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

Example 11 with TypeDefn

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

the class JsonGenerator method generateElement.

private void generateElement(ElementDefn root, ElementDefn e, Set<String> required, JsonObject props, boolean relative) throws Exception {
    if (e.getTypes().size() > 1 || (e.getTypes().size() == 1 && e.getTypes().get(0).isWildcardType())) {
        if (!e.getName().contains("[x]"))
            throw new Exception("Element " + e.getName() + " in " + root.getName() + " has multiple types as a choice doesn't have a [x] in the element name");
        if (e.getTypes().size() == 1)
            generateAny(root, e, e.getName().replace("[x]", ""), props, relative);
        else {
            for (TypeRef t : e.getTypes()) {
                JsonObject property = new JsonObject();
                JsonObject property_ = null;
                TypeDefn td = null;
                if (definitions.getConstraints().containsKey(t.getName()))
                    td = definitions.getElementDefn(definitions.getConstraints().get(t.getName()).getBaseType());
                else if (definitions.hasElementDefn(t.getName()))
                    td = definitions.getElementDefn(t.getName());
                String en = e.getName().replace("[x]", "");
                props.add(en + upFirst(td == null ? t.getName() : td.getName()), property);
                property.addProperty("description", e.getDefinition());
                String tref = null;
                String type = null;
                String pattern = null;
                if (definitions.getPrimitives().containsKey(t.getName())) {
                    DefinedCode def = definitions.getPrimitives().get(t.getName());
                    type = def.getJsonType();
                    pattern = def.getRegex();
                    if (!Utilities.noString(pattern))
                        property.addProperty("pattern", "^" + pattern + "$");
                    property.addProperty("type", type);
                    property_ = new JsonObject();
                    props.add("_" + en + upFirst(t.getName()), property_);
                    property_.addProperty("description", "Extensions for " + en + upFirst(t.getName()));
                    tref = (relative ? "#" : "Element.schema.json#") + "/definitions/Element";
                    property_.addProperty("$ref", tref);
                } else {
                    String tn = encodeType(e, t, true);
                    tref = (relative ? "#" : tn.replace(".", "_") + ".schema.json#") + "/definitions/" + tn.replace(".", "_");
                    property.addProperty("$ref", tref);
                }
            }
        }
    } else {
        JsonObject property = new JsonObject();
        JsonObject property_ = null;
        props.add(e.getName(), property);
        property.addProperty("description", e.getDefinition());
        String tref = null;
        String type = null;
        String pattern = null;
        if (e.usesCompositeType()) /* && types.containsKey(root.getElementByName(e.typeCode().substring(1)))*/
        {
            ElementDefn ref = root.getElementByName(definitions, e.typeCode().substring(1), true, false, null);
            String rtn = types.get(ref);
            if (rtn == null)
                throw new Exception("logic error in schema generator (null composite reference in " + types.toString() + ")");
            if (rtn == "Type")
                rtn = "Element";
            type = rtn;
            tref = "#/definitions/" + rtn.replace(".", "_");
        } else if (e.getTypes().size() == 0 && e.getElements().size() > 0) {
            tref = "#/definitions/" + types.get(e).replace(".", "_");
            type = types.get(e).replace(".", "_");
        } else if (e.getTypes().size() == 1) {
            String tn = encodeType(e, e.getTypes().get(0), true);
            tref = "#/definitions/" + tn;
            if (definitions.getPrimitives().containsKey(e.typeCode())) {
                DefinedCode def = definitions.getPrimitives().get(e.typeCode());
                if (e.getName().equals("id")) {
                    tref = (relative ? "#" : tn.replace(".", "_") + ".schema.json#") + "/definitions/" + tn.replace(".", "_");
                    property.addProperty("$ref", tref);
                } else {
                    property_ = new JsonObject();
                    props.add("_" + e.getName(), property_);
                    property_.addProperty("description", "Extensions for " + e.getName());
                    BindingSpecification cd = e.getBinding();
                    if (cd != null && (cd.getBinding() == BindingSpecification.BindingMethod.CodeList)) {
                        ValueSet vs = cd.getValueSet();
                        if (vs != null) {
                            ValueSet ex = workerContext.expandVS(vs, true, false).getValueset();
                            JsonArray enums = new JsonArray();
                            for (ValueSetExpansionContainsComponent cc : ex.getExpansion().getContains()) {
                                enums.add(new JsonPrimitive(cc.getCode()));
                            }
                            property.add("enum", enums);
                            pattern = null;
                        }
                    } else {
                        property.addProperty("$ref", tref);
                    }
                    tref = (relative ? "#" : "Element.schema.json#") + "/definitions/Element";
                }
            } else {
                tref = (relative ? "#" : tn.replace(".", "_") + ".schema.json#") + "/definitions/" + tn.replace(".", "_");
            }
        } else
            throw new Exception("how do we get here? " + e.getName() + " in " + root.getName() + " " + Integer.toString(e.getTypes().size()));
        if (property_ != null) {
            if (!Utilities.noString(type))
                property.addProperty("type", type);
            if (!Utilities.noString(pattern))
                property.addProperty("pattern", "^" + pattern + "$");
            if (!Utilities.noString(tref))
                property_.addProperty("$ref", tref);
        } else if ("div".equals(e.getName()) && "xhtml".equals(type)) {
            // Is there a better type, or ref for html?
            property.addProperty("type", "string");
        } else {
            property.addProperty("$ref", tref);
        }
        if (e.unbounded()) {
            makeArray(property);
            if (property_ != null)
                makeArray(property_);
        }
        if (e.getMinCardinality() > 0 && property_ == null)
            required.add(e.getName());
    }
}

Example 12 with TypeDefn

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

the class FhirTurtleGenerator method genElementDefn.

/**
 * TypeDefinition generator (e.g. code, id, markdown, uuid)
 *
 * @param td definition to generate
 * @throws Exception
 */
private void genElementDefn(TypeDefn td) throws Exception {
    String typeName = td.getName();
    StructureDefinition typeSd = td.getProfile();
    String parentURL = typeSd.getBaseDefinitionElement().getValue();
    String parentName = null;
    // TODO: Figure out how to do this properly
    if (parentURL != null)
        parentName = parentURL.substring(parentURL.lastIndexOf("/") + 1);
    FHIRResource typeRes = (td.getTypes().isEmpty() ? fact.fhir_class(typeName) : fact.fhir_class(typeName, parentName)).addTitle(td.getShortDefn()).addDefinition(td.getDefinition());
    processTypes(typeName, typeRes, td, typeName, false);
}

Example 13 with TypeDefn

use of org.hl7.fhir.definitions.model.TypeDefn 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 14 with TypeDefn

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

the class SourceParser method convertToExpression.

private String convertToExpression(ResourceDefn rd, List<String> pn, Set<String> targets, SearchParameterDefn sp) throws Exception {
    StringBuilder b = new StringBuilder();
    boolean first = true;
    for (String p : pn) {
        StringBuilder bp = new StringBuilder();
        ElementDefn ed;
        List<ElementDefn> trace = new ArrayList<ElementDefn>();
        if (p.startsWith(rd.getName() + ".")) {
            ed = rd.getRoot().getElementByName(p, true, definitions, "search parameter generation", true, trace);
        } else if (p.startsWith("{{name}}.")) {
            ed = rd.getRoot().getElementByName(p.replace("{{name}}", rd.getName()), true, definitions, "search parameter generation", true, trace);
        } else
            throw new Exception("huh?");
        if (ed == null)
            throw new Exception("not found: " + p);
        for (ElementDefn t : trace) {
            if (t.getStandardsStatus() != null && t.getStandardsStatus().isLowerThan(sp.getStandardsStatus()))
                sp.setStandardsStatus(t.getStandardsStatus(), t.getNormativeVersion(rd));
            try {
                if (definitions.hasPrimitiveType(t.typeCodeNoParams())) {
                    sp.setStandardsStatus(StandardsStatus.NORMATIVE, t.getNormativeVersion(rd));
                } else if (Utilities.noString(t.typeCode())) {
                // nothing, this is part of the resource.
                } else if (t.getTypes().size() == 1 && !t.getTypes().get(0).getName().startsWith("@")) {
                    TypeDefn tt = definitions.getElementDefn(t.typeCodeNoParams());
                    if (tt.getStandardsStatus() != null && tt.getStandardsStatus().isLowerThan(sp.getStandardsStatus())) {
                        sp.setStandardsStatus(tt.getStandardsStatus(), t.getNormativeVersion(rd));
                    }
                }
            } catch (Exception e) {
            // nothing
            }
        }
        if (ed.getName().endsWith("[x]"))
            if (p.endsWith("[x]"))
                bp.append(p.substring(0, p.length() - 3));
            else {
                int lp = p.lastIndexOf(".") + ed.getName().length() - 2;
                String tn = p.substring(lp);
                if (definitions.hasPrimitiveType(Utilities.uncapitalize(tn)))
                    bp.append("(" + p.substring(0, lp) + " as " + Utilities.uncapitalize(tn) + ")");
                else
                    bp.append("(" + p.substring(0, lp) + " as " + tn + ")");
            }
        else
            bp.append(p);
        if (!targets.isEmpty() && !matchesElementDefinition(targets, ed.getTypes())) {
            bp.append(".where(");
            boolean innerFirst = true;
            for (String t : targets) {
                if (innerFirst)
                    innerFirst = false;
                else
                    bp.append(" or ");
                bp.append("resolve() is " + t);
            }
            bp.append(")");
        }
        if (first)
            first = false;
        else
            b.append(" | ");
        b.append(bp.toString());
    }
    return b.toString();
}

Example 15 with TypeDefn

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

the class Publisher method getSnapShotForProfile.

public StructureDefinition getSnapShotForProfile(String base) throws Exception {
    String[] parts = base.split("#");
    if (parts[0].startsWith("http://hl7.org/fhir/StructureDefinition/") && parts.length == 1) {
        String name = base.substring(40);
        if (page.getDefinitions().hasResource(name))
            return page.getDefinitions().getSnapShotForType(name);
        else if (page.getDefinitions().hasType(name)) {
            TypeDefn t = page.getDefinitions().getElementDefn(name);
            if (t.getProfile().hasSnapshot())
                return t.getProfile();
            throw new Exception("unable to find snapshot for " + name);
        }
    // else
    // throw new Exception("unable to find base definition for "+name);
    }
    StructureDefinition p = new ProfileUtilities(page.getWorkerContext(), page.getValidationErrors(), page).getProfile(null, parts[0]);
    if (p == null)
        throw new Exception("unable to find base definition for " + base);
    if (parts.length == 1) {
        if (p.getSnapshot() == null)
            // or else we could fill it in?
            throw new Exception("StructureDefinition " + base + " has no snapshot");
        return p;
    }
    for (Resource r : p.getContained()) {
        if (r instanceof StructureDefinition && r.getId().equals(parts[1])) {
            StructureDefinition pc = (StructureDefinition) r;
            if (pc.getSnapshot() == null) {
                StructureDefinition ps = getSnapShotForProfile(pc.getBaseDefinition());
                processProfile(pc);
            }
            return pc;
        }
    }
    throw new Exception("Unable to find snapshot for " + base);
}