mirror of
https://github.com/hapifhir/org.hl7.fhir.core.git
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unit test conversions r3r4
This commit is contained in:
Oliver Egger
parent
4ca4a595b2
commit
992f870cb4
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4
context
model
utils
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests
@ -289,6 +289,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
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}
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}
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}
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this.version = pi.version();
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}
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public void loadFromFile(String file, IContextResourceLoader loader) throws IOException, FHIRException {
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@ -73,8 +73,13 @@ public class XhtmlType extends Element {
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@Override
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public Base setProperty(int hash, String name, Base value) throws FHIRException {
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if ("value".equals(name)) {
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place.setDiv(castToXhtml(value));
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return value;
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if (value instanceof StringType) {
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// div is already generated with getValue, we cannot just overwrite it
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place.getDiv().setValueAsString(((StringType) value).asStringValue());
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} else {
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place.setDiv(castToXhtml(value));
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}
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return value;
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} else
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return super.setProperty(hash, name, value);
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}
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@ -2889,7 +2889,7 @@ public class FHIRPathEngine {
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if (!Utilities.noString(f)) {
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if (exp.getParameters().size() != 2) {
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if (exp.getParameters().size() == 2) {
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String t = convertToString(execute(context, focus, exp.getParameters().get(0), true));
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String r = convertToString(execute(context, focus, exp.getParameters().get(1), true));
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@ -1402,7 +1402,7 @@ public class StructureMapUtilities {
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}
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} else if (rule.getSource().size() == 1 && rule.getSourceFirstRep().hasVariable() && rule.getTarget().size() == 1 && rule.getTargetFirstRep().hasVariable() && rule.getTargetFirstRep().getTransform() == StructureMapTransform.CREATE && !rule.getTargetFirstRep().hasParameter()) {
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// simple inferred, map by type
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System.out.println(v.summary());
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log(v.summary());
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Base src = v.get(VariableMode.INPUT, rule.getSourceFirstRep().getVariable());
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Base tgt = v.get(VariableMode.OUTPUT, rule.getTargetFirstRep().getVariable());
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String srcType = src.fhirType();
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@ -1493,7 +1493,9 @@ public class StructureMapUtilities {
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if (value.contains("*")) {
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for (StructureMap sm : worker.listTransforms()) {
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if (urlMatches(value, sm.getUrl())) {
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res.add(sm);
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if (!res.contains(sm)) {
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res.add(sm);
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}
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}
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}
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} else {
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@ -25,6 +25,7 @@ import java.io.IOException;
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import java.util.List;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r5.model.StringType;
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import org.hl7.fhir.utilities.xhtml.NodeType;
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import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
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import org.hl7.fhir.utilities.xhtml.XhtmlNode;
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@ -72,7 +73,12 @@ public class XhtmlType extends Element {
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@Override
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public Base setProperty(int hash, String name, Base value) throws FHIRException {
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if ("value".equals(name)) {
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place.setDiv(castToXhtml(value));
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if (value instanceof StringType) {
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// div is already generated with getValue, we cannot just overwrite it
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place.getDiv().setValueAsString(((StringType) value).asStringValue());
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} else {
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place.setDiv(castToXhtml(value));
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}
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return value;
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} else
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return super.setProperty(hash, name, value);
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@ -2896,7 +2896,7 @@ public class FHIRPathEngine {
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if (!Utilities.noString(f)) {
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if (exp.getParameters().size() != 2) {
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if (exp.getParameters().size() == 2) {
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String t = convertToString(execute(context, focus, exp.getParameters().get(0), true));
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String r = convertToString(execute(context, focus, exp.getParameters().get(1), true));
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@ -33,18 +33,20 @@ import org.hl7.fhir.r4.model.Resource;
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import org.hl7.fhir.r4.model.ResourceFactory;
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import org.hl7.fhir.r4.model.StructureDefinition;
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import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
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import org.hl7.fhir.r4.test.utils.TestingUtilities;
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import org.hl7.fhir.r4.model.StructureMap;
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import org.hl7.fhir.r4.model.UriType;
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import org.hl7.fhir.r4.test.utils.TestingUtilities;
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import org.hl7.fhir.r4.utils.IResourceValidator;
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import org.hl7.fhir.r4.utils.IResourceValidator.IValidatorResourceFetcher;
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import org.hl7.fhir.r4.utils.IResourceValidator.ReferenceValidationPolicy;
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import org.hl7.fhir.r4.utils.StructureMapUtilities;
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import org.hl7.fhir.r4.utils.StructureMapUtilities.ITransformerServices;
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import org.hl7.fhir.r5.validation.InstanceValidatorFactory;
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import org.hl7.fhir.r4.validation.InstanceValidatorFactory;
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import org.hl7.fhir.utilities.IniFile;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.cache.PackageCacheManager;
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import org.hl7.fhir.utilities.cache.ToolsVersion;
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import org.hl7.fhir.utilities.validation.ValidationMessage;
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import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
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import org.junit.Test;
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@ -63,12 +65,14 @@ import com.google.gson.JsonPrimitive;
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public class R3R4ConversionTests implements ITransformerServices, IValidatorResourceFetcher {
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private static final boolean SAVING = true;
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private PackageCacheManager pcm = null;
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@Parameters(name = "{index}: id {0}")
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public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
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if (!(new File(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")).exists()))
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throw new Error("You must set the default directory to the build directory when you execute these tests");
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r3r4Outcomes = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
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r3r4Outcomes = (JsonObject) new com.google.gson.JsonParser().parse(
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TextFile.fileToString(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
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rules = new IniFile(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-rules.ini"));
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String srcFile = Utilities.path(TestingUtilities.home(), "source", "release3", "examples.zip");
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@ -79,7 +83,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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filter = filter.toLowerCase();
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Map<String, byte[]> examples = new HashMap<String, byte[]>();
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ZipEntry entry;
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while((entry = stream.getNextEntry())!=null) {
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while ((entry = stream.getNextEntry()) != null) {
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String n = entry.getName();
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byte[] buffer = new byte[2048];
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ByteArrayOutputStream output = null;
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@ -97,7 +101,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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List<Object[]> objects = new ArrayList<Object[]>(examples.size());
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for (String id : names) {
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objects.add(new Object[] { id, examples.get(id)});
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objects.add(new Object[] { id, examples.get(id) });
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}
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return objects;
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@ -137,7 +141,8 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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extras = new ArrayList<Resource>();
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// load the example (r3)
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org.hl7.fhir.r4.elementmodel.Element r3 = new org.hl7.fhir.r4.elementmodel.XmlParser(contextR3).parse(new ByteArrayInputStream(content));
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org.hl7.fhir.r4.elementmodel.Element r3 = new org.hl7.fhir.r4.elementmodel.XmlParser(contextR3)
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.parse(new ByteArrayInputStream(content));
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tn = r3.fhirType();
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workingid = r3.getChildValue("id");
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if (SAVING) {
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@ -145,13 +150,14 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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new org.hl7.fhir.r4.elementmodel.JsonParser(contextR3).compose(r3, bso, OutputStyle.PRETTY, null);
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cnt = bso.toByteArray();
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Utilities.createDirectory(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output"));
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TextFile.bytesToFile(cnt, Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", tn+"-"+workingid+".input.json"));
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TextFile.bytesToFile(cnt, Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output",
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tn + "-" + workingid + ".input.json"));
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}
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// load the r3 to R4 map
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String mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R3toR4", r3.fhirType()+".map");
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if (new File(mapFile).exists()) {
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StructureMap sm = smu4.parse(TextFile.fileToString(mapFile), mapFile);
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tn = smu4.getTargetType(sm).getType();
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// convert from r3 to r4
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@ -161,11 +167,13 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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ByteArrayOutputStream bs = new ByteArrayOutputStream();
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new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r4);
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if (SAVING) {
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TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", tn+"-"+workingid+".r4.json"));
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TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps",
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"test-output", tn + "-" + workingid + ".r4.json"));
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for (Resource r : extras) {
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bs = new ByteArrayOutputStream();
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new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r);
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TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", r.fhirType()+"-"+r.getId()+".r4.json"));
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TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps",
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"test-output", r.fhirType() + "-" + r.getId() + ".r4.json"));
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}
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}
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@ -176,8 +184,6 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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validator.validate(null, r4validationErrors, r4);
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// load the R4 to R3 map
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// mapFile = Utilities.path(root, "implementations", "r3maps", "R4toR3", r3.fhirType()+".map");
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// s = sm.parse(TextFile.fileToString(mapFile));
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mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R4toR3", getMapFor(r4.fhirType(), r3.fhirType())+".map");
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sm = smu3.parse(TextFile.fileToString(mapFile), mapFile);
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@ -190,15 +196,17 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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bs = new ByteArrayOutputStream();
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new org.hl7.fhir.r4.elementmodel.JsonParser(contextR3).compose(ro3, bs, OutputStyle.PRETTY, null);
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if (SAVING)
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TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", tn+"-"+workingid+".output.json"));
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TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps",
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"test-output", tn + "-" + workingid + ".output.json"));
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// check(errors, tn, workingid);
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roundTripError = TestingUtilities.checkJsonSrcIsSame(new String(cnt), new String(bs.toByteArray()), filter != null);
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if (roundTripError != null && roundTripError.equals(rules.getStringProperty(tn+"/"+workingid, "roundtrip")))
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// check(errors, tn, workingid);
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roundTripError = TestingUtilities.checkJsonSrcIsSame(new String(cnt), new String(bs.toByteArray()),
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filter != null);
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if (roundTripError != null && roundTripError.equals(rules.getStringProperty(tn + "/" + workingid, "roundtrip")))
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roundTripError = null;
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} else {
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if (loadErrors.containsKey(r3.fhirType()+".map")) {
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executionError = loadErrors.get(r3.fhirType()+".map");
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if (loadErrors.containsKey(r3.fhirType() + ".map")) {
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executionError = loadErrors.get(r3.fhirType() + ".map");
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}
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}
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} catch (Exception e) {
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@ -216,10 +224,11 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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if (r3.equals("ReferralRequest"))
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return "ServiceRequestRR";
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// if (r3.equals("ProcedureRequest"))
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return "ServiceRequestPR";
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return "ServiceRequestPR";
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}
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private void updateOutcomes(String tn, String id, Exception executionError, List<ValidationMessage> r4validationErrors, String roundTripError) throws IOException {
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private void updateOutcomes(String tn, String id, Exception executionError,
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List<ValidationMessage> r4validationErrors, String roundTripError) throws IOException {
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JsonObject r = r3r4Outcomes.getAsJsonObject(tn);
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if (r == null) {
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r = new JsonObject();
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@ -238,7 +247,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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i.addProperty("execution", true);
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else
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i.addProperty("execution", executionError.getMessage());
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// round-trip check
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// round-trip check
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if (i.has("round-trip"))
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i.remove("round-trip");
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if (roundTripError != null)
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@ -251,11 +260,12 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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JsonArray arr = new JsonArray();
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i.add("r4.errors", arr);
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for (ValidationMessage e : r4validationErrors)
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arr.add(new JsonPrimitive(e.summary()));
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arr.add(new JsonPrimitive(e.summary()));
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}
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Gson gson = new GsonBuilder().setPrettyPrinting().create();
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String json = gson.toJson(r3r4Outcomes);
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TextFile.stringToFile(json, (Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
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TextFile.stringToFile(json,
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(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
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}
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@ -266,7 +276,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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break;
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if (vm.getMessage().contains("Error null validating Coding"))
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break;
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String s = rules.getStringProperty(tn+"/"+id, "validation");
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String s = rules.getStringProperty(tn + "/" + id, "validation");
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if (!Utilities.noString(s)) {
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boolean ok = false;
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for (String m : s.split("\\;"))
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@ -285,7 +295,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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break;
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}
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if (vm.getLevel() == IssueSeverity.ERROR || vm.getLevel() == IssueSeverity.FATAL) {
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b.append("[R4 validation error] "+vm.getLocation()+": "+vm.getMessage()+"\r\n");
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b.append("[R4 validation error] " + vm.getLocation() + ": " + vm.getMessage() + "\r\n");
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}
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}
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if (b.length() > 0)
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@ -293,32 +303,31 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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}
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/*
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* Supporting multiple versions at once is a little tricky. We're going to have 2 contexts:
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* - an R3 context which is used to read/write R3 instances
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* - an R4 context which is used to perform the transforms
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* Supporting multiple versions at once is a little tricky. We're going to have
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* 2 contexts: - an R3 context which is used to read/write R3 instances - an R4
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* context which is used to perform the transforms
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*
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* R3 structure definitions are cloned into R3 context with a modified URL (as
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* 3.0/)
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*
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* R3 structure definitions are cloned into R3 context with a modified URL (as 3.0/)
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*
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*/
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private void checkLoad() throws IOException, FHIRException {
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private void checkLoad() throws IOException, FHIRException, Exception {
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if (contextR3 != null)
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return;
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pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
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R3ToR4Loader ldr = new R3ToR4Loader().setPatchUrls(true).setKillPrimitives(true);
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System.out.println("loading R3");
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contextR3 = new SimpleWorkerContext();
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contextR3.setAllowLoadingDuplicates(true);
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contextR3.setOverrideVersionNs("http://hl7.org/fhir/3.0/StructureDefinition");
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contextR3.loadFromFile(Utilities.path(TestingUtilities.home(),"source","release3","profiles-types.xml"), ldr);
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contextR3.loadFromFile(Utilities.path(TestingUtilities.home(),"source","release3","profiles-resources.xml"), ldr);
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contextR3.loadFromFile(Utilities.path(TestingUtilities.home(),"source","release3","expansions.xml"), ldr);
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contextR3.loadFromPackage(pcm.loadPackage("hl7.fhir.core", "3.0.1"), ldr, new String[] {});
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System.out.println("loading R4");
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contextR4 = new SimpleWorkerContext();
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contextR4.setAllowLoadingDuplicates(true);
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contextR4.loadFromFile(Utilities.path(TestingUtilities.content(),"profiles-types.xml"), null);
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contextR4.loadFromFile(Utilities.path(TestingUtilities.content(),"profiles-resources.xml"), null);
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contextR4.loadFromFile(Utilities.path(TestingUtilities.content(),"extension-definitions.xml"), null);
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contextR4.loadFromFile(Utilities.path(TestingUtilities.content(),"valuesets.xml"), null);
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contextR4 = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
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contextR4.setCanRunWithoutTerminology(true);
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for (StructureDefinition sd : contextR3.allStructures()) {
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@ -332,7 +341,8 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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contextR3.cacheResource(sd);
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StructureDefinition sdn = sd.copy();
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sdn.setUrl(sdn.getUrl().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/3.0/"));
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sdn.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").setValue(new UriType("http://hl7.org/fhir"));
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sdn.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace")
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.setValue(new UriType("http://hl7.org/fhir"));
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contextR3.cacheResource(sdn);
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contextR4.cacheResource(sdn);
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}
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@ -342,11 +352,15 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
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contextR4.setExpansionProfile(new org.hl7.fhir.r4.model.Parameters());
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contextR3.setName("R3");
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contextR4.setName("R4");
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contextR4.setValidatorFactory(new InstanceValidatorFactory());
|
||||
// TODO: this has to be R% now... contextR4.setValidatorFactory(new InstanceValidatorFactory());
|
||||
|
||||
System.out.println("loading Maps");
|
||||
loadLib(Utilities.path(TestingUtilities.home(),"implementations","r3maps", "R3toR4"));
|
||||
loadLib(Utilities.path(TestingUtilities.home(),"implementations","r3maps", "R4toR3"));
|
||||
|
||||
loadLib(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R4toR3"));
|
||||
loadLib(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R3toR4"));
|
||||
|
||||
System.out.println("loaded");
|
||||
}
|
||||
|
||||
@ -361,30 +375,31 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
|
||||
for (Resource r : sm.getContained()) {
|
||||
if (r instanceof MetadataResource) {
|
||||
MetadataResource mr = (MetadataResource) r.copy();
|
||||
mr.setUrl(sm.getUrl()+"#"+r.getId());
|
||||
mr.setUrl(sm.getUrl() + "#" + r.getId());
|
||||
contextR3.cacheResource(mr);
|
||||
contextR4.cacheResource(mr);
|
||||
}
|
||||
}
|
||||
} catch (FHIRException e) {
|
||||
System.out.println("Unable to load "+Utilities.path(dir, s)+": "+e.getMessage());
|
||||
System.out.println("Unable to load " + Utilities.path(dir, s) + ": " + e.getMessage());
|
||||
loadErrors.put(s, e);
|
||||
// e.printStackTrace();
|
||||
// e.printStackTrace();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void log(String message) {
|
||||
System.out.println(message);
|
||||
System.out.println(message);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
|
||||
if (res instanceof Resource && (res.fhirType().equals("CodeSystem") || res.fhirType().equals("CareTeam")) || res.fhirType().equals("PractitionerRole")) {
|
||||
if (res instanceof Resource && (res.fhirType().equals("CodeSystem") || res.fhirType().equals("CareTeam")
|
||||
|| res.fhirType().equals("PractitionerRole"))) {
|
||||
Resource r = (Resource) res;
|
||||
extras.add(r);
|
||||
r.setId(workingid+"-"+extras.size());
|
||||
r.setId(workingid + "-" + extras.size());
|
||||
}
|
||||
return res;
|
||||
}
|
||||
@ -398,9 +413,10 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
|
||||
public Base createType(Object appInfo, String name) throws FHIRException {
|
||||
BaseWorkerContext context = (BaseWorkerContext) appInfo;
|
||||
if (context == contextR3) {
|
||||
StructureDefinition sd = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/3.0/StructureDefinition/"+name);
|
||||
StructureDefinition sd = context.fetchResource(StructureDefinition.class,
|
||||
"http://hl7.org/fhir/3.0/StructureDefinition/" + name);
|
||||
if (sd == null)
|
||||
throw new FHIRException("Type not found: '"+name+"'");
|
||||
throw new FHIRException("Type not found: '" + name + "'");
|
||||
return Manager.build(context, sd);
|
||||
} else
|
||||
return ResourceFactory.createResourceOrType(name);
|
||||
@ -414,7 +430,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
|
||||
if (url.equals(mr.getUrl()))
|
||||
return mr;
|
||||
}
|
||||
if (url.equals(r.fhirType()+"/"+r.getId()))
|
||||
if (url.equals(r.fhirType() + "/" + r.getId()))
|
||||
return r;
|
||||
}
|
||||
|
||||
@ -429,7 +445,8 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
|
||||
String[] vals = parts[1].split("\\=");
|
||||
if (vals.length == 2 && vals[0].equals("practitioner"))
|
||||
for (Resource r : extras) {
|
||||
if (r instanceof PractitionerRole && ((PractitionerRole) r).getPractitioner().getReference().equals("Practitioner/"+vals[1])) {
|
||||
if (r instanceof PractitionerRole
|
||||
&& ((PractitionerRole) r).getPractitioner().getReference().equals("Practitioner/" + vals[1])) {
|
||||
results.add(r);
|
||||
}
|
||||
}
|
||||
@ -438,7 +455,8 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
|
||||
}
|
||||
|
||||
@Override
|
||||
public Element fetch(Object appContext, String url) throws FHIRFormatError, DefinitionException, IOException, FHIRException {
|
||||
public Element fetch(Object appContext, String url)
|
||||
throws FHIRFormatError, DefinitionException, IOException, FHIRException {
|
||||
return null;
|
||||
}
|
||||
|
||||
@ -451,6 +469,4 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
|
||||
public boolean resolveURL(Object appContext, String path, String url) throws IOException, FHIRException {
|
||||
return true;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user