Examples with StructureDefinition org.hl7.fhir.dstu2016may.model.StructureDefinition used on opensource projects

Example 51 with StructureDefinition

use of org.hl7.fhir.dstu2016may.model.StructureDefinition in project kindling by HL7.

the class OldSpreadsheetParser method parseConformancePackage.

public void parseConformancePackage(Profile ap, Definitions definitions, String folder, String usage, List<ValidationMessage> issues, WorkGroup wg) throws Exception {
    try {
        isProfile = true;
        this.folder = folder;
        checkMappings(ap);
        Sheet sheet = loadSheet("Bindings");
        if (sheet != null)
            readBindings(sheet);
        sheet = loadSheet("Metadata");
        for (int row = 0; row < sheet.rows.size(); row++) {
            String n = sheet.getColumn(row, "Name");
            String v = sheet.getColumn(row, "Value");
            if (n != null && v != null) {
                if (ap.getMetadata().containsKey(n))
                    ap.getMetadata().get(n).add(v);
                else {
                    ArrayList<String> vl = new ArrayList<String>();
                    vl.add(v);
                    ap.getMetadata().put(n, vl);
                }
            }
        }
        if (!Utilities.noString(ap.metadata("category")))
            usage = ap.metadata("category");
        if (ap.hasMetadata("name"))
            ap.setTitle(ap.metadata("name"));
        if (ap.hasMetadata("introduction"))
            ap.setIntroduction(Utilities.path(folder, ap.metadata("introduction")));
        if (ap.hasMetadata("notes"))
            ap.setNotes(Utilities.path(folder, ap.metadata("notes")));
        if (!ap.hasMetadata("id"))
            throw new Exception("Error parsing " + ap.getId() + "/" + ap.getTitle() + " no 'id' found in metadata");
        if (!ap.metadata("id").matches(FormatUtilities.ID_REGEX))
            throw new Exception("Error parsing " + ap.getId() + "/" + ap.getTitle() + " 'id' is not a valid id");
        if (wg == null)
            wg = workgroups.get(ap.metadata("workgroup"));
        if (wg == null)
            wg = committee;
        if (wg == null)
            throw new Exception("Error parsing " + ap.getId() + "/" + ap.getTitle() + " : no workgroup value in the metadata");
        if (!ap.metadata("id").equals(ap.metadata("id").toLowerCase()))
            throw new Exception("Error parsing " + ap.getId() + "/" + ap.getTitle() + " 'id' must be all lowercase");
        this.profileExtensionBase = ap.metadata("extension.uri");
        if (ig == null || ig.isCore()) {
            if (!profileExtensionBase.startsWith("http://hl7.org/fhir/StructureDefinition/") && !profileExtensionBase.startsWith("http://fhir-registry.smarthealthit.org/StructureDefinition/"))
                throw new Exception("Core extensions must have a url starting with http://hl7.org/fhir/StructureDefinition/ for " + ap.getId());
        } else {
            if (!profileExtensionBase.startsWith("http://hl7.org/fhir/StructureDefinition/" + ig.getCode() + "-"))
                throw new Exception("Core extensions must have a url starting with http://hl7.org/fhir/StructureDefinition/" + ig.getCode() + "- for " + ap.getId());
        }
        Map<String, Invariant> invariants = null;
        sheet = loadSheet("Extensions-Inv");
        if (sheet != null) {
            invariants = readInvariants(sheet, "", "Extensions-Inv");
        }
        sheet = loadSheet("Extensions");
        if (sheet != null) {
            int row = 0;
            while (row < sheet.rows.size()) {
                if (sheet.getColumn(row, "Code").startsWith("!"))
                    row++;
                else
                    row = processExtension(null, sheet, row, definitions, ap.metadata("extension.uri"), ap, issues, invariants, wg);
            }
        }
        List<String> namedSheets = new ArrayList<String>();
        if (ap.getMetadata().containsKey("published.structure")) {
            for (String n : ap.getMetadata().get("published.structure")) {
                if (!Utilities.noString(n)) {
                    if (ig != null && !ig.isCore() && !n.toLowerCase().startsWith(ig.getCode() + "-"))
                        throw new Exception("Error: published structure names must start with the implementation guide code (" + ig.getCode() + "-)");
                    String fmm = ap.metadata("fmm-" + n);
                    if (Utilities.noString(fmm))
                        fmm = ap.metadata("fmm");
                    if (Utilities.noString(fmm))
                        // default fmm value
                        fmm = "1";
                    ap.getProfiles().add(parseProfileSheet(definitions, ap, n, namedSheets, true, usage, issues, wg, fmm));
                }
            }
        }
        int i = 0;
        while (i < namedSheets.size()) {
            String fmm = ap.metadata("fmm-" + namedSheets.get(i));
            if (Utilities.noString(fmm))
                fmm = ap.metadata("fmm");
            if (Utilities.noString(fmm))
                // default fmm value
                fmm = "1";
            ap.getProfiles().add(parseProfileSheet(definitions, ap, namedSheets.get(i), namedSheets, false, usage, issues, wg, fmm));
            i++;
        }
        if (namedSheets.isEmpty() && xls.getSheets().containsKey("Search"))
            readSearchParams(ap, xls.getSheets().get("Search"), this.profileExtensionBase);
        if (xls.getSheets().containsKey("Operations"))
            readOperations(ap.getOperations(), loadSheet("Operations"));
    } catch (Exception e) {
        throw new Exception("exception parsing pack " + ap.getSource() + ": " + e.getMessage(), e);
    }
}

Example 52 with StructureDefinition

use of org.hl7.fhir.dstu2016may.model.StructureDefinition 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 53 with StructureDefinition

use of org.hl7.fhir.dstu2016may.model.StructureDefinition 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);
        }
    }
}

Example 54 with StructureDefinition

use of org.hl7.fhir.dstu2016may.model.StructureDefinition in project kindling by HL7.

the class SourceParser method genTypeProfile.

private void genTypeProfile(org.hl7.fhir.definitions.model.TypeDefn t) throws Exception {
    StructureDefinition profile;
    try {
        profile = new ProfileGenerator(definitions, context, page, genDate, version, null, fpUsages, page.getFolders().rootDir, page.getUml(), page.getRc()).generate(t);
        t.setProfile(profile);
        DataTypeTableGenerator dtg = new DataTypeTableGenerator(dstDir, page, t.getName(), true, version);
        t.getProfile().getText().setDiv(new XhtmlNode(NodeType.Element, "div"));
        t.getProfile().getText().getDiv().getChildNodes().add(dtg.generate(t, null, false));
        if (context.hasResource(StructureDefinition.class, t.getProfile().getUrl()))
            throw new Exception("Duplicate Profile " + t.getProfile().getUrl());
        context.cacheResource(t.getProfile());
    } catch (Exception e) {
        throw new Exception("Error generating profile for '" + t.getName() + "': " + e.getMessage(), e);
    }
}

Example 55 with StructureDefinition

use of org.hl7.fhir.dstu2016may.model.StructureDefinition in project kindling by HL7.

the class SourceParser method loadConformancePackage.

private void loadConformancePackage(Profile ap, List<ValidationMessage> issues, WorkGroup wg) throws FileNotFoundException, IOException, Exception {
    if (ap.getSourceType() == ConformancePackageSourceType.Spreadsheet) {
        OldSpreadsheetParser sparser = new OldSpreadsheetParser(ap.getCategory(), new CSFileInputStream(ap.getSource()), Utilities.noString(ap.getId()) ? ap.getSource() : ap.getId(), ap.getSource(), definitions, srcDir, logger, registry, version, context, genDate, false, page, false, ini, wg, definitions.getProfileIds(), fpUsages, page.getConceptMaps(), exceptionIfExcelNotNormalised, page.packageInfo(), page.getRc());
        sparser.setFolder(Utilities.getDirectoryForFile(ap.getSource()));
        sparser.parseConformancePackage(ap, definitions, Utilities.getDirectoryForFile(ap.getSource()), ap.getCategory(), issues, wg);
        errors.addAll(sparser.getErrors());
    } else if (ap.getSourceType() == ConformancePackageSourceType.StructureDefinition) {
        Resource rf;
        try {
            rf = new XmlParser().parse(new CSFileInputStream(ap.getSource()));
        } catch (Exception e) {
            throw new Exception("Error parsing " + ap.getSource() + ": " + e.getMessage(), e);
        }
        if (!(rf instanceof StructureDefinition))
            throw new Exception("Error parsing Profile: not a structure definition");
        StructureDefinition sd = (StructureDefinition) rf;
        sd.setVersion(version.toCode());
        ap.putMetadata("id", sd.getId() + "-pack");
        ap.putMetadata("date", sd.getDateElement().asStringValue());
        ap.putMetadata("title", sd.getTitle());
        ap.putMetadata("status", sd.getStatus().toCode());
        ap.putMetadata("description", new XhtmlComposer(XhtmlComposer.HTML).compose(sd.getText().getDiv()));
        if (ToolingExtensions.hasExtension(sd, "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg")) {
            wg = definitions.getWorkgroups().get(ToolingExtensions.readStringExtension(sd, "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"));
            ap.putMetadata("workgroup", wg.getCode());
        }
        ap.setTitle(sd.getTitle());
        new ProfileUtilities(page.getWorkerContext(), null, null).setIds(sd, false);
        ap.getProfiles().add(new ConstraintStructure(sd, definitions.getUsageIG(ap.getCategory(), "Parsing " + ap.getSource()), wg == null ? wg(sd) : wg, fmm(sd), sd.getExperimental()));
    } else if (ap.getSource() != null) {
        parseConformanceDocument(ap, ap.getId(), new CSFile(ap.getSource()), ap.getCategory(), wg);
    }
}