Skip to content

Commit

Permalink
Merge pull request #1866 from hapifhir/2024-12-gg-test-instance-gener…
Browse files Browse the repository at this point in the history 
…ation-2

2024 12 gg test instance generation 2
  • Loading branch information
@grahamegrieve
grahamegrieve authored Dec 24, 2024
2 parents e021fb3 + 7170545 commit 22eacf9
Show file tree
Hide file tree
Showing 54 changed files with 3,075 additions and 531 deletions.
18 changes: 9 additions & 9 deletions org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/analytics/PackageVisitor.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
import org.hl7.fhir.utilities.json.parser.JsonParser;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackagedResourceFile;
import org.hl7.fhir.utilities.npm.PackageClient;
import org.hl7.fhir.utilities.npm.PackageInfo;
import org.hl7.fhir.utilities.npm.PackageServer;
Expand Down Expand Up @@ -357,6 +358,7 @@ private void processPackage(String pid, String v, int i, int t) throws IOExcepti
npm = pcm.loadPackage(pid, v);
} catch (Throwable e) {
System.out.println("Unable to load package: "+pid+"#"+v+": "+e.getMessage());
return;
}

try {
Expand All @@ -378,15 +380,13 @@ private void processPackage(String pid, String v, int i, int t) throws IOExcepti
if (ok) {
int c = 0;
if (fv != null && (versions.isEmpty() || versions.contains(fv))) {
for (String type : resourceTypes) {
for (String s : npm.listResources(type)) {
c++;
try {
processor.processResource(ctxt, context, type, s, TextFile.streamToBytes(npm.load("package", s)));
} catch (Exception e) {
System.out.println("####### Error loading "+pid+"#"+v +"["+fv+"]/"+type+" ####### "+e.getMessage());
e.printStackTrace();
}
for (PackagedResourceFile p : npm.listAllResources(resourceTypes)) {
c++;
try {
processor.processResource(ctxt, context, p.getResourceType(), p.getFilename(), TextFile.streamToBytes(npm.load(p.getFolder(), p.getFilename())));
} catch (Exception e) {
System.out.println("####### Error loading "+pid+"#"+v +"["+fv+"]/"+p.getResourceType()+" ####### "+e.getMessage());
e.printStackTrace();
}
}
}
Expand Down
64 changes: 55 additions & 9 deletions ...nvertors/src/main/java/org/hl7/fhir/convertors/analytics/TestGenerationDataGenerator.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,17 @@

import org.hl7.fhir.convertors.analytics.PackageVisitor.IPackageVisitorProcessor;
import org.hl7.fhir.convertors.analytics.PackageVisitor.PackageContext;
import org.hl7.fhir.convertors.loaders.loaderR5.ILoaderKnowledgeProviderR5;
import org.hl7.fhir.convertors.loaders.loaderR5.NullLoaderKnowledgeProviderR5;
import org.hl7.fhir.convertors.loaders.loaderR5.R2016MayToR5Loader;
import org.hl7.fhir.convertors.loaders.loaderR5.R2ToR5Loader;
import org.hl7.fhir.convertors.loaders.loaderR5.R3ToR5Loader;
import org.hl7.fhir.convertors.loaders.loaderR5.R4BToR5Loader;
import org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader;
import org.hl7.fhir.convertors.loaders.loaderR5.R5ToR5Loader;
import org.hl7.fhir.convertors.loaders.loaderR5.R6ToR5Loader;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IContextResourceLoader;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext.SimpleWorkerContextBuilder;
Expand All @@ -37,6 +47,7 @@
import org.hl7.fhir.utilities.http.ManagedWebAccess.WebAccessPolicy;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackagedResourceFile;
import org.xml.sax.SAXException;

public class TestGenerationDataGenerator implements IPackageVisitorProcessor {
Expand Down Expand Up @@ -67,6 +78,7 @@ public void alreadyVisited(String pid) {

@Override
public Object startPackage(PackageContext ctxt) {
System.out.println("Process Package "+ctxt.getPid()+"#"+ctxt.getVersion()+" ("+ctxt.getNpm().fhirVersion()+")");
return null;
}

Expand All @@ -77,22 +89,45 @@ public void processResource(PackageContext ctxt, Object context, String type, St
if (worker == null) {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
NpmPackage npm = pcm.loadPackage(VersionUtilities.packageForVersion(version));
SimpleWorkerContext swc = new SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).fromPackage(npm);
IContextResourceLoader loader = makeLoader(ctxt.getNpm().fhirVersion(), new NullLoaderKnowledgeProviderR5());
SimpleWorkerContext swc = new SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).fromPackage(npm, loader, true);
contexts.put(version, swc);
worker = swc;
}
List<ValidatedFragment> res = Manager.parse(worker, new ByteArrayInputStream(content), FhirFormat.JSON);
if (res.size() > 0) {
try {
processElement(res.get(0).getElement());
processElement(res.get(0).getElement(), null);
} catch (SQLException e) {
throw new FHIRException(e);
}
}
}

private void processElement(Element element) throws SQLException {
String id = element.getProperty().getDefinition().getId();
private IContextResourceLoader makeLoader(String version, ILoaderKnowledgeProviderR5 loader) {
if (VersionUtilities.isR2Ver(version)) {
return new R2ToR5Loader(Utilities.strings("Conformance", "StructureDefinition", "ValueSet", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"), loader);
}
if (VersionUtilities.isR2BVer(version)) {
return new R2016MayToR5Loader(Utilities.strings("Conformance", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"), loader); // special case
}
if (VersionUtilities.isR3Ver(version)) {
return new R3ToR5Loader(Utilities.strings("CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"), loader);
}
if (VersionUtilities.isR4Ver(version)) {
return new R4ToR5Loader(Utilities.strings("CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"), loader, version);
}
if (VersionUtilities.isR4BVer(version)) {
return new R4BToR5Loader(Utilities.strings("CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"), loader, version);
}
if (VersionUtilities.isR6Ver(version)) {
return new R6ToR5Loader(Utilities.strings("CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"), loader);
}
return new R5ToR5Loader(Utilities.strings("CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"), loader);
}

private void processElement(Element element, String path) throws SQLException {
String id = path != null ? path : element.getProperty().getDefinition().getId();
switch (element.fhirType()) {
case "Address":
recordValue(id, "Address", getValues(element, "use", "type", "text", "line", "city", "district", "state", "postalCode", "country"));
Expand Down Expand Up @@ -161,12 +196,23 @@ private void processElement(Element element) throws SQLException {
break;
default:
if (element.isPrimitive()) {
recordValue(id, element.fhirType(), element.primitiveValue());
if (!element.getProperty().getDefinition().getId().equals("Extension.url")) {
recordValue(id, element.fhirType(), element.primitiveValue());
}
} else {
for (Element child : element.getChildren()) {
if (!child.fhirType().equals("Extension") && !child.getPath().endsWith(".id") && !child.getPath().endsWith(".linkId")) {
if (child.fhirType().equals("Extension")) {
String url = child.getChildValue("url");
String npath;
if (Utilities.isAbsoluteUrl(url) || path == null) {
npath = url;
} else {
npath = path+"."+url;
}
processElement(child, npath);
} else if (!child.getPath().endsWith(".id") && !child.getPath().endsWith(".linkId")) {
if (!child.isResource() || !Utilities.existsInList(child.fhirType(), "Bundle", "CapabilityStatement", "CodeSystem", "ConceptMap", "GraphDefinition", "ImplementationGuide", "MessageHeader", "NamingSystem", "OperationDefinition", "OperationOutcome", "Parameters", "SearchParameter", "StructureDefinition", "StructureMap", "TerminologyCapabilities", "ValueSet")) {
processElement(child);
processElement(child, path);
}
}
}
Expand Down Expand Up @@ -325,9 +371,9 @@ private void processPackage(NpmPackage npm) throws IOException, FHIRException, E
for (String type : resourceTypes) {
List<String> rt = new ArrayList<String>();
rt.add(type);
for (StringPair s : npm.listAllResources(rt)) {
for (PackagedResourceFile s : npm.listAllResources(rt)) {
c++;
processResource(ctxt, context, type, s.getName(), TextFile.streamToBytes(npm.load(s.getName(), s.getValue())));
processResource(ctxt, context, type, s.getFilename(), TextFile.streamToBytes(npm.load(s.getFolder(), s.getFilename())));
}
}
}
Expand Down
65 changes: 32 additions & 33 deletions org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/profilemodel/PEBuilder.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,7 @@ public PEDefinition buildPEDefinition(StructureDefinition profile) {
if (!profile.hasSnapshot()) {
throw new DefinitionException("Profile '"+profile.getVersionedUrl()+"' does not have a snapshot");
}
return new PEDefinitionResource(this, profile, profile.getName());
return new PEDefinitionResource(this, profile, null);
}

/**
Expand Down Expand Up @@ -342,6 +342,7 @@ private StructureDefinition getProfile(String url, String version) {

protected List<PEDefinition> listChildren(boolean allFixed, PEDefinition parent, StructureDefinition profileStructure, ElementDefinition definition, String url, String... omitList) {
StructureDefinition profile = profileStructure;
boolean inExtension = profile.getDerivation() == TypeDerivationRule.CONSTRAINT && "Extension".equals(profile.getType());
List<ElementDefinition> list = pu.getChildList(profile, definition);
if (definition.getType().size() == 1 || (!definition.getPath().contains(".")) || list.isEmpty()) {
assert url == null || checkType(definition, url);
Expand All @@ -359,43 +360,38 @@ protected List<PEDefinition> listChildren(boolean allFixed, PEDefinition parent,
while (i < list.size()) {
ElementDefinition defn = list.get(i);
if (!defn.getMax().equals("0") && (allFixed || include(defn))) {
if (passElementPropsCheck(defn) && !Utilities.existsInList(defn.getName(), omitList)) {
if (defn.getType().size() > 1) {
// Debug/Utilities.breakpoint();
i++;
} else {
String name = uniquefy(names, defn.getName());
PEDefinitionElement pe = new PEDefinitionElement(this, name, profile, defn, parent.path());
pe.setRecursing(definition == defn || (profile.getDerivation() == TypeDerivationRule.SPECIALIZATION && profile.getType().equals("Extension")));
if (context.isPrimitiveType(definition.getTypeFirstRep().getWorkingCode()) && "value".equals(pe.name())) {
pe.setMustHaveValue(definition.getMustHaveValue());
if (passElementPropsCheck(defn, inExtension) && !Utilities.existsInList(defn.getName(), omitList)) {
String name = uniquefy(names, defn.getName());
PEDefinitionElement pe = new PEDefinitionElement(this, name, profile, defn, parent.path());
pe.setRecursing(definition == defn || (profile.getDerivation() == TypeDerivationRule.SPECIALIZATION && profile.getType().equals("Extension")));
if (context.isPrimitiveType(definition.getTypeFirstRep().getWorkingCode()) && "value".equals(pe.name())) {
pe.setMustHaveValue(definition.getMustHaveValue());
}
pe.setInFixedValue(definition.hasFixed() || definition.hasPattern() || parent.isInFixedValue());
if (defn.hasSlicing()) {
if (defn.getSlicing().getRules() != SlicingRules.CLOSED) {
res.add(pe);
pe.setSlicer(true);
}
pe.setInFixedValue(definition.hasFixed() || definition.hasPattern() || parent.isInFixedValue());
if (defn.hasSlicing()) {
if (defn.getSlicing().getRules() != SlicingRules.CLOSED) {
res.add(pe);
pe.setSlicer(true);
}
i++;
while (i < list.size() && list.get(i).getPath().equals(defn.getPath())) {
StructureDefinition ext = getExtensionDefinition(list.get(i));
if (ext != null) {
res.add(new PEDefinitionExtension(this, uniquefy(names, list.get(i).getSliceName()), profile, list.get(i), defn, ext, parent.path()));
} else if (isTypeSlicing(defn)) {
res.add(new PEDefinitionTypeSlice(this, uniquefy(names, list.get(i).getSliceName()), profile, list.get(i), defn, parent.path()));
i++;
while (i < list.size() && list.get(i).getPath().equals(defn.getPath())) {
StructureDefinition ext = getExtensionDefinition(list.get(i));
if (ext != null) {
res.add(new PEDefinitionExtension(this, uniquefy(names, list.get(i).getSliceName()), profile, list.get(i), defn, ext, parent.path()));
} else if (isTypeSlicing(defn)) {
res.add(new PEDefinitionTypeSlice(this, uniquefy(names, list.get(i).getSliceName()), profile, list.get(i), defn, parent.path()));
} else {
if (ProfileUtilities.isComplexExtension(profile) && defn.getPath().endsWith(".extension")) {
res.add(new PEDefinitionSubExtension(this, profile, list.get(i), parent.path()));
} else {
if (ProfileUtilities.isComplexExtension(profile) && defn.getPath().endsWith(".extension")) {
res.add(new PEDefinitionSubExtension(this, profile, list.get(i), parent.path()));
} else {
res.add(new PEDefinitionSlice(this, uniquefy(names, list.get(i).getSliceName()), profile, list.get(i), defn, parent.path()));
}
res.add(new PEDefinitionSlice(this, uniquefy(names, list.get(i).getSliceName()), profile, list.get(i), defn, parent.path()));
}
i++;
}
} else {
res.add(pe);
i++;
}
} else {
res.add(pe);
i++;
}
} else {
i++;
Expand Down Expand Up @@ -434,7 +430,10 @@ protected PEDefinition makeChild(PEDefinition parent, StructureDefinition profil
return pe;
}

private boolean passElementPropsCheck(ElementDefinition bdefn) {
private boolean passElementPropsCheck(ElementDefinition bdefn, boolean inExtension) {
if (inExtension) {
return !Utilities.existsInList(bdefn.getBase().getPath(), "Element.id");
}
switch (elementProps) {
case EXTENSION:
return !Utilities.existsInList(bdefn.getBase().getPath(), "Element.id");
Expand Down
32 changes: 31 additions & 1 deletion org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/profilemodel/PEDefinition.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,9 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
import org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.Type;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.profilemodel.PEDefinition.PEDefinitionElementMode;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;

public abstract class PEDefinition {
Expand Down Expand Up @@ -84,7 +86,7 @@ protected PEDefinition(PEBuilder builder, String name, StructureDefinition profi
this.name = name;
this.profile = profile;
this.definition = definition;
this.path = path == null ? name : ppath+"."+name;
this.path = ppath == null ? name : ppath+"."+name;
}


Expand Down Expand Up @@ -392,6 +394,34 @@ public boolean isExtension() {
return false;
}

public String getExtensionUrl() {
return null;
}

public ValueSet valueSet() {
if (definition.getBinding().hasValueSet()) {
return builder.getContext().fetchResource(ValueSet.class, definition.getBinding().getValueSet());
}
return null;
}


public PEBuilder getBuilder() {
return builder;
}

public String typeSummary() {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (PEType t : types()) {
b.append(t.getName());
}
return b.toString();
}


public boolean isSlice() {
return definition.hasSliceName();
}
}


6 changes: 5 additions & 1 deletion org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/profilemodel/PEDefinitionExtension.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -114,5 +114,9 @@ public boolean isExtension() {
return true;
}



public String getExtensionUrl() {
return extension.getUrl();
}

}
3 changes: 3 additions & 0 deletions org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/profilemodel/PEDefinitionSubExtension.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -113,5 +113,8 @@ public boolean isExtension() {
return true;
}

public String getExtensionUrl() {
return ued.getFixed().primitiveValue();
}

}
16 changes: 9 additions & 7 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfilePathProcessor.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -652,13 +652,15 @@ private ElementDefinition processSimplePathWithOneMatchingElementInDifferential(
}
}
}
template = src.copy().setPath(currentBase.getPath());
template.setSliceName(null);
// temporary work around
if (!"Extension".equals(diffMatches.get(0).getType().get(0).getCode())) {
template.setMin(currentBase.getMin());
template.setMax(currentBase.getMax());
}
if (Utilities.existsInList(currentBase.typeSummary(), "Extension", "Resource")) {
template = src.copy().setPath(currentBase.getPath());
template.setSliceName(null);
// temporary work around
if (!"Extension".equals(diffMatches.get(0).getType().get(0).getCode())) {
template.setMin(currentBase.getMin());
template.setMax(currentBase.getMax());
}
}
}
}
if (template == null)
Expand Down
Loading

0 comments on commit 22eacf9

Please sign in to comment.