myPeriodIndexEndOfTime;
private NormalizedQuantitySearchLevel myNormalizedQuantitySearchLevel;
-
+
/**
* Constructor
*/
@@ -576,6 +576,47 @@ public class ModelConfig {
myPeriodIndexEndOfTime = thePeriodIndexEndOfTime;
}
+ /**
+ * Toggles whether Quantity searches support value normalization when using valid UCUM coded values.
+ *
+ *
+ * The default value is {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED} which is current behavior.
+ *
+ *
+ * Here is the UCUM service support level
+ *
+ * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED}, default, Quantity is stored in {@link ResourceIndexedSearchParamQuantity} only and it is used by searching.
+ * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_STORAGE_SUPPORTED}, Quantity is stored in both {@link ResourceIndexedSearchParamQuantity} and {@link ResourceIndexedSearchParamQuantityNormalized}, but {@link ResourceIndexedSearchParamQuantity} is used by searching.
+ * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_SUPPORTED}, Quantity is stored in both {@link ResourceIndexedSearchParamQuantity} and {@link ResourceIndexedSearchParamQuantityNormalized}, {@link ResourceIndexedSearchParamQuantityNormalized} is used by searching.
+ *
+ *
+ *
+ * @since 5.3.0
+ */
+ public NormalizedQuantitySearchLevel getNormalizedQuantitySearchLevel() {
+ return myNormalizedQuantitySearchLevel;
+ }
+
+ /**
+ * Toggles whether Quantity searches support value normalization when using valid UCUM coded values.
+ *
+ *
+ * The default value is {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED} which is current behavior.
+ *
+ *
+ * Here is the UCUM service support level
+ *
+ * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED}, default, Quantity is stored in {@link ResourceIndexedSearchParamQuantity} only and it is used by searching.
+ * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_STORAGE_SUPPORTED}, Quantity is stored in both {@link ResourceIndexedSearchParamQuantity} and {@link ResourceIndexedSearchParamQuantityNormalized}, but {@link ResourceIndexedSearchParamQuantity} is used by searching.
+ * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_SUPPORTED}, Quantity is stored in both {@link ResourceIndexedSearchParamQuantity} and {@link ResourceIndexedSearchParamQuantityNormalized}, {@link ResourceIndexedSearchParamQuantityNormalized} is used by searching.
+ *
+ *
+ *
+ * @since 5.3.0
+ */
+ public void setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel theNormalizedQuantitySearchLevel) {
+ myNormalizedQuantitySearchLevel = theNormalizedQuantitySearchLevel;
+ }
private static void validateTreatBaseUrlsAsLocal(String theUrl) {
Validate.notBlank(theUrl, "Base URL must not be null or empty");
@@ -589,43 +630,4 @@ public class ModelConfig {
}
- /**
- * Set the UCUM service support level
- *
- *
- * The default value is {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED} which is current behavior.
- *
- *
- * Here is the UCUM service support level
- *
- * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED}, default, Quantity is stored in {@link ResourceIndexedSearchParamQuantity} only and it is used by searching.
- * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_STORAGE_SUPPORTED}, Quantity is stored in both {@link ResourceIndexedSearchParamQuantity} and {@link ResourceIndexedSearchParamQuantityNormalized}, but {@link ResourceIndexedSearchParamQuantity} is used by searching.
- * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_SUPPORTED}, Quantity is stored in both {@link ResourceIndexedSearchParamQuantity} and {@link ResourceIndexedSearchParamQuantityNormalized}, {@link ResourceIndexedSearchParamQuantityNormalized} is used by searching.
- * - {@link NormalizedQuantitySearchLevel#NORMALIZED_QUANTITY_SEARCH_FULL_SUPPORTED}, Quantity is stored in only in {@link ResourceIndexedSearchParamQuantityNormalized}, {@link ResourceIndexedSearchParamQuantityNormalized} is used by searching. NOTE： this option is not supported yet.
- *
- *
- *
- * @since 5.3.0
- */
- public NormalizedQuantitySearchLevel getNormalizedQuantitySearchLevel() {
- return myNormalizedQuantitySearchLevel;
- }
- public void setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel theNormalizedQuantitySearchLevel) {
- myNormalizedQuantitySearchLevel = theNormalizedQuantitySearchLevel;
- }
- public boolean isNormalizedQuantitySearchSupported() {
- return myNormalizedQuantitySearchLevel.equals(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_SUPPORTED);
- }
- public boolean isNormalizedQuantityStorageSupported() {
- return myNormalizedQuantitySearchLevel.equals(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_STORAGE_SUPPORTED);
- }
- public void setNormalizedQuantitySearchNotSupported() {
- myNormalizedQuantitySearchLevel = NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED;
- }
- public void setNormalizedQuantityStorageSupported() {
- myNormalizedQuantitySearchLevel = NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_STORAGE_SUPPORTED;
- }
- public void setNormalizedQuantitySearchSupported() {
- myNormalizedQuantitySearchLevel = NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_SUPPORTED;
- }
}
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/NormalizedQuantitySearchLevel.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/NormalizedQuantitySearchLevel.java
index f7c819b5a92..56b9dee8b31 100644
--- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/NormalizedQuantitySearchLevel.java
+++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/NormalizedQuantitySearchLevel.java
@@ -53,5 +53,6 @@ public enum NormalizedQuantitySearchLevel {
* The existing non normalized quantity will be not supported
* NOTE： this option is not supported in this release
*/
+ // When this is enabled, we can enable testSortByQuantityWithNormalizedQuantitySearchFullSupported()
//NORMALIZED_QUANTITY_SEARCH_FULL_SUPPORTED,
}
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java
index 75e99a94150..51e587fa29d 100644
--- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java
+++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java
@@ -69,7 +69,7 @@ public class ResourceIndexedSearchParamQuantity extends ResourceIndexedSearchPar
@Column(name = "SP_VALUE", nullable = true)
@ScaledNumberField
- public BigDecimal myValue;
+ public Double myValue;
public ResourceIndexedSearchParamQuantity() {
super();
@@ -99,11 +99,11 @@ public class ResourceIndexedSearchParamQuantity extends ResourceIndexedSearchPar
}
public BigDecimal getValue() {
- return myValue;
+ return myValue != null ? new BigDecimal(myValue) : null;
}
public ResourceIndexedSearchParamQuantity setValue(BigDecimal theValue) {
- myValue = theValue;
+ myValue = theValue != null ? theValue.doubleValue() : null;
return this;
}
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java
index 0234d0fa4a2..03a89138db1 100644
--- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java
+++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java
@@ -40,7 +40,6 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.fhir.ucum.Pair;
-import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.ScaledNumberField;
@@ -84,23 +83,14 @@ public class ResourceIndexedSearchParamQuantityNormalized extends ResourceIndexe
super();
}
- public ResourceIndexedSearchParamQuantityNormalized(PartitionSettings thePartitionSettings, String theResourceType, String theParamName, BigDecimal theValue, String theSystem, String theUnits) {
+ public ResourceIndexedSearchParamQuantityNormalized(PartitionSettings thePartitionSettings, String theResourceType, String theParamName, double theValue, String theSystem, String theUnits) {
this();
setPartitionSettings(thePartitionSettings);
setResourceType(theResourceType);
setParamName(theParamName);
setSystem(theSystem);
-
- //-- convert the value/unit to the canonical form if any, otherwise store the original value/units pair
- Pair canonicalForm = UcumServiceUtil.getCanonicalForm(theSystem, theValue, theUnits);
- if (canonicalForm != null) {
- setValue(Double.parseDouble(canonicalForm.getValue().asDecimal()));
- setUnits(canonicalForm.getCode());
- } else {
- setValue(theValue);
- setUnits(theUnits);
- }
-
+ setValue(theValue);
+ setUnits(theUnits);
calculateHashes();
}
@@ -123,17 +113,13 @@ public class ResourceIndexedSearchParamQuantityNormalized extends ResourceIndexe
public ResourceIndexedSearchParamQuantityNormalized setValue(Double theValue) {
myValue = theValue;
return this;
- }
- public void setValue(BigDecimal theValue) {
- if (theValue != null)
- myValue = theValue.doubleValue();
}
- public BigDecimal getValueBigDecimal() {
- if (myValue == null)
- return null;
- return new BigDecimal(myValue);
+
+ public ResourceIndexedSearchParamQuantityNormalized setValue(double theValue) {
+ myValue = theValue;
+ return this;
}
-
+
//-- myId
@Override
public Long getId() {
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/UcumServiceUtil.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/UcumServiceUtil.java
index 3224067fbc0..d718eaaedb6 100644
--- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/UcumServiceUtil.java
+++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/UcumServiceUtil.java
@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.model.util;
import java.io.InputStream;
import java.math.BigDecimal;
+import ca.uhn.fhir.rest.param.QuantityParam;
import org.fhir.ucum.Decimal;
import org.fhir.ucum.Pair;
import org.fhir.ucum.UcumEssenceService;
@@ -32,6 +33,8 @@ import org.slf4j.LoggerFactory;
import ca.uhn.fhir.util.ClasspathUtil;
+import javax.annotation.Nullable;
+
/**
* It's a wrapper of UcumEssenceService
*
@@ -85,7 +88,7 @@ public class UcumServiceUtil {
return null;
init();
- Pair theCanonicalPair = null;
+ Pair theCanonicalPair;
try {
Decimal theDecimal = new Decimal(theValue.toPlainString(), theValue.precision());
@@ -97,4 +100,19 @@ public class UcumServiceUtil {
return theCanonicalPair;
}
+ @Nullable
+ public static QuantityParam toCanonicalQuantityOrNull(QuantityParam theQuantityParam) {
+ Pair canonicalForm = getCanonicalForm(theQuantityParam.getSystem(), theQuantityParam.getValue(), theQuantityParam.getUnits());
+ if (canonicalForm != null) {
+ BigDecimal valueValue = new BigDecimal(canonicalForm.getValue().asDecimal());
+ String unitsValue = canonicalForm.getCode();
+ return new QuantityParam()
+ .setSystem(theQuantityParam.getSystem())
+ .setValue(valueValue)
+ .setUnits(unitsValue)
+ .setPrefix(theQuantityParam.getPrefix());
+ } else {
+ return null;
+ }
+ }
}
diff --git a/hapi-fhir-jpaserver-model/src/test/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalizedTest.java b/hapi-fhir-jpaserver-model/src/test/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalizedTest.java
index 4affba1865c..1e3b5d94727 100644
--- a/hapi-fhir-jpaserver-model/src/test/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalizedTest.java
+++ b/hapi-fhir-jpaserver-model/src/test/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalizedTest.java
@@ -1,34 +1,13 @@
package ca.uhn.fhir.jpa.model.entity;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
-import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
-
import org.junit.jupiter.api.Test;
-import java.math.BigDecimal;
-
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
public class ResourceIndexedSearchParamQuantityNormalizedTest {
- private ResourceIndexedSearchParamQuantityNormalized createParam(String theParamName, String theValue, String theSystem, String theUnits) {
- ResourceIndexedSearchParamQuantityNormalized token = new ResourceIndexedSearchParamQuantityNormalized(new PartitionSettings(), "Observation", theParamName, new BigDecimal(theValue), theSystem, theUnits);
- token.setResource(new ResourceTable().setResourceType("Patient"));
- return token;
- }
-
- @Test
- public void testHashFunctions() {
- ResourceIndexedSearchParamQuantityNormalized token = createParam("Quanity", "123.001", UcumServiceUtil.UCUM_CODESYSTEM_URL, "cm");
- token.calculateHashes();
-
- // Make sure our hashing function gives consistent results
- assertEquals(5219730978980909111L, token.getHashIdentity().longValue());
- assertEquals(-2454931617586657338L, token.getHashIdentityAndUnits().longValue());
- assertEquals(878263047209296227L, token.getHashIdentitySystemAndUnits().longValue());
- }
-
@Test
public void testEquals() {
@@ -46,37 +25,5 @@ public class ResourceIndexedSearchParamQuantityNormalizedTest {
assertNotEquals(val1, "");
}
- @Test
- public void testUcum() {
-
- //-- system is ucum
- ResourceIndexedSearchParamQuantityNormalized token1 = createParam("Quanity", "123.001", UcumServiceUtil.UCUM_CODESYSTEM_URL, "cm");
- token1.calculateHashes();
-
- assertEquals("m", token1.getUnits());
- assertEquals(Double.parseDouble("1.23001"), token1.getValue());
-
- //-- small number
- token1 = createParam("Quanity", "0.000001", UcumServiceUtil.UCUM_CODESYSTEM_URL, "mm");
- token1.calculateHashes();
-
- assertEquals("m", token1.getUnits());
- assertEquals(Double.parseDouble("0.000000001"), token1.getValue());
-
-
- // -- non ucum system
- ResourceIndexedSearchParamQuantityNormalized token2 = createParam("Quanity", "123.001", "http://abc.org", "cm");
- token2.calculateHashes();
-
- assertEquals("cm", token2.getUnits());
- assertEquals(Double.parseDouble("123.001"), token2.getValue());
-
- // -- unsupported ucum code
- ResourceIndexedSearchParamQuantityNormalized token3 = createParam("Quanity", "123.001", UcumServiceUtil.UCUM_CODESYSTEM_URL, "unknown");
- token3.calculateHashes();
-
- assertEquals("unknown", token3.getUnits());
- assertEquals(Double.parseDouble("123.001"), token3.getValue());
- }
}
diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
index 25af4ddb6c4..d2324ef102f 100644
--- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
+++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
@@ -30,6 +30,7 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamCoords;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
@@ -38,6 +39,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantityNormalized
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
+import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.model.primitive.BoundCodeDt;
@@ -49,7 +51,7 @@ import com.google.common.collect.Sets;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
-import org.hibernate.search.engine.spatial.GeoPoint;
+import org.fhir.ucum.Pair;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseEnumeration;
@@ -78,7 +80,6 @@ import java.util.TreeSet;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
-import static ca.uhn.fhir.jpa.searchparam.extractor.GeopointNormalizer.normalizeLongitude;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
@@ -201,10 +202,14 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
extractor = createReferenceExtractor();
return extractReferenceParamsAsQueryTokens(theSearchParam, theResource, extractor);
case QUANTITY:
- if (myModelConfig.isNormalizedQuantitySearchSupported())
- extractor = createQuantityNormalizedExtractor(theResource);
- else
+ if (myModelConfig.getNormalizedQuantitySearchLevel().equals(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_SUPPORTED)) {
+ extractor = new CompositeExtractor(
+ createQuantityExtractor(theResource),
+ createQuantityNormalizedExtractor(theResource)
+ );
+ } else {
extractor = createQuantityExtractor(theResource);
+ }
break;
case URI:
extractor = createUriExtractor(theResource);
@@ -216,6 +221,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
default:
throw new UnsupportedOperationException("Type " + theSearchParam.getParamType() + " not supported for extraction");
}
+
return extractParamsAsQueryTokens(theSearchParam, theResource, extractor);
}
@@ -377,14 +383,14 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.QUANTITY);
}
-
+
@Override
public SearchParamSet extractSearchParamQuantityNormalized(IBaseResource theResource) {
IExtractor extractor = createQuantityNormalizedExtractor(theResource);
return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.QUANTITY);
}
-
- private IExtractor createQuantityExtractor(IBaseResource theResource) {
+
+ private IExtractor createQuantityExtractor(IBaseResource theResource) {
return (params, searchParam, value, path) -> {
if (value.getClass().equals(myLocationPositionDefinition.getImplementingClass())) {
return;
@@ -394,7 +400,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
String resourceType = toRootTypeName(theResource);
switch (nextType) {
case "Quantity":
- addQuantity_Quantity(resourceType, params, searchParam, value);
+ addQuantity_Quantity(resourceType, params, searchParam, value);
break;
case "Money":
addQuantity_Money(resourceType, params, searchParam, value);
@@ -406,11 +412,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
addUnexpectedDatatypeWarning(params, searchParam, value);
break;
}
- };
+ };
}
-
+
private IExtractor createQuantityNormalizedExtractor(IBaseResource theResource) {
-
+
return (params, searchParam, value, path) -> {
if (value.getClass().equals(myLocationPositionDefinition.getImplementingClass())) {
return;
@@ -434,7 +440,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
};
}
-
+
@Override
public SearchParamSet extractSearchParamStrings(IBaseResource theResource) {
IExtractor extractor = createStringExtractor(theResource);
@@ -546,24 +552,31 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
String code = extractValueAsString(myQuantityCodeValueChild, theValue);
ResourceIndexedSearchParamQuantity nextEntity = new ResourceIndexedSearchParamQuantity(myPartitionSettings, theResourceType, theSearchParam.getName(), nextValueValue, system, code);
-
- theParams.add(nextEntity);
+
+ theParams.add(nextEntity);
}
}
-
-
- private void addQuantity_QuantityNormalized(String theResourceType, Set theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
+
+
+ private void addQuantity_QuantityNormalized(String theResourceType, Set theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
Optional> valueField = myQuantityValueValueChild.getAccessor().getFirstValueOrNull(theValue);
if (valueField.isPresent() && valueField.get().getValue() != null) {
BigDecimal nextValueValue = valueField.get().getValue();
String system = extractValueAsString(myQuantitySystemValueChild, theValue);
String code = extractValueAsString(myQuantityCodeValueChild, theValue);
- ResourceIndexedSearchParamQuantityNormalized nextEntity = new ResourceIndexedSearchParamQuantityNormalized(myPartitionSettings, theResourceType, theSearchParam.getName(), nextValueValue, system, code);
- theParams.add(nextEntity);
+ //-- convert the value/unit to the canonical form if any
+ Pair canonicalForm = UcumServiceUtil.getCanonicalForm(system, nextValueValue, code);
+ if (canonicalForm != null) {
+ double canonicalValue = Double.parseDouble(canonicalForm.getValue().asDecimal());
+ String canonicalUnits = canonicalForm.getCode();
+ ResourceIndexedSearchParamQuantityNormalized nextEntity = new ResourceIndexedSearchParamQuantityNormalized(myPartitionSettings, theResourceType, theSearchParam.getName(), canonicalValue, system, canonicalUnits);
+ theParams.add(nextEntity);
+ }
+
}
}
-
+
private void addQuantity_Money(String theResourceType, Set theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
Optional> valueField = myMoneyValueChild.getAccessor().getFirstValueOrNull(theValue);
if (valueField.isPresent() && valueField.get().getValue() != null) {
@@ -572,14 +585,14 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
String nextValueString = "urn:iso:std:iso:4217";
String nextValueCode = extractValueAsString(myMoneyCurrencyChild, theValue);
String searchParamName = theSearchParam.getName();
-
+
ResourceIndexedSearchParamQuantity nextEntity = new ResourceIndexedSearchParamQuantity(myPartitionSettings, theResourceType, searchParamName, nextValueValue, nextValueString, nextValueCode);
theParams.add(nextEntity);
- }
+ }
}
-
- private void addQuantity_MoneyNormalized(String theResourceType, Set theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
+
+ private void addQuantity_MoneyNormalized(String theResourceType, Set theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
Optional> valueField = myMoneyValueChild.getAccessor().getFirstValueOrNull(theValue);
if (valueField.isPresent() && valueField.get().getValue() != null) {
BigDecimal nextValueValue = valueField.get().getValue();
@@ -587,22 +600,22 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
String nextValueString = "urn:iso:std:iso:4217";
String nextValueCode = extractValueAsString(myMoneyCurrencyChild, theValue);
String searchParamName = theSearchParam.getName();
-
- ResourceIndexedSearchParamQuantityNormalized nextEntityNormalized = new ResourceIndexedSearchParamQuantityNormalized(myPartitionSettings, theResourceType, searchParamName, nextValueValue, nextValueString, nextValueCode);
- theParams.add(nextEntityNormalized);
+
+ ResourceIndexedSearchParamQuantityNormalized nextEntityNormalized = new ResourceIndexedSearchParamQuantityNormalized(myPartitionSettings, theResourceType, searchParamName, nextValueValue.doubleValue(), nextValueString, nextValueCode);
+ theParams.add(nextEntityNormalized);
}
}
-
-
+
+
private void addQuantity_Range(String theResourceType, Set theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
Optional low = myRangeLowValueChild.getAccessor().getFirstValueOrNull(theValue);
low.ifPresent(theIBase -> addQuantity_Quantity(theResourceType, theParams, theSearchParam, theIBase));
Optional high = myRangeHighValueChild.getAccessor().getFirstValueOrNull(theValue);
- high.ifPresent(theIBase -> addQuantity_Quantity(theResourceType, theParams, theSearchParam, theIBase));
+ high.ifPresent(theIBase -> addQuantity_Quantity(theResourceType, theParams, theSearchParam, theIBase));
}
-
+
private void addQuantity_RangeNormalized(String theResourceType, Set theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
Optional low = myRangeLowValueChild.getAccessor().getFirstValueOrNull(theValue);
low.ifPresent(theIBase -> addQuantity_QuantityNormalized(theResourceType, theParams, theSearchParam, theIBase));
@@ -610,7 +623,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
Optional high = myRangeHighValueChild.getAccessor().getFirstValueOrNull(theValue);
high.ifPresent(theIBase -> addQuantity_QuantityNormalized(theResourceType, theParams, theSearchParam, theIBase));
}
-
+
private void addToken_Identifier(String theResourceType, Set theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
String system = extractValueAsString(myIdentifierSystemValueChild, theValue);
String value = extractValueAsString(myIdentifierValueValueChild, theValue);
@@ -1163,11 +1176,27 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
@FunctionalInterface
private interface IExtractor {
-
void extract(SearchParamSet theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath);
}
+ private static class CompositeExtractor implements IExtractor {
+
+ private final IExtractor myExtractor0;
+ private final IExtractor myExtractor1;
+
+ private CompositeExtractor(IExtractor theExtractor0, IExtractor theExtractor1) {
+ myExtractor0 = theExtractor0;
+ myExtractor1 = theExtractor1;
+ }
+
+ @Override
+ public void extract(SearchParamSet theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath) {
+ myExtractor0.extract(theParams, theSearchParam, theValue, thePath);
+ myExtractor1.extract(theParams, theSearchParam, theValue, thePath);
+ }
+ }
+
private class ResourceLinkExtractor implements IExtractor {
private PathAndRef myPathAndRef = null;
diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParams.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParams.java
index 3006df3ddec..656a3cbb50a 100644
--- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParams.java
+++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParams.java
@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamCoords;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
@@ -36,9 +37,14 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
+import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Sets;
+import com.google.common.collect.Streams;
import org.apache.commons.lang3.StringUtils;
import java.util.ArrayList;
@@ -51,6 +57,7 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.function.Predicate;
+import java.util.stream.Stream;
import static org.apache.commons.lang3.StringUtils.compare;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -158,21 +165,30 @@ public final class ResourceIndexedSearchParams {
return myPopulatedResourceLinkParameters;
}
- public boolean matchParam(ModelConfig theModelConfig, String theResourceName, String theParamName, RuntimeSearchParam theParamDef, IQueryParameterType theParam) {
+ public boolean matchParam(ModelConfig theModelConfig, String theResourceName, String theParamName, RuntimeSearchParam theParamDef, IQueryParameterType theValue) {
if (theParamDef == null) {
return false;
}
- Collection resourceParams;
+ Collection resourceParams = null;
+ IQueryParameterType value = theValue;
switch (theParamDef.getParamType()) {
case TOKEN:
resourceParams = myTokenParams;
break;
case QUANTITY:
- if (theModelConfig.isNormalizedQuantitySearchSupported())
- resourceParams = myQuantityNormalizedParams;
- else
- resourceParams = myQuantityParams;
+ if (theModelConfig.getNormalizedQuantitySearchLevel().equals(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_SUPPORTED)) {
+ QuantityParam quantity = QuantityParam.toQuantityParam(theValue);
+ QuantityParam normalized = UcumServiceUtil.toCanonicalQuantityOrNull(quantity);
+ if (normalized != null) {
+ resourceParams = myQuantityNormalizedParams;
+ value = normalized;
+ }
+ }
+
+ if (resourceParams == null) {
+ resourceParams = myQuantityParams;
+ }
break;
case STRING:
resourceParams = myStringParams;
@@ -187,7 +203,7 @@ public final class ResourceIndexedSearchParams {
resourceParams = myDateParams;
break;
case REFERENCE:
- return matchResourceLinks(theModelConfig, theResourceName, theParamName, theParam, theParamDef.getPath());
+ return matchResourceLinks(theModelConfig, theResourceName, theParamName, value, theParamDef.getPath());
case COMPOSITE:
case HAS:
case SPECIAL:
@@ -197,11 +213,16 @@ public final class ResourceIndexedSearchParams {
if (resourceParams == null) {
return false;
}
- Predicate namedParamPredicate = param ->
- param.getParamName().equalsIgnoreCase(theParamName) &&
- param.matches(theParam);
- return resourceParams.stream().anyMatch(namedParamPredicate);
+ for (BaseResourceIndexedSearchParam nextParam : resourceParams) {
+ if (nextParam.getParamName().equalsIgnoreCase(theParamName)) {
+ if (nextParam.matches(value)) {
+ return true;
+ }
+ }
+ }
+
+ return false;
}
/**
@@ -275,10 +296,7 @@ public final class ResourceIndexedSearchParams {
public void findMissingSearchParams(PartitionSettings thePartitionSettings, ModelConfig theModelConfig, ResourceTable theEntity, Set> theActiveSearchParams) {
findMissingSearchParams(thePartitionSettings, theModelConfig, theEntity, theActiveSearchParams, RestSearchParameterTypeEnum.STRING, myStringParams);
findMissingSearchParams(thePartitionSettings, theModelConfig, theEntity, theActiveSearchParams, RestSearchParameterTypeEnum.NUMBER, myNumberParams);
- if (theModelConfig.isNormalizedQuantitySearchSupported())
- findMissingSearchParams(thePartitionSettings, theModelConfig, theEntity, theActiveSearchParams, RestSearchParameterTypeEnum.QUANTITY, myQuantityNormalizedParams);
- else
- findMissingSearchParams(thePartitionSettings, theModelConfig, theEntity, theActiveSearchParams, RestSearchParameterTypeEnum.QUANTITY, myQuantityParams);
+ findMissingSearchParams(thePartitionSettings, theModelConfig, theEntity, theActiveSearchParams, RestSearchParameterTypeEnum.QUANTITY, myQuantityParams);
findMissingSearchParams(thePartitionSettings, theModelConfig, theEntity, theActiveSearchParams, RestSearchParameterTypeEnum.DATE, myDateParams);
findMissingSearchParams(thePartitionSettings, theModelConfig, theEntity, theActiveSearchParams, RestSearchParameterTypeEnum.URI, myUriParams);
findMissingSearchParams(thePartitionSettings, theModelConfig, theEntity, theActiveSearchParams, RestSearchParameterTypeEnum.TOKEN, myTokenParams);
@@ -309,10 +327,7 @@ public final class ResourceIndexedSearchParams {
param = new ResourceIndexedSearchParamNumber();
break;
case QUANTITY:
- if (theModelConfig.isNormalizedQuantitySearchSupported())
- param = new ResourceIndexedSearchParamQuantityNormalized();
- else
- param = new ResourceIndexedSearchParamQuantity();
+ param = new ResourceIndexedSearchParamQuantity();
break;
case STRING:
param = new ResourceIndexedSearchParamString()
diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3.java
index 89074ba36ad..e92e62dc9d9 100644
--- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3.java
+++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3.java
@@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
*/
import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
@@ -50,9 +49,9 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
// This constructor is used by tests
@VisibleForTesting
- public SearchParamExtractorDstu3(ModelConfig theModelConfig, PartitionSettings thePartitionSettings, FhirContext theCtx, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry) {
+ public SearchParamExtractorDstu3(ModelConfig theModelConfig, PartitionSettings thePartitionSettings, FhirContext theCtx, ISearchParamRegistry theSearchParamRegistry) {
super(theModelConfig, thePartitionSettings, theCtx, theSearchParamRegistry);
- initFhirPathEngine(theValidationSupport);
+ initFhirPathEngine();
start();
}
@@ -75,13 +74,12 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
public void start() {
super.start();
if (myFhirPathEngine == null) {
- IValidationSupport support = myApplicationContext.getBean(IValidationSupport.class);
- initFhirPathEngine(support);
+ initFhirPathEngine();
}
}
- public void initFhirPathEngine(IValidationSupport theSupport) {
- IWorkerContext worker = new HapiWorkerContext(getContext(), theSupport);
+ public void initFhirPathEngine() {
+ IWorkerContext worker = new HapiWorkerContext(getContext(), getContext().getValidationSupport());
myFhirPathEngine = new FHIRPathEngine(worker);
}
diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java
index 60701fb23b3..5e61663ab01 100644
--- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java
+++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java
@@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
*/
import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
@@ -62,9 +61,9 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
// This constructor is used by tests
@VisibleForTesting
- public SearchParamExtractorR4(ModelConfig theModelConfig, PartitionSettings thePartitionSettings, FhirContext theCtx, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry) {
+ public SearchParamExtractorR4(ModelConfig theModelConfig, PartitionSettings thePartitionSettings, FhirContext theCtx, ISearchParamRegistry theSearchParamRegistry) {
super(theModelConfig, thePartitionSettings, theCtx, theSearchParamRegistry);
- initFhirPath(theValidationSupport);
+ initFhirPath();
start();
}
@@ -82,13 +81,12 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
public void start() {
super.start();
if (myFhirPathEngine == null) {
- IValidationSupport support = myApplicationContext.getBean(IValidationSupport.class);
- initFhirPath(support);
+ initFhirPath();
}
}
- public void initFhirPath(IValidationSupport theSupport) {
- IWorkerContext worker = new HapiWorkerContext(getContext(), theSupport);
+ public void initFhirPath() {
+ IWorkerContext worker = new HapiWorkerContext(getContext(), getContext().getValidationSupport());
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR4HostServices());
}
@@ -96,7 +94,7 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
private static class SearchParamExtractorR4HostServices implements FHIRPathEngine.IEvaluationContext {
- private Map myResourceTypeToStub = Collections.synchronizedMap(new HashMap<>());
+ private final Map myResourceTypeToStub = Collections.synchronizedMap(new HashMap<>());
@Override
public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java
index af1e43bd107..38e6b082f12 100644
--- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java
+++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java
@@ -21,8 +21,6 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
*/
import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
-import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
@@ -58,9 +56,9 @@ public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements
/**
* Constructor for unit tests
*/
- public SearchParamExtractorR5(ModelConfig theModelConfig, PartitionSettings thePartitionSettings, FhirContext theCtx, DefaultProfileValidationSupport theDefaultProfileValidationSupport, ISearchParamRegistry theSearchParamRegistry) {
+ public SearchParamExtractorR5(ModelConfig theModelConfig, PartitionSettings thePartitionSettings, FhirContext theCtx, ISearchParamRegistry theSearchParamRegistry) {
super(theModelConfig, thePartitionSettings, theCtx, theSearchParamRegistry);
- initFhirPath(theDefaultProfileValidationSupport);
+ initFhirPath();
start();
}
@@ -69,13 +67,12 @@ public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements
public void start() {
super.start();
if (myFhirPathEngine == null) {
- IValidationSupport support = myApplicationContext.getBean(IValidationSupport.class);
- initFhirPath(support);
+ initFhirPath();
}
}
- public void initFhirPath(IValidationSupport theSupport) {
- IWorkerContext worker = new HapiWorkerContext(getContext(), theSupport);
+ public void initFhirPath() {
+ IWorkerContext worker = new HapiWorkerContext(getContext(), getContext().getValidationSupport());
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR5HostServices());
}
@@ -88,7 +85,7 @@ public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements
private static class SearchParamExtractorR5HostServices implements FHIRPathEngine.IEvaluationContext {
- private Map myResourceTypeToStub = Collections.synchronizedMap(new HashMap<>());
+ private final Map myResourceTypeToStub = Collections.synchronizedMap(new HashMap<>());
@Override
public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java
index 1727f6a1ba4..43d0945b341 100644
--- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java
+++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java
@@ -31,6 +31,7 @@ import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamCoords;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
@@ -119,8 +120,8 @@ public class SearchParamExtractorService {
ISearchParamExtractor.SearchParamSet quantities = extractSearchParamQuantity(theResource);
handleWarnings(theRequestDetails, myInterceptorBroadcaster, quantities);
theParams.myQuantityParams.addAll(quantities);
-
- if (myModelConfig.isNormalizedQuantityStorageSupported()|| myModelConfig.isNormalizedQuantitySearchSupported()) {
+
+ if (myModelConfig.getNormalizedQuantitySearchLevel().equals(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_STORAGE_SUPPORTED) || myModelConfig.getNormalizedQuantitySearchLevel().equals(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_SUPPORTED)) {
ISearchParamExtractor.SearchParamSet quantitiesNormalized = extractSearchParamQuantityNormalized(theResource);
handleWarnings(theRequestDetails, myInterceptorBroadcaster, quantitiesNormalized);
theParams.myQuantityNormalizedParams.addAll(quantitiesNormalized);
diff --git a/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/IndexStressTest.java b/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/IndexStressTest.java
index cd6ffa86f18..bbb7ef23b6b 100644
--- a/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/IndexStressTest.java
+++ b/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/IndexStressTest.java
@@ -9,9 +9,6 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu3;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.util.StopWatch;
-import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
-import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
-import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.dstu3.model.Patient;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
@@ -23,7 +20,6 @@ import java.util.stream.Collectors;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.ArgumentMatchers.eq;
-import static org.mockito.Mockito.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@@ -43,9 +39,8 @@ public class IndexStressTest {
FhirContext ctx = FhirContext.forDstu3();
IValidationSupport mockValidationSupport = mock(IValidationSupport.class);
when(mockValidationSupport.getFhirContext()).thenReturn(ctx);
- IValidationSupport validationSupport = new CachingValidationSupport(new ValidationSupportChain(new DefaultProfileValidationSupport(ctx), mockValidationSupport));
ISearchParamRegistry searchParamRegistry = mock(ISearchParamRegistry.class);
- SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ctx, validationSupport, searchParamRegistry);
+ SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ctx, searchParamRegistry);
extractor.start();
Map spMap = ctx
diff --git a/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3Test.java b/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3Test.java
index 11bd9c98f6d..4a6106d9fea 100644
--- a/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3Test.java
+++ b/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3Test.java
@@ -1,11 +1,10 @@
package ca.uhn.fhir.jpa.searchparam.extractor;
import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.context.phonetic.IPhoneticEncoder;
-import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
-import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.cache.ResourceChangeResult;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
@@ -33,7 +32,6 @@ import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.text.Normalizer;
@@ -51,8 +49,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
public class SearchParamExtractorDstu3Test {
- private static FhirContext ourCtx = FhirContext.forDstu3();
- private static IValidationSupport ourValidationSupport;
+ private static FhirContext ourCtx = FhirContext.forCached(FhirVersionEnum.DSTU3);
@Test
public void testParamWithOrInPath() {
@@ -61,7 +58,7 @@ public class SearchParamExtractorDstu3Test {
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
- SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, ourValidationSupport, searchParamRegistry);
+ SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, searchParamRegistry);
extractor.start();
Set tokens = extractor.extractSearchParamTokens(obs);
assertEquals(1, tokens.size());
@@ -84,7 +81,7 @@ public class SearchParamExtractorDstu3Test {
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
- SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, ourValidationSupport, searchParamRegistry);
+ SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, searchParamRegistry);
extractor.start();
Set params = extractor.extractSearchParamStrings(questionnaire);
assertEquals(1, params.size());
@@ -102,7 +99,7 @@ public class SearchParamExtractorDstu3Test {
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
- SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, ourValidationSupport, searchParamRegistry);
+ SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, searchParamRegistry);
extractor.start();
Set params = extractor.extractSearchParamNumber(enc);
assertEquals(1, params.size());
@@ -120,7 +117,7 @@ public class SearchParamExtractorDstu3Test {
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
- SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, ourValidationSupport, searchParamRegistry);
+ SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, searchParamRegistry);
extractor.start();
Set params = extractor.extractSearchParamNumber(enc);
assertEquals(1, params.size());
@@ -132,7 +129,7 @@ public class SearchParamExtractorDstu3Test {
public void testEmptyPath() {
MySearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
- SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, ourValidationSupport, searchParamRegistry);
+ SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, searchParamRegistry);
extractor.start();
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "", RestSearchParameterTypeEnum.STRING, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
@@ -148,7 +145,7 @@ public class SearchParamExtractorDstu3Test {
public void testStringMissingResourceType() {
MySearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
- SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, ourValidationSupport, searchParamRegistry);
+ SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, searchParamRegistry);
extractor.start();
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "communication.language.coding.system | communication.language.coding.code", RestSearchParameterTypeEnum.STRING, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
@@ -165,7 +162,7 @@ public class SearchParamExtractorDstu3Test {
public void testInvalidType() {
MySearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
- SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, ourValidationSupport, searchParamRegistry);
+ SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, searchParamRegistry);
extractor.start();
{
@@ -216,7 +213,7 @@ public class SearchParamExtractorDstu3Test {
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
- SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, ourValidationSupport, searchParamRegistry);
+ SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, searchParamRegistry);
extractor.start();
ISearchParamExtractor.SearchParamSet coords = extractor.extractSearchParamTokens(loc);
assertEquals(1, coords.size());
@@ -227,7 +224,7 @@ public class SearchParamExtractorDstu3Test {
private static class MySearchParamRegistry implements ISearchParamRegistry {
- private List myAddedSearchParams = new ArrayList<>();
+ private final List myAddedSearchParams = new ArrayList<>();
public void addSearchParam(RuntimeSearchParam... theSearchParam) {
myAddedSearchParams.clear();
@@ -306,9 +303,4 @@ public class SearchParamExtractorDstu3Test {
TestUtil.clearAllStaticFieldsForUnitTest();
}
- @BeforeAll
- public static void beforeClass() {
- ourValidationSupport = new DefaultProfileValidationSupport(ourCtx);
- }
-
}
diff --git a/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorMegaTest.java b/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorMegaTest.java
index bd1744df856..97185778d9a 100644
--- a/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorMegaTest.java
+++ b/hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorMegaTest.java
@@ -17,7 +17,6 @@ import ca.uhn.fhir.context.RuntimePrimitiveDatatypeXhtmlHl7OrgDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.context.phonetic.IPhoneticEncoder;
-import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.jpa.cache.ResourceChangeResult;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
@@ -66,15 +65,15 @@ public class SearchParamExtractorMegaTest {
ctx = FhirContext.forDstu3();
searchParamRegistry = new MySearchParamRegistry(ctx);
- process(ctx, new SearchParamExtractorDstu3(new ModelConfig(), partitionSettings, ctx, new DefaultProfileValidationSupport(ctx), searchParamRegistry));
+ process(ctx, new SearchParamExtractorDstu3(new ModelConfig(), partitionSettings, ctx, searchParamRegistry));
ctx = FhirContext.forR4();
searchParamRegistry = new MySearchParamRegistry(ctx);
- process(ctx, new SearchParamExtractorR4(new ModelConfig(), partitionSettings, ctx, new DefaultProfileValidationSupport(ctx), searchParamRegistry));
+ process(ctx, new SearchParamExtractorR4(new ModelConfig(), partitionSettings, ctx, searchParamRegistry));
ctx = FhirContext.forR5();
searchParamRegistry = new MySearchParamRegistry(ctx);
- process(ctx, new SearchParamExtractorR5(new ModelConfig(), partitionSettings, ctx, new DefaultProfileValidationSupport(ctx), searchParamRegistry));
+ process(ctx, new SearchParamExtractorR5(new ModelConfig(), partitionSettings, ctx, searchParamRegistry));
}
private void process(FhirContext theCtx, BaseSearchParamExtractor theExtractor) throws Exception {
diff --git a/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/BaseValidatingInterceptor.java b/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/BaseValidatingInterceptor.java
index c352102c51f..b84e30a6490 100644
--- a/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/BaseValidatingInterceptor.java
+++ b/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/BaseValidatingInterceptor.java
@@ -45,7 +45,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* request with an {@link UnprocessableEntityException HTTP 422 Unprocessable Entity}.
*/
@Interceptor
-public abstract class BaseValidatingInterceptor {
+public abstract class BaseValidatingInterceptor extends ValidationResultEnrichingInterceptor {
/**
* Default value:
diff --git a/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/RequestValidatingInterceptor.java b/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/RequestValidatingInterceptor.java
index a046dbf7304..25c035c8692 100644
--- a/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/RequestValidatingInterceptor.java
+++ b/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/RequestValidatingInterceptor.java
@@ -31,8 +31,6 @@ import ca.uhn.fhir.rest.server.method.ResourceParameter;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import ca.uhn.fhir.validation.ValidationResult;
-import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
-import org.hl7.fhir.instance.model.api.IBaseResource;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@@ -51,11 +49,6 @@ public class RequestValidatingInterceptor extends BaseValidatingInterceptor validationResult = (List) theRequestDetails.getUserData().remove(REQUEST_VALIDATION_RESULT);
+ if (validationResult != null) {
+ for (ValidationResult next : validationResult) {
+ next.populateOperationOutcome(oo);
+ }
+ }
+ }
+
+ }
+
+ return true;
+ }
+
+
+ @SuppressWarnings("unchecked")
+ public static void addValidationResultToRequestDetails(@Nullable RequestDetails theRequestDetails, @Nonnull ValidationResult theValidationResult) {
+ if (theRequestDetails != null) {
+ List results = (List) theRequestDetails.getUserData().computeIfAbsent(REQUEST_VALIDATION_RESULT, t -> new ArrayList<>(2));
+ results.add(theValidationResult);
+ }
+ }
+}
diff --git a/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java b/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java
index 60c32608290..32d6ab8b196 100644
--- a/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java
+++ b/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java
@@ -9,15 +9,14 @@ import fr.inria.lille.shexjava.schema.parsing.GenParser;
import fr.inria.lille.shexjava.validation.RecursiveValidation;
import fr.inria.lille.shexjava.validation.ValidationAlgorithm;
import org.apache.commons.rdf.api.Graph;
-import org.apache.commons.rdf.api.IRI;
+import org.apache.commons.rdf.api.RDFTerm;
import org.apache.commons.rdf.rdf4j.RDF4J;
import org.eclipse.rdf4j.model.Model;
-import org.eclipse.rdf4j.model.impl.SimpleIRI;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.eclipse.rdf4j.rio.Rio;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Base;
-import org.hl7.fhir.r4.model.DomainResource;
+import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.MethodSource;
@@ -25,8 +24,10 @@ import org.springframework.core.io.Resource;
import org.springframework.core.io.support.PathMatchingResourcePatternResolver;
import org.springframework.core.io.support.ResourcePatternResolver;
+import java.io.ByteArrayInputStream;
import java.io.FileInputStream;
import java.io.IOException;
+import java.io.InputStream;
import java.io.StringReader;
import java.nio.file.Path;
import java.nio.file.Paths;
@@ -53,6 +54,15 @@ public class RDFParserTest extends BaseTest {
fhirSchema = GenParser.parseSchema(schemaFile, Collections.emptyList());
}
+ // If we can't round-trip JSON, we skip the Turtle round-trip test.
+ private static ArrayList jsonRoundTripErrors = new ArrayList();
+ @AfterAll
+ static void reportJsonRoundTripErrors() {
+ System.out.println(jsonRoundTripErrors.size() + " tests disqualified because of JSON round-trip errors");
+ for (String e : jsonRoundTripErrors)
+ System.out.println(e);
+ }
+
/**
* This test method has a method source for each JSON file in the resources/rdf-test-input directory (see #getInputFiles).
* Each input file is expected to be a JSON representation of an R4 FHIR resource.
@@ -62,71 +72,48 @@ public class RDFParserTest extends BaseTest {
* 3. Perform a graph validation on the resulting RDF using ShEx and ShEx-java -- ensure validation passed
* 4. Parse the RDF string into the HAPI object model -- ensure resource instance is not null
* 5. Perform deep equals comparison of JSON-originated instance and RDF-originated instance -- ensure equality
- * @param inputFile -- path to resource file to be tested
+ * @param referenceFilePath -- path to resource file to be tested
* @throws IOException -- thrown when parsing RDF string into graph model
*/
@ParameterizedTest
@MethodSource("getInputFiles")
- public void testRDFRoundTrip(String inputFile) throws IOException {
- FileInputStream inputStream = new FileInputStream(inputFile);
- IBaseResource resource;
- String resourceType;
- // Parse JSON input as Resource
- resource = ourCtx.newJsonParser().parseResource(inputStream);
- assertNotNull(resource);
- resourceType = resource.fhirType();
-
- // Write the resource out to an RDF String
- String rdfContent = ourCtx.newRDFParser().encodeResourceToString(resource);
- assertNotNull(rdfContent);
+ public void testRDFRoundTrip(String referenceFilePath) throws IOException {
+ String referenceFileName = referenceFilePath.substring(referenceFilePath.lastIndexOf("/")+1);
+ IBaseResource referenceResource = parseJson(new FileInputStream(referenceFilePath));
+ String referenceJson = serializeJson(ourCtx, referenceResource);
// Perform ShEx validation on RDF
- RDF4J factory = new RDF4J();
- GlobalFactory.RDFFactory = factory; //set the global factory used in shexjava
+ String turtleString = serializeRdf(ourCtx, referenceResource);
+ validateRdf(turtleString, referenceFileName, referenceResource);
- // load the model
- String baseIRI = "http://a.example.shex/";
- Model data = Rio.parse(new StringReader(rdfContent), baseIRI, RDFFormat.TURTLE);
+ // If we can round-trip JSON
+ IBaseResource viaJsonResource = parseJson(new ByteArrayInputStream(referenceJson.getBytes()));
+ if (((Base)viaJsonResource).equalsDeep((Base)referenceResource)) {
- String rootSubjectIri = null;
- for (org.eclipse.rdf4j.model.Resource resourceStream : data.subjects()) {
- if (resourceStream instanceof SimpleIRI) {
- Model filteredModel = data.filter(resourceStream, factory.getValueFactory().createIRI(NODE_ROLE_IRI), factory.getValueFactory().createIRI(TREE_ROOT_IRI), (org.eclipse.rdf4j.model.Resource)null);
- if (filteredModel != null && filteredModel.subjects().size() == 1) {
- Optional rootResource = filteredModel.subjects().stream().findFirst();
- if (rootResource.isPresent()) {
- rootSubjectIri = rootResource.get().stringValue();
- break;
- }
+ // Parse RDF content as resource
+ IBaseResource viaTurtleResource = parseRdf(ourCtx, new StringReader(turtleString));
+ assertNotNull(viaTurtleResource);
- }
+ // Compare original JSON-based resource against RDF-based resource
+ String viaTurtleJson = serializeJson(ourCtx, viaTurtleResource);
+ if (!((Base)viaTurtleResource).equalsDeep((Base)referenceResource)) {
+ String failMessage = referenceFileName + ": failed to round-trip Turtle ";
+ if (referenceJson.equals(viaTurtleJson))
+ throw new Error(failMessage
+ + "\nttl: " + turtleString
+ + "\nexp: " + referenceJson);
+ else
+ assertEquals(referenceJson, viaTurtleJson, failMessage + "\nttl: " + turtleString);
}
- }
-
- // create the graph
- Graph dataGraph = factory.asGraph(data);
-
- // choose focus node and shapelabel
- IRI focusNode = factory.createIRI(rootSubjectIri);
- Label shapeLabel = new Label(factory.createIRI(FHIR_SHAPE_PREFIX + resourceType));
-
- ValidationAlgorithm validation = new RecursiveValidation(fhirSchema, dataGraph);
- validation.validate(focusNode, shapeLabel);
- boolean result = validation.getTyping().isConformant(focusNode, shapeLabel);
- assertTrue(result);
-
- // Parse RDF content as resource
- IBaseResource parsedResource = ourCtx.newRDFParser().parseResource(new StringReader(rdfContent));
- assertNotNull(parsedResource);
-
- // Compare original JSON-based resource against RDF-based resource
- if (parsedResource instanceof DomainResource) {
- // This is a hack because this initializes the collection if it is empty
- ((DomainResource) parsedResource).getContained();
- boolean deepEquals = ((Base)parsedResource).equalsDeep((Base)resource);
- assertTrue(deepEquals);
} else {
- ourLog.warn("Input JSON did not yield a DomainResource");
+ String gotString = serializeJson(ourCtx, viaJsonResource);
+ String skipMessage = referenceFileName + ": failed to round-trip JSON" +
+ (referenceJson.equals(gotString)
+ ? "\ngot: " + gotString + "\nexp: " + referenceJson
+ : "\nsome inequality not visible in: " + referenceJson);
+ System.out.println(referenceFileName + " skipped");
+ // Specific messages are printed at end of run.
+ jsonRoundTripErrors.add(skipMessage);
}
}
@@ -135,11 +122,98 @@ public class RDFParserTest extends BaseTest {
List resourceList = new ArrayList<>();
ResourcePatternResolver resolver = new PathMatchingResourcePatternResolver(cl);
Resource[] resources = resolver.getResources("classpath:rdf-test-input/*.json") ;
- for (Resource resource: resources){
+ for (Resource resource: resources)
resourceList.add(resource.getFile().getPath());
- }
return resourceList.stream();
}
+ // JSON functions
+ public IBaseResource parseJson(InputStream inputStream) {
+ IParser refParser = ourCtx.newJsonParser();
+ refParser.setStripVersionsFromReferences(false);
+ // parser.setDontStripVersionsFromReferencesAtPaths();
+ IBaseResource ret = refParser.parseResource(inputStream);
+ assertNotNull(ret);
+ return ret;
+ }
+
+ public String serializeJson(FhirContext ctx, IBaseResource resource) {
+ IParser jsonParser = ctx.newJsonParser();
+ jsonParser.setStripVersionsFromReferences(false);
+ String ret = jsonParser.encodeResourceToString(resource);
+ assertNotNull(ret);
+ return ret;
+ }
+
+ // Rdf (Turtle) functions
+ public IBaseResource parseRdf(FhirContext ctx, StringReader inputStream) {
+ IParser refParser = ctx.newRDFParser();
+ IBaseResource ret = refParser.parseResource(inputStream);
+ assertNotNull(ret);
+ return ret;
+ }
+
+ public String serializeRdf(FhirContext ctx, IBaseResource resource) {
+ IParser rdfParser = ourCtx.newRDFParser();
+ rdfParser.setStripVersionsFromReferences(false);
+ rdfParser.setServerBaseUrl("http://a.example/fhir/");
+ String ret = rdfParser.encodeResourceToString(resource);
+ assertNotNull(ret);
+ return ret;
+ }
+
+ public void validateRdf(String rdfContent, String referenceFileName, IBaseResource referenceResource) throws IOException {
+ String baseIRI = "http://a.example/shex/";
+ RDF4J factory = new RDF4J();
+ GlobalFactory.RDFFactory = factory; //set the global factory used in shexjava
+ Model data = Rio.parse(new StringReader(rdfContent), baseIRI, RDFFormat.TURTLE);
+ FixedShapeMapEntry fixedMapEntry = new FixedShapeMapEntry(factory, data, referenceResource.fhirType(), baseIRI);
+ Graph dataGraph = factory.asGraph(data); // create the graph
+ ValidationAlgorithm validation = new RecursiveValidation(fhirSchema, dataGraph);
+ validation.validate(fixedMapEntry.node, fixedMapEntry.shape);
+ boolean result = validation.getTyping().isConformant(fixedMapEntry.node, fixedMapEntry.shape);
+ assertTrue(result,
+ referenceFileName + ": failed to validate " + fixedMapEntry
+ + "\n" + referenceFileName
+ + "\n" + rdfContent
+ );
+ }
+
+ // Shape Expressions functions
+ class FixedShapeMapEntry {
+ RDFTerm node;
+ Label shape;
+
+ FixedShapeMapEntry(RDF4J factory, Model data, String resourceType, String baseIRI) {
+ String rootSubjectIri = null;
+ // StmtIterator i = data.listStatements();
+ for (org.eclipse.rdf4j.model.Resource resourceStream : data.subjects()) {
+// if (resourceStream instanceof SimpleIRI) {
+ Model filteredModel = data.filter(resourceStream, factory.getValueFactory().createIRI(NODE_ROLE_IRI), factory.getValueFactory().createIRI(TREE_ROOT_IRI), (org.eclipse.rdf4j.model.Resource)null);
+ if (filteredModel != null && filteredModel.subjects().size() == 1) {
+ Optional rootResource = filteredModel.subjects().stream().findFirst();
+ if (rootResource.isPresent()) {
+ rootSubjectIri = rootResource.get().stringValue();
+ break;
+ }
+
+ }
+// }
+ }
+
+ // choose focus node and shapelabel
+ this.node = rootSubjectIri.indexOf(":") == -1
+ ? factory.createBlankNode(rootSubjectIri)
+ : factory.createIRI(rootSubjectIri);
+ Label shapeLabel = new Label(factory.createIRI(FHIR_SHAPE_PREFIX + resourceType));
+// this.node = focusNode;
+ this.shape = shapeLabel;
+ }
+
+ public String toString() {
+ return "<" + node.toString() + ">@" + shape.toPrettyString();
+ }
+ }
+
}
diff --git a/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/README.md b/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/README.md
new file mode 100644
index 00000000000..43a69e1cb67
--- /dev/null
+++ b/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/README.md
@@ -0,0 +1,5 @@
+# Why is this disabled?
+
+| file | reason |
+| - | - |
+| [bundle-response](bundle-response.json) | [entry\[0\].response.outcome.issue](bundle-response.json#L50-L61) is not in [R4 Resource](http://hl7.org/fhir/resource.html#Resource) |
diff --git a/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/bundle-response.json b/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/bundle-response.json
similarity index 100%
rename from hapi-fhir-structures-r4/src/test/resources/rdf-test-input/bundle-response.json
rename to hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/bundle-response.json
diff --git a/hapi-fhir-structures-r4/src/test/resources/rdf-validation/fhir-r4.shex b/hapi-fhir-structures-r4/src/test/resources/rdf-validation/fhir-r4.shex
index 040ca2b9c67..ec75815f9e1 100644
--- a/hapi-fhir-structures-r4/src/test/resources/rdf-validation/fhir-r4.shex
+++ b/hapi-fhir-structures-r4/src/test/resources/rdf-validation/fhir-r4.shex
@@ -13267,7 +13267,7 @@ fhirvs:contact-point-use ["home" "work" "temp" "old" "mobile"]
fhirvs:immunization-status ["completed" "entered-in-error" "not-done"]
# This value set includes all possible codes from BCP-13 (http://tools.ietf.org/html/bcp13)
-fhirvs:mimetypes EXTERNAL
+fhirvs:mimetypes .
# The use of an address.
fhirvs:address-use ["home" "work" "temp" "old" "billing"]
diff --git a/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/FhirInstanceValidator.java b/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/FhirInstanceValidator.java
index 5a5354aa8ca..8b8175683d9 100644
--- a/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/FhirInstanceValidator.java
+++ b/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/FhirInstanceValidator.java
@@ -29,6 +29,8 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
private BestPracticeWarningLevel myBestPracticeWarningLevel;
private IValidationSupport myValidationSupport;
private boolean noTerminologyChecks = false;
+ private boolean noExtensibleWarnings = false;
+ private boolean noBindingMsgSuppressed = false;
private volatile VersionSpecificWorkerContextWrapper myWrappedWorkerContext;
private boolean errorForUnknownProfiles;
private boolean assumeValidRestReferences;
@@ -184,6 +186,34 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
noTerminologyChecks = theNoTerminologyChecks;
}
+ /**
+ * If set to {@literal true} (default is false) no extensible warnings suppressed
+ */
+ public boolean isNoExtensibleWarnings() {
+ return noExtensibleWarnings;
+ }
+
+ /**
+ * If set to {@literal true} (default is false) no extensible warnings is suppressed
+ */
+ public void setNoExtensibleWarnings(final boolean theNoExtensibleWarnings) {
+ noExtensibleWarnings = theNoExtensibleWarnings;
+ }
+
+ /**
+ * If set to {@literal true} (default is false) no binding message is suppressed
+ */
+ public boolean isNoBindingMsgSuppressed() {
+ return noBindingMsgSuppressed;
+ }
+
+ /**
+ * If set to {@literal true} (default is false) no binding message is suppressed
+ */
+ public void setNoBindingMsgSuppressed(final boolean theNoBindingMsgSuppressed) {
+ noBindingMsgSuppressed = theNoBindingMsgSuppressed;
+ }
+
public List getExtensionDomains() {
return myExtensionDomains;
}
@@ -198,6 +228,8 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
.setErrorForUnknownProfiles(isErrorForUnknownProfiles())
.setExtensionDomains(getExtensionDomains())
.setNoTerminologyChecks(isNoTerminologyChecks())
+ .setNoExtensibleWarnings(isNoExtensibleWarnings())
+ .setNoBindingMsgSuppressed(isNoBindingMsgSuppressed())
.setValidatorResourceFetcher(getValidatorResourceFetcher())
.setAssumeValidRestReferences(isAssumeValidRestReferences())
.validate(wrappedWorkerContext, theValidationCtx);
diff --git a/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/ValidatorWrapper.java b/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/ValidatorWrapper.java
index 9452feb433a..33817480b03 100644
--- a/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/ValidatorWrapper.java
+++ b/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/ValidatorWrapper.java
@@ -38,6 +38,8 @@ class ValidatorWrapper {
private boolean myErrorForUnknownProfiles;
private boolean myNoTerminologyChecks;
private boolean myAssumeValidRestReferences;
+ private boolean myNoExtensibleWarnings;
+ private boolean myNoBindingMsgSuppressed;
private Collection myExtensionDomains;
private IResourceValidator.IValidatorResourceFetcher myValidatorResourceFetcher;
@@ -77,6 +79,16 @@ class ValidatorWrapper {
return this;
}
+ public ValidatorWrapper setNoExtensibleWarnings(boolean theNoExtensibleWarnings) {
+ myNoExtensibleWarnings = theNoExtensibleWarnings;
+ return this;
+ }
+
+ public ValidatorWrapper setNoBindingMsgSuppressed(boolean theNoBindingMsgSuppressed) {
+ myNoBindingMsgSuppressed = theNoBindingMsgSuppressed;
+ return this;
+ }
+
public ValidatorWrapper setExtensionDomains(Collection theExtensionDomains) {
myExtensionDomains = theExtensionDomains;
return this;
@@ -105,6 +117,8 @@ class ValidatorWrapper {
v.setErrorForUnknownProfiles(myErrorForUnknownProfiles);
v.getExtensionDomains().addAll(myExtensionDomains);
v.setFetcher(myValidatorResourceFetcher);
+ v.setNoExtensibleWarnings(myNoExtensibleWarnings);
+ v.setNoBindingMsgSuppressed(myNoBindingMsgSuppressed);
v.setAllowXsiLocation(true);
List messages = new ArrayList<>();
diff --git a/pom.xml b/pom.xml
index d94a6d732f6..142adf8cf1f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -531,6 +531,10 @@
basecade
Anders Havn
+
+ vedion
+ Anders Havn
+
zaewonyx
@@ -744,7 +748,7 @@
2.3.0.1
2.3.1
3.16.0
- 2.25.1
+ 3.0.0
9.4.35.v20201120
3.0.2
@@ -758,19 +762,19 @@
6.1.5.Final
4.4.13
4.5.13
- 2.11.2
+ 2.12.1
2.11.2
3.1.0
1.8
4.0.0.Beta3
- 5.2.0
- 9.3.8
+ 5.6.5
+ 9.5.4
2.8.8
9.8.0-15
1.2_5
1.7.30
2.11.1
- 5.3.2
+ 5.3.3
2.4.2
4.2.3.RELEASE
@@ -888,6 +892,12 @@
com.helger
ph-schematron
${ph_schematron_version}
+
+
+ jakarta.xml.bind
+ jakarta.xml.bind-api
+
+
com.helger
@@ -927,7 +937,7 @@
org.apache.commons
commons-collections4
- 4.3
+ 4.4
org.apache.commons
@@ -1351,7 +1361,7 @@
org.fusesource.jansi
jansi
- 1.18
+ 2.1.1
org.glassfish
@@ -1956,7 +1966,7 @@
org.jacoco
jacoco-maven-plugin
- 0.8.5
+ 0.8.6
ca/uhn/fhir/model/dstu2/**/*.class