Examples with Element org.hl7.fhir.r5.elementmodel.Element used on opensource projects

Example 76 with Element

use of org.hl7.fhir.r5.elementmodel.Element 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 77 with Element

use of org.hl7.fhir.r5.elementmodel.Element in project org.hl7.fhir.core by hapifhir.

the class ArgonautConverter method processMedicationsSection.

private void processMedicationsSection(CDAUtilities cda, Convert convert, Element section, Context context) throws Exception {
    scanSection("Medications", section);
    ListResource list = new ListResource();
    list.setId(context.getBaseId() + "-list-medications");
    list.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/list-daf-dafmedicationlist");
    list.setSubject(context.getSubjectRef());
    list.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")), null));
    list.setTitle(cda.getChild(section, "title").getTextContent());
    list.setStatus(ListStatus.CURRENT);
    list.setMode(ListMode.SNAPSHOT);
    list.setDateElement(context.getNow());
    list.setSource(context.getAuthorRef());
    buildNarrative(list, cda.getChild(section, "text"));
    int i = 0;
    for (Element c : cda.getChildren(section, "entry")) {
        // allergy problem act
        Element sa = cda.getChild(c, "substanceAdministration");
        MedicationStatement ms = new MedicationStatement();
        ms.setId(context.getBaseId() + "-medication-" + i);
        ms.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/medicationstatement-daf-dafmedicationstatement");
        i++;
        ms.setSubject(context.getSubjectRef());
        boolean found = false;
        for (Element e : cda.getChildren(sa, "id")) {
            Identifier id = convert.makeIdentifierFromII(e);
            ms.getIdentifier().add(id);
        }
        if (!found) {
            ms.setStatus(MedicationStatementStatus.COMPLETED);
            list.addEntry().setItem(new Reference().setReference("MedicationStatement/" + ms.getId()));
            // allergy observation
            Element mm = cda.getChild(cda.getChild(cda.getChild(sa, "consumable"), "manufacturedProduct"), "manufacturedMaterial");
            ms.setMedication(new Reference().setReference("#med"));
            Medication med = new Medication();
            med.setId("med");
            med.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(mm, "code")), null));
            ms.getContained().add(med);
            Dosage dosage = ms.addDosage();
            // allergy observation
            Element qty = cda.getChild(sa, "doseQuantity");
            try {
                if (cda.getChild(qty, "low") != null) {
                    // todo: this is not correct?
                    dosage.getExtension().add(new Extension().setUrl("http://healthintersections.com.au/fhir/extensions/medication-statement-range").setValue(convert.makeRangeFromIVLPQ(qty)));
                } else {
                    dosage.setDose(convert.makeQuantityFromPQ(qty));
                }
            } catch (Exception e) {
                System.out.println("  invalid dose quantity '" + qty.getAttribute("value") + " " + qty.getAttribute("unit") + "' (" + e.getClass().getName() + ") in " + context.getBaseId());
            }
            dosage.setRoute(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(sa, "routeCode")), null));
            Type t = convert.makeSomethingFromGTS(cda.getChildren(sa, "effectiveTime"));
            if (t instanceof Timing) {
                dosage.setTiming((Timing) t);
                if (dosage.getTiming().hasRepeat() && dosage.getTiming().getRepeat().hasBounds())
                    ms.setEffective(dosage.getTiming().getRepeat().getBounds());
            } else if (t instanceof Period)
                ms.setEffective(t);
            else
                throw new Exception("Undecided how to handle " + t.getClass().getName());
            for (Element e : cda.getChildren(sa, "author")) {
                if (ms.hasInformationSource())
                    throw new Error("additional author discovered");
                Practitioner p = processPerformer(cda, convert, context, e, "assignedAuthor", "assignedPerson");
                Reference ref = new Reference().setReference("Practitioner/" + p.getId()).setDisplay(p.getUserString("display"));
                ms.setInformationSource(ref);
                ms.setDateAssertedElement(convert.makeDateTimeFromTS(cda.getChild(e, "time")));
            }
            saveResource(ms);
        }
    }
    saveResource(list);
}

Example 78 with Element

use of org.hl7.fhir.r5.elementmodel.Element in project org.hl7.fhir.core by hapifhir.

the class ADLImporter method execute.

private void execute() throws Exception {
    // load config
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();
    adlConfig = builder.parse(new FileInputStream(config)).getDocumentElement();
    // load ADL
    builder = factory.newDocumentBuilder();
    adl = builder.parse(new FileInputStream(source)).getDocumentElement();
    check("root", adl.getNamespaceURI(), "http://schemas.openehr.org/v1", "Wrong namespace for ADL XML");
    check("root", adl.getNodeName(), "archetype", "Wrong XML for ADL XML");
    check("root", XMLUtil.getNamedChild(adl, "adl_version").getTextContent(), "1.4", "unsupported ADL version");
    String id = XMLUtil.getFirstChild(XMLUtil.getNamedChild(adl, "archetype_id")).getTextContent().split("\\.")[1];
    // create structure definition
    StructureDefinition sd = new StructureDefinition();
    sd.setId(id);
    // populate metadata
    Element description = XMLUtil.getNamedChild(adl, "description");
    Element details = XMLUtil.getNamedChild(description, "details");
    sd.setDescription(XMLUtil.getNamedChild(details, "purpose").getTextContent());
    sd.setCopyright(XMLUtil.getNamedChild(details, "copyright").getTextContent());
    sd.setPurpose("Use:\r\n" + XMLUtil.getNamedChild(details, "use").getTextContent() + "\r\n\r\nMisuse:\r\n" + XMLUtil.getNamedChild(details, "misuse").getTextContent());
    List<Element> set = new ArrayList<Element>();
    XMLUtil.getNamedChildren(details, "keywords", set);
    for (Element e : set) sd.addKeyword().setDisplay(e.getTextContent());
    String status = XMLUtil.getNamedChild(description, "lifecycle_state").getTextContent();
    if ("CommitteeDraft".equals(status) || "AuthorDraft".equals(status))
        sd.setStatus(PublicationStatus.DRAFT);
    else
        throw new Exception("Unknown life cycle state " + XMLUtil.getNamedChild(description, "lifecycle_state").getTextContent());
    // load texts from ontology
    Element ontology = XMLUtil.getNamedChild(adl, "ontology");
    Element term_definitions = XMLUtil.getNamedChild(ontology, "term_definitions");
    set.clear();
    XMLUtil.getNamedChildren(term_definitions, "items", set);
    for (Element item : set) {
        processTextItem(item);
    }
    // load data and protocol
    Element definition = XMLUtil.getNamedChild(adl, "definition");
    NodeTreeEntry root = new NodeTreeEntry();
    root.setTypeName(XMLUtil.getNamedChild(definition, "rm_type_name").getTextContent());
    root.setAtCode(XMLUtil.getNamedChild(definition, "node_id").getTextContent());
    root.setName(generateToken(root.getAtCode(), true));
    sd.setName(root.getName());
    root.setCardinality(readCardinality("root", XMLUtil.getNamedChild(definition, "occurrences")));
    set.clear();
    XMLUtil.getNamedChildren(definition, "attributes", set);
    for (Element item : set) {
        // we're actually skipping this level - we don't care about data protocol etc.
        // XMLUtil.getNamedChild(XMLUtil.getNamedChild(item, "children"), "attributes");
        Element attributes = item;
        loadChildren(root.getAtCode(), root, attributes);
    }
    dumpChildren("", root);
    genElements(sd, root.getName(), root);
    // save
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), sd);
    System.out.println("done. saved as " + dest);
}

Example 79 with Element

use of org.hl7.fhir.r5.elementmodel.Element in project org.hl7.fhir.core by hapifhir.

the class LoincToDEConvertor method processLoincCodes.

private void processLoincCodes() {
    Element row = XMLUtil.getFirstChild(xml.getDocumentElement());
    int i = 0;
    while (row != null) {
        i++;
        if (i % 1000 == 0)
            System.out.print(".");
        String code = col(row, "LOINC_NUM");
        String comp = col(row, "COMPONENT");
        DataElement de = new DataElement();
        de.setId("loinc-" + code);
        de.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
        bundle.getEntry().add(new BundleEntryComponent().setResource(de));
        Identifier id = new Identifier();
        id.setSystem("http://hl7.org/fhir/commondataelement/loinc");
        id.setValue(code);
        de.addIdentifier(id);
        de.setPublisher("Regenstrief + FHIR Project Team");
        if (!col(row, "STATUS").equals("ACTIVE"))
            // till we get good at this
            de.setStatus(ConformanceResourceStatus.DRAFT);
        else
            de.setStatus(ConformanceResourceStatus.RETIRED);
        de.setDateElement(DateTimeType.now());
        de.setName(comp);
        ElementDefinition dee = de.addElement();
        // PROPERTY	ignore
        // TIME_ASPCT
        // SYSTEM
        // SCALE_TYP
        // METHOD_TYP
        // dee.getCategory().add(new CodeableConcept().setText(col(row, "CLASS")));
        // SOURCE
        // DATE_LAST_CHANGED - should be in ?
        // CHNG_TYPE
        dee.setComments(col(row, "COMMENTS"));
        if (hasCol(row, "CONSUMER_NAME"))
            dee.addAlias(col(row, "CONSUMER_NAME"));
        // SURVEY_QUEST_SRC
        if (hasCol(row, "RELATEDNAMES2")) {
            String n = col(row, "RELATEDNAMES2");
            for (String s : n.split("\\;")) {
                if (!Utilities.noString(s))
                    dee.addAlias(s);
            }
        }
        dee.addAlias(col(row, "SHORTNAME"));
        // ORDER_OBS
        // CDISC Code
        // HL7_FIELD_SUBFIELD_ID
        // ------------------ EXTERNAL_COPYRIGHT_NOTICE todo
        dee.setDefinition(col(row, "LONG_COMMON_NAME"));
        // HL7_V2_DATATYPE
        String cc = makeType(col(row, "HL7_V3_DATATYPE"), code);
        if (cc != null)
            dee.addType().setCode(cc);
        // todo... CURATED_RANGE_AND_UNITS
        // todo: DOCUMENT_SECTION
        // STATUS_REASON
        // STATUS_TEXT
        // CHANGE_REASON_PUBLIC
        // COMMON_TEST_RANK
        // COMMON_ORDER_RANK
        // COMMON_SI_TEST_RANK
        // HL7_ATTACHMENT_STRUCTURE
        // units:
        // UNITSREQUIRED
        // SUBMITTED_UNITS
        ToolingExtensions.setAllowableUnits(dee, makeUnits(col(row, "EXAMPLE_UNITS"), col(row, "EXAMPLE_UCUM_UNITS")));
        // EXAMPLE_SI_UCUM_UNITS
        row = XMLUtil.getNextSibling(row);
    }
    System.out.println("done");
}

Example 80 with Element

use of org.hl7.fhir.r5.elementmodel.Element in project org.hl7.fhir.core by hapifhir.

the class FHIRPathEngine method getChildTypesByName.

private void getChildTypesByName(String type, String name, TypeDetails result) throws PathEngineException, DefinitionException {
    if (Utilities.noString(type))
        throw new PathEngineException("No type provided in BuildToolPathEvaluator.getChildTypesByName");
    if (type.equals("xhtml"))
        return;
    String url = null;
    if (type.contains(".")) {
        url = "http://hl7.org/fhir/StructureDefinition/" + type.substring(0, type.indexOf("."));
    } else {
        url = "http://hl7.org/fhir/StructureDefinition/" + type;
    }
    String tail = "";
    StructureDefinition sd = worker.fetchResource(StructureDefinition.class, url);
    if (sd == null)
        // this really is an error, because we can only get to here if the internal infrastrucgture is wrong
        throw new DefinitionException("Unknown type " + type);
    List<StructureDefinition> sdl = new ArrayList<StructureDefinition>();
    ElementDefinitionMatch m = null;
    if (type.contains("."))
        m = getElementDefinition(sd, type, false);
    if (m != null && hasDataType(m.definition)) {
        if (m.fixedType != null) {
            StructureDefinition dt = worker.fetchTypeDefinition(m.fixedType);
            if (dt == null)
                throw new DefinitionException("unknown data type " + m.fixedType);
            sdl.add(dt);
        } else
            for (TypeRefComponent t : m.definition.getType()) {
                StructureDefinition dt = worker.fetchTypeDefinition(t.getCode());
                if (dt == null)
                    throw new DefinitionException("unknown data type " + t.getCode());
                sdl.add(dt);
            }
    } else {
        sdl.add(sd);
        if (type.contains("."))
            tail = type.substring(type.indexOf("."));
    }
    for (StructureDefinition sdi : sdl) {
        String path = sdi.getSnapshot().getElement().get(0).getPath() + tail + ".";
        if (name.equals("**")) {
            assert (result.getCollectionStatus() == CollectionStatus.UNORDERED);
            for (ElementDefinition ed : sdi.getSnapshot().getElement()) {
                if (ed.getPath().startsWith(path))
                    for (TypeRefComponent t : ed.getType()) {
                        if (t.hasCode() && t.getCodeElement().hasValue()) {
                            String tn = null;
                            if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement"))
                                tn = ed.getPath();
                            else
                                tn = t.getCode();
                            if (t.getCode().equals("Resource")) {
                                for (String rn : worker.getResourceNames()) {
                                    if (!result.hasType(worker, rn)) {
                                        result.addType(rn);
                                        getChildTypesByName(rn, "**", result);
                                    }
                                }
                            } else if (!result.hasType(worker, tn)) {
                                result.addType(tn);
                                getChildTypesByName(tn, "**", result);
                            }
                        }
                    }
            }
        } else if (name.equals("*")) {
            assert (result.getCollectionStatus() == CollectionStatus.UNORDERED);
            for (ElementDefinition ed : sdi.getSnapshot().getElement()) {
                if (ed.getPath().startsWith(path) && !ed.getPath().substring(path.length()).contains("."))
                    for (TypeRefComponent t : ed.getType()) {
                        if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement"))
                            result.addType(ed.getPath());
                        else if (t.getCode().equals("Resource"))
                            result.addTypes(worker.getResourceNames());
                        else
                            result.addType(t.getCode());
                    }
            }
        } else {
            path = sdi.getSnapshot().getElement().get(0).getPath() + tail + "." + name;
            ElementDefinitionMatch ed = getElementDefinition(sdi, path, false);
            if (ed != null) {
                if (!Utilities.noString(ed.getFixedType()))
                    result.addType(ed.getFixedType());
                else
                    for (TypeRefComponent t : ed.getDefinition().getType()) {
                        if (Utilities.noString(t.getCode()))
                            // throw new PathEngineException("Illegal reference to primitive value attribute @ "+path);
                            break;
                        if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement"))
                            result.addType(path);
                        else if (t.getCode().equals("Resource"))
                            result.addTypes(worker.getResourceNames());
                        else
                            result.addType(t.getCode());
                    }
            }
        }
    }
}