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Merge pull request #480 from hapifhir/gg-202104-bugfixes 

Gg 202104 bugfixes
This commit is contained in:
Grahame Grieve 2021-04-21 21:41:04 +10:00 committed by GitHub
parent ba18e1c11a 6af6219dcc
commit ab9698d5bc
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GPG Key ID: 4AEE18F83AFDEB23
17 changed files with 84 additions and 20 deletions
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5
RELEASE_NOTES.md
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@ -0,0 +1,5 @@
* Breaking Change: Fix issue where primitive elements with required bindings must have a value, but this wasn't be checked
* Fix bug with value set imports not working
* Fix bug with base definitions not working properly for logical models
* Better memory tracking for validator
* Get code generator compiling

0
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/tests/RoundTripTests.java → org.hl7.fhir.core.generator/configuration/tests/RoundTripTests.java
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2
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/JavaResourceGenerator.java
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@ -996,7 +996,7 @@ private void generatePropertyMaker(Analysis analysis, TypeInfo ti, String indent
private List<TypeRefComponent> getTypes(List<TypeRefComponent> types) {
if (types.size() == 1 && types.get(0).getName().equals("*")) {
List<TypeRefComponent> t = new ArrayList<TypeRefComponent>();
for (String s : TypesUtilities.wildcardTypes()) {
for (String s : TypesUtilities.wildcardTypes("5.0")) {
t.add(new TypeRefComponent(s));
}
return t;

4
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/engine/DefinitionsLoader.java
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@ -13,8 +13,8 @@ import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
public class DefinitionsLoader {

6
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/engine/JavaCoreGenerator.java
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@ -30,9 +30,9 @@ import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
public class JavaCoreGenerator {

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
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@ -2989,7 +2989,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (!ok) {
StructureDefinition sdt = context.fetchTypeDefinition(tt);
if (sdt != null && sdt.getAbstract()) {
if (sdt != null && (sdt.getAbstract() || sdt.getKind() == StructureDefinitionKind.LOGICAL)) {
StructureDefinition sdb = context.fetchTypeDefinition(t);
while (sdb != null && !ok) {
ok = sdb.getType().equals(sdt.getType());

22
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
View File

@ -923,13 +923,21 @@ public class ValueSetRenderer extends TerminologyRenderer {
}
} else {
li.tx("Import all the codes that are contained in ");
boolean first = true;
for (UriType vs : inc.getValueSet()) {
if (first)
first = false;
else
li.tx(", ");
AddVsRef(vs.asStringValue(), li);
if (inc.getValueSet().size() < 4) {
boolean first = true;
for (UriType vs : inc.getValueSet()) {
if (first)
first = false;
else
li.tx(", ");
AddVsRef(vs.asStringValue(), li);
}
} else {
XhtmlNode xul = li.ul();
for (UriType vs : inc.getValueSet()) {
AddVsRef(vs.asStringValue(), xul.li());
}
}
}
return hasExtensions;

21
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetExpanderSimple.java
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@ -510,10 +510,31 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
if (!existsInParams(exp.getParameter(), p.getName(), p.getValue()))
exp.getParameter().add(p);
}
copyExpansion(vso.getValueset().getExpansion().getContains());
canBeHeirarchy = false; // if we're importing a value set, we have to be combining, so we won't try for a heirarchy
return vso.getValueset();
}
public void copyExpansion(List<ValueSetExpansionContainsComponent> list) {
for (ValueSetExpansionContainsComponent cc : list) {
ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
n.setSystem(cc.getSystem());
n.setCode(cc.getCode());
n.setAbstract(cc.getAbstract());
n.setInactive(cc.getInactive());
n.setDisplay(cc.getDisplay());
n.getDesignation().addAll(cc.getDesignation());
String s = key(n);
if (!map.containsKey(s) && !excludeKeys.contains(s)) {
codes.add(n);
map.put(s, n);
total++;
}
copyExpansion(cc.getContains());
}
}
private void addErrors(List<String> errs) {
for (String s : errs) {
if (!allErrors.contains(s)) {

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/OperationOutcomeUtilities.java
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@ -54,9 +54,9 @@ public class OperationOutcomeUtilities {
issue.addExpression(message.getLocation());
}
// pass through line/col if they're present
if (message.getLine() != 0)
if (message.getLine() >= 0)
issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_LINE).setValue(new IntegerType(message.getLine()));
if (message.getCol() != 0)
if (message.getCol() >= 0)
issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_COL).setValue(new IntegerType(message.getCol()));
issue.setSeverity(convert(message.getLevel()));
CodeableConcept c = new CodeableConcept();

15
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
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@ -1346,6 +1346,21 @@ public class Utilities {
return length + BT;
}
public static String describeSize(long length) {
if (length < 0) throw new IllegalArgumentException("File length of < 0 passed in...");
if (length > Math.pow(ONE_MB, 3)) {
return length / ((long) Math.pow(ONE_MB, 3)) + GB;
}
if (length > Math.pow(ONE_MB, 2)) {
return length / ((long) Math.pow(ONE_MB, 2)) + MB;
}
if (length > ONE_MB) {
return length / (ONE_MB) + KB;
}
return length + BT;
}
public static List<byte[]> splitBytes(byte[] array, byte[] delimiter) {
List<byte[]> byteArrays = new LinkedList<byte[]>();
if (delimiter.length == 0)

1
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
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@ -386,6 +386,7 @@ public class I18nConstants {
public static final String TERMINOLOGY_TX_CODE_NOTVALID = "Terminology_TX_Code_NotValid";
public static final String TERMINOLOGY_TX_CODE_UNKNOWN = "Terminology_TX_Code_Unknown";
public static final String TERMINOLOGY_TX_CODE_VALUESET = "Terminology_TX_Code_ValueSet";
public static final String Terminology_TX_Code_ValueSet_MISSING = "Terminology_TX_Code_ValueSet_MISSING";
public static final String TERMINOLOGY_TX_CODE_VALUESETMAX = "Terminology_TX_Code_ValueSetMax";
public static final String TERMINOLOGY_TX_CODE_VALUESET_EXT = "Terminology_TX_Code_ValueSet_Ext";
public static final String TERMINOLOGY_TX_CODING_COUNT = "Terminology_TX_Coding_Count";

3
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/validation/ValidationMessage.java
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@ -164,6 +164,9 @@ public class ValidationMessage implements Comparator<ValidationMessage>, Compara
public boolean isError() {
return this == FATAL || this == ERROR;
}
public boolean isHint() {
return this == INFORMATION;
}
}
public enum IssueType {

1
org.hl7.fhir.utilities/src/main/resources/Messages.properties
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@ -130,6 +130,7 @@ Terminology_TX_Binding_NoSource2 = Binding has no source, so can''t be checked
Terminology_TX_Code_NotValid = Code {0} is not a valid code in code system {1}
Terminology_TX_Code_Unknown = Unknown Code ({0}#{1})
Terminology_TX_Code_ValueSet = No code provided, and a code is required from the value set {0} ({1})
Terminology_TX_Code_ValueSet_MISSING = No code provided, and a code is required from the value set
Terminology_TX_Code_ValueSetMax = No code provided, and a code must be provided from the value set {0} (max value set {1})
Terminology_TX_Code_ValueSet_Ext = No code provided, and a code should be provided from the value set {0} ({1})
Terminology_TX_Coding_Count = Expected {0} but found {1} coding elements

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidatorCli.java
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@ -61,6 +61,7 @@ POSSIBILITY OF SUCH DAMAGE.
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.services.ComparisonService;
@ -238,6 +239,6 @@ public class ValidatorCli {
}
break;
}
System.out.println("Done. " + tt.report());
System.out.println("Done. " + tt.report()+". Max Memory = "+Utilities.describeSize(Runtime.getRuntime().maxMemory()));
}
}

10
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
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@ -24,6 +24,8 @@ import org.hl7.fhir.validation.cli.utils.EngineMode;
import org.hl7.fhir.validation.cli.utils.VersionSourceInformation;
import java.io.FileOutputStream;
import java.lang.management.ManagementFactory;
import java.lang.management.MemoryMXBean;
import java.util.ArrayList;
import java.util.List;
@ -66,6 +68,7 @@ public class ValidationService {
messages.forEach(outcome::addMessage);
response.addOutcome(outcome);
}
System.out.println(" Max Memory: "+Runtime.getRuntime().maxMemory());
return response;
}
@ -87,7 +90,8 @@ public class ValidationService {
List<ValidationRecord> records = new ArrayList<>();
Resource r = validator.validate(cliContext.getSources(), cliContext.getProfiles(), records);
int ec = 0;
System.out.println("Done. " + validator.getContext().clock().report());
MemoryMXBean mbean = ManagementFactory.getMemoryMXBean();
System.out.println("Done. " + validator.getContext().clock().report()+". Memory = "+Utilities.describeSize(mbean.getHeapMemoryUsage().getUsed()+mbean.getNonHeapMemoryUsage().getUsed()));
System.out.println();
if (cliContext.getOutput() == null) {
@ -211,7 +215,9 @@ public class ValidationService {
public String initializeValidator(CliContext cliContext, String definitions, TimeTracker tt, String sessionId) throws Exception {
tt.milestone();
if (!sessionCache.sessionExists(sessionId)) {
System.out.println("No such cached session exists for session id " + sessionId + ", re-instantiating validator.");
if (sessionId != null) {
System.out.println("No such cached session exists for session id " + sessionId + ", re-instantiating validator.");
}
System.out.print(" Load FHIR v" + cliContext.getSv() + " from " + definitions);
ValidationEngine validator = new ValidationEngine(definitions, cliContext.getSv(), tt);
sessionId = sessionCache.cacheSession(validator);

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -1907,6 +1907,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_NOTEMPTY);
else if (StringUtils.isWhitespace(e.primitiveValue()))
warning(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_WS);
if (context.hasBinding()) {
rule(errors, IssueType.CODEINVALID, e.line(), e.col(), path, context.getBinding().getStrength() != BindingStrength.REQUIRED, I18nConstants.Terminology_TX_Code_ValueSet_MISSING);
}
return;
}
String regex = context.getExtensionString(ToolingExtensions.EXT_REGEX);

2
pom.xml
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@ -19,7 +19,7 @@
<properties>
<hapi_fhir_version>5.1.0</hapi_fhir_version>
<validator_test_case_version>1.1.59</validator_test_case_version>
<validator_test_case_version>1.1.60-SNAPSHOT</validator_test_case_version>
<junit_jupiter_version>5.7.1</junit_jupiter_version>
<junit_platform_launcher_version>1.7.1</junit_platform_launcher_version>
<maven_surefire_version>3.0.0-M4</maven_surefire_version>