Examples with TypeRef org.hl7.fhir.definitions.model.TypeRef used on opensource projects

Example 1 with TypeRef

use of org.hl7.fhir.definitions.model.TypeRef in project kindling by HL7.

the class TypeParser method convert.

public List<TypeRefComponent> convert(IWorkerContext context, String path, List<TypeRef> types, boolean resource, ElementDefinition ed) throws Exception {
    List<TypeRefComponent> list = new ArrayList<TypeRefComponent>();
    for (TypeRef t : types) {
        // Expand any Resource(A|B|C) references
        if (t.hasParams() && !("Reference".equals(t.getName()) || "canonical".equals(t.getName()))) {
            throw new Exception("Only resource references can specify parameters.  Path " + path);
        }
        if (t.getParams().size() > 0) {
            if (t.getProfile() != null && t.getParams().size() != 1) {
                throw new Exception("Cannot declare profile on a resource reference declaring multiple resource types.  Path " + path);
            }
            if (t.getProfile() != null) {
                TypeRefComponent childType = getTypeComponent(list, t.getName());
                if (t.getVersioning() != null)
                    childType.setVersioning(t.getVersioning());
                if (t.getName().equals("Reference") || t.getName().equals("canonical"))
                    childType.addTargetProfile(t.getProfile());
                else
                    childType.addProfile(t.getProfile());
            } else
                for (String param : t.getParams()) {
                    TypeRefComponent childType = getTypeComponent(list, t.getName());
                    if (t.getVersioning() != null)
                        childType.setVersioning(t.getVersioning());
                    String p = "Any".equals(param) ? "Resource" : param;
                    if (t.getName().equals("Reference") || t.getName().equals("canonical"))
                        childType.addTargetProfile("http://hl7.org/fhir/StructureDefinition/" + p);
                    else
                        childType.addProfile("http://hl7.org/fhir/StructureDefinition/" + p);
                }
        } else if (t.isWildcardType()) {
            // this list is filled out manually because it may be running before the types referred to have been loaded
            for (String n : TypesUtilities.wildcardTypes(version)) {
                TypeRefComponent tc = new TypeRefComponent().setCode(n);
                if (t.getVersioning() != null)
                    tc.setVersioning(t.getVersioning());
                list.add(tc);
            }
        } else if (Utilities.noString(t.getName()) && t.getProfile() != null) {
            StructureDefinition sd = context.fetchResource(StructureDefinition.class, t.getProfile());
            TypeRefComponent tc = getTypeComponent(list, sd != null ? sd.getType() : t.getName());
            if (t.getVersioning() != null)
                tc.setVersioning(t.getVersioning());
            if (t.getName().equals("Reference"))
                tc.addTargetProfile(t.getProfile());
            else
                tc.addProfile(t.getProfile());
        } else if (t.getName().startsWith("=")) {
            if (resource)
                list.add(new TypeRefComponent().setCode("BackboneElement"));
            else
                list.add(new TypeRefComponent().setCode("Element"));
            ToolingExtensions.addStringExtension(ed, "http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name", t.getName().substring(1));
        } else {
            StructureDefinition sd = context.fetchTypeDefinition(t.getName());
            if (sd == null)
                throw new Exception("Unknown type '" + t.getName() + "'");
            TypeRefComponent tc = getTypeComponent(list, sd.getType());
            if (t.getVersioning() != null)
                tc.setVersioning(t.getVersioning());
            if (t.getName().equals("Reference")) {
                if (t.hasProfile())
                    tc.addTargetProfile(t.getProfile());
            } else if (t.hasProfile())
                tc.addProfile(t.getProfile());
        }
    }
    // no duplicates
    for (TypeRefComponent tr1 : list) {
        for (TypeRefComponent tr2 : list) {
            if (tr1 != tr2) {
                if (tr1.getWorkingCode().equals(tr2.getWorkingCode()))
                    throw new Exception("duplicate code " + tr1.getWorkingCode());
            }
        }
    }
    return list;
}

Example 2 with TypeRef

use of org.hl7.fhir.definitions.model.TypeRef in project kindling by HL7.

the class ValueSetGenerator method genDataTypes.

private void genDataTypes(ValueSet vs) throws Exception {
    if (!vs.hasCompose())
        vs.setCompose(new ValueSetComposeComponent());
    vs.getCompose().addInclude().setSystem("http://hl7.org/fhir/data-types");
    vs.setUserData("filename", "valueset-" + vs.getId());
    if (!vs.hasExtension(ToolingExtensions.EXT_WORKGROUP)) {
        vs.addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType("fhir"));
    } else {
        String ec = ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_WORKGROUP);
        if (!ec.equals("fhir"))
            System.out.println("ValueSet " + vs.getUrl() + " WG mismatch 6: is " + ec + ", want to set to " + "fhir");
    }
    vs.setUserData("path", "valueset-" + vs.getId() + ".html");
    CodeSystem cs = new CodeSystem();
    CodeSystemConvertor.populate(cs, vs);
    cs.setUrl("http://hl7.org/fhir/data-types");
    cs.setVersion(version);
    cs.setCaseSensitive(true);
    cs.setContent(CodeSystemContentMode.COMPLETE);
    definitions.getCodeSystems().see(cs, packageInfo);
    List<String> codes = new ArrayList<String>();
    for (TypeRef t : definitions.getKnownTypes()) codes.add(t.getName());
    Collections.sort(codes);
    for (String s : codes) {
        if (!definitions.dataTypeIsSharedInfo(s)) {
            ConceptDefinitionComponent c = cs.addConcept();
            c.setCode(s);
            c.setDisplay(s);
            if (definitions.getPrimitives().containsKey(s))
                c.setDefinition(definitions.getPrimitives().get(s).getDefinition());
            else if (definitions.getConstraints().containsKey(s))
                // don't add these: c.setDefinition(definitions.getConstraints().get(s).getDefinition());
                ;
            else if (definitions.hasElementDefn(s))
                c.setDefinition(definitions.getElementDefn(s).getDefinition());
            else
                c.setDefinition("...to do...");
        }
    }
    ToolingExtensions.addCSComment(cs.addConcept().setCode("xhtml").setDisplay("XHTML").setDefinition("XHTML format, as defined by W3C, but restricted usage (mainly, no active content)"), "Special case: xhtml can only be used in the narrative Data Type");
    markSpecialStatus(vs, cs, true);
}

Example 3 with TypeRef

use of org.hl7.fhir.definitions.model.TypeRef in project kindling by HL7.

the class OldSpreadsheetParser method parseProfileSheet.

private ConstraintStructure parseProfileSheet(Definitions definitions, Profile ap, String n, List<String> namedSheets, boolean published, String usage, List<ValidationMessage> issues, WorkGroup wg, String fmm) throws Exception {
    Sheet sheet;
    ResourceDefn resource = new ResourceDefn();
    sheet = loadSheet(n + "-Inv");
    Map<String, Invariant> invariants = null;
    if (sheet != null) {
        invariants = readInvariants(sheet, n, n + "-Inv");
    } else {
        invariants = new HashMap<String, Invariant>();
    }
    sheet = loadSheet(n);
    if (sheet == null)
        throw new Exception("The StructureDefinition referred to a tab by the name of '" + n + "', but no tab by the name could be found");
    for (int row = 0; row < sheet.rows.size(); row++) {
        ElementDefn e = processLine(resource, sheet, row, invariants, true, ap, row == 0);
        if (e != null)
            for (TypeRef t : e.getTypes()) {
                if (t.getProfile() != null && !t.getName().equals("Extension") && t.getProfile().startsWith("#")) {
                    if (!namedSheets.contains(t.getProfile().substring(1)))
                        namedSheets.add(t.getProfile().substring(1));
                }
            }
    }
    sheet = loadSheet(n + "-Extensions");
    if (sheet != null) {
        int row = 0;
        while (row < sheet.rows.size()) {
            if (sheet.getColumn(row, "Code").startsWith("!"))
                row++;
            else
                row = processExtension(resource.getRoot().getElementByName(definitions, "extensions", true, false), sheet, row, definitions, ap.metadata("extension.uri"), ap, issues, invariants, wg);
        }
    }
    sheet = loadSheet(n + "-Search");
    if (sheet != null) {
        readSearchParams(resource, sheet, true);
    }
    if (invariants != null) {
        for (Invariant inv : invariants.values()) {
            if (Utilities.noString(inv.getContext()))
                throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " has no context");
            else {
                ElementDefn ed = findContext(resource.getRoot(), inv.getContext(), "Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " Context");
                // TODO: Need to resolve context based on element name, not just path
                if (ed.getName().endsWith("[x]") && !inv.getContext().endsWith("[x]"))
                    inv.setFixedName(inv.getContext().substring(inv.getContext().lastIndexOf(".") + 1));
                ed.getInvariants().put(inv.getId(), inv);
                if (Utilities.noString(inv.getXpath())) {
                    throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " (" + inv.getEnglish() + ") has no XPath statement");
                } else if (inv.getXpath().contains("\""))
                    throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " (" + inv.getEnglish() + ") contains a \" character");
            // if (Utilities.noString(inv.getExpression()))
            // throw new Exception("Type "+resource.getRoot().getName()+" Invariant "+inv.getId()+" ("+inv.getEnglish()+") has no Expression statement (in FHIRPath format)");
            }
        }
    }
    resource.getRoot().setProfileName(n);
    if (n.toLowerCase().equals(ap.getId()))
        throw new Exception("Duplicate Profile Name: Package id " + ap.getId() + " and profile id " + n.toLowerCase() + " are the same");
    if (profileIds.containsKey(n.toLowerCase()))
        throw new Exception("Duplicate Profile Name: " + n.toLowerCase() + " in " + ap.getId() + ", already registered in " + profileIds.get(n.toLowerCase()).getOwner());
    ConstraintStructure p = new ConstraintStructure(n.toLowerCase(), resource.getRoot().getProfileName(), resource, ig != null ? ig : definitions.getUsageIG(usage, "Parsing " + name), wg, fmm, Utilities.existsInList(ap.metadata("Experimental"), "y", "Y", "true", "TRUE", "1"));
    p.setOwner(ap.getId());
    profileIds.put(n.toLowerCase(), p);
    return p;
}

Example 4 with TypeRef

use of org.hl7.fhir.definitions.model.TypeRef in project kindling by HL7.

the class OldSpreadsheetParser method resolveElementReferences.

private void resolveElementReferences(ResourceDefn parent, ElementDefn root) throws Exception {
    for (TypeRef ref : root.getTypes()) {
        if (ref.isElementReference()) {
            ElementDefn referredElement = parent.getRoot().getElementByName(definitions, ref.getName().substring(1), true, false, null);
            if (referredElement == null)
                throw new Exception("Element reference " + ref.getName() + " cannot be found in type " + parent.getName());
            if (referredElement.getDeclaredTypeName() == null)
                throw new Exception("Element reference " + ref.getName() + " in " + parent.getName() + " refers to an anonymous group of elements. Please specify names with the '=<name>' construct in the typename column.");
            ref.setResolvedTypeName(referredElement.getDeclaredTypeName());
        }
    }
    for (ElementDefn element : root.getElements()) {
        resolveElementReferences(parent, element);
    }
}

Example 5 with TypeRef

use of org.hl7.fhir.definitions.model.TypeRef in project kindling by HL7.

the class SourceParser method loadCompositeType.

private String loadCompositeType(String n, Map<String, org.hl7.fhir.definitions.model.TypeDefn> map, String fmm, boolean isAbstract) throws Exception {
    TypeParser tp = new TypeParser(version.toString());
    List<TypeRef> ts = tp.parse(n, false, null, context, true);
    definitions.getKnownTypes().addAll(ts);
    StandardsStatus status = loadStatus(n);
    String nv = loadNormativeVersion(n);
    try {
        TypeRef t = ts.get(0);
        File csv = new CSFile(dtDir + t.getName().toLowerCase() + ".xml");
        if (csv.exists()) {
            OldSpreadsheetParser p = new OldSpreadsheetParser("core", new CSFileInputStream(csv), csv.getName(), csv.getAbsolutePath(), definitions, srcDir, logger, registry, version, context, genDate, isAbstract, page, true, ini, wg("fhir"), definitions.getProfileIds(), fpUsages, page.getConceptMaps(), exceptionIfExcelNotNormalised, page.packageInfo(), page.getRc());
            org.hl7.fhir.definitions.model.TypeDefn el = p.parseCompositeType();
            el.setFmmLevel(fmm);
            el.setStandardsStatus(status);
            el.setNormativeVersion(nv);
            map.put(t.getName(), el);
            genTypeProfile(el);
            errors.addAll(p.getErrors());
            return el.getName();
        } else {
            String p = ini.getStringProperty("types", n);
            csv = new CSFile(dtDir + p.toLowerCase() + ".xml");
            if (!csv.exists())
                throw new Exception("unable to find a definition for " + n + " in " + p);
            XLSXmlParser xls = new XLSXmlParser(new CSFileInputStream(csv), csv.getAbsolutePath());
            new XLSXmlNormaliser(csv.getAbsolutePath(), exceptionIfExcelNotNormalised).go();
            Sheet sheet = xls.getSheets().get("Restrictions");
            boolean found = false;
            for (int i = 0; i < sheet.rows.size(); i++) {
                if (sheet.getColumn(i, "Name").equals(n)) {
                    found = true;
                    Invariant inv = new Invariant();
                    inv.setId(n);
                    inv.setEnglish(sheet.getColumn(i, "Rules"));
                    inv.setOcl(sheet.getColumn(i, "OCL"));
                    inv.setXpath(sheet.getColumn(i, "XPath"));
                    inv.setExpression(sheet.getColumn(i, "Expression"));
                    inv.setExplanation(sheet.getColumn(i, "Explanation"));
                    inv.setTurtle(sheet.getColumn(i, "RDF"));
                    ProfiledType pt = new ProfiledType();
                    pt.setDefinition(sheet.getColumn(i, "Definition"));
                    pt.setDescription(sheet.getColumn(i, "Rules"));
                    String structure = sheet.getColumn(i, "Structure");
                    if (!Utilities.noString(structure)) {
                        String[] parts = structure.split("\\;");
                        for (String pp : parts) {
                            String[] words = pp.split("\\=");
                            pt.getRules().put(words[0], words[1]);
                        }
                    }
                    pt.setName(n);
                    pt.setBaseType(p);
                    pt.setInvariant(inv);
                    definitions.getConstraints().put(n, pt);
                }
            }
            if (!found)
                throw new Exception("Unable to find definition for " + n);
            return n;
        }
    } catch (Exception e) {
        throw new Exception("Unable to load " + n + ": " + e.getMessage(), e);
    }
}