Examples with Element org.hl7.fhir.r4b.elementmodel.Element used on opensource projects

Example 36 with Element

use of org.hl7.fhir.r4b.elementmodel.Element in project kindling by HL7.

the class XmlValidator method checkBySchema.

public Element checkBySchema(String fileToCheck, boolean wantThrow) throws FileNotFoundException, SAXException, IOException, ParserConfigurationException, FHIRException {
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    factory.setValidating(false);
    factory.setSchema(schema);
    DocumentBuilder builder = factory.newDocumentBuilder();
    MyErrorHandler err = new MyErrorHandler(errors, fileToCheck);
    builder.setErrorHandler(err);
    CSFileInputStream f = new CSFileInputStream(new CSFile(fileToCheck));
    Document doc = builder.parse(f);
    if (wantThrow && err.getErrors().size() > 0)
        throw new FHIRException("File " + fileToCheck + " failed schema validation");
    return doc.getDocumentElement();
}

Example 37 with Element

use of org.hl7.fhir.r4b.elementmodel.Element in project kindling by HL7.

the class ResourceParser method parseED.

private void parseED(ProfileUtilities pu, ElementDefn ed, ElementDefinition focus, StructureDefinition sd, String parentName) throws IOException {
    ed.setMinCardinality(focus.getMin());
    ed.setMaxCardinality("*".equals(focus.getMax()) ? Integer.MAX_VALUE : Integer.parseInt(focus.getMax()));
    ed.setIsModifier(focus.getIsModifier());
    ed.setModifierReason(focus.getIsModifierReason());
    ed.setMustSupport(focus.getMustSupport());
    ed.setSummaryItem(focus.getIsSummary());
    ed.setRegex(ToolingExtensions.readStringExtension(focus, ToolingExtensions.EXT_REGEX));
    ed.setXmlAttribute(focus.hasRepresentation(PropertyRepresentation.XMLATTR));
    if (ToolingExtensions.hasExtension(focus, BuildExtensions.EXT_UML_DIR)) {
        ed.setUmlDir(ToolingExtensions.readStringExtension(focus, BuildExtensions.EXT_UML_DIR));
    }
    if (ToolingExtensions.hasExtension(focus, BuildExtensions.EXT_UML_BREAK)) {
        ed.setUmlBreak(ToolingExtensions.readBoolExtension(focus, BuildExtensions.EXT_UML_BREAK));
    }
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_SVG)) {
        String svg = BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_SVG);
        if (svg.contains("w=")) {
            ed.setSvgWidth(Integer.parseInt(svg.substring(svg.indexOf("w=") + 2)));
            svg = svg.substring(0, svg.indexOf(";"));
        }
        ed.setSvgLeft(Integer.parseInt(svg.substring(0, svg.indexOf(","))));
        ed.setSvgTop(Integer.parseInt(svg.substring(svg.indexOf(",") + 1)));
    }
    ed.setName(tail(focus.getPath()));
    ed.setShortDefn(focus.getShort());
    ed.setDefinition(focus.getDefinition());
    ed.setRequirements(focus.getRequirements());
    ed.setComments(focus.getComment());
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_TODO)) {
        ed.setTodo(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_TODO));
    }
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_COMMITTEE_NOTES)) {
        ed.setCommitteeNotes(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_COMMITTEE_NOTES));
    }
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_HINT)) {
        ed.setDisplayHint(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_HINT));
    }
    if (focus.hasExtension(BuildExtensions.EXT_NO_BINDING)) {
        ed.setNoBindingAllowed(focus.getExtensionString(BuildExtensions.EXT_NO_BINDING).equals("true"));
    }
    for (StringType t : focus.getAlias()) {
        ed.getAliases().add(t.getValue());
    }
    if (focus.hasMaxLength()) {
        ed.setMaxLength(Integer.toString(focus.getMaxLength()));
    }
    ed.setExample(focus.getExampleFirstRep().getValue());
    ed.setMeaningWhenMissing(focus.getMeaningWhenMissing());
    if (ToolingExtensions.hasExtension(focus, BuildExtensions.EXT_TRANSLATABLE)) {
        ed.setTranslatable(ToolingExtensions.readBoolExtension(focus, BuildExtensions.EXT_TRANSLATABLE));
    }
    ed.setOrderMeaning(focus.getOrderMeaning());
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_STANDARDS_STATUS)) {
        ed.setStandardsStatus(StandardsStatus.fromCode(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_STANDARDS_STATUS)));
    }
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_NORMATIVE_VERSION)) {
        ed.setNormativeVersion(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_NORMATIVE_VERSION));
    }
    for (ElementDefinitionConstraintComponent cst : focus.getConstraint()) {
        Invariant inv = new Invariant();
        inv.setContext(focus.getPath());
        inv.setEnglish(cst.getHuman());
        if (cst.hasExtension(BuildExtensions.EXT_OCL)) {
            inv.setOcl(cst.getExtensionString(BuildExtensions.EXT_OCL));
        }
        inv.setXpath(cst.getXpath());
        inv.setId(cst.getKey());
        if (cst.hasExtension(BuildExtensions.EXT_FIXED_NAME)) {
            inv.setFixedName(cst.getExtensionString(BuildExtensions.EXT_FIXED_NAME));
        }
        inv.setSeverity(cst.getSeverity().toCode());
        if (cst.hasExtension(BuildExtensions.EXT_BEST_PRACTICE)) {
            inv.setSeverity("best-practice");
        }
        if (cst.hasExtension(BuildExtensions.EXT_TURTLE)) {
            inv.setTurtle(cst.getExtensionString(BuildExtensions.EXT_TURTLE));
        }
        inv.setRequirements(cst.getRequirements());
        inv.setExpression(cst.getExpression());
        if (cst.hasExtension(BuildExtensions.EXT_BEST_PRACTICE_EXPLANATION)) {
            inv.setExplanation(cst.getExtensionString(BuildExtensions.EXT_BEST_PRACTICE_EXPLANATION));
        }
        ed.getInvariants().put(inv.getId(), inv);
        invariants.put(inv.getId(), inv);
    }
    for (IdType cnd : focus.getCondition()) {
        Invariant inv = invariants.get(cnd.primitiveValue());
        if (inv == null) {
            System.out.println("Unable to find invariant " + cnd.primitiveValue());
        } else {
            ed.getStatedInvariants().add(inv);
        }
    }
    for (ElementDefinitionMappingComponent map : focus.getMapping()) {
        String uri = getMappingUri(sd, map.getIdentity());
        if ("http://hl7.org/fhir/fivews".equals(uri)) {
            ed.setW5(reverseW5(map.getMap()));
        } else {
            ed.getMappings().put(uri, map.getMap());
        }
    }
    if (focus.hasContentReference()) {
        ed.getTypes().add(new TypeRef("@" + focus.getContentReference().substring(1)));
    } else {
        for (TypeRefComponent tr : focus.getType()) {
            if (!Utilities.existsInList(tr.getCode(), "Element", "BackboneElement")) {
                TypeRef t = new TypeRef();
                ed.getTypes().add(t);
                if (tr.hasExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type")) {
                    t.setName(tr.getExtensionString("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"));
                } else {
                    t.setName(tr.getCode());
                }
                if (ToolingExtensions.hasExtension(tr, BuildExtensions.EXT_HIERARCHY)) {
                    ed.setHierarchy(ToolingExtensions.readBoolExtension(tr, BuildExtensions.EXT_HIERARCHY));
                }
                for (CanonicalType u : tr.getProfile()) {
                    t.setProfile(u.getValue().replace("http://hl7.org/fhir/StructureDefinition/", ""));
                }
                for (CanonicalType u : tr.getTargetProfile()) {
                    String s = u.getValue().replace("http://hl7.org/fhir/StructureDefinition/", "");
                    if ("Resource".equals(s)) {
                        t.getParams().add("Any");
                    } else {
                        t.getParams().add(s);
                    }
                }
                if (t.getName().equals("Quantity") && "SimpleQuantity".equals(t.getProfile())) {
                    t.setName("SimpleQuantity");
                    t.setProfile(null);
                }
                if ("Resource".equals(t.getProfile())) {
                    t.setProfile("Any");
                }
                if (t.getParams().toString().equals("[ActivityDefinition, EventDefinition, EvidenceVariable, Measure, OperationDefinition, PlanDefinition, Questionnaire, SubscriptionTopic]")) {
                    t.getParams().clear();
                    t.getParams().add("Definition");
                }
            }
        }
        if (ed.getTypes().size() == STAR_TYPES_COUNT) {
            ed.getTypes().clear();
            ed.getTypes().add(new TypeRef("*"));
        }
    }
    String name = parentName + Utilities.capitalize(ed.getName());
    if (focus.hasExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name")) {
        ed.setStatedType(focus.getExtensionString("http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name"));
        ed.setDeclaredTypeName(ed.getStatedType());
    } else if (ed.getTypes().isEmpty() && !focus.hasContentReference()) {
        ed.setDeclaredTypeName(name + "Component");
    }
    if (focus.hasBinding()) {
        ed.setBinding(parseBinding(focus.getBinding()));
    }
    for (ElementDefinition child : pu.getChildList(sd, focus, true, false)) {
        ElementDefn c = new ElementDefn();
        ed.getElements().add(c);
        parseED(pu, c, child, sd, name);
    }
// todo:
// private ElementDefinition derivation;
}

Example 38 with Element

use of org.hl7.fhir.r4b.elementmodel.Element in project kindling by HL7.

the class SvgGenerator method drawElement.

private ClassItem drawElement(XMLWriter xml, String[] classNames) throws Exception {
    // classNames.length == 1 && classNames[0].equals("Base");
    boolean onlyElement = false;
    if (classNames != null) {
        for (String cn : classNames) {
            if (definitions.getPrimitives().containsKey(cn)) {
                DefinedCode cd = definitions.getPrimitives().get(cn);
                ElementDefn fake = fakes.get(cn);
                if (cd instanceof DefinedStringPattern) {
                    links.add(new Link(classes.get(fakes.get(((DefinedStringPattern) cd).getBase())), drawClass(xml, fake, false, null, true, null, cd, StandardsStatus.NORMATIVE), LinkType.SPECIALIZATION, null, null, PointKind.unknown, null, null));
                } else {
                    ClassItem parent = classes.get(definitions.getElementDefn(version.isR4B() ? "Element" : "PrimitiveType"));
                    if (parent == null) {
                        drawClass(xml, fake, false, null, true, null, cd, StandardsStatus.NORMATIVE);
                    } else {
                        links.add(new Link(parent, drawClass(xml, fake, false, null, true, null, cd, StandardsStatus.NORMATIVE), LinkType.SPECIALIZATION, null, null, PointKind.unknown, null, null));
                    }
                }
            } else if ("xhtml".equals(cn)) {
                DefinedCode cd = new DefinedCode("xhtml", "XHTML for resource narrative", null);
                ElementDefn fake = fakes.get(cn);
                ClassItem parent = classes.get(definitions.getElementDefn(version.isR4B() ? "Element" : "DataType"));
                if (parent == null) {
                    drawClass(xml, fake, false, null, true, null, cd, StandardsStatus.NORMATIVE);
                } else {
                    links.add(new Link(parent, drawClass(xml, fake, false, null, true, null, cd, StandardsStatus.NORMATIVE), LinkType.SPECIALIZATION, null, null, PointKind.unknown, null, null));
                }
            } else if (definitions.getConstraints().containsKey(cn)) {
                ProfiledType cd = definitions.getConstraints().get(cn);
                ElementDefn fake = fakes.get(cn);
                ClassItem parent = classes.get(definitions.getElementDefn(cd.getBaseType()));
                links.add(new Link(parent, drawClass(xml, fake, false, null, true, null, null, StandardsStatus.NORMATIVE), LinkType.CONSTRAINT, null, null, PointKind.unknown, null, null));
            } else if (definitions.getPrimitives().containsKey(cn)) {
                DefinedCode cd = new DefinedCode("xhtml", "XHTML for resource narrative", null);
                ElementDefn fake = fakes.get(cn);
                // links.add(new Link(item,
                // , LinkType.SPECIALIZATION, null, null, PointKind.unknown, null, null));
                drawClass(xml, fake, false, null, true, null, cd, StandardsStatus.NORMATIVE);
            } else if (!onlyElement) {
                ElementDefn e = definitions.getElementDefn(cn);
                ClassItem parent = Utilities.noString(e.typeCode()) ? null : classes.get(definitions.getElementDefn(e.typeCode()));
                if (parent == null) {
                    drawClass(xml, e, false, null, true, cn, null, e.getStandardsStatus());
                } else {
                    links.add(new Link(parent, drawClass(xml, e, false, null, true, cn, null, e.getStandardsStatus()), LinkType.SPECIALIZATION, null, null, PointKind.unknown, null, null));
                }
            }
        }
    }
    return null;
}

Example 39 with Element

use of org.hl7.fhir.r4b.elementmodel.Element in project kindling by HL7.

the class SvgGenerator method determineMetrics.

private Point determineMetrics(String[] classNames) throws Exception {
    double width = textWidth("Element") * 1.8;
    double height = HEADER_HEIGHT + GAP_HEIGHT * 2;
    // if ("true".equals(ini.getStringProperty("diagram", "element-attributes"))) {
    // height = height + LINE_HEIGHT + GAP_HEIGHT;
    // width = textWidth("extension : Extension 0..*");
    // }
    Point p = new Point(0, 0, PointKind.unknown);
    ClassItem item = new ClassItem(p.x, p.y, width, height, id);
    classes.put(null, item);
    double x = item.right() + MARGIN_X;
    double y = item.bottom() + MARGIN_Y;
    if (classNames != null) {
        for (String cn : classNames) {
            if (definitions.getPrimitives().containsKey(cn)) {
                DefinedCode cd = definitions.getPrimitives().get(cn);
                ElementDefn fake = new ElementDefn();
                fake.setName(cn);
                fakes.put(cn, fake);
                if (cd instanceof DefinedStringPattern)
                    p = determineMetrics(fake, classes.get(fakes.get(((DefinedStringPattern) cd).getBase())), cn, false, cd);
                else
                    p = determineMetrics(fake, item, cn, false, cd);
            } else if ("xhtml".equals(cn)) {
                ElementDefn fake = new ElementDefn();
                fake.setName("xhtml");
                fakes.put("xhtml", fake);
                DefinedCode cd = new DefinedCode("xhtml", "XHTML for resource narrative", null);
                p = determineMetrics(fake, item, cn, false, cd);
            } else if (definitions.getConstraints().containsKey(cn)) {
                ProfiledType cd = definitions.getConstraints().get(cn);
                ElementDefn ed = definitions.getElementDefn(cd.getBaseType());
                ClassItem parentClss = classes.get(ed);
                ElementDefn fake = new ElementDefn();
                fake.setName(cn);
                fakes.put(cn, fake);
                p = determineMetrics(fake, parentClss, cn, false, null);
            } else {
                ElementDefn c = definitions.getElementDefn(cn);
                p = determineMetrics(c, item, c.getName(), false, null);
            }
            x = Math.max(x, p.x + MARGIN_X);
            y = Math.max(y, p.y + MARGIN_Y);
        }
    }
    return new Point(x, y, PointKind.unknown);
}

Example 40 with Element

use of org.hl7.fhir.r4b.elementmodel.Element in project kindling by HL7.

the class TurtleSpecGenerator method generateInner.

private void generateInner(ElementDefn root, boolean resource, boolean isAbstract) throws IOException, Exception {
    String rn;
    if (root.getName().equals("Extension"))
        rn = "extension|modifierExtension";
    else if (root.getName().equals("Meta"))
        rn = "meta";
    else if (root.getTypes().size() > 0 && (root.getTypes().get(0).getName().equals("Type") || (root.getTypes().get(0).getName().equals("Structure"))) || isAbstract)
        rn = "[name]";
    else
        rn = root.getName();
    write("@prefix fhir: <http://hl7.org/fhir/> .");
    if (resource)
        write("<span style=\"float: right\"><a title=\"Documentation for this format\" href=\"" + prefix + "rdf.html\"><img src=\"" + prefix + "help.png\" alt=\"doco\"/></a></span>\r\n");
    write("\r\n");
    write("\r\n");
    if (resource) {
        write("[ a fhir:");
        if (defPage == null)
            write("<span title=\"" + Utilities.escapeXml(root.getDefinition()) + "\"><b>");
        else
            write("<a href=\"" + (defPage + "#" + root.getName()) + "\" title=\"" + Utilities.escapeXml(root.getDefinition()) + "\" class=\"dict\"><b>");
        write(rn);
        if ((defPage == null))
            write("</b></span>;");
        else
            write("</b></a>;");
        write("\r\n  fhir:nodeRole fhir:treeRoot; # if this is the parser root\r\n");
    } else
        write("[");
    write("\r\n");
    if (rn.equals(root.getName()) && resource) {
        if (!Utilities.noString(root.typeCode())) {
            write("  # from <a href=\"" + prefix + "resource.html\">Resource</a>: <a href=\"" + prefix + "resource.html#id\">.id</a>, <a href=\"" + prefix + "resource.html#meta\">.meta</a>, <a href=\"" + prefix + "resource.html#implicitRules\">.implicitRules</a>, and <a href=\"" + prefix + "resource.html#language\">.language</a>\r\n");
            if (root.typeCode().equals("DomainResource"))
                write("  # from <a href=\"" + prefix + "domainresource.html\">DomainResource</a>: <a href=\"" + prefix + "narrative.html#Narrative\">.text</a>, <a href=\"" + prefix + "references.html#contained\">.contained</a>, <a href=\"" + prefix + "extensibility.html\">.extension</a>, and <a href=\"" + prefix + "extensibility.html#modifierExtension\">.modifierExtension</a>\r\n");
        }
    } else {
        if (root.typeCode().equals("BackboneElement"))
            write(" # from BackboneElement: <a href=\"" + prefix + "extensibility.html\">Element.extension</a>, <a href=\"" + prefix + "extensibility.html\">BackboneElement.modifierextension</a>\r\n");
        else
            write(" # from Element: <a href=\"" + prefix + "extensibility.html\">Element.extension</a>\r\n");
    }
    for (ElementDefn elem : root.getElements()) {
        generateCoreElem(elem, 1, root.getName(), rn.equals(root.getName()) && resource);
    }
    write("]\r\n");
}