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org.hl7.fhir.core
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Merge remote-tracking branch 'origin/master'

This commit is contained in:
Grahame Grieve 2023-10-05 15:22:10 +03:00
parent 0927f0bbfa 9ec1c68cfc
commit c52d5a71b4
26 changed files with 222 additions and 145 deletions
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6
RELEASE_NOTES.md
View File

@ -1,9 +1,7 @@
## Validator Changes
* Fix FHIRPath type resolution for logical models
* Update parsers to record the element format for logical model validation
* fix profile matching for CDA logical models
* no changes
## Other code changes
* Upgrade PackageVisitor for XIG
* no changes

2
org.hl7.fhir.convertors/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

56
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/CmdLineApp.java
View File

@ -10,22 +10,33 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
<<<<<<< HEAD
import org.hl7.fhir.r4.formats.XmlParser;
=======
>>>>>>> master
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.CapabilityStatement;
<<<<<<< HEAD
import org.hl7.fhir.r4.model.CodeSystem;
=======
>>>>>>> master
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Condition;
<<<<<<< HEAD
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
=======
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Immunization;
>>>>>>> master
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Period;
import org.hl7.fhir.r4.model.Procedure;
@ -68,8 +79,11 @@ public class CmdLineApp {
finished = true;
} else if (p.length == 1 && p[0].equals("?")) {
genMenu();
<<<<<<< HEAD
} else if (p.length == 1 && p[0].equals("?tx")) {
genMenuTx();
=======
>>>>>>> master
} else if (p.length >= 1 && p[0].equals("c")) {
if (p.length == 1) {
connectToServer("http://hapi.fhir.org/baseR4");
@ -115,10 +129,15 @@ public class CmdLineApp {
select("Patient", p[1]);
} else if (p.length == 3 && p[0].equals("e")) {
edit(p[1], p[2]);
<<<<<<< HEAD
} else if (p.length > 3 && p[0].equals("tx")) {
tx(p);
} else {
tx(p);
=======
} else {
System.out.println("Command unknown or not understood: "+cmd);
>>>>>>> master
}
} catch (Exception e) {
System.out.println("Error executing command "+p[0]+": "+e.getMessage());
@ -128,6 +147,7 @@ public class CmdLineApp {
System.out.println("Finished!");
}
<<<<<<< HEAD
private boolean tx(String[] p) throws IOException {
if (p[1].equals("l")) {
if (p.length == 4) {
@ -170,6 +190,9 @@ public class CmdLineApp {
}
private void getImmunizations() throws IOException {
=======
private void getImmunizations() {
>>>>>>> master
Bundle bnd = client.search("Immunization", "?patient="+currentId);
System.out.println(""+bnd.getTotal()+" Immunizations found. Printing "+bnd.getEntry().size());
@ -180,7 +203,11 @@ public class CmdLineApp {
}
}
<<<<<<< HEAD
private void getProcedures() throws IOException {
=======
private void getProcedures() {
>>>>>>> master
Bundle bnd = client.search("Procedure", "?patient="+currentId);
System.out.println(""+bnd.getTotal()+" Procedures found. Printing "+bnd.getEntry().size());
@ -191,7 +218,11 @@ public class CmdLineApp {
}
}
<<<<<<< HEAD
private void getConditions() throws IOException {
=======
private void getConditions() {
>>>>>>> master
Bundle bnd = client.search("Condition", "?patient="+currentId);
System.out.println(""+bnd.getTotal()+" Conditions found. Printing "+bnd.getEntry().size());
@ -226,7 +257,10 @@ public class CmdLineApp {
case "boolean" : return new BooleanType(value);
case "code" : return new CodeType(value);
case "string" : return new StringType(value);
<<<<<<< HEAD
case "date" : return new DateType(value);
=======
>>>>>>> master
}
throw new FHIRException("Unhandled type "+p.getTypeCode());
}
@ -244,7 +278,11 @@ public class CmdLineApp {
System.out.println(new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(currentResource));
}
<<<<<<< HEAD
private void select(String type, String id) throws IOException {
=======
private void select(String type, String id) {
>>>>>>> master
if (type.equals("Patient")) {
currentResource = client.fetchResource(Patient.class, id);
} else if (type.equals("Immunization")) {
@ -260,8 +298,12 @@ public class CmdLineApp {
System.out.println("Resource = "+currentId+" "+summary(currentResource));
}
<<<<<<< HEAD
private String summary(Resource r) throws IOException {
// return new XmlParser().composeString(r);
=======
private String summary(Resource r) {
>>>>>>> master
if (r instanceof Patient) {
Patient pat = (Patient) r;
return pat.getIdBase()+" "+pat.getGender()+" "+pat.getBirthDateElement().asStringValue()+" "+name(pat);
@ -324,7 +366,11 @@ public class CmdLineApp {
return "";
}
<<<<<<< HEAD
private void search(String[] p) throws IOException {
=======
private void search(String[] p) {
>>>>>>> master
if (client == null) {
throw new FHIRException("Not connected to to a server");
}
@ -332,7 +378,11 @@ public class CmdLineApp {
if (p.length > 2) {
search = search +"&gender="+p[2];
if (p.length > 3) {
<<<<<<< HEAD
search = search +"&birthdate="+p[3];
=======
search = search +"&dob="+p[3];
>>>>>>> master
}
}
Bundle bnd = client.search("Patient", search);
@ -368,6 +418,7 @@ public class CmdLineApp {
private void connectToServer(String url) throws URISyntaxException {
client = new FHIRToolingClient(url, "FHIR-Command-Line-App");
CapabilityStatement cs = client.getCapabilitiesStatementQuick();
<<<<<<< HEAD
System.out.println("Connected to "+url+": "+cs.getSoftware().getName()+", version "+cs.getFhirVersion().toCode());
}
@ -380,6 +431,11 @@ public class CmdLineApp {
System.out.println(" x - exit");
}
=======
System.out.println("Connected to "+url+": "+cs.getSoftware().getName()+".");
}
>>>>>>> master
private void genMenu() {
System.out.println("Simple Client. Commands you can run:");
System.out.println(" c {url} - connect to a server");

2
org.hl7.fhir.r4b/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/FmlParser.java
View File

@ -50,9 +50,9 @@ public class FmlParser extends ParserBase {
ByteArrayInputStream stream = new ByteArrayInputStream(content);
String text = TextFile.streamToString(stream);
List<ValidatedFragment> result = new ArrayList<>();
ValidatedFragment ctxt = new ValidatedFragment("focus", "fml", content);
ctxt.setElement(parse(ctxt.getErrors(), text));
result.add(ctxt);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "fml", content, false);
focusFragment.setElement(parse(focusFragment.getErrors(), text));
result.add(focusFragment);
return result;
}

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
View File

@ -123,7 +123,7 @@ public class JsonParser extends ParserBase {
public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
// long start = System.currentTimeMillis();
byte[] content = TextFile.streamToBytes(inStream);
ValidatedFragment ctxt = new ValidatedFragment("focus", "json", content);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "json", content, false);
ByteArrayInputStream stream = new ByteArrayInputStream(content);
@ -135,17 +135,17 @@ public class JsonParser extends ParserBase {
try {
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true);
} catch (Exception e) {
logError(ctxt.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1,context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1,context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
}
} else {
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true);
}
if (obj != null) {
ctxt.setElement(parse(ctxt.getErrors(), obj));
focusFragment.setElement(parse(focusFragment.getErrors(), obj));
}
List<ValidatedFragment> res = new ArrayList<>();
res.add(ctxt);
res.add(focusFragment);
// long t =System.currentTimeMillis()-start;
// System.out.println("json parser: "+(t)+"ms, "+(content.length/1024)+"kb "+(t == 0 ? "" : " @ "+(content.length / t)+"kb/s"));

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/SHCParser.java
View File

@ -83,7 +83,7 @@ public class SHCParser extends ParserBase {
byte[] content = TextFile.streamToBytes(inStream);
ByteArrayInputStream stream = new ByteArrayInputStream(content);
List<ValidatedFragment> res = new ArrayList<>();
ValidatedFragment shc = new ValidatedFragment("shc", "txt", content);
ValidatedFragment shc = new ValidatedFragment("shc", "txt", content, false);
res.add(shc);
String src = TextFile.streamToString(stream).trim();
@ -121,7 +121,7 @@ public class SHCParser extends ParserBase {
return res;
}
ValidatedFragment bnd = new ValidatedFragment("payload", "json", jwt.payloadSrc);
ValidatedFragment bnd = new ValidatedFragment("payload", "json", jwt.payloadSrc, true);
res.add(bnd);
checkNamedProperties(shc.getErrors(), jwt.getPayload(), prefix+"payload", "iss", "nbf", "vc");
checkProperty(shc.getErrors(), jwt.getPayload(), prefix+"payload", "iss", true, "String");

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/SHLParser.java
View File

@ -280,7 +280,7 @@ public class SHLParser extends ParserBase {
}
private ValidatedFragment addNamedElement(List<ValidatedFragment> res, String name, String type, byte[] content) {
ValidatedFragment result = new ValidatedFragment(name, type, content);
ValidatedFragment result = new ValidatedFragment(name, type, content, true);
res.add(result);
return result;
}

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/TurtleParser.java
View File

@ -83,7 +83,7 @@ public class TurtleParser extends ParserBase {
@Override
public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
byte[] content = TextFile.streamToBytes(inStream);
ValidatedFragment ctxt = new ValidatedFragment("focus", "ttl", content);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "ttl", content, false);
ByteArrayInputStream stream = new ByteArrayInputStream(content);
Turtle src = new Turtle();
@ -91,16 +91,16 @@ public class TurtleParser extends ParserBase {
try {
src.parse(TextFile.streamToString(stream));
} catch (Exception e) {
logError(ctxt.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1, "(document)", IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_TURTLE_, e.getMessage()), IssueSeverity.FATAL);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1, "(document)", IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_TURTLE_, e.getMessage()), IssueSeverity.FATAL);
return null;
}
ctxt.setElement(parse(ctxt.getErrors(), src));
focusFragment.setElement(parse(focusFragment.getErrors(), src));
} else {
src.parse(TextFile.streamToString(stream));
ctxt.setElement(parse(ctxt.getErrors(), src));
focusFragment.setElement(parse(focusFragment.getErrors(), src));
}
List<ValidatedFragment> res = new ArrayList<>();
res.add(ctxt);
res.add(focusFragment);
return res;
}

54
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ValidatedFragment.java
View File

@ -3,63 +3,55 @@ package org.hl7.fhir.r5.elementmodel;
import java.util.ArrayList;
import java.util.List;
import lombok.Getter;
import lombok.Setter;
import org.hl7.fhir.utilities.validation.ValidationMessage;
public class ValidatedFragment {
@Getter
private String name;
@Getter @Setter
private String elementPath;
@Getter
private String extension;
@Getter @Setter
private Element element;
@Getter @Setter
private byte[] content;
@Getter
private final boolean isDerivedContent;
public final static String FOCUS_NAME = "focus";
@Getter
private List<ValidationMessage> errors = new ArrayList<>();
public ValidatedFragment(String name, String extension, Element element, byte[] content) {
public ValidatedFragment(String name, String extension, Element element, byte[] content, boolean isDerivedContent) {
super();
this.name = name;
this.element = element;
this.content = content;
this.extension = extension;
this.isDerivedContent = isDerivedContent;
}
public ValidatedFragment(String name, String extension, byte[] content) {
public ValidatedFragment(String name, String extension, byte[] content, boolean isDerivedContent) {
super();
this.name = name;
this.content = content;
this.extension = extension;
this.isDerivedContent = isDerivedContent;
}
public String getName() {
return name;
}
public Element getElement() {
return element;
}
public byte[] getContent() {
return content;
}
public List<ValidationMessage> getErrors() {
return errors;
}
public void setElement(Element element) {
this.element = element;
}
public String getFilename() {
return name+"."+extension;
}
public String getElementPath() {
return elementPath;
}
public void setElementPath(String elementPath) {
this.elementPath = elementPath;
}
public String path() {
return elementPath == null ? name : elementPath;
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/VerticalBarParser.java
View File

@ -465,7 +465,7 @@ public class VerticalBarParser extends ParserBase {
while (!reader.isFinished()) // && (getOptions().getSegmentLimit() == 0 || getOptions().getSegmentLimit() > message.getSegments().size()))
readSegment(message, reader);
List<ValidatedFragment> res = new ArrayList<>();
res.add(new ValidatedFragment("focus", "hl7", message, content));
res.add(new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "hl7", message, content, false));
return res;
}

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
View File

@ -118,7 +118,7 @@ public class XmlParser extends ParserBase {
public List<ValidatedFragment> parse(InputStream inStream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
byte[] content = TextFile.streamToBytes(inStream);
ValidatedFragment context = new ValidatedFragment("focus", "xml", content);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "xml", content, false);
ByteArrayInputStream stream = new ByteArrayInputStream(content);
Document doc = null;
@ -138,7 +138,7 @@ public class XmlParser extends ParserBase {
// if we can, we'll inspect the header/encoding ourselves
stream.mark(1024);
version = checkHeader(context.getErrors(), stream);
version = checkHeader(focusFragment.getErrors(), stream);
stream.reset();
// use a slower parser that keeps location data
@ -172,17 +172,17 @@ public class XmlParser extends ParserBase {
if (e.getMessage().contains("lineNumber:") && e.getMessage().contains("columnNumber:")) {
int line = Utilities.parseInt(extractVal(e.getMessage(), "lineNumber"), 0);
int col = Utilities.parseInt(extractVal(e.getMessage(), "columnNumber"), 0);
logError(context.getErrors(), ValidationMessage.NO_RULE_DATE, line, col, "(xml)", IssueType.INVALID, e.getMessage().substring(e.getMessage().lastIndexOf(";")+1).trim(), IssueSeverity.FATAL);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, line, col, "(xml)", IssueType.INVALID, e.getMessage().substring(e.getMessage().lastIndexOf(";")+1).trim(), IssueSeverity.FATAL);
} else {
logError(context.getErrors(), ValidationMessage.NO_RULE_DATE, 0, 0, "(xml)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, 0, 0, "(xml)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
}
doc = null;
}
if (doc != null) {
context.setElement(parse(context.getErrors(), doc));
focusFragment.setElement(parse(focusFragment.getErrors(), doc));
}
List<ValidatedFragment> res = new ArrayList<>();
res.add(context);
res.add(focusFragment);
return res;
}

6
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/sql/SQLOnFhirTestCases.java → org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/sql/SQLOnFhirTests.java
View File

@ -14,10 +14,8 @@ import javax.xml.parsers.ParserConfigurationException;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Factory;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ResourceFactory;
import org.hl7.fhir.r5.sql.SQLOnFhirTestCases.RowSorter;
import org.hl7.fhir.r5.test.utils.CompareUtilities;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.sql.Provider;
@ -28,12 +26,13 @@ import org.hl7.fhir.utilities.json.model.JsonElement;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.xml.sax.SAXException;
public class SQLOnFhirTestCases {
public class SQLOnFhirTests {
public class TestProvider implements Provider {
@ -110,6 +109,7 @@ public class SQLOnFhirTestCases {
@SuppressWarnings("deprecation")
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
@Disabled
public void test(String name, TestDetails test) throws FileNotFoundException, IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException, UcumException {
this.details = test;
Runner runner = new Runner();

2
org.hl7.fhir.report/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -249,7 +249,7 @@ Validation_VAL_Profile_MultipleMatches_other = Found multiple matching profiles
Validation_VAL_Profile_NoDefinition = No definition found for resource type ''{0}''
Validation_VAL_Profile_NoMatch = Unable to find a match for the specified profile among choices: {0}
Validation_VAL_Profile_NoSnapshot = StructureDefinition {0} has no snapshot - validation is against the snapshot, so it must be provided
Validation_VAL_Profile_NoType = The type of element {0} is not known - it couild not be determined from the information available. Valid types at this point are {1}
Validation_VAL_Profile_NoType = The type of element {0} is not known - it could not be determined from the information available. Valid types at this point are {1}
Validation_VAL_Profile_NotAllowed = This element is not allowed by the profile {0}
Validation_VAL_Profile_NotSlice = This element does not match any known slice {0} and slicing is CLOSED: {1}
Validation_VAL_Profile_OutOfOrder = As specified by profile {0}, Element ''{1}'' is out of order (found after {2})

2
org.hl7.fhir.validation.cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

13
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -32,12 +32,8 @@ import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContextManager;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.context.SystemOutLoggingService;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.*;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.elementmodel.ObjectConverter;
import org.hl7.fhir.r5.elementmodel.ParserBase;
import org.hl7.fhir.r5.elementmodel.SHCParser;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
@ -635,6 +631,13 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
return results.getEntryFirstRep().getResource();
}
public List<ValidatedFragment> validateAsFragments(byte[] source, FhirFormat cntType, List<String> profiles, List<ValidationMessage> messages) throws FHIRException, IOException, EOperationOutcome {
InstanceValidator validator = getValidator(cntType);
validator.validate(null, messages, new ByteArrayInputStream(source), cntType, asSdList(profiles));
return validator.validatedContent;
}
public OperationOutcome validate(byte[] source, FhirFormat cntType, List<String> profiles, List<ValidationMessage> messages) throws FHIRException, IOException, EOperationOutcome {
InstanceValidator validator = getValidator(cntType);

46
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
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@ -29,6 +29,7 @@ import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.LanguageUtils;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.elementmodel.ValidatedFragment;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Bundle;
@ -61,10 +62,7 @@ import org.hl7.fhir.utilities.i18n.XLIFFProducer;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.IgLoader;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.ValidationRecord;
import org.hl7.fhir.validation.ValidatorUtils;
import org.hl7.fhir.validation.*;
import org.hl7.fhir.validation.ValidatorUtils.SourceFile;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.model.FileInfo;
@ -114,13 +112,43 @@ public class ValidationService {
ValidationResponse response = new ValidationResponse().setSessionId(sessionId);
for (FileInfo fp : request.getFilesToValidate()) {
for (FileInfo fileToValidate : request.getFilesToValidate()) {
if (fileToValidate.getFileType() == null) {
Manager.FhirFormat format = ResourceChecker.checkIsResource(validator.getContext(),
false,
fileToValidate.getFileContent().getBytes(),
fileToValidate.getFileName(),
false);
fileToValidate.setFileType(format.getExtension());
}
List<ValidationMessage> messages = new ArrayList<>();
validator.validate(fp.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fp.getFileType()),
List<ValidatedFragment> validatedFragments = validator.validateAsFragments(fileToValidate.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fileToValidate.getFileType()),
request.getCliContext().getProfiles(), messages);
ValidationOutcome outcome = new ValidationOutcome().setFileInfo(fp);
messages.forEach(outcome::addMessage);
response.addOutcome(outcome);
if (validatedFragments.size() == 1 && !validatedFragments.get(0).isDerivedContent()) {
ValidatedFragment validatedFragment = validatedFragments.get(0);
ValidationOutcome outcome = new ValidationOutcome();
FileInfo fileInfo = new FileInfo(
fileToValidate.getFileName(),
new String(validatedFragment.getContent()),
validatedFragment.getExtension());
outcome.setMessages(validatedFragment.getErrors());
outcome.setFileInfo(fileInfo);
response.addOutcome(outcome);
} else {
for (ValidatedFragment validatedFragment : validatedFragments) {
ValidationOutcome outcome = new ValidationOutcome();
FileInfo fileInfo = new FileInfo(
validatedFragment.getFilename(),
new String(validatedFragment.getContent()),
validatedFragment.getExtension());
outcome.setMessages(validatedFragment.getErrors());
outcome.setFileInfo(fileInfo);
response.addOutcome(outcome);
}
}
}
System.out.println(" Max Memory: "+Runtime.getRuntime().maxMemory());
return response;

4
pom.xml
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@ -14,13 +14,13 @@
HAPI FHIR
-->
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.1.11-SNAPSHOT</version>
<version>6.1.13-SNAPSHOT</version>
<packaging>pom</packaging>
<properties>
<guava_version>32.0.1-jre</guava_version>
<hapi_fhir_version>6.4.1</hapi_fhir_version>
<validator_test_case_version>1.4.7</validator_test_case_version>
<validator_test_case_version>1.4.8</validator_test_case_version>
<jackson_version>2.15.2</jackson_version>
<junit_jupiter_version>5.9.2</junit_jupiter_version>
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>