Examples with Sheet org.hl7.fhir.utilities.xls.XLSXmlParser.Sheet used on opensource projects

Example 46 with Sheet

use of org.hl7.fhir.utilities.xls.XLSXmlParser.Sheet 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 47 with Sheet

use of org.hl7.fhir.utilities.xls.XLSXmlParser.Sheet in project kindling by HL7.

the class OldSpreadsheetParser method parseCodes.

private void parseCodes(List<DefinedCode> codes, Sheet sheet) throws Exception {
    for (int row = 0; row < sheet.rows.size(); row++) {
        DefinedCode c = new DefinedCode();
        c.setId(sheet.getColumn(row, "Id"));
        c.setAbstract(sheet.getColumn(row, "Abstract").toUpperCase().equals("Y"));
        c.setCode(sheet.getColumn(row, "Code"));
        c.setDisplay(sheet.getColumn(row, "Display"));
        if (c.hasCode() && !c.hasDisplay())
            c.setDisplay(Utilities.humanize(c.getCode()));
        c.setSystem(sheet.getColumn(row, "System"));
        c.setDefinition(Utilities.appendPeriod(processDefinition(sheet.getColumn(row, "Definition"))));
        c.setComment(Utilities.appendPeriod(sheet.getColumn(row, "Comment")));
        c.setParent(sheet.getColumn(row, "Parent"));
        c.setV2Map(sheet.getColumn(row, "v2"));
        c.setV3Map(sheet.getColumn(row, "v3"));
        for (String ct : sheet.columns) if (ct.startsWith("Display:") && !Utilities.noString(sheet.getColumn(row, ct)))
            c.getLangs().put(ct.substring(8), sheet.getColumn(row, ct));
        if (Utilities.noString(c.getId()) && Utilities.noString(c.getSystem()))
            throw new Exception("code has no id or system (" + sheet.title + ") " + getLocation(row));
        codes.add(c);
    }
}

Example 48 with Sheet

use of org.hl7.fhir.utilities.xls.XLSXmlParser.Sheet in project kindling by HL7.

the class OldSpreadsheetParser method readInvariants.

private Map<String, Invariant> readInvariants(Sheet sheet, String id, String sheetName) throws Exception {
    Map<String, Invariant> result = new HashMap<String, Invariant>();
    for (int row = 0; row < sheet.rows.size(); row++) {
        Invariant inv = new Invariant();
        String s = sheet.getColumn(row, "Id");
        if (!s.startsWith("!")) {
            inv.setId(s.contains("-") ? s : getAbbreviationFor(id) + "-" + s);
            inv.setRequirements(sheet.getColumn(row, "Requirements"));
            inv.setContext(sheet.getColumn(row, "Context"));
            inv.setEnglish(sheet.getColumn(row, "English"));
            inv.setXpath(sheet.getColumn(row, "XPath"));
            inv.setExpression(sheet.getColumn(row, "Expression"));
            inv.setExplanation(sheet.getColumn(row, "Explanation"));
            if (Utilities.noString(inv.getExpression()))
                throw new Exception("missing expression " + getLocation(row));
            inv.setSeverity(sheet.getColumn(row, "Severity"));
            inv.setTurtle(sheet.getColumn(row, "RDF"));
            inv.setOcl(sheet.getColumn(row, "OCL"));
            if (s.equals("") || result.containsKey(s))
                throw new Exception("duplicate or missing invariant id " + getLocation(row));
            result.put(s, inv);
        }
    }
    return result;
}

Example 49 with Sheet

use of org.hl7.fhir.utilities.xls.XLSXmlParser.Sheet in project kindling by HL7.

the class OldSpreadsheetParser method parseExtensionElement.

private void parseExtensionElement(Sheet sheet, int row, Definitions definitions, ElementDefn exe, boolean nested) throws Exception {
    // things that go on Extension
    String[] card = sheet.getColumn(row, "Card.").split("\\.\\.");
    if (card.length != 2 || !Utilities.isInteger(card[0]) || (!"*".equals(card[1]) && !Utilities.isInteger(card[1])))
        throw new Exception("Unable to parse Cardinality " + sheet.getColumn(row, "Card.") + " in " + getLocation(row));
    exe.setMinCardinality(Integer.parseInt(card[0]));
    exe.setMaxCardinality("*".equals(card[1]) ? Integer.MAX_VALUE : Integer.parseInt(card[1]));
    exe.setDefinition(Utilities.appendPeriod(processDefinition(sheet.getColumn(row, "Definition"))));
    exe.setRequirements(Utilities.appendPeriod(sheet.getColumn(row, "Requirements")));
    exe.setComments(Utilities.appendPeriod(sheet.getColumn(row, "Comments")));
    doAliases(sheet, row, exe);
    for (String n : mappings.keySet()) {
        exe.addMapping(n, sheet.getColumn(row, mappings.get(n).getColumnName()).trim());
    }
    exe.setTodo(Utilities.appendPeriod(sheet.getColumn(row, "To Do")));
    exe.setCommitteeNotes(Utilities.appendPeriod(sheet.getColumn(row, "Committee Notes")));
    exe.setShortDefn(sheet.getColumn(row, "Short Name"));
    exe.setIsModifier(parseBoolean(sheet.getColumn(row, "Is Modifier"), row, null));
    if (exe.isModifier()) {
        String reason = sheet.getColumn(row, "Modifier Reason");
        if (Utilities.noString(reason)) {
            System.out.println("Missing IsModifierReason on extension @ " + getLocation(row));
            reason = "Not known why this is labelled a modifier";
        }
        exe.setModifierReason(reason);
    }
    if (nested && exe.isModifier())
        throw new Exception("Cannot create a nested extension that is a modifier @" + getLocation(row));
    exe.getTypes().add(new TypeRef().setName("Extension"));
    // things that go on Extension.value
    if (!Utilities.noString(sheet.getColumn(row, "Type"))) {
        ElementDefn exv = new ElementDefn();
        exv.setName("value[x]");
        exv.getTypes().addAll(new TypeParser(version.toCode()).parse(sheet.getColumn(row, "Type"), true, profileExtensionBase, context, false, sheet.title));
        /*      if (!exv.getName().equals("value[x]")) {
        ElementDefn exd = new ElementDefn();
        exd.setName("value[x]");
        exd.setMaxCardinality(1);
        exd.getTypes().add(new TypeRef(exv.getTypes().get(0).getName()));
        List<String> discriminator = new ArrayList<String>();
        discriminator.add("@type");
        exd.setDiscriminator(discriminator);
        exe.getElements().add(exd);
        exv.setProfileName("value");
      }*/
        exe.getElements().add(exv);
        String bindingName = sheet.getColumn(row, "Binding");
        if (!Utilities.noString(bindingName)) {
            BindingSpecification binding = bindings.get(bindingName);
            if (binding == null && definitions != null)
                binding = definitions.getCommonBindings().get(bindingName);
            if (binding == null) {
                if (bindingName.startsWith("!"))
                    exv.setNoBindingAllowed(true);
                else
                    throw new Exception("Binding name " + bindingName + " could not be resolved in local spreadsheet");
            }
            exv.setBinding(binding);
            if (binding != null && !binding.getUseContexts().contains(name))
                binding.getUseContexts().add(name);
        }
        // exv.setBinding();
        exv.setMaxLength(sheet.getColumn(row, "Max Length"));
        exv.setExample(processValue(sheet, row, "Example", sheet.getColumn(row, "Example"), exv));
    }
}

Example 50 with Sheet

use of org.hl7.fhir.utilities.xls.XLSXmlParser.Sheet in project kindling by HL7.

the class SourceParser method loadPrimitives.

private void loadPrimitives() throws Exception {
    XLSXmlParser xls = new XLSXmlParser(new CSFileInputStream(dtDir + "primitives.xml"), "primitives");
    new XLSXmlNormaliser(dtDir + "primitives.xml", exceptionIfExcelNotNormalised).go();
    Sheet sheet = xls.getSheets().get("Imports");
    for (int row = 0; row < sheet.rows.size(); row++) {
        processImport(sheet, row);
    }
    sheet = xls.getSheets().get("Patterns");
    for (int row = 0; row < sheet.rows.size(); row++) {
        processStringPattern(sheet, row);
    }
}