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hapi-fhir
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Work on refactor

This commit is contained in:
James 2017-07-09 16:38:28 -04:00
parent 0059f2e48e
commit 6464ce9304
391 changed files with 1144936 additions and 7012 deletions
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18
example-projects/hapi-fhir-base-example-embedded-ws/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>
@ -12,6 +12,17 @@
<artifactId>hapi-fhir-base-example-embedded-ws</artifactId>
<dependencies>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
@ -44,11 +55,6 @@
<artifactId>cors-filter</artifactId>
<version>1.0.1</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>

77
example-projects/hapi-fhir-standalone-overlay-example/pom.xml
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@ -4,43 +4,21 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-standalone-overlay-example</artifactId>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<overlays>
<overlay>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
</overlay>
</overlays>
<warName>fhirtester</warName>
<failOnMissingWebXml>true</failOnMissingWebXml>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
@ -85,4 +63,37 @@
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<overlays>
<overlay>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
</overlay>
</overlays>
<warName>fhirtester</warName>
<failOnMissingWebXml>true</failOnMissingWebXml>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</build>
</project>

8
example-projects/hapi-fhir-standalone-overlay-example/src/main/java/embedded/example/FhirTesterConfig.java
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@ -2,19 +2,17 @@ package embedded.example;
import javax.servlet.http.HttpServletRequest;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.*;
import com.google.common.base.Strings;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor;
import ca.uhn.fhir.rest.server.util.ITestingUiClientFactory;
import ca.uhn.fhir.to.FhirTesterMvcConfig;
import ca.uhn.fhir.to.TesterConfig;
import ca.uhn.fhir.util.ITestingUiClientFactory;
//@formatter:off
/**

2
examples/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

12
examples/src/main/java/example/AuthorizationInterceptors.java
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@ -8,20 +8,14 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.auth.IAuthRule;
import ca.uhn.fhir.rest.server.interceptor.auth.RuleBuilder;
import ca.uhn.fhir.rest.server.interceptor.auth.*;
public class AuthorizationInterceptors {

4
examples/src/main/java/example/AuthorizingTesterUiClientFactory.java
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@ -3,9 +3,9 @@ package example;
import javax.servlet.http.HttpServletRequest;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor;
import ca.uhn.fhir.util.ITestingUiClientFactory;
import ca.uhn.fhir.rest.server.util.ITestingUiClientFactory;
public class AuthorizingTesterUiClientFactory implements ITestingUiClientFactory {

6
examples/src/main/java/example/BundleFetcher.java
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@ -2,11 +2,13 @@ package example;
import java.util.HashSet;
import java.util.Set;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.RelatedPerson;
import ca.uhn.fhir.rest.client.IGenericClient;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import ca.uhn.fhir.rest.client.api.IGenericClient;
/**
* @author Bill de Beaubien on 1/13/2016.

5
examples/src/main/java/example/ClientExamples.java
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@ -4,11 +4,10 @@ import org.hl7.fhir.dstu3.model.Bundle;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.okhttp.client.OkHttpRestfulClientFactory;
import ca.uhn.fhir.rest.client.*;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.client.apache.GZipContentInterceptor;
import ca.uhn.fhir.rest.client.api.IBasicClient;
import ca.uhn.fhir.rest.client.api.*;
import ca.uhn.fhir.rest.client.interceptor.*;
import ca.uhn.fhir.rest.server.EncodingEnum;
public class ClientExamples {

11
examples/src/main/java/example/ClientTransactionExamples.java
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@ -3,15 +3,10 @@ package example;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
import ca.uhn.fhir.model.dstu2.valueset.ObservationStatusEnum;
import ca.uhn.fhir.model.dstu2.resource.*;
import ca.uhn.fhir.model.dstu2.valueset.*;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
public class ClientTransactionExamples {

2
examples/src/main/java/example/Dstu2Examples.java
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@ -6,7 +6,7 @@ import javax.servlet.ServletException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;

10
examples/src/main/java/example/ExtensionsDstu3.java
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@ -3,18 +3,12 @@ package example;
import java.io.IOException;
import java.util.List;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.HumanName;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.StringType;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
public class ExtensionsDstu3 {

18
examples/src/main/java/example/FhirDataModel.java
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@ -1,26 +1,16 @@
package example;
import java.util.Date;
import java.util.List;
import java.util.Set;
import java.util.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.composite.SimpleQuantityDt;
import ca.uhn.fhir.model.dstu2.composite.*;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
import ca.uhn.fhir.model.dstu2.valueset.MaritalStatusCodesEnum;
import ca.uhn.fhir.model.dstu2.valueset.ObservationStatusEnum;
import ca.uhn.fhir.model.dstu2.valueset.*;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
public class FhirDataModel {

22
examples/src/main/java/example/GenericClientExample.java
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@ -9,27 +9,15 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.PerformanceOptionsEnum;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Conformance;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
import ca.uhn.fhir.model.dstu2.resource.*;
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome.Issue;
import ca.uhn.fhir.model.dstu2.resource.Organization;
import ca.uhn.fhir.model.dstu2.resource.Parameters;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.resource.Provenance;
import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
import ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum;
import ca.uhn.fhir.model.primitive.DateDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.ServerValidationModeEnum;
import ca.uhn.fhir.model.primitive.*;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.method.SearchStyleEnum;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;

8
examples/src/main/java/example/HttpProxy.java
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@ -3,17 +3,13 @@ package example;
import org.apache.http.HttpHost;
import org.apache.http.auth.AuthScope;
import org.apache.http.auth.UsernamePasswordCredentials;
import org.apache.http.client.AuthenticationStrategy;
import org.apache.http.client.CredentialsProvider;
import org.apache.http.impl.client.BasicCredentialsProvider;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.client.ProxyAuthenticationStrategy;
import org.apache.http.impl.client.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
public class HttpProxy {

12
examples/src/main/java/example/JaxRsClient.java
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@ -1,18 +1,8 @@
package example;
import java.util.ArrayList;
import java.util.List;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jaxrs.client.JaxRsRestfulClientFactory;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.client.api.IGenericClient;
@SuppressWarnings(value= {"serial"})
public class JaxRsClient {

2
examples/src/main/java/example/JaxRsConformanceProvider.java
View File

@ -9,7 +9,7 @@ import javax.ws.rs.Produces;
import javax.ws.rs.core.MediaType;
import ca.uhn.fhir.jaxrs.server.AbstractJaxRsConformanceProvider;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.IResourceProvider;
/**

20
examples/src/main/java/example/JaxRsPatientRestProvider.java
View File

@ -1,14 +1,8 @@
package example;
import java.lang.reflect.InvocationTargetException;
import javax.ejb.Local;
import javax.ejb.Stateless;
import javax.ws.rs.GET;
import javax.ws.rs.POST;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.*;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
@ -17,16 +11,8 @@ import ca.uhn.fhir.model.dstu2.resource.Parameters;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.*;
/**
* A demo JaxRs Patient Rest Provider

2
examples/src/main/java/example/PagingPatientProvider.java
View File

@ -9,8 +9,8 @@ import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.IResourceProvider;
@SuppressWarnings("null")

2
examples/src/main/java/example/RequestExceptionInterceptor.java
View File

@ -6,7 +6,7 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;

62
examples/src/main/java/example/RestfulPatientResourceProviderMore.java
View File

@ -2,15 +2,13 @@ package example;
import java.io.IOException;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Set;
import java.util.*;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
@ -18,63 +16,17 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.annotation.AddTags;
import ca.uhn.fhir.rest.annotation.At;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.annotation.Count;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.Delete;
import ca.uhn.fhir.rest.annotation.DeleteTags;
import ca.uhn.fhir.rest.annotation.Elements;
import ca.uhn.fhir.rest.annotation.GetTags;
import ca.uhn.fhir.rest.annotation.History;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.IncludeParam;
import ca.uhn.fhir.rest.annotation.Metadata;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.annotation.Since;
import ca.uhn.fhir.rest.annotation.Sort;
import ca.uhn.fhir.rest.annotation.TagListParam;
import ca.uhn.fhir.rest.annotation.Transaction;
import ca.uhn.fhir.rest.annotation.TransactionParam;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.annotation.Validate;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.client.api.IBasicClient;
import ca.uhn.fhir.rest.client.api.IRestfulClient;
import ca.uhn.fhir.rest.param.CompositeParam;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.exceptions.*;
@SuppressWarnings("unused")
public abstract class RestfulPatientResourceProviderMore implements IResourceProvider {

2
examples/src/main/java/example/SecurityInterceptors.java
View File

@ -5,7 +5,7 @@ import javax.servlet.http.HttpServletResponse;
import org.apache.commons.codec.binary.Base64;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;

6
examples/src/main/java/example/TagsExamples.java
View File

@ -4,12 +4,10 @@ import java.util.ArrayList;
import java.util.List;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
public class TagsExamples {

23
examples/src/main/java/example/ValidatorExamples.java
View File

@ -8,32 +8,17 @@ import javax.servlet.ServletException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.filefilter.WildcardFileFilter;
import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.hapi.validation.*;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.ContactPoint.ContactPointSystem;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.OperationOutcome;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.instance.model.ValueSet;
import org.hl7.fhir.instance.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.instance.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.SchemaBaseValidator;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationResult;
import ca.uhn.fhir.validation.*;
import ca.uhn.fhir.validation.schematron.SchematronBaseValidator;
@SuppressWarnings("serial")

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-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-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

8
hapi-fhir-base-test-mindeps-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -64,12 +64,12 @@
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu</artifactId>
<artifactId>hapi-fhir-client</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<artifactId>woodstox-core-asl</artifactId>
<groupId>org.codehaus.woodstox</groupId>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</exclusion>
</exclusions>
</dependency>

5
hapi-fhir-base-test-mindeps-client/src/test/java/ca/uhn/fhir/rest/client/ClientTest.java
View File

@ -6,13 +6,14 @@ import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.dstu.resource.Patient;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
import ca.uhn.fhir.rest.gclient.ITransactionTyped;
public class ClientTest {
private static FhirContext ctx = FhirContext.forDstu1();
private static FhirContext ctx = FhirContext.forDstu2();
@Test
public void testTransaction() {

62
hapi-fhir-base-test-mindeps-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -54,25 +54,6 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<artifactId>woodstox-core-asl</artifactId>
<groupId>org.codehaus.woodstox</groupId>
</exclusion>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
<exclusion>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<artifactId>woodstox-core-asl</artifactId>
@ -89,6 +70,47 @@
<artifactId>woodstox-core-asl</artifactId>
<groupId>org.codehaus.woodstox</groupId>
</exclusion>
<exclusion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<artifactId>woodstox-core-asl</artifactId>
<groupId>org.codehaus.woodstox</groupId>
</exclusion>
<exclusion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</exclusion>
</exclusions>
</dependency>

10
hapi-fhir-base-test-mindeps-server/src/test/java/ca/uhn/fhir/parser/MultiVersionJsonParserTest.java
View File

@ -6,8 +6,8 @@ import static org.junit.Assert.fail;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu.composite.QuantityDt;
import ca.uhn.fhir.model.dstu.resource.Patient;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.resource.Patient;
public class MultiVersionJsonParserTest {
@ -16,14 +16,14 @@ public class MultiVersionJsonParserTest {
@Test
public void testEncodeExtensionFromDifferentVersion() {
Patient p = new Patient();
p.addIdentifier("urn:sys", "001");
p.addIdentifier().setSystem("urn:sys").setValue("001");
p.addUndeclaredExtension(false, "http://foo#ext", new QuantityDt(2.2));
try {
FhirContext.forDstu2().newJsonParser().encodeResourceToString(p);
FhirContext.forDstu3().newJsonParser().encodeResourceToString(p);
fail();
} catch (IllegalArgumentException e) {
assertEquals("This parser is for FHIR version DSTU2 - Can not encode a structure for version DSTU1", e.getMessage());
assertEquals("This parser is for FHIR version DSTU3 - Can not encode a structure for version DSTU2", e.getMessage());
}
}

28
hapi-fhir-base-test-mindeps-server/src/test/java/ca/uhn/fhir/parser/MultiVersionXmlParserTest.java
View File

@ -1,8 +1,6 @@
package ca.uhn.fhir.parser;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import static org.junit.Assert.*;
import org.hamcrest.Matchers;
import org.junit.AfterClass;
@ -10,16 +8,16 @@ import org.junit.Test;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu.composite.QuantityDt;
import ca.uhn.fhir.model.dstu.resource.Organization;
import ca.uhn.fhir.model.dstu.resource.Patient;
import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.resource.Organization;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.valueset.QuantityComparatorEnum;
import ca.uhn.fhir.util.TestUtil;
public class MultiVersionXmlParserTest {
private static FhirContext ourCtxDstu1 = FhirContext.forDstu1();
private static FhirContext ourCtxDstu2 = FhirContext.forDstu2();
private static FhirContext ourCtxDstu3 = FhirContext.forDstu3();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(MultiVersionXmlParserTest.class);
@ -31,11 +29,11 @@ public class MultiVersionXmlParserTest {
@Test
public void testEncodeExtensionFromDifferentVersion() {
Patient p = new Patient();
p.addIdentifier("urn:sys", "001");
p.addUndeclaredExtension(false, "http://foo#ext", new QuantityDt(QuantityCompararatorEnum.LESSTHAN, 2.2, "g/L"));
p.addIdentifier().setSystem("urn:sys").setValue("001");
p.addUndeclaredExtension(false, "http://foo#ext", new QuantityDt(QuantityComparatorEnum.LESS_THAN, 2.2, "g/L"));
String str;
str = ourCtxDstu1.newXmlParser().encodeResourceToString(p);
str = ourCtxDstu2.newXmlParser().encodeResourceToString(p);
ourLog.info(str);
assertThat(str, Matchers.stringContainsInOrder("<extension url=\"http://foo#ext\"><valueQuantity><value value=\"2.2\"", "<comparator value=\"&lt;\"", "<units value=\"g/L\"",
"</valueQuantity></extension>"));
@ -52,7 +50,7 @@ public class MultiVersionXmlParserTest {
public void testParseResourceReference() {
Organization o = new Organization();
o.getName().setValue("Some Org");
o.getNameElement().setValue("Some Org");
o.getPartOf().setDisplay("Part Of");
Patient p = new Patient();
@ -60,16 +58,16 @@ public class MultiVersionXmlParserTest {
p.getManagingOrganization().setDisplay("RR Display");
p.getManagingOrganization().setResource(o);
String res = ourCtxDstu1.newXmlParser().encodeResourceToString(p);
String res = ourCtxDstu2.newXmlParser().encodeResourceToString(p);
try {
ourCtxDstu1.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Patient.class, res);
ourCtxDstu2.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Patient.class, res);
fail();
} catch (ConfigurationException e) {
assertEquals("This context is for FHIR version \"DSTU1\" but the class \"ca.uhn.fhir.model.dstu2.resource.Patient\" is for version \"DSTU2\"", e.getMessage());
}
try {
ourCtxDstu2.newXmlParser().parseResource(ca.uhn.fhir.model.dstu.resource.Patient.class, res);
ourCtxDstu3.newXmlParser().parseResource(Patient.class, res);
fail();
} catch (ConfigurationException e) {
assertEquals("This context is for FHIR version \"DSTU2\" but the class \"ca.uhn.fhir.model.dstu.resource.Patient\" is for version \"DSTU1\"", e.getMessage());

4
hapi-fhir-base-test-mindeps-server/src/test/java/ca/uhn/fhir/testmindeps/FhirContextTest.java
View File

@ -1,12 +1,12 @@
package ca.uhn.fhir.testmindeps;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.dstu.resource.Patient;
import ca.uhn.fhir.model.dstu2.resource.Patient;
public class FhirContextTest {

31
hapi-fhir-base-test-mindeps-server/src/test/java/ca/uhn/fhir/testmindeps/ReadTest.java
View File

@ -6,28 +6,25 @@ import static org.junit.Assert.assertNotNull;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.IOUtils;
import org.apache.http.Header;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.*;
import org.mortbay.jetty.Server;
import org.mortbay.jetty.servlet.ServletHandler;
import org.mortbay.jetty.servlet.ServletHolder;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu.resource.Binary;
import ca.uhn.fhir.model.dstu.resource.Patient;
import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu2.resource.Binary;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.util.PortUtil;
@ -53,10 +50,10 @@ public class ReadTest {
assertEquals(200, status.getStatusLine().getStatusCode());
IdentifierDt dt = ourCtx.newXmlParser().parseResource(Patient.class,responseContent).getIdentifierFirstRep();
assertEquals("1", dt.getSystem().getValueAsString());
assertEquals(null, dt.getValue().getValueAsString());
assertEquals("1", dt.getSystemElement().getValueAsString());
assertEquals(null, dt.getValueElement().getValueAsString());
Header cl = status.getFirstHeader(Constants.HEADER_CONTENT_LOCATION_LC);
org.apache.http.Header cl = status.getFirstHeader(Constants.HEADER_CONTENT_LOCATION_LC);
assertNotNull(cl);
assertEquals("http://localhost:" + ourPort + "/Patient/1/_history/1", cl.getValue());
@ -77,11 +74,11 @@ public class ReadTest {
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals("application/x-foo", status.getEntity().getContentType().getValue());
Header cl = status.getFirstHeader(Constants.HEADER_CONTENT_LOCATION_LC);
org.apache.http.Header cl = status.getFirstHeader(Constants.HEADER_CONTENT_LOCATION_LC);
assertNotNull(cl);
assertEquals("http://localhost:" + ourPort + "/Binary/1/_history/1", cl.getValue());
Header cd = status.getFirstHeader("content-disposition");
org.apache.http.Header cd = status.getFirstHeader("content-disposition");
assertNotNull(cd);
assertEquals("Attachment;", cd.getValue());
@ -104,10 +101,10 @@ public class ReadTest {
assertEquals(200, status.getStatusLine().getStatusCode());
IdentifierDt dt = ourCtx.newXmlParser().parseResource(Patient.class,responseContent).getIdentifierFirstRep();
assertEquals("1", dt.getSystem().getValueAsString());
assertEquals("2", dt.getValue().getValueAsString());
assertEquals("1", dt.getSystemElement().getValueAsString());
assertEquals("2", dt.getValueElement().getValueAsString());
Header cl = status.getFirstHeader(Constants.HEADER_CONTENT_LOCATION_LC);
org.apache.http.Header cl = status.getFirstHeader(Constants.HEADER_CONTENT_LOCATION_LC);
assertNotNull(cl);
assertEquals("http://localhost:" + ourPort + "/Patient/1/_history/1", cl.getValue());
}
@ -149,7 +146,7 @@ public class ReadTest {
@Read(version = true)
public Patient findPatient(@IdParam IdDt theId) {
Patient patient = new Patient();
patient.addIdentifier(theId.getIdPart(), theId.getVersionIdPart());
patient.addIdentifier().setSystem(theId.getIdPart()).setValue(theId.getVersionIdPart());
patient.setId("Patient/1/_history/1");
return patient;
}

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

47
hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/HapiLocalizer.java
View File

@ -32,17 +32,20 @@ import java.util.ResourceBundle;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import ca.uhn.fhir.context.ConfigurationException;
/**
* This feature is not yet in its final state and should be considered an internal part of HAPI for now - use with caution
*/
public class HapiLocalizer {
public static final String UNKNOWN_I18N_KEY_MESSAGE = "!MESSAGE!";
private static boolean ourFailOnMissingMessage;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HapiLocalizer.class);
private List<ResourceBundle> myBundle = new ArrayList<ResourceBundle>();
public static final String UNKNOWN_I18N_KEY_MESSAGE = "!MESSAGE!";
private final Map<String, MessageFormat> myKeyToMessageFormat = new ConcurrentHashMap<String, MessageFormat>();
private List<ResourceBundle> myBundle = new ArrayList<ResourceBundle>();
private String[] myBundleNames;
private final Map<String, MessageFormat> myKeyToMessageFormat = new ConcurrentHashMap<String, MessageFormat>();
public HapiLocalizer() {
this(HapiLocalizer.class.getPackage().getName() + ".hapi-messages");
@ -53,12 +56,6 @@ public class HapiLocalizer {
init();
}
protected void init() {
for (String nextName : myBundleNames) {
myBundle.add(ResourceBundle.getBundle(nextName));
}
}
private String findFormatString(String theQualifiedKey) {
String formatString = null;
for (ResourceBundle nextBundle : myBundle) {
@ -72,11 +69,25 @@ public class HapiLocalizer {
if (formatString == null) {
ourLog.warn("Unknown localization key: {}", theQualifiedKey);
if (ourFailOnMissingMessage) {
throw new ConfigurationException("Unknown localization key: " + theQualifiedKey);
}
formatString = UNKNOWN_I18N_KEY_MESSAGE;
}
return formatString;
}
public Set<String> getAllKeys(){
HashSet<String> retVal = new HashSet<String>();
for (ResourceBundle nextBundle : myBundle) {
Enumeration<String> keysEnum = nextBundle.getKeys();
while (keysEnum.hasMoreElements()) {
retVal.add(keysEnum.nextElement());
}
}
return retVal;
}
public String getMessage(Class<?> theType, String theKey, Object... theParameters) {
return getMessage(theType.getName() + '.' + theKey, theParameters);
}
@ -98,15 +109,19 @@ public class HapiLocalizer {
return retVal;
}
public Set<String> getAllKeys(){
HashSet<String> retVal = new HashSet<String>();
for (ResourceBundle nextBundle : myBundle) {
Enumeration<String> keysEnum = nextBundle.getKeys();
while (keysEnum.hasMoreElements()) {
retVal.add(keysEnum.nextElement());
protected void init() {
for (String nextName : myBundleNames) {
myBundle.add(ResourceBundle.getBundle(nextName));
}
}
return retVal;
/**
* This <b>global setting</b> causes the localizer to fail if any attempts
* are made to retrieve a key that does not exist. This method is primarily for
* unit tests.
*/
public static void setOurFailOnMissingMessage(boolean ourFailOnMissingMessage) {
HapiLocalizer.ourFailOnMissingMessage = ourFailOnMissingMessage;
}
}

65
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ParameterUtil.java
View File

@ -27,14 +27,13 @@ import java.util.*;
import org.hl7.fhir.instance.model.api.IIdType;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.param.binder.QueryParameterAndBinder;
import ca.uhn.fhir.util.ReflectionUtil;
import ca.uhn.fhir.util.UrlUtil;
@ -64,6 +63,64 @@ public class ParameterUtil {
return (T) value;
}
/**
* This is a utility method intended provided to help the JPA module.
*/
public static IQueryParameterAnd<?> parseQueryParams(FhirContext theContext, RestSearchParameterTypeEnum paramType,
String theUnqualifiedParamName, List<QualifiedParamList> theParameters) {
QueryParameterAndBinder binder = null;
switch (paramType) {
case COMPOSITE:
throw new UnsupportedOperationException();
case DATE:
binder = new QueryParameterAndBinder(DateAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case NUMBER:
binder = new QueryParameterAndBinder(NumberAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case QUANTITY:
binder = new QueryParameterAndBinder(QuantityAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case REFERENCE:
binder = new QueryParameterAndBinder(ReferenceAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case STRING:
binder = new QueryParameterAndBinder(StringAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case TOKEN:
binder = new QueryParameterAndBinder(TokenAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case URI:
binder = new QueryParameterAndBinder(UriAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case HAS:
binder = new QueryParameterAndBinder(HasAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
}
// FIXME null access
return binder.parse(theContext, theUnqualifiedParamName, theParameters);
}
/**
* This is a utility method intended provided to help the JPA module.
*/
public static IQueryParameterAnd<?> parseQueryParams(FhirContext theContext, RuntimeSearchParam theParamDef,
String theUnqualifiedParamName, List<QualifiedParamList> theParameters) {
RestSearchParameterTypeEnum paramType = theParamDef.getParamType();
return parseQueryParams(theContext, paramType, theUnqualifiedParamName, theParameters);
}
/**
* Escapes a string according to the rules for parameter escaping specified in the <a href="http://www.hl7.org/implement/standards/fhir/search.html#escaping">FHIR Specification Escaping
* Section</a>

2
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/BaseBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/BaseBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.client.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L

5
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseJavaPrimitiveBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/BaseJavaPrimitiveBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.server.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L
@ -28,8 +28,7 @@ import java.util.List;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;

6
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/CalendarBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/CalendarBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.server.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L
@ -24,8 +24,8 @@ import java.util.Calendar;
import ca.uhn.fhir.model.primitive.InstantDt;
final class CalendarBinder extends BaseJavaPrimitiveBinder<Calendar> {
CalendarBinder() {
public final class CalendarBinder extends BaseJavaPrimitiveBinder<Calendar> {
public CalendarBinder() {
}
@Override

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

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.param;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L

6
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/DateBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/DateBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.server.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L
@ -24,8 +24,8 @@ import java.util.Date;
import ca.uhn.fhir.model.primitive.InstantDt;
final class DateBinder extends BaseJavaPrimitiveBinder<Date> {
DateBinder() {
public final class DateBinder extends BaseJavaPrimitiveBinder<Date> {
public DateBinder() {
}
@Override

6
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/FhirPrimitiveBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/FhirPrimitiveBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.client.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L
@ -24,11 +24,11 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.util.ReflectionUtil;
final class FhirPrimitiveBinder extends BaseJavaPrimitiveBinder<IPrimitiveType<?>> {
public final class FhirPrimitiveBinder extends BaseJavaPrimitiveBinder<IPrimitiveType<?>> {
private Class<IPrimitiveType<?>> myType;
FhirPrimitiveBinder(Class<IPrimitiveType<?>> theType) {
public FhirPrimitiveBinder(Class<IPrimitiveType<?>> theType) {
myType = theType;
}

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/IParamBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/IParamBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.server.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L
@ -28,7 +28,7 @@ import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
interface IParamBinder<T> {
public interface IParamBinder<T> {
List<IQueryParameterOr<?>> encode(FhirContext theContext, T theString) throws InternalErrorException;

10
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/QueryParameterAndBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/QueryParameterAndBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.server.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L
@ -23,16 +23,14 @@ package ca.uhn.fhir.rest.server.method;
import java.util.List;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
final class QueryParameterAndBinder extends BaseBinder<IQueryParameterAnd<?>> implements IParamBinder<IQueryParameterAnd<?>> {
public final class QueryParameterAndBinder extends BaseBinder<IQueryParameterAnd<?>> implements IParamBinder<IQueryParameterAnd<?>> {
QueryParameterAndBinder(Class<? extends IQueryParameterAnd<?>> theType, List<Class<? extends IQueryParameterType>> theCompositeTypes) {
public QueryParameterAndBinder(Class<? extends IQueryParameterAnd<?>> theType, List<Class<? extends IQueryParameterType>> theCompositeTypes) {
super(theType, theCompositeTypes);
}

6
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/QueryParameterOrBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/QueryParameterOrBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.client.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L
@ -30,9 +30,9 @@ import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
final class QueryParameterOrBinder extends BaseBinder<IQueryParameterOr<?>> implements IParamBinder<IQueryParameterOr<?>> {
public final class QueryParameterOrBinder extends BaseBinder<IQueryParameterOr<?>> implements IParamBinder<IQueryParameterOr<?>> {
QueryParameterOrBinder(Class<? extends IQueryParameterOr<?>> theType, List<Class<? extends IQueryParameterType>> theCompositeTypes) {
public QueryParameterOrBinder(Class<? extends IQueryParameterOr<?>> theType, List<Class<? extends IQueryParameterType>> theCompositeTypes) {
super(theType, theCompositeTypes);
}

6
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/QueryParameterTypeBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/QueryParameterTypeBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.client.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L
@ -33,9 +33,9 @@ import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
final class QueryParameterTypeBinder extends BaseBinder<IQueryParameterType> implements IParamBinder<IQueryParameterType> {
public final class QueryParameterTypeBinder extends BaseBinder<IQueryParameterType> implements IParamBinder<IQueryParameterType> {
QueryParameterTypeBinder(Class<? extends IQueryParameterType> theType, List<Class<? extends IQueryParameterType>> theCompositeTypes) {
public QueryParameterTypeBinder(Class<? extends IQueryParameterType> theType, List<Class<? extends IQueryParameterType>> theCompositeTypes) {
super(theType, theCompositeTypes);
}

6
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/StringBinder.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/binder/StringBinder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.rest.client.method;
package ca.uhn.fhir.rest.param.binder;
/*
* #%L
@ -20,8 +20,8 @@ package ca.uhn.fhir.rest.client.method;
* #L%
*/
final class StringBinder extends BaseJavaPrimitiveBinder<String> {
StringBinder() {
public final class StringBinder extends BaseJavaPrimitiveBinder<String> {
public StringBinder() {
}
@Override

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

@ -157,7 +157,8 @@ public class ReflectionUtil {
if (fhirServerVersion == null) {
try {
Class<?> type = Class.forName(theType);
Validate.isTrue(IFhirVersion.class.isAssignableFrom(type));
Class<?> serverType = Class.forName("ca.uhn.fhir.rest.api.server.IFhirVersionServer");
Validate.isTrue(serverType.isAssignableFrom(type));
fhirServerVersion = type.newInstance();
} catch (Exception e) {
throw new ConfigurationException("Unable to instantiate server framework. Please make sure that hapi-fhir-server library is on your classpath!", e);

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

@ -29,6 +29,7 @@ import java.util.TimeZone;
import org.slf4j.LoggerFactory;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.HapiLocalizer;
import ch.qos.logback.classic.Level;
import ch.qos.logback.classic.Logger;
import ch.qos.logback.classic.LoggerContext;
@ -44,6 +45,7 @@ public class TestUtil {
* static fields seems to solve this.
*/
public static void clearAllStaticFieldsForUnitTest() {
HapiLocalizer.setOurFailOnMissingMessage(true);
Class<?> theType;
try {

52
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -8,41 +8,41 @@ ca.uhn.fhir.context.FhirContext.noStructuresForSpecifiedVersion=Could not find t
ca.uhn.fhir.context.RuntimeResourceDefinition.nonInstantiableType=Resource type "{0}" can not be instantiated. Check that this class has a no-argument constructor, and that it is static if it is a nested type. Error is: {1}
ca.uhn.fhir.context.RuntimeResourceDefinition.typeWrongVersion=This context is for FHIR version "{0}" but the class "{1}" is for version "{2}"
ca.uhn.fhir.rest.client.BaseClient.ioExceptionDuringOperation=Encountered IOException when performing {0} to URL {1} - {2}
ca.uhn.fhir.rest.client.BaseClient.failedToParseResponse=Failed to parse response from server when performing {0} to URL {1} - {2}
ca.uhn.fhir.rest.client.impl.BaseClient.ioExceptionDuringOperation=Encountered IOException when performing {0} to URL {1} - {2}
ca.uhn.fhir.rest.client.impl.BaseClient.failedToParseResponse=Failed to parse response from server when performing {0} to URL {1} - {2}
ca.uhn.fhir.rest.client.GenericClient.cantDetermineRequestType=Unable to determing encoding of request (body does not appear to be valid XML or JSON)
ca.uhn.fhir.rest.client.GenericClient.noPagingLinkFoundInBundle=Can not perform paging operation because no link was found in Bundle with relation "{0}"
ca.uhn.fhir.rest.client.GenericClient.noVersionIdForVread=No version specified in URL for 'vread' operation: {0}
ca.uhn.fhir.rest.client.GenericClient.incompleteUriForRead=The given URI is not an absolute URL and is not usable for this operation: {0}
ca.uhn.fhir.rest.client.GenericClient.cannotDetermineResourceTypeFromUri=Unable to determine the resource type from the given URI: {0}
ca.uhn.fhir.rest.client.RestfulClientFactory.failedToRetrieveConformance=Failed to retrieve the server metadata statement during client initialization. URL used was {0}
ca.uhn.fhir.rest.client.RestfulClientFactory.wrongVersionInConformance=The server at base URL "{0}" returned a conformance statement indicating that it supports FHIR version "{1}" which corresponds to {2}, but this client is configured to use {3} (via the FhirContext).
ca.uhn.fhir.rest.client.impl.GenericClient.cantDetermineRequestType=Unable to determing encoding of request (body does not appear to be valid XML or JSON)
ca.uhn.fhir.rest.client.impl.GenericClient.noPagingLinkFoundInBundle=Can not perform paging operation because no link was found in Bundle with relation "{0}"
ca.uhn.fhir.rest.client.impl.GenericClient.noVersionIdForVread=No version specified in URL for 'vread' operation: {0}
ca.uhn.fhir.rest.client.impl.GenericClient.incompleteUriForRead=The given URI is not an absolute URL and is not usable for this operation: {0}
ca.uhn.fhir.rest.client.impl.GenericClient.cannotDetermineResourceTypeFromUri=Unable to determine the resource type from the given URI: {0}
ca.uhn.fhir.rest.client.impl.RestfulClientFactory.failedToRetrieveConformance=Failed to retrieve the server metadata statement during client initialization. URL used was {0}
ca.uhn.fhir.rest.client.impl.RestfulClientFactory.wrongVersionInConformance=The server at base URL "{0}" returned a conformance statement indicating that it supports FHIR version "{1}" which corresponds to {2}, but this client is configured to use {3} (via the FhirContext).
ca.uhn.fhir.rest.method.BaseOutcomeReturningMethodBindingWithResourceParam.incorrectIdForUpdate=Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of "{0}" does not match URL ID of "{1}"
ca.uhn.fhir.rest.method.BaseOutcomeReturningMethodBindingWithResourceParam.noIdInBodyForUpdate=Can not update resource, resource body must contain an ID element for update (PUT) operation
ca.uhn.fhir.rest.method.BaseOutcomeReturningMethodBindingWithResourceParam.noIdInUrlForUpdate=Can not update resource, request URL must contain an ID element for update (PUT) operation (it must be of the form [base]/[resource type]/[id])
ca.uhn.fhir.rest.method.BaseOutcomeReturningMethodBindingWithResourceParam.idInUrlForCreate=Can not create resource with ID "{0}", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)
ca.uhn.fhir.rest.method.BaseOutcomeReturningMethodBindingWithResourceParam.idInBodyForCreate=Can not create resource with ID "{0}", an ID element must not be supplied in the resource body on a create (POST) operation
ca.uhn.fhir.rest.server.method.BaseOutcomeReturningMethodBindingWithResourceParam.incorrectIdForUpdate=Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of "{0}" does not match URL ID of "{1}"
ca.uhn.fhir.rest.server.method.BaseOutcomeReturningMethodBindingWithResourceParam.noIdInBodyForUpdate=Can not update resource, resource body must contain an ID element for update (PUT) operation
ca.uhn.fhir.rest.server.method.BaseOutcomeReturningMethodBindingWithResourceParam.noIdInUrlForUpdate=Can not update resource, request URL must contain an ID element for update (PUT) operation (it must be of the form [base]/[resource type]/[id])
ca.uhn.fhir.rest.server.method.BaseOutcomeReturningMethodBindingWithResourceParam.idInUrlForCreate=Can not create resource with ID "{0}", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)
ca.uhn.fhir.rest.server.method.BaseOutcomeReturningMethodBindingWithResourceParam.idInBodyForCreate=Can not create resource with ID "{0}", an ID element must not be supplied in the resource body on a create (POST) operation
ca.uhn.fhir.rest.method.OperationMethodBinding.methodNotSupported=HTTP Method {0} is not allowed for this operation. Allowed method(s): {1}
ca.uhn.fhir.rest.method.OperationParameter.urlParamNotPrimitive=Can not invoke operation {0} using HTTP GET because parameter {1} is not a primitive datatype
ca.uhn.fhir.rest.method.IncludeParameter.invalidIncludeNameInRequest=Invalid {2} parameter value: "{0}". Valid values are: {1}
ca.uhn.fhir.rest.method.IncludeParameter.orIncludeInRequest='OR' query parameters (values containing ',') are not supported in _include parameters
ca.uhn.fhir.rest.server.method.OperationMethodBinding.methodNotSupported=HTTP Method {0} is not allowed for this operation. Allowed method(s): {1}
ca.uhn.fhir.rest.server.method.OperationParameter.urlParamNotPrimitive=Can not invoke operation {0} using HTTP GET because parameter {1} is not a primitive datatype
ca.uhn.fhir.rest.server.method.IncludeParameter.invalidIncludeNameInRequest=Invalid {2} parameter value: "{0}". Valid values are: {1}
ca.uhn.fhir.rest.server.method.IncludeParameter.orIncludeInRequest='OR' query parameters (values containing ',') are not supported in _include parameters
ca.uhn.fhir.rest.method.PageMethodBinding.unknownSearchId=Search ID "{0}" does not exist and may have expired
ca.uhn.fhir.rest.server.method.PageMethodBinding.unknownSearchId=Search ID "{0}" does not exist and may have expired
ca.uhn.fhir.rest.method.SearchMethodBinding.invalidSpecialParamName=Method [{0}] in provider [{1}] contains search parameter annotated to use name [{2}] - This name is reserved according to the FHIR specification and can not be used as a search parameter name.
ca.uhn.fhir.rest.method.SearchMethodBinding.idWithoutCompartment=Method [{0}] in provider [{1}] has an @IdParam parameter. This is only allowable for compartment search (e.g. @Search(compartment="foo") )
ca.uhn.fhir.rest.method.SearchMethodBinding.idNullForCompartmentSearch=ID parameter can not be null or empty for compartment search
ca.uhn.fhir.rest.server.method.SearchMethodBinding.invalidSpecialParamName=Method [{0}] in provider [{1}] contains search parameter annotated to use name [{2}] - This name is reserved according to the FHIR specification and can not be used as a search parameter name.
ca.uhn.fhir.rest.server.method.SearchMethodBinding.idWithoutCompartment=Method [{0}] in provider [{1}] has an @IdParam parameter. This is only allowable for compartment search (e.g. @Search(compartment="foo") )
ca.uhn.fhir.rest.server.method.SearchMethodBinding.idNullForCompartmentSearch=ID parameter can not be null or empty for compartment search
ca.uhn.fhir.rest.method.SummaryEnumParameter.cantCombineText=Can not combine _summary=text with other values for _summary
ca.uhn.fhir.rest.server.method.SummaryEnumParameter.cantCombineText=Can not combine _summary=text with other values for _summary
ca.uhn.fhir.rest.param.BaseParam.chainNotSupported=Invalid search parameter "{0}". Parameter contains a chain ({1}) and chains are not supported for this parameter (chaining is only allowed on reference parameters)
ca.uhn.fhir.rest.param.ResourceParameter.invalidContentTypeInRequest=Incorrect Content-Type header value of "{0}" was provided in the request. A FHIR Content-Type is required for "{1}" operation
ca.uhn.fhir.rest.param.ResourceParameter.noContentTypeInRequest=No Content-Type header was provided in the request. This is required for "{0}" operation
ca.uhn.fhir.rest.param.ResourceParameter.failedToParseRequest=Failed to parse request body as {0} resource. Error was: {1}
ca.uhn.fhir.rest.server.method.ResourceParameter.invalidContentTypeInRequest=Incorrect Content-Type header value of "{0}" was provided in the request. A FHIR Content-Type is required for "{1}" operation
ca.uhn.fhir.rest.server.method.ResourceParameter.noContentTypeInRequest=No Content-Type header was provided in the request. This is required for "{0}" operation
ca.uhn.fhir.rest.server.method.ResourceParameter.failedToParseRequest=Failed to parse request body as {0} resource. Error was: {1}
ca.uhn.fhir.parser.ParserState.wrongResourceTypeFound=Incorrect resource type found, expected "{0}" but found "{1}"
ca.uhn.fhir.rest.server.RestfulServer.getPagesNonHttpGet=Requests for _getpages must use HTTP GET

7
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>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -23,6 +23,11 @@
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli-jpaserver</artifactId>

7
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/BaseCommand.java
View File

@ -1,13 +1,10 @@
package ca.uhn.fhir.cli;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
public abstract class BaseCommand implements Comparable<BaseCommand> {

39
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ExampleDataUploader.java
View File

@ -3,29 +3,13 @@ package ca.uhn.fhir.cli;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.BufferedInputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.io.*;
import java.util.*;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.BooleanUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.cli.*;
import org.apache.commons.io.*;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
@ -34,18 +18,11 @@ import org.apache.http.impl.client.HttpClientBuilder;
import org.fusesource.jansi.Ansi;
import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.*;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
@ -54,9 +31,9 @@ import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.valueset.BundleTypeEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.api.IVersionSpecificBundleFactory;
import ca.uhn.fhir.rest.client.apache.GZipContentInterceptor;
import ca.uhn.fhir.rest.server.IVersionSpecificBundleFactory;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.ResourceReferenceInfo;

4
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu2.java
View File

@ -7,8 +7,8 @@ import org.hl7.fhir.instance.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
public class LoadingValidationSupportDstu2 implements IValidationSupport {

4
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu3.java
View File

@ -11,8 +11,8 @@ import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
public class LoadingValidationSupportDstu3 implements IValidationSupport {

11
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
View File

@ -3,19 +3,14 @@ package ca.uhn.fhir.cli;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.apache.commons.cli.*;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.BearerTokenAuthInterceptor;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;

31
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ValidateCommand.java
View File

@ -1,39 +1,22 @@
package ca.uhn.fhir.cli;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.leftPad;
import static org.apache.commons.lang3.StringUtils.*;
import static org.fusesource.jansi.Ansi.ansi;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.*;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionGroup;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.text.WordUtils;
import org.fusesource.jansi.Ansi.Color;
import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.dstu3.hapi.validation.*;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.instance.model.api.IBaseResource;
import com.phloc.commons.io.file.FileUtils;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.method.MethodUtil;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationResult;
import ca.uhn.fhir.validation.*;
public class ValidateCommand extends BaseCommand {
@ -89,7 +72,7 @@ public class ValidateCommand extends BaseCommand {
ourLog.info("Fully read - Size is {}", FileUtils.getFileSizeDisplay(contents.length()));
}
EncodingEnum enc = MethodUtil.detectEncodingNoDefault(defaultString(contents));
ca.uhn.fhir.rest.api.EncodingEnum enc = ca.uhn.fhir.rest.api.EncodingEnum.detectEncodingNoDefault(defaultString(contents));
if (enc == null) {
throw new ParseException("Could not detect encoding (json/xml) of contents");
}
@ -108,7 +91,7 @@ public class ValidateCommand extends BaseCommand {
throw new ParseException("Failed to load file '" + localProfile + "' - Error: " + e.toString());
}
localProfileResource = MethodUtil.detectEncodingNoDefault(input).newParser(ctx).parseResource(input);
localProfileResource = ca.uhn.fhir.rest.api.EncodingEnum.detectEncodingNoDefault(input).newParser(ctx).parseResource(input);
}
if (theCommandLine.hasOption("p")) {

11
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ValidationDataUploader.java
View File

@ -6,10 +6,7 @@ import java.io.IOException;
import java.util.Collections;
import java.util.Comparator;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.CapabilityStatement;
@ -21,11 +18,9 @@ import org.springframework.core.io.support.ResourcePatternResolver;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.*;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.model.dstu2.resource.StructureDefinition;
import ca.uhn.fhir.model.dstu2.resource.ValueSet;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
public class ValidationDataUploader extends BaseCommand {

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

32
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java
View File

@ -1,13 +1,9 @@
package ca.uhn.fhir.jpa.demo;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.*;
import javax.servlet.ServletException;
import org.hl7.fhir.dstu3.model.Meta;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.web.cors.CorsConfiguration;
@ -16,22 +12,14 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu1;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.jpa.provider.dstu3.*;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.*;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
@ -80,9 +68,7 @@ public class JpaServerDemo extends RestfulServer {
* transaction, and global history.
*/
List<Object> systemProvider = new ArrayList<Object>();
if (fhirVersion == FhirVersionEnum.DSTU1) {
systemProvider.add(myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class));
} else if (fhirVersion == FhirVersionEnum.DSTU2) {
if (fhirVersion == FhirVersionEnum.DSTU2) {
systemProvider.add(myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class));
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
systemProvider.add(myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class));
@ -97,13 +83,7 @@ public class JpaServerDemo extends RestfulServer {
* this server. The JPA version adds resource counts to the exported statement, so it
* is a nice addition.
*/
if (fhirVersion == FhirVersionEnum.DSTU1) {
IFhirSystemDao<List<IResource>, MetaDt> systemDao = myAppCtx.getBean("mySystemDaoDstu1",
IFhirSystemDao.class);
JpaConformanceProviderDstu1 confProvider = new JpaConformanceProviderDstu1(this, systemDao);
confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.DSTU2) {
if (fhirVersion == FhirVersionEnum.DSTU2) {
IFhirSystemDao<Bundle, MetaDt> systemDao = myAppCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao,
myAppCtx.getBean(DaoConfig.class));

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-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>2.6-SNAPSHOT</version>
<version>3.0.0-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>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

6
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/GenericClient.java
View File

@ -169,9 +169,9 @@ import ca.uhn.fhir.util.UrlUtil;
*/
public class GenericClient extends BaseClient implements IGenericClient {
private static final String I18N_CANNOT_DETEMINE_RESOURCE_TYPE = "ca.uhn.fhir.rest.client.GenericClient.cannotDetermineResourceTypeFromUri";
private static final String I18N_INCOMPLETE_URI_FOR_READ = "ca.uhn.fhir.rest.client.GenericClient.incompleteUriForRead";
private static final String I18N_NO_VERSION_ID_FOR_VREAD = "ca.uhn.fhir.rest.client.GenericClient.noVersionIdForVread";
private static final String I18N_CANNOT_DETEMINE_RESOURCE_TYPE = GenericClient.class.getName() + ".cannotDetermineResourceTypeFromUri";
private static final String I18N_INCOMPLETE_URI_FOR_READ = GenericClient.class.getName() + ".incompleteUriForRead";
private static final String I18N_NO_VERSION_ID_FOR_VREAD = GenericClient.class.getName() + ".noVersionIdForVread";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(GenericClient.class);
private FhirContext myContext;
private IHttpRequest myLastRequest;

70
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/BaseJavaPrimitiveBinder.java
View File

@ -1,70 +0,0 @@
package ca.uhn.fhir.rest.client.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.util.Collections;
import java.util.List;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
abstract class BaseJavaPrimitiveBinder<T>implements IParamBinder<T> {
public BaseJavaPrimitiveBinder() {
super();
}
protected abstract String doEncode(T theString);
protected abstract T doParse(String theString);
@SuppressWarnings("unchecked")
@Override
public List<IQueryParameterOr<?>> encode(FhirContext theContext, T theString) throws InternalErrorException {
String retVal = doEncode(theString);
if (isBlank(retVal)) {
return Collections.emptyList();
}
List<?> retValList = Collections.singletonList(ParameterUtil.singleton(new StringParam(retVal), null));
return (List<IQueryParameterOr<?>>) retValList;
}
@Override
public T parse(FhirContext theContext, String theName, List<QualifiedParamList> theParams) throws InternalErrorException, InvalidRequestException {
if (theParams.size() == 0 || theParams.get(0).size() == 0) {
return null;
}
if (theParams.size() > 1 || theParams.get(0).size() > 1) {
throw new InvalidRequestException("Multiple values detected for non-repeatable parameter '" + theName + "'. This server is not configured to allow multiple (AND) values for this param.");
}
T value = doParse(theParams.get(0).get(0));
return value;
}
}

42
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/CalendarBinder.java
View File

@ -1,42 +0,0 @@
package ca.uhn.fhir.rest.client.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Calendar;
import ca.uhn.fhir.model.primitive.InstantDt;
final class CalendarBinder extends BaseJavaPrimitiveBinder<Calendar> {
CalendarBinder() {
}
@Override
protected String doEncode(Calendar theString) {
return new InstantDt(theString).getValueAsString();
}
@Override
protected Calendar doParse(String theString) {
return new InstantDt(theString).getValueAsCalendar();
}
}

42
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/DateBinder.java
View File

@ -1,42 +0,0 @@
package ca.uhn.fhir.rest.client.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Date;
import ca.uhn.fhir.model.primitive.InstantDt;
final class DateBinder extends BaseJavaPrimitiveBinder<Date> {
DateBinder() {
}
@Override
protected String doEncode(Date theString) {
return new InstantDt(theString).getValueAsString();
}
@Override
protected Date doParse(String theString) {
return new InstantDt(theString).getValue();
}
}

37
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/IParamBinder.java
View File

@ -1,37 +0,0 @@
package ca.uhn.fhir.rest.client.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.List;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
interface IParamBinder<T> {
List<IQueryParameterOr<?>> encode(FhirContext theContext, T theString) throws InternalErrorException;
T parse(FhirContext theContext, String theName, List<QualifiedParamList> theList) throws InternalErrorException, InvalidRequestException;
}

60
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/MethodUtil.java
View File

@ -22,7 +22,8 @@ import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.impl.BaseHttpClientInvocation;
import ca.uhn.fhir.rest.client.method.OperationParameter.IOperationParamConverter;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.param.binder.CollectionBinder;
import ca.uhn.fhir.util.*;
/*
@ -533,62 +534,6 @@ public class MethodUtil {
}
}
/**
* This is a utility method intended provided to help the JPA module.
*/
public static IQueryParameterAnd<?> parseQueryParams(FhirContext theContext, RuntimeSearchParam theParamDef,
String theUnqualifiedParamName, List<QualifiedParamList> theParameters) {
RestSearchParameterTypeEnum paramType = theParamDef.getParamType();
return parseQueryParams(theContext, paramType, theUnqualifiedParamName, theParameters);
}
/**
* This is a utility method intended provided to help the JPA module.
*/
public static IQueryParameterAnd<?> parseQueryParams(FhirContext theContext, RestSearchParameterTypeEnum paramType,
String theUnqualifiedParamName, List<QualifiedParamList> theParameters) {
QueryParameterAndBinder binder = null;
switch (paramType) {
case COMPOSITE:
throw new UnsupportedOperationException();
case DATE:
binder = new QueryParameterAndBinder(DateAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case NUMBER:
binder = new QueryParameterAndBinder(NumberAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case QUANTITY:
binder = new QueryParameterAndBinder(QuantityAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case REFERENCE:
binder = new QueryParameterAndBinder(ReferenceAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case STRING:
binder = new QueryParameterAndBinder(StringAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case TOKEN:
binder = new QueryParameterAndBinder(TokenAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case URI:
binder = new QueryParameterAndBinder(UriAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
case HAS:
binder = new QueryParameterAndBinder(HasAndListParam.class,
Collections.<Class<? extends IQueryParameterType>> emptyList());
break;
}
// FIXME null access
return binder.parse(theContext, theUnqualifiedParamName, theParameters);
}
public static MethodOutcome process2xxResponse(FhirContext theContext, int theResponseStatusCode,
String theResponseMimeType, Reader theResponseReader, Map<String, List<String>> theHeaders) {
List<String> locationHeaders = new ArrayList<String>();
@ -642,7 +587,6 @@ public class MethodUtil {
return retVal;
}
public static void addAcceptHeaderToRequest(EncodingEnum theEncoding, IHttpRequest theHttpRequest,
FhirContext theContext) {
if (theEncoding == null) {

57
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/QueryParameterAndBinder.java
View File

@ -1,57 +0,0 @@
package ca.uhn.fhir.rest.client.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.List;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
final class QueryParameterAndBinder extends BaseBinder<IQueryParameterAnd<?>> implements IParamBinder<IQueryParameterAnd<?>> {
QueryParameterAndBinder(Class<? extends IQueryParameterAnd<?>> theType, List<Class<? extends IQueryParameterType>> theCompositeTypes) {
super(theType, theCompositeTypes);
}
@SuppressWarnings("unchecked")
@Override
public List<IQueryParameterOr<?>> encode(FhirContext theContext, IQueryParameterAnd<?> theString) throws InternalErrorException {
List<IQueryParameterOr<?>> retVal = (List<IQueryParameterOr<?>>) ((IQueryParameterAnd<?>) theString).getValuesAsQueryTokens();
return retVal;
}
@Override
public IQueryParameterAnd<?> parse(FhirContext theContext, String theParamName, List<QualifiedParamList> theString) throws InternalErrorException, InvalidRequestException {
IQueryParameterAnd<?> dt;
try {
dt = newInstance();
dt.setValuesAsQueryTokens(theContext, theParamName, theString);
} catch (SecurityException e) {
throw new InternalErrorException(e);
}
return dt;
}
}

3
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/ResourceParameter.java
View File

@ -20,9 +20,10 @@ public class ResourceParameter implements IParameter {
*/
@SuppressWarnings("unchecked")
public ResourceParameter(Class<?> theParameterType) {
Validate.isTrue(IBaseResource.class.isAssignableFrom(theParameterType));
if (IBaseResource.class.isAssignableFrom(theParameterType)) {
myResourceType = (Class<? extends IBaseResource>) theParameterType;
}
}
@Override
public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {

1
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/SearchParameter.java
View File

@ -33,6 +33,7 @@ import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.param.binder.*;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.CollectionUtil;

14
hapi-fhir-converter/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -26,36 +26,36 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<optional>true</optional>
</dependency>
</dependencies>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-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>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>2.6-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

87
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu1Config.java
View File

@ -1,87 +0,0 @@
package ca.uhn.fhir.jpa.config;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.List;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
import ca.uhn.fhir.jpa.dao.SearchParamExtractorDstu1;
import ca.uhn.fhir.jpa.dao.SearchParamRegistryDstu1;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu1;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
@Configuration
public class BaseDstu1Config extends BaseConfig {
private static FhirContext ourFhirContextDstu1;
@Bean
@Primary
public FhirContext defaultFhirContext() {
return fhirContextDstu1();
}
@Bean(name = "myFhirContextDstu1")
@Lazy
public FhirContext fhirContextDstu1() {
if (ourFhirContextDstu1 == null) {
ourFhirContextDstu1 = FhirContext.forDstu1();
}
return ourFhirContextDstu1;
}
@Bean(name = "mySystemDaoDstu1", autowire = Autowire.BY_NAME)
public ca.uhn.fhir.jpa.dao.IFhirSystemDao<List<IResource>, MetaDt> fhirSystemDaoDstu1() {
ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu1 retVal = new ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu1();
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public SearchParamExtractorDstu1 searchParamExtractor() {
return new SearchParamExtractorDstu1();
}
@Bean
public ISearchParamRegistry searchParamRegistry() {
return new SearchParamRegistryDstu1();
}
@Bean(name = "mySystemProviderDstu1")
public ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1 systemDaoDstu1() {
ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1 retVal = new ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1();
retVal.setDao(fhirSystemDaoDstu1());
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvc terminologyService() {
return new HapiTerminologySvcDstu1();
}
}

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

@ -1952,7 +1952,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
}
if (Constants.PARAM_HAS.equals(nextParamName)) {
IQueryParameterAnd<?> param = ca.uhn.fhir.rest.client.method.MethodUtil.parseQueryParams(theContext, RestSearchParameterTypeEnum.HAS, nextParamName, paramList);
IQueryParameterAnd<?> param = ParameterUtil.parseQueryParams(theContext, RestSearchParameterTypeEnum.HAS, nextParamName, paramList);
paramMap.add(nextParamName, param);
continue;
}
@ -1985,7 +1985,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
"Failed to parse match URL[" + theMatchUrl + "] - Resource type " + resourceDef.getName() + " does not have a parameter with name: " + nextParamName);
}
IQueryParameterAnd<?> param = ca.uhn.fhir.rest.client.method.MethodUtil.parseQueryParams(theContext, paramDef, nextParamName, paramList);
IQueryParameterAnd<?> param = ParameterUtil.parseQueryParams(theContext, paramDef, nextParamName, paramList);
paramMap.add(nextParamName, param);
}
}

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -23,7 +23,6 @@ package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.*;
import java.util.Map.Entry;
import javax.annotation.PostConstruct;
import javax.persistence.NoResultException;
@ -38,38 +37,29 @@ import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.interceptor.IJpaServerInterceptor;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.DeleteConflict;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.*;
import ca.uhn.fhir.rest.method.SearchMethodBinding.QualifierDetails;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.param.QualifierDetails;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerOperationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.OperationOutcomeUtil;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import ca.uhn.fhir.rest.server.interceptor.IServerOperationInterceptor;
import ca.uhn.fhir.rest.server.method.MethodUtil;
import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
import ca.uhn.fhir.util.*;
@Transactional(propagation = Propagation.REQUIRED)
public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends BaseHapiFhirDao<T> implements IFhirResourceDao<T> {
@ -1070,7 +1060,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
if (isNotBlank(nextValue)) {
QualifiedParamList qualifiedParam = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifiedParamName.getWholeQualifier(), nextValue);
List<QualifiedParamList> paramList = Collections.singletonList(qualifiedParam);
IQueryParameterAnd<?> parsedParam = MethodUtil.parseQueryParams(getContext(), paramDef, nextParamName, paramList);
IQueryParameterAnd<?> parsedParam = ParameterUtil.parseQueryParams(getContext(), paramDef, nextParamName, paramList);
theTarget.add(qualifiedParamName.getParamName(), parsedParam);
}
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
View File

@ -24,16 +24,11 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
import java.util.*;
import java.util.concurrent.locks.ReentrantLock;
import javax.persistence.Query;
import javax.persistence.Tuple;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Root;
import javax.persistence.*;
import javax.persistence.criteria.*;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.annotation.Propagation;
@ -50,8 +45,8 @@ import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;

71
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu1.java
View File

@ -1,71 +0,0 @@
package ca.uhn.fhir.jpa.dao;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.dstu.resource.OperationOutcome;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.util.FhirTerser;
public class FhirResourceDaoDstu1<T extends IResource> extends BaseHapiFhirResourceDao<T> {
@Override
protected List<Object> getIncludeValues(FhirTerser t, Include next, IBaseResource nextResource, RuntimeResourceDefinition def) {
List<Object> values;
if ("*".equals(next.getValue())) {
values = new ArrayList<Object>();
values.addAll(t.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class));
} else if (next.getValue().startsWith(def.getName() + ".")) {
values = t.getValues(nextResource, next.getValue());
} else {
values = Collections.emptyList();
}
return values;
}
@Override
public MethodOutcome validate(T theResource, IIdType theId, String theRawResource, EncodingEnum theEncoding, ValidationModeEnum theMode, String theProfile, RequestDetails theRequestDetails) {
throw new UnsupportedOperationException();
}
@Override
protected IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode) {
OperationOutcome oo = new OperationOutcome();
oo.getIssueFirstRep().getSeverityElement().setValue(theSeverity);
oo.getIssueFirstRep().getDetailsElement().setValue(theMessage);
return oo;
}
}

41
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2.java
View File

@ -1,43 +1,30 @@
package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.*;
import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.instance.model.api.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.util.DeleteConflict;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
import ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ValidationResult;
import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import ca.uhn.fhir.validation.*;
/*
* #%L

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoEncounterDstu2.java
View File

@ -31,9 +31,9 @@ import ca.uhn.fhir.jpa.dao.SearchParameterMap.EverythingModeEnum;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.Encounter;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
public class FhirResourceDaoEncounterDstu2 extends FhirResourceDaoDstu2<Encounter>implements IFhirResourceDaoEncounter<Encounter> {
@ -52,7 +52,7 @@ public class FhirResourceDaoEncounterDstu2 extends FhirResourceDaoDstu2<Encounte
if (theId != null) {
paramMap.add("_id", new StringParam(theId.getIdPart()));
}
ca.uhn.fhir.rest.server.IBundleProvider retVal = search(paramMap);
IBundleProvider retVal = search(paramMap);
return retVal;
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoPatientDstu2.java
View File

@ -30,14 +30,10 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.jpa.dao.SearchParameterMap.EverythingModeEnum;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>implements IFhirResourceDaoPatient<Patient> {

25
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java
View File

@ -22,14 +22,10 @@ package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.*;
import javax.persistence.Query;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionChannelTypeEnum;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -37,9 +33,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.scheduling.annotation.Scheduled;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.*;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallback;
@ -48,23 +42,18 @@ import org.springframework.transaction.support.TransactionTemplate;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.data.ISubscriptionFlaggedResourceDataDao;
import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.SubscriptionFlaggedResource;
import ca.uhn.fhir.jpa.entity.SubscriptionTable;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.dstu2.resource.Subscription;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionChannelTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
public class FhirResourceDaoSubscriptionDstu2 extends FhirResourceDaoDstu2<Subscription> implements IFhirResourceDaoSubscription<Subscription> {

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
View File

@ -23,10 +23,7 @@ package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import java.util.*;
import javax.annotation.PostConstruct;
@ -43,16 +40,13 @@ import ca.uhn.fhir.jpa.entity.BaseHasResource;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.resource.ValueSet;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.ComposeInclude;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.ComposeIncludeConcept;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.ExpansionContains;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.*;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;

294
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu1.java
View File

@ -1,294 +0,0 @@
package ca.uhn.fhir.jpa.dao;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.jpa.entity.BaseHasResource;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.dstu.resource.OperationOutcome;
import ca.uhn.fhir.model.dstu.valueset.IssueSeverityEnum;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.FhirTerser;
public class FhirSystemDaoDstu1 extends BaseHapiFhirSystemDao<List<IResource>, MetaDt> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu1.class);
@Override
public MetaDt metaGetOperation(RequestDetails theRequestDetails) {
throw new NotImplementedOperationException("meta not supported in DSTU1");
}
@Transactional(propagation = Propagation.REQUIRED)
@Override
public List<IResource> transaction(RequestDetails theRequestDetails, List<IResource> theResources) {
ourLog.info("Beginning transaction with {} resources", theResources.size());
// Notify interceptors
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails);
notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);
long start = System.currentTimeMillis();
Set<IdDt> allIds = new HashSet<IdDt>();
for (int i = 0; i < theResources.size(); i++) {
IResource res = theResources.get(i);
if (res.getId().hasIdPart() && !res.getId().hasResourceType() && !isPlaceholder(res.getId())) {
res.setId(new IdDt(toResourceName(res.getClass()), res.getId().getIdPart()));
}
/*
* Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
*/
if (isPlaceholder(res.getId())) {
if (!allIds.add(res.getId())) {
throw new InvalidRequestException("Transaction bundle contains multiple resources with ID: " + res.getId());
}
} else if (res.getId().hasResourceType() && res.getId().hasIdPart()) {
IdDt nextId = res.getId().toUnqualifiedVersionless();
if (!allIds.add(nextId)) {
throw new InvalidRequestException("Transaction bundle contains multiple resources with ID: " + nextId);
}
}
}
FhirTerser terser = getContext().newTerser();
int creations = 0;
int updates = 0;
Map<IdDt, IdDt> idConversions = new HashMap<IdDt, IdDt>();
List<ResourceTable> persistedResources = new ArrayList<ResourceTable>();
List<IResource> retVal = new ArrayList<IResource>();
OperationOutcome oo = new OperationOutcome();
retVal.add(oo);
Date updateTime = new Date();
for (int resourceIdx = 0; resourceIdx < theResources.size(); resourceIdx++) {
IResource nextResource = theResources.get(resourceIdx);
IdDt nextId = nextResource.getId();
if (nextId == null) {
nextId = new IdDt();
}
String resourceName = toResourceName(nextResource);
BundleEntryTransactionMethodEnum nextResouceOperationIn = ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get(nextResource);
if (nextResouceOperationIn == null && hasValue(ResourceMetadataKeyEnum.DELETED_AT.get(nextResource))) {
nextResouceOperationIn = BundleEntryTransactionMethodEnum.DELETE;
}
String matchUrl = ResourceMetadataKeyEnum.LINK_SEARCH.get(nextResource);
Set<Long> candidateMatches = null;
if (StringUtils.isNotBlank(matchUrl)) {
candidateMatches = processMatchUrl(matchUrl, nextResource.getClass());
}
ResourceTable entity;
if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.POST) {
entity = null;
} else if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.PUT || nextResouceOperationIn == BundleEntryTransactionMethodEnum.DELETE) {
if (candidateMatches == null || candidateMatches.size() == 0) {
if (nextId == null || StringUtils.isBlank(nextId.getIdPart())) {
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionOperationFailedNoId", nextResouceOperationIn.name()));
}
entity = tryToLoadEntity(nextId);
if (entity == null) {
if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.PUT) {
ourLog.debug("Attempting to UPDATE resource with unknown ID '{}', will CREATE instead", nextId);
} else if (candidateMatches == null) {
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionOperationFailedUnknownId", nextResouceOperationIn.name(), nextId));
} else {
ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
persistedResources.add(null);
retVal.add(nextResource);
continue;
}
}
} else if (candidateMatches.size() == 1) {
entity = loadFirstEntityFromCandidateMatches(candidateMatches);
} else {
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionOperationWithMultipleMatchFailure", nextResouceOperationIn.name(), matchUrl, candidateMatches.size()));
}
} else if (nextId.isEmpty() || isPlaceholder(nextId)) {
entity = null;
} else {
entity = tryToLoadEntity(nextId);
}
BundleEntryTransactionMethodEnum nextResouceOperationOut;
if (entity == null) {
nextResouceOperationOut = BundleEntryTransactionMethodEnum.POST;
// entity = toEntity(nextResource);
entity = new ResourceTable();
populateResourceIntoEntity(nextResource, entity, false);
entity.setResourceType(resourceName);
entity.setUpdated(updateTime);
entity.setPublished(updateTime);
if (nextId.getIdPart() != null && nextId.getIdPart().startsWith("cid:")) {
ourLog.debug("Resource in transaction has ID[{}], will replace with server assigned ID", nextId.getIdPart());
} else if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.POST) {
if (nextId.isEmpty() == false) {
ourLog.debug("Resource in transaction has ID[{}] but is marked for CREATE, will ignore ID", nextId.getIdPart());
}
if (candidateMatches != null) {
if (candidateMatches.size() == 1) {
ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
BaseHasResource existingEntity = loadFirstEntityFromCandidateMatches(candidateMatches);
IResource existing = (IResource) toResource(existingEntity, false);
persistedResources.add(null);
retVal.add(existing);
continue;
}
if (candidateMatches.size() > 1) {
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionOperationWithMultipleMatchFailure", BundleEntryTransactionMethodEnum.POST.name(), matchUrl, candidateMatches.size()));
}
}
} else {
createForcedIdIfNeeded(entity, nextId);
}
myEntityManager.persist(entity);
if (entity.getForcedId() != null) {
myEntityManager.persist(entity.getForcedId());
}
creations++;
ourLog.info("Resource Type[{}] with ID[{}] does not exist, creating it", resourceName, nextId);
} else {
nextResouceOperationOut = nextResouceOperationIn;
if (nextResouceOperationOut == null) {
nextResouceOperationOut = BundleEntryTransactionMethodEnum.PUT;
}
updates++;
ourLog.info("Resource Type[{}] with ID[{}] exists, updating it", resourceName, nextId);
}
persistedResources.add(entity);
retVal.add(nextResource);
ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(nextResource, nextResouceOperationOut);
}
ourLog.info("Flushing transaction to database");
myEntityManager.flush();
for (int i = 0; i < persistedResources.size(); i++) {
ResourceTable entity = persistedResources.get(i);
String resourceName = toResourceName(theResources.get(i));
IdDt nextId = theResources.get(i).getId();
IdDt newId;
if (entity == null) {
newId = retVal.get(i + 1).getId().toUnqualifiedVersionless();
} else {
newId = entity.getIdDt().toUnqualifiedVersionless();
}
if (nextId == null || nextId.isEmpty()) {
ourLog.info("Transaction resource (with no preexisting ID) has been assigned new ID[{}]", nextId, newId);
} else {
if (nextId.toUnqualifiedVersionless().equals(newId)) {
ourLog.info("Transaction resource ID[{}] is being updated", newId);
} else {
if (isPlaceholder(nextId)) {
// nextId = new IdDt(resourceName, nextId.getIdPart());
ourLog.info("Transaction resource ID[{}] has been assigned new ID[{}]", nextId, newId);
idConversions.put(nextId, newId);
idConversions.put(new IdDt(resourceName + "/" + nextId.getValue()), newId);
}
}
}
}
for (IResource nextResource : theResources) {
List<BaseResourceReferenceDt> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class);
for (BaseResourceReferenceDt nextRef : allRefs) {
IdDt nextId = nextRef.getReference();
if (idConversions.containsKey(nextId)) {
IdDt newId = idConversions.get(nextId);
ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
nextRef.setReference(newId);
} else {
ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
}
}
}
ourLog.info("Re-flushing updated resource references and extracting search criteria");
for (int i = 0; i < theResources.size(); i++) {
IResource resource = theResources.get(i);
ResourceTable table = persistedResources.get(i);
if (table == null) {
continue;
}
InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(resource);
Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
if (deletedInstantOrNull == null && ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get(resource) == BundleEntryTransactionMethodEnum.DELETE) {
deletedTimestampOrNull = updateTime;
ResourceMetadataKeyEnum.DELETED_AT.put(resource, new InstantDt(deletedTimestampOrNull));
}
updateEntity(resource, table, deletedTimestampOrNull, updateTime);
}
long delay = System.currentTimeMillis() - start;
ourLog.info("Transaction completed in {}ms with {} creations and {} updates", new Object[] { delay, creations, updates });
oo.addIssue().setSeverity(IssueSeverityEnum.INFORMATION).setDetails("Transaction completed in " + delay + "ms with " + creations + " creations and " + updates + " updates");
return retVal;
}
private static boolean isPlaceholder(IdDt theId) {
if (theId.getIdPart() != null && theId.getIdPart().startsWith("cid:")) {
return true;
}
return false;
}
}

45
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java
View File

@ -19,23 +19,9 @@ package ca.uhn.fhir.jpa.dao;
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.*;
import javax.persistence.TypedQuery;
@ -43,9 +29,7 @@ import org.apache.http.NameValuePair;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.*;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallback;
@ -66,26 +50,18 @@ import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.model.dstu2.resource.Bundle.EntryResponse;
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
import ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum;
import ca.uhn.fhir.model.dstu2.valueset.*;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.BaseMethodBinding;
import ca.uhn.fhir.rest.method.BaseResourceReturningMethodBinding;
import ca.uhn.fhir.rest.method.BaseResourceReturningMethodBinding.ResourceOrDstu1Bundle;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
import ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.UrlUtil;
@ -580,8 +556,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
if (method instanceof BaseResourceReturningMethodBinding) {
try {
ResourceOrDstu1Bundle responseData = ((BaseResourceReturningMethodBinding) method).doInvokeServer(theRequestDetails.getServer(), requestDetails);
IBaseResource resource = responseData.getResource();
IBaseResource resource = ((BaseResourceReturningMethodBinding) method).doInvokeServer(theRequestDetails.getServer(), requestDetails);
if (paramValues.containsKey(Constants.PARAM_SUMMARY) || paramValues.containsKey(Constants.PARAM_CONTENT)) {
resource = filterNestedBundle(requestDetails, resource);
}

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
View File

@ -22,26 +22,16 @@ package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.*;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.*;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.lucene.analysis.Analyzer;
import org.apache.lucene.search.Query;
import org.apache.lucene.search.highlight.*;
import org.apache.lucene.search.highlight.Formatter;
import org.apache.lucene.search.highlight.Highlighter;
import org.apache.lucene.search.highlight.QueryScorer;
import org.apache.lucene.search.highlight.Scorer;
import org.apache.lucene.search.highlight.TokenGroup;
import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.FullTextQuery;
import org.hibernate.search.query.dsl.BooleanJunction;
@ -55,8 +45,8 @@ import com.google.common.collect.Sets;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.dstu.resource.BaseResource;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoEncounter.java
View File

@ -21,14 +21,11 @@ import javax.servlet.http.HttpServletRequest;
* limitations under the License.
* #L%
*/
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.instance.model.api.*;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
public interface IFhirResourceDaoEncounter<T extends IBaseResource> extends IFhirResourceDao<T> {

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoPatient.java
View File

@ -21,17 +21,13 @@ import javax.servlet.http.HttpServletRequest;
* limitations under the License.
* #L%
*/
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
public interface IFhirResourceDaoPatient<T extends IBaseResource> extends IFhirResourceDao<T> {

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

@ -26,8 +26,8 @@ import java.util.Map;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
/**
* @param <T>

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaValidationSupportDstu2.java
View File

@ -31,8 +31,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
@Transactional(value=TxType.REQUIRED)
public class JpaValidationSupportDstu2 implements IJpaValidationSupportDstu2 {

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
View File

@ -1,7 +1,5 @@
package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.defaultString;
/*
* #%L
* HAPI FHIR JPA Server
@ -21,9 +19,7 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.math.BigDecimal;
import java.math.MathContext;
@ -60,11 +56,8 @@ import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.util.UrlUtil;

475
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamExtractorDstu1.java
View File

@ -1,475 +0,0 @@
package ca.uhn.fhir.jpa.dao;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.measure.quantity.Quantity;
import javax.measure.unit.NonSI;
import javax.measure.unit.Unit;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.model.api.IDatatype;
import ca.uhn.fhir.model.api.IPrimitiveDatatype;
import ca.uhn.fhir.model.base.composite.BaseHumanNameDt;
import ca.uhn.fhir.model.dstu.composite.AddressDt;
import ca.uhn.fhir.model.dstu.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu.composite.CodingDt;
import ca.uhn.fhir.model.dstu.composite.ContactDt;
import ca.uhn.fhir.model.dstu.composite.DurationDt;
import ca.uhn.fhir.model.dstu.composite.HumanNameDt;
import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu.composite.PeriodDt;
import ca.uhn.fhir.model.dstu.composite.QuantityDt;
import ca.uhn.fhir.model.primitive.BaseDateTimeDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
public class SearchParamExtractorDstu1 extends BaseSearchParamExtractor implements ISearchParamExtractor {
@Override
public Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource) {
return Collections.emptySet();
}
@Override
public Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) {
HashSet<ResourceIndexedSearchParamDate> retVal = new HashSet<ResourceIndexedSearchParamDate>();
Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
for (RuntimeSearchParam nextSpDef : searchParams) {
if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.DATE) {
continue;
}
String nextPath = nextSpDef.getPath();
if (isBlank(nextPath)) {
continue;
}
boolean multiType = false;
if (nextPath.endsWith("[x]")) {
multiType = true;
}
for (Object nextObject : extractValues(nextPath, theResource)) {
if (nextObject == null) {
continue;
}
ResourceIndexedSearchParamDate nextEntity;
if (nextObject instanceof BaseDateTimeDt) {
BaseDateTimeDt nextValue = (BaseDateTimeDt) nextObject;
if (nextValue.isEmpty()) {
continue;
}
nextEntity = new ResourceIndexedSearchParamDate(nextSpDef.getName(), nextValue.getValue(), nextValue.getValue());
} else if (nextObject instanceof PeriodDt) {
PeriodDt nextValue = (PeriodDt) nextObject;
if (nextValue.isEmpty()) {
continue;
}
nextEntity = new ResourceIndexedSearchParamDate(nextSpDef.getName(), nextValue.getStart().getValue(), nextValue.getEnd().getValue());
} else {
if (!multiType) {
throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());
} else {
continue;
}
}
if (nextEntity != null) {
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
}
}
}
return retVal;
}
@Override
public HashSet<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IBaseResource theResource) {
HashSet<ResourceIndexedSearchParamNumber> retVal = new HashSet<ResourceIndexedSearchParamNumber>();
Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
for (RuntimeSearchParam nextSpDef : searchParams) {
if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.NUMBER) {
continue;
}
String nextPath = nextSpDef.getPath();
if (isBlank(nextPath)) {
continue;
}
for (Object nextObject : extractValues(nextPath, theResource)) {
if (nextObject == null || ((IDatatype) nextObject).isEmpty()) {
continue;
}
String resourceName = nextSpDef.getName();
boolean multiType = false;
if (nextPath.endsWith("[x]")) {
multiType = true;
}
if (nextObject instanceof DurationDt) {
DurationDt nextValue = (DurationDt) nextObject;
if (nextValue.getValue().isEmpty()) {
continue;
}
if (new UriDt(BaseHapiFhirDao.UCUM_NS).equals(nextValue.getSystem())) {
if (isNotBlank(nextValue.getCode().getValue())) {
Unit<? extends Quantity> unit = Unit.valueOf(nextValue.getCode().getValue());
javax.measure.converter.UnitConverter dayConverter = unit.getConverterTo(NonSI.DAY);
double dayValue = dayConverter.convert(nextValue.getValue().getValue().doubleValue());
DurationDt newValue = new DurationDt();
newValue.setSystem(BaseHapiFhirDao.UCUM_NS);
newValue.setCode(NonSI.DAY.toString());
newValue.setValue(dayValue);
nextValue = newValue;
/*
* @SuppressWarnings("unchecked") PhysicsUnit<? extends
* org.unitsofmeasurement.quantity.Quantity<?>> unit = (PhysicsUnit<? extends
* org.unitsofmeasurement.quantity.Quantity<?>>)
* UCUMFormat.getCaseInsensitiveInstance().parse(nextValue.getCode().getValue(), null); if
* (unit.isCompatible(UCUM.DAY)) {
*
* @SuppressWarnings("unchecked") PhysicsUnit<org.unitsofmeasurement.quantity.Time> timeUnit
* = (PhysicsUnit<Time>) unit; UnitConverter conv = timeUnit.getConverterTo(UCUM.DAY);
* double dayValue = conv.convert(nextValue.getValue().getValue().doubleValue()); DurationDt
* newValue = new DurationDt(); newValue.setSystem(UCUM_NS);
* newValue.setCode(UCUM.DAY.getSymbol()); newValue.setValue(dayValue); nextValue=newValue;
* }
*/
}
}
ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, nextValue.getValue().getValue());
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
} else if (nextObject instanceof QuantityDt) {
QuantityDt nextValue = (QuantityDt) nextObject;
if (nextValue.getValue().isEmpty()) {
continue;
}
ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, nextValue.getValue().getValue());
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
} else if (nextObject instanceof IntegerDt) {
IntegerDt nextValue = (IntegerDt) nextObject;
if (nextValue.getValue() == null) {
continue;
}
ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, new BigDecimal(nextValue.getValue()));
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
} else {
if (!multiType) {
throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass());
} else {
continue;
}
}
}
}
return retVal;
}
@Override
public Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IBaseResource theResource) {
HashSet<ResourceIndexedSearchParamQuantity> retVal = new HashSet<ResourceIndexedSearchParamQuantity>();
Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
for (RuntimeSearchParam nextSpDef : searchParams) {
if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.QUANTITY) {
continue;
}
String nextPath = nextSpDef.getPath();
if (isBlank(nextPath)) {
continue;
}
for (Object nextObject : extractValues(nextPath, theResource)) {
if (nextObject == null || ((IDatatype) nextObject).isEmpty()) {
continue;
}
String resourceName = nextSpDef.getName();
boolean multiType = false;
if (nextPath.endsWith("[x]")) {
multiType = true;
}
if (nextObject instanceof QuantityDt) {
QuantityDt nextValue = (QuantityDt) nextObject;
if (nextValue.getValue().isEmpty()) {
continue;
}
ResourceIndexedSearchParamQuantity nextEntity = new ResourceIndexedSearchParamQuantity(resourceName, nextValue.getValue().getValue(), nextValue.getSystem().getValueAsString(), nextValue.getUnits().getValue());
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
} else {
if (!multiType) {
throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass());
} else {
continue;
}
}
}
}
return retVal;
}
@Override
public Set<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IBaseResource theResource) {
HashSet<ResourceIndexedSearchParamString> retVal = new HashSet<ResourceIndexedSearchParamString>();
Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
for (RuntimeSearchParam nextSpDef : searchParams) {
if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.STRING) {
continue;
}
String nextPath = nextSpDef.getPath();
if (isBlank(nextPath)) {
// TODO: implement phoenetic, and any others that have no path
continue;
}
for (Object nextObject : extractValues(nextPath, theResource)) {
if (nextObject == null || ((IDatatype) nextObject).isEmpty()) {
continue;
}
String resourceName = nextSpDef.getName();
boolean multiType = false;
if (nextPath.endsWith("[x]")) {
multiType = true;
}
if (nextObject instanceof IPrimitiveDatatype<?>) {
IPrimitiveDatatype<?> nextValue = (IPrimitiveDatatype<?>) nextObject;
String searchTerm = nextValue.getValueAsString();
if (searchTerm.length() > ResourceIndexedSearchParamString.MAX_LENGTH) {
searchTerm = searchTerm.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
}
ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, BaseHapiFhirDao.normalizeString(searchTerm), searchTerm);
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
} else {
if (nextObject instanceof BaseHumanNameDt) {
ArrayList<StringDt> allNames = new ArrayList<StringDt>();
HumanNameDt nextHumanName = (HumanNameDt) nextObject;
allNames.addAll(nextHumanName.getFamily());
allNames.addAll(nextHumanName.getGiven());
for (StringDt nextName : allNames) {
if (nextName.isEmpty()) {
continue;
}
ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, BaseHapiFhirDao.normalizeString(nextName.getValueAsString()), nextName.getValueAsString());
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
}
} else if (nextObject instanceof AddressDt) {
ArrayList<StringDt> allNames = new ArrayList<StringDt>();
AddressDt nextAddress = (AddressDt) nextObject;
allNames.addAll(nextAddress.getLine());
allNames.add(nextAddress.getCity());
allNames.add(nextAddress.getState());
allNames.add(nextAddress.getCountry());
allNames.add(nextAddress.getZip());
for (StringDt nextName : allNames) {
if (nextName.isEmpty()) {
continue;
}
ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, BaseHapiFhirDao.normalizeString(nextName.getValueAsString()), nextName.getValueAsString());
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
}
} else if (nextObject instanceof ContactDt) {
ContactDt nextContact = (ContactDt) nextObject;
if (nextContact.getValue().isEmpty() == false) {
ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, BaseHapiFhirDao.normalizeString(nextContact.getValue().getValueAsString()), nextContact.getValue().getValueAsString());
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
}
} else {
if (!multiType) {
throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass());
}
}
}
}
}
return retVal;
}
@Override
public Set<BaseResourceIndexedSearchParam> extractSearchParamTokens(ResourceTable theEntity, IBaseResource theResource) {
HashSet<BaseResourceIndexedSearchParam> retVal = new HashSet<BaseResourceIndexedSearchParam>();
Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
for (RuntimeSearchParam nextSpDef : searchParams) {
if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.TOKEN) {
continue;
}
String nextPath = nextSpDef.getPath();
if (isBlank(nextPath)) {
continue;
}
boolean multiType = false;
if (nextPath.endsWith("[x]")) {
multiType = true;
}
List<String> systems = new ArrayList<String>();
List<String> codes = new ArrayList<String>();
for (Object nextObject : extractValues(nextPath, theResource)) {
if (nextObject instanceof IdentifierDt) {
IdentifierDt nextValue = (IdentifierDt) nextObject;
if (nextValue.isEmpty()) {
continue;
}
systems.add(nextValue.getSystem().getValueAsString());
codes.add(nextValue.getValue().getValue());
} else if (nextObject instanceof IPrimitiveDatatype<?>) {
IPrimitiveDatatype<?> nextValue = (IPrimitiveDatatype<?>) nextObject;
if (nextValue.isEmpty()) {
continue;
}
systems.add(null);
codes.add(nextValue.getValueAsString());
} else if (nextObject instanceof CodeableConceptDt) {
CodeableConceptDt nextCC = (CodeableConceptDt) nextObject;
if (!nextCC.getText().isEmpty()) {
ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(nextSpDef.getName(), BaseHapiFhirDao.normalizeString(nextCC.getText().getValue()), nextCC.getText().getValue());
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
}
for (CodingDt nextCoding : nextCC.getCoding()) {
if (nextCoding.isEmpty()) {
continue;
}
String nextSystem = nextCoding.getSystem().getValueAsString();
String nextCode = nextCoding.getCode().getValue();
if (isNotBlank(nextSystem) || isNotBlank(nextCode)) {
systems.add(nextSystem);
codes.add(nextCode);
}
if (!nextCoding.getDisplay().isEmpty()) {
systems.add(null);
codes.add(nextCoding.getDisplay().getValue());
}
}
} else {
if (!multiType) {
throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());
} else {
continue;
}
}
}
assert systems.size() == codes.size() : "Systems contains " + systems + ", codes contains: " + codes;
Set<Pair<String, String>> haveValues = new HashSet<Pair<String, String>>();
for (int i = 0; i < systems.size(); i++) {
String system = systems.get(i);
String code = codes.get(i);
if (isBlank(system) && isBlank(code)) {
continue;
}
if (system != null && system.length() > ResourceIndexedSearchParamToken.MAX_LENGTH) {
system = system.substring(0, ResourceIndexedSearchParamToken.MAX_LENGTH);
}
if (code != null && code.length() > ResourceIndexedSearchParamToken.MAX_LENGTH) {
code = code.substring(0, ResourceIndexedSearchParamToken.MAX_LENGTH);
}
Pair<String, String> nextPair = Pair.of(system, code);
if (haveValues.contains(nextPair)) {
continue;
}
haveValues.add(nextPair);
ResourceIndexedSearchParamToken nextEntity;
nextEntity = new ResourceIndexedSearchParamToken(nextSpDef.getName(), system, code);
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
}
}
return retVal;
}
@Override
public Set<ResourceIndexedSearchParamUri> extractSearchParamUri(ResourceTable theEntity, IBaseResource theResource) {
return Collections.emptySet();
}
}

46
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamExtractorDstu2.java
View File

@ -23,12 +23,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.*;
import javax.measure.quantity.Quantity;
import javax.measure.unit.NonSI;
@ -39,45 +34,18 @@ import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.model.api.IDatatype;
import ca.uhn.fhir.model.api.IPrimitiveDatatype;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.base.composite.BaseHumanNameDt;
import ca.uhn.fhir.model.dstu2.composite.AddressDt;
import ca.uhn.fhir.model.dstu2.composite.*;
import ca.uhn.fhir.model.dstu2.composite.BoundCodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.composite.ContactPointDt;
import ca.uhn.fhir.model.dstu2.composite.DurationDt;
import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.resource.*;
import ca.uhn.fhir.model.dstu2.resource.Conformance.RestSecurity;
import ca.uhn.fhir.model.dstu2.resource.Location;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.resource.Patient.Communication;
import ca.uhn.fhir.model.dstu2.resource.Questionnaire;
import ca.uhn.fhir.model.dstu2.resource.ValueSet;
import ca.uhn.fhir.model.dstu2.valueset.RestfulSecurityServiceEnum;
import ca.uhn.fhir.model.primitive.BaseDateTimeDt;
import ca.uhn.fhir.model.primitive.BoundCodeDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
import ca.uhn.fhir.model.primitive.*;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implements ISearchParamExtractor {

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamRegistryDstu1.java
View File

@ -1,26 +0,0 @@
package ca.uhn.fhir.jpa.dao;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public class SearchParamRegistryDstu1 extends BaseSearchParamRegistry {
// nothing yet
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParameterMap.java
View File

@ -29,17 +29,10 @@ import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.SearchParameterMap.IncludeComparator;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.UrlUtil;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -22,34 +22,24 @@ package ca.uhn.fhir.jpa.dao.dstu3;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Set;
import java.util.*;
import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport.CodeValidationResult;
import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.instance.model.api.*;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;

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