Examples with Package org.hl7.fhir.utilities.graphql.Package used on opensource projects

Example 1 with Package

use of org.hl7.fhir.utilities.graphql.Package in project beneficiary-fhir-data by CMSgov.

the class SamhsaMatcherFromClaimTransformerTest method verifySamhsaMatcherForDiagnosisPackage.

/**
 * Verify SAMHSA matcher for package with the given system, code and if the expectation is that
 * there should be a match for this combination.
 *
 * @param system the system value
 * @param code the code
 * @param shouldMatch if the matcher should match on this combination
 */
private void verifySamhsaMatcherForDiagnosisPackage(String system, String code, boolean shouldMatch, ExplanationOfBenefit explanationOfBenefit) {
    ExplanationOfBenefit modifiedEob = explanationOfBenefit.copy();
    // Set diagnosis DRG
    for (ExplanationOfBenefit.DiagnosisComponent diagnosisComponent : modifiedEob.getDiagnosis()) {
        if (diagnosisComponent.getDiagnosisCodeableConcept() != null) {
            diagnosisComponent.getDiagnosisCodeableConcept().setCoding(new ArrayList<>());
        }
        CodeableConcept codeableConcept = new CodeableConcept();
        Coding coding = new Coding(system, code, null);
        codeableConcept.setCoding(Collections.singletonList(coding));
        diagnosisComponent.setPackageCode(codeableConcept);
    }
    // Set procedure to empty so we dont check it for matches
    for (ExplanationOfBenefit.ProcedureComponent diagnosisComponent : modifiedEob.getProcedure()) {
        CodeableConcept codeableConcept = diagnosisComponent.getProcedureCodeableConcept();
        ArrayList<Coding> codingList = new ArrayList<>();
        codeableConcept.setCoding(codingList);
    }
    // Set item coding to non-SAMHSA so we dont check it for matches
    List<Coding> codings = new ArrayList<>();
    Coding coding = new Coding();
    coding.setSystem(TransformerConstants.CODING_SYSTEM_HCPCS);
    coding.setCode(NON_SAMHSA_HCPCS_CODE);
    codings.add(coding);
    modifiedEob.getItem().get(0).getService().setCoding(codings);
    assertEquals(shouldMatch, samhsaMatcher.test(modifiedEob));
}

Example 2 with Package

use of org.hl7.fhir.utilities.graphql.Package in project beneficiary-fhir-data by CMSgov.

the class SamhsaMatcherR4FromClaimTransformerV2Test method verifyNoItemCodingsTriggersSamhsaFiltering.

/**
 * Verifies that a claim with no samhsa diagnosis, procedure, or item-level HCPCS codes does
 * trigger filtering because the code array is empty and therefore does not contain known systems.
 *
 * @param expectMatch if the test is expecting a filtering match
 * @param explanationOfBenefit the loaded benefit to use for the test
 */
private void verifyNoItemCodingsTriggersSamhsaFiltering(ExplanationOfBenefit explanationOfBenefit, boolean expectMatch) {
    ExplanationOfBenefit modifiedEob = explanationOfBenefit.copy();
    // Set Top level diagnosis and package code to null and coding to empty
    for (ExplanationOfBenefit.DiagnosisComponent diagnosisComponent : modifiedEob.getDiagnosis()) {
        diagnosisComponent.getDiagnosisCodeableConcept().setCoding(new ArrayList<>());
        diagnosisComponent.setPackageCode(null);
    }
    // Set procedure to empty
    modifiedEob.setProcedure(new ArrayList<>());
    // Set item level codings to non-SAMHSA
    modifiedEob.getItem().get(0).setProductOrService(null);
    // When
    boolean isMatch = samhsaMatcherV2.test(modifiedEob);
    // Then
    assertEquals(expectMatch, isMatch);
}

Example 3 with Package

use of org.hl7.fhir.utilities.graphql.Package in project beneficiary-fhir-data by CMSgov.

the class SamhsaMatcherR4FromClaimTransformerV2Test method verifySamhsaMatcherForItemWithMultiCoding.

/**
 * Verify SAMHSA matcher for item with the given system, code and if the expectation is that there
 * should be a match for this combination.
 *
 * @param system the system value of the first coding
 * @param code the code of the first coding
 * @param system2 the system value of the second coding
 * @param code2 the code of the second coding
 * @param shouldMatch if the matcher should match on this combination
 * @param explanationOfBenefit the explanation of benefit
 */
private void verifySamhsaMatcherForItemWithMultiCoding(String system, String code, String system2, String code2, boolean shouldMatch, ExplanationOfBenefit explanationOfBenefit) {
    ExplanationOfBenefit modifiedEob = explanationOfBenefit.copy();
    // Set Top level diagnosis and package code to null so we can test item logic
    for (ExplanationOfBenefit.DiagnosisComponent diagnosisComponent : modifiedEob.getDiagnosis()) {
        CodeableConcept codeableConcept = diagnosisComponent.getDiagnosisCodeableConcept();
        codeableConcept.setCoding(new ArrayList<>());
        diagnosisComponent.setPackageCode(null);
    }
    List<Coding> codings = new ArrayList<>();
    Coding coding = new Coding();
    coding.setSystem(system);
    coding.setCode(code);
    Coding coding2 = new Coding();
    coding2.setSystem(system2);
    coding2.setCode(code2);
    codings.add(coding);
    codings.add(coding2);
    modifiedEob.getItem().get(0).getProductOrService().setCoding(codings);
    assertEquals(shouldMatch, samhsaMatcherV2.test(modifiedEob));
}

Example 4 with Package

use of org.hl7.fhir.utilities.graphql.Package in project kindling by HL7.

the class BuildWorkerContext method loadFromPackageInt.

public int loadFromPackageInt(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
    int t = 0;
    System.out.println("Load Package " + pi.name() + "#" + pi.version());
    if (loadedPackages.contains(pi.id() + "#" + pi.version())) {
        return 0;
    }
    loadedPackages.add(pi.id() + "#" + pi.version());
    if ((types == null || types.length == 0) && loader != null) {
        types = loader.getTypes();
    }
    for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
        try {
            registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version()));
            t++;
        } catch (FHIRException e) {
            throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
        }
    }
    for (String s : pi.list("other")) {
        binaries.put(s, TextFile.streamToBytes(pi.load("other", s)));
    }
    if (version == null) {
        version = pi.version();
    }
    return t;
}

Example 5 with Package

use of org.hl7.fhir.utilities.graphql.Package in project kindling by HL7.

the class OldSpreadsheetParser method parseProfileSheet.

private ConstraintStructure parseProfileSheet(Definitions definitions, Profile ap, String n, List<String> namedSheets, boolean published, String usage, List<ValidationMessage> issues, WorkGroup wg, String fmm) throws Exception {
    Sheet sheet;
    ResourceDefn resource = new ResourceDefn();
    sheet = loadSheet(n + "-Inv");
    Map<String, Invariant> invariants = null;
    if (sheet != null) {
        invariants = readInvariants(sheet, n, n + "-Inv");
    } else {
        invariants = new HashMap<String, Invariant>();
    }
    sheet = loadSheet(n);
    if (sheet == null)
        throw new Exception("The StructureDefinition referred to a tab by the name of '" + n + "', but no tab by the name could be found");
    for (int row = 0; row < sheet.rows.size(); row++) {
        ElementDefn e = processLine(resource, sheet, row, invariants, true, ap, row == 0);
        if (e != null)
            for (TypeRef t : e.getTypes()) {
                if (t.getProfile() != null && !t.getName().equals("Extension") && t.getProfile().startsWith("#")) {
                    if (!namedSheets.contains(t.getProfile().substring(1)))
                        namedSheets.add(t.getProfile().substring(1));
                }
            }
    }
    sheet = loadSheet(n + "-Extensions");
    if (sheet != null) {
        int row = 0;
        while (row < sheet.rows.size()) {
            if (sheet.getColumn(row, "Code").startsWith("!"))
                row++;
            else
                row = processExtension(resource.getRoot().getElementByName(definitions, "extensions", true, false), sheet, row, definitions, ap.metadata("extension.uri"), ap, issues, invariants, wg);
        }
    }
    sheet = loadSheet(n + "-Search");
    if (sheet != null) {
        readSearchParams(resource, sheet, true);
    }
    if (invariants != null) {
        for (Invariant inv : invariants.values()) {
            if (Utilities.noString(inv.getContext()))
                throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " has no context");
            else {
                ElementDefn ed = findContext(resource.getRoot(), inv.getContext(), "Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " Context");
                // TODO: Need to resolve context based on element name, not just path
                if (ed.getName().endsWith("[x]") && !inv.getContext().endsWith("[x]"))
                    inv.setFixedName(inv.getContext().substring(inv.getContext().lastIndexOf(".") + 1));
                ed.getInvariants().put(inv.getId(), inv);
                if (Utilities.noString(inv.getXpath())) {
                    throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " (" + inv.getEnglish() + ") has no XPath statement");
                } else if (inv.getXpath().contains("\""))
                    throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " (" + inv.getEnglish() + ") contains a \" character");
            // if (Utilities.noString(inv.getExpression()))
            // throw new Exception("Type "+resource.getRoot().getName()+" Invariant "+inv.getId()+" ("+inv.getEnglish()+") has no Expression statement (in FHIRPath format)");
            }
        }
    }
    resource.getRoot().setProfileName(n);
    if (n.toLowerCase().equals(ap.getId()))
        throw new Exception("Duplicate Profile Name: Package id " + ap.getId() + " and profile id " + n.toLowerCase() + " are the same");
    if (profileIds.containsKey(n.toLowerCase()))
        throw new Exception("Duplicate Profile Name: " + n.toLowerCase() + " in " + ap.getId() + ", already registered in " + profileIds.get(n.toLowerCase()).getOwner());
    ConstraintStructure p = new ConstraintStructure(n.toLowerCase(), resource.getRoot().getProfileName(), resource, ig != null ? ig : definitions.getUsageIG(usage, "Parsing " + name), wg, fmm, Utilities.existsInList(ap.metadata("Experimental"), "y", "Y", "true", "TRUE", "1"));
    p.setOwner(ap.getId());
    profileIds.put(n.toLowerCase(), p);
    return p;
}