValueSet resources | ||
| * @return List of PhemaConceptSets | ||
| * @throws IOException | ||
| * @throws OmopRepositoryException | ||
| * @throws InvalidFormatException | ||
| * @throws ValuesetServiceException | ||
| */ | ||
| public List<PhemaConceptSet> getConceptSets(List<ValueSet> valueSets) throws IOException, OmopRepositoryException, InvalidFormatException, ValuesetServiceException { | ||
| List<PhemaConceptSet> conceptSets = new ArrayList<PhemaConceptSet>(valueSets.size()); | ||
| for (int index = 0; index < valueSets.size(); index++) { | ||
| ValueSet valueSet = valueSets.get(index); | ||
| conceptSets.add(getConceptSet(valueSet, index)); | ||
| } | ||
| return conceptSets; | ||
| } | ||
|
|
||
| /** | ||
| * Convert a ValueSet to a PhemaConceptSet | ||
| * @param valueSet FHIR ValueSet resource to convert | ||
| * @param index The index the valueset appears - must be unique | ||
| * @return PhemaConceptSet containing all codes from the value set | ||
| * @throws OmopRepositoryException | ||
| * @throws ValuesetServiceException | ||
| */ | ||
| private PhemaConceptSet getConceptSet(ValueSet valueSet, int index) throws OmopRepositoryException, ValuesetServiceException { | ||
| // TODO - account for more than just "include", but this will work for now | ||
| List<Concept> concepts = new ArrayList<>(); | ||
| List<ValueSet.ConceptSetComponent> components = valueSet.getCompose().getInclude(); | ||
| for (ValueSet.ConceptSetComponent component : components) { | ||
| String codeSystem = component.getSystem(); | ||
| if (!codeSystemUriToOmopName.containsKey(codeSystem)) { | ||
| throw new ValuesetServiceException(String.format("Unable to transform the code system %s", codeSystem)); | ||
| } | ||
| codeSystem = codeSystemUriToOmopName.get(codeSystem); | ||
| for (ValueSet.ConceptReferenceComponent concept : component.getConcept()) { | ||
| concepts.addAll(repository.vocabularySearch(concept.getCode(), codeSystem)); | ||
| } | ||
| } | ||
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| PhemaConceptSet conceptSet = new PhemaConceptSet(); | ||
| conceptSet.setOid(valueSet.getIdElement().getIdPart()); | ||
| conceptSet.id = index; | ||
| conceptSet.name = valueSet.getName(); | ||
| ArrayList<ConceptSetExpression.ConceptSetItem> itemsList = new ArrayList<>(); | ||
| for (Concept concept : concepts) { | ||
| ConceptSetExpression.ConceptSetItem item = new ConceptSetExpression.ConceptSetItem(); | ||
| item.concept = concept; | ||
| itemsList.add(item); | ||
| } | ||
|
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| ConceptSetExpression.ConceptSetItem[] items = new ConceptSetExpression.ConceptSetItem[itemsList.size()]; | ||
| ConceptSetExpression expression = new ConceptSetExpression(); | ||
| expression.items = itemsList.toArray(items); | ||
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| conceptSet.expression = expression; | ||
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| return conceptSet; | ||
| } | ||
| } |
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