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org.hl7.fhir.core
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fix issues in testing

This commit is contained in:
Grahame Grieve 2020-07-21 06:16:45 +10:00
parent 27e8aa0bec
commit acbba54d25
4 changed files with 171 additions and 58 deletions
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100
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -78,6 +78,9 @@ import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.BasePackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.NpmPackage.PackageResourceInformation;
import org.hl7.fhir.utilities.i18n.I18nConstants;
@ -141,7 +144,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
private boolean ignoreProfileErrors;
private boolean progress;
private List<String> loadedPackages = new ArrayList<String>();
public SimpleWorkerContext() throws FileNotFoundException, IOException, FHIRException {
super();
}
@ -170,6 +173,11 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
validatorFactory = other.validatorFactory;
}
public List<String> getLoadedPackages() {
return loadedPackages;
}
// -- Initializations
/**
* Load the working context from the validation pack
@ -189,13 +197,9 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
}
public static SimpleWorkerContext fromPackage(NpmPackage pi, boolean allowDuplicates) throws FileNotFoundException, IOException, FHIRException {
return fromPackage(pi, allowDuplicates, null);
}
public static SimpleWorkerContext fromPackage(NpmPackage pi, boolean allowDuplicates, ILoadFilter filter) throws FileNotFoundException, IOException, FHIRException {
SimpleWorkerContext res = new SimpleWorkerContext();
res.setAllowLoadingDuplicates(allowDuplicates);
res.loadFromPackage(pi, null, filter);
res.loadFromPackage(pi, null);
return res;
}
@ -206,14 +210,10 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
}
public static SimpleWorkerContext fromPackage(NpmPackage pi, IContextResourceLoader loader) throws FileNotFoundException, IOException, FHIRException {
return fromPackage(pi, loader, null);
}
public static SimpleWorkerContext fromPackage(NpmPackage pi, IContextResourceLoader loader, ILoadFilter filter) throws FileNotFoundException, IOException, FHIRException {
SimpleWorkerContext res = new SimpleWorkerContext();
res.setAllowLoadingDuplicates(true);
res.version = pi.getNpm().get("version").getAsString();
res.loadFromPackage(pi, loader, filter);
res.loadFromPackage(pi, loader);
res.finishLoading();
return res;
}
@ -356,46 +356,62 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
loadFromStream(new CSFileInputStream(path), loader);
}
public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, ILoadFilter filter) throws IOException {
// public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, ILoadFilter filter) throws IOException {
// if (progress) {
// System.out.println("Load Package "+pi.name()+"#"+pi.version());
// }
// loadedPackages.add(pi.id()+"#"+pi.version());
// String [] types = loader != null ? loader.getTypes() : new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem" };
// for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
// try {
// registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version()));
// } catch (FHIRException e) {
// throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
// }
// }
// for (String s : pi.list("other")) {
// binaries.put(s, TextFile.streamToBytes(pi.load("other", s)));
// }
// if (version == null) {
// version = pi.version();
// }
// }
@Override
public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
if (progress) {
System.out.println("Load Package "+pi.name()+"#"+pi.version());
}
loadedPackages.add(pi.id()+"#"+pi.version());
String [] types = loader != null ? loader.getTypes() : new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem" };
for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
try {
registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version()));
} catch (FHIRException e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
}
}
for (String s : pi.list("other")) {
binaries.put(s, TextFile.streamToBytes(pi.load("other", s)));
}
if (version == null) {
version = pi.version();
}
}
@Override
public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
if (progress) {
System.out.println("Load Package "+pi.name()+"#"+pi.version());
}
loadedPackages.add(pi.id()+"#"+pi.version());
if (types.length == 0 && loader != null) {
types = loader.getTypes();
}
if (types.length == 0) {
types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem" };
}
for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
try {
registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version()));
} catch (FHIRException e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
if (VersionUtilities.isR2Ver(pi.fhirVersion())) {
// can't lazy load R2 because of valueset/codesystem implementation
if (types.length == 0) {
types = new String[] { "StructureDefinition", "ValueSet", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem" };
}
}
for (String s : pi.listResources(loader.getTypes())) {
try {
loadDefinitionItem(s, pi.load("package", s), loader, null, new PackageVersion(pi.id(), pi.version()));
} catch (FHIRException e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, s, pi.name(), pi.version(), e.getMessage()), e);
}
}
} else {
if (types.length == 0) {
types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem" };
}
for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
try {
registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version()));
} catch (FHIRException e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
}
}
}
for (String s : pi.list("other")) {
binaries.put(s, TextFile.streamToBytes(pi.load("other", s)));
}

115
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetExpanderSimple.java
View File

@ -83,6 +83,9 @@ import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionDesignationComponent;
import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent;
import org.hl7.fhir.r5.model.CodeSystem.PropertyComponent;
import org.hl7.fhir.r5.model.CodeSystem.PropertyType;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.Enumerations.FilterOperator;
@ -101,11 +104,75 @@ import org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpanderSimple.AllConceptsFilter;
import org.hl7.fhir.r5.terminologies.ValueSetExpanderSimple.IConceptFilter;
import org.hl7.fhir.r5.terminologies.ValueSetExpanderSimple.PropertyFilter;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
public class ValueSetExpanderSimple implements ValueSetExpander {
public class PropertyFilter implements IConceptFilter {
private ConceptSetFilterComponent filter;
private PropertyComponent property;
public PropertyFilter(ConceptSetFilterComponent fc, PropertyComponent propertyDefinition) {
this.filter = fc;
this.property = propertyDefinition;
}
@Override
public boolean includeConcept(CodeSystem cs, ConceptDefinitionComponent def) {
ConceptPropertyComponent pc = getPropertyForConcept(def);
if (pc != null) {
String v = pc.getValue().isPrimitive() ? pc.getValue().primitiveValue() : null;
switch (filter.getOp()) {
case DESCENDENTOF: throw new FHIRException("not supported yet");
case EQUAL: return filter.getValue().equals(v);
case EXISTS: throw new FHIRException("not supported yet");
case GENERALIZES: throw new FHIRException("not supported yet");
case IN: throw new FHIRException("not supported yet");
case ISA: throw new FHIRException("not supported yet");
case ISNOTA: throw new FHIRException("not supported yet");
case NOTIN: throw new FHIRException("not supported yet");
case NULL: throw new FHIRException("not supported yet");
case REGEX: throw new FHIRException("not supported yet");
default:
throw new FHIRException("Shouldn't get here");
}
} else if (property.getType() == PropertyType.BOOLEAN && filter.getOp() == FilterOperator.EQUAL) {
return "false".equals(filter.getValue());
} else {
return false;
}
}
private ConceptPropertyComponent getPropertyForConcept(ConceptDefinitionComponent def) {
for (ConceptPropertyComponent pc : def.getProperty()) {
if (pc.getCode().equals(property.getCode())) {
return pc;
}
}
return null;
}
}
public class AllConceptsFilter implements IConceptFilter {
@Override
public boolean includeConcept(CodeSystem cs, ConceptDefinitionComponent def) {
return true;
}
}
public interface IConceptFilter {
boolean includeConcept(CodeSystem cs, ConceptDefinitionComponent def);
}
private List<ValueSetExpansionContainsComponent> codes = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
private List<ValueSetExpansionContainsComponent> roots = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
private Map<String, ValueSetExpansionContainsComponent> map = new HashMap<String, ValueSet.ValueSetExpansionContainsComponent>();
@ -214,7 +281,7 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
return list;
}
private void addCodeAndDescendents(CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, ConceptDefinitionComponent exclusion) throws FHIRException {
private void addCodeAndDescendents(CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, ConceptDefinitionComponent exclusion, IConceptFilter filterFunc) throws FHIRException {
def.checkNoModifiers("Code in Code System", "expanding");
if (exclusion != null) {
if (exclusion.getCode().equals(def.getCode()))
@ -224,24 +291,25 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
ValueSetExpansionContainsComponent np = null;
boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
boolean inc = CodeSystemUtilities.isInactive(cs, def);
if (includeAbstract || !abs)
if ((includeAbstract || !abs) && filterFunc.includeConcept(cs, def)) {
np = addCode(system, def.getCode(), def.getDisplay(), parent, def.getDesignation(), expParams, abs, inc, filters);
}
for (ConceptDefinitionComponent c : def.getConcept()) {
addCodeAndDescendents(cs, system, c, np, expParams, filters, exclusion);
addCodeAndDescendents(cs, system, c, np, expParams, filters, exclusion, filterFunc);
}
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children)
addCodeAndDescendents(cs, system, c, np, expParams, filters, exclusion);
addCodeAndDescendents(cs, system, c, np, expParams, filters, exclusion, filterFunc);
}
} else {
for (ConceptDefinitionComponent c : def.getConcept()) {
addCodeAndDescendents(cs, system, c, null, expParams, filters, exclusion);
addCodeAndDescendents(cs, system, c, null, expParams, filters, exclusion, filterFunc);
}
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children)
addCodeAndDescendents(cs, system, c, null, expParams, filters, exclusion);
addCodeAndDescendents(cs, system, c, null, expParams, filters, exclusion, filterFunc);
}
}
@ -517,7 +585,7 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null);
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter());
}
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
@ -556,14 +624,14 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null);
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter());
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISNOTA) {
// special: all codes in the target code system that are not under the value
ConceptDefinitionComponent defEx = getConceptForCode(cs.getConcept(), fc.getValue());
if (defEx == null)
throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, defEx);
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter());
}
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
// special: all codes in the target code system under the value
@ -571,11 +639,11 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
if (def == null)
throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent c : def.getConcept())
addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null);
addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter());
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children)
addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null);
addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter());
}
} else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
@ -590,11 +658,34 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
}
}
}
} else
} else if (isDefinedProperty(cs, fc.getProperty())) {
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(fc, getPropertyDefinition(cs, fc.getProperty())));
}
} else {
throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
}
}
}
private PropertyComponent getPropertyDefinition(CodeSystem cs, String property) {
for (PropertyComponent cp : cs.getProperty()) {
if (cp.getCode().equals(property)) {
return cp;
}
}
return null;
}
private boolean isDefinedProperty(CodeSystem cs, String property) {
for (PropertyComponent cp : cs.getProperty()) {
if (cp.getCode().equals(property)) {
return true;
}
}
return false;
}
private void addFragmentWarning(ValueSetExpansionComponent exp, CodeSystem cs) {
for (Extension ex : cs.getExtensionsByUrl(ToolingExtensions.EXT_EXP_FRAGMENT)) {
if (ex.getValue().primitiveValue().equals(cs.getUrl())) {

12
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -261,7 +261,6 @@ public class ValidationEngine implements IValidatorResourceFetcher {
private FilesystemPackageCacheManager pcm;
private PrintWriter mapLog;
private boolean debug;
private Set<String> loadedIgs = new HashSet<>();
private IValidatorResourceFetcher fetcher;
private boolean assumeValidRestReferences;
private boolean noExtensibleBindingMessages;
@ -608,10 +607,10 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
public Map<String, byte[]> loadPackage(NpmPackage pi) throws Exception {
loadedIgs.add(pi.name()+"#"+pi.version());
context.getLoadedPackages().add(pi.name()+"#"+pi.version());
Map<String, byte[]> res = new HashMap<String, byte[]>();
for (String s : pi.dependencies()) {
if (!loadedIgs.contains(s)) {
if (! context.getLoadedPackages().contains(s)) {
if (!VersionUtilities.isCorePackage(s)) {
System.out.println("+ .. load IG from "+s);
res.putAll(fetchByPackage(s));
@ -772,6 +771,13 @@ public class ValidationEngine implements IValidatorResourceFetcher {
public void loadIg(String src, boolean recursive) throws IOException, FHIRException, Exception {
NpmPackage npm = pcm.loadPackage(src, null);
if (npm != null) {
for (String s : npm.dependencies()) {
if (!context.getLoadedPackages().contains(s)) {
if (!VersionUtilities.isCorePackage(s)) {
loadIg(s, false);
}
}
}
context.loadFromPackage(npm, loaderForVersion(npm.fhirVersion()));
} else {
String canonical = null;

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/R3R4ConversionTests.java
View File

@ -287,7 +287,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
return;
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
R3ToR4Loader ldr = new R3ToR4Loader().setPatchUrls(true).setKillPrimitives(true);
R3ToR4Loader ldr = (R3ToR4Loader) new R3ToR4Loader().setPatchUrls(true).setKillPrimitives(true);
System.out.println("loading R3");
contextR3 = new SimpleWorkerContext();