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

Example 21 with WorkGroup

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

the class PageProcessor method loadXmlNotes.

public String loadXmlNotes(String name, String suffix, boolean checkHeaders, String definition, ResourceDefn resource, List<String> tabs, ImplementationGuideDefn ig, WorkGroup wg) throws Exception {
    String filename;
    if (definitions.hasLogicalModel(name)) {
        LogicalModel lm = definitions.getLogicalModel(name);
        filename = Utilities.changeFileExt(lm.getSource(), "-" + suffix + ".xml");
    } else
        filename = folders.srcDir + name + File.separatorChar + name + "-" + suffix + ".xml";
    return loadXmlNotesFromFile(filename, checkHeaders, definition, resource, tabs, ig, wg);
}

Example 22 with WorkGroup

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

the class PageProcessor method loadXmlNotesFromFile.

public String loadXmlNotesFromFile(String filename, boolean checkHeaders, String definition, ResourceDefn r, List<String> tabs, ImplementationGuideDefn ig, WorkGroup wg) throws Exception {
    if (!new CSFile(filename).exists()) {
        TextFile.stringToFile(HTML_PREFIX1 + "\r\n<!-- content goes here -->\r\n\r\n" + HTML_SUFFIX, filename);
        return "";
    }
    String res;
    String cnt = TextFile.fileToString(filename);
    Map<String, String> others = new HashMap<String, String>();
    others.put("definition", definition);
    cnt = processPageIncludes(filename, cnt, "notes", others, null, tabs, "--", ig, r, wg).trim() + "\r\n";
    if (cnt.startsWith("<div")) {
        if (!cnt.startsWith(HTML_PREFIX1) && !cnt.startsWith(HTML_PREFIX2))
            throw new Exception("unable to process start xhtml content " + filename + " : \r\n" + cnt.substring(0, HTML_PREFIX1.length()) + " - should be \r\n'" + HTML_PREFIX1 + "' or \r\n'" + HTML_PREFIX2 + "'");
        else if (!cnt.endsWith(HTML_SUFFIX))
            throw new Exception("unable to process end xhtml content " + filename + " : " + cnt.substring(cnt.length() - HTML_SUFFIX.length()));
        else if (cnt.startsWith(HTML_PREFIX2))
            res = cnt.substring(HTML_PREFIX2.length(), cnt.length() - (HTML_SUFFIX.length())).trim();
        else
            res = cnt.substring(HTML_PREFIX1.length(), cnt.length() - (HTML_SUFFIX.length())).trim();
    } else {
        res = HTML_PREFIX1 + cnt + HTML_SUFFIX;
        TextFile.stringToFile(res, filename);
    }
    if (checkHeaders) {
        checkFormat(filename, res, r);
    }
    return res;
}

Example 23 with WorkGroup

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

the class OldSpreadsheetParser method processExtension.

private int processExtension(ElementDefn extensions, Sheet sheet, int row, Definitions definitions, String uri, Profile ap, List<ValidationMessage> issues, Map<String, Invariant> invariants, WorkGroup wg) throws Exception {
    // first, we build the extension definition
    StructureDefinition ex = new StructureDefinition();
    ex.setUserData(ToolResourceUtilities.NAME_RES_IG, ig == null ? "core" : ig.getCode());
    ex.setUserData("profile", ap);
    ex.setKind(StructureDefinitionKind.COMPLEXTYPE);
    ex.setType("Extension");
    ex.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/Extension");
    ex.setDerivation(TypeDerivationRule.CONSTRAINT);
    ex.setAbstract(false);
    ex.setFhirVersion(version);
    ex.setVersion(version.toCode());
    if (wg != null)
        ToolingExtensions.setCodeExtension(ex, ToolingExtensions.EXT_WORKGROUP, wg.getCode());
    String fmm = sheet.getColumn(row, "FMM");
    if (Utilities.noString(fmm))
        // default fmm value for extensions
        fmm = "1";
    ToolingExtensions.addIntegerExtension(ex, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(fmm));
    if (ap.hasMetadata("fmm-level"))
        ToolingExtensions.addIntegerExtension(ex, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(ap.getFmmLevel()));
    if (ap.hasMetadata("workgroup"))
        ToolingExtensions.setCodeExtension(ex, ToolingExtensions.EXT_WORKGROUP, ap.getWg());
    ToolResourceUtilities.updateUsage(ex, ap.getCategory());
    String name = sheet.getColumn(row, "Code");
    String context = null;
    if (Utilities.noString(name))
        throw new Exception("No code found on Extension at " + getLocation(row));
    if (name.contains("."))
        throw new Exception("Extension Definition Error: Extension names cannot contain '.': " + name + "  at " + getLocation(row));
    ex.setUrl(uri + name);
    ex.setId(tail(ex.getUrl()));
    ex.setUserData("path", "extension-" + ex.getId().toLowerCase() + ".html");
    ap.getExtensions().add(ex);
    if (context == null) {
        ExtensionContextType ct = readContextType(sheet.getColumn(row, "Context Type"), row);
        if (sheet.hasColumn("Context Invariant"))
            for (String s : sheet.getColumn(row, "Context Invariant").split("~")) ex.addContextInvariant(s);
        String cc = checkContextMacro(sheet.getColumn(row, "Context"));
        if (!Utilities.noString(cc))
            for (String c : cc.split("\\;")) {
                StructureDefinitionContextComponent ec = ex.addContext();
                ec.setExpression(c.trim());
                ec.setType(ct);
                if (definitions != null) {
                    definitions.checkContextValid(ec, this.name, this.context);
                }
            }
    }
    ex.setTitle(sheet.getColumn(row, "Display"));
    ElementDefn exe = new ElementDefn();
    exe.setName(sheet.getColumn(row, "Code"));
    ElementDefn exu = new ElementDefn();
    exu.setName("url");
    exu.setXmlAttribute(true);
    exe.getElements().add(exu);
    exu.setFixed(new UriType(ex.getUrl()));
    exu.getTypes().add(new TypeRef().setName("uri"));
    if (invariants != null) {
        for (Invariant inv : invariants.values()) {
            if (inv.getContext().equals(name))
                exe.getInvariants().put(inv.getId(), inv);
        }
    }
    parseExtensionElement(sheet, row, definitions, exe, false);
    String sl = exe.getShortDefn();
    ex.setName(sheet.getColumn(row, "Name"));
    if (!ex.hasName())
        ex.setName(exe.getName());
    if (!ex.hasName())
        ex.setName(ex.getTitle());
    if (!ex.hasName() && !Utilities.noString(sl))
        ex.setName(sl);
    if (!ex.hasName())
        throw new Exception("Extension " + ex.getUrl() + " missing name at " + getLocation(row));
    ex.setDescription(preProcessMarkdown(exe.getDefinition(), "Extension Definition"));
    ex.setPublisher(ap.metadata("author.name"));
    if (ap.hasMetadata("author.reference"))
        ex.addContact().getTelecom().add(Factory.newContactPoint(ContactPointSystem.URL, ap.metadata("author.reference")));
    // <code> opt Zero+ Coding assist with indexing and finding</code>
    if (ap.hasMetadata("date"))
        ex.setDateElement(Factory.newDateTime(ap.metadata("date").substring(0, 10)));
    else
        ex.setDate(genDate.getTime());
    if (ap.hasMetadata("status"))
        ex.setStatus(PublicationStatus.fromCode(ap.metadata("status")));
    row++;
    if (ig == null || ig.isCore()) {
        if (!ex.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/") && !ex.getUrl().startsWith("http://fhir-registry.smarthealthit.org/StructureDefinition/"))
            throw new Exception("extension " + ex.getUrl() + " is not valid in the publication tooling");
    } else {
        if (!ex.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/" + ig.getCode() + "-"))
            throw new Exception("extension " + ex.getUrl() + " is not valid for the IG " + ig.getCode() + " in the publication tooling");
    }
    while (row < sheet.getRows().size() && sheet.getColumn(row, "Code").startsWith(name + ".")) {
        String n = sheet.getColumn(row, "Code");
        ElementDefn p = findContext(exe, n.substring(0, n.lastIndexOf(".")), "Extension Definition " + name);
        ElementDefn child = new ElementDefn();
        p.getElements().add(child);
        child.setName(n.substring(n.lastIndexOf(".") + 1));
        child.setProfileName(child.getName());
        parseExtensionElement(sheet, row, definitions, child, true);
        if (invariants != null) {
            for (Invariant inv : invariants.values()) {
                if (inv.getContext().equals(n))
                    child.getInvariants().put(inv.getId(), inv);
            }
        }
        row++;
    }
    ProfileGenerator gen = new ProfileGenerator(definitions, null, pkp, null, version, null, fpUsages, null, null, rc);
    ProfileUtilities utils = new ProfileUtilities(this.context, issues, pkp);
    gen.convertElements(exe, ex, null);
    ex.getDifferential().getElementFirstRep().getType().clear();
    utils.setIds(ex, false);
    StructureDefinition base = definitions != null ? definitions.getSnapShotForType("Extension") : this.context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Extension");
    List<String> errors = new ArrayList<String>();
    utils.sortDifferential(base, ex, "extension " + ex.getUrl(), errors, false);
    assert (errors.size() == 0);
    utils.generateSnapshot(base, ex, ex.getUrl(), "http://hl7.org/fhir", ex.getName());
    utils.setIds(ex, true);
    new ExtensionDefinitionValidator(context).validate(ex);
    this.context.cacheResource(ex);
    return row;
}

Example 24 with WorkGroup

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

the class SourceParser method parseConformanceDocument.

private void parseConformanceDocument(Profile pack, String n, File file, String usage, WorkGroup wg) throws Exception {
    try {
        Resource rf = new XmlParser().parse(new CSFileInputStream(file));
        if (!(rf instanceof Bundle))
            throw new Exception("Error parsing Profile: neither a spreadsheet nor a bundle");
        Bundle b = (Bundle) rf;
        if (b.getType() != BundleType.DOCUMENT)
            throw new Exception("Error parsing profile: neither a spreadsheet nor a bundle that is a document");
        for (BundleEntryComponent ae : ((Bundle) rf).getEntry()) {
            if (ae.getResource() instanceof Composition)
                pack.loadFromComposition((Composition) ae.getResource(), file.getAbsolutePath());
            else if (ae.getResource() instanceof StructureDefinition && !((StructureDefinition) ae.getResource()).getType().equals("Extension")) {
                StructureDefinition ed = (StructureDefinition) ae.getResource();
                for (StructureDefinitionContextComponent s : ed.getContext()) definitions.checkContextValid(s, file.getName(), this.context);
                ToolResourceUtilities.updateUsage(ed, pack.getCategory());
                pack.getProfiles().add(new ConstraintStructure(ed, definitions.getUsageIG(usage, "Parsing " + file.getAbsolutePath()), wg == null ? wg(ed) : wg, fmm(ed), ed.getExperimental()));
            } else if (ae.getResource() instanceof StructureDefinition) {
                StructureDefinition ed = (StructureDefinition) ae.getResource();
                if (Utilities.noString(ed.getBaseDefinition()))
                    ed.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/Extension");
                ed.setDerivation(TypeDerivationRule.CONSTRAINT);
                if (ToolingExtensions.readStringExtension(ed, ToolingExtensions.EXT_WORKGROUP) == null)
                    ToolingExtensions.setCodeExtension(ed, ToolingExtensions.EXT_WORKGROUP, wg.getCode());
                if (!ed.hasUrl())
                    if (ae.hasFullUrl())
                        ed.setUrl(ae.getFullUrl());
                    else
                        ed.setUrl("http://hl7.org/fhir/StructureDefinition/" + ed.getId());
                context.cacheResource(ed);
                pack.getExtensions().add(ed);
            }
        }
    } catch (Exception e) {
        throw new Exception("Error Parsing profile: '" + n + "': " + e.getMessage(), e);
    }
}

Example 25 with WorkGroup

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

the class SourceParser method loadResource.

private ResourceDefn loadResource(String n, Map<String, ResourceDefn> map, boolean isAbstract, boolean isTemplate, String t, boolean isInterface) throws Exception {
    String folder = n;
    WorkGroup wg = definitions.getWorkgroups().get(ini.getStringProperty("workgroups", n));
    if (wg == null)
        throw new Exception("No Workgroup found for resource " + n + ": '" + ini.getStringProperty("workgroups", n) + "'");
    File f = new File(Utilities.path(srcDir, folder, n + ".svg"));
    if (isTemplate) {
        File spreadsheet = new CSFile((srcDir) + folder + File.separatorChar + n + "-spreadsheet.xml");
        OldSpreadsheetParser sparser = new OldSpreadsheetParser("core", new CSFileInputStream(spreadsheet), spreadsheet.getName(), spreadsheet.getAbsolutePath(), definitions, srcDir, logger, registry, version, context, genDate, isAbstract, page, false, ini, wg, definitions.getProfileIds(), fpUsages, page.getConceptMaps(), exceptionIfExcelNotNormalised, page.packageInfo(), page.getRc());
        ResourceDefn root;
        try {
            root = sparser.parseResource(isTemplate);
        } catch (Exception e) {
            throw new Exception("Error Parsing Resource " + n + ": " + e.getMessage(), e);
        }
        root.setAbstract(isAbstract);
        root.setInterface(isInterface);
        errors.addAll(sparser.getErrors());
        setResourceProps(n, wg, root);
        String sc = ini.getStringProperty("security-categorization", root.getName().toLowerCase());
        if (sc != null) {
            root.setSecurityCategorization(SecurityCategorization.fromCode(sc));
        } else if (!Utilities.existsInList(root.getName(), "Resource", "DomainResource", "CanonicalResource", "MetadataResource", "MetadataPattern"))
            throw new Exception("Must have an entry in the security-categorization section of fhir.ini for the resource " + root.getName());
        for (EventDefn e : sparser.getEvents()) {
            processEvent(e, root.getRoot());
        }
        if (map != null) {
            map.put(root.getName(), root);
        }
        if (!isTemplate) {
            definitions.getKnownResources().put(root.getName(), new DefinedCode(root.getName(), root.getRoot().getDefinition(), n));
            context.getResourceNames().add(root.getName());
        }
        if (root.getNormativeVersion() != null || root.getNormativePackage() != null) {
            root.setStatus(StandardsStatus.NORMATIVE);
        }
        if (f.exists()) {
            parseSvgFile(f, root.getLayout(), f.getName());
        }
        if (map != null) {
            map.put(root.getName(), root);
        }
        return root;
    } else {
        try {
            new SpreadSheetReloader(context, srcDir, t, version.toCode()).process();
        } catch (Exception e) {
            System.out.println("Error loading spreadsheet for resource " + t + ": " + e.getMessage());
        }
        new SpreadSheetCreator(context, srcDir, t).generateSpreadsheet();
        ResourceDefn rootNew = new ResourceParser(srcDir, definitions, context, wg, registry, version.toCode(), page.getConceptMaps()).parse(n, t);
        if (f.exists()) {
            parseSvgFile(f, rootNew.getLayout(), f.getName());
        }
        if (!isTemplate) {
            definitions.getKnownResources().put(rootNew.getName(), new DefinedCode(rootNew.getName(), rootNew.getRoot().getDefinition(), n));
            context.getResourceNames().add(rootNew.getName());
        }
        setResourceProps(n, wg, rootNew);
        if (map != null) {
            map.put(rootNew.getName(), rootNew);
        }
        return rootNew;
    }
}