Examples with ProfileUtilities org.hl7.fhir.r5.conformance.ProfileUtilities used on opensource projects

Example 36 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class SimpleWorkerContext method generateSnapshot.

@Override
public void generateSnapshot(StructureDefinition p, boolean logical) throws FHIRException {
    if ((!p.hasSnapshot() || isProfileNeedsRegenerate(p)) && (logical || p.getKind() != StructureDefinitionKind.LOGICAL)) {
        if (!p.hasBaseDefinition())
            throw new DefinitionException(formatMessage(I18nConstants.PROFILE___HAS_NO_BASE_AND_NO_SNAPSHOT, p.getName(), p.getUrl()));
        StructureDefinition sd = fetchResource(StructureDefinition.class, p.getBaseDefinition());
        if (sd == null && "http://hl7.org/fhir/StructureDefinition/Base".equals(p.getBaseDefinition())) {
            sd = ProfileUtilities.makeBaseDefinition(p.getFhirVersion());
        }
        if (sd == null) {
            throw new DefinitionException(formatMessage(I18nConstants.PROFILE___BASE__COULD_NOT_BE_RESOLVED, p.getName(), p.getUrl(), p.getBaseDefinition()));
        }
        List<ValidationMessage> msgs = new ArrayList<ValidationMessage>();
        List<String> errors = new ArrayList<String>();
        ProfileUtilities pu = new ProfileUtilities(this, msgs, this);
        pu.setAutoFixSliceNames(true);
        pu.setThrowException(false);
        if (xverManager == null) {
            xverManager = new XVerExtensionManager(this);
        }
        pu.setXver(xverManager);
        if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
            pu.sortDifferential(sd, p, p.getUrl(), errors, true);
        }
        pu.setDebug(false);
        for (String err : errors) msgs.add(new ValidationMessage(Source.ProfileValidator, IssueType.EXCEPTION, p.getUserString("path"), "Error sorting Differential: " + err, ValidationMessage.IssueSeverity.ERROR));
        pu.generateSnapshot(sd, p, p.getUrl(), sd.getUserString("webroot"), p.getName());
        for (ValidationMessage msg : msgs) {
            if ((!ignoreProfileErrors && msg.getLevel() == ValidationMessage.IssueSeverity.ERROR) || msg.getLevel() == ValidationMessage.IssueSeverity.FATAL)
                throw new DefinitionException(formatMessage(I18nConstants.PROFILE___ELEMENT__ERROR_GENERATING_SNAPSHOT_, p.getName(), p.getUrl(), msg.getLocation(), msg.getMessage()));
        }
        if (!p.hasSnapshot())
            throw new FHIRException(formatMessage(I18nConstants.PROFILE___ERROR_GENERATING_SNAPSHOT, p.getName(), p.getUrl()));
        pu = null;
    }
}

Example 37 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class SnapShotGenerationTests method testGen.

private void testGen(boolean fail, TestDetails test, SnapShotGenerationTestsContext context) throws Exception {
    if (!Utilities.noString(test.register)) {
        List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
        ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null);
        pu.setNewSlicingProcessing(true);
        for (StructureDefinition sd : test.included) {
            pu.setIds(sd, false);
        }
        for (StructureDefinition sd : test.included) {
            if (!TestingUtilities.getSharedWorkerContext().hasResource(StructureDefinition.class, sd.getUrl())) {
                TestingUtilities.getSharedWorkerContext().cacheResource(sd);
            }
        }
        StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, test.included.get(0).getBaseDefinition());
        if (base != null) {
            pu.generateSnapshot(base, test.included.get(0), test.included.get(0).getUrl(), "http://test.org/profile", test.included.get(0).getName());
        }
        int ec = 0;
        for (ValidationMessage vm : messages) {
            if (vm.getLevel() == IssueSeverity.ERROR) {
                System.out.println(vm.summary());
                ec++;
            }
        }
        if (ec > 0)
            throw new FHIRException("register gen failed: " + messages.toString());
    }
    StructureDefinition base = getSD(test.getSource().getBaseDefinition(), context);
    if (!base.getUrl().equals(test.getSource().getBaseDefinition()))
        throw new Exception("URL mismatch on base: " + base.getUrl() + " wanting " + test.getSource().getBaseDefinition());
    StructureDefinition output = test.getSource().copy();
    ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, new TestPKP());
    pu.setNewSlicingProcessing(test.isNewSliceProcessing());
    pu.setThrowException(false);
    pu.setDebug(test.isDebug());
    pu.setIds(test.getSource(), false);
    if (!TestingUtilities.getSharedWorkerContext().hasPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER)) {
        NpmPackage npm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER);
        TestingUtilities.getSharedWorkerContext().loadFromPackage(npm, new TestPackageLoader(new String[] { "StructureDefinition" }), new String[] { "StructureDefinition" });
    }
    pu.setXver(new XVerExtensionManager(TestingUtilities.getSharedWorkerContext()));
    if (test.isSort()) {
        List<String> errors = new ArrayList<String>();
        int lastCount = output.getDifferential().getElement().size();
        pu.sortDifferential(base, output, test.getSource().getName(), errors, false);
        if (errors.size() > 0)
            throw new FHIRException("Sort failed: " + errors.toString());
    }
    try {
        messages.clear();
        pu.generateSnapshot(base, output, test.getSource().getUrl(), "http://test.org/profile", test.getSource().getName());
        List<ValidationMessage> ml = new ArrayList<>();
        for (ValidationMessage vm : messages) {
            if (vm.getLevel() == IssueSeverity.ERROR) {
                ml.add(vm);
            }
        }
        if (ml.size() > 0) {
            throw new FHIRException("Snapshot Generation failed: " + ml.toString());
        }
    } catch (Throwable e) {
        System.out.println("\r\nException: " + e.getMessage());
        throw e;
    }
    if (output.getDifferential().hasElement()) {
        RenderingContext rc = new RenderingContext(TestingUtilities.getSharedWorkerContext(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
        rc.setDestDir(Utilities.path("[tmp]", "snapshot"));
        rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), null, new TestPKP()));
        RendererFactory.factory(output, rc).render(output);
    }
    if (!fail) {
        test.output = output;
        TestingUtilities.getSharedWorkerContext().cacheResource(output);
        File dst = new File(TestingUtilities.tempFile("snapshot", test.getId() + "-expected.xml"));
        if (dst.exists())
            dst.delete();
        IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", test.getId() + "-expected.xml"), new FileOutputStream(dst));
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("snapshot", test.getId() + "-actual.xml")), output);
        StructureDefinition t1 = test.expected.copy();
        t1.setText(null);
        StructureDefinition t2 = test.output.copy();
        t2.setText(null);
        Assertions.assertTrue(t1.equalsDeep(t2), "Output does not match expected");
    }
}

Example 38 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilitiesTests method testCardinalityChange.

/**
 * Change one cardinality.
 */
@Test
void testCardinalityChange() {
    StructureDefinition focus = new StructureDefinition();
    StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
    focus.setUrl(Utilities.makeUuidUrn());
    focus.setBaseDefinition(base.getUrl());
    focus.setType(base.getType());
    focus.setDerivation(TypeDerivationRule.CONSTRAINT);
    ElementDefinition id = focus.getDifferential().addElement();
    id.setPath("Patient.identifier");
    id.setMin(1);
    List<ValidationMessage> messages = new ArrayList<>();
    new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "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);
            b.setRequirements(null);
            f.setRequirements(null);
            for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
                c.setSource(null);
            }
            for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
                c.setSource(null);
            }
            if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
                ok = false;
            } else {
                if (f.getPath().equals("Patient.identifier")) {
                    ok = f.getMin() == 1;
                    if (ok) {
                        f.setMin(0);
                    }
                }
                if (!Base.compareDeep(b, f, true)) {
                    ok = Base.compareDeep(b, f, true);
                }
            }
        }
    }
    Assertions.assertTrue(ok);
}

Example 39 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class StructureMapUtilities method analyse.

/**
 * Given a structure map, return a set of analyses on it.
 *
 * Returned:
 *   - a list or profiles for what it will create. First profile is the target
 *   - a table with a summary (in xhtml) for easy human undertanding of the mapping
 *
 * @param appInfo
 * @param map
 * @return
 * @throws Exception
 */
public StructureMapAnalysis analyse(Object appInfo, StructureMap map) throws Exception {
    ids.clear();
    StructureMapAnalysis result = new StructureMapAnalysis();
    TransformContext context = new TransformContext(appInfo);
    VariablesForProfiling vars = new VariablesForProfiling(false, false);
    StructureMapGroupComponent start = map.getGroup().get(0);
    for (StructureMapGroupInputComponent t : start.getInput()) {
        PropertyWithType ti = resolveType(map, t.getType(), t.getMode());
        if (t.getMode() == StructureMapInputMode.SOURCE)
            vars.add(VariableMode.INPUT, t.getName(), ti);
        else
            vars.add(VariableMode.OUTPUT, t.getName(), createProfile(map, result.profiles, ti, start.getName(), start));
    }
    result.summary = new XhtmlNode(NodeType.Element, "table").setAttribute("class", "grid");
    XhtmlNode tr = result.summary.addTag("tr");
    tr.addTag("td").addTag("b").addText("Source");
    tr.addTag("td").addTag("b").addText("Target");
    log("Start Profiling Transform " + map.getUrl());
    analyseGroup("", context, map, vars, start, result);
    ProfileUtilities pu = new ProfileUtilities(worker, null, pkp);
    for (StructureDefinition sd : result.getProfiles()) pu.cleanUpDifferential(sd);
    return result;
}

Example 40 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class QuestionnaireBuilder method selectTypes.

private void selectTypes(StructureDefinition profile, QuestionnaireItemComponent sub, TypeRefComponent t, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> source, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> dest) throws FHIRFormatError {
    List<QuestionnaireResponse.QuestionnaireResponseItemComponent> temp = new ArrayList<QuestionnaireResponse.QuestionnaireResponseItemComponent>();
    for (QuestionnaireResponse.QuestionnaireResponseItemComponent g : source) if (instanceOf(t, (Element) g.getUserData("object")))
        temp.add(g);
    for (QuestionnaireResponse.QuestionnaireResponseItemComponent g : temp) source.remove(g);
    for (QuestionnaireResponse.QuestionnaireResponseItemComponent g : temp) {
        // it should be empty
        assert (g.getItem().size() == 0);
        QuestionnaireResponse.QuestionnaireResponseItemComponent q = g.addItem();
        q.setLinkId(g.getLinkId() + "._type");
        q.setText("type");
        Coding cc = new Coding();
        QuestionnaireResponseItemAnswerComponent a = q.addAnswer();
        a.setValue(cc);
        if (t.getCode().equals("Reference") && t.hasTargetProfile() && t.getTargetProfile().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
            cc.setCode(t.getTargetProfile().substring(40));
            cc.setSystem("http://hl7.org/fhir/resource-types");
        } else {
            ProfileUtilities pu = new ProfileUtilities(context, null, null);
            StructureDefinition ps = null;
            if (t.hasTargetProfile())
                ps = pu.getProfile(profile, t.getTargetProfile());
            else if (t.hasProfile())
                ps = pu.getProfile(profile, t.getProfile());
            if (ps != null) {
                cc.setCode(t.getProfile());
                cc.setSystem("http://hl7.org/fhir/resource-types");
            } else {
                cc.setCode(t.getCode());
                cc.setSystem("http://hl7.org/fhir/data-types");
            }
        }
        // 1st: create the subgroup
        QuestionnaireResponse.QuestionnaireResponseItemComponent subg = a.addItem();
        dest.add(subg);
        subg.setLinkId(sub.getLinkId());
        subg.setText(sub.getText());
        subg.setUserData("object", g.getUserData("object"));
    }
}