(click to expand)
+EHRbase is an [openEHR](https://www.openehr.org/) Clinical Data Repository, providing a standard-based backend for
+interoperable clinical applications. It implements the latest version of the openEHR Reference Model (RM 1.1.0) and
+version 1.4 of the Archetype Definition Language (ADL). Applications can use the capabilities of EHRbase through the
+latest version of the [openEHR REST API](https://specifications.openehr.org/releases/ITS-REST/latest/) and model-based
+queries using the [Archetype Query Language](https://specifications.openehr.org/releases/QUERY/latest/AQL.html).
-Please check the [CHANGELOG](https://github.com/ehrbase/ehrbase/blob/develop/CHANGELOG.md) and/or [EHRbase Documentation](https://ehrbase.readthedocs.io/en/latest/) for more details.
-
-##### WIP: 2021, XYZ 00
-v?.?.? - (...)
+----
-**Important:** Please note that this release introduces [Archie's](https://github.com/openEHR/archie) new strict invariant checks. Depending on existing data and clients this might be a breaking change. Please carefully check the EHRbase output and update your input data if EHRbase rejects it. The strict validation can also be deactivated via configuration, but caution in advised!
+## Release notes
-##### 2021, Sep 9
-v0.17.2 - **beta** release. Bug fixes, enhancements, automatic Docker Hub deployments via Github Actions.
+Please check the [CHANGELOG](https://github.com/ehrbase/ehrbase/blob/develop/CHANGELOG.md)
-##### 2021, Aug 12
-v0.17.1 - **beta** release. Default handling for audit metadata, bug fixes and SDK version update.
-
-##### 2021, Aug 04
-v0.17.0 - fifth **beta** release. validation using an external terminology server, Attribute-based Access Control, AQL fixes and other enhancements
-
-##### 2021, March 30
-v0.16.0 - fourth **beta** release. New endpoints for versioned Compositions, ATNA Logging, AQL fixes and other enhancements.
-
-##### 2021, February 25
-v0.15.0 - third **beta** release. New admin API endpoints for EHRs, Compositions and Contributions. Fixes and other enhancements.
-
-##### 2020, October 1
-v0.14.0 - second **beta** release.
-
-##### 2020, May 14
-This release of EHRbase (v0.13.0) is the first **beta** release.
-
-
-
-Please check the [CHANGELOG](https://github.com/ehrbase/ehrbase/blob/develop/CHANGELOG.md) and/or [EHRbase Documentation](https://ehrbase.readthedocs.io/en/latest/) for more details.
+## Documentation
+Check out the documentation at https://docs.ehrbase.org
+## Quick Start: Run EHRbase with Docker
-## 📝 Documentation
-[EHRbase Documentation](https://ehrbase.readthedocs.io/en/latest/) is build with Sphinx and hosted on [Read the Docs](https://readthedocs.org/).
+> [!TIP]
+> The fastest way to get started with EHRbase and openEHR is the **EHRbase Sandbox** available at https://sandkiste.ehrbase.org/.
+>
+> For a deployment on premise read below.
-## Quick Start: Run EHRbase with Docker
-See our [Run EHRbase + DB with Docker-Compose](https://ehrbase.readthedocs.io/en/latest/03_development/04_docker_images/01_ehrbase/02_use_image/index.html#run-ehrbase-db-with-docker-compose) documentation page for a quick start.
+Check out the Installation guide at https://docs.ehrbase.org/docs/EHRbase/installation
## Building and Installing EHRbase
-These instructions will get you a copy of the project up and running on your local machine **for development and testing purposes**. Please read these instructions carefully. See [deployment](#deployment) for notes on how to deploy the project on a live system.
+
+These instructions will get you a copy of the project up and running on your local machine **for development and testing
+purposes**. Please read these instructions carefully. See [deployment](#deployment) for notes on how to deploy the
+project on a live system.
### Prerequisites
-You will need Java JDK/JRE 11 (preferably openJDK: e.g. from https://adoptopenjdk.net/)
-
-You will need a Postgres Database (Docker image or local installation). We recommend the Docker image to get started quickly.
-
-When installing locally, the Postgres Database (at least Version 10.4) needs the following extensions:
- * [temporal tables](https://github.com/arkhipov/temporal_tables)
- ```bash
- git clone https://github.com/arkhipov/temporal_tables.git
- make
- sudo make install
- make installcheck
- ```
- * [jsquery](https://github.com/postgrespro/jsquery)
- ```bash
- git clone https://github.com/postgrespro/jsquery.git
- cd jsquery
- make USE_PGXS=1
- sudo make USE_PGXS=1 install
- make USE_PGXS=1 installcheck
- ```
+You will need Java JDK/JRE 21 (preferably openJDK: e.g. from https://adoptopenjdk.net/)
+
+You will need a Postgres Database (at least Version 15 or higher, Version 16 recommended) (Docker image or local installation).
+We recommend the Docker image to get started quickly.
### Installing
#### 1. Setup database
-> NOTE: Building EHRbase requires a properly set up and running DB for the following steps.
+> NOTE: Building EHRbase requires a properly set-up and running DB for the following steps.
-Run `./db-setup/createdb.sql` as `postgres` User.
+Run `./createdb.sql` as `postgres` User.
You can also use this Docker image which is a preconfigured Postgres database:
+
```shell
docker network create ehrbase-net
- docker run --name ehrdb --network ehrbase-net -e POSTGRES_PASSWORD=postgres -d -p 5432:5432 ehrbase/ehrbase-postgres:latest
+ docker run --name ehrdb --network ehrbase-net -e POSTGRES_PASSWORD=postgres -d -p 5432:5432 ehrbase/ehrbase-v2-postgres:16.2
```
-(For a preconfigured EHRbase application Docker image and its usage see the [documentation](https://ehrbase.readthedocs.io/en/latest/03_development/04_docker_images/index.html))
+(For a preconfigured EHRbase application Docker image and its usage see the [Installation](https://docs.ehrbase.org/docs/EHRbase/installation) guide.
+
#### 2. Setup Maven environment
Edit the database properties in `./pom.xml` if necessary
#### 3. Build EHRbase
+
Run `mvn package`
#### 4. Run EHRbase
-Replace the * with the current version, e.g. `application/target/application-0.9.0.jar`
+Replace the * with the current version, e.g. `application/target/ehrbase-2.0.0.jar`
-`java -jar application/target/application-*.jar`
+`java -jar application/target/ehrbase-*.jar`
### Authentication Types
@@ -117,7 +90,7 @@ Currently we have support one user with password which can be set via environmen
and can be overridden by environment values. Alternatively you can set them inside the corresponding application.yml
file.
-The same applies to the *admin* user, via `SECURITY_AUTHADMINUSER`, `SECURITY_AUTHADMINPASSWORD`
+The same applies to the *admin* user, via `SECURITY_AUTHADMINUSER`, `SECURITY_AUTHADMINPASSWORD`
and their default values of `ehrbase-admin` and `EvenMoreSecretPassword`.
#### 2. OAuth2
@@ -127,53 +100,89 @@ Environment variable `SECURITY_AUTHTYPE=OAUTH` is enabling OAuth2 authentication
Additionally, setting the following variable to point to the existing OAuth2 server and realm is necessary:
`SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_ISSUERURI=http://localhost:8081/auth/realms/ehrbase`
-
Two roles are available: a user role, and admin role. By default, these roles are expected to be named `USER` and
`ADMIN`. The names of these roles can be customised through the `SECURITY_OAUTH2USERROLE` and `SECURITY_OAUTH2ADMINROLE`
environment variables. Users should have their roles assigned accordingly, either in the `realm_access.roles` or `scope`
claim of the JWT used for authentication.
-## Running the tests
+## Contributing
-This command will run all tests from `tests/robot` folder.
-DB and server application will be started/stopped by the tests accordingly. You *must not* start them by hand.
+### Codestyle/Formatting
-> NOTE: Make sure you meet the PREREQUISITES mentioned in tests/README.md prior to test execution.
->
-> Please Check the README in `tests` folder for more details.
+EHRbase java sourcecode is using [palantir-java-format](https://github.com/palantir/palantir-java-format) codestyle.
+The formatting is checked and applied using
+the [spotless-maven-plugin](https://github.com/diffplug/spotless/tree/main/plugin-maven).
+To apply the codestyle run the `com.diffplug.spotless:spotless-maven-plugin:apply` maven goal in the root directory of
+the project.
+To check if the code conforms to the codestyle run the `com.diffplug.spotless:spotless-maven-plugin:check` maven goal in
+the root directory of the project.
+These maven goals can also be run for a single module by running them in the modules' subdirectory.
-```bash
-cd tests
-./run_local_tests.sh
+To make sure all code conforms to the codestyle, the "check-codestyle" check is run on all pull requests.
+Pull requests not passing this check shall not be merged.
+
+If you wish to automatically apply the formatting on commit for *.java files, a simple pre-commit hook script "
+pre-commit.sh" is available in the root directory of this repository.
+To enable the hook you can either copy the script to or create a symlink for it at `.git/hooks/pre-commit`.
+The git hook will run the "apply" goal for the whole project, but formatting changes will only be staged for already
+staged files, to avoid including unrelated changes.
+
+In case there is a section of code that you carefully formatted in a special way the formatting can be turned off for
+that section like this:
+
+```
+everything here will be reformatted..
+
+// @formatter:off
+
+ This is not affected by spotless-plugin reformatting...
+ And will stay as is it is!
+
+// @formatter:on
+
+everything here will be reformatted..
```
+Please be aware that `@formatter:off/on` should only be used on rare occasions to increase readability of complex code and shall be looked at critically when reviewing merge requests.
+
+## Running the tests
+
+For integration tests please refer to the [integration-test](https://github.com/ehrbase/integration-tests) repository
## Deployment
- 1. `java -jar application/target/application-*.jar` You can override the application properties (like database settings) using the normal spring boot mechanism: [Command-Line Arguments in Spring Boot](https://www.baeldung.com/spring-boot-command-line-arguments)
+ 1. `java -jar application/target/ehrbase-*.jar` You can override the application properties (like database settings) using the normal spring boot mechanism: [Command-Line Arguments in Spring Boot](https://www.baeldung.com/spring-boot-command-line-arguments)
2. Browse to Swagger UI --> http://localhost:8080/ehrbase/swagger-ui.html
+## Updating
+Before updating to a new version of EHRBase check [UPDATING.md](UPDATING.md) for any backwards-incompatible changes and additional
+steps needed in EHRBase. New Releases may introduce DB changes. It is thus recommend to make a DB backup before
+updating.
## Built With
* [Maven](https://maven.apache.org/) - Dependency Management
+----
+## Acknowledgments
-## License
-
-EHRbase uses the Apache License, Version 2.0 (https://www.apache.org/licenses/LICENSE-2.0)
+EHRbase contains code and derived code from EtherCIS (ethercis.org) which has been developed by Christian Chevalley (
+ADOC Software Development Co.,Ltd).
+Dr. Tony Shannon and Phil Berret of the [Ripple Foundation CIC Ltd, UK](https://ripple.foundation/) and Dr. Ian
+McNicoll (FreshEHR Ltd.) greatly contributed to EtherCIS.
-## Acknowledgments
+EHRbase heavily relies on the openEHR Reference Model implementation ([Archie](https://github.com/openEHR/archie)) made
+by Nedap. Many thanks to Pieter Bos and his team for their work!
-EHRbase contains code and derived code from EtherCIS (ethercis.org) which has been developed by Christian Chevalley (ADOC Software Development Co.,Ltd).
-Dr. Tony Shannon and Phil Berret of the [Ripple Foundation CIC Ltd, UK](https://ripple.foundation/) and Dr. Ian McNicoll (FreshEHR Ltd.) greatly contributed to EtherCIS.
+EHRbase is jointly developed by [Vitasystems GmbH](https://www.vitagroup.ag/de_DE/Ueber-uns/vitasystems)
+and [Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School](https://www.plri.de/)
-EHRbase heavily relies on the openEHR Reference Model implementation ([Archie](https://github.com/openEHR/archie)) made by Nedap. Many thanks to Pieter Bos and his team for their work!
-EHRbase is jointly developed by [Vitasystems GmbH](https://www.vitagroup.ag/de_DE/Ueber-uns/vitasystems) and [Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School](plri.de)
+## License
+EHRbase uses the [Apache License, Version 2.0](https://www.apache.org/licenses/LICENSE-2.0)
## Stargazers over time
diff --git a/SECURITY.md b/SECURITY.md
new file mode 100644
index 0000000000..e4ae0ac5e7
--- /dev/null
+++ b/SECURITY.md
@@ -0,0 +1,27 @@
+# Responsible disclosure of security issues
+
+## Report a vulnerability
+
+We're extremely grateful for users that identify and report vulnerabilities to the EHRbase community. All reports are thoroughly investigated, confirmed and patched as soon as possible.
+
+Given that EHRbase is used to handle sensitive, medical data, we would like to ask you to submit the vulnerability to [ehrbase-security@vitagroup.ag](mailto:ehrbase-security@vitagroup.ag), to allow triaging and handling of the vulnerability with standardized processes and response times.
+
+Reporting vulnerabilities according to [regular responsible disclosure policies](https://www.bugcrowd.com/resource/what-is-responsible-disclosure/) allows us to confirm and provide a patch based on your report before a full disclosure, preventing in-the-wild exploitation of the vulnerability.
+
+## When should I report a vulnerability?
+
+- You think you discovered a potential security vulnerability in EHRbase
+- You are unsure how a vulnerability affects EHRbase
+
+## When should I **not** report a vulnerability?
+
+- You need support in securely deploying/operating EHRbase
+- You need support for additional environment-dependent security measures
+- You need support in security related updates
+- Your issue is not related to security
+
+## Security vulnerability response
+
+Each report is acknowledged, analyzed and responded to by the team as soon as possible.
+
+We will notify you as soon as the issue is triaged and we identify a fix and a release date, and create a full disclosure after a patch is released.
\ No newline at end of file
diff --git a/UPDATING.md b/UPDATING.md
index fea8e9f9ca..521034ca64 100644
--- a/UPDATING.md
+++ b/UPDATING.md
@@ -1,14 +1,70 @@
# Updating EHRbase
-This file documents any backwards-incompatible changes in EHRBase deployment and
-assists users migrating to a new version.
-
-## EHRbase 1.0.0
-### Database Configuration
-The creation of the DB must ensure that SQL interval type is ISO-8601 compliant. This is required to ensure proper
-formatting of the resultset.
-Scripts provided ensure this encoding is done properly (see `base/db-setup`) with the following statement:
-```
--- ensure INTERVAL is ISO8601 encoded
-alter database ehrbase SET intervalstyle = 'iso_8601';
-```
\ No newline at end of file
+This file documents any backwards-incompatible changes in EHRBase and assists users migrating to a new version.
+
+## EHRbase 2.0.0
+
+### Migrating data
+
+EHRbase 2.0.0 comes with a completely overhauled data structure that is not automatically migrated when deploying this
+new version over an older data structure.
+
+To support the migrating of data from systems `pre-2.0.0` to `2.0.0`, a migration tool and instructions are provided
+at https://github.com/ehrbase/migration-tool.
+
+
+## EHRbase 2.7.0
+
+### EHR_STATUS and FOLDER consistency check
+
+Updating an `EHR_STATUS` or `FOLDER` did not check the `If-Match header` against the DB. This allowed to pass in an
+invalid identifier that does not match the existing in the DB. This may have lead to inconsistent data in some systems.
+
+To check if any `EHR_STATUS` or `FOLDER` is affected run [ehrbase_2.7.0_check_ehr_status_and_folder_void](db_scripts/ehrbase_2.7.0_check_ehr_status_and_folder_void.sql).
+In case you see an output like:
+```text
+Inconsistent EHR_STATUS found
+Inconsistent FOLDER found
+```
+Please open an issue so that a fix can be provided.
+
+## EHRbase 2.10.0
+
+Starting from version 2.0.0 the ehrscape API was deprecated.
+With the release of version 2.10.0, the API is now disabled by default,
+but can still be enabled by setting the configuration property or environment variable `ehrbase.rest.ehrscape.enabled` to `true`.
+
+A validation that compositions only contain nodes that are defined by the template has been added.
+This behavior can be disabled by setting the configuration property or environment variable `ehrbase.validation.checkForExtraNodes` to `false`.
+
+## EHRbase 2.11.0
+
+The new data model for FOLDER items requires a full migration of the ehr_folder_data table, which may take a while.
+As only local VERSIONED_COMPOSITION references are supported, existing data is rewritten accordingly.
+If entries of FOLDER.items.id.value exist that do not comply with the UUID format, the migration will fail.
+These entries will have to be fixed manually.
+
+## EHRbase 2.13.0
+
+The openEHR terminology has been update to version 2.4.0.
+As the code for the composition category 'episodic' has changed from 435 to 451, existing templates and compositions may be inconsistent.
+For smaller systems this can be checked via AQL:
+`SELECT c/archetype_details/template_id/value, count(*) FROM COMPOSITION c WHERE c/category/code/value = '435'`.
+Please open an issue on github in case you need instructions on correcting the data.
+
+## EHRbase 2.21.0
+
+In AQL queries CONTAINS expressions with a node predicate now exclude results from nested archetypes.
+
+Example:
+```
+SELECT el
+FROM OBSERVATION[openEHR-EHR-OBSERVATION.blood_pressure.v2] CONTAINS ELEMENT el[at0004]
+```
+will be no longer contain from ELEMENTs returned by
+```
+SELECT el
+FROM OBSERVATION[openEHR-EHR-OBSERVATION.blood_pressure.v2] CONTAINS CLUSTER c[openEHR-EHR-CLUSTER.device.v1] CONTAINS ELEMENT el[at0004]
+```
+
+To restore the previous behaviour set `ehrbase.aql.archetype-local-node-predicates = false`
diff --git a/api/pom.xml b/api/pom.xml
index 3ef80a53ae..73d7ba4ac3 100644
--- a/api/pom.xml
+++ b/api/pom.xml
@@ -1,7 +1,7 @@
-
+4.0.0org.ehrbase.openehrserver
- 0.20.0-SNAPSHOT
+ 2.23.0-SNAPSHOTapi
+ EHRbase Internal API
+
+ org.aspectj
+ aspectjweaver
+
+
com.fasterxml.jackson.datatypejackson-datatype-jsr310
@@ -62,15 +66,20 @@
com.nedap.healthcare.archieopenehr-rm
+
org.assertjassertj-core
+ test
- junit
- junit
+ org.junit.jupiter
+ junit-jupitertest
+
-
\ No newline at end of file
+
+
+
diff --git a/api/src/main/java/org/ehrbase/api/annotations/EhrbaseSecurity.java b/api/src/main/java/org/ehrbase/api/annotations/EhrbaseSecurity.java
new file mode 100644
index 0000000000..b616e380f1
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/annotations/EhrbaseSecurity.java
@@ -0,0 +1,28 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.annotations;
+
+import static java.lang.annotation.RetentionPolicy.RUNTIME;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.Target;
+
+@Retention(RUNTIME)
+@Target(ElementType.METHOD)
+public @interface EhrbaseSecurity {}
diff --git a/api/src/main/java/org/ehrbase/api/aspect/AnnotationAspect.java b/api/src/main/java/org/ehrbase/api/aspect/AnnotationAspect.java
new file mode 100644
index 0000000000..f116c068b2
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/aspect/AnnotationAspect.java
@@ -0,0 +1,28 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.aspect;
+
+import java.lang.annotation.Annotation;
+import java.util.List;
+import org.aspectj.lang.ProceedingJoinPoint;
+
+public interface AnnotationAspect {
+ public List> matchAnnotations();
+
+ public Object action(ProceedingJoinPoint pjp, List annotations) throws Throwable;
+}
diff --git a/api/src/main/java/org/ehrbase/api/aspect/AuthorizationAspect.java b/api/src/main/java/org/ehrbase/api/aspect/AuthorizationAspect.java
new file mode 100644
index 0000000000..fc3048866f
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/aspect/AuthorizationAspect.java
@@ -0,0 +1,20 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.aspect;
+
+public interface AuthorizationAspect extends AnnotationAspect {}
diff --git a/api/src/main/java/org/ehrbase/api/definitions/OperationalTemplateFormat.java b/api/src/main/java/org/ehrbase/api/definitions/OperationalTemplateFormat.java
index e4674a9870..a8b8392560 100644
--- a/api/src/main/java/org/ehrbase/api/definitions/OperationalTemplateFormat.java
+++ b/api/src/main/java/org/ehrbase/api/definitions/OperationalTemplateFormat.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,9 +15,9 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.definitions;
public enum OperationalTemplateFormat {
- XML, JSON
+ XML,
+ JSON
}
diff --git a/api/src/main/java/org/ehrbase/api/definitions/QueryMode.java b/api/src/main/java/org/ehrbase/api/definitions/QueryMode.java
deleted file mode 100644
index 131350b2b1..0000000000
--- a/api/src/main/java/org/ehrbase/api/definitions/QueryMode.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright (c) 2019 Vitasystems GmbH and Hannover Medical School.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.api.definitions;
-
-public enum QueryMode {
- SQL("sql"), AQL("aql");
-
- private final String code;
-
- QueryMode(String code) {
- this.code = code;
- }
-
- public String getCode() {
- return code;
- }
-}
diff --git a/api/src/main/java/org/ehrbase/api/definitions/ServerConfig.java b/api/src/main/java/org/ehrbase/api/definitions/ServerConfig.java
deleted file mode 100644
index c07d243d43..0000000000
--- a/api/src/main/java/org/ehrbase/api/definitions/ServerConfig.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package org.ehrbase.api.definitions;
-
-public interface ServerConfig {
-
- int getPort();
-
- void setPort(int port);
-
- String getNodename();
-
- void setNodename(String nodename);
-
- String getAqlIterationSkipList();
-
- Integer getAqlDepth();
-
- Boolean getUseJsQuery();
-
- void setUseJsQuery(boolean b);
-
- public boolean isDisableStrictValidation();
-}
diff --git a/api/src/main/java/org/ehrbase/api/dto/AqlQueryContext.java b/api/src/main/java/org/ehrbase/api/dto/AqlQueryContext.java
new file mode 100644
index 0000000000..ce2a27a80d
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/dto/AqlQueryContext.java
@@ -0,0 +1,73 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.dto;
+
+import java.net.URI;
+import org.ehrbase.openehr.sdk.response.dto.MetaData;
+
+public interface AqlQueryContext {
+
+ String BEAN_NAME = "scopedAqlQueryContext";
+
+ interface MetaProperty {
+ String propertyName();
+ }
+
+ enum EhrbaseMetaProperty implements MetaProperty {
+ OFFSET("offset"),
+ FETCH("fetch"),
+ DEFAULT_LIMIT("default-limit"),
+ MAX_LIMIT("max-limit"),
+ MAX_FETCH("max-fetch"),
+ RESULT_SIZE("resultsize"),
+ DRY_RUN("dry_run"),
+ EXECUTED_SQL("executed_sql"),
+ QUERY_PLAN("query_plan");
+
+ private final String propertyName;
+
+ EhrbaseMetaProperty(String propertyName) {
+ this.propertyName = propertyName;
+ }
+
+ @Override
+ public String propertyName() {
+ return propertyName;
+ }
+ }
+
+ String OPENEHR_REST_API_VERSION = "1.0.3";
+
+ MetaData createMetaData(URI location);
+
+ boolean showExecutedAql();
+
+ boolean isDryRun();
+
+ boolean showExecutedSql();
+
+ boolean showQueryPlan();
+
+ boolean isPathSkipping();
+
+ boolean isArchetypeLocalNodePredicates();
+
+ void setExecutedAql(String executedAql);
+
+ void setMetaProperty(MetaProperty property, Object value);
+}
diff --git a/api/src/main/java/org/ehrbase/api/dto/AqlQueryRequest.java b/api/src/main/java/org/ehrbase/api/dto/AqlQueryRequest.java
new file mode 100644
index 0000000000..03c880bb5c
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/dto/AqlQueryRequest.java
@@ -0,0 +1,64 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.dto;
+
+import java.util.Map;
+import java.util.Optional;
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import org.ehrbase.api.exception.IllegalAqlException;
+import org.ehrbase.api.service.AqlQueryService;
+import org.ehrbase.openehr.sdk.aql.dto.AqlQuery;
+import org.ehrbase.openehr.sdk.aql.parser.AqlParseException;
+import org.ehrbase.openehr.sdk.aql.parser.AqlQueryParser;
+
+/**
+ * The requested AQL to be executed by {@link AqlQueryService#query(AqlQueryRequest)}.
+ *
+ * @param aqlQuery the actual aql query
+ * @param parameters additional query parameters
+ * @param fetch query limit to apply
+ * @param offset query offset to apply
+ */
+public record AqlQueryRequest(
+ @Nonnull AqlQuery aqlQuery,
+ @Nullable Map parameters,
+ @Nullable Long fetch,
+ @Nullable Long offset) {
+
+ /**
+ * Create a new {@link AqlQueryRequest} by parsing the given AQL queryString.
+ *
+ * @see AqlQueryRequest
+ */
+ public static AqlQueryRequest prepare(
+ @Nonnull String queryString,
+ @Nullable Map parameters,
+ @Nullable Long fetch,
+ @Nullable Long offset) {
+ try {
+ AqlQuery aqlQuery = AqlQueryParser.parse(queryString);
+ return new AqlQueryRequest(aqlQuery, parameters, fetch, offset);
+ } catch (AqlParseException e) {
+ throw new IllegalAqlException(
+ "Could not parse AQL query: "
+ + Optional.of(e).map(Throwable::getCause).orElse(e).getMessage(),
+ e);
+ }
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/dto/EhrDto.java b/api/src/main/java/org/ehrbase/api/dto/EhrDto.java
new file mode 100644
index 0000000000..3e53ce5c0d
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/dto/EhrDto.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2019 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.dto;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonRootName;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
+import com.nedap.archie.rm.datavalues.quantity.datetime.DvDateTime;
+import com.nedap.archie.rm.support.identification.HierObjectId;
+import java.util.List;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.CompositionDto;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.ContributionDto;
+
+/**
+ * Basic set of response data regarding EHR_STATUS. operations. Used as default or when PREFER
+ * header requests minimal response.
+ */
+@JsonRootName(value = "EHR")
+@JacksonXmlRootElement(localName = "ehr")
+public record EhrDto(
+ @JsonProperty(value = "system_id") HierObjectId systemId,
+ @JsonProperty(value = "ehr_id") HierObjectId ehrId,
+ @JsonProperty(value = "ehr_status") EhrStatusDto ehrStatus,
+ @JsonProperty(value = "time_created") DvDateTime timeCreated,
+ @JsonProperty(value = "compositions") List compositions,
+ @JsonProperty(value = "contributions") List contributions) {}
diff --git a/api/src/main/java/org/ehrbase/api/dto/EhrStatusDto.java b/api/src/main/java/org/ehrbase/api/dto/EhrStatusDto.java
new file mode 100644
index 0000000000..555ecb2968
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/dto/EhrStatusDto.java
@@ -0,0 +1,59 @@
+/*
+ * Copyright (c) 2019-2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.dto;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonRootName;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
+import com.nedap.archie.rm.archetyped.Archetyped;
+import com.nedap.archie.rm.archetyped.FeederAudit;
+import com.nedap.archie.rm.datastructures.ItemStructure;
+import com.nedap.archie.rm.datavalues.DvText;
+import com.nedap.archie.rm.generic.PartySelf;
+import com.nedap.archie.rm.support.identification.UIDBasedId;
+import javax.annotation.Nullable;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+/**
+ * Request/Response data of an EHR_STATUS.
+ */
+@JsonRootName(value = "EHR_STATUS")
+@JacksonXmlRootElement(localName = "ehr_status")
+@XmlType(name = "EHR_STATUS")
+public record EhrStatusDto(
+ @JsonProperty(value = "uid") @XmlElement UIDBasedId uid,
+ @JsonProperty(value = "archetype_node_id", required = true) @XmlAttribute(name = "archetype_node_id")
+ String archetypeNodeId,
+ @JsonProperty(value = "name") @XmlElement DvText name,
+ @JsonProperty(value = "archetype_details") @XmlElement(name = "archetype_details") @Nullable
+ Archetyped archetypeDetails,
+ @JsonProperty(value = "feeder_audit") @XmlElement(name = "feeder_audit") @Nullable FeederAudit feederAudit,
+ @JsonProperty(value = "subject") @XmlElement PartySelf subject,
+ @JsonProperty(value = "is_queryable") @XmlElement(name = "is_queryable") Boolean isQueryable,
+ @JsonProperty(value = "is_modifiable") @XmlElement(name = "is_modifiable") Boolean isModifiable,
+ @JsonProperty(value = "other_details") @XmlElement(name = "other_details") @Nullable
+ ItemStructure otherDetails) {
+
+ @JsonProperty(value = "_type", required = true)
+ @XmlElement(name = "_type")
+ public String type() {
+ return "EHR_STATUS";
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/dto/FolderDto.java b/api/src/main/java/org/ehrbase/api/dto/FolderDto.java
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/api/src/main/java/org/ehrbase/api/dto/VersionedCompositionDto.java b/api/src/main/java/org/ehrbase/api/dto/VersionedCompositionDto.java
new file mode 100644
index 0000000000..c33960cea5
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/dto/VersionedCompositionDto.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2019-2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.dto;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonRootName;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
+import com.nedap.archie.rm.support.identification.HierObjectId;
+import com.nedap.archie.rm.support.identification.ObjectId;
+import com.nedap.archie.rm.support.identification.ObjectRef;
+
+/**
+ * Response data of a VERSIONED_COMPOSITION.
+ */
+@JsonRootName(value = "VERSIONED_COMPOSITION")
+@JacksonXmlRootElement(localName = "versioned_composition")
+public record VersionedCompositionDto(
+ @JsonProperty(value = "uid") HierObjectId uid,
+ @JsonProperty(value = "owner_id") ObjectRef ownerId,
+ @JsonProperty(value = "time_created") String timeCreated) {
+
+ @JsonProperty(value = "_type")
+ public String type() {
+ return "VERSIONED_COMPOSITION";
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/dto/VersionedEhrStatusDto.java b/api/src/main/java/org/ehrbase/api/dto/VersionedEhrStatusDto.java
new file mode 100644
index 0000000000..b9d24292a4
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/dto/VersionedEhrStatusDto.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2019-2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.dto;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonRootName;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
+import com.nedap.archie.rm.support.identification.HierObjectId;
+import com.nedap.archie.rm.support.identification.ObjectId;
+import com.nedap.archie.rm.support.identification.ObjectRef;
+
+/**
+ * Response data of a VERSIONED_EHR_STATUS.
+ */
+@JsonRootName(value = "VERSIONED_EHR_STATUS")
+@JacksonXmlRootElement(localName = "versioned_ehr_status")
+public record VersionedEhrStatusDto(
+ @JsonProperty(value = "uid") HierObjectId uid,
+ @JsonProperty(value = "owner_id") ObjectRef ownerId,
+ @JsonProperty(value = "time_created") String timeCreated) {
+
+ @JsonProperty(value = "_type")
+ public String type() {
+ return "VERSIONED_EHR_STATUS";
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/dto/experimental/ItemTagDto.java b/api/src/main/java/org/ehrbase/api/dto/experimental/ItemTagDto.java
new file mode 100644
index 0000000000..7d7705aac9
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/dto/experimental/ItemTagDto.java
@@ -0,0 +1,166 @@
+/*
+ * Copyright (c) 2019-2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.dto.experimental;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import java.util.Objects;
+import java.util.UUID;
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+
+public final class ItemTagDto {
+ private UUID id;
+ private UUID ownerId;
+ private UUID target;
+ private ItemTagRMType targetType;
+ private String targetPath;
+ private String key;
+ private String value;
+
+ public ItemTagDto() {
+ // NOOP - For Jackson
+ }
+
+ /**
+ * @param id Identifier of the tag
+ * @param ownerId Identifier of owner object, such as EHR.
+ * @param target Identifier of target, which may be a VERSIONED_OBJECT<T> or a VERSION<T>.
+ * @param targetType RM type of the tag
+ * @param targetPath Optional archetype (i.e. AQL) or RM path within target, used to tag a fine-grained element.
+ * @param key The tag key. May not be empty or contain leading or trailing whitespace.
+ * @param value The value. If set, may not be empty.
+ */
+ public ItemTagDto(
+ UUID id,
+ UUID ownerId, // obtained by path for PUT
+ UUID target, // obtained by path for PUT
+ ItemTagRMType targetType, // obtained by path for PUT
+ String targetPath,
+ String key,
+ String value) {
+ this.id = id;
+ this.ownerId = ownerId;
+ this.target = target;
+ this.targetType = targetType;
+ this.targetPath = targetPath;
+ this.key = key;
+ this.value = value;
+ }
+
+ @Nullable
+ public UUID getId() {
+ return id;
+ }
+
+ public void setId(@Nullable final UUID id) {
+ this.id = id;
+ }
+
+ @JsonProperty(value = "owner_id")
+ @Nullable
+ public UUID getOwnerId() {
+ return ownerId;
+ }
+
+ public void setOwnerId(@Nullable final UUID ownerId) {
+ this.ownerId = ownerId;
+ }
+
+ @Nullable
+ public UUID getTarget() {
+ return target;
+ }
+
+ public void setTarget(@Nullable final UUID target) {
+ this.target = target;
+ }
+
+ @JsonProperty(value = "target_type")
+ @Nullable
+ public ItemTagRMType getTargetType() {
+ return targetType;
+ }
+
+ public void setTargetType(@Nullable final ItemTagRMType targetType) {
+ this.targetType = targetType;
+ }
+
+ @JsonProperty(value = "target_path")
+ @Nullable
+ public String getTargetPath() {
+ return targetPath;
+ }
+
+ public void setTargetPath(@Nullable final String targetPath) {
+ this.targetPath = targetPath;
+ }
+
+ @Nonnull
+ public String getKey() {
+ return key;
+ }
+
+ public void setKey(@Nonnull final String key) {
+ this.key = key;
+ }
+
+ @Nullable
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(@Nullable final String value) {
+ this.value = value;
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (obj == this) return true;
+ if (obj == null || obj.getClass() != this.getClass()) return false;
+ var that = (ItemTagDto) obj;
+ return Objects.equals(this.id, that.id)
+ && Objects.equals(this.ownerId, that.ownerId)
+ && Objects.equals(this.target, that.target)
+ && Objects.equals(this.targetType, that.targetType)
+ && Objects.equals(this.targetPath, that.targetPath)
+ && Objects.equals(this.key, that.key)
+ && Objects.equals(this.value, that.value);
+ }
+
+ @Override
+ public int hashCode() {
+ return Objects.hash(id, ownerId, target, targetType, targetPath, key, value);
+ }
+
+ @Override
+ public String toString() {
+ return "ItemTagDto[" + "id="
+ + id + ", " + "ownerId="
+ + ownerId + ", " + "target="
+ + target + ", " + "targetType="
+ + targetType + ", " + "targetPath="
+ + targetPath + ", " + "key="
+ + key + ", " + "value="
+ + value + ']';
+ }
+
+ public enum ItemTagRMType {
+ EHR_STATUS,
+ COMPOSITION
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/exception/AqlFeatureNotImplementedException.java b/api/src/main/java/org/ehrbase/api/exception/AqlFeatureNotImplementedException.java
new file mode 100644
index 0000000000..f4fdb4bbad
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/exception/AqlFeatureNotImplementedException.java
@@ -0,0 +1,24 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.exception;
+
+public class AqlFeatureNotImplementedException extends AqlRuntimeException {
+ public AqlFeatureNotImplementedException(String message) {
+ super("Not implemented: %s".formatted(message));
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/exception/AqlRuntimeException.java b/api/src/main/java/org/ehrbase/api/exception/AqlRuntimeException.java
new file mode 100644
index 0000000000..83d8ee2930
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/exception/AqlRuntimeException.java
@@ -0,0 +1,33 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.exception;
+
+public abstract class AqlRuntimeException extends RuntimeException {
+
+ public AqlRuntimeException(String s) {
+ super(s);
+ }
+
+ public AqlRuntimeException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+ public AqlRuntimeException(Throwable cause) {
+ super(cause.getMessage(), cause);
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/exception/BadGatewayException.java b/api/src/main/java/org/ehrbase/api/exception/BadGatewayException.java
index 8dff1e63ae..27a49f961a 100644
--- a/api/src/main/java/org/ehrbase/api/exception/BadGatewayException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/BadGatewayException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,7 +15,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
/**
@@ -23,7 +22,7 @@
* status 502 "Bad gateway" or whatever is appropriate.
* Proxied connection failed, e.g. the server could not contact the clustered note that processes the specified query (EhrScape API example).
*/
-public class BadGatewayException extends RuntimeException{
+public class BadGatewayException extends RuntimeException {
public BadGatewayException(String message) {
super(message);
diff --git a/api/src/main/java/org/ehrbase/api/exception/DuplicateObjectException.java b/api/src/main/java/org/ehrbase/api/exception/DuplicateObjectException.java
deleted file mode 100644
index 38d00b10a2..0000000000
--- a/api/src/main/java/org/ehrbase/api/exception/DuplicateObjectException.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright (c) 2019 Vitasystems GmbH and Hannover Medical School.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.api.exception;
-
-public class DuplicateObjectException extends RuntimeException {
-
- private String type;
-
- public DuplicateObjectException(String type, String message) {
- super(message);
- this.type = type;
- }
-
- public DuplicateObjectException(String type, String message, Throwable cause) {
- super(message, cause);
- this.type = type;
- }
-
- public String getType() {
- return type;
- }
-}
diff --git a/api/src/main/java/org/ehrbase/api/exception/GeneralRequestProcessingException.java b/api/src/main/java/org/ehrbase/api/exception/GeneralRequestProcessingException.java
index 02300e3021..3cbcfaec01 100644
--- a/api/src/main/java/org/ehrbase/api/exception/GeneralRequestProcessingException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/GeneralRequestProcessingException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,7 +15,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
/**
@@ -23,7 +22,7 @@
* status 400 "Bad Request" or whatever is appropriate.
* To be thrown in all cases where part of the request leads to problems, like malformed queries or non-existent referenced objects.
*/
-public class GeneralRequestProcessingException extends RuntimeException {
+public class GeneralRequestProcessingException extends RuntimeException {
public GeneralRequestProcessingException(String message) {
super(message);
diff --git a/api/src/main/java/org/ehrbase/api/exception/IllegalAqlException.java b/api/src/main/java/org/ehrbase/api/exception/IllegalAqlException.java
new file mode 100644
index 0000000000..a004d9ef3d
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/exception/IllegalAqlException.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.exception;
+
+public class IllegalAqlException extends AqlRuntimeException {
+ public IllegalAqlException(String message) {
+ super(message);
+ }
+
+ public IllegalAqlException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+ public IllegalAqlException(Throwable cause) {
+ super(cause.getMessage(), cause);
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/exception/InternalServerException.java b/api/src/main/java/org/ehrbase/api/exception/InternalServerException.java
index 2dd28bc87c..07a9bf6f11 100644
--- a/api/src/main/java/org/ehrbase/api/exception/InternalServerException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/InternalServerException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,7 +15,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
/**
@@ -29,11 +28,11 @@ public InternalServerException(String message) {
super(message);
}
- public InternalServerException(String message, Exception cause) {
+ public InternalServerException(String message, Throwable cause) {
super(message, cause);
}
- public InternalServerException(Exception cause) {
- super(cause);
+ public InternalServerException(Throwable cause) {
+ super(cause.getMessage(), cause);
}
}
diff --git a/api/src/main/java/org/ehrbase/api/exception/InvalidApiParameterException.java b/api/src/main/java/org/ehrbase/api/exception/InvalidApiParameterException.java
index 4371f3d6b1..9e65c6dd66 100644
--- a/api/src/main/java/org/ehrbase/api/exception/InvalidApiParameterException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/InvalidApiParameterException.java
@@ -1,11 +1,13 @@
/*
- * Copyright 2019-2022 vitasystems GmbH and Hannover Medical School.
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * https://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -13,16 +15,15 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
public class InvalidApiParameterException extends RuntimeException {
- public InvalidApiParameterException(String message) {
- super(message);
- }
+ public InvalidApiParameterException(String message) {
+ super(message);
+ }
- public InvalidApiParameterException(String message, Throwable cause) {
- super(message, cause);
- }
+ public InvalidApiParameterException(String message, Throwable cause) {
+ super(message, cause);
+ }
}
diff --git a/api/src/main/java/org/ehrbase/api/exception/NotAcceptableException.java b/api/src/main/java/org/ehrbase/api/exception/NotAcceptableException.java
index 3ce803bc98..99a9f42f2b 100644
--- a/api/src/main/java/org/ehrbase/api/exception/NotAcceptableException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/NotAcceptableException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,7 +15,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
public class NotAcceptableException extends RuntimeException {
diff --git a/api/src/main/java/org/ehrbase/api/exception/ObjectNotFoundException.java b/api/src/main/java/org/ehrbase/api/exception/ObjectNotFoundException.java
index 1fda474069..28b286e061 100644
--- a/api/src/main/java/org/ehrbase/api/exception/ObjectNotFoundException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/ObjectNotFoundException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,7 +15,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
/**
@@ -25,7 +24,7 @@
*/
public class ObjectNotFoundException extends RuntimeException {
- private String type;
+ private final String type;
public ObjectNotFoundException(String type, String message) {
super(message);
diff --git a/api/src/main/java/org/ehrbase/api/exception/PreconditionFailedException.java b/api/src/main/java/org/ehrbase/api/exception/PreconditionFailedException.java
index 8e583eca36..5cc4a0ea75 100644
--- a/api/src/main/java/org/ehrbase/api/exception/PreconditionFailedException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/PreconditionFailedException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,7 +15,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
/**
@@ -23,7 +22,7 @@
* status 412 "Precondition Failed" or whatever is appropriate.
* To be thrown in all cases where part of the request leads to problems, like malformed queries or non-existent referenced objects.
*/
-public class PreconditionFailedException extends RuntimeException {
+public class PreconditionFailedException extends RuntimeException {
private final String currentVersionUid;
private final String url;
@@ -56,4 +55,4 @@ public String getCurrentVersionUid() {
public String getUrl() {
return url;
}
-}
\ No newline at end of file
+}
diff --git a/api/src/main/java/org/ehrbase/api/exception/StateConflictException.java b/api/src/main/java/org/ehrbase/api/exception/StateConflictException.java
index 715afb1052..5b92d265e4 100644
--- a/api/src/main/java/org/ehrbase/api/exception/StateConflictException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/StateConflictException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,7 +15,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
/**
@@ -23,7 +22,7 @@
* status 409 "Conflict" or whatever is appropriate.
* Request is in conflict with current state, e.g. referenced version of object is not the last version.
*/
-public class StateConflictException extends RuntimeException{
+public class StateConflictException extends RuntimeException {
public StateConflictException(String message) {
super(message);
diff --git a/api/src/main/java/org/ehrbase/api/exception/UnexpectedSwitchCaseException.java b/api/src/main/java/org/ehrbase/api/exception/UnexpectedSwitchCaseException.java
index 761961c9fb..be48a4f875 100644
--- a/api/src/main/java/org/ehrbase/api/exception/UnexpectedSwitchCaseException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/UnexpectedSwitchCaseException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Hannover Medical School.
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,38 +15,31 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
import org.apache.commons.lang3.StringUtils;
/**
*
- * Diese Exception wird geworfen, wenn in einem Switch-Block ein Case eingetreten ist, der nicht korrekt behandelt werden kann. Eigentlich
- * sollte dieser Fall nicht auftreten (außer man ignoriert die Eclipse-Warning zum unvollständigen Switch).
+ * This exception is thrown when a case has occurred in a switch block that cannot be handled correctly.
*
*
- * Typische Verwendungen in einer Switch-Definition:
+ * Typical uses in a switch statement:
*
- *
Im unerwarteten default-Case
- *
Im explizit nicht sinnvoll behandelbaren Case
- *
Im unerwarteten default-Case eines Switch mit Fall-Through von nicht sinnvoll behandelbaren Cases (Kombination aus 1. und 2.)
+ *
unexpected default case
+ *
explicitly not sensibly treatable case
+ *
unexpected default case with fall-through of not sensibly treatable case (combination of 1. and 2.)
*
- * @author Jan Falkenstern, Stefan Kock
*/
public class UnexpectedSwitchCaseException extends RuntimeException {
private static final long serialVersionUID = 5695009820197756438L;
/**
- * Erzeugt aus dem übergebenen enumValue eine message.
- * Ausgegeben in der Exception-Message wird enumValue.name(),
- * damit z.B. bei lokalisierten Enums immer denselbe Wert ausgegeben wird.
+ * Creates a message from the enumValue parameter.
+ * The message is based on enumValue.name(),
+ * so that the format is stable, e.g. in case of i18n.
*
* @param enumValue must not be null
*/
@@ -55,9 +48,9 @@ public UnexpectedSwitchCaseException(Enum enumValue) {
}
/**
- * Erzeugt aus dem übergebenen enumValue eine message.
- * Ausgegeben in der Exception-Message wird enumValue.name(),
- * damit z.B. bei lokalisierten Enums immer denselbe Wert ausgegeben wird.
+ * Creates a message from the enumValue parameter.
+ * The message is based on enumValue.name(),
+ * so that the format is stable, e.g. in case of i18n.
*
* @param enumValue must not be null
* @param additionalMessage additional text for generated message
@@ -67,7 +60,7 @@ public UnexpectedSwitchCaseException(Enum enumValue, String additionalMessage
}
/**
- * Erzeugt aus dem übergebenen intValue eine message.
+ * Creates a message from the intValue parameter
*
* @param intValue
*/
@@ -76,7 +69,7 @@ public UnexpectedSwitchCaseException(Integer intValue) {
}
/**
- * Erzeugt aus dem übergebenen intValue eine message.
+ * Creates a message from the intValue parameter
*
* @param intValue
* @param additionalMessage additional text for generated message
@@ -86,13 +79,7 @@ public UnexpectedSwitchCaseException(Integer intValue, String additionalMessage)
}
/**
- * Erzeugt aus dem übergebenen stringValue eine message.
- *
- *
- *
Achtung: Breaking Change!
- *
Mit Version 0.1.3-SNAPSHOT hat sich die Bedeutung des Konstruktors geändert!
- * Statt der Meldung wird jetzt nur der Wert angegeben!
- *
+ * Creates a message from the stringValue parameter
*
* @param stringValue
*/
@@ -101,7 +88,7 @@ public UnexpectedSwitchCaseException(String stringValue) {
}
/**
- * Erzeugt aus dem übergebenen stringValue eine message.
+ * Creates a message from the stringValue parameter
*
* @param stringValue
* @param additionalMessage additional text for generated message
@@ -111,10 +98,9 @@ public UnexpectedSwitchCaseException(String stringValue, String additionalMessag
}
/**
- * Erzeugt die Message der {@link UnexpectedSwitchCaseException} anhand der übergebenen Parameter mit Ausgabe von
- * enumValue.getClass().getSimpleName().
- * Ausgegeben in der Exception-Message wird enumValue.name(),
- * damit z.B. bei lokalisierten Enums immer denselbe Wert ausgegeben wird.
+ * Creates the message of a {@link UnexpectedSwitchCaseException} containing the simple class name of the enumValue parameter.
+ * The message is based on enumValue.name(),
+ * so that the format is stable, e.g. in case of i18n.
*
* @param enumValue must not be null
* @param additionalMessage additional text for generated message (optional)
@@ -126,7 +112,7 @@ public static String formatMessage(Enum enumValue, String additionalMessage)
}
/**
- * Erzeugt die Message der {@link UnexpectedSwitchCaseException} anhand der übergebenen Parameter.
+ * Creates the message of a {@link UnexpectedSwitchCaseException} based on the given parameters.
*
* @param value
* @param additionalMessage additional text for generated message (optional)
@@ -138,7 +124,7 @@ public static String formatMessage(Object value, String additionalMessage) {
}
/**
- * Erzeugt die Message der {@link UnexpectedSwitchCaseException} anhand der übergebenen Parameter.
+ * Creates the message of a {@link UnexpectedSwitchCaseException} based on the given parameters.
*
* @param type e.g. enumValue.getClass().getSimpleName()
* @param value unsupported value in switch
@@ -166,4 +152,4 @@ public static String formatMessage(String type, Object value, String additionalM
return sb.toString();
}
-}
\ No newline at end of file
+}
diff --git a/api/src/main/java/org/ehrbase/api/exception/UnprocessableEntityException.java b/api/src/main/java/org/ehrbase/api/exception/UnprocessableEntityException.java
index d8da677be5..05ae453c58 100644
--- a/api/src/main/java/org/ehrbase/api/exception/UnprocessableEntityException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/UnprocessableEntityException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,7 +15,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
/**
@@ -27,4 +26,8 @@ public class UnprocessableEntityException extends RuntimeException {
public UnprocessableEntityException(String message) {
super(message);
}
+
+ public UnprocessableEntityException(String message, Throwable e) {
+ super(message, e);
+ }
}
diff --git a/api/src/main/java/org/ehrbase/api/exception/UnsupportedMediaTypeException.java b/api/src/main/java/org/ehrbase/api/exception/UnsupportedMediaTypeException.java
index 6f013b262e..11d7e3b26f 100644
--- a/api/src/main/java/org/ehrbase/api/exception/UnsupportedMediaTypeException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/UnsupportedMediaTypeException.java
@@ -1,3 +1,20 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
package org.ehrbase.api.exception;
/**
@@ -14,6 +31,7 @@ public class UnsupportedMediaTypeException extends RuntimeException {
public UnsupportedMediaTypeException(String message) {
super(message);
}
+
public UnsupportedMediaTypeException(String message, Throwable cause) {
super(message, cause);
}
diff --git a/api/src/main/java/org/ehrbase/api/exception/ValidationException.java b/api/src/main/java/org/ehrbase/api/exception/ValidationException.java
index ccfced4fb3..af5a4d9838 100644
--- a/api/src/main/java/org/ehrbase/api/exception/ValidationException.java
+++ b/api/src/main/java/org/ehrbase/api/exception/ValidationException.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Christian Chevalley (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,7 +15,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.exception;
/**
@@ -23,7 +22,7 @@
* status 400 "Bad Request" or whatever is appropriate.
* To be thrown in all cases where part of the request leads to problems, like malformed queries or non-existent referenced objects.
*/
-public class ValidationException extends RuntimeException {
+public class ValidationException extends RuntimeException {
public ValidationException(String message) {
super(message);
@@ -33,7 +32,7 @@ public ValidationException(String message, Throwable cause) {
super(message, cause);
}
- public ValidationException(Exception otherException){
- super(otherException);
+ public ValidationException(Exception cause) {
+ super(cause.getMessage(), cause);
}
}
diff --git a/api/src/main/java/org/ehrbase/api/knowledge/KnowledgeCacheService.java b/api/src/main/java/org/ehrbase/api/knowledge/KnowledgeCacheService.java
new file mode 100644
index 0000000000..96c4852294
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/knowledge/KnowledgeCacheService.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.knowledge;
+
+import java.io.InputStream;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import org.ehrbase.openehr.sdk.webtemplate.model.WebTemplate;
+import org.openehr.schemas.v1.OPERATIONALTEMPLATE;
+
+public interface KnowledgeCacheService {
+
+ String addOperationalTemplate(OPERATIONALTEMPLATE template);
+
+ List listAllOperationalTemplates();
+
+ Map findAllTemplateIds();
+
+ /**
+ * retrieve an operational template document instance
+ *
+ * @param key the name of the operational template
+ * @return an OPERATIONALTEMPLATE document instance or null
+ * @see org.openehr.schemas.v1.OPERATIONALTEMPLATE
+ */
+ Optional retrieveOperationalTemplate(String key);
+
+ WebTemplate getInternalTemplate(String templateId);
+
+ /**
+ * Deletes a given operational template physically from cache and from template storage and from cache. Should only
+ * be executed if the template is no longer referenced by any Composition. Make sure you check for references before
+ * deleting a template otherwise this causes inconsistencies and no longer deliverable Composition entries.
+ *
+ * @param template - The template instance to delete
+ */
+ void deleteOperationalTemplate(OPERATIONALTEMPLATE template);
+
+ Optional findTemplateIdByUuid(UUID uuid);
+
+ Optional findUuidByTemplateId(String templateId);
+
+ String adminUpdateOperationalTemplate(InputStream content);
+
+ int deleteAllOperationalTemplates();
+}
diff --git a/api/src/main/java/org/ehrbase/api/knowledge/TemplateMetaData.java b/api/src/main/java/org/ehrbase/api/knowledge/TemplateMetaData.java
new file mode 100644
index 0000000000..f420c25064
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/knowledge/TemplateMetaData.java
@@ -0,0 +1,71 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.knowledge;
+
+import java.time.OffsetDateTime;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+import org.openehr.schemas.v1.OPERATIONALTEMPLATE;
+
+public class TemplateMetaData {
+ private OPERATIONALTEMPLATE operationaltemplate;
+ private OffsetDateTime createdOn;
+
+ private UUID internalId;
+
+ private List errorList;
+
+ public OPERATIONALTEMPLATE getOperationaltemplate() {
+ return operationaltemplate;
+ }
+
+ public void setOperationalTemplate(OPERATIONALTEMPLATE operationaltemplate) {
+ this.operationaltemplate = operationaltemplate;
+ }
+
+ public OffsetDateTime getCreatedOn() {
+ return createdOn;
+ }
+
+ public void setCreatedOn(OffsetDateTime createdOn) {
+ this.createdOn = createdOn;
+ }
+
+ public void setInternalId(UUID internalId) {
+ this.internalId = internalId;
+ }
+
+ public UUID getInternalId() {
+ return internalId;
+ }
+
+ public List getErrorList() {
+ if (this.errorList == null) {
+ this.errorList = new ArrayList<>();
+ }
+ return errorList;
+ }
+
+ public void addError(String error) {
+ if (this.errorList == null) {
+ this.errorList = new ArrayList<>();
+ }
+ this.errorList.add(error);
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/mapper/StructuredStringJSonSerializer.java b/api/src/main/java/org/ehrbase/api/mapper/StructuredStringJSonSerializer.java
index b258e96523..22a88f39ad 100644
--- a/api/src/main/java/org/ehrbase/api/mapper/StructuredStringJSonSerializer.java
+++ b/api/src/main/java/org/ehrbase/api/mapper/StructuredStringJSonSerializer.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) Stefan Spiska (Vitasystems GmbH) and Hannover Medical School.
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,17 +15,15 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.mapper;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializerProvider;
import com.fasterxml.jackson.dataformat.xml.ser.ToXmlGenerator;
-import org.ehrbase.api.exception.UnexpectedSwitchCaseException;
-import org.ehrbase.response.ehrscape.StructuredString;
-
import java.io.IOException;
+import org.ehrbase.api.exception.UnexpectedSwitchCaseException;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.StructuredString;
public class StructuredStringJSonSerializer extends JsonSerializer {
@Override
@@ -55,5 +53,3 @@ public void serialize(StructuredString value, JsonGenerator jgen, SerializerProv
}
}
}
-
-
diff --git a/api/src/main/java/org/ehrbase/api/repository/KeyValuePair.java b/api/src/main/java/org/ehrbase/api/repository/KeyValuePair.java
new file mode 100644
index 0000000000..58e21db89e
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/repository/KeyValuePair.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.repository;
+
+import java.util.UUID;
+
+public interface KeyValuePair {
+
+ public static KeyValuePair of(String pluginId, String key, String value) {
+ return KeyValuePair.of(UUID.randomUUID(), pluginId, key, value);
+ }
+
+ public static KeyValuePair of(UUID id, String pluginId, String key, String value) {
+ return new KeyValueEntry(id, pluginId, key, value);
+ }
+
+ public UUID getId();
+
+ public String getContext();
+
+ public String getKey();
+
+ public String getValue();
+}
+
+class KeyValueEntry implements KeyValuePair {
+
+ private final UUID id;
+ private final String context;
+ private final String key;
+ private final String value;
+
+ KeyValueEntry(UUID id, String pluginId, String key, String value) {
+ this.id = id;
+ this.context = pluginId;
+ this.key = key;
+ this.value = value;
+ }
+
+ public UUID getId() {
+ return id;
+ }
+
+ public String getContext() {
+ return context;
+ }
+
+ public String getKey() {
+ return key;
+ }
+
+ public String getValue() {
+ return value;
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/repository/KeyValuePairRepository.java b/api/src/main/java/org/ehrbase/api/repository/KeyValuePairRepository.java
new file mode 100644
index 0000000000..e654330f01
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/repository/KeyValuePairRepository.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.repository;
+
+import java.util.List;
+import java.util.Optional;
+import java.util.UUID;
+
+public interface KeyValuePairRepository {
+
+ public List findAllBy(String context);
+
+ public Optional findBy(String context, String key);
+
+ public Optional findBy(UUID uid);
+
+ public KeyValuePair save(KeyValuePair kve);
+
+ public boolean deleteBy(UUID uid);
+}
diff --git a/api/src/main/java/org/ehrbase/api/rest/EHRbaseHeader.java b/api/src/main/java/org/ehrbase/api/rest/EHRbaseHeader.java
new file mode 100644
index 0000000000..afcef5a77a
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/rest/EHRbaseHeader.java
@@ -0,0 +1,53 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.rest;
+
+/**
+ * EHRbase specific HTTP headers that are not part of the openEHR standard.
+ */
+public final class EHRbaseHeader {
+
+ private EHRbaseHeader() {}
+
+ public static final String TEMPLATE_ID = "EHRBase-Template-ID";
+
+ /**
+ * Used by the /query endpoint to perform only a dry run query.
+ */
+ public static final String AQL_DRY_RUN = "EHRbase-AQL-Dry-Run";
+
+ /**
+ * Used by the /query endpoint to provide the executed SQL statement in the return metadata.
+ */
+ public static final String AQL_EXECUTED_SQL = "EHRbase-AQL-Executed-SQL";
+
+ /**
+ * Used by the /query endpoint to provide the database query plan in the return metadata.
+ */
+ public static final String AQL_QUERY_PLAN = "EHRbase-AQL-Query-Plan";
+
+ /**
+ * In AQL queries with paths containing consecutive node predicates: Skip nodes implied by the archetype definitions
+ */
+ public static final String AQL_PATH_SKIPPING = "EHRbase-AQL-Path-Skipping";
+
+ /**
+ * In AQL queries CONTAINS expressions with a node predicate: Exclude results from nested archetypes
+ */
+ public static final String AQL_ARCHETYPE_LOCAL_NODE_PREDICATES = "EHRbase-AQL-Archetype-Local-Node-Predicates";
+}
diff --git a/api/src/main/java/org/ehrbase/api/rest/HttpRestContext.java b/api/src/main/java/org/ehrbase/api/rest/HttpRestContext.java
new file mode 100644
index 0000000000..da0311a1ad
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/rest/HttpRestContext.java
@@ -0,0 +1,100 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.rest;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+
+public class HttpRestContext {
+
+ public interface HttpCtx {
+ T get(CtxAttr attr);
+ }
+
+ public static final class CtxAttr {}
+
+ public static final CtxAttr QUERY = new CtxAttr<>();
+ public static final CtxAttr QUERY_ID = new CtxAttr<>();
+ public static final CtxAttr LOCATION = new CtxAttr<>();
+ public static final CtxAttr VERSION = new CtxAttr<>();
+ public static final CtxAttr EHR_ID = new CtxAttr<>();
+ public static final CtxAttr TEMPLATE_ID = new CtxAttr<>();
+ public static final CtxAttr COMPOSITION_ID = new CtxAttr<>();
+ public static final CtxAttr DIRECTORY_ID = new CtxAttr<>();
+ public static final CtxAttr CONTRIBUTION_ID = new CtxAttr<>();
+ public static final CtxAttr> REMOVED_PATIENTS = new CtxAttr<>();
+ public static final CtxAttr QUERY_EXECUTE_ENDPOINT = new CtxAttr<>();
+
+ private static final ThreadLocal, Object>> httpContext = ThreadLocal.withInitial(HashMap::new);
+
+ public static void clear() {
+ httpContext.remove();
+ }
+
+ public static void register(CtxAttr key, V value) {
+ httpContext.get().put(key, value);
+ }
+
+ public static void register(CtxAttr key0, V0 value0, CtxAttr key1, V1 value1) {
+ Map, Object> map = httpContext.get();
+ map.put(key0, value0);
+ map.put(key1, value1);
+ }
+
+ public static void register(
+ CtxAttr key0, V0 value0, CtxAttr key1, V1 value1, CtxAttr key2, V2 value2) {
+ Map, Object> map = httpContext.get();
+ map.put(key0, value0);
+ map.put(key1, value1);
+ map.put(key2, value2);
+ }
+
+ public static void register(
+ CtxAttr key0,
+ V0 value0,
+ CtxAttr key1,
+ V1 value1,
+ CtxAttr key2,
+ V2 value2,
+ CtxAttr key3,
+ V3 value3) {
+ Map, Object> map = httpContext.get();
+ map.put(key0, value0);
+ map.put(key1, value1);
+ map.put(key2, value2);
+ map.put(key3, value3);
+ }
+
+ @SuppressWarnings("unchecked")
+ public static T get(CtxAttr attr) {
+ Map, Object> ctxAttrObjectMap = httpContext.get();
+ return (T) ctxAttrObjectMap.get(attr);
+ }
+
+ public static void handle(HttpRestContextHandler handler) {
+ Map, Object> ctxAttrObjectMap = httpContext.get();
+ handler.handle(new HttpCtx() {
+ @Override
+ public T get(CtxAttr attr) {
+ return (T) ctxAttrObjectMap.get(attr);
+ }
+ });
+ }
+}
diff --git a/api/src/main/java/org/ehrbase/api/rest/HttpRestContextHandler.java b/api/src/main/java/org/ehrbase/api/rest/HttpRestContextHandler.java
new file mode 100644
index 0000000000..1569a1d4d0
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/rest/HttpRestContextHandler.java
@@ -0,0 +1,25 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.rest;
+
+import org.ehrbase.api.rest.HttpRestContext.HttpCtx;
+
+public interface HttpRestContextHandler {
+
+ void handle(HttpCtx context);
+}
diff --git a/api/src/main/java/org/ehrbase/api/service/AqlQueryService.java b/api/src/main/java/org/ehrbase/api/service/AqlQueryService.java
new file mode 100644
index 0000000000..73eb7fe6ad
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/service/AqlQueryService.java
@@ -0,0 +1,33 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.service;
+
+import org.ehrbase.api.dto.AqlQueryRequest;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.QueryResultDto;
+
+public interface AqlQueryService {
+
+ /**
+ * simple query where the full json expression contains both query (key = 'q') and optional
+ * parameters (key = 'query-parameters')
+ *
+ * @param aqlQueryRequest to perform
+ * @return aqlQueryResult
+ */
+ QueryResultDto query(AqlQueryRequest aqlQueryRequest);
+}
diff --git a/api/src/main/java/org/ehrbase/api/service/BaseService.java b/api/src/main/java/org/ehrbase/api/service/BaseService.java
deleted file mode 100644
index 3d9cc96679..0000000000
--- a/api/src/main/java/org/ehrbase/api/service/BaseService.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.api.service;
-
-import org.ehrbase.api.definitions.ServerConfig;
-
-import java.util.UUID;
-
-/**
- * Basic service interface, foundation of all service interfaces
- */
-public interface BaseService {
-
- UUID getSystemUuid();
-
- ServerConfig getServerConfig();
-}
diff --git a/api/src/main/java/org/ehrbase/api/service/CompositionService.java b/api/src/main/java/org/ehrbase/api/service/CompositionService.java
index 50b61860f1..23e9e7ae00 100644
--- a/api/src/main/java/org/ehrbase/api/service/CompositionService.java
+++ b/api/src/main/java/org/ehrbase/api/service/CompositionService.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Stefan Spiska (Vitasystems GmbH), Jake Smolka (Hannover Medical School), and Luis Marco-Ruiz (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,49 +15,45 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.service;
import com.nedap.archie.rm.changecontrol.OriginalVersion;
import com.nedap.archie.rm.composition.Composition;
import com.nedap.archie.rm.ehr.VersionedComposition;
import com.nedap.archie.rm.generic.RevisionHistory;
-import org.ehrbase.api.exception.InternalServerException;
-import org.ehrbase.api.exception.ObjectNotFoundException;
-import org.ehrbase.response.ehrscape.CompositionDto;
-import org.ehrbase.response.ehrscape.CompositionFormat;
-import org.ehrbase.response.ehrscape.StructuredString;
-
-import java.time.LocalDateTime;
+import java.time.OffsetDateTime;
import java.util.Optional;
import java.util.UUID;
+import javax.annotation.Nullable;
+import org.ehrbase.api.exception.InternalServerException;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.CompositionDto;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.CompositionFormat;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.StructuredString;
+
+public interface CompositionService extends VersionedObjectService {
+
+ static CompositionDto from(UUID ehrId, Composition composition) {
+
+ return new CompositionDto(
+ composition,
+ composition.getArchetypeDetails().getTemplateId().getValue(),
+ UUID.fromString(composition.getUid().getRoot().getValue()),
+ ehrId);
+ }
-public interface CompositionService extends BaseService, VersionedObjectService {
/**
* @param compositionId The {@link UUID} of the composition to be returned.
+ * @param ehrId The {@link UUID} of the ehr wich contains the composition
* @param version The version to returned. If null return the latest
* @return
* @throws InternalServerException
*/
- Optional retrieve(UUID compositionId, Integer version);
+ Optional retrieve(UUID ehrId, UUID compositionId, Integer version);
/**
- * TODO: untested because not needed, yet
- *
- * Gets the composition that is closest in time before timestamp
- *
- * @param compositionId UUID (versioned_object_id) of composition
- * @param timestamp Given time
- * @return Optional of CompositionDto closest in time before timestamp
- */
- Optional retrieveByTimestamp(UUID compositionId, LocalDateTime timestamp);
-
- /**
- * Public serializer entry point which will be called with
- * composition dto fetched from database and the
- * desired target serialized string format.
- * Will parse the composition dto into target format either
- * with a custom lambda expression for desired target format
+ * Public serializer entry point which will be called with composition dto fetched from database
+ * and the desired target serialized string format. Will parse the composition dto into target
+ * format either with a custom lambda expression for desired target format
*
* @param composition Composition dto from database
* @param format Target format
@@ -65,75 +61,90 @@ public interface CompositionService extends BaseService, VersionedObjectService<
*/
StructuredString serialize(CompositionDto composition, CompositionFormat format);
- Integer getLastVersionNumber(UUID compositionId);
-
/**
- * Helper function to read UUID from given composition input in stated format.
- * @param content Composition input
- * @param format Composition format
- * @return The UUID or null when not available.
+ * Retrieve the latest version number for the given composition ID.
+ *
+ * @param compositionId The {@link UUID} of the composition to be returned.
+ * @return latestVersion of the existing composition.
*/
- String getUidFromInputComposition(String content, CompositionFormat format);
+ int getLastVersionNumber(UUID ehrId, UUID compositionId);
/**
- * Helper function to read the template ID from given composition input in stated format.
- * @param content Composition input
- * @param format Composition format
- * @return The UUID or null when not available.
+ * Retrieves the template ID associated with a given composition ID.
+ *
+ * @param compositionId The UUID of the composition for which to retrieve the template ID
+ * @return The template ID associated with the given composition ID
*/
- String getTemplateIdFromInputComposition(String content, CompositionFormat format);
+ String retrieveTemplateId(UUID compositionId);
/**
* Gets the version of a composition that is closest in time before timestamp
+ *
* @param compositionId UUID (versioned_object_id) of composition
- * @param timestamp Given time
+ * @param timestamp Given time
* @return Version closest in time before given timestamp, or `null` in case of error.
*/
- Integer getVersionByTimestamp(UUID compositionId, LocalDateTime timestamp);
+ int getVersionByTimestamp(UUID compositionId, OffsetDateTime timestamp);
/**
- * Checks if given ID is a valid composition ID.
+ * Checks if given ID is already used.
+ *
* @param versionedObjectId ID to check
- * @return True if ID exists
- * @throws ObjectNotFoundException if ID does not exist
+ * @return if ID already exists
*/
boolean exists(UUID versionedObjectId);
/**
* Checks if given composition ID is ID of a logically deleted composition.
+ *
+ * @param ehrId EHRid to delete composition for
* @param versionedObjectId ID to check
+ * @param version Version to delete, option uses head as default
* @return True if deleted, false if not
*/
- boolean isDeleted(UUID versionedObjectId);
+ boolean isDeleted(UUID ehrId, UUID versionedObjectId, @Nullable Integer version);
/**
* Admin method to delete a Composition from the DB. See EHRbase Admin API specification for details.
+ *
* @param compositionId Composition to delete
*/
void adminDelete(UUID compositionId);
/**
* Gets version container Composition associated with given EHR and Composition ID.
- * @param ehrUid Given EHR ID
- * @param composition Given Composition ID
+ *
+ * @param ehrUid Given EHR ID
+ * @param compositionId Given Composition ID
* @return Version container object
*/
- VersionedComposition getVersionedComposition(UUID ehrUid, UUID composition);
+ VersionedComposition getVersionedComposition(UUID ehrUid, UUID compositionId);
/**
* Gets revision history of given composition.
- * @param composition Given composition.
+ *
+ * @param compositionId Given composition.
* @return Revision history
*/
- RevisionHistory getRevisionHistoryOfVersionedComposition(UUID composition);
+ RevisionHistory getRevisionHistoryOfVersionedComposition(UUID ehrUid, UUID compositionId);
/**
* Gets Original Version container class representation of the given composition at given version.
+ *
* @param versionedObjectUid Given composition Uid.
- * @param version Given version number.
+ * @param version Given version number.
* @return Original Version container class representation.
*/
- Optional> getOriginalVersionComposition(UUID versionedObjectUid, int version);
+ Optional> getOriginalVersionComposition(
+ UUID ehrUid, UUID versionedObjectUid, int version);
Composition buildComposition(String content, CompositionFormat format, String templateId);
+
+ /**
+ * Gets the EHR id for the given Composition id.
+ *
+ * @param compositionId Given composition Uid.
+ * @return EHR UID for the given Composition
+ */
+ Optional getEhrIdForComposition(UUID compositionId);
}
diff --git a/api/src/main/java/org/ehrbase/api/service/ContributionService.java b/api/src/main/java/org/ehrbase/api/service/ContributionService.java
index fc8c1e4224..59905ca70a 100644
--- a/api/src/main/java/org/ehrbase/api/service/ContributionService.java
+++ b/api/src/main/java/org/ehrbase/api/service/ContributionService.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,61 +15,103 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.service;
-import java.util.Set;
-import org.ehrbase.api.exception.InternalServerException;
-import org.ehrbase.response.ehrscape.CompositionFormat;
-import org.ehrbase.response.ehrscape.ContributionDto;
-
-import java.util.Optional;
+import com.nedap.archie.rm.datavalues.DvCodedText;
+import com.nedap.archie.rm.generic.AuditDetails;
import java.util.UUID;
+import java.util.stream.Stream;
+import javax.annotation.Nonnull;
+import org.ehrbase.api.exception.InternalServerException;
+import org.ehrbase.api.exception.ValidationException;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.ContributionDto;
/**
* Interface for contribution service roughly based on openEHR SM "I_EHR_CONTRIBUTION Interface",
* see: https://specifications.openehr.org/releases/SM/latest/openehr_platform.html#_i_ehr_contribution_interface
*/
-public interface ContributionService extends BaseService {
+public interface ContributionService {
- /**
- * Check if given contribution exists and is part of given EHR.
- * @param ehrId ID of EHR
- * @param contributionId ID of contribution
- * @return True if exists and part of EHR, false if not
- */
- boolean hasContribution(UUID ehrId, UUID contributionId);
+ enum ContributionChangeType {
+ CREATION(249),
+ AMENDMENT(250),
+ MODIFICATION(251),
+ SYNTHESIS(252),
+ UNKNOWN(253),
+ DELETED(523);
+ final int code;
+
+ ContributionChangeType(int code) {
+ this.code = code;
+ }
+
+ public static ContributionChangeType fromAuditDetails(AuditDetails commitAudit) {
+ DvCodedText changeType = commitAudit.getChangeType();
+
+ if (!"openehr"
+ .equals(changeType.getDefiningCode().getTerminologyId().getValue())) {
+ throw new ValidationException("Unsupported change type terminology: %s"
+ .formatted(
+ changeType.getDefiningCode().getTerminologyId().getValue()));
+ }
+
+ ContributionChangeType byCode =
+ getByCode(changeType.getDefiningCode().getCodeString());
+ if (byCode.name().equalsIgnoreCase(changeType.getValue())) {
+ return byCode;
+ } else {
+ throw new ValidationException("Inconsistent change type: %s for code %s"
+ .formatted(
+ changeType.getValue(),
+ changeType.getDefiningCode().getCodeString()));
+ }
+ }
+
+ private static ContributionChangeType getByCode(String codeString) {
+
+ int code;
+ try {
+ code = Integer.parseInt(codeString);
+ } catch (NumberFormatException e) {
+ throw new ValidationException("Unknown change type code %s".formatted(codeString));
+ }
+
+ return Stream.of(ContributionChangeType.values())
+ .filter(t -> t.code == code)
+ .findFirst()
+ .orElseThrow(() -> new ValidationException("Unknown change type code %s".formatted(codeString)));
+ }
+
+ public int getCode() {
+ return code;
+ }
+ }
/**
* Return the Contribution with given id in given EHR.
- * @param ehrId ID of EHR
+ *
+ * @param ehrId ID of EHR
* @param contributionId ID of contribution
- * @return {@link Optional} containing a {@link ContributionDto} if successful, empty if not
*/
- Optional getContribution(UUID ehrId, UUID contributionId);
+ @Nonnull
+ ContributionDto getContribution(UUID ehrId, UUID contributionId);
/**
* Commit a CONTRIBUTION containing any number of serialized VERSION objects.
- * @param ehrId ID of EHR
+ *
+ * @param ehrId ID of EHR
* @param content serialized content, containing version objects and audit object in given format
- * @param format format of serialized versions
* @return ID of successfully committed contribution
* @throws IllegalArgumentException when input can't be processed
- * @throws InternalServerException when DB is inconsistent
+ * @throws InternalServerException when DB is inconsistent
*/
- UUID commitContribution(UUID ehrId, String content, CompositionFormat format);
+ UUID commitContribution(UUID ehrId, String content);
/**
* Admin method to delete a Contribution from the DB. See EHRbase Admin API specification for details.
+ *
+ * @param ehrId
* @param contributionId Contribution to delete
*/
- void adminDelete(UUID contributionId);
-
- /**
- * Extracts set of used templates in payload's compositions.
- * @param contribution Contribution request content
- * @param format Format of that content
- * @return Set of templates used by compositions
- */
- Set getListOfTemplates(String contribution, CompositionFormat format);
+ void adminDelete(UUID ehrId, UUID contributionId);
}
diff --git a/api/src/main/java/org/ehrbase/api/service/DirectoryService.java b/api/src/main/java/org/ehrbase/api/service/DirectoryService.java
new file mode 100644
index 0000000000..6284d941a3
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/service/DirectoryService.java
@@ -0,0 +1,85 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.service;
+
+import com.nedap.archie.rm.directory.Folder;
+import com.nedap.archie.rm.support.identification.ObjectVersionId;
+import java.time.OffsetDateTime;
+import java.util.Optional;
+import java.util.UUID;
+import javax.annotation.Nullable;
+
+public interface DirectoryService {
+
+ int EHR_DIRECTORY_FOLDER_IDX = 1;
+
+ /**
+ * Get the Folder for Ehr with id equal ehrId
+ *
+ * @param ehrId
+ * @param folderId if null latest version will be returned
+ * @param path optional return folder at path
+ * @return
+ */
+ Optional get(UUID ehrId, @Nullable ObjectVersionId folderId, @Nullable String path);
+
+ /**
+ * Get the Folder for Ehr with id equal ehrId for a specific point in time;
+ *
+ * @param ehrId
+ * @param time
+ * @param path optional return folder at path
+ * @return
+ */
+ Optional getByTime(UUID ehrId, OffsetDateTime time, @Nullable String path);
+
+ /**
+ * Create a new folder for Ehr with id equal ehrId
+ *
+ * @param ehrId
+ * @param folder
+ * @return
+ */
+ Folder create(UUID ehrId, Folder folder);
+
+ /**
+ * Update the folder for Ehr with id equal ehrId
+ *
+ * @param ehrId
+ * @param folder
+ * @param ifMatches expected version before update for optimistic looking
+ * @return
+ */
+ Folder update(UUID ehrId, Folder folder, ObjectVersionId ifMatches);
+
+ /**
+ * delete the folder for Ehr with id equal ehrId
+ *
+ * @param ehrId
+ * @param ifMatches expected version before delete for optimistic looking
+ */
+ void delete(UUID ehrId, ObjectVersionId ifMatches);
+
+ /**
+ * Physical delete a folder with all History
+ *
+ * @param ehrId
+ * @param folderId
+ */
+ void adminDeleteFolder(UUID ehrId, UUID folderId);
+}
diff --git a/api/src/main/java/org/ehrbase/api/service/EhrService.java b/api/src/main/java/org/ehrbase/api/service/EhrService.java
index d8e3c0e914..5aa35c400e 100644
--- a/api/src/main/java/org/ehrbase/api/service/EhrService.java
+++ b/api/src/main/java/org/ehrbase/api/service/EhrService.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Stefan Spiska (Vitasystems GmbH) and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,165 +15,172 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.service;
import com.nedap.archie.rm.changecontrol.OriginalVersion;
+import com.nedap.archie.rm.changecontrol.VersionedObject;
import com.nedap.archie.rm.datavalues.quantity.datetime.DvDateTime;
-import com.nedap.archie.rm.ehr.EhrStatus;
-import com.nedap.archie.rm.ehr.VersionedEhrStatus;
import com.nedap.archie.rm.generic.RevisionHistory;
-import org.ehrbase.api.exception.DuplicateObjectException;
-import org.ehrbase.api.exception.InternalServerException;
-import org.ehrbase.response.ehrscape.CompositionFormat;
-import org.ehrbase.response.ehrscape.EhrStatusDto;
-
-import java.sql.Timestamp;
+import com.nedap.archie.rm.support.identification.ObjectVersionId;
+import java.time.OffsetDateTime;
import java.util.Optional;
import java.util.UUID;
+import javax.annotation.Nullable;
+import org.ehrbase.api.dto.EhrStatusDto;
+import org.ehrbase.api.exception.ObjectNotFoundException;
+import org.ehrbase.api.exception.StateConflictException;
+import org.ehrbase.api.exception.ValidationException;
+
+public interface EhrService {
+
+ /**
+ * Wrapper for {@link #create(UUID, EhrStatusDto)} response that contains the EHR id as well as the
+ * {@link EhrStatusDto} and it's {@link ObjectVersionId}. This prevents to call {@link #getEhrStatus(UUID)} with an
+ * additional DB round trip.
+ *
+ * @param ehrId ID of the created EHR
+ * @param statusVersionId the {@link ObjectVersionId} of the @{@link EhrStatusDto}
+ * @param status initial {@link EhrStatusDto} version
+ */
+ record EhrResult(UUID ehrId, ObjectVersionId statusVersionId, EhrStatusDto status) {}
-public interface EhrService extends BaseService {
/**
* Creates new EHR instance, with default settings and values when no status or ID is supplied.
- * @param status Optional, sets custom status
+ *
* @param ehrId Optional, sets custom ID
- * @return UUID of new EHR instance
- * @throws DuplicateObjectException when given party/subject already has an EHR
- * @throws InternalServerException when unspecified error occurs
+ * @param status Optional, sets custom status
+ * @return {@link EhrResult} of new EHR instance
+ * @throws StateConflictException when an EHR with the given id already exist
+ * @throws ValidationException when given status is invalid, e.g. not a valid openEHR RM object
*/
- UUID create(EhrStatus status, UUID ehrId);
+ EhrResult create(@Nullable UUID ehrId, @Nullable EhrStatusDto status);
- @Deprecated
- Optional getEhrStatusEhrScape(UUID ehrUuid, CompositionFormat format);
+ /**
+ * Update the EHR_STATUS linked to the given EHR
+ *
+ * @param ehrId ID of linked EHR
+ * @param status input EHR_STATUS
+ * @param contribution Optional ID of custom contribution. Can be null.
+ * @param audit Audit event id
+ * @return {@link EhrResult} of the updated status
+ * @throws ObjectNotFoundException if no EHR is found
+ * @throws ValidationException when given status is invalid, e.g. not a valid openEHR RM object
+ */
+ EhrResult updateStatus(UUID ehrId, EhrStatusDto status, ObjectVersionId targetObjId, UUID contribution, UUID audit);
/**
* Gets latest EHR_STATUS of the given EHR.
+ *
* @param ehrUuid EHR subject
- * @return Latest EHR_STATUS or empty
+ * @return Latest EHR_STATUS
+ * @throws ObjectNotFoundException if no EHR is found
*/
- Optional getEhrStatus(UUID ehrUuid);
+ EhrResult getEhrStatus(UUID ehrUuid);
/**
* Gets particular EHR_STATUS matching the given version Uid.
- * @param ehrUuid Root EHR
+ *
+ * @param ehrUuid Root EHR
* @param versionedObjectUid Given Uid of EHR_STATUS
- * @param version Given version of EHR_STATUS
+ * @param version Given version of EHR_STATUS
* @return Matching EHR_STATUS or empty
+ * @throws ObjectNotFoundException if no EHR is found
*/
- Optional> getEhrStatusAtVersion(UUID ehrUuid, UUID versionedObjectUid, int version);
+ Optional> getEhrStatusAtVersion(UUID ehrUuid, UUID versionedObjectUid, int version);
/**
- * Update the EHR_STATUS linked to the given EHR
- * @param ehrId ID of linked EHR
- * @param status input EHR_STATUS
- * @param contribution Optional ID of custom contribution. Can be null.
- * @return {@link Optional} containing the updated status on success
- * @throws org.ehrbase.api.exception.ObjectNotFoundException when given ehrId cannot be found
- * @throws org.ehrbase.api.exception.InvalidApiParameterException when given status is invalid, e.g. not a valid openEHR RM object
- */
- Optional updateStatus(UUID ehrId, EhrStatus status, UUID contribution);
-
- Optional findBySubject(String subjectId, String nameSpace);
-
- /**
- * Checks if there is an ehr entry existing for specified ehrId.
+ * Search for an EHR_STATUS based on the given subject id and namespace
*
- * @param ehrId - Target EHR identified
- * @return EHR with id exists
+ * @param subjectId ID of the EHR_STATUS subject
+ * @param nameSpace of the EHR_STATUS subject
+ * @return {@link Optional} of the matching EHR_STATUS
*/
- boolean doesEhrExist(UUID ehrId);
+ Optional findBySubject(String subjectId, String nameSpace);
/**
* Get latest version UID of an EHR_STATUS by given associated EHR UID.
+ *
* @param ehrId EHR ID
* @return EHR_STATUS version UID
+ * @throws ObjectNotFoundException if no EHR is found
*/
- String getLatestVersionUidOfStatus(UUID ehrId);
-
- DvDateTime getCreationTime(UUID ehrId);
+ ObjectVersionId getLatestVersionUidOfStatus(UUID ehrId);
/**
* Get version number of EHR_STATUS associated with given EHR UID at given timestamp.
- * @param ehrUid EHR UID
+ *
+ * @param ehrUid EHR UID
* @param timestamp Timestamp of point in time
* @return version number
+ * @throws ObjectNotFoundException if no EHR is found
+ */
+ ObjectVersionId getEhrStatusVersionByTimestamp(UUID ehrUid, OffsetDateTime timestamp);
+
+ /**
+ * Provides the creation time of the given EHR id.
+ *
+ * @param ehrId ID of the EHR
+ * @return {@link DvDateTime} of the EHR creation
*/
- Integer getEhrStatusVersionByTimestamp(UUID ehrUid, Timestamp timestamp);
+ DvDateTime getCreationTime(UUID ehrId);
/**
* Return True if a EHR with identifier ehrId exists.
* Implements has_ehr from the openEHR Platform Abstract Service Model.
+ *
* @param ehrId identifier to test
* @return True when existing, false if not
*/
boolean hasEhr(UUID ehrId);
- /**
- * Return True if a EHR_STATUS with identifier statusId exists.
- * @param statusId identifier to test
- * @return True when existing, false if not
- */
- boolean hasStatus(UUID statusId);
-
- /**
- * Helper to get (Versioned Object) Uid of EHR_STATUS of given EHR.
- * @param ehrUid Uid of EHR
- * @return UUID of corresponding EHR_STATUS
- */
- UUID getEhrStatusVersionedObjectUidByEhr(UUID ehrUid);
-
/**
* Gets version container EhrStatus associated with given EHR.
- * @param ehrUid Given EHR ID
+ *
+ * @param ehrId Given EHR ID
* @return Version container object
+ * @throws ObjectNotFoundException if no EHR is found
*/
- VersionedEhrStatus getVersionedEhrStatus(UUID ehrUid);
+ VersionedObject getVersionedEhrStatus(UUID ehrId);
/**
* Gets revision history of EhrStatus associated with given EHR.
- * @param ehrUid Given EHR ID
+ *
+ * @param ehrId Given EHR ID
* @return Revision history object
+ * @throws ObjectNotFoundException if no EHR is found
*/
- RevisionHistory getRevisionHistoryOfVersionedEhrStatus(UUID ehrUid);
+ RevisionHistory getRevisionHistoryOfVersionedEhrStatus(UUID ehrId);
/**
- * Reads the EHR entry from database and returns the ID of the root directory entry.
+ * Admin method to delete an EHR from the DB. See EHRbase Admin API specification for details.
*
- * @param ehrId - EHR id to find the directory for
- * @return UUID of the root directory if existing
+ * @param ehrId EHR to delete
*/
- UUID getDirectoryId(UUID ehrId);
+ void adminDeleteEhr(UUID ehrId);
/**
- * Removes the directory information from EHR table entry after deletion of the corresponding folder from
- * folders table. If there were no such folder it will return a successful deletion.
+ * Helper to directly get the external subject reference form the linked subject to given EHR.
*
- * @param ehrId - Target EHR id
- * @return Directory entry is now 'null'
- */
- boolean removeDirectory(UUID ehrId);
-
- /**
- * Admin method to delete an EHR from the DB. See EHRbase Admin API specification for details.
- * @param ehrId EHR to delete
+ * @param ehrId Given EHR ID
+ * @return Linked external subject reference or null
+ * @throws ObjectNotFoundException if no EHR is found
*/
- void adminDeleteEhr(UUID ehrId);
-
- void adminPurgePartyIdentified();
-
- void adminDeleteOrphanHistory();
+ String getSubjectExtRef(String ehrId);
/**
- * Helper to directly get the linked subject ID to given EHR.
- * @param ehrId Given EHR ID
- * @return Linked subject ID or null
+ * Checks if an EHR with the given UUID exists.
+ *
+ * @param ehrId EHR ID to check
+ * @throws ObjectNotFoundException if no EHR is found
*/
- UUID getSubjectUuid(String ehrId);
+ void checkEhrExists(UUID ehrId);
/**
- * Helper to directly get the external subject reference form the linked subject to given EHR.
- * @param ehrId Given EHR ID
- * @return Linked external subject reference or null
+ * Checks if the EHR with the given UUID is modifiable.
+ *
+ * @param ehrId EHR ID to check
+ * @throws ObjectNotFoundException if no EHR is found.
+ * @throws StateConflictException if the EHR is not modifiable.
*/
- String getSubjectExtRef(String ehrId);
+ void checkEhrExistsAndIsModifiable(UUID ehrId);
}
diff --git a/api/src/main/java/org/ehrbase/api/service/FolderService.java b/api/src/main/java/org/ehrbase/api/service/FolderService.java
deleted file mode 100644
index 8fbe57c96e..0000000000
--- a/api/src/main/java/org/ehrbase/api/service/FolderService.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
- * Copyright (c) 2019 Vitasystems GmbH and Hannover Medical School.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.api.service;
-
-import com.nedap.archie.rm.directory.Folder;
-import com.nedap.archie.rm.support.identification.ObjectVersionId;
-import org.ehrbase.api.exception.ObjectNotFoundException;
-import org.ehrbase.response.ehrscape.FolderDto;
-import org.ehrbase.response.ehrscape.StructuredString;
-import org.ehrbase.response.ehrscape.StructuredStringFormat;
-
-import java.sql.Timestamp;
-import java.util.Optional;
-import java.util.UUID;
-
-public interface FolderService extends BaseService, VersionedObjectService {
-
- /**
- * Retrieves a folder from database identified by object_version_uid and
- * extracts the given sub path of existing. If the object_version_uid does
- * not contain a version number the latest entry will be returned. A path
- * with common unix like root notation '/' will be treated as if there is
- * no path specified and the full tree will be returned.
- *
- * @param folderId - object_version_uid for target folder
- * @param path - Optional path to sub folder to extract
- * @return FolderDTO for further usage in upper layers
- */
- Optional get(ObjectVersionId folderId, String path);
-
- /**
- * Fetches the latest entry from database. This will be
- * @param folderId - object_version_uid for target folder
- * @param path - Optional path to sub folder to extract
- * @return FolderDTO for further usage in other layers
- */
- Optional getLatest(ObjectVersionId folderId, String path);
-
- /**
- * Fetches an folder entry from database identified by the root folder uid
- * and the given timestamp. If the current version has ben modified after
- * the given timestamp the folder will be searched inside the folder history
- * table.
- *
- * @param folderId - object_version_uid for target folder
- * @param timestamp - Timestamp of folder version to find
- * @param path - Optional path to sub folder to extract
- * @return FolderDTO for further usage in other layers
- */
- Optional getByTimeStamp(ObjectVersionId folderId, Timestamp timestamp, String path);
-
- /**
- * Serializes folder content from request body into a structured string
- * that can be used by database save mechanism to parse in into jsonb
- * format that will be saved at the database.
- *
- * @param folder - Folder to serialize
- * @param format - Source format of the folder
- * @return Structured string that can be parsed into jsonb
- */
- StructuredString serialize(Folder folder, StructuredStringFormat format);
-
- /**
- * Searches the last version number of a given folder entry from database.
- * This will be executed against the folder table which contains the latest
- * entry of a folder. The version will be extracted from there.
- *
- * @param folderId - Id of the folder to search for the latest version
- * @return Version number of the latest folder entry
- * @throws ObjectNotFoundException - Folder entry does not exist
- */
- Integer getLastVersionNumber(ObjectVersionId folderId);
-
-
- /**
- * Searches for the folder version that was the current version at the
- * given timestamp. If the entry from folder table has a later timestamp
- * the folder history will be queried to find the version at the timestamp
- *
- * @param folderId - Id of the folder to search the version
- * @param timestamp - Timestamp to look for the version number
- * @return - Version number that was actual at the timestamp
- * @throws ObjectNotFoundException - Folder entry does not exist at the time
- */
- Integer getVersionNumberForTimestamp(ObjectVersionId folderId, Timestamp timestamp);
-
- /**
- * Admin method to delete a Folder from the DB. See EHRbase Admin API specification for details.
- * @param folderId Folder to delete
- */
- void adminDeleteFolder(UUID folderId);
-}
diff --git a/api/src/main/java/org/ehrbase/api/service/QueryService.java b/api/src/main/java/org/ehrbase/api/service/QueryService.java
deleted file mode 100644
index 1a25530f79..0000000000
--- a/api/src/main/java/org/ehrbase/api/service/QueryService.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright (c) 2019 Stefan Spiska (Vitasystems GmbH) and Hannover Medical School.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.api.service;
-
-import org.ehrbase.api.definitions.QueryMode;
-import org.ehrbase.response.ehrscape.QueryDefinitionResultDto;
-import org.ehrbase.response.ehrscape.QueryResultDto;
-
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-public interface QueryService extends BaseService {
- /**
- * simple query where the full json expression contains both query (key = 'q') and optional
- * parameters (key = 'query-parameters')
- * @param queryString
- * @param queryMode
- * @param explain
- * @return
- */
- QueryResultDto query(String queryString, QueryMode queryMode, boolean explain);
-
- QueryResultDto query(String queryString, Map parameters, QueryMode queryMode, boolean explain);
-
- //=== DEFINITION: manage stored queries
- List retrieveStoredQueries(String fullyQualifiedName);
-
- QueryDefinitionResultDto retrieveStoredQuery(String qualifiedName, String version);
-
- //=== DEFINITION: manage stored queries
- QueryDefinitionResultDto createStoredQuery(String qualifiedName, String version, String queryString);
-
- QueryDefinitionResultDto updateStoredQuery(String qualifiedName, String version, String queryString);
-
- QueryDefinitionResultDto deleteStoredQuery(String qualifiedName, String version);
-
- //the audit variables
- Map> getAuditResultMap();
-}
diff --git a/api/src/main/java/org/ehrbase/api/service/StatusService.java b/api/src/main/java/org/ehrbase/api/service/StatusService.java
index 3c126c4e66..29c2bb8341 100644
--- a/api/src/main/java/org/ehrbase/api/service/StatusService.java
+++ b/api/src/main/java/org/ehrbase/api/service/StatusService.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2020 Axel Siebert (Vitasystems GmbH) and Hannover Medical School.
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -20,7 +20,7 @@
/**
* Status service to get information about the running EHRbase instance
*/
-public interface StatusService extends BaseService {
+public interface StatusService {
/**
* Returns information on the current operating system this EHRbase instance is running on.
@@ -64,9 +64,9 @@ public interface StatusService extends BaseService {
String getArchieVersion();
/**
- * Returns the current version of openEHR_SDK which has been used to build the running EHRbase instance.
+ * Returns the current version of ehrbase SDK which has been used to build the running EHRbase instance.
*
- * @return Current used openEHR_SDK version
+ * @return Current used ehrbase SDK version
*/
String getOpenEHR_SDK_Version();
}
diff --git a/api/src/main/java/org/ehrbase/api/service/StoredQueryService.java b/api/src/main/java/org/ehrbase/api/service/StoredQueryService.java
new file mode 100644
index 0000000000..701052e581
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/service/StoredQueryService.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.service;
+
+import java.util.List;
+import org.ehrbase.api.exception.ObjectNotFoundException;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.QueryDefinitionResultDto;
+
+public interface StoredQueryService {
+
+ // === DEFINITION: manage stored queries
+ List retrieveStoredQueries(String fullyQualifiedName);
+
+ QueryDefinitionResultDto retrieveStoredQuery(String qualifiedName, String version) throws ObjectNotFoundException;
+
+ // === DEFINITION: manage stored queries
+ QueryDefinitionResultDto createStoredQuery(String qualifiedName, String version, String queryString);
+
+ void deleteStoredQuery(String qualifiedName, String version);
+}
diff --git a/api/src/main/java/org/ehrbase/api/service/SystemService.java b/api/src/main/java/org/ehrbase/api/service/SystemService.java
new file mode 100644
index 0000000000..196043a025
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/service/SystemService.java
@@ -0,0 +1,22 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.service;
+
+public interface SystemService {
+ String getSystemId();
+}
diff --git a/api/src/main/java/org/ehrbase/api/service/TemplateService.java b/api/src/main/java/org/ehrbase/api/service/TemplateService.java
index 045536d0bf..3390efc61b 100644
--- a/api/src/main/java/org/ehrbase/api/service/TemplateService.java
+++ b/api/src/main/java/org/ehrbase/api/service/TemplateService.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Stefan Spiska (Vitasystems GmbH) and Jake Smolka (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,46 +15,51 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.service;
-import org.ehrbase.api.definitions.OperationalTemplateFormat;
-import org.ehrbase.response.ehrscape.CompositionFormat;
-import org.ehrbase.response.ehrscape.StructuredString;
-import org.ehrbase.response.ehrscape.TemplateMetaDataDto;
-
+import com.nedap.archie.rm.composition.Composition;
import java.util.List;
+import java.util.Map;
+import java.util.UUID;
+import org.ehrbase.api.definitions.OperationalTemplateFormat;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.TemplateMetaDataDto;
+import org.ehrbase.openehr.sdk.webtemplate.model.WebTemplate;
+import org.openehr.schemas.v1.OPERATIONALTEMPLATE;
-public interface TemplateService extends BaseService {
+public interface TemplateService {
List getAllTemplates();
- StructuredString buildExample(String templateId, CompositionFormat format);
+ Map findAllTemplateIds();
+
+ Composition buildExample(String templateId);
- org.ehrbase.webtemplate.model.WebTemplate findTemplate(String templateId);
+ WebTemplate findWebTemplate(String templateId);
/**
* Finds and returns the given operational template as string represented in requested format.
+ *
* @param templateId - Unique name of operational template
* @param format - As enum value from {@link OperationalTemplateFormat}
* @return
- * @throws RuntimeException When the template couldn't be found, the format isn't support or in case of another error.
+ * @throws RuntimeException When the template couldn't be found, the format isn't support or in
+ * case of another error.
*/
String findOperationalTemplate(String templateId, OperationalTemplateFormat format) throws RuntimeException;
- String create(String content);
+ String create(OPERATIONALTEMPLATE content);
/**
- * Deletes a given template from storage physically. The template is no longer available. If you try to delete a
- * template that is used in at least one Composition Entry or in one history entry the deletion will be rejected.
+ * Deletes a given template from storage physically. The template is no longer available. If you
+ * try to delete a template that is used in at least one Composition Entry or in one history entry
+ * the deletion will be rejected.
*
* @param templateId - Template id to delete, e.g. "IDCR Allergies List.v0"
- * @return - Whether the template could be removed or not
*/
- boolean adminDeleteTemplate(String templateId);
+ void adminDeleteTemplate(String templateId);
/**
- * Replaces a given template in the storage and updates the cache with the new template content. Will be rejected
- * if the template has referencing Compositions.
+ * Replaces a given template in the storage and updates the cache with the new template content.
+ * Will be rejected if the template has referencing Compositions.
*
* @param templateId - Tempalte id to update, e.g. "IDCR Allergies List.v0"
* @param content - New content to overwrite the template with
@@ -63,11 +68,11 @@ public interface TemplateService extends BaseService {
String adminUpdateTemplate(String templateId, String content);
/**
- * Deletes all templates from target template storage and returns the number of deleted templates. If any template
- * is referenced by at least one Composition the deletion will be rejected and no template will be removed.
+ * Deletes all templates from target template storage and returns the number of deleted templates.
+ * If any template is referenced by at least one Composition the deletion will be rejected and no
+ * template will be removed.
*
* @return - Number of deleted templates
*/
int adminDeleteAllTemplates();
-
}
diff --git a/api/src/main/java/org/ehrbase/api/service/TerminologyServer.java b/api/src/main/java/org/ehrbase/api/service/TerminologyServer.java
index c3c05e839a..9a4ba1ca73 100644
--- a/api/src/main/java/org/ehrbase/api/service/TerminologyServer.java
+++ b/api/src/main/java/org/ehrbase/api/service/TerminologyServer.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2020 Vitasystems GmbH, Hannover Medical School, and Luis Marco-Ruiz (Hannover Medical School).
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -19,8 +19,7 @@
import java.util.EnumSet;
import java.util.List;
-
-import com.nedap.archie.rm.datavalues.DvCodedText;
+import org.apache.commons.lang3.EnumUtils;
/***
*@Created by Luis Marco-Ruiz on Feb 12, 2020
@@ -29,83 +28,85 @@
* @param generic id type to specify the data type used for the identifier of the concept in the terminology server of choice.
* @param generic type for parameters that are custom to each operation implementation.
*/
-
public interface TerminologyServer {
-/**
- * Expands the value set identified by the provided ID.
- * @param valueSetId
- * @return Returns the list of concepts of type T that conform the expansion of the value set.
- */
- List expand(ID valueSetId);
-
- /**
- * Expands the value set identified by the provided ID.
- * @param valueSetId
- * @return Returns the list of concepts of type T that conform the expansion of the value set.
- */
- List expandWithParameters(ID valueSetId, @SuppressWarnings("unchecked") U...operationParams);//warning is ignored because the specific implementation will type the method avoiding possible heap pollution
-
- /**
- * Searches all the attributes associated with the concept that corresponds to the provided ID.
- * @param conceptId
- * @return A complex Object of type T that contains all the attributes directly associated to the concept identified by the provided ID.
- */
- T lookUp(ID conceptId);
- /**
- * Evaluates if the concept provided T belongs to the value set identified by the provided ID.
- * @param concept to evaluate.
- * @param valueSetId
- * @return true if the concept belongs to the specified value set.
- */
- Boolean validate(T concept, ID valueSetId);
-
- /**
- * Evaluates if the concept provided as one operationParams belongs to the value set provided as another operationParam.
- * @param dynamic list of parameters to perform the operation against an external terminology server.
- * @return true if the concept belongs to the specified value set.
- */
- Boolean validate(U...operationParams);
- /**
- * Evaluates if the concept B subsumes concept A.
- * @param concept that is subsumed by the concept in the second param.
- * @param concept that subsumes the concept in the first param.
- * @return {@link org.ehrbase.aql.compiler.tsclient.TerminologyServer.SubsumptionResult} indicating the result of the subsumption evaluation.
- */
- SubsumptionResult subsumes(T conceptA, T conceptB);
- /**
- *
- * Possible subsumption evaluation results.
- *
- */
- public enum SubsumptionResult{
-
- EQUIVALENT, SUBSUMES, SUBSUMEDBY, NOTSUBSUMED;
- }
-
- public enum TerminologyAdapter{
- FHIR("hl7.org/fhir/R4"),
- OCEAN("OTS.OCEANHEALTHSYSTEMS.COM"),
- BETTER("bts.better.care"),
- DTS4("dts4.apelon.com"),
- INDIZEN("cts2.indizen.com");
-
- private String adapterId;
- public String getAdapterId() {
- return adapterId;
- }
+ /**
+ * Expands the value set identified by the provided ID.
+ * @param valueSetId
+ * @return Returns the list of concepts of type T that conform the expansion of the value set.
+ */
+ List expand(ID valueSetId);
+
+ /**
+ * Expands the value set identified by the provided ID.
+ * @param valueSetId
+ * @return Returns the list of concepts of type T that conform the expansion of the value set.
+ */
+ List expandWithParameters(
+ ID valueSetId,
+ @SuppressWarnings("unchecked")
+ U... operationParams); // warning is ignored because the specific implementation will type the
+ // method avoiding possible heap pollution
+
+ /**
+ * Searches all the attributes associated with the concept that corresponds to the provided ID.
+ * @param conceptId
+ * @return A complex Object of type T that contains all the attributes directly associated to the concept identified by the provided ID.
+ */
+ T lookUp(ID conceptId);
+ /**
+ * Evaluates if the concept provided T belongs to the value set identified by the provided ID.
+ * @param concept to evaluate.
+ * @param valueSetId
+ * @return true if the concept belongs to the specified value set.
+ */
+ Boolean validate(T concept, ID valueSetId);
+
+ /**
+ * Evaluates if the concept provided as one operationParams belongs to the value set provided as another operationParam.
+ * @param operationParams dynamic list of parameters to perform the operation against an external terminology server.
+ * @return true if the concept belongs to the specified value set.
+ */
+ Boolean validate(U... operationParams);
+ /**
+ * Evaluates if the concept B subsumes concept A.
+ * @param conceptA concept that is subsumed by the concept in the second param.
+ * @param conceptB concept that subsumes the concept in the first param.
+ * @return {@link TerminologyServer.SubsumptionResult} indicating the result of the subsumption evaluation.
+ */
+ SubsumptionResult subsumes(T conceptA, T conceptB);
+ /**
+ *
+ * Possible subsumption evaluation results.
+ *
+ */
+ public enum SubsumptionResult {
+ EQUIVALENT,
+ SUBSUMES,
+ SUBSUMEDBY,
+ NOTSUBSUMED;
+ }
+
+ enum TerminologyAdapter {
+ FHIR("hl7.org/fhir/R4"),
+ OCEAN("OTS.OCEANHEALTHSYSTEMS.COM"),
+ BETTER("bts.better.care"),
+ DTS4("dts4.apelon.com"),
+ INDIZEN("cts2.indizen.com");
+
+ private String adapterId;
+
+ public String getAdapterId() {
+ return adapterId;
+ }
+
+ private static EnumSet supportedAdapters = EnumSet.of(FHIR);
+
+ TerminologyAdapter(String adapterId) {
+ this.adapterId = adapterId;
+ }
- private static EnumSet supportedAdapters = EnumSet.of(FHIR);
-
- private TerminologyAdapter(String adapterId) {
- this.adapterId = adapterId;
- }
-
- public static boolean isAdapterSupported(String adapterToCheck) {
- for(TerminologyAdapter ta: supportedAdapters) {
- if(ta.name().equals(adapterToCheck))
- {return true;} }
- return false;
- }
- }
-
+ public static boolean isAdapterSupported(String adapterToCheck) {
+ return EnumUtils.isValidEnum(TerminologyAdapter.class, adapterToCheck);
+ }
+ }
}
diff --git a/api/src/main/java/org/ehrbase/api/service/ValidationService.java b/api/src/main/java/org/ehrbase/api/service/ValidationService.java
index 8af9b5c6f9..1e4b33f946 100644
--- a/api/src/main/java/org/ehrbase/api/service/ValidationService.java
+++ b/api/src/main/java/org/ehrbase/api/service/ValidationService.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Vitasystems GmbH and Hannover Medical School.
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,11 +15,12 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.service;
import com.nedap.archie.rm.composition.Composition;
-import com.nedap.archie.rm.ehr.EhrStatus;
+import javax.annotation.Nonnull;
+import org.ehrbase.api.dto.EhrStatusDto;
+import org.ehrbase.openehr.sdk.response.dto.ContributionCreateDto;
/**
* ValidationService
@@ -32,29 +33,27 @@
*/
public interface ValidationService {
- /**
- * check a composition based on the operation template constraints
- *
- * @param templateID the template Id (String)
- * @param composition the RM composition
- * @throws Exception if the validation fails or the template cannot be resolved
- */
- void check(String templateID, Composition composition) throws Exception;
-
- /**
- * initially check if the composition is valid for further processing
- *
- * @param composition
- * @throws IllegalArgumentException
- */
- void check(Composition composition) throws Exception;
+ /**
+ * Initially check if the composition is valid for further processing.
+ *
+ * @param composition to validate
+ * @throws IllegalArgumentException in case the given composition is invalid.
+ */
+ void check(Composition composition);
- /**
- * initially check if ehrstatus is valid for further processing
- *
- * @param ehrStatus
- * @throws IllegalArgumentException
- */
- void check(EhrStatus ehrStatus);
+ /**
+ * Initially check if ehrStatus is valid for further processing.
+ *
+ * @param ehrStatus to validate
+ * @throws IllegalArgumentException in case the given ehrStatus is invalid.
+ */
+ void check(@Nonnull EhrStatusDto ehrStatus);
+ /**
+ * Initially check if contribution is valid for further processing.
+ *
+ * @param contribution to validate
+ * @throws IllegalArgumentException in case the given contribution is invalid.
+ */
+ void check(ContributionCreateDto contribution);
}
diff --git a/api/src/main/java/org/ehrbase/api/service/VersionedObjectService.java b/api/src/main/java/org/ehrbase/api/service/VersionedObjectService.java
index 6056ee6e9c..65283124fa 100644
--- a/api/src/main/java/org/ehrbase/api/service/VersionedObjectService.java
+++ b/api/src/main/java/org/ehrbase/api/service/VersionedObjectService.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2021 Jake Smolka (Hannover Medical School) and Vitasystems GmbH.
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,108 +15,122 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.api.service;
import com.nedap.archie.rm.archetyped.Locatable;
import com.nedap.archie.rm.support.identification.ObjectVersionId;
import java.util.Optional;
import java.util.UUID;
+import org.ehrbase.openehr.sdk.response.dto.ehrscape.FolderDto;
/**
* Service layer interface for versioned openEHR objects.
* Helps to always handle the necessary metadata and streamlines C(R)UD operations.
* Retrieval is
* @param Class of target versioned object, e.g. {@link com.nedap.archie.rm.directory.Folder}.
- * @param Class of return value of create and update methods. For instance, {@link org.ehrbase.response.ehrscape.FolderDto}. Will be wrapped in an {@link Optional}.
+ * @param Class of return value of create and update methods. For instance, {@link FolderDto}. Will be wrapped in an {@link Optional}.
*/
public interface VersionedObjectService {
- /**
- * Creation with given audit meta-data. Will create a new ad-hoc contribution.
- * @param ehrId EHR ID of context
- * @param objData Payload object data
- * @param systemId Audit system ID
- * @param committerId Audit committer ID
- * @param description Optional audit description text
- * @return {@link T} typed response wrapped in {@link Optional}
- */
- Optional create(UUID ehrId, T objData, UUID systemId, UUID committerId, String description);
-
- /**
- * Creation with a given contribution, and its audit meta-data.
- * @param ehrId EHR ID of context
- * @param objData Payload object data
- * @param contribution Contribution for operation
- * @return {@link T} typed response wrapped in {@link Optional}
- */
- Optional create(UUID ehrId, T objData, UUID contribution);
+ /**
+ * Creation with given audit meta-data. Will create a new ad-hoc contribution.
+ * @param ehrId EHR ID of context
+ * @param objData Payload object data
+ * @param systemId Audit system ID
+ * @param committerId Audit committer ID
+ * @param description Optional audit description text
+ * @return {@link T} typed response wrapped in {@link Optional}
+ */
+ @Deprecated(forRemoval = true)
+ default Optional create(UUID ehrId, T objData, UUID systemId, UUID committerId, String description) {
+ throw new UnsupportedOperationException();
+ }
- /**
- * Creation with default audit meta-data. Will create a new ad-hoc contribution.
- * @param ehrId EHR ID of context
- * @param objData Payload object data
- * @return {@link T} typed response wrapped in {@link Optional}
- */
- Optional create(UUID ehrId, T objData);
+ /**
+ * Creation with a given contribution, and its audit meta-data.
+ *
+ * @param ehrId EHR ID of context
+ * @param objData Payload object data
+ * @param contribution Contribution for operation
+ * @param audit
+ * @return {@link T} typed response wrapped in {@link Optional}
+ */
+ Optional create(UUID ehrId, T objData, UUID contribution, UUID audit);
- /**
- * Update with given audit meta-data. Will create a new ad-hoc contribution.
- * @param ehrId EHR ID of context
- * @param targetObjId ID of target object
- * @param objData Payload object data
- * @param systemId Audit system ID
- * @param committerId Audit committer ID
- * @param description Optional audit description text
- * @return {@link T} typed response wrapped in {@link Optional}
- */
- Optional update(UUID ehrId, ObjectVersionId targetObjId, T objData, UUID systemId, UUID committerId, String description);
+ /**
+ * Creation with default audit meta-data. Will create a new ad-hoc contribution.
+ * @param ehrId EHR ID of context
+ * @param objData Payload object data
+ * @return {@link T} typed response wrapped in {@link Optional}
+ */
+ Optional create(UUID ehrId, T objData);
- /**
- * Update with a given contribution, and its audit meta-data.
- * @param ehrId EHR ID of context
- * @param targetObjId ID of target object
- * @param objData Payload object data
- * @param contribution Contribution for operation
- * @return {@link T} typed response wrapped in {@link Optional}
- */
- Optional update(UUID ehrId, ObjectVersionId targetObjId, T objData, UUID contribution);
+ /**
+ * Update with given audit meta-data. Will create a new ad-hoc contribution.
+ * @param ehrId EHR ID of context
+ * @param targetObjId ID of target object
+ * @param objData Payload object data
+ * @param systemId Audit system ID
+ * @param committerId Audit committer ID
+ * @param description Optional audit description text
+ * @return {@link T} typed response wrapped in {@link Optional}
+ */
+ @Deprecated(forRemoval = true)
+ default Optional update(
+ UUID ehrId, ObjectVersionId targetObjId, T objData, UUID systemId, UUID committerId, String description) {
+ throw new UnsupportedOperationException();
+ }
- /**
- * Update with default audit meta-data. Will create a new ad-hoc contribution.
- * @param ehrId EHR ID of context
- * @param targetObjId ID of target object
- * @param objData Payload object data
- * @return {@link T} typed response wrapped in {@link Optional}
- */
- Optional update(UUID ehrId, ObjectVersionId targetObjId, T objData);
+ /**
+ * Update with a given contribution, and its audit meta-data.
+ *
+ * @param ehrId EHR ID of context
+ * @param targetObjId ID of target object
+ * @param objData Payload object data
+ * @param contribution Contribution for operation
+ * @param audit
+ * @return {@link T} typed response wrapped in {@link Optional}
+ */
+ Optional update(UUID ehrId, ObjectVersionId targetObjId, T objData, UUID contribution, UUID audit);
- /**
- * Deletion with given audit meta-data. Will create a new ad-hoc contribution.
- * @param ehrId EHR ID of context
- * @param targetObjId ID of target object
- * @param systemId Audit system ID
- * @param committerId Audit committer ID
- * @param description Optional audit description text
- * @return True if successful
- */
- boolean delete(UUID ehrId, ObjectVersionId targetObjId, UUID systemId, UUID committerId, String description);
+ /**
+ * Update with default audit meta-data. Will create a new ad-hoc contribution.
+ * @param ehrId EHR ID of context
+ * @param targetObjId ID of target object
+ * @param objData Payload object data
+ * @return {@link T} typed response wrapped in {@link Optional}
+ */
+ Optional update(UUID ehrId, ObjectVersionId targetObjId, T objData);
- /**
- * Deletion with a given contribution, and its audit meta-data.
- * @param ehrId EHR ID of context
- * @param targetObjId ID of target object
- * @param contribution Contribution for operation
- * @return True if successful
- */
- boolean delete(UUID ehrId, ObjectVersionId targetObjId, UUID contribution);
+ /**
+ * Deletion with given audit meta-data. Will create a new ad-hoc contribution.
+ *
+ * @param ehrId EHR ID of context
+ * @param targetObjId ID of target object
+ * @param systemId Audit system ID
+ * @param committerId Audit committer ID
+ * @param description Optional audit description text
+ */
+ @Deprecated(forRemoval = true)
+ default void delete(UUID ehrId, ObjectVersionId targetObjId, UUID systemId, UUID committerId, String description) {
+ throw new UnsupportedOperationException();
+ }
- /**
- * Deletion with default audit meta-data. Will create a new ad-hoc contribution.
- * @param ehrId EHR ID of context
- * @param targetObjId ID of target object
- * @return True if successful
- */
- boolean delete(UUID ehrId, ObjectVersionId targetObjId);
+ /**
+ * Deletion with a given contribution, and its audit meta-data.
+ *
+ * @param ehrId EHR ID of context
+ * @param targetObjId ID of target object
+ * @param contribution Contribution for operation
+ * @param audit
+ */
+ void delete(UUID ehrId, ObjectVersionId targetObjId, UUID contribution, UUID audit);
+ /**
+ * Deletion with default audit meta-data. Will create a new ad-hoc contribution.
+ *
+ * @param ehrId EHR ID of context
+ * @param targetObjId ID of target object
+ */
+ void delete(UUID ehrId, ObjectVersionId targetObjId);
}
diff --git a/api/src/main/java/org/ehrbase/api/service/experimental/ItemTagService.java b/api/src/main/java/org/ehrbase/api/service/experimental/ItemTagService.java
new file mode 100644
index 0000000000..5b968a80ed
--- /dev/null
+++ b/api/src/main/java/org/ehrbase/api/service/experimental/ItemTagService.java
@@ -0,0 +1,83 @@
+/*
+ * Copyright (c) 2019-2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.service.experimental;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.UUID;
+import javax.annotation.Nonnull;
+import org.ehrbase.api.dto.experimental.ItemTagDto;
+import org.ehrbase.api.dto.experimental.ItemTagDto.ItemTagRMType;
+
+/**
+ * Service manages the ITEM_TAG
+ * Class.
+ *
+ * All operations on tags are implemented as bulk operations.
+ */
+public interface ItemTagService {
+
+ /**
+ * Performs a bulk update/create operation for the given ItemTag into the tag list
+ * of the owner.
+ *
+ * @param ownerId Identifier of owner object, such as EHR.
+ * @param targetId VERSIONED_OBJECT<T> Identifier of target.
+ * @param targetType Type of the target object.
+ * @param itemTagsDto Content of the ItemTag containing the key, value parameter.
+ * @return tagUUIDs of the update/create ItemTags
+ */
+ List bulkUpsert(
+ @Nonnull UUID ownerId,
+ @Nonnull UUID targetId,
+ @Nonnull ItemTagRMType targetType,
+ @Nonnull List itemTagsDto);
+
+ /**
+ * Performs a bulk get operation for the given ItemTagIDs and/or
+ * keys.
+ *
+ * @param ownerId Identifier of owner object, such as EHR.
+ * @param targetId VERSIONED_OBJECT<T> Identifier of target.
+ * @param targetType Type of the target object.
+ * @param ids Identifier ItemTag to search for.
+ * @param keys ItemTag keys to search for.
+ * @return tags Matching the ownerId, targetId and optional ids, keys
+ */
+ List findItemTag(
+ @Nonnull UUID ownerId,
+ @Nonnull UUID targetId,
+ @Nonnull ItemTagRMType targetType,
+ @Nonnull Collection ids,
+ @Nonnull Collection keys);
+
+ /**
+ * Performs a bulk delete operation for the given ItemTagids. This method
+ * will simply return in cases where the given IDs does not exist.
+ *
+ * @param ownerId Identifier of owner object, such as EHR.
+ * @param targetId VERSIONED_OBJECT<T> Identifier of target.
+ * @param targetType Type of the target object.
+ * @param ids Identifier ItemTag to delete.
+ */
+ void bulkDelete(
+ @Nonnull UUID ownerId,
+ @Nonnull UUID targetId,
+ @Nonnull ItemTagRMType targetType,
+ @Nonnull Collection ids);
+}
diff --git a/api/src/main/java/org/ehrbase/api/util/VersionUidHelper.java b/api/src/main/java/org/ehrbase/api/util/VersionUidHelper.java
deleted file mode 100644
index ba33ee8c3f..0000000000
--- a/api/src/main/java/org/ehrbase/api/util/VersionUidHelper.java
+++ /dev/null
@@ -1,117 +0,0 @@
-/*
- * Copyright (c) 2019 Vitasystems GmbH and Hannover Medical School.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.api.util;
-
-
-import java.util.UUID;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class VersionUidHelper {
-
- public static final Pattern UUID_PATTERN = Pattern.compile("^([a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12})");
- public static final Pattern VERSION_PATTERN = Pattern.compile("::(\\d+)$");
- public static final Pattern SYSTEM_ID_PATTERN = Pattern.compile("::(\\w+.\\w+.\\w+)");
- public static final Pattern VERSION_UID_PATTERN =
- Pattern.compile(
- UUID_PATTERN.toString() +
- SYSTEM_ID_PATTERN.toString() +
- VERSION_PATTERN.toString()
- );
-
- private UUID uuid;
- private String systemId;
- private int version;
-
- public VersionUidHelper(String versionUid) {
- if (!VERSION_UID_PATTERN.matcher(versionUid).matches()) {
- throw new IllegalArgumentException("Version uid " + versionUid + " is not a valid version_uid,");
- }
- this.uuid = extractUUID(versionUid);
- this.systemId = extractSystemId(versionUid);
- this.version = extractVersion(versionUid);
- }
-
- public static boolean isVersionUid(String testString) {
- return VERSION_UID_PATTERN.matcher(testString).matches();
- }
-
- public static boolean isUUID(String testString) {
- return UUID_PATTERN.matcher(testString).matches();
- }
-
- public static boolean isSystemId(String testString) {
- return SYSTEM_ID_PATTERN.matcher(testString).matches();
- }
-
- public static boolean isVersion(String testString) {
- return VERSION_PATTERN.matcher(testString).matches();
- }
-
-
- public static UUID extractUUID(String versionUid) {
- Matcher matcher = UUID_PATTERN.matcher(versionUid);
- if (matcher.find()) {
- return UUID.fromString(matcher.group(1));
- }
- return null;
- }
-
-
- public static String extractSystemId(String versionUid) {
- Matcher matcher = SYSTEM_ID_PATTERN.matcher(versionUid);
- if (matcher.find()) {
- return matcher.group(1);
- }
- return null;
- }
-
-
- public static int extractVersion(String versionUid) {
- Matcher matcher = VERSION_PATTERN.matcher(versionUid);
- if (matcher.find()) {
- return Integer.parseInt(matcher.group(1));
- }
- return 1;
- }
-
- public String toString() {
- return this.uuid.toString() + "::" + this.systemId + "::" + this.version;
- }
-
- public UUID getUuid() {
- return this.uuid;
- }
- public void setUuid(UUID uuid) {
- this.uuid = uuid;
- }
- public String getSystemId() {
- return systemId;
- }
- public void setSystemId(String systemId) {
- this.systemId = systemId;
- }
- public int getVersion() {
- return version;
- }
- public void setVersion(int version) {
- this.version = version;
- }
-
-}
diff --git a/api/src/test/java/org/ehrbase/api/dto/AqlQueryRequestTest.java b/api/src/test/java/org/ehrbase/api/dto/AqlQueryRequestTest.java
new file mode 100644
index 0000000000..6d8f9aeb80
--- /dev/null
+++ b/api/src/test/java/org/ehrbase/api/dto/AqlQueryRequestTest.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright (c) 2025 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.api.dto;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.util.Map;
+import org.assertj.core.api.Assertions;
+import org.ehrbase.api.exception.IllegalAqlException;
+import org.ehrbase.openehr.sdk.aql.dto.AqlQuery;
+import org.junit.jupiter.api.Test;
+
+class AqlQueryRequestTest {
+
+ @Test
+ void prepareAqlQueryRequest() {
+
+ AqlQueryRequest request = AqlQueryRequest.prepare("SELECT e/ehr_id/value FROM EHR e", Map.of(), null, null);
+ assertThat(request.aqlQuery().render()).isEqualTo("SELECT e/ehr_id/value FROM EHR e");
+ assertThat(request.parameters()).isEmpty();
+ assertThat(request.fetch()).isNull();
+ assertThat(request.offset()).isNull();
+ }
+
+ @Test
+ void prepareInvalidAql() {
+
+ Map parameter = Map.of();
+ Assertions.assertThatThrownBy(
+ () -> AqlQueryRequest.prepare("SELECT invalid FROM INVALID i", parameter, null, null))
+ .isInstanceOf(IllegalAqlException.class);
+ }
+
+ @Test
+ void withLimitAndFetch() {
+
+ AqlQueryRequest request = new AqlQueryRequest(new AqlQuery(), Map.of(), 10L, 25L);
+ assertThat(request.parameters()).isEmpty();
+ assertThat(request.fetch()).isEqualTo(10L);
+ assertThat(request.offset()).isEqualTo(25L);
+ }
+}
diff --git a/api/src/test/java/org/ehrbase/api/util/VersionUidHelperTest.java b/api/src/test/java/org/ehrbase/api/util/VersionUidHelperTest.java
deleted file mode 100644
index d714c12853..0000000000
--- a/api/src/test/java/org/ehrbase/api/util/VersionUidHelperTest.java
+++ /dev/null
@@ -1,78 +0,0 @@
-package org.ehrbase.api.util;
-
-import java.util.UUID;
-
-import org.junit.Test;
-
-import static org.assertj.core.api.Assertions.assertThat;
-
-
-public class VersionUidHelperTest {
-
- static final String VALID_VERSION_UID = "1234abcd-5678-ef12-ab34-cd56ef78ab90::test.ehrbase.org::10";
-
- @Test
- public void acceptsValidVersionUid() {
- assertThat(VersionUidHelper.isVersionUid(VALID_VERSION_UID)).isTrue();
- }
-
- @Test
- public void rejectsInvalidVersionUid() {
- String testString = "1234invalid";
- assertThat(VersionUidHelper.isVersionUid(testString)).isFalse();
- }
-
- @Test
- public void acceptsValidUUID() {
- String testString = "abcd1234-ef56-ab78-cd90-ef12ab34cd56";
- assertThat(VersionUidHelper.isUUID(testString)).isTrue();
- }
-
- @Test
- public void rejectsInvalidUUID() {
- String testString = "invalid-uuid";
- assertThat(VersionUidHelper.isUUID(testString)).isFalse();
- }
-
- @Test
- public void acceptsValidSystemId() {
- String testString = "::test123.ehrbase.org";
- assertThat(VersionUidHelper.isSystemId(testString)).isTrue();
- }
-
- @Test
- public void rejectsInvalidSystemId() {
- String testString = "this/is/not/a/valid/system/id";
- assertThat(VersionUidHelper.isSystemId(testString)).isFalse();
- }
-
- @Test
- public void acceptsValidVersion() {
- String testString = "::562";
- assertThat(VersionUidHelper.isVersion(testString)).isTrue();
- }
-
- @Test
- public void rejectsInvalidVersion() {
- String testString = "::invalid123";
- assertThat(VersionUidHelper.isVersion(testString)).isFalse();
- }
-
- @Test
- public void extractsUUID() {
- UUID expected = UUID.fromString("1234abcd-5678-ef12-ab34-cd56ef78ab90");
- assertThat(VersionUidHelper.extractUUID(VALID_VERSION_UID)).isEqualTo(expected);
- }
-
- @Test
- public void extractsSystemId() {
- String expected = "test.ehrbase.org";
- assertThat(VersionUidHelper.extractSystemId(VALID_VERSION_UID)).isEqualTo(expected);
- }
-
- @Test
- public void extractsVersion() {
- int expected = 10;
- assertThat(VersionUidHelper.extractVersion(VALID_VERSION_UID)).isEqualTo(expected);
- }
-}
\ No newline at end of file
diff --git a/application/Dockerfile b/application/Dockerfile
deleted file mode 100644
index 6a7b9d3f90..0000000000
--- a/application/Dockerfile
+++ /dev/null
@@ -1,9 +0,0 @@
-FROM adoptopenjdk:11-jre-openj9
-ARG JAR_FILE
-ENV AUTH_TYPE="BASIC"
-ENV AUTH_USER="ehrbase-user"
-ENV AUTH_PASSWORD="SuperSecretPassword"
-COPY application/target/${JAR_FILE} app.jar
-RUN mkdir -p file_repo/knowledge/archetypes && mkdir -p file_repo/knowledge/operational_templates && mkdir -p file_repo/knowledge/templates
-EXPOSE 8080
-ENTRYPOINT ["java","-Dspring.profiles.active=docker", "-Dsecurity.authType=${AUTH_TYPE}", "-Dsecurity.authUser=${AUTH_USER}", "-Dsecurity.authPassword=${AUTH_PASSWORD}" ,"-jar","/app.jar"]
diff --git a/application/pom.xml b/application/pom.xml
index 36bc6df005..92a21b2a37 100644
--- a/application/pom.xml
+++ b/application/pom.xml
@@ -1,7 +1,7 @@
-
- 4.0.0
+ 4.0.0
-
- org.ehrbase.openehr
- server
- 0.20.0-SNAPSHOT
-
+
+ org.ehrbase.openehr
+ server
+ 2.23.0-SNAPSHOT
+
- application
+ application
+ jar
+ EHRbase Application
-
- vitasystems/hip-openehr
-
+
+ false
+
-
-
- org.springframework.boot
- spring-boot-starter-web
-
-
- org.springframework.boot
- spring-boot-starter-actuator
-
-
- org.springframework.boot
- spring-boot-starter-cache
-
-
- org.springframework.boot
- spring-boot-starter-tomcat
- provided
-
-
- org.springframework.boot
- spring-boot-starter-security
-
-
- org.springframework.boot
- spring-boot-starter-oauth2-resource-server
-
-
- org.springframework.boot
- spring-boot-configuration-processor
- true
-
-
- org.springframework.boot
- spring-boot-starter-jdbc
-
-
- org.springframework.boot
- spring-boot-starter-validation
-
-
- io.micrometer
- micrometer-registry-prometheus
-
-
- org.flywaydb
- flyway-core
-
-
- org.ehrbase.openehr
- service
-
-
- org.ehrbase.openehr
- rest-ehr-scape
-
-
- org.ehrbase.openehr
- api
-
-
- org.ehrbase.openehr.sdk
- serialisation
-
-
- org.ehrbase.openehr
- rest-openehr
-
-
- org.ehrbase.openehr
- base
-
-
- org.springdoc
- springdoc-openapi-ui
-
-
- net.bull.javamelody
- javamelody-spring-boot-starter
-
-
- org.springframework.boot
- spring-boot-starter-test
- test
-
-
- org.junit.vintage
- junit-vintage-engine
- test
-
-
- org.springframework.security
- spring-security-oauth2-client
- test
-
-
- org.springframework.security
- spring-security-test
- test
-
-
- org.ehrbase.openehr.sdk
- test-data
- test
-
-
+
+
+ org.ehrbase.openehr
+ configuration
+
+
+ org.ehrbase.openehr
+ cli
+
+
-
-
-
- org.springframework.boot
- spring-boot-maven-plugin
-
-
-
- repackage
-
-
- org.ehrbase.application.EhrBase
-
-
-
-
-
- com.spotify
- dockerfile-maven-plugin
-
-
-
-
-
-
-
\ No newline at end of file
+
+ ehrbase
+
+
+
+ src/main/resources
+ true
+
+
+
+
+
+ org.springframework.boot
+ spring-boot-maven-plugin
+
+
+
+ repackage
+
+
+
+
+ org.ehrbase.application.EhrBase
+ ${ehrbase.spring-boot-plugin.skip}
+
+
+
+
+
diff --git a/application/src/main/java/org/ehrbase/application/EhrBase.java b/application/src/main/java/org/ehrbase/application/EhrBase.java
index 4d2c97c36c..dd7292e340 100644
--- a/application/src/main/java/org/ehrbase/application/EhrBase.java
+++ b/application/src/main/java/org/ehrbase/application/EhrBase.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2019 Stefan Spiska (Vitasystems GmbH) and Hannover Medical School.
+ * Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
@@ -7,7 +7,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,30 +15,20 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package org.ehrbase.application;
-import org.ehrbase.ServiceModuleConfiguration;
-import org.ehrbase.rest.RestModuleConfiguration;
-import org.ehrbase.rest.ehrscape.RestEHRScapeModuleConfiguration;
+import java.util.Arrays;
+import org.ehrbase.application.cli.EhrBaseCli;
+import org.ehrbase.application.server.EhrBaseServer;
+import org.ehrbase.cli.CliRunner;
import org.springframework.boot.SpringApplication;
-import org.springframework.boot.actuate.autoconfigure.security.servlet.ManagementWebSecurityAutoConfiguration;
-import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.boot.autoconfigure.security.servlet.SecurityAutoConfiguration;
-import org.springframework.context.annotation.Import;
-@SpringBootApplication(exclude = {
- SecurityAutoConfiguration.class,
- ManagementWebSecurityAutoConfiguration.class
-})
-@Import({
- ServiceModuleConfiguration.class,
- RestEHRScapeModuleConfiguration.class,
- RestModuleConfiguration.class,
-})
public class EhrBase {
- public static void main(String[] args) {
- SpringApplication.run(EhrBase.class, args);
- }
+ public static void main(String[] args) {
+
+ SpringApplication app =
+ Arrays.asList(args).contains(CliRunner.CLI) ? EhrBaseCli.build(args) : EhrBaseServer.build(args);
+ app.run(args);
+ }
}
diff --git a/application/src/main/java/org/ehrbase/application/abac/AbacConfig.java b/application/src/main/java/org/ehrbase/application/abac/AbacConfig.java
deleted file mode 100644
index 0fe4fb9060..0000000000
--- a/application/src/main/java/org/ehrbase/application/abac/AbacConfig.java
+++ /dev/null
@@ -1,164 +0,0 @@
-/*
- * Copyright (c) 2021 Jake Smolka (Hannover Medical School) and Vitasystems GmbH.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.abac;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-import org.apache.http.HttpResponse;
-import org.apache.http.client.HttpClient;
-import org.apache.http.client.methods.HttpPost;
-import org.apache.http.entity.ContentType;
-import org.apache.http.entity.StringEntity;
-import org.ehrbase.api.exception.InternalServerException;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.boot.context.properties.EnableConfigurationProperties;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-
-import java.io.IOException;
-import java.net.URI;
-import java.util.Map;
-
-@ConditionalOnProperty(name = "abac.enabled")
-@Configuration
-@EnableConfigurationProperties
-@ConfigurationProperties(prefix = "abac")
-@SuppressWarnings("java:S6212")
-public class AbacConfig {
-
- public enum AbacType {
- EHR, EHR_STATUS, COMPOSITION, CONTRIBUTION, QUERY
- }
-
- public enum PolicyParameter {
- ORGANIZATION, PATIENT, TEMPLATE
- }
-
- static class Policy {
- private String name;
- private PolicyParameter[] parameters;
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public PolicyParameter[] getParameters() {
- return parameters;
- }
-
- public void setParameters(PolicyParameter[] parameters) {
- this.parameters = parameters;
- }
- }
-
- private URI server;
- private String organizationClaim;
- private String patientClaim;
- private Map policy;
-
- @Bean
- public AbacCheck abacCheck(HttpClient httpClient) {
- return new AbacCheck(httpClient);
- }
-
- public URI getServer() {
- return server;
- }
-
- public void setServer(URI server) {
- this.server = server;
- }
-
- public String getOrganizationClaim() {
- return organizationClaim;
- }
-
- public void setOrganizationClaim(String organizationClaim) {
- this.organizationClaim = organizationClaim;
- }
-
- public String getPatientClaim() {
- return patientClaim;
- }
-
- public void setPatientClaim(String patientClaim) {
- this.patientClaim = patientClaim;
- }
-
- public Map getPolicy() {
- return policy;
- }
-
- public void setPolicy(
- Map policy) {
- this.policy = policy;
- }
-
- /*
- This class has only some extracted methods to handle ABAC server connection and requests.
- It is mainly a separate class so it can be overwritten by a MockBean in the context of tests.
- */
- public static class AbacCheck {
-
- private final HttpClient httpClient;
-
- public AbacCheck(HttpClient httpClient) {
- this.httpClient = httpClient;
- }
-
- /**
- * Helper to build and send the actual HTTP request to the ABAC server.
- *
- * @param url URL for ABAC server request
- * @param bodyMap Map of attributes for the request
- * @return HTTP response
- * @throws IOException On error during attribute or HTTP handling
- */
- public boolean execute(String url, Map bodyMap)
- throws IOException {
- return evaluateResponse(send(url, bodyMap));
- }
-
- private HttpResponse send(String url, Map bodyMap)
- throws IOException {
- // convert bodyMap to JSON
- ObjectMapper objectMapper = new ObjectMapper();
- String requestBody = objectMapper
- .writerWithDefaultPrettyPrinter()
- .writeValueAsString(bodyMap);
-
- HttpPost request = new HttpPost(url);
- request.setEntity(new StringEntity(requestBody, ContentType.APPLICATION_JSON));
-
- try {
- return httpClient.execute(request);
- } catch (Exception e) {
- throw new InternalServerException("ABAC: Connection with ABAC server failed. Check configuration. Error: " + e.getMessage());
- }
- }
-
- private boolean evaluateResponse(HttpResponse response) {
- return response.getStatusLine().getStatusCode() == 200;
- }
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/abac/CustomMethodSecurityExpressionHandler.java b/application/src/main/java/org/ehrbase/application/abac/CustomMethodSecurityExpressionHandler.java
deleted file mode 100644
index 738d70ac12..0000000000
--- a/application/src/main/java/org/ehrbase/application/abac/CustomMethodSecurityExpressionHandler.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Copyright (c) 2021 Jake Smolka (Hannover Medical School) and Vitasystems GmbH.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.abac;
-
-import org.aopalliance.intercept.MethodInvocation;
-import org.ehrbase.api.service.CompositionService;
-import org.ehrbase.api.service.ContributionService;
-import org.ehrbase.api.service.EhrService;
-import org.ehrbase.application.abac.AbacConfig.AbacCheck;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
-import org.springframework.context.annotation.Lazy;
-import org.springframework.security.access.expression.method.DefaultMethodSecurityExpressionHandler;
-import org.springframework.security.access.expression.method.MethodSecurityExpressionOperations;
-import org.springframework.security.authentication.AuthenticationTrustResolver;
-import org.springframework.security.authentication.AuthenticationTrustResolverImpl;
-import org.springframework.security.core.Authentication;
-import org.springframework.stereotype.Component;
-
-@ConditionalOnProperty(name = "abac.enabled")
-@Component
-public class CustomMethodSecurityExpressionHandler extends DefaultMethodSecurityExpressionHandler {
-
- private final AbacConfig abacConfig;
- private final AuthenticationTrustResolver trustResolver =
- new AuthenticationTrustResolverImpl();
- private final CompositionService compositionService;
- private final ContributionService contributionService;
- private final EhrService ehrService;
- private final AbacCheck abacCheck;
-
- @Lazy
- public CustomMethodSecurityExpressionHandler(AbacConfig abacConfig,
- CompositionService compositionService,
- ContributionService contributionService, EhrService ehrService,
- AbacCheck abacCheck) {
- this.abacConfig = abacConfig;
- this.compositionService = compositionService;
- this.contributionService = contributionService;
- this.ehrService = ehrService;
- this.abacCheck = abacCheck;
- }
-
- @Override
- protected MethodSecurityExpressionOperations createSecurityExpressionRoot(
- Authentication authentication, MethodInvocation invocation) {
- CustomMethodSecurityExpressionRoot root =
- new CustomMethodSecurityExpressionRoot(authentication, abacConfig, abacCheck);
- root.setCompositionService(this.compositionService);
- root.setContributionService(this.contributionService);
- root.setEhrService(this.ehrService);
- root.setPermissionEvaluator(getPermissionEvaluator());
- root.setTrustResolver(this.trustResolver);
- root.setRoleHierarchy(getRoleHierarchy());
- return root;
- }
-
-}
diff --git a/application/src/main/java/org/ehrbase/application/abac/CustomMethodSecurityExpressionRoot.java b/application/src/main/java/org/ehrbase/application/abac/CustomMethodSecurityExpressionRoot.java
deleted file mode 100644
index c55945be4f..0000000000
--- a/application/src/main/java/org/ehrbase/application/abac/CustomMethodSecurityExpressionRoot.java
+++ /dev/null
@@ -1,547 +0,0 @@
-/*
- * Copyright (c) 2021 Jake Smolka (Hannover Medical School) and Vitasystems GmbH.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.abac;
-
-import com.nedap.archie.rm.composition.Composition;
-import com.nedap.archie.rm.support.identification.ObjectVersionId;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.Optional;
-import java.util.Set;
-import java.util.UUID;
-import org.ehrbase.api.exception.InternalServerException;
-import org.ehrbase.api.service.CompositionService;
-import org.ehrbase.api.service.ContributionService;
-import org.ehrbase.api.service.EhrService;
-import org.ehrbase.application.abac.AbacConfig.AbacCheck;
-import org.ehrbase.application.abac.AbacConfig.AbacType;
-import org.ehrbase.application.abac.AbacConfig.Policy;
-import org.ehrbase.application.abac.AbacConfig.PolicyParameter;
-import org.ehrbase.aql.compiler.AuditVariables;
-import org.ehrbase.response.ehrscape.CompositionDto;
-import org.ehrbase.response.ehrscape.CompositionFormat;
-import org.ehrbase.response.openehr.OriginalVersionResponseData;
-import org.ehrbase.rest.BaseController;
-import org.ehrbase.rest.openehr.OpenehrQueryController;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.MediaType;
-import org.springframework.http.ResponseEntity;
-import org.springframework.security.access.expression.SecurityExpressionRoot;
-import org.springframework.security.access.expression.method.MethodSecurityExpressionOperations;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.oauth2.server.resource.authentication.JwtAuthenticationToken;
-
-/**
- * Implementation of custom security expression, to be used in e.g. @PreAuthorize(..) to allow ABAC
- * requests.
- */
-public class CustomMethodSecurityExpressionRoot extends SecurityExpressionRoot implements
- MethodSecurityExpressionOperations {
-
- static final String ORGANIZATION = "organization";
- static final String PATIENT = "patient";
- static final String TEMPLATE = "template";
- static final String PRE = "pre";
- static final String POST = "post";
-
- private final AbacConfig abacConfig;
- private final AbacCheck abacCheck;
- private CompositionService compositionService;
- private ContributionService contributionService;
- private EhrService ehrService;
- private Object filterObject;
- private Object returnObject;
-
- public CustomMethodSecurityExpressionRoot(Authentication authentication,
- AbacConfig abacConfig, AbacCheck abacCheck) {
- super(authentication);
- this.abacConfig = abacConfig;
- this.abacCheck = abacCheck;
- }
-
- public void setCompositionService(CompositionService compositionService) {
- this.compositionService = compositionService;
- }
-
- public void setContributionService(ContributionService contributionService) {
- this.contributionService = contributionService;
- }
-
- public void setEhrService(EhrService ehrService) {
- this.ehrService = ehrService;
- }
-
- /**
- * Custom SpEL expression to be used to check if the remote ABAC allows the operation by given
- * data. For @PostAuthorize cases.
- *
- * @param type Type of scope's resource
- * @param subject Subject ID from the current EHR context
- * @param payload Payload object, either request's input or response's output
- * @param contentType Content type from the scope
- * @return True if ABAC authorizes given attributes
- * @throws IOException On parsing error
- * @throws InterruptedException On error while communicating with the ABAC server
- */
- public boolean checkAbacPost(String type, String subject, Object payload,
- String contentType)
- throws IOException, InterruptedException {
-
- return checkAbac(type, subject, payload, contentType, POST);
- }
-
- public boolean checkAbacPostQuery(Object payload)
- throws IOException, InterruptedException {
-
- return checkAbac(OpenehrQueryController.QUERY, null, payload, null, POST);
- }
-
- /**
- * Custom SpEL expression to be used to check if the remote ABAC allows the operation by given
- * data. For @PreAuthorize cases.
- *
- * @param type Type of scope's resource
- * @param subject Subject ID from the current EHR context
- * @param payload Payload object, either request's input or response's output
- * @param contentType Content type from the scope
- * @return True if ABAC authorizes given attributes
- * @throws IOException On parsing error
- * @throws InterruptedException On error while communicating with the ABAC server
- */
- public boolean checkAbacPre(String type, String subject, Object payload,
- String contentType)
- throws IOException, InterruptedException {
-
- // @PreAuthorize will give different types, e.g. String (for composition), EhrStatus,...
- // so just pipe it through to templateHandling and make by-type handling there
-
- return checkAbac(type, subject, payload, contentType, PRE);
- }
-
- /*
- Short call with less parameters.
- */
- public boolean checkAbacPre(String type, String subject)
- throws IOException, InterruptedException {
-
- return checkAbac(type, subject, null, null, PRE);
- }
-
- /**
- * Builds the ABAC request with given data and evaluates the ABAC's response.
- * @param type Object type of scope
- * @param subject Subject ID from the current EHR context
- * @param payload Payload object, either request's input or response's output
- * @param contentType Content type from the scope
- * @param authType Pre- or PostAuthorize, determines payload style (string or object)
- * @return True if ABAC returns a positive feedback, False if not
- * @throws IOException On parsing error
- * @throws InterruptedException On error while communicating with the ABAC server
- */
- private boolean checkAbac(String type, String subject, Object payload,
- String contentType, String authType) throws IOException, InterruptedException {
- // Set type specific settings:
- // Extract and set parameters according to which parameters are configured
- List policyParameters;
- // Build abac server request, depending on type
- var requestUrl = abacConfig.getServer().toString();
-
- Map policy = abacConfig.getPolicy();
-
- switch (type) {
- case BaseController.EHR:
- policyParameters = Arrays.asList(policy.get(AbacType.EHR).getParameters());
- requestUrl = requestUrl.concat(policy.get(AbacType.EHR).getName());
- break;
- case BaseController.EHR_STATUS:
- policyParameters = Arrays.asList(policy.get(AbacType.EHR_STATUS).getParameters());
- requestUrl = requestUrl.concat(policy.get(AbacType.EHR_STATUS).getName());
- break;
- case BaseController.COMPOSITION:
- policyParameters = Arrays.asList(policy.get(AbacType.COMPOSITION).getParameters());
- requestUrl = requestUrl.concat(policy.get(AbacType.COMPOSITION).getName());
- break;
- case BaseController.CONTRIBUTION:
- policyParameters = Arrays.asList(policy.get(AbacType.CONTRIBUTION).getParameters());
- requestUrl = requestUrl.concat(policy.get(AbacType.CONTRIBUTION).getName());
- break;
- case BaseController.QUERY:
- policyParameters = Arrays.asList(policy.get(AbacType.QUERY).getParameters());
- requestUrl = requestUrl.concat(policy.get(AbacType.QUERY).getName());
- break;
- default:
- throw new InternalServerException("ABAC: Invalid type given from Pre- or PostAuthorize");
- }
-
- // Check and extract JWT
- var jwt = getJwtAuthenticationToken(this.authentication);
-
- // Request body map. will result in simple JSON like {"patient_id":"...", ...}
- // but requires "Object" for template handling, which can have a Set for multiple IDs
- Map requestMap = new HashMap<>();
-
- // Organization attribute handling
- if (policyParameters.contains(PolicyParameter.ORGANIZATION)) {
- organizationHandling(jwt, requestMap);
- }
-
- // Patient attribute handling
- if (policyParameters.contains(PolicyParameter.PATIENT)) {
- // populate requestMap, but also already check if subject from token and request matches
- boolean patientMatch = patientHandling(jwt, subject, requestMap, type, payload);
- if (!patientMatch) {
- // doesn't match -> requesting data for patient X with token for patient Y
- return false;
- }
- }
-
- // Extract template ID from object of type "type"
- if (policyParameters.contains(PolicyParameter.TEMPLATE)) {
- templateHandling(type, payload, contentType, requestMap, authType);
- }
-
- // Final check, if request would be empty even though params were configured to be used
- if ((policyParameters.contains(PolicyParameter.ORGANIZATION) ||
- policyParameters.contains(PolicyParameter.PATIENT) ||
- policyParameters.contains(PolicyParameter.TEMPLATE))
- && requestMap.size() == 0) {
- throw new InternalServerException("ABAC: Parameters were configured, but request parameters "
- + "are empty.");
- }
-
- return abacCheckRequest(requestUrl, requestMap);
- }
-
- /**
- * Handles organization ID extraction. Uses token's claim.
- * @param jwt Token
- * @param requestMap ABAC request attribute map to add the result
- */
- private void organizationHandling(JwtAuthenticationToken jwt, Map requestMap) {
- if (jwt.getTokenAttributes().containsKey(abacConfig.getOrganizationClaim())) {
- String orgaId = (String) jwt.getTokenAttributes().get(abacConfig.getOrganizationClaim());
- requestMap.put(ORGANIZATION, orgaId);
- } else {
- // organization configured but claim not available
- throw new IllegalArgumentException("ABAC use of an organization claim is configured but "
- + "can't be retrieved from the given JWT.");
- }
- }
-
- /**
- * Handles patient ID extraction. Either uses token's claim or EHR's subject.
- * @param jwt Token
- * @param subject Subject from EHR
- * @param requestMap ABAC request attribute map to add the result
- */
- private boolean patientHandling(JwtAuthenticationToken jwt, String subject,
- Map requestMap, String type, Object payload) {
-
- if (!jwt.getTokenAttributes().containsKey(abacConfig.getPatientClaim())) {
- throw new IllegalArgumentException("ABAC: Patient parameter configured, but no claim "
- + "attribute available.");
- }
- String tokenPatient = (String) jwt.getTokenAttributes().get(abacConfig.getPatientClaim());
-
- if (type.equals(BaseController.QUERY)) {
- // special case of type QUERY, where multiple subjects are possible
- if (payload instanceof Map) {
- if (((Map) payload).containsKey(AuditVariables.EHR_PATH)) {
- Set ehrs = (Set) ((Map) payload).get(AuditVariables.EHR_PATH);
- Set patientSet = new HashSet<>();
- for (UUID ehr : ehrs) {
- String subjectId = ehrService.getSubjectExtRef(ehr.toString());
- // check if patient token is available and if it matches OR internal reference is null
- if (tokenPatient.equals(subjectId) || subjectId == null) {
- // matches OR EHR's external ref is null, so add our subject from token
- patientSet.add(tokenPatient);
- } else {
- // doesn't match -> requesting data for patient X with token for patient Y
- return false;
- }
-
- }
- // put result set into the requestMap and exit
- requestMap.put(PATIENT, patientSet);
- return true;
- } else {
- throw new InternalServerException("ABAC: AQL audit patient data unavailable.");
- }
- } else {
- throw new InternalServerException("ABAC: AQL audit patient data malformed.");
- }
- }
-
- // in all other cases just handle the one String "subject" variable
- // check if matches (to block accessing patient X with token from patient Y) OR null reference
- if (tokenPatient.equals(subject) || subject == null) {
- // matches OR EHR's external ref is null, so add our subject from token
- requestMap.put(PATIENT, tokenPatient);
- } else {
- // doesn't match -> requesting data for patient X with token for patient Y
- return false;
- }
-
- return true;
- }
-
- /**
- * Handles template ID extraction of specific payload.
- *
- * Payload will be a response body string, in case of @PostAuthorize.
- *
- * Payload will be request body string, or already deserialized object (e.g. EhrStatus), in case of @PreAuthorize.
- * @param type Object type of scope
- * @param payload Payload object, either request's input or response's output
- * @param contentType Content type from the scope
- * @param requestMap ABAC request attribute map to add the result
- * @param authType Pre- or PostAuthorize, determines payload style (string or object)
- */
- private void templateHandling(String type, Object payload, String contentType, Map requestMap, String authType) {
- switch (type) {
- case BaseController.EHR:
- throw new IllegalArgumentException("ABAC: Unsupported configuration: Can't set template ID for EHR type.");
- case BaseController.EHR_STATUS:
- throw new IllegalArgumentException("ABAC: Unsupported configuration: Can't set template ID for EHR_STATUS type.");
- case BaseController.COMPOSITION:
- String content = "";
- if (authType.equals(POST)) {
- // @PostAuthorize gives a ResponseEntity type for "returnObject", so payload is of that type
- if (((ResponseEntity) payload).hasBody()) {
- Object body = ((ResponseEntity) payload).getBody();
- // can have "No content" here (even with some data in the body) if the compo was (logically) deleted
- if (((ResponseEntity) payload).getStatusCode().equals(HttpStatus.NO_CONTENT)) {
- if (body instanceof Map) {
- Object error = ((Map) body).get("error");
- if (error != null) {
- if (((String) error).contains("delet")) {
- //composition was deleted, so nothing to check here, skip
- break;
- }
- }
- }
- throw new InternalServerException("ABAC: Unexpected empty response from composition reuquest");
- }
- if (body instanceof OriginalVersionResponseData) {
- // case of versioned_composition --> fast path, because template is easy to get
- if (((OriginalVersionResponseData) body).getData() instanceof Composition) {
- String template = Objects.requireNonNull(
- ((Composition) ((OriginalVersionResponseData) body).getData())
- .getArchetypeDetails().getTemplateId()).getValue();
- requestMap.put(TEMPLATE, template);
- break; // special case, so done here, exit
- }
- } else if (body instanceof String) {
- content = (String) body;
- } else {
- throw new InternalServerException("ABAC: unexpected composition payload object");
- }
- } else {
- throw new InternalServerException("ABAC: unexpected empty response body");
- }
- } else if (authType.equals(PRE)) {
- try {
- // try if this is the Delete composition case. Payload would contain the UUID of the compo.
- ObjectVersionId versionId = new ObjectVersionId((String) payload);
- UUID compositionUid = UUID.fromString(versionId.getRoot().getValue());
- Optional compoDto = compositionService.retrieve(compositionUid, null);
- if (compoDto.isPresent()) {
- Composition c = compoDto.get().getComposition();
- requestMap.put(TEMPLATE, c.getArchetypeDetails().getTemplateId().getValue());
- break; // special case, so done here, exit
- } else {
- throw new InternalServerException(
- "ABAC: unexpected empty response from composition delete");
- }
- } catch (IllegalArgumentException e) {
- // if not an UUID, the payload is a composition itself so continue
- content = (String) payload;
- }
- } else {
- throw new InternalServerException("ABAC: invalid auth type given.");
- }
- String templateId;
- if (MediaType.parseMediaType(contentType).isCompatibleWith(MediaType.APPLICATION_JSON)) {
- templateId = compositionService.getTemplateIdFromInputComposition(content, CompositionFormat.JSON);
- } else if (MediaType.parseMediaType(contentType).isCompatibleWith(MediaType.APPLICATION_XML)) {
- templateId = compositionService.getTemplateIdFromInputComposition(content, CompositionFormat.XML);
- } else {
- throw new IllegalArgumentException("ABAC: Only JSON and XML composition are supported.");
- }
- requestMap.put(TEMPLATE, templateId);
- break;
- case BaseController.CONTRIBUTION:
- CompositionFormat format;
- if (MediaType.parseMediaType(contentType).isCompatibleWith(MediaType.APPLICATION_JSON)) {
- format = CompositionFormat.JSON;
- } else if (MediaType.parseMediaType(contentType).isCompatibleWith(MediaType.APPLICATION_XML)) {
- format = CompositionFormat.XML;
- } else {
- throw new IllegalArgumentException("ABAC: Only JSON and XML composition are supported.");
- }
- if (payload instanceof String) {
- Set templates = contributionService.getListOfTemplates((String) payload, format);
- requestMap.put(TEMPLATE, templates);
- break;
- } else {
- throw new InternalServerException("ABAC: invalid POST contribution payload.");
- }
- case BaseController.QUERY:
- // special case of type QUERY, where multiple subjects are possible
- if (payload instanceof Map) {
- if (((Map) payload).containsKey(AuditVariables.TEMPLATE_PATH)) {
- Set templates = (Set) ((Map) payload).get(AuditVariables.TEMPLATE_PATH);
- Set templateSet = new HashSet<>(templates);
- // put result set into the requestMap and exit
- requestMap.put(TEMPLATE, templateSet);
- break;
- } else {
- throw new InternalServerException("ABAC: AQL audit template data unavailable.");
- }
- } else {
- throw new InternalServerException("ABAC: AQL audit template data malformed.");
- }
- default:
- throw new InternalServerException("ABAC: Invalid type given from Pre- or PostAuthorize");
- }
- }
-
- private boolean abacCheckRequest(String url, Map bodyMap)
- throws IOException, InterruptedException {
- // prepare request attributes and convert from to
- Map request = new HashMap<>();
- if (bodyMap.containsKey(ORGANIZATION)) {
- request.put(ORGANIZATION, (String) bodyMap.get(ORGANIZATION));
- }
- // check if patient attribues are available and see if it contains a Set or simple String
- if (bodyMap.containsKey(PATIENT)) {
- if (bodyMap.get(PATIENT) instanceof Set) {
- // check if templates are also configured
- if (bodyMap.containsKey(TEMPLATE)) {
- if (bodyMap.get(TEMPLATE) instanceof Set) {
- // multiple templates possible: need cartesian product of n patients and m templates
- // so: for each patient, go through templates and do a request each
- Set setP = (Set) bodyMap.get(PATIENT);
- for (String p : setP) {
- request.put(PATIENT, p);
- boolean success = sendRequestForEach(TEMPLATE, url, bodyMap, request);
- if (!success) {
- return false;
- }
- }
- // in case all combinations were validated successfully
- return true;
- }
- } else {
- // only patients (or + orga) set. So run request for each patient, without template.
- return sendRequestForEach(PATIENT, url, bodyMap, request);
- }
- } else if (bodyMap.get(PATIENT) instanceof String) {
- request.put(PATIENT, (String) bodyMap.get(PATIENT));
- } else {
- // if it is just a String, set it and continue normal
- throw new InternalServerException("ABAC: Invalid patient attribute content.");
- }
- }
- // check if template attributes are available and see if it contains a Set or simple String
- if (bodyMap.containsKey(TEMPLATE)) {
- if (bodyMap.get(TEMPLATE) instanceof Set) {
- // set each template and send separate ABAC requests
- return sendRequestForEach(TEMPLATE, url, bodyMap, request);
- } else if (bodyMap.get(TEMPLATE) instanceof String) {
- // if it is just a String, set it and continue normal
- request.put(TEMPLATE, (String) bodyMap.get(TEMPLATE));
- } else {
- throw new InternalServerException("ABAC: Invalid template attribute content.");
- }
- }
- return abacCheck.execute(url, request);
- }
-
- /**
- * Goes through all template IDs and sends an ABAC request for each.
- * @param type Type, either ORGANIZATION, TEMPLATE, PATIENT
- * @param url ABAC server request URL
- * @param bodyMap Unprocessed attributes for the request
- * @param request Processed attributes for the request
- * @return True on success, False if one combinations is rejected by the ABAC server
- * @throws IOException On error during attribute or HTTP handling
- * @throws InterruptedException On error during HTTP handling
- */
- private boolean sendRequestForEach(String type, String url, Map bodyMap,
- Map request) throws IOException, InterruptedException {
- Set set = (Set) bodyMap.get(type);
- for (String s : set) {
- request.put(type, s);
- boolean allowed = abacCheck.execute(url, request);
- if (!allowed) {
- // if only one combination of attributes is rejected by ABAC return false for all
- return false;
- }
- }
- // in case all combinations were validated successfully
- return true;
- }
-
- /**
- * Extracts the JWT auth token.
- * @param auth Auth object.
- * @return JWT Auth Token
- */
- private JwtAuthenticationToken getJwtAuthenticationToken(Authentication auth) {
- JwtAuthenticationToken jwt;
- if (auth instanceof JwtAuthenticationToken) {
- jwt = (JwtAuthenticationToken) auth;
- } else {
- throw new IllegalArgumentException("ABAC: Invalid authentication, no JWT available.");
- }
- return jwt;
- }
-
- @Override
- public Object getFilterObject() {
- return this.filterObject;
- }
-
- @Override
- public void setFilterObject(Object filterObject) {
- this.filterObject = filterObject;
- }
-
- @Override
- public Object getReturnObject() {
- return this.returnObject;
- }
-
- @Override
- public void setReturnObject(Object returnObject) {
- this.returnObject = returnObject;
- }
-
- @Override
- public Object getThis() {
- return this;
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/abac/MethodSecurityConfig.java b/application/src/main/java/org/ehrbase/application/abac/MethodSecurityConfig.java
deleted file mode 100644
index a18cb87274..0000000000
--- a/application/src/main/java/org/ehrbase/application/abac/MethodSecurityConfig.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * Copyright (c) 2021 Jake Smolka (Hannover Medical School) and Vitasystems GmbH.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.abac;
-
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.security.access.expression.method.MethodSecurityExpressionHandler;
-import org.springframework.security.config.annotation.method.configuration.EnableGlobalMethodSecurity;
-import org.springframework.security.config.annotation.method.configuration.GlobalMethodSecurityConfiguration;
-
-@ConditionalOnProperty(name = "abac.enabled")
-@Configuration
-@EnableGlobalMethodSecurity(prePostEnabled = true)
-public class MethodSecurityConfig extends GlobalMethodSecurityConfiguration {
-
- private final AbacConfig abacConfig;
-
- public MethodSecurityConfig(AbacConfig abacConfig) {
- this.abacConfig = abacConfig;
- }
-
- /**
- * Registration of custom SpEL expressions, here to include ABAC checks.
- */
- @Override
- protected MethodSecurityExpressionHandler createExpressionHandler() {
- // "null" for beans here, but autowiring will make the beans available on runtime
- return new CustomMethodSecurityExpressionHandler(abacConfig, null, null, null, null);
- }
-
-}
diff --git a/application/src/main/java/org/ehrbase/application/cli/EhrBaseCli.java b/application/src/main/java/org/ehrbase/application/cli/EhrBaseCli.java
new file mode 100644
index 0000000000..8bf902a44e
--- /dev/null
+++ b/application/src/main/java/org/ehrbase/application/cli/EhrBaseCli.java
@@ -0,0 +1,60 @@
+/*
+ * Copyright (c) 2019-2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.application.cli;
+
+import java.util.Map;
+import org.ehrbase.cli.CliConfiguration;
+import org.ehrbase.cli.CliRunner;
+import org.ehrbase.configuration.EhrBaseCliConfiguration;
+import org.springframework.boot.Banner;
+import org.springframework.boot.CommandLineRunner;
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.WebApplicationType;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.autoconfigure.data.redis.RedisAutoConfiguration;
+import org.springframework.boot.autoconfigure.web.servlet.WebMvcAutoConfiguration;
+import org.springframework.boot.builder.SpringApplicationBuilder;
+import org.springframework.context.annotation.Import;
+
+@SpringBootApplication(exclude = {WebMvcAutoConfiguration.class, RedisAutoConfiguration.class})
+@Import({EhrBaseCliConfiguration.class, CliConfiguration.class})
+public class EhrBaseCli implements CommandLineRunner {
+
+ public static SpringApplication build(String[] args) {
+ return new SpringApplicationBuilder(EhrBaseCli.class)
+ .web(WebApplicationType.NONE)
+ .headless(true)
+ .properties(Map.of(
+ "spring.main.allow-bean-definition-overriding", "true",
+ "spring.banner.location", "classpath:banner-cli.txt"))
+ .bannerMode(Banner.Mode.CONSOLE)
+ .logStartupInfo(false)
+ .build(args);
+ }
+
+ private final CliRunner cliRunner;
+
+ public EhrBaseCli(CliRunner cliRunner) {
+ this.cliRunner = cliRunner;
+ }
+
+ @Override
+ public void run(String... args) {
+ cliRunner.run(args);
+ }
+}
diff --git a/application/src/main/java/org/ehrbase/application/config/HttpClientConfig.java b/application/src/main/java/org/ehrbase/application/config/HttpClientConfig.java
deleted file mode 100644
index 53a2d7131c..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/HttpClientConfig.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * Copyright (c) 2021 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-
-package org.ehrbase.application.config;
-
-import java.net.InetSocketAddress;
-import java.net.ProxySelector;
-import java.net.URI;
-import java.net.http.HttpClient;
-import java.net.http.HttpClient.Redirect;
-import java.net.http.HttpClient.Version;
-import java.time.Duration;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.boot.context.properties.EnableConfigurationProperties;
-import org.springframework.context.annotation.Configuration;
-
-@Configuration
-@EnableConfigurationProperties
-@ConfigurationProperties(prefix = "httpclient")
-public class HttpClientConfig {
-
- private HttpClient client;
-
- private URI proxy;
- private int proxyPort;
-
- /**
- * General HTTP client with central configuration.
- */
- public HttpClient getClient() {
- if (this.client == null) {
- var builder = HttpClient.newBuilder()
- .version(Version.HTTP_2)
- .followRedirects(Redirect.NEVER)
- .connectTimeout(Duration.ofSeconds(20));
-
- if (proxy != null && proxyPort != 0) {
- builder.proxy(ProxySelector.of(new InetSocketAddress(proxy.toString(), proxyPort)));
- }
-
- // TODO: allow configuration of authentication
- //builder.authenticator(Authenticator.getDefault());
-
- this.client = builder.build();
- }
- return client;
- }
-
- public URI getProxy() {
- return proxy;
- }
-
- public void setProxy(URI proxy) {
- this.proxy = proxy;
- }
-
- public int getProxyPort() {
- return proxyPort;
- }
-
- public void setProxyPort(int proxyPort) {
- this.proxyPort = proxyPort;
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/JacksonConfiguration.java b/application/src/main/java/org/ehrbase/application/config/JacksonConfiguration.java
deleted file mode 100644
index eaca874549..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/JacksonConfiguration.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright (c) 2019 Stefan Spiska (Vitasystems GmbH) and Hannover Medical School.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config;
-
-import com.fasterxml.jackson.dataformat.xml.XmlMapper;
-import com.fasterxml.jackson.dataformat.xml.ser.ToXmlGenerator;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import com.nedap.archie.rm.RMObject;
-import com.nedap.archie.rm.directory.Folder;
-import com.nedap.archie.rm.ehr.EhrStatus;
-import org.ehrbase.api.mapper.StructuredStringJSonSerializer;
-import org.ehrbase.response.ehrscape.StructuredString;
-import org.ehrbase.serialisation.mapper.RmObjectJsonDeSerializer;
-import org.ehrbase.serialisation.mapper.RmObjectJsonSerializer;
-import org.springframework.boot.autoconfigure.jackson.Jackson2ObjectMapperBuilderCustomizer;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Primary;
-import org.springframework.http.converter.json.Jackson2ObjectMapperBuilder;
-import org.springframework.http.converter.xml.MappingJackson2XmlHttpMessageConverter;
-
-@Configuration
-public class JacksonConfiguration {
-
- @Bean
- public Jackson2ObjectMapperBuilderCustomizer addCustomSerialization() {
- return jacksonObjectMapperBuilder -> jacksonObjectMapperBuilder
- .serializerByType(StructuredString.class, new StructuredStringJSonSerializer())
- .serializerByType(RMObject.class, new RmObjectJsonSerializer())
- .deserializerByType(EhrStatus.class, new RmObjectJsonDeSerializer())
- .deserializerByType(Folder.class, new RmObjectJsonDeSerializer())
- .modules(new JavaTimeModule());
- }
-
- @Bean
- @Primary
- public MappingJackson2XmlHttpMessageConverter mappingJackson2XmlHttpMessageConverter(
- Jackson2ObjectMapperBuilder builder) {
- XmlMapper objectMapper = builder.createXmlMapper(true).build();
- objectMapper.configure(ToXmlGenerator.Feature.WRITE_XML_DECLARATION, true);
- return new MappingJackson2XmlHttpMessageConverter(
- objectMapper);
- }
-}
\ No newline at end of file
diff --git a/application/src/main/java/org/ehrbase/application/config/ServerConfigImp.java b/application/src/main/java/org/ehrbase/application/config/ServerConfigImp.java
deleted file mode 100644
index 9b6e6e9200..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/ServerConfigImp.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * Copyright (c) 2020 Vitasystems GmbH and Hannover Medical School.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.ehrbase.application.config;
-
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.context.annotation.Configuration;
-
-import javax.validation.constraints.Max;
-import javax.validation.constraints.Min;
-
-@Configuration
-@ConfigurationProperties(prefix = "server")
-public class ServerConfigImp implements org.ehrbase.api.definitions.ServerConfig {
-
- @Min(1025)
- @Max(65536)
- private int port;
- private String nodename = "local.ehrbase.org";
- private AqlConfig aqlConfig;
- private boolean disableStrictValidation = false;
-
- public int getPort() {
- return port;
- }
-
- public void setPort(int port) {
- this.port = port;
- }
-
- public String getNodename() {
- return nodename;
- }
-
- public void setNodename(String nodename) {
- this.nodename = nodename;
- }
-
- @Override
- public String getAqlIterationSkipList() {
- return aqlConfig.getIgnoreIterativeNodeList();
- }
-
- @Override
- public Integer getAqlDepth() {
- return aqlConfig.getIterationScanDepth();
- }
-
- @Override
- public Boolean getUseJsQuery() {
- return aqlConfig.getUseJsQuery();
- }
-
- @Override
- public void setUseJsQuery(boolean b) {
- aqlConfig.setUseJsQuery(b);
- }
-
- public AqlConfig getAqlConfig() {
- return aqlConfig;
- }
-
- public void setAqlConfig(AqlConfig aqlConfig) {
- this.aqlConfig = aqlConfig;
- }
-
- public static class AqlConfig {
-
- private Boolean useJsQuery;
- private String ignoreIterativeNodeList;
- private Integer iterationScanDepth = 1;
-
- public Boolean getUseJsQuery() {
- return useJsQuery;
- }
-
- public String getIgnoreIterativeNodeList() {
- return ignoreIterativeNodeList;
- }
-
- public Integer getIterationScanDepth() {
- return iterationScanDepth;
- }
-
- public void setUseJsQuery(Boolean useJsQuery) {
- this.useJsQuery = useJsQuery;
- }
-
- public void setIgnoreIterativeNodeList(String ignoreIterativeNodeList) {
- this.ignoreIterativeNodeList = ignoreIterativeNodeList;
- }
-
- public void setIterationScanDepth(Integer iterationScanDepth) {
- this.iterationScanDepth = iterationScanDepth;
- }
- }
-
- @Override
- public boolean isDisableStrictValidation() {
- return disableStrictValidation;
- }
-
- public void setDisableStrictValidation(boolean disableStrictValidation) {
- this.disableStrictValidation = disableStrictValidation;
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/SwaggerConfiguration.java b/application/src/main/java/org/ehrbase/application/config/SwaggerConfiguration.java
deleted file mode 100644
index 628eec5bf2..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/SwaggerConfiguration.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package org.ehrbase.application.config;
-
-import io.swagger.v3.oas.models.ExternalDocumentation;
-import io.swagger.v3.oas.models.OpenAPI;
-import io.swagger.v3.oas.models.info.Info;
-import io.swagger.v3.oas.models.info.License;
-import org.springdoc.core.GroupedOpenApi;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-
-@Configuration
-public class SwaggerConfiguration {
-
- @Bean
- public GroupedOpenApi openEhrApi() {
- return GroupedOpenApi.builder()
- .group("1. openEHR API")
- .pathsToMatch("/rest/openehr/**")
- .build();
- }
-
- @Bean
- public GroupedOpenApi ehrScapeApi() {
- return GroupedOpenApi.builder()
- .group("2. EhrScape API")
- .pathsToMatch("/rest/ecis/**")
- .build();
- }
-
- @Bean
- public GroupedOpenApi statusApi() {
- return GroupedOpenApi.builder()
- .group("3. EHRbase Status Endpoint")
- .pathsToMatch("/rest/status")
- .build();
- }
-
- @Bean
- public GroupedOpenApi adminApi() {
- return GroupedOpenApi.builder()
- .group("4. EHRbase Admin API")
- .pathsToMatch("/rest/admin/**")
- .build();
- }
-
- @Bean
- public GroupedOpenApi actuatorApi() {
- return GroupedOpenApi.builder()
- .group("5. Management API")
- .pathsToMatch("/management/**")
- .build();
- }
-
- @Bean
- public OpenAPI ehrBaseOpenAPI() {
- return new OpenAPI()
- .info(
- new Info()
- .title("EHRbase API")
- .description("EHRbase implements the [official openEHR REST API](https://specifications.openehr.org/releases/ITS-REST/latest/) and "
- + "a subset of the [EhrScape API](https://www.ehrscape.com/). "
- + "Additionally, EHRbase provides a custom `status` heartbeat endpoint, "
- + "an [Admin API](https://ehrbase.readthedocs.io/en/latest/03_development/07_admin/index.html) (if activated) "
- + "and a [Status and Metrics API](https://ehrbase.readthedocs.io/en/latest/03_development/08_status_and_metrics/index.html?highlight=status) (if activated) "
- + "for monitoring and maintenance. "
- + "Please select the definition in the top right."
- + " "
- + "Note: The openEHR REST API and the EhrScape API are documented in their official documentation, not here. Please refer to their separate documentation.")
- .version("v1")
- .license(
- new License()
- .name("Apache 2.0")
- .url("https://github.com/ehrbase/ehrbase/blob/develop/LICENSE.md")))
- .externalDocs(
- new ExternalDocumentation()
- .description("EHRbase Documentation")
- .url("https://ehrbase.readthedocs.io/"));
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/cache/CacheConfiguration.java b/application/src/main/java/org/ehrbase/application/config/cache/CacheConfiguration.java
deleted file mode 100644
index 542e54ddec..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/cache/CacheConfiguration.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2021 vitasystems GmbH and Hannover Medical School.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * https://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.cache;
-
-import org.ehrbase.cache.CacheOptions;
-import org.ehrbase.service.KnowledgeCacheService;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
-import org.springframework.boot.context.properties.EnableConfigurationProperties;
-import org.springframework.cache.annotation.EnableCaching;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-
-/**
- * {@link Configuration} for EhCache using JCache.
- *
- * @author Renaud Subiger
- * @since 1.0.0
- */
-@Configuration(proxyBeanMethods = false)
-@EnableConfigurationProperties(CacheProperties.class)
-@EnableCaching
-public class CacheConfiguration {
-
- @Bean
- public CacheOptions cacheOptions(CacheProperties properties) {
- var options = new CacheOptions();
- options.setPreBuildQueries(properties.isPreBuildQueries());
- options.setPreBuildQueriesDepth(properties.getPreBuildQueriesDepth());
- return options;
- }
-
- @Bean
- @ConditionalOnProperty(prefix = "cache", name = "init-on-startup", havingValue = "true")
- public CacheInitializer cacheInitializer(KnowledgeCacheService knowledgeCacheService) {
- return new CacheInitializer(knowledgeCacheService);
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/cache/CacheInitializer.java b/application/src/main/java/org/ehrbase/application/config/cache/CacheInitializer.java
deleted file mode 100644
index d8d5c1afdc..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/cache/CacheInitializer.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Copyright 2021-2022 vitasystems GmbH and Hannover Medical School.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * https://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.cache;
-
-import javax.annotation.PostConstruct;
-import org.ehrbase.service.KnowledgeCacheService;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * Initializes caches during application startup.
- *
- * @author Renaud Subiger
- * @since 1.0.0
- */
-public class CacheInitializer {
-
- private final Logger logger = LoggerFactory.getLogger(getClass());
-
- private final KnowledgeCacheService knowledgeCacheService;
-
- public CacheInitializer(KnowledgeCacheService knowledgeCacheService) {
- this.knowledgeCacheService = knowledgeCacheService;
- }
-
- @PostConstruct
- public void initialize() {
- logger.info("Initializing EHRbase caches");
- knowledgeCacheService.initializeCaches();
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/cache/CacheProperties.java b/application/src/main/java/org/ehrbase/application/config/cache/CacheProperties.java
deleted file mode 100644
index 8fbc23c782..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/cache/CacheProperties.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * Copyright 2021 vitasystems GmbH and Hannover Medical School.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * https://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.cache;
-
-import org.springframework.boot.context.properties.ConfigurationProperties;
-
-/**
- * {@link ConfigurationProperties} for EHRbase cache configuration.
- *
- * @author Renaud Subiger
- * @since 1.0.0
- */
-@ConfigurationProperties(prefix = "cache")
-public class CacheProperties {
-
- /**
- * Whether to initialize the caches during application startup.
- */
- private boolean initOnStartup = true;
-
- /**
- * Whether to pre-build queries when a new template is added.
- */
- private boolean preBuildQueries = true;
-
- /**
- * The default node depth for pre-built queries.
- */
- private Integer preBuildQueriesDepth = 4;
-
- public boolean isInitOnStartup() {
- return initOnStartup;
- }
-
- public void setInitOnStartup(boolean initOnStartup) {
- this.initOnStartup = initOnStartup;
- }
-
- public boolean isPreBuildQueries() {
- return preBuildQueries;
- }
-
- public void setPreBuildQueries(boolean preBuildQueries) {
- this.preBuildQueries = preBuildQueries;
- }
-
- public Integer getPreBuildQueriesDepth() {
- return preBuildQueriesDepth;
- }
-
- public void setPreBuildQueriesDepth(Integer preBuildQueriesDepth) {
- this.preBuildQueriesDepth = preBuildQueriesDepth;
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/client/HttpClientConfiguration.java b/application/src/main/java/org/ehrbase/application/config/client/HttpClientConfiguration.java
deleted file mode 100644
index d9de537376..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/client/HttpClientConfiguration.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/*
- * Copyright (c) 2021 Vitasystems GmbH.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.client;
-
-import org.apache.http.HttpHost;
-import org.apache.http.auth.AuthScope;
-import org.apache.http.auth.UsernamePasswordCredentials;
-import org.apache.http.client.HttpClient;
-import org.apache.http.conn.ssl.NoopHostnameVerifier;
-import org.apache.http.conn.ssl.TrustAllStrategy;
-import org.apache.http.impl.client.BasicCredentialsProvider;
-import org.apache.http.impl.client.HttpClientBuilder;
-import org.apache.http.impl.client.HttpClients;
-import org.apache.http.ssl.SSLContextBuilder;
-import org.springframework.boot.context.properties.EnableConfigurationProperties;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.util.ResourceUtils;
-
-import javax.net.ssl.SSLContext;
-import java.io.IOException;
-import java.security.KeyManagementException;
-import java.security.KeyStoreException;
-import java.security.NoSuchAlgorithmException;
-import java.security.UnrecoverableKeyException;
-import java.security.cert.CertificateException;
-
-/**
- * {@link Configuration} for Apache HTTP Client.
- */
-@Configuration
-@EnableConfigurationProperties(HttpClientProperties.class)
-@SuppressWarnings("java:S6212")
-public class HttpClientConfiguration {
-
- @Bean
- public HttpClient httpClient(HttpClientProperties properties) throws UnrecoverableKeyException, CertificateException,
- NoSuchAlgorithmException, KeyStoreException, IOException, KeyManagementException {
-
- HttpClientBuilder builder = HttpClients.custom();
-
- if (properties.getSsl().isEnabled()) {
- builder.setSSLContext(buildSSLContext(properties.getSsl()));
- builder.setSSLHostnameVerifier(NoopHostnameVerifier.INSTANCE);
- }
-
- if (properties.getProxy().getHost() != null && properties.getProxy().getPort() != null) {
- builder.setProxy(new HttpHost(properties.getProxy().getHost(), properties.getProxy().getPort()));
-
- if (properties.getProxy().getUsername() != null && properties.getProxy().getPassword() != null) {
- UsernamePasswordCredentials credentials =
- new UsernamePasswordCredentials(properties.getProxy().getUsername(), properties.getProxy().getPassword());
- BasicCredentialsProvider credentialsProvider = new BasicCredentialsProvider();
- credentialsProvider.setCredentials(AuthScope.ANY, credentials);
- builder.setDefaultCredentialsProvider(credentialsProvider);
- }
- }
-
- return builder.build();
- }
-
- private SSLContext buildSSLContext(HttpClientProperties.Ssl properties) throws UnrecoverableKeyException, CertificateException,
- NoSuchAlgorithmException, KeyStoreException, IOException, KeyManagementException {
-
- SSLContextBuilder builder = SSLContextBuilder.create();
-
- if (properties.getKeyStoreType() != null) {
- builder.setKeyStoreType(properties.getKeyStoreType());
- }
- builder.loadKeyMaterial(ResourceUtils.getFile(properties.getKeyStore()),
- properties.getKeyStorePassword().toCharArray(),
- properties.getKeyPassword().toCharArray());
-
- if (properties.getTrustStoreType() != null) {
- builder.setKeyStoreType(properties.getTrustStoreType());
- }
- builder.loadTrustMaterial(ResourceUtils.getFile(properties.getTrustStore()),
- properties.getTrustStorePassword().toCharArray(), TrustAllStrategy.INSTANCE);
-
- return builder.build();
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/security/BasicAuthSecurityConfiguration.java b/application/src/main/java/org/ehrbase/application/config/security/BasicAuthSecurityConfiguration.java
deleted file mode 100644
index c1ec1b8c7e..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/security/BasicAuthSecurityConfiguration.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- * Copyright 2021-2022 vitasystems GmbH and Hannover Medical School.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * https://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.security;
-
-import static org.ehrbase.application.config.security.SecurityProperties.ADMIN;
-import static org.ehrbase.application.config.security.SecurityProperties.USER;
-
-import javax.annotation.PostConstruct;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.security.config.annotation.authentication.builders.AuthenticationManagerBuilder;
-import org.springframework.security.config.annotation.web.builders.HttpSecurity;
-import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
-import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
-import org.springframework.security.config.http.SessionCreationPolicy;
-
-/**
- * {@link Configuration} for Basic authentication.
- *
- * @author Jake Smolka
- * @author Renaud Subiger
- * @since 1.0.0
- */
-@Configuration
-@ConditionalOnProperty(prefix = "security", name = "authType", havingValue = "basic")
-@EnableWebSecurity
-public class BasicAuthSecurityConfiguration extends WebSecurityConfigurerAdapter {
-
- private final Logger logger = LoggerFactory.getLogger(getClass());
-
- private final SecurityProperties properties;
-
- public BasicAuthSecurityConfiguration(SecurityProperties securityProperties) {
- this.properties = securityProperties;
- }
-
- @PostConstruct
- public void initialize() {
- logger.info("Using basic authentication");
- }
-
- @Override
- public void configure(AuthenticationManagerBuilder auth) throws Exception {
- // @formatter:off
- auth
- .inMemoryAuthentication()
- .withUser(properties.getAuthUser())
- .password("{noop}" + properties.getAuthPassword())
- .roles(USER)
- .and()
- .withUser(properties.getAuthAdminUser())
- .password("{noop}" + properties.getAuthAdminPassword())
- .roles(ADMIN);
- // @formatter:on
- }
-
- @Override
- protected void configure(HttpSecurity http) throws Exception {
- // @formatter:off
- http
- .cors()
- .and()
- .csrf()
- .ignoringAntMatchers("/rest/**")
- .and()
- .authorizeRequests()
- .antMatchers("/rest/admin/**", "/management/**").hasRole(ADMIN)
- .anyRequest().hasAnyRole(ADMIN, USER)
- .and()
- .sessionManagement()
- .sessionCreationPolicy(SessionCreationPolicy.STATELESS)
- .and()
- .httpBasic();
- // @formatter:on
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/security/NoOpSecurityConfiguration.java b/application/src/main/java/org/ehrbase/application/config/security/NoOpSecurityConfiguration.java
deleted file mode 100644
index b0489f151e..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/security/NoOpSecurityConfiguration.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2021-2022 vitasystems GmbH and Hannover Medical School.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * https://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.security;
-
-import javax.annotation.PostConstruct;
-import org.ehrbase.service.IAuthenticationFacade;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Primary;
-import org.springframework.security.authentication.AnonymousAuthenticationToken;
-import org.springframework.security.web.authentication.AnonymousAuthenticationFilter;
-
-/**
- * {@link Configuration} used when security is disabled.
- *
- * @author Renaud Subiger
- * @since 1.0.0
- */
-@Configuration(proxyBeanMethods = false)
-@ConditionalOnProperty(prefix = "security", name = "auth-type", havingValue = "none")
-public class NoOpSecurityConfiguration {
-
- private final Logger logger = LoggerFactory.getLogger(getClass());
-
- @PostConstruct
- public void initialize() {
- logger.warn("Security is disabled. Configure 'security.auth-type' to disable this warning.");
- }
-
- @Bean
- @Primary
- public IAuthenticationFacade anonymousAuthentication() {
- var filter = new AnonymousAuthenticationFilter("key");
- return () -> new AnonymousAuthenticationToken("key", filter.getPrincipal(),
- filter.getAuthorities());
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/security/OAuth2SecurityConfiguration.java b/application/src/main/java/org/ehrbase/application/config/security/OAuth2SecurityConfiguration.java
deleted file mode 100644
index ddfab5812a..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/security/OAuth2SecurityConfiguration.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- * Copyright 2021-2022 vitasystems GmbH and Hannover Medical School.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * https://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.security;
-
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.stream.Collectors;
-import javax.annotation.PostConstruct;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
-import org.springframework.boot.autoconfigure.security.oauth2.resource.OAuth2ResourceServerProperties;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.core.convert.converter.Converter;
-import org.springframework.security.authentication.AbstractAuthenticationToken;
-import org.springframework.security.config.annotation.web.builders.HttpSecurity;
-import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
-import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
-import org.springframework.security.core.GrantedAuthority;
-import org.springframework.security.core.authority.SimpleGrantedAuthority;
-import org.springframework.security.oauth2.jwt.Jwt;
-import org.springframework.security.oauth2.server.resource.authentication.JwtAuthenticationConverter;
-
-/**
- * {@link Configuration} for OAuth2 authentication.
- *
- * @author Jake Smolka
- * @since 1.0.0
- */
-@Configuration
-@ConditionalOnProperty(prefix = "security", name = "auth-type", havingValue = "oauth")
-@EnableWebSecurity
-public class OAuth2SecurityConfiguration extends WebSecurityConfigurerAdapter {
-
- public static final String PROFILE_SCOPE = "PROFILE";
-
- private final Logger logger = LoggerFactory.getLogger(getClass());
-
- private final SecurityProperties securityProperties;
-
- private final OAuth2ResourceServerProperties oAuth2rProperties;
-
- public OAuth2SecurityConfiguration(SecurityProperties securityProperties,
- OAuth2ResourceServerProperties oAuth2rProperties) {
- this.securityProperties = securityProperties;
- this.oAuth2rProperties = oAuth2rProperties;
- }
-
- @PostConstruct
- public void initialize() {
- logger.info("Using OAuth2 authentication");
- logger.debug("Using issuer URI: {}", oAuth2rProperties.getJwt().getIssuerUri());
- logger.debug("Using user role: {}", securityProperties.getOauth2UserRole());
- logger.debug("Using admin role: {}", securityProperties.getOauth2AdminRole());
- }
-
- @Override
- protected void configure(HttpSecurity http) throws Exception {
- String userRole = securityProperties.getOauth2UserRole();
- String adminRole = securityProperties.getOauth2AdminRole();
-
- // @formatter:off
- http
- .cors()
- .and()
- .authorizeRequests()
- .antMatchers("/rest/admin/**", "/management/**").hasRole(adminRole)
- .anyRequest().hasAnyRole(adminRole, userRole, PROFILE_SCOPE)
- .and()
- .oauth2ResourceServer()
- .jwt()
- .jwtAuthenticationConverter(getJwtAuthenticationConverter());
- // @formatter:on
- }
-
- // Converter creates list of "ROLE_*" (upper case) authorities for each "realm access" role
- // and "roles" role from JWT
- @SuppressWarnings("unchecked")
- private Converter getJwtAuthenticationConverter() {
- var converter = new JwtAuthenticationConverter();
- converter.setJwtGrantedAuthoritiesConverter(jwt -> {
- Map realmAccess;
- realmAccess = (Map) jwt.getClaims().get("realm_access");
-
- Collection authority = new HashSet<>();
- if (realmAccess != null && realmAccess.containsKey("roles")) {
- authority.addAll(((List) realmAccess.get("roles")).stream()
- .map(roleName -> "ROLE_" + roleName.toUpperCase()).map(SimpleGrantedAuthority::new)
- .collect(Collectors.toList()));
- }
-
- if (jwt.getClaims().containsKey("scope")) {
- authority.addAll(Arrays.stream(jwt.getClaims().get("scope").toString().split(" "))
- .map(roleName -> "ROLE_" + roleName.toUpperCase()).map(SimpleGrantedAuthority::new)
- .collect(Collectors.toList()));
- }
- return authority;
- });
- return converter;
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/security/SecurityConfiguration.java b/application/src/main/java/org/ehrbase/application/config/security/SecurityConfiguration.java
deleted file mode 100644
index 79c34b0f76..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/security/SecurityConfiguration.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * Copyright (c) 2020 Vitasystems GmbH and Hannover Medical School.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.security;
-
-import org.springframework.boot.context.properties.EnableConfigurationProperties;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
-
-@Configuration(proxyBeanMethods = false)
-@EnableConfigurationProperties(SecurityProperties.class)
-@Import({NoOpSecurityConfiguration.class, BasicAuthSecurityConfiguration.class})
-public class SecurityConfiguration {
-
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/security/SecurityProperties.java b/application/src/main/java/org/ehrbase/application/config/security/SecurityProperties.java
deleted file mode 100644
index 8d485b3128..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/security/SecurityProperties.java
+++ /dev/null
@@ -1,124 +0,0 @@
-/*
- * Copyright (c) 2020 Vitasystems GmbH and Hannover Medical School.
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.ehrbase.application.config.security;
-
-import org.springframework.boot.context.properties.ConfigurationProperties;
-
-@ConfigurationProperties(prefix = "security")
-public class SecurityProperties {
-
- // Roles, when not using OAuth2
- public static final String ADMIN = "ADMIN";
-
- public static final String USER = "USER";
-
- /**
- * Authentication type.
- */
- private AuthTypes authType;
-
- /**
- * Username.
- */
- private String authUser;
-
- /**
- * Password for the user.
- */
- private String authPassword;
-
- /**
- * Admin username.
- */
- private String authAdminUser;
-
- /**
- * Password for the admin user.
- */
- private String authAdminPassword;
-
- /**
- * User role name used with OAuth2 authentication type.
- */
- private String oauth2UserRole;
-
- /**
- * Admin role name used with OAuth2 authentication type.
- */
- private String oauth2AdminRole;
-
- public AuthTypes getAuthType() {
- return authType;
- }
-
- public void setAuthType(AuthTypes authType) {
- this.authType = authType;
- }
-
- public String getAuthUser() {
- return authUser;
- }
-
- public void setAuthUser(String authUser) {
- this.authUser = authUser;
- }
-
- public String getAuthPassword() {
- return authPassword;
- }
-
- public void setAuthPassword(String authPassword) {
- this.authPassword = authPassword;
- }
-
- public String getAuthAdminUser() {
- return authAdminUser;
- }
-
- public void setAuthAdminUser(String authAdminUser) {
- this.authAdminUser = authAdminUser;
- }
-
- public String getAuthAdminPassword() {
- return authAdminPassword;
- }
-
- public void setAuthAdminPassword(String authAdminPassword) {
- this.authAdminPassword = authAdminPassword;
- }
-
- public String getOauth2UserRole() {
- return oauth2UserRole;
- }
-
- public void setOauth2UserRole(String oauth2UserRole) {
- this.oauth2UserRole = oauth2UserRole.toUpperCase();
- }
-
- public String getOauth2AdminRole() {
- return oauth2AdminRole;
- }
-
- public void setOauth2AdminRole(String oauth2AdminRole) {
- this.oauth2AdminRole = oauth2AdminRole.toUpperCase();
- }
-
- public enum AuthTypes {
- NONE, BASIC, OAUTH
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/validation/ValidationConfiguration.java b/application/src/main/java/org/ehrbase/application/config/validation/ValidationConfiguration.java
deleted file mode 100644
index f227f9c5a9..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/validation/ValidationConfiguration.java
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- * Copyright 2021-2022 vitasystems GmbH and Hannover Medical School.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * https://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.validation;
-
-import java.util.Map;
-import org.apache.http.client.HttpClient;
-import org.ehrbase.validation.terminology.ExternalTerminologyValidation;
-import org.ehrbase.validation.terminology.ExternalTerminologyValidationChain;
-import org.ehrbase.validation.terminology.FhirTerminologyValidation;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
-import org.springframework.boot.context.properties.EnableConfigurationProperties;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-
-/**
- * {@link Configuration} for external terminology validation.
- *
- * @author Renaud Subiger
- * @since 1.0.0
- */
-@Configuration
-@ConditionalOnProperty(name = "validation.external-terminology.enabled", havingValue = "true")
-@EnableConfigurationProperties(ValidationProperties.class)
-@SuppressWarnings("java:S6212")
-public class ValidationConfiguration {
-
- private final Logger logger = LoggerFactory.getLogger(getClass());
-
- private final ValidationProperties properties;
-
- private final HttpClient httpClient;
-
- public ValidationConfiguration(ValidationProperties properties, HttpClient httpClient) {
- this.properties = properties;
- this.httpClient = httpClient;
- }
-
- @Bean
- public ExternalTerminologyValidation externalTerminologyValidator() {
- Map providers = properties.getProvider();
-
- if (providers.isEmpty()) {
- throw new IllegalStateException(
- "At least one external terminology provider must be defined " +
- "if 'validation.external-validation.enabled' is set to 'true'");
- } else if (providers.size() == 1) {
- Map.Entry provider = providers.entrySet().iterator()
- .next();
- return buildExternalTerminologyValidation(provider);
- } else {
- ExternalTerminologyValidationChain chain = new ExternalTerminologyValidationChain();
- for (Map.Entry provider : providers.entrySet()) {
- chain.addExternalTerminologyValidationSupport(buildExternalTerminologyValidation(provider));
- }
- return chain;
- }
- }
-
- private ExternalTerminologyValidation buildExternalTerminologyValidation(
- Map.Entry provider) {
- logger.info("Initializing '{}' external terminology provider (type: {})", provider.getKey(),
- provider.getValue().getType());
- if (provider.getValue().getType() == ValidationProperties.ProviderType.FHIR) {
- return fhirTerminologyValidation(provider.getValue().getUrl());
- }
- throw new IllegalArgumentException("Invalid provider type: " + provider.getValue().getType());
- }
-
- private FhirTerminologyValidation fhirTerminologyValidation(String url) {
- return new FhirTerminologyValidation(url, properties.isFailOnError(), httpClient);
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/validation/ValidationProperties.java b/application/src/main/java/org/ehrbase/application/config/validation/ValidationProperties.java
deleted file mode 100644
index b703a5bab6..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/validation/ValidationProperties.java
+++ /dev/null
@@ -1,67 +0,0 @@
-package org.ehrbase.application.config.validation;
-
-import org.springframework.boot.context.properties.ConfigurationProperties;
-
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * {@link ConfigurationProperties} for external terminology validation.
- */
-@ConfigurationProperties(prefix = "validation.external-terminology")
-public class ValidationProperties {
-
- private boolean enabled = false;
-
- private boolean failOnError = false;
-
- private final Map provider = new HashMap<>();
-
- public boolean isEnabled() {
- return enabled;
- }
-
- public void setEnabled(boolean enabled) {
- this.enabled = enabled;
- }
-
- public boolean isFailOnError() {
- return failOnError;
- }
-
- public void setFailOnError(boolean failOnError) {
- this.failOnError = failOnError;
- }
-
- public Map getProvider() {
- return provider;
- }
-
- public enum ProviderType {
-
- FHIR
- }
-
- public static class Provider {
-
- private ProviderType type;
-
- private String url;
-
- public ProviderType getType() {
- return type;
- }
-
- public void setType(ProviderType type) {
- this.type = type;
- }
-
- public String getUrl() {
- return url;
- }
-
- public void setUrl(String url) {
- this.url = url;
- }
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/config/web/WebConfiguration.java b/application/src/main/java/org/ehrbase/application/config/web/WebConfiguration.java
deleted file mode 100644
index 26dad5c30f..0000000000
--- a/application/src/main/java/org/ehrbase/application/config/web/WebConfiguration.java
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
- * Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.config.web;
-
-import org.ehrbase.api.service.CompositionService;
-import org.ehrbase.api.service.EhrService;
-import org.ehrbase.application.util.IsoDateTimeConverter;
-import org.ehrbase.rest.openehr.audit.CompositionAuditInterceptor;
-import org.ehrbase.rest.openehr.audit.EhrAuditInterceptor;
-import org.ehrbase.rest.openehr.audit.QueryAuditInterceptor;
-import org.openehealth.ipf.commons.audit.AuditContext;
-import org.springframework.boot.context.properties.EnableConfigurationProperties;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.format.FormatterRegistry;
-import org.springframework.lang.NonNull;
-import org.springframework.web.servlet.config.annotation.CorsRegistry;
-import org.springframework.web.servlet.config.annotation.InterceptorRegistry;
-import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
-
-/**
- * {@link Configuration} from Spring Web MVC.
- */
-@Configuration(proxyBeanMethods = false)
-@EnableConfigurationProperties(CorsProperties.class)
-public class WebConfiguration implements WebMvcConfigurer {
-
- private final CorsProperties properties;
-
- private final AuditContext auditContext;
-
- private final EhrService ehrService;
-
- private final CompositionService compositionService;
-
- public WebConfiguration(CorsProperties properties, AuditContext auditContext,
- EhrService ehrService, CompositionService compositionService) {
- this.properties = properties;
- this.auditContext = auditContext;
- this.ehrService = ehrService;
- this.compositionService = compositionService;
- }
-
- @Override
- public void addFormatters(FormatterRegistry registry) {
- registry.addConverter(new IsoDateTimeConverter()); // Converter for version_at_time and other ISO date params
- }
-
- @Override
- public void addCorsMappings(CorsRegistry registry) {
- registry.addMapping("/**")
- .combine(properties.toCorsConfiguration());
- }
-
- @Override
- public void addInterceptors(@NonNull InterceptorRegistry registry) {
- if (auditContext.isAuditEnabled()) {
- // Composition endpoint
- registry
- .addInterceptor(new CompositionAuditInterceptor(auditContext, ehrService, compositionService))
- .addPathPatterns("/rest/openehr/v1/**/composition/**");
- // Ehr endpoint
- registry
- .addInterceptor(new EhrAuditInterceptor(auditContext, ehrService))
- .addPathPatterns("/rest/openehr/v1/ehr", "/rest/openehr/v1/ehr/*");
- // Query endpoint
- registry
- .addInterceptor(new QueryAuditInterceptor(auditContext, ehrService))
- .addPathPatterns("/rest/openehr/v1/query/**");
- }
- }
-}
diff --git a/application/src/main/java/org/ehrbase/application/server/EhrBaseServer.java b/application/src/main/java/org/ehrbase/application/server/EhrBaseServer.java
new file mode 100644
index 0000000000..e5559057a1
--- /dev/null
+++ b/application/src/main/java/org/ehrbase/application/server/EhrBaseServer.java
@@ -0,0 +1,45 @@
+/*
+ * Copyright (c) 2019-2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.application.server;
+
+import org.ehrbase.configuration.EhrBaseServerConfiguration;
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.WebApplicationType;
+import org.springframework.boot.actuate.autoconfigure.security.servlet.ManagementWebSecurityAutoConfiguration;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.autoconfigure.r2dbc.R2dbcAutoConfiguration;
+import org.springframework.boot.autoconfigure.security.servlet.SecurityAutoConfiguration;
+import org.springframework.boot.builder.SpringApplicationBuilder;
+import org.springframework.context.annotation.Import;
+
+@SpringBootApplication(
+ exclude = {
+ ManagementWebSecurityAutoConfiguration.class,
+ R2dbcAutoConfiguration.class,
+ SecurityAutoConfiguration.class
+ })
+@Import({EhrBaseServerConfiguration.class})
+@SuppressWarnings("java:S1118")
+public class EhrBaseServer {
+
+ public static SpringApplication build(String[] args) {
+ return new SpringApplicationBuilder(EhrBaseServer.class)
+ .web(WebApplicationType.SERVLET)
+ .build(args);
+ }
+}
diff --git a/application/src/main/java/org/ehrbase/application/web/LoggingContextFilter.java b/application/src/main/java/org/ehrbase/application/web/LoggingContextFilter.java
deleted file mode 100644
index 12805d58c9..0000000000
--- a/application/src/main/java/org/ehrbase/application/web/LoggingContextFilter.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * Copyright 2022 vitasystems GmbH and Hannover Medical School.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * https://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.web;
-
-import java.io.IOException;
-import java.util.UUID;
-import javax.servlet.FilterChain;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import org.slf4j.MDC;
-import org.springframework.core.Ordered;
-import org.springframework.core.annotation.Order;
-import org.springframework.lang.NonNull;
-import org.springframework.stereotype.Component;
-import org.springframework.web.filter.OncePerRequestFilter;
-
-/**
- * Filter implementation that associates a unique traceId for logging purposes to each
- * incoming request.
- *
- * @author Renaud Subiger
- * @since 1.0.0
- */
-@Component
-@Order(Ordered.HIGHEST_PRECEDENCE)
-public class LoggingContextFilter extends OncePerRequestFilter {
-
- @Override
- protected void doFilterInternal(@NonNull HttpServletRequest request,
- @NonNull HttpServletResponse response,
- @NonNull FilterChain filterChain)
- throws ServletException, IOException {
-
- try {
- MDC.put("traceId", generateId());
- logger.trace("Set traceId for current request");
-
- filterChain.doFilter(request, response);
- } finally {
- MDC.remove("traceId");
- }
- }
-
- private String generateId() {
- return UUID.randomUUID().toString();
- }
-}
diff --git a/application/src/main/resources/application-cloud.yml b/application/src/main/resources/application-cloud.yml
deleted file mode 100644
index fcdba00efe..0000000000
--- a/application/src/main/resources/application-cloud.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-spring:
- datasource:
- url: jdbc:postgresql://localhost:5432/ehrbase
- username: ehrbase
- password: ehrbase
- hikari:
- maximum-pool-size: 50
- max-lifetime: 1800000
- minimum-idle: 10
-
-security:
- authType: NONE
-
-
-server:
- port: 8080
- # Optional custom server nodename
- # nodename: 'local.test.org'
-
- aqlConfig:
- # if true, WHERE clause is using jsquery, false uses SQL only
- useJsQuery: false
- # ignore unbounded item in path starting with one of
- ignoreIterativeNodeList: 'events,activities,content'
- # how many embedded jsonb_array_elements(..) are acceptable? Recommended == 1
- iterationScanDepth: 1
-
- servlet:
- context-path: /ehrbase
diff --git a/application/src/main/resources/application-docker.yml b/application/src/main/resources/application-docker.yml
deleted file mode 100644
index 10e0552948..0000000000
--- a/application/src/main/resources/application-docker.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright (c) 2019 Vitasystems GmbH and Hannover Medical School.
-#
-# This file is part of Project EHRbase
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-spring:
- datasource:
- url: ${DB_URL}
- username: ${DB_USER}
- password: ${DB_PASS}
- hikari:
- maximum-pool-size: 50
- max-lifetime: 1800000
- minimum-idle: 10
-
-security:
- authType: NONE
-
-server:
- port: 8080
- # Optional custom server nodename
- # nodename: 'local.test.org'
- servlet:
- context-path: /ehrbase
-
- aqlConfig:
- # if true, WHERE clause is using jsquery, false uses SQL only
- useJsQuery: false
- # ignore unbounded item in path starting with one of
- ignoreIterativeNodeList: 'events,activities,content'
- # how many embedded jsonb_array_elements(..) are acceptable? Recommended == 1
- iterationScanDepth: 1
diff --git a/application/src/main/resources/application-local.yml b/application/src/main/resources/application-local.yml
deleted file mode 100644
index 97da688f5a..0000000000
--- a/application/src/main/resources/application-local.yml
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright (c) 2019 Vitasystems GmbH and Hannover Medical School.
-#
-# This file is part of Project EHRbase
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-spring:
- datasource:
- url: jdbc:postgresql://localhost:5432/ehrbase
- username: ehrbase
- password: ehrbase
- tomcat:
- maxIdle: 10
- max-active: 50
- max-wait: 10000
-
-server:
- port: 8080
- # Optional custom server nodename
- # nodename: 'local.test.org'
- servlet:
- context-path: /ehrbase
-
- aqlConfig:
- # if true, WHERE clause is using jsquery, false uses SQL only
- useJsQuery: false
- # ignore unbounded item in path starting with one of
- ignoreIterativeNodeList: 'dummy'
- # how many embedded jsonb_array_elements(..) are acceptable? Recommended == 2
- iterationScanDepth: 20
-
-security:
- authType: NONE
-
-#use admin for cleaning up the db during tests
-admin-api:
- active: true
- allowDeleteAll: true
-
-terminology_server:
- tsUrl: 'https://r4.ontoserver.csiro.au/fhir/'
- codePath: '$["expansion"]["contains"][*]["code"]'
- systemPath: '$["expansion"]["contains"][*]["system"]'
- displayPath: '$["expansion"]["contains"][*]["display"]'
\ No newline at end of file
diff --git a/application/src/main/resources/application.yml b/application/src/main/resources/application.yml
deleted file mode 100644
index ef979602dd..0000000000
--- a/application/src/main/resources/application.yml
+++ /dev/null
@@ -1,208 +0,0 @@
-# Copyright (c) 2019 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
-#
-# This file is part of Project EHRbase
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-# ------------------------------------------------------------------------------
-# General How-to:
-#
-# You can set all config values here or via an corresponding environment variable which is named as the property you
-# want to set. Replace camel case (aB) as all upper case (AB), dashes (-) and low dashes (_) just get ignored adn words
-# will be in one word. Each nesting step of properties will be separated by low dash in environment variable name.
-# E.g. if you want to allow the delete all endpoints in the admin api set an environment variable like this:
-# ADMINAPI_ALLOWDELETEALL=true
-#
-# See https://docs.spring.io/spring-boot/docs/2.5.0/reference/html/features.html#features.external-config.typesafe-configuration-properties.relaxed-binding.environment-variables
-# for official documentation on this feature.
-#
-# Also see the documentation on externalized configuration in general:
-# https://docs.spring.io/spring-boot/docs/2.5.0/reference/html/features.html#features.external-config
-
-spring:
- application:
- name: ehrbase
-
- cache:
- jcache:
- config: classpath:ehcache.xml
-
- security:
- oauth2:
- resourceserver:
- jwt:
- issuer-uri: # http://localhost:8081/auth/realms/ehrbase # Example issuer URI - or set via env var
- profiles:
- active: local
- datasource:
- driver-class-name: org.postgresql.Driver
-
- flyway:
- schemas: ehr
-
- jackson:
- default-property-inclusion: NON_NULL
-
-security:
- authType: BASIC
- authUser: ehrbase-user
- authPassword: SuperSecretPassword
- authAdminUser: ehrbase-admin
- authAdminPassword: EvenMoreSecretPassword
- oauth2UserRole: USER
- oauth2AdminRole: ADMIN
-
-# Attribute Based Access Control
-abac:
- enabled: false
- # Server URL incl. trailing "/"!
- server: http://localhost:3001/rest/v1/policy/execute/name/
- # Definition of the JWT claim which contains the organization ID.
- organizationClaim: 'organization_id'
- # Definition of the JWT claim which contains the patient ID. Falls back to the EHR's subject.
- patientClaim: 'patient_id'
- # Policies need to be named and configured for each resource. Available parameters are
- # - organization
- # - patient
- # - template
- policy:
- ehr:
- name: 'has_consent_patient'
- parameters: 'organization, patient'
- ehrstatus:
- name: 'has_consent_patient'
- parameters: 'organization, patient'
- composition:
- name: 'has_consent_template'
- parameters: 'organization, patient, template'
- #parameters: 'template' # for manual testing, doesn't depend on real claims in JWT
- contribution:
- name: 'has_consent_template'
- parameters: 'organization, patient, template'
- query:
- name: 'has_consent_template'
- parameters: 'organization, patient, template'
-
-httpclient:
-#proxy: 'localhost'
-#proxyPort: 1234
-
-cache:
- init-on-startup: true
- pre-build-queries: true
- pre-build-queries-depth: 4
-
-system:
- allow-template-overwrite: false
-
-openehr-api:
- context-path: /rest/openehr
-admin-api:
- active: false
- allowDeleteAll: false
- context-path: /rest/admin
-
-# Logging Properties
-logging:
- level:
- org.ehcache: info
- org.jooq: info
- org.springframework: info
- pattern:
- console: '%clr(%d{yyyy-MM-dd HH:mm:ss.SSS}){faint} %clr(%5p) %clr([%X]){faint} %clr(${PID}){magenta} %clr(---){faint} %clr([%15.15t]){faint} %clr(%-40.40logger{39}){cyan} %clr(:){faint} %m%n%wEx'
-
-server:
- # Optional custom server nodename
- # nodename: 'local.test.org'
-
- aqlConfig:
- # if true, WHERE clause is using jsquery, false uses SQL only
- useJsQuery: false
- # ignore unbounded item in path starting with one of
- ignoreIterativeNodeList: 'activities,content'
- # how many embedded jsonb_array_elements(..) are acceptable? Recommended == 2
- iterationScanDepth: 2
-
- # Option to disable strict invariant validation.
- # disable-strict-validation: true
-
-
-terminology-server:
- tsUrl: 'https://r4.ontoserver.csiro.au/fhir/'
- codePath: '$["expansion"]["contains"][*]["code"]'
- systemPath: '$["expansion"]["contains"][*]["system"]'
- displayPath: '$["expansion"]["contains"][*]["display"]'
-
-# Configuration of actuator for reporting and health endpoints
-management:
- endpoints:
- # Disable all endpoint by default to opt-in enabled endpoints
- enabled-by-default: false
- web:
- base-path: '/management'
- exposure:
- include: 'env, health, info, metrics, prometheus'
- # Per endpoint settings
- endpoint:
- # Env endpoint - Shows information on environment of EHRbase
- env:
- # Enable / disable env endpoint
- enabled: false
- # Health endpoint - Shows information on system status
- health:
- # Enable / disable health endpoint
- enabled: false
- # Show components in health endpoint. Can be "never", "when-authorized" or "always"
- show-components: 'when-authorized'
- # Show details in health endpoint. Can be "never", "when-authorized" or "always"
- show-details: 'when-authorized'
- # Show additional information on used systems. See https://docs.spring.io/spring-boot/docs/current/reference/html/production-ready-features.html#production-ready-health-indicators for available keys
- datasource:
- # Enable / disable report if datasource connection could be established
- enabled: true
- # Info endpoint - Shows information on the application as build infor, etc.
- info:
- # Enable / disable info endpoint
- enabled: false
- # Metrics endpoint - Shows several metrics on running EHRbase
- metrics:
- # Enable / disable metrics endpoint
- enabled: false
- # Prometheus metric endpoint - Special metrics format to display in microservice observer solutions
- prometheus:
- # Enable / disable prometheus endpoint
- enabled: false
- # Metrics settings
- metrics:
- export:
- prometheus:
- enabled: true
-
-# Audit Properties
-ipf:
- atna:
- audit-enabled: false
-
-# External Terminology Validation Properties
-validation:
- external-terminology:
- enabled: false
-
-# SSL Properties (used by Spring WebClient and Apache HTTP Client)
-client:
- ssl:
- enabled: false
-
-# JavaMelody
-javamelody:
- enabled: false
\ No newline at end of file
diff --git a/application/src/main/resources/banner-cli.txt b/application/src/main/resources/banner-cli.txt
new file mode 100644
index 0000000000..4b5d029f60
--- /dev/null
+++ b/application/src/main/resources/banner-cli.txt
@@ -0,0 +1 @@
+${AnsiColor.BLUE}EHRbase CLI (Spring Boot ${spring-boot.version} EHRbase @project.version@ https://ehrbase.org/)${AnsiBackground.DEFAULT}${AnsiColor.DEFAULT}
\ No newline at end of file
diff --git a/application/src/main/resources/banner.txt b/application/src/main/resources/banner.txt
index 842966cbae..aaea7d2c91 100644
--- a/application/src/main/resources/banner.txt
+++ b/application/src/main/resources/banner.txt
@@ -6,5 +6,5 @@ ${AnsiColor.BLUE}
| |____| | | | | \ \| |_) | (_| \__ \ __/
|______|_| |_|_| \_\_.__/ \__,_|___/\___|
Spring Boot ${spring-boot.version}
-EHRbase ${application.formatted-version}
+EHRbase @project.version@
https://ehrbase.org/ ${AnsiBackground.DEFAULT}${AnsiColor.DEFAULT}
\ No newline at end of file
diff --git a/application/src/main/resources/ehcache.xml b/application/src/main/resources/ehcache.xml
deleted file mode 100644
index 5bbc8b860c..0000000000
--- a/application/src/main/resources/ehcache.xml
+++ /dev/null
@@ -1,84 +0,0 @@
-
-
-
-
-
-
-
-
-
- java.util.UUID
- org.ehrbase.webtemplate.model.WebTemplate
-
-
-
- org.ehrbase.aql.containment.TemplateIdQueryTuple
- org.ehrbase.aql.containment.JsonPathQueryResult
-
-
-
- org.ehrbase.aql.containment.TemplateIdAqlTuple
- org.ehrbase.aql.sql.queryimpl.ItemInfo
-
-
-
- java.lang.String
- java.util.List
-
-
-
-
-
-
-
- 300
- 400
-
-
-
-
-
-
-
-
- 200
- 400
-
-
-
\ No newline at end of file
diff --git a/application/src/main/resources/static/img/ehrbase.png b/application/src/main/resources/static/img/ehrbase.png
new file mode 100644
index 0000000000..684e11c78d
Binary files /dev/null and b/application/src/main/resources/static/img/ehrbase.png differ
diff --git a/application/src/main/resources/static/img/favicons/apple-icon-120x120.png b/application/src/main/resources/static/img/favicons/apple-icon-120x120.png
new file mode 100644
index 0000000000..d84a25a295
Binary files /dev/null and b/application/src/main/resources/static/img/favicons/apple-icon-120x120.png differ
diff --git a/application/src/main/resources/static/img/favicons/apple-icon-152x152.png b/application/src/main/resources/static/img/favicons/apple-icon-152x152.png
new file mode 100644
index 0000000000..7232b8bf53
Binary files /dev/null and b/application/src/main/resources/static/img/favicons/apple-icon-152x152.png differ
diff --git a/application/src/main/resources/static/img/favicons/apple-icon-60x60.png b/application/src/main/resources/static/img/favicons/apple-icon-60x60.png
new file mode 100644
index 0000000000..416ad41cc6
Binary files /dev/null and b/application/src/main/resources/static/img/favicons/apple-icon-60x60.png differ
diff --git a/application/src/main/resources/static/img/favicons/apple-icon-76x76.png b/application/src/main/resources/static/img/favicons/apple-icon-76x76.png
new file mode 100644
index 0000000000..e8ba74a888
Binary files /dev/null and b/application/src/main/resources/static/img/favicons/apple-icon-76x76.png differ
diff --git a/application/src/main/resources/static/img/favicons/favicon-16x16.png b/application/src/main/resources/static/img/favicons/favicon-16x16.png
new file mode 100644
index 0000000000..6c5d991539
Binary files /dev/null and b/application/src/main/resources/static/img/favicons/favicon-16x16.png differ
diff --git a/application/src/main/resources/static/img/favicons/favicon-32x32.png b/application/src/main/resources/static/img/favicons/favicon-32x32.png
new file mode 100644
index 0000000000..0a49b0e9a7
Binary files /dev/null and b/application/src/main/resources/static/img/favicons/favicon-32x32.png differ
diff --git a/application/src/main/resources/static/index.html b/application/src/main/resources/static/index.html
new file mode 100644
index 0000000000..2c11459ef9
--- /dev/null
+++ b/application/src/main/resources/static/index.html
@@ -0,0 +1,31 @@
+
+
+
+
+
+
+ EHRbase Open Source
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/application/src/test/java/org/ehrbase/application/abac/AbacIntegrationTest.java b/application/src/test/java/org/ehrbase/application/abac/AbacIntegrationTest.java
deleted file mode 100644
index 511d5be6b3..0000000000
--- a/application/src/test/java/org/ehrbase/application/abac/AbacIntegrationTest.java
+++ /dev/null
@@ -1,437 +0,0 @@
-/*
- * Copyright (c) 2021 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.abac;
-
-import static org.junit.jupiter.api.Assertions.assertNotEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-import static org.mockito.ArgumentMatchers.anyMap;
-import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.BDDMockito.given;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.verify;
-import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.jwt;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.delete;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.put;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-import com.jayway.jsonpath.JsonPath;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.UUID;
-import org.apache.commons.io.IOUtils;
-import org.ehrbase.test_data.composition.CompositionTestDataCanonicalJson;
-import org.ehrbase.test_data.operationaltemplate.OperationalTemplateTestData;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.condition.EnabledIfEnvironmentVariable;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.boot.test.mock.mockito.MockBean;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.MediaType;
-import org.springframework.security.oauth2.core.user.OAuth2UserAuthority;
-import org.springframework.test.context.ActiveProfiles;
-import org.springframework.test.context.junit4.SpringRunner;
-import org.springframework.test.web.servlet.MockMvc;
-import org.springframework.test.web.servlet.MvcResult;
-import org.springframework.util.ResourceUtils;
-
-@RunWith(SpringRunner.class)
-@SpringBootTest
-@ActiveProfiles({"local", "test"})
-@EnabledIfEnvironmentVariable(named = "EHRBASE_ABAC_IT_TEST", matches = "true")
-@AutoConfigureMockMvc
-class AbacIntegrationTest {
-
- private static final String ORGA_ID = "f47bfc11-ec8d-412e-aebf-c6953cc23e7d";
-
- @MockBean
- private AbacConfig.AbacCheck abacCheck;
-
- @Autowired
- private MockMvc mockMvc;
-
- @Autowired
- private AbacConfig abacConfig;
-
- @Test
- /*
- * This test requires a new and clean DB state to run successfully.
- */
- void testAbacIntegrationTest() throws Exception {
- /*
- ----------------- TEST CONTEXT SETUP -----------------
- */
- // Configure the mock bean of the ABAC server, so we can test with this external service.
- given(this.abacCheck.execute(anyString(), anyMap())).willReturn(true);
-
- Map attributes = new HashMap<>();
- attributes.put("sub", "my-id");
- attributes.put("email", "test@test.org");
-
- // Counters to keep track of number of requests to mock ABAC server bean
- int hasConsentPatientCount = 0;
- int hasConsentTemplateCount = 0;
-
- String externalSubjectRef = UUID.randomUUID().toString();
-
- String ehrStatus =
- String.format(IOUtils.toString(ResourceUtils.getURL("classpath:ehr_status.json"),
- StandardCharsets.UTF_8),
- externalSubjectRef);
-
- MvcResult result = mockMvc.perform(post("/rest/openehr/v1/ehr")
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE)
- .contentType(MediaType.APPLICATION_JSON)
- .content(ehrStatus)
- )
- .andExpectAll(status().isCreated(),
- jsonPath("$.ehr_id.value").exists())
- .andReturn();
-
- String ehrId = JsonPath.read(result.getResponse().getContentAsString(), "$.ehr_id.value");
- Assertions.assertNotNull(ehrId);
- assertNotEquals("", ehrId);
-
- InputStream stream = OperationalTemplateTestData.CORONA_ANAMNESE.getStream();
- Assertions.assertNotNull(stream);
- String streamString = IOUtils.toString(stream, StandardCharsets.UTF_8);
-
- mockMvc.perform(post("/rest/openehr/v1/definition/template/adl1.4/")
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .content(streamString)
- .contentType(MediaType.APPLICATION_XML)
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_XML)
- )
- .andExpect(r -> assertTrue(
- // created 201 or conflict 409 are okay
- r.getResponse().getStatus() == HttpStatus.CREATED.value() ||
- r.getResponse().getStatus() == HttpStatus.CONFLICT.value()));
-
- stream = CompositionTestDataCanonicalJson.CORONA.getStream();
- Assertions.assertNotNull(stream);
- streamString = IOUtils.toString(stream, StandardCharsets.UTF_8);
-
- /*
- ----------------- TEST CASES -----------------
- */
-
- /*
- GET EHR
- */
- mockMvc.perform(get(String.format("/rest/openehr/v1/ehr/%s", ehrId))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isOk());
-
- verify(abacCheck, times(++hasConsentPatientCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_patient", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- }});
- /*
- GET EHR_STATUS
- */
- result = mockMvc.perform(get(String.format("/rest/openehr/v1/ehr/%s/ehr_status", ehrId))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isOk())
- .andReturn();
-
- verify(abacCheck, times(++hasConsentPatientCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_patient", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- }});
-
- String ehrStatusVersionUid = JsonPath.read(result.getResponse().getContentAsString(),
- "$.uid.value");
- Assertions.assertNotNull(ehrStatusVersionUid);
- assertNotEquals("", ehrStatusVersionUid);
-
- /*
- PUT EHR_STATUS
- */
- mockMvc.perform(put(String.format("/rest/openehr/v1/ehr/%s/ehr_status", ehrId))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .header("If-Match", ehrStatusVersionUid)
- .header("PREFER", "return=representation")
- .content(ehrStatus)
- .contentType(MediaType.APPLICATION_JSON)
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isOk());
-
- verify(abacCheck, times(++hasConsentPatientCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_patient", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- }});
- /*
- GET VERSIONED_EHR_STATUS
- */
- mockMvc.perform(
- get(String.format("/rest/openehr/v1/ehr/%s/versioned_ehr_status/version", ehrId))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isOk());
-
- verify(abacCheck, times(++hasConsentPatientCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_patient", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- }});
- /*
- POST COMPOSITION
- */
- result = mockMvc.perform(post(String.format("/rest/openehr/v1/ehr/%s/composition", ehrId))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .content(streamString)
- .contentType(MediaType.APPLICATION_JSON)
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isCreated())
- .andReturn();
-
- String compositionVersionUid = JsonPath.read(result.getResponse().getContentAsString(),
- "$.uid.value");
- Assertions.assertNotNull(compositionVersionUid);
- assertNotEquals("", compositionVersionUid);
- assertTrue(compositionVersionUid.contains("::"));
-
- verify(abacCheck, times(++hasConsentTemplateCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- put("template", "Corona_Anamnese");
- }});
- /*
- GET VERSIONED_COMPOSITION
- */
- mockMvc.perform(get(String.format("/rest/openehr/v1/ehr/%s/versioned_composition/%s/version/%s",
- ehrId, compositionVersionUid.split("::")[0], compositionVersionUid))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isOk());
-
- verify(abacCheck, times(++hasConsentTemplateCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- put("template", "Corona_Anamnese");
- }});
-
- /*
- GET COMPOSITION (here of deleted composition)
- */
- mockMvc.perform(
- get(String.format("/rest/openehr/v1/ehr/%s/composition/%s", ehrId, compositionVersionUid))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isOk());
-
- // Failing: Does not call ABAC Server. Deleted composition does not need to call ABAC server?
- verify(abacCheck, times(++hasConsentTemplateCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- put("template", "Corona_Anamnese");
- }});
-
- /*
- DELETE COMPOSITION
- */
- mockMvc.perform(delete(
- String.format("/rest/openehr/v1/ehr/%s/composition/%s", ehrId, compositionVersionUid))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isNoContent());
-
- verify(abacCheck, times(++hasConsentTemplateCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- put("template", "Corona_Anamnese");
- }});
-
- String contribution =
- String.format(IOUtils.toString(ResourceUtils.getURL("classpath:contribution.json"),
- StandardCharsets.UTF_8),
- streamString);
- /*
- POST CONTRIBUTION
- */
- mockMvc.perform(post(String.format("/rest/openehr/v1/ehr/%s/contribution", ehrId))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .content(contribution)
- .contentType(MediaType.APPLICATION_JSON)
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isCreated())
- .andReturn();
-
- verify(abacCheck, times(++hasConsentTemplateCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- put("template", "Corona_Anamnese");
- }});
-
- /*
- POST QUERY
- */
- mockMvc.perform(post("/rest/openehr/v1/query/aql")
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .content("{\n"
- + " \"q\": \"select e/ehr_id/value, c/uid/value, c/archetype_details/template_id/value, c/feeder_audit from EHR e CONTAINS composition c\"\n"
- + "}")
- .contentType(MediaType.APPLICATION_JSON)
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isOk());
-
- verify(abacCheck, times(++hasConsentTemplateCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- put("template", "Corona_Anamnese");
- }});
-
- /*
- GET QUERY
- */
- String pathQuery = "select e/ehr_id/value, c/uid/value, c/archetype_details/template_id/value, c/feeder_audit from EHR e CONTAINS composition c";
-
- mockMvc.perform(get(String.format("/rest/openehr/v1/query/aql?q=%s", pathQuery))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- )
- .andExpect(status().isOk());
-
- verify(abacCheck, times(++hasConsentTemplateCount)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template", new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- put("template", "Corona_Anamnese");
- }});
-
- /*
- GET QUERY WITH MULTIPLE EHRs AND TEMPLATES (incl. posting those)
- */
- // post another template
- stream = OperationalTemplateTestData.MINIMAL_EVALUATION.getStream();
- Assertions.assertNotNull(stream);
- streamString = IOUtils.toString(stream, StandardCharsets.UTF_8);
-
- mockMvc.perform(post("/rest/openehr/v1/definition/template/adl1.4/")
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .content(streamString)
- .contentType(MediaType.APPLICATION_XML)
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_XML)
- )
- .andExpect(r -> assertTrue(
- // created 201 or conflict 409 are okay
- r.getResponse().getStatus() == HttpStatus.CREATED.value() ||
- r.getResponse().getStatus() == HttpStatus.CONFLICT.value()));
-
- streamString = IOUtils.toString(ResourceUtils.getURL("classpath:composition.json"),
- StandardCharsets.UTF_8);
-
- mockMvc.perform(post(String.format("/rest/openehr/v1/ehr/%s/composition", ehrId))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- .content(streamString)
- .contentType(MediaType.APPLICATION_JSON)
- .header("PREFER", "return=representation")
- .accept(MediaType.APPLICATION_JSON_VALUE))
- .andExpect(status().isCreated())
- .andReturn();
-
- verify(abacCheck).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template",
- new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- put("template", "minimal_evaluation.en.v1");
- }});
-
- mockMvc.perform(get(String.format("/rest/openehr/v1/query/aql?q=%s", pathQuery))
- .with(jwt().authorities(new OAuth2UserAuthority("ROLE_USER", attributes)).
- jwt(token -> token.claim(abacConfig.getPatientClaim(), externalSubjectRef)
- .claim(abacConfig.getOrganizationClaim(), ORGA_ID)))
- )
- .andExpect(status().isOk());
-
-// verify(abacCheck, times(++hasConsentTemplateCount)).execute(
-// "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template", new HashMap<>() {{
-// put("patient", externalSubjectRef);
-// put("organization", ORGA_ID);
-// put("template", "Corona_Anamnese");
-// }});
-
- verify(abacCheck, times(3)).execute(
- "http://localhost:3001/rest/v1/policy/execute/name/has_consent_template",
- new HashMap<>() {{
- put("patient", externalSubjectRef);
- put("organization", ORGA_ID);
- put("template", "minimal_evaluation.en.v1");
- }});
-
- }
-}
\ No newline at end of file
diff --git a/application/src/test/java/org/ehrbase/application/abac/FlywayTestConfiguration.java b/application/src/test/java/org/ehrbase/application/abac/FlywayTestConfiguration.java
deleted file mode 100644
index 861be79ba7..0000000000
--- a/application/src/test/java/org/ehrbase/application/abac/FlywayTestConfiguration.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package org.ehrbase.application.abac;
-
-import org.springframework.boot.autoconfigure.flyway.FlywayMigrationStrategy;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-
-@Configuration
-public class FlywayTestConfiguration {
-
- @Bean
- public FlywayMigrationStrategy clean() {
- return flyway -> {
- flyway.clean();
- flyway.migrate();
- };
- }
-}
diff --git a/application/src/test/java/org/ehrbase/application/cors/CorsBasicAuthIT.java b/application/src/test/java/org/ehrbase/application/cors/CorsBasicAuthIT.java
deleted file mode 100644
index 98d13ada4d..0000000000
--- a/application/src/test/java/org/ehrbase/application/cors/CorsBasicAuthIT.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package org.ehrbase.application.cors;
-
-import org.junit.jupiter.api.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.test.web.servlet.MockMvc;
-
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.options;
-import static org.springframework.test.web.servlet.result.MockMvcResultHandlers.print;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-@SpringBootTest(properties = {
- "security.authType=basic",
- "spring.cache.type=simple"
-})
-@AutoConfigureMockMvc
-class CorsBasicAuthIT {
-
- @Autowired
- private MockMvc mockMvc;
-
- @Test
- void testCors() throws Exception {
- mockMvc.perform(options("/rest/openehr/v1/definition/template/adl1.4")
- .header("Access-Control-Request-Method", "GET")
- .header("Origin", "https://client.ehrbase.org"))
- .andDo(print())
- .andExpect(status().isOk());
- }
-}
diff --git a/application/src/test/java/org/ehrbase/application/cors/CorsNoAuthIT.java b/application/src/test/java/org/ehrbase/application/cors/CorsNoAuthIT.java
deleted file mode 100644
index 422c1664f2..0000000000
--- a/application/src/test/java/org/ehrbase/application/cors/CorsNoAuthIT.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package org.ehrbase.application.cors;
-
-import org.junit.jupiter.api.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.test.web.servlet.MockMvc;
-
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.options;
-import static org.springframework.test.web.servlet.result.MockMvcResultHandlers.print;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-@SpringBootTest(properties = {
- "spring.cache.type=simple"
-})
-@AutoConfigureMockMvc
-class CorsNoAuthIT {
-
- @Autowired
- private MockMvc mockMvc;
-
- @Test
- void testCors() throws Exception {
- mockMvc.perform(options("/rest/openehr/v1/definition/template/adl1.4")
- .header("Access-Control-Request-Method", "GET")
- .header("Origin", "https://client.ehrbase.org"))
- .andDo(print())
- .andExpect(status().isOk());
- }
-}
diff --git a/aql-engine/pom.xml b/aql-engine/pom.xml
new file mode 100644
index 0000000000..fd21453049
--- /dev/null
+++ b/aql-engine/pom.xml
@@ -0,0 +1,119 @@
+
+
+ 4.0.0
+
+ org.ehrbase.openehr
+ server
+ 2.23.0-SNAPSHOT
+
+
+ aql-engine
+ EHRbase AQL Engine
+
+
+ 21
+ 21
+ UTF-8
+
+
+
+
+
+ org.ehrbase.openehr
+ rm-db-format
+
+
+ org.ehrbase.openehr
+ api
+
+
+ org.ehrbase.openehr
+ jooq-pg
+
+
+ org.ehrbase.openehr.sdk
+ validation
+
+
+
+
+ org.springframework
+ spring-context
+
+
+ org.springframework
+ spring-core
+
+
+ org.springframework
+ spring-tx
+
+
+ org.springframework
+ spring-web
+
+
+
+
+ org.springframework.boot
+ spring-boot
+
+
+
+
+ org.apache.commons
+ commons-lang3
+
+
+
+
+ org.junit.jupiter
+ junit-jupiter
+ test
+
+
+ org.mockito
+ mockito-core
+ test
+
+
+
+ client
+ org.ehrbase.openehr.sdk
+ test
+
+
+ org.ehrbase.openehr.sdk
+ test-data
+ test
+
+
+ org.springframework.boot
+ spring-boot-starter-test
+ test
+
+
+ net.java
+ quickcheck
+ 0.6
+ test
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-jar-plugin
+
+
+
+ test-jar
+
+
+
+
+
+
+
diff --git a/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlConfigurationProperties.java b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlConfigurationProperties.java
new file mode 100644
index 0000000000..26d22e41da
--- /dev/null
+++ b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlConfigurationProperties.java
@@ -0,0 +1,83 @@
+/*
+ * Copyright (c) 2019-2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.openehr.aqlengine;
+
+import org.ehrbase.openehr.aqlengine.AqlConfigurationProperties.Experimental.AqlOnFolder;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+/**
+ * AQL features that can be optionally enabled.
+ *
+ *
+ *
pg-llj-workaround Enables fix for an old postgresql bug where filters in lateral left joins inside a left join are not respected, default: true
+ *
experimental.aql-on-folder.enabled if enabled allow to query EHRFOLDER using AQL, default: false
+ *
+ */
+@ConfigurationProperties(prefix = "ehrbase.aql")
+public final class AqlConfigurationProperties {
+ private boolean pgLljWorkaround;
+ private boolean archetypeLocalNodePredicates = true;
+ private boolean pathNodeSkipping;
+ private Experimental experimental = new Experimental(new AqlOnFolder(false));
+
+ public boolean pgLljWorkaround() {
+ return pgLljWorkaround;
+ }
+
+ public boolean archetypeLocalNodePredicates() {
+ return archetypeLocalNodePredicates;
+ }
+
+ public boolean pathNodeSkipping() {
+ return pathNodeSkipping;
+ }
+
+ public Experimental experimental() {
+ return experimental;
+ }
+
+ public void setPgLljWorkaround(final boolean pgLljWorkaround) {
+ this.pgLljWorkaround = pgLljWorkaround;
+ }
+
+ public void setArchetypeLocalNodePredicates(final boolean archetypeLocalNodePredicates) {
+ this.archetypeLocalNodePredicates = archetypeLocalNodePredicates;
+ }
+
+ public void setPathNodeSkipping(final boolean pathNodeSkipping) {
+ this.pathNodeSkipping = pathNodeSkipping;
+ }
+
+ public void setExperimental(final Experimental experimental) {
+ this.experimental = experimental;
+ }
+
+ @Override
+ public String toString() {
+ return "AqlConfigurationProperties[" + "pgLljWorkaround="
+ + pgLljWorkaround + ", " + "archetypeLocalNodePredicates="
+ + archetypeLocalNodePredicates + ", " + "pathNodeSkipping="
+ + pathNodeSkipping + ", " + "experimental="
+ + experimental + ']';
+ }
+
+ public record Experimental(AqlOnFolder aqlOnFolder) {
+
+ public record AqlOnFolder(boolean enabled) {}
+ }
+}
diff --git a/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlEhrPathPostProcessor.java b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlEhrPathPostProcessor.java
new file mode 100644
index 0000000000..52aeec987d
--- /dev/null
+++ b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlEhrPathPostProcessor.java
@@ -0,0 +1,162 @@
+/*
+ * Copyright (c) 2025 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.openehr.aqlengine;
+
+import java.util.Comparator;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.regex.Pattern;
+import java.util.stream.Stream;
+import org.apache.commons.collections4.CollectionUtils;
+import org.ehrbase.api.dto.AqlQueryContext;
+import org.ehrbase.api.dto.AqlQueryRequest;
+import org.ehrbase.api.exception.AqlFeatureNotImplementedException;
+import org.ehrbase.openehr.sdk.aql.dto.AqlQuery;
+import org.ehrbase.openehr.sdk.aql.dto.containment.AbstractContainmentExpression;
+import org.ehrbase.openehr.sdk.aql.dto.containment.ContainmentClassExpression;
+import org.ehrbase.openehr.sdk.aql.dto.containment.ContainmentSetOperator;
+import org.ehrbase.openehr.sdk.aql.dto.containment.ContainmentSetOperatorSymbol;
+import org.ehrbase.openehr.sdk.aql.dto.operand.IdentifiedPath;
+import org.ehrbase.openehr.sdk.aql.dto.path.AqlObjectPath;
+import org.ehrbase.openehr.sdk.aql.dto.path.AqlObjectPath.PathNode;
+import org.ehrbase.openehr.sdk.aql.util.AqlUtil;
+import org.ehrbase.openehr.sdk.util.rmconstants.RmConstants;
+import org.springframework.stereotype.Component;
+
+/**
+ * Replaces paths targeting EHR_STATUS, but starting at EHR. For more information {@see replaceEhrPaths}
+ */
+@Component
+public class AqlEhrPathPostProcessor implements AqlQueryParsingPostProcessor {
+ @Override
+ public void afterParseAql(final AqlQuery aqlQuery, final AqlQueryRequest request, final AqlQueryContext ctx) {
+ replaceEhrPaths(aqlQuery);
+ }
+
+ @Override
+ public int getOrder() {
+ return EHR_PATH_PRECEDENCE;
+ }
+
+ /**
+ * Rephrases EHR.status to CONTAINS statements so that they can be handled regularly by the aql engine.
+ * I.e. SELECT e/ehr_status FROM EHR is rewritten as SELECT s FROM EHR e CONTAINS EHR_STATUS s.
+ * EHR/composition, EHR/directory, and EHR/folders are not supported because the path syntax implies that the objects are optional (vs. CONTAINS).
+ */
+ static void replaceEhrPaths(AqlQuery aqlQuery) {
+ replaceEhrPath(aqlQuery, "ehr_status", RmConstants.EHR_STATUS, "s");
+ }
+
+ /**
+ * Rephrases a path from EHR to EHR_STATUS as CONTAINS statement so that it can be handled regularly by the aql engine.
+ * E.g. SELECT e/status FROM EHR is rewritten as SELECT s FROM EHR e CONTAINS EHR_STATUS s.
+ */
+ static void replaceEhrPath(AqlQuery aqlQuery, String ehrPath, String type, String aliasPrefix) {
+
+ // gather paths that contain EHR/status.
+ List ehrPaths = AqlQueryUtils.allIdentifiedPaths(aqlQuery)
+ // EHR
+ .filter(ip -> ip.getRoot() instanceof ContainmentClassExpression cce
+ && cce.getType().equals(RmConstants.EHR))
+ // EHR.ehrPath...
+ .filter(ip -> Optional.of(ip)
+ .map(IdentifiedPath::getPath)
+ .map(AqlObjectPath::getPathNodes)
+ .map(List::getFirst)
+ .map(PathNode::getAttribute)
+ .filter(ehrPath::equals)
+ .isPresent())
+ .toList();
+
+ if (ehrPaths.isEmpty()) {
+ return;
+ }
+
+ if (ehrPaths.stream()
+ .map(IdentifiedPath::getRoot)
+ .map(AbstractContainmentExpression::getIdentifier)
+ .distinct()
+ .count()
+ > 1) {
+ throw new AqlFeatureNotImplementedException("Multiple EHR in FROM are not supported");
+ }
+
+ if (ehrPaths.stream().map(IdentifiedPath::getRootPredicate).anyMatch(CollectionUtils::isNotEmpty)) {
+ throw new AqlFeatureNotImplementedException(
+ "Root predicates for EHR/%s are not supported".formatted(ehrPath));
+ }
+
+ if (ehrPaths.stream()
+ .map(IdentifiedPath::getPath)
+ .map(p -> p.getPathNodes().getFirst().getPredicateOrOperands())
+ .distinct()
+ .count()
+ > 1) {
+ // could result in multiple containments
+ throw new AqlFeatureNotImplementedException(
+ "Specifying different predicates for EHR/%s is not supported".formatted(ehrPath));
+ }
+ // determine unused alias
+ String alias = AqlUtil.streamContainments(aqlQuery.getFrom())
+ .map(AbstractContainmentExpression::getIdentifier)
+ .filter(Objects::nonNull)
+ .filter(s -> s.matches(Pattern.quote(aliasPrefix) + "\\d*"))
+ .map(s -> aliasPrefix.equals(s) ? 0 : Long.parseLong(s.substring(1)))
+ .max(Comparator.naturalOrder())
+ .map(i -> aliasPrefix + (i + 1))
+ .orElse(aliasPrefix);
+
+ // insert CONTAINS [type] (AND if needed)
+ // what about "SELECT e[ehr_id=…]/status from EHR e"?
+ ContainmentClassExpression ehrContainment =
+ (ContainmentClassExpression) ehrPaths.getFirst().getRoot();
+
+ ContainmentClassExpression ehrStatusContainment = new ContainmentClassExpression();
+ ehrStatusContainment.setType(type);
+ ehrStatusContainment.setIdentifier(alias);
+
+ // copy first predicate (all all are the same)
+ ehrPaths.stream()
+ .findFirst()
+ .map(IdentifiedPath::getPath)
+ .map(p -> p.getPathNodes().getFirst().getPredicateOrOperands())
+ .ifPresent(ehrStatusContainment::setPredicates);
+
+ // add containment
+ if (ehrContainment.getContains() == null) {
+ ehrContainment.setContains(ehrStatusContainment);
+ } else if (ehrContainment.getContains() instanceof ContainmentSetOperator cse
+ && cse.getSymbol() == ContainmentSetOperatorSymbol.AND) {
+ cse.setValues(Stream.concat(Stream.of(ehrStatusContainment), cse.getValues().stream())
+ .toList());
+ } else {
+ ContainmentSetOperator and = new ContainmentSetOperator();
+ and.setSymbol(ContainmentSetOperatorSymbol.AND);
+ and.setValues(List.of(ehrStatusContainment, ehrContainment.getContains()));
+ ehrContainment.setContains(and);
+ }
+
+ // rewrite paths
+ ehrPaths.forEach(ip -> {
+ ip.setRoot(ehrStatusContainment);
+ List pathNodes = ip.getPath().getPathNodes();
+ ip.setPath(pathNodes.size() == 1 ? null : new AqlObjectPath(pathNodes.subList(1, pathNodes.size())));
+ });
+ }
+}
diff --git a/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlEngineModuleConfiguration.java b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlEngineModuleConfiguration.java
new file mode 100644
index 0000000000..c56cd87e16
--- /dev/null
+++ b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlEngineModuleConfiguration.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.openehr.aqlengine;
+
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.EnableAspectJAutoProxy;
+
+@Configuration
+@ComponentScan
+@EnableAspectJAutoProxy
+@EnableConfigurationProperties(AqlConfigurationProperties.class)
+public class AqlEngineModuleConfiguration {}
diff --git a/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlFromEhrOptimisationPostProcessor.java b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlFromEhrOptimisationPostProcessor.java
new file mode 100644
index 0000000000..a8a94a784d
--- /dev/null
+++ b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlFromEhrOptimisationPostProcessor.java
@@ -0,0 +1,60 @@
+/*
+ * Copyright (c) 2025 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.openehr.aqlengine;
+
+import org.ehrbase.api.dto.AqlQueryContext;
+import org.ehrbase.api.dto.AqlQueryRequest;
+import org.ehrbase.openehr.sdk.aql.dto.AqlQuery;
+import org.ehrbase.openehr.sdk.aql.dto.containment.ContainmentClassExpression;
+import org.ehrbase.openehr.sdk.util.rmconstants.RmConstants;
+import org.springframework.stereotype.Component;
+
+/**
+ * Removes unused EHR at the start of the FROM statement of an {@link AqlQuery} for simple cases.
+ */
+@Component
+public class AqlFromEhrOptimisationPostProcessor implements AqlQueryParsingPostProcessor {
+ @Override
+ public int getOrder() {
+ return FROM_EHR_OPTIMISATION_PRECEDENCE;
+ }
+
+ @Override
+ public void afterParseAql(final AqlQuery aqlQuery, final AqlQueryRequest request, final AqlQueryContext ctx) {
+ // remove unused FROM EHR
+ if (aqlQuery.getFrom() instanceof ContainmentClassExpression containment
+ && RmConstants.EHR.equals(containment.getType())
+ && containment.getContains() instanceof ContainmentClassExpression childContainment
+ && !isReferenced(containment, aqlQuery)) {
+ aqlQuery.setFrom(childContainment);
+ }
+ }
+
+ protected static boolean isReferenced(ContainmentClassExpression containment, AqlQuery aqlQuery) {
+ if (containment.getPredicates() != null) {
+ return true;
+ }
+ String identifier = containment.getIdentifier();
+ if (identifier == null) {
+ return false;
+ } else {
+ return AqlQueryUtils.allIdentifiedPaths(aqlQuery)
+ .anyMatch(p -> p.getRoot().equals(containment));
+ }
+ }
+}
diff --git a/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlLimitPostProcessor.java b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlLimitPostProcessor.java
new file mode 100644
index 0000000000..623b4e72d7
--- /dev/null
+++ b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlLimitPostProcessor.java
@@ -0,0 +1,133 @@
+/*
+ * Copyright (c) 2025 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.openehr.aqlengine;
+
+import org.apache.commons.lang3.ObjectUtils;
+import org.ehrbase.api.dto.AqlQueryContext;
+import org.ehrbase.api.dto.AqlQueryRequest;
+import org.ehrbase.api.exception.UnprocessableEntityException;
+import org.ehrbase.openehr.sdk.aql.dto.AqlQuery;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Component;
+
+/**
+ * Applies upper bounds and/or defaults for limit/fetch to an {@link AqlQuery}.
+ */
+@Component
+public class AqlLimitPostProcessor implements AqlQueryParsingPostProcessor {
+
+ public enum FetchPrecedence {
+ /**
+ * Fail if both fetch and limit are present
+ */
+ REJECT,
+ /**
+ * Take minimum of fetch and limit for limit;
+ * fail if query has offset
+ */
+ MIN_FETCH
+ }
+
+ private final Long defaultLimit;
+ private final Long maxLimit;
+ private final Long maxFetch;
+ private final FetchPrecedence fetchPrecedence;
+
+ public AqlLimitPostProcessor(
+ @Value("${ehrbase.rest.aql.default-limit:}") Long defaultLimit,
+ @Value("${ehrbase.rest.aql.max-limit:}") Long maxLimit,
+ @Value("${ehrbase.rest.aql.max-fetch:}") Long maxFetch,
+ @Value("${ehrbase.rest.aql.fetch-precedence:REJECT}") FetchPrecedence fetchPrecedence) {
+ this.defaultLimit = defaultLimit;
+ this.maxLimit = maxLimit;
+ this.maxFetch = maxFetch;
+ this.fetchPrecedence = fetchPrecedence;
+ }
+
+ @Override
+ public int getOrder() {
+ return LIMIT_CONSTRAINT_PRECEDENCE;
+ }
+
+ @Override
+ public void afterParseAql(final AqlQuery aqlQuery, final AqlQueryRequest request, final AqlQueryContext ctx) {
+
+ // add defaults and upper bounds to meta information
+ if (defaultLimit != null) {
+ ctx.setMetaProperty(AqlQueryContext.EhrbaseMetaProperty.DEFAULT_LIMIT, defaultLimit);
+ }
+ if (maxLimit != null) {
+ ctx.setMetaProperty(AqlQueryContext.EhrbaseMetaProperty.MAX_LIMIT, maxLimit);
+ }
+ if (maxFetch != null) {
+ ctx.setMetaProperty(AqlQueryContext.EhrbaseMetaProperty.MAX_FETCH, maxFetch);
+ }
+
+ // apply limit and offset - where the definitions from the aql are the precedence
+ Long fetchParam = request.fetch();
+ Long offsetParam = request.offset();
+
+ Long queryLimit = aqlQuery.getLimit();
+ Long queryOffset = aqlQuery.getOffset();
+
+ if (queryLimit != null && maxLimit != null && queryLimit > maxLimit) {
+ throw new UnprocessableEntityException(
+ "Query LIMIT %d exceeds maximum limit %d".formatted(queryLimit, maxLimit));
+ }
+
+ if (fetchParam != null && maxFetch != null && fetchParam > maxFetch) {
+ throw new UnprocessableEntityException(
+ "Fetch parameter %d exceeds maximum fetch %d".formatted(fetchParam, maxFetch));
+ }
+
+ Long limit = applyFetchPrecedence(fetchPrecedence, queryLimit, queryOffset, fetchParam, offsetParam);
+
+ aqlQuery.setLimit(ObjectUtils.firstNonNull(limit, defaultLimit));
+ aqlQuery.setOffset(ObjectUtils.firstNonNull(offsetParam, queryOffset));
+ }
+
+ private static Long applyFetchPrecedence(
+ FetchPrecedence fetchPrecedence, Long queryLimit, Long queryOffset, Long fetchParam, Long offsetParam) {
+
+ if (fetchParam == null) {
+ if (offsetParam != null) {
+ throw new UnprocessableEntityException("Query parameter for offset provided, but no fetch parameter");
+ }
+ return queryLimit;
+ } else if (queryLimit == null) {
+ assert queryOffset == null;
+ return fetchParam;
+ }
+
+ return switch (fetchPrecedence) {
+ case REJECT -> {
+ throw new UnprocessableEntityException(
+ "Query contains a LIMIT clause, fetch and offset parameters must not be used (with fetch precedence %s)"
+ .formatted(fetchPrecedence));
+ }
+ case MIN_FETCH -> {
+ if (queryOffset != null) {
+ throw new UnprocessableEntityException(
+ "Query contains a OFFSET clause, fetch parameter must not be used (with fetch precedence %s)"
+ .formatted(fetchPrecedence));
+ }
+ yield Math.min(queryLimit, fetchParam);
+ }
+ };
+ }
+}
diff --git a/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlParameterPostProcessor.java b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlParameterPostProcessor.java
new file mode 100644
index 0000000000..7018e5ca8c
--- /dev/null
+++ b/aql-engine/src/main/java/org/ehrbase/openehr/aqlengine/AqlParameterPostProcessor.java
@@ -0,0 +1,579 @@
+/*
+ * Copyright (c) 2024 vitasystems GmbH.
+ *
+ * This file is part of project EHRbase
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ehrbase.openehr.aqlengine;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Map;
+import java.util.Optional;
+import java.util.function.BiFunction;
+import java.util.function.Consumer;
+import java.util.function.Function;
+import java.util.regex.Pattern;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
+import java.util.stream.Stream;
+import org.apache.commons.collections4.MapUtils;
+import org.ehrbase.api.dto.AqlQueryContext;
+import org.ehrbase.api.dto.AqlQueryRequest;
+import org.ehrbase.openehr.aqlengine.asl.model.AslRmTypeAndConcept;
+import org.ehrbase.openehr.sdk.aql.dto.AqlQuery;
+import org.ehrbase.openehr.sdk.aql.dto.condition.ComparisonOperatorCondition;
+import org.ehrbase.openehr.sdk.aql.dto.condition.ExistsCondition;
+import org.ehrbase.openehr.sdk.aql.dto.condition.LikeCondition;
+import org.ehrbase.openehr.sdk.aql.dto.condition.LogicalOperatorCondition;
+import org.ehrbase.openehr.sdk.aql.dto.condition.MatchesCondition;
+import org.ehrbase.openehr.sdk.aql.dto.condition.NotCondition;
+import org.ehrbase.openehr.sdk.aql.dto.condition.WhereCondition;
+import org.ehrbase.openehr.sdk.aql.dto.containment.AbstractContainmentExpression;
+import org.ehrbase.openehr.sdk.aql.dto.containment.Containment;
+import org.ehrbase.openehr.sdk.aql.dto.containment.ContainmentClassExpression;
+import org.ehrbase.openehr.sdk.aql.dto.containment.ContainmentNotOperator;
+import org.ehrbase.openehr.sdk.aql.dto.containment.ContainmentSetOperator;
+import org.ehrbase.openehr.sdk.aql.dto.containment.ContainmentVersionExpression;
+import org.ehrbase.openehr.sdk.aql.dto.operand.AggregateFunction;
+import org.ehrbase.openehr.sdk.aql.dto.operand.BooleanPrimitive;
+import org.ehrbase.openehr.sdk.aql.dto.operand.ComparisonLeftOperand;
+import org.ehrbase.openehr.sdk.aql.dto.operand.DoublePrimitive;
+import org.ehrbase.openehr.sdk.aql.dto.operand.IdentifiedPath;
+import org.ehrbase.openehr.sdk.aql.dto.operand.LikeOperand;
+import org.ehrbase.openehr.sdk.aql.dto.operand.LongPrimitive;
+import org.ehrbase.openehr.sdk.aql.dto.operand.MatchesOperand;
+import org.ehrbase.openehr.sdk.aql.dto.operand.Operand;
+import org.ehrbase.openehr.sdk.aql.dto.operand.PathPredicateOperand;
+import org.ehrbase.openehr.sdk.aql.dto.operand.Primitive;
+import org.ehrbase.openehr.sdk.aql.dto.operand.QueryParameter;
+import org.ehrbase.openehr.sdk.aql.dto.operand.SingleRowFunction;
+import org.ehrbase.openehr.sdk.aql.dto.operand.StringPrimitive;
+import org.ehrbase.openehr.sdk.aql.dto.operand.TemporalPrimitive;
+import org.ehrbase.openehr.sdk.aql.dto.operand.TerminologyFunction;
+import org.ehrbase.openehr.sdk.aql.dto.orderby.OrderByExpression;
+import org.ehrbase.openehr.sdk.aql.dto.path.AndOperatorPredicate;
+import org.ehrbase.openehr.sdk.aql.dto.path.AqlObjectPath;
+import org.ehrbase.openehr.sdk.aql.dto.path.AqlObjectPathUtil;
+import org.ehrbase.openehr.sdk.aql.dto.path.ComparisonOperatorPredicate;
+import org.ehrbase.openehr.sdk.aql.dto.select.SelectClause;
+import org.ehrbase.openehr.sdk.aql.dto.select.SelectExpression;
+import org.ehrbase.openehr.sdk.aql.parser.AqlParseException;
+import org.springframework.stereotype.Component;
+
+/**
+ * Replaces parameters in an AQL query
+ */
+@Component
+public class AqlParameterPostProcessor implements AqlQueryParsingPostProcessor {
+
+ @Override
+ public void afterParseAql(final AqlQuery aqlQuery, final AqlQueryRequest request, final AqlQueryContext ctx) {
+ replaceParameters(aqlQuery, request.parameters());
+ }
+
+ @Override
+ public int getOrder() {
+ return PARAMETER_REPLACEMENT_PRECEDENCE;
+ }
+ /**
+ * Replaces all parameters in the aqlQuery with values from the parameterMap.
+ * The replacement is performed in-place, modifying the source object.
+ * Missing parameter values are set to NULL.
+ *
+ * @param aqlQuery the query to me modified
+ * @param parameterMap a map of parameter values
+ */
+ public static void replaceParameters(AqlQuery aqlQuery, Map parameterMap) {
+ if (MapUtils.isNotEmpty(parameterMap)) {
+ // SELECT
+ SelectParams.replaceParameters(aqlQuery.getSelect(), parameterMap);
+ // FROM
+ ContainmentParams.replaceParameters(aqlQuery.getFrom(), parameterMap);
+ // WHERE
+ WhereParams.replaceParameters(aqlQuery.getWhere(), parameterMap);
+ // ORDER BY
+ OrderByParams.replaceParameters(parameterMap, aqlQuery.getOrderBy());
+ }
+ }
+
+ public static void replaceIdentifiedPathParameters(
+ IdentifiedPath identifiedPath, Map parameterMap) {
+ // revise root predicates in-place
+ Optional.of(identifiedPath).map(IdentifiedPath::getRootPredicate).stream()
+ .flatMap(List::stream)
+ .map(AndOperatorPredicate::getOperands)
+ .flatMap(List::stream)
+ .forEach(co -> ObjectPathParams.replaceComparisonOperatorParameters(co, parameterMap));
+ ObjectPathParams.replaceParameters(identifiedPath.getPath(), parameterMap)
+ .ifPresent(identifiedPath::setPath);
+ }
+
+ /**
+ * @param operand
+ * @param parameterMap
+ * @return a Stream of new primitive, if the operand needs to be replaced
+ */
+ private static Stream replaceOperandParameters(Operand operand, Map parameterMap) {
+
+ return switch (operand) {
+ case QueryParameter qp -> resolveParameters(qp, parameterMap);
+ case IdentifiedPath path -> {
+ replaceIdentifiedPathParameters(path, parameterMap);
+ yield null;
+ }
+ case SingleRowFunction func -> {
+ replaceFunctionParameters(func, parameterMap);
+ yield null;
+ }
+ case TerminologyFunction __ -> null;
+ case Primitive __ -> null;
+ };
+ }
+
+ private static void replaceFunctionParameters(SingleRowFunction func, Map parameterMap) {
+ Utils.reviseList(func.getOperandList(), o -> replaceOperandParameters(o, parameterMap));
+ }
+
+ private static Stream resolveParameters(QueryParameter param, Map parameterMap) {
+ String paramName = param.getName();
+ Object paramValue = parameterMap.get(paramName);
+
+ return switch (paramValue) {
+ case Collection c -> c.stream().map(e -> toPrimitive(param.getName(), e));
+ case null -> throw new AqlParseException("Missing parameter '%s'".formatted(paramName));
+ default -> Stream.of(toPrimitive(param.getName(), paramValue));
+ };
+ }
+
+ private static Primitive toPrimitive(String name, Object paramValue) {
+ return switch (paramValue) {
+ case null -> throw new AqlParseException("Missing parameter '%s'".formatted(name));
+ case Integer i -> new LongPrimitive(i.longValue());
+ case Long i -> new LongPrimitive(i);
+ case Number nr -> new DoublePrimitive(nr.doubleValue());
+ case String str -> Utils.stringToPrimitive(str);
+ case Boolean b -> new BooleanPrimitive(b);
+ default -> {
+ throw new IllegalArgumentException("Type of parameter '%s' is not supported".formatted(name));
+ }
+ };
+ }
+
+ private record ModifiedElement(int index, T node) {}
+
+ private static final class OrderByParams {
+
+ public static void replaceParameters(Map parameterMap, List orderBy) {
+ if (orderBy != null) {
+ orderBy.stream()
+ .map(OrderByExpression::getStatement)
+ .forEach(path -> replaceIdentifiedPathParameters(path, parameterMap));
+ }
+ }
+ }
+
+ private static final class SelectParams {
+
+ public static void replaceParameters(SelectClause selectClause, Map parameterMap) {
+ selectClause.getStatement().stream()
+ .map(SelectExpression::getColumnExpression)
+ .forEach(ce -> {
+ switch (ce) {
+ case SingleRowFunction func -> replaceFunctionParameters(func, parameterMap);
+ case AggregateFunction aFunc -> replaceIdentifiedPathParameters(
+ aFunc.getIdentifiedPath(), parameterMap);
+ case IdentifiedPath identifiedPath -> replaceIdentifiedPathParameters(
+ identifiedPath, parameterMap);
+ case Primitive __ -> {
+ /* No parameters */
+ }
+ case TerminologyFunction __ -> {
+ /* No parameters */
+ }
+ }
+ });
+ }
+ }
+
+ private static final class WhereParams {
+ public static void replaceParameters(WhereCondition condition, Map parameterMap) {
+ switch (condition) {
+ case null -> {
+ /* NOOP */
+ }
+ case ComparisonOperatorCondition c -> {
+ replaceComparisonLeftOperandParameters(c.getStatement(), parameterMap);
+ ensureSingleElement(replaceOperandParameters(c.getValue(), parameterMap), c::setValue);
+ }
+ case NotCondition c -> replaceParameters(c.getConditionDto(), parameterMap);
+ case MatchesCondition c -> Utils.reviseList(
+ c.getValues(), o -> replaceMatchesParameters(o, parameterMap));
+ case LikeCondition c -> replaceLikeOperandParameters(c.getValue(), parameterMap)
+ .ifPresent(c::setValue);
+ case LogicalOperatorCondition c -> c.getValues().forEach(v -> replaceParameters(v, parameterMap));
+ case ExistsCondition __ -> {
+ /* NOOP */
+ }
+ default -> throw new IllegalStateException("Unexpected value: " + condition);
+ }
+ }
+
+ private static Optional replaceLikeOperandParameters(
+ LikeOperand value, Map parameterMap) {
+ if (value instanceof QueryParameter qp) {
+ return Optional.of(qp.getName())
+ .map(parameterMap::get)
+ .map(Object::toString)
+ .map(Utils::stringToPrimitive)
+ .or(() -> Optional.of(new StringPrimitive(null)));
+ } else {
+ return Optional.empty();
+ }
+ }
+
+ private static Stream replaceMatchesParameters(
+ MatchesOperand operand, Map parameterMap) {
+ if (operand instanceof QueryParameter qp) {
+ return resolveParameters(qp, parameterMap);
+ } else {
+ return null;
+ }
+ }
+
+ private static void replaceComparisonLeftOperandParameters(
+ ComparisonLeftOperand statement, Map parameterMap) {
+ switch (statement) {
+ case SingleRowFunction func -> replaceFunctionParameters(func, parameterMap);
+ case IdentifiedPath path -> replaceIdentifiedPathParameters(path, parameterMap);
+ case TerminologyFunction __ -> {
+ /* cannot contain parameters */
+ }
+ }
+ }
+ }
+
+ private static final class ContainmentParams {
+ public static void replaceParameters(Containment containment, Map parameterMap) {
+ switch (containment) {
+ case null -> {
+ /*NOOP*/
+ }
+ case ContainmentSetOperator cso -> cso.getValues().forEach(c -> replaceParameters(c, parameterMap));
+ case ContainmentNotOperator cno -> replaceParameters(cno.getContainmentExpression(), parameterMap);
+ case ContainmentClassExpression cce -> replaceContainmentClassExpressionParameters(cce, parameterMap);
+ case ContainmentVersionExpression cve -> replaceContainmentVersionExpressionParameters(
+ cve, parameterMap);
+ }
+ }
+
+ private static void replaceContainmentClassExpressionParameters(
+ ContainmentClassExpression cce, Map parameterMap) {
+ streamComparisonOperatorPredicates(cce)
+ .forEach(op -> ObjectPathParams.replaceComparisonOperatorParameters(op, parameterMap));
+ replaceParameters(cce.getContains(), parameterMap);
+ }
+
+ private static void replaceContainmentVersionExpressionParameters(
+ ContainmentVersionExpression cve, Map parameterMap) {
+ Optional.of(cve)
+ .map(ContainmentVersionExpression::getPredicate)
+ .ifPresent(op -> ObjectPathParams.replaceComparisonOperatorParameters(op, parameterMap));
+ replaceParameters(cve.getContains(), parameterMap);
+ }
+
+ private static Stream streamComparisonOperatorPredicates(
+ ContainmentClassExpression cce) {
+ return Optional.of(cce)
+ .filter(AbstractContainmentExpression::hasPredicates)
+ .map(AbstractContainmentExpression::getPredicates)
+ .stream()
+ .flatMap(List::stream)
+ .map(AndOperatorPredicate::getOperands)
+ .flatMap(Collection::stream);
+ }
+ }
+
+ private static final class ObjectPathParams {
+
+ /**
+ * Replaces all parameters.
+ * If parameters were replaced, the modified AqlObjectPath is returned.
+ * The provided path object remains unchanged.
+ *
+ * @param path
+ * @param parameterMap
+ * @return
+ */
+ public static Optional replaceParameters(AqlObjectPath path, Map parameterMap) {
+ if (path == null) {
+ return Optional.empty();
+ }
+ return Utils.replaceChildParameters(
+ path.getPathNodes(), ObjectPathParams::replacePathNodeParameters, parameterMap)
+ .map(AqlObjectPath::new);
+ }
+
+ private static Optional replaceComparisonOperatorPredicateParameters(
+ ComparisonOperatorPredicate n, Map parameterMap) {
+ Optional replacedPath = replaceParameters(n.getPath(), parameterMap);
+
+ Optional replacedValue =
+ switch (n.getValue()) {
+ case QueryParameter qp -> Optional.of((PathPredicateOperand) ensureSingleElement(
+ resolveParameters(qp, parameterMap), p -> validateParameterSyntax(n.getPath(), p)));
+ case Primitive __ -> Optional.empty();
+ case AqlObjectPath p -> replaceParameters(p, parameterMap)
+ .map(PathPredicateOperand.class::cast);
+ default -> throw new IllegalStateException("Unexpected value: " + n.getValue());
+ };
+
+ if (replacedPath.isEmpty() && replacedValue.isEmpty()) {
+ return Optional.empty();
+ }
+
+ return Optional.of(new ComparisonOperatorPredicate(
+ replacedPath.orElse(n.getPath()), n.getOperator(), replacedValue.orElse(n.getValue())));
+ }
+
+ /**
+ * if ARCHETYPE_NODE_ID: check syntax
+ * @param path
+ * @param p
+ */
+ private static void validateParameterSyntax(AqlObjectPath path, Primitive p) {
+ if (AqlObjectPathUtil.ARCHETYPE_NODE_ID.equals(path)) {
+ if (p instanceof StringPrimitive sp) {
+ try {
+ AslRmTypeAndConcept.fromArchetypeNodeId(sp.getValue());
+ } catch (IllegalArgumentException e) {
+ throw new AqlParseException(
+ "Invalid parameter for %s".formatted(AqlObjectPathUtil.ARCHETYPE_NODE_ID));
+ }
+ } else {
+ throw new AqlParseException(
+ "Invalid parameter type for %s".formatted(AqlObjectPathUtil.ARCHETYPE_NODE_ID));
+ }
+ }
+ }
+
+ private static Optional replaceAndOperatorPredicateParameters(
+ AndOperatorPredicate and, Map parameterMap) {
+ return Utils.replaceChildParameters(
+ and.getOperands(),
+ ObjectPathParams::replaceComparisonOperatorPredicateParameters,
+ parameterMap)
+ .map(AndOperatorPredicate::new);
+ }
+
+ private static Optional replacePathNodeParameters(
+ AqlObjectPath.PathNode node, Map parameterMap) {
+ return Utils.replaceChildParameters(
+ node.getPredicateOrOperands(),
+ ObjectPathParams::replaceAndOperatorPredicateParameters,
+ parameterMap)
+ .map(l -> new AqlObjectPath.PathNode(node.getAttribute(), l));
+ }
+
+ /**
+ * {@link ComparisonOperatorPredicate}s are used in
+ *
+
+
\ No newline at end of file
diff --git a/application/src/test/java/org/ehrbase/application/abac/AbacIntegrationTest.java b/application/src/test/java/org/ehrbase/application/abac/AbacIntegrationTest.java
deleted file mode 100644
index 511d5be6b3..0000000000
--- a/application/src/test/java/org/ehrbase/application/abac/AbacIntegrationTest.java
+++ /dev/null
@@ -1,437 +0,0 @@
-/*
- * Copyright (c) 2021 Vitasystems GmbH and Jake Smolka (Hannover Medical School).
- *
- * This file is part of project EHRbase
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.ehrbase.application.abac;
-
-import static org.junit.jupiter.api.Assertions.assertNotEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-import static org.mockito.ArgumentMatchers.anyMap;
-import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.BDDMockito.given;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.verify;
-import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.jwt;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.delete;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.put;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-import com.jayway.jsonpath.JsonPath;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.UUID;
-import org.apache.commons.io.IOUtils;
-import org.ehrbase.test_data.composition.CompositionTestDataCanonicalJson;
-import org.ehrbase.test_data.operationaltemplate.OperationalTemplateTestData;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.condition.EnabledIfEnvironmentVariable;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.boot.test.mock.mockito.MockBean;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.MediaType;
-import org.springframework.security.oauth2.core.user.OAuth2UserAuthority;
-import org.springframework.test.context.ActiveProfiles;
-import org.springframework.test.context.junit4.SpringRunner;
-import org.springframework.test.web.servlet.MockMvc;
-import org.springframework.test.web.servlet.MvcResult;
-import org.springframework.util.ResourceUtils;
-
-@RunWith(SpringRunner.class)
-@SpringBootTest
-@ActiveProfiles({"local", "test"})
-@EnabledIfEnvironmentVariable(named = "EHRBASE_ABAC_IT_TEST", matches = "true")
-@AutoConfigureMockMvc
-class AbacIntegrationTest {
-
- private static final String ORGA_ID = "f47bfc11-ec8d-412e-aebf-c6953cc23e7d";
-
- @MockBean
- private AbacConfig.AbacCheck abacCheck;
-
- @Autowired
- private MockMvc mockMvc;
-
- @Autowired
- private AbacConfig abacConfig;
-
- @Test
- /*
- * This test requires a new and clean DB state to run successfully.
- */
- void testAbacIntegrationTest() throws Exception {
- /*
- ----------------- TEST CONTEXT SETUP -----------------
- */
- // Configure the mock bean of the ABAC server, so we can test with this external service.
- given(this.abacCheck.execute(anyString(), anyMap())).willReturn(true);
-
- Map