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Upgrade dependencies to HAPI-FHIR 6.10.0
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@qligier
qligier committed Nov 29, 2023
1 parent 5b830e7 commit 47fbd5f
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Showing 14 changed files with 9,629 additions and 9,414 deletions.
9 changes: 5 additions & 4 deletions matchbox-engine/src/main/java/ch/ahdis/matchbox/engine/MatchboxEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.r5.utils.validation.IResourceValidator;
import org.hl7.fhir.utilities.ByteProvider;
import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
Expand Down Expand Up @@ -246,8 +247,8 @@ public Resource transformToFhir(String input, boolean inputJson, String mapUri)
public String transform(String input, boolean inputJson, String mapUri, boolean outputJson)
throws FHIRException, IOException {
log.info("Start transform: " + mapUri);
Element transformed = transform(input.getBytes("UTF-8"), (inputJson ? FhirFormat.JSON : FhirFormat.XML),
mapUri);
Element transformed = transform(ByteProvider.forBytes(input.getBytes("UTF-8")), (inputJson ? FhirFormat.JSON : FhirFormat.XML),
mapUri);
ByteArrayOutputStream boas = new ByteArrayOutputStream();
if (outputJson)
new org.hl7.fhir.r5.elementmodel.JsonParser(getContext()).compose(transformed, boas,
Expand All @@ -268,10 +269,10 @@ public String transform(String input, boolean inputJson, String mapUri, boolean
* MatchboxStructureMapUtilities
*/
@Override
public org.hl7.fhir.r5.elementmodel.Element transform(byte[] source, FhirFormat cntType, String mapUri)
public org.hl7.fhir.r5.elementmodel.Element transform(ByteProvider source, FhirFormat cntType, String mapUri)
throws FHIRException, IOException {
SimpleWorkerContext context = this.getContext();
org.hl7.fhir.r5.elementmodel.Element src = Manager.parseSingle(context, new ByteArrayInputStream(source),
org.hl7.fhir.r5.elementmodel.Element src = Manager.parseSingle(context, new ByteArrayInputStream(source.getBytes()),
cntType);
return transform(src, mapUri);
}
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269 changes: 239 additions & 30 deletions matchbox-engine/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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50 changes: 39 additions & 11 deletions matchbox-engine/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,9 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
import org.hl7.fhir.utilities.xml.XMLWriter;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.xml.sax.ErrorHandler;
import org.xml.sax.InputSource;
import org.xml.sax.SAXParseException;
import org.xml.sax.XMLReader;

public class XmlParser extends ParserBase {
Expand All @@ -98,8 +100,6 @@ public void setSchemaPath(String schemaPath) {
this.schemaPath = schemaPath;
}



public boolean isAllowXsiLocation() {
return allowXsiLocation;
}
Expand Down Expand Up @@ -154,6 +154,7 @@ public List<NamedElement> parse(InputStream stream) throws FHIRFormatError, Defi
nullTransformer.transform(saxSource, domResult);
} else {
DocumentBuilder builder = factory.newDocumentBuilder();
builder.setErrorHandler(new NullErrorHandler());
doc = builder.parse(stream);
}
} catch (Exception e) {
Expand Down Expand Up @@ -296,19 +297,29 @@ public Element parse(org.w3c.dom.Element base, String type) throws Exception {
private void parseChildren(String path, org.w3c.dom.Element node, Element element) throws FHIRFormatError, FHIRException, IOException, DefinitionException {
// this parsing routine retains the original order in a the XML file, to support validation
reapComments(node, element);

String xsiType = XMLUtil.getXsiType(node);
List<Property> properties = element.getProperty().getChildProperties(element.getName(), xsiType);
List<Property> properties = element.getProperty().getChildProperties(element.getName(), XMLUtil.getXsiType(node));

String text = XMLUtil.getDirectText(node).trim();
int line = line(node, false);
int col = col(node, false);
if (!Utilities.noString(text)) {
Property property = getTextProp(properties);
if (property != null) {
Element n = new Element(property.getName(), property, property.getType(), text).markLocation(line, col);
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
if ("ED.data[x]".equals(property.getDefinition().getId()) || (property.getDefinition()!=null && property.getDefinition().getBase()!=null && "ED.data[x]".equals(property.getDefinition().getBase().getPath()))) {
if ("B64".equals(node.getAttribute("representation"))) {
Element n = new Element("dataBase64Binary", property, "base64Binary", text).markLocation(line, col);
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
} else {
Element n = new Element("dataString", property, "string", text).markLocation(line, col);
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
}
} else {
Element n = new Element(property.getName(), property, property.getType(), text).markLocation(line, col);
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
}
}
else {
Node n = node.getFirstChild();
Expand Down Expand Up @@ -416,7 +427,7 @@ private void parseChildren(String path, org.w3c.dom.Element node, Element elemen
boolean ok = true;
if (property.isChoice()) {
if (property.getDefinition().hasRepresentation(PropertyRepresentation.TYPEATTR)) {
xsiType = ((org.w3c.dom.Element) child).getAttributeNS(FormatUtilities.NS_XSI, "type");
String xsiType = ((org.w3c.dom.Element) child).getAttributeNS(FormatUtilities.NS_XSI, "type");
if (Utilities.noString(xsiType)) {
if (ToolingExtensions.hasExtension(property.getDefinition(), "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaulttype")) {
xsiType = ToolingExtensions.readStringExtension(property.getDefinition(), "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaulttype");
Expand All @@ -442,8 +453,9 @@ private void parseChildren(String path, org.w3c.dom.Element node, Element elemen
parseChildren(npath, (org.w3c.dom.Element) child, n);
}
}
} else
logError(ValidationMessage.NO_RULE_DATE, line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ELEMENT_, child.getLocalName()), IssueSeverity.ERROR);
} else {
logError(ValidationMessage.NO_RULE_DATE, line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ELEMENT_, child.getLocalName(), path), IssueSeverity.ERROR);
}
} else if (child.getNodeType() == Node.CDATA_SECTION_NODE){
logError(ValidationMessage.NO_RULE_DATE, line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.CDATA_IS_NOT_ALLOWED), IssueSeverity.ERROR);
} else if (!Utilities.existsInList(child.getNodeType(), 3, 8)) {
Expand Down Expand Up @@ -823,4 +835,20 @@ private String checkHeader(InputStream stream) throws IOException {
return "?xml-p2?";
}

class NullErrorHandler implements ErrorHandler {
@Override
public void fatalError(SAXParseException e) {
// do nothing
}

@Override
public void error(SAXParseException e) {
// do nothing
}

@Override
public void warning(SAXParseException e) {
// do nothing
}
}
}
1 change: 1 addition & 0 deletions matchbox-engine/src/main/java/org/hl7/fhir/r5/utils/structuremap/FFHIRPathHostServices.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathUtilityClasses.FunctionDetails;
import org.hl7.fhir.r5.utils.validation.IResourceValidator;
import org.hl7.fhir.utilities.validation.ValidationMessage;

Expand Down
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