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org.hl7.fhir.core
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Merge branch 'hapifhir:master' into master

This commit is contained in:
Deepak Sharma 2023-02-27 14:04:23 -06:00 committed by GitHub
parent e513ca022d b0daf66672
commit 83a323ac33
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91 changed files with 3963 additions and 1872 deletions
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27
checkstyle.xml Normal file
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@ -0,0 +1,27 @@
<?xml version="1.0"?>
<!DOCTYPE module PUBLIC
"-//Puppy Crawl//DTD Check Configuration 1.3//EN"
"http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
<module name="Checker">
<property name="severity" value="error"/>
<property name="charset" value="UTF-8"/>
<property name="fileExtensions" value="java, properties, xml, js, json"/>
<module name="TreeWalker">
<!--
<module name="TodoComment">-->
<!-- The (?i) below means Case Insensitive -->
<!--<property name="format" value="(?i)FIXME"/>
-->
<module name="RegexpSinglelineJava">
<property name="format" value="org\.jetbrains\.annotations\.NotNull"/>
</module>
<module name="RegexpSinglelineJava">
<property name="format" value="org\.jetbrains\.annotations\.Nullable"/>
</module>
<module name="RegexpSinglelineJava">
<property name="format" value="org\.jetbrains\.annotations\.\*"/>
</module>
</module>
</module>

8
codecov.yml Normal file
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@ -0,0 +1,8 @@
coverage:
status:
project:
default:
informational: true
patch:
default:
informational: true

8
org.hl7.fhir.convertors/checkstyle_suppressions.xml Normal file
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@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

4
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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -87,7 +87,7 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
</dependency>

105
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/BaseLoaderR5.java
View File

@ -3,8 +3,22 @@ package org.hl7.fhir.convertors.loaders.loaderR5;
import java.io.IOException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.OperationDefinition;
import org.hl7.fhir.r5.model.OperationDefinition.OperationDefinitionParameterComponent;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.NpmPackage;
@ -18,12 +32,8 @@ import lombok.experimental.Accessors;
public abstract class BaseLoaderR5 implements IContextResourceLoader {
protected final String URL_BASE = "http://hl7.org/fhir/";
protected final String URL_DSTU2 = "http://hl7.org/fhir/1.0/";
protected final String URL_DSTU2016MAY = "http://hl7.org/fhir/1.4/";
protected final String URL_DSTU3 = "http://hl7.org/fhir/3.0/";
protected final String URL_R4 = "http://hl7.org/fhir/4.0/";
protected final String URL_ELEMENT_DEF_NAMESPACE = "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace";
@Getter @Setter protected boolean patchUrls;
protected boolean patchUrls;
@Getter @Setter protected boolean killPrimitives;
@Getter protected String[] types;
protected ILoaderKnowledgeProviderR5 lkp;
@ -73,4 +83,87 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
}
}
}
public boolean isPatchUrls() {
return patchUrls;
}
public void setPatchUrls(boolean patchUrls) {
this.patchUrls = patchUrls;
}
protected abstract String versionString();
@Override
public String patchUrl(String url, String type) {
if (!patchUrls || url == null) {
return url;
} else if (url.startsWith("http://hl7.org/fhir/"+type+"/")) {
return "http://hl7.org/fhir/"+versionString()+"/"+url.substring(20);
} else if ("CodeSystem".equals(type) && url.startsWith("http://hl7.org/fhir/")) {
return "http://hl7.org/fhir/"+versionString()+"/"+url.substring(20);
} else {
return url;
}
}
// we don't patch everything. It's quite hard work to do that,
// and we only patch URLs to support version transforms
// so we just patch sd/od -> vs -> cs
protected void doPatchUrls(Resource resource) {
if (resource instanceof CanonicalResource) {
CanonicalResource cr = (CanonicalResource) resource;
cr.setUrl(patchUrl(cr.getUrl(), cr.fhirType()));
if (cr instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) cr;
sd.setBaseDefinition(patchUrl(sd.getBaseDefinition(), sd.fhirType()));
new ProfileUtilities(null, null, null, null).setIds(sd, false);
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
}
if (cr instanceof ValueSet) {
ValueSet vs = (ValueSet) cr;
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
inc.setSystem(patchUrl(inc.getSystem(), "CodeSystem"));
}
for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
inc.setSystem(patchUrl(inc.getSystem(), "CodeSystem"));
}
}
if (cr instanceof OperationDefinition) {
OperationDefinition od = (OperationDefinition) cr;
for (OperationDefinitionParameterComponent param : od.getParameter()) {
patchUrls(param);
}
}
}
}
private void patchUrls(OperationDefinitionParameterComponent param) {
if (param.hasBinding()) {
param.getBinding().setValueSet(patchUrl(param.getBinding().getValueSet(), "ValueSet"));
}
for (OperationDefinitionParameterComponent p : param.getPart()) {
patchUrls(p);
}
}
private void patchUrl(ElementDefinition ed) {
for (TypeRefComponent tr : ed.getType()) {
if (!Utilities.isAbsoluteUrl(tr.getCode())) {
tr.setCode(URL_BASE+versionString()+"/StructureDefinition/"+tr.getCode());
}
for (CanonicalType s : tr.getTargetProfile()) {
s.setValue(patchUrl(s.getValue(), "StructureDefinitino"));
}
}
if (ed.hasBinding()) {
ed.getBinding().setValueSet(patchUrl(ed.getBinding().getValueSet(), "ValueSet"));
}
}
}

36
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R2016MayToR5Loader.java
View File

@ -98,13 +98,10 @@ public class R2016MayToR5Loader extends BaseLoaderR5 {
}
b.getEntry().removeAll(remove);
}
for (BundleEntryComponent be : b.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
new ProfileUtilities(null, null, null, null).setIds(sd, false);
if (patchUrls) {
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_DSTU2016MAY));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
if (patchUrls) {
for (BundleEntryComponent be : b.getEntry()) {
if (be.hasResource()) {
doPatchUrls(be.getResource());
}
}
}
@ -128,33 +125,20 @@ public class R2016MayToR5Loader extends BaseLoaderR5 {
throw new FHIRException("Cannot kill primitives when using deferred loading");
}
if (patchUrls) {
if (r5 instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r5;
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
}
doPatchUrls(r5);
}
return r5;
}
private void patchUrl(ElementDefinition ed) {
for (TypeRefComponent tr : ed.getType()) {
for (CanonicalType s : tr.getTargetProfile()) {
s.setValue(s.getValue().replace(URL_BASE, URL_DSTU2016MAY));
}
for (CanonicalType s : tr.getProfile()) {
s.setValue(s.getValue().replace(URL_BASE, URL_DSTU2016MAY));
}
}
}
@Override
public List<CodeSystem> getCodeSystems() {
return new ArrayList<>();
}
@Override
protected String versionString() {
return "4.3";
}
}

32
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R2ToR5Loader.java
View File

@ -102,10 +102,8 @@ public class R2ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
}
if (patchUrls) {
for (BundleEntryComponent be : b.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_DSTU2));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
if (be.hasResource()) {
doPatchUrls(be.getResource());
}
}
}
@ -126,30 +124,11 @@ public class R2ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
throw new FHIRException("Cannot kill primitives when using deferred loading");
}
if (patchUrls) {
if (r5 instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r5;
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
}
doPatchUrls(r5);
}
return r5;
}
private void patchUrl(ElementDefinition ed) {
for (TypeRefComponent tr : ed.getType()) {
for (CanonicalType s : tr.getTargetProfile()) {
s.setValue(s.getValue().replace(URL_BASE, URL_DSTU2));
}
for (CanonicalType s : tr.getProfile()) {
s.setValue(s.getValue().replace(URL_BASE, URL_DSTU2));
}
}
}
@Override
public List<CodeSystem> getCodeSystems() {
List<CodeSystem> list = new ArrayList<>();
@ -160,4 +139,9 @@ public class R2ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
return list;
}
@Override
protected String versionString() {
return "1.0";
}
}

38
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R3ToR5Loader.java
View File

@ -99,15 +99,9 @@ public class R3ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
}
if (patchUrls) {
for (BundleEntryComponent be : b.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_DSTU3));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
}
if (be.hasResource()) {
doPatchUrls(be.getResource());
}
}
}
return b;
@ -130,33 +124,19 @@ public class R3ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
throw new FHIRException("Cannot kill primitives when using deferred loading");
}
if (patchUrls) {
if (r5 instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r5;
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
}
doPatchUrls(r5);
}
return r5;
}
private void patchUrl(ElementDefinition ed) {
for (TypeRefComponent tr : ed.getType()) {
for (CanonicalType s : tr.getTargetProfile()) {
s.setValue(s.getValue().replace(URL_BASE, URL_DSTU3));
}
for (CanonicalType s : tr.getProfile()) {
s.setValue(s.getValue().replace(URL_BASE, URL_DSTU3));
}
}
}
@Override
public List<CodeSystem> getCodeSystems() {
return new ArrayList<>();
}
@Override
protected String versionString() {
return "3.0";
}
}

36
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R4BToR5Loader.java
View File

@ -103,14 +103,8 @@ public class R4BToR5Loader extends BaseLoaderR5 implements IContextResourceLoade
}
if (patchUrls) {
for (BundleEntryComponent be : b.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
if (be.hasResource()) {
doPatchUrls(be.getResource());
}
}
}
@ -137,34 +131,20 @@ public class R4BToR5Loader extends BaseLoaderR5 implements IContextResourceLoade
r5 = new StructureDefinitionHacker(version).fixSD((StructureDefinition) r5);
}
if (patchUrls) {
if (r5 instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r5;
sd.setUrl(sd.getUrl().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType("http://hl7.org/fhir"));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
}
doPatchUrls(r5);
}
return r5;
}
private void patchUrl(ElementDefinition ed) {
for (TypeRefComponent tr : ed.getType()) {
for (CanonicalType s : tr.getTargetProfile()) {
s.setValue(s.getValue().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
}
for (CanonicalType s : tr.getProfile()) {
s.setValue(s.getValue().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
}
}
}
@Override
public List<CodeSystem> getCodeSystems() {
return new ArrayList<>();
}
@Override
protected String versionString() {
return "4.3";
}
}

35
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R4ToR5Loader.java
View File

@ -103,14 +103,8 @@ public class R4ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
}
if (patchUrls) {
for (BundleEntryComponent be : b.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
if (be.hasResource()) {
doPatchUrls(be.getResource());
}
}
}
@ -137,34 +131,21 @@ public class R4ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
r5 = new StructureDefinitionHacker(version).fixSD((StructureDefinition) r5);
}
if (patchUrls) {
if (r5 instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r5;
sd.setUrl(sd.getUrl().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType("http://hl7.org/fhir"));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
}
doPatchUrls(r5);
}
return r5;
}
private void patchUrl(ElementDefinition ed) {
for (TypeRefComponent tr : ed.getType()) {
for (CanonicalType s : tr.getTargetProfile()) {
s.setValue(s.getValue().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
}
for (CanonicalType s : tr.getProfile()) {
s.setValue(s.getValue().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
}
}
}
@Override
public List<CodeSystem> getCodeSystems() {
return new ArrayList<>();
}
@Override
protected String versionString() {
return "4.0";
}
}

36
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R5ToR5Loader.java
View File

@ -96,14 +96,8 @@ public class R5ToR5Loader extends BaseLoaderR5 {
}
if (patchUrls) {
for (BundleEntryComponent be : b.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
if (be.hasResource()) {
doPatchUrls(be.getResource());
}
}
}
@ -126,34 +120,20 @@ public class R5ToR5Loader extends BaseLoaderR5 {
throw new FHIRException("Cannot kill primitives when using deferred loading");
}
if (patchUrls) {
if (r5 instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r5;
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement())
patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement())
patchUrl(ed);
}
doPatchUrls(r5);
}
return r5;
}
private void patchUrl(ElementDefinition ed) {
for (TypeRefComponent tr : ed.getType()) {
for (CanonicalType s : tr.getTargetProfile()) {
s.setValue(s.getValue().replace(URL_BASE, URL_R4));
}
for (CanonicalType s : tr.getProfile()) {
s.setValue(s.getValue().replace(URL_BASE, URL_R4));
}
}
}
@Override
public List<CodeSystem> getCodeSystems() {
return new ArrayList<>();
}
@Override
protected String versionString() {
return "5.0";
}
}

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientFactory.java
View File

@ -60,7 +60,7 @@ public class TerminologyClientFactory {
private static String checkEndsWith(String term, String url) {
if (url.endsWith(term))
return url;
if (url.startsWith("http://tx.fhir.org"))
if (url.startsWith("http://tx.fhir.org") || url.startsWith("https://tx.fhir.org"))
return Utilities.pathURL(url, term);
if (url.equals("http://local.fhir.org:8080"))
return Utilities.pathURL(url, term);

74
org.hl7.fhir.convertors/src/test/java/org/hl7/fhir/convertors/txClient/TerminologyClientFactoryTest.java Normal file
View File

@ -0,0 +1,74 @@
package org.hl7.fhir.convertors.txClient;
import org.hl7.fhir.r5.terminologies.TerminologyClient;
import org.hl7.fhir.utilities.FhirPublication;
import org.junit.jupiter.api.Test;
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;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertThrows;
public class TerminologyClientFactoryTest {
public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
List<Arguments> objects = new ArrayList<>();
objects.addAll(getDefaultServerArgs("tx.fhir.org/r4", "tx.fhir.org", FhirPublication.R4));
objects.addAll(getHttpAndHttpsArgs("tx.fhir.org", null, "tx.fhir.org/r4"));
objects.addAll(getHttpAndHttpsArgs("tx.fhir.org/r4", null, "tx.fhir.org/r4"));
objects.addAll(getDefaultServerArgs("tx.fhir.org/r2", "tx.fhir.org", FhirPublication.DSTU2));
objects.addAll(getDefaultServerArgs("tx.fhir.org/r3", "tx.fhir.org", FhirPublication.DSTU2016May));
objects.addAll(getDefaultServerArgs("tx.fhir.org/r4", "tx.fhir.org", FhirPublication.R4B));
objects.addAll(getDefaultServerArgs("tx.fhir.org/r4", "tx.fhir.org", FhirPublication.R5));
objects.addAll(getDefaultServerArgs("tx.fhir.org/r3", "tx.fhir.org", FhirPublication.STU3));
objects.addAll(getHttpAndHttpsArgs("someserver.org", FhirPublication.R4, "someserver.org"));
objects.addAll(getHttpAndHttpsArgs("someserver.org", null, "someserver.org"));
return objects.stream();
}
private static List<Arguments> getDefaultServerArgs(String explicitUrl, String baseUrl, FhirPublication fhirPublication) {
List<Arguments> objects = new ArrayList<>();
objects.addAll(getHttpAndHttpsArgs(baseUrl, fhirPublication, explicitUrl));
objects.addAll(getHttpAndHttpsArgs(explicitUrl, fhirPublication, explicitUrl));
return objects;
}
private static List<Arguments> getHttpAndHttpsArgs(String baseUrl, FhirPublication fhirPublication, String baseExpectedAddress) {
return List.of(
Arguments.of("https://" + baseUrl, fhirPublication, "https://" + baseExpectedAddress),
Arguments.of("http://" + baseUrl, fhirPublication, "http://" + baseExpectedAddress)
);
}
@ParameterizedTest
@MethodSource("data")
public void testMakeClient(String url, FhirPublication fhirPublication, String expectedAddress) throws URISyntaxException {
TerminologyClient terminologyClient = TerminologyClientFactory.makeClient(url, "dummyUserAgent", fhirPublication);
assertEquals(expectedAddress, terminologyClient.getAddress());
}
@Test
public void testMakeClientDstu1Fails() throws URISyntaxException {
assertThrows(Error.class, () -> {
TerminologyClient terminologyClient = TerminologyClientFactory.makeClient("urldoesnotmatter", "dummyUserAgent", FhirPublication.DSTU1);
}
);
}
@Test
public void testMakeClientNullFails() throws URISyntaxException {
assertThrows(Error.class, () -> {
TerminologyClient terminologyClient = TerminologyClientFactory.makeClient("urldoesnotmatter", "dummyUserAgent", FhirPublication.NULL);
}
);
}
}

84
org.hl7.fhir.core.generator/configuration/RdfParser.java
View File

@ -29,8 +29,8 @@ public class RdfParser extends RdfParserBase {
private void composeEnum(Complex parent, String parentType, String name, Enumeration<? extends Enum> value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
decorateCode(t, value);
}
@ -39,24 +39,24 @@ public class RdfParser extends RdfParserBase {
protected void composeDate(Complex parent, String parentType, String name, DateType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeDateTime(Complex parent, String parentType, String name, DateTimeType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeCode(Complex parent, String parentType, String name, CodeType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
decorateCode(t, value);
}
@ -64,136 +64,136 @@ public class RdfParser extends RdfParserBase {
protected void composeString(Complex parent, String parentType, String name, StringType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeInteger(Complex parent, String parentType, String name, IntegerType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeInteger64(Complex parent, String parentType, String name, Integer64Type value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeOid(Complex parent, String parentType, String name, OidType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeCanonical(Complex parent, String parentType, String name, CanonicalType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeUri(Complex parent, String parentType, String name, UriType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeUuid(Complex parent, String parentType, String name, UuidType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeUrl(Complex parent, String parentType, String name, UrlType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeInstant(Complex parent, String parentType, String name, InstantType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeBoolean(Complex parent, String parentType, String name, BooleanType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeBase64Binary(Complex parent, String parentType, String name, Base64BinaryType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeUnsignedInt(Complex parent, String parentType, String name, UnsignedIntType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeMarkdown(Complex parent, String parentType, String name, MarkdownType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeTime(Complex parent, String parentType, String name, TimeType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeId(Complex parent, String parentType, String name, IdType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composePositiveInt(Complex parent, String parentType, String name, PositiveIntType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}
protected void composeDecimal(Complex parent, String parentType, String name, DecimalType value, int index) {
if (value == null)
return;
Complex t = parent.predicate("fhir:"+parentType+"."+name);
t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
Complex t = parent.predicate("fhir:"+name, index > -1);
t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
composeElement(t, parentType, name, value, index);
}

2
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/JavaParserRdfGenerator.java
View File

@ -108,7 +108,7 @@ public class JavaParserRdfGenerator extends JavaBaseGenerator {
composer.append(" if (Utilities.noString(parentType))\r\n");
composer.append(" t = parent;\r\n");
composer.append(" else {\r\n");
composer.append(" t = parent.predicate(\"fhir:\"+parentType+'.'+name);\r\n");
composer.append(" t = parent.predicate(\"fhir:\"+name,index > -1);\r\n");
composer.append(" }\r\n");
composer.append(" compose"+ti.getAncestorName()+"(t, \""+ti.getDefn().getName()+"\", name, element, index);\r\n");
if (tn.equals("Coding"))

8
org.hl7.fhir.dstu2/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

5
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/ProfileUtilities.java
View File

@ -79,6 +79,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xml.SchematronWriter;
@ -1183,7 +1184,7 @@ public class ProfileUtilities {
public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, Set<String> outputTracker) throws IOException, FHIRException {
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false);
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false, TableGenerationMode.XML);
boolean deep = false;
boolean vdeep = false;
@ -1447,7 +1448,7 @@ public class ProfileUtilities {
public XhtmlNode generateTable(String defFile, StructureDefinition profile, boolean diff, String imageFolder, boolean inlineGraphics, String profileBaseFileName, boolean snapshot, String corePath, Set<String> outputTracker) throws IOException, FHIRException {
assert(diff != snapshot);// check it's ok to get rid of one of these
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false);
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false, TableGenerationMode.XML);
List<ElementDefinition> list = diff ? profile.getDifferential().getElement() : profile.getSnapshot().getElement();
List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
profiles.add(profile);

8
org.hl7.fhir.dstu2016may/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

5
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/ProfileUtilities.java
View File

@ -80,6 +80,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xml.SchematronWriter;
@ -1184,7 +1185,7 @@ public class ProfileUtilities {
public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, Set<String> outputTracker) throws IOException, FHIRException {
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false);
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false, TableGenerationMode.XML);
boolean deep = false;
boolean vdeep = false;
@ -1446,7 +1447,7 @@ public class ProfileUtilities {
public XhtmlNode generateTable(String defFile, StructureDefinition profile, boolean diff, String imageFolder, boolean inlineGraphics, String profileBaseFileName, boolean snapshot, String corePath, boolean logicalModel, Set<String> outputTracker) throws IOException, FHIRException {
assert(diff != snapshot);// check it's ok to get rid of one of these
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false);
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false, TableGenerationMode.XML);
List<ElementDefinition> list = diff ? profile.getDifferential().getElement() : profile.getSnapshot().getElement();
List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
profiles.add(profile);

8
org.hl7.fhir.dstu3/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

4
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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -55,7 +55,7 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
</dependency>

5
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/conformance/ProfileUtilities.java
View File

@ -102,6 +102,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xml.SchematronWriter;
@ -1621,7 +1622,7 @@ public class ProfileUtilities extends TranslatingUtilities {
public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, String imagePath, Set<String> outputTracker) throws IOException, FHIRException {
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
gen.setTranslator(getTranslator());
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false);
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false, TableGenerationMode.XML);
boolean deep = false;
String m = "";
@ -1990,7 +1991,7 @@ public class ProfileUtilities extends TranslatingUtilities {
assert(diff != snapshot);// check it's ok to get rid of one of these
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
gen.setTranslator(getTranslator());
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false);
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false, TableGenerationMode.XML);
List<ElementDefinition> list = diff ? profile.getDifferential().getElement() : profile.getSnapshot().getElement();
List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
profiles.add(profile);

8
org.hl7.fhir.r4/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

4
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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -67,7 +67,7 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
</dependency>
<dependency>

5
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/conformance/ProfileUtilities.java
View File

@ -110,6 +110,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xml.SchematronWriter;
@ -2149,7 +2150,7 @@ public class ProfileUtilities extends TranslatingUtilities {
public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, String imagePath, Set<String> outputTracker) throws IOException, FHIRException {
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
gen.setTranslator(getTranslator());
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false);
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false, TableGenerationMode.XML);
boolean deep = false;
String m = "";
@ -2519,7 +2520,7 @@ public class ProfileUtilities extends TranslatingUtilities {
assert(diff != snapshot);// check it's ok to get rid of one of these
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
gen.setTranslator(getTranslator());
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false);
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false, TableGenerationMode.XML);
List<ElementDefinition> list = diff ? profile.getDifferential().getElement() : profile.getSnapshot().getElement();
List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
profiles.add(profile);

6
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/StructureMapUtilities.java
View File

@ -265,8 +265,10 @@ public class StructureMapUtilities {
public StructureMapUtilities(IWorkerContext worker) {
super();
this.worker = worker;
fpe = new FHIRPathEngine(worker);
fpe.setHostServices(new FFHIRPathHostServices());
if (worker != null) {
fpe = new FHIRPathEngine(worker);
fpe.setHostServices(new FFHIRPathHostServices());
}
}
public static String render(StructureMap map) {

8
org.hl7.fhir.r4b/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

8
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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -61,19 +61,19 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>logging-interceptor</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>mockwebserver</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
<scope>test</scope>
</dependency>

5
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/conformance/ProfileUtilities.java
View File

@ -130,6 +130,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xml.SchematronWriter;
@ -3471,7 +3472,7 @@ public class ProfileUtilities extends TranslatingUtilities {
public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, String imagePath, Set<String> outputTracker, RenderingContext rc) throws IOException, FHIRException {
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
gen.setTranslator(getTranslator());
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId()+(full ? "f" : "n"), true);
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId()+(full ? "f" : "n"), true, TableGenerationMode.XHTML);
boolean deep = false;
String m = "";
@ -3988,7 +3989,7 @@ public class ProfileUtilities extends TranslatingUtilities {
assert(diff != snapshot);// check it's ok to get rid of one of these
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
gen.setTranslator(getTranslator());
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), active);
TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), active, active ? TableGenerationMode.XHTML : TableGenerationMode.XML);
List<ElementDefinition> list = new ArrayList<>();
if (diff)
list.addAll(profile.getDifferential().getElement());

58
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/model/BaseResource.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r4b.model;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import org.hl7.fhir.instance.model.api.IAnyResource;
@ -58,7 +58,7 @@ public abstract class BaseResource extends Base implements IAnyResource, IElemen
@Override
public FhirVersionEnum getStructureFhirVersionEnum() {
return FhirVersionEnum.R5; // to: change to R5
return FhirVersionEnum.R4B;
}
@Override

8
org.hl7.fhir.r5/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

8
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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -111,13 +111,13 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>logging-interceptor</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
</dependency>
@ -148,7 +148,7 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>mockwebserver</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
<scope>test</scope>
</dependency>

80
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ContextUtilities.java
View File

@ -23,6 +23,7 @@ import org.hl7.fhir.r5.model.NamingSystem.NamingSystemIdentifierType;
import org.hl7.fhir.r5.model.NamingSystem.NamingSystemUniqueIdComponent;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.r5.model.Identifier;
@ -42,6 +43,9 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
private boolean ignoreProfileErrors;
private XVerExtensionManager xverManager;
private Map<String, String> oidCache = new HashMap<>();
private List<StructureDefinition> allStructuresList = new ArrayList<StructureDefinition>();
private List<String> canonicalResourceNames;
private List<String> concreteResourceNames;
public ContextUtilities(IWorkerContext context) {
super();
@ -196,41 +200,46 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
* @return a list of the resource names that are canonical resources defined for this version
*/
public List<String> getCanonicalResourceNames() {
List<String> names = new ArrayList<>();
for (StructureDefinition sd : allStructures()) {
if (sd.getKind() == StructureDefinitionKind.RESOURCE && !sd.getAbstract() && hasUrlProperty(sd)) {
names.add(sd.getType());
if (canonicalResourceNames == null) {
canonicalResourceNames = new ArrayList<>();
Set<String> names = new HashSet<>();
for (StructureDefinition sd : allStructures()) {
if (sd.getKind() == StructureDefinitionKind.RESOURCE && !sd.getAbstract() && hasUrlProperty(sd)) {
names.add(sd.getType());
}
}
canonicalResourceNames.addAll(Utilities.sorted(names));
}
return names;
return canonicalResourceNames;
}
/**
* @return a list of all structure definitions, with snapshots generated (if possible)
*/
public List<StructureDefinition> allStructures(){
List<StructureDefinition> result = new ArrayList<StructureDefinition>();
Set<StructureDefinition> set = new HashSet<StructureDefinition>();
for (StructureDefinition sd : getStructures()) {
if (!set.contains(sd)) {
try {
generateSnapshot(sd);
// new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "snapshot", tail(sd.getUrl())+".xml")), sd);
} catch (Exception e) {
if (!isSuppressDebugMessages()) {
System.out.println("Unable to generate snapshot for "+tail(sd.getUrl()) +" from "+tail(sd.getBaseDefinition())+" because "+e.getMessage());
if (context.getLogger().isDebugLogging()) {
e.printStackTrace();
if (allStructuresList.isEmpty()) {
Set<StructureDefinition> set = new HashSet<StructureDefinition>();
for (StructureDefinition sd : getStructures()) {
if (!set.contains(sd)) {
try {
generateSnapshot(sd);
// new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "snapshot", tail(sd.getUrl())+".xml")), sd);
} catch (Exception e) {
if (!isSuppressDebugMessages()) {
System.out.println("Unable to generate snapshot for "+tail(sd.getUrl()) +" from "+tail(sd.getBaseDefinition())+" because "+e.getMessage());
if (context.getLogger().isDebugLogging()) {
e.printStackTrace();
}
}
}
allStructuresList.add(sd);
set.add(sd);
}
result.add(sd);
set.add(sd);
}
}
return result;
return allStructuresList;
}
/**
* @return a list of all structure definitions, without trying to generate snapshots
*/
@ -368,5 +377,32 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
return null;
}
public List<String> getConcreteResources() {
if (concreteResourceNames == null) {
concreteResourceNames = new ArrayList<>();
Set<String> names = new HashSet<>();
for (StructureDefinition sd : allStructures()) {
if (sd.getKind() == StructureDefinitionKind.RESOURCE && !sd.getAbstract()) {
names.add(sd.getType());
}
}
concreteResourceNames.addAll(Utilities.sorted(names));
}
return concreteResourceNames;
}
public List<StructureMap> listMaps(String url) {
List<StructureMap> res = new ArrayList<>();
String start = url.substring(0, url.indexOf("*"));
String end = url.substring(url.indexOf("*")+1);
for (StructureMap map : context.fetchResourcesByType(StructureMap.class)) {
String u = map.getUrl();
if (u.startsWith(start) && u.endsWith(end)) {
res.add(map);
}
}
return res;
}
}

18
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
View File

@ -320,7 +320,23 @@ public interface IWorkerContext {
*
* @return
*/
List<CodeSystem> getCodeSystems();
List<CodeSystem> getCodeSystems();
/**
* if this is true, then the loader will patch canonical URLs and cross-links
* to add /X.X/ into the URL so that different versions can be loaded safely
*
* default is false
*/
void setPatchUrls(boolean value);
/**
* patch the URL if necessary
*
* @param url
* @return
*/
String patchUrl(String url, String resourceType);
}
/**

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -97,7 +97,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
private final IContextResourceLoader loader;
public PackageResourceLoader(PackageResourceInformation pri, IContextResourceLoader loader) {
super(pri.getResourceType(), pri.getId(), pri.getUrl(),pri.getVersion());
super(pri.getResourceType(), pri.getId(), loader == null ? pri.getUrl() :loader.patchUrl(pri.getUrl(), pri.getResourceType()), pri.getVersion());
this.filename = pri.getFilename();
this.loader = loader;
}

44
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java
View File

@ -129,6 +129,7 @@ public class Element extends Base {
private int instanceId;
private boolean isNull;
private Base source;
private boolean ignorePropertyOrder;
public Element(String name) {
super();
@ -148,6 +149,9 @@ public class Element extends Base {
super();
this.name = name;
this.property = property;
if (property.isResource()) {
children = new ArrayList<>();
}
}
public Element(String name, Property property, String type, String value) {
@ -211,8 +215,9 @@ public class Element extends Base {
this.value = value;
}
public void setType(String type) {
public Element setType(String type) {
this.type = type;
return this;
}
@ -287,9 +292,21 @@ public class Element extends Base {
if (name.equals(child.getName()))
return child.getValue();
}
for (Element child : children) {
if (name.equals(child.getNameBase()))
return child.getValue();
}
return null;
}
private String getNameBase() {
if (property.isChoice()) {
return property.getName().replace("[x]", "");
} else {
return getName();
}
}
public void setChildValue(String name, String value) {
if (children == null)
children = new ArrayList<Element>();
@ -538,6 +555,16 @@ public class Element extends Base {
Element ne = new Element(name, p);
children.add(ne);
return ne;
} else if (p.getDefinition().isChoice() && name.startsWith(p.getName().replace("[x]", ""))) {
String type = name.substring(p.getName().length()-3);
if (new ContextUtilities(property.getContext()).isPrimitiveDatatype(Utilities.uncapitalize(type))) {
type = Utilities.uncapitalize(type);
}
Element ne = new Element(name, p);
ne.setType(type);
children.add(ne);
return ne;
}
}
@ -598,7 +625,7 @@ public class Element extends Base {
@Override
public String primitiveValue() {
if (isPrimitive())
if (isPrimitive() || value != null)
return value;
else {
if (hasPrimitiveValue() && children != null) {
@ -1360,6 +1387,19 @@ public class Element extends Base {
setChildValue(name, value.primitiveValue());
return this;
}
public boolean isIgnorePropertyOrder() {
return ignorePropertyOrder;
}
public void setIgnorePropertyOrder(boolean ignorePropertyOrder) {
this.ignorePropertyOrder = ignorePropertyOrder;
if (children != null) {
for (Element e : children) {
e.setIgnorePropertyOrder(ignorePropertyOrder);
}
}
}
}

585
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/FmlParser.java Normal file
View File

@ -0,0 +1,585 @@
package org.hl7.fhir.r5.elementmodel;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.ConceptMap.ConceptMapGroupUnmappedMode;
import org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupTypeMode;
import org.hl7.fhir.r5.model.StructureMap.StructureMapTransform;
import org.hl7.fhir.r5.utils.FHIRLexer;
import org.hl7.fhir.r5.utils.FHIRLexer.FHIRLexerException;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.utilities.SourceLocation;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
public class FmlParser extends ParserBase {
private FHIRPathEngine fpe;
public FmlParser(IWorkerContext context) {
super(context);
fpe = new FHIRPathEngine(context);
}
@Override
public List<NamedElement> parse(InputStream stream) throws IOException, FHIRFormatError, DefinitionException, FHIRException {
String text = TextFile.streamToString(stream);
List<NamedElement> result = new ArrayList<>();
result.add(new NamedElement(null, parse(text)));
return result;
}
@Override
public void compose(Element e, OutputStream destination, OutputStyle style, String base)
throws FHIRException, IOException {
throw new Error("Not done yet");
}
public Element parse(String text) throws FHIRException {
FHIRLexer lexer = new FHIRLexer(text, "source", true);
if (lexer.done())
throw lexer.error("Map Input cannot be empty");
Element result = Manager.build(context, context.fetchTypeDefinition("StructureMap"));
try {
if (lexer.hasToken("map")) {
lexer.token("map");
result.makeElement("url").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
lexer.token("=");
result.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("name"));
if (lexer.hasComments()) {
result.makeElement("description").markLocation(lexer.getCurrentLocation()).setValue(lexer.getAllComments());
}
} else {
while (lexer.hasToken("///")) {
lexer.next();
String fid = lexer.takeDottedToken();
Element e = result.makeElement(fid).markLocation(lexer.getCurrentLocation());
lexer.token("=");
e.setValue(lexer.readConstant("meta value"));
}
}
lexer.setMetadataFormat(false);
while (lexer.hasToken("conceptmap"))
parseConceptMap(result, lexer);
while (lexer.hasToken("uses"))
parseUses(result, lexer);
while (lexer.hasToken("imports"))
parseImports(result, lexer);
while (!lexer.done()) {
parseGroup(result, lexer);
}
} catch (FHIRLexerException e) {
logError("2023-02-24", e.getLocation().getLine(), e.getLocation().getColumn(), "??", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
} catch (Exception e) {
logError("2023-02-24", -1, -1, "?", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
}
if (!result.hasChild("status")) {
result.makeElement("status").setValue("draft");
}
result.setIgnorePropertyOrder(true);
return result;
}
private void parseConceptMap(Element result, FHIRLexer lexer) throws FHIRLexerException {
lexer.token("conceptmap");
Element map = Manager.build(context, context.fetchTypeDefinition("ConceptMap"));
Element eid = map.makeElement("id").markLocation(lexer.getCurrentLocation());
String id = lexer.readConstant("map id");
if (id.startsWith("#"))
throw lexer.error("Concept Map identifier must start with #");
eid.setValue(id);
map.makeElement("status").setValue(PublicationStatus.DRAFT.toCode()); // todo: how to add this to the text format
result.makeElement("contained").setElement("resource", map);
lexer.token("{");
// lexer.token("source");
// map.setSource(new UriType(lexer.readConstant("source")));
// lexer.token("target");
// map.setSource(new UriType(lexer.readConstant("target")));
Map<String, String> prefixes = new HashMap<String, String>();
while (lexer.hasToken("prefix")) {
lexer.token("prefix");
String n = lexer.take();
lexer.token("=");
String v = lexer.readConstant("prefix url");
prefixes.put(n, v);
}
while (lexer.hasToken("unmapped")) {
lexer.token("unmapped");
lexer.token("for");
String n = readPrefix(prefixes, lexer);
Element g = getGroupE(map, n, null);
lexer.token("=");
SourceLocation loc = lexer.getCurrentLocation();
String v = lexer.take();
if (v.equals("provided")) {
g.makeElement("unmapped").makeElement("mode").markLocation(loc).setValue(ConceptMapGroupUnmappedMode.USESOURCECODE.toCode());
} else
throw lexer.error("Only unmapped mode PROVIDED is supported at this time");
}
while (!lexer.hasToken("}")) {
String srcs = readPrefix(prefixes, lexer);
lexer.token(":");
SourceLocation scloc = lexer.getCurrentLocation();
String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
SourceLocation relLoc = lexer.getCurrentLocation();
ConceptMapRelationship rel = readRelationship(lexer);
String tgts = readPrefix(prefixes, lexer);
Element g = getGroupE(map, srcs, tgts);
Element e = g.addElement("element");
e.makeElement("code").markLocation(scloc).setValue(sc.startsWith("\"") ? lexer.processConstant(sc) : sc);
Element tgt = e.addElement("target");
tgt.makeElement("relationship").markLocation(relLoc).setValue(rel.toCode());
lexer.token(":");
tgt.makeElement("code").markLocation(lexer.getCurrentLocation()).setValue(lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take());
if (lexer.hasComments()) {
tgt.makeElement("comment").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
}
lexer.token("}");
}
private Element getGroupE(Element map, String srcs, String tgts) {
for (Element grp : map.getChildrenByName("group")) {
if (grp.getChildValue("source").equals(srcs)) {
Element tgt = grp.getNamedChild("target");
if (tgt == null || tgts == null || tgts.equals(tgt.getValue())) {
if (tgt == null && tgts != null)
grp.makeElement("target").setValue(tgts);
return grp;
}
}
}
Element grp = map.addElement("group");
grp.makeElement("source").setValue(srcs);
grp.makeElement("target").setValue(tgts);
return grp;
}
private String readPrefix(Map<String, String> prefixes, FHIRLexer lexer) throws FHIRLexerException {
String prefix = lexer.take();
if (!prefixes.containsKey(prefix))
throw lexer.error("Unknown prefix '" + prefix + "'");
return prefixes.get(prefix);
}
private ConceptMapRelationship readRelationship(FHIRLexer lexer) throws FHIRLexerException {
String token = lexer.take();
if (token.equals("-"))
return ConceptMapRelationship.RELATEDTO;
if (token.equals("=="))
return ConceptMapRelationship.EQUIVALENT;
if (token.equals("!="))
return ConceptMapRelationship.NOTRELATEDTO;
if (token.equals("<="))
return ConceptMapRelationship.SOURCEISNARROWERTHANTARGET;
if (token.equals(">="))
return ConceptMapRelationship.SOURCEISBROADERTHANTARGET;
throw lexer.error("Unknown relationship token '" + token + "'");
}
private void parseUses(Element result, FHIRLexer lexer) throws FHIRException {
lexer.token("uses");
Element st = result.addElement("structure");
st.makeElement("url").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
if (lexer.hasToken("alias")) {
lexer.token("alias");
st.makeElement("alias").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
lexer.token("as");
st.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
lexer.skipToken(";");
if (lexer.hasComments()) {
st.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
}
private void parseImports(Element result, FHIRLexer lexer) throws FHIRException {
lexer.token("imports");
result.addElement("import").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
lexer.skipToken(";");
}
private void parseGroup(Element result, FHIRLexer lexer) throws FHIRException {
SourceLocation commLoc = lexer.getCommentLocation();
String comment = lexer.getAllComments();
lexer.token("group");
Element group = result.addElement("group").markLocation(lexer.getCurrentLocation());
if (!Utilities.noString(comment)) {
group.makeElement("documentation").markLocation(commLoc).setValue(comment);
}
boolean newFmt = false;
if (lexer.hasToken("for")) {
lexer.token("for");
SourceLocation loc = lexer.getCurrentLocation();
if ("type".equals(lexer.getCurrent())) {
lexer.token("type");
lexer.token("+");
lexer.token("types");
group.makeElement("typeMode").markLocation(loc).setValue(StructureMapGroupTypeMode.TYPEANDTYPES.toCode());
} else {
lexer.token("types");
group.makeElement("typeMode").markLocation(loc).setValue(StructureMapGroupTypeMode.TYPES.toCode());
}
}
group.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
if (lexer.hasToken("(")) {
newFmt = true;
lexer.take();
while (!lexer.hasToken(")")) {
parseInput(group, lexer, true);
if (lexer.hasToken(","))
lexer.token(",");
}
lexer.take();
}
if (lexer.hasToken("extends")) {
lexer.next();
group.makeElement("extends").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (newFmt) {
if (lexer.hasToken("<")) {
lexer.token("<");
lexer.token("<");
if (lexer.hasToken("types")) {
group.makeElement("typeMode").markLocation(lexer.getCurrentLocation()).setValue(StructureMapGroupTypeMode.TYPES.toCode());
} else {
group.makeElement("typeMode").markLocation(lexer.getCurrentLocation()).setValue(StructureMapGroupTypeMode.TYPEANDTYPES.toCode());
lexer.token("type");
lexer.token("+");
}
lexer.token(">");
lexer.token(">");
}
lexer.token("{");
}
if (newFmt) {
while (!lexer.hasToken("}")) {
if (lexer.done())
throw lexer.error("premature termination expecting 'endgroup'");
parseRule(result, group, lexer, true);
}
} else {
while (lexer.hasToken("input"))
parseInput(group, lexer, false);
while (!lexer.hasToken("endgroup")) {
if (lexer.done())
throw lexer.error("premature termination expecting 'endgroup'");
parseRule(result, group, lexer, false);
}
}
lexer.next();
if (newFmt && lexer.hasToken(";"))
lexer.next();
}
private void parseRule(Element map, Element context, FHIRLexer lexer, boolean newFmt) throws FHIRException {
Element rule = context.addElement("rule").markLocation(lexer.getCurrentLocation());
if (!newFmt) {
rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.takeDottedToken());
lexer.token(":");
lexer.token("for");
} else {
if (lexer.hasComments()) {
rule.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
}
boolean done = false;
while (!done) {
parseSource(rule, lexer);
done = !lexer.hasToken(",");
if (!done)
lexer.next();
}
if ((newFmt && lexer.hasToken("->")) || (!newFmt && lexer.hasToken("make"))) {
lexer.token(newFmt ? "->" : "make");
done = false;
while (!done) {
parseTarget(rule, lexer);
done = !lexer.hasToken(",");
if (!done)
lexer.next();
}
}
if (lexer.hasToken("then")) {
lexer.token("then");
if (lexer.hasToken("{")) {
lexer.token("{");
while (!lexer.hasToken("}")) {
if (lexer.done())
throw lexer.error("premature termination expecting '}' in nested group");
parseRule(map, rule, lexer, newFmt);
}
lexer.token("}");
} else {
done = false;
while (!done) {
parseRuleReference(rule, lexer);
done = !lexer.hasToken(",");
if (!done)
lexer.next();
}
}
}
if (!rule.hasChild("documentation") && lexer.hasComments()) {
rule.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
if (isSimpleSyntax(rule)) {
rule.forceElement("source").makeElement("variable").setValue(StructureMapUtilities.AUTO_VAR_NAME);
rule.forceElement("target").makeElement("variable").setValue(StructureMapUtilities.AUTO_VAR_NAME);
rule.forceElement("target").makeElement("transform").setValue(StructureMapTransform.CREATE.toCode());
Element dep = rule.forceElement("dependent");
dep.makeElement("name").setValue(StructureMapUtilities.DEF_GROUP_NAME);
dep.makeElement("parameter").makeElement("valueId").setValue(StructureMapUtilities.AUTO_VAR_NAME);
dep.makeElement("parameter").makeElement("valueId").setValue(StructureMapUtilities.AUTO_VAR_NAME);
// no dependencies - imply what is to be done based on types
}
if (newFmt) {
if (lexer.isConstant()) {
if (lexer.isStringConstant()) {
rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("ruleName"));
} else {
rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
} else {
if (rule.getChildrenByName("source").size() != 1 || !rule.getChildrenByName("source").get(0).hasChild("element"))
throw lexer.error("Complex rules must have an explicit name");
if (rule.getChildrenByName("source").get(0).hasChild("type"))
rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + rule.getChildrenByName("source").get(0).getNamedChildValue("type"));
else
rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element"));
}
lexer.token(";");
}
}
private void parseRuleReference(Element rule, FHIRLexer lexer) throws FHIRLexerException {
Element ref = rule.addElement("dependent");
ref.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
lexer.token("(");
boolean done = false;
while (!done) {
parseParameter(ref, lexer);
done = !lexer.hasToken(",");
if (!done)
lexer.next();
}
lexer.token(")");
}
private void parseSource(Element rule, FHIRLexer lexer) throws FHIRException {
Element source = rule.addElement("source").markLocation(lexer.getCurrentLocation());
source.makeElement("context").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
if (source.getChildValue("context").equals("search") && lexer.hasToken("(")) {
source.makeElement("context").markLocation(lexer.getCurrentLocation()).setValue("@search");
lexer.take();
SourceLocation loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
source.setUserData(StructureMapUtilities.MAP_SEARCH_EXPRESSION, node);
source.makeElement("element").markLocation(loc).setValue(node.toString());
lexer.token(")");
} else if (lexer.hasToken(".")) {
lexer.token(".");
source.makeElement("element").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (lexer.hasToken(":")) {
// type and cardinality
lexer.token(":");
source.makeElement("type").markLocation(lexer.getCurrentLocation()).setValue(lexer.takeDottedToken());
}
if (Utilities.isInteger(lexer.getCurrent())) {
source.makeElement("min").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
lexer.token("..");
source.makeElement("max").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (lexer.hasToken("default")) {
lexer.token("default");
source.makeElement("defaultValue").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("default value"));
}
if (Utilities.existsInList(lexer.getCurrent(), "first", "last", "not_first", "not_last", "only_one")) {
source.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (lexer.hasToken("as")) {
lexer.take();
source.makeElement("variable").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (lexer.hasToken("where")) {
lexer.take();
SourceLocation loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
source.setUserData(StructureMapUtilities.MAP_WHERE_EXPRESSION, node);
source.makeElement("condition").markLocation(loc).setValue(node.toString());
}
if (lexer.hasToken("check")) {
lexer.take();
SourceLocation loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
source.setUserData(StructureMapUtilities.MAP_WHERE_CHECK, node);
source.makeElement("check").markLocation(loc).setValue(node.toString());
}
if (lexer.hasToken("log")) {
lexer.take();
SourceLocation loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
source.setUserData(StructureMapUtilities.MAP_WHERE_CHECK, node);
source.makeElement("logMessage").markLocation(loc).setValue(lexer.take());
}
}
private void parseTarget(Element rule, FHIRLexer lexer) throws FHIRException {
Element target = rule.addElement("target").markLocation(lexer.getCurrentLocation());
SourceLocation loc = lexer.getCurrentLocation();
String start = lexer.take();
if (lexer.hasToken(".")) {
target.makeElement("context").markLocation(loc).setValue(start);
start = null;
lexer.token(".");
target.makeElement("element").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
String name;
boolean isConstant = false;
if (lexer.hasToken("=")) {
if (start != null) {
target.makeElement("context").markLocation(loc).setValue(start);
}
lexer.token("=");
isConstant = lexer.isConstant();
loc = lexer.getCurrentLocation();
name = lexer.take();
} else {
loc = lexer.getCurrentLocation();
name = start;
}
if ("(".equals(name)) {
// inline fluentpath expression
target.makeElement("transform").markLocation(lexer.getCurrentLocation()).setValue(StructureMapTransform.EVALUATE.toCode());
loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
target.setUserData(StructureMapUtilities.MAP_EXPRESSION, node);
target.addElement("parameter").markLocation(loc).makeElement("valueString").setValue(node.toString());
lexer.token(")");
} else if (lexer.hasToken("(")) {
target.makeElement("transform").markLocation(loc).setValue(name);
lexer.token("(");
if (target.getChildValue("transform").equals(StructureMapTransform.EVALUATE.toCode())) {
parseParameter(target, lexer);
lexer.token(",");
loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
target.setUserData(StructureMapUtilities.MAP_EXPRESSION, node);
target.addElement("parameter").markLocation(loc).setValue(node.toString());
} else {
while (!lexer.hasToken(")")) {
parseParameter(target, lexer);
if (!lexer.hasToken(")"))
lexer.token(",");
}
}
lexer.token(")");
} else if (name != null) {
target.makeElement("transform").markLocation(loc).setValue(StructureMapTransform.COPY.toCode());
if (!isConstant) {
loc = lexer.getCurrentLocation();
String id = name;
while (lexer.hasToken(".")) {
id = id + lexer.take() + lexer.take();
}
target.addElement("parameter").markLocation(loc).setValue(id);
} else {
target.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(readConstant(name, lexer));
}
}
if (lexer.hasToken("as")) {
lexer.take();
target.makeElement("variable").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
while (Utilities.existsInList(lexer.getCurrent(), "first", "last", "share", "collate")) {
if (lexer.getCurrent().equals("share")) {
target.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
target.makeElement("listRuleId").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
} else {
target.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
}
}
private void parseParameter(Element ref, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
if (!lexer.isConstant()) {
ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).makeElement("valueId").setValue(lexer.take());
} else if (lexer.isStringConstant())
ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).makeElement("valueString").setValue(lexer.readConstant("??"));
else {
ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).makeElement("valueString").setValue(readConstant(lexer.take(), lexer));
}
}
private void parseInput(Element group, FHIRLexer lexer, boolean newFmt) throws FHIRException {
Element input = group.addElement("input");
if (newFmt) {
input.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
} else
lexer.token("input");
input.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
if (lexer.hasToken(":")) {
lexer.token(":");
input.makeElement("type").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (!newFmt) {
lexer.token("as");
input.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
if (lexer.hasComments()) {
input.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
lexer.skipToken(";");
}
}
private boolean isSimpleSyntax(Element rule) {
return
(rule.getChildren("source").size() == 1 && rule.getChildren("source").get(0).hasChild("context") && rule.getChildren("source").get(0).hasChild("element") && !rule.getChildren("source").get(0).hasChild("variable")) &&
(rule.getChildren("target").size() == 1 && rule.getChildren("target").get(0).hasChild("context") && rule.getChildren("target").get(0).hasChild("element") && !rule.getChildren("target").get(0).hasChild("variable") &&
!rule.getChildren("target").get(0).hasChild("parameter")) &&
(rule.getChildren("dependent").size() == 0 && rule.getChildren("rule").size() == 0);
}
private String readConstant(String s, FHIRLexer lexer) throws FHIRLexerException {
if (Utilities.isInteger(s))
return s;
else if (Utilities.isDecimal(s, false))
return s;
else if (Utilities.existsInList(s, "true", "false"))
return s;
else
return lexer.processConstant(s);
}
}

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

@ -48,7 +48,7 @@ import org.hl7.fhir.r5.model.StructureDefinition;
public class Manager {
//TODO use EnumMap
public enum FhirFormat { XML, JSON, TURTLE, TEXT, VBAR, SHC;
public enum FhirFormat { XML, JSON, TURTLE, TEXT, VBAR, SHC, FML;
// SHC = smart health cards, including as text versions of QR codes
public String getExtension() {
@ -65,6 +65,8 @@ public class Manager {
return "hl7";
case SHC:
return "shc";
case FML:
return "fml";
}
return null;
}
@ -81,6 +83,8 @@ public class Manager {
return TEXT;
case "hl7":
return VBAR;
case "fml":
return FML;
}
return null;
}
@ -115,6 +119,7 @@ public class Manager {
case TURTLE : return new TurtleParser(context);
case VBAR : return new VerticalBarParser(context);
case SHC : return new SHCParser(context);
case FML : return new FmlParser(context);
case TEXT : throw new Error("Programming logic error: do not call makeParser for a text resource");
}
return null;
@ -123,6 +128,7 @@ public class Manager {
public static Element build(IWorkerContext context, StructureDefinition sd) {
Property p = new Property(context, sd.getSnapshot().getElementFirstRep(), sd);
Element e = new Element(p.getName(), p);
e.setPath(sd.getType());
return e;
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Property.java
View File

@ -270,8 +270,9 @@ public class Property {
String tc = definition.getType().get(0).getCode();
return definition.getType().size() == 1 && (("Resource".equals(tc) || "DomainResource".equals(tc)) || Utilities.existsInList(tc, context.getResourceNames()));
}
else
else {
return !definition.getPath().contains(".") && (structure.getKind() == StructureDefinitionKind.RESOURCE);
}
}
public boolean isList() {

83
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/TurtleParser.java
View File

@ -333,22 +333,24 @@ public class TurtleParser extends ParserBase {
}
String subjId = genSubjectId(e);
String ontologyId = subjId.replace(">", ".ttl>");
Section ontology = ttl.section("ontology header");
ontology.triple(ontologyId, "a", "owl:Ontology");
ontology.triple(ontologyId, "owl:imports", "fhir:fhir.ttl");
if(ontologyId.startsWith("<" + FHIR_URI_BASE))
ontology.triple(ontologyId, "owl:versionIRI", ontologyId.replace(FHIR_URI_BASE, FHIR_VERSION_BASE));
Subject subject;
if (hasModifierExtension(e))
subject = section.triple(subjId, "a", "fhir:_" + e.getType());
else
subject = section.triple(subjId, "a", "fhir:" + e.getType());
subject.linkedPredicate("fhir:nodeRole", "fhir:treeRoot", linkResolver == null ? null : linkResolver.resolvePage("rdf.html#tree-root"), null);
Subject subject = section.triple(subjId, "a", "fhir:" + e.getType());
subject.linkedPredicate("fhir:nodeRole", "fhir:treeRoot", linkResolver == null ? null : linkResolver.resolvePage("rdf.html#tree-root"), null);
for (Element child : e.getChildren()) {
composeElement(section, subject, child, null);
}
for (Element child : e.getChildren()) {
composeElement(section, subject, child, null);
}
}
private boolean hasModifierExtension(Element e) {
return e.getChildren().stream().anyMatch(p -> p.getName().equals("modifierExtension"));
}
protected String getURIType(String uri) {
if(uri.startsWith("<" + FHIR_URI_BASE))
if(uri.substring(FHIR_URI_BASE.length() + 1).contains("/"))
@ -415,17 +417,18 @@ public class TurtleParser extends ParserBase {
Complex t;
if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY && parent != null && parent.getNamedChildValue("fullUrl") != null) {
String url = "<"+parent.getNamedChildValue("fullUrl")+">";
ctxt.linkedPredicate("fhir:"+en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment);
ctxt.linkedPredicate("fhir:"+en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment, element.getProperty().isList());
t = section.subject(url);
} else {
t = ctxt.linkedPredicate("fhir:"+en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment);
t = ctxt.linkedPredicate("fhir:"+en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment, element.getProperty().isList());
}
if (element.getProperty().getName().endsWith("[x]") && !element.hasValue()) {
t.linkedPredicate("a", "fhir:" + element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()), null);
}
if (element.getSpecial() != null)
t.linkedPredicate("a", "fhir:"+element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()), null);
if (element.hasValue())
t.linkedPredicate("fhir:value", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()), null);
if (element.getProperty().isList() && (!element.isResource() || element.getSpecial() == SpecialElement.CONTAINED))
t.linkedPredicate("fhir:index", Integer.toString(element.getIndex()), linkResolver == null ? null : linkResolver.resolvePage("rdf.html#index"), null);
t.linkedPredicate("fhir:v", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()), null);
if ("Coding".equals(element.getType()))
decorateCoding(t, element, section);
@ -463,37 +466,27 @@ public class TurtleParser extends ParserBase {
private String getFormalName(Element element) {
String en = null;
if (element.getSpecial() == null) {
if (element.getProperty().getDefinition().hasBase())
en = element.getProperty().getDefinition().getBase().getPath();
}
if (element.getSpecial() == null)
en = element.getProperty().getName();
else if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY)
en = "Bundle.entry.resource";
en = "resource";
else if (element.getSpecial() == SpecialElement.BUNDLE_OUTCOME)
en = "Bundle.entry.response.outcome";
en = "outcome";
else if (element.getSpecial() == SpecialElement.PARAMETER)
en = element.getElementProperty().getDefinition().getPath();
else // CONTAINED
en = "DomainResource.contained";
en = "contained";
if (en == null)
en = element.getProperty().getDefinition().getPath();
boolean doType = false;
if (en.endsWith("[x]")) {
en = en.substring(0, en.length()-3);
doType = true;
}
if (doType || (element.getProperty().getDefinition().getType().size() > 1 && !allReference(element.getProperty().getDefinition().getType())))
en = en + Utilities.capitalize(element.getType());
return en;
}
private boolean allReference(List<TypeRefComponent> types) {
for (TypeRefComponent t : types) {
if (!t.getCode().equals("Reference"))
return false;
}
return true;
if (en == null)
en = element.getProperty().getName();
if (en.endsWith("[x]"))
en = en.substring(0, en.length()-3);
if (hasModifierExtension(element))
return "_" + en;
else
return en;
}
static public String ttlLiteral(String value, String type) {
@ -550,10 +543,14 @@ public class TurtleParser extends ParserBase {
else
t.linkedPredicate("a", "sct:" + urlescape(code), null, null);
} else if ("http://loinc.org".equals(system)) {
t.prefix("loinc", "http://loinc.org/rdf#");
t.prefix("loinc", "https://loinc.org/rdf/");
t.linkedPredicate("a", "loinc:"+urlescape(code).toUpperCase(), null, null);
} else if ("https://www.nlm.nih.gov/mesh".equals(system)) {
t.prefix("mesh", "http://id.nlm.nih.gov/mesh/");
t.linkedPredicate("a", "mesh:"+urlescape(code), null, null);
}
}
private void generateLinkedPredicate(Complex t, String code) throws FHIRException {
Expression expression = SnomedExpressions.parse(code);

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/FormatUtilities.java
View File

@ -80,7 +80,11 @@ public abstract class FormatUtilities {
public static final String XHTML_NS = "http://www.w3.org/1999/xhtml";
public static final String NS_XSI = "http://www.w3.org/2001/XMLSchema-instance";
private static final int MAX_SCAN_LENGTH = 1000; // how many characters to scan into content when autodetermining format
public static final String MAP_ATTRIBUTE_NAME = "mapAttribute";
public static final String PROPERTY_NAME = "property";
public static String WORKING_CM_PROP_NAME = PROPERTY_NAME;
protected String toString(String value) {
return value;
}

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/JsonParser.java
View File

@ -9418,10 +9418,10 @@ public class JsonParser extends JsonParserBase {
protected void parseConceptMapOtherElementComponentProperties(JsonObject json, ConceptMap.OtherElementComponent res) throws IOException, FHIRFormatError {
parseBackboneElementProperties(json, res);
if (json.has("property"))
res.setPropertyElement(parseUri(json.get("property").getAsString()));
if (json.has("_property"))
parseElementProperties(getJObject(json, "_property"), res.getPropertyElement());
if (json.has(FormatUtilities.WORKING_CM_PROP_NAME))
res.setPropertyElement(parseUri(json.get(FormatUtilities.WORKING_CM_PROP_NAME).getAsString()));
if (json.has("_"+FormatUtilities.WORKING_CM_PROP_NAME))
parseElementProperties(getJObject(json, "_"+FormatUtilities.WORKING_CM_PROP_NAME), res.getPropertyElement());
DataType value = parseType("value", json);
if (value != null)
res.setValue(value);
@ -44920,8 +44920,8 @@ public class JsonParser extends JsonParserBase {
protected void composeOtherElementComponentProperties(ConceptMap.OtherElementComponent element) throws IOException {
composeBackboneElementProperties(element);
if (element.hasPropertyElement()) {
composeUriCore("property", element.getPropertyElement(), false);
composeUriExtras("property", element.getPropertyElement(), false);
composeUriCore(FormatUtilities.WORKING_CM_PROP_NAME, element.getPropertyElement(), false);
composeUriExtras(FormatUtilities.WORKING_CM_PROP_NAME, element.getPropertyElement(), false);
}
if (element.hasValue()) {
composeType("value", element.getValue());

1690
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/RdfParser.java
View File

File diff suppressed because it is too large Load Diff

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/RdfParserBase.java
View File

@ -122,10 +122,10 @@ public abstract class RdfParserBase extends ParserBase implements IParser {
return;
if ("http://snomed.info/sct".equals(element.getSystem())) {
t.prefix("sct", "http://snomed.info/sct/");
t.predicate("a", "sct:"+element.getCode());
t.predicate("a", "sct:"+element.getCode(), false);
} else if ("http://snomed.info/sct".equals(element.getSystem())) {
t.prefix("loinc", "http://loinc.org/rdf#");
t.predicate("a", "loinc:"+element.getCode());
t.predicate("a", "loinc:"+element.getCode(), false);
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/XmlParser.java
View File

@ -8204,7 +8204,7 @@ public class XmlParser extends XmlParserBase {
}
protected boolean parseConceptMapOtherElementComponentContent(int eventType, XmlPullParser xpp, ConceptMap.OtherElementComponent res) throws XmlPullParserException, IOException, FHIRFormatError {
if (eventType == XmlPullParser.START_TAG && xpp.getName().equals("property")) {
if (eventType == XmlPullParser.START_TAG && xpp.getName().equals(FormatUtilities.WORKING_CM_PROP_NAME)) {
res.setPropertyElement(parseUri(xpp));
} else if (eventType == XmlPullParser.START_TAG && nameIsTypeName(xpp, "value")) {
res.setValue(parseType("value", xpp));
@ -38972,7 +38972,7 @@ public class XmlParser extends XmlParserBase {
protected void composeConceptMapOtherElementComponentElements(ConceptMap.OtherElementComponent element) throws IOException {
composeBackboneElementElements(element);
if (element.hasPropertyElement()) {
composeUri("property", element.getPropertyElement());
composeUri(FormatUtilities.WORKING_CM_PROP_NAME, element.getPropertyElement());
}
if (element.hasValue()) {
composeType("value", element.getValue());

15
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/DomainResource.java
View File

@ -34,7 +34,11 @@ package org.hl7.fhir.r5.model;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.r5.model.Enumerations.*;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.StandardsStatus;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.ICompositeType;
@ -467,7 +471,7 @@ public void checkNoModifiers(String noun, String verb) throws FHIRException {
}
}
public Resource getContained(String ref) {
public Resource getContained(String ref) {
if (ref == null)
return null;
@ -509,6 +513,15 @@ public void checkNoModifiers(String noun, String verb) throws FHIRException {
}
return Collections.unmodifiableList(retVal);
}
public StandardsStatus getStandardsStatus() {
return ToolingExtensions.getStandardsStatus(this);
}
public void setStandardsStatus(StandardsStatus status) {
ToolingExtensions.setStandardsStatus(this, status, null);
}
// end addition
}

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Element.java
View File

@ -34,8 +34,11 @@ package org.hl7.fhir.r5.model;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import org.hl7.fhir.utilities.StandardsStatus;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.r5.model.Enumerations.*;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.ICompositeType;
@ -430,6 +433,15 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
return ext.get(0).getValue().primitiveValue();
}
public StandardsStatus getStandardsStatus() {
return ToolingExtensions.getStandardsStatus(this);
}
public void setStandardsStatus(StandardsStatus status) {
ToolingExtensions.setStandardsStatus(this, status, null);
}
// end addition
}

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ElementDefinition.java
View File

@ -13521,6 +13521,9 @@ If a pattern[x] is declared on a repeating element, the pattern applies to all r
return hasPath() ? getPath().contains(".") ? getPath().substring(getPath().lastIndexOf(".")+1) : getPath() : null;
}
public String getNameBase() {
return getName().replace("[x]", "");
}
public boolean unbounded() {
return getMax().equals("*") || Integer.parseInt(getMax()) > 1;
}
@ -13554,6 +13557,8 @@ If a pattern[x] is declared on a repeating element, the pattern applies to all r
return getMin() == 1;
}
// end addition
}

80
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/TypeDetails.java
View File

@ -115,10 +115,13 @@ public class TypeDetails {
public boolean isSystemType() {
return uri.startsWith(FP_NS);
}
}
private List<ProfiledType> types = new ArrayList<ProfiledType>();
private CollectionStatus collectionStatus;
private Set<String> targets; // or, not and, canonical urls
public TypeDetails(CollectionStatus collectionStatus, String... names) {
super();
this.collectionStatus = collectionStatus;
@ -151,6 +154,7 @@ public class TypeDetails {
addType(pt);
return res;
}
public void addType(ProfiledType pt) {
for (ProfiledType et : types) {
if (et.uri.equals(pt.uri)) {
@ -175,7 +179,29 @@ public class TypeDetails {
}
types.add(pt);
}
public void addType(CollectionStatus status, ProfiledType pt) {
addType(pt);
if (collectionStatus == null) {
collectionStatus = status;
} else {
switch (status) {
case ORDERED:
if (collectionStatus == CollectionStatus.SINGLETON) {
collectionStatus = status;
}
break;
case SINGLETON:
break;
case UNORDERED:
collectionStatus = status;
break;
default:
break;
}
}
}
public void addTypes(Collection<String> names) {
for (String n : names)
addType(new ProfiledType(n));
@ -245,7 +271,14 @@ public class TypeDetails {
collectionStatus = source.collectionStatus;
else
collectionStatus = CollectionStatus.ORDERED;
if (source.targets != null) {
if (targets == null) {
targets = new HashSet<>();
}
targets.addAll(source.targets);
}
}
public TypeDetails union(TypeDetails right) {
TypeDetails result = new TypeDetails(null);
if (right.collectionStatus == CollectionStatus.UNORDERED || collectionStatus == CollectionStatus.UNORDERED)
@ -256,6 +289,16 @@ public class TypeDetails {
result.addType(pt);
for (ProfiledType pt : right.types)
result.addType(pt);
if (targets != null || right.targets != null) {
result.targets = new HashSet<>();
if (targets != null) {
result.targets.addAll(targets);
}
if (right.targets != null) {
result.targets.addAll(right.targets);
}
}
return result;
}
@ -274,6 +317,15 @@ public class TypeDetails {
}
for (ProfiledType pt : right.types)
result.addType(pt);
if (targets != null && right.targets != null) {
result.targets = new HashSet<>();
for (String s : targets) {
if (right.targets.contains(s)) {
result.targets.add(s);
}
}
}
return result;
}
@ -359,5 +411,31 @@ public class TypeDetails {
return null;
}
public void addTarget(String url) {
if (targets == null) {
targets = new HashSet<>();
}
targets.add(url);
}
public Set<String> getTargets() {
return targets;
}
public boolean typesHaveTargets() {
for (ProfiledType pt : types) {
if (Utilities.existsInList(pt.getUri(), "Reference", "CodeableReference", "canonical", "http://hl7.org/fhir/StructureDefinition/Reference", "http://hl7.org/fhir/StructureDefinition/CodeableReference", "http://hl7.org/fhir/StructureDefinition/canonical")) {
return true;
}
}
return false;
}
public void addTargets(Set<String> src) {
if (src != null) {
for (String s : src) {
addTarget(s);
}
}
}
}

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ConceptMapRenderer.java
View File

@ -212,7 +212,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
} else
tr.td().b().tx("Code");
for (String s : sources.keySet()) {
if (!s.equals("code")) {
if (s != null && !s.equals("code")) {
if (sources.get(s).size() == 1) {
String url = sources.get(s).iterator().next();
renderCSDetailsLink(tr, url, false);
@ -229,7 +229,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
} else
tr.td().b().tx("Code");
for (String s : targets.keySet()) {
if (!s.equals("code")) {
if (s != null && !s.equals("code")) {
if (targets.get(s).size() == 1) {
String url = targets.get(s).iterator().next();
renderCSDetailsLink(tr, url, false);
@ -291,7 +291,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
td.style("border-top-style: none; border-left-width: 0px");
}
for (String s : sources.keySet()) {
if (!s.equals("code")) {
if (s != null && !s.equals("code")) {
td = tr.td();
if (first) {
td.addText(getValue(ccm.getDependsOn(), s, sources.get(s).size() != 1));
@ -323,7 +323,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
tr.td().style("border-left-width: 0px").tx(display == null ? "" : display);
for (String s : targets.keySet()) {
if (!s.equals("code")) {
if (s != null && !s.equals("code")) {
td = tr.td();
td.addText(getValue(ccm.getProduct(), s, targets.get(s).size() != 1));
display = getDisplay(ccm.getProduct(), s);

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DiagnosticReportRenderer.java
View File

@ -125,7 +125,11 @@ public class DiagnosticReportRenderer extends ResourceRenderer {
pw = getProperty(dr, "conclusion");
if (valued(pw)) {
render(x.para(), pw.value());
if (pw.fhirType().equals("markdown")) {
render(x, pw.value());
} else {
render(x.para(), pw.value());
}
}
pw = getProperty(dr, "conclusionCode");

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ResourceRenderer.java
View File

@ -223,12 +223,15 @@ public abstract class ResourceRenderer extends DataRenderer {
tr = resolveReference(rw, r.getReference());
if (!r.getReference().startsWith("#")) {
if (tr != null && tr.getReference() != null)
if (tr != null && tr.getReference() != null) {
c = x.ah(tr.getReference());
else
} else if (r.getReference().contains("?")) {
x.tx("Conditional Reference: ");
c = x.code("");
} else {
c = x.ah(r.getReference());
}
} else {
c = x.ah(r.getReference());
}
} else {

7
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/StructureDefinitionRenderer.java
View File

@ -77,6 +77,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Title;
import org.hl7.fhir.utilities.xhtml.NodeType;
@ -324,7 +325,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
model = initCustomTable(gen, corePath, false, true, profile.getId()+(diff ? "d" : "s"), rc.getRules() == GenerationRules.IG_PUBLISHER, columns);
break;
case SUMMARY:
model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), rc.getRules() == GenerationRules.IG_PUBLISHER);
model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), rc.getRules() == GenerationRules.IG_PUBLISHER, rc.getRules() == GenerationRules.IG_PUBLISHER ? TableGenerationMode.XHTML : TableGenerationMode.XML);
break;
default:
throw new Error("Unknown structure mode");
@ -2052,7 +2053,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
} else if (definition.hasExample()) {
for (ElementDefinitionExampleComponent ex : definition.getExample()) {
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, "Example'"+("".equals("General")? "" : " "+ex.getLabel()+"'")+": ", null).addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, "Example'"+("".equals("General")? "": " "+ex.getLabel()+"'")+": ", "").addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, buildJson(ex.getValue()), null).addStyle("color: darkgreen")));
}
}
@ -2667,7 +2668,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, String imagePath, Set<String> outputTracker, RenderingContext rc) throws IOException, FHIRException {
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
gen.setTranslator(getTranslator());
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId()+(full ? "f" : "n"), true);
TableModel model = gen.initNormalTable(corePath, false, true, ed.getId()+(full ? "f" : "n"), true, TableGenerationMode.XHTML);
boolean deep = false;
String m = "";

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestPackageLoader.java
View File

@ -52,4 +52,14 @@ public class TestPackageLoader implements IContextResourceLoader {
return new ArrayList<>();
}
@Override
public void setPatchUrls(boolean value) {
}
@Override
public String patchUrl(String url, String resourceType) {
return url;
}
}

29
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRLexer.java
View File

@ -89,6 +89,7 @@ public class FHIRLexer {
private String name;
private boolean liquidMode; // in liquid mode, || terminates the expression and hands the parser back to the host
private SourceLocation commentLocation;
private boolean metadataFormat;
public FHIRLexer(String source, String name) throws FHIRLexerException {
this.source = source == null ? "" : source;
@ -102,6 +103,13 @@ public class FHIRLexer {
currentLocation = new SourceLocation(1, 1);
next();
}
public FHIRLexer(String source, String name, boolean metadataFormat) throws FHIRLexerException {
this.source = source == null ? "" : source;
this.name = name == null ? "??" : name;
this.metadataFormat = metadataFormat;
currentLocation = new SourceLocation(1, 1);
next();
}
public String getCurrent() {
return current;
}
@ -211,10 +219,13 @@ public class FHIRLexer {
} else if (ch == '/') {
cursor++;
if (cursor < source.length() && (source.charAt(cursor) == '/')) {
// this is en error - should already have been skipped
error("This shouldn't happen?");
// we've run into metadata
cursor++;
cursor++;
current = source.substring(currentStart, cursor);
} else {
current = source.substring(currentStart, cursor);
}
current = source.substring(currentStart, cursor);
} else if (ch == '$') {
cursor++;
while (cursor < source.length() && (source.charAt(cursor) >= 'a' && source.charAt(cursor) <= 'z'))
@ -309,7 +320,7 @@ public class FHIRLexer {
boolean last13 = false;
boolean done = false;
while (cursor < source.length() && !done) {
if (cursor < source.length() -1 && "//".equals(source.substring(cursor, cursor+2))) {
if (cursor < source.length() -1 && "//".equals(source.substring(cursor, cursor+2)) && !isMetadataStart()) {
commentLocation = currentLocation;
int start = cursor+2;
while (cursor < source.length() && !((source.charAt(cursor) == '\r') || source.charAt(cursor) == '\n')) {
@ -338,6 +349,10 @@ public class FHIRLexer {
}
}
private boolean isMetadataStart() {
return metadataFormat && cursor < source.length() - 2 && "///".equals(source.substring(cursor, cursor+3));
}
private boolean isDateChar(char ch,int start) {
int eot = source.charAt(start+1) == 'T' ? 10 : 20;
@ -550,5 +565,11 @@ public class FHIRLexer {
public SourceLocation getCommentLocation() {
return this.commentLocation;
}
public boolean isMetadataFormat() {
return metadataFormat;
}
public void setMetadataFormat(boolean metadataFormat) {
this.metadataFormat = metadataFormat;
}
}

218
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -30,6 +30,7 @@ import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.BaseDateTimeType;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.DateTimeType;
@ -386,6 +387,7 @@ public class FHIRPathEngine {
}
}
initFlags();
cu = new ContextUtilities(worker);
}
private void initFlags() {
@ -578,6 +580,23 @@ public class FHIRPathEngine {
* @if the path is not valid
*/
public TypeDetails check(Object appContext, String resourceType, String context, ExpressionNode expr) throws FHIRLexerException, PathEngineException, DefinitionException {
return check(appContext, resourceType, context, expr, null);
}
/**
* check that paths referred to in the ExpressionNode are valid
*
* xPathStartsWithValueRef is a hack work around for the fact that FHIR Path sometimes needs a different starting point than the xpath
*
* returns a list of the possible types that might be returned by executing the ExpressionNode against a particular context
*
* @param context - the logical type against which this path is applied
* @throws DefinitionException
* @throws PathEngineException
* @if the path is not valid
*/
public TypeDetails check(Object appContext, String resourceType, String context, ExpressionNode expr, Set<ElementDefinition> elementDependencies) throws FHIRLexerException, PathEngineException, DefinitionException {
// if context is a path that refers to a type, do that conversion now
TypeDetails types;
if (context == null) {
@ -610,7 +629,33 @@ public class FHIRPathEngine {
}
}
return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, true);
return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, elementDependencies, true);
}
/**
* check that paths referred to in the ExpressionNode are valid
*
* xPathStartsWithValueRef is a hack work around for the fact that FHIR Path sometimes needs a different starting point than the xpath
*
* returns a list of the possible types that might be returned by executing the ExpressionNode against a particular context
*
* @throws DefinitionException
* @throws PathEngineException
* @if the path is not valid
*/
public TypeDetails check(Object appContext, String resourceType, List<String> resourceTypes, ExpressionNode expr, Set<ElementDefinition> elementDependencies) throws FHIRLexerException, PathEngineException, DefinitionException {
// if context is a path that refers to a type, do that conversion now
TypeDetails types = null;
for (String rt : resourceTypes) {
if (types == null) {
types = new TypeDetails(CollectionStatus.SINGLETON, rt);
} else {
types.addType(rt);
}
}
return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, elementDependencies, true);
}
private FHIRException makeExceptionPlural(Integer num, ExpressionNode holder, String constName, Object... args) {
@ -659,13 +704,13 @@ public class FHIRPathEngine {
}
}
return executeType(new ExecutionTypeContext(appContext, sd.getUrl(), types, types), types, expr, true);
return executeType(new ExecutionTypeContext(appContext, sd.getUrl(), types, types), types, expr, null, true);
}
public TypeDetails check(Object appContext, StructureDefinition sd, ExpressionNode expr) throws FHIRLexerException, PathEngineException, DefinitionException {
// if context is a path that refers to a type, do that conversion now
TypeDetails types = null; // this is a special case; the first path reference will have to resolve to something in the context
return executeType(new ExecutionTypeContext(appContext, sd == null ? null : sd.getUrl(), null, types), types, expr, true);
return executeType(new ExecutionTypeContext(appContext, sd == null ? null : sd.getUrl(), null, types), types, expr, null, true);
}
public TypeDetails check(Object appContext, String resourceType, String context, String expr) throws FHIRLexerException, PathEngineException, DefinitionException {
@ -1557,7 +1602,7 @@ public class FHIRPathEngine {
return new TypeDetails(CollectionStatus.SINGLETON, exp.getName());
}
private TypeDetails executeType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, boolean atEntry) throws PathEngineException, DefinitionException {
private TypeDetails executeType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, Set<ElementDefinition> elementDependencies, boolean atEntry) throws PathEngineException, DefinitionException {
TypeDetails result = new TypeDetails(null);
switch (exp.getKind()) {
case Name:
@ -1571,7 +1616,7 @@ public class FHIRPathEngine {
result.update(executeContextType(context, exp.getName(), exp));
} else {
for (String s : focus.getTypes()) {
result.update(executeType(s, exp, atEntry));
result.update(executeType(s, exp, atEntry, focus, elementDependencies));
}
if (result.hasNoTypes()) {
throw makeException(exp, I18nConstants.FHIRPATH_UNKNOWN_NAME, exp.getName(), focus.describe());
@ -1579,7 +1624,7 @@ public class FHIRPathEngine {
}
break;
case Function:
result.update(evaluateFunctionType(context, focus, exp));
result.update(evaluateFunctionType(context, focus, exp, elementDependencies));
break;
case Unary:
result.addType(TypeDetails.FP_Integer);
@ -1590,12 +1635,12 @@ public class FHIRPathEngine {
result.update(resolveConstantType(context, exp.getConstant(), exp));
break;
case Group:
result.update(executeType(context, focus, exp.getGroup(), atEntry));
result.update(executeType(context, focus, exp.getGroup(), elementDependencies, atEntry));
}
exp.setTypes(result);
if (exp.getInner() != null) {
result = executeType(context, result, exp.getInner(), false);
result = executeType(context, result, exp.getInner(), elementDependencies, false);
}
if (exp.isProximal() && exp.getOperation() != null) {
@ -1606,7 +1651,7 @@ public class FHIRPathEngine {
if (last.getOperation() == Operation.Is || last.getOperation() == Operation.As) {
work = executeTypeName(context, focus, next, atEntry);
} else {
work = executeType(context, focus, next, atEntry);
work = executeType(context, focus, next, elementDependencies, atEntry);
}
result = operateTypes(result, last.getOperation(), work, last);
last = next;
@ -1917,7 +1962,12 @@ public class FHIRPathEngine {
case LessOrEqual: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case GreaterOrEqual: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case Is: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case As: return new TypeDetails(CollectionStatus.SINGLETON, right.getTypes());
case As:
TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON, right.getTypes());
if (td.typesHaveTargets()) {
td.addTargets(left.getTargets());
}
return td;
case Union: return left.union(right);
case Or: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case And: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
@ -3102,12 +3152,12 @@ public class FHIRPathEngine {
return hostServices.resolveConstantType(context.appInfo, name);
}
private TypeDetails executeType(String type, ExpressionNode exp, boolean atEntry) throws PathEngineException, DefinitionException {
private TypeDetails executeType(String type, ExpressionNode exp, boolean atEntry, TypeDetails focus, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
if (atEntry && Character.isUpperCase(exp.getName().charAt(0)) && hashTail(type).equals(exp.getName())) { // special case for start up
return new TypeDetails(CollectionStatus.SINGLETON, type);
}
TypeDetails result = new TypeDetails(null);
getChildTypesByName(type, exp.getName(), result, exp);
getChildTypesByName(type, exp.getName(), result, exp, focus, elementDependencies);
return result;
}
@ -3118,7 +3168,7 @@ public class FHIRPathEngine {
@SuppressWarnings("unchecked")
private TypeDetails evaluateFunctionType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp) throws PathEngineException, DefinitionException {
private TypeDetails evaluateFunctionType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
List<TypeDetails> paramTypes = new ArrayList<TypeDetails>();
if (exp.getFunction() == Function.Is || exp.getFunction() == Function.As || exp.getFunction() == Function.OfType) {
paramTypes.add(new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
@ -3126,9 +3176,9 @@ public class FHIRPathEngine {
int i = 0;
for (ExpressionNode expr : exp.getParameters()) {
if (isExpressionParameter(exp, i)) {
paramTypes.add(executeType(changeThis(context, focus), focus, expr, true));
paramTypes.add(executeType(changeThis(context, focus), focus, expr, elementDependencies, true));
} else {
paramTypes.add(executeType(context, context.thisItem, expr, true));
paramTypes.add(executeType(context, context.thisItem, expr, elementDependencies, true));
}
i++;
}
@ -3159,11 +3209,11 @@ public class FHIRPathEngine {
case Where :
return focus;
case Select :
return anything(focus.getCollectionStatus());
return paramTypes.get(0);
case All :
return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case Repeat :
return anything(focus.getCollectionStatus());
return paramTypes.get(0); // this might be a little more complicated...
case Aggregate :
return anything(focus.getCollectionStatus());
case Item : {
@ -3172,12 +3222,20 @@ public class FHIRPathEngine {
return focus;
}
case As : {
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
return new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
if (td.typesHaveTargets()) {
td.addTargets(focus.getTargets());
}
return td;
}
case OfType : {
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
return new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
if (td.typesHaveTargets()) {
td.addTargets(focus.getTargets());
}
return td;
}
case Type : {
boolean s = false;
@ -3326,11 +3384,19 @@ public class FHIRPathEngine {
return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_DateTime);
case Resolve : {
checkContextReference(focus, "resolve", exp);
return new TypeDetails(CollectionStatus.SINGLETON, "DomainResource");
return new TypeDetails(CollectionStatus.ORDERED, "DomainResource");
}
case Extension : {
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
return new TypeDetails(CollectionStatus.SINGLETON, "Extension");
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
ExpressionNode p = exp.getParameters().get(0);
if (p.getKind() == Kind.Constant && p.getConstant() != null) {
String url = exp.getParameters().get(0).getConstant().primitiveValue();
StructureDefinition sd = worker.fetchResource(StructureDefinition.class, url);
if (sd != null) {
return new TypeDetails(CollectionStatus.ORDERED, new ProfiledType(url));
}
return new TypeDetails(CollectionStatus.SINGLETON, "Extension");
}
}
case AnyTrue:
return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
@ -3572,7 +3638,7 @@ public class FHIRPathEngine {
private TypeDetails childTypes(TypeDetails focus, String mask, ExpressionNode expr) throws PathEngineException, DefinitionException {
TypeDetails result = new TypeDetails(CollectionStatus.UNORDERED);
for (String f : focus.getTypes()) {
getChildTypesByName(f, mask, result, expr);
getChildTypesByName(f, mask, result, expr, null, null);
}
return result;
}
@ -4011,6 +4077,7 @@ public class FHIRPathEngine {
}
private static final char[] HEX_ARRAY = "0123456789ABCDEF".toCharArray();
private ContextUtilities cu;
public static String bytesToHex(byte[] bytes) {
char[] hexChars = new char[bytes.length * 2];
for (int j = 0; j < bytes.length; j++) {
@ -5693,7 +5760,7 @@ public class FHIRPathEngine {
}
private void getChildTypesByName(String type, String name, TypeDetails result, ExpressionNode expr) throws PathEngineException, DefinitionException {
private void getChildTypesByName(String type, String name, TypeDetails result, ExpressionNode expr, TypeDetails focus, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
if (Utilities.noString(type)) {
throw makeException(expr, I18nConstants.FHIRPATH_NO_TYPE, "", "getChildTypesByName");
}
@ -5737,11 +5804,11 @@ public class FHIRPathEngine {
if (dt == null) {
throw makeException(expr, I18nConstants.FHIRPATH_NO_TYPE, ProfileUtilities.sdNs(t.getCode(), null), "getChildTypesByName");
}
addTypeAndDescendents(sdl, dt, new ContextUtilities(worker).allStructures());
addTypeAndDescendents(sdl, dt, cu.allStructures());
// also add any descendant types
}
} else {
addTypeAndDescendents(sdl, sd, new ContextUtilities(worker).allStructures());
addTypeAndDescendents(sdl, sd, cu.allStructures());
if (type.contains("#")) {
tail = type.substring(type.indexOf("#")+1);
tail = tail.substring(tail.indexOf("."));
@ -5753,26 +5820,44 @@ public class FHIRPathEngine {
if (name.equals("**")) {
assert(result.getCollectionStatus() == CollectionStatus.UNORDERED);
for (ElementDefinition ed : sdi.getSnapshot().getElement()) {
if (ed.getPath().startsWith(path))
for (TypeRefComponent t : ed.getType()) {
if (t.hasCode() && t.getCodeElement().hasValue()) {
String tn = null;
if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement")) {
tn = sdi.getType()+"#"+ed.getPath();
} else {
tn = t.getCode();
if (ed.getPath().startsWith(path)) {
if (ed.hasContentReference()) {
String cpath = ed.getContentReference();
String tn = sdi.getType()+cpath;
if (!result.hasType(worker, tn)) {
if (elementDependencies != null) {
elementDependencies.add(ed);
}
if (t.getCode().equals("Resource")) {
for (String rn : worker.getResourceNames()) {
if (!result.hasType(worker, rn)) {
getChildTypesByName(result.addType(rn), "**", result, expr);
}
getChildTypesByName(result.addType(tn), "**", result, expr, null, elementDependencies);
}
} else {
for (TypeRefComponent t : ed.getType()) {
if (t.hasCode() && t.getCodeElement().hasValue()) {
String tn = null;
if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement")) {
tn = sdi.getType()+"#"+ed.getPath();
} else {
tn = t.getCode();
}
if (t.getCode().equals("Resource")) {
for (String rn : worker.getResourceNames()) {
if (!result.hasType(worker, rn)) {
if (elementDependencies != null) {
elementDependencies.add(ed);
}
getChildTypesByName(result.addType(rn), "**", result, expr, null, elementDependencies);
}
}
} else if (!result.hasType(worker, tn)) {
if (elementDependencies != null) {
elementDependencies.add(ed);
}
getChildTypesByName(result.addType(tn), "**", result, expr, null, elementDependencies);
}
} else if (!result.hasType(worker, tn)) {
getChildTypesByName(result.addType(tn), "**", result, expr);
}
}
}
}
}
} else if (name.equals("*")) {
assert(result.getCollectionStatus() == CollectionStatus.UNORDERED);
@ -5780,13 +5865,26 @@ public class FHIRPathEngine {
if (ed.getPath().startsWith(path) && !ed.getPath().substring(path.length()).contains("."))
for (TypeRefComponent t : ed.getType()) {
if (Utilities.noString(t.getCode())) { // Element.id or Extension.url
if (elementDependencies != null) {
elementDependencies.add(ed);
}
result.addType("System.string");
} else if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement")) {
if (elementDependencies != null) {
elementDependencies.add(ed);
}
result.addType(sdi.getType()+"#"+ed.getPath());
} else if (t.getCode().equals("Resource")) {
if (elementDependencies != null) {
elementDependencies.add(ed);
}
result.addTypes(worker.getResourceNames());
} else {
if (elementDependencies != null) {
elementDependencies.add(ed);
}
result.addType(t.getCode());
copyTargetProfiles(ed, t, focus, result);
}
}
}
@ -5795,12 +5893,18 @@ public class FHIRPathEngine {
ElementDefinitionMatch ed = getElementDefinition(sdi, path, isAllowPolymorphicNames(), expr);
if (ed != null) {
if (!Utilities.noString(ed.getFixedType()))
if (!Utilities.noString(ed.getFixedType())) {
if (elementDependencies != null) {
elementDependencies.add(ed.definition);
}
result.addType(ed.getFixedType());
else {
} else {
for (TypeRefComponent t : ed.getDefinition().getType()) {
if (Utilities.noString(t.getCode())) {
if (Utilities.existsInList(ed.getDefinition().getId(), "Element.id", "Extension.url") || Utilities.existsInList(ed.getDefinition().getBase().getPath(), "Resource.id", "Element.id", "Extension.url")) {
if (elementDependencies != null) {
elementDependencies.add(ed.definition);
}
result.addType(TypeDetails.FP_NS, "string");
}
break; // throw new PathEngineException("Illegal reference to primitive value attribute @ "+path);
@ -5810,6 +5914,9 @@ public class FHIRPathEngine {
if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement")) {
pt = new ProfiledType(sdi.getUrl()+"#"+path);
} else if (t.getCode().equals("Resource")) {
if (elementDependencies != null) {
elementDependencies.add(ed.definition);
}
result.addTypes(worker.getResourceNames());
} else {
pt = new ProfiledType(t.getCode());
@ -5821,7 +5928,11 @@ public class FHIRPathEngine {
if (ed.getDefinition().hasBinding()) {
pt.addBinding(ed.getDefinition().getBinding());
}
result.addType(pt);
if (elementDependencies != null) {
elementDependencies.add(ed.definition);
}
result.addType(ed.definition.unbounded() ? CollectionStatus.ORDERED : CollectionStatus.SINGLETON, pt);
copyTargetProfiles(ed.getDefinition(), t, focus, result);
}
}
}
@ -5831,6 +5942,18 @@ public class FHIRPathEngine {
}
}
private void copyTargetProfiles(ElementDefinition ed, TypeRefComponent t, TypeDetails focus, TypeDetails result) {
if (t.hasTargetProfile()) {
for (CanonicalType u : t.getTargetProfile()) {
result.addTarget(u.primitiveValue());
}
} else if (focus != null && focus.hasType("CodeableReference") && ed.getPath().endsWith(".reference") && focus.getTargets() != null) { // special case, targets are on parent
for (String s : focus.getTargets()) {
result.addTarget(s);
}
}
}
private void addTypeAndDescendents(List<StructureDefinition> sdl, StructureDefinition dt, List<StructureDefinition> types) {
sdl.add(dt);
for (StructureDefinition sd : types) {
@ -5860,7 +5983,7 @@ public class FHIRPathEngine {
}
private ElementDefinitionMatch getElementDefinition(StructureDefinition sd, String path, boolean allowTypedName, ExpressionNode expr) throws PathEngineException {
public ElementDefinitionMatch getElementDefinition(StructureDefinition sd, String path, boolean allowTypedName, ExpressionNode expr) throws PathEngineException {
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.getPath().equals(path)) {
if (ed.hasContentReference()) {
@ -6229,5 +6352,8 @@ public class FHIRPathEngine {
this.liquidMode = liquidMode;
}
public ProfileUtilities getProfileUtilities() {
return profileUtilities;
}
}

536
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/structuremap/StructureMapUtilities.java
View File

@ -103,7 +103,8 @@ public class StructureMapUtilities {
public static final String MAP_SEARCH_EXPRESSION = "map.search.expression";
public static final String MAP_EXPRESSION = "map.transform.expression";
private static final boolean RENDER_MULTIPLE_TARGETS_ONELINE = true;
private static final String AUTO_VAR_NAME = "vvv";
public static final String AUTO_VAR_NAME = "vvv";
public static final String DEF_GROUP_NAME = "DefaultMappingGroupAnonymousAlias";
private final IWorkerContext worker;
private final FHIRPathEngine fpe;
@ -619,15 +620,38 @@ public class StructureMapUtilities {
}
public StructureMap parse(String text, String srcName) throws FHIRException {
FHIRLexer lexer = new FHIRLexer(text, srcName);
FHIRLexer lexer = new FHIRLexer(Utilities.stripBOM(text), srcName, true);
if (lexer.done())
throw lexer.error("Map Input cannot be empty");
lexer.token("map");
StructureMap result = new StructureMap();
result.setUrl(lexer.readConstant("url"));
lexer.token("=");
result.setName(lexer.readConstant("name"));
result.setDescription(lexer.getAllComments());
if (lexer.hasToken("map")) {
lexer.token("map");
result.setUrl(lexer.readConstant("url"));
lexer.token("=");
result.setName(lexer.readConstant("name"));
result.setDescription(lexer.getAllComments());
result.setStatus(PublicationStatus.DRAFT);
} else {
while (lexer.hasToken("///")) {
lexer.next();
String fid = lexer.takeDottedToken();
lexer.token("=");
switch (fid) {
case "url" :
result.setUrl(lexer.readConstant("url"));
break;
case "name" :
result.setName(lexer.readConstant("name"));
break;
case "title" :
result.setTitle(lexer.readConstant("title"));
break;
default:
lexer.readConstant("nothing");
// nothing
}
}
}
while (lexer.hasToken("conceptmap"))
parseConceptMap(result, lexer);
@ -643,37 +667,7 @@ public class StructureMapUtilities {
return result;
}
public Element parseEM(String text, String srcName, List<ValidationMessage> list) throws FHIRException {
FHIRLexer lexer = new FHIRLexer(text, srcName);
if (lexer.done())
throw lexer.error("Map Input cannot be empty");
lexer.token("map");
Element result = Manager.build(worker, worker.fetchTypeDefinition("StructureMap"));
try {
result.makeElement("url").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
lexer.token("=");
result.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("name"));
result.makeElement("description").markLocation(lexer.getCurrentLocation()).setValue(lexer.getAllComments());
while (lexer.hasToken("conceptmap"))
parseConceptMapEM(result, lexer);
while (lexer.hasToken("uses"))
parseUsesEM(result, lexer);
while (lexer.hasToken("imports"))
parseImportsEM(result, lexer);
while (!lexer.done()) {
parseGroupEM(result, lexer);
}
} catch (FHIRLexerException e) {
list.add(new ValidationMessage(Source.InstanceValidator, IssueType.INVALID, e.getLocation().getLine(), e.getLocation().getColumn(), null, e.getMessage(), IssueSeverity.FATAL));
} catch (Exception e) {
list.add(new ValidationMessage(Source.InstanceValidator, IssueType.INVALID, null, e.getMessage(), IssueSeverity.FATAL));
}
return result;
}
private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
lexer.token("conceptmap");
ConceptMap map = new ConceptMap();
@ -730,63 +724,7 @@ public class StructureMapUtilities {
lexer.token("}");
}
private void parseConceptMapEM(Element result, FHIRLexer lexer) throws FHIRLexerException {
lexer.token("conceptmap");
Element map = Manager.build(worker, worker.fetchTypeDefinition("ConceptMap"));
Element eid = map.makeElement("id").markLocation(lexer.getCurrentLocation());
String id = lexer.readConstant("map id");
if (id.startsWith("#"))
throw lexer.error("Concept Map identifier must start with #");
eid.setValue(id);
map.makeElement("status").setValue(PublicationStatus.DRAFT.toCode()); // todo: how to add this to the text format
result.makeElement("contained").setElement("resource", map);
lexer.token("{");
// lexer.token("source");
// map.setSource(new UriType(lexer.readConstant("source")));
// lexer.token("target");
// map.setSource(new UriType(lexer.readConstant("target")));
Map<String, String> prefixes = new HashMap<String, String>();
while (lexer.hasToken("prefix")) {
lexer.token("prefix");
String n = lexer.take();
lexer.token("=");
String v = lexer.readConstant("prefix url");
prefixes.put(n, v);
}
while (lexer.hasToken("unmapped")) {
lexer.token("unmapped");
lexer.token("for");
String n = readPrefix(prefixes, lexer);
Element g = getGroupE(map, n, null);
lexer.token("=");
SourceLocation loc = lexer.getCurrentLocation();
String v = lexer.take();
if (v.equals("provided")) {
g.makeElement("unmapped").makeElement("mode").markLocation(loc).setValue(ConceptMapGroupUnmappedMode.USESOURCECODE.toCode());
} else
throw lexer.error("Only unmapped mode PROVIDED is supported at this time");
}
while (!lexer.hasToken("}")) {
String srcs = readPrefix(prefixes, lexer);
lexer.token(":");
SourceLocation scloc = lexer.getCurrentLocation();
String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
SourceLocation relLoc = lexer.getCurrentLocation();
ConceptMapRelationship rel = readRelationship(lexer);
String tgts = readPrefix(prefixes, lexer);
Element g = getGroupE(map, srcs, tgts);
Element e = g.addElement("element");
e.makeElement("code").markLocation(scloc).setValue(sc.startsWith("\"") ? lexer.processConstant(sc) : sc);
Element tgt = e.addElement("target");
tgt.makeElement("relationship").markLocation(relLoc).setValue(rel.toCode());
lexer.token(":");
tgt.makeElement("code").markLocation(lexer.getCurrentLocation()).setValue(lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take());
if (lexer.hasComments()) {
tgt.makeElement("comment").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
}
lexer.token("}");
}
private ConceptMapGroupComponent getGroup(ConceptMap map, String srcs, String tgts) {
for (ConceptMapGroupComponent grp : map.getGroup()) {
@ -803,23 +741,7 @@ public class StructureMapUtilities {
return grp;
}
private Element getGroupE(Element map, String srcs, String tgts) {
for (Element grp : map.getChildrenByName("group")) {
if (grp.getChildValue("source").equals(srcs)) {
Element tgt = grp.getNamedChild("target");
if (tgt == null || tgts == null || tgts.equals(tgt.getValue())) {
if (tgt == null && tgts != null)
grp.makeElement("target").setValue(tgts);
return grp;
}
}
}
Element grp = map.addElement("group");
grp.makeElement("source").setValue(srcs);
grp.makeElement("target").setValue(tgts);
return grp;
}
private String readPrefix(Map<String, String> prefixes, FHIRLexer lexer) throws FHIRLexerException {
String prefix = lexer.take();
@ -859,21 +781,7 @@ public class StructureMapUtilities {
st.setDocumentation(lexer.getFirstComment());
}
private void parseUsesEM(Element result, FHIRLexer lexer) throws FHIRException {
lexer.token("uses");
Element st = result.addElement("structure");
st.makeElement("url").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
if (lexer.hasToken("alias")) {
lexer.token("alias");
st.makeElement("alias").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
lexer.token("as");
st.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
lexer.skipToken(";");
if (lexer.hasComments()) {
st.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
}
private void parseImports(StructureMap result, FHIRLexer lexer) throws FHIRException {
lexer.token("imports");
@ -881,12 +789,6 @@ public class StructureMapUtilities {
lexer.skipToken(";");
}
private void parseImportsEM(Element result, FHIRLexer lexer) throws FHIRException {
lexer.token("imports");
result.addElement("import").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
lexer.skipToken(";");
}
private void parseGroup(StructureMap result, FHIRLexer lexer) throws FHIRException {
String comment = lexer.getAllComments();
lexer.token("group");
@ -959,78 +861,7 @@ public class StructureMapUtilities {
lexer.next();
}
private void parseGroupEM(Element result, FHIRLexer lexer) throws FHIRException {
SourceLocation commLoc = lexer.getCommentLocation();
String comment = lexer.getAllComments();
lexer.token("group");
Element group = result.addElement("group");
if (comment != null) {
group.makeElement("documentation").markLocation(commLoc).setValue(comment);
}
boolean newFmt = false;
if (lexer.hasToken("for")) {
lexer.token("for");
SourceLocation loc = lexer.getCurrentLocation();
if ("type".equals(lexer.getCurrent())) {
lexer.token("type");
lexer.token("+");
lexer.token("types");
group.makeElement("typeMode").markLocation(loc).setValue(StructureMapGroupTypeMode.TYPEANDTYPES.toCode());
} else {
lexer.token("types");
group.makeElement("typeMode").markLocation(loc).setValue(StructureMapGroupTypeMode.TYPES.toCode());
}
}
group.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
if (lexer.hasToken("(")) {
newFmt = true;
lexer.take();
while (!lexer.hasToken(")")) {
parseInputEM(group, lexer, true);
if (lexer.hasToken(","))
lexer.token(",");
}
lexer.take();
}
if (lexer.hasToken("extends")) {
lexer.next();
group.makeElement("extends").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (newFmt) {
if (lexer.hasToken("<")) {
lexer.token("<");
lexer.token("<");
if (lexer.hasToken("types")) {
group.makeElement("typeMode").markLocation(lexer.getCurrentLocation()).setValue(StructureMapGroupTypeMode.TYPES.toCode());
} else {
group.makeElement("typeMode").markLocation(lexer.getCurrentLocation()).setValue(StructureMapGroupTypeMode.TYPEANDTYPES.toCode());
lexer.token("type");
lexer.token("+");
}
lexer.token(">");
lexer.token(">");
}
lexer.token("{");
}
if (newFmt) {
while (!lexer.hasToken("}")) {
if (lexer.done())
throw lexer.error("premature termination expecting 'endgroup'");
parseRuleEM(result, group, lexer, true);
}
} else {
while (lexer.hasToken("input"))
parseInputEM(group, lexer, false);
while (!lexer.hasToken("endgroup")) {
if (lexer.done())
throw lexer.error("premature termination expecting 'endgroup'");
parseRuleEM(result, group, lexer, false);
}
}
lexer.next();
if (newFmt && lexer.hasToken(";"))
lexer.next();
}
private void parseInput(StructureMapGroupComponent group, FHIRLexer lexer, boolean newFmt) throws FHIRException {
StructureMapGroupInputComponent input = group.addInput();
@ -1051,26 +882,7 @@ public class StructureMapUtilities {
}
}
private void parseInputEM(Element group, FHIRLexer lexer, boolean newFmt) throws FHIRException {
Element input = group.addElement("input");
if (newFmt) {
input.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
} else
lexer.token("input");
input.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
if (lexer.hasToken(":")) {
lexer.token(":");
input.makeElement("type").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (!newFmt) {
lexer.token("as");
input.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
if (lexer.hasComments()) {
input.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
lexer.skipToken(";");
}
}
private void parseRule(StructureMap map, List<StructureMapGroupRuleComponent> list, FHIRLexer lexer, boolean newFmt) throws FHIRException {
StructureMapGroupRuleComponent rule = new StructureMapGroupRuleComponent();
@ -1147,84 +959,6 @@ public class StructureMapUtilities {
}
}
private void parseRuleEM(Element map, Element context, FHIRLexer lexer, boolean newFmt) throws FHIRException {
Element rule = context.addElement("rule");
if (!newFmt) {
rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.takeDottedToken());
lexer.token(":");
lexer.token("for");
} else {
if (lexer.hasComments()) {
rule.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
}
boolean done = false;
while (!done) {
parseSourceEM(rule, lexer);
done = !lexer.hasToken(",");
if (!done)
lexer.next();
}
if ((newFmt && lexer.hasToken("->")) || (!newFmt && lexer.hasToken("make"))) {
lexer.token(newFmt ? "->" : "make");
done = false;
while (!done) {
parseTargetEM(rule, lexer);
done = !lexer.hasToken(",");
if (!done)
lexer.next();
}
}
if (lexer.hasToken("then")) {
lexer.token("then");
if (lexer.hasToken("{")) {
lexer.token("{");
while (!lexer.hasToken("}")) {
if (lexer.done())
throw lexer.error("premature termination expecting '}' in nested group");
parseRuleEM(map, rule, lexer, newFmt);
}
lexer.token("}");
} else {
done = false;
while (!done) {
parseRuleReferenceEM(rule, lexer);
done = !lexer.hasToken(",");
if (!done)
lexer.next();
}
}
}
if (!rule.hasChild("documentation") && lexer.hasComments()) {
rule.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
}
if (isSimpleSyntaxEM(rule)) {
rule.forceElement("source").makeElement("variable").setValue(AUTO_VAR_NAME);
rule.forceElement("target").makeElement("variable").setValue(AUTO_VAR_NAME);
rule.forceElement("target").makeElement("transform").setValue(StructureMapTransform.CREATE.toCode());
// no dependencies - imply what is to be done based on types
}
if (newFmt) {
if (lexer.isConstant()) {
if (lexer.isStringConstant()) {
rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("ruleName"));
} else {
rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
} else {
if (rule.getChildrenByName("source").size() != 1 || !rule.getChildrenByName("source").get(0).hasChild("element"))
throw lexer.error("Complex rules must have an explicit name");
if (rule.getChildrenByName("source").get(0).hasChild("type"))
rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + "-" + rule.getChildrenByName("source").get(0).getNamedChildValue("type"));
else
rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element"));
}
lexer.token(";");
}
}
private boolean isSimpleSyntax(StructureMapGroupRuleComponent rule) {
return
(rule.getSource().size() == 1 && rule.getSourceFirstRep().hasContext() && rule.getSourceFirstRep().hasElement() && !rule.getSourceFirstRep().hasVariable()) &&
@ -1233,14 +967,7 @@ public class StructureMapUtilities {
}
private boolean isSimpleSyntaxEM(Element rule) {
return
(rule.getChildren("source").size() == 1 && rule.getChildren("source").get(0).hasChild("context") && rule.getChildren("source").get(0).hasChild("element") && !rule.getChildren("source").get(0).hasChild("variable")) &&
(rule.getChildren("target").size() == 1 && rule.getChildren("target").get(0).hasChild("context") && rule.getChildren("target").get(0).hasChild("element") && !rule.getChildren("target").get(0).hasChild("variable") &&
!rule.getChildren("target").get(0).hasChild("parameter")) &&
(rule.getChildren("dependent").size() == 0 && rule.getChildren("rule").size() == 0);
}
private void parseRuleReference(StructureMapGroupRuleComponent rule, FHIRLexer lexer) throws FHIRLexerException {
StructureMapGroupRuleDependentComponent ref = rule.addDependent();
ref.setName(lexer.take());
@ -1255,20 +982,7 @@ public class StructureMapUtilities {
lexer.token(")");
}
private void parseRuleReferenceEM(Element rule, FHIRLexer lexer) throws FHIRLexerException {
Element ref = rule.addElement("dependent");
rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
lexer.token("(");
boolean done = false;
while (!done) {
parseParameterEM(ref, lexer);
done = !lexer.hasToken(",");
if (!done)
lexer.next();
}
lexer.token(")");
}
private void parseSource(StructureMapGroupRuleComponent rule, FHIRLexer lexer) throws FHIRException {
StructureMapGroupRuleSourceComponent source = rule.addSource();
source.setContext(lexer.take());
@ -1287,11 +1001,11 @@ public class StructureMapUtilities {
// type and cardinality
lexer.token(":");
source.setType(lexer.takeDottedToken());
if (!lexer.hasToken("as", "first", "last", "not_first", "not_last", "only_one", "default")) {
source.setMin(lexer.takeInt());
lexer.token("..");
source.setMax(lexer.take());
}
}
if (Utilities.isInteger(lexer.getCurrent())) {
source.setMin(lexer.takeInt());
lexer.token("..");
source.setMax(lexer.take());
}
if (lexer.hasToken("default")) {
lexer.token("default");
@ -1324,66 +1038,7 @@ public class StructureMapUtilities {
}
}
private void parseSourceEM(Element rule, FHIRLexer lexer) throws FHIRException {
Element source = rule.addElement("source");
source.makeElement("context").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
if (source.getChildValue("context").equals("search") && lexer.hasToken("(")) {
source.makeElement("context").markLocation(lexer.getCurrentLocation()).setValue("@search");
lexer.take();
SourceLocation loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
source.setUserData(MAP_SEARCH_EXPRESSION, node);
source.makeElement("element").markLocation(loc).setValue(node.toString());
lexer.token(")");
} else if (lexer.hasToken(".")) {
lexer.token(".");
source.makeElement("element").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (lexer.hasToken(":")) {
// type and cardinality
lexer.token(":");
source.setType(lexer.takeDottedToken());
if (!lexer.hasToken("as", "first", "last", "not_first", "not_last", "only_one", "default")) {
source.makeElement("min").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
lexer.token("..");
source.makeElement("max").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
}
if (lexer.hasToken("default")) {
lexer.token("default");
source.makeElement("defaultValue").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("default value"));
}
if (Utilities.existsInList(lexer.getCurrent(), "first", "last", "not_first", "not_last", "only_one")) {
source.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (lexer.hasToken("as")) {
lexer.take();
source.makeElement("variable").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
if (lexer.hasToken("where")) {
lexer.take();
SourceLocation loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
source.setUserData(MAP_WHERE_EXPRESSION, node);
source.makeElement("condition").markLocation(loc).setValue(node.toString());
}
if (lexer.hasToken("check")) {
lexer.take();
SourceLocation loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
source.setUserData(MAP_WHERE_CHECK, node);
source.makeElement("check").markLocation(loc).setValue(node.toString());
}
if (lexer.hasToken("log")) {
lexer.take();
SourceLocation loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
source.setUserData(MAP_WHERE_CHECK, node);
source.makeElement("logMessage").markLocation(loc).setValue(lexer.take());
}
}
private void parseTarget(StructureMapGroupRuleComponent rule, FHIRLexer lexer) throws FHIRException {
StructureMapGroupRuleTargetComponent target = rule.addTarget();
String start = lexer.take();
@ -1458,85 +1113,7 @@ public class StructureMapUtilities {
}
}
private void parseTargetEM(Element rule, FHIRLexer lexer) throws FHIRException {
Element target = rule.addElement("target");
SourceLocation loc = lexer.getCurrentLocation();
String start = lexer.take();
if (lexer.hasToken(".")) {
target.makeElement("context").markLocation(loc).setValue(start);
start = null;
lexer.token(".");
target.makeElement("element").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
String name;
boolean isConstant = false;
if (lexer.hasToken("=")) {
if (start != null) {
target.makeElement("context").markLocation(loc).setValue(start);
}
lexer.token("=");
isConstant = lexer.isConstant();
loc = lexer.getCurrentLocation();
name = lexer.take();
} else {
loc = lexer.getCurrentLocation();
name = start;
}
if ("(".equals(name)) {
// inline fluentpath expression
target.makeElement("transform").markLocation(lexer.getCurrentLocation()).setValue(StructureMapTransform.EVALUATE.toCode());
loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
target.setUserData(MAP_EXPRESSION, node);
target.addElement("parameter").markLocation(loc).setValue(node.toString());
lexer.token(")");
} else if (lexer.hasToken("(")) {
target.makeElement("transform").markLocation(loc).setValue(name);
lexer.token("(");
if (target.getChildValue("transform").equals(StructureMapTransform.EVALUATE.toCode())) {
parseParameterEM(target, lexer);
lexer.token(",");
loc = lexer.getCurrentLocation();
ExpressionNode node = fpe.parse(lexer);
target.setUserData(MAP_EXPRESSION, node);
target.addElement("parameter").markLocation(loc).setValue(node.toString());
} else {
while (!lexer.hasToken(")")) {
parseParameterEM(target, lexer);
if (!lexer.hasToken(")"))
lexer.token(",");
}
}
lexer.token(")");
} else if (name != null) {
target.makeElement("transform").markLocation(loc).setValue(StructureMapTransform.COPY.toCode());
if (!isConstant) {
loc = lexer.getCurrentLocation();
String id = name;
while (lexer.hasToken(".")) {
id = id + lexer.take() + lexer.take();
}
target.addElement("parameter").markLocation(loc).setValue(id);
} else {
target.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(readConstantEM(name, lexer));
}
}
if (lexer.hasToken("as")) {
lexer.take();
target.makeElement("variable").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
while (Utilities.existsInList(lexer.getCurrent(), "first", "last", "share", "collate")) {
if (lexer.getCurrent().equals("share")) {
target.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
target.makeElement("listRuleId").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
} else {
target.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
}
}
}
private void parseParameter(StructureMapGroupRuleDependentComponent ref, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
if (!lexer.isConstant()) {
ref.addParameter().setValue(new IdType(lexer.take()));
@ -1557,16 +1134,7 @@ public class StructureMapUtilities {
}
}
private void parseParameterEM(Element ref, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
if (!lexer.isConstant()) {
ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
} else if (lexer.isStringConstant())
ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("??"));
else {
ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(readConstantEM(lexer.take(), lexer));
}
}
private DataType readConstant(String s, FHIRLexer lexer) throws FHIRLexerException {
if (Utilities.isInteger(s))
return new IntegerType(s);
@ -1578,16 +1146,6 @@ public class StructureMapUtilities {
return new StringType(lexer.processConstant(s));
}
private String readConstantEM(String s, FHIRLexer lexer) throws FHIRLexerException {
if (Utilities.isInteger(s))
return s;
else if (Utilities.isDecimal(s, false))
return s;
else if (Utilities.existsInList(s, "true", "false"))
return s;
else
return lexer.processConstant(s);
}
public StructureDefinition getTargetType(StructureMap map) throws FHIRException {
boolean found = false;

18
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/StructureMapUtilitiesTest.java
View File

@ -91,24 +91,6 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
assertSerializeDeserialize(map);
}
@Test
public void testSyntaxEM() throws IOException, FHIRException {
StructureMapUtilities scu = new StructureMapUtilities(context, this);
String fileMap = TestingUtilities.loadTestResource("r5", "structure-mapping", "syntax.map");
System.out.println(fileMap);
Element structureMap = scu.parseEM(fileMap, "Syntax", null);
// assertSerializeDeserialize(structureMap);
//
// String renderedMap = StructureMapUtilities.render(structureMap);
// StructureMap map = scu.parse(renderedMap, "Syntax");
// System.out.println(map);
// assertSerializeDeserialize(map);
}
@Override
public void log(String message) {
}

8
org.hl7.fhir.report/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

4
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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -90,7 +90,7 @@
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<configuration>
<skip>true</skip>
<skipStaging>true</skipStaging>
</configuration>
</plugin>
<plugin>

8
org.hl7.fhir.utilities/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

6
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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -45,7 +45,7 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
</dependency>
@ -159,7 +159,7 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>logging-interceptor</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<scope>compile</scope>
</dependency>
-->

119
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/MarkDownProcessor.java
View File

@ -69,6 +69,125 @@ public class MarkDownProcessor {
}
}
/**
* Returns true if this is intended to be processed as markdown
*
* this is guess, based on textual analysis of the content.
*
* Uses of this routine:
* In general, the main use of this is to decide to escape the string so erroneous markdown processing doesn't munge characters
* If it's a plain string, and it's being put into something that's markdown, then you should escape the content
* If it's markdown, but you're not sure whether to process it as markdown
*
* The underlying problem is that markdown processing plain strings is problematic because some technical characters might
* get lost. So it's good to escape them... but if it's meant to be markdown, then it'll get trashed.
*
* This method works by looking for character patterns that are unlikely to occur outside markdown - but it's still only unlikely
*
* @param content
* @return
*/
// todo: dialect dependency?
public boolean isProbablyMarkdown(String content, boolean mdIfParagrapghs) {
if (mdIfParagrapghs && content.contains("\n")) {
return true;
}
String[] lines = content.split("\\r?\\n");
for (String s : lines) {
if (s.startsWith("* ") || isHeading(s) || s.startsWith("1. ") || s.startsWith(" ")) {
return true;
}
if (s.contains("```") || s.contains("~~~") || s.contains("[[[")) {
return true;
}
if (hasLink(s)) {
return true;
}
if (hasTextSpecial(s, '*') || hasTextSpecial(s, '_') ) {
return true;
}
}
return false;
}
private boolean isHeading(String s) {
if (s.length() > 7 && s.startsWith("###### ") && !Character.isWhitespace(s.charAt(7))) {
return true;
}
if (s.length() > 6 && s.startsWith("##### ") && !Character.isWhitespace(s.charAt(6))) {
return true;
}
if (s.length() > 5 && s.startsWith("#### ") && !Character.isWhitespace(s.charAt(5))) {
return true;
}
if (s.length() > 4 && s.startsWith("### ") && !Character.isWhitespace(s.charAt(4))) {
return true;
}
if (s.length() > 3 && s.startsWith("## ") && !Character.isWhitespace(s.charAt(3))) {
return true;
}
//
// not sure about this one. # [string] is something that could easily arise in non-markdown,
// so this appearing isn't enough to call it markdown
//
// if (s.length() > 2 && s.startsWith("# ") && !Character.isWhitespace(s.charAt(2))) {
// return true;
// }
return false;
}
private boolean hasLink(String s) {
int left = -1;
int mid = -1;
for (int i = 0; i < s.length(); i++) {
char c = s.charAt(i);
if (c == '[') {
mid = -1;
left = i;
} else if (left > -1 && i < s.length()-1 && c == ']' && s.charAt(i+1) == '(') {
mid = i;
} else if (left > -1 && c == ']') {
left = -1;
} else if (left > -1 && mid > -1 && c == ')') {
return true;
} else if (mid > -1 && c == '[' || c == ']' || (c == '(' && i > mid+1)) {
left = -1;
mid = -1;
}
}
return false;
}
private boolean hasTextSpecial(String s, char c) {
boolean second = false;
for (int i = 0; i < s.length(); i++) {
char prev = i == 0 ? ' ' : s.charAt(i-1);
char next = i < s.length() - 1 ? s.charAt(i+1) : ' ';
if (s.charAt(i) != c) {
// nothing
} else if (second) {
if (Character.isWhitespace(next) && (isPunctation(prev) || Character.isLetterOrDigit(prev))) {
return true;
}
second = false;
} else {
if (Character.isWhitespace(prev) && (isPunctation(next) || Character.isLetterOrDigit(next))) {
second = true;
}
}
}
return false;
}
private boolean isPunctation(char ch) {
return Utilities.existsInList(ch, '.', ',', '!', '?');
}
/**
* This deals with a painful problem created by the intersection of previous publishing processes
* and the way commonmark specifies that < is handled in content. For control reasons, the FHIR specification does

14
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java
View File

@ -214,9 +214,17 @@ public class VersionUtilities {
} else if (Utilities.charCount(version, '.') == 2) {
String[] p = version.split("\\.");
return p[0]+"."+p[1];
} else {
return null;
}
} else if (Utilities.existsInList(version, "R2", "R2B", "R3", "R4", "R4B", "R5")) {
switch (version) {
case "R2": return "1.0";
case "R2B": return "1.4";
case "R3": return "3.0";
case "R4": return "4.0";
case "R4B": return "4.3";
case "R5": return "5.0";
}
}
return null;
}
public static String getPatch(String version) {

38
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -774,6 +774,44 @@ public class I18nConstants {
public static final String EXT_VER_URL_REVERSION = "EXT_VER_URL_REVERSION";
public static final String ILLEGAL_COMMENT_TYPE = "ILLEGAL_COMMENT_TYPE";
public static final String SD_NO_SLICING_ON_ROOT = "SD_NO_SLICING_ON_ROOT";
public static final String REFERENCE_REF_QUERY_INVALID = "REFERENCE_REF_QUERY_INVALID";
public static final String SM_RULEGROUP_NOT_FOUND = "SM_RULEGROUP_NOT_FOUND";
public static final String SM_NAME_INVALID = "SM_NAME_INVALID";
public static final String SM_GROUP_INPUT_DUPLICATE = "SM_GROUP_INPUT_DUPLICATE";
public static final String SM_GROUP_INPUT_MODE_INVALID = "SM_GROUP_INPUT_MODE_INVALID";
public static final String SM_GROUP_INPUT_NO_TYPE = "SM_GROUP_INPUT_NO_TYPE";
public static final String SM_GROUP_INPUT_TYPE_NOT_DECLARED = "SM_GROUP_INPUT_TYPE_NOT_DECLARED";
public static final String SM_GROUP_INPUT_MODE_MISMATCH = "SM_GROUP_INPUT_MODE_MISMATCH";
public static final String SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE = "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE";
public static final String SM_GROUP_INPUT_TYPE_UNKNOWN_TYPE = "SM_GROUP_INPUT_TYPE_UNKNOWN_TYPE";
public static final String SM_SOURCE_CONTEXT_UNKNOWN = "SM_SOURCE_CONTEXT_UNKNOWN";
public static final String SM_SOURCE_PATH_INVALID = "SM_SOURCE_PATH_INVALID";
public static final String SM_RULE_SOURCE_MIN_REDUNDANT = "SM_RULE_SOURCE_MIN_REDUNDANT";
public static final String SM_RULE_SOURCE_MAX_REDUNDANT = "SM_RULE_SOURCE_MAX_REDUNDANT";
public static final String SM_RULE_SOURCE_LISTMODE_REDUNDANT = "SM_RULE_SOURCE_LISTMODE_REDUNDANT";
public static final String SM_TARGET_CONTEXT_UNKNOWN = "SM_TARGET_CONTEXT_UNKNOWN";
public static final String SM_TARGET_PATH_INVALID = "SM_TARGET_PATH_INVALID";
public static final String SM_NO_LIST_MODE_NEEDED = "SM_NO_LIST_MODE_NEEDED";
public static final String SM_NO_LIST_RULE_ID_NEEDED = "SM_NO_LIST_RULE_ID_NEEDED";
public static final String SM_LIST_RULE_ID_ONLY_WHEN_SHARE = "SM_LIST_RULE_ID_ONLY_WHEN_SHARE";
public static final String SM_RULE_SOURCE_UNASSIGNED = "SM_RULE_SOURCE_UNASSIGNED";
public static final String SM_TARGET_PATH_MULTIPLE_MATCHES = "SM_TARGET_PATH_MULTIPLE_MATCHES";
public static final String SM_SOURCE_TYPE_INVALID = "SM_SOURCE_TYPE_INVALID";
public static final String SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE = "SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE";
public static final String SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE = "SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE";
public static final String SM_TARGET_TRANSFORM_NOT_CHECKED = "SM_TARGET_TRANSFORM_NOT_CHECKED";
public static final String SM_TARGET_NO_TRANSFORM_NO_CHECKED = "SM_TARGET_NO_TRANSFORM_NO_CHECKED";
public static final String SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE = "SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE";
public static final String SM_TARGET_TRANSFORM_PARAM_UNPROCESSIBLE = "SM_TARGET_TRANSFORM_PARAM_UNPROCESSIBLE";
public static final String SM_TARGET_TRANSFORM_EXPRESSION_ERROR = "SM_TARGET_TRANSFORM_EXPRESSION_ERROR";
public static final String SM_IMPORT_NOT_FOUND = "SM_IMPORT_NOT_FOUND";
public static final String SM_TARGET_TYPE_MULTIPLE_POSSIBLE = "SM_TARGET_TYPE_MULTIPLE_POSSIBLE";
public static final String SM_DEPENDENT_PARAM_MODE_MISMATCH = "SM_DEPENDENT_PARAM_MODE_MISMATCH";
public static final String SM_DEPENDENT_PARAM_TYPE_MISMATCH = "SM_DEPENDENT_PARAM_TYPE_MISMATCH";
public static final String SM_ORPHAN_GROUP = "SM_ORPHAN_GROUP";
public static final String SM_SOURCE_TYPE_NOT_FOUND = "SM_SOURCE_TYPE_NOT_FOUND";
public static final String SM_TARGET_TYPE_NOT_FOUND = "SM_TARGET_TYPE_NOT_FOUND";
public static final String SM_MATCHING_RULEGROUP_NOT_FOUND = "SM_MATCHING_RULEGROUP_NOT_FOUND";
}

8
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageClient.java
View File

@ -27,19 +27,13 @@ public class PackageClient {
private PackageServer server;
private String cacheFolder;
private String address;
public PackageClient(PackageServer server) {
super();
this.server = server;
address = server.getUrl();
try {
cacheFolder = Utilities.path(System.getProperty("user.home"), ".fhir", "package-client");
Utilities.createDirectory(cacheFolder);
} catch (IOException e) {
}
address = this.server.getUrl();
}
public boolean exists(String id, String ver) throws IOException {

120
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/turtle/Turtle.java
View File

@ -72,22 +72,35 @@ public class Turtle {
protected List<Predicate> predicates = new ArrayList<Predicate>();
public Complex predicate(String predicate, String object) {
return predicate(predicate, object, false);
}
public Complex predicate(String predicate, String object, boolean asList) {
predicateSet.add(predicate);
objectSet.add(object);
return predicate(predicate, new StringType(object));
return predicate(predicate, new StringType(object), asList);
}
public Complex linkedPredicate(String predicate, String object, String link, String comment) {
public Complex linkedPredicate(String predicate, String object, String link, String comment) {
return linkedPredicate(predicate, object, link, comment, false);
}
public Complex linkedPredicate(String predicate, String object, String link, String comment, boolean asList) {
predicateSet.add(predicate);
objectSet.add(object);
return linkedPredicate(predicate, new StringType(object), link, comment);
return linkedPredicate(predicate, new StringType(object), link, comment, asList);
}
public Complex predicate(String predicate, Triple object) {
return predicate(predicate, object, false);
}
public Complex predicate(String predicate, Triple object) {
public Complex predicate(String predicate, Triple object, boolean asList) {
Predicate p = getPredicate(predicate);
if (p == null) {
p = new Predicate();
p.predicate = predicate;
p.asList = asList;
predicateSet.add(predicate);
predicates.add(p);
}
@ -95,7 +108,7 @@ public class Turtle {
objectSet.add(((StringType) object).value);
p.objects.add(object);
return this;
}
}
protected Predicate getPredicate(String predicate) {
for (Predicate p : predicates)
@ -103,14 +116,19 @@ public class Turtle {
return p;
return null;
}
public Complex linkedPredicate(String predicate, Triple object, String link, String comment) {
return linkedPredicate(predicate, object, link, comment, false);
}
public Complex linkedPredicate(String predicate, Triple object, String link, String comment, boolean asList) {
Predicate p = getPredicate(predicate);
if (p == null) {
p = new Predicate();
p.predicate = predicate;
p.link = link;
p.comment = comment;
p.asList = asList;
predicateSet.add(predicate);
predicates.add(p);
}
@ -119,18 +137,26 @@ public class Turtle {
p.objects.add(object);
return this;
}
public Complex predicate(String predicate) {
return predicate(predicate, false);
}
public Complex predicate(String predicate) {
predicateSet.add(predicate);
Complex c = complex();
predicate(predicate, c);
return c;
}
public Complex predicate(String predicate, boolean asList) {
predicateSet.add(predicate);
Complex c = complex();
predicate(predicate, c, asList);
return c;
}
public Complex linkedPredicate(String predicate, String link, String comment) {
public Complex linkedPredicate(String predicate, String link, String comment) {
return linkedPredicate(predicate, link, comment, false);
}
public Complex linkedPredicate(String predicate, String link, String comment, boolean asList) {
predicateSet.add(predicate);
Complex c = complex();
linkedPredicate(predicate, c, link, comment);
linkedPredicate(predicate, c, link, comment, asList);
return c;
}
@ -144,6 +170,7 @@ public class Turtle {
protected String link;
protected List<Triple> objects = new ArrayList<Turtle.Triple>();
protected String comment;
protected boolean asList = false;
public String getPredicate() {
return predicate;
@ -183,15 +210,15 @@ public class Turtle {
public void comment(String comment) {
if (!Utilities.noString(comment)) {
predicate("rdfs:comment", literal(comment));
predicate("dcterms:description", literal(comment));
predicate("rdfs:comment", literal(comment), false);
predicate("dcterms:description", literal(comment), false);
}
}
public void label(String label) {
if (!Utilities.noString(label)) {
predicate("rdfs:label", literal(label));
predicate("dc:title", literal(label));
predicate("rdfs:label", literal(label), false);
predicate("dc:title", literal(label), false);
}
}
@ -445,7 +472,7 @@ public class Turtle {
writer.ln();
if (!section.comments.isEmpty()) {
for (String s : section.comments) {
writer.ln("# "+s);
writer.ln("# "+formatMultilineComment(s));
}
writer.ln();
}
@ -464,10 +491,13 @@ public class Turtle {
writer.write(" ");
boolean first = true;
for (Triple o : p.getObjects()) {
if (first)
if (first) {
first = false;
else
writer.write(", ");
if (p.asList) writer.write("( ");
} else {
if (!p.asList) writer.write(", ");
else writer.write(" ");
}
if (o instanceof StringType)
writer.write(((StringType) o).value);
else {
@ -478,10 +508,11 @@ public class Turtle {
writer.write("]");
}
}
String comment = p.comment == null? "" : " # "+p.comment;
String comment = p.comment == null? "" : " # "+formatMultilineComment(p.comment);
if (p.asList) writer.write(" )");
i++;
if (i < sbj.predicates.size())
writer.write(";"+comment+"\r\n ");
writer.write(" ;"+comment+"\r\n ");
else {
if (Utilities.noString(sbj.id))
writer.write("]");
@ -490,6 +521,11 @@ public class Turtle {
}
}
}
private String formatMultilineComment(String s) {
return s.replace("\n", "\n#");
}
private void commitSection(StringBuilder b, Section section) throws Exception {
b.append("# - "+section.name+" "+Utilities.padLeft("", '-', 75-section.name.length())+"\r\n");
@ -511,10 +547,12 @@ public class Turtle {
b.append(" ");
boolean first = true;
for (Triple o : p.getObjects()) {
if (first)
first = false;
else
b.append(", ");
if (first) {
first = false;
if (p.asList) b.append("( ");
} else
if (!p.asList) b.append(", ");
else b.append(" ");
if (o instanceof StringType)
b.append(Utilities.escapeXml(((StringType) o).value));
else {
@ -525,12 +563,13 @@ public class Turtle {
b.append("]");
}
}
String comment = p.comment == null? "" : " # "+p.comment;
String comment = p.comment == null? "" : " # "+formatMultilineComment(p.comment);
if (p.asList) b.append(" )");
i++;
if (i < sbj.predicates.size())
b.append(";"+Utilities.escapeXml(comment)+"\r\n ");
b.append(" ;"+Utilities.escapeXml(comment)+"\r\n ");
else
b.append("."+Utilities.escapeXml(comment)+"\r\n\r\n");
b.append(" ."+Utilities.escapeXml(comment)+"\r\n\r\n");
}
}
}
@ -566,8 +605,11 @@ public class Turtle {
if (first) {
first = false;
writer.write(left+" "+po.getPredicate()+" ");
} else
writer.write(", ");
if (po.asList) writer.write("( ");
} else {
if (!po.asList) writer.write(", ");
else writer.write(" ");
}
if (o instanceof StringType)
writer.write(((StringType) o).value);
else {
@ -578,9 +620,10 @@ public class Turtle {
writer.write(" ]");
}
}
if (po.asList) writer.write(" )");
i++;
if (i < complex.predicates.size())
writer.write(";");
writer.write(" ;");
if (!Utilities.noString(po.comment))
writer.write(" # "+escape(po.comment, false));
}
@ -602,9 +645,11 @@ public class Turtle {
for (Triple o : po.getObjects()) {
if (first) {
first = false;
b.append(left+" "+po.makelink()+" ");
if (po.asList) b.append(left+"( ");
b.append(po.makelink()+" ");
} else
b.append(", ");
if (!po.asList) b.append(", ");
else b.append(" ");
if (o instanceof StringType)
b.append(Utilities.escapeXml(((StringType) o).value));
else {
@ -615,9 +660,10 @@ public class Turtle {
b.append(" ]");
}
}
if (po.asList) b.append(" )");
i++;
if (i < complex.predicates.size())
b.append(";");
b.append(" ;");
if (!Utilities.noString(po.comment))
b.append(" # "+Utilities.escapeXml(escape(po.comment, false)));
}

26
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java
View File

@ -83,9 +83,14 @@ import org.commonmark.renderer.html.HtmlRenderer;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.TranslatingUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
public class HierarchicalTableGenerator extends TranslatingUtilities {
public enum TableGenerationMode {
XML, XHTML
}
public static final String TEXT_ICON_REFERENCE = "Reference to another Resource";
public static final String TEXT_ICON_PRIMITIVE = "Primitive Data Type";
public static final String TEXT_ICON_KEY = "JSON Key Value";
@ -599,6 +604,8 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
*/
private boolean inLineGraphics;
private TableGenerationMode mode;
public HierarchicalTableGenerator() {
super();
}
@ -626,7 +633,9 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
checkSetup();
}
public TableModel initNormalTable(String prefix, boolean isLogical, boolean alternating, String id, boolean isActive) {
public TableModel initNormalTable(String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, TableGenerationMode mode) {
this.mode = mode;
TableModel model = new TableModel(id, isActive);
model.setAlternating(alternating);
@ -686,12 +695,16 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
tr.setAttribute("style", "border: " + Integer.toString(1 + border) + "px #F0F0F0 solid; font-size: 11px; font-family: verdana; vertical-align: top");
XhtmlNode tc = null;
for (Title t : model.getTitles()) {
tc = renderCell(tr, t, "th", null, null, null, false, null, "white", 0, imagePath, border, outputTracker, model, null);
tc = renderCell(tr, t, "th", null, null, null, false, null, "white", 0, imagePath, border, outputTracker, model, null, true);
if (t.width != 0)
tc.setAttribute("style", "width: "+Integer.toString(t.width)+"px");
}
if (tc != null && model.getDocoRef() != null) {
XhtmlNode img = tc.addTag("span").setAttribute("style", "float: right").addTag("a").setAttribute("title", "Legend for this format").setAttribute("href", model.getDocoRef()).addTag("img");
XhtmlNode a = tc.addTag("span").setAttribute("style", "float: right").addTag("a").setAttribute("title", "Legend for this format").setAttribute("href", model.getDocoRef());
if (mode == TableGenerationMode.XHTML) {
a.setAttribute("no-external", "true");
}
XhtmlNode img = a.addTag("img");
img.setAttribute("alt", "doco").setAttribute("style", "background-color: inherit").setAttribute("src", model.getDocoImg());
if (model.isActive()) {
img.setAttribute("onLoad", "fhirTableInit(this)");
@ -732,7 +745,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
}
boolean first = true;
for (Cell t : r.getCells()) {
renderCell(tr, t, "td", first ? r.getIcon() : null, first ? r.getHint() : null, first ? indents : null, !r.getSubRows().isEmpty(), first ? r.getAnchor() : null, color, r.getLineColor(), imagePath, border, outputTracker, model, r);
renderCell(tr, t, "td", first ? r.getIcon() : null, first ? r.getHint() : null, first ? indents : null, !r.getSubRows().isEmpty(), first ? r.getAnchor() : null, color, r.getLineColor(), imagePath, border, outputTracker, model, r, first);
first = false;
}
table.addText("\r\n");
@ -751,7 +764,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
}
private XhtmlNode renderCell(XhtmlNode tr, Cell c, String name, String icon, String hint, List<Integer> indents, boolean hasChildren, String anchor, String color, int lineColor, String imagePath, int border, Set<String> outputTracker, TableModel table, Row row) throws IOException {
private XhtmlNode renderCell(XhtmlNode tr, Cell c, String name, String icon, String hint, List<Integer> indents, boolean hasChildren, String anchor, String color, int lineColor, String imagePath, int border, Set<String> outputTracker, TableModel table, Row row, boolean suppressExternals) throws IOException {
XhtmlNode tc = tr.addTag(name);
tc.setAttribute("class", "hierarchy");
if (c.span > 1) {
@ -837,6 +850,9 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
} else if (!Utilities.noString(p.getReference())) {
XhtmlNode a = addStyle(tc.addTag("a"), p);
a.setAttribute("href", p.getReference());
if (mode == TableGenerationMode.XHTML && suppressExternals) {
a.setAttribute("no-external", "true");
}
if (!Utilities.noString(p.getHint()))
a.setAttribute("title", p.getHint());
if (p.getText() != null) {

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlFluent.java
View File

@ -150,7 +150,9 @@ public abstract class XhtmlFluent {
public XhtmlNode code(String text) {
return addTag("code").tx(text);
XhtmlNode code = addTag("code");
code.tx(text);
return code;
}
public XhtmlNode code() {

40
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -824,5 +824,45 @@ EXT_VER_URL_NOT_ALLOWED = The extension URL must not contain a version
EXT_VER_URL_REVERSION = The extension URL must not contain a version. The extension was validated against version {0} of the extension
ILLEGAL_COMMENT_TYPE = The fhir_comments property must be an array of strings
SD_NO_SLICING_ON_ROOT = Slicing is not allowed at the root of a profile
REFERENCE_REF_QUERY_INVALID = The query part of the conditional reference is not a valid query string ({0})
SM_RULEGROUP_NOT_FOUND = The group {0} could not be resolved
SM_NAME_INVALID = The name {0} is not valid
SM_GROUP_INPUT_DUPLICATE = The name {0} is already used
SM_GROUP_INPUT_MODE_INVALID = The group parameter {0} mode {1} isn''t valid
SM_GROUP_INPUT_NO_TYPE = The group parameter {0} has no type, so the paths cannot be validated
SM_GROUP_INPUT_TYPE_NOT_DECLARED = The type {0} is not declared and is unknown
SM_GROUP_INPUT_MODE_MISMATCH = The type {0} has mode {1} which doesn''t match the structure definition {2}
SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE = The type {0} which maps to the canonical URL {1} is not known, so the paths cannot be validated
SM_GROUP_INPUT_TYPE_UNKNOWN_TYPE = The type {0} is not known, so the paths cannot be validated
SM_SOURCE_CONTEXT_UNKNOWN = The source context {0} is not known at this point
SM_SOURCE_PATH_INVALID = The source path {0}.{1} refers to the path {2} which is unknown
SM_RULE_SOURCE_MIN_REDUNDANT = The min value of {0} is redundant since the valid min is {0}
SM_RULE_SOURCE_MAX_REDUNDANT = The max value of {0} is redundant since the valid max is {0}
SM_RULE_SOURCE_LISTMODE_REDUNDANT = The listMode value of {0} is redundant since the valid max is {0}
SM_TARGET_CONTEXT_UNKNOWN = The target context {0} is not known at this point
SM_TARGET_PATH_INVALID = The target path {0}.{1} refers to the path {2} which is unknown
SM_NO_LIST_MODE_NEEDED = A list mode should not be provided since this is a rule that can only be executed once
SM_NO_LIST_RULE_ID_NEEDED = A list ruleId should not be provided since this is a rule that can only be executed once
SM_LIST_RULE_ID_ONLY_WHEN_SHARE = A ruleId should only be provided when the rule mode is ''share''
SM_RULE_SOURCE_UNASSIGNED = The source statement doesn''t assign a variable to the source - check that this is what is intended
SM_TARGET_PATH_MULTIPLE_MATCHES = The target path {0}.{1} refers to the path {2} which is could be a reference to multiple elements ({3}). No further checking can be performed
SM_SOURCE_TYPE_INVALID = The type {0} is not valid in this source context {1}. The possible types are [{2}]
SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE = Transform {0} takes {1}-{2} parameter(s) but {3} were found
SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE = Transform {0} takes {1} parameter(s) but {2} were found
SM_TARGET_TRANSFORM_NOT_CHECKED = Transform {0} not checked yet
SM_TARGET_NO_TRANSFORM_NO_CHECKED = When there is no transform, parameters can''t be provided
SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE = The value of the type parameter could not be processed
SM_TARGET_TRANSFORM_PARAM_UNPROCESSIBLE = The parameter at index {0} could not be processed (type = {1})
SM_TARGET_TRANSFORM_EXPRESSION_ERROR = The FHIRPath expression passed as the evaluate parameter is invalid: {0}
SM_IMPORT_NOT_FOUND = No maps were found to match {0} - validation may be wrong
SM_TARGET_TYPE_MULTIPLE_POSSIBLE = Multiple types are possible here ({0}) so further type checking is not possible
SM_DEPENDENT_PARAM_MODE_MISMATCH = The parameter {0} refers to the variable {1} but it''s mode is {2} which is not the same as the mode required for the group {3}
SM_DEPENDENT_PARAM_TYPE_MISMATCH = The parameter {0} refers to the variable {1} but it''s type is {2} which is not compatible with the type required for the group {3}
SM_ORPHAN_GROUP = This group is not called from within this mapping script, and does not have types on it's inputs, so type verification is not possible
SM_SOURCE_TYPE_NOT_FOUND = No source type was found, so the default group for this implied dependent rule could not be determined
SM_TARGET_TYPE_NOT_FOUND = No target type was found, so the default group for this implied dependent rule could not be determined
SM_MATCHING_RULEGROUP_NOT_FOUND = Unable to find a default rule for the type pair source={0} and target={1}

2
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/FTPClientTest.java
View File

@ -30,7 +30,7 @@ public class FTPClientTest implements ResourceLoaderTests {
public static final String DUMMY_FILE_TO_DELETE = "dummyFileToDelete";
public static final String DUMMY_FILE_TO_UPLOAD = "dummyFileToUpload";
public static final int FAKE_FTP_PORT = 8021;
public static final int FAKE_FTP_PORT = 8022;
public static final String DUMMY_FILE_CONTENT = "Dummy file content\nMore content\n";
public static final String LOCALHOST = "localhost";

57
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/MarkdownTests.java
View File

@ -2,15 +2,72 @@ package org.hl7.fhir.utilities;
import static org.junit.jupiter.api.Assertions.*;
import org.hl7.fhir.utilities.MarkDownProcessor.Dialect;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
class MarkdownTests {
@Test
void testMarkdownDetection() {
testMarkdown("this is a test string", false);
testMarkdown("this is a \r\ntest string", false);
testMarkdown("this is a \r\ntest string", true, true);
testMarkdown("this is a t*est strin*g", false);
testMarkdown("this is a *test strin*g", false);
testMarkdown("this is a *test string*", true);
testMarkdown("this is a *test *string", false);
testMarkdown("this is a *test* string", true);
testMarkdown("this [is] a test string", false);
testMarkdown("this [is](link) a test string", true);
testMarkdown("this [is](link a test string", false);
testMarkdown("this [is] (link) a test string", false);
testMarkdown("this [is(link)] a test string", false);
testMarkdown("this [is](link a test string", false);
testMarkdown("this [i]s] (link) a test string", false);
testMarkdown("## heading", true);
testMarkdown("# heading", false);
testMarkdown("## heading", false);
testMarkdown("###", false);
}
private void testMarkdown(String content, boolean isMD) {
testMarkdown(content, isMD, false);
}
private void testMarkdown(String content, boolean isMD, boolean ifLines) {
boolean test = new MarkDownProcessor(Dialect.COMMON_MARK).isProbablyMarkdown(content, ifLines);
assertEquals(isMD, test);
}
@Test
void testStringToMarkdown() {
// first, we test the need for replacing
Assertions.assertEquals("<p>This is a string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is a string", null).trim());
Assertions.assertEquals("<p>This is *a string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is *a string", null).trim());
Assertions.assertNotEquals("<p>This is *a* string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is *a* string", null).trim());
Assertions.assertEquals("<p>This is *a *string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is *a *string", null).trim());
Assertions.assertNotEquals("<p>This genomic study analyzes CYP2D6*1 and CYP2D6*2</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This genomic study analyzes CYP2D6*1 and CYP2D6*2", null).trim());
Assertions.assertEquals("<p>This genomic study analyzes CYP2D6*1 and CYP2D6*2</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This genomic study analyzes CYP2D6*1 and CYP2D6\\*2", null).trim());
Assertions.assertEquals("This is \\*a test\\*", MarkDownProcessor.makeStringSafeAsMarkdown("This is *a test*"));
Assertions.assertEquals("This is *a test*", MarkDownProcessor.makeMarkdownForString("This is \\*a test\\*"));
}
}
//
//case '*':
//case '&':
//case '#':
//case '[':
//case '>':
//case '<':
//case '`':
// -
// |
// :
// ~
// ^
// =

8
org.hl7.fhir.validation.cli/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

8
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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -225,7 +225,7 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>mockwebserver</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>false</optional>
<scope>compile</scope>
</dependency>
@ -273,7 +273,7 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
</dependency>
<dependency>
<groupId>com.atlassian.commonmark</groupId>
@ -310,7 +310,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.2</version>
<version>${maven-jar-plugin.version}</version>
<configuration>
<archive>
<manifest>

8
org.hl7.fhir.validation/checkstyle_suppressions.xml Normal file
View File

@ -0,0 +1,8 @@
<?xml version="1.0"?>
<!DOCTYPE suppressions PUBLIC
"-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
"https://checkstyle.org/dtds/suppressions_1_2.dtd">
<suppressions>
</suppressions>

4
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>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -154,7 +154,7 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>4.9.0</version>
<version>${okhttp.version}</version>
<optional>true</optional>
</dependency>

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java
View File

@ -1065,7 +1065,7 @@ public class BaseValidator implements IValidationContextResourceLoader {
if (!context.getResourceNames().contains(tn)) {
return false;
} else {
return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+))*");
return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*))*");
}
}

22
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/IgLoader.java
View File

@ -20,6 +20,7 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_43_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.formats.JsonParser;
@ -112,7 +113,9 @@ public class IgLoader {
if (!srcPackage.contains("#")) {
System.out.print("#" + npm.version());
}
int count = getContext().loadFromPackage(npm, ValidatorUtils.loaderForVersion(npm.fhirVersion()));
IContextResourceLoader loader = ValidatorUtils.loaderForVersion(npm.fhirVersion());
loader.setPatchUrls(VersionUtilities.isCorePackage(npm.id()));
int count = getContext().loadFromPackage(npm, loader);
System.out.println(" - " + count + " resources (" + getContext().clock().milestone() + ")");
} else {
System.out.print(" Load " + srcPackage);
@ -183,8 +186,10 @@ public class IgLoader {
res.cntType = Manager.FhirFormat.TURTLE;
else if (t.getKey().endsWith(".shc"))
res.cntType = Manager.FhirFormat.SHC;
else if (t.getKey().endsWith(".txt") || t.getKey().endsWith(".map"))
else if (t.getKey().endsWith(".txt"))
res.cntType = Manager.FhirFormat.TEXT;
else if (t.getKey().endsWith(".fml") || t.getKey().endsWith(".map"))
res.cntType = Manager.FhirFormat.FML;
else
throw new FHIRException("Todo: Determining resource type is not yet done");
}
@ -762,6 +767,7 @@ public class IgLoader {
if (isDebug() || ((e.getMessage() != null && e.getMessage().contains("cannot be cast")))) {
e.printStackTrace();
}
e.printStackTrace();
}
return r;
}
@ -774,7 +780,7 @@ public class IgLoader {
res = new org.hl7.fhir.dstu3.formats.XmlParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.dstu3.formats.JsonParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".txt") || fn.endsWith(".map"))
else if (fn.endsWith(".txt") || fn.endsWith(".map") || fn.endsWith(".fml"))
res = new org.hl7.fhir.dstu3.utils.StructureMapUtilities(null).parse(new String(content));
else
throw new FHIRException("Unsupported format for " + fn);
@ -785,7 +791,7 @@ public class IgLoader {
res = new org.hl7.fhir.r4.formats.XmlParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.r4.formats.JsonParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".txt") || fn.endsWith(".map"))
else if (fn.endsWith(".txt") || fn.endsWith(".map") || fn.endsWith(".fml"))
res = new org.hl7.fhir.r4.utils.StructureMapUtilities(null).parse(new String(content), fn);
else
throw new FHIRException("Unsupported format for " + fn);
@ -796,7 +802,7 @@ public class IgLoader {
res = new org.hl7.fhir.r4b.formats.XmlParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.r4b.formats.JsonParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".txt") || fn.endsWith(".map"))
else if (fn.endsWith(".txt") || fn.endsWith(".map") || fn.endsWith(".fml"))
res = new org.hl7.fhir.r4b.utils.structuremap.StructureMapUtilities(null).parse(new String(content), fn);
else
throw new FHIRException("Unsupported format for " + fn);
@ -819,15 +825,15 @@ public class IgLoader {
else
throw new FHIRException("Unsupported format for " + fn);
r = VersionConvertorFactory_10_50.convertResource(res, new org.hl7.fhir.convertors.misc.IGR2ConvertorAdvisor5());
} else if (fhirVersion.startsWith("5.0")) {
} else if (fhirVersion.startsWith("5.0") || "current".equals(fhirVersion)) {
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
r = new XmlParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
r = new JsonParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".txt"))
r = new StructureMapUtilities(getContext(), null, null).parse(TextFile.bytesToString(content), fn);
else if (fn.endsWith(".map"))
r = new StructureMapUtilities(null).parse(new String(content), fn);
else if (fn.endsWith(".map") || fn.endsWith(".fml"))
r = new StructureMapUtilities(context).parse(new String(content), fn);
else
throw new FHIRException("Unsupported format for " + fn);
} else

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ResourceChecker.java
View File

@ -43,8 +43,8 @@ public class ResourceChecker {
if (Utilities.existsInList(ext, "ttl")) {
return FhirFormat.TURTLE;
}
if (Utilities.existsInList(ext, "map")) {
return Manager.FhirFormat.TEXT;
if (Utilities.existsInList(ext, "map", "fml")) {
return Manager.FhirFormat.FML;
}
if (Utilities.existsInList(ext, "jwt", "jws")) {
return Manager.FhirFormat.SHC;

18
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -219,6 +219,8 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
@Getter @Setter private Coding jurisdiction;
private ContextUtilities cu = null;
/**
* Creating a validation engine is an expensive operation - takes seconds.
* Once you have a validation engine created, you can quickly clone it to
@ -842,7 +844,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
new org.hl7.fhir.dstu3.formats.XmlParser().setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
new org.hl7.fhir.dstu3.formats.JsonParser().setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".txt") || fn.endsWith(".map"))
else if (fn.endsWith(".txt") || fn.endsWith(".map") || fn.endsWith(".fml"))
TextFile.stringToStream(org.hl7.fhir.dstu3.utils.StructureMapUtilities.render((org.hl7.fhir.dstu3.model.StructureMap) res), s, false);
else
throw new FHIRException("Unsupported format for " + fn);
@ -852,7 +854,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
new org.hl7.fhir.r4.formats.XmlParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".txt") || fn.endsWith(".map"))
else if (fn.endsWith(".txt") || fn.endsWith(".map") || fn.endsWith(".fml"))
TextFile.stringToStream(org.hl7.fhir.r4.utils.StructureMapUtilities.render((org.hl7.fhir.r4.model.StructureMap) res), s, false);
else
throw new FHIRException("Unsupported format for " + fn);
@ -877,7 +879,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
new XmlParser().setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(s, r);
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
new JsonParser().setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(s, r);
else if (fn.endsWith(".txt") || fn.endsWith(".map"))
else if (fn.endsWith(".txt") || fn.endsWith(".map") || fn.endsWith(".fml"))
TextFile.stringToStream(StructureMapUtilities.render((org.hl7.fhir.r5.model.StructureMap) r), s, false);
else
throw new FHIRException("Unsupported format for " + fn);
@ -1061,6 +1063,16 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
resolvedUrls.put(type+"|"+url, false);
return false; // todo... how to access settings from here?
}
if (url.contains("*") && !url.contains("?")) {
if (cu == null) {
cu = new ContextUtilities(context);
}
List<StructureMap> maps = cu.listMaps(url);
if (!maps.isEmpty()) {
return true;
}
}
if (fetcher != null) {
try {
boolean ok = fetcher.resolveURL(validator, appContext, path, url, type);

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java
View File

@ -105,6 +105,8 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
}
if (base.equals("http://terminology.hl7.org")) {
pid = "hl7.terminology";
} else if (base.equals("http://hl7.org/fhir")) {
return false;
} else if (url.startsWith("http://hl7.org/fhir")) {
pid = pcm.getPackageId(base);
} else {

24
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java
View File

@ -14,6 +14,7 @@ import org.hl7.fhir.validation.cli.model.HtmlInMarkdownCheck;
public class Params {
public static final String VERSION = "-version";
public static final String ALT_VERSION = "-alt-version";
public static final String OUTPUT = "-output";
public static final String OUTPUT_SUFFIX = "-outputSuffix";
@ -307,9 +308,29 @@ public class Params {
if (version == null) {
cliContext.addIg(s);
} else {
cliContext.setSv(version);
String v = getParam(args, VERSION);
if (v != null && !v.equals(version)) {
throw new Error("Parameters are inconsistent: specified version is "+v+" but -ig parameter "+s+" implies a different version");
} else if (cliContext.getSv() != null && !version.equals(cliContext.getSv())) {
throw new Error("Parameters are inconsistent: multiple -ig parameters implying differetion versions ("+cliContext.getSv()+","+version+")");
} else {
cliContext.setSv(version);
}
}
}
} else if (args[i].equals(ALT_VERSION)) {
if (i + 1 == args.length)
throw new Error("Specified " + args[i] + " without indicating version");
else {
String s = args[++i];
String v = VersionUtilities.getMajMin(s);
if (v == null) {
throw new Error("Unsupported FHIR Version "+s);
}
String pid = VersionUtilities.packageForVersion(v);
pid = pid + "#"+VersionUtilities.getCurrentPackageVersion(v);
cliContext.addIg(pid);
}
} else if (args[i].equals(MAP)) {
if (cliContext.getMap() == null) {
if (i + 1 == args.length)
@ -336,6 +357,7 @@ public class Params {
cliContext.addSource(args[i]);
}
}
return cliContext;
}

24
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -189,6 +189,7 @@ import org.hl7.fhir.validation.instance.type.MeasureValidator;
import org.hl7.fhir.validation.instance.type.QuestionnaireValidator;
import org.hl7.fhir.validation.instance.type.SearchParameterValidator;
import org.hl7.fhir.validation.instance.type.StructureDefinitionValidator;
import org.hl7.fhir.validation.instance.type.StructureMapValidator;
import org.hl7.fhir.validation.instance.type.ValueSetValidator;
import org.hl7.fhir.validation.instance.utils.ChildIterator;
import org.hl7.fhir.validation.instance.utils.ElementInfo;
@ -3262,6 +3263,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
refType = "bundled";
}
}
boolean conditional = ref.contains("?") && Utilities.existsInList(ref.substring(0, ref.indexOf("?")), context.getResourceNames());
ReferenceValidationPolicy pol;
if (refType.equals("contained") || refType.equals("bundled")) {
pol = ReferenceValidationPolicy.CHECK_VALID;
@ -3273,7 +3275,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
if (pol.checkExists()) {
if (conditional) {
String query = ref.substring(ref.indexOf("?"));
boolean test = !Utilities.noString(query) && query.matches("\\?([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*))*");
//("^\\?([\\w-]+(=[\\w-]*)?(&[\\w-]+(=[\\w-]*)?)*)?$"),
ok = rule(errors, "2023-02-20", IssueType.INVALID, element.line(), element.col(), path, test, I18nConstants.REFERENCE_REF_QUERY_INVALID, ref) && ok;
} else if (pol.checkExists()) {
if (we == null) {
if (!refType.equals("contained")) {
if (fetcher == null) {
@ -3766,7 +3774,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
TypedElementDefinition ted = null;
String fp = FHIRPathExpressionFixer.fixExpr(discriminator, null);
String fp = FHIRPathExpressionFixer.fixExpr(discriminator, null, context.getVersion());
ExpressionNode expr = null;
try {
expr = fpe.parse(fp);
@ -4384,7 +4392,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
try {
n = fpe.parse(FHIRPathExpressionFixer.fixExpr(expression.toString(), null));
n = fpe.parse(FHIRPathExpressionFixer.fixExpr(expression.toString(), null, context.getVersion()));
} catch (FHIRLexerException e) {
if (STACK_TRACE) e.printStackTrace();
throw new FHIRException(context.formatMessage(I18nConstants.PROBLEM_PROCESSING_EXPRESSION__IN_PROFILE__PATH__, expression, profile.getVersionedUrl(), path, e.getMessage()));
@ -4993,6 +5001,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return new SearchParameterValidator(context, timeTracker, fpe, xverManager, jurisdiction).validateSearchParameter(errors, element, stack);
} else if (element.getType().equals("StructureDefinition")) {
return new StructureDefinitionValidator(context, timeTracker, fpe, wantCheckSnapshotUnchanged, xverManager, jurisdiction).validateStructureDefinition(errors, element, stack);
} else if (element.getType().equals("StructureMap")) {
return new StructureMapValidator(context, timeTracker, fpe, xverManager,profileUtilities, jurisdiction).validateStructureMap(errors, element, stack);
} else if (element.getType().equals("ValueSet")) {
return new ValueSetValidator(context, timeTracker, this, xverManager, jurisdiction).validateValueSet(errors, element, stack);
} else {
@ -5849,7 +5859,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
if (!ToolingExtensions.readBoolExtension(profile, "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-no-order")) {
boolean ok = (ei.definition == null) || (ei.index >= last) || isXmlAttr;
boolean ok = (ei.definition == null) || (ei.index >= last) || isXmlAttr || ei.getElement().isIgnorePropertyOrder();
rule(errors, NO_RULE_DATE, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), ok, I18nConstants.VALIDATION_VAL_PROFILE_OUTOFORDER, profile.getVersionedUrl(), ei.getName(), lastei == null ? "(null)" : lastei.getName());
}
if (ei.slice != null && ei.index == last && ei.slice.getSlicing().getOrdered()) {
@ -6010,7 +6020,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
List<ValidationMessage> invErrors = null;
// We key based on inv.expression rather than inv.key because expressions can change in derived profiles and aren't guaranteed to be consistent across profiles.
String key = FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey());
String key = FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey(), context.getVersion());
if (!invMap.keySet().contains(key)) {
invErrors = new ArrayList<ValidationMessage>();
invMap.put(key, invErrors);
@ -6064,7 +6074,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (n == null) {
long t = System.nanoTime();
try {
String expr = FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey());
String expr = FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey(), context.getVersion());
n = fpe.parse(expr);
} catch (FHIRException e) {
rule(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, false, I18nConstants.PROBLEM_PROCESSING_EXPRESSION__IN_PROFILE__PATH__, inv.getExpression(), profile.getVersionedUrl(), path, e.getMessage());
@ -6275,7 +6285,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
ExpressionNode n = (ExpressionNode) inv.getUserData("validator.expression.cache");
if (n == null) {
n = fpe.parse(FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey()));
n = fpe.parse(FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey(), context.getVersion()));
inv.setUserData("validator.expression.cache", n);
}
fpe.check(null, sd.getKind() == StructureDefinitionKind.RESOURCE ? sd.getType() : "DomainResource", ed.getPath(), n);

958
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureMapValidator.java Normal file
View File

@ -0,0 +1,958 @@
package org.hl7.fhir.validation.instance.type;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupComponent;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupInputComponent;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupTypeMode;
import org.hl7.fhir.r5.model.StructureMap.StructureMapInputMode;
import org.hl7.fhir.r5.model.StructureMap.StructureMapModelMode;
import org.hl7.fhir.r5.model.StructureMap.StructureMapStructureComponent;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class StructureMapValidator extends BaseValidator {
public class ElementDefinitionSource {
private StructureDefinition sd;
private ElementDefinition ed;
protected ElementDefinitionSource(StructureDefinition sd, ElementDefinition ed) {
super();
this.sd = sd;
this.ed = ed;
}
public StructureDefinition getSd() {
return sd;
}
public ElementDefinition getEd() {
return ed;
}
}
public class RuleInformation {
int maxCount = 1;
String defVariable;
public void seeCardinality(int max) {
if (max == Integer.MAX_VALUE || maxCount == Integer.MAX_VALUE) {
maxCount = Integer.MAX_VALUE;
} else {
maxCount = maxCount * max;
}
}
public boolean isList() {
return maxCount > 1;
}
public int getMaxCount() {
return maxCount;
}
public String getDefVariable() {
return defVariable;
}
public void setDefVariable(String defVariable) {
this.defVariable = defVariable;
}
}
public class VariableDefn {
private String name;
private String mode;
private int max;
private StructureDefinition sd;
private ElementDefinition ed;
private String type;
protected VariableDefn(String name, String mode) {
super();
this.name = name;
this.mode = mode;
}
public VariableDefn setType(int max, StructureDefinition sd, ElementDefinition ed, String type) {
this.max = max;
this.sd = sd;
this.ed = ed;
this.type = type;
return this;
}
public String getName() {
return name;
}
public String getMode() {
return mode;
}
public VariableDefn copy() {
VariableDefn n = new VariableDefn(name, mode);
n.max = max;
n.sd = sd;
n.ed = ed;
n.type = type;
return n;
}
public boolean hasTypeInfo() {
return sd != null;
}
public int getMax() {
return max;
}
public StructureDefinition getSd() {
return sd;
}
public ElementDefinition getEd() {
return ed;
}
public String getType() {
return type;
}
public void setType(String type) {
this.type = type;
}
public String getWorkingType() {
if (type != null) {
return type;
}
if (ed != null && ed.getType().size() == 1) {
return ed.getType().get(0).getWorkingCode();
}
return null;
}
}
public class VariableSet {
private List<VariableDefn> list = new ArrayList<>();
public boolean hasVariable(String name) {
for (VariableDefn v : list) {
if (name.equals(v.getName())) {
return true;
}
}
return false;
}
public boolean hasVariable(String name, boolean source) {
for (VariableDefn v : list) {
if (name.equals(v.getName()) && source == ("source".equals(v.getMode()))) {
return true;
}
}
return false;
}
public VariableDefn add(String name, String mode) {
list.removeIf(item -> item.getName().equals(name) && item.getMode().equals(mode));
VariableDefn v = new VariableDefn(name, mode);
list.add(v);
return v;
}
//
// public void add(VariableDefn v) {
// list.removeIf(item -> item.getName().equals(v.getName()) && item.getMode().equals(v.getMode()));
// list.add(v);
// }
//
public VariableSet copy() {
VariableSet set = new VariableSet();
for (VariableDefn v : list) {
set.list.add(v.copy());
}
return set;
}
public VariableDefn getVariable(String name, boolean source) {
for (VariableDefn v : list) {
if (name.equals(v.getName()) && source == ("source".equals(v.getMode()))) {
return v;
}
}
return null;
}
public void add(String pname, VariableDefn v) {
VariableDefn vn = v.copy();
vn.name = pname;
list.add(vn);
}
}
private static final boolean SOURCE = true;
private static final boolean TARGET = false;
private FHIRPathEngine fpe;
private ProfileUtilities profileUtilities;
private ContextUtilities cu;
private List<StructureMap> imports = new ArrayList<>();
public StructureMapValidator(IWorkerContext context, TimeTracker timeTracker, FHIRPathEngine fpe, XVerExtensionManager xverManager, ProfileUtilities profileUtilities, Coding jurisdiction) {
super(context, xverManager);
source = Source.InstanceValidator;
this.fpe = fpe;
this.timeTracker = timeTracker;
this.jurisdiction = jurisdiction;
this.profileUtilities = profileUtilities;
this.cu = new ContextUtilities(context);
}
public boolean validateStructureMap(List<ValidationMessage> errors, Element src, NodeStack stack) {
boolean ok = true;
List<Element> imports = src.getChildrenByName("import");
int cc = 0;
for (Element import_ : imports) {
ok = validateImport(errors, src, import_, stack.push(import_, cc, null, null)) && ok;
cc++;
}
List<Element> groups = src.getChildrenByName("group");
// we iterate the groups repeatedly, validating them if they have stated types or found types, until nothing happens
boolean fired = false;
do {
fired = false;
cc = 0;
for (Element group : groups) {
if (!group.hasUserData("structuremap.validated")) {
if (hasInputTypes(group) || group.hasUserData("structuremap.parameters")) {
group.setUserData("structuremap.validated", true);
fired = true;
ok = validateGroup(errors, src, group, stack.push(group, cc, null, null)) && ok;
}
}
cc++;
}
} while (fired);
cc = 0;
for (Element group : groups) {
if (!group.hasUserData("structuremap.validated")) {
hint(errors, "2023-03-01", IssueType.INFORMATIONAL, group.line(), group.col(), stack.getLiteralPath(), ok, I18nConstants.SM_ORPHAN_GROUP);
ok = validateGroup(errors, src, group, stack.push(group, cc, null, null)) && ok;
}
cc++;
}
return ok;
}
private boolean hasInputTypes(Element group) {
List<Element> inputs = group.getChildrenByName("input");
for (Element input : inputs) {
if (!input.hasChild("type")) {
return false;
}
}
return true;
}
private boolean validateImport(List<ValidationMessage> errors, Element src, Element import_, NodeStack stack) {
String url = import_.primitiveValue();
boolean ok = false;
StructureMap map = context.fetchResource(StructureMap.class, url);
if (map != null) {
imports.add(map);
ok = true;
} else if (url.contains("*")) {
List<StructureMap> maps = cu.listMaps(url);
ok = !maps.isEmpty();
imports.addAll(maps);
}
warning(errors, "2023-03-01", IssueType.INVALID, import_.line(), import_.col(), stack.getLiteralPath(), ok, I18nConstants.SM_IMPORT_NOT_FOUND, url);
return true;
}
private boolean validateGroup(List<ValidationMessage> errors, Element src, Element group, NodeStack stack) {
String name = group.getChildValue("name");
boolean ok = rule(errors, "2023-03-01", IssueType.INVALID, group.line(), group.col(), stack.getLiteralPath(), idIsValid(name), I18nConstants.SM_NAME_INVALID, name);
Element extend = group.getNamedChild("extends");
if (extend != null) {
StructureMapGroupComponent grp = resolveGroup(extend.primitiveValue(), src);
if (rule(errors, "2023-03-01", IssueType.NOTSUPPORTED, extend.line(), extend.col(), stack.push(extend, -1, null, null).getLiteralPath(), grp != null, I18nConstants.SM_RULEGROUP_NOT_FOUND, extend.primitiveValue())) {
// check inputs
} else {
ok = false;
}
}
VariableSet variables = new VariableSet();
VariableSet pvars = (VariableSet) group.getUserData("structuremap.parameters");
// first, load all the inputs
List<Element> inputs = group.getChildrenByName("input");
List<Element> structures = src.getChildrenByName("structure");
int cc = 0;
for (Element input : inputs) {
ok = validateInput(errors, src, group, input, stack.push(input, cc, null, null), structures, variables, pvars) && ok;
cc++;
}
// now check the rules.
List<Element> rules = group.getChildrenByName("rule");
cc = 0;
for (Element rule : rules) {
ok = validateRule(errors, src, group, rule, stack.push(rule, cc, null, null), variables) && ok;
cc++;
}
return ok;
}
private StructureMapGroupComponent resolveGroup(String grpName, Element src) {
if (grpName == null) {
return null;
}
List<Element> groups = src.getChildrenByName("group");
for (Element group : groups) {
String name = group.getChildValue("name");
if (grpName.equals(name)) {
return makeGroupComponent(group);
}
}
for (StructureMap map : imports) {
for (StructureMapGroupComponent grp : map.getGroup()) {
if (grpName.equals(grp.getName())) {
return grp;
}
}
}
return null;
}
private StructureMapGroupComponent makeGroupComponent(Element group) {
StructureMapGroupComponent grp = new StructureMapGroupComponent();
grp.setUserData("element.source", group);
grp.setName(group.getChildValue("name"));
List<Element> inputs = group.getChildrenByName("input");
for (Element input : inputs) {
StructureMapGroupInputComponent inp = grp.addInput();
inp.setName(input.getChildValue("name"));
inp.setType(input.getChildValue("type"));
try {
inp.setMode(StructureMapInputMode.fromCode(input.getChildValue("mode")));
} catch (Exception e) {
// nothing; will be an error elsewhere
}
}
return grp;
}
private boolean validateInput(List<ValidationMessage> errors, Element src, Element group, Element input, NodeStack stack, List<Element> structures, VariableSet variables, VariableSet pvars) {
boolean ok = false;
String name = input.getChildValue("name");
String mode = input.getChildValue("mode");
String type = input.getChildValue("type");
VariableDefn pv = null;
if (type == null && pvars != null) {
pv = pvars.getVariable(name, mode.equals("source"));
if (pv != null) {
type = pv.getWorkingType();
}
}
if (rule(errors, "2023-03-01", IssueType.NOTSUPPORTED, input.line(), input.col(), stack.getLiteralPath(), idIsValid(name), I18nConstants.SM_NAME_INVALID, name) && // the name {0} is not valid)
rule(errors, "2023-03-01", IssueType.DUPLICATE, input.line(), input.col(), stack.getLiteralPath(), !variables.hasVariable(name), I18nConstants.SM_GROUP_INPUT_DUPLICATE, name)) { // the name {0} is not valid)
VariableDefn v = variables.add(name, mode);
if (rule(errors, "2023-03-01", IssueType.INVALID, input.line(), input.col(), stack.getLiteralPath(), Utilities.existsInList(mode, "source", "target"), I18nConstants.SM_GROUP_INPUT_MODE_INVALID, name, mode) && // the group parameter {0} mode {1} isn't valid
warning(errors, "2023-03-01", IssueType.NOTSUPPORTED, input.line(), input.col(), stack.getLiteralPath(), type != null, I18nConstants.SM_GROUP_INPUT_NO_TYPE, name)) { // the group parameter {0} has no type, so the paths cannot be validated
String smode = null;
StructureDefinition sd = null;
ElementDefinition ed = null;
if (pv != null) {
sd = pv.getSd();
ed = pv.getEd();
} else {
Element structure = findStructure(structures, type);
if (structure != null) {
smode = structure.getChildValue("mode");
String url = structure.getChildValue("url");
sd = context.fetchResource(StructureDefinition.class, url);
if (sd == null) {
rule(errors, "2023-03-01", IssueType.INVALID, input.line(), input.col(), stack.getLiteralPath(), sd != null, I18nConstants.SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE, type, url);
}
} else if (type != null) {
sd = context.fetchTypeDefinition(type);
if (sd == null) {
rule(errors, "2023-03-01", IssueType.INVALID, input.line(), input.col(), stack.getLiteralPath(), sd != null, I18nConstants.SM_GROUP_INPUT_TYPE_UNKNOWN_TYPE, type);
}
} else {
rule(errors, "2023-03-01", IssueType.NOTSUPPORTED, input.line(), input.col(), stack.getLiteralPath(), structure != null, I18nConstants.SM_GROUP_INPUT_TYPE_NOT_DECLARED, type);
ok = false;
}
if (sd != null) {
ed = sd.getSnapshot().getElementFirstRep();
}
}
if (rule(errors, "2023-03-01", IssueType.NOTSUPPORTED, input.line(), input.col(), stack.getLiteralPath(), smode == null || mode.equals(smode), I18nConstants.SM_GROUP_INPUT_MODE_MISMATCH, type, mode, smode)) { // the type {0} has mode {1} which doesn't match the structure definition {2}
v.setType(1, sd, ed, null);
ok = true;
}
}
}
return ok;
}
private Element findStructure(List<Element> structures, String type) {
for (Element structure : structures ) {
String t = structure.getChildValue("alias");
if (type.equals(t)) {
return structure;
}
}
return null;
}
private boolean idIsValid(String name) {
return name != null && name.matches("[a-zA-Z][a-zA-Z0-9]*");
}
private boolean validateRule(List<ValidationMessage> errors, Element src, Element group, Element rule, NodeStack stack, VariableSet variables) {
String name = rule.getChildValue("name");
boolean ok = rule(errors, "2023-03-01", IssueType.INVALID, rule.line(), rule.col(), stack.getLiteralPath(), idIsValid(name), I18nConstants.SM_NAME_INVALID, name);
RuleInformation ruleInfo = new RuleInformation();
// process the sources
VariableSet lvars = variables.copy();
List<Element> sources = rule.getChildrenByName("source");
int cc = 0;
for (Element source : sources) {
ok = validateRuleSource(errors, src, group, rule, source, stack.push(source, cc, null, null), lvars, ruleInfo, cc) && ok;
cc++;
}
// process the targets
List<Element> targets = rule.getChildrenByName("target");
cc = 0;
for (Element target : targets) {
ok = validateRuleTarget(errors, src, group, rule, target, stack.push(target, cc, null, null), lvars, ruleInfo) && ok;
cc++;
}
// process the targets
List<Element> rules = rule.getChildrenByName("rule");
cc = 0;
for (Element child : rules) {
ok = validateRule(errors, src, group, child, stack.push(child, cc, null, null), lvars) && ok;
cc++;
}
// todo: check dependents
List<Element> dependents = rule.getChildrenByName("dependent");
cc = 0;
for (Element dependent : dependents) {
ok = validateDependent(errors, src, group, dependent, stack.push(dependent, cc, null, null), lvars) && ok;
cc++;
}
return ok;
}
private boolean validateRuleSource(List<ValidationMessage> errors, Element src, Element group, Element rule, Element source, NodeStack stack, VariableSet variables, RuleInformation ruleInfo, int loopCounter) {
String context = source.getChildValue("context");
if (loopCounter > 0) {
ruleInfo.setDefVariable(null);
}
boolean ok = rule(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), idIsValid(context), I18nConstants.SM_NAME_INVALID, context) &&
rule(errors, "2023-03-01", IssueType.UNKNOWN, source.line(), source.col(), stack.getLiteralPath(), variables.hasVariable(context, SOURCE), I18nConstants.SM_SOURCE_CONTEXT_UNKNOWN, context);
if (ok) {
VariableDefn v = variables.getVariable(context, SOURCE);
if (v.hasTypeInfo()) { // if it doesn't, that's already an issue elsewhere
// check type
// check defaultValue
// check element
String element = source.getChildValue("element");
if (element != null) {
String path = v.getEd().getPath()+"."+element;
String variable = source.getChildValue("variable");
VariableDefn vn = null;
if (hint(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), variable != null, I18nConstants.SM_RULE_SOURCE_UNASSIGNED)) {
if (rule(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), idIsValid(variable), I18nConstants.SM_NAME_INVALID, variable)) {
vn = variables.add(variable, v.getMode()); // may overwrite
if (loopCounter == 0) {
ruleInfo.setDefVariable(variable);
}
} else {
ok = false;
}
}
List<ElementDefinitionSource> els = getElementDefinitions(v.getSd(), v.getEd(), v.getType(), element);
if (rule(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), !els.isEmpty(), I18nConstants.SM_SOURCE_PATH_INVALID, context, element, path)) {
if (warning(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), els.size() == 1, I18nConstants.SM_TARGET_PATH_MULTIPLE_MATCHES, context, element, v.getEd().getPath()+"."+element, render(els))) {
ElementDefinitionSource el = els.get(0);
String type = source.getChildValue("type");
if (type != null) {
ok = rule(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), hasType(el.getEd(), type), I18nConstants.SM_SOURCE_TYPE_INVALID, type, path, el.getEd().typeSummary()) && ok;
}
String min = source.getChildValue("min");
hint(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), min == null || isMoreOrEqual(min, v.getEd().getMin()), I18nConstants.SM_RULE_SOURCE_MIN_REDUNDANT, min, v.getEd().getMin());
int existingMax = multiplyCardinality(v.getMax(), el.getEd().getMax());
String max = source.getChildValue("max");
int iMax = readMax(max, existingMax);
warning(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), iMax <= existingMax, I18nConstants.SM_RULE_SOURCE_MAX_REDUNDANT, max, v.getMax());
ruleInfo.seeCardinality(iMax);
if (vn != null) {
vn.setType(iMax, el.getSd(), el.getEd(), type); // may overwrite
}
}
} else {
ok = false;
}
}
// check condition
// check check
}
}
return ok;
}
private boolean hasType(ElementDefinition ed, String type) {
for (TypeRefComponent td : ed.getType()) {
if (type.equals(td.getWorkingCode())) {
return true;
}
}
return false;
}
private int readMax(String max, int existingMax) {
if (max == null || !Utilities.isInteger(max)) {
return existingMax;
} else {
return Integer.parseInt(max);
}
}
private int multiplyCardinality(int max, String max2) {
if (max == Integer.MAX_VALUE || "*".equals(max2)) {
return Integer.MAX_VALUE;
} else {
return max * Integer.parseInt(max2);
}
}
private boolean validateRuleTarget(List<ValidationMessage> errors, Element src, Element group, Element rule, Element target, NodeStack stack, VariableSet variables, RuleInformation ruleInfo) {
String context = target.getChildValue("context");
if (context == null) {
return true;
}
boolean ok = rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), idIsValid(context), I18nConstants.SM_NAME_INVALID, context) &&
rule(errors, "2023-03-01", IssueType.UNKNOWN, target.line(), target.col(), stack.getLiteralPath(), variables.hasVariable(context, TARGET), I18nConstants.SM_TARGET_CONTEXT_UNKNOWN, context);
if (ok) {
VariableDefn v = variables.getVariable(context, TARGET);
if (v.hasTypeInfo()) {
String listMode = target.getChildValue("listMode");
String listRuleId = target.getChildValue("listRuleId");
warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), listRuleId == null || "share".equals(listMode), I18nConstants.SM_LIST_RULE_ID_ONLY_WHEN_SHARE);
if (!ruleInfo.isList()) {
warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), listMode == null, I18nConstants.SM_NO_LIST_MODE_NEEDED);
warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), listRuleId == null, I18nConstants.SM_NO_LIST_RULE_ID_NEEDED);
}
VariableDefn vn = null;
String variable = target.getChildValue("variable");
if (variable != null) {
if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), idIsValid(variable), I18nConstants.SM_NAME_INVALID, variable)) {
vn = variables.add(variable, v.getMode()); // may overwrite
} else {
ok = false;
}
}
String element = target.getChildValue("element");
if (element != null) {
List<ElementDefinitionSource> els = getElementDefinitions(v.getSd(), v.getEd(), v.getType(), element);
if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), !els.isEmpty(), I18nConstants.SM_TARGET_PATH_INVALID, context, element, v.getEd().getPath()+"."+element)) {
if (warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), els.size() == 1, I18nConstants.SM_TARGET_PATH_MULTIPLE_MATCHES, context, element, v.getEd().getPath()+"."+element, render(els))) {
ElementDefinitionSource el = els.get(0);
String transform = target.getChildValue("transform");
List<Element> params = target.getChildren("parameter");
if (transform == null) {
transform = "create"; // implied
rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() == 0, I18nConstants.SM_TARGET_NO_TRANSFORM_NO_CHECKED, transform);
}
// List<String> types = listTypes(el.getEd().getType());
String type = null;
if (el.getEd().getType().size() == 1) {
type = el.getEd().getTypeFirstRep().getWorkingCode();
} else {
type = inferType(ruleInfo, variables, rule, transform, params);
}
switch (transform) {
case "create":
if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() < 2, I18nConstants.SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE, "create", "0", "1", params.size())) {
if (params.size() == 1) {
type = params.get(0).getChildValue("value");
warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(),type != null, I18nConstants.SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE);
} else {
// maybe can guess? maybe not ... type =
}
} else {
ok = false;
}
break;
case "copy": // logic is the same as create?
if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() < 2, I18nConstants.SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE, "create", "0", "1", params.size())) {
if (params.size() == 1) {
type = params.get(0).getChildValue("value");
warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(),type != null, I18nConstants.SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE);
} else {
// maybe can guess? maybe not ... type =
}
} else {
ok = false;
}
break;
case "reference":
if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() == 1, I18nConstants.SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE, "reference", "0", "1", params.size())) {
type = "string";
} else {
ok = false;
}
break;
case "evaluate":
if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() == 1, I18nConstants.SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE, "evaluate", "1", params.size())) {
String exp = params.get(0).getChildValue("value");
if (rule(errors, "2023-03-01", IssueType.INVALID, params.get(0).line(), params.get(0).col(), stack.getLiteralPath(), exp != null, I18nConstants.SM_TARGET_TRANSFORM_PARAM_UNPROCESSIBLE, "0", params.size())) {
try {
TypeDetails td = fpe.check(null, v.getSd().getType(), v.getEd().getPath(), fpe.parse(exp));
if (td.getTypes().size() == 1) {
type = td.getType();
}
} catch (Exception e) {
rule(errors, "2023-03-01", IssueType.INVALID, params.get(0).line(), params.get(0).col(), stack.getLiteralPath(), false, I18nConstants.SM_TARGET_TRANSFORM_EXPRESSION_ERROR, e.getMessage());
}
} else {
ok = false;
}
} else {
ok = false;
}
break;
default:
rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), false, I18nConstants.SM_TARGET_TRANSFORM_NOT_CHECKED, transform);
ok = false;
}
if (vn != null) {
// it's just a warning: maybe this'll work out at run time?
warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), type != null, I18nConstants.SM_TARGET_TYPE_MULTIPLE_POSSIBLE, el.getEd().typeSummary());
vn.setType(ruleInfo.getMaxCount(), el.getSd(), el.getEd(), type); // may overwrite
}
}
} else {
ok = false;
}
}
//
}
}
return ok;
}
private String inferType(RuleInformation ruleInfo, VariableSet variables, Element rule, String transform, List<Element> params) {
// under some special conditions, we can infer what the type will be:
// * there's a nominated default variable
// * that variable has as single type
// * there's a create with no param
// * there's a single dependent rule with name = StructureMapUtilities.DEF_GROUP_NAME
// * there's a default type group for the type of the source type
// otherwise, we can't know the target type.
if (ruleInfo.getDefVariable() != null && "create".equals(transform) && params.isEmpty()) {
VariableDefn v = variables.getVariable(ruleInfo.getDefVariable(), SOURCE);
if (v != null && (v.getEd().getType().size() == 1 || v.getType() != null)) {
List<Element> dependents = rule.getChildrenByName("dependent");
if (dependents.size() == 1 && StructureMapUtilities.DEF_GROUP_NAME.equals(dependents.get(0).getChildValue("name"))) {
String type = v.getType() != null ? v.getType() : v.getEd().getTypeFirstRep().getWorkingCode();
// now, we look for a default group.
// todo: look in this source
// now look through the inputs
for (StructureMap map : imports) {
for (StructureMapGroupComponent grp : map.getGroup()) {
if (grp.getTypeMode() == StructureMapGroupTypeMode.TYPEANDTYPES && grp.getInput().size() == 2) {
String grpType = getTypeForGroupInput(map, grp, grp.getInput().get(0));
if (sameTypes(type, grpType)) {
String tgtType = getTypeForGroupInput(map, grp, grp.getInput().get(1));
if (tgtType != null) {
return tgtType;
}
}
}
}
}
}
}
}
return null;
}
private boolean sameTypes(String type1, String type2) {
if (type1 == null || type2 == null) {
return false;
}
if (!Utilities.isAbsoluteUrl(type1)) {
type1 = "http://hl7.org/fhir/StructureDefinition/"+type1;
}
if (!Utilities.isAbsoluteUrl(type2)) {
type2 = "http://hl7.org/fhir/StructureDefinition/"+type2;
}
return type1.equals(type2);
}
private String getTypeForGroupInput(StructureMap map, StructureMapGroupComponent grp, StructureMapGroupInputComponent input) {
String type = input.getType();
StructureMapModelMode mode = input.getMode() == StructureMapInputMode.SOURCE ? StructureMapModelMode.SOURCE : StructureMapModelMode.TARGET;
if (input == null) {
return null;
}
for (StructureMapStructureComponent st : map.getStructure()) {
if (type.equals(st.getAlias()) && mode == st.getMode()) {
return st.getUrl();
}
}
return type;
}
private List<String> listTypes(List<TypeRefComponent> types) {
List<String> res = new ArrayList<>();
for (TypeRefComponent td : types) {
res.add(td.getWorkingCode());
}
Collections.sort(res);
return res;
}
private String render(List<ElementDefinitionSource> list) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (ElementDefinitionSource t : list) {
b.append(t.getEd().getId());
}
return b.toString();
}
private List<ElementDefinitionSource> getElementDefinitions(StructureDefinition sd, ElementDefinition ed, String type, String element) {
List<ElementDefinitionSource> result = new ArrayList<>();
List<ElementDefinition> children = profileUtilities.getChildList(sd, ed);
if (children == null || children.isEmpty()) {
getElementDefinitionChildrenFromTypes(result, sd, ed, type, element);
} else {
for (ElementDefinition t : children) {
if (t.getNameBase().equals(element)) {
result.add(new ElementDefinitionSource(sd, t));
}
}
}
return result;
}
private void getElementDefinitionChildrenFromTypes(List<ElementDefinitionSource> result, StructureDefinition sd, ElementDefinition ed, String type, String element) {
for (TypeRefComponent td : ed.getType()) {
if (type == null | td.getWorkingCode().equals(type)) {
StructureDefinition tsd = context.fetchTypeDefinition(td.getWorkingCode());
if (tsd != null) {
for (ElementDefinition t : tsd.getSnapshot().getElement()) {
if (Utilities.charCount(t.getPath(), '.') == 1 && t.getNameBase().equals(element)) {
result.add(new ElementDefinitionSource(tsd, t));
}
}
} else {
System.out.println("Unable to find type "+type);
}
}
}
}
private boolean isLessOrEqual(String value, String limit) {
if (Utilities.isInteger(value) || !Utilities.isInteger(limit)) {
int v = Integer.parseInt(value);
int l = Integer.parseInt(limit);
return v <= l;
}
return true; // no issue in this case
}
private boolean isMoreOrEqual(String value, int limit) {
if (Utilities.isInteger(value)) {
int v = Integer.parseInt(value);
return v >= limit;
}
return true; // no issue in this case
}
private boolean validateDependent(List<ValidationMessage> errors, Element src, Element group, Element dependent, NodeStack stack, VariableSet variables) {
boolean ok = true;
String name = dependent.getChildValue("name");
if (StructureMapUtilities.DEF_GROUP_NAME.equals(name)) {
VariableDefn srcVar = variables.getVariable(StructureMapUtilities.AUTO_VAR_NAME, true);
VariableDefn tgtVar = variables.getVariable(StructureMapUtilities.AUTO_VAR_NAME, false);
if (srcVar != null && srcVar.hasTypeInfo() && tgtVar != null && tgtVar.hasTypeInfo()) {
String srcType = srcVar.getWorkingType();
String tgtType = tgtVar.getWorkingType();
if (rule(errors, "2023-03-01", IssueType.NOTFOUND, dependent.line(), dependent.col(), stack.getLiteralPath(), srcType != null, I18nConstants.SM_SOURCE_TYPE_NOT_FOUND) &&
rule(errors, "2023-03-01", IssueType.NOTFOUND, dependent.line(), dependent.col(), stack.getLiteralPath(), tgtType != null, I18nConstants.SM_TARGET_TYPE_NOT_FOUND)) {
StructureMapGroupComponent grp = findDefaultGroup(src, srcType, tgtType);
ok = rule(errors, "2023-03-01", IssueType.NOTFOUND, dependent.line(), dependent.col(), stack.getLiteralPath(), grp != null, I18nConstants.SM_MATCHING_RULEGROUP_NOT_FOUND, srcType, tgtType) && ok;
} else {
ok = false;
}
}
} else {
StructureMapGroupComponent grp = resolveGroup(name, src);
if (rule(errors, "2023-03-01", IssueType.NOTFOUND, dependent.line(), dependent.col(), stack.getLiteralPath(), grp != null, I18nConstants.SM_RULEGROUP_NOT_FOUND, name)) {
List<Element> params = dependent.getChildren("parameter");
if (rule(errors, "2023-03-01", IssueType.INVALID, dependent.line(), dependent.col(), stack.getLiteralPath(), params.size() == grp.getInput().size(), I18nConstants.SM_RULEGROUP_NOT_FOUND, params.size(), grp.getInput().size())) {
VariableSet lvars = new VariableSet();
int cc = 0;
for (Element param : params) {
NodeStack pstack = stack.push(param, cc, null, null);
StructureMapGroupInputComponent input = grp.getInput().get(cc);
String pname = input.getName();
VariableDefn v = getParameter(errors, param, pstack, variables, input.getMode());
if (v != null) {
if (rule(errors, "2023-03-01", IssueType.INVALID, param.line(), param.col(), pstack.getLiteralPath(), v.mode.equals(input.getMode().toCode()), I18nConstants.SM_DEPENDENT_PARAM_MODE_MISMATCH, param.getChildValue("name"), v.mode, input.getMode().toCode()) &&
rule(errors, "2023-03-01", IssueType.INVALID, param.line(), param.col(), pstack.getLiteralPath(), typesMatch(v, input.getType()), I18nConstants.SM_DEPENDENT_PARAM_TYPE_MISMATCH, param.getChildValue("name"), v, input.getType())) {
lvars.add(pname, v);
} else {
ok = false;
}
} else {
ok = false;
}
cc++;
}
if (ok && grp.hasUserData("element.source")) {
Element g = (Element) grp.getUserData("element.source");
if (g.hasUserData("structuremap.parameters")) {
throw new Error("bang! - this situation is not handled");
} else {
g.setUserData("structuremap.parameters", lvars);
}
}
}
} else {
ok = false;
}
}
return ok;
}
private StructureMapGroupComponent findDefaultGroup(Element src, String srcType, String tgtType) {
List<Element> groups = src.getChildrenByName("group");
for (Element group : groups) {
if (Utilities.existsInList(group.getChildValue("typeMode"), "types", "type-and-types")) {
List<Element> inputs = group.getChildrenByName("input");
if (inputs.size() == 2 && "source".equals(inputs.get(0).getChildValue("mode")) && "source".equals(inputs.get(0).getChildValue("mode"))) {
String srcT = resolveInputType(src, inputs.get(0));
String tgtT = resolveInputType(src, inputs.get(1));
if (sameTypes(srcT, srcType) && sameTypes(tgtT, tgtType)) {
return makeGroupComponent(group);
}
}
}
}
for (StructureMap map : imports) {
for (StructureMapGroupComponent grp : map.getGroup()) {
if ((grp.getTypeMode() == StructureMapGroupTypeMode.TYPES || grp.getTypeMode() == StructureMapGroupTypeMode.TYPEANDTYPES) &&
grp.getInput().size() == 2 && grp.getInput().get(0).getMode() == StructureMapInputMode.SOURCE && grp.getInput().get(1).getMode() == StructureMapInputMode.TARGET) {
String srcT = resolveInputType(map, grp.getInput().get(0));
String tgtT = resolveInputType(map, grp.getInput().get(1));
if (sameTypes(srcT, srcType) && sameTypes(tgtT, tgtType)) {
return grp;
}
}
}
}
return null;
}
private String resolveInputType(StructureMap map, StructureMapGroupInputComponent input) {
String type = input.getType();
if (type == null) {
return null;
}
for (StructureMapStructureComponent structure : map.getStructure()) {
if (type.equals(structure.getAlias())) {
return structure.getUrl();
}
}
StructureDefinition sd = context.fetchTypeDefinition(type);
return sd == null ? null : sd.getUrl();
}
private String resolveInputType(Element src, Element input) {
String type = input.getChildValue("type");
if (type == null) {
return null;
}
for (Element structure : input.getChildren("structure")) {
if (type.equals(structure.getChildValue("alias"))) {
return structure.getChildValue("url");
}
}
StructureDefinition sd = context.fetchTypeDefinition(type);
return sd == null ? null : sd.getUrl();
}
private boolean typesMatch(VariableDefn v, String type) {
if (type == null) {
return true;
} else {
return false;
}
}
private VariableDefn getParameter(List<ValidationMessage> errors, Element param, NodeStack pstack, VariableSet variables, StructureMapInputMode mode) {
Element v = param.getNamedChild("value");
if (v.fhirType().equals("id")) {
return variables.getVariable(v.primitiveValue(), mode == StructureMapInputMode.SOURCE);
} else {
String type = v.fhirType();
StructureDefinition sd = context.fetchTypeDefinition(type);
return new VariableDefn("$", "source").setType(1, sd, sd.getSnapshot().getElementFirstRep(), null);
}
}
}

22
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/FHIRPathExpressionFixer.java
View File

@ -1,16 +1,22 @@
package org.hl7.fhir.validation.instance.utils;
import org.hl7.fhir.utilities.VersionUtilities;
public class FHIRPathExpressionFixer {
public static String fixExpr(String expr, String key) {
public static String fixExpr(String expr, String key, String version) {
// this is a hack work around for past publication of wrong FHIRPath expressions
// R4
// waiting for 4.0.2
boolean r5 = VersionUtilities.isR5Ver(version);
// if (r5) {
// return expr;
// }
//TODO is this expression below correct? @grahamegrieve
if ("probability is decimal implies (probability as decimal) <= 100".equals(expr)) {
return "probability.empty() or ((probability is decimal) implies ((probability as decimal) <= 100))";
}
// if ("probability is decimal implies (probability as decimal) <= 100".equals(expr)) {
// return "probability.empty() or ((probability is decimal) implies ((probability as decimal) <= 100))";
// }
if ("enableWhen.count() > 2 implies enableBehavior.exists()".equals(expr)) {
return "enableWhen.count() >= 2 implies enableBehavior.exists()";
}
@ -52,10 +58,10 @@ public class FHIRPathExpressionFixer {
}
// clarification in FHIRPath spec
if ("eld-19".equals(key)) {
if (!r5 && "eld-19".equals(key)) {
return "path.matches('^[^\\\\s\\\\.,:;\\\\\\'\"\\\\/|?!@#$%&*()\\\\[\\\\]{}]{1,64}(\\\\.[^\\\\s\\\\.,:;\\\\\\'\"\\\\/|?!@#$%&*()\\\\[\\\\]{}]{1,64}(\\\\[x\\\\])?(\\\\:[^\\\\s\\\\.]+)?)*$')";
}
if ("eld-20".equals(key)) {
if (!r5 && "eld-20".equals(key)) {
return "path.matches('^[A-Za-z][A-Za-z0-9]*(\\\\.[a-z][A-Za-z0-9]*(\\\\[x])?)*$')";
}

10
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/5.0.0/ucum.cache
View File

@ -79,3 +79,13 @@ v: {
"system" : "http://unitsofmeasure.org"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "cm"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "cm",
"code" : "cm",
"system" : "http://unitsofmeasure.org"
}
-------------------------------------------------------------------------------------

26
pom.xml
View File

@ -14,7 +14,7 @@
HAPI FHIR
-->
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.99-SNAPSHOT</version>
<version>5.6.100-SNAPSHOT</version>
<packaging>pom</packaging>
<properties>
@ -24,6 +24,7 @@
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
<maven_surefire_version>3.0.0-M5</maven_surefire_version>
<maven_clean_version>3.1.0</maven_clean_version>
<okhttp.version>4.9.3</okhttp.version>
<jacoco_version>0.8.8</jacoco_version>
<info_cqframework_version>1.5.1</info_cqframework_version>
<lombok_version>1.18.22</lombok_version>
@ -36,6 +37,7 @@
<maven.compiler.testRelease>11</maven.compiler.testRelease>
<maven.compiler.testSource>11</maven.compiler.testSource>
<maven.compiler.testTarget>11</maven.compiler.testTarget>
<maven-jar-plugin.version>3.2.2</maven-jar-plugin.version>
</properties>
<name>HL7 Core Artifacts</name>
@ -182,9 +184,22 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
<executions>
<execution>
<phase>process-sources</phase>
<goals>
<goal>checkstyle</goal>
</goals>
<configuration>
<failsOnError>true</failsOnError>
<suppressionsLocation>${project.basedir}/checkstyle_suppressions.xml</suppressionsLocation>
<enableRulesSummary>true</enableRulesSummary>
<enableSeveritySummary>true</enableSeveritySummary>
<consoleOutput>true</consoleOutput>
<configLocation>${project.basedir}/../checkstyle.xml</configLocation>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@ -228,7 +243,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
<version>${maven-jar-plugin.version}</version>
<executions>
<execution>
<goals>
@ -415,6 +430,7 @@
</executions>
</plugin>
</plugins>
</build>
<profiles>

19
pull-request-pipeline-parameterized.yml
View File

@ -1,7 +1,7 @@
jobs:
- ${{ each image in parameters.images }}:
- job:
dependsOn: [ 'setup' ]
displayName: ${{image.displayName}}
pool:
@ -9,15 +9,21 @@ jobs:
variables:
currentImage: ${{image.vmImage}}
currentName: ${{image.displayName}}
codecov: $(CODECOV_TOKEN)
VERSION:
JAVA_TOOL_OPTIONS: ${{image.javaToolOptions}}
steps:
# Runs 'mvn clean install'
- task: Cache@2
inputs:
key: maven | $(Build.BuildId)
path: $(MAVEN_CACHE_FOLDER)
# Runs 'mvn install'
- task: Maven@3
inputs:
mavenPomFile: 'pom.xml'
options: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
mavenOptions: '-Xmx3072m'
javaHomeOption: 'JDKVersion'
jdkVersionOption: '${{image.jdkVersion}}'
@ -33,21 +39,22 @@ jobs:
javaHomeOption: 'JDKVersion'
jdkVersionOption: '${{image.jdkVersion}}'
jdkArchitectureOption: 'x64'
options: '-pl org.hl7.fhir.validation.cli'
options: '-pl org.hl7.fhir.validation.cli -Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
publishJUnitResults: false
testResultsFiles: '**/surefire-reports/TEST-*.xml'
goals: 'exec:exec'
# Upload test results to codecov
# Upload test results to codecov
- script: bash <(curl https://codecov.io/bash) -t $(codecov)
displayName: 'codecov Bash Uploader'
condition: eq(variables.currentImage, 'ubuntu-latest')
condition: eq(variables.currentName, 'ubuntu-latest-java-11')
# Publishes the test results to build artifacts.
- task: PublishCodeCoverageResults@1
displayName: 'Publish JaCoCo test results'
condition: eq(variables.currentImage, 'ubuntu-latest')
condition: eq(variables.currentName, 'ubuntu-latest-java-11')
inputs:
codeCoverageTool: 'JaCoCo'
summaryFileLocation: '$(System.DefaultWorkingDirectory)/org.hl7.fhir.report/target/site/jacoco-aggregate/jacoco.xml'
reportDirectory: '$(System.DefaultWorkingDirectory)/org.hl7.fhir.report/target/site/jacoco-aggregate/'

38
pull-request-pipeline.yml
View File

@ -1,3 +1,6 @@
variables:
MAVEN_CACHE_FOLDER: $(Pipeline.Workspace)/.m2/repository
trigger: none
pr:
@ -7,6 +10,41 @@ pr:
# Different users have different machine setups, we run the build three times, on ubuntu, osx, and windows.
# Azure doesn't always have the same Java versions on each system, so they are enumerated for each system independently.
jobs:
- job: setup
displayName: cache-maven-dependencies
pool:
vmImage: ubuntu-latest
steps:
- checkout: self
fetchDepth: 1
- task: Cache@2
inputs:
key: maven | $(Build.BuildId)
path: $(MAVEN_CACHE_FOLDER)
- task: Bash@3
inputs:
targetType: 'inline'
script: mkdir -p $(MAVEN_CACHE_FOLDER); pwd; ls -al $(MAVEN_CACHE_FOLDER)
- task: Maven@3
inputs:
mavenPomFile: 'pom.xml'
options: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
mavenOptions: '-Xmx3072m'
javaHomeOption: 'JDKVersion'
jdkVersionOption: '1.11'
jdkArchitectureOption: 'x64'
publishJUnitResults: false
goals: 'dependency:resolve'
- task: Maven@3
inputs:
mavenPomFile: 'pom.xml'
options: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
mavenOptions: '-Xmx3072m'
javaHomeOption: 'JDKVersion'
jdkVersionOption: '1.11'
jdkArchitectureOption: 'x64'
publishJUnitResults: false
goals: 'dependency:resolve-plugins'
- template: pull-request-pipeline-parameterized.yml
parameters:
images: