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Merge branch 'master' into 2849_add_new_mdm_param

This commit is contained in:
Jaison B 2021-09-17 10:18:24 -06:00
parent 35aaa98431 75bb6e3f7a
commit 8bb9aca8df
274 changed files with 53127 additions and 2151 deletions
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2
hapi-deployable-pom/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
View File

@ -225,6 +225,14 @@ public class FhirContext {
}
/**
* @since 5.6.0
*/
public static FhirContext forDstu2Cached() {
return forCached(FhirVersionEnum.DSTU2);
}
/**
* @since 5.5.0
*/

13
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ModelScanner.java
View File

@ -73,7 +73,6 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
class ModelScanner {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ModelScanner.class);
private Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinitions = new HashMap<>();
private FhirContext myContext;
private Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = new HashMap<>();
@ -90,6 +89,7 @@ class ModelScanner {
@Nonnull Collection<Class<? extends IBase>> theResourceTypes) throws ConfigurationException {
myContext = theContext;
myVersion = theVersion;
Set<Class<? extends IBase>> toScan = new HashSet<>(theResourceTypes);
init(theExistingDefinitions, toScan);
}
@ -405,8 +405,8 @@ class ModelScanner {
List<RuntimeSearchParam.Component> components = null;
if (paramType == RestSearchParameterTypeEnum.COMPOSITE) {
components = new ArrayList<>();
for (String next : searchParam.compositeOf()) {
String ref = "http://hl7.org/fhir/SearchParameter/" + theResourceDef.getName().toLowerCase() + "-" + next;
for (String name : searchParam.compositeOf()) {
String ref = toCanonicalSearchParameterUri(theResourceDef, name);
components.add(new RuntimeSearchParam.Component(null, ref));
}
}
@ -414,7 +414,8 @@ class ModelScanner {
Collection<String> base = Collections.singletonList(theResourceDef.getName());
String url = null;
if (theResourceDef.isStandardType()) {
url = "http://hl7.org/fhir/SearchParameter/" + theResourceDef.getName().toLowerCase() + "-" + searchParam.name();
String name = searchParam.name();
url = toCanonicalSearchParameterUri(theResourceDef, name);
}
RuntimeSearchParam param = new RuntimeSearchParam(null, url, searchParam.name(), searchParam.description(), searchParam.path(), paramType, providesMembershipInCompartments, toTargetList(searchParam.target()), RuntimeSearchParamStatusEnum.ACTIVE, null, components, base);
theResourceDef.addSearchParam(param);
@ -424,6 +425,10 @@ class ModelScanner {
}
private String toCanonicalSearchParameterUri(RuntimeResourceDefinition theResourceDef, String theName) {
return "http://hl7.org/fhir/SearchParameter/" + theResourceDef.getName() + "-" + theName;
}
private Set<String> toTargetList(Class<? extends IBaseResource>[] theTarget) {
HashSet<String> retVal = new HashSet<>();

48
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeSearchParam.java
View File

@ -233,18 +233,7 @@ public class RuntimeSearchParam {
}
public List<String> getPathsSplit() {
String path = getPath();
if (path.indexOf('|') == -1) {
return Collections.singletonList(path);
}
List<String> retVal = new ArrayList<>();
StringTokenizer tok = new StringTokenizer(path, "|");
while (tok.hasMoreElements()) {
String nextPath = tok.nextToken().trim();
retVal.add(nextPath.trim());
}
return retVal;
return getPathsSplitForResourceType(null);
}
/**
@ -266,6 +255,41 @@ public class RuntimeSearchParam {
return myPhoneticEncoder.encode(theString);
}
public List<String> getPathsSplitForResourceType(@Nullable String theResourceName) {
String path = getPath();
if (path.indexOf('|') == -1) {
if (theResourceName != null && !pathMatchesResourceType(theResourceName, path)) {
return Collections.emptyList();
}
return Collections.singletonList(path);
}
List<String> retVal = new ArrayList<>();
StringTokenizer tok = new StringTokenizer(path, "|");
while (tok.hasMoreElements()) {
String nextPath = tok.nextToken().trim();
if (theResourceName != null && !pathMatchesResourceType(theResourceName, nextPath)) {
continue;
}
retVal.add(nextPath.trim());
}
return retVal;
}
private boolean pathMatchesResourceType(String theResourceName, String thePath) {
if (thePath.startsWith(theResourceName + ".")) {
return true;
}
if (thePath.startsWith("Resouce.") || thePath.startsWith("DomainResource.")) {
return true;
}
if (Character.isLowerCase(thePath.charAt(0))) {
return true;
}
return false;
}
public enum RuntimeSearchParamStatusEnum {
ACTIVE,
DRAFT,

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -961,6 +961,7 @@ public class FhirTerser {
for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {
List<?> values = nextChild.getAccessor().getValues(theElement);
if (values != null) {
for (Object nextValueObject : values) {
IBase nextValue;

7
hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IAnyResource.java
View File

@ -28,13 +28,6 @@ import ca.uhn.fhir.rest.gclient.TokenClientParam;
*/
public interface IAnyResource extends IBaseResource {
/**
* Search parameter constant for <b>_language</b>
*/
@SearchParamDefinition(name="_language", path="", description="The language of the resource", type="string" )
String SP_RES_LANGUAGE = "_language";
/**
* Search parameter constant for <b>_id</b>
*/

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

@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

8
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java
View File

@ -282,7 +282,7 @@ public abstract class BaseApp {
}
private Optional<BaseCommand> parseCommand(String[] theArgs) {
Optional<BaseCommand> commandOpt = getNextCommand(theArgs);
Optional<BaseCommand> commandOpt = getNextCommand(theArgs, 0);
if (! commandOpt.isPresent()) {
String message = "Unrecognized command: " + ansi().bold().fg(Ansi.Color.RED) + theArgs[0] + ansi().boldOff().fg(Ansi.Color.WHITE);
@ -294,8 +294,8 @@ public abstract class BaseApp {
return commandOpt;
}
private Optional<BaseCommand> getNextCommand(String[] theArgs) {
return ourCommands.stream().filter(cmd -> cmd.getCommandName().equals(theArgs[0])).findFirst();
private Optional<BaseCommand> getNextCommand(String[] theArgs, int thePosition) {
return ourCommands.stream().filter(cmd -> cmd.getCommandName().equals(theArgs[thePosition])).findFirst();
}
private void processHelp(String[] theArgs) {
@ -303,7 +303,7 @@ public abstract class BaseApp {
logUsage();
return;
}
Optional<BaseCommand> commandOpt = getNextCommand(theArgs);
Optional<BaseCommand> commandOpt = getNextCommand(theArgs, 1);
if (! commandOpt.isPresent()) {
String message = "Unknown command: " + theArgs[1];
System.err.println(message);

31
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/BaseAppTest.java Normal file
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@ -0,0 +1,31 @@
package ca.uhn.fhir.cli;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.io.ByteArrayOutputStream;
import java.io.PrintStream;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
public class BaseAppTest {
private final PrintStream standardOut = System.out;
private final ByteArrayOutputStream outputStreamCaptor = new ByteArrayOutputStream();
@BeforeEach
public void setUp() {
System.setOut(new PrintStream(outputStreamCaptor));
}
@AfterEach
public void tearDown() {
System.setOut(standardOut);
}
@Test
public void testHelpOption() {
App.main(new String[]{"help", "create-package"});
assertThat(outputStreamCaptor.toString().trim(), outputStreamCaptor.toString().trim(), containsString("Usage"));
}
}

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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-deployable-pom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

5
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java
View File

@ -30,6 +30,7 @@ import org.apache.commons.lang3.time.DateUtils;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -65,8 +66,8 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(myDataSource);
retVal.setJpaProperties(myJpaProperties);

5
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java
View File

@ -30,6 +30,7 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -62,8 +63,8 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(myDataSource);
retVal.setJpaProperties(myJpaProperties);

5
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigR4.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -60,8 +61,8 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(myDataSource);
retVal.setJpaProperties(myJpaProperties);

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-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>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-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>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2457-fix-single-threaded-search-execution.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: perf
issue: 2457
title: "A regression in HAPI FHIR 5.3.0 resulted in concurrent searches being executed in a sequential
(and not parallel) fashion in some circumstances."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2790-correct-searchparameter-urls-in-jps.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: fix
issue: 2790
title: "The SearchParameter canonical URLs exported by the JPA server have been adjusted to match the URLs
specified in the FHIR specification."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2790-remove-language-from-jpa.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: change
issue: 2790
title: "Support for the `_language` search parameter has been dropped from the JPA server. This search parameter
was specified in FHIR DSTU1 but was dropped in later versions. It is rarely used in practice and imposes
an indexing cost, so it has now been removed. A custom search parameter may be used in order to achieve
the same functionality if needed."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2901-autoversionatpaths-with-autocreateplaceholders-no-null-pointer.yml Normal file
View File

@ -0,0 +1,5 @@
---
type: fix
issue: 2901
jira: SMILE-3004
title: "Processing transactions with AutoversionAtPaths set should create those resources (if AutoCreatePlaceholders is set) and use latest version as expected"

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2958-procedure-patient-consistent-error-handling.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 2958
jira: SMILE-643
title: "Fixed issue where the processing of queries like Procedure?patient= before a cache search would cause the parameter key to be removed.
Additionally, ensured that requests like Procedure?patient= cause HTTP 400 Bad Request instead of HTTP 500 Internal Error."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2962-custom-elastic-prefixes.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: fix
issue: 2962
jira: SMILE-720
title: "Added a new DaoConfig setting called `setElasticSearchIndexPrefix(String prefix)` which will cause Hibernate search to prefix all of its tables with the provided value."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2967-hybrid-search-chain.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: fix
issue: 2967
jira: SMILE-2899
title: "Previously, the system would only traverse references to discrete resources while performing a chained search.
This fix adds support for traversing references to contained resources as well, with the limitation that the reference
to the contained resource must be the last reference in the chain."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2973-CLI-option-help-fails.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 2973
title: "CLI `smileutil help {command}` returns `Unknown command` which should return the usage of `command`. This has been corrected."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2975-elastic-improvements.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 2975
title: "Two improvements have been made to the connection to Elasticsearch. First, null username and password values are now permitted. Second, multiple hosts are now permitted via the `setHosts()` method on the ElasticHibernatePropertiesBuilder, allowing you to
connect to multiple elasticsearch clusters at once. Thanks to Dušan Marković for the contribution!"

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2978-bundle-batch-tag-bug.yaml Normal file
View File

@ -0,0 +1,3 @@
---
type: fix
title: "Fixed a bug where two identical tags in parallel entries being created in a batch would fail."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2987-validate-conditional-urls.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: change
jira: SMILE-2927
title: "During transactions, any resources that were PUT or POSTed with a conditional URL now receive extra validation. There is now a final
storage step which ensures that the stored resource actually matches the conditional URL."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2991-eliminate-search-coordinator-threadpool.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: change
issue: 2991
title: "This PR eliminates the search coordinator threadpool, and executes searches synchronously on the HTTP client
thread. The idea of using a separate pool was supposed to help improve server scalability, but ultimately created
false bottlenecks and reduced the utility of monitoring infrastructure so it has been eliminated."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/lastn.md
View File

@ -31,12 +31,11 @@ In addition, the Elasticsearch client service, `ElasticsearchSvcImpl` will need
```java
@Bean()
public ElasticsearchSvcImpl elasticsearchSvc() {
String elasticsearchHost = "localhost";
String elasticsearchUserId = "elastic";
String elasticsearchHost = "localhost:9200";
String elasticsearchUsername = "elastic";
String elasticsearchPassword = "changeme";
int elasticsearchPort = 9301;
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUserId, elasticsearchPassword);
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword);
}
```

10
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md
View File

@ -302,6 +302,14 @@ If the server has been configured with a [Resource Server ID Strategy](/apidocs/
Contains the specific version (starting with 1) of the resource that this row corresponds to.
</td>
</tr>
<tr>
<td>RESOURCE_TYPE</td>
<td></td>
<td>String</td>
<td>
Contains the string specifying the type of the resource (Patient, Observation, etc).
</td>
</tr>
</tbody>
</table>
@ -476,7 +484,7 @@ The following columns are common to **all HFJ_SPIDX_xxx tables**.
<tr>
<td>RES_ID</td>
<td>FK to <a href="#HFJ_RESOURCE">HFJ_RESOURCE</a></td>
<td>String</td>
<td>Long</td>
<td></td>
<td>
Contains the PID of the resource being indexed.

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

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-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>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

28
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
View File

@ -258,6 +258,11 @@ public class DaoConfig {
private boolean myAccountForDateIndexNulls;
private boolean myTriggerSubscriptionsForNonVersioningChanges;
/**
* @since 5.6.0
*/
private String myElasicSearchIndexPrefix;
/**
* @since 5.6.0
*/
@ -269,6 +274,7 @@ public class DaoConfig {
private Integer myBundleBatchPoolSize = DEFAULT_BUNDLE_BATCH_POOL_SIZE;
private Integer myBundleBatchMaxPoolSize = DEFAULT_BUNDLE_BATCH_MAX_POOL_SIZE;
/**
* Constructor
*/
@ -2643,6 +2649,28 @@ public class DaoConfig {
return retval;
}
/**
*
* Sets a prefix for any indexes created when interacting with elasticsearch. This will apply to fulltext search indexes
* and terminology expansion indexes.
*
* @since 5.6.0
*/
public String getElasticSearchIndexPrefix() {
return myElasicSearchIndexPrefix;
}
/**
*
* Sets a prefix for any indexes created when interacting with elasticsearch. This will apply to fulltext search indexes
* and terminology expansion indexes.
*
* @since 5.6.0
*/
public void setElasticSearchIndexPrefix(String thePrefix) {
myElasicSearchIndexPrefix = thePrefix;
}
public enum StoreMetaSourceInformationEnum {
NONE(false, false),
SOURCE_URI(true, false),

1
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirSystemDao.java
View File

@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.api.dao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.rest.annotation.Offset;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseBundle;

2
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/model/LazyDaoMethodOutcome.java
View File

@ -52,13 +52,11 @@ public class LazyDaoMethodOutcome extends DaoMethodOutcome {
private void tryToRunSupplier() {
if (myEntitySupplier != null) {
EntityAndResource entityAndResource = myEntitySupplier.get();
setEntity(entityAndResource.getEntity());
setResource(entityAndResource.getResource());
setId(entityAndResource.getResource().getIdElement());
myEntitySupplierUseCallback.run();
}
}

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE3-SNAPSHOT</version>
<version>5.6.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/job/model/PartitionedUrl.java
View File

@ -54,4 +54,8 @@ public class PartitionedUrl implements IModelJson {
public void setRequestPartitionId(RequestPartitionId theRequestPartitionId) {
myRequestPartitionId = theRequestPartitionId;
}
public boolean isPartitioned() {
return myRequestPartitionId != null && !myRequestPartitionId.isDefaultPartition();
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/MdmBatchJobSubmitterFactoryImpl.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.batch.mdm;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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 ca.uhn.fhir.mdm.api.IMdmBatchJobSubmitterFactory;
import ca.uhn.fhir.mdm.api.IMdmClearJobSubmitter;
import org.springframework.beans.factory.annotation.Autowired;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processor/PidToIBaseResourceProcessor.java
View File

@ -69,7 +69,7 @@ public class PidToIBaseResourceProcessor implements ItemProcessor<List<ResourceP
List<IBaseResource> outgoing = new ArrayList<>();
sb.loadResourcesByPid(theResourcePersistentId, Collections.emptyList(), outgoing, false, null);
ourLog.trace("Loaded resources: {}", outgoing.stream().map(t->t.getIdElement().getValue()).collect(Collectors.joining(", ")));
ourLog.trace("Loaded resources: {}", outgoing.stream().filter(t -> t != null).map(t -> t.getIdElement().getValue()).collect(Collectors.joining(", ")));
return outgoing;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/reader/BaseReverseCronologicalBatchPidReader.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.batch.reader;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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 ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;

102
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/cache/ResourceVersionSvcDaoImpl.java vendored
View File

@ -24,18 +24,23 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.annotation.Nonnull;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import static org.slf4j.LoggerFactory.getLogger;
@ -52,17 +57,19 @@ public class ResourceVersionSvcDaoImpl implements IResourceVersionSvc {
DaoRegistry myDaoRegistry;
@Autowired
IResourceTableDao myResourceTableDao;
@Autowired
IdHelperService myIdHelperService;
@Override
@Nonnull
public ResourceVersionMap getVersionMap(String theResourceName, SearchParameterMap theSearchParamMap) {
public ResourceVersionMap getVersionMap(RequestPartitionId theRequestPartitionId, String theResourceName, SearchParameterMap theSearchParamMap) {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(theResourceName);
if (ourLog.isDebugEnabled()) {
ourLog.debug("About to retrieve version map for resource type: {}", theResourceName);
}
List<Long> matchingIds = dao.searchForIds(theSearchParamMap, new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.allPartitions())).stream()
List<Long> matchingIds = dao.searchForIds(theSearchParamMap, new SystemRequestDetails().setRequestPartitionId(theRequestPartitionId)).stream()
.map(ResourcePersistentId::getIdAsLong)
.collect(Collectors.toList());
@ -74,4 +81,95 @@ public class ResourceVersionSvcDaoImpl implements IResourceVersionSvc {
return ResourceVersionMap.fromResourceTableEntities(allById);
}
@Override
/**
* Retrieves the latest versions for any resourceid that are found.
* If they are not found, they will not be contained in the returned map.
* The key should be the same value that was passed in to allow
* consumer to look up the value using the id they already have.
*
* This method should not throw, so it can safely be consumed in
* transactions.
*
* @param theRequestPartitionId - request partition id
* @param theIds - list of IIdTypes for resources of interest.
* @return
*/
public ResourcePersistentIdMap getLatestVersionIdsForResourceIds(RequestPartitionId theRequestPartitionId, List<IIdType> theIds) {
ResourcePersistentIdMap idToPID = new ResourcePersistentIdMap();
HashMap<String, List<IIdType>> resourceTypeToIds = new HashMap<>();
for (IIdType id : theIds) {
String resourceType = id.getResourceType();
if (!resourceTypeToIds.containsKey(resourceType)) {
resourceTypeToIds.put(resourceType, new ArrayList<>());
}
resourceTypeToIds.get(resourceType).add(id);
}
for (String resourceType : resourceTypeToIds.keySet()) {
ResourcePersistentIdMap idAndPID = getIdsOfExistingResources(theRequestPartitionId,
resourceTypeToIds.get(resourceType));
idToPID.putAll(idAndPID);
}
return idToPID;
}
/**
* Helper method to determine if some resources exist in the DB (without throwing).
* Returns a set that contains the IIdType for every resource found.
* If it's not found, it won't be included in the set.
*
* @param theIds - list of IIdType ids (for the same resource)
* @return
*/
private ResourcePersistentIdMap getIdsOfExistingResources(RequestPartitionId thePartitionId,
Collection<IIdType> theIds) {
// these are the found Ids that were in the db
ResourcePersistentIdMap retval = new ResourcePersistentIdMap();
if (theIds == null || theIds.isEmpty()) {
return retval;
}
List<ResourcePersistentId> resourcePersistentIds = myIdHelperService.resolveResourcePersistentIdsWithCache(thePartitionId,
theIds.stream().collect(Collectors.toList()));
// we'll use this map to fetch pids that require versions
HashMap<Long, ResourcePersistentId> pidsToVersionToResourcePid = new HashMap<>();
// fill in our map
for (ResourcePersistentId pid : resourcePersistentIds) {
if (pid.getVersion() == null) {
pidsToVersionToResourcePid.put(pid.getIdAsLong(), pid);
}
Optional<IIdType> idOp = theIds.stream()
.filter(i -> i.getIdPart().equals(pid.getAssociatedResourceId().getIdPart()))
.findFirst();
// this should always be present
// since it was passed in.
// but land of optionals...
idOp.ifPresent(id -> {
retval.put(id, pid);
});
}
// set any versions we don't already have
if (!pidsToVersionToResourcePid.isEmpty()) {
Collection<Object[]> resourceEntries = myResourceTableDao
.getResourceVersionsForPid(new ArrayList<>(pidsToVersionToResourcePid.keySet()));
for (Object[] record : resourceEntries) {
// order matters!
Long retPid = (Long) record[0];
String resType = (String) record[1];
Long version = (Long) record[2];
pidsToVersionToResourcePid.get(retPid).setVersion(version);
}
}
return retval;
}
}

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

@ -122,6 +122,7 @@ import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchResultCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexer;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
@ -155,6 +156,7 @@ import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.ApplicationContext;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -288,8 +290,8 @@ public abstract class BaseConfig {
* bean, but it provides a partially completed entity manager
* factory with HAPI FHIR customizations
*/
protected LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean();
protected LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory);
configureEntityManagerFactory(retVal, fhirContext());
return retVal;
}
@ -378,17 +380,6 @@ public abstract class BaseConfig {
return new TermConceptMappingSvcImpl();
}
@Bean
public ThreadPoolTaskExecutor searchCoordinatorThreadFactory() {
final ThreadPoolTaskExecutor threadPoolTaskExecutor = new ThreadPoolTaskExecutor();
threadPoolTaskExecutor.setThreadNamePrefix("search_coord_");
threadPoolTaskExecutor.setCorePoolSize(searchCoordCorePoolSize);
threadPoolTaskExecutor.setMaxPoolSize(searchCoordMaxPoolSize);
threadPoolTaskExecutor.setQueueCapacity(searchCoordQueueCapacity);
threadPoolTaskExecutor.initialize();
return threadPoolTaskExecutor;
}
@Bean
public TaskScheduler taskScheduler() {
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
@ -849,8 +840,8 @@ public abstract class BaseConfig {
}
@Bean
public ISearchCoordinatorSvc searchCoordinatorSvc(ThreadPoolTaskExecutor searchCoordinatorThreadFactory) {
return new SearchCoordinatorSvcImpl(searchCoordinatorThreadFactory);
public ISearchCoordinatorSvc searchCoordinatorSvc() {
return new SearchCoordinatorSvcImpl();
}
@Bean
@ -919,6 +910,11 @@ public abstract class BaseConfig {
return new PredicateBuilderFactory(theApplicationContext);
}
@Bean
public IndexNamePrefixLayoutStrategy indexLayoutStrategy() {
return new IndexNamePrefixLayoutStrategy();
}
@Bean
public JpaResourceLoader jpaResourceLoader() {
return new JpaResourceLoader();

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HapiFhirLocalContainerEntityManagerFactoryBean.java
View File

@ -23,6 +23,9 @@ package ca.uhn.fhir.jpa.config;
import org.hibernate.cfg.AvailableSettings;
import org.hibernate.query.criteria.LiteralHandlingMode;
import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.orm.hibernate5.SpringBeanContainer;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import java.util.Map;
@ -32,6 +35,14 @@ import java.util.Map;
* that sets some sensible default property values
*/
public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContainerEntityManagerFactoryBean {
//https://stackoverflow.com/questions/57902388/how-to-inject-spring-beans-into-the-hibernate-envers-revisionlistener
ConfigurableListableBeanFactory myConfigurableListableBeanFactory;
public HapiFhirLocalContainerEntityManagerFactoryBean(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
myConfigurableListableBeanFactory = theConfigurableListableBeanFactory;
}
@Override
public Map<String, Object> getJpaPropertyMap() {
Map<String, Object> retVal = super.getJpaPropertyMap();
@ -63,6 +74,11 @@ public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContain
if (!retVal.containsKey(AvailableSettings.BATCH_VERSIONED_DATA)) {
retVal.put(AvailableSettings.BATCH_VERSIONED_DATA, "true");
}
// Why is this here, you ask? LocalContainerEntityManagerFactoryBean actually clobbers the setting hibernate needs
// in order to be able to resolve beans, so we add it back in manually here
if (!retVal.containsKey(AvailableSettings.BEAN_CONTAINER)) {
retVal.put(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(myConfigurableListableBeanFactory));
}
return retVal;
}

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

@ -1207,7 +1207,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
if (thePerformIndexing || ((ResourceTable) theEntity).getVersion() == 1) {
newParams = new ResourceIndexedSearchParams();
mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theTransactionDetails, entity, theResource, existingParams, theRequest, thePerformIndexing);
changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);
@ -1229,12 +1228,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
}
entity.setUpdated(theTransactionDetails.getTransactionDate());
if (theResource instanceof IResource) {
entity.setLanguage(((IResource) theResource).getLanguage().getValue());
} else {
entity.setLanguage(((IAnyResource) theResource).getLanguageElement().getValue());
}
newParams.populateResourceTableSearchParamsPresentFlags(entity);
entity.setIndexStatus(INDEX_STATUS_INDEXED);
}

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

@ -136,9 +136,12 @@ import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.UUID;

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
View File

@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
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;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;

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

@ -25,19 +25,18 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.model.LazyDaoMethodOutcome;
import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
import ca.uhn.fhir.jpa.cache.ResourcePersistentIdMap;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.util.JpaParamUtil;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
@ -45,12 +44,16 @@ import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.QualifierDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.OperationOutcomeUtil;
@ -91,6 +94,10 @@ public abstract class BaseStorageDao {
protected DaoRegistry myDaoRegistry;
@Autowired
protected ModelConfig myModelConfig;
@Autowired
protected IResourceVersionSvc myResourceVersionSvc;
@Autowired
protected DaoConfig myDaoConfig;
@VisibleForTesting
public void setSearchParamRegistry(ISearchParamRegistry theSearchParamRegistry) {
@ -204,10 +211,33 @@ public abstract class BaseStorageDao {
for (IBaseReference nextReference : referencesToVersion) {
IIdType referenceElement = nextReference.getReferenceElement();
if (!referenceElement.hasBaseUrl()) {
String resourceType = referenceElement.getResourceType();
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceType);
String targetVersionId = dao.getCurrentVersionId(referenceElement);
String newTargetReference = referenceElement.withVersion(targetVersionId).getValue();
ResourcePersistentIdMap resourceVersionMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(RequestPartitionId.allPartitions(),
Collections.singletonList(referenceElement)
);
// 3 cases:
// 1) there exists a resource in the db with some version (use this version)
// 2) no resource exists, but we will create one (eventually). The version is 1
// 3) no resource exists, and none will be made -> throw
Long version;
if (resourceVersionMap.containsKey(referenceElement)) {
// the resource exists... latest id
// will be the value in the ResourcePersistentId
version = resourceVersionMap.getResourcePersistentId(referenceElement).getVersion();
} else if (myDaoConfig.isAutoCreatePlaceholderReferenceTargets()) {
// if idToPID doesn't contain object
// but autcreateplaceholders is on
// then the version will be 1 (the first version)
version = 1L;
}
else {
// resource not found
// and no autocreateplaceholders set...
// we throw
throw new ResourceNotFoundException(referenceElement);
}
String newTargetReference = referenceElement.withVersion(version.toString()).getValue();
nextReference.setReference(newTargetReference);
}
}

621
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.interceptor.model.TransactionWriteOperationsDetails;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
@ -34,6 +35,9 @@ import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.model.DeleteConflict;
import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.api.model.LazyDaoMethodOutcome;
import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
import ca.uhn.fhir.jpa.cache.ResourcePersistentIdMap;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
@ -41,7 +45,9 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryMatchResult;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
import ca.uhn.fhir.jpa.searchparam.matcher.SearchParamMatcher;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.parser.DataFormatException;
@ -61,6 +67,7 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
import ca.uhn.fhir.rest.server.exceptions.PayloadTooLargeException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
import ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding;
@ -68,15 +75,16 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletSubRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.rest.server.util.ServletRequestUtil;
import ca.uhn.fhir.util.AsyncUtil;
import ca.uhn.fhir.util.ElementUtil;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.AsyncUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.exceptions.FHIRException;
@ -90,7 +98,6 @@ import org.hl7.fhir.instance.model.api.IBaseReference;
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.r4.model.Task;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -117,11 +124,11 @@ import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.TreeSet;
import java.util.concurrent.Callable;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.TimeUnit;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import static ca.uhn.fhir.util.StringUtil.toUtf8String;
import static org.apache.commons.lang3.StringUtils.defaultString;
@ -154,9 +161,14 @@ public abstract class BaseTransactionProcessor {
private ModelConfig myModelConfig;
@Autowired
private InMemoryResourceMatcher myInMemoryResourceMatcher;
@Autowired
private SearchParamMatcher mySearchParamMatcher;
private TaskExecutor myExecutor ;
@Autowired
private IResourceVersionSvc myResourceVersionSvc;
@VisibleForTesting
public void setDaoConfig(DaoConfig theDaoConfig) {
myDaoConfig = theDaoConfig;
@ -252,8 +264,10 @@ public abstract class BaseTransactionProcessor {
myVersionAdapter.populateEntryWithOperationOutcome(caughtEx, nextEntry);
}
private void handleTransactionCreateOrUpdateOutcome(Map<IIdType, IIdType> idSubstitutions, Map<IIdType, DaoMethodOutcome> idToPersistedOutcome, IIdType nextResourceId, DaoMethodOutcome outcome,
IBase newEntry, String theResourceType, IBaseResource theRes, RequestDetails theRequestDetails) {
private void handleTransactionCreateOrUpdateOutcome(Map<IIdType, IIdType> idSubstitutions, Map<IIdType, DaoMethodOutcome> idToPersistedOutcome,
IIdType nextResourceId, DaoMethodOutcome outcome,
IBase newEntry, String theResourceType,
IBaseResource theRes, RequestDetails theRequestDetails) {
IIdType newId = outcome.getId().toUnqualified();
IIdType resourceId = isPlaceholder(nextResourceId) ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
if (newId.equals(resourceId) == false) {
@ -267,7 +281,9 @@ public abstract class BaseTransactionProcessor {
idSubstitutions.put(id, newId);
}
}
idToPersistedOutcome.put(newId, outcome);
populateIdToPersistedOutcomeMap(idToPersistedOutcome, newId, outcome);
if (outcome.getCreated()) {
myVersionAdapter.setResponseStatus(newEntry, toStatusString(Constants.STATUS_HTTP_201_CREATED));
} else {
@ -291,6 +307,21 @@ public abstract class BaseTransactionProcessor {
}
/** Method which populates entry in idToPersistedOutcome.
* Will store whatever outcome is sent, unless the key already exists, then we only replace an instance if we find that the instance
* we are replacing with is non-lazy. This allows us to evaluate later more easily, as we _know_ we need access to these.
*/
private void populateIdToPersistedOutcomeMap(Map<IIdType, DaoMethodOutcome> idToPersistedOutcome, IIdType newId, DaoMethodOutcome outcome) {
//Prefer real method outcomes over lazy ones.
if (idToPersistedOutcome.containsKey(newId)) {
if (!(outcome instanceof LazyDaoMethodOutcome)) {
idToPersistedOutcome.put(newId, outcome);
}
} else {
idToPersistedOutcome.put(newId, outcome);
}
}
private Date getLastModified(IBaseResource theRes) {
return theRes.getMeta().getLastUpdated();
}
@ -359,8 +390,8 @@ public abstract class BaseTransactionProcessor {
IBase nextRequestEntry = null;
for (int i=0; i<requestEntriesSize; i++ ) {
nextRequestEntry = requestEntries.get(i);
BundleTask bundleTask = new BundleTask(completionLatch, theRequestDetails, responseMap, i, nextRequestEntry, theNestedMode);
getTaskExecutor().execute(bundleTask);
RetriableBundleTask retriableBundleTask = new RetriableBundleTask(completionLatch, theRequestDetails, responseMap, i, nextRequestEntry, theNestedMode);
getTaskExecutor().execute(retriableBundleTask);
}
// waiting for all tasks to be completed
@ -394,7 +425,8 @@ public abstract class BaseTransactionProcessor {
myHapiTransactionService = theHapiTransactionService;
}
private IBaseBundle processTransaction(final RequestDetails theRequestDetails, final IBaseBundle theRequest, final String theActionName, boolean theNestedMode) {
private IBaseBundle processTransaction(final RequestDetails theRequestDetails, final IBaseBundle theRequest,
final String theActionName, boolean theNestedMode) {
validateDependencies();
String transactionType = myVersionAdapter.getBundleType(theRequest);
@ -412,7 +444,8 @@ public abstract class BaseTransactionProcessor {
throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + transactionType);
}
int numberOfEntries = myVersionAdapter.getEntries(theRequest).size();
List<IBase> requestEntries = myVersionAdapter.getEntries(theRequest);
int numberOfEntries = requestEntries.size();
if (myDaoConfig.getMaximumTransactionBundleSize() != null && numberOfEntries > myDaoConfig.getMaximumTransactionBundleSize()) {
throw new PayloadTooLargeException("Transaction Bundle Too large. Transaction bundle contains " +
@ -425,8 +458,6 @@ public abstract class BaseTransactionProcessor {
final TransactionDetails transactionDetails = new TransactionDetails();
final StopWatch transactionStopWatch = new StopWatch();
List<IBase> requestEntries = myVersionAdapter.getEntries(theRequest);
// Do all entries have a verb?
for (int i = 0; i < numberOfEntries; i++) {
IBase nextReqEntry = requestEntries.get(i);
@ -450,10 +481,11 @@ public abstract class BaseTransactionProcessor {
List<IBase> getEntries = new ArrayList<>();
final IdentityHashMap<IBase, Integer> originalRequestOrder = new IdentityHashMap<>();
for (int i = 0; i < requestEntries.size(); i++) {
originalRequestOrder.put(requestEntries.get(i), i);
IBase requestEntry = requestEntries.get(i);
originalRequestOrder.put(requestEntry, i);
myVersionAdapter.addEntry(response);
if (myVersionAdapter.getEntryRequestVerb(myContext, requestEntries.get(i)).equals("GET")) {
getEntries.add(requestEntries.get(i));
if (myVersionAdapter.getEntryRequestVerb(myContext, requestEntry).equals("GET")) {
getEntries.add(requestEntry);
}
}
@ -472,16 +504,43 @@ public abstract class BaseTransactionProcessor {
}
entries.sort(new TransactionSorter(placeholderIds));
doTransactionWriteOperations(theRequestDetails, theActionName, transactionDetails, transactionStopWatch, response, originalRequestOrder, entries);
// perform all writes
prepareThenExecuteTransactionWriteOperations(theRequestDetails, theActionName,
transactionDetails, transactionStopWatch,
response, originalRequestOrder, entries);
// perform all gets
// (we do these last so that the gets happen on the final state of the DB;
// see above note)
doTransactionReadOperations(theRequestDetails, response,
getEntries, originalRequestOrder,
transactionStopWatch, theNestedMode);
// Interceptor broadcast: JPA_PERFTRACE_INFO
if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO, myInterceptorBroadcaster, theRequestDetails)) {
String taskDurations = transactionStopWatch.formatTaskDurations();
StorageProcessingMessage message = new StorageProcessingMessage();
message.setMessage("Transaction timing:\n" + taskDurations);
HookParams params = new HookParams()
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(StorageProcessingMessage.class, message);
CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_INFO, params);
}
return response;
}
private void doTransactionReadOperations(final RequestDetails theRequestDetails, IBaseBundle theResponse,
List<IBase> theGetEntries, IdentityHashMap<IBase, Integer> theOriginalRequestOrder,
StopWatch theTransactionStopWatch, boolean theNestedMode) {
if (theGetEntries.size() > 0) {
theTransactionStopWatch.startTask("Process " + theGetEntries.size() + " GET entries");
/*
* Loop through the request and process any entries of type GET
*/
if (getEntries.size() > 0) {
transactionStopWatch.startTask("Process " + getEntries.size() + " GET entries");
}
for (IBase nextReqEntry : getEntries) {
for (IBase nextReqEntry : theGetEntries) {
if (theNestedMode) {
throw new InvalidRequestException("Can not invoke read operation on nested transaction");
}
@ -491,8 +550,8 @@ public abstract class BaseTransactionProcessor {
}
ServletRequestDetails srd = (ServletRequestDetails) theRequestDetails;
Integer originalOrder = originalRequestOrder.get(nextReqEntry);
IBase nextRespEntry = (IBase) myVersionAdapter.getEntries(response).get(originalOrder);
Integer originalOrder = theOriginalRequestOrder.get(nextReqEntry);
IBase nextRespEntry = (IBase) myVersionAdapter.getEntries(theResponse).get(originalOrder);
ArrayListMultimap<String, String> paramValues = ArrayListMultimap.create();
@ -519,7 +578,6 @@ public abstract class BaseTransactionProcessor {
Validate.isTrue(method instanceof BaseResourceReturningMethodBinding, "Unable to handle GET {}", url);
try {
BaseResourceReturningMethodBinding methodBinding = (BaseResourceReturningMethodBinding) method;
requestDetails.setRestOperationType(methodBinding.getRestOperationType());
@ -536,23 +594,9 @@ public abstract class BaseTransactionProcessor {
myVersionAdapter.setResponseStatus(nextRespEntry, toStatusString(e.getStatusCode()));
populateEntryWithOperationOutcome(e, nextRespEntry);
}
}
transactionStopWatch.endCurrentTask();
// Interceptor broadcast: JPA_PERFTRACE_INFO
if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO, myInterceptorBroadcaster, theRequestDetails)) {
String taskDurations = transactionStopWatch.formatTaskDurations();
StorageProcessingMessage message = new StorageProcessingMessage();
message.setMessage("Transaction timing:\n" + taskDurations);
HookParams params = new HookParams()
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(StorageProcessingMessage.class, message);
CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_INFO, params);
theTransactionStopWatch.endCurrentTask();
}
return response;
}
/**
@ -564,13 +608,69 @@ public abstract class BaseTransactionProcessor {
* heavy load with lots of concurrent transactions using all available
* database connections.
*/
private void doTransactionWriteOperations(RequestDetails theRequestDetails, String theActionName, TransactionDetails theTransactionDetails, StopWatch theTransactionStopWatch, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries) {
TransactionWriteOperationsDetails writeOperationsDetails = null;
if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, myInterceptorBroadcaster, theRequestDetails) ||
CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_POST, myInterceptorBroadcaster, theRequestDetails)) {
private void prepareThenExecuteTransactionWriteOperations(RequestDetails theRequestDetails, String theActionName,
TransactionDetails theTransactionDetails, StopWatch theTransactionStopWatch,
IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder,
List<IBase> theEntries) {
TransactionWriteOperationsDetails writeOperationsDetails = null;
if (haveWriteOperationsHooks(theRequestDetails)) {
writeOperationsDetails = buildWriteOperationsDetails(theEntries);
callWriteOperationsHook(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, theRequestDetails, theTransactionDetails, writeOperationsDetails);
}
TransactionCallback<Map<IBase, IIdType>> txCallback = status -> {
final Set<IIdType> allIds = new LinkedHashSet<>();
final Map<IIdType, IIdType> idSubstitutions = new HashMap<>();
final Map<IIdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
Map<IBase, IIdType> retVal = doTransactionWriteOperations(theRequestDetails, theActionName,
theTransactionDetails, allIds,
idSubstitutions, idToPersistedOutcome,
theResponse, theOriginalRequestOrder,
theEntries, theTransactionStopWatch);
theTransactionStopWatch.startTask("Commit writes to database");
return retVal;
};
Map<IBase, IIdType> entriesToProcess;
try {
entriesToProcess = myHapiTransactionService.execute(theRequestDetails, theTransactionDetails, txCallback);
} finally {
if (haveWriteOperationsHooks(theRequestDetails)) {
callWriteOperationsHook(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_POST, theRequestDetails, theTransactionDetails, writeOperationsDetails);
}
}
theTransactionStopWatch.endCurrentTask();
for (Map.Entry<IBase, IIdType> nextEntry : entriesToProcess.entrySet()) {
String responseLocation = nextEntry.getValue().toUnqualified().getValue();
String responseEtag = nextEntry.getValue().getVersionIdPart();
myVersionAdapter.setResponseLocation(nextEntry.getKey(), responseLocation);
myVersionAdapter.setResponseETag(nextEntry.getKey(), responseEtag);
}
}
private boolean haveWriteOperationsHooks(RequestDetails theRequestDetails) {
return CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, myInterceptorBroadcaster, theRequestDetails) ||
CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_POST, myInterceptorBroadcaster, theRequestDetails);
}
private void callWriteOperationsHook(Pointcut thePointcut, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails, TransactionWriteOperationsDetails theWriteOperationsDetails) {
HookParams params = new HookParams()
.add(TransactionDetails.class, theTransactionDetails)
.add(TransactionWriteOperationsDetails.class, theWriteOperationsDetails);
CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, thePointcut, params);
}
private TransactionWriteOperationsDetails buildWriteOperationsDetails(List<IBase> theEntries) {
TransactionWriteOperationsDetails writeOperationsDetails;
List<String> updateRequestUrls = new ArrayList<>();
List<String> conditionalCreateRequestUrls = new ArrayList<>();
//Extract
for (IBase nextEntry : theEntries) {
String method = myVersionAdapter.getEntryRequestVerb(myContext, nextEntry);
if ("PUT".equals(method)) {
@ -589,43 +689,7 @@ public abstract class BaseTransactionProcessor {
writeOperationsDetails = new TransactionWriteOperationsDetails();
writeOperationsDetails.setUpdateRequestUrls(updateRequestUrls);
writeOperationsDetails.setConditionalCreateRequestUrls(conditionalCreateRequestUrls);
HookParams params = new HookParams()
.add(TransactionDetails.class, theTransactionDetails)
.add(TransactionWriteOperationsDetails.class, writeOperationsDetails);
CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, params);
}
TransactionCallback<Map<IBase, IIdType>> txCallback = status -> {
final Set<IIdType> allIds = new LinkedHashSet<>();
final Map<IIdType, IIdType> idSubstitutions = new HashMap<>();
final Map<IIdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
Map<IBase, IIdType> retVal = doTransactionWriteOperations(theRequestDetails, theActionName, theTransactionDetails, allIds, idSubstitutions, idToPersistedOutcome, theResponse, theOriginalRequestOrder, theEntries, theTransactionStopWatch);
theTransactionStopWatch.startTask("Commit writes to database");
return retVal;
};
Map<IBase, IIdType> entriesToProcess;
try {
entriesToProcess = myHapiTransactionService.execute(theRequestDetails, theTransactionDetails, txCallback);
} finally {
if (writeOperationsDetails != null) {
HookParams params = new HookParams()
.add(TransactionDetails.class, theTransactionDetails)
.add(TransactionWriteOperationsDetails.class, writeOperationsDetails);
CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_POST, params);
}
}
theTransactionStopWatch.endCurrentTask();
for (Map.Entry<IBase, IIdType> nextEntry : entriesToProcess.entrySet()) {
String responseLocation = nextEntry.getValue().toUnqualified().getValue();
String responseEtag = nextEntry.getValue().getVersionIdPart();
myVersionAdapter.setResponseLocation(nextEntry.getKey(), responseLocation);
myVersionAdapter.setResponseETag(nextEntry.getKey(), responseEtag);
}
return writeOperationsDetails;
}
private boolean isValidVerb(String theVerb) {
@ -664,34 +728,19 @@ public abstract class BaseTransactionProcessor {
myModelConfig = theModelConfig;
}
protected Map<IBase, IIdType> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName, TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries, StopWatch theTransactionStopWatch) {
theTransactionDetails.beginAcceptingDeferredInterceptorBroadcasts(
Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED,
Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED,
Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED
);
try {
Set<String> deletedResources = new HashSet<>();
DeleteConflictList deleteConflicts = new DeleteConflictList();
Map<IBase, IIdType> entriesToProcess = new IdentityHashMap<>();
Set<IIdType> nonUpdatedEntities = new HashSet<>();
Set<IBasePersistedResource> updatedEntities = new HashSet<>();
List<IBaseResource> updatedResources = new ArrayList<>();
Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<>();
/*
* Look for duplicate conditional creates and consolidate them
/**
* Searches for duplicate conditional creates and consolidates them.
*
* @param theEntries
*/
private void consolidateDuplicateConditionals(List<IBase> theEntries) {
final HashMap<String, String> keyToUuid = new HashMap<>();
for (int index = 0, originalIndex = 0; index < theEntries.size(); index++, originalIndex++) {
IBase nextReqEntry = theEntries.get(index);
IBaseResource resource = myVersionAdapter.getResource(nextReqEntry);
if (resource != null) {
String verb = myVersionAdapter.getEntryRequestVerb(myContext, nextReqEntry);
String entryUrl = myVersionAdapter.getFullUrl(nextReqEntry);
String entryFullUrl = myVersionAdapter.getFullUrl(nextReqEntry);
String requestUrl = myVersionAdapter.getEntryRequestUrl(nextReqEntry);
String ifNoneExist = myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry);
String key = verb + "|" + requestUrl + "|" + ifNoneExist;
@ -699,7 +748,7 @@ public abstract class BaseTransactionProcessor {
// Conditional UPDATE
boolean consolidateEntry = false;
if ("PUT".equals(verb)) {
if (isNotBlank(entryUrl) && isNotBlank(requestUrl)) {
if (isNotBlank(entryFullUrl) && isNotBlank(requestUrl)) {
int questionMarkIndex = requestUrl.indexOf('?');
if (questionMarkIndex >= 0 && requestUrl.length() > (questionMarkIndex + 1)) {
consolidateEntry = true;
@ -709,8 +758,8 @@ public abstract class BaseTransactionProcessor {
// Conditional CREATE
if ("POST".equals(verb)) {
if (isNotBlank(entryUrl) && isNotBlank(requestUrl) && isNotBlank(ifNoneExist)) {
if (!entryUrl.equals(requestUrl)) {
if (isNotBlank(entryFullUrl) && isNotBlank(requestUrl) && isNotBlank(ifNoneExist)) {
if (!entryFullUrl.equals(requestUrl)) {
consolidateEntry = true;
}
}
@ -718,12 +767,24 @@ public abstract class BaseTransactionProcessor {
if (consolidateEntry) {
if (!keyToUuid.containsKey(key)) {
keyToUuid.put(key, entryUrl);
keyToUuid.put(key, entryFullUrl);
} else {
ourLog.info("Discarding transaction bundle entry {} as it contained a duplicate conditional {}", originalIndex, verb);
theEntries.remove(index);
index--;
String existingUuid = keyToUuid.get(key);
replaceReferencesInEntriesWithConsolidatedUUID(theEntries, entryFullUrl, existingUuid);
}
}
}
}
}
/**
* Iterates over all entries, and if it finds any which have references which match the fullUrl of the entry that was consolidated out
* replace them with our new consolidated UUID
*/
private void replaceReferencesInEntriesWithConsolidatedUUID(List<IBase> theEntries, String theEntryFullUrl, String existingUuid) {
for (IBase nextEntry : theEntries) {
IBaseResource nextResource = myVersionAdapter.getResource(nextEntry);
for (IBaseReference nextReference : myContext.newTerser().getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class)) {
@ -733,36 +794,29 @@ public abstract class BaseTransactionProcessor {
if (isBlank(nextReferenceId) && nextReference.getResource() != null) {
nextReferenceId = nextReference.getResource().getIdElement().getValue();
}
if (entryUrl.equals(nextReferenceId)) {
if (theEntryFullUrl.equals(nextReferenceId)) {
nextReference.setReference(existingUuid);
nextReference.setResource(null);
}
}
}
}
}
}
}
/*
* Loop through the request and process any entries of type
* PUT, POST or DELETE
/**
* Retrieves the next resource id (IIdType) from the base resource and next request entry.
* @param theBaseResource - base resource
* @param theNextReqEntry - next request entry
* @param theAllIds - set of all IIdType values
* @return
*/
for (int i = 0; i < theEntries.size(); i++) {
if (i % 250 == 0) {
ourLog.debug("Processed {} non-GET entries out of {} in transaction", i, theEntries.size());
}
IBase nextReqEntry = theEntries.get(i);
IBaseResource res = myVersionAdapter.getResource(nextReqEntry);
private IIdType getNextResourceIdFromBaseResource(IBaseResource theBaseResource,
IBase theNextReqEntry,
Set<IIdType> theAllIds) {
IIdType nextResourceId = null;
if (res != null) {
if (theBaseResource != null) {
nextResourceId = theBaseResource.getIdElement();
nextResourceId = res.getIdElement();
String fullUrl = myVersionAdapter.getFullUrl(nextReqEntry);
String fullUrl = myVersionAdapter.getFullUrl(theNextReqEntry);
if (isNotBlank(fullUrl)) {
IIdType fullUrlIdType = newIdType(fullUrl);
if (isPlaceholder(fullUrlIdType)) {
@ -777,8 +831,8 @@ public abstract class BaseTransactionProcessor {
}
if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !isPlaceholder(nextResourceId)) {
nextResourceId = newIdType(toResourceName(res.getClass()), nextResourceId.getIdPart());
res.setId(nextResourceId);
nextResourceId = newIdType(toResourceName(theBaseResource.getClass()), nextResourceId.getIdPart());
theBaseResource.setId(nextResourceId);
}
/*
@ -797,6 +851,52 @@ public abstract class BaseTransactionProcessor {
}
return nextResourceId;
}
/** After pre-hooks have been called
*
*/
protected Map<IBase, IIdType> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName,
TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder,
List<IBase> theEntries, StopWatch theTransactionStopWatch) {
// During a transaction, we don't execute hooks, instead, we execute them all post-transaction.
theTransactionDetails.beginAcceptingDeferredInterceptorBroadcasts(
Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED,
Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED,
Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED
);
try {
Set<String> deletedResources = new HashSet<>();
DeleteConflictList deleteConflicts = new DeleteConflictList();
Map<IBase, IIdType> entriesToProcess = new IdentityHashMap<>();
Set<IIdType> nonUpdatedEntities = new HashSet<>();
Set<IBasePersistedResource> updatedEntities = new HashSet<>();
Map<String, IIdType> conditionalUrlToIdMap = new HashMap<>();
List<IBaseResource> updatedResources = new ArrayList<>();
Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<>();
/*
* Look for duplicate conditional creates and consolidate them
*/
consolidateDuplicateConditionals(theEntries);
/*
* Loop through the request and process any entries of type
* PUT, POST or DELETE
*/
for (int i = 0; i < theEntries.size(); i++) {
if (i % 250 == 0) {
ourLog.debug("Processed {} non-GET entries out of {} in transaction", i, theEntries.size());
}
IBase nextReqEntry = theEntries.get(i);
IBaseResource res = myVersionAdapter.getResource(nextReqEntry);
IIdType nextResourceId = getNextResourceIdFromBaseResource(res, nextReqEntry, theAllIds);
String verb = myVersionAdapter.getEntryRequestVerb(myContext, nextReqEntry);
String resourceType = res != null ? myContext.getResourceType(res) : null;
Integer order = theOriginalRequestOrder.get(nextReqEntry);
@ -815,6 +915,7 @@ public abstract class BaseTransactionProcessor {
String matchUrl = myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry);
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
outcome = resourceDao.create(res, matchUrl, false, theTransactionDetails, theRequest);
setConditionalUrlToBeValidatedLater(conditionalUrlToIdMap, matchUrl, outcome.getId());
res.setId(outcome.getId());
if (nextResourceId != null) {
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequest);
@ -849,6 +950,7 @@ public abstract class BaseTransactionProcessor {
String matchUrl = parts.getResourceType() + '?' + parts.getParams();
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
DeleteMethodOutcome deleteOutcome = dao.deleteByUrl(matchUrl, deleteConflicts, theRequest);
setConditionalUrlToBeValidatedLater(conditionalUrlToIdMap, matchUrl, deleteOutcome.getId());
List<ResourceTable> allDeleted = deleteOutcome.getDeletedEntities();
for (ResourceTable deleted : allDeleted) {
deletedResources.add(deleted.getIdDt().toUnqualifiedVersionless().getValueAsString());
@ -891,6 +993,7 @@ public abstract class BaseTransactionProcessor {
}
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
outcome = resourceDao.update(res, matchUrl, false, false, theRequest, theTransactionDetails);
setConditionalUrlToBeValidatedLater(conditionalUrlToIdMap, matchUrl, outcome.getId());
if (Boolean.TRUE.equals(outcome.getCreated())) {
conditionalRequestUrls.put(matchUrl, res.getClass());
}
@ -904,7 +1007,8 @@ public abstract class BaseTransactionProcessor {
}
}
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequest);
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId,
outcome, nextRespEntry, resourceType, res, theRequest);
entriesToProcess.put(nextRespEntry, outcome.getId());
break;
}
@ -948,6 +1052,7 @@ public abstract class BaseTransactionProcessor {
IFhirResourceDao<? extends IBaseResource> dao = toDao(parts, verb, url);
IIdType patchId = myContext.getVersion().newIdType().setValue(parts.getResourceId());
DaoMethodOutcome outcome = dao.patch(patchId, matchUrl, patchType, patchBody, patchBodyParameters, theRequest);
setConditionalUrlToBeValidatedLater(conditionalUrlToIdMap, matchUrl, outcome.getId());
updatedEntities.add(outcome.getEntity());
if (outcome.getResource() != null) {
updatedResources.add(outcome.getResource());
@ -971,52 +1076,24 @@ public abstract class BaseTransactionProcessor {
* was also deleted as a part of this transaction, which is why we check this now at the
* end.
*/
for (Iterator<DeleteConflict> iter = deleteConflicts.iterator(); iter.hasNext(); ) {
DeleteConflict nextDeleteConflict = iter.next();
checkForDeleteConflicts(deleteConflicts, deletedResources, updatedResources);
/*
* If we have a conflict, it means we can't delete Resource/A because
* Resource/B has a reference to it. We'll ignore that conflict though
* if it turns out we're also deleting Resource/B in this transaction.
*/
if (deletedResources.contains(nextDeleteConflict.getSourceId().toUnqualifiedVersionless().getValue())) {
iter.remove();
continue;
}
/*
* And then, this is kind of a last ditch check. It's also ok to delete
* Resource/A if Resource/B isn't being deleted, but it is being UPDATED
* in this transaction, and the updated version of it has no references
* to Resource/A any more.
*/
String sourceId = nextDeleteConflict.getSourceId().toUnqualifiedVersionless().getValue();
String targetId = nextDeleteConflict.getTargetId().toUnqualifiedVersionless().getValue();
Optional<IBaseResource> updatedSource = updatedResources
.stream()
.filter(t -> sourceId.equals(t.getIdElement().toUnqualifiedVersionless().getValue()))
.findFirst();
if (updatedSource.isPresent()) {
List<ResourceReferenceInfo> referencesInSource = myContext.newTerser().getAllResourceReferences(updatedSource.get());
boolean sourceStillReferencesTarget = referencesInSource
.stream()
.anyMatch(t -> targetId.equals(t.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue()));
if (!sourceStillReferencesTarget) {
iter.remove();
}
}
}
DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(myContext, deleteConflicts);
theIdToPersistedOutcome.entrySet().forEach(t -> theTransactionDetails.addResolvedResourceId(t.getKey(), t.getValue().getPersistentId()));
theIdToPersistedOutcome.entrySet().forEach(idAndOutcome -> {
theTransactionDetails.addResolvedResourceId(idAndOutcome.getKey(), idAndOutcome.getValue().getPersistentId());
});
/*
* Perform ID substitutions and then index each resource we have saved
*/
resolveReferencesThenSaveAndIndexResources(theRequest, theTransactionDetails, theIdSubstitutions, theIdToPersistedOutcome, theTransactionStopWatch, entriesToProcess, nonUpdatedEntities, updatedEntities);
resolveReferencesThenSaveAndIndexResources(theRequest, theTransactionDetails,
theIdSubstitutions, theIdToPersistedOutcome,
theTransactionStopWatch, entriesToProcess,
nonUpdatedEntities, updatedEntities);
theTransactionStopWatch.endCurrentTask();
// flush writes to db
theTransactionStopWatch.startTask("Flush writes to database");
flushSession(theIdToPersistedOutcome);
@ -1032,6 +1109,15 @@ public abstract class BaseTransactionProcessor {
if (!myDaoConfig.isMassIngestionMode()) {
validateNoDuplicates(theRequest, theActionName, conditionalRequestUrls, theIdToPersistedOutcome.values());
}
theTransactionStopWatch.endCurrentTask();
if (conditionalUrlToIdMap.size() > 0) {
theTransactionStopWatch.startTask("Check that all conditionally created/updated entities actually match their conditionals.");
}
if (!myDaoConfig.isMassIngestionMode()) {
validateAllInsertsMatchTheirConditionalUrls(theIdToPersistedOutcome, conditionalUrlToIdMap, theRequest);
}
theTransactionStopWatch.endCurrentTask();
for (IIdType next : theAllIds) {
@ -1070,6 +1156,86 @@ public abstract class BaseTransactionProcessor {
}
}
private void setConditionalUrlToBeValidatedLater(Map<String, IIdType> theConditionalUrlToIdMap, String theMatchUrl, IIdType theId) {
if (!StringUtils.isBlank(theMatchUrl)) {
theConditionalUrlToIdMap.put(theMatchUrl, theId);
}
}
/**
* After transaction processing and resolution of indexes and references, we want to validate that the resources that were stored _actually_
* match the conditional URLs that they were brought in on.
* @param theIdToPersistedOutcome
* @param conditionalUrlToIdMap
*/
private void validateAllInsertsMatchTheirConditionalUrls(Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, Map<String, IIdType> conditionalUrlToIdMap, RequestDetails theRequest) {
conditionalUrlToIdMap.entrySet().stream()
.filter(entry -> entry.getKey() != null)
.forEach(entry -> {
String matchUrl = entry.getKey();
IIdType value = entry.getValue();
DaoMethodOutcome daoMethodOutcome = theIdToPersistedOutcome.get(value);
if (daoMethodOutcome != null && !daoMethodOutcome.isNop() && daoMethodOutcome.getResource() != null) {
InMemoryMatchResult match = mySearchParamMatcher.match(matchUrl, daoMethodOutcome.getResource(), theRequest);
if (ourLog.isDebugEnabled()) {
ourLog.debug("Checking conditional URL [{}] against resource with ID [{}]: Supported?:[{}], Matched?:[{}]", matchUrl, value, match.supported(), match.matched());
}
if (match.supported()) {
if (!match.matched()) {
throw new PreconditionFailedException("Invalid conditional URL \"" + matchUrl + "\". The given resource is not matched by this URL.");
};
}
}
});
}
/**
* Checks for any delete conflicts.
* @param theDeleteConflicts - set of delete conflicts
* @param theDeletedResources - set of deleted resources
* @param theUpdatedResources - list of updated resources
*/
private void checkForDeleteConflicts(DeleteConflictList theDeleteConflicts,
Set<String> theDeletedResources,
List<IBaseResource> theUpdatedResources) {
for (Iterator<DeleteConflict> iter = theDeleteConflicts.iterator(); iter.hasNext(); ) {
DeleteConflict nextDeleteConflict = iter.next();
/*
* If we have a conflict, it means we can't delete Resource/A because
* Resource/B has a reference to it. We'll ignore that conflict though
* if it turns out we're also deleting Resource/B in this transaction.
*/
if (theDeletedResources.contains(nextDeleteConflict.getSourceId().toUnqualifiedVersionless().getValue())) {
iter.remove();
continue;
}
/*
* And then, this is kind of a last ditch check. It's also ok to delete
* Resource/A if Resource/B isn't being deleted, but it is being UPDATED
* in this transaction, and the updated version of it has no references
* to Resource/A any more.
*/
String sourceId = nextDeleteConflict.getSourceId().toUnqualifiedVersionless().getValue();
String targetId = nextDeleteConflict.getTargetId().toUnqualifiedVersionless().getValue();
Optional<IBaseResource> updatedSource = theUpdatedResources
.stream()
.filter(t -> sourceId.equals(t.getIdElement().toUnqualifiedVersionless().getValue()))
.findFirst();
if (updatedSource.isPresent()) {
List<ResourceReferenceInfo> referencesInSource = myContext.newTerser().getAllResourceReferences(updatedSource.get());
boolean sourceStillReferencesTarget = referencesInSource
.stream()
.anyMatch(t -> targetId.equals(t.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue()));
if (!sourceStillReferencesTarget) {
iter.remove();
}
}
}
DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(myContext, theDeleteConflicts);
}
/**
* This method replaces any placeholder references in the
* source transaction Bundle with their actual targets, then stores the resource contents and indexes
@ -1092,7 +1258,10 @@ public abstract class BaseTransactionProcessor {
* pass because it's too complex to try and insert the auto-versioned references and still
* account for NOPs, so we block NOPs in that pass.
*/
private void resolveReferencesThenSaveAndIndexResources(RequestDetails theRequest, TransactionDetails theTransactionDetails, Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, StopWatch theTransactionStopWatch, Map<IBase, IIdType> entriesToProcess, Set<IIdType> nonUpdatedEntities, Set<IBasePersistedResource> updatedEntities) {
private void resolveReferencesThenSaveAndIndexResources(RequestDetails theRequest, TransactionDetails theTransactionDetails,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
StopWatch theTransactionStopWatch, Map<IBase, IIdType> entriesToProcess,
Set<IIdType> nonUpdatedEntities, Set<IBasePersistedResource> updatedEntities) {
FhirTerser terser = myContext.newTerser();
theTransactionStopWatch.startTask("Index " + theIdToPersistedOutcome.size() + " resources");
IdentityHashMap<DaoMethodOutcome, Set<IBaseReference>> deferredIndexesForAutoVersioning = null;
@ -1114,8 +1283,15 @@ public abstract class BaseTransactionProcessor {
Set<IBaseReference> referencesToAutoVersion = BaseStorageDao.extractReferencesToAutoVersion(myContext, myModelConfig, nextResource);
if (referencesToAutoVersion.isEmpty()) {
resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails, theIdSubstitutions, theIdToPersistedOutcome, entriesToProcess, nonUpdatedEntities, updatedEntities, terser, nextOutcome, nextResource, referencesToAutoVersion);
// no references to autoversion - we can do the resolve and save now
resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails,
theIdSubstitutions, theIdToPersistedOutcome,
entriesToProcess, nonUpdatedEntities,
updatedEntities, terser,
nextOutcome, nextResource,
referencesToAutoVersion); // this is empty
} else {
// we have autoversioned things to defer until later
if (deferredIndexesForAutoVersioning == null) {
deferredIndexesForAutoVersioning = new IdentityHashMap<>();
}
@ -1129,12 +1305,24 @@ public abstract class BaseTransactionProcessor {
DaoMethodOutcome nextOutcome = nextEntry.getKey();
Set<IBaseReference> referencesToAutoVersion = nextEntry.getValue();
IBaseResource nextResource = nextOutcome.getResource();
resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails, theIdSubstitutions, theIdToPersistedOutcome, entriesToProcess, nonUpdatedEntities, updatedEntities, terser, nextOutcome, nextResource, referencesToAutoVersion);
resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails,
theIdSubstitutions, theIdToPersistedOutcome,
entriesToProcess, nonUpdatedEntities,
updatedEntities, terser,
nextOutcome, nextResource,
referencesToAutoVersion);
}
}
}
private void resolveReferencesThenSaveAndIndexResource(RequestDetails theRequest, TransactionDetails theTransactionDetails, Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, Map<IBase, IIdType> entriesToProcess, Set<IIdType> nonUpdatedEntities, Set<IBasePersistedResource> updatedEntities, FhirTerser terser, DaoMethodOutcome nextOutcome, IBaseResource nextResource, Set<IBaseReference> theReferencesToAutoVersion) {
private void resolveReferencesThenSaveAndIndexResource(RequestDetails theRequest, TransactionDetails theTransactionDetails,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
Map<IBase, IIdType> entriesToProcess, Set<IIdType> nonUpdatedEntities,
Set<IBasePersistedResource> updatedEntities, FhirTerser terser,
DaoMethodOutcome nextOutcome, IBaseResource nextResource,
Set<IBaseReference> theReferencesToAutoVersion) {
// References
List<ResourceReferenceInfo> allRefs = terser.getAllResourceReferences(nextResource);
for (ResourceReferenceInfo nextRef : allRefs) {
@ -1175,9 +1363,34 @@ public abstract class BaseTransactionProcessor {
} else if (nextId.getValue().startsWith("urn:")) {
throw new InvalidRequestException("Unable to satisfy placeholder ID " + nextId.getValue() + " found in element named '" + nextRef.getName() + "' within resource of type: " + nextResource.getIdElement().getResourceType());
} else {
// get a map of
// existing ids -> PID (for resources that exist in the DB)
// should this be allPartitions?
ResourcePersistentIdMap resourceVersionMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(RequestPartitionId.allPartitions(),
theReferencesToAutoVersion.stream()
.map(IBaseReference::getReferenceElement).collect(Collectors.toList()));
for (IBaseReference baseRef : theReferencesToAutoVersion) {
IIdType id = baseRef.getReferenceElement();
if (!resourceVersionMap.containsKey(id)
&& myDaoConfig.isAutoCreatePlaceholderReferenceTargets()) {
// not in the db, but autocreateplaceholders is true
// so the version we'll set is "1" (since it will be
// created later)
String newRef = id.withVersion("1").getValue();
id.setValue(newRef);
} else {
// we will add the looked up info to the transaction
// for later
theTransactionDetails.addResolvedResourceId(id,
resourceVersionMap.getResourcePersistentId(id));
}
}
if (theReferencesToAutoVersion.contains(resourceReference)) {
DaoMethodOutcome outcome = theIdToPersistedOutcome.get(nextId);
if (!outcome.isNop() && !Boolean.TRUE.equals(outcome.getCreated())) {
if (outcome != null && !outcome.isNop() && !Boolean.TRUE.equals(outcome.getCreated())) {
addRollbackReferenceRestore(theTransactionDetails, resourceReference);
resourceReference.setReference(nextId.getValue());
resourceReference.setResource(null);
@ -1266,7 +1479,7 @@ public abstract class BaseTransactionProcessor {
thePersistedOutcomes
.stream()
.filter(t -> !t.isNop())
.filter(t -> t.getEntity() instanceof ResourceTable)
.filter(t -> t.getEntity() instanceof ResourceTable)//N.B. GGG: This validation never occurs for mongo, as nothing is a ResourceTable.
.filter(t -> t.getEntity().getDeleted() == null)
.filter(t -> t.getResource() != null)
.forEach(t -> resourceToIndexedParams.put(t.getResource(), new ResourceIndexedSearchParams((ResourceTable) t.getEntity())));
@ -1565,30 +1778,29 @@ public abstract class BaseTransactionProcessor {
return theStatusCode + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
}
public class BundleTask implements Runnable {
public class RetriableBundleTask implements Runnable {
private CountDownLatch myCompletedLatch;
private RequestDetails myRequestDetails;
private IBase myNextReqEntry;
private Map<Integer, Object> myResponseMap;
private int myResponseOrder;
private boolean myNestedMode;
private final CountDownLatch myCompletedLatch;
private final RequestDetails myRequestDetails;
private final IBase myNextReqEntry;
private final Map<Integer, Object> myResponseMap;
private final int myResponseOrder;
private final boolean myNestedMode;
private BaseServerResponseException myLastSeenException;
protected BundleTask(CountDownLatch theCompletedLatch, RequestDetails theRequestDetails, Map<Integer, Object> theResponseMap, int theResponseOrder, IBase theNextReqEntry, boolean theNestedMode) {
protected RetriableBundleTask(CountDownLatch theCompletedLatch, RequestDetails theRequestDetails, Map<Integer, Object> theResponseMap, int theResponseOrder, IBase theNextReqEntry, boolean theNestedMode) {
this.myCompletedLatch = theCompletedLatch;
this.myRequestDetails = theRequestDetails;
this.myNextReqEntry = theNextReqEntry;
this.myResponseMap = theResponseMap;
this.myResponseOrder = theResponseOrder;
this.myNestedMode = theNestedMode;
this.myLastSeenException = null;
}
@Override
public void run() {
BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
try {
private void processBatchEntry() {
IBaseBundle subRequestBundle = myVersionAdapter.createBundle(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION.toCode());
myVersionAdapter.addEntry(subRequestBundle, (IBase) myNextReqEntry);
myVersionAdapter.addEntry(subRequestBundle, myNextReqEntry);
IBaseBundle nextResponseBundle = processTransactionAsSubRequest(myRequestDetails, subRequestBundle, "Batch sub-request", myNestedMode);
@ -1602,22 +1814,45 @@ public abstract class BaseTransactionProcessor {
IBase nextResponseBundleFirstEntry = (IBase) myVersionAdapter.getEntries(nextResponseBundle).get(0);
myResponseMap.put(myResponseOrder, nextResponseBundleFirstEntry);
}
}
private boolean processBatchEntryWithRetry() {
int maxAttempts =3;
for (int attempt = 1;; attempt++) {
try {
processBatchEntry();
return true;
} catch (BaseServerResponseException e) {
caughtEx.setException(e);
//If we catch a known and structured exception from HAPI, just fail.
myLastSeenException = e;
return false;
} catch (Throwable t) {
myLastSeenException = new InternalErrorException(t);
//If we have caught a non-tag-storage failure we are unfamiliar with, or we have exceeded max attempts, exit.
if (!DaoFailureUtil.isTagStorageFailure(t) || attempt >= maxAttempts) {
ourLog.error("Failure during BATCH sub transaction processing", t);
caughtEx.setException(new InternalErrorException(t));
return false;
}
}
}
}
if (caughtEx.getException() != null) {
// add exception to the response map
myResponseMap.put(myResponseOrder, caughtEx);
@Override
public void run() {
boolean success = processBatchEntryWithRetry();
if (!success) {
populateResponseMapWithLastSeenException();
}
// checking for the parallelism
ourLog.debug("processing bacth for {} is completed", myVersionAdapter.getEntryRequestUrl((IBase)myNextReqEntry));
ourLog.debug("processing batch for {} is completed", myVersionAdapter.getEntryRequestUrl(myNextReqEntry));
myCompletedLatch.countDown();
}
private void populateResponseMapWithLastSeenException() {
BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
caughtEx.setException(myLastSeenException);
myResponseMap.put(myResponseOrder, caughtEx);
}
}
}

38
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoFailureUtil.java Normal file
View File

@ -0,0 +1,38 @@
package ca.uhn.fhir.jpa.dao;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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 org.apache.commons.lang3.StringUtils;
/**
* Utility class to help identify classes of failure.
*/
public class DaoFailureUtil {
public static boolean isTagStorageFailure(Throwable t) {
if (StringUtils.isBlank(t.getMessage())) {
return false;
} else {
String msg = t.getMessage().toLowerCase();
return msg.contains("hfj_tag_def") || msg.contains("hfj_res_tag");
}
}
}

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

@ -100,6 +100,16 @@ public interface IResourceTableDao extends JpaRepository<ResourceTable, Long> {
@Query("SELECT t.myVersion FROM ResourceTable t WHERE t.myId = :pid")
Long findCurrentVersionByPid(@Param("pid") Long thePid);
/**
* This query will return rows with the following values:
* Id (resource pid - long), ResourceType (Patient, etc), version (long)
* Order matters!
* @param pid - list of pids to get versions for
* @return
*/
@Query("SELECT t.myId, t.myResourceType, t.myVersion FROM ResourceTable t WHERE t.myId IN ( :pid )")
Collection<Object[]> getResourceVersionsForPid(@Param("pid") List<Long> pid);
@Query("SELECT t FROM ResourceTable t LEFT JOIN FETCH t.myForcedId WHERE t.myPartitionId.myPartitionId IS NULL AND t.myId = :pid")
Optional<ResourceTable> readByPartitionIdNull(@Param("pid") Long theResourceId);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
View File

@ -94,7 +94,6 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
throw new InvalidRequestException("Resource " + resName + "/" + idPart + " not found, specified in path: " + theSourcePath);
}
resolvedResource = createdTableOpt.get();
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
View File

@ -34,6 +34,7 @@ import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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 com.google.common.annotations.VisibleForTesting;
@ -204,7 +205,11 @@ public class IdHelperService {
*/
@Nonnull
public List<ResourcePersistentId> resolveResourcePersistentIdsWithCache(RequestPartitionId theRequestPartitionId, List<IIdType> theIds) {
theIds.forEach(id -> Validate.isTrue(id.hasIdPart()));
for (IIdType id : theIds) {
if (!id.hasIdPart()) {
throw new InvalidRequestException("Parameter value missing in request");
}
}
if (theIds.isEmpty()) {
return Collections.emptyList();
@ -303,7 +308,7 @@ public class IdHelperService {
if (forcedId.isPresent()) {
retVal.setValue(theResourceType + '/' + forcedId.get());
} else {
retVal.setValue(theResourceType + '/' + theId.toString());
retVal.setValue(theResourceType + '/' + theId);
}
return retVal;

47
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java
View File

@ -559,11 +559,6 @@ class PredicateBuilderReference extends BasePredicateBuilder {
myPredicateBuilder.addPredicateResourceId(theAndOrParams, theResourceName, theRequestPartitionId);
break;
case IAnyResource.SP_RES_LANGUAGE:
addPredicateLanguage(theAndOrParams,
null);
break;
case Constants.PARAM_HAS:
addPredicateHas(theResourceName, theAndOrParams, theRequest, theRequestPartitionId);
break;
@ -733,9 +728,6 @@ class PredicateBuilderReference extends BasePredicateBuilder {
null,
theFilter.getValue());
return myPredicateBuilder.addPredicateResourceId(Collections.singletonList(Collections.singletonList(param)), myResourceName, theFilter.getOperation(), theRequestPartitionId);
} else if (theFilter.getParamPath().getName().equals(IAnyResource.SP_RES_LANGUAGE)) {
return addPredicateLanguage(Collections.singletonList(Collections.singletonList(new StringParam(theFilter.getValue()))),
theFilter.getOperation());
}
RuntimeSearchParam searchParam = mySearchParamRegistry.getActiveSearchParam(theResourceName, theFilter.getParamPath().getName());
@ -828,45 +820,6 @@ class PredicateBuilderReference extends BasePredicateBuilder {
return qp;
}
private Predicate addPredicateLanguage(List<List<IQueryParameterType>> theList,
SearchFilterParser.CompareOperation operation) {
for (List<? extends IQueryParameterType> nextList : theList) {
Set<String> values = new HashSet<>();
for (IQueryParameterType next : nextList) {
if (next instanceof StringParam) {
String nextValue = ((StringParam) next).getValue();
if (isBlank(nextValue)) {
continue;
}
values.add(nextValue);
} else {
throw new InternalErrorException("Language parameter must be of type " + StringParam.class.getCanonicalName() + " - Got " + next.getClass().getCanonicalName());
}
}
if (values.isEmpty()) {
continue;
}
Predicate predicate;
if ((operation == null) ||
(operation == SearchFilterParser.CompareOperation.eq)) {
predicate = myQueryStack.get("myLanguage").as(String.class).in(values);
} else if (operation == SearchFilterParser.CompareOperation.ne) {
predicate = myQueryStack.get("myLanguage").as(String.class).in(values).not();
} else {
throw new InvalidRequestException("Unsupported operator specified in language query, only \"eq\" and \"ne\" are supported");
}
myQueryStack.addPredicate(predicate);
if (operation != null) {
return predicate;
}
}
return null;
}
private void addPredicateSource(List<List<IQueryParameterType>> theAndOrParams, RequestDetails theRequest) {
for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
addPredicateSource(nextAnd, SearchFilterParser.CompareOperation.eq, theRequest);

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderToken.java
View File

@ -261,6 +261,9 @@ class PredicateBuilderToken extends BasePredicateBuilder implements IPredicateBu
if (theSearchParam != null) {
Set<String> valueSetUris = Sets.newHashSet();
for (String nextPath : theSearchParam.getPathsSplit()) {
if (!nextPath.startsWith(myResourceType + ".")) {
continue;
}
BaseRuntimeChildDefinition def = myContext.newTerser().getDefinition(myResourceType, nextPath);
if (def instanceof BaseRuntimeDeclaredChildDefinition) {
String valueSet = ((BaseRuntimeDeclaredChildDefinition) def).getBindingValueSet();

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSearchParameterR4.java
View File

@ -92,11 +92,15 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
for (IPrimitiveType<?> nextBaseType : theResource.getBase()) {
String nextBase = nextBaseType.getValueAsString();
RuntimeSearchParam existingSearchParam = theSearchParamRegistry.getActiveSearchParam(nextBase, theResource.getCode());
if (existingSearchParam != null && existingSearchParam.getId() == null) {
if (existingSearchParam != null) {
boolean isBuiltIn = existingSearchParam.getId() == null;
isBuiltIn |= existingSearchParam.getUri().startsWith("http://hl7.org/fhir/SearchParameter/");
if (isBuiltIn) {
throw new UnprocessableEntityException("Can not override built-in search parameter " + nextBase + ":" + theResource.getCode() + " because overriding is disabled on this server");
}
}
}
}
/*
* Everything below is validating that the SP is actually valid. We'll only do that if the

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.model.ResourceVersionConflictResolutionStrategy;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.DaoFailureUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -93,10 +94,9 @@ public class HapiTransactionService {
* known to the system already, they'll both try to create a row in HFJ_TAG_DEF,
* which is the tag definition table. In that case, a constraint error will be
* thrown by one of the client threads, so we auto-retry in order to avoid
* annopying spurious failures for the client.
* annoying spurious failures for the client.
*/
if (e.getMessage().contains("HFJ_TAG_DEF") || e.getMessage().contains("hfj_tag_def") ||
e.getMessage().contains("HFJ_RES_TAG") || e.getMessage().contains("hfj_res_tag")) {
if (DaoFailureUtil.isTagStorageFailure(e)) {
maxRetries = 3;
}

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

@ -82,7 +82,6 @@ import org.springframework.data.domain.Sort;
import org.springframework.orm.jpa.JpaDialect;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.stereotype.Component;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
@ -111,7 +110,6 @@ import java.util.UUID;
import java.util.concurrent.Callable;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
@ -123,7 +121,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
public static final Integer INTEGER_0 = 0;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchCoordinatorSvcImpl.class);
private final ConcurrentHashMap<String, SearchTask> myIdToSearchTask = new ConcurrentHashMap<>();
private final ExecutorService myExecutor;
@Autowired
private FhirContext myContext;
@Autowired
@ -162,8 +159,13 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
* Constructor
*/
@Autowired
public SearchCoordinatorSvcImpl(ThreadPoolTaskExecutor searchCoordinatorThreadFactory) {
myExecutor = searchCoordinatorThreadFactory.getThreadPoolExecutor();
public SearchCoordinatorSvcImpl() {
super();
}
@VisibleForTesting
Set<String> getActiveSearchIds() {
return myIdToSearchTask.keySet();
}
@VisibleForTesting
@ -274,7 +276,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(theRequestDetails, resourceType, params, null);
SearchContinuationTask task = new SearchContinuationTask(search, resourceDao, params, resourceType, theRequestDetails, requestPartitionId);
myIdToSearchTask.put(search.getUuid(), task);
myExecutor.submit(task);
task.call();
}
}
@ -406,7 +408,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
SearchTask task = new SearchTask(theSearch, theCallingDao, theParams, theResourceType, theRequestDetails, theRequestPartitionId);
myIdToSearchTask.put(theSearch.getUuid(), task);
myExecutor.submit(task);
task.call();
PersistedJpaSearchFirstPageBundleProvider retVal = myPersistedJpaBundleProviderFactory.newInstanceFirstPage(theRequestDetails, theSearch, task, theSb);
@ -1087,7 +1089,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
ourLog.trace("Performing count");
ISearchBuilder sb = newSearchBuilder();
Iterator<Long> countIterator = sb.createCountQuery(myParams, mySearch.getUuid(), myRequest, myRequestPartitionId);
Long count = countIterator.hasNext() ? countIterator.next() : 0;
Long count = countIterator.hasNext() ? countIterator.next() : 0L;
ourLog.trace("Got count {}", count);
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);

88
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
View File

@ -434,9 +434,6 @@ public class QueryStack {
param.setValueAsQueryToken(null, null, null, theFilter.getValue());
return theQueryStack3.createPredicateResourceId(null, Collections.singletonList(Collections.singletonList(param)), theResourceName, theFilter.getOperation(), theRequestPartitionId);
}
case IAnyResource.SP_RES_LANGUAGE: {
return theQueryStack3.createPredicateLanguage(Collections.singletonList(Collections.singletonList(new StringParam(theFilter.getValue()))), theFilter.getOperation());
}
case Constants.PARAM_SOURCE: {
TokenParam param = new TokenParam();
param.setValueAsQueryToken(null, null, null, theFilter.getValue());
@ -579,44 +576,6 @@ public class QueryStack {
return toAndPredicate(andPredicates);
}
public Condition createPredicateLanguage(List<List<IQueryParameterType>> theList, Object theOperation) {
ResourceTablePredicateBuilder rootTable = mySqlBuilder.getOrCreateResourceTablePredicateBuilder();
List<Condition> predicates = new ArrayList<>();
for (List<? extends IQueryParameterType> nextList : theList) {
Set<String> values = new HashSet<>();
for (IQueryParameterType next : nextList) {
if (next instanceof StringParam) {
String nextValue = ((StringParam) next).getValue();
if (isBlank(nextValue)) {
continue;
}
values.add(nextValue);
} else {
throw new InternalErrorException("Language parameter must be of type " + StringParam.class.getCanonicalName() + " - Got " + next.getClass().getCanonicalName());
}
}
if (values.isEmpty()) {
continue;
}
if ((theOperation == null) ||
(theOperation == SearchFilterParser.CompareOperation.eq)) {
predicates.add(rootTable.createLanguagePredicate(values, false));
} else if (theOperation == SearchFilterParser.CompareOperation.ne) {
predicates.add(rootTable.createLanguagePredicate(values, true));
} else {
throw new InvalidRequestException("Unsupported operator specified in language query, only \"eq\" and \"ne\" are supported");
}
}
return toAndPredicate(predicates);
}
public Condition createPredicateNumber(@Nullable DbColumn theSourceJoinColumn, String theResourceName,
String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
@ -729,7 +688,7 @@ public class QueryStack {
return predicateBuilder.createPredicate(theRequest, theResourceName, theParamName, theList, theOperation, theRequestPartitionId);
}
private Condition createPredicateReferenceForContainedResource(@Nullable DbColumn theSourceJoinColumn,
public Condition createPredicateReferenceForContainedResource(@Nullable DbColumn theSourceJoinColumn,
String theResourceName, String theParamName, RuntimeSearchParam theSearchParam,
List<? extends IQueryParameterType> theList, SearchFilterParser.CompareOperation theOperation,
RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
@ -794,31 +753,31 @@ public class QueryStack {
switch (targetParamDefinition.getParamType()) {
case DATE:
containedCondition = createPredicateDate(null, theResourceName, spnamePrefix, targetParamDefinition,
containedCondition = createPredicateDate(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
orValues, theOperation, theRequestPartitionId);
break;
case NUMBER:
containedCondition = createPredicateNumber(null, theResourceName, spnamePrefix, targetParamDefinition,
containedCondition = createPredicateNumber(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
orValues, theOperation, theRequestPartitionId);
break;
case QUANTITY:
containedCondition = createPredicateQuantity(null, theResourceName, spnamePrefix, targetParamDefinition,
containedCondition = createPredicateQuantity(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
orValues, theOperation, theRequestPartitionId);
break;
case STRING:
containedCondition = createPredicateString(null, theResourceName, spnamePrefix, targetParamDefinition,
containedCondition = createPredicateString(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
orValues, theOperation, theRequestPartitionId);
break;
case TOKEN:
containedCondition = createPredicateToken(null, theResourceName, spnamePrefix, targetParamDefinition,
containedCondition = createPredicateToken(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
orValues, theOperation, theRequestPartitionId);
break;
case COMPOSITE:
containedCondition = createPredicateComposite(null, theResourceName, spnamePrefix, targetParamDefinition,
containedCondition = createPredicateComposite(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
orValues, theRequestPartitionId);
break;
case URI:
containedCondition = createPredicateUri(null, theResourceName, spnamePrefix, targetParamDefinition,
containedCondition = createPredicateUri(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
orValues, theOperation, theRequest, theRequestPartitionId);
break;
case HAS:
@ -1099,9 +1058,6 @@ public class QueryStack {
case IAnyResource.SP_RES_ID:
return createPredicateResourceId(theSourceJoinColumn, theAndOrParams, theResourceName, null, theRequestPartitionId);
case IAnyResource.SP_RES_LANGUAGE:
return createPredicateLanguage(theAndOrParams, null);
case Constants.PARAM_HAS:
return createPredicateHas(theSourceJoinColumn, theResourceName, theAndOrParams, theRequest, theRequestPartitionId);
@ -1162,11 +1118,25 @@ public class QueryStack {
break;
case REFERENCE:
for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
if (theSearchContainedMode.equals(SearchContainedModeEnum.TRUE))
andPredicates.add(createPredicateReferenceForContainedResource(theSourceJoinColumn, theResourceName, theParamName, nextParamDef, nextAnd, null, theRequest, theRequestPartitionId));
else
if (theSearchContainedMode.equals(SearchContainedModeEnum.TRUE)) {
// TODO: The _contained parameter is not intended to control search chain interpretation like this.
// See SMILE-2898 for details.
// For now, leave the incorrect implementation alone, just in case someone is relying on it,
// until the complete fix is available.
andPredicates.add(createPredicateReferenceForContainedResource(null, theResourceName, theParamName, nextParamDef, nextAnd, null, theRequest, theRequestPartitionId));
} else if (isEligibleForContainedResourceSearch(nextAnd)) {
// TODO for now, restrict contained reference traversal to the last reference in the chain
// We don't seem to be indexing the outbound references of a contained resource, so we can't
// include them in search chains.
// It would be nice to eventually relax this constraint, but no client seems to be asking for it.
andPredicates.add(toOrPredicate(
createPredicateReference(theSourceJoinColumn, theResourceName, theParamName, nextAnd, null, theRequest, theRequestPartitionId),
createPredicateReferenceForContainedResource(theSourceJoinColumn, theResourceName, theParamName, nextParamDef, nextAnd, null, theRequest, theRequestPartitionId)
));
} else {
andPredicates.add(createPredicateReference(theSourceJoinColumn, theResourceName, theParamName, nextAnd, null, theRequest, theRequestPartitionId));
}
}
break;
case STRING:
for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
@ -1243,6 +1213,14 @@ public class QueryStack {
return toAndPredicate(andPredicates);
}
private boolean isEligibleForContainedResourceSearch(List<? extends IQueryParameterType> nextAnd) {
return myModelConfig.isIndexOnContainedResources() &&
nextAnd.stream()
.filter(t -> t instanceof ReferenceParam)
.map(t -> (ReferenceParam) t)
.noneMatch(t -> t.getChain().contains("."));
}
public void addPredicateCompositeUnique(String theIndexString, RequestPartitionId theRequestPartitionId) {
ComboUniqueSearchParameterPredicateBuilder predicateBuilder = mySqlBuilder.addComboUniquePredicateBuilder();
Condition predicate = predicateBuilder.createPredicateIndexString(theRequestPartitionId, theIndexString);

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
View File

@ -377,7 +377,7 @@ public class SearchBuilder implements ISearchBuilder {
SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(myContext, myDaoConfig.getModelConfig(), myPartitionSettings, myRequestPartitionId, sqlBuilderResourceName, mySqlBuilderFactory, myDialectProvider, theCount);
QueryStack queryStack3 = new QueryStack(theParams, myDaoConfig, myDaoConfig.getModelConfig(), myContext, sqlBuilder, mySearchParamRegistry, myPartitionSettings);
if (theParams.keySet().size() > 1 || theParams.getSort() != null || theParams.keySet().contains(Constants.PARAM_HAS)) {
if (theParams.keySet().size() > 1 || theParams.getSort() != null || theParams.keySet().contains(Constants.PARAM_HAS) || isPotentiallyContainedReferenceParameterExistsAtRoot(theParams)) {
List<RuntimeSearchParam> activeComboParams = mySearchParamRegistry.getActiveComboSearchParams(myResourceName, theParams.keySet());
if (activeComboParams.isEmpty()) {
sqlBuilder.setNeedResourceTableRoot(true);
@ -487,6 +487,13 @@ public class SearchBuilder implements ISearchBuilder {
return Optional.of(executor);
}
private boolean isPotentiallyContainedReferenceParameterExistsAtRoot(SearchParameterMap theParams) {
return myModelConfig.isIndexOnContainedResources() && theParams.values().stream()
.flatMap(Collection::stream)
.flatMap(Collection::stream)
.anyMatch(t -> t instanceof ReferenceParam);
}
private List<Long> normalizeIdListForLastNInClause(List<Long> lastnResourceIds) {
/*
The following is a workaround to a known issue involving Hibernate. If queries are used with "in" clauses with large and varying

32
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java
View File

@ -38,20 +38,18 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderReference;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
import ca.uhn.fhir.jpa.search.builder.QueryStack;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.search.builder.QueryStack;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
import ca.uhn.fhir.jpa.searchparam.util.JpaParamUtil;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.CompositeParam;
@ -66,6 +64,8 @@ import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import com.google.common.collect.Lists;
import com.healthmarketscience.sqlbuilder.BinaryCondition;
import com.healthmarketscience.sqlbuilder.ComboCondition;
@ -341,7 +341,7 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
List<Condition> orPredicates = new ArrayList<>();
boolean paramInverted = false;
QueryStack childQueryFactory = myQueryStack.newChildQueryFactoryWithFullBuilderReuse();
for (String nextType : resourceTypes) {
String chain = theReferenceParam.getChain();
String remainingChain = null;
@ -351,15 +351,6 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
chain = chain.substring(0, chainDotIndex);
}
RuntimeResourceDefinition typeDef = getFhirContext().getResourceDefinition(nextType);
String subResourceName = typeDef.getName();
IDao dao = myDaoRegistry.getResourceDao(nextType);
if (dao == null) {
ourLog.debug("Don't have a DAO for type {}", nextType);
continue;
}
int qualifierIndex = chain.indexOf(':');
String qualifier = null;
if (qualifierIndex != -1) {
@ -368,6 +359,18 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
}
boolean isMeta = ResourceMetaParams.RESOURCE_META_PARAMS.containsKey(chain);
for (String nextType : resourceTypes) {
RuntimeResourceDefinition typeDef = getFhirContext().getResourceDefinition(nextType);
String subResourceName = typeDef.getName();
IDao dao = myDaoRegistry.getResourceDao(nextType);
if (dao == null) {
ourLog.debug("Don't have a DAO for type {}", nextType);
continue;
}
RuntimeSearchParam param = null;
if (!isMeta) {
param = mySearchParamRegistry.getActiveSearchParam(nextType, chain);
@ -408,7 +411,6 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
andPredicates.add(childQueryFactory.searchForIdsWithAndOr(myColumnTargetResourceId, subResourceName, chain, chainParamValues, theRequest, theRequestPartitionId, SearchContainedModeEnum.FALSE));
orPredicates.add(toAndPredicate(andPredicates));
}
if (candidateTargetTypes.isEmpty()) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/TokenPredicateBuilder.java
View File

@ -222,7 +222,7 @@ public class TokenPredicateBuilder extends BaseSearchParamPredicateBuilder {
if (retVal == null) {
if (theSearchParam != null) {
Set<String> valueSetUris = Sets.newHashSet();
for (String nextPath : theSearchParam.getPathsSplit()) {
for (String nextPath : theSearchParam.getPathsSplitForResourceType(getResourceType())) {
Class<? extends IBaseResource> type = getFhirContext().getResourceDefinition(getResourceType()).getImplementingClass();
BaseRuntimeChildDefinition def = getFhirContext().newTerser().getDefinition(type, nextPath);
if (def instanceof BaseRuntimeDeclaredChildDefinition) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java
View File

@ -549,7 +549,7 @@ public class SearchQueryBuilder {
}
public ComboCondition addPredicateLastUpdated(DateRangeParam theDateRange) {
ResourceTablePredicateBuilder resourceTableRoot = getOrCreateResourceTablePredicateBuilder();
ResourceTablePredicateBuilder resourceTableRoot = getOrCreateResourceTablePredicateBuilder(false);
List<Condition> conditions = new ArrayList<>(2);
if (theDateRange.getLowerBoundAsInstant() != null) {

32
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/ElasticsearchHibernatePropertiesBuilder.java
View File

@ -37,6 +37,7 @@ import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchIndexSettings
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
import org.slf4j.Logger;
import javax.annotation.Nullable;
import java.io.IOException;
import java.util.Arrays;
import java.util.Properties;
@ -52,10 +53,10 @@ public class ElasticsearchHibernatePropertiesBuilder {
private static final Logger ourLog = getLogger(ElasticsearchHibernatePropertiesBuilder.class);
private IndexStatus myRequiredIndexStatus = IndexStatus.YELLOW.YELLOW;
private IndexStatus myRequiredIndexStatus = IndexStatus.YELLOW;
private SchemaManagementStrategyName myIndexSchemaManagementStrategy = SchemaManagementStrategyName.CREATE;
private String myRestUrl;
private String myHosts;
private String myUsername;
private String myPassword;
private long myIndexManagementWaitTimeoutMillis = 10000L;
@ -77,11 +78,8 @@ public class ElasticsearchHibernatePropertiesBuilder {
// the below properties are used for ElasticSearch integration
theProperties.put(BackendSettings.backendKey(BackendSettings.TYPE), "elasticsearch");
theProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.ANALYSIS_CONFIGURER), HapiElasticsearchAnalysisConfigurer.class.getName());
theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS), myRestUrl);
theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS), myHosts);
theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.PROTOCOL), myProtocol);
if (StringUtils.isNotBlank(myUsername)) {
@ -99,8 +97,10 @@ public class ElasticsearchHibernatePropertiesBuilder {
theProperties.put(HibernateOrmMapperSettings.AUTOMATIC_INDEXING_SYNCHRONIZATION_STRATEGY, myDebugSyncStrategy);
theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.LOG_JSON_PRETTY_PRINTING), Boolean.toString(myDebugPrettyPrintJsonLog));
injectStartupTemplate(myProtocol, myRestUrl, myUsername, myPassword);
//This tells elasticsearch to use our custom index naming strategy.
theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.LAYOUT_STRATEGY), IndexNamePrefixLayoutStrategy.class.getName());
injectStartupTemplate(myProtocol, myHosts, myUsername, myPassword);
}
public ElasticsearchHibernatePropertiesBuilder setRequiredIndexStatus(IndexStatus theRequiredIndexStatus) {
@ -108,11 +108,8 @@ public class ElasticsearchHibernatePropertiesBuilder {
return this;
}
public ElasticsearchHibernatePropertiesBuilder setRestUrl(String theRestUrl) {
if (theRestUrl.contains("://")) {
throw new ConfigurationException("Elasticsearch URL cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.");
}
myRestUrl = theRestUrl;
public ElasticsearchHibernatePropertiesBuilder setHosts(String hosts) {
myHosts = hosts;
return this;
}
@ -147,18 +144,13 @@ public class ElasticsearchHibernatePropertiesBuilder {
* TODO GGG HS: In HS6.1, we should have a native way of performing index settings manipulation at bootstrap time, so this should
* eventually be removed in favour of whatever solution they come up with.
*/
void injectStartupTemplate(String theProtocol, String theHostAndPort, String theUsername, String thePassword) {
void injectStartupTemplate(String theProtocol, String theHosts, @Nullable String theUsername, @Nullable String thePassword) {
PutIndexTemplateRequest ngramTemplate = new PutIndexTemplateRequest("ngram-template")
.patterns(Arrays.asList("resourcetable-*", "termconcept-*"))
.patterns(Arrays.asList("*resourcetable-*", "*termconcept-*"))
.settings(Settings.builder().put("index.max_ngram_diff", 50));
int colonIndex = theHostAndPort.indexOf(":");
String host = theHostAndPort.substring(0, colonIndex);
Integer port = Integer.valueOf(theHostAndPort.substring(colonIndex + 1));
String qualifiedHost = theProtocol + "://" + host;
try {
RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(qualifiedHost, port, theUsername, thePassword);
RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theProtocol, theHosts, theUsername, thePassword);
ourLog.info("Adding starter template for large ngram diffs");
AcknowledgedResponse acknowledgedResponse = elasticsearchHighLevelRestClient.indices().putTemplate(ngramTemplate, RequestOptions.DEFAULT);
assert acknowledgedResponse.isAcknowledged();

99
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/IndexNamePrefixLayoutStrategy.java Normal file
View File

@ -0,0 +1,99 @@
package ca.uhn.fhir.jpa.search.elastic;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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 ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import org.apache.commons.lang3.StringUtils;
import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;
import org.hibernate.search.backend.elasticsearch.logging.impl.Log;
import org.hibernate.search.util.common.logging.impl.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.lang.invoke.MethodHandles;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* This class instructs hibernate search on how to create index names for indexed entities.
* In our case, we use this class to add an optional prefix to all indices which are created, which can be controlled via
* {@link DaoConfig#setElasticSearchIndexPrefix(String)}.
*/
@Service
public class IndexNamePrefixLayoutStrategy implements IndexLayoutStrategy {
@Autowired
private DaoConfig myDaoConfig;
static final Log log = LoggerFactory.make(Log.class, MethodHandles.lookup());
public static final String NAME = "prefix";
public static final Pattern UNIQUE_KEY_EXTRACTION_PATTERN = Pattern.compile("(.*)-\\d{6}");
public String createInitialElasticsearchIndexName(String hibernateSearchIndexName) {
return addPrefixIfNecessary(hibernateSearchIndexName + "-000001");
}
public String createWriteAlias(String hibernateSearchIndexName) {
return addPrefixIfNecessary(hibernateSearchIndexName +"-write");
}
public String createReadAlias(String hibernateSearchIndexName) {
return addPrefixIfNecessary(hibernateSearchIndexName + "-read");
}
private String addPrefixIfNecessary(String theCandidateName) {
validateDaoConfigIsPresent();
if (!StringUtils.isBlank(myDaoConfig.getElasticSearchIndexPrefix())) {
return myDaoConfig.getElasticSearchIndexPrefix() + "-" + theCandidateName;
} else {
return theCandidateName;
}
}
public String extractUniqueKeyFromHibernateSearchIndexName(String hibernateSearchIndexName) {
return hibernateSearchIndexName;
}
public String extractUniqueKeyFromElasticsearchIndexName(String elasticsearchIndexName) {
Matcher matcher = UNIQUE_KEY_EXTRACTION_PATTERN.matcher(elasticsearchIndexName);
if (!matcher.matches()) {
throw log.invalidIndexPrimaryName(elasticsearchIndexName, UNIQUE_KEY_EXTRACTION_PATTERN);
} else {
String candidateUniqueKey= matcher.group(1);
return removePrefixIfNecessary(candidateUniqueKey);
}
}
private String removePrefixIfNecessary(String theCandidateUniqueKey) {
validateDaoConfigIsPresent();
if (!StringUtils.isBlank(myDaoConfig.getElasticSearchIndexPrefix())) {
return theCandidateUniqueKey.replace(myDaoConfig.getElasticSearchIndexPrefix() + "-", "");
} else {
return theCandidateUniqueKey;
}
}
private void validateDaoConfigIsPresent() {
if (myDaoConfig == null) {
throw new ConfigurationException("While attempting to boot HAPI FHIR, the Hibernate Search bootstrapper failed to find the DaoConfig. This probably means Hibernate Search has been recently upgraded, or somebody modified HapiFhirLocalContainerEntityManagerFactoryBean.");
}
}
}

56
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/ElasticsearchRestClientFactory.java
View File

@ -20,6 +20,8 @@ package ca.uhn.fhir.jpa.search.lastn;
* #L%
*/
import ca.uhn.fhir.context.ConfigurationException;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.Header;
import org.apache.http.HttpHost;
import org.apache.http.auth.AuthScope;
@ -27,41 +29,47 @@ import org.apache.http.auth.UsernamePasswordCredentials;
import org.apache.http.client.CredentialsProvider;
import org.apache.http.impl.client.BasicCredentialsProvider;
import org.apache.http.message.BasicHeader;
import org.elasticsearch.client.Node;
import org.elasticsearch.client.RestClient;
import org.elasticsearch.client.RestClientBuilder;
import org.elasticsearch.client.RestHighLevelClient;
import javax.annotation.Nullable;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
public class ElasticsearchRestClientFactory {
private static String determineScheme(String theHostname) {
int schemeIdx = theHostname.indexOf("://");
if (schemeIdx > 0) {
return theHostname.substring(0, schemeIdx);
} else {
return "http";
static public RestHighLevelClient createElasticsearchHighLevelRestClient(
String protocol, String hosts, @Nullable String theUsername, @Nullable String thePassword) {
if (hosts.contains("://")) {
throw new ConfigurationException("Elasticsearch URLs cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.");
}
String[] hostArray = hosts.split(",");
List<Node> clientNodes = Arrays.stream(hostArray)
.map(String::trim)
.filter(s -> s.contains(":"))
.map(h -> {
int colonIndex = h.indexOf(":");
String host = h.substring(0, colonIndex);
int port = Integer.parseInt(h.substring(colonIndex + 1));
return new Node(new HttpHost(host, port, protocol));
})
.collect(Collectors.toList());
if (hostArray.length != clientNodes.size()) {
throw new ConfigurationException("Elasticsearch URLs have to contain ':' as a host:port separator. Example: localhost:9200,localhost:9201,localhost:9202");
}
private static String stripHostOfScheme(String theHostname) {
int schemeIdx = theHostname.indexOf("://");
if (schemeIdx > 0) {
return theHostname.substring(schemeIdx + 3);
} else {
return theHostname;
}
}
static public RestHighLevelClient createElasticsearchHighLevelRestClient(String theHostname, int thePort, String theUsername, String thePassword) {
final CredentialsProvider credentialsProvider =
new BasicCredentialsProvider();
credentialsProvider.setCredentials(AuthScope.ANY,
new UsernamePasswordCredentials(theUsername, thePassword));
RestClientBuilder clientBuilder = RestClient.builder(
new HttpHost(stripHostOfScheme(theHostname), thePort, determineScheme(theHostname)))
.setHttpClientConfigCallback(httpClientBuilder -> httpClientBuilder
RestClientBuilder clientBuilder = RestClient.builder(clientNodes.toArray(new Node[0]));
if (StringUtils.isNotBlank(theUsername) && StringUtils.isNotBlank(thePassword)) {
final CredentialsProvider credentialsProvider = new BasicCredentialsProvider();
credentialsProvider.setCredentials(AuthScope.ANY, new UsernamePasswordCredentials(theUsername, thePassword));
clientBuilder.setHttpClientConfigCallback(httpClientBuilder -> httpClientBuilder
.setDefaultCredentialsProvider(credentialsProvider));
}
Header[] defaultHeaders = new Header[]{new BasicHeader("Content-Type", "application/json")};
clientBuilder.setDefaultHeaders(defaultHeaders);

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/ElasticsearchSvcImpl.java
View File

@ -68,11 +68,11 @@ import org.elasticsearch.search.aggregations.bucket.terms.ParsedTerms;
import org.elasticsearch.search.aggregations.bucket.terms.Terms;
import org.elasticsearch.search.aggregations.bucket.terms.TermsAggregationBuilder;
import org.elasticsearch.search.aggregations.metrics.ParsedTopHits;
import org.elasticsearch.search.aggregations.support.ValueType;
import org.elasticsearch.search.builder.SearchSourceBuilder;
import org.elasticsearch.search.sort.SortOrder;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nullable;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
@ -125,13 +125,13 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
private PartitionSettings myPartitionSettings;
//This constructor used to inject a dummy partitionsettings in test.
public ElasticsearchSvcImpl(PartitionSettings thePartitionSetings, String theHostname, int thePort, String theUsername, String thePassword) {
this(theHostname, thePort, theUsername, thePassword);
public ElasticsearchSvcImpl(PartitionSettings thePartitionSetings, String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
this(theHostname, theUsername, thePassword);
this.myPartitionSettings = thePartitionSetings;
}
public ElasticsearchSvcImpl(String theHostname, int thePort, String theUsername, String thePassword) {
myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theHostname, thePort, theUsername, thePassword);
public ElasticsearchSvcImpl(String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient("http", theHostname, theUsername, thePassword);
try {
createObservationIndexIfMissing();

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

@ -172,6 +172,10 @@ public class MemoryCacheService {
return (Cache<K, T>) myCaches.get(theCache);
}
public long getEstimatedSize(CacheEnum theCache) {
return getCache(theCache).estimatedSize();
}
public enum CacheEnum {
TAG_DEFINITION(TagDefinitionCacheKey.class),

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SqlQuery.java
View File

@ -126,5 +126,8 @@ public class SqlQuery {
}
@Override
public String toString() {
return getSql(true, true);
}
}

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportProviderTest.java
View File

@ -1,16 +1,15 @@
package ca.uhn.fhir.jpa.bulk;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportResponseJson;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportResponseJson;
import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
import ca.uhn.fhir.rest.client.apache.ResourceEntity;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -55,11 +54,8 @@ import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.notNullValue;
import static org.hamcrest.Matchers.nullValue;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyBoolean;
import static org.mockito.ArgumentMatchers.isNull;
import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.Mockito.eq;
import static org.mockito.Mockito.times;
@ -74,7 +70,7 @@ public class BulkDataExportProviderTest {
private static final String GROUP_ID = "Group/G2401";
private static final String G_JOB_ID = "0000000-GGGGGG";
private Server myServer;
private final FhirContext myCtx = FhirContext.forCached(FhirVersionEnum.R4);
private final FhirContext myCtx = FhirContext.forR4Cached();
private int myPort;
@Mock
private IBulkDataExportSvc myBulkDataExportSvc;
@ -478,7 +474,7 @@ public class BulkDataExportProviderTest {
when(myBulkDataExportSvc.submitJob(any(), any(), nullable(RequestDetails.class))).thenReturn(jobInfo);
String url = "http://localhost:" + myPort + "/" + "Group/123/" +JpaConstants.OPERATION_EXPORT
+ "?" + JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT + "=" + UrlUtil.escapeUrlParam(Constants.CT_FHIR_NDJSON);;
+ "?" + JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT + "=" + UrlUtil.escapeUrlParam(Constants.CT_FHIR_NDJSON);
HttpGet get = new HttpGet(url);
get.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/cache/ResourceVersionCacheSvcTest.java vendored
View File

@ -21,12 +21,12 @@ public class ResourceVersionCacheSvcTest extends BaseJpaR4Test {
IIdType patientId = myPatientDao.create(patient).getId();
ResourceVersionMap versionMap = myResourceVersionCacheSvc.getVersionMap("Patient", SearchParameterMap.newSynchronous());
assertEquals(1, versionMap.size());
assertEquals("1", versionMap.getVersion(patientId));
assertEquals(1L, versionMap.getVersion(patientId));
patient.setGender(Enumerations.AdministrativeGender.MALE);
myPatientDao.update(patient);
versionMap = myResourceVersionCacheSvc.getVersionMap("Patient", SearchParameterMap.newSynchronous());
assertEquals(1, versionMap.size());
assertEquals("2", versionMap.getVersion(patientId));
assertEquals(2L, versionMap.getVersion(patientId));
}
}

147
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/ElasticsearchWithPrefixConfig.java Normal file
View File

@ -0,0 +1,147 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.config.BlockLargeNumbersOfParamsListener;
import ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect;
import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
import ca.uhn.fhir.jpa.dao.r4.ElasticsearchPrefixTest;
import ca.uhn.fhir.jpa.search.elastic.HapiElasticsearchAnalysisConfigurer;
import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
import ca.uhn.fhir.jpa.search.lastn.config.TestElasticsearchContainerHelper;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import org.elasticsearch.action.support.master.AcknowledgedResponse;
import org.elasticsearch.client.RequestOptions;
import org.elasticsearch.client.RestHighLevelClient;
import org.elasticsearch.client.indices.PutIndexTemplateRequest;
import org.elasticsearch.common.settings.Settings;
import org.hibernate.dialect.H2Dialect;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchBackendSettings;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchIndexSettings;
import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.testcontainers.elasticsearch.ElasticsearchContainer;
import javax.sql.DataSource;
import java.io.IOException;
import java.util.Arrays;
import java.util.Properties;
import java.util.concurrent.TimeUnit;
/**
* The only reason this is its own class is so that we can set a dao config setting before the whole test framework comes online.
* We need to do this as it is during bean creation that HS bootstrapping occurs.
*/
@Configuration
public class ElasticsearchWithPrefixConfig {
@Bean
public DaoConfig daoConfig() {
DaoConfig daoConfig = new DaoConfig();
daoConfig.setElasticSearchIndexPrefix(ElasticsearchPrefixTest.ELASTIC_PREFIX);
return daoConfig;
}
@Bean
public IndexNamePrefixLayoutStrategy indexNamePrefixLayoutStrategy() {
return new IndexNamePrefixLayoutStrategy();
}
@Bean
public FhirContext fhirContext() {
return FhirContext.forR4();
}
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean(theConfigurableListableBeanFactory);
retVal.setJpaDialect(new HapiFhirHibernateJpaDialect(fhirContext().getLocalizer()));
retVal.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");
retVal.setPersistenceProvider(new HibernatePersistenceProvider());
retVal.setPersistenceUnitName("PU_HapiFhirJpaR4");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());
return retVal;
}
@Bean
public DataSource dataSource() {
BasicDataSource retVal = new BasicDataSource();
retVal.setDriver(new org.h2.Driver());
retVal.setUrl("jdbc:h2:mem:testdb_r4");
retVal.setMaxWaitMillis(30000);
retVal.setUsername("");
retVal.setPassword("");
retVal.setMaxTotal(5);
SLF4JLogLevel level = SLF4JLogLevel.INFO;
DataSource dataSource = ProxyDataSourceBuilder
.create(retVal)
.logSlowQueryBySlf4j(10, TimeUnit.SECONDS, level)
.beforeQuery(new BlockLargeNumbersOfParamsListener())
.afterQuery(new CurrentThreadCaptureQueriesListener())
.build();
return dataSource;
}
@Bean
public Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.dialect", H2Dialect.class.getName());
//Override default lucene settings
// Force elasticsearch to start first
int httpPort = elasticContainer().getMappedPort(9200);//9200 is the HTTP port
String host = elasticContainer().getHost();
// the below properties are used for ElasticSearch integration
extraProperties.put(BackendSettings.backendKey(BackendSettings.TYPE), "elasticsearch");
extraProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.ANALYSIS_CONFIGURER), HapiElasticsearchAnalysisConfigurer.class.getName());
extraProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS), host + ":" + httpPort);
extraProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.PROTOCOL), "http");
extraProperties.put(HibernateOrmMapperSettings.SCHEMA_MANAGEMENT_STRATEGY, SchemaManagementStrategyName.CREATE.externalRepresentation());
extraProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.SCHEMA_MANAGEMENT_MINIMAL_REQUIRED_STATUS_WAIT_TIMEOUT), Long.toString(10000));
extraProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.SCHEMA_MANAGEMENT_MINIMAL_REQUIRED_STATUS), IndexStatus.YELLOW.externalRepresentation());
// Need the mapping to be dynamic because of terminology indexes.
extraProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.DYNAMIC_MAPPING), "true");
// Only for unit tests
extraProperties.put(HibernateOrmMapperSettings.AUTOMATIC_INDEXING_SYNCHRONIZATION_STRATEGY, "read-sync");
extraProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.LOG_JSON_PRETTY_PRINTING), Boolean.toString(true));
//This tells elasticsearch to use our custom index naming strategy.
extraProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.LAYOUT_STRATEGY), IndexNamePrefixLayoutStrategy.class.getName());
PutIndexTemplateRequest ngramTemplate = new PutIndexTemplateRequest("ngram-template")
.patterns(Arrays.asList("*resourcetable-*", "*termconcept-*"))
.settings(Settings.builder().put("index.max_ngram_diff", 50));
try {
RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient("http", host + ":" + httpPort, "", "");
AcknowledgedResponse acknowledgedResponse = elasticsearchHighLevelRestClient.indices().putTemplate(ngramTemplate, RequestOptions.DEFAULT);
assert acknowledgedResponse.isAcknowledged();
} catch (IOException theE) {
theE.printStackTrace();
throw new ConfigurationException("Couldn't connect to the elasticsearch server to create necessary templates. Ensure the Elasticsearch user has permissions to create templates.");
}
return extraProperties;
}
@Bean
public ElasticsearchContainer elasticContainer() {
ElasticsearchContainer embeddedElasticSearch = TestElasticsearchContainerHelper.getEmbeddedElasticSearch();
embeddedElasticSearch.start();
return embeddedElasticSearch;
}
}

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java
View File

@ -16,6 +16,7 @@ import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -134,8 +135,8 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu2");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java
View File

@ -15,6 +15,7 @@ import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -138,8 +139,8 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu3");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestJPAConfig.java
View File

@ -3,12 +3,14 @@ package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
import ca.uhn.fhir.jpa.subscription.match.deliver.resthook.SubscriptionDeliveringRestHookSubscriber;
import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.batch.svc.BatchJobSubmitterImpl;
@ -14,6 +15,8 @@ import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.dialect.H2Dialect;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -138,10 +141,15 @@ public class TestR4Config extends BaseJavaConfigR4 {
return new SingleQueryCountHolder();
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean(theConfigurableListableBeanFactory);
configureEntityManagerFactory(retVal, fhirContext());
retVal.setJpaDialect(new HapiFhirHibernateJpaDialect(fhirContext().getLocalizer()));
retVal.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");
retVal.setPersistenceProvider(new HibernatePersistenceProvider());
retVal.setPersistenceUnitName("PU_HapiFhirJpaR4");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticSearch.java
View File

@ -1,13 +1,19 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
import ca.uhn.fhir.jpa.search.lastn.config.TestElasticsearchContainerHelper;
import org.h2.index.Index;
import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.DependsOn;
import org.testcontainers.elasticsearch.ElasticsearchContainer;
import javax.annotation.PreDestroy;
@ -35,7 +41,7 @@ public class TestR4ConfigWithElasticSearch extends TestR4Config {
.setIndexSchemaManagementStrategy(SchemaManagementStrategyName.CREATE)
.setIndexManagementWaitTimeoutMillis(10000)
.setRequiredIndexStatus(IndexStatus.YELLOW)
.setRestUrl(host+ ":" + httpPort)
.setHosts(host + ":" + httpPort)
.setProtocol("http")
.setUsername("")
.setPassword("")

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticsearchClient.java
View File

@ -21,7 +21,7 @@ public class TestR4ConfigWithElasticsearchClient extends TestR4ConfigWithElastic
public ElasticsearchSvcImpl myElasticsearchSvc() {
int elasticsearchPort = elasticContainer().getMappedPort(9200);
String host = elasticContainer().getHost();
return new ElasticsearchSvcImpl(host, elasticsearchPort, "", "");
return new ElasticsearchSvcImpl(host + ":" + elasticsearchPort, null, null);
}
@PreDestroy

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4WithLuceneDisabledConfig.java
View File

@ -3,9 +3,11 @@ package ca.uhn.fhir.jpa.config;
import java.util.Properties;
import org.hibernate.dialect.H2Dialect;
import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;
import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@ -27,8 +29,8 @@ public class TestR4WithLuceneDisabledConfig extends TestR4Config {
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());
return retVal;

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR5Config.java
View File

@ -16,6 +16,7 @@ import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -138,8 +139,8 @@ public class TestR5Config extends BaseJavaConfigR5 {
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("PU_HapiFhirJpaR5");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDaoTest.java
View File

@ -13,6 +13,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
class BaseHapiFhirResourceDaoTest {
TestResourceDao mySvc = new TestResourceDao();
@Test

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

@ -721,6 +721,4 @@ public abstract class BaseJpaTest extends BaseTest {
}
Thread.sleep(500);
}
}

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TolerantJsonParserR4Test.java
View File

@ -1,19 +1,18 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.LenientErrorHandler;
import org.hl7.fhir.r4.model.Observation;
import org.junit.jupiter.api.Test;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.hamcrest.MatcherAssert.assertThat;
public class TolerantJsonParserR4Test {
private FhirContext myFhirContext = FhirContext.forCached(FhirVersionEnum.R4);
private final FhirContext myFhirContext = FhirContext.forR4Cached();
@Test
public void testParseInvalidNumeric_LeadingDecimal() {

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java
View File

@ -1,10 +1,10 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.interceptor.executor.InterceptorService;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
@ -13,6 +13,7 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
import ca.uhn.fhir.jpa.searchparam.matcher.SearchParamMatcher;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hibernate.Session;
import org.hibernate.internal.SessionImpl;
@ -70,6 +71,10 @@ public class TransactionProcessorTest {
private MatchUrlService myMatchUrlService;
@MockBean
private IRequestPartitionHelperSvc myRequestPartitionHelperSvc;
@MockBean
private IResourceVersionSvc myResourceVersionSvc;
@MockBean
private SearchParamMatcher mySearchParamMatcher;
@MockBean(answer = Answers.RETURNS_DEEP_STUBS)
private SessionImpl mySession;
@ -120,7 +125,7 @@ public class TransactionProcessorTest {
@Bean
public FhirContext fhirContext() {
return FhirContext.forCached(FhirVersionEnum.R4);
return FhirContext.forR4Cached();
}
@Bean

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java
View File

@ -1033,7 +1033,7 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
myPatientDao.search(map).size();
fail();
} catch (InvalidRequestException e) {
assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
}
}
@ -1070,7 +1070,7 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
myPatientDao.search(map).size();
fail();
} catch (InvalidRequestException e) {
assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
}
// Try with normal gender SP

148
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java
View File

@ -727,9 +727,6 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
params.add("_id", new StringDt("TEST"));
assertEquals(1, toList(myPatientDao.search(params)).size());
params.add("_language", new StringParam("TEST"));
assertEquals(1, toList(myPatientDao.search(params)).size());
params.add(Patient.SP_IDENTIFIER, new TokenParam("TEST", "TEST"));
assertEquals(1, toList(myPatientDao.search(params)).size());
@ -744,9 +741,6 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
params.add("_id", new StringDt("TEST"));
assertEquals(0, toList(myPatientDao.search(params)).size());
params.add("_language", new StringParam("TEST"));
assertEquals(0, toList(myPatientDao.search(params)).size());
params.add(Patient.SP_IDENTIFIER, new TokenParam("TEST", "TEST"));
assertEquals(0, toList(myPatientDao.search(params)).size());
@ -766,148 +760,6 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
}
}
@Test
public void testSearchLanguageParam() {
IIdType id1;
{
Patient patient = new Patient();
patient.getLanguage().setValue("en_CA");
patient.addIdentifier().setSystem("urn:system").setValue("001");
patient.addName().addFamily("testSearchLanguageParam").addGiven("Joe");
id1 = myPatientDao.create(patient, mySrd).getId();
}
IIdType id2;
{
Patient patient = new Patient();
patient.getLanguage().setValue("en_US");
patient.addIdentifier().setSystem("urn:system").setValue("002");
patient.addName().addFamily("testSearchLanguageParam").addGiven("John");
id2 = myPatientDao.create(patient, mySrd).getId();
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(BaseResource.SP_RES_LANGUAGE, new StringParam("en_CA"));
List<IResource> patients = toList(myPatientDao.search(params));
assertEquals(1, patients.size());
assertEquals(id1.toUnqualifiedVersionless(), patients.get(0).getId().toUnqualifiedVersionless());
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(BaseResource.SP_RES_LANGUAGE, new StringParam("en_US"));
List<Patient> patients = toList(myPatientDao.search(params));
assertEquals(1, patients.size());
assertEquals(id2.toUnqualifiedVersionless(), patients.get(0).getId().toUnqualifiedVersionless());
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(BaseResource.SP_RES_LANGUAGE, new StringParam("en_GB"));
List<Patient> patients = toList(myPatientDao.search(params));
assertEquals(0, patients.size());
}
}
@Test
public void testSearchLanguageParamAndOr() {
IIdType id1;
{
Patient patient = new Patient();
patient.getLanguage().setValue("en_CA");
patient.addIdentifier().setSystem("urn:system").setValue("001");
patient.addName().addFamily("testSearchLanguageParam").addGiven("Joe");
id1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Date betweenTime = new Date();
IIdType id2;
{
Patient patient = new Patient();
patient.getLanguage().setValue("en_US");
patient.addIdentifier().setSystem("urn:system").setValue("002");
patient.addName().addFamily("testSearchLanguageParam").addGiven("John");
id2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(BaseResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("en_US")));
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1, id2));
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(BaseResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("en_US")));
params.setLastUpdated(new DateRangeParam(betweenTime, null));
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id2));
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(BaseResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")));
params.add(BaseResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("ZZZZZ")));
params.add(BaseResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty());
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("ZZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
params.add(BaseResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty());
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("")).addOr(new StringParam(null)));
params.add(BaseResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add("_id", new StringParam(id1.getIdPart()));
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("")).addOr(new StringParam(null)));
params.add(BaseResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("")).addOr(new StringParam(null)));
params.add(BaseResource.SP_RES_LANGUAGE, and);
params.add("_id", new StringParam(id1.getIdPart()));
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
}
@Test
public void testSearchLastUpdatedParam() throws InterruptedException {
String methodName = "testSearchLastUpdatedParam";

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
View File

@ -224,7 +224,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
}
@Test
public void testCantSearchForDeletedResourceByLanguageOrTag() {
public void testCantSearchForDeletedResourceByTag() {
String methodName = "testCantSearchForDeletedResourceByLanguageOrTag";
Organization org = new Organization();
org.setLanguage(new CodeDt("EN_ca"));
@ -236,9 +236,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map = new SearchParameterMap();
map.add("_language", new StringParam("EN_ca"));
assertEquals(1, myOrganizationDao.search(map).size().intValue());
SearchParameterMap map;
map = new SearchParameterMap();
map.add("_tag", new TokenParam(methodName, methodName));
@ -246,10 +244,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
myOrganizationDao.delete(orgId, mySrd);
map = new SearchParameterMap();
map.add("_language", new StringParam("EN_ca"));
assertEquals(0, myOrganizationDao.search(map).size().intValue());
map = new SearchParameterMap();
map.add("_tag", new TokenParam(methodName, methodName));
assertEquals(0, myOrganizationDao.search(map).size().intValue());
@ -1603,7 +1597,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
found = toList(myPatientDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Patient.SP_BIRTHDATE + "AAAA", new DateParam(ParamPrefixEnum.GREATERTHAN, "2000-01-01"))));
assertEquals(0, found.size());
} catch (InvalidRequestException e) {
assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, careprovider, deathdate, deceased, email, family, gender, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java
View File

@ -1015,7 +1015,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
myPatientDao.search(map).size();
fail();
} catch (InvalidRequestException e) {
assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
}
}
@ -1053,7 +1053,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
myPatientDao.search(map).size();
fail();
} catch (InvalidRequestException e) {
assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
assertEquals("Unknown search parameter \"foo\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
}
// Try with normal gender SP

147
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java
View File

@ -1192,11 +1192,6 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
params.add("_id", new StringParam("TEST"));
assertEquals(1, toList(myPatientDao.search(params)).size());
params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add("_language", new StringParam("TEST"));
assertEquals(1, toList(myPatientDao.search(params)).size());
params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(Patient.SP_IDENTIFIER, new TokenParam("TEST", "TEST"));
@ -1214,11 +1209,6 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
params.add("_id", new StringParam("TEST"));
assertEquals(0, toList(myPatientDao.search(params)).size());
params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add("_language", new StringParam("TEST"));
assertEquals(0, toList(myPatientDao.search(params)).size());
params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(Patient.SP_IDENTIFIER, new TokenParam("TEST", "TEST"));
@ -1241,143 +1231,6 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
}
}
@Test
public void testSearchLanguageParam() {
IIdType id1;
{
Patient patient = new Patient();
patient.getLanguageElement().setValue("en_CA");
patient.addIdentifier().setSystem("urn:system").setValue("001");
patient.addName().setFamily("testSearchLanguageParam").addGiven("Joe");
id1 = myPatientDao.create(patient, mySrd).getId();
}
IIdType id2;
{
Patient patient = new Patient();
patient.getLanguageElement().setValue("en_US");
patient.addIdentifier().setSystem("urn:system").setValue("002");
patient.addName().setFamily("testSearchLanguageParam").addGiven("John");
id2 = myPatientDao.create(patient, mySrd).getId();
}
SearchParameterMap params;
{
params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(IAnyResource.SP_RES_LANGUAGE, new StringParam("en_CA"));
List<IBaseResource> patients = toList(myPatientDao.search(params));
assertEquals(1, patients.size());
assertEquals(id1.toUnqualifiedVersionless(), patients.get(0).getIdElement().toUnqualifiedVersionless());
}
{
params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(IAnyResource.SP_RES_LANGUAGE, new StringParam("en_US"));
List<Patient> patients = toList(myPatientDao.search(params));
assertEquals(1, patients.size());
assertEquals(id2.toUnqualifiedVersionless(), patients.get(0).getIdElement().toUnqualifiedVersionless());
}
{
params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add(IAnyResource.SP_RES_LANGUAGE, new StringParam("en_GB"));
List<Patient> patients = toList(myPatientDao.search(params));
assertEquals(0, patients.size());
}
}
@Test
public void testSearchLanguageParamAndOr() {
IIdType id1;
{
Patient patient = new Patient();
patient.getLanguageElement().setValue("en_CA");
patient.addIdentifier().setSystem("urn:system").setValue("001");
patient.addName().setFamily("testSearchLanguageParam").addGiven("Joe");
id1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
TestUtil.sleepOneClick();
Date betweenTime = new Date();
IIdType id2;
{
Patient patient = new Patient();
patient.getLanguageElement().setValue("en_US");
patient.addIdentifier().setSystem("urn:system").setValue("002");
patient.addName().setFamily("testSearchLanguageParam").addGiven("John");
id2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
{
SearchParameterMap params = new SearchParameterMap();
params.add(IAnyResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("en_US")));
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1, id2));
}
{
SearchParameterMap params = new SearchParameterMap();
params.add(IAnyResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("en_US")));
params.setLastUpdated(new DateRangeParam(betweenTime, null));
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id2));
}
{
SearchParameterMap params = new SearchParameterMap();
params.add(IAnyResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
{
SearchParameterMap params = new SearchParameterMap();
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")));
params.add(IAnyResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
{
SearchParameterMap params = new SearchParameterMap();
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("ZZZZZ")));
params.add(IAnyResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty());
}
{
SearchParameterMap params = new SearchParameterMap();
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("ZZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
params.add(IAnyResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty());
}
{
SearchParameterMap params = new SearchParameterMap();
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("")).addOr(new StringParam(null)));
params.add(IAnyResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
{
SearchParameterMap params = new SearchParameterMap();
params.add("_id", new StringParam(id1.getIdPart()));
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("")).addOr(new StringParam(null)));
params.add(IAnyResource.SP_RES_LANGUAGE, and);
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
{
SearchParameterMap params = new SearchParameterMap();
StringAndListParam and = new StringAndListParam();
and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
and.addAnd(new StringOrListParam().addOr(new StringParam("")).addOr(new StringParam(null)));
params.add(IAnyResource.SP_RES_LANGUAGE, and);
params.add("_id", new StringParam(id1.getIdPart()));
assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
}
}
@Test
public void testSearchLastUpdatedParam() {
String methodName = "testSearchLastUpdatedParam";

11
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
View File

@ -206,21 +206,12 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map = new SearchParameterMap();
map.add("_language", new StringParam("EN_ca"));
assertEquals(1, myOrganizationDao.search(map).size().intValue());
map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add("_tag", new TokenParam(methodName, methodName));
assertEquals(1, myOrganizationDao.search(map).size().intValue());
myOrganizationDao.delete(orgId, mySrd);
map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add("_language", new StringParam("EN_ca"));
assertEquals(0, myOrganizationDao.search(map).size().intValue());
map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add("_tag", new TokenParam(methodName, methodName));
@ -2014,7 +2005,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_BIRTHDATE + "AAAA", new DateParam(ParamPrefixEnum.GREATERTHAN, "2000-01-01")).setLoadSynchronous(true)));
assertEquals(0, found.size());
} catch (InvalidRequestException e) {
assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _language, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
assertEquals("Unknown search parameter \"birthdateAAAA\" for resource type \"Patient\". Valid search parameters for this search are: [_id, _lastUpdated, active, address, address-city, address-country, address-postalcode, address-state, address-use, animal-breed, animal-species, birthdate, death-date, deceased, email, family, gender, general-practitioner, given, identifier, language, link, name, organization, phone, phonetic, telecom]", e.getMessage());
}
}

35
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/index/IdHelperServiceTest.java
View File

@ -1,35 +0,0 @@
package ca.uhn.fhir.jpa.dao.index;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
public class IdHelperServiceTest {
@Test
public void testReplaceDefault_AllPartitions() {
IdHelperService svc = new IdHelperService();
PartitionSettings partitionSettings = new PartitionSettings();
partitionSettings.setDefaultPartitionId(1);
svc.setPartitionSettingsForUnitTest(partitionSettings);
RequestPartitionId outcome = svc.replaceDefault(RequestPartitionId.allPartitions());
assertSame(RequestPartitionId.allPartitions(), outcome);
}
@Test
public void testReplaceDefault_DefaultPartition() {
IdHelperService svc = new IdHelperService();
PartitionSettings partitionSettings = new PartitionSettings();
partitionSettings.setDefaultPartitionId(1);
svc.setPartitionSettingsForUnitTest(partitionSettings);
RequestPartitionId outcome = svc.replaceDefault(RequestPartitionId.defaultPartition());
assertEquals(1, outcome.getPartitionIds().get(0));
}
}

209
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/index/ResourceVersionSvcTest.java Normal file
View File

@ -0,0 +1,209 @@
package ca.uhn.fhir.jpa.dao.index;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.cache.ResourcePersistentIdMap;
import ca.uhn.fhir.jpa.cache.ResourceVersionSvcDaoImpl;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Path;
import javax.persistence.criteria.Root;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertSame;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class ResourceVersionSvcTest {
// helper class to package up data for helper methods
private class ResourceIdPackage {
public IIdType MyResourceId;
public ResourcePersistentId MyPid;
public Long MyVersion;
public ResourceIdPackage(IIdType id,
ResourcePersistentId pid,
Long version) {
MyResourceId = id;
MyPid = pid;
MyVersion = version;
}
}
@Mock
DaoRegistry myDaoRegistry;
@Mock
IResourceTableDao myResourceTableDao;
@Mock
IdHelperService myIdHelperService;
// TODO KHS move the methods that use this out to a separate test class
@InjectMocks
private ResourceVersionSvcDaoImpl myResourceVersionSvc;
/**
* Gets a ResourceTable record for getResourceVersionsForPid
* Order matters!
* @param resourceType
* @param pid
* @param version
* @return
*/
private Object[] getResourceTableRecordForResourceTypeAndPid(String resourceType, long pid, long version) {
return new Object[] {
pid, // long
resourceType, // string
version // long
};
}
/**
* Helper function to mock out resolveResourcePersistentIdsWithCache
* to return empty lists (as if no resources were found).
*/
private void mock_resolveResourcePersistentIdsWithCache_toReturnNothing() {
CriteriaBuilder cb = Mockito.mock(CriteriaBuilder.class);
CriteriaQuery<ForcedId> criteriaQuery = Mockito.mock(CriteriaQuery.class);
Root<ForcedId> from = Mockito.mock(Root.class);
Path path = Mockito.mock(Path.class);
TypedQuery<ForcedId> queryMock = Mockito.mock(TypedQuery.class);
}
/**
* Helper function to mock out getIdsOfExistingResources
* to return the matches and resources matching those provided
* by parameters.
* @param theResourcePacks
*/
private void mockReturnsFor_getIdsOfExistingResources(ResourceIdPackage... theResourcePacks) {
List<ResourcePersistentId> resourcePersistentIds = new ArrayList<>();
List<Object[]> matches = new ArrayList<>();
for (ResourceIdPackage pack : theResourcePacks) {
resourcePersistentIds.add(pack.MyPid);
matches.add(getResourceTableRecordForResourceTypeAndPid(
pack.MyResourceId.getResourceType(),
pack.MyPid.getIdAsLong(),
pack.MyVersion
));
}
ResourcePersistentId first = resourcePersistentIds.remove(0);
if (resourcePersistentIds.isEmpty()) {
when(myIdHelperService.resolveResourcePersistentIdsWithCache(any(), any())).thenReturn(Collections.singletonList(first));
}
else {
when(myIdHelperService.resolveResourcePersistentIdsWithCache(any(), any())).thenReturn(resourcePersistentIds);
}
}
@Test
public void getLatestVersionIdsForResourceIds_whenResourceExists_returnsMapWithPIDAndVersion() {
IIdType type = new IdDt("Patient/RED");
ResourcePersistentId pid = new ResourcePersistentId(1L);
pid.setAssociatedResourceId(type);
HashMap<IIdType, ResourcePersistentId> map = new HashMap<>();
map.put(type, pid);
ResourceIdPackage pack = new ResourceIdPackage(type, pid, 2L);
// when
mockReturnsFor_getIdsOfExistingResources(pack);
// test
ResourcePersistentIdMap retMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(RequestPartitionId.allPartitions(),
Collections.singletonList(type));
Assertions.assertTrue(retMap.containsKey(type));
Assertions.assertEquals(pid.getVersion(), map.get(type).getVersion());
}
@Test
public void getLatestVersionIdsForResourceIds_whenResourceDoesNotExist_returnsEmptyMap() {
IIdType type = new IdDt("Patient/RED");
// when
mock_resolveResourcePersistentIdsWithCache_toReturnNothing();
// test
ResourcePersistentIdMap retMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(RequestPartitionId.allPartitions(),
Collections.singletonList(type));
Assertions.assertTrue(retMap.isEmpty());
}
@Test
public void getLatestVersionIdsForResourceIds_whenSomeResourcesDoNotExist_returnsOnlyExistingElements() {
// resource to be found
IIdType type = new IdDt("Patient/RED");
ResourcePersistentId pid = new ResourcePersistentId(1L);
pid.setAssociatedResourceId(type);
ResourceIdPackage pack = new ResourceIdPackage(type, pid, 2L);
// resource that won't be found
IIdType type2 = new IdDt("Patient/BLUE");
// when
mock_resolveResourcePersistentIdsWithCache_toReturnNothing();
mockReturnsFor_getIdsOfExistingResources(pack);
// test
ResourcePersistentIdMap retMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(
RequestPartitionId.allPartitions(),
Arrays.asList(type, type2)
);
// verify
Assertions.assertEquals(1, retMap.size());
Assertions.assertTrue(retMap.containsKey(type));
Assertions.assertFalse(retMap.containsKey(type2));
}
@Test
public void testReplaceDefault_AllPartitions() {
IdHelperService svc = new IdHelperService();
PartitionSettings partitionSettings = new PartitionSettings();
partitionSettings.setDefaultPartitionId(1);
svc.setPartitionSettingsForUnitTest(partitionSettings);
RequestPartitionId outcome = svc.replaceDefault(RequestPartitionId.allPartitions());
assertSame(RequestPartitionId.allPartitions(), outcome);
}
@Test
public void testReplaceDefault_DefaultPartition() {
IdHelperService svc = new IdHelperService();
PartitionSettings partitionSettings = new PartitionSettings();
partitionSettings.setDefaultPartitionId(1);
svc.setPartitionSettingsForUnitTest(partitionSettings);
RequestPartitionId outcome = svc.replaceDefault(RequestPartitionId.defaultPartition());
assertEquals(1, outcome.getPartitionIds().get(0));
}
}

388
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/ChainingR4SearchTest.java Normal file
View File

@ -0,0 +1,388 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class ChainingR4SearchTest extends BaseJpaR4Test {
@Autowired
MatchUrlService myMatchUrlService;
@AfterEach
public void after() throws Exception {
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
myDaoConfig.setCountSearchResultsUpTo(new DaoConfig().getCountSearchResultsUpTo());
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
myModelConfig.setIndexOnContainedResources(false);
myModelConfig.setIndexOnContainedResources(new ModelConfig().isIndexOnContainedResources());
}
@BeforeEach
public void before() throws Exception {
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myDaoConfig.setAllowMultipleDelete(true);
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
myModelConfig.setIndexOnContainedResources(true);
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Test
public void testShouldResolveATwoLinkChainWithStandAloneResources() throws Exception {
// setup
IIdType oid1;
{
Patient p = new Patient();
p.setId(IdType.newRandomUuid());
p.addName().setFamily("Smith").addGiven("John");
myPatientDao.create(p, mySrd);
Observation obs = new Observation();
obs.getCode().setText("Observation 1");
obs.getSubject().setReference(p.getId());
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject.name=Smith";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
public void testShouldResolveATwoLinkChainWithAContainedResource() throws Exception {
// setup
IIdType oid1;
{
Patient p = new Patient();
p.setId("pat");
p.addName().setFamily("Smith").addGiven("John");
Observation obs = new Observation();
obs.getContained().add(p);
obs.getCode().setText("Observation 1");
obs.setValue(new StringType("Test"));
obs.getSubject().setReference("#pat");
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject.name=Smith";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
public void testShouldResolveAThreeLinkChainWhereAllResourcesStandAlone() throws Exception {
// setup
IIdType oid1;
{
Organization org = new Organization();
org.setId(IdType.newRandomUuid());
org.setName("HealthCo");
myOrganizationDao.create(org, mySrd);
Patient p = new Patient();
p.setId(IdType.newRandomUuid());
p.addName().setFamily("Smith").addGiven("John");
p.getManagingOrganization().setReference(org.getId());
myPatientDao.create(p, mySrd);
Observation obs = new Observation();
obs.getCode().setText("Observation 1");
obs.getSubject().setReference(p.getId());
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject.organization.name=HealthCo";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
public void testShouldResolveAThreeLinkChainWithAContainedResourceAtTheEndOfTheChain() throws Exception {
// This is the case that is most relevant to SMILE-2899
// setup
IIdType oid1;
{
Organization org = new Organization();
org.setId("org");
org.setName("HealthCo");
Patient p = new Patient();
p.setId(IdType.newRandomUuid());
p.getContained().add(org);
p.addName().setFamily("Smith").addGiven("John");
p.getManagingOrganization().setReference("#org");
myPatientDao.create(p, mySrd);
Observation obs = new Observation();
obs.getCode().setText("Observation 1");
obs.getSubject().setReference(p.getId());
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject.organization.name=HealthCo";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
@Disabled
public void testShouldResolveAThreeLinkChainWithAContainedResourceAtTheBeginningOfTheChain() throws Exception {
// We do not currently support this case - we may not be indexing the references of contained resources
// setup
IIdType oid1;
{
Organization org = new Organization();
org.setId(IdType.newRandomUuid());
org.setName("HealthCo");
myOrganizationDao.create(org, mySrd);
Patient p = new Patient();
p.setId("pat");
p.addName().setFamily("Smith").addGiven("John");
p.getManagingOrganization().setReference(org.getId());
Observation obs = new Observation();
obs.getContained().add(p);
obs.getCode().setText("Observation 1");
obs.getSubject().setReference("#pat");
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject.organization.name=HealthCo";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
public void testShouldResolveAThreeLinkChainWithQualifiersWhereAllResourcesStandAlone() throws Exception {
// setup
IIdType oid1;
{
Organization org = new Organization();
org.setId(IdType.newRandomUuid());
org.setName("HealthCo");
myOrganizationDao.create(org, mySrd);
Patient p = new Patient();
p.setId(IdType.newRandomUuid());
p.addName().setFamily("Smith").addGiven("John");
p.getManagingOrganization().setReference(org.getId());
myPatientDao.create(p, mySrd);
Observation obs = new Observation();
obs.getCode().setText("Observation 1");
obs.getSubject().setReference(p.getId());
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject:Patient.organization:Organization.name=HealthCo";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
public void testShouldResolveAThreeLinkChainWithQualifiersWithAContainedResourceAtTheEndOfTheChain() throws Exception {
// This is the case that is most relevant to SMILE-2899
// setup
IIdType oid1;
{
Organization org = new Organization();
org.setId("org");
org.setName("HealthCo");
Patient p = new Patient();
p.setId(IdType.newRandomUuid());
p.getContained().add(org);
p.addName().setFamily("Smith").addGiven("John");
p.getManagingOrganization().setReference("#org");
myPatientDao.create(p, mySrd);
Observation obs = new Observation();
obs.getCode().setText("Observation 1");
obs.getSubject().setReference(p.getId());
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject:Patient.organization:Organization.name=HealthCo";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
public void testShouldResolveAFourLinkChainWhereAllResourcesStandAlone() throws Exception {
// setup
IIdType oid1;
{
Organization org = new Organization();
org.setId(IdType.newRandomUuid());
org.setName("HealthCo");
myOrganizationDao.create(org, mySrd);
Organization partOfOrg = new Organization();
partOfOrg.setId(IdType.newRandomUuid());
partOfOrg.getPartOf().setReference(org.getId());
myOrganizationDao.create(partOfOrg, mySrd);
Patient p = new Patient();
p.setId(IdType.newRandomUuid());
p.addName().setFamily("Smith").addGiven("John");
p.getManagingOrganization().setReference(partOfOrg.getId());
myPatientDao.create(p, mySrd);
Observation obs = new Observation();
obs.getCode().setText("Observation 1");
obs.getSubject().setReference(p.getId());
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject.organization.partof.name=HealthCo";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
public void testShouldResolveAFourLinkChainWhereTheLastReferenceIsContained() throws Exception {
// setup
IIdType oid1;
{
Organization org = new Organization();
org.setId("parent");
org.setName("HealthCo");
Organization partOfOrg = new Organization();
partOfOrg.setId(IdType.newRandomUuid());
partOfOrg.getContained().add(org);
partOfOrg.getPartOf().setReference("#parent");
myOrganizationDao.create(partOfOrg, mySrd);
Patient p = new Patient();
p.setId(IdType.newRandomUuid());
p.addName().setFamily("Smith").addGiven("John");
p.getManagingOrganization().setReference(partOfOrg.getId());
myPatientDao.create(p, mySrd);
Observation obs = new Observation();
obs.getCode().setText("Observation 1");
obs.getSubject().setReference(p.getId());
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject.organization.partof.name=HealthCo";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
private List<String> searchAndReturnUnqualifiedVersionlessIdValues(String theUrl) throws IOException {
List<String> ids = new ArrayList<>();
ResourceSearch search = myMatchUrlService.getResourceSearch(theUrl);
SearchParameterMap map = search.getSearchParameterMap();
map.setLoadSynchronous(true);
IBundleProvider result = myObservationDao.search(map);
return result.getAllResourceIds();
}
}

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