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

Example 41 with Sheet

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

the class ReviewSpreadsheetGenerator method generateReviewSheet.

private void generateReviewSheet(HSSFWorkbook workbook, StructureDefinition profile) throws FHIRException {
    HSSFSheet sheet = workbook.createSheet(sanitize(profile.getName()));
    sheet.setColumnWidth(0, 8000);
    sheet.setColumnWidth(3, 100);
    HSSFFont font = workbook.createFont();
    font.setBold(true);
    font.setFontName("Calibri");
    HSSFCellStyle style = workbook.createCellStyle();
    style.setFont(font);
    style.setBorderBottom(BorderStyle.THIN);
    style.setFillBackgroundColor(IndexedColors.LAVENDER.getIndex());
    style.setFillForegroundColor(IndexedColors.LAVENDER.getIndex());
    style.setFillPattern(FillPatternType.SOLID_FOREGROUND);
    addRow(sheet, style, "Path", "StructureDefinition", "Value Set", "Definition", "Your Comments").setRowStyle(style);
    font = workbook.createFont();
    font.setFontName("Calibri");
    style = workbook.createCellStyle();
    ElementDefinition ed = profile.getSnapshot().getElement().get(0);
    String path = ed.getPath();
    addRow(sheet, style, path + " : " + profile.getType(), profile.getName(), "", ed.getDefinition(), "");
    processRows(workbook, path, profile, profile.getSnapshot().getElement(), 1, sheet, "  ");
}

Example 42 with Sheet

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

the class OldSpreadsheetParser method readPackages.

private void readPackages(ResourceDefn defn, Sheet sheet) throws Exception {
    if (sheet != null) {
        for (int row = 0; row < sheet.rows.size(); row++) {
            String name = sheet.getColumn(row, "Name");
            if (name != null && !name.equals("") && !name.startsWith("!")) {
                Profile pack = new Profile(sheet.getColumn(row, "IG Name"));
                if (Utilities.noString(pack.getCategory()))
                    throw new Exception("Missing IG Name at " + getLocation(row));
                if (!definitions.getIgs().containsKey(pack.getCategory()))
                    throw new Exception("IG Name '" + pack.getCategory() + "' is not registered in [igs] in fhir.ini at " + getLocation(row));
                ImplementationGuideDefn ig = definitions.getIgs().get(pack.getCategory());
                if (!Utilities.noString(ig.getSource()))
                    throw new Exception("Implementation Guides that have their own structured definition cannot be registered directly in a source spreadsheet (" + name + ")");
                pack.setTitle(name);
                // todo-profile
                pack.setSource(checkFile(sheet, row, "Source", false, sheet.getColumn(row, "Filename")));
                String type = sheet.getColumn(row, "Type");
                if ("bundle".equalsIgnoreCase(type))
                    pack.setSourceType(ConformancePackageSourceType.Bundle);
                else if ("spreadsheet".equalsIgnoreCase(type))
                    pack.setSourceType(ConformancePackageSourceType.Spreadsheet);
                else if ("structuredefinition".equalsIgnoreCase(type))
                    pack.setSourceType(ConformancePackageSourceType.StructureDefinition);
                else
                    throw new Exception("Unknown source type: " + type + " at " + getLocation(row));
                // todo-profile
                String example = checkFile(sheet, row, "Example", true, null);
                if (example != null)
                    pack.getExamples().add(new Example(example, Utilities.fileTitle(example), "General Example for " + pack.getSource(), new File(example), true, ExampleType.XmlFile, isAbstract));
                defn.getConformancePackages().add(pack);
            }
        }
    }
}

Example 43 with Sheet

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

the class OldSpreadsheetParser method processLine.

private ElementDefn processLine(ResourceDefn root, Sheet sheet, int row, Map<String, Invariant> invariants, boolean profile, Profile pack, boolean firstTime) throws Exception {
    ElementDefn e;
    String path = sheet.getColumn(row, "Element");
    if (path.startsWith("!"))
        return null;
    if (Utilities.noString(path))
        throw new Exception("Error reading definitions - no path found @ " + getLocation(row));
    if (path.contains("#"))
        throw new Exception("Old path style @ " + getLocation(row));
    String profileName = isProfile ? sheet.getColumn(row, "Profile Name") : "";
    String discriminator = isProfile ? sheet.getColumn(row, "Discriminator") : "";
    boolean isRoot = !path.contains(".");
    if (isRoot) {
        if (root.getRoot() != null)
            throw new Exception("Definitions in " + getLocation(row) + " contain two roots: " + path + " in " + root.getName());
        root.setName(path);
        e = new TypeDefn();
        e.setName(path);
        root.setRoot((TypeDefn) e);
        if (template != null)
            e.copyFrom(template.getRoot(), root.getName(), templateTitle);
    } else {
        e = makeFromPath(root.getRoot(), path, row, profileName, true);
        if (template != null) {
            ElementDefn ted = getTemplateDefinition(path);
            if (ted != null) {
                e.copyFrom(ted, root.getName(), templateTitle);
            }
        }
    }
    e.setStandardsStatus(StandardsStatus.fromCode(sheet.getColumn(row, "Standards-Status")));
    e.setNormativeVersion(sheet.getColumn(row, "Normative-Version"));
    if (e.getName().startsWith("@")) {
        e.setName(e.getName().substring(1));
        e.setXmlAttribute(true);
    }
    String c = sheet.getColumn(row, "Card.");
    if (c == null || c.equals("") || c.startsWith("!")) {
        if (!isRoot && !profile && (template == null))
            throw new Exception("Missing cardinality at " + getLocation(row) + " on " + path);
        if (isRoot && (template == null)) {
            e.setMinCardinality(0);
            e.setMaxCardinality(Integer.MAX_VALUE);
        }
    } else {
        String[] card = c.split("\\.\\.");
        if (card.length != 2 || !Utilities.isInteger(card[0]) || (!"*".equals(card[1]) && !Utilities.isInteger(card[1])))
            throw new Exception("Unable to parse Cardinality '" + c + "' " + c + " in " + getLocation(row) + " on " + path);
        e.setMinCardinality(Integer.parseInt(card[0]));
        e.setMaxCardinality("*".equals(card[1]) ? Integer.MAX_VALUE : Integer.parseInt(card[1]));
    }
    if (profileName.startsWith("#"))
        throw new Exception("blah: " + profileName);
    e.setProfileName(profileName);
    e.setSliceDescription(isProfile ? sheet.getColumn(row, "Slice Description") : "");
    for (String d : discriminator.split("\\,")) if (!Utilities.noString(d))
        e.getDiscriminator().add(d);
    doAliases(sheet, row, e);
    if (sheet.hasColumn(row, "Must Understand"))
        throw new Exception("Column 'Must Understand' has been renamed to 'Is Modifier'");
    if (sheet.hasColumn(row, "Is Modifier")) {
        e.setIsModifier(parseBoolean(sheet.getColumn(row, "Is Modifier"), row, null));
        String reason = sheet.getColumn(row, "Modifier Reason");
        if (Utilities.noString(reason) && e.getName().toLowerCase().contains("status") && sheet.getColumn(row, "Short Name").contains("error"))
            reason = "This element is labelled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid";
        if (Utilities.noString(reason) && e.getName().equals("active"))
            reason = "This element is labelled as a modifier because it is a status element that can indicate that a record should not be treated as valid";
        if (Utilities.noString(reason)) {
            System.out.println("Missing IsModifierReason on " + path);
            reason = "Not known why this is labelled a modifier";
        }
        e.setModifierReason(reason);
    }
    if (isProfile) {
        // later, this will get hooked in from the underlying definitions, but we need to know this now to validate the extension modifier matching
        if (e.getName().equals("modifierExtension"))
            e.setIsModifier(true);
        e.setMustSupport(parseBoolean(sheet.getColumn(row, "Must Support"), row, null));
    }
    if (sheet.hasColumn(row, "Summary"))
        e.setSummaryItem(parseBoolean(sheet.getColumn(row, "Summary"), row, null));
    e.setRegex(sheet.getColumn(row, "Regex"));
    String uml = sheet.getColumn(row, "UML");
    if (uml != null) {
        if (uml.contains(";")) {
            String[] parts = uml.split("\\;");
            e.setSvgLeft(Integer.parseInt(parts[0]));
            e.setSvgTop(Integer.parseInt(parts[1]));
            if (parts.length > 2)
                e.setSvgWidth(Integer.parseInt(parts[2]));
            e.setUmlDir("");
        } else if (uml.startsWith("break:")) {
            e.setUmlBreak(true);
            e.setUmlDir(uml.substring(6));
        } else {
            e.setUmlDir(uml);
        }
    }
    String s = sheet.getColumn(row, "Condition");
    if (s != null && !s.equals(""))
        throw new Exception("Found Condition in spreadsheet " + getLocation(row));
    s = sheet.getColumn(row, "Inv.");
    if (s != null && !s.equals("")) {
        for (String sn : s.split(",")) {
            if (!sn.startsWith("!")) {
                Invariant inv = invariants.get(sn);
                if (inv == null)
                    throw new Exception("unable to find Invariant '" + sn + "' " + getLocation(row));
                e.getStatedInvariants().add(inv);
            }
        }
    }
    TypeParser tp = new TypeParser(version.toCode());
    e.getTypes().addAll(tp.parse(sheet.getColumn(row, "Type"), isProfile, profileExtensionBase, context, !path.contains("."), this.name));
    if (isRoot && e.getTypes().size() == 1 && definitions != null) {
        String t = e.getTypes().get(0).getName();
        if (definitions.getResourceTemplates().containsKey(t)) {
            // we've got a template in play.
            template = definitions.getResourceTemplates().get(t);
            templateTitle = Utilities.unCamelCase(e.getName());
            e.getTypes().get(0).setName(template.getRoot().getTypes().get(0).getName());
        } else if (definitions.getBaseResources().containsKey(t) && definitions.getBaseResources().get(t).isInterface()) {
            // we've got a template in play.
            template = definitions.getBaseResources().get(t);
            templateTitle = Utilities.unCamelCase(e.getName());
        }
    }
    if (isProfile && ((path.endsWith(".extension") || path.endsWith(".modifierExtension")) && (e.getTypes().size() == 1) && e.getTypes().get(0).hasProfile()) && Utilities.noString(profileName))
        throw new Exception("need to have a profile name if a profiled extension is referenced for " + e.getTypes().get(0).getProfile());
    if (sheet.hasColumn(row, "Concept Domain"))
        throw new Exception("Column 'Concept Domain' has been retired in " + path);
    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("!"))
                e.setNoBindingAllowed(true);
            else
                throw new Exception("Binding name " + bindingName + " could not be resolved in local spreadsheet");
        }
        e.setBinding(binding);
        if (binding != null && !binding.getUseContexts().contains(name))
            binding.getUseContexts().add(name);
    } else if (e.getBinding() != null) {
        if (!e.getBinding().getUseContexts().contains(name))
            e.getBinding().getUseContexts().add(name);
    }
    if (!Utilities.noString(sheet.getColumn(row, "Short Label")))
        throw new Exception("Short Label is no longer used");
    if (// todo: make this a warning when a fair chunk of the spreadsheets have been converted
    sheet.hasColumn(row, "Short Name"))
        if (sheet.getColumn(row, "Short Name").startsWith("&"))
            e.setShortDefn(e.getShortDefn() + sheet.getColumn(row, "Short Name").substring(1));
        else
            e.setShortDefn(sheet.getColumn(row, "Short Name"));
    if (!isProfile && e.getShortDefn() == null)
        throw new Exception("A short definition is required for " + e.getName() + " at " + getLocation(row));
    if (sheet.hasColumn(row, "Definition"))
        if (sheet.getColumn(row, "Definition").startsWith("&"))
            e.setDefinition(Utilities.appendPeriod(e.getDefinition() + processDefinition(sheet.getColumn(row, "Definition")).substring(1)));
        else
            e.setDefinition(Utilities.appendPeriod(processDefinition(sheet.getColumn(row, "Definition"))));
    if (isRoot) {
        root.setDefinition(e.getDefinition());
    }
    if (isProfile || isLogicalModel)
        e.setMaxLength(sheet.getColumn(row, "Max Length"));
    if (sheet.hasColumn(row, "Requirements"))
        if (sheet.getColumn(row, "Requirements").startsWith("&"))
            e.setRequirements(Utilities.appendPeriod(e.getRequirements() + sheet.getColumn(row, "Requirements").substring(1)));
        else
            e.setRequirements(Utilities.appendPeriod(sheet.getColumn(row, "Requirements")));
    if (sheet.hasColumn(row, "Comments"))
        if (sheet.getColumn(row, "Comments").startsWith("&"))
            e.setComments(Utilities.appendPeriod(e.getComments() + Utilities.appendPeriod(sheet.getColumn(row, "Comments").substring(1))));
        else
            e.setComments(Utilities.appendPeriod(Utilities.appendPeriod(sheet.getColumn(row, "Comments"))));
    for (String n : mappings.keySet()) {
        String ms = sheet.getColumn(row, mappings.get(n).getColumnName());
        if (mappings.get(n).getColumnName().equals("Snomed Code") && !Utilities.noString(ms))
            System.out.println("!!");
        e.addMapping(n, ms.trim());
    }
    if (pack != null) {
        for (String n : pack.getMappingSpaces().keySet()) {
            e.addMapping(n, sheet.getColumn(row, pack.getMappingSpaces().get(n).getColumnName()).trim());
        }
    }
    if (sheet.hasColumn("Hierarchy"))
        e.setHierarchy(parseBoolean(sheet.getColumn(row, "Hierarchy"), row, null));
    if (sheet.hasColumn(row, "To Do"))
        e.setTodo(Utilities.appendPeriod(sheet.getColumn(row, "To Do")));
    if (sheet.hasColumn(row, "Example"))
        e.setExample(processValue(sheet, row, "Example", sheet.getColumn(row, "Example"), e));
    processOtherExamples(e, sheet, row);
    if (sheet.hasColumn(row, "Committee Notes"))
        e.setCommitteeNotes(Utilities.appendPeriod(sheet.getColumn(row, "Committee Notes")));
    if (sheet.hasColumn(row, "Display Hint"))
        e.setDisplayHint(sheet.getColumn(row, "Display Hint"));
    if (isProfile) {
        e.setFixed(processValue(sheet, row, "Value", sheet.getColumn(row, "Value"), e));
        e.setPattern(processValue(sheet, row, "Pattern", sheet.getColumn(row, "Pattern"), e));
    } else {
        if (sheet.hasColumn(row, "Default Value"))
            errors.add(path + ": Default value '" + sheet.getColumn(row, "Default Value") + "' found @ " + getLocation(row));
        if (sheet.hasColumn(row, "Missing Meaning"))
            e.setMeaningWhenMissing(sheet.getColumn(row, "Missing Meaning"));
    }
    if (sheet.hasColumn(row, "w5"))
        e.setW5(checkW5(sheet.getColumn(row, "w5"), path));
    if (sheet.hasColumn(row, "Translatable"))
        e.setTranslatable(parseBoolean(sheet.getColumn(row, "Translatable"), row, false));
    if (sheet.hasColumn(row, "Order Meaning"))
        e.setOrderMeaning(sheet.getColumn(row, "Order Meaning"));
    return e;
}

Example 44 with Sheet

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

the class OldSpreadsheetParser method processValue.

private DataType processValue(Sheet sheet, int row, String column, String source, ElementDefn e) throws Exception {
    if (Utilities.noString(source))
        return null;
    if (e.getTypes().size() != 1)
        throw new Exception("Unable to process " + column + " unless a single type is specified (types = " + e.typeCode() + ") " + getLocation(row) + ", column = " + column);
    String type = e.typeCode();
    if (definitions != null) {
        if (definitions.getConstraints().containsKey(type))
            type = definitions.getConstraints().get(type).getBaseType();
    } else {
        StructureDefinition sd = context.fetchTypeDefinition(type);
        if (// not loaded yet?
        sd != null)
            type = sd.getType();
        if (type.equals("SimpleQuantity"))
            type = "Quantity";
    }
    if (source.startsWith("{")) {
        JsonParser json = new JsonParser();
        return json.parseType(source, type);
    } else if (source.startsWith("<")) {
        XmlParser xml = new XmlParser();
        return xml.parseType(source, type);
    } else {
        if (source.startsWith("\"") && source.endsWith("\""))
            source = source.substring(1, source.length() - 1);
        if (type.equals("string"))
            return new StringType(source);
        if (type.equals("boolean"))
            return new BooleanType(Boolean.valueOf(source));
        if (type.equals("integer"))
            return new IntegerType(Integer.valueOf(source));
        if (type.equals("integer64"))
            return new Integer64Type(Long.valueOf(source));
        if (type.equals("unsignedInt"))
            return new UnsignedIntType(Integer.valueOf(source));
        if (type.equals("positiveInt"))
            return new PositiveIntType(Integer.valueOf(source));
        if (type.equals("decimal"))
            return new DecimalType(new BigDecimal(source));
        if (type.equals("base64Binary"))
            return new Base64BinaryType(Base64.decode(source.toCharArray()));
        if (type.equals("instant"))
            return new InstantType(source);
        if (type.equals("uri"))
            return new UriType(source);
        if (type.equals("url"))
            return new UrlType(source);
        if (type.equals("canonical"))
            return new CanonicalType(source);
        if (type.equals("date"))
            return new DateType(source);
        if (type.equals("dateTime"))
            return new DateTimeType(source);
        if (type.equals("time"))
            return new TimeType(source);
        if (type.equals("code"))
            return new CodeType(source);
        if (type.equals("oid"))
            return new OidType(source);
        if (type.equals("uuid"))
            return new UuidType(source);
        if (type.equals("id"))
            return new IdType(source);
        if (type.startsWith("Reference(")) {
            Reference r = new Reference();
            r.setReference(source);
            return r;
        }
        if (type.equals("Period")) {
            if (source.contains("->")) {
                String[] parts = source.split("\\-\\>");
                Period p = new Period();
                p.setStartElement(new DateTimeType(parts[0].trim()));
                if (parts.length > 1)
                    p.setEndElement(new DateTimeType(parts[1].trim()));
                return p;
            } else
                throw new Exception("format not understood parsing " + source + " into a period");
        }
        if (type.equals("CodeableConcept")) {
            CodeableConcept cc = new CodeableConcept();
            if (source.contains(":")) {
                String[] parts = source.split("\\:");
                String system = "";
                if (parts[0].equalsIgnoreCase("SCT"))
                    system = "http://snomed.info/sct";
                else if (parts[0].equalsIgnoreCase("LOINC"))
                    system = "http://loinc.org";
                else if (parts[0].equalsIgnoreCase("AMTv2"))
                    system = "http://nehta.gov.au/amtv2";
                else
                    system = "http://hl7.org/fhir/" + parts[0];
                String code = parts[1];
                String display = parts.length > 2 ? parts[2] : null;
                cc.addCoding().setSystem(system).setCode(code).setDisplay(display);
            } else
                throw new Exception("format not understood parsing " + source + " into a codeable concept");
            return cc;
        }
        if (type.equals("Identifier")) {
            Identifier id = new Identifier();
            id.setSystem("urn:ietf:rfc:3986");
            id.setValue(source);
            return id;
        }
        if (type.equals("Quantity")) {
            int s = 0;
            if (source.startsWith("<=") || source.startsWith("=>"))
                s = 2;
            else if (source.startsWith("<") || source.startsWith(">"))
                s = 1;
            int i = s;
            while (i < source.length() && Character.isDigit(source.charAt(i))) i++;
            Quantity q = new Quantity();
            if (s > 0)
                q.setComparator(QuantityComparator.fromCode(source.substring(0, s)));
            if (i > s)
                q.setValue(new BigDecimal(source.substring(s, i)));
            if (i < source.length())
                q.setUnit(source.substring(i).trim());
            return q;
        }
        throw new Exception("Unable to process primitive value '" + source + "' provided for " + column + " - unhandled type " + type + " @ " + getLocation(row));
    }
}

Example 45 with Sheet

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

the class OldSpreadsheetParser method parseLogicalModel.

public LogicalModel parseLogicalModel() throws Exception {
    ResourceDefn resource = new ResourceDefn();
    isLogicalModel = true;
    Sheet sheet = loadSheet("Bindings");
    if (sheet != null)
        readBindings(sheet);
    sheet = loadSheet("Invariants");
    Map<String, Invariant> invariants = null;
    if (sheet != null)
        invariants = readInvariants(sheet, title, "Invariants");
    sheet = loadSheet("Data Elements");
    if (sheet == null)
        throw new Exception("No Sheet found for Data Elements");
    for (int row = 0; row < sheet.rows.size(); row++) {
        processLine(resource, sheet, row, invariants, false, null, row == 0);
    }
    parseMetadata(resource);
    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");
                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)");
            }
        }
    }
    // EK: Future types. But those won't get there.
    if (bindings != null)
        resource.getRoot().getNestedBindings().putAll(bindings);
    scanNestedTypes(resource, resource.getRoot(), resource.getName());
    resolveElementReferences(resource, resource.getRoot());
    LogicalModel lm = new LogicalModel();
    lm.setResource(resource);
    lm.setWg(definitions.getWorkgroups().get("fhir"));
    return lm;
}