Examples with CodeSystemComparison org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison used on opensource projects

Example 11 with CodeSystemComparison

use of org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison in project org.hl7.fhir.core by hapifhir.

the class CodeSystemComparer method compareConcepts.

private void compareConcepts(List<ConceptDefinitionComponent> left, List<ConceptDefinitionComponent> right, StructuralMatch<ConceptDefinitionComponent> combined, List<ConceptDefinitionComponent> union, List<ConceptDefinitionComponent> intersection, CodeSystem csU, CodeSystem csI, CodeSystemComparison res, String path) {
    List<ConceptDefinitionComponent> matchR = new ArrayList<>();
    for (ConceptDefinitionComponent l : left) {
        ConceptDefinitionComponent r = findInList(right, l);
        if (r == null) {
            union.add(l);
            combined.getChildren().add(new StructuralMatch<CodeSystem.ConceptDefinitionComponent>(l, vmI(IssueSeverity.INFORMATION, "Removed this concept", path)));
        } else {
            matchR.add(r);
            ConceptDefinitionComponent cdM = merge(l, r, csU.getProperty(), res);
            ConceptDefinitionComponent cdI = intersect(l, r, res);
            union.add(cdM);
            intersection.add(cdI);
            StructuralMatch<ConceptDefinitionComponent> sm = new StructuralMatch<CodeSystem.ConceptDefinitionComponent>(l, r);
            compare(sm.getMessages(), l, r, path + ".where(code='" + l.getCode() + "')", res);
            combined.getChildren().add(sm);
            compareConcepts(l.getConcept(), r.getConcept(), sm, cdM.getConcept(), cdI.getConcept(), csU, csI, res, path + ".where(code='" + l.getCode() + "').concept");
        }
    }
    for (ConceptDefinitionComponent r : right) {
        if (!matchR.contains(r)) {
            union.add(r);
            combined.getChildren().add(new StructuralMatch<CodeSystem.ConceptDefinitionComponent>(vmI(IssueSeverity.INFORMATION, "Added this concept", path), r));
        }
    }
}

Example 12 with CodeSystemComparison

use of org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison in project org.hl7.fhir.core by hapifhir.

the class CodeSystemComparer method merge.

private ConceptDefinitionComponent merge(ConceptDefinitionComponent l, ConceptDefinitionComponent r, List<PropertyComponent> destProps, CodeSystemComparison res) {
    ConceptDefinitionComponent cd = l.copy();
    if (!l.hasDisplay() && r.hasDisplay()) {
        cd.setDisplay(r.getDisplay());
    }
    if (!l.hasDefinition() && r.hasDefinition()) {
        cd.setDefinition(r.getDefinition());
    }
    mergeProps(cd, l, r, destProps, res);
    mergeDesignations(cd, l, r);
    return cd;
}

Example 13 with CodeSystemComparison

use of org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison in project org.hl7.fhir.core by hapifhir.

the class ComparisonTests method test.

@ParameterizedTest(name = "{index}: id {0}")
@MethodSource("data")
public void test(String name, JsonObject content) throws Exception {
    this.content = content;
    if (content.has("use-test") && !content.get("use-test").getAsBoolean())
        return;
    if (context == null) {
        System.out.println("---- Load R5 ----------------------------------------------------------------");
        context = TestingUtilities.getSharedWorkerContext();
        FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
        NpmPackage npm = pcm.loadPackage("hl7.fhir.us.core#3.1.0");
        BaseWorkerContext bc = (BaseWorkerContext) context;
        boolean dupl = bc.isAllowLoadingDuplicates();
        bc.setAllowLoadingDuplicates(true);
        context.loadFromPackage(npm, new R4ToR5Loader(new String[] { "CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem" }, new NullLoaderKnowledgeProviderR5(), context.getVersion()));
        bc.setAllowLoadingDuplicates(dupl);
    }
    if (!new File(Utilities.path("[tmp]", "comparison")).exists()) {
        System.out.println("---- Set up Output ----------------------------------------------------------");
        Utilities.createDirectory(Utilities.path("[tmp]", "comparison"));
        FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
        NpmPackage npm = pcm.loadPackage(CommonPackages.ID_PUBPACK, CommonPackages.VER_PUBPACK);
        for (String f : npm.list("other")) {
            TextFile.streamToFile(npm.load("other", f), Utilities.path("[tmp]", "comparison", f));
        }
    }
    System.out.println("---- " + name + " ----------------------------------------------------------------");
    CanonicalResource left = load("left");
    CanonicalResource right = load("right");
    ComparisonSession session = new ComparisonSession(context, context, "Comparison Tests", null);
    if (left instanceof CodeSystem && right instanceof CodeSystem) {
        CodeSystemComparer cs = new CodeSystemComparer(session);
        CodeSystemComparison csc = cs.compare((CodeSystem) left, (CodeSystem) right);
        Assertions.assertTrue(csc.getUnion().getConcept().size() > csc.getIntersection().getConcept().size());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-union.json")), csc.getUnion());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-intersection.json")), csc.getIntersection());
        String xmle = new XhtmlComposer(true).compose(cs.renderErrors(csc));
        String xml1 = new XhtmlComposer(true).compose(cs.renderMetadata(csc, "", ""));
        String xml2 = new XhtmlComposer(true).compose(cs.renderConcepts(csc, "", ""));
        TextFile.stringToFile(HEADER + hd("Messages") + xmle + BREAK + hd("Metadata") + xml1 + BREAK + hd("Concepts") + xml2 + FOOTER, Utilities.path("[tmp]", "comparison", name + ".html"));
        checkOutcomes(csc.getMessages(), content);
    } else if (left instanceof ValueSet && right instanceof ValueSet) {
        ValueSetComparer cs = new ValueSetComparer(session);
        ValueSetComparison csc = cs.compare((ValueSet) left, (ValueSet) right);
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-union.json")), csc.getUnion());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-intersection.json")), csc.getIntersection());
        String xmle = new XhtmlComposer(true).compose(cs.renderErrors(csc));
        String xml1 = new XhtmlComposer(true).compose(cs.renderMetadata(csc, "", ""));
        String xml2 = new XhtmlComposer(true).compose(cs.renderCompose(csc, "", ""));
        String xml3 = new XhtmlComposer(true).compose(cs.renderExpansion(csc, "", ""));
        TextFile.stringToFile(HEADER + hd("Messages") + xmle + BREAK + hd("Metadata") + xml1 + BREAK + hd("Definition") + xml2 + BREAK + hd("Expansion") + xml3 + FOOTER, Utilities.path("[tmp]", "comparison", name + ".html"));
        checkOutcomes(csc.getMessages(), content);
    } else if (left instanceof StructureDefinition && right instanceof StructureDefinition) {
        ProfileUtilities utils = new ProfileUtilities(context, null, null);
        genSnapshot(utils, (StructureDefinition) left);
        genSnapshot(utils, (StructureDefinition) right);
        ProfileComparer pc = new ProfileComparer(session, utils, utils);
        ProfileComparison csc = pc.compare((StructureDefinition) left, (StructureDefinition) right);
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-union.json")), csc.getUnion());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-intersection.json")), csc.getIntersection());
        String xmle = new XhtmlComposer(true).compose(pc.renderErrors(csc));
        String xml1 = new XhtmlComposer(true).compose(pc.renderMetadata(csc, "", ""));
        String xml2 = new XhtmlComposer(true).compose(pc.renderStructure(csc, "", "", "http://hl7.org/fhir"));
        // String xml3 = new XhtmlComposer(true).compose(cs.renderExpansion(csc, "", ""));
        TextFile.stringToFile(HEADER + hd("Messages") + xmle + BREAK + hd("Metadata") + xml1 + BREAK + hd("Structure") + xml2 + FOOTER, Utilities.path("[tmp]", "comparison", name + ".html"));
        checkOutcomes(csc.getMessages(), content);
    } else if (left instanceof CapabilityStatement && right instanceof CapabilityStatement) {
        CapabilityStatementComparer pc = new CapabilityStatementComparer(session);
        CapabilityStatementComparison csc = pc.compare((CapabilityStatement) left, (CapabilityStatement) right);
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-union.json")), csc.getUnion());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-intersection.json")), csc.getIntersection());
        String xmle = new XhtmlComposer(true).compose(pc.renderErrors(csc));
        String xml1 = new XhtmlComposer(true).compose(pc.renderMetadata(csc, "", ""));
        String xml2 = new XhtmlComposer(true).compose(pc.renderStatements(csc, "", ""));
        // String xml3 = new XhtmlComposer(true).compose(cs.renderExpansion(csc, "", ""));
        TextFile.stringToFile(HEADER + hd("Messages") + xmle + BREAK + hd("Metadata") + xml1 + BREAK + hd("Structure") + xml2 + FOOTER, Utilities.path("[tmp]", "comparison", name + ".html"));
        checkOutcomes(csc.getMessages(), content);
    } else {
        throw new FHIRException("Can't compare " + left.fhirType() + " to " + right.fhirType());
    }
}

Example 14 with CodeSystemComparison

use of org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison in project org.hl7.fhir.core by hapifhir.

the class CodeSystemComparer method mergeProps.

private void mergeProps(ConceptDefinitionComponent cd, ConceptDefinitionComponent l, ConceptDefinitionComponent r, List<PropertyComponent> destProps, CodeSystemComparison res) {
    List<ConceptPropertyComponent> matchR = new ArrayList<>();
    for (ConceptPropertyComponent lp : l.getProperty()) {
        ConceptPropertyComponent rp = findRightProp(r.getProperty(), lp, res);
        if (rp == null) {
            cd.getProperty().add(lp);
        } else {
            matchR.add(rp);
            cd.getProperty().add(lp);
            if (lp.getValue().equalsDeep(rp.getValue())) {
                cd.getProperty().add(rp.setCode(res.getPropMap().get(rp.getCode())));
            }
        }
    }
    for (ConceptPropertyComponent rp : r.getProperty()) {
        if (!matchR.contains(rp)) {
            cd.getProperty().add(rp.setCode(res.getPropMap().get(rp.getCode())));
        }
    }
}

Example 15 with CodeSystemComparison

use of org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison in project org.hl7.fhir.core by hapifhir.

the class CodeSystemComparer method renderConcepts.

public XhtmlNode renderConcepts(CodeSystemComparison comparison, String id, String prefix) throws FHIRException, IOException {
    // columns: code, display (left|right), properties (left|right)
    HierarchicalTableGenerator gen = new HierarchicalTableGenerator(Utilities.path("[tmp]", "compare"), false);
    TableModel model = gen.new TableModel(id, true);
    model.setAlternating(true);
    model.getTitles().add(gen.new Title(null, null, "Code", "The code for the concept", null, 100));
    model.getTitles().add(gen.new Title(null, null, "Display", "The display for the concept", null, 200, 2));
    for (PropertyComponent p : comparison.getUnion().getProperty()) {
        model.getTitles().add(gen.new Title(null, null, p.getCode(), p.getDescription(), null, 100, 2));
    }
    model.getTitles().add(gen.new Title(null, null, "Comments", "Additional information about the comparison", null, 200));
    for (StructuralMatch<ConceptDefinitionComponent> t : comparison.getCombined().getChildren()) {
        addRow(gen, model.getRows(), t, comparison);
    }
    return gen.generate(model, prefix, 0, null);
}