- This is the home for the FHIR test server operated by - University Health Network. This server - (and the testing application you are currently using to access it) - is entirely built using - HAPI-FHIR, - a 100% open-source Java implementation of the - FHIR specification. -
-- Here are some things you might wish to try: -
-- You are accessing the public FHIR server - . This server is hosted elsewhere on the internet - but is being accessed using the HAPI client implementation. -
-- - This is not a production server! - Do not store any information here that contains personal health information - or any other confidential information. This server will be regularly purged - and reloaded with fixed test data. -
-DataSource properties
- such as serverName, databaseName
- and portNumber, the more specific properties will
- take precedence and url will be ignored.
-
- ]]>
- - This schema document describes the XML namespace, in a form - suitable for import by other schema documents. -
-- See - http://www.w3.org/XML/1998/namespace.html and - - http://www.w3.org/TR/REC-xml for information - about this namespace. -
-- Note that local names in this namespace are intended to be - defined only by the World Wide Web Consortium or its subgroups. - The names currently defined in this namespace are listed below. - They should not be used with conflicting semantics by any Working - Group, specification, or document instance. -
-- See further below in this document for more information about how to refer to this schema document from your own - XSD schema documents and about the - namespace-versioning policy governing this schema document. -
-- denotes an attribute whose value - is a language code for the natural language of the content of - any element; its value is inherited. This name is reserved - by virtue of its definition in the XML specification.
- -- Attempting to install the relevant ISO 2- and 3-letter - codes as the enumerated possible values is probably never - going to be a realistic possibility. -
-- See BCP 47 at - http://www.rfc-editor.org/rfc/bcp/bcp47.txt - and the IANA language subtag registry at - - http://www.iana.org/assignments/language-subtag-registry - for further information. -
-- The union allows for the 'un-declaration' of xml:lang with - the empty string. -
-- denotes an attribute whose - value is a keyword indicating what whitespace processing - discipline is intended for the content of the element; its - value is inherited. This name is reserved by virtue of its - definition in the XML specification.
- -- denotes an attribute whose value - provides a URI to be used as the base for interpreting any - relative URIs in the scope of the element on which it - appears; its value is inherited. This name is reserved - by virtue of its definition in the XML Base specification.
- -- See http://www.w3.org/TR/xmlbase/ - for information about this attribute. -
-- denotes an attribute whose value - should be interpreted as if declared to be of type ID. - This name is reserved by virtue of its definition in the - xml:id specification.
- -- See http://www.w3.org/TR/xml-id/ - for information about this attribute. -
-- denotes Jon Bosak, the chair of - the original XML Working Group. This name is reserved by - the following decision of the W3C XML Plenary and - XML Coordination groups: -
---- In appreciation for his vision, leadership and - dedication the W3C XML Plenary on this 10th day of - February, 2000, reserves for Jon Bosak in perpetuity - the XML name "xml:Father". -
-
- This schema defines attributes and an attribute group suitable
- for use by schemas wishing to allow xml:base,
- xml:lang, xml:space or
- xml:id attributes on elements they define.
-
- To enable this, such a schema must import this schema for - the XML namespace, e.g. as follows: -
-- <schema . . .> - . . . - <import namespace="http://www.w3.org/XML/1998/namespace" - schemaLocation="http://www.w3.org/2001/xml.xsd"/> --
- or -
-- <import namespace="http://www.w3.org/XML/1998/namespace" - schemaLocation="http://www.w3.org/2009/01/xml.xsd"/> --
- Subsequently, qualified reference to any of the attributes or the - group defined below will have the desired effect, e.g. -
-- <type . . .> - . . . - <attributeGroup ref="xml:specialAttrs"/> --
- will define a type which will schema-validate an instance element - with any of those attributes. -
-- In keeping with the XML Schema WG's standard versioning - policy, this schema document will persist at - - http://www.w3.org/2009/01/xml.xsd. -
-- At the date of issue it can also be found at - - http://www.w3.org/2001/xml.xsd. -
-- The schema document at that URI may however change in the future, - in order to remain compatible with the latest version of XML - Schema itself, or with the XML namespace itself. In other words, - if the XML Schema or XML namespaces change, the version of this - document at - http://www.w3.org/2001/xml.xsd - - will change accordingly; the version at - - http://www.w3.org/2009/01/xml.xsd - - will not change. -
-- Previous dated (and unchanging) versions of this schema - document are at: -
- -This project has been built with hapi-fhir-jpaserver-example as a base. It has been made more dynamic by replacing web.xml with ca.uhn.fhir.jpa.demo.WebInitializer class which extends Spring org.springframework.web.WebApplicationInitializer class and loads application contexts in a dynamic manner, so that based on environment and/or property variables it can be started either as dstu2 or dstu3 version of HAPI-FHIR JPA Server. Some of the classes have been also refactored to make them more generic.
There are number of environment variables that will control the behavior of the application at run time (such as start as dstu2 or dstu3 version, whether database schema gets recreated or no, database url, etc..). They can also be defined in Property files, see section below. These are environment variables that can be set before application starts:
-DB_URL - database url in a standard jdbc url format, specific to a database of your choosing. For example for Postgres it will be: jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>. So far support has been added for MySQL, derby and Postgres databases.
DATABASE_URL - if you deploy your server to HEROKU and create a Postgres database, its URL will be exposed through DATABASE_URL environment variable set by HEROKU. If DATABASE_URL is present it will overwrite DB_URL and its value will be used as jdbc url. This implementations assumes that Heroku will be setup with Postgres database, so current implementation handles postgres DATABASE_URL that gets set in this format: postgres://<username>:<password>@<hostname>:5432/<databaseName>. We convert it into standard jdbc format: jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>
SCHEMA_NAME - used only if DATABASE_URL is set, which is expected to be Postgres database url set by HEROKU. If it's set currentSchema parameter will be added to the jdbc url, e.g.:
jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>¤tScema=<schemaName>. Note that schema has to be created beforehand and user should have the right permissions to create tables.
STU_VERSION - can be set to dstu2 or dstu3. If not set by default dstu3 will be used. Corresponding classes will get dynamically loaded at a server startup.
ENV - environment this server will run in, and based on which corresponding property files will be loaded.
It can be one of those values: local, dev, stg, prod. Based on the value one of the property files will be loaded: resources/config/<STU_VERSION>/app_<ENV>.properties.
So for example if ENV=local and STU_VERSION=dstu3 this file will be loaded:
resources/config/dstu3/app_local.properties
HIBERNATE_CREATE - can be set to true or false. If set to true database schema will be dropped and recreated again upon application startup. If set to false hibernate will run with validate as a schema setting.
There are number of property files created for different environments: local, dev, stg, prod. So if ENV environment variable is set to one of those values corresponding property file will be loaded at a run time, by default local files will be loaded. Property files are located at: src/main/resources/config/dstu2 and src/main/resources/config/dstu3s directories. These are the files:
app_local.properties
- app_dev.properties
- app_stg.properties
- app_prod.properties
- immutable.properties - DO NOT modify any of the properties defined in that file.
-Any of the Environment variables can be defined in one of the app_<ENV>.properties property files. If a property is also defined as Environment variable it will overwrite value defined in property file. Properties defined in immutable.properties should not be changed, those are servlet/Spring mappings and names of classes that will be loaded at a run time and are specific to dstu version being used.
You can run the web application with webapp-runner and pass environment variables to it.
-Here is a sample command to run the webapp runner which will start dynamic HAPI-FHIR server with version dstu3, postgres database and hibernate schema being dropped and re-created.
-Note optional command to unset DATABASE_URL, so that only DB_URL is used locally. Also make sure to replace placeholder parameters <databasename>, <username> and <password> with actual values.
mvn clean install
-
-unset DATABASE_URL
-
-java $JAVA_OPTS -DSTU_VERSION=dstu3 -DHIBERNATE_CREATE=true -DDB_URL='jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>' -DENV=local -jar target/dependency/webapp-runner.jar target/*.war
-You should be able to access HAPI_FHIR server at: http://localhost:8080/ .
-If you'd like to open a debugging port run this command and attach remote debugger in IDE of your choice to port 5000. Again make sure to replace placeholder parameters with actual values before you run the command.
-java $JAVA_OPTS -Xdebug -Xrunjdwp:transport=dt_socket,server=y,address=5000,suspend=n -DSTU_VERSION=dstu3 -DHIBERNATE_CREATE=false -DDB_URL='jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>' -DENV=local -jar target/dependency/webapp-runner.jar target/*.war
-Install Tomcat.
-Make sure you have Tomcat set up in IntelliJ.
-Add a Run Configuration for running hapi-fhir-jpaserver-dynamic under Tomcat
-Run the configuration.
-Point your browser (or fiddler, or what have you) to http://localhost:8080/fhir/base/Patient
You should get an empty bundle back.
-Execute the build-docker-image.sh script to build the docker image.
Use this command to start the container: docker run -d --name hapi-fhir-jpaserver-dynamic -p 8080:8080 hapi-fhir/hapi-fhir-jpaserver-dynamic
Note: with this command data is persisted across container restarts, but not after removal of the container. Use a docker volume mapping on /var/lib/jetty/target to achieve this.
-There is also Dockerfile.tomcat which contains docker commands to run hapi-fhir-jpaserver-dynamic within tomcat. Rename Dockerfile.tomcat to Dockerfile if you would rather use tomcat as your application container.
- - diff --git a/example-projects/hapi-fhir-jpaserver-dynamic/.gitignore b/example-projects/hapi-fhir-jpaserver-dynamic/.gitignore deleted file mode 100644 index b72be74147a..00000000000 --- a/example-projects/hapi-fhir-jpaserver-dynamic/.gitignore +++ /dev/null @@ -1,130 +0,0 @@ -/target -/jpaserver_derby_files -*.log -ca.uhn.fhir.jpa.entity.ResourceTable/ - -# Created by https://www.gitignore.io - -### Java ### -*.class - -# Mobile Tools for Java (J2ME) -.mtj.tmp/ - -# Package Files # -*.jar -*.war -*.ear - -overlays/ - -# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml -hs_err_pid* - - -### Maven ### -target/ -pom.xml.tag -pom.xml.releaseBackup -pom.xml.versionsBackup -pom.xml.next -release.properties -dependency-reduced-pom.xml -buildNumber.properties - - -### Vim ### -[._]*.s[a-w][a-z] -[._]s[a-w][a-z] -*.un~ -Session.vim -.netrwhist -*~ - - -### Intellij ### -# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm - -*.iml - -## Directory-based project format: -.idea/ -# if you remove the above rule, at least ignore the following: - -# User-specific stuff: -# .idea/workspace.xml -# .idea/tasks.xml -# .idea/dictionaries - -# Sensitive or high-churn files: -# .idea/dataSources.ids -# .idea/dataSources.xml -# .idea/sqlDataSources.xml -# .idea/dynamic.xml -# .idea/uiDesigner.xml - -# Gradle: -# .idea/gradle.xml -# .idea/libraries - -# Mongo Explorer plugin: -# .idea/mongoSettings.xml - -## File-based project format: -*.ipr -*.iws - -## Plugin-specific files: - -# IntelliJ -/out/ - -# mpeltonen/sbt-idea plugin -.idea_modules/ - -# JIRA plugin -atlassian-ide-plugin.xml - -# Crashlytics plugin (for Android Studio and IntelliJ) -com_crashlytics_export_strings.xml -crashlytics.properties -crashlytics-build.properties - - - -### Eclipse ### -*.pydevproject -.metadata -.gradle -bin/ -tmp/ -*.tmp -*.bak -*.swp -*~.nib -local.properties -.loadpath - -# Eclipse Core -.project - -# External tool builders -.externalToolBuilders/ - -# Locally stored "Eclipse launch configurations" -*.launch - -# CDT-specific -.cproject - -# JDT-specific (Eclipse Java Development Tools) - -# PDT-specific -.buildpath - -# sbteclipse plugin -.target - -# TeXlipse plugin -.texlipse - diff --git a/example-projects/hapi-fhir-jpaserver-dynamic/Dockerfile b/example-projects/hapi-fhir-jpaserver-dynamic/Dockerfile deleted file mode 100644 index ddd9c750572..00000000000 --- a/example-projects/hapi-fhir-jpaserver-dynamic/Dockerfile +++ /dev/null @@ -1,4 +0,0 @@ -FROM jetty:9-jre8-alpine -USER jetty:jetty -ADD ./target/hapi-fhir-jpaserver-dynamic.war /var/lib/jetty/webapps/root.war -EXPOSE 8080 \ No newline at end of file diff --git a/example-projects/hapi-fhir-jpaserver-dynamic/Dockerfile.tomcat b/example-projects/hapi-fhir-jpaserver-dynamic/Dockerfile.tomcat deleted file mode 100644 index 27876fb10fa..00000000000 --- a/example-projects/hapi-fhir-jpaserver-dynamic/Dockerfile.tomcat +++ /dev/null @@ -1,4 +0,0 @@ -FROM tomcat:8 -COPY ["./hapi-fhir-jpaserver-dynamic.war","/usr/local/tomcat/webapps/"] -CMD ["catalina.sh","run"] -EXPOSE 8080 diff --git a/example-projects/hapi-fhir-jpaserver-dynamic/README.md b/example-projects/hapi-fhir-jpaserver-dynamic/README.md deleted file mode 100644 index c76de2c0e02..00000000000 --- a/example-projects/hapi-fhir-jpaserver-dynamic/README.md +++ /dev/null @@ -1,107 +0,0 @@ -## Description -This project has been built with hapi-fhir-jpaserver-example as a base. It has been made more dynamic by replacing `web.xml` with `ca.uhn.fhir.jpa.demo.WebInitializer` class which extends -Spring `org.springframework.web.WebApplicationInitializer` class and loads application contexts in a dynamic manner, so that based on environment and/or property variables it can be started either as dstu2 or dstu3 version of HAPI-FHIR JPA Server. Some of the classes have been also refactored to make them more generic. - -#### Environment variables -There are number of environment variables that will control the behavior of the application at run time (such as start as dstu2 or dstu3 version, whether -database schema gets recreated or no, database url, etc..). They can also be defined in Property files, see section below. These are environment variables that can be set before application starts: - * `DB_URL` - database url in a standard jdbc url format, specific to a database of your choosing. For example for Postgres it will be: `jdbc:postgresql://localhost:5432/- This is the home for the FHIR test server operated by - University Health Network. This server - (and the testing application you are currently using to access it) - is entirely built using - HAPI-FHIR, - a 100% open-source Java implementation of the - FHIR specification. -
-- Here are some things you might wish to try: -
-- You are accessing the public FHIR server - . This server is hosted elsewhere on the internet - but is being accessed using the HAPI client implementation. -
-- - This is not a production server! - Do not store any information here that contains personal health information - or any other confidential information. This server will be regularly purged - and reloaded with fixed test data. -
-DataSource properties
- such as serverName, databaseName
- and portNumber, the more specific properties will
- take precedence and url will be ignored.
-
- ]]>
- - This schema document describes the XML namespace, in a form - suitable for import by other schema documents. -
-- See - http://www.w3.org/XML/1998/namespace.html and - - http://www.w3.org/TR/REC-xml for information - about this namespace. -
-- Note that local names in this namespace are intended to be - defined only by the World Wide Web Consortium or its subgroups. - The names currently defined in this namespace are listed below. - They should not be used with conflicting semantics by any Working - Group, specification, or document instance. -
-- See further below in this document for more information about how to refer to this schema document from your own - XSD schema documents and about the - namespace-versioning policy governing this schema document. -
-- denotes an attribute whose value - is a language code for the natural language of the content of - any element; its value is inherited. This name is reserved - by virtue of its definition in the XML specification.
- -- Attempting to install the relevant ISO 2- and 3-letter - codes as the enumerated possible values is probably never - going to be a realistic possibility. -
-- See BCP 47 at - http://www.rfc-editor.org/rfc/bcp/bcp47.txt - and the IANA language subtag registry at - - http://www.iana.org/assignments/language-subtag-registry - for further information. -
-- The union allows for the 'un-declaration' of xml:lang with - the empty string. -
-- denotes an attribute whose - value is a keyword indicating what whitespace processing - discipline is intended for the content of the element; its - value is inherited. This name is reserved by virtue of its - definition in the XML specification.
- -- denotes an attribute whose value - provides a URI to be used as the base for interpreting any - relative URIs in the scope of the element on which it - appears; its value is inherited. This name is reserved - by virtue of its definition in the XML Base specification.
- -- See http://www.w3.org/TR/xmlbase/ - for information about this attribute. -
-- denotes an attribute whose value - should be interpreted as if declared to be of type ID. - This name is reserved by virtue of its definition in the - xml:id specification.
- -- See http://www.w3.org/TR/xml-id/ - for information about this attribute. -
-- denotes Jon Bosak, the chair of - the original XML Working Group. This name is reserved by - the following decision of the W3C XML Plenary and - XML Coordination groups: -
---- In appreciation for his vision, leadership and - dedication the W3C XML Plenary on this 10th day of - February, 2000, reserves for Jon Bosak in perpetuity - the XML name "xml:Father". -
-
- This schema defines attributes and an attribute group suitable
- for use by schemas wishing to allow xml:base,
- xml:lang, xml:space or
- xml:id attributes on elements they define.
-
- To enable this, such a schema must import this schema for - the XML namespace, e.g. as follows: -
-- <schema . . .> - . . . - <import namespace="http://www.w3.org/XML/1998/namespace" - schemaLocation="http://www.w3.org/2001/xml.xsd"/> --
- or -
-- <import namespace="http://www.w3.org/XML/1998/namespace" - schemaLocation="http://www.w3.org/2009/01/xml.xsd"/> --
- Subsequently, qualified reference to any of the attributes or the - group defined below will have the desired effect, e.g. -
-- <type . . .> - . . . - <attributeGroup ref="xml:specialAttrs"/> --
- will define a type which will schema-validate an instance element - with any of those attributes. -
-- In keeping with the XML Schema WG's standard versioning - policy, this schema document will persist at - - http://www.w3.org/2009/01/xml.xsd. -
-- At the date of issue it can also be found at - - http://www.w3.org/2001/xml.xsd. -
-- The schema document at that URI may however change in the future, - in order to remain compatible with the latest version of XML - Schema itself, or with the XML namespace itself. In other words, - if the XML Schema or XML namespaces change, the version of this - document at - http://www.w3.org/2001/xml.xsd - - will change accordingly; the version at - - http://www.w3.org/2009/01/xml.xsd - - will not change. -
-- Previous dated (and unchanging) versions of this schema - document are at: -
- -- This is the home for the FHIR test server operated by - University Health Network. This server - (and the testing application you are currently using to access it) - is entirely built using - HAPI-FHIR, - a 100% open-source Java implementation of the - FHIR specification. -
-- Here are some things you might wish to try: -
-- You are accessing the public FHIR server - . This server is hosted elsewhere on the internet - but is being accessed using the HAPI client implementation. -
-- - This is not a production server! - Do not store any information here that contains personal health information - or any other confidential information. This server will be regularly purged - and reloaded with fixed test data. -
-DataSource properties
- such as serverName, databaseName
- and portNumber, the more specific properties will
- take precedence and url will be ignored.
-
- ]]>
- - This schema document describes the XML namespace, in a form - suitable for import by other schema documents. -
-- See - http://www.w3.org/XML/1998/namespace.html and - - http://www.w3.org/TR/REC-xml for information - about this namespace. -
-- Note that local names in this namespace are intended to be - defined only by the World Wide Web Consortium or its subgroups. - The names currently defined in this namespace are listed below. - They should not be used with conflicting semantics by any Working - Group, specification, or document instance. -
-- See further below in this document for more information about how to refer to this schema document from your own - XSD schema documents and about the - namespace-versioning policy governing this schema document. -
-- denotes an attribute whose value - is a language code for the natural language of the content of - any element; its value is inherited. This name is reserved - by virtue of its definition in the XML specification.
- -- Attempting to install the relevant ISO 2- and 3-letter - codes as the enumerated possible values is probably never - going to be a realistic possibility. -
-- See BCP 47 at - http://www.rfc-editor.org/rfc/bcp/bcp47.txt - and the IANA language subtag registry at - - http://www.iana.org/assignments/language-subtag-registry - for further information. -
-- The union allows for the 'un-declaration' of xml:lang with - the empty string. -
-- denotes an attribute whose - value is a keyword indicating what whitespace processing - discipline is intended for the content of the element; its - value is inherited. This name is reserved by virtue of its - definition in the XML specification.
- -- denotes an attribute whose value - provides a URI to be used as the base for interpreting any - relative URIs in the scope of the element on which it - appears; its value is inherited. This name is reserved - by virtue of its definition in the XML Base specification.
- -- See http://www.w3.org/TR/xmlbase/ - for information about this attribute. -
-- denotes an attribute whose value - should be interpreted as if declared to be of type ID. - This name is reserved by virtue of its definition in the - xml:id specification.
- -- See http://www.w3.org/TR/xml-id/ - for information about this attribute. -
-- denotes Jon Bosak, the chair of - the original XML Working Group. This name is reserved by - the following decision of the W3C XML Plenary and - XML Coordination groups: -
---- In appreciation for his vision, leadership and - dedication the W3C XML Plenary on this 10th day of - February, 2000, reserves for Jon Bosak in perpetuity - the XML name "xml:Father". -
-
- This schema defines attributes and an attribute group suitable
- for use by schemas wishing to allow xml:base,
- xml:lang, xml:space or
- xml:id attributes on elements they define.
-
- To enable this, such a schema must import this schema for - the XML namespace, e.g. as follows: -
-- <schema . . .> - . . . - <import namespace="http://www.w3.org/XML/1998/namespace" - schemaLocation="http://www.w3.org/2001/xml.xsd"/> --
- or -
-- <import namespace="http://www.w3.org/XML/1998/namespace" - schemaLocation="http://www.w3.org/2009/01/xml.xsd"/> --
- Subsequently, qualified reference to any of the attributes or the - group defined below will have the desired effect, e.g. -
-- <type . . .> - . . . - <attributeGroup ref="xml:specialAttrs"/> --
- will define a type which will schema-validate an instance element - with any of those attributes. -
-- In keeping with the XML Schema WG's standard versioning - policy, this schema document will persist at - - http://www.w3.org/2009/01/xml.xsd. -
-- At the date of issue it can also be found at - - http://www.w3.org/2001/xml.xsd. -
-- The schema document at that URI may however change in the future, - in order to remain compatible with the latest version of XML - Schema itself, or with the XML namespace itself. In other words, - if the XML Schema or XML namespaces change, the version of this - document at - http://www.w3.org/2001/xml.xsd - - will change accordingly; the version at - - http://www.w3.org/2009/01/xml.xsd - - will not change. -
-- Previous dated (and unchanging) versions of this schema - document are at: -
- - theCodeSystemUrl, IPrimitiveType theVersion, IPrimitiveType theCode,
- IPrimitiveType theDisplay, Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
+ public CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType theCodeSystemUrl, IPrimitiveType theVersion, IPrimitiveType theCode,
+ IPrimitiveType theDisplay, Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
throw new UnsupportedOperationException();
}
-
+
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
index 4750d9bb0dc..6ddf296d402 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
@@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* #L%
*/
+import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
-import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -30,6 +30,8 @@ import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
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;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -37,8 +39,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.util.Date;
-import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
-
public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao implements IFhirResourceDaoConceptMap {
@Autowired
private ITermConceptMappingSvc myTermConceptMappingSvc;
@@ -53,7 +53,6 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao implements IFhirResourceDaoValueSet {
@@ -54,15 +54,15 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao expandMdmBySourceResourcePid(Long theSourceResourcePid) {
ourLog.debug("About to expand source resource with PID {}", theSourceResourcePid);
List goldenPidSourcePidTuples = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(theSourceResourcePid, MdmMatchResultEnum.MATCH);
+ return flattenPidTuplesToSet(theSourceResourcePid, goldenPidSourcePidTuples);
+ }
+
+ /**
+ * Given a PID of a golden resource, perform MDM expansion and return all the resource IDs of all resources that are
+ * MDM-Matched to this golden resource.
+ *
+ * @param theGoldenResourcePid The PID of the golden resource to MDM-Expand.
+ * @return A set of strings representing the FHIR ids of the expanded resources.
+ */
+ public Set expandMdmByGoldenResourceId(Long theGoldenResourcePid) {
+ ourLog.debug("About to expand golden resource with PID {}", theGoldenResourcePid);
+ List goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH);
+ return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples);
+ }
+
+
+ /**
+ * Given a resource ID of a golden resource, perform MDM expansion and return all the resource IDs of all resources that are
+ * MDM-Matched to this golden resource.
+ *
+ * @param theGoldenResourcePid The resource ID of the golden resource to MDM-Expand.
+ * @return A set of strings representing the FHIR ids of the expanded resources.
+ */
+ public Set expandMdmByGoldenResourcePid(Long theGoldenResourcePid) {
+ ourLog.debug("About to expand golden resource with PID {}", theGoldenResourcePid);
+ List goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH);
+ return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples);
+ }
+ public Set expandMdmByGoldenResourceId(IdDt theId) {
+ ourLog.debug("About to expand golden resource with golden resource id {}", theId);
+ Long pidOrThrowException = myIdHelperService.getPidOrThrowException(theId);
+ return expandMdmByGoldenResourcePid(pidOrThrowException);
+ }
+
+ @Nonnull
+ private Set flattenPidTuplesToSet(Long initialPid, List goldenPidSourcePidTuples) {
Set flattenedPids = new HashSet<>();
goldenPidSourcePidTuples.forEach(tuple -> {
flattenedPids.add(tuple.getSourcePid());
flattenedPids.add(tuple.getGoldenPid());
});
Set resourceIds = myIdHelperService.translatePidsToFhirResourceIds(flattenedPids);
- ourLog.debug("Pid {} has been expanded to [{}]", theSourceResourcePid, String.join(",", resourceIds));
+ ourLog.debug("Pid {} has been expanded to [{}]", initialPid, String.join(",", resourceIds));
return resourceIds;
}
-
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
index 740fd8b1492..03642eeb588 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
@@ -38,6 +38,8 @@ import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -149,7 +151,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao
@Override
public ValueSet expandByIdentifier(String theUri, ValueSetExpansionOptions theOptions) {
org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, theUri);
- return ValueSet40_50.convertValueSet(canonicalOutput);
+ return (ValueSet) VersionConvertorFactory_40_50.convertResource(canonicalOutput, new BaseAdvisor_40_50(false));
}
@Override
public ValueSet expand(ValueSet theSource, ValueSetExpansionOptions theOptions) {
- org.hl7.fhir.r4.model.ValueSet canonicalInput = ValueSet40_50.convertValueSet(theSource);
+ org.hl7.fhir.r4.model.ValueSet canonicalInput = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(theSource, new BaseAdvisor_40_50(false));
org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, canonicalInput);
- return ValueSet40_50.convertValueSet(canonicalOutput);
+ return (ValueSet) VersionConvertorFactory_40_50.convertResource(canonicalOutput, new BaseAdvisor_40_50(false));
}
@Override
@@ -82,7 +83,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao
if (getConfig().isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
- myTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSet));
+ myTerminologySvc.storeTermValueSet(retVal, (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(valueSet, new BaseAdvisor_40_50(false)));
} else {
myTerminologySvc.deleteValueSetAndChildren(retVal);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java
index 4516e342a14..1ec7b3593c9 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java
@@ -76,8 +76,16 @@ public class MdmSearchExpandingInterceptor {
if (iQueryParameterType instanceof ReferenceParam) {
ReferenceParam refParam = (ReferenceParam) iQueryParameterType;
if (refParam.isMdmExpand()) {
- ourLog.debug("Found a reference parameter to expand: {}", refParam.toString());
+ ourLog.debug("Found a reference parameter to expand: {}", refParam);
+ //First, attempt to expand as a source resource.
Set expandedResourceIds = myMdmLinkExpandSvc.expandMdmBySourceResourceId(new IdDt(refParam.getValue()));
+
+ // If we failed, attempt to expand as a golden resource
+ if (expandedResourceIds.isEmpty()) {
+ expandedResourceIds = myMdmLinkExpandSvc.expandMdmByGoldenResourceId(new IdDt(refParam.getValue()));
+ }
+
+ //Rebuild the search param list.
if (!expandedResourceIds.isEmpty()) {
ourLog.debug("Parameter has been expanded to: {}", String.join(", ", expandedResourceIds));
toRemove.add(refParam);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
index 806ace404ac..b0ce5830e2b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
@@ -40,6 +40,10 @@ import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.base.Charsets;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimap;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.ICompositeType;
@@ -58,10 +62,7 @@ import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import static org.apache.commons.lang3.StringUtils.isBlank;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import static org.apache.commons.lang3.StringUtils.trim;
-import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
+import static org.apache.commons.lang3.StringUtils.*;
public class TerminologyUploaderProvider extends BaseJpaProvider {
@@ -308,10 +309,10 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
CodeSystem nextCodeSystem;
switch (getContext().getVersion().getVersion()) {
case DSTU3:
- nextCodeSystem = convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem);
+ nextCodeSystem = (CodeSystem) VersionConvertorFactory_30_40.convertResource((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem, new BaseAdvisor_30_40(false));
break;
case R5:
- nextCodeSystem = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem);
+ nextCodeSystem = (CodeSystem) VersionConvertorFactory_40_50.convertResource((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem, new BaseAdvisor_40_50(false));
break;
default:
nextCodeSystem = (CodeSystem) theCodeSystem;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderConceptMapDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderConceptMapDstu3.java
index dd7f18e713b..1627544a315 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderConceptMapDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderConceptMapDstu3.java
@@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.provider.dstu3;
* #L%
*/
+import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
-import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl;
import ca.uhn.fhir.rest.annotation.IdParam;
@@ -31,7 +31,8 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -45,8 +46,6 @@ import org.hl7.fhir.exceptions.FHIRException;
import javax.servlet.http.HttpServletRequest;
-import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
-
public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderDstu3 {
@Operation(name = JpaConstants.OPERATION_TRANSLATE, idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1, max = 1),
@@ -82,7 +81,7 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
&& theSourceValueSet.hasValue();
boolean haveSourceCoding = theSourceCoding != null
&& theSourceCoding.hasCode();
- boolean haveSourceCodeableConcept= theSourceCodeableConcept != null
+ boolean haveSourceCodeableConcept = theSourceCodeableConcept != null
&& theSourceCodeableConcept.hasCoding()
&& theSourceCodeableConcept.getCodingFirstRep().hasCode();
boolean haveTargetValueSet = theTargetValueSet != null
@@ -100,46 +99,46 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
TranslationRequest translationRequest = new TranslationRequest();
try {
-
+
if (haveUrl) {
- translationRequest.setUrl(VersionConvertor_30_40.convertUri(theUrl));
+ translationRequest.setUrl((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theUrl, new BaseAdvisor_30_40(false)));
}
-
+
if (haveConceptMapVersion) {
- translationRequest.setConceptMapVersion(VersionConvertor_30_40.convertString(theConceptMapVersion));
+ translationRequest.setConceptMapVersion((org.hl7.fhir.r4.model.StringType) VersionConvertorFactory_30_40.convertType(theConceptMapVersion, new BaseAdvisor_30_40(false)));
}
-
+
// Convert from DSTU3 to R4
if (haveSourceCode) {
- translationRequest.getCodeableConcept().addCoding().setCodeElement(VersionConvertor_30_40.convertCode(theSourceCode));
+ translationRequest.getCodeableConcept().addCoding().setCodeElement((org.hl7.fhir.r4.model.CodeType) VersionConvertorFactory_30_40.convertType(theSourceCode, new BaseAdvisor_30_40(false)));
if (haveSourceCodeSystem) {
- translationRequest.getCodeableConcept().getCodingFirstRep().setSystemElement(VersionConvertor_30_40.convertUri(theSourceCodeSystem));
+ translationRequest.getCodeableConcept().getCodingFirstRep().setSystemElement((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theSourceCodeSystem, new BaseAdvisor_30_40(false)));
}
if (haveSourceCodeSystemVersion) {
- translationRequest.getCodeableConcept().getCodingFirstRep().setVersionElement(VersionConvertor_30_40.convertString(theSourceCodeSystemVersion));
+ translationRequest.getCodeableConcept().getCodingFirstRep().setVersionElement((org.hl7.fhir.r4.model.StringType) VersionConvertorFactory_30_40.convertType(theSourceCodeSystemVersion, new BaseAdvisor_30_40(false)));
}
} else if (haveSourceCoding) {
- translationRequest.getCodeableConcept().addCoding(VersionConvertor_30_40.convertCoding(theSourceCoding));
+ translationRequest.getCodeableConcept().addCoding((org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_30_40.convertType(theSourceCoding, new BaseAdvisor_30_40(false)));
} else {
- translationRequest.setCodeableConcept(VersionConvertor_30_40.convertCodeableConcept(theSourceCodeableConcept));
+ translationRequest.setCodeableConcept((org.hl7.fhir.r4.model.CodeableConcept) VersionConvertorFactory_30_40.convertType(theSourceCodeableConcept, new BaseAdvisor_30_40(false)));
}
if (haveSourceValueSet) {
- translationRequest.setSource(VersionConvertor_30_40.convertUri(theSourceValueSet));
+ translationRequest.setSource((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theSourceValueSet, new BaseAdvisor_30_40(false)));
}
if (haveTargetValueSet) {
- translationRequest.setTarget(VersionConvertor_30_40.convertUri(theTargetValueSet));
+ translationRequest.setTarget((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theTargetValueSet, new BaseAdvisor_30_40(false)));
}
if (haveTargetCodeSystem) {
- translationRequest.setTargetSystem(VersionConvertor_30_40.convertUri(theTargetCodeSystem));
+ translationRequest.setTargetSystem((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theTargetCodeSystem, new BaseAdvisor_30_40(false)));
}
if (haveReverse) {
- translationRequest.setReverse(VersionConvertor_30_40.convertBoolean(theReverse));
+ translationRequest.setReverse((org.hl7.fhir.r4.model.BooleanType) VersionConvertorFactory_30_40.convertType(theReverse, new BaseAdvisor_30_40(false)));
}
if (haveId) {
@@ -155,7 +154,7 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
TranslateConceptResults result = dao.translate(translationRequest, theRequestDetails);
// Convert from R4 to DSTU3
- return convertParameters(TermConceptMappingSvcImpl.toParameters(result));
+ return (Parameters) VersionConvertorFactory_30_40.convertResource(TermConceptMappingSvcImpl.toParameters(result), new BaseAdvisor_30_40(false));
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
} finally {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaResourceProviderDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaResourceProviderDstu3.java
index cc96142c495..b9c118d3de8 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaResourceProviderDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaResourceProviderDstu3.java
@@ -24,8 +24,6 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider;
import org.hl7.fhir.instance.model.api.IAnyResource;
-import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
-
public class JpaResourceProviderDstu3 extends BaseJpaResourceProvider {
public JpaResourceProviderDstu3() {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaSystemProviderDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaSystemProviderDstu3.java
index e622c3d82dc..3a18e6c6da9 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaSystemProviderDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaSystemProviderDstu3.java
@@ -24,7 +24,6 @@ import java.util.Map.Entry;
import java.util.TreeMap;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
-import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
/*
* #%L
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderConceptMapR5.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderConceptMapR5.java
index 4e80fe87662..b7cd93d5fd9 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderConceptMapR5.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderConceptMapR5.java
@@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.provider.r5;
* #L%
*/
+import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
-import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl;
import ca.uhn.fhir.rest.annotation.IdParam;
@@ -30,7 +30,8 @@ import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import org.hl7.fhir.convertors.VersionConvertor_40_50;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.CodeableConcept;
@@ -52,7 +53,7 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5 dao = (IFhirResourceDaoConceptMap) getDao();
TranslateConceptResults result = dao.translate(translationRequest, theRequestDetails);
org.hl7.fhir.r4.model.Parameters parameters = TermConceptMappingSvcImpl.toParameters(result);
- return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
+ return (Parameters) VersionConvertorFactory_40_50.convertResource(parameters, new BaseAdvisor_40_50(false));
} finally {
endRequest(theServletRequest);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
index 5fdec9ec884..38ddcb8077b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
@@ -41,6 +41,7 @@ import ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum;
import ca.uhn.fhir.jpa.util.InterceptorUtil;
+import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.model.primitive.InstantDt;
@@ -74,6 +75,7 @@ import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.function.Function;
+import java.util.stream.Collectors;
public class PersistedJpaBundleProvider implements IBundleProvider {
@@ -409,19 +411,25 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
// Note: Leave as protected, HSPC depends on this
@SuppressWarnings("WeakerAccess")
protected List toResourceList(ISearchBuilder theSearchBuilder, List thePids) {
- Set includedPids = new HashSet<>();
+ List includedPidList = new ArrayList<>();
if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) {
Integer maxIncludes = myDaoConfig.getMaximumIncludesToLoadPerPage();
- includedPids.addAll(theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated(), myUuid, myRequest, maxIncludes));
+
+ // Load _revincludes
+ Set includedPids = theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated(), myUuid, myRequest, maxIncludes);
if (maxIncludes != null) {
maxIncludes -= includedPids.size();
}
- includedPids.addAll(theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated(), myUuid, myRequest, maxIncludes));
- }
+ thePids.addAll(includedPids);
+ includedPidList.addAll(includedPids);
- List includedPidList = new ArrayList<>(includedPids);
- thePids.addAll(includedPidList);
+ // Load _includes
+ Set revIncludedPids = theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated(), myUuid, myRequest, maxIncludes);
+ thePids.addAll(revIncludedPids);
+ includedPidList.addAll(revIncludedPids);
+
+ }
// Execute the query and make sure we return distinct results
List resources = new ArrayList<>();
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
index dba0366e468..4d266271bd9 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
@@ -536,19 +536,22 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
* individually for pages as we return them to clients
*/
+ // _includes
Integer maxIncludes = myDaoConfig.getMaximumIncludesToLoadPerPage();
final Set includedPids = theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated(), "(synchronous)", theRequestDetails, maxIncludes);
-
if (maxIncludes != null) {
maxIncludes -= includedPids.size();
}
-
- if (theParams.getEverythingMode() == null && (maxIncludes == null || maxIncludes > 0)) {
- includedPids.addAll(theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)", theRequestDetails, maxIncludes));
- }
-
+ pids.addAll(includedPids);
List includedPidsList = new ArrayList<>(includedPids);
- pids.addAll(includedPidsList);
+
+ // _revincludes
+ if (theParams.getEverythingMode() == null && (maxIncludes == null || maxIncludes > 0)) {
+ Set revIncludedPids = theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)", theRequestDetails, maxIncludes);
+ includedPids.addAll(revIncludedPids);
+ pids.addAll(revIncludedPids);
+ includedPidsList.addAll(revIncludedPids);
+ }
List resources = new ArrayList<>();
theSb.loadResourcesByPid(pids, includedPidsList, resources, false, theRequestDetails);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
index 10ea71cc4d5..9f14b0bd4d5 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
@@ -220,9 +220,14 @@ public class SearchBuilder implements ISearchBuilder {
}
SearchContainedModeEnum searchContainedMode = theParams.getSearchContainedMode();
-
+
+ // Handle _id last, since it can typically be tacked onto a different parameter
+ List paramNames = myParams.keySet().stream().filter(t -> !t.equals(IAnyResource.SP_RES_ID)).collect(Collectors.toList());
+ if (myParams.containsKey(IAnyResource.SP_RES_ID)) {
+ paramNames.add(IAnyResource.SP_RES_ID);
+ }
+
// Handle each parameter
- List paramNames = new ArrayList<>(myParams.keySet());
for (String nextParamName : paramNames) {
if (myParams.isLastN() && LastNParameterHelper.isLastNParameter(nextParamName, myContext)) {
// Skip parameters for Subject, Patient, Code and Category for LastN as these will be filtered by Elasticsearch
@@ -857,7 +862,7 @@ public class SearchBuilder implements ISearchBuilder {
resourceLink = (Long) ((Object[]) nextRow)[0];
version = (Long) ((Object[]) nextRow)[1];
} else {
- resourceLink = (Long)nextRow;
+ resourceLink = (Long) nextRow;
}
pidsToInclude.add(new ResourcePersistentId(resourceLink, version));
@@ -926,8 +931,8 @@ public class SearchBuilder implements ISearchBuilder {
if (resourceLink != null) {
ResourcePersistentId persistentId;
if (findVersionFieldName != null) {
- persistentId = new ResourcePersistentId(((Object[])resourceLink)[0]);
- persistentId.setVersion((Long) ((Object[])resourceLink)[1]);
+ persistentId = new ResourcePersistentId(((Object[]) resourceLink)[0]);
+ persistentId.setVersion((Long) ((Object[]) resourceLink)[1]);
} else {
persistentId = new ResourcePersistentId(resourceLink);
}
@@ -977,7 +982,7 @@ public class SearchBuilder implements ISearchBuilder {
.add(IPreResourceAccessDetails.class, accessDetails)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest);
- CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.STORAGE_PREACCESS_RESOURCES, params);
+ CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.STORAGE_PREACCESS_RESOURCES, params);
for (int i = includedPidList.size() - 1; i >= 0; i--) {
if (accessDetails.isDontReturnResourceAtIndex(i)) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/BasePredicateBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/BasePredicateBuilder.java
index 0e6d710c478..0dbaa55fde1 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/BasePredicateBuilder.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/BasePredicateBuilder.java
@@ -82,8 +82,8 @@ public class BasePredicateBuilder {
return mySearchSqlBuilder.createConditionForValueWithComparator(theComparator, theColumn, theValue);
}
- protected BaseJoiningPredicateBuilder getOrCreateQueryRootTable() {
- return mySearchSqlBuilder.getOrCreateFirstPredicateBuilder();
+ protected BaseJoiningPredicateBuilder getOrCreateQueryRootTable(boolean theIncludeResourceTypeAndNonDeletedFlag) {
+ return mySearchSqlBuilder.getOrCreateFirstPredicateBuilder(theIncludeResourceTypeAndNonDeletedFlag);
}
public void addJoin(DbTable theFromTable, DbTable theToTable, DbColumn theFromColumn, DbColumn theToColumn) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceIdPredicateBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceIdPredicateBuilder.java
index cacd54cc387..3709146db1c 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceIdPredicateBuilder.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceIdPredicateBuilder.java
@@ -65,6 +65,7 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
Set allOrPids = null;
SearchFilterParser.CompareOperation defaultOperation = SearchFilterParser.CompareOperation.eq;
+ boolean allIdsAreForcedIds = true;
for (List nextValue : theValues) {
Set orPids = new HashSet<>();
boolean haveValue = false;
@@ -76,6 +77,9 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
IdType valueAsId = new IdType(value);
if (isNotBlank(value)) {
+ if (!myIdHelperService.idRequiresForcedId(valueAsId.getIdPart()) && allIdsAreForcedIds) {
+ allIdsAreForcedIds = false;
+ }
haveValue = true;
try {
ResourcePersistentId pid = myIdHelperService.resolveResourcePersistentIds(theRequestPartitionId, theResourceName, valueAsId.getIdPart());
@@ -114,7 +118,7 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
List resourceIds = ResourcePersistentId.toLongList(allOrPids);
if (theSourceJoinColumn == null) {
- BaseJoiningPredicateBuilder queryRootTable = super.getOrCreateQueryRootTable();
+ BaseJoiningPredicateBuilder queryRootTable = super.getOrCreateQueryRootTable(!allIdsAreForcedIds);
Condition predicate;
switch (operation) {
default:
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java
index 582e4eebbaf..ca3314c0c2e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java
@@ -469,18 +469,31 @@ public class SearchQueryBuilder {
* If at least one predicate builder already exists, return the last one added to the chain. If none has been selected, create a builder on HFJ_RESOURCE, add it and return it.
*/
public BaseJoiningPredicateBuilder getOrCreateFirstPredicateBuilder() {
+ return getOrCreateFirstPredicateBuilder(true);
+ }
+
+ /**
+ * If at least one predicate builder already exists, return the last one added to the chain. If none has been selected, create a builder on HFJ_RESOURCE, add it and return it.
+ */
+ public BaseJoiningPredicateBuilder getOrCreateFirstPredicateBuilder(boolean theIncludeResourceTypeAndNonDeletedFlag) {
if (myFirstPredicateBuilder == null) {
- getOrCreateResourceTablePredicateBuilder();
+ getOrCreateResourceTablePredicateBuilder(theIncludeResourceTypeAndNonDeletedFlag);
}
return myFirstPredicateBuilder;
}
public ResourceTablePredicateBuilder getOrCreateResourceTablePredicateBuilder() {
+ return getOrCreateResourceTablePredicateBuilder(true);
+ }
+
+ public ResourceTablePredicateBuilder getOrCreateResourceTablePredicateBuilder(boolean theIncludeResourceTypeAndNonDeletedFlag) {
if (myResourceTableRoot == null) {
ResourceTablePredicateBuilder resourceTable = mySqlBuilderFactory.resourceTable(this);
addTable(resourceTable, null);
- Condition typeAndDeletionPredicate = resourceTable.createResourceTypeAndNonDeletedPredicates();
- addPredicate(typeAndDeletionPredicate);
+ if (theIncludeResourceTypeAndNonDeletedFlag) {
+ Condition typeAndDeletionPredicate = resourceTable.createResourceTypeAndNonDeletedPredicates();
+ addPredicate(typeAndDeletionPredicate);
+ }
myResourceTableRoot = resourceTable;
}
return myResourceTableRoot;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
index 124a0a50c90..8f9c583ce23 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
@@ -42,7 +42,7 @@ import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.concurrent.BasicThreadFactory;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.r4.model.InstantType;
-import org.jetbrains.annotations.Nullable;
+import javax.annotation.Nullable;
import org.quartz.JobExecutionContext;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java
index 5ed129c071e..eafe533f2d3 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java
@@ -9,8 +9,8 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.ValidateUtil;
-import org.hl7.fhir.convertors.VersionConvertor_30_40;
-import org.hl7.fhir.convertors.conv30_40.CodeSystem30_40;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
@@ -25,8 +25,6 @@ import org.springframework.transaction.PlatformTransactionManager;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
-import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
-
/*
* #%L
* HAPI FHIR JPA Server
@@ -67,7 +65,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = toCanonicalValueSet(theValueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(theExpansionOptions, valueSetToExpandR4);
- return new ValueSetExpansionOutcome(convertValueSet(expandedR4), null);
+ return new ValueSetExpansionOutcome(VersionConvertorFactory_30_40.convertResource(expandedR4, new BaseAdvisor_30_40(false)), null);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@@ -81,7 +79,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(theExpansionOptions, valueSetToExpandR4);
- return convertValueSet(expandedR4);
+ return VersionConvertorFactory_30_40.convertResource(expandedR4, new BaseAdvisor_30_40(false));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@@ -90,31 +88,31 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
@Override
protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws FHIRException {
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
- valueSetToExpandR4 = convertValueSet((ValueSet) theValueSet);
+ valueSetToExpandR4 = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_30_40.convertResource((ValueSet) theValueSet, new BaseAdvisor_30_40(false));
return valueSetToExpandR4;
}
@Override
protected org.hl7.fhir.r4.model.CodeSystem toCanonicalCodeSystem(IBaseResource theCodeSystem) {
- return CodeSystem30_40.convertCodeSystem((CodeSystem)theCodeSystem);
+ return (org.hl7.fhir.r4.model.CodeSystem) VersionConvertorFactory_30_40.convertResource((CodeSystem)theCodeSystem, new BaseAdvisor_30_40(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseDatatype theCoding) {
- return VersionConvertor_30_40.convertCoding((org.hl7.fhir.dstu3.model.Coding) theCoding);
+ return (org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_30_40.convertType((Coding) theCoding, new BaseAdvisor_30_40(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseCoding theCoding) {
- return VersionConvertor_30_40.convertCoding((org.hl7.fhir.dstu3.model.Coding) theCoding);
+ return (org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_30_40.convertType((org.hl7.fhir.dstu3.model.Coding) theCoding, new BaseAdvisor_30_40(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCoding) {
- return VersionConvertor_30_40.convertCodeableConcept((org.hl7.fhir.dstu3.model.CodeableConcept) theCoding);
+ return (org.hl7.fhir.r4.model.CodeableConcept) VersionConvertorFactory_30_40.convertType((CodeableConcept) theCoding, new BaseAdvisor_30_40(false));
}
@@ -160,7 +158,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
public IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(ConceptValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
- org.hl7.fhir.r4.model.ValueSet valueSetR4 = convertValueSet(valueSet);
+ org.hl7.fhir.r4.model.ValueSet valueSetR4 = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_30_40.convertResource(valueSet, new BaseAdvisor_30_40(false));
Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = null;
@@ -184,7 +182,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
- org.hl7.fhir.r4.model.ValueSet valueSetR4 = convertValueSet(valueSet);
+ org.hl7.fhir.r4.model.ValueSet valueSetR4 = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_30_40.convertResource(valueSet, new BaseAdvisor_30_40(false));
return super.isValueSetPreExpandedForCodeValidation(valueSetR4);
}
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java
index 5c2f7c08d86..56c14ea5d94 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java
@@ -10,8 +10,8 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
import ca.uhn.fhir.util.ValidateUtil;
-import org.hl7.fhir.convertors.VersionConvertor_40_50;
-import org.hl7.fhir.convertors.conv40_50.CodeSystem40_50;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -19,8 +19,6 @@ import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ValueSet;
-import org.hl7.fhir.utilities.TerminologyServiceOptions;
-import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
@@ -59,15 +57,16 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Transactional(dontRollbackOn = {ExpansionTooCostlyException.class})
public ValueSetExpansionOutcome expandValueSet(ValidationSupportContext theValidationSupportContext, ValueSetExpansionOptions theExpansionOptions, @Nonnull IBaseResource theValueSetToExpand) {
ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
- org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(theExpansionOptions, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetToExpand));
- return new ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(expandedR4));
+ org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(theExpansionOptions,
+ (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(valueSetToExpand, new BaseAdvisor_40_50(false)));
+ return new ValueSetExpansionOutcome(VersionConvertorFactory_40_50.convertResource(expandedR4, new BaseAdvisor_40_50(false)));
}
@Override
public IBaseResource expandValueSet(ValueSetExpansionOptions theExpansionOptions, IBaseResource theInput) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = toCanonicalValueSet(theInput);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSet(theExpansionOptions, valueSetToExpand);
- return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR4);
+ return VersionConvertorFactory_40_50.convertResource(valueSetR4, new BaseAdvisor_40_50(false));
}
@Override
@@ -79,7 +78,7 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Override
protected org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
ValueSet valueSetR5 = myDaoRegistry.getResourceDao("ValueSet").toResource(ValueSet.class, theResourceTable, null, false);
- return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR5);
+ return (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(valueSetR5, new BaseAdvisor_40_50(false));
}
@Override
@@ -110,30 +109,30 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseDatatype theCoding) {
- return VersionConvertor_40_50.convertCoding((Coding) theCoding);
+ return (org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_40_50.convertType((Coding) theCoding, new BaseAdvisor_40_50(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseCoding theCoding) {
- return VersionConvertor_40_50.convertCoding((Coding) theCoding);
+ return (org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_40_50.convertType((Coding) theCoding, new BaseAdvisor_40_50(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCoding) {
- return VersionConvertor_40_50.convertCodeableConcept((CodeableConcept) theCoding);
+ return (org.hl7.fhir.r4.model.CodeableConcept) VersionConvertorFactory_40_50.convertType((CodeableConcept) theCoding, new BaseAdvisor_40_50(false));
}
@Override
protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws org.hl7.fhir.exceptions.FHIRException {
- return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet((ValueSet) theValueSet);
+ return (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource((ValueSet) theValueSet, new BaseAdvisor_40_50(false));
}
@Override
protected org.hl7.fhir.r4.model.CodeSystem toCanonicalCodeSystem(IBaseResource theCodeSystem) {
- return CodeSystem40_50.convertCodeSystem((CodeSystem) theCodeSystem);
+ return (org.hl7.fhir.r4.model.CodeSystem) VersionConvertorFactory_40_50.convertResource((CodeSystem) theCodeSystem, new BaseAdvisor_40_50(false));
}
@Override
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu3.java
index 2933d256a7b..446a5188cfa 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu3.java
@@ -25,6 +25,8 @@ import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.UrlUtil;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.dstu3.model.ValueSet;
@@ -36,9 +38,6 @@ import org.springframework.context.event.ContextRefreshedEvent;
import org.springframework.context.event.EventListener;
import static org.apache.commons.lang3.StringUtils.isBlank;
-import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
-import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
-import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
@@ -56,7 +55,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
/**
* Initialize the beans that are used by this service.
- *
+ *
* Note: There is a circular dependency here where the CodeSystem DAO
* needs terminology services, and the term services need the CodeSystem DAO.
* So we look these up in a refresh event instead of just autowiring them
@@ -70,11 +69,11 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
myConceptMapResourceDao = (IFhirResourceDao) myAppCtx.getBean("myConceptMapDaoDstu3");
}
- @Override
+ @Override
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, RequestDetails theRequestDetails) {
CodeSystem resourceToStore;
try {
- resourceToStore = convertCodeSystem(theCodeSystemResource);
+ resourceToStore = (CodeSystem) VersionConvertorFactory_30_40.convertResource(theCodeSystemResource, new BaseAdvisor_30_40(false));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@@ -91,7 +90,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap resourceToStore;
try {
- resourceToStore = convertConceptMap(theConceptMap);
+ resourceToStore = (ConceptMap) VersionConvertorFactory_30_40.convertResource(theConceptMap, new BaseAdvisor_30_40(false));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@@ -107,7 +106,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetDstu3;
try {
- valueSetDstu3 = convertValueSet(theValueSet);
+ valueSetDstu3 = (ValueSet) VersionConvertorFactory_30_40.convertResource(theValueSet, new BaseAdvisor_30_40(false));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR5.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR5.java
index f0664b99564..93e96974d27 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR5.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR5.java
@@ -24,6 +24,8 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.util.UrlUtil;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ConceptMap;
@@ -63,7 +65,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, RequestDetails theRequestDetails) {
validateCodeSystemForStorage(theCodeSystemResource);
- CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(theCodeSystemResource);
+ CodeSystem codeSystemR4 = (CodeSystem) VersionConvertorFactory_40_50.convertResource(theCodeSystemResource, new BaseAdvisor_40_50(false));
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(codeSystemR4, matchUrl, theRequestDetails).getId();
@@ -75,7 +77,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
@Override
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
- ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap40_50.convertConceptMap(theConceptMap);
+ ConceptMap conceptMapR4 = (ConceptMap) VersionConvertorFactory_40_50.convertResource(theConceptMap, new BaseAdvisor_40_50(false));
if (isBlank(theConceptMap.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
@@ -88,7 +90,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
@Override
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
- ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(theValueSet);
+ ValueSet valueSetR4 = (ValueSet) VersionConvertorFactory_40_50.convertResource(theValueSet, new BaseAdvisor_40_50(false));
if (isBlank(theValueSet.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java
index d10ad96f738..290adfab468 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java
@@ -27,7 +27,9 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import org.hl7.fhir.common.hapi.validation.validator.VersionSpecificWorkerContextWrapper;
+import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r5.elementmodel.Element;
@@ -39,6 +41,9 @@ import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.PostConstruct;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
import java.util.Locale;
public class ValidatorResourceFetcher implements IResourceValidator.IValidatorResourceFetcher {
@@ -60,10 +65,8 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
myVersionSpecificCOntextWrapper = VersionSpecificWorkerContextWrapper.newVersionSpecificWorkerContextWrapper(myValidationSupport);
}
-
@Override
- public Element fetch(Object appContext, String theUrl) throws FHIRException {
-
+ public Element fetch(IResourceValidator iResourceValidator, Object appContext, String theUrl) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
IdType id = new IdType(theUrl);
String resourceType = id.getResourceType();
IFhirResourceDao dao = myDaoRegistry.getResourceDao(resourceType);
@@ -83,7 +86,8 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
}
@Override
- public IResourceValidator.ReferenceValidationPolicy validationPolicy(Object appContext, String path, String url) {
+ public IResourceValidator.ReferenceValidationPolicy validationPolicy(IResourceValidator iResourceValidator,
+ Object appContext, String path, String url) {
int slashIdx = url.indexOf("/");
if (slashIdx > 0 && myFhirContext.getResourceTypes().contains(url.substring(0, slashIdx))) {
return myValidationSettings.getLocalReferenceValidationDefaultPolicy();
@@ -93,12 +97,12 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
}
@Override
- public boolean resolveURL(Object appContext, String path, String url, String type) throws FHIRException {
+ public boolean resolveURL(IResourceValidator iResourceValidator, Object o, String s, String s1, String s2) throws IOException, FHIRException {
return true;
}
@Override
- public byte[] fetchRaw(String url) {
+ public byte[] fetchRaw(IResourceValidator iResourceValidator, String s) throws MalformedURLException, IOException {
throw new UnsupportedOperationException();
}
@@ -109,13 +113,12 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
}
@Override
- public CanonicalResource fetchCanonicalResource(String url) {
- throw new UnsupportedOperationException();
+ public CanonicalResource fetchCanonicalResource(IResourceValidator iResourceValidator, String s) throws URISyntaxException {
+ return null;
}
@Override
- public boolean fetchesCanonicalResource(String url) {
+ public boolean fetchesCanonicalResource(IResourceValidator iResourceValidator, String s) {
return false;
}
-
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java
index 8b8289a3980..1dbade8c828 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java
@@ -78,7 +78,8 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
- assertFalse(result.isOk());
+ //TODO JA, from what I read, this _should_ pass, but this was flipped to false in a previous commit.
+ assertTrue(result.isOk());
}
@Test
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
index 0f7ac511ac6..7714d442b05 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
@@ -38,7 +38,6 @@ import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
-import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
import ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl;
@@ -53,10 +52,13 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.session.SearchSession;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.AllergyIntolerance;
import org.hl7.fhir.dstu3.model.Appointment;
import org.hl7.fhir.dstu3.model.AuditEvent;
@@ -125,7 +127,6 @@ import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.Map;
-import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
import static org.junit.jupiter.api.Assertions.fail;
@ExtendWith(SpringExtension.class)
@@ -378,7 +379,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@BeforeEach
public void beforeFlushFT() {
runInTransaction(() -> {
- SearchSession searchSession = Search.session(myEntityManager);
+ SearchSession searchSession = Search.session(myEntityManager);
searchSession.workspace(ResourceTable.class).purge();
// searchSession.workspace(ResourceIndexedSearchParamString.class).purge();
searchSession.indexingPlan().execute();
@@ -462,7 +463,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
*/
public static ConceptMap createConceptMap() {
try {
- return convertConceptMap(BaseJpaR4Test.createConceptMap());
+ return (ConceptMap) VersionConvertorFactory_30_40.convertResource(BaseJpaR4Test.createConceptMap(), new BaseAdvisor_30_40(false));
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
index 716db77adef..95a9732fed5 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
@@ -103,6 +103,7 @@ import org.hl7.fhir.r4.model.AllergyIntolerance;
import org.hl7.fhir.r4.model.Appointment;
import org.hl7.fhir.r4.model.AuditEvent;
import org.hl7.fhir.r4.model.Binary;
+import org.hl7.fhir.r4.model.BodyStructure;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CapabilityStatement;
import org.hl7.fhir.r4.model.CarePlan;
@@ -371,6 +372,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@Qualifier("myBinaryDaoR4")
protected IFhirResourceDao myBinaryDao;
@Autowired
+ @Qualifier("myBodyStructureDaoR4")
+ protected IFhirResourceDao myBodyStructureDao;
+ @Autowired
@Qualifier("myDocumentReferenceDaoR4")
protected IFhirResourceDao myDocumentReferenceDao;
@Autowired
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConcurrentWriteTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConcurrentWriteTest.java
index 01f28434035..714c6b70b9f 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConcurrentWriteTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConcurrentWriteTest.java
@@ -155,12 +155,12 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
}
+ logAllResourceLinks();
runInTransaction(() -> {
Map counts = getResourceCountMap();
assertEquals(1, counts.get("Patient"), counts.toString());
assertEquals(1, counts.get("Observation"), counts.toString());
- logAllResourceLinks();
assertEquals(6, myResourceLinkDao.count());
assertEquals(6, myResourceTableDao.count());
assertEquals(14, myResourceHistoryTableDao.count());
@@ -194,12 +194,12 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
}
+ logAllResourceLinks();
runInTransaction(() -> {
Map counts = getResourceCountMap();
assertEquals(1, counts.get("Patient"), counts.toString());
assertEquals(1, counts.get("Observation"), counts.toString());
- logAllResourceLinks();
assertEquals(6, myResourceLinkDao.count());
assertEquals(6, myResourceTableDao.count());
assertEquals(14, myResourceHistoryTableDao.count());
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java
index 75ba865d268..7a18b4ed391 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java
@@ -929,7 +929,7 @@ public class FhirResourceDaoR4LegacySearchBuilderTest extends BaseJpaR4Test {
List actual = toUnqualifiedVersionlessIds(resp);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(actual, containsInAnyOrder(orgId, medId, patId, moId, patId2));
- assertEquals(6, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
+ assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
// Specific patient ID with linked stuff
request = mock(HttpServletRequest.class);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchIncludeTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchIncludeTest.java
index 575b71648ab..a95130ace11 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchIncludeTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchIncludeTest.java
@@ -1,17 +1,25 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
+import ca.uhn.fhir.jpa.search.PersistedJpaSearchFirstPageBundleProvider;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import org.hamcrest.Matcher;
+import org.hamcrest.Matchers;
import org.hamcrest.collection.IsIterableContainingInAnyOrder;
+import org.hl7.fhir.r4.model.BodyStructure;
import org.hl7.fhir.r4.model.CarePlan;
+import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.EpisodeOfCare;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Procedure;
import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.SearchParameter;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Test;
@@ -23,7 +31,10 @@ import java.util.stream.IntStream;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.equalTo;
+import static org.hl7.fhir.r4.model.ResourceType.BodyStructure;
import static org.hl7.fhir.r4.model.ResourceType.Patient;
+import static org.hl7.fhir.r4.model.ResourceType.Procedure;
+import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
@SuppressWarnings({"unchecked", "Duplicates"})
@@ -114,6 +125,61 @@ public class FhirResourceDaoR4SearchIncludeTest extends BaseJpaR4Test {
}
}
+
+ @Test
+ public void testRevIncludeOnIncludedResource() {
+ SearchParameter sp = new SearchParameter();
+ sp.addBase("Procedure");
+ sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+ sp.setCode("focalAccess");
+ sp.setType(Enumerations.SearchParamType.REFERENCE);
+ sp.setExpression("Procedure.extension('http://fkcfhir.org/fhir/cs/CS1MachNumber')");
+ sp.addTarget("BodyStructure");
+ mySearchParameterDao.create(sp, mySrd);
+ mySearchParamRegistry.forceRefresh();
+
+ BodyStructure bs = new BodyStructure();
+ bs.setId("B51936689");
+ bs.setDescription("Foo");
+ myBodyStructureDao.update(bs, mySrd);
+
+ Procedure p = new Procedure();
+ p.setId("PRA8780542726");
+ p.setStatus(org.hl7.fhir.r4.model.Procedure.ProcedureStatus.COMPLETED);
+ myProcedureDao.update(p, mySrd);
+
+ p = new Procedure();
+ p.setId("PRA8780542785");
+ p.addPartOf().setReference("Procedure/PRA8780542726");
+ p.setStatus(org.hl7.fhir.r4.model.Procedure.ProcedureStatus.COMPLETED);
+ p.addExtension("http://fkcfhir.org/fhir/cs/CS1MachNumber", new Reference("BodyStructure/B51936689"));
+ myProcedureDao.update(p, mySrd);
+
+ logAllResources();
+ logAllResourceLinks();
+
+ // Non synchronous
+ SearchParameterMap map = new SearchParameterMap();
+ map.add("_id", new TokenParam("PRA8780542726"));
+ map.addRevInclude(new Include("Procedure:part-of"));
+ map.addInclude(new Include("Procedure:focalAccess").asRecursive());
+ IBundleProvider outcome = myProcedureDao.search(map, mySrd);
+ assertEquals(PersistedJpaSearchFirstPageBundleProvider.class, outcome.getClass());
+ List ids = toUnqualifiedVersionlessIdValues(outcome);
+ assertThat(ids.toString(), ids, Matchers.containsInAnyOrder("Procedure/PRA8780542726", "Procedure/PRA8780542785", "BodyStructure/B51936689"));
+
+ // Synchronous
+ map = new SearchParameterMap().setLoadSynchronous(true);
+ map.add("_id", new TokenParam("PRA8780542726"));
+ map.addRevInclude(new Include("Procedure:part-of"));
+ map.addInclude(new Include("Procedure:focalAccess").asRecursive());
+ outcome = myProcedureDao.search(map, mySrd);
+ assertEquals(SimpleBundleProvider.class, outcome.getClass());
+ ids = toUnqualifiedVersionlessIdValues(outcome);
+ assertThat(ids.toString(), ids, Matchers.containsInAnyOrder("Procedure/PRA8780542726", "Procedure/PRA8780542785", "BodyStructure/B51936689"));
+ }
+
+
@Test
public void testRevIncludesPaged_AsyncSearch() {
int eocCount = 10;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java
index 19076e16b97..6e1adee1f66 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java
@@ -33,6 +33,7 @@ public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
// Set up search parameters that will return 75 Observations.
SearchParameterMap params = new SearchParameterMap();
+ params.setLoadSynchronous(true);
ReferenceParam subjectParam1 = new ReferenceParam("Patient", "", patient0Id.getValue());
ReferenceParam subjectParam2 = new ReferenceParam("Patient", "", patient1Id.getValue());
ReferenceParam subjectParam3 = new ReferenceParam("Patient", "", patient2Id.getValue());
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
index c5cfa742aa0..25eecd5c164 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
@@ -778,7 +778,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
List actual = toUnqualifiedVersionlessIds(resp);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(actual, containsInAnyOrder(orgId, medId, patId, moId, patId2));
- assertEquals(5, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
+ assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
// Specific patient ID with linked stuff
request = mock(HttpServletRequest.class);
@@ -1475,21 +1475,28 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
id2 = myOrganizationDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
}
+ // FIXME: restore
+
+ int size;
SearchParameterMap params = new SearchParameterMap();
+// params.setLoadSynchronous(true);
+// assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id1));
+//
+// params = new SearchParameterMap();
+// params.add("_id", new StringParam(id1));
+// assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id1));
+//
+// params = new SearchParameterMap();
+// params.add("_id", new StringParam("9999999999999999"));
+// assertEquals(0, toList(myPatientDao.search(params)).size());
+
+ myCaptureQueriesListener.clear();
+ params = new SearchParameterMap();
params.setLoadSynchronous(true);
- assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id1));
-
- params = new SearchParameterMap();
- params.add("_id", new StringParam(id1));
- assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id1));
-
- params = new SearchParameterMap();
- params.add("_id", new StringParam("9999999999999999"));
- assertEquals(0, toList(myPatientDao.search(params)).size());
-
- params = new SearchParameterMap();
params.add("_id", new StringParam(id2));
- assertEquals(0, toList(myPatientDao.search(params)).size());
+ size = toList(myPatientDao.search(params)).size();
+ myCaptureQueriesListener.logAllQueries();
+ assertEquals(0, size);
}
@@ -1596,8 +1603,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertEquals(1, countMatches(sqlQuery, "res_id = '123'"), sqlQuery);
assertEquals(1, countMatches(sqlQuery, "join"), sqlQuery);
assertEquals(1, countMatches(sqlQuery, "hash_sys_and_value"), sqlQuery);
- assertEquals(1, countMatches(sqlQuery, "res_type = 'diagnosticreport"), sqlQuery); // could be 0
- assertEquals(1, countMatches(sqlQuery, "res_deleted_at"), sqlQuery); // could be 0
+ assertEquals(0, countMatches(sqlQuery, "res_type = 'diagnosticreport"), sqlQuery); // could be 0
+ assertEquals(0, countMatches(sqlQuery, "res_deleted_at"), sqlQuery); // could be 0
}
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
index 66201cfddba..a84edb5bdc9 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
@@ -18,6 +19,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.apache.commons.lang3.StringUtils;
@@ -26,6 +28,8 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Enumerations;
+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.Reference;
@@ -797,6 +801,112 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
assertEquals(1, StringUtils.countMatches(selectQuery, "SELECT"));
}
+ /**
+ * Make sure that if we're performing a query where the resource type is implicitly known,
+ * we don't include a selector for the resource type
+ *
+ * This test is for queries with _id where the ID is a forced ID
+ */
+ @Test
+ public void testSearchOnIdAndReference_SearchById() {
+
+ Patient p = new Patient();
+ p.setId("B");
+ myPatientDao.update(p);
+
+ Observation obs = new Observation();
+ obs.setId("A");
+ obs.setSubject(new Reference("Patient/B"));
+ obs.setStatus(Observation.ObservationStatus.FINAL);
+ myObservationDao.update(obs);
+
+ Observation obs2 = new Observation();
+ obs2.setSubject(new Reference("Patient/B"));
+ obs2.setStatus(Observation.ObservationStatus.FINAL);
+ String obs2id = myObservationDao.create(obs2).getId().getIdPart();
+ assertThat(obs2id, matchesPattern("^[0-9]+$"));
+
+ // Search by ID where all IDs are forced IDs
+ {
+ SearchParameterMap map = SearchParameterMap.newSynchronous();
+ map.add("_id", new TokenParam("A"));
+ map.add("subject", new ReferenceParam("Patient/B"));
+ map.add("status", new TokenParam("final"));
+ myCaptureQueriesListener.clear();
+ IBundleProvider outcome = myObservationDao.search(map, new SystemRequestDetails());
+ assertEquals(1, outcome.getResources(0, 999).size());
+ myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+
+ String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "forcedid0_.resource_type='observation'"), selectQuery);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "forcedid0_.forced_id in ('a')"), selectQuery);
+
+ selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, false);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "select t1.res_id from hfj_resource t1"), selectQuery);
+ assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), "t1.res_type = 'observation'"), selectQuery);
+ assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), "t1.res_deleted_at is null"), selectQuery);
+ }
+
+ // Search by ID where at least one ID is a numeric ID
+ {
+ SearchParameterMap map = SearchParameterMap.newSynchronous();
+ map.add("_id", new TokenOrListParam(null, "A", obs2id));
+ myCaptureQueriesListener.clear();
+ IBundleProvider outcome = myObservationDao.search(map, new SystemRequestDetails());
+ assertEquals(2, outcome.size());
+ assertEquals(2, outcome.getResources(0, 999).size());
+ myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+ String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, false);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "select t0.res_id from hfj_resource t0"), selectQuery);
+ // Because we included a non-forced ID, we need to verify the type
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_type = 'observation'"), selectQuery);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_deleted_at is null"), selectQuery);
+ }
+
+ // Delete the resource - The searches should generate similar SQL now, but
+ // not actually return the result
+ myObservationDao.delete(new IdType("Observation/A"));
+ myObservationDao.delete(new IdType("Observation/" + obs2id));
+
+ // Search by ID where all IDs are forced IDs
+ {
+ SearchParameterMap map = SearchParameterMap.newSynchronous();
+ map.add("_id", new TokenParam("A"));
+ myCaptureQueriesListener.clear();
+ IBundleProvider outcome = myObservationDao.search(map, new SystemRequestDetails());
+ assertEquals(0, outcome.size());
+ assertEquals(0, outcome.getResources(0, 999).size());
+ myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+
+ String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "forcedid0_.resource_type='observation'"), selectQuery);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "forcedid0_.forced_id in ('a')"), selectQuery);
+
+ selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, false);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "select t0.res_id from hfj_resource t0"), selectQuery);
+ assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_type = 'observation'"), selectQuery);
+ assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_deleted_at is null"), selectQuery);
+ }
+
+ // Search by ID where at least one ID is a numeric ID
+ {
+ SearchParameterMap map = SearchParameterMap.newSynchronous();
+ map.add("_id", new TokenOrListParam(null, "A", obs2id));
+ myCaptureQueriesListener.clear();
+ IBundleProvider outcome = myObservationDao.search(map, new SystemRequestDetails());
+ assertEquals(0, outcome.size());
+ assertEquals(0, outcome.getResources(0, 999).size());
+ myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+ String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, false);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "select t0.res_id from hfj_resource t0"), selectQuery);
+ // Because we included a non-forced ID, we need to verify the type
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_type = 'observation'"), selectQuery);
+ assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_deleted_at is null"), selectQuery);
+ }
+
+ }
+
+
@AfterEach
public void afterResetDao() {
myDaoConfig.setResourceMetaCountHardLimit(new DaoConfig().getResourceMetaCountHardLimit());
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java
index 76ebb3e0b74..67e43f02edf 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java
@@ -779,7 +779,5 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
assertEquals(observationId.getValue(), resources.get(0).getIdElement().getValue());
assertEquals(patientId.withVersion("2").getValue(), resources.get(1).getIdElement().getValue());
}
-
}
-
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
index 7c753d06320..a1b7bb0ae52 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
@@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
@@ -63,6 +64,7 @@ import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
+import org.hl7.fhir.r4.model.Task;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
@@ -1002,6 +1004,23 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
}
+ @Test
+ public void testTransactionNoContainedRedux() throws IOException {
+ //Pre-create the patient, which will cause the ifNoneExist to prevent a new creation during bundle transaction
+ Patient patient = loadResourceFromClasspath(Patient.class, "/r4/preexisting-patient.json");
+ myPatientDao.create(patient);
+
+ //Post the Bundle containing a conditional POST with an identical patient from the above resource.
+ Bundle request = loadResourceFromClasspath(Bundle.class, "/r4/transaction-no-contained-2.json");
+
+ Bundle outcome = mySystemDao.transaction(mySrd, request);
+
+ IdType taskId = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
+ Task task = myTaskDao.read(taskId, mySrd);
+
+ assertThat(task.getBasedOn().get(0).getReference(), matchesPattern("Patient/[0-9]+"));
+ }
+
@Test
public void testTransactionNoContained() throws IOException {
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchCoordinatorSvcImplTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchCoordinatorSvcImplTest.java
index 4eb8f636121..5f983a7ce1f 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchCoordinatorSvcImplTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchCoordinatorSvcImplTest.java
@@ -10,10 +10,8 @@ import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
-import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.lang3.time.DateUtils;
import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
@@ -40,7 +38,7 @@ public class SearchCoordinatorSvcImplTest extends BaseJpaR4Test {
private ISearchCoordinatorSvc mySearchCoordinator;
@Autowired
- private ISearchCacheSvc myDataaseCacheSvc;
+ private ISearchCacheSvc myDatabaseCacheSvc;
@AfterEach
public void after() {
@@ -92,7 +90,7 @@ public class SearchCoordinatorSvcImplTest extends BaseJpaR4Test {
assertEquals(30, mySearchResultDao.count());
});
- myDataaseCacheSvc.pollForStaleSearchesAndDeleteThem();
+ myDatabaseCacheSvc.pollForStaleSearchesAndDeleteThem();
runInTransaction(()->{
// We should delete up to 10, but 3 don't get deleted since they have too many results to delete in one pass
assertEquals(13, mySearchDao.count());
@@ -101,7 +99,7 @@ public class SearchCoordinatorSvcImplTest extends BaseJpaR4Test {
assertEquals(15, mySearchResultDao.count());
});
- myDataaseCacheSvc.pollForStaleSearchesAndDeleteThem();
+ myDatabaseCacheSvc.pollForStaleSearchesAndDeleteThem();
runInTransaction(()->{
// Once again we attempt to delete 10, but the first 3 don't get deleted and still remain
// (total is 6 because 3 weren't deleted, and they blocked another 3 that might have been)
@@ -110,7 +108,7 @@ public class SearchCoordinatorSvcImplTest extends BaseJpaR4Test {
assertEquals(0, mySearchResultDao.count());
});
- myDataaseCacheSvc.pollForStaleSearchesAndDeleteThem();
+ myDatabaseCacheSvc.pollForStaleSearchesAndDeleteThem();
runInTransaction(()->{
assertEquals(0, mySearchDao.count());
assertEquals(0, mySearchDao.countDeleted());
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptorTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptorTest.java
index 0f28baac6cf..0a05a8ac464 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptorTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptorTest.java
@@ -343,8 +343,8 @@ public class PatientIdPartitionInterceptorTest extends BaseJpaR4SystemTest {
.stream()
.collect(MultimapCollector.toMultimap(t -> new IdType(t.getResponse().getLocation()).toUnqualifiedVersionless().getResourceType(), t -> new IdType(t.getResponse().getLocation()).toUnqualifiedVersionless().getValue()));
+ logAllResources();
Multimap resourcesByType = runInTransaction(() -> {
- logAllResources();
return myResourceTableDao.findAll().stream().collect(MultimapCollector.toMultimap(t -> t.getResourceType(), t -> t.getPartitionId().getPartitionId()));
});
@@ -378,8 +378,8 @@ public class PatientIdPartitionInterceptorTest extends BaseJpaR4SystemTest {
String patientId = resourceIds.get("Patient").get(0);
+ logAllResources();
Multimap resourcesByType = runInTransaction(() -> {
- logAllResources();
return myResourceTableDao.findAll().stream().collect(MultimapCollector.toMultimap(t -> t.getResourceType(), t -> t.getPartitionId().getPartitionId()));
});
@@ -426,8 +426,8 @@ public class PatientIdPartitionInterceptorTest extends BaseJpaR4SystemTest {
String patientId = resourceIds.get("Patient").get(0);
+ logAllResources();
Multimap resourcesByType = runInTransaction(() -> {
- logAllResources();
return myResourceTableDao.findAll().stream().collect(MultimapCollector.toMultimap(t -> t.getResourceType(), t -> t.getPartitionId().getPartitionId()));
});
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SearchParameterMapTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SearchParameterMapTest.java
index d5210186f4e..39f995742a4 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SearchParameterMapTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SearchParameterMapTest.java
@@ -1,8 +1,10 @@
package ca.uhn.fhir.jpa.provider;
import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
@@ -41,6 +43,24 @@ public class SearchParameterMapTest {
assertEquals("?birthdate=ge2001&birthdate=lt2002&name=bouvier,simpson&name=homer,jay&name:exact=ZZZ?", UrlUtil.unescape(queryString));
}
+ @Test
+ public void testContainedParameterIsIncludedInNormalizedString() {
+ SearchParameterMap map = new SearchParameterMap();
+ map.add("name", new StringParam("Smith"));
+ map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
+ String containedQueryString = map.toNormalizedQueryString(ourCtx);
+
+ SearchParameterMap uncontainedMap = new SearchParameterMap();
+ uncontainedMap.add("name", new StringParam("Smith"));
+ uncontainedMap.setSearchContainedMode(SearchContainedModeEnum.FALSE);
+ String uncontainedQueryString = uncontainedMap.toNormalizedQueryString(ourCtx);
+
+ ourLog.info(containedQueryString);
+ ourLog.info(uncontainedQueryString);
+ assertNotEquals(containedQueryString, uncontainedQueryString);
+
+ }
+
@Test
public void testToQueryStringEmpty() {
SearchParameterMap map = new SearchParameterMap();
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4BundleTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4BundleTest.java
index 6c349b33e97..3be614e3bbd 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4BundleTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4BundleTest.java
@@ -1,22 +1,50 @@
package ca.uhn.fhir.jpa.provider.r4;
-import ca.uhn.fhir.jpa.model.util.JpaConstants;
-import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Bundle.BundleType;
-import org.hl7.fhir.r4.model.Parameters;
-import org.hl7.fhir.r4.model.Patient;
-import org.junit.jupiter.api.Test;
-
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Bundle.BundleType;
+import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
+import org.hl7.fhir.r4.model.Condition;
+import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
+import org.hl7.fhir.r4.model.OperationOutcome;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
public class ResourceProviderR4BundleTest extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4BundleTest.class);
+ @BeforeEach
+ @Override
+ public void before() throws Exception {
+ super.before();
+ myDaoConfig.setBundleBatchPoolSize(20);
+ myDaoConfig.setBundleBatchMaxPoolSize(100);
+ }
+
+ @AfterEach
+ @Override
+ public void after() throws Exception {
+ super.after();
+ myDaoConfig.setBundleBatchPoolSize(DaoConfig.DEFAULT_BUNDLE_BATCH_POOL_SIZE);
+ myDaoConfig.setBundleBatchMaxPoolSize(DaoConfig.DEFAULT_BUNDLE_BATCH_MAX_POOL_SIZE);
+ }
/**
* See #401
*/
@@ -58,5 +86,181 @@ public class ResourceProviderR4BundleTest extends BaseResourceProviderR4Test {
}
+ @Test
+ public void testBundleBatch() {
+ List ids = createPatients(50);
+
+ Bundle input = new Bundle();
+ input.setType(BundleType.BATCH);
+
+ for (String id : ids)
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(id);
+
+ Bundle output = myClient.transaction().withBundle(input).execute();
+
+ //ourLog.info("Bundle: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
+
+ assertEquals(50, output.getEntry().size());
+ List bundleEntries = output.getEntry();
+
+ int i=0;
+ for (BundleEntryComponent bundleEntry : bundleEntries) {
+ assertEquals(ids.get(i++), bundleEntry.getResource().getIdElement().toUnqualifiedVersionless().getValueAsString());
+ }
+
+ }
+
+ @Test
+ public void testBundleBatchWithSingleThread() {
+ List ids = createPatients(50);
+
+ myDaoConfig.setBundleBatchPoolSize(1);
+ myDaoConfig.setBundleBatchMaxPoolSize(1);
+
+ Bundle input = new Bundle();
+ input.setType(BundleType.BATCH);
+
+ for (String id : ids)
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(id);
+
+ Bundle output = myClient.transaction().withBundle(input).execute();
+
+ //ourLog.info("Bundle: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
+
+ assertEquals(50, output.getEntry().size());
+ List bundleEntries = output.getEntry();
+
+ int i=0;
+ for (BundleEntryComponent bundleEntry : bundleEntries) {
+ assertEquals(ids.get(i++), bundleEntry.getResource().getIdElement().toUnqualifiedVersionless().getValueAsString());
+ }
+
+
+ }
+ @Test
+ public void testBundleBatchWithError() {
+ List ids = createPatients(5);
+
+ Bundle input = new Bundle();
+ input.setType(BundleType.BATCH);
+
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(0));
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl("Patient/1000"); // not exist
+
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(1));
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(2));
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl("Patient/2000"); // not exist
+
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(3));
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl("Patient/3000"); // not exist
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(4));
+
+
+ Bundle output = myClient.transaction().withBundle(input).execute();
+
+ //ourLog.info("Bundle: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
+
+ assertEquals(8, output.getEntry().size());
+
+ List bundleEntries = output.getEntry();
+
+ // patient 1
+ assertEquals(ids.get(0), bundleEntries.get(0).getResource().getIdElement().toUnqualifiedVersionless().getValueAsString());
+
+ // patient 10 - error outcomes
+ assertThat(((OperationOutcome)bundleEntries.get(1).getResponse().getOutcome()).getIssueFirstRep().getDiagnostics(), containsString("Patient/1000"));
+
+ // patient 2
+ assertEquals(ids.get(1), bundleEntries.get(2).getResource().getIdElement().toUnqualifiedVersionless().getValueAsString());
+
+ // patient 3
+ assertEquals(ids.get(2), bundleEntries.get(3).getResource().getIdElement().toUnqualifiedVersionless().getValueAsString());
+
+ // patient 20 - error outcomes
+ assertThat(((OperationOutcome)bundleEntries.get(4).getResponse().getOutcome()).getIssueFirstRep().getDiagnostics(), containsString("Patient/2000"));
+
+ // patient 4
+ assertEquals(ids.get(3), bundleEntries.get(5).getResource().getIdElement().toUnqualifiedVersionless().getValueAsString());
+
+ // patient 30 - error outcomes
+ assertThat(((OperationOutcome)bundleEntries.get(6).getResponse().getOutcome()).getIssueFirstRep().getDiagnostics(), containsString("Patient/3000"));
+
+ // patient 5
+ assertEquals(ids.get(4), bundleEntries.get(7).getResource().getIdElement().toUnqualifiedVersionless().getValueAsString());
+
+ }
+
+ @Test
+ public void testBundleBatchWithCreate() {
+
+ List ids = createPatients(5);
+
+ Bundle input = new Bundle();
+ input.setType(BundleType.BATCH);
+
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(0));
+
+ Patient p = new Patient();
+ p.setId("100");
+ p.setGender(AdministrativeGender.MALE);
+ p.addIdentifier().setSystem("urn:foo").setValue("A");
+ p.addName().setFamily("Smith");
+ input.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST);
+
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(1));
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(2));
+
+ Condition c = new Condition();
+ c.getSubject().setReference(ids.get(0));
+ input.addEntry().setResource(c).getRequest().setMethod(HTTPVerb.POST);
+
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(3));
+ input.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl(ids.get(4));
+
+ //ourLog.info("Bundle: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input));
+
+ Bundle output = myClient.transaction().withBundle(input).execute();
+
+ //ourLog.info("Bundle: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
+
+ assertEquals(7, output.getEntry().size());
+
+ List