Examples with Source org.hl7.fhir.utilities.validation.ValidationMessage.Source used on opensource projects

Example 41 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source 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 42 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source 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 43 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method expand.

@Override
public ValueSetExpansionOutcome expand(ValueSet source) {
    try {
        focus = source.copy();
        focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
        focus.getExpansion().setTimestampElement(DateTimeType.now());
        focus.getExpansion().setIdentifier(Factory.createUUID());
        handleDefine(source, focus.getExpansion().getParameter());
        if (source.hasCompose())
            handleCompose(source.getCompose(), focus.getExpansion().getParameter());
        for (ValueSetExpansionContainsComponent c : codes) {
            if (map.containsKey(key(c))) {
                focus.getExpansion().getContains().add(c);
            }
        }
        return new ValueSetExpansionOutcome(focus, null);
    } catch (Exception e) {
        // that might fail too, but it might not, later.
        return new ValueSetExpansionOutcome(new ValueSetCheckerSimple(source, factory, context), e.getMessage());
    }
}

Example 44 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class RdfParser method composeDocumentManifest.

protected void composeDocumentManifest(Complex parent, String parentType, String name, DocumentManifest element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeDomainResource(t, "DocumentManifest", name, element, index);
    if (element.hasMasterIdentifier())
        composeIdentifier(t, "DocumentManifest", "masterIdentifier", element.getMasterIdentifier(), -1);
    for (int i = 0; i < element.getIdentifier().size(); i++) composeIdentifier(t, "DocumentManifest", "identifier", element.getIdentifier().get(i), i);
    if (element.hasSubject())
        composeReference(t, "DocumentManifest", "subject", element.getSubject(), -1);
    for (int i = 0; i < element.getRecipient().size(); i++) composeReference(t, "DocumentManifest", "recipient", element.getRecipient().get(i), i);
    if (element.hasType())
        composeCodeableConcept(t, "DocumentManifest", "type", element.getType(), -1);
    for (int i = 0; i < element.getAuthor().size(); i++) composeReference(t, "DocumentManifest", "author", element.getAuthor().get(i), i);
    if (element.hasCreatedElement())
        composeDateTime(t, "DocumentManifest", "created", element.getCreatedElement(), -1);
    if (element.hasSourceElement())
        composeUri(t, "DocumentManifest", "source", element.getSourceElement(), -1);
    if (element.hasStatusElement())
        composeEnum(t, "DocumentManifest", "status", element.getStatusElement(), -1);
    if (element.hasDescriptionElement())
        composeString(t, "DocumentManifest", "description", element.getDescriptionElement(), -1);
    for (int i = 0; i < element.getContent().size(); i++) composeDocumentManifestDocumentManifestContentComponent(t, "DocumentManifest", "content", element.getContent().get(i), i);
    for (int i = 0; i < element.getRelated().size(); i++) composeDocumentManifestDocumentManifestRelatedComponent(t, "DocumentManifest", "related", element.getRelated().get(i), i);
}

Example 45 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method expand.

@Override
public ValueSetExpansionOutcome expand(ValueSet source) {
    try {
        focus = source.copy();
        focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
        focus.getExpansion().setTimestampElement(DateTimeType.now());
        focus.getExpansion().setIdentifier(Factory.createUUID());
        if (source.hasCompose())
            handleCompose(source.getCompose(), focus.getExpansion().getParameter());
        for (ValueSetExpansionContainsComponent c : codes) {
            if (map.containsKey(key(c))) {
                focus.getExpansion().getContains().add(c);
            }
        }
        return new ValueSetExpansionOutcome(focus, null);
    } catch (RuntimeException e) {
        // it swallows bugs.. what would be expected to be caught there?
        throw e;
    } catch (Exception e) {
        // that might fail too, but it might not, later.
        return new ValueSetExpansionOutcome(new ValueSetCheckerSimple(source, factory, context), e.getMessage());
    }
}