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

Example 46 with ProfileUtilities

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

the class SnapShotGenerationTests method getSD.

private StructureDefinition getSD(String url, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException, IOException {
    StructureDefinition sd = context.getByUrl(url);
    if (sd == null) {
        sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
    }
    if (sd == null) {
        throw new DefinitionException("Unable to find profile " + url);
    }
    if (!sd.hasSnapshot()) {
        StructureDefinition base = getSD(sd.getBaseDefinition(), context);
        ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, new TestPKP());
        pu.setNewSlicingProcessing(true);
        List<String> errors = new ArrayList<String>();
        pu.sortDifferential(base, sd, url, errors, false);
        if (!errors.isEmpty())
            throw new FHIRException(errors.get(0));
        pu.setIds(sd, false);
        pu.generateSnapshot(base, sd, sd.getUrl(), "http://test.org/profile", sd.getName());
    }
    return sd;
}

Example 47 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.context(), messages, null);
        pu.setNewSlicingProcessing(true);
        for (StructureDefinition sd : test.included) {
            pu.setIds(sd, false);
        }
        for (StructureDefinition sd : test.included) {
            if (!TestingUtilities.context().hasResource(StructureDefinition.class, sd.getUrl())) {
                TestingUtilities.context().cacheResource(sd);
            }
        }
        StructureDefinition base = TestingUtilities.context().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.context(), messages, new TestPKP());
    pu.setNewSlicingProcessing(test.isNewSliceProcessing());
    pu.setThrowException(false);
    pu.setDebug(test.isDebug());
    pu.setIds(test.getSource(), false);
    if (!TestingUtilities.context().hasPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER)) {
        NpmPackage npm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER);
        TestingUtilities.context().loadFromPackage(npm, new TestLoader(new String[] { "StructureDefinition" }), new String[] { "StructureDefinition" });
    }
    pu.setXver(new XVerExtensionManager(TestingUtilities.context()));
    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.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
        rc.setDestDir(Utilities.path("[tmp]", "snapshot"));
        rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.context(), null, new TestPKP()));
        RendererFactory.factory(output, rc).render(output);
    }
    if (!fail) {
        test.output = output;
        TestingUtilities.context().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 48 with ProfileUtilities

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

the class ComparisonRenderer method renderProfile.

private void renderProfile(String id, ProfileComparison comp) throws IOException {
    String template = templates.get("Profile");
    Map<String, Base> vars = new HashMap<>();
    ProfileComparer cs = new ProfileComparer(session, new ProfileUtilities(session.getContextLeft(), null, session.getPkp()), new ProfileUtilities(session.getContextRight(), null, session.getPkp()));
    vars.put("left", new StringType(comp.getLeft().present()));
    vars.put("right", new StringType(comp.getRight().present()));
    vars.put("leftId", new StringType(comp.getLeft().getId()));
    vars.put("rightId", new StringType(comp.getRight().getId()));
    vars.put("leftUrl", new StringType(comp.getLeft().getUrl()));
    vars.put("rightUrl", new StringType(comp.getRight().getUrl()));
    vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
    vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
    vars.put("structure", new StringType(new XhtmlComposer(true).compose(cs.renderStructure(comp, "", "", "http://hl7.org/fhir"))));
    String cnt = processTemplate(template, "CodeSystem", vars);
    TextFile.stringToFile(cnt, file(comp.getId() + ".html"));
    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-union.json")), comp.getUnion());
    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-intersection.json")), comp.getIntersection());
}

Example 49 with ProfileUtilities

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

the class QuestionnaireBuilder method makeTypeList.

private ValueSet makeTypeList(StructureDefinition profile, List<TypeRefComponent> types, String path) {
    ValueSet vs = new ValueSet();
    vs.setName("Type options for " + path);
    vs.setDescription(vs.present());
    vs.setStatus(PublicationStatus.ACTIVE);
    vs.setExpansion(new ValueSetExpansionComponent());
    vs.getExpansion().setIdentifier(Factory.createUUID());
    vs.getExpansion().setTimestampElement(DateTimeType.now());
    for (TypeRefComponent t : types) {
        if (t.hasTarget()) {
            for (UriType u : t.getTargetProfile()) {
                if (u.getValue().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
                    ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
                    cc.setCode(u.getValue().substring(40));
                    cc.setSystem("http://hl7.org/fhir/resource-types");
                    cc.setDisplay(cc.getCode());
                }
            }
        } else if (!t.hasProfile()) {
            ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
            cc.setCode(t.getWorkingCode());
            cc.setDisplay(t.getWorkingCode());
            cc.setSystem("http://hl7.org/fhir/data-types");
        } else
            for (UriType u : t.getProfile()) {
                ProfileUtilities pu = new ProfileUtilities(context, null, null);
                StructureDefinition ps = pu.getProfile(profile, u.getValue());
                if (ps != null) {
                    ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
                    cc.setCode(u.getValue());
                    cc.setDisplay(ps.getType());
                    cc.setSystem("http://hl7.org/fhir/resource-types");
                }
            }
    }
    return vs;
}

Example 50 with ProfileUtilities

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

the class StructureDefinitionValidator method validateStructureDefinition.

public void validateStructureDefinition(List<ValidationMessage> errors, Element src, NodeStack stack) {
    StructureDefinition sd = null;
    try {
        sd = loadAsSD(src);
        List<ElementDefinition> snapshot = sd.getSnapshot().getElement();
        sd.setSnapshot(null);
        StructureDefinition base = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
        if (warning(errors, IssueType.NOTFOUND, stack.getLiteralPath(), base != null, I18nConstants.UNABLE_TO_FIND_BASE__FOR_, sd.getBaseDefinition(), "StructureDefinition, so can't check the differential")) {
            if (rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), sd.hasDerivation(), I18nConstants.SD_MUST_HAVE_DERIVATION, sd.getUrl())) {
                if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
                    List<ValidationMessage> msgs = new ArrayList<>();
                    ProfileUtilities pu = new ProfileUtilities(context, msgs, null);
                    pu.setXver(xverManager);
                    pu.generateSnapshot(base, sd, sd.getUrl(), "http://hl7.org/fhir/R4/", sd.getName());
                    if (msgs.size() > 0) {
                        for (ValidationMessage msg : msgs) {
                            // we need to set the location for the context
                            String loc = msg.getLocation();
                            if (loc.contains("#")) {
                                msg.setLocation(stack.getLiteralPath() + ".differential.element.where(path = '" + loc.substring(loc.indexOf("#") + 1) + "')");
                            } else {
                                msg.setLocation(stack.getLiteralPath());
                            }
                            errors.add(msg);
                        }
                    }
                    if (!snapshot.isEmpty() && wantCheckSnapshotUnchanged) {
                        int was = snapshot.size();
                        int is = sd.getSnapshot().getElement().size();
                        rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), was == is, I18nConstants.SNAPSHOT_EXISTING_PROBLEM, was, is);
                    }
                }
            }
            if ("constraint".equals(src.getChildValue("derivation"))) {
                rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), base.getKindElement().primitiveValue().equals(src.getChildValue("kind")), I18nConstants.SD_DERIVATION_KIND_MISMATCH, base.getKindElement().primitiveValue(), src.getChildValue("kind"));
            }
        }
    } catch (FHIRException | IOException e) {
        rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), false, I18nConstants.ERROR_GENERATING_SNAPSHOT, e.getMessage());
    }
    List<Element> differentials = src.getChildrenByName("differential");
    List<Element> snapshots = src.getChildrenByName("snapshot");
    for (Element differential : differentials) {
        validateElementList(errors, differential, stack.push(differential, -1, null, null), false, snapshots.size() > 0, sd);
    }
    for (Element snapshot : snapshots) {
        validateElementList(errors, snapshot, stack.push(snapshot, -1, null, null), true, true, sd);
    }
}