Examples with Extension org.hl7.fhir.r5.model.Extension used on opensource projects

Example 46 with Extension

use of org.hl7.fhir.r5.model.Extension in project kindling by HL7.

the class DefinitionsUsageTracker method usage.

private void usage(org.hl7.fhir.r5.elementmodel.Element instance, ElementDefn definition, String path) throws Exception {
    definition.setCoveredByExample(true);
    for (Element c : instance.getChildren()) {
        String p = c.getProperty().getDefinition().getPath();
        ElementDefn ed = definitions.getElementByPath(p.split("\\."), "example usage", true);
        if (ed != null)
            usage(c, ed, path + "." + c.getName());
    // else if (!c.getName().equals("extension"))
    // System.out.println("error finding "+c.getName()+" at "+path);
    }
}

Example 47 with Extension

use of org.hl7.fhir.r5.model.Extension in project kindling by HL7.

the class CDAGenerator method addCDExtensions.

private void addCDExtensions(List<ElementDefinition> list, String n) {
    ElementDefinition ed = new ElementDefinition();
    ed.setPath(n + ".valueSet");
    seePath(ed);
    ed.setMin(0);
    ed.setMax("1");
    ed.addType().setCode("string");
    ed.addRepresentation(PropertyRepresentation.XMLATTR);
    ed.setDefinition("The valueSet extension adds an attribute for elements with a CD dataType which indicates the particular value set constraining the coded concept");
    ed.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").setValue(new UriType("urn:hl7-org:sdtc"));
    ed = new ElementDefinition();
    ed.setPath(n + ".valueSetVersion");
    seePath(ed);
    ed.setMin(0);
    ed.setMax("1");
    ed.addType().setCode("string");
    ed.addRepresentation(PropertyRepresentation.XMLATTR);
    ed.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").setValue(new UriType("urn:hl7-org:sdtc"));
    ed.setDefinition("The valueSetVersion extension adds an attribute for elements with a CD dataType which indicates the version of the particular value set constraining the coded concept.");
    list.add(ed);
}

Example 48 with Extension

use of org.hl7.fhir.r5.model.Extension 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 49 with Extension

use of org.hl7.fhir.r5.model.Extension in project kindling by HL7.

the class OldSpreadsheetParser method readSearchParams.

private void readSearchParams(ResourceDefn root2, Sheet sheet, boolean forProfile) throws Exception {
    if (sheet != null) {
        for (int row = 0; row < sheet.rows.size(); row++) {
            if (!sheet.hasColumn(row, "Name"))
                throw new Exception("Search Param has no name " + getLocation(row));
            String n = sheet.getColumn(row, "Name");
            if (!n.startsWith("!")) {
                if (!sheet.hasColumn(row, "Type"))
                    throw new Exception("Search Param " + root2.getName() + "/" + n + " has no type " + getLocation(row));
                if (n.endsWith("-before") || n.endsWith("-after"))
                    throw new Exception("Search Param " + root2.getName() + "/" + n + " includes relative time " + getLocation(row));
                if (root2.getSearchParams().containsKey(n))
                    throw new Exception("Search Param " + root2.getName() + "/" + n + ": duplicate name " + getLocation(row));
                String d = sheet.getColumn(row, "Description");
                SearchType t = readSearchType(sheet.getColumn(row, "Type"), row);
                SearchParameter.XPathUsageType pu = readSearchXPathUsage(sheet.getColumn(row, "Path Usage"), row);
                if (Utilities.noString(sheet.getColumn(row, "Path")) && !root2.getName().equals("Resource") && !root2.getName().equals("DomainResource"))
                    throw new Exception("Search Param " + root2.getName() + "/" + n + " has no path at " + getLocation(row));
                SearchParameterDefn sp = null;
                if (t == SearchType.composite) {
                    List<CompositeDefinition> pn = new ArrayList<CompositeDefinition>();
                    if (Utilities.noString(d))
                        throw new Exception("Search Param " + root2.getName() + "/" + n + " has no description " + getLocation(row));
                    String[] pl = sheet.getColumn(row, "Path").split("\\&");
                    String[] pe = sheet.getColumn(row, "Expression").split("\\;");
                    if (pe.length != pl.length + 1)
                        throw new Exception("Composite Search Param " + root2.getName() + "/" + n + " needs expressions " + getLocation(row));
                    int i = 0;
                    for (String pi : pl) {
                        String p = pi.trim();
                        i++;
                        String e = pe[i].trim();
                        if (!root2.getSearchParams().containsKey(p)) {
                            boolean found = false;
                            if (p.endsWith("[x]"))
                                for (String pan : root2.getSearchParams().keySet()) {
                                    if (pan.startsWith(p.substring(0, p.length() - 3)))
                                        found = true;
                                }
                            if (!found)
                                throw new Exception("Composite Search Param " + root2.getName() + "/" + n + "  refers to an unknown component " + p + " at " + getLocation(row));
                        }
                        pn.add(new CompositeDefinition(p, e));
                    }
                    StandardsStatus ss = root2.getStatus();
                    if (!Utilities.noString(sheet.getColumn(row, "Standards-Status")))
                        ss = StandardsStatus.fromCode(sheet.getColumn(row, "Standards-Status"));
                    sp = new SearchParameterDefn(n, d, t, pu, ss);
                    sp.setExpression(pe[0].trim());
                    sp.getComposites().addAll(pn);
                } else {
                    List<String> pn = new ArrayList<String>();
                    String xp = sheet.getColumn(row, "XPath");
                    String[] pl = sheet.getColumn(row, "Path").split("\\|");
                    boolean hierarchy = false;
                    for (String pi : pl) {
                        String p = pi.trim();
                        ElementDefn e = null;
                        if (!Utilities.noString(p) && !p.startsWith("!") && !p.startsWith("Extension{") && definitions != null) {
                            e = root2.getRoot().getElementForPath(trimIndexes(p), definitions, "search param", true, true);
                        }
                        if (e != null && e.hasHierarchy() && e.getHierarchy())
                            hierarchy = true;
                        if (Utilities.noString(d) && e != null)
                            d = e.getShortDefn();
                        if (p.startsWith("Extension(")) {
                            String url = extractExtensionUrl(p);
                            StructureDefinition ex = context.fetchResource(StructureDefinition.class, url);
                            if (ex == null)
                                throw new Exception("Search Param " + root2.getName() + "/" + n + " refers to unknown extension '" + url + "' " + getLocation(row));
                            if (Utilities.noString(d))
                                d = ex.getDescription();
                            pn.add(p);
                        }
                        if (d == null)
                            throw new Exception("Search Param " + root2.getName() + "/" + n + " has no description " + getLocation(row));
                        if (e != null)
                            pn.add(p);
                        if (t == SearchType.reference) {
                            if (e == null && !forProfile && !sheet.hasColumn(row, "Target Types"))
                                throw new Exception("Search Param " + root2.getName() + "/" + n + " of type reference has wrong path '" + p + "' at " + getLocation(row));
                            if (!forProfile && e != null && (!e.hasType("Reference")) && (!e.hasType("canonical")) && (!e.hasType("Resource")))
                                throw new Exception("Search Param " + root2.getName() + "/" + n + " wrong type. The search type is reference, but the element type is " + e.typeCode());
                        } else {
                            if (e != null && e.hasOnlyType("Reference"))
                                throw new Exception("Search Param " + root2.getName() + "/" + n + " wrong type. The search type is " + t.toString() + ", but the element type is " + e.typeCode());
                            if (t == SearchType.uri) {
                                if (e != null && !(e.typeCode().equals("uri") || e.typeCode().equals("url") || e.typeCode().equals("oid") || e.typeCode().startsWith("canonical(")))
                                    throw new Exception("Search Param " + root2.getName() + "/" + n + " wrong type. The search type is " + t.toString() + ", but the element type is " + e.typeCode());
                            } else {
                                if (e != null && e.typeCode().equals("uri"))
                                    throw new Exception("Search Param " + root2.getName() + "/" + n + " wrong type. The search type is " + t.toString() + ", but the element type is " + e.typeCode());
                            }
                        }
                    }
                    if (!forProfile && t == SearchType.reference && pn.size() == 0 && !sheet.hasColumn(row, "Target Types"))
                        throw new Exception("Search Param " + root2.getName() + "/" + n + " of type reference has no path(s) " + getLocation(row));
                    StandardsStatus ss = root2.getStatus();
                    if (!Utilities.noString(sheet.getColumn(row, "Standards-Status")))
                        ss = StandardsStatus.fromCode(sheet.getColumn(row, "Standards-Status"));
                    sp = new SearchParameterDefn(n, d, t, pu, ss);
                    sp.getPaths().addAll(pn);
                    if (!Utilities.noString(xp))
                        sp.setXPath(xp);
                    if (!Utilities.noString(sheet.getColumn(row, "Expression")))
                        sp.setExpression(sheet.getColumn(row, "Expression"));
                    if (!Utilities.noString(sheet.getColumn(row, "Target Types"))) {
                        sp.setManualTypes(sheet.getColumn(row, "Target Types").split("\\,"));
                    }
                    sp.setHierarchy(hierarchy);
                    CommonSearchParameter csp = definitions.getCommonSearchParameters().get(root2.getName() + "::" + n);
                    if (csp != null)
                        for (String s : csp.getResources()) {
                            if (!root2.getName().equals(s))
                                sp.getOtherResources().add(s);
                        }
                }
                root2.getSearchParams().put(n, sp);
            }
        }
    }
}

Example 50 with Extension

use of org.hl7.fhir.r5.model.Extension in project kindling by HL7.

the class OldSpreadsheetParser method readSearchParams.

/* for profiles that have a "search" tab not tied to a structure */
private void readSearchParams(Profile pack, Sheet sheet, String prefix) throws Exception {
    for (int row = 0; row < sheet.rows.size(); row++) {
        if (!sheet.hasColumn(row, "Name"))
            throw new Exception("Search Param has no name " + getLocation(row));
        String n = sheet.getColumn(row, "Name");
        if (!n.startsWith("!")) {
            SearchParameter sp = new SearchParameter();
            if (!sheet.hasColumn(row, "Type"))
                throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has no type " + getLocation(row));
            if (n.endsWith("-before") || n.endsWith("-after"))
                throw new Exception("Search Param " + pack.getTitle() + "/" + n + " includes relative time " + getLocation(row));
            // if (!n.toLowerCase().equals(n))
            // throw new Exception("Search Param "+pack.getTitle()+"/"+n+" must be all lowercase "+ getLocation(row));
            sp.setVersion(version.toCode());
            sp.setName(n);
            sp.setCode(n);
            if (pack.getProfiles().size() > 0 && pack.getProfiles().get(0).getResource() != null) {
                sp.setStatus(pack.getProfiles().get(0).getResource().getStatus());
                sp.setExperimental(pack.getProfiles().get(0).getResource().getExperimental());
            } else {
                // we just guess
                sp.setStatus(PublicationStatus.DRAFT);
                sp.setExperimental(true);
            }
            String d = sheet.getColumn(row, "Description");
            sp.setType(SearchParamType.fromCode(sheet.getColumn(row, "Type")));
            List<String> pn = new ArrayList<String>();
            String path = sheet.getColumn(row, "Path");
            if (Utilities.noString(path))
                throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has no path");
            if (!path.contains(".") && !path.startsWith("#"))
                throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has an invalid path: " + path);
            ResourceDefn root2 = null;
            if (!path.startsWith("#")) {
                path = path.substring(0, path.indexOf('.'));
                if (!pkp.isResource(path))
                    throw new Exception("Ilegal Search Parameter path " + sheet.getColumn(row, "Path"));
                sp.addBase(path);
                sp.setId(pack.getId() + "-" + path + "-" + sp.getName());
                if (definitions != null) {
                    // igtodo (and below)
                    root2 = definitions.getResourceByName(path);
                    if (root2 == null)
                        throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has an invalid path (resource not found)");
                    if (!pkp.isResource(root2.getName()))
                        throw new Exception("Ilegal Search Parameter path " + sheet.getColumn(row, "Path"));
                    sp.getBase().clear();
                    sp.addBase(root2.getName());
                    sp.setId(pack.getId() + "-" + (root2 == null ? "all" : root2.getName()) + "-" + sp.getName());
                }
            }
            if (!Utilities.noString(sheet.getColumn(row, "Target Types")))
                throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has manually specified targets (not allowed)");
            if (root2 != null && root2.getSearchParams().containsKey(n))
                throw new Exception("Search Param " + root2.getName() + "/" + n + ": duplicate name " + getLocation(row));
            if (sp.getType() == SearchParamType.COMPOSITE) {
                throw new Exception("not supported");
            } else {
                String[] pl = sheet.getColumn(row, "Path").split("\\|");
                String xp = sheet.getColumn(row, "XPath");
                for (String pi : pl) {
                    String p = pi.trim();
                    ElementDefn e = null;
                    if (Utilities.noString(p))
                        throw new Exception("Search Param " + root2.getName() + "/" + n + ": empty path " + getLocation(row));
                    if (p.startsWith("#")) {
                        // root less extension search parameter
                        StructureDefinition ex = pack.getExtension(prefix + p.substring(1));
                        if (ex == null)
                            throw new Exception("Search Param " + pack.getTitle() + "/" + n + " refers to unknown extension '" + p + "' " + getLocation(row));
                        e = definitions.getElementDefn("Extension");
                        if (ex.getContext().size() != 1 || ex.getContext().get(0).getType() != ExtensionContextType.ELEMENT)
                            throw new Exception("Search Param " + pack.getTitle() + "/" + n + " refers to an extension with multiple contexts, not not an element context - not supported '" + p + "' " + getLocation(row));
                        path = ex.getContext().get(0).getExpression();
                        if (Utilities.noString(path))
                            throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has no path");
                        if (path.contains("."))
                            path = path.substring(0, path.indexOf('.'));
                        sp.setId(pack.getId() + "-" + path + "-" + sp.getName());
                        root2 = definitions.getResourceByName(path);
                        if (root2 == null)
                            throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has an invalid path (resource not found)");
                        if (root2 != null && root2.getSearchParams().containsKey(n))
                            throw new Exception("Search Param " + root2.getName() + "/" + n + ": duplicate name " + getLocation(row));
                        sp.setId(pack.getId() + "-" + path + "-" + sp.getName());
                        pn.add(ex.getContext().get(0).getExpression() + ".extension{" + ex.getUrl() + "}");
                    } else if (p.contains(".extension{")) {
                        String url = extractExtensionUrl(p);
                        // not created yet?
                        StructureDefinition ex = context.fetchResource(StructureDefinition.class, url);
                        if (ex == null)
                            ex = context.getExtensionStructure(null, url);
                        if (ex == null)
                            throw new Exception("Search Param " + pack.getTitle() + "/" + n + " refers to unknown extension '" + url + "' " + getLocation(row));
                        if (Utilities.noString(d))
                            d = ex.getDescription();
                        if (definitions != null)
                            e = definitions.getElementDefn("Extension");
                        pn.add(p);
                    } else if (!p.startsWith("!") && !p.startsWith("Extension{") && root2 != null) {
                        e = root2.getRoot().getElementForPath(p, definitions, "search param", true, true);
                    }
                    if (e == null && Utilities.noString(d))
                        throw new Exception("unable to resolve sarch param " + p);
                    if (e == null)
                        sp.setExpression(p);
                    if (Utilities.noString(d) && e != null)
                        d = e.getShortDefn();
                    if (d == null)
                        throw new Exception("Search Param " + root2.getName() + "/" + n + " has no description " + getLocation(row));
                    if (e != null)
                        pn.add(p);
                    if (sp.getType() == SearchParamType.REFERENCE) {
                    // no check?
                    } else if (e != null && e.typeCode().startsWith("Reference("))
                        throw new Exception("Search Param " + root2.getName() + "/" + n + " wrong type. The search type is " + sp.getType().toCode() + ", but the element type is " + e.typeCode());
                    sp.setDescription(d);
                }
                sp.setXpath(Utilities.noString(xp) ? new XPathQueryGenerator(definitions, log, null).generateXpath(pn, null) : xp);
                sp.setXpathUsage(readSearchXPathUsage(sheet.getColumn(row, "Path Usage"), row));
            }
            sp.setUrl("http://hl7.org/fhir/SearchParameter/" + sp.getId());
            if (definitions != null)
                definitions.addNs(sp.getUrl(), "Search Parameter " + sp.getName(), pack.getId() + ".html#search");
            if (context.getSearchParameter(sp.getUrl()) != null)
                throw new Exception("Duplicated Search Parameter " + sp.getUrl());
            context.cacheResource(sp);
            pack.getSearchParameters().add(sp);
        }
    }
}