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Gg 202302 fhirpath as (#1102) 

* fix type of issue source extension

* update extension extractor

* FHIRPath changes for as - case and singleton issues

* minor fixes for extension rendering

* Update test cases version

---------

Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
This commit is contained in:
Grahame Grieve 2023-02-04 05:14:51 +11:00 committed by GitHub
parent ea41a8b6a6
commit ea9333b322
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
10 changed files with 181 additions and 25 deletions
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56
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExtensionExtractor.java
View File

@ -5,6 +5,8 @@ import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Set;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.CanonicalResourceManager;
@ -21,17 +23,21 @@ import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
public class ExtensionExtractor {
public static void main(String[] args) throws FHIRFormatError, FileNotFoundException, IOException {
new ExtensionExtractor().process(args[0]);
}
private void process(String dst) throws IOException {
Set<String> ids = new HashSet<>();
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
NpmPackage r5 = pcm.loadPackage("hl7.fhir.r5.core", "current");
CanonicalResourceManager<CodeSystem> cslist = new CanonicalResourceManager<CodeSystem>(true);
@ -67,7 +73,7 @@ public class ExtensionExtractor {
sd.setSnapshot(null);
String fn;
if (sd.getContext().size() == 0) {
save(sd, dst,"none");
save(sd, dst,"none", ids);
} else if (sd.getContext().size() > 1) {
boolean dt = true;
for (StructureDefinitionContextComponent x : sd.getContext()) {
@ -75,16 +81,16 @@ public class ExtensionExtractor {
dt = dt && isDataType(s);
}
if (dt) {
save(sd, dst,"datatypes");
save(sd, dst,"datatypes", ids);
} else {
save(sd, dst,"multiple");
save(sd, dst,"multiple", ids);
}
} else {
String s = extractType(sd.getContextFirstRep().getExpression());
if (isDataType(s)) {
save(sd, dst,"datatypes");
save(sd, dst,"datatypes", ids);
} else {
save(sd, dst,s);
save(sd, dst,s, ids);
}
}
} else {
@ -118,21 +124,53 @@ public class ExtensionExtractor {
for (ValueSet vs : vslist.getList()) {
StructureDefinition sd = (StructureDefinition) vs.getUserData("ext");
String s = sd.getUserString("folder");
save(vs, dst, s);
save(vs, dst, s, ids);
}
for (CodeSystem cs : cslist.getList()) {
ValueSet vs = ((ArrayList<ValueSet>) cs.getUserData("vsl")).get(0);
String s = vs.getUserString("folder");
save(cs, dst,s);
save(cs, dst,s, ids);
}
deleteMatchingResources(ids, new File("/Users/grahamegrieve/work/r5/source"));
}
private void save(CanonicalResource cr, String dst, String folder) throws IOException {
private void deleteMatchingResources(Set<String> ids, File folder) {
for (File f : folder.listFiles()) {
if (f.isDirectory()) {
deleteMatchingResources(ids, f);
} else if (f.getName().endsWith(".json")) {
try {
JsonObject json = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(f);
if (json.has("resourceType") && json.has("id") && ids.contains(json.asString("id"))) {
System.out.println("Delete "+f.getAbsolutePath());
f.delete();
}
} catch (Exception e) {
// nothing
}
} else if (f.getName().endsWith(".xml")) {
try {
Element xml = XMLUtil.parseFileToDom(f.getAbsolutePath()).getDocumentElement();
if (XMLUtil.hasNamedChild(xml, "id") && ids.contains(XMLUtil.getNamedChildValue(xml, "id"))) {
System.out.println("Delete "+f.getAbsolutePath());
f.delete();
}
} catch (Exception e) {
// nothing
}
}
}
}
private void save(CanonicalResource cr, String dst, String folder, Set<String> ids) throws IOException {
// TODO Auto-generated method stub
cr.setText(null);
if (!cr.hasTitle()) {
cr.setTitle(Utilities.unCamelCase(cr.getName()));
}
ids.add(cr.getId());
String fn = Utilities.path(dst, folder, cr.fhirType()+"-"+cr.getId()+".xml");
cr.setUserData("folder", folder);
if (!new File(fn).exists()) {

46
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/FHIRPathEngine.java
View File

@ -61,6 +61,7 @@ import org.hl7.fhir.utilities.MergedList;
import org.hl7.fhir.utilities.MergedList.MergeNode;
import org.hl7.fhir.utilities.SourceLocation;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.xhtml.NodeType;
@ -260,6 +261,8 @@ public class FHIRPathEngine {
private boolean allowPolymorphicNames;
private boolean doImplicitStringConversion;
private boolean liquidMode; // in liquid mode, || terminates the expression and hands the parser back to the host
private boolean doNotEnforceAsSingletonRule;
private boolean doNotEnforceAsCaseSensitive;
// if the fhir path expressions are allowed to use constants beyond those defined in the specification
// the application can implement them by providing a constant resolver
@ -369,8 +372,15 @@ public class FHIRPathEngine {
primitiveTypes.add(sd.getName());
}
}
initFlags();
}
private void initFlags() {
if (!VersionUtilities.isR5VerOrLater(worker.getVersion())) {
doNotEnforceAsCaseSensitive = true;
doNotEnforceAsSingletonRule = true;
}
}
// --- 3 methods to override in children -------------------------------------------------------
// if you don't override, it falls through to the using the base reference implementation
@ -453,6 +463,22 @@ public class FHIRPathEngine {
this.doImplicitStringConversion = doImplicitStringConversion;
}
public boolean isDoNotEnforceAsSingletonRule() {
return doNotEnforceAsSingletonRule;
}
public void setDoNotEnforceAsSingletonRule(boolean doNotEnforceAsSingletonRule) {
this.doNotEnforceAsSingletonRule = doNotEnforceAsSingletonRule;
}
public boolean isDoNotEnforceAsCaseSensitive() {
return doNotEnforceAsCaseSensitive;
}
public void setDoNotEnforceAsCaseSensitive(boolean doNotEnforceAsCaseSensitive) {
this.doNotEnforceAsCaseSensitive = doNotEnforceAsCaseSensitive;
}
// --- public API -------------------------------------------------------
/**
* Parse a path for later use using execute
@ -1789,11 +1815,11 @@ public class FHIRPathEngine {
if (!isKnownType(tn)) {
throw new PathEngineException("The type "+tn+" is not valid");
}
if (left.size() > 1) {
throw new PathEngineException("Attempt to use as on more than one item ("+left.size()+")");
if (!doNotEnforceAsSingletonRule && left.size() > 1) {
throw new PathEngineException("Attempt to use as on more than one item ("+left.size()+", '"+expr.toString()+"')");
}
for (Base nextLeft : left) {
if (tn.equals(nextLeft.fhirType())) {
if (compareTypeNames(tn, nextLeft.fhirType())) {
result.add(nextLeft);
}
}
@ -1801,9 +1827,19 @@ public class FHIRPathEngine {
return result;
}
private boolean compareTypeNames(String left, String right) {
if (doNotEnforceAsCaseSensitive) {
return left.equalsIgnoreCase(right);
} else {
return left.equals(right);
}
}
private boolean isKnownType(String tn) {
if (!tn.contains(".")) {
if (Utilities.existsInList(tn, "String", "Boolean", "Integer", "Decimal", "Quantity", "DateTime", "Time", "SimpleTypeInfo", "ClassInfo")) {
return true;
}
try {
return worker.fetchTypeDefinition(tn) != null;
} catch (Exception e) {
@ -4584,7 +4620,7 @@ public class FHIRPathEngine {
if (!isKnownType(tn)) {
throw new PathEngineException("The type "+tn+" is not valid");
}
if (focus.size() > 1) {
if (!doNotEnforceAsSingletonRule && focus.size() > 1) {
throw new PathEngineException("Attempt to use as() on more than one item ("+focus.size()+")");
}
@ -4603,7 +4639,7 @@ public class FHIRPathEngine {
} else {
StructureDefinition sd = worker.fetchTypeDefinition(b.fhirType());
while (sd != null) {
if (tnp.equals(sd.getType())) {
if (compareTypeNames(tnp, sd.getType())) {
result.add(b);
break;
}

3
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/FHIRPathTests.java
View File

@ -201,6 +201,9 @@ public class FHIRPathTests {
}
}
fp.setDoNotEnforceAsCaseSensitive(false);
fp.setDoNotEnforceAsSingletonRule(false);
if (node != null) {
try {
outcome = fp.evaluate(res, node);

46
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/FHIRPathEngine.java
View File

@ -62,6 +62,7 @@ import org.hl7.fhir.utilities.MergedList;
import org.hl7.fhir.utilities.MergedList.MergeNode;
import org.hl7.fhir.utilities.SourceLocation;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.xhtml.NodeType;
@ -257,6 +258,8 @@ public class FHIRPathEngine {
private boolean allowPolymorphicNames;
private boolean doImplicitStringConversion;
private boolean liquidMode; // in liquid mode, || terminates the expression and hands the parser back to the host
private boolean doNotEnforceAsSingletonRule;
private boolean doNotEnforceAsCaseSensitive;
// if the fhir path expressions are allowed to use constants beyond those defined in the specification
// the application can implement them by providing a constant resolver
@ -366,8 +369,15 @@ public class FHIRPathEngine {
primitiveTypes.add(sd.getName());
}
}
initFlags();
}
private void initFlags() {
if (!VersionUtilities.isR5VerOrLater(worker.getVersion())) {
doNotEnforceAsCaseSensitive = true;
doNotEnforceAsSingletonRule = true;
}
}
// --- 3 methods to override in children -------------------------------------------------------
// if you don't override, it falls through to the using the base reference implementation
@ -450,6 +460,22 @@ public class FHIRPathEngine {
this.doImplicitStringConversion = doImplicitStringConversion;
}
public boolean isDoNotEnforceAsSingletonRule() {
return doNotEnforceAsSingletonRule;
}
public void setDoNotEnforceAsSingletonRule(boolean doNotEnforceAsSingletonRule) {
this.doNotEnforceAsSingletonRule = doNotEnforceAsSingletonRule;
}
public boolean isDoNotEnforceAsCaseSensitive() {
return doNotEnforceAsCaseSensitive;
}
public void setDoNotEnforceAsCaseSensitive(boolean doNotEnforceAsCaseSensitive) {
this.doNotEnforceAsCaseSensitive = doNotEnforceAsCaseSensitive;
}
// --- public API -------------------------------------------------------
/**
* Parse a path for later use using execute
@ -1785,11 +1811,11 @@ public class FHIRPathEngine {
if (!isKnownType(tn)) {
throw new PathEngineException("The type "+tn+" is not valid");
}
if (left.size() > 1) {
throw new PathEngineException("Attempt to use as on more than one item ("+left.size()+")");
if (!doNotEnforceAsSingletonRule && left.size() > 1) {
throw new PathEngineException("Attempt to use as on more than one item ("+left.size()+", '"+expr.toString()+"')");
}
for (Base nextLeft : left) {
if (tn.equals(nextLeft.fhirType())) {
if (compareTypeNames(tn, nextLeft.fhirType())) {
result.add(nextLeft);
}
}
@ -1797,9 +1823,19 @@ public class FHIRPathEngine {
return result;
}
private boolean compareTypeNames(String left, String right) {
if (doNotEnforceAsCaseSensitive) {
return left.equalsIgnoreCase(right);
} else {
return left.equals(right);
}
}
private boolean isKnownType(String tn) {
if (!tn.contains(".")) {
if (Utilities.existsInList(tn, "String", "Boolean", "Integer", "Decimal", "Quantity", "DateTime", "Time", "SimpleTypeInfo", "ClassInfo")) {
return true;
}
try {
return worker.fetchTypeDefinition(tn) != null;
} catch (Exception e) {
@ -4580,7 +4616,7 @@ public class FHIRPathEngine {
if (!isKnownType(tn)) {
throw new PathEngineException("The type "+tn+" is not valid");
}
if (focus.size() > 1) {
if (!doNotEnforceAsSingletonRule && focus.size() > 1) {
throw new PathEngineException("Attempt to use as() on more than one item ("+focus.size()+")");
}
@ -4599,7 +4635,7 @@ public class FHIRPathEngine {
} else {
StructureDefinition sd = worker.fetchTypeDefinition(b.fhirType());
while (sd != null) {
if (tnp.equals(sd.getType())) {
if (compareTypeNames(tnp, sd.getType())) {
result.add(b);
break;
}

3
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/FHIRPathTests.java
View File

@ -201,6 +201,9 @@ public class FHIRPathTests {
}
}
fp.setDoNotEnforceAsCaseSensitive(false);
fp.setDoNotEnforceAsSingletonRule(false);
if (node != null) {
try {
outcome = fp.evaluate(res, node);

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java
View File

@ -3864,5 +3864,9 @@ public class ProfileUtilities extends TranslatingUtilities {
return null;
}
public static boolean isExtensionDefinition(StructureDefinition sd) {
return sd.getDerivation() == TypeDerivationRule.CONSTRAINT && sd.getType().equals("Extension");
}
}

16
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ContextUtilities.java
View File

@ -136,12 +136,24 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
* @return a list of the resource and type names defined for this version
*/
public List<String> getTypeNames() {
List<String> result = new ArrayList<String>();
Set<String> result = new HashSet<String>();
for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) {
if (sd.getKind() != StructureDefinitionKind.LOGICAL && sd.getDerivation() == TypeDerivationRule.SPECIALIZATION)
result.add(sd.getName());
}
return Utilities.sorted(result);
}
/**
* @return a set of the resource and type names defined for this version
*/
public Set<String> getTypeNameSet() {
Set<String> result = new HashSet<String>();
for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) {
if (sd.getKind() != StructureDefinitionKind.LOGICAL && sd.getDerivation() == TypeDerivationRule.SPECIALIZATION)
result.add(sd.getName());
}
Collections.sort(result);
return result;
}

28
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -64,6 +64,7 @@ import org.hl7.fhir.utilities.MergedList;
import org.hl7.fhir.utilities.MergedList.MergeNode;
import org.hl7.fhir.utilities.SourceLocation;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.xhtml.NodeType;
@ -264,6 +265,7 @@ public class FHIRPathEngine {
private boolean doImplicitStringConversion;
private boolean liquidMode; // in liquid mode, || terminates the expression and hands the parser back to the host
private boolean doNotEnforceAsSingletonRule;
private boolean doNotEnforceAsCaseSensitive;
// if the fhir path expressions are allowed to use constants beyond those defined in the specification
// the application can implement them by providing a constant resolver
@ -373,8 +375,15 @@ public class FHIRPathEngine {
primitiveTypes.add(sd.getName());
}
}
initFlags();
}
private void initFlags() {
if (!VersionUtilities.isR5VerOrLater(worker.getVersion())) {
doNotEnforceAsCaseSensitive = true;
doNotEnforceAsSingletonRule = true;
}
}
// --- 3 methods to override in children -------------------------------------------------------
// if you don't override, it falls through to the using the base reference implementation
@ -465,6 +474,14 @@ public class FHIRPathEngine {
this.doNotEnforceAsSingletonRule = doNotEnforceAsSingletonRule;
}
public boolean isDoNotEnforceAsCaseSensitive() {
return doNotEnforceAsCaseSensitive;
}
public void setDoNotEnforceAsCaseSensitive(boolean doNotEnforceAsCaseSensitive) {
this.doNotEnforceAsCaseSensitive = doNotEnforceAsCaseSensitive;
}
// --- public API -------------------------------------------------------
/**
* Parse a path for later use using execute
@ -1804,7 +1821,7 @@ public class FHIRPathEngine {
throw new PathEngineException("Attempt to use as on more than one item ("+left.size()+", '"+expr.toString()+"')");
}
for (Base nextLeft : left) {
if (tn.equals(nextLeft.fhirType())) {
if (compareTypeNames(tn, nextLeft.fhirType())) {
result.add(nextLeft);
}
}
@ -1812,6 +1829,13 @@ public class FHIRPathEngine {
return result;
}
private boolean compareTypeNames(String left, String right) {
if (doNotEnforceAsCaseSensitive) {
return left.equalsIgnoreCase(right);
} else {
return left.equals(right);
}
}
private boolean isKnownType(String tn) {
if (!tn.contains(".")) {
@ -4617,7 +4641,7 @@ public class FHIRPathEngine {
} else {
StructureDefinition sd = worker.fetchTypeDefinition(b.fhirType());
while (sd != null) {
if (tnp.equals(sd.getType())) {
if (compareTypeNames(tnp, sd.getType())) {
result.add(b);
break;
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ToolingExtensions.java
View File

@ -250,7 +250,7 @@ public class ToolingExtensions {
Extension ex = new Extension();
// todo: write this up and get it published with the pack (and handle the redirect?)
ex.setUrl(ToolingExtensions.EXT_ISSUE_SOURCE);
CodeType c = new CodeType();
StringType c = new StringType();
c.setValue(source.toString());
ex.setValue(c);
return ex;

2
pom.xml
View File

@ -19,7 +19,7 @@
<properties>
<hapi_fhir_version>6.2.1</hapi_fhir_version>
<validator_test_case_version>1.2.10</validator_test_case_version>
<validator_test_case_version>1.2.11-SNAPSHOT</validator_test_case_version>
<junit_jupiter_version>5.7.1</junit_jupiter_version>
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
<maven_surefire_version>3.0.0-M5</maven_surefire_version>