Examples with ProfileUtilities org.hl7.fhir.r4b.conformance.ProfileUtilities used on opensource projects

Example 11 with ProfileUtilities

use of org.hl7.fhir.r4b.conformance.ProfileUtilities in project kindling by HL7.

the class ResourceParser method parseTypeDefinition.

private TypeDefn parseTypeDefinition(ProfileUtilities pu, ElementDefinition focus, StructureDefinition sd) throws IOException {
    TypeDefn ed = new TypeDefn();
    parseED(pu, ed, focus, sd, "");
    return ed;
}

Example 12 with ProfileUtilities

use of org.hl7.fhir.r4b.conformance.ProfileUtilities in project kindling by HL7.

the class ProfileGenerator method generate.

public StructureDefinition generate(ProfiledType pt, List<ValidationMessage> issues) throws Exception {
    StructureDefinition p = new StructureDefinition();
    p.setId(pt.getName());
    p.setUrl("http://hl7.org/fhir/StructureDefinition/" + pt.getName());
    p.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/" + pt.getBaseType());
    p.setKind(StructureDefinitionKind.COMPLEXTYPE);
    p.setType(pt.getBaseType());
    p.setDerivation(TypeDerivationRule.CONSTRAINT);
    p.setAbstract(false);
    p.setUserData("filename", pt.getName().toLowerCase());
    p.setUserData("path", "datatypes.html#" + pt.getName());
    p.setFhirVersion(version);
    p.setVersion(version.toCode());
    ToolingExtensions.setStandardsStatus(p, StandardsStatus.NORMATIVE, "4.0.0");
    p.setStatus(PublicationStatus.fromCode("active"));
    ToolResourceUtilities.updateUsage(p, "core");
    p.setName(pt.getName());
    p.setPublisher("HL7 FHIR Standard");
    p.addContact().getTelecom().add(Factory.newContactPoint(ContactPointSystem.URL, "http://hl7.org/fhir"));
    p.setDescription("Base StructureDefinition for Type " + pt.getName() + ": " + pt.getDefinition());
    p.setDescription(pt.getDefinition());
    p.setDate(genDate.getTime());
    // first, the differential
    p.setName(pt.getName());
    ElementDefinition e = new ElementDefinition();
    String idroot = e.getId();
    e.setPath(pt.getBaseType());
    // e.setSliceName(pt.getName());
    e.setShort(pt.getDefinition());
    e.setDefinition(preProcessMarkdown(pt.getDescription(), "??"));
    e.setMin(0);
    e.setMax("*");
    e.setIsModifier(false);
    String s = definitions.getTLAs().get(pt.getName().toLowerCase());
    if (s == null)
        throw new Exception("There is no TLA for '" + pt.getName() + "' in fhir.ini");
    ElementDefinitionConstraintComponent inv = new ElementDefinitionConstraintComponent();
    inv.setKey(s + "-1");
    inv.setRequirements(pt.getInvariant().getRequirements());
    inv.setSeverity(ConstraintSeverity.ERROR);
    inv.setHuman(pt.getInvariant().getEnglish());
    if (!"n/a".equals(pt.getInvariant().getExpression())) {
        fpUsages.add(new FHIRPathUsage(pt.getName(), pt.getName(), pt.getName(), null, pt.getInvariant().getExpression()));
        inv.setExpression(pt.getInvariant().getExpression());
    }
    inv.setXpath(pt.getInvariant().getXpath());
    e.getConstraint().add(inv);
    p.setDifferential(new StructureDefinitionDifferentialComponent());
    p.getDifferential().getElement().add(e);
    StructureDefinition base = getTypeSnapshot(pt.getBaseType());
    if (!pt.getRules().isEmpty()) {
        // throw new Exception("todo");
        for (String rule : pt.getRules().keySet()) {
            String[] parts = rule.split("\\.");
            String value = pt.getRules().get(rule);
            ElementDefinition er = findElement(p.getDifferential(), pt.getBaseType() + '.' + parts[0]);
            if (er == null) {
                er = new ElementDefinition();
                er.setId(pt.getBaseType() + ':' + p.getId() + '.' + parts[0]);
                er.setPath(pt.getBaseType() + '.' + parts[0]);
                p.getDifferential().getElement().add(er);
            }
            if (parts[1].equals("min"))
                er.setMin(Integer.parseInt(value));
            else if (parts[1].equals("max"))
                er.setMax(value);
            else if (parts[1].equals("defn"))
                er.setDefinition(preProcessMarkdown(value, "er"));
        }
        List<String> errors = new ArrayList<String>();
        new ProfileUtilities(context, null, pkp).sortDifferential(base, p, p.getName(), errors, true);
        for (String se : errors) issues.add(new ValidationMessage(Source.ProfileValidator, IssueType.STRUCTURE, -1, -1, p.getUrl(), se, IssueSeverity.WARNING));
    }
    reset();
    // now, the snapshot
    new ProfileUtilities(context, issues, pkp).generateSnapshot(base, p, "http://hl7.org/fhir/StructureDefinition/" + pt.getBaseType(), "http://hl7.org/fhir", p.getName());
    // for (ElementDefinition ed : p.getSnapshot().getElement())
    // generateElementDefinition(ed, getParent(ed, p.getSnapshot().getElement()));
    p.getDifferential().getElement().get(0).getType().clear();
    p.getSnapshot().getElement().get(0).getType().clear();
    XhtmlNode div = new XhtmlNode(NodeType.Element, "div");
    div.addTag("h2").addText("Data type " + pt.getName());
    div.addTag("p").addText(pt.getDefinition());
    div.addTag("h3").addText("Rule");
    div.addTag("p").addText(pt.getInvariant().getEnglish());
    div.addTag("p").addText("XPath:");
    div.addTag("blockquote").addTag("pre").addText(pt.getInvariant().getXpath());
    p.setText(new Narrative());
    p.getText().setStatus(NarrativeStatus.GENERATED);
    p.getText().setDiv(div);
    addElementConstraintToSnapshot(p);
    new ProfileUtilities(context, issues, pkp).setIds(p, false);
    checkHasTypes(p);
    return p;
}

Example 13 with ProfileUtilities

use of org.hl7.fhir.r4b.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class ExtensionDefinitionGenerator method loadSource.

private List<StructureDefinition> loadSource() throws IOException, FHIRException {
    List<StructureDefinition> list = new ArrayList<>();
    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
    NpmPackage npm = pcm.loadPackage("hl7.fhir.core", sourceVersion.toCode());
    if (sourceVersion == FHIRVersion._4_0_0)
        context = SimpleWorkerContext.fromPackage(npm);
    else if (sourceVersion == FHIRVersion._3_0_1)
        context = SimpleWorkerContext.fromPackage(npm, new R3ToR4Loader());
    else if (sourceVersion == FHIRVersion._1_4_0)
        context = SimpleWorkerContext.fromPackage(npm, new R2016MayToR4Loader());
    else if (sourceVersion == FHIRVersion._1_0_2)
        context = SimpleWorkerContext.fromPackage(npm, new R2ToR4Loader());
    pu = new ProfileUtilities(context, null, null);
    for (String fn : npm.listResources("StructureDefinition")) {
        list.add((StructureDefinition) loadResource(npm.load("package", fn), sourceVersion));
    }
    for (StructureDefinition sd : list) if (sd.getName().equals("Extension")) {
        extbase = sd;
        extv = extbase.getSnapshot().getElement().get(extbase.getSnapshot().getElement().size() - 1);
    }
    return list;
}

Example 14 with ProfileUtilities

use of org.hl7.fhir.r4b.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilitiesTests method textTypeNarrowing1.

/**
 * check that narrowing types is working
 * this one doesn't rename the path
 *
 * @param context2
 * @
 * @throws EOperationOutcome
 */
private void textTypeNarrowing1() throws EOperationOutcome, Exception {
    StructureDefinition focus = new StructureDefinition();
    StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
    focus.setUrl(Utilities.makeUuidUrn());
    focus.setBase(base.getUrl());
    ElementDefinition id = focus.getDifferential().addElement();
    id.setPath("Patient.deceased[x]");
    id.addType().setCode("dateTime");
    List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
    new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test");
    boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
    for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
        if (ok) {
            ElementDefinition b = base.getSnapshot().getElement().get(i);
            ElementDefinition f = focus.getSnapshot().getElement().get(i);
            if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath()))
                ok = false;
            else {
                f.setBase(null);
                if (f.getPath().equals("Patient.deceasedDateTime")) {
                    ok = f.getType().size() == 1 && f.getType().get(0).getCode().equals("dateTime");
                    if (ok) {
                        f.getType().clear();
                        b.getType().clear();
                        f.setPath(b.getPath());
                    }
                }
                ok = ok && Base.compareDeep(b, f, true);
            }
        }
    }
    if (!ok) {
        compareXml(base, focus);
        throw new FHIRException("Snap shot generation narrow type 1 failed");
    } else
        System.out.println("Snap shot generation narrow type 1 test passed");
}

Example 15 with ProfileUtilities

use of org.hl7.fhir.r4b.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilitiesTests method testSlicingTask8742.

private void testSlicingTask8742() throws EOperationOutcome, Exception {
    StructureDefinition focus = new StructureDefinition();
    StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Organization").copy();
    focus.setUrl(Utilities.makeUuidUrn());
    focus.setBase(base.getUrl());
    ElementDefinition id = focus.getDifferential().addElement();
    id.setPath("Organization.address");
    id.setMin(1);
    id.setMax("1");
    id.setMustSupport(true);
    id = focus.getDifferential().addElement();
    id.setPath("Organization.address.extension");
    id.setName("USLabCountycodes");
    id.getSlicing().setOrdered(false).setRules(SlicingRules.OPEN).addDiscriminator("url");
    id.setShort("County/Parish FIPS codes");
    id.setDefinition("County/Parish FIPS codes.");
    id.setRequirements("County/Parish Code SHALL use FIPS 6-4  ( INCITS 31:2009).");
    id.setMin(0);
    id.setMax("1");
    id.addType().setCode("Extension").addProfile("http://hl7.org/fhir/StructureDefinition/us-core-county");
    id.setMustSupport(true);
    id.getBinding().setStrength(BindingStrength.REQUIRED).setDescription("FIPS codes for US counties and county equivalent entities.").setValueSet(new Reference().setReference("http://hl7.org/fhir/ValueSet/fips-county"));
    List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
    new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test");
    // 14 for address with one sliced extension
    boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 13;
    if (!ok) {
        compareXml(base, focus);
        throw new FHIRException("Snap shot generation test 8742 failed");
    } else
        System.out.println("Snap shot generation test 8742 passed");
}