Examples with ValueSet org.hl7.fhir.r4.model.ValueSet used on opensource projects

Example 41 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project kindling by HL7.

the class XSDGenerator method generateEnum.

private void generateEnum(String en) throws IOException {
    if (allenums.contains(en))
        return;
    allenums.add(en);
    write("  <xs:simpleType name=\"" + en + "-list\">\r\n");
    write("    <xs:restriction base=\"code-primitive\">\r\n");
    ValueSet vs = enums.get(en);
    vs.setUserData(ToolResourceUtilities.NAME_VS_USE_MARKER, true);
    ValueSet ex = workerContext.expandVS(vs, true, false).getValueset();
    for (ValueSetExpansionContainsComponent cc : ex.getExpansion().getContains()) {
        genIncludedCode(cc);
    }
    write("    </xs:restriction>\r\n");
    write("  </xs:simpleType>\r\n");
    write("  <xs:complexType name=\"" + en + "\">\r\n");
    write("    <xs:annotation>\r\n");
    write("      <xs:documentation xml:lang=\"en\">" + Utilities.escapeXml(enumDefs.get(en)) + "</xs:documentation>\r\n");
    write("      <xs:documentation xml:lang=\"en\">If the element is present, it must have either a @value, an @id, or extensions</xs:documentation>\r\n");
    write("    </xs:annotation>\r\n");
    write("    <xs:complexContent>\r\n");
    write("      <xs:extension base=\"Element\">\r\n");
    write("        <xs:attribute name=\"value\" type=\"" + en + "-list\" use=\"optional\"/>\r\n");
    write("      </xs:extension>\r\n");
    write("    </xs:complexContent>\r\n");
    write("  </xs:complexType>\r\n");
}

Example 42 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project kindling by HL7.

the class JsonSpecGenerator method generateCoreElem.

@SuppressWarnings("rawtypes")
private void generateCoreElem(List<ElementDefinition> elements, ElementDefinition elem, int indent, String pathName, boolean asValue, TypeRefComponent type, boolean last, boolean complex) throws Exception {
    if (elem.getPath().endsWith(".id"))
        return;
    if (!complex && elem.getPath().endsWith(".extension"))
        return;
    if (elem.getMax().equals("0"))
        return;
    String indentS = "";
    for (int i = 0; i < indent; i++) {
        indentS += "  ";
    }
    write(indentS);
    List<ElementDefinition> children = getChildren(elements, elem);
    String name = tail(elem.getPath());
    String en = asValue ? "value[x]" : name;
    String tc = type.getWorkingCode();
    if (en.contains("[x]"))
        en = en.replace("[x]", upFirst(tc));
    boolean unbounded = elem.hasMax() && elem.getMax().equals("*");
    // 1. name
    write("\"<a href=\"" + (defPage + "#" + pathName + "." + en) + "\" title=\"" + Utilities.escapeXml(getEnhancedDefinition(elem)) + "\" class=\"dict\"><span style=\"text-decoration: underline\">" + en + "</span></a>\" : ");
    // 2. value
    boolean delayedCloseArray = false;
    if (unbounded)
        write("[");
    if (type == null) {
        // inline definition
        assert (children.size() > 0);
        write("{");
        delayedCloseArray = true;
    } else if (definitions.getPrimitives().containsKey(tc)) {
        if (!(tc.equals("integer") || tc.equals("boolean") || tc.equals("decimal")))
            write("\"");
        if (elem.hasFixed())
            write(Utilities.escapeJson(((PrimitiveType) elem.getFixed()).asStringValue()));
        else
            write("&lt;<span style=\"color: darkgreen\"><a href=\"" + prefix + (dtRoot + definitions.getSrcFile(tc) + ".html#" + tc) + "\">" + tc + "</a></span>&gt;");
        if (!(tc.equals("integer") || tc.equals("boolean") || tc.equals("decimal")))
            write("\"");
    } else {
        write("{ ");
        write("<span style=\"color: darkgreen\"><a href=\"" + prefix + (dtRoot + definitions.getSrcFile(tc) + ".html#" + tc) + "\">" + tc + "</a></span>");
        if (type.hasProfile()) {
            if (type.getProfile().get(0).getValue().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
                String t = type.getProfile().get(0).getValue().substring(40);
                if (definitions.hasType(t))
                    write("(<span style=\"color: darkgreen\"><a href=\"" + prefix + (dtRoot + definitions.getSrcFile(t) + ".html#" + t) + "\">" + t + "</a></span>)");
                else if (definitions.hasResource(t))
                    write("(<span style=\"color: darkgreen\"><a href=\"" + prefix + dtRoot + t.toLowerCase() + ".html\">" + t + "</a></span>)");
                else
                    write("(" + t + ")");
            } else
                write("(" + type.getProfile() + ")");
        }
        if (type.hasTargetProfile()) {
            if (type.getTargetProfile().get(0).getValue().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
                String t = type.getTargetProfile().get(0).getValue().substring(40);
                if (definitions.hasType(t))
                    write("(<span style=\"color: darkgreen\"><a href=\"" + prefix + (dtRoot + definitions.getSrcFile(t) + ".html#" + t) + "\">" + t + "</a></span>)");
                else if (definitions.hasResource(t))
                    write("(<span style=\"color: darkgreen\"><a href=\"" + prefix + dtRoot + t.toLowerCase() + ".html\">" + t + "</a></span>)");
                else
                    write("(" + t + ")");
            } else
                write("(" + type.getTargetProfile() + ")");
        }
        write(" }");
    }
    if (!delayedCloseArray) {
        if (unbounded)
            write("]");
        if (!last)
            write(",");
    }
    write(" <span style=\"color: Gray\">//</span>");
    // 3. optionality
    writeCardinality(elem);
    // 4. doco
    if (!elem.hasFixed()) {
        if (elem.hasBinding() && elem.getBinding().hasValueSet()) {
            ValueSet vs = resolveValueSet(elem.getBinding().getValueSet());
            if (vs != null)
                write("<span style=\"color: navy; opacity: 0.8\"><a href=\"" + (Utilities.isAbsoluteUrl(vs.getUserString("path")) ? "" : prefix) + vs.getUserData("path") + "\" style=\"color: navy\">" + Utilities.escapeXml(elem.getShort()) + "</a></span>");
            else
                write("<span style=\"color: navy; opacity: 0.8\"><a href=\"" + elem.getBinding().getValueSet() + ".html\" style=\"color: navy\">" + Utilities.escapeXml(elem.getShort()) + "</a></span>");
        } else
            write("<span style=\"color: navy; opacity: 0.8\">" + Utilities.escapeXml(elem.getShort()) + "</span>");
    }
    write("\r\n");
    if (delayedCloseArray) {
        int c = 0;
        for (ElementDefinition child : children) {
            if (child.getType().size() == 1)
                generateCoreElem(elements, child, indent + 1, pathName + "." + name, false, child.getType().get(0), ++c == children.size(), false);
            else {
                write("<span style=\"color: Gray\">// value[x]: <span style=\"color: navy; opacity: 0.8\">" + Utilities.escapeXml(child.getShort()) + "</span>. One of these " + Integer.toString(child.getType().size()) + ":</span>\r\n");
                for (TypeRefComponent t : child.getType()) generateCoreElem(elements, child, indent + 1, pathName + "." + name, false, t, ++c == children.size(), false);
            }
        }
        write("}]");
        if (!last)
            write(",");
    }
}

Example 43 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project kindling by HL7.

the class ProfileGenerator method convertElements.

public void convertElements(ElementDefn src, StructureDefinition ed, String path) throws Exception {
    ElementDefinition dst = new ElementDefinition();
    if (!ed.hasDifferential())
        ed.setDifferential(new StructureDefinitionDifferentialComponent());
    ed.getDifferential().getElement().add(dst);
    String thisPath = path == null ? "Extension" : path;
    dst.setId(thisPath);
    dst.setPath(thisPath);
    if (!Utilities.noString(src.getProfileName()))
        dst.setSliceName(src.getProfileName());
    dst.setShort(src.getShortDefn());
    dst.setDefinition(preProcessMarkdown(src.getDefinition(), "Element Definition"));
    dst.setComment(preProcessMarkdown(src.getComments(), "Element Comments"));
    if (src.getMaxCardinality() != null) {
        if (src.getMaxCardinality() == Integer.MAX_VALUE)
            dst.setMax("*");
        else
            dst.setMax(src.getMaxCardinality().toString());
    }
    if (src.getMinCardinality() != null)
        dst.setMin(src.getMinCardinality());
    if (src.getFixed() != null)
        dst.setFixed(src.getFixed());
    if (src.hasMustSupport())
        dst.setMustSupport(src.isMustSupport());
    if (src.hasModifier())
        dst.setIsModifier(src.isModifier());
    if (dst.getIsModifier())
        dst.setIsModifierReason(src.getModifierReason());
    if (src.hasSummaryItem() && dst.getPath().contains("."))
        dst.setIsSummaryElement(Factory.newBoolean(src.isSummary()));
    for (Invariant id : src.getStatedInvariants()) dst.addCondition(id.getId());
    // dDst.
    for (TypeRef t : src.getTypes()) {
        if (t.hasParams()) {
            for (String tp : t.getParams()) {
                if (definitions.hasLogicalModel(tp)) {
                    for (String tpn : definitions.getLogicalModel(tp).getImplementations()) {
                        ElementDefinition.TypeRefComponent type = dst.getType(t.getName());
                        String pr = "http://hl7.org/fhir/StructureDefinition/" + tpn;
                        type.addTargetProfile(pr);
                    }
                } else {
                    ElementDefinition.TypeRefComponent type = dst.getType(t.getName());
                    String pr = t.hasProfile() ? t.getProfile() : // this should only happen if t.getParams().size() == 1
                    "http://hl7.org/fhir/StructureDefinition/" + (tp.equals("Any") ? "Resource" : tp);
                    if (type.getWorkingCode().equals("Reference") || type.getWorkingCode().equals("canonical") || type.getWorkingCode().equals("CodeableReference"))
                        type.addTargetProfile(pr);
                    else
                        type.addProfile(pr);
                }
            }
        } else if (t.isWildcardType()) {
            for (String n : TypesUtilities.wildcardTypes(version.toString())) dst.getType(n);
        } else {
            if (definitions != null && definitions.getConstraints().containsKey(t.getName())) {
                ProfiledType ct = definitions.getConstraints().get(t.getName());
                ElementDefinition.TypeRefComponent type = dst.getType(ct.getBaseType());
                type.addProfile("http://hl7.org/fhir/StructureDefinition/" + ct.getName());
            } else if ("Extension.url".equals(path)) {
            // juat don't populate it
            // ElementDefinition.TypeRefComponent tt = dst.addType();
            // tt.setCodeElement(new UriType());
            // tt.getFormatCommentsPre().add("Note: special primitive values do not have an assigned type. e.g. this is compiler magic. XML, JSON and RDF types provided by extension");
            // ToolingExtensions.addStringExtension(tt.getCodeElement(), ToolingExtensions.EXT_JSON_TYPE, "string");
            // ToolingExtensions.addStringExtension(tt.getCodeElement(), ToolingExtensions.EXT_XML_TYPE, "xs:anyURI");
            // ToolingExtensions.addStringExtension(tt.getCodeElement(), ToolingExtensions.EXT_RDF_TYPE, "xs:anyURI");
            } else {
                ElementDefinition.TypeRefComponent type = dst.getType(t.getName());
                if (t.hasProfile())
                    if (type.getWorkingCode().equals("Reference") || type.getWorkingCode().equals("CodeableReference"))
                        type.addTargetProfile(t.getProfile());
                    else
                        type.addProfile(t.getProfile());
            }
        }
    }
    if (definitions != null) {
        // igtodo - catch this
        for (String mu : definitions.getMapTypes().keySet()) {
            if (src.hasMapping(mu)) {
                addMapping(ed, dst, mu, src.getMapping(mu), null);
            }
        }
    }
    for (String in : src.getInvariants().keySet()) {
        ElementDefinitionConstraintComponent con = new ElementDefinitionConstraintComponent();
        Invariant inv = src.getInvariants().get(in);
        con.setKey(inv.getId());
        if (!con.hasKey()) {
            extensionCounter++;
            con.setKey("exd-" + Integer.toString(extensionCounter));
        }
        con.setRequirements(inv.getRequirements());
        if (Utilities.noString(inv.getSeverity()))
            con.setSeverity(ConstraintSeverity.ERROR);
        else
            con.setSeverity(ConstraintSeverity.fromCode(inv.getSeverity()));
        con.setHuman(inv.getEnglish());
        con.setXpath(inv.getXpath());
        if (!"n/a".equals(inv.getExpression()))
            con.setExpression(inv.getExpression());
        dst.getConstraint().add(con);
    }
    if (src.hasBinding())
        dst.setBinding(generateBinding(src.getBinding()));
    if (src.getElements().isEmpty()) {
        if (path == null)
            throw new Exception("?error parsing extension");
    } else {
        ElementDefn url = src.getElements().get(0);
        if (!url.getName().equals("url"))
            throw new Exception("first child of extension should be 'url', not " + url.getName() + " for structure definition " + ed.getUrl());
        convertElements(url, ed, thisPath + ".url");
        // this pair might leave elements out of order, but we're going to sort them later
        if (!hasValue(src)) {
            ElementDefn value = new ElementDefn();
            value.setName("value[x]");
            value.setMinCardinality(0);
            value.setMaxCardinality(0);
            convertElements(value, ed, thisPath + ".value[x]");
        } else {
            ElementDefn ext = new ElementDefn();
            // can't have an extension if you have a value
            ext.setName("extension");
            ext.setMaxCardinality(0);
            convertElements(ext, ed, thisPath + ".extension");
        }
        if (src.getElements().size() == 2 && src.getElements().get(0).getName().equals("url") && src.getElements().get(1).getName().equals("value[x]")) {
            ElementDefn value = src.getElements().get(1);
            value.setMinCardinality(1);
            convertElements(value, ed, thisPath + ".value[x]");
        } else {
            for (ElementDefn child : src.getElements()) {
                if (child != url) {
                    if (child.getName().startsWith("value") && !child.getName().startsWith("valueSet"))
                        convertElements(child, ed, thisPath + "." + child.getName());
                    else {
                        if (child.getElements().size() == 0 || !child.getElements().get(0).getName().equals("url")) {
                            ElementDefn childUrl = new ElementDefn();
                            childUrl.setName("url");
                            childUrl.setXmlAttribute(true);
                            childUrl.getTypes().add(new TypeRef("uri"));
                            childUrl.setFixed(new UriType(child.getName()));
                            child.getElements().add(0, childUrl);
                        }
                        if (!hasValue(child)) {
                            ElementDefn value = new ElementDefn();
                            value.setName("value[x]");
                            value.setMinCardinality(0);
                            value.setMaxCardinality(0);
                            child.getElements().add(value);
                        }
                        convertElements(child, ed, thisPath + ".extension");
                    }
                }
            }
        }
    }
}

Example 44 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project kindling by HL7.

the class ResourceDependencyGenerator method addBindingToAnalysis.

private void addBindingToAnalysis(HierarchicalTableGenerator gen, Row row, Cell dc, boolean req, StandardsStatus elementStatus, BindingSpecification binding) throws FHIRException {
    String tgtFMM = null;
    StandardsStatus tgtSS = null;
    ValueSet vs = binding.getValueSet();
    if (vs != null) {
        tgtFMM = ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_FMM_LEVEL);
        tgtSS = ToolingExtensions.getStandardsStatus(vs);
    } else if (Utilities.existsInList(binding.getReference(), "http://www.rfc-editor.org/bcp/bcp13.txt")) {
        tgtFMM = "5";
        tgtSS = StandardsStatus.EXTERNAL;
    }
    if (elementStatus == null)
        elementStatus = sstatus;
    if (tgtFMM == null)
        addError(gen, row, dc, "Binding Error: Unable to resolve vs '" + binding.getReference() + "' to check dependencies", null);
    else {
        boolean ok = elementStatus.canDependOn(tgtSS);
        if (ok)
            ok = fmm.compareTo(tgtFMM) <= 0;
        if (ok)
            // addInfo(gen, row, dc, "Binding OK (ValueSet = FMM"+tgtFMM+"-"+tgtSS.toDisplay()+" vs. Element = FMM"+fmm+"-"+elementStatus.toDisplay()+")", null);
            ;
        else
            addError(gen, row, dc, "Binding Error: (ValueSet = FMM" + tgtFMM + "-" + tgtSS.toDisplay() + " vs. Element = FMM" + fmm + "-" + elementStatus.toDisplay() + ")", vs.getUserString("path"));
    }
}

Example 45 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project health-patterns by LinuxForHealth.

the class TerminologyService method translateResource.

/**
 * Translates the given single FHIR resource represented as a {@link JsonNode}.
 *
 * @param resource the FHIR resource to translate
 * @returns true if there was something to translate, false otherwise
 * @throws DeIdentifierException if there is an error in the de-identification REST API or parsing the JSON
 * @throws IllegalArgumentException if the given JSON does not have a 'resource' object
 */
private boolean translateResource(JsonNode resource) {
    boolean translatedSomething = false;
    String resourceType = getResourceType(resource);
    boolean isTranslatable = StringUtils.equalsAny(resourceType, TRANSLATABLE_FHIR_TYPES);
    if (!isTranslatable) {
        return translatedSomething;
    }
    ArrayNode extensions = (ArrayNode) resource.get(EXTENSION_OBJECT);
    if (extensions == null) {
        return translatedSomething;
    }
    for (int i = 0; i < extensions.size(); i++) {
        JsonNode extension = extensions.get(i);
        JsonNode urlJson = extension.get(URL_OBJECT);
        JsonNode valueCodeJson = extension.get(VALUE_CODE_OBJECT);
        if (urlJson == null || valueCodeJson == null) {
            // In order to do a translation we need both the url and the valueCode
            continue;
        }
        // The resource's extension URL is the URL for the StructureDefinition, so we resolve a ValueSet if known
        String structureDefinitionURL = urlJson.asText();
        String valueSetURL = valueSetForStructureDefinition.get(structureDefinitionURL);
        // and if known we check the FHIR Server's known ConceptMaps to see if there is a corresponding one
        // http://4603f72b-us-south.lb.appdomain.cloud/fhir-server/api/v4/ConceptMap?_format=json&source-uri=http://hl7.org/fhir/us/core/ValueSet/birthsex
        Bundle bundle = fhirClient.search().forResource(ConceptMap.class).where(ConceptMap.SOURCE_URI.hasId(valueSetURL)).returnBundle(Bundle.class).execute();
        String conceptMapId;
        if (!bundle.getEntry().isEmpty()) {
            Resource conceptMap = bundle.getEntry().get(0).getResource();
            if (bundle.getEntry().size() > 1) {
                System.err.println("Found multiple ConceptMaps that will map " + valueSetURL + " for this StructureDefinition, will use the first one " + conceptMap.getId());
            } else {
                System.out.println("Found ConceptMap for " + valueSetURL + ": " + conceptMap.getId() + " !!");
            }
            conceptMapId = conceptMap.getIdElement().getIdPart();
        } else {
            System.out.println("Did not find ConceptMap for " + valueSetURL + "!!");
            continue;
        }
        // "POST ${FHIR_URL}/${conceptMapID}/$translate?code=${code}&system=${valueSet}&_format=json
        String valueCode = valueCodeJson.asText();
        String url = String.format("%s/ConceptMap/%s/$translate?code=%s&system=%s&_format=json", fhirClient.getServerBase(), conceptMapId, valueCode, valueSetURL);
        Parameters translationResponse = fhirClient.fetchResourceFromUrl(Parameters.class, url);
        // This is what comes back from the server
        // {
        // "resourceType": "Parameters",
        // "parameter": [
        // {
        // "name": "result",
        // "valueBoolean": true
        // },
        // {
        // "name": "match",
        // "part": [
        // {
        // "name": "equivalence",
        // "valueCode": "equivalent"
        // },
        // {
        // "name": "concept",
        // "valueCoding": {
        // "system": "http://ibm.com/fhir/cdm/ValueSet/sex-assigned-at-birth",
        // "code": "male",
        // "display": "Male"
        // }
        // }
        // ]
        // }
        // ]
        // }
        Coding translatedCode = null;
        List<ParametersParameterComponent> parameters = translationResponse.getParameter();
        for (ParametersParameterComponent parameter : parameters) {
            if (parameter.getName().equals(MATCH_VALUE)) {
                List<ParametersParameterComponent> parts = parameter.getPart();
                for (ParametersParameterComponent part : parts) {
                    if (part.getName().equals(CONCEPT_VALUE)) {
                        try {
                            translatedCode = (Coding) part.getValue();
                        } catch (ClassCastException e) {
                            String jsonResponse = fhirClient.getFhirContext().newJsonParser().encodeResourceToString(translationResponse);
                            System.err.println("Found a ConceptMap that will map " + valueSetURL + " for this StructureDefinition, but the FHIR server returned an unknown $translate response (expected a 'valueCoding' part): " + jsonResponse);
                        }
                    }
                }
            }
        }
        if (translatedCode == null) {
            String jsonResponse = fhirClient.getFhirContext().newJsonParser().encodeResourceToString(translationResponse);
            System.err.println("Found a ConceptMap that will map " + valueSetURL + " for this StructureDefinition, but the FHIR server returned an unknown $translate response: " + jsonResponse);
            continue;
        }
        System.out.printf("Found ConceptMap %s which translates (valueCode, system) = (%s, %s) for StructureDefinition %s to (valueCode, system) = (%s, %s) %n", conceptMapId, valueCode, valueSetURL, structureDefinitionURL, translatedCode.getCode(), translatedCode.getSystem());
        String translatedStructuredData = valueSetForStructureDefinition.get(translatedCode.getSystem());
        if (translatedStructuredData == null) {
            System.err.printf("Cannot find the mapping from ValueSet '%s' to its corresponding StructureData for this translation, make sure the corresponding mappings configuration file has it.%n", translatedCode.getSystem());
            continue;
        }
        ((ObjectNode) extension).set(URL_OBJECT, JsonNodeFactory.instance.textNode(translatedStructuredData));
        ((ObjectNode) extension).set(VALUE_CODE_OBJECT, JsonNodeFactory.instance.textNode(translatedCode.getCode()));
        translatedSomething = true;
    }
    return translatedSomething;
}