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DO-20250204-1 #1896

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Feb 6, 2025
Merged

DO-20250204-1 #1896

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dotasek Feb 4, 2025
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Merge branch 'master' into do-20250204-1
dotasek Feb 6, 2025
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dotasek Feb 6, 2025
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2 changes: 1 addition & 1 deletion org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/SpecDifferenceEvaluator.java
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Expand Up @@ -123,7 +123,7 @@ public class SpecDifferenceEvaluator {
// b.append(self.getDiffAsHtml(null));
// b.append("</body>\r\n");
// b.append("</html>\r\n");
// TextFile.stringToFile(b.toString(), Utilities.path("[tmp]", "diff.html"));
// FileUtilities.stringToFile(b.toString(), Utilities.path("[tmp]", "diff.html"));
// System.out.println("done");
// }
//
Expand Down
4 changes: 2 additions & 2 deletions org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/Convert.java
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Expand Up @@ -67,7 +67,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
import org.hl7.fhir.dstu3.model.Timing.UnitsOfTime;
import org.hl7.fhir.dstu3.model.Type;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.OIDUtils;
import org.hl7.fhir.utilities.OIDUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
Expand Down Expand Up @@ -139,7 +139,7 @@ else if (UriForOid(r) != null)
}

private String UriForOid(String r) {
String uri = OIDUtils.getUriForOid(r);
String uri = OIDUtilities.getUriForOid(r);
if (uri != null)
return uri;
else {
Expand Down
2 changes: 1 addition & 1 deletion ...l7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExamplesPackageBuilder.java
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Expand Up @@ -35,7 +35,7 @@ private void process(String source) throws FHIRFormatError, FileNotFoundExceptio
content = r5ToR4B(content);
FileUtilities.bytesToFile(content, f);
}
// TextFile.bytesToFile(content, Utilities.path(dest2, type+"-"+id+".json"));
// FileUtilities.bytesToFile(content, Utilities.path(dest2, type+"-"+id+".json"));
// if (!set.contains(type+"/"+id)) {
// set.add(type+"/"+id);
// pck.addFile(Category.RESOURCE, type+"-"+id+".json", content);
Expand Down
2 changes: 1 addition & 1 deletion org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/PhinVadsImporter.java
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Expand Up @@ -28,7 +28,7 @@ public PhinVadsImporter() throws FHIRException, IOException {
}

public static void main(String[] args) throws FHIRException, IOException, ParseException {
// new PhinVadsImporter().importValueSet(TextFile.fileToBytes("C:\\work\\org.hl7.fhir\\packages\\us.cdc.phinvads-source\\source\\PHVS_BirthDefectsLateralityatDiagnosis_HL7_V1.txt"));
// new PhinVadsImporter().importValueSet(FileUtilities.fileToBytes("C:\\work\\org.hl7.fhir\\packages\\us.cdc.phinvads-source\\source\\PHVS_BirthDefectsLateralityatDiagnosis_HL7_V1.txt"));
PhinVadsImporter self = new PhinVadsImporter();
self.process(args[0], args[1]);
}
Expand Down
6 changes: 2 additions & 4 deletions org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/SPDXImporter.java
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@@ -1,8 +1,5 @@
package org.hl7.fhir.convertors.misc;

import java.io.FileInputStream;
import java.io.FileOutputStream;

import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
Expand All @@ -12,6 +9,7 @@
import org.hl7.fhir.r4.terminologies.CodeSystemUtilities;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.FileUtilities;
import org.hl7.fhir.utilities.OIDUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonObject;
Expand Down Expand Up @@ -79,7 +77,7 @@ private boolean allPlusMinus(String cc) {
protected String makeConst(String cc) {
if (cc.equals("*"))
cc = "ASTERISK";
if (Utilities.isOid(cc) && Utilities.charCount(cc, '.') > 2)
if (OIDUtilities.isValidOID(cc) && Utilities.charCount(cc, '.') > 2)
cc = "OID_"+cc;
if (cc.equals("%"))
cc = "pct";
Expand Down
2 changes: 1 addition & 1 deletion ...tors/src/main/java/org/hl7/fhir/convertors/misc/searchparam/SearchParameterProcessor.java
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Expand Up @@ -73,7 +73,7 @@ public class SearchParameterProcessor {
// }
// b.append(s+"\r\n");
// }
// TextFile.stringToFile(b.toString(), name);
// FileUtilities.stringToFile(b.toString(), name);
// }
//
public static void main(String[] args) throws IOException, FHIRException {
Expand Down
6 changes: 3 additions & 3 deletions org.hl7.fhir.core.generator/configuration/tests/RoundTripTests.java
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Expand Up @@ -16,7 +16,7 @@
import org.hl7.fhir.{{jid}}.model.DomainResource;
import org.hl7.fhir.{{jid}}.model.Resource;
import org.hl7.fhir.{{jid}}.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.FileUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
Expand Down Expand Up @@ -52,7 +52,7 @@ public RoundTripTests(String name, String unused) {

@Test
public void test() throws FileNotFoundException, IOException {
byte[] src = TextFile.fileToBytes(Utilities.path(EXAMPLES_DIR, name));
byte[] src = FileUtilities.fileToBytes(Utilities.path(EXAMPLES_DIR, name));
Resource r = new XmlParser().parse(src);
assertNotNull(r);
byte[] cnt = new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(r);
Expand Down Expand Up @@ -81,7 +81,7 @@ private void save(byte[] src, String path) throws IOException {
if (f.exists()) {
f.delete();
}
TextFile.bytesToFile(src, f);
FileUtilities.bytesToFile(src, f);


}
Expand Down
6 changes: 3 additions & 3 deletions org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/Configuration.java
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Expand Up @@ -9,7 +9,7 @@
import java.util.Map;

import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.FileUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;

Expand All @@ -22,11 +22,11 @@ public static final SimpleDateFormat DATE_FORMAT() {
private Map<String, String> adornments = new HashMap<>();

public Configuration(String path) throws FileNotFoundException, IOException {
license = TextFile.fileToString(Utilities.path(path, "license.txt"));
license = FileUtilities.fileToString(Utilities.path(path, "license.txt"));
ini = new IniFile(Utilities.path(path, "configuration.ini"));
for (File jfn : ManagedFileAccess.file(path).listFiles()) {
if (jfn.getName().endsWith(".java")) {
adornments.put(Utilities.changeFileExt(jfn.getName(), ""), TextFile.fileToString(jfn));
adornments.put(Utilities.changeFileExt(jfn.getName(), ""), FileUtilities.fileToString(jfn));
}
}
}
Expand Down
6 changes: 2 additions & 4 deletions org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/BaseWorkerContext.java
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Expand Up @@ -31,14 +31,12 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS

import java.io.FileNotFoundException;
import java.io.IOException;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.ResourceBundle;
import java.util.Set;

Expand Down Expand Up @@ -68,7 +66,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
import org.hl7.fhir.dstu2.terminologies.ValueSetExpansionCache;
import org.hl7.fhir.dstu2.utils.client.FHIRToolingClient;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.UUIDUtilities;
import org.hl7.fhir.utilities.i18n.I18nBase;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;

Expand Down Expand Up @@ -318,7 +316,7 @@ else if (codeSystems.containsKey(system) || vs.hasExpansion())
@Override
public ValidationResult validateCode(String system, String code, String display, ConceptSetComponent vsi) {
try {
ValueSet vs = new ValueSet().setUrl(Utilities.makeUuidUrn());
ValueSet vs = new ValueSet().setUrl(UUIDUtilities.makeUuidUrn());
vs.getCompose().addInclude(vsi);
return verifyCodeExternal(vs, new Coding().setSystem(system).setCode(code).setDisplay(display), true);
} catch (Exception e) {
Expand Down
30 changes: 14 additions & 16 deletions org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/ProfileUtilitiesTests.java
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@@ -1,8 +1,6 @@
package org.hl7.fhir.dstu2.test;

import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
Expand All @@ -24,8 +22,8 @@
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.UUIDUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFile;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
Expand Down Expand Up @@ -162,7 +160,7 @@ private void testSimple() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test");
Expand Down Expand Up @@ -200,7 +198,7 @@ private void testSimple2() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test");
Expand Down Expand Up @@ -236,7 +234,7 @@ private void testCardinalityChange() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Patient.identifier");
Expand Down Expand Up @@ -280,7 +278,7 @@ private void testDocumentationAppend() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Patient.identifier");
Expand Down Expand Up @@ -326,7 +324,7 @@ private void textTypeNarrowing1() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Patient.deceased[x]");
Expand Down Expand Up @@ -373,7 +371,7 @@ private void textTypeNarrowing2() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Patient.deceasedDateTime");
Expand Down Expand Up @@ -420,7 +418,7 @@ private void testMapping() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Patient.identifier");
Expand Down Expand Up @@ -466,7 +464,7 @@ private void testTypeWalk() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Patient.identifier");
Expand Down Expand Up @@ -517,7 +515,7 @@ private void testTypeWalk2() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Patient.identifier.system");
Expand Down Expand Up @@ -561,7 +559,7 @@ private void testSlicingSimple() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());

// set the slice up
Expand Down Expand Up @@ -650,7 +648,7 @@ private void testSlicingExtension(boolean implicit) throws EOperationOutcome, Ex
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());

// set the slice up
Expand Down Expand Up @@ -740,7 +738,7 @@ private void testSlicingExtensionComplex(boolean implicit) throws EOperationOutc
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());

// set the slice up
Expand Down Expand Up @@ -868,7 +866,7 @@ private void testSlicingTask8742() throws EOperationOutcome, Exception {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = context
.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Organization").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setUrl(UUIDUtilities.makeUuidUrn());
focus.setBase(base.getUrl());

ElementDefinition id = focus.getDifferential().addElement();
Expand Down
4 changes: 2 additions & 2 deletions org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/metamodel/Tester.java
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Expand Up @@ -60,8 +60,8 @@ public static void main(String[] args) throws Exception {
System.out.print("convert " + f);
// Manager.convert(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML,
// ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")), FhirFormat.JSON, OutputStyle.PRETTY);
// String src = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")));
// String tgt = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".json")));
// String src = normalise(FileUtilities.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")));
// String tgt = normalise(FileUtilities.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".json")));
Element e = Manager.parse(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\" + f),
FhirFormat.XML);
Manager.compose(context, e,
Expand Down
6 changes: 2 additions & 4 deletions org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/BaseWorkerContext.java
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Expand Up @@ -31,14 +31,12 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS

import java.io.FileNotFoundException;
import java.io.IOException;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.ResourceBundle;
import java.util.Set;

Expand Down Expand Up @@ -68,7 +66,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpansionCache;
import org.hl7.fhir.dstu2016may.utils.client.FHIRToolingClient;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.UUIDUtilities;
import org.hl7.fhir.utilities.i18n.I18nBase;

public abstract class BaseWorkerContext extends I18nBase implements IWorkerContext {
Expand Down Expand Up @@ -339,7 +337,7 @@ public ValidationResult validateCode(String system, String code, String display,
@Override
public ValidationResult validateCode(String system, String code, String display, ConceptSetComponent vsi) {
try {
ValueSet vs = new ValueSet().setUrl(Utilities.makeUuidUrn());
ValueSet vs = new ValueSet().setUrl(UUIDUtilities.makeUuidUrn());
vs.getCompose().addInclude(vsi);
return verifyCodeExternal(vs, new Coding().setSystem(system).setCode(code).setDisplay(display), true);
} catch (Exception e) {
Expand Down
6 changes: 2 additions & 4 deletions ...l7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/SimpleWorkerContext.java
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Expand Up @@ -30,8 +30,6 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
*/

import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
Expand Down Expand Up @@ -71,7 +69,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.OIDUtils;
import org.hl7.fhir.utilities.OIDUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
Expand Down Expand Up @@ -396,7 +394,7 @@ public List<StructureDefinition> allStructures() {

@Override
public String oid2Uri(String oid) {
String uri = OIDUtils.getUriForOid(oid);
String uri = OIDUtilities.getUriForOid(oid);
if (uri != null)
return uri;
for (NamingSystem ns : systems) {
Expand Down
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