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Merge branch 'master' into jakarta-upgrade-md

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This commit is contained in:
Tadgh 2023-12-12 10:25:36 -08:00
commit 5dcbbae8b2
794 changed files with 4467 additions and 3650 deletions
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2
.pre-commit-config.yaml
View File

@ -4,7 +4,7 @@
repos:
- repo: https://github.com/ejba/pre-commit-maven
rev: v0.3.3
rev: v0.3.4
hooks:
- id: maven-spotless-apply
stages: [pre-push]

2
hapi-deployable-pom/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

8
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -116,10 +116,16 @@
</dependency>
<!-- @Nonnull annotation -->
<!-- We need to leave this in because otherwise hapi-fhir-structures-dstu3: will fail to generate javadoc -->
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</dependency>
<dependency>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/BaseRuntimeElementDefinition.java
View File

@ -21,6 +21,8 @@ package ca.uhn.fhir.context;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.util.UrlUtil;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
@ -31,8 +33,6 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
public abstract class BaseRuntimeElementDefinition<T extends IBase> {

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
View File

@ -49,6 +49,8 @@ import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ReflectionUtil;
import ca.uhn.fhir.util.VersionUtil;
import ca.uhn.fhir.validation.FhirValidator;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.apache.jena.riot.Lang;
@ -77,8 +79,6 @@ import java.util.Optional;
import java.util.Properties;
import java.util.Set;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
/**
* The FHIR context is the central starting point for the use of the HAPI FHIR API. It should be created once, and then

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ModelScanner.java
View File

@ -38,6 +38,7 @@ import ca.uhn.fhir.model.primitive.BoundCodeDt;
import ca.uhn.fhir.model.primitive.XhtmlDt;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.util.ReflectionUtil;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
@ -67,7 +68,6 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
import javax.annotation.Nonnull;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -498,7 +498,7 @@ class ModelScanner {
nextElementType = ReflectionUtil.getGenericCollectionTypeOfField(next);
} else if (Collection.class.isAssignableFrom(nextElementType)) {
throw new ConfigurationException(Msg.code(1722) + "Field '" + next.getName() + "' in type '"
+ next.getClass().getCanonicalName()
+ nextElementType.getCanonicalName()
+ "' is a Collection - Only java.util.List curently supported");
}
return nextElementType;

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeSearchParam.java
View File

@ -21,6 +21,8 @@ package ca.uhn.fhir.context;
import ca.uhn.fhir.context.phonetic.IPhoneticEncoder;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
@ -37,8 +39,6 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.StringTokenizer;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/DefaultProfileValidationSupport.java
View File

@ -23,6 +23,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.util.ILockable;
import ca.uhn.fhir.util.ReflectionUtil;
import jakarta.annotation.Nullable;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -32,7 +33,6 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import javax.annotation.Nullable;
/**
* This class returns the vocabulary that is shipped with the base FHIR

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/DefaultProfileValidationSupportBundleStrategy.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.ClasspathUtil;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -43,7 +44,6 @@ import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Properties;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

59
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
View File

@ -24,6 +24,8 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.ParametersUtil;
import ca.uhn.fhir.util.UrlUtil;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
@ -42,8 +44,6 @@ import java.util.List;
import java.util.Set;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -295,8 +295,8 @@ public interface IValidationSupport {
*/
@Nullable
default CodeValidationResult validateCode(
@Nonnull ValidationSupportContext theValidationSupportContext,
@Nonnull ConceptValidationOptions theOptions,
ValidationSupportContext theValidationSupportContext,
ConceptValidationOptions theOptions,
String theCodeSystem,
String theCode,
String theDisplay,
@ -526,8 +526,13 @@ public interface IValidationSupport {
public String getPropertyName() {
return myPropertyName;
}
public abstract String getType();
}
String TYPE_STRING = "string";
String TYPE_CODING = "Coding";
class StringConceptProperty extends BaseConceptProperty {
private final String myValue;
@ -544,6 +549,10 @@ public interface IValidationSupport {
public String getValue() {
return myValue;
}
public String getType() {
return TYPE_STRING;
}
}
class CodingConceptProperty extends BaseConceptProperty {
@ -574,6 +583,10 @@ public interface IValidationSupport {
public String getDisplay() {
return myDisplay;
}
public String getType() {
return TYPE_CODING;
}
}
class CodeValidationResult {
@ -881,25 +894,35 @@ public interface IValidationSupport {
}
for (BaseConceptProperty next : myProperties) {
String propertyName = next.getPropertyName();
if (!properties.isEmpty()) {
if (!properties.contains(next.getPropertyName())) {
continue;
}
if (!properties.isEmpty() && !properties.contains(propertyName)) {
continue;
}
IBase property = ParametersUtil.addParameterToParameters(theContext, retVal, "property");
ParametersUtil.addPartCode(theContext, property, "code", next.getPropertyName());
ParametersUtil.addPartCode(theContext, property, "code", propertyName);
if (next instanceof StringConceptProperty) {
StringConceptProperty prop = (StringConceptProperty) next;
ParametersUtil.addPartString(theContext, property, "value", prop.getValue());
} else if (next instanceof CodingConceptProperty) {
CodingConceptProperty prop = (CodingConceptProperty) next;
ParametersUtil.addPartCoding(
theContext, property, "value", prop.getCodeSystem(), prop.getCode(), prop.getDisplay());
} else {
throw new IllegalStateException(Msg.code(1739) + "Don't know how to handle " + next.getClass());
String propertyType = next.getType();
switch (propertyType) {
case TYPE_STRING:
StringConceptProperty stringConceptProperty = (StringConceptProperty) next;
ParametersUtil.addPartString(
theContext, property, "value", stringConceptProperty.getValue());
break;
case TYPE_CODING:
CodingConceptProperty codingConceptProperty = (CodingConceptProperty) next;
ParametersUtil.addPartCoding(
theContext,
property,
"value",
codingConceptProperty.getCodeSystem(),
codingConceptProperty.getCode(),
codingConceptProperty.getDisplay());
break;
default:
throw new IllegalStateException(
Msg.code(1739) + "Don't know how to handle " + next.getClass());
}
}
}

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/fhirpath/IFhirPath.java
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@ -19,11 +19,11 @@
*/
package ca.uhn.fhir.fhirpath;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBase;
import java.util.List;
import java.util.Optional;
import javax.annotation.Nonnull;
public interface IFhirPath {

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/fhirpath/IFhirPathEvaluationContext.java
View File

@ -19,12 +19,11 @@
*/
package ca.uhn.fhir.fhirpath;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IIdType;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
public interface IFhirPathEvaluationContext {
/**

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/HookParams.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.interceptor.api;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import com.google.common.collect.Multimaps;
import jakarta.annotation.Nonnull;
import org.apache.commons.lang3.Validate;
import java.util.Collection;
@ -29,7 +30,6 @@ import java.util.Collections;
import java.util.List;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
public class HookParams {

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/IBaseInterceptorService.java
View File

@ -19,10 +19,11 @@
*/
package ca.uhn.fhir.interceptor.api;
import jakarta.annotation.Nullable;
import java.util.Collection;
import java.util.List;
import java.util.function.Predicate;
import javax.annotation.Nullable;
public interface IBaseInterceptorService<POINTCUT extends IPointcut> extends IBaseInterceptorBroadcaster<POINTCUT> {

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/IPointcut.java
View File

@ -19,8 +19,9 @@
*/
package ca.uhn.fhir.interceptor.api;
import jakarta.annotation.Nonnull;
import java.util.List;
import javax.annotation.Nonnull;
public interface IPointcut {
@Nonnull

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.validation.ValidationResult;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBaseConformance;
import java.io.Writer;
@ -33,7 +34,6 @@ import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.annotation.Nonnull;
/**
* Value for {@link Hook#value()}

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/executor/BaseInterceptorService.java
View File

@ -31,6 +31,8 @@ import ca.uhn.fhir.util.ReflectionUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
@ -57,8 +59,6 @@ import java.util.Optional;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Predicate;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
public abstract class BaseInterceptorService<POINTCUT extends Enum<POINTCUT> & IPointcut>
implements IBaseInterceptorService<POINTCUT>, IBaseInterceptorBroadcaster<POINTCUT> {

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/model/RequestPartitionId.java
View File

@ -24,6 +24,8 @@ import ca.uhn.fhir.util.JsonUtil;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
@ -37,8 +39,6 @@ import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/BaseNarrativeGenerator.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.Logs;
import jakarta.annotation.Nullable;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.INarrative;
@ -37,7 +38,6 @@ import java.util.EnumSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.defaultIfEmpty;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/INarrativeTemplateManifest.java
View File

@ -20,12 +20,12 @@
package ca.uhn.fhir.narrative2;
import ca.uhn.fhir.context.FhirContext;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBase;
import java.util.Collection;
import java.util.EnumSet;
import java.util.List;
import javax.annotation.Nonnull;
public interface INarrativeTemplateManifest {
List<INarrativeTemplate> getTemplateByResourceName(

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/NarrativeTemplateManifest.java
View File

@ -28,6 +28,7 @@ import com.google.common.base.Charsets;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import com.google.common.collect.Multimaps;
import jakarta.annotation.Nonnull;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
@ -53,7 +54,6 @@ import java.util.Objects;
import java.util.Properties;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -45,6 +45,7 @@ import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import jakarta.annotation.Nullable;
import org.apache.commons.io.output.StringBuilderWriter;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
@ -78,7 +79,6 @@ import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

33
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/jackson/JacksonStructure.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.parser.json.BaseJsonLikeWriter;
import ca.uhn.fhir.parser.json.JsonLikeStructure;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.core.StreamReadConstraints;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.JsonNode;
@ -114,14 +115,38 @@ public class JacksonStructure implements JsonLikeStructure {
setNativeArray((ArrayNode) OBJECT_MAPPER.readTree(pbr));
}
} catch (Exception e) {
if (e.getMessage().startsWith("Unexpected char 39")) {
String message;
if (e instanceof JsonProcessingException) {
/*
* Currently there is no way of preventing Jackson from adding this
* annoying REDACTED message from certain messages we get back from
* the parser, so we just manually strip them. Hopefully Jackson
* will accept this request at some point:
* https://github.com/FasterXML/jackson-core/issues/1158
*/
JsonProcessingException jpe = (JsonProcessingException) e;
StringBuilder messageBuilder = new StringBuilder();
String originalMessage = jpe.getOriginalMessage();
originalMessage = originalMessage.replace(
"Source: REDACTED (`StreamReadFeature.INCLUDE_SOURCE_IN_LOCATION` disabled); ", "");
messageBuilder.append(originalMessage);
if (jpe.getLocation() != null) {
messageBuilder.append("\n at [");
jpe.getLocation().appendOffsetDescription(messageBuilder);
messageBuilder.append("]");
}
message = messageBuilder.toString();
} else {
message = e.getMessage();
}
if (message.startsWith("Unexpected char 39")) {
throw new DataFormatException(
Msg.code(1860) + "Failed to parse JSON encoded FHIR content: " + e.getMessage() + " - "
Msg.code(1860) + "Failed to parse JSON encoded FHIR content: " + message + " - "
+ "This may indicate that single quotes are being used as JSON escapes where double quotes are required",
e);
}
throw new DataFormatException(
Msg.code(1861) + "Failed to parse JSON encoded FHIR content: " + e.getMessage(), e);
throw new DataFormatException(Msg.code(1861) + "Failed to parse JSON encoded FHIR content: " + message, e);
}
}

32
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/jackson/JacksonWriter.java
View File

@ -45,29 +45,15 @@ public class JacksonWriter extends BaseJsonLikeWriter {
@Override
public BaseJsonLikeWriter init() {
if (isPrettyPrint()) {
DefaultPrettyPrinter prettyPrinter = new DefaultPrettyPrinter() {
/**
* Objects should serialize as
* <pre>
* {
* "key": "value"
* }
* </pre>
* in order to be consistent with Gson behaviour, instead of the jackson default
* <pre>
* {
* "key" : "value"
* }
* </pre>
*/
@Override
public DefaultPrettyPrinter withSeparators(Separators separators) {
_separators = separators;
_objectFieldValueSeparatorWithSpaces = separators.getObjectFieldValueSeparator() + " ";
return this;
}
};
DefaultPrettyPrinter prettyPrinter = new DefaultPrettyPrinter()
.withSeparators(new Separators(
Separators.DEFAULT_ROOT_VALUE_SEPARATOR,
':',
Separators.Spacing.AFTER,
',',
Separators.Spacing.NONE,
',',
Separators.Spacing.NONE));
prettyPrinter = prettyPrinter.withObjectIndenter(new DefaultIndenter(" ", "\n"));
myJsonGenerator.setPrettyPrinter(prettyPrinter);

15
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
View File

@ -220,21 +220,6 @@ public class Constants {
public static final String PARAM_TEXT = "_text";
public static final String PARAM_VALIDATE = "_validate";
/**
* $member-match operation
*/
public static final String PARAM_MEMBER_PATIENT = "MemberPatient";
public static final String PARAM_MEMBER_IDENTIFIER = "MemberIdentifier";
public static final String COVERAGE_TO_MATCH = "CoverageToMatch";
public static final String COVERAGE_TO_LINK = "CoverageToLink";
public static final String PARAM_CONSENT = "Consent";
public static final String PARAM_MEMBER_PATIENT_NAME = PARAM_MEMBER_PATIENT + " Name";
public static final String PARAM_MEMBER_PATIENT_BIRTHDATE = PARAM_MEMBER_PATIENT + " Birthdate";
public static final String PARAM_CONSENT_PATIENT_REFERENCE = PARAM_CONSENT + "'s Patient Reference";
public static final String PARAM_CONSENT_PERFORMER_REFERENCE = PARAM_CONSENT + "'s Performer Reference";
public static final String PARAMQUALIFIER_MISSING = ":missing";
public static final String PARAMQUALIFIER_MISSING_FALSE = "false";
public static final String PARAMQUALIFIER_MISSING_TRUE = "true";

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/IVersionSpecificBundleFactory.java
View File

@ -22,6 +22,8 @@ package ca.uhn.fhir.rest.api;
import ca.uhn.fhir.context.api.BundleInclusionRule;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.valueset.BundleTypeEnum;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -29,8 +31,6 @@ import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Set;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
/**
* This interface should be considered experimental and will likely change in future releases of HAPI. Use with caution!

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/PatchTypeEnum.java
View File

@ -23,10 +23,10 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.annotation.Patch;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import jakarta.annotation.Nonnull;
import java.util.HashMap;
import java.util.Map;
import javax.annotation.Nonnull;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/PreferHeader.java
View File

@ -19,7 +19,7 @@
*/
package ca.uhn.fhir.rest.api;
import javax.annotation.Nullable;
import jakarta.annotation.Nullable;
public class PreferHeader {

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/PreferReturnEnum.java
View File

@ -19,8 +19,9 @@
*/
package ca.uhn.fhir.rest.api;
import jakarta.annotation.Nullable;
import java.util.HashMap;
import javax.annotation.Nullable;
/**
* Represents values for "return" value as provided in the the <a href="https://tools.ietf.org/html/rfc7240#section-4.2">HTTP Prefer header</a>.

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/RestOperationTypeEnum.java
View File

@ -20,11 +20,11 @@
package ca.uhn.fhir.rest.api;
import ca.uhn.fhir.util.CoverageIgnore;
import jakarta.annotation.Nonnull;
import org.apache.commons.lang3.Validate;
import java.util.HashMap;
import java.util.Map;
import javax.annotation.Nonnull;
@CoverageIgnore
public enum RestOperationTypeEnum {

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/api/IRestfulClient.java
View File

@ -24,10 +24,9 @@ import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.RequestFormatParamStyleEnum;
import ca.uhn.fhir.rest.api.SummaryEnum;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBaseResource;
import javax.annotation.Nonnull;
public interface IRestfulClient {
/**

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java
View File

@ -27,6 +27,7 @@ import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.DateUtils;
import jakarta.annotation.Nonnull;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -34,7 +35,6 @@ import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import javax.annotation.Nonnull;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.EQUAL;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN_OR_EQUALS;

124
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleBuilder.java
View File

@ -25,6 +25,8 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.primitive.IdDt;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
@ -36,8 +38,6 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.Date;
import java.util.Objects;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
/**
* This class can be used to build a Bundle resource to be used as a FHIR transaction. Convenience methods provide
@ -196,11 +196,7 @@ public class BundleBuilder {
public UpdateBuilder addTransactionUpdateEntry(IBaseResource theResource) {
Validate.notNull(theResource, "theResource must not be null");
IIdType id = theResource.getIdElement();
if (id.hasIdPart() && !id.hasResourceType()) {
String resourceType = myContext.getResourceType(theResource);
id = id.withResourceType(resourceType);
}
IIdType id = getIdTypeForUpdate(theResource);
String requestUrl = id.toUnqualifiedVersionless().getValue();
String fullUrl = id.getValue();
@ -225,13 +221,29 @@ public class BundleBuilder {
myEntryRequestUrlChild.getMutator().setValue(request, url);
// Bundle.entry.request.method
IPrimitiveType<?> method = (IPrimitiveType<?>)
myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
method.setValueAsString(theHttpVerb);
myEntryRequestMethodChild.getMutator().setValue(request, method);
addRequestMethod(request, theHttpVerb);
return url;
}
/**
* Adds an entry containing an update (UPDATE) request without the body of the resource.
* Also sets the Bundle.type value to "transaction" if it is not already set.
*
* @param theResource The resource to update.
*/
public void addTransactionUpdateIdOnlyEntry(IBaseResource theResource) {
setBundleField("type", "transaction");
Validate.notNull(theResource, "theResource must not be null");
IIdType id = getIdTypeForUpdate(theResource);
String requestUrl = id.toUnqualifiedVersionless().getValue();
String fullUrl = id.getValue();
String httpMethod = "PUT";
addIdOnlyEntry(requestUrl, httpMethod, fullUrl);
}
/**
* Adds an entry containing an create (POST) request.
* Also sets the Bundle.type value to "transaction" if it is not already set.
@ -247,20 +259,47 @@ public class BundleBuilder {
String resourceType = myContext.getResourceType(theResource);
// Bundle.entry.request.url
IPrimitiveType<?> url =
(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
url.setValueAsString(resourceType);
myEntryRequestUrlChild.getMutator().setValue(request, url);
addRequestUrl(request, resourceType);
// Bundle.entry.request.url
IPrimitiveType<?> method = (IPrimitiveType<?>)
myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
method.setValueAsString("POST");
myEntryRequestMethodChild.getMutator().setValue(request, method);
// Bundle.entry.request.method
addRequestMethod(request, "POST");
return new CreateBuilder(request);
}
/**
* Adds an entry containing a create (POST) request without the body of the resource.
* Also sets the Bundle.type value to "transaction" if it is not already set.
*
* @param theResource The resource to create
*/
public void addTransactionCreateEntryIdOnly(IBaseResource theResource) {
setBundleField("type", "transaction");
String requestUrl = myContext.getResourceType(theResource);
String fullUrl = theResource.getIdElement().getValue();
String httpMethod = "POST";
addIdOnlyEntry(requestUrl, httpMethod, fullUrl);
}
private void addIdOnlyEntry(String theRequestUrl, String theHttpMethod, String theFullUrl) {
IBase entry = addEntry();
// Bundle.entry.request
IBase request = myEntryRequestDef.newInstance();
myEntryRequestChild.getMutator().setValue(entry, request);
// Bundle.entry.request.url
addRequestUrl(request, theRequestUrl);
// Bundle.entry.request.method
addRequestMethod(request, theHttpMethod);
// Bundle.entry.fullUrl
addFullUrl(entry, theFullUrl);
}
/**
* Adds an entry containing a delete (DELETE) request.
* Also sets the Bundle.type value to "transaction" if it is not already set.
@ -341,20 +380,44 @@ public class BundleBuilder {
IBase request = addEntryAndReturnRequest();
// Bundle.entry.request.url
IPrimitiveType<?> url =
(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
url.setValueAsString(theDeleteUrl);
myEntryRequestUrlChild.getMutator().setValue(request, url);
addRequestUrl(request, theDeleteUrl);
// Bundle.entry.request.method
IPrimitiveType<?> method = (IPrimitiveType<?>)
myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
method.setValueAsString("DELETE");
myEntryRequestMethodChild.getMutator().setValue(request, method);
addRequestMethod(request, "DELETE");
return new DeleteBuilder();
}
private IIdType getIdTypeForUpdate(IBaseResource theResource) {
IIdType id = theResource.getIdElement();
if (id.hasIdPart() && !id.hasResourceType()) {
String resourceType = myContext.getResourceType(theResource);
id = id.withResourceType(resourceType);
}
return id;
}
private void addFullUrl(IBase theEntry, String theFullUrl) {
IPrimitiveType<?> fullUrl =
(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
fullUrl.setValueAsString(theFullUrl);
myEntryFullUrlChild.getMutator().setValue(theEntry, fullUrl);
}
private void addRequestUrl(IBase request, String theRequestUrl) {
IPrimitiveType<?> url =
(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
url.setValueAsString(theRequestUrl);
myEntryRequestUrlChild.getMutator().setValue(request, url);
}
private void addRequestMethod(IBase theRequest, String theMethod) {
IPrimitiveType<?> method = (IPrimitiveType<?>)
myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
method.setValueAsString(theMethod);
myEntryRequestMethodChild.getMutator().setValue(theRequest, method);
}
/**
* Adds an entry for a Collection bundle type
*/
@ -406,10 +469,7 @@ public class BundleBuilder {
IBase entry = addEntry();
// Bundle.entry.fullUrl
IPrimitiveType<?> fullUrl =
(IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
fullUrl.setValueAsString(theFullUrl);
myEntryFullUrlChild.getMutator().setValue(entry, fullUrl);
addFullUrl(entry, theFullUrl);
// Bundle.entry.resource
myEntryResourceChild.getMutator().setValue(entry, theResource);

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleUtil.java
View File

@ -35,6 +35,7 @@ import ca.uhn.fhir.util.bundle.EntryListAccumulator;
import ca.uhn.fhir.util.bundle.ModifiableBundleEntry;
import ca.uhn.fhir.util.bundle.SearchBundleEntryParts;
import com.google.common.collect.Sets;
import jakarta.annotation.Nonnull;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBinary;
@ -54,7 +55,6 @@ import java.util.Objects;
import java.util.Set;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.instance.model.api.IBaseBundle.LINK_PREV;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ClasspathUtil.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import com.google.common.base.Charsets;
import jakarta.annotation.Nonnull;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.BOMInputStream;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -37,7 +38,6 @@ import java.io.Reader;
import java.nio.charset.StandardCharsets;
import java.util.function.Function;
import java.util.zip.GZIPInputStream;
import javax.annotation.Nonnull;
/**
* Use this API with caution, it may change!

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/CompositionBuilder.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.util;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseReference;
@ -29,7 +30,6 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.Date;
import javax.annotation.Nonnull;
/**
* This class can be used to generate <code>Composition</code> resources in

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/DateRangeUtil.java
View File

@ -20,10 +20,10 @@
package ca.uhn.fhir.util;
import ca.uhn.fhir.rest.param.DateRangeParam;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import java.util.Date;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
public class DateRangeUtil {

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ExtensionUtil.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.util;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import jakarta.annotation.Nonnull;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
@ -33,7 +34,6 @@ import java.util.List;
import java.util.Optional;
import java.util.function.Predicate;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
/**
* Utility for modifying with extensions in a FHIR version-independent approach.

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -42,6 +42,8 @@ import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.parser.DataFormatException;
import com.google.common.collect.Lists;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
@ -71,8 +73,6 @@ import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/JsonUtil.java
View File

@ -27,12 +27,12 @@ import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import jakarta.annotation.Nonnull;
import java.io.IOException;
import java.io.StringWriter;
import java.io.Writer;
import java.util.List;
import javax.annotation.Nonnull;
public class JsonUtil {

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/OperationOutcomeUtil.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import jakarta.annotation.Nullable;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
@ -36,7 +37,6 @@ import org.hl7.fhir.instance.model.api.ICompositeType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.List;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java
View File

@ -27,6 +27,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.primitive.StringDt;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
@ -45,7 +46,6 @@ import java.util.List;
import java.util.Optional;
import java.util.function.Function;
import java.util.stream.Collectors;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.isBlank;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ReflectionUtil.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.util;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import jakarta.annotation.Nonnull;
import org.apache.commons.lang3.Validate;
import java.lang.reflect.Constructor;
@ -39,7 +40,6 @@ import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.concurrent.ConcurrentHashMap;
import javax.annotation.Nonnull;
public class ReflectionUtil {

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/SearchParameterUtil.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.i18n.Msg;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -34,7 +35,6 @@ import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import javax.annotation.Nullable;
public class SearchParameterUtil {

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/StringUtil.java
View File

@ -19,11 +19,12 @@
*/
package ca.uhn.fhir.util;
import jakarta.annotation.Nonnull;
import java.io.CharArrayWriter;
import java.nio.charset.StandardCharsets;
import java.text.Normalizer;
import java.util.Arrays;
import javax.annotation.Nonnull;
public class StringUtil {

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlUtil.java
View File

@ -28,6 +28,8 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.google.common.escape.Escaper;
import com.google.common.net.PercentEscaper;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.NameValuePair;
import org.apache.http.client.utils.URLEncodedUtils;
@ -50,8 +52,6 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.StringTokenizer;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.defaultString;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/IValidationContext.java
View File

@ -21,9 +21,9 @@ package ca.uhn.fhir.validation;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.EncodingEnum;
import jakarta.annotation.Nonnull;
import java.util.List;
import javax.annotation.Nonnull;
public interface IValidationContext<T> {

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/ValidationContext.java
View File

@ -26,11 +26,11 @@ import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ObjectUtil;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.ArrayList;
import java.util.List;
import javax.annotation.Nonnull;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;

2
hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IPrimitiveType.java
View File

@ -19,7 +19,7 @@
*/
package org.hl7.fhir.instance.model.api;
import javax.annotation.Nullable;
import jakarta.annotation.Nullable;
public interface IPrimitiveType<T> extends IBaseDatatype {

7
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -206,10 +206,3 @@ ca.uhn.fhir.jpa.provider.DiffProvider.cantDiffDifferentTypes=Unable to diff two
ca.uhn.fhir.jpa.interceptor.validation.RuleRequireProfileDeclaration.noMatchingProfile=Resource of type "{0}" does not declare conformance to profile from: {1}
ca.uhn.fhir.jpa.interceptor.validation.RuleRequireProfileDeclaration.illegalProfile=Resource of type "{0}" must not declare conformance to profile: {1}
operation.member.match.error.coverage.not.found=Could not find coverage for member based on coverage id or coverage identifier.
operation.member.match.error.beneficiary.not.found=Could not find beneficiary for coverage.
operation.member.match.error.missing.parameter=Parameter "{0}" is required.
operation.member.match.error.beneficiary.without.identifier=Coverage beneficiary does not have an identifier.
operation.member.match.error.patient.not.found=Could not find matching patient for coverage.
operation.member.match.error.consent.release.data.mismatch=Consent policy does not match the data release segmentation capabilities.

2
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/TaskChunkerTest.java
View File

@ -8,7 +8,7 @@ import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import javax.annotation.Nonnull;
import jakarta.annotation.Nonnull;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.verify;

4
hapi-fhir-bom/pom.xml
View File

@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
@ -12,7 +12,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-checkstyle/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

10
hapi-fhir-checkstyle/src/checkstyle/hapi-base-checkstyle.xml
View File

@ -31,9 +31,19 @@
</module>
<module name="RegexpSinglelineJava">
<property name="format" value="org\.jetbrains\.annotations\.NotNull"/>
<property name="message" value="Incorrect &quot;org.jetbrains.annotation.NotNull&quot; annotation used: The &quot;jakarta.annotation.Nonnull&quot; annotation should be used for non-null values"/>
</module>
<module name="RegexpSinglelineJava">
<property name="format" value="org\.jetbrains\.annotations\.Nullable"/>
<property name="message" value="Incorrect &quot;org.jetbrains.annotation.Nullable&quot; annotation used: The &quot;jakarta.annotation.Nullable&quot; annotation should be used for nullable values"/>
</module>
<module name="RegexpSinglelineJava">
<property name="format" value="javax\.annotation\.Nonnull"/>
<property name="message" value="Incorrect &quot;javax.annotation.Nonnull&quot; used: &quot;jakarta.annotation.Nonnull&quot; should be used for non-null values"/>
</module>
<module name="RegexpSinglelineJava">
<property name="format" value="javax\.annotation\.Nullable"/>
<property name="message" value="Incorrect &quot;javax.annotation.Nullable&quot; used: &quot;jakarta.annotation.Nonnull&quot; should be used for nullable values"/>
</module>
<!-- Should always use the Spring transactional interface, per: https://stackoverflow.com/questions/26387399/javax-transaction-transactional-vs-org-springframework-transaction-annotation-tr -->
<module name="RegexpSinglelineJava">

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseCommand.java
View File

@ -34,6 +34,7 @@ import com.google.common.base.Charsets;
import com.google.common.collect.Sets;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
import jakarta.annotation.Nullable;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionGroup;
@ -75,7 +76,6 @@ import java.util.Optional;
import java.util.concurrent.ExecutionException;
import java.util.stream.Collectors;
import java.util.zip.GZIPInputStream;
import javax.annotation.Nullable;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

2
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BulkImportCommand.java
View File

@ -31,6 +31,7 @@ import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.ParametersUtil;
import jakarta.annotation.Nonnull;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
@ -68,7 +69,6 @@ import java.util.List;
import java.util.Locale;
import java.util.concurrent.ExecutionException;
import java.util.zip.GZIPInputStream;
import javax.annotation.Nonnull;
public class BulkImportCommand extends BaseCommand {

2
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ReindexTerminologyCommand.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.util.ParametersUtil;
import jakarta.annotation.Nonnull;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.ParseException;
import org.hl7.fhir.instance.model.api.IBaseParameters;
@ -31,7 +32,6 @@ import org.hl7.fhir.r4.model.Parameters;
import java.util.List;
import java.util.Optional;
import javax.annotation.Nonnull;
import static ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider.RESP_PARAM_SUCCESS;

2
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiClearMigrationLockCommandTest.java
View File

@ -14,7 +14,7 @@ import org.springframework.jdbc.core.support.AbstractLobCreatingPreparedStatemen
import org.springframework.jdbc.support.lob.DefaultLobHandler;
import org.springframework.jdbc.support.lob.LobCreator;
import javax.annotation.Nonnull;
import jakarta.annotation.Nonnull;
import java.io.File;
import java.io.IOException;
import java.sql.PreparedStatement;

2
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiFlywayMigrateDatabaseCommandTest.java
View File

@ -20,7 +20,7 @@ import org.springframework.jdbc.core.support.AbstractLobCreatingPreparedStatemen
import org.springframework.jdbc.support.lob.DefaultLobHandler;
import org.springframework.jdbc.support.lob.LobCreator;
import javax.annotation.Nonnull;
import jakarta.annotation.Nonnull;
import java.io.File;
import java.io.IOException;
import java.sql.PreparedStatement;

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/BaseClient.java
View File

@ -58,6 +58,7 @@ import ca.uhn.fhir.util.BinaryUtil;
import ca.uhn.fhir.util.OperationOutcomeUtil;
import ca.uhn.fhir.util.XmlDetectionUtil;
import com.google.common.base.Charsets;
import jakarta.annotation.Nonnull;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
@ -79,7 +80,6 @@ import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.annotation.Nonnull;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

2
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/tls/TlsAuthenticationSvc.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.tls.KeyStoreInfo;
import ca.uhn.fhir.tls.PathType;
import ca.uhn.fhir.tls.TlsAuthentication;
import ca.uhn.fhir.tls.TrustStoreInfo;
import jakarta.annotation.Nonnull;
import org.apache.commons.lang3.Validate;
import org.apache.http.conn.ssl.DefaultHostnameVerifier;
import org.apache.http.conn.ssl.NoopHostnameVerifier;
@ -37,7 +38,6 @@ import java.io.FileInputStream;
import java.io.InputStream;
import java.security.KeyStore;
import java.util.Optional;
import javax.annotation.Nonnull;
import javax.net.ssl.HostnameVerifier;
import javax.net.ssl.SSLContext;
import javax.net.ssl.TrustManager;

2
hapi-fhir-converter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/src/main/java/ca/uhn/hapi/converters/canonical/VersionCanonicalizer.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.util.HapiExtensions;
import jakarta.annotation.Nonnull;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_40;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_50;
@ -69,7 +70,6 @@ import java.util.Date;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import static org.apache.commons.lang3.StringUtils.isBlank;

3
hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor10_30.java
View File

@ -19,13 +19,12 @@
*/
package org.hl7.fhir.converter;
import jakarta.annotation.Nullable;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_30;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.exceptions.FHIRException;
import javax.annotation.Nullable;
public class NullVersionConverterAdvisor10_30 extends BaseAdvisor_10_30 {
@Nullable

3
hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor10_40.java
View File

@ -19,13 +19,12 @@
*/
package org.hl7.fhir.converter;
import jakarta.annotation.Nullable;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_40;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
import javax.annotation.Nullable;
public class NullVersionConverterAdvisor10_40 extends BaseAdvisor_10_40 {
@Nullable

2
hapi-fhir-dist/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/BalpExample.java
View File

@ -26,11 +26,11 @@ import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.storage.interceptor.balp.AsyncMemoryQueueBackedFhirClientBalpSink;
import ca.uhn.fhir.storage.interceptor.balp.IBalpAuditContextServices;
import ca.uhn.fhir.storage.interceptor.balp.IBalpAuditEventSink;
import jakarta.annotation.Nonnull;
import jakarta.servlet.ServletException;
import org.hl7.fhir.r4.model.Reference;
import java.util.List;
import javax.annotation.Nonnull;
public class BalpExample {

2
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/PagingPatientProvider.java
View File

@ -25,12 +25,12 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.method.ResponsePage;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Patient;
import java.util.List;
import javax.annotation.Nonnull;
@SuppressWarnings("null")
// START SNIPPET: provider

2
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ValidatorExamples.java
View File

@ -36,6 +36,7 @@ import ca.uhn.fhir.validation.SchemaBaseValidator;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationResult;
import ca.uhn.fhir.validation.schematron.SchematronBaseValidator;
import jakarta.annotation.Nonnull;
import jakarta.servlet.ServletException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.filefilter.WildcardFileFilter;
@ -60,7 +61,6 @@ import org.hl7.fhir.r4.model.ValueSet;
import java.io.File;
import java.io.FileReader;
import java.util.List;
import javax.annotation.Nonnull;
@SuppressWarnings({"serial", "unused"})
public class ValidatorExamples {

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5340-update-hapifhir-document.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 5340
title: "Updated documentation specifying the correct status (CANCELLED) to set the job status to if a job is cancelled."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5493-linked-resources-for-several-partitions-are-not-returned-in-the-everything-operation.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
jira: SMILE-7624
title: "Previously, it was impossible to find all resources from different partitions for $everything operation
with partitioning.cross_partition_reference_mode=ALLOWED_UNQUALIFIED and dao_config.client_id_mode=ANY.
It's fixed now"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5498-add-empty-and-id-only-payload-content-support-for-topic-subscriptions.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 5498
title: "Added support for `id-only` and `empty` payload content types for notifications
triggered by R5, R4B, and R4 back-ported topic subscriptions."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5505-remove-broken-member-match-from-hapi.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: remove
issue: 5505
title: "Removed an incorrect implementation of $member-match."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5512-codesystem-lookup-with-designation-no-language-nullpointerexception.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 5511
title: 'Previously, CodeSystem `$lookup` with Remote Terminology Service enabled would throw NullPointerException
when the CodeSystem included designations with no language value. Also, there was an inconsistency between
input and output type `string` vs. `code` for property parameters. These issues have been fixed.'

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5523-case-sensitive-package-ids.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: fix
issue: 5523
jira: SMILE-7729
title: "Previously, it was possible to store NPM Packages where the package name's case did not match the package ID's case, e.g. `my-package` was different than `MY-PACKAGE`. Names are now normalized to lower case before queries occur."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5536-sql-migration-lowercase-and-custom-column-type-sql.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: add
issue: 5536
title: "In code: Support lowercase for SQL columns and overridden column type/driver type SQL type string rules"

17
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/changes.yaml
View File

@ -4,13 +4,20 @@
title: "The version of a few dependencies have been bumped to the latest versions
(dependent HAPI modules listed in brackets):
<ul>
<li>Spring Framework (JPA): 5.3.27 -&gt; 6.0.12</li>
<li>Spring Data BOM (JPA): 2021.2.2 -&gt; 2023.0.0</li>
<li>Hibernate (JPA): 5.6.15.Final -&gt; 6.2.8.Final</li>
<li>Jackson (Base): 2.15.3 -&gt; 2.16.0</li>
<li>SLF4j (Base): 2.0.3 -&gt; 2.0.9</li>
<li>Logback (Base): 1.4.7 -&gt; 1.4.14</li>
<li>Caffeine (Base): 3.1.1 -&gt; 3.1.8</li>
<li>Spring Framework (JPA): 5.3.27 -&gt; 6.1.1</li>
<li>Spring Boot (JPA-Starter): 5.3.27 -&gt; 6.2.0</li>
<li>Spring Data BOM (JPA): 2021.2.2 -&gt; 2023.1.0</li>
<li>Hibernate (JPA): 5.6.15.Final -&gt; 6.4.0.Final</li>
<li>Hibernate Validator (JPA): 6.1.5.Final -&gt; 8.0.0.Final</li>
<li>Hibernate Search (JPA): 6.1.6.Final -&gt; 6.2.1.Final</li>
<li>Hibernate Search (JPA): 6.1.6.Final -&gt; 6.2.2.Final</li>
<li>Commons-DBCP2 (JPA): 2.9.0 -&gt; 2.11.0</li>
<li>Spring Boot (Boot+Starter): 2.7.12 -&gt; 3.1.4</li>
<li>Jetty (CLI): 10.0.14 -&gt; 12.0.2</li>
<li>Jetty (CLI): 10.0.14 -&gt; 12.0.3</li>
<li>Jansi (CLI): 2.4.0 -&gt; 2.4.1</li>
<li>Phloc Schematron (Schematron Validator): 5.6.5 -&gt; 7.1.2</li>
<li>RestEasy (JAX-RS Server): 5.0.2.Final -&gt; 6.2.5.Final</li>
</ul>"

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_batch/introduction.md
View File

@ -31,7 +31,7 @@ HAPI-FHIR Batch Jobs run based on job notification messages. The process is kic
The handler then does the following:
1. Change the work chunk status from QUEUED to IN_PROGRESS
2. Change the Job Instance status from QUEUED to IN_PROGRESS
3. If the Job Instance is cancelled, change the status to COMPLETED and abort processing.
3. If the Job Instance is cancelled, change the status to CANCELLED and abort processing.
4. The first step of the job definition is executed with the job parameters
5. This step creates new work chunks. For each work chunk it creates, it json serializes the work chunk data, stores it in the database, and publishes a new message to the Batch Notification Message Channel to notify worker threads that there are new work chunks waiting to be processed.
6. If the step succeeded, the work chunk status is changed from IN_PROGRESS to COMPLETED, and the data it contained is deleted.

2
hapi-fhir-jacoco/pom.xml
View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/util/JaxRsResponse.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jaxrs.server.util;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.BaseRestfulResponse;
import ca.uhn.fhir.util.IoUtil;
import jakarta.annotation.Nonnull;
import jakarta.ws.rs.core.Response;
import jakarta.ws.rs.core.Response.ResponseBuilder;
import org.apache.commons.lang3.StringUtils;
@ -34,7 +35,6 @@ import java.io.StringWriter;
import java.io.Writer;
import java.util.List;
import java.util.Map.Entry;
import javax.annotation.Nonnull;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

2
hapi-fhir-jpa/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

3
hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/nickname/NicknameMap.java
View File

@ -19,6 +19,8 @@
*/
package ca.uhn.fhir.jpa.nickname;
import jakarta.annotation.Nonnull;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.Reader;
@ -27,7 +29,6 @@ import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.annotation.Nonnull;
class NicknameMap {
private final Map<String, List<String>> myFormalToNick = new HashMap<>();

2
hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/nickname/NicknameSvc.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.nickname;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.i18n.Msg;
import jakarta.annotation.Nonnull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.io.ClassPathResource;
@ -34,7 +35,6 @@ import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.annotation.Nonnull;
/**
* Nickname service is used to load nicknames

2
hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/sched/BaseHapiScheduler.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Sets;
import jakarta.annotation.Nonnull;
import org.apache.commons.lang3.Validate;
import org.quartz.JobDataMap;
import org.quartz.JobKey;
@ -47,7 +48,6 @@ import java.util.Properties;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
public abstract class BaseHapiScheduler implements IHapiScheduler {
private static final Logger ourLog = LoggerFactory.getLogger(BaseHapiScheduler.class);

3
hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/util/ISequenceValueMassager.java
View File

@ -19,10 +19,9 @@
*/
package ca.uhn.fhir.jpa.util;
import jakarta.annotation.Nullable;
import org.hibernate.service.Service;
import javax.annotation.Nullable;
/**
* This is an internal API and may change or disappear without notice
*

4
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.5-SNAPSHOT</version>
<version>6.11.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -578,8 +578,8 @@
</dialect>
<dialect>
<className>ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect</className>
<prependFile>classpath:ca/uhn/fhir/jpa/docs/database/hapifhirpostgres94-init01.sql</prependFile>
<targetFileName>postgres.sql</targetFileName>
<appendFile>classpath:ca/uhn/fhir/jpa/docs/database/hapifhirpostgres94-init01.sql</appendFile>
</dialect>
</dialects>
<outputDirectory>${project.build.directory}/classes/ca/uhn/hapi/fhir/jpa/docs/database</outputDirectory>

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JobInstanceUtil.java
View File

@ -23,8 +23,7 @@ import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
import ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity;
import javax.annotation.Nonnull;
import jakarta.annotation.Nonnull;
class JobInstanceUtil {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java
View File

@ -47,6 +47,8 @@ import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ObjectNode;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import jakarta.persistence.EntityManager;
import jakarta.persistence.LockModeType;
import jakarta.persistence.Query;
@ -72,8 +74,6 @@ import java.util.UUID;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import static ca.uhn.fhir.batch2.coordinator.WorkChunkProcessor.MAX_CHUNK_ERROR_COUNT;
import static ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity.ERROR_MSG_MAX_LENGTH;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/DatabaseBlobBinaryStorageSvcImpl.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import com.google.common.hash.HashingInputStream;
import com.google.common.io.ByteStreams;
import jakarta.annotation.Nonnull;
import jakarta.persistence.EntityManager;
import jakarta.persistence.PersistenceContext;
import jakarta.persistence.PersistenceContextType;
@ -47,7 +48,6 @@ import java.sql.Blob;
import java.sql.SQLException;
import java.util.Date;
import java.util.Optional;
import javax.annotation.Nonnull;
@Transactional
public class DatabaseBlobBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportJobSchedulingHelperImpl.java
View File

@ -34,6 +34,7 @@ import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.util.Batch2JobDefinitionConstants;
import ca.uhn.fhir.util.JsonUtil;
import jakarta.annotation.Nonnull;
import jakarta.annotation.PostConstruct;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateUtils;
@ -55,7 +56,6 @@ import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import javax.annotation.Nonnull;
import static org.slf4j.LoggerFactory.getLogger;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessor.java
View File

@ -58,6 +58,7 @@ import ca.uhn.fhir.util.ExtensionUtil;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.Logs;
import ca.uhn.fhir.util.SearchParameterUtil;
import jakarta.annotation.Nonnull;
import jakarta.persistence.EntityManager;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseExtension;
@ -79,7 +80,6 @@ import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import static ca.uhn.fhir.rest.api.Constants.PARAM_HAS;
import static ca.uhn.fhir.rest.api.Constants.PARAM_ID;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImpl.java
View File

@ -40,6 +40,7 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.Logs;
import ca.uhn.fhir.util.ValidateUtil;
import com.apicatalog.jsonld.StringUtils;
import jakarta.annotation.Nonnull;
import jakarta.annotation.PostConstruct;
import org.apache.commons.lang3.time.DateUtils;
import org.quartz.JobExecutionContext;
@ -59,7 +60,6 @@ import java.util.Objects;
import java.util.Optional;
import java.util.UUID;
import java.util.concurrent.Semaphore;
import javax.annotation.Nonnull;
import static ca.uhn.fhir.batch2.jobs.importpull.BulkImportPullConfig.BULK_IMPORT_JOB_NAME;

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