Examples with CqlRule org.hl7.davinci.endpoint.cql.CqlRule used on opensource projects

Example 1 with CqlRule

use of org.hl7.davinci.endpoint.cql.CqlRule in project CRD by HL7-DaVinci.

the class CqlRule method getFhirVersionFromCqlFile.

private static String getFhirVersionFromCqlFile(byte[] cql) {
    String fhirVersion = "";
    UsingDef usingDef = new UsingDef();
    Pattern pattern = Pattern.compile("using (.*?) version '(.*?)'");
    try {
        Matcher matcher = pattern.matcher(new String(cql));
        while (fhirVersion.isEmpty()) {
            matcher.find();
            if (matcher.groupCount() != 2) {
                throw new RuntimeException("Encountered bad CQL file, could not detect library identifier.");
            }
            if (matcher.group(1).equalsIgnoreCase("FHIR")) {
                fhirVersion = matcher.group(2);
            }
        }
    } catch (Exception e) {
        logger.warn("exception in CqlRule::getFhirVersionFromCqlFile(): " + e.getMessage());
    }
    return fhirVersion;
}

Example 2 with CqlRule

use of org.hl7.davinci.endpoint.cql.CqlRule in project CRD by HL7-DaVinci.

the class CqlExecutionContextBuilder method getExecutionContext.

public static Context getExecutionContext(CqlRule cqlRule, HashMap<String, Resource> cqlParams, String baseUrl) {
    ModelManager modelManager = new ModelManager();
    LibraryManager libraryManager = new LibraryManager(modelManager);
    libraryManager.getLibrarySourceLoader().clearProviders();
    Library library = null;
    LibraryLoader libraryLoader = null;
    if (cqlRule.isPrecompiled()) {
    // todo
    } else {
        libraryManager.getLibrarySourceLoader().registerProvider(cqlRule.getRawCqlLibrarySourceProvider(CQL_VERSION));
        libraryLoader = new LocalLibraryLoader(libraryManager);
        try {
            library = CqlExecution.translate(cqlRule.getRawMainCqlLibrary(CQL_VERSION), libraryManager, modelManager);
        } catch (Exception e) {
            throw new RuntimeException(e);
        }
    }
    FhirContext fhirContext = FhirContext.forR4();
    Context context = new Context(library);
    context.registerLibraryLoader(libraryLoader);
    context.setExpressionCaching(true);
    R4FhirModelResolver modelResolver = new R4FhirModelResolver();
    RestFhirRetrieveProvider retrieveProvider = new RestFhirRetrieveProvider(new SearchParameterResolver(fhirContext), fhirContext.newRestfulGenericClient("http://fhirtest.uhn.ca/baseR4"));
    CompositeDataProvider provider = new CompositeDataProvider(modelResolver, retrieveProvider);
    context.registerDataProvider("http://hl7.org/fhir", provider);
    for (Map.Entry<String, org.hl7.fhir.r4.model.Resource> entry : cqlParams.entrySet()) {
        context.setParameter(null, entry.getKey(), entry.getValue());
    }
    context.setParameter(null, "base_url", baseUrl);
    return context;
}

Example 3 with CqlRule

use of org.hl7.davinci.endpoint.cql.CqlRule in project CRD by HL7-DaVinci.

the class FhirBundleProcessor method buildExecutionContexts.

private void buildExecutionContexts(List<CoverageRequirementRuleCriteria> criteriaList, HashMap<String, Resource> cqlParams) {
    for (CoverageRequirementRuleCriteria criteria : criteriaList) {
        logger.info("FhirBundleProcessor::buildExecutionContexts() criteria: " + criteria.toString());
        List<RuleMapping> rules = fileStore.findRules(criteria);
        for (RuleMapping rule : rules) {
            CoverageRequirementRuleResult result = new CoverageRequirementRuleResult();
            result.setCriteria(criteria).setTopic(rule.getTopic());
            try {
                logger.info("FhirBundleProcessor::buildExecutionContexts() found rule topic: " + rule.getTopic());
                // get the CqlRule
                CqlRule cqlRule = fileStore.getCqlRule(rule.getTopic(), rule.getFhirVersion());
                result.setContext(CqlExecutionContextBuilder.getExecutionContext(cqlRule, cqlParams, baseUrl));
                results.add(result);
            } catch (Exception e) {
                logger.info("r4/FhirBundleProcessor::buildExecutionContexts: failed processing cql bundle: " + e.getMessage());
            }
        }
    }
}

Example 4 with CqlRule

use of org.hl7.davinci.endpoint.cql.CqlRule in project CRD by HL7-DaVinci.

the class CqlRule method build.

private void build(HashMap<String, byte[]> cqlFiles, HashMap<String, byte[]> jsonElmFiles, HashMap<String, byte[]> xmlElmFiles) {
    // build a list of all of the CQL Libraries
    List<CqlRule.CqlLibrary> cqlLibraries = new ArrayList<>();
    for (String fileName : cqlFiles.keySet()) {
        logger.debug("CqlRule: file: " + fileName);
        CqlRule.CqlLibrary cqlLibrary = new CqlRule.CqlLibrary();
        cqlLibrary.cql = cqlFiles.get(fileName);
        // only add those that are the right fhir version
        String fhirVersionFromCql = getFhirVersionFromCqlFile(cqlLibrary.cql);
        // last character of fhirVersion ("R4" => "4") and first character of FHIR version from file ("3.0.0" => "3")
        if (fhirVersion.substring(fhirVersion.length() - 1).equalsIgnoreCase(fhirVersionFromCql.substring(0, 1))) {
            String fileNameWithoutExtension = fileName.substring(0, fileName.length() - 4);
            String xmlElmName = fileNameWithoutExtension + ".xml";
            if (xmlElmFiles.containsKey(xmlElmName)) {
                cqlLibrary.xlmElm = true;
                cqlLibrary.elm = xmlElmFiles.get(xmlElmName);
            }
            String jsonElmName = fileNameWithoutExtension + ".json";
            if (jsonElmFiles.containsKey(jsonElmName)) {
                cqlLibrary.xlmElm = false;
                cqlLibrary.elm = jsonElmFiles.get(jsonElmName);
            }
            cqlLibraries.add(cqlLibrary);
        }
    }
    precompiled = false;
    for (CqlLibrary cqlLibrary : cqlLibraries) {
        if (precompiled) {
            if (cqlLibrary.elm == null) {
                throw new RuntimeException("Package indicated CQL was precompiled, but elm xml missing.");
            }
        // TODO: need to set rulePackage.elmLibraries and mainCqlLibraryId
        } else {
            InputStream cqlStream = new ByteArrayInputStream(cqlLibrary.cql);
            VersionedIdentifier id = getIdFromCqlFile(cqlLibrary.cql);
            String fhirVersionFromFile = getFhirVersionFromCqlFile(cqlLibrary.cql);
            logger.info("CqlRule::Constructor() add id: " + id.getId() + ", fhir version: " + fhirVersionFromFile);
            if (rawCqlLibraries.containsKey(fhirVersionFromFile)) {
                // logger.info("CqlRule::Constructor() add rawCqlLibraries add: " + id.getId());
                rawCqlLibraries.get(fhirVersionFromFile).put(id, cqlStream);
            } else {
                HashMap<VersionedIdentifier, InputStream> map = new HashMap<>();
                map.put(id, cqlStream);
                // logger.info("CqlRule::Constructor() add rawCqlLibraries new: " + id.getId());
                rawCqlLibraries.put(fhirVersionFromFile, map);
            }
            if (id.getId().equals(mainCqlLibraryName)) {
                // logger.info("CqlRule::Constructor() add mainCqlLibraryId: " + id.getId());
                mainCqlLibraryId.put(fhirVersionFromFile, id);
            }
        }
    }
}

Example 5 with CqlRule

use of org.hl7.davinci.endpoint.cql.CqlRule in project CRD by HL7-DaVinci.

the class GitHubFileStore method getCqlRule.

public CqlRule getCqlRule(String topic, String fhirVersion) {
    logger.info("GitHubFileStore::getCqlRule(): " + topic + "/" + fhirVersion);
    // load CQL files needed for the CRD Rule
    HashMap<String, byte[]> cqlFiles = new HashMap<>();
    String rulePath = config.getGitHubConfig().getRulePath();
    String examplesPath = config.getGitHubConfig().getExamplesPath();
    String mainCqlLibraryName = topic + "Rule";
    String mainCqlFile = findGitHubFile(topic, fhirVersion, mainCqlLibraryName, FileStore.CQL_EXTENSION);
    if (mainCqlFile == null) {
        logger.warn("GitHubFileStore::getCqlRule(): failed to find main CQL file");
    } else {
        String mainCqlFilePath = rulePath + topic + "/" + fhirVersion + "/files/" + mainCqlFile;
        try {
            InputStream inputStream = connection.getFile(mainCqlFilePath);
            if (inputStream == null) {
                // look for the main cql file in the examples path as well
                mainCqlFilePath = examplesPath + topic + "/" + fhirVersion + "/files/" + mainCqlFile;
                inputStream = connection.getFile(mainCqlFilePath);
            }
            cqlFiles.put(mainCqlFile, IOUtils.toByteArray(inputStream));
            logger.info("GitHubFileStore::getCqlRule(): added mainCqlFile: " + mainCqlFile);
        } catch (IOException e) {
            logger.warn("GitHubFileStore::getCqlRule(): failed to open main cql file: " + e.getMessage());
        }
    }
    String helperCqlFile = findGitHubFile(FileStore.SHARED_TOPIC, fhirVersion, FileStore.FHIR_HELPERS_FILENAME, FileStore.CQL_EXTENSION);
    if (helperCqlFile == null) {
        logger.warn("GitHubFileStore::getCqlRule(): failed to find FHIR helper CQL file");
    } else {
        String helperCqlFilePath = rulePath + "Shared/" + fhirVersion + "/files/" + helperCqlFile;
        try {
            InputStream inputStream = connection.getFile(helperCqlFilePath);
            if (inputStream == null) {
                // look for the helper cql file in the examples path as well
                helperCqlFilePath = examplesPath + "Shared/" + fhirVersion + "/files/" + helperCqlFile;
                inputStream = connection.getFile(helperCqlFilePath);
            }
            cqlFiles.put(helperCqlFile, IOUtils.toByteArray(inputStream));
            logger.info("GitHubFileStore::getCqlRule(): added helperCqlFile: " + helperCqlFile);
        } catch (IOException e) {
            logger.warn("GitHubFileStore::getCqlRule(): failed to open file FHIR helper cql file: " + e.getMessage());
        }
    }
    return new CqlRule(mainCqlLibraryName, cqlFiles, fhirVersion);
}