Examples with ConceptSetComponent org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent used on opensource projects

Example 76 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project snowstorm by IHTSDO.

the class FHIRHelper method convertToECL.

public String convertToECL(ConceptSetComponent setDefn) throws FHIROperationException {
    String ecl = "";
    boolean firstItem = true;
    for (ConceptReferenceComponent concept : setDefn.getConcept()) {
        if (firstItem) {
            firstItem = false;
        } else {
            ecl += " OR ";
        }
        ecl += concept.getCode() + "|" + concept.getDisplay() + "|";
    }
    ecl += convertFilterToECL(setDefn, firstItem);
    return ecl;
}

Example 77 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project snowstorm by IHTSDO.

the class FHIRValueSetProvider method obtainConsistentCodeSystemVersionFromCompose.

private BranchPath obtainConsistentCodeSystemVersionFromCompose(ValueSetComposeComponent compose, BranchPath branchPath) throws FHIROperationException {
    String system = null;
    String version = null;
    // Check all include and exclude elements to ensure they have a consistent snomed URI
    List<ConceptSetComponent> allIncludeExcludes = new ArrayList<>(compose.getInclude());
    allIncludeExcludes.addAll(compose.getExclude());
    for (ConceptSetComponent thisIncludeExclude : allIncludeExcludes) {
        if (thisIncludeExclude.getSystem() != null && !thisIncludeExclude.getSystem().contains(SNOMED_URI)) {
            throw new FHIROperationException(IssueType.NOTSUPPORTED, "Server currently limited to compose elements using SNOMED CT code system");
        }
        if (thisIncludeExclude.getSystem() != null && system == null) {
            system = thisIncludeExclude.getSystem();
        }
        if (thisIncludeExclude.getVersion() != null && version == null) {
            version = thisIncludeExclude.getVersion();
        }
        if (system != null && thisIncludeExclude.getSystem() != null && !system.equals(thisIncludeExclude.getSystem())) {
            String msg = "Server currently requires consistency in ValueSet compose element code systems.";
            msg += " Encoundered both '" + system + "' and '" + thisIncludeExclude.getSystem() + "'.";
            throw new FHIROperationException(IssueType.NOTSUPPORTED, msg);
        }
        if (version != null && thisIncludeExclude.getVersion() != null && !version.equals(thisIncludeExclude.getVersion())) {
            throw new FHIROperationException(IssueType.NOTSUPPORTED, "Server currently requires consistency in ValueSet compose element code system versions");
        }
    }
    StringType codeSystemVersionUri;
    if (version == null) {
        if (system == null) {
            return branchPath;
        } else {
            codeSystemVersionUri = new StringType(system);
        }
    } else {
        codeSystemVersionUri = new StringType(version);
    }
    return fhirHelper.getBranchPathFromURI(codeSystemVersionUri);
}

Example 78 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project snowstorm by IHTSDO.

the class FHIRValueSetProvider method covertComposeToEcl.

public String covertComposeToEcl(ValueSetComposeComponent compose) throws FHIROperationException {
    // Successive include elements will be added using 'OR'
    // While the excludes will be added using 'MINUS'
    String ecl = "";
    boolean isFirstInclude = true;
    for (ConceptSetComponent include : compose.getInclude()) {
        if (isFirstInclude) {
            isFirstInclude = false;
        } else {
            ecl += " OR ";
        }
        ecl += "( " + fhirHelper.convertToECL(include) + " )";
    }
    // We need something to minus!
    if (isFirstInclude) {
        throw new FHIROperationException(IssueType.VALUE, "Invalid use of exclude without include in ValueSet compose element.");
    }
    for (ConceptSetComponent exclude : compose.getExclude()) {
        ecl += " MINUS ( " + fhirHelper.convertToECL(exclude) + " )";
    }
    return ecl;
}

Example 79 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project snowstorm by IHTSDO.

the class FHIRValueSetProvider method doExplicitExpansion.

/**
 * An explicit ValueSet has been saved on the server with a name and id, and
 * is defined by use of the "compose" element within the valueset resource.
 * @param branchPathForced
 */
private Page<ConceptMini> doExplicitExpansion(ValueSet vs, Boolean active, String filter, BranchPath branchPath, List<LanguageDialect> designations, PageRequest pageRequest, boolean branchPathForced) throws FHIROperationException {
    Page<ConceptMini> conceptMiniPage = new PageImpl<>(new ArrayList<>());
    if (vs != null && vs.getCompose() != null && !vs.getCompose().isEmpty()) {
        if (!branchPathForced) {
            branchPath.set(obtainConsistentCodeSystemVersionFromCompose(vs.getCompose(), branchPath));
        }
        ValueSetComposeComponent compose = vs.getCompose();
        Set<String> conceptIds = new HashSet<>();
        StringBuilder filterECL = new StringBuilder();
        boolean firstItem = true;
        for (ConceptSetComponent include : compose.getInclude()) {
            conceptIds.addAll(include.getConcept().stream().map(ValueSet.ConceptReferenceComponent::getCode).collect(Collectors.toSet()));
            filterECL.append(fhirHelper.convertFilterToECL(include, firstItem));
            if (firstItem) {
                firstItem = false;
            }
        }
        firstItem = true;
        for (ConceptSetComponent exclude : compose.getExclude()) {
            conceptIds.addAll(exclude.getConcept().stream().map(ValueSet.ConceptReferenceComponent::getCode).collect(Collectors.toSet()));
            filterECL.append(fhirHelper.convertFilterToECL(exclude, firstItem));
            if (firstItem) {
                firstItem = false;
            }
        }
        String branch = branchPath.toString();
        Collection<ConceptMini> fromService = conceptService.findConceptMinis(branch, conceptIds, designations).getResultsMap().values();
        logger.info("Recovered {} Concepts from branch {} with Compose.", fromService.size(), branch);
        String ecl = filterECL.toString();
        Page<ConceptMini> page = fhirHelper.eclSearch(ecl, active, filter, designations, branchPath, pageRequest);
        Collection<ConceptMini> fromECL = page.getContent();
        logger.info("Recovered {} Concepts from branch {} with ECL {}.", page.getTotalElements(), branch, filterECL);
        List<ConceptMini> conceptMinis = new ArrayList<>();
        conceptMinis.addAll(fromService);
        conceptMinis.addAll(fromECL);
        long totalCount = fromService.size() + page.getTotalElements();
        conceptMiniPage = new PageImpl<ConceptMini>(conceptMinis, page.getPageable(), totalCount);
        logger.info("Collectively recovered {} Concepts from branch {}.", conceptMiniPage.getTotalElements(), branch);
    } else {
        String msg = "Compose element(s) or 'url' parameter is expected to be present for an expansion, containing eg http://snomed.info/sct?fhir_vs=ecl/ or http://snomed.info/sct/45991000052106?fhir_vs=ecl/ ";
        // We don't need ECL if we're expanding a named valueset
        if (vs != null) {
            logger.warn(msg + " when expanding " + vs.getId());
        } else {
            throw new FHIROperationException(IssueType.VALUE, msg);
        }
    }
    return conceptMiniPage;
}

Example 80 with ConceptSetComponent

use of org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent in project quality-measure-and-cohort-service by Alvearie.

the class R4FileSystemFhirTerminologyProvider method loadFromFile.

/**
 * Loads ValueSet definitions from the filesystem or S3 compatible location
 * ValueSet definitions are expected to be stored in FHIR xml or JSON format
 * named using the valueSet id (ie 2.16.840.1.113762.1.4.1114.7.json)
 *
 * @param valueSetInfo contains information for teh VlaueSet we want to load
 */
protected void loadFromFile(ValueSetInfo valueSetInfo) throws RuntimeException {
    LOG.debug("Entry: loadFromFile() ValueSet.getId=[{}] version=[{}]", valueSetInfo.getId(), valueSetInfo.getVersion());
    VersionedIdentifier valueSetIdentifier = createVersionedIdentifierForValueSet(valueSetInfo);
    String valueSetId = valueSetIdentifier.getId();
    // get the valueSet codes from the cache if it is there
    Map<String, Set<String>> codesToCodeSystems = valueSetToCodesCache.get(valueSetIdentifier);
    List<Code> codeList = valueSetCodeCache.get(valueSetIdentifier);
    if (codesToCodeSystems == null || codeList == null) {
        LOG.debug("loadFromFile() valueSetId={} not found in cache, attempting to load from file", valueSetId);
        FileStatus[] valueSetFiles;
        FileSystem fileSystem;
        // List the files in the terminology directory that end in xml or json
        try {
            fileSystem = terminologyDirectory.getFileSystem(configuration);
            valueSetFiles = fileSystem.listStatus(terminologyDirectory, new PathFilter() {

                @Override
                public boolean accept(Path path) {
                    return path.getName().equalsIgnoreCase(valueSetId + ".json") || path.getName().equalsIgnoreCase(valueSetId + ".xml");
                }
            });
        } catch (ConfigurationException | DataFormatException | IOException e) {
            LOG.error("Error attempting to get ValueSet file for ValueSet [" + valueSetId + " from " + terminologyDirectory.toString(), e);
            throw new RuntimeException("Error attempting to get ValueSet file for ValueSet [" + valueSetId + " from " + terminologyDirectory.toString(), e);
        }
        if (valueSetFiles.length == 0) {
            LOG.error("No valueSet file " + valueSetId + ".json or " + valueSetId + ".xml found in terminology directory " + terminologyDirectory.toString());
            throw new RuntimeException("No valueSet file " + valueSetId + ".json or " + valueSetId + ".xml found in terminology directory " + terminologyDirectory.toString());
        } else {
            if (valueSetFiles.length > 1) {
                LOG.warn("Multiple ValueSet files found for ValueSet {} in terminology directory {}. File {} will be used.", valueSetId, terminologyDirectory.toString(), valueSetFiles[0].toString());
            }
            ValueSet valueSetFhirR4 = null;
            try {
                // Use the fhir parsers to convert file contents back into ValueSet fhir object
                if (valueSetFiles[0].getPath().getName().toLowerCase().endsWith(".xml")) {
                    valueSetFhirR4 = (ValueSet) fhirContext.newXmlParser().parseResource(new InputStreamReader(fileSystem.open(valueSetFiles[0].getPath())));
                    LOG.info("Unmarshalled xml {}", valueSetFhirR4.getId());
                } else if (valueSetFiles[0].getPath().getName().toLowerCase().endsWith(".json")) {
                    valueSetFhirR4 = (ValueSet) fhirContext.newJsonParser().parseResource(new InputStreamReader(fileSystem.open(valueSetFiles[0].getPath())));
                    LOG.info("Unmarshalled json {}", valueSetFhirR4.getId());
                }
                // This improves performance for the in() method for code lookup in large valuesets
                codesToCodeSystems = new HashMap<String, Set<String>>();
                // cache the list of code objects for the expand method
                codeList = new ArrayList<Code>();
                for (ConceptSetComponent csc : valueSetFhirR4.getCompose().getInclude()) {
                    for (ConceptReferenceComponent cfc : csc.getConcept()) {
                        codeList.add(new Code().withCode(cfc.getCode()).withDisplay(cfc.getDisplay()).withSystem(csc.getSystem()).withVersion(csc.getVersion()));
                        Set<String> codeSystems = codesToCodeSystems.get(cfc.getCode());
                        if (codeSystems == null) {
                            codeSystems = new HashSet<String>();
                            codesToCodeSystems.put(cfc.getCode(), codeSystems);
                        }
                        codeSystems.add(csc.getSystem());
                    }
                }
                valueSetToCodesCache.put(valueSetIdentifier, codesToCodeSystems);
                valueSetCodeCache.put(valueSetIdentifier, codeList);
            } catch (ConfigurationException | DataFormatException | IOException e) {
                LOG.error("Error attempting to deserialize ValueSet " + valueSetFiles[0].getPath().toString(), e);
                throw new RuntimeException("Error attempting to deserialize ValueSet " + valueSetFiles[0].getPath().toString(), e);
            }
        }
    }
    LOG.debug("Exit: loadFromFile() ValueSet.getId=[{}] version=[{}]", valueSetInfo.getId(), valueSetInfo.getVersion());
}