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

Example 26 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project org.hl7.fhir.core by hapifhir.

the class SearchParameter10_50 method convertSearchParameter.

public static org.hl7.fhir.dstu2.model.SearchParameter convertSearchParameter(org.hl7.fhir.r5.model.SearchParameter src) throws FHIRException {
    if (src == null || src.isEmpty())
        return null;
    org.hl7.fhir.dstu2.model.SearchParameter tgt = new org.hl7.fhir.dstu2.model.SearchParameter();
    ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().copyDomainResource(src, tgt);
    if (src.hasUrlElement())
        tgt.setUrlElement(Uri10_50.convertUri(src.getUrlElement()));
    if (src.hasNameElement())
        tgt.setNameElement(String10_50.convertString(src.getNameElement()));
    if (src.hasStatus())
        tgt.setStatusElement(Enumerations10_50.convertConformanceResourceStatus(src.getStatusElement()));
    if (src.hasExperimental())
        tgt.setExperimentalElement(Boolean10_50.convertBoolean(src.getExperimentalElement()));
    if (src.hasDate())
        tgt.setDateElement(DateTime10_50.convertDateTime(src.getDateElement()));
    if (src.hasPublisherElement())
        tgt.setPublisherElement(String10_50.convertString(src.getPublisherElement()));
    for (org.hl7.fhir.r5.model.ContactDetail t : src.getContact()) tgt.addContact(convertSearchParameterContactComponent(t));
    if (src.hasPurpose())
        tgt.setRequirements(src.getPurpose());
    if (src.hasCodeElement())
        tgt.setCodeElement(Code10_50.convertCode(src.getCodeElement()));
    for (CodeType t : src.getBase()) tgt.setBase(t.asStringValue());
    if (src.hasType())
        tgt.setTypeElement(Enumerations10_50.convertSearchParamType(src.getTypeElement()));
    if (src.hasDescription())
        tgt.setDescription(src.getDescription());
    org.hl7.fhir.dstu2.utils.ToolingExtensions.setStringExtension(tgt, ToolingExtensions.EXT_EXPRESSION, src.getExpression());
    if (src.hasXpathElement())
        tgt.setXpathElement(String10_50.convertString(src.getXpathElement()));
    if (src.hasXpathUsage())
        tgt.setXpathUsageElement(convertXPathUsageType(src.getXpathUsageElement()));
    for (CodeType t : src.getTarget()) tgt.addTarget(t.getValue());
    return tgt;
}

Example 27 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project org.hl7.fhir.core by hapifhir.

the class IEEE11073Convertor method generateMDC.

public static CodeSystem generateMDC(String src, String dst, UcumService ucum) throws IOException, FHIRException {
    CSVReader csv = new CSVReader(new FileInputStream(src));
    csv.readHeaders();
    CodeSystem cs = new CodeSystem();
    Map<String, String> ucumIssues = new HashMap<String, String>();
    int errorCount = 0;
    cs.setId("MDC");
    cs.setUrl("urn:iso:std:iso:11073:10101");
    cs.setVersion("[todo]");
    cs.setName("11073:10101 codes for the FHIR community");
    cs.setStatus(PublicationStatus.ACTIVE);
    cs.setExperimental(false);
    cs.setDateElement(new DateTimeType());
    cs.setPublisher("HL7 (FHIR Project)");
    ContactDetail cd = cs.addContact();
    ContactPoint cp = cd.addTelecom();
    cp.setSystem(ContactPointSystem.URL);
    cp.setValue("http://ieee?");
    cs.setDescription("1073 Codes for the FHIR community (generated from the Rosetta data");
    Identifier i = new Identifier();
    cs.setIdentifier(i);
    i.setSystem("urn:ietf:rfc:3986");
    i.setValue("urn:oid:2.16.840.1.113883.6.24");
    cs.setCaseSensitive(false);
    cs.setContent(CodeSystemContentMode.COMPLETE);
    cs.addProperty().setCode("ucum").setDescription("UCUM units associated with Concept").setType(PropertyType.STRING);
    cs.addProperty().setCode("unit").setDescription("MDC units associated with Concept").setType(PropertyType.STRING);
    cs.addProperty().setCode("refid").setDescription("MDC Reference Id for Concept").setType(PropertyType.CODE);
    Set<String> codes = new HashSet<String>();
    while (csv.line()) {
        if (csv.has("CF_CODE10")) {
            String code = csv.cell("CF_CODE10");
            if (codes.contains(code))
                System.out.println("Duplicate Code " + code);
            else {
                codes.add(code);
                ConceptDefinitionComponent c = cs.addConcept();
                c.setCode(code);
                c.setDisplay(csv.cell("Common Term"));
                c.setDefinition(csv.cell("Term Description"));
                String vd = csv.cell("Vendor_Description");
                if (!c.hasDefinition())
                    c.setDefinition(vd);
                if (!c.hasDisplay())
                    c.setDisplay(vd);
                String refid = csv.cell("REFID");
                c.addProperty().setCode("refid").setValue(new CodeType().setValue(refid));
                if (csv.has("Synonym"))
                    c.addDesignation().setValue(csv.cell("Synonym")).setUse(new Coding().setSystem("http://hl7.org/fhir/designation-use").setCode("synonym"));
                if (csv.has("Acronym"))
                    c.addDesignation().setValue(csv.cell("Acronym")).setUse(new Coding().setSystem("http://hl7.org/fhir/designation-use").setDisplay("acronym"));
                if (csv.has("Systematic Name")) {
                    String sysName = csv.cell("Systematic Name");
                    if (!c.hasDefinition())
                        c.setDefinition(sysName);
                    c.addDesignation().setValue(sysName).setUse(new Coding().setSystem("http://hl7.org/fhir/designation-use").setCode("structured-name"));
                }
                if (csv.has("UOM_MDC"))
                    c.addProperty().setCode("unit").setValue(new StringType().setValue(csv.cell("UOM_MDC")));
                if (csv.has("UOM_UCUM")) {
                    CommaSeparatedStringBuilder ul = new CommaSeparatedStringBuilder();
                    for (String u : csv.cell("UOM_UCUM").split(" ")) {
                        String msg = ucum.validate(u);
                        if (msg != null) {
                            errorCount++;
                            ucumIssues.put(u, msg);
                        } else
                            ul.append(u);
                    }
                    if (ul.length() > 0)
                        c.addProperty().setCode("ucum").setValue(new StringType().setValue(ul.toString()));
                }
            }
        }
    }
    csv.close();
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "codesystem-" + cs.getId() + ".xml")), cs);
    System.out.println(errorCount + "UCUM errors");
    for (String u : sorted(ucumIssues.keySet())) System.out.println("Invalid UCUM code: " + u + " because " + ucumIssues.get(u));
    return cs;
}

Example 28 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project org.hl7.fhir.core by hapifhir.

the class CountryCodesConverter method execute.

private void execute() throws ParserConfigurationException, SAXException, IOException {
    Document src = load();
    CodeSystem cs1 = new CodeSystem();
    CodeSystem cs2 = new CodeSystem();
    CodeSystem cs3 = new CodeSystem();
    setMetadata(src, cs1, "iso3166", "urn:iso:std:iso:3166", "", "");
    setMetadata(src, cs2, "iso3166-2", "urn:iso:std:iso:3166:-2", "Part2", " Part 2");
    cs1.addProperty().setCode("canonical").setDescription("The 2 letter code that identifies the same country (so 2/3/numeric codes can be aligned)").setType(PropertyType.CODE);
    cs2.addProperty().setCode("country").setDescription("The 2 letter code that identifies the country for the subdivision").setType(PropertyType.CODE);
    for (Element e : XMLUtil.getNamedChildren(src.getDocumentElement(), "country")) {
        System.out.println(e.getAttribute("id"));
        String c2 = XMLUtil.getNamedChildText(e, "alpha-2-code");
        String c3 = XMLUtil.getNamedChildText(e, "alpha-3-code");
        String cN = XMLUtil.getNamedChildText(e, "numeric-code");
        Element n = XMLUtil.getNamedChildByAttribute(e, "short-name", "lang3code", "eng");
        if (n == null)
            n = XMLUtil.getNamedChildByAttribute(e, "short-name-upper-case", "lang3code", "eng");
        if (n == null)
            continue;
        String name = n.getTextContent();
        n = XMLUtil.getNamedChildByAttribute(e, "full-name", "lang3code", "eng");
        if (n == null)
            n = XMLUtil.getNamedChildByAttribute(e, "full-name-upper-case", "lang3code", "eng");
        if (n == null)
            n = XMLUtil.getNamedChildByAttribute(e, "short-name", "lang3code", "eng");
        if (n == null)
            n = XMLUtil.getNamedChildByAttribute(e, "short-name-upper-case", "lang3code", "eng");
        String desc = n.getTextContent();
        ConceptDefinitionComponent cc = cs1.addConcept();
        cc.setCode(c2);
        cc.setDisplay(name);
        cc.setDefinition(desc);
        poplang(e, cc);
        if (c3 != null) {
            cc = cs1.addConcept();
            cc.setCode(c3);
            cc.setDisplay(name);
            cc.setDefinition(desc);
            cc.addProperty().setCode("canonical").setValue(new CodeType(c2));
            poplang(e, cc);
        }
        if (cN != null) {
            cc = cs1.addConcept();
            cc.setCode(cN);
            cc.setDisplay(name);
            cc.setDefinition(desc);
            cc.addProperty().setCode("canonical").setValue(new CodeType(c2));
            poplang(e, cc);
        }
        for (Element sd : XMLUtil.getNamedChildren(e, "subdivision")) {
            cc = cs2.addConcept();
            cc.setCode(XMLUtil.getNamedChildText(sd, "subdivision-code"));
            Element l = XMLUtil.getNamedChild(sd, "subdivision-locale");
            cc.setDisplay(XMLUtil.getNamedChildText(l, "subdivision-locale-name"));
            cc.addProperty().setCode("country").setValue(new CodeType(c2));
        }
    }
    cs1.setCount(cs1.getConcept().size());
    cs2.setCount(cs2.getConcept().size());
    throw new Error("Needs revisiting");
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166.json")), cs1);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166.json")), cs1); // format hasn't changed
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166-2.json")), cs2);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166-2.json")), cs2); // format hasn't changed
}

Example 29 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project org.hl7.fhir.core by hapifhir.

the class ICD11Generator method processMMSEntity.

private void processMMSEntity(CodeSystem cs, String base, String ref, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String dest) throws IOException {
    System.out.print(".");
    JsonObject entity = fetchJson(url(base, ref));
    cc.setId(tail(ref));
    if (entity.has("code") && !Utilities.noString(entity.get("code").getAsString())) {
        cc.setCode(entity.get("code").getAsString());
    } else if (entity.has("blockId") && !Utilities.noString(entity.get("blockId").getAsString())) {
        cc.setCode(entity.get("blockId").getAsString());
    } else {
        cc.setCode(cc.getId());
        cc.addProperty().setCode("abstract").setValue(new BooleanType(true));
    }
    if (entity.has("classKind") && !Utilities.noString(entity.get("classKind").getAsString()) && !"category".equals(entity.get("classKind").getAsString())) {
        cc.addProperty().setCode("kind").setValue(new CodeType(entity.get("classKind").getAsString()));
    }
    cc.setDisplay(readString(entity, "title"));
    StringBuilder defn = new StringBuilder();
    String d = readString(entity, "definition");
    if (d != null) {
        defn.append(d);
    }
    if (d == null && (entity.has("inclusion") || entity.has("exclusion"))) {
        defn.append(cc.getDisplay());
    }
    if (entity.has("inclusion")) {
        defn.append(". Includes: ");
        boolean first = true;
        for (JsonElement child : entity.getAsJsonArray("inclusion")) {
            if (first)
                first = false;
            else
                defn.append(", ");
            defn.append(readString((JsonObject) child, "label"));
        }
    }
    if (entity.has("exclusion")) {
        defn.append(". Excludes: ");
        boolean first = true;
        for (JsonElement child : entity.getAsJsonArray("exclusion")) {
            if (first)
                first = false;
            else
                defn.append(", ");
            JsonObject co = (JsonObject) child;
            String v = readString(co, "label");
            if (v != null) {
                defn.append(v);
                if (co.has("linearizationReference")) {
                    cc.addProperty().setValue(new Coding().setSystem("http://id.who.int/icd11/mms").setCode(tail(co.get("linearizationReference").getAsString())).setDisplay(v)).setCode("exclusion");
                }
            }
        }
    }
    cc.setDefinition(defn.toString());
    addDesignation(readString(entity, "longDefinition"), cc, "http://id.who.int/icd11/mms/designation", "longDefinition");
    addDesignation(readString(entity, "fullySpecifiedName"), cc, "http://snomed.info/sct", "900000000000003001");
    addProperty(readString(entity, "codingNote"), cc, "codingNote");
    if (entity.has("indexTerm")) {
        // }
        for (JsonElement child : entity.getAsJsonArray("indexTerm")) {
            processIndexTerm(cc, (JsonObject) child);
        }
    }
    if (entity.has("postcoordinationScale")) {
        for (JsonElement child : entity.getAsJsonArray("postcoordinationScale")) {
            JsonObject o = (JsonObject) child;
            String name = tail(o.get("axisName").getAsString());
            ConceptPropertyComponent prop = cc.addProperty();
            prop.setCode("postcoordinationScale");
            prop.setValue(new CodeType(name));
            ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/required", o.get("requiredPostcoordination").getAsBoolean());
            ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/repeats", o.get("allowMultipleValues").getAsBoolean());
            if (o.has("scaleEntity")) {
                ToolingExtensions.addUriExtension(prop, "http://id.who.int/icd11/extensions/valueSet", buildValueSet(cs, cc.getCode(), name, o, dest));
            }
        }
    }
    if (entity.has("child")) {
        for (JsonElement child : entity.getAsJsonArray("child")) {
            processMMSEntity(cs, base, child.getAsString(), cc.addConcept(), dest);
        }
    }
}

Example 30 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method renderLeaf.

private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints) throws FHIRException, UnsupportedEncodingException, IOException {
    if (ew == null)
        return;
    Base e = ew.getBase();
    if (e instanceof StringType)
        x.addText(((StringType) e).getValue());
    else if (e instanceof CodeType)
        x.addText(((CodeType) e).getValue());
    else if (e instanceof IdType)
        x.addText(((IdType) e).getValue());
    else if (e instanceof Extension)
        x.addText("Extensions: Todo");
    else if (e instanceof InstantType)
        x.addText(((InstantType) e).toHumanDisplay());
    else if (e instanceof DateTimeType)
        x.addText(((DateTimeType) e).toHumanDisplay());
    else if (e instanceof Base64BinaryType)
        x.addText(new Base64().encodeAsString(((Base64BinaryType) e).getValue()));
    else if (e instanceof org.hl7.fhir.dstu2.model.DateType)
        x.addText(((org.hl7.fhir.dstu2.model.DateType) e).toHumanDisplay());
    else if (e instanceof Enumeration) {
        Object ev = ((Enumeration<?>) e).getValue();
        // todo: look up a display name if there is one
        x.addText(ev == null ? "" : ev.toString());
    } else if (e instanceof BooleanType)
        x.addText(((BooleanType) e).getValue().toString());
    else if (e instanceof CodeableConcept) {
        renderCodeableConcept((CodeableConcept) e, x, showCodeDetails);
    } else if (e instanceof Coding) {
        renderCoding((Coding) e, x, showCodeDetails);
    } else if (e instanceof Annotation) {
        renderAnnotation((Annotation) e, x);
    } else if (e instanceof Identifier) {
        renderIdentifier((Identifier) e, x);
    } else if (e instanceof org.hl7.fhir.dstu2.model.IntegerType) {
        x.addText(Integer.toString(((org.hl7.fhir.dstu2.model.IntegerType) e).getValue()));
    } else if (e instanceof org.hl7.fhir.dstu2.model.DecimalType) {
        x.addText(((org.hl7.fhir.dstu2.model.DecimalType) e).getValue().toString());
    } else if (e instanceof HumanName) {
        renderHumanName((HumanName) e, x);
    } else if (e instanceof SampledData) {
        renderSampledData((SampledData) e, x);
    } else if (e instanceof Address) {
        renderAddress((Address) e, x);
    } else if (e instanceof ContactPoint) {
        renderContactPoint((ContactPoint) e, x);
    } else if (e instanceof UriType) {
        renderUri((UriType) e, x);
    } else if (e instanceof Timing) {
        renderTiming((Timing) e, x);
    } else if (e instanceof Range) {
        renderRange((Range) e, x);
    } else if (e instanceof Quantity) {
        renderQuantity((Quantity) e, x, showCodeDetails);
    } else if (e instanceof Ratio) {
        renderQuantity(((Ratio) e).getNumerator(), x, showCodeDetails);
        x.addText("/");
        renderQuantity(((Ratio) e).getDenominator(), x, showCodeDetails);
    } else if (e instanceof Period) {
        Period p = (Period) e;
        x.addText(!p.hasStart() ? "??" : p.getStartElement().toHumanDisplay());
        x.addText(" --> ");
        x.addText(!p.hasEnd() ? "(ongoing)" : p.getEndElement().toHumanDisplay());
    } else if (e instanceof Reference) {
        Reference r = (Reference) e;
        XhtmlNode c = x;
        ResourceWithReference tr = null;
        if (r.hasReferenceElement()) {
            tr = resolveReference(res, r.getReference());
            if (!r.getReference().startsWith("#")) {
                if (tr != null && tr.getReference() != null)
                    c = x.addTag("a").attribute("href", tr.getReference());
                else
                    c = x.addTag("a").attribute("href", r.getReference());
            }
        }
        // what to display: if text is provided, then that. if the reference was resolved, then show the generated narrative
        if (r.hasDisplayElement()) {
            c.addText(r.getDisplay());
            if (tr != null) {
                c.addText(". Generated Summary: ");
                generateResourceSummary(c, tr.getResource(), true, r.getReference().startsWith("#"));
            }
        } else if (tr != null) {
            generateResourceSummary(c, tr.getResource(), r.getReference().startsWith("#"), r.getReference().startsWith("#"));
        } else {
            c.addText(r.getReference());
        }
    } else if (e instanceof Resource) {
        return;
    } else if (e instanceof ElementDefinition) {
        x.addText("todo-bundle");
    } else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta))
        throw new NotImplementedException("type " + e.getClass().getName() + " not handled yet");
}