Examples with Interval org.opencds.cqf.cql.engine.runtime.Interval used on opensource projects

Example 1 with Interval

use of org.opencds.cqf.cql.engine.runtime.Interval in project cqf-ruler by DBCG.

the class LibraryEvaluationProvider method evaluate.

@SuppressWarnings({ "unchecked" })
@Operation(name = "$evaluate", idempotent = true, type = Library.class)
public Bundle evaluate(@IdParam IdType theId, @OperationParam(name = "patientId") String patientId, @OperationParam(name = "periodStart") String periodStart, @OperationParam(name = "periodEnd") String periodEnd, @OperationParam(name = "productLine") String productLine, @OperationParam(name = "terminologyEndpoint") Endpoint terminologyEndpoint, @OperationParam(name = "dataEndpoint") Endpoint dataEndpoint, @OperationParam(name = "context") String contextParam, @OperationParam(name = "executionResults") String executionResults, @OperationParam(name = "parameters") Parameters parameters, @OperationParam(name = "additionalData") Bundle additionalData, RequestDetails theRequestDetails) {
    log.info("Library evaluation started..");
    if (patientId == null && contextParam != null && contextParam.equals("Patient")) {
        log.error("Patient id null");
        throw new IllegalArgumentException("Must specify a patientId when executing in Patient context.");
    }
    Bundle libraryBundle = new Bundle();
    Library theResource = null;
    if (additionalData != null) {
        for (Bundle.BundleEntryComponent entry : additionalData.getEntry()) {
            if (entry.getResource().fhirType().equals("Library")) {
                libraryBundle.addEntry(entry);
                if (entry.getResource().getIdElement().equals(theId)) {
                    theResource = (Library) entry.getResource();
                }
            }
        }
    }
    if (theResource == null) {
        theResource = read(theId, theRequestDetails);
    }
    VersionedIdentifier libraryIdentifier = new VersionedIdentifier().withId(theResource.getName()).withVersion(theResource.getVersion());
    TerminologyProvider terminologyProvider;
    if (terminologyEndpoint != null) {
        IGenericClient client = Clients.forEndpoint(getFhirContext(), terminologyEndpoint);
        terminologyProvider = new R4FhirTerminologyProvider(client);
    } else {
        terminologyProvider = myJpaTerminologyProviderFactory.create(new SystemRequestDetails());
    }
    DataProvider dataProvider;
    if (dataEndpoint != null) {
        List<RetrieveProvider> retrieveProviderList = new ArrayList<>();
        IGenericClient client = Clients.forEndpoint(dataEndpoint);
        RestFhirRetrieveProvider retriever = new RestFhirRetrieveProvider(new SearchParameterResolver(getFhirContext()), client);
        retriever.setTerminologyProvider(terminologyProvider);
        if (terminologyEndpoint == null || (terminologyEndpoint != null && !terminologyEndpoint.getAddress().equals(dataEndpoint.getAddress()))) {
            retriever.setExpandValueSets(true);
        }
        retrieveProviderList.add(retriever);
        if (additionalData != null) {
            BundleRetrieveProvider bundleProvider = new BundleRetrieveProvider(getFhirContext(), additionalData);
            bundleProvider.setTerminologyProvider(terminologyProvider);
            retrieveProviderList.add(bundleProvider);
            PriorityRetrieveProvider priorityProvider = new PriorityRetrieveProvider(retrieveProviderList);
            dataProvider = new CompositeDataProvider(myModelResolver, priorityProvider);
        } else {
            dataProvider = new CompositeDataProvider(myModelResolver, retriever);
        }
    } else {
        List<RetrieveProvider> retrieveProviderList = new ArrayList<>();
        JpaFhirRetrieveProvider retriever = new JpaFhirRetrieveProvider(getDaoRegistry(), new SearchParameterResolver(getFhirContext()));
        retriever.setTerminologyProvider(terminologyProvider);
        // Assume it's a different server, therefore need to expand.
        if (terminologyEndpoint != null) {
            retriever.setExpandValueSets(true);
        }
        retrieveProviderList.add(retriever);
        if (additionalData != null) {
            BundleRetrieveProvider bundleProvider = new BundleRetrieveProvider(getFhirContext(), additionalData);
            bundleProvider.setTerminologyProvider(terminologyProvider);
            retrieveProviderList.add(bundleProvider);
            PriorityRetrieveProvider priorityProvider = new PriorityRetrieveProvider(retrieveProviderList);
            dataProvider = new CompositeDataProvider(myModelResolver, priorityProvider);
        } else {
            dataProvider = new CompositeDataProvider(myModelResolver, retriever);
        }
    }
    LibraryContentProvider bundleLibraryProvider = new BundleFhirLibraryContentProvider(this.getFhirContext(), libraryBundle, adapterFactory, libraryVersionSelector);
    LibraryContentProvider jpaLibraryContentProvider = this.myJpaLibraryContentProviderFactory.create(theRequestDetails);
    List<LibraryContentProvider> sourceProviders = new ArrayList<LibraryContentProvider>(Arrays.asList(bundleLibraryProvider, jpaLibraryContentProvider));
    LibraryLoader libraryLoader = this.myLibraryLoaderFactory.create(sourceProviders);
    CqlEngine engine = new CqlEngine(libraryLoader, Collections.singletonMap("http://hl7.org/fhir", dataProvider), terminologyProvider);
    Map<String, Object> resolvedParameters = new HashMap<>();
    if (parameters != null) {
        for (Parameters.ParametersParameterComponent pc : parameters.getParameter()) {
            resolvedParameters.put(pc.getName(), pc.getValue());
        }
    }
    if (periodStart != null && periodEnd != null) {
        // resolve the measurement period
        Interval measurementPeriod = new Interval(Operations.resolveRequestDate(periodStart, true), true, Operations.resolveRequestDate(periodEnd, false), true);
        resolvedParameters.put("Measurement Period", new Interval(DateTime.fromJavaDate((Date) measurementPeriod.getStart()), true, DateTime.fromJavaDate((Date) measurementPeriod.getEnd()), true));
    }
    if (productLine != null) {
        resolvedParameters.put("Product Line", productLine);
    }
    EvaluationResult evalResult = engine.evaluate(libraryIdentifier, null, Pair.of(contextParam != null ? contextParam : "Unspecified", patientId == null ? "null" : patientId), resolvedParameters, this.getDebugMap());
    List<Resource> results = new ArrayList<>();
    FhirMeasureBundler bundler = new FhirMeasureBundler();
    if (evalResult != null && evalResult.expressionResults != null) {
        for (Map.Entry<String, Object> def : evalResult.expressionResults.entrySet()) {
            Parameters result = new Parameters();
            try {
                result.setId(def.getKey());
                Object res = def.getValue();
                if (res == null) {
                    result.addParameter().setName("value").setValue(new StringType("null"));
                } else if (res instanceof List<?>) {
                    if (((List<?>) res).size() > 0 && ((List<?>) res).get(0) instanceof Resource) {
                        if (executionResults != null && executionResults.equals("Summary")) {
                            result.addParameter().setName("value").setValue(new StringType(((Resource) ((List<?>) res).get(0)).getIdElement().getResourceType() + "/" + ((Resource) ((List<?>) res).get(0)).getIdElement().getIdPart()));
                        } else {
                            result.addParameter().setName("value").setResource(bundler.bundle((Iterable<Resource>) res, theRequestDetails.getFhirServerBase()));
                        }
                    } else {
                        result.addParameter().setName("value").setValue(new StringType(res.toString()));
                    }
                } else if (res instanceof Iterable) {
                    result.addParameter().setName("value").setResource(bundler.bundle((Iterable<Resource>) res, theRequestDetails.getFhirServerBase()));
                } else if (res instanceof Resource) {
                    if (executionResults != null && executionResults.equals("Summary")) {
                        result.addParameter().setName("value").setValue(new StringType(((Resource) res).getIdElement().getResourceType() + "/" + ((Resource) res).getIdElement().getIdPart()));
                    } else {
                        result.addParameter().setName("value").setResource((Resource) res);
                    }
                } else if (res instanceof Type) {
                    result.addParameter().setName("value").setValue((Type) res);
                } else {
                    result.addParameter().setName("value").setValue(new StringType(res.toString()));
                }
                result.addParameter().setName("resultType").setValue(new StringType(resolveType(res)));
            } catch (RuntimeException re) {
                re.printStackTrace();
                String message = re.getMessage() != null ? re.getMessage() : re.getClass().getName();
                result.addParameter().setName("error").setValue(new StringType(message));
            }
            results.add(result);
        }
    }
    return bundler.bundle(results, theRequestDetails.getFhirServerBase());
}

Example 2 with Interval

use of org.opencds.cqf.cql.engine.runtime.Interval in project cqf-ruler by DBCG.

the class PrefetchDataProviderR4 method retrieve.

@Override
public Iterable<Object> retrieve(String context, String contextPath, Object contextValue, String dataType, String templateId, String codePath, Iterable<Code> codes, String valueSet, String datePath, String dateLowPath, String dateHighPath, Interval dateRange) {
    if (codePath == null && (codes != null || valueSet != null)) {
        throw new IllegalArgumentException("A code path must be provided when filtering on codes or a valueset.");
    }
    if (dataType == null) {
        throw new IllegalArgumentException("A data type (i.e. Procedure, Valueset, etc...) must be specified for clinical data retrieval");
    }
    // not be in the pre-fetch bundle, or might required a lookup by Id
    if (context.equals("Patient") && contextPath == null) {
        return Collections.emptyList();
    }
    List<Object> resourcesOfType = prefetchResources.get(dataType);
    if (resourcesOfType == null) {
        return Collections.emptyList();
    }
    // no resources or no filtering -> return list
    if (resourcesOfType.isEmpty() || (dateRange == null && codePath == null)) {
        return resourcesOfType;
    }
    List<Object> returnList = new ArrayList<>();
    for (Object resource : resourcesOfType) {
        boolean includeResource = true;
        if (dateRange != null) {
            if (datePath != null) {
                if (dateHighPath != null || dateLowPath != null) {
                    throw new IllegalArgumentException("If the datePath is specified, the dateLowPath and dateHighPath attributes must not be present.");
                }
                Object dateObject = PrefetchDataProviderHelper.getR4DateTime(this.resolver.resolvePath(resource, datePath));
                DateTime date = dateObject instanceof DateTime ? (DateTime) dateObject : null;
                Interval dateInterval = dateObject instanceof Interval ? (Interval) dateObject : null;
                String precision = PrefetchDataProviderHelper.getPrecision(Arrays.asList(dateRange, date));
                if (date != null && !(InEvaluator.in(date, dateRange, precision))) {
                    includeResource = false;
                } else // TODO - add precision to includes evaluator
                if (dateInterval != null && !(IncludesEvaluator.includes(dateRange, dateInterval, precision))) {
                    includeResource = false;
                }
            } else {
                if (dateHighPath == null && dateLowPath == null) {
                    throw new IllegalArgumentException("If the datePath is not given, either the lowDatePath or highDatePath must be provided.");
                }
                DateTime lowDate = dateLowPath == null ? null : (DateTime) PrefetchDataProviderHelper.getR4DateTime(this.resolver.resolvePath(resource, dateLowPath));
                DateTime highDate = dateHighPath == null ? null : (DateTime) PrefetchDataProviderHelper.getR4DateTime(this.resolver.resolvePath(resource, dateHighPath));
                String precision = PrefetchDataProviderHelper.getPrecision(Arrays.asList(dateRange, lowDate, highDate));
                Interval interval = new Interval(lowDate, true, highDate, true);
                // TODO - add precision to includes evaluator
                if (!IncludesEvaluator.includes(dateRange, interval, precision)) {
                    includeResource = false;
                }
            }
        }
        if (codePath != null && !codePath.equals("") && includeResource) {
            if (valueSet != null && terminologyProvider != null) {
                if (valueSet.startsWith("urn:oid:")) {
                    valueSet = valueSet.replace("urn:oid:", "");
                }
                ValueSetInfo valueSetInfo = new ValueSetInfo().withId(valueSet);
                codes = terminologyProvider.expand(valueSetInfo);
            }
            if (codes != null) {
                Object codeObject = PrefetchDataProviderHelper.getR4Code(this.resolver.resolvePath(resource, codePath));
                includeResource = PrefetchDataProviderHelper.checkCodeMembership(codes, codeObject, this.codeUtil);
            }
        }
        if (includeResource) {
            returnList.add(resource);
        }
    }
    return returnList;
}

Example 3 with Interval

use of org.opencds.cqf.cql.engine.runtime.Interval in project cqf-ruler by DBCG.

the class PrefetchDataProviderStu3 method retrieve.

@Override
public Iterable<Object> retrieve(String context, String contextPath, Object contextValue, String dataType, String templateId, String codePath, Iterable<Code> codes, String valueSet, String datePath, String dateLowPath, String dateHighPath, Interval dateRange) {
    if (codePath == null && (codes != null || valueSet != null)) {
        throw new IllegalArgumentException("A code path must be provided when filtering on codes or a valueset.");
    }
    if (dataType == null) {
        throw new IllegalArgumentException("A data type (i.e. Procedure, Valueset, etc...) must be specified for clinical data retrieval");
    }
    // not be in the pre-fetch bundle, or might required a lookup by Id
    if (context.equals("Patient") && contextPath == null) {
        return Collections.emptyList();
    }
    List<Object> resourcesOfType = prefetchResources.get(dataType);
    if (resourcesOfType == null) {
        return Collections.emptyList();
    }
    // no resources or no filtering -> return list
    if (resourcesOfType.isEmpty() || (dateRange == null && codePath == null)) {
        return resourcesOfType;
    }
    List<Object> returnList = new ArrayList<>();
    for (Object resource : resourcesOfType) {
        boolean includeResource = true;
        if (dateRange != null) {
            if (datePath != null) {
                if (dateHighPath != null || dateLowPath != null) {
                    throw new IllegalArgumentException("If the datePath is specified, the dateLowPath and dateHighPath attributes must not be present.");
                }
                Object dateObject = PrefetchDataProviderHelper.getStu3DateTime(this.resolver.resolvePath(resource, datePath));
                DateTime date = dateObject instanceof DateTime ? (DateTime) dateObject : null;
                Interval dateInterval = dateObject instanceof Interval ? (Interval) dateObject : null;
                String precision = PrefetchDataProviderHelper.getPrecision(Arrays.asList(dateRange, date));
                if (date != null && !(InEvaluator.in(date, dateRange, precision))) {
                    includeResource = false;
                } else // TODO - add precision to includes evaluator
                if (dateInterval != null && !(IncludesEvaluator.includes(dateRange, dateInterval, precision))) {
                    includeResource = false;
                }
            } else {
                if (dateHighPath == null && dateLowPath == null) {
                    throw new IllegalArgumentException("If the datePath is not given, either the lowDatePath or highDatePath must be provided.");
                }
                DateTime lowDate = dateLowPath == null ? null : (DateTime) PrefetchDataProviderHelper.getStu3DateTime(this.resolver.resolvePath(resource, dateLowPath));
                DateTime highDate = dateHighPath == null ? null : (DateTime) PrefetchDataProviderHelper.getStu3DateTime(this.resolver.resolvePath(resource, dateHighPath));
                String precision = PrefetchDataProviderHelper.getPrecision(Arrays.asList(dateRange, lowDate, highDate));
                Interval interval = new Interval(lowDate, true, highDate, true);
                // TODO - add precision to includes evaluator
                if (!IncludesEvaluator.includes(dateRange, interval, precision)) {
                    includeResource = false;
                }
            }
        }
        if (codePath != null && !codePath.equals("") && includeResource) {
            if (valueSet != null && terminologyProvider != null) {
                if (valueSet.startsWith("urn:oid:")) {
                    valueSet = valueSet.replace("urn:oid:", "");
                }
                ValueSetInfo valueSetInfo = new ValueSetInfo().withId(valueSet);
                codes = terminologyProvider.expand(valueSetInfo);
            }
            if (codes != null) {
                Object codeObject = PrefetchDataProviderHelper.getStu3Code(this.resolver.resolvePath(resource, codePath));
                includeResource = PrefetchDataProviderHelper.checkCodeMembership(codes, codeObject, this.codeUtil);
            }
        }
        if (includeResource) {
            returnList.add(resource);
        }
    }
    return returnList;
}

Example 4 with Interval

use of org.opencds.cqf.cql.engine.runtime.Interval in project cqf-ruler by DBCG.

the class PrefetchDataProviderDstu2 method retrieve.

@Override
public Iterable<Object> retrieve(String context, String contextPath, Object contextValue, String dataType, String templateId, String codePath, Iterable<Code> codes, String valueSet, String datePath, String dateLowPath, String dateHighPath, Interval dateRange) {
    if (codePath == null && (codes != null || valueSet != null)) {
        throw new IllegalArgumentException("A code path must be provided when filtering on codes or a valueset.");
    }
    if (dataType == null) {
        throw new IllegalArgumentException("A data type (i.e. Procedure, Valueset, etc...) must be specified for clinical data retrieval");
    }
    // not be in the pre-fetch bundle, or might required a lookup by Id
    if (context.equals("Patient") && contextPath == null) {
        return Collections.emptyList();
    }
    List<Object> resourcesOfType = prefetchResources.get(dataType);
    if (resourcesOfType == null) {
        return Collections.emptyList();
    }
    // no resources or no filtering -> return list
    if (resourcesOfType.isEmpty() || (dateRange == null && codePath == null)) {
        return resourcesOfType;
    }
    List<Object> returnList = new ArrayList<>();
    for (Object resource : resourcesOfType) {
        boolean includeResource = true;
        if (dateRange != null) {
            if (datePath != null) {
                if (dateHighPath != null || dateLowPath != null) {
                    throw new IllegalArgumentException("If the datePath is specified, the dateLowPath and dateHighPath attributes must not be present.");
                }
                Object dateObject = PrefetchDataProviderHelper.getDstu2DateTime(this.resolver.resolvePath(resource, datePath));
                DateTime date = dateObject instanceof DateTime ? (DateTime) dateObject : null;
                Interval dateInterval = dateObject instanceof Interval ? (Interval) dateObject : null;
                String precision = PrefetchDataProviderHelper.getPrecision(Arrays.asList(dateRange, date));
                if (date != null && !(InEvaluator.in(date, dateRange, precision))) {
                    includeResource = false;
                } else // TODO - add precision to includes evaluator
                if (dateInterval != null && !(IncludesEvaluator.includes(dateRange, dateInterval, precision))) {
                    includeResource = false;
                }
            } else {
                if (dateHighPath == null && dateLowPath == null) {
                    throw new IllegalArgumentException("If the datePath is not given, either the lowDatePath or highDatePath must be provided.");
                }
                DateTime lowDate = dateLowPath == null ? null : (DateTime) PrefetchDataProviderHelper.getDstu2DateTime(this.resolver.resolvePath(resource, dateLowPath));
                DateTime highDate = dateHighPath == null ? null : (DateTime) PrefetchDataProviderHelper.getDstu2DateTime(this.resolver.resolvePath(resource, dateHighPath));
                String precision = PrefetchDataProviderHelper.getPrecision(Arrays.asList(dateRange, lowDate, highDate));
                Interval interval = new Interval(lowDate, true, highDate, true);
                // TODO - add precision to includes evaluator
                if (!IncludesEvaluator.includes(dateRange, interval, precision)) {
                    includeResource = false;
                }
            }
        }
        if (codePath != null && !codePath.equals("") && includeResource) {
            if (valueSet != null && terminologyProvider != null) {
                if (valueSet.startsWith("urn:oid:")) {
                    valueSet = valueSet.replace("urn:oid:", "");
                }
                ValueSetInfo valueSetInfo = new ValueSetInfo().withId(valueSet);
                codes = terminologyProvider.expand(valueSetInfo);
            }
            if (codes != null) {
                Object codeObject = PrefetchDataProviderHelper.getDstu2Code(this.resolver.resolvePath(resource, codePath));
                includeResource = PrefetchDataProviderHelper.checkCodeMembership(codes, codeObject, this.codeUtil);
            }
        }
        if (includeResource) {
            returnList.add(resource);
        }
    }
    return returnList;
}

Example 5 with Interval

use of org.opencds.cqf.cql.engine.runtime.Interval in project quality-measure-and-cohort-service by Alvearie.

the class CQLToFHIRMeasureReportHelperTest method testIntervalDate_shouldReturnNull.

@Test
public void testIntervalDate_shouldReturnNull() {
    Interval interval = new Interval(new Date("2020-01-02"), true, new Date("2020-06-04"), true);
    assertNull(CQLToFHIRMeasureReportHelper.getFhirTypeValue(interval));
}