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Feature/opends 0.4.0 #63

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merged 6 commits into from
Nov 12, 2024
Merged

Feature/opends 0.4.0 #63

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3b0e6b8
Update to opends 0.4.0
samleeflang Nov 11, 2024
c20483a
Merge branch 'main' into feature/opends-0.4.0
samleeflang Nov 11, 2024
500b60e
Add correct agents
samleeflang Nov 11, 2024
843a9f9
Remove exceptions
samleeflang Nov 11, 2024
94d6c25
Code review
samleeflang Nov 12, 2024
270d58e
Code review
samleeflang Nov 12, 2024
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3 changes: 0 additions & 3 deletions .github/workflows/.trivyignore
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# September 20, 2024
# Vulnerability in io.kubernetes java client, may be fixed in 21.0.1 but not sure
CVE-2024-7254
19 changes: 9 additions & 10 deletions pom.xml
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Expand Up @@ -16,10 +16,9 @@
<description>Backend for orchestration service</description>
<properties>
<java.version>17</java.version>
<apachecommons.version>4.4</apachecommons.version>
<k8s-client-java.version>21.0.0</k8s-client-java.version>
<k8s-client-java.version>22.0.0</k8s-client-java.version>
<json-patch.version>1.13</json-patch.version>
<testcontainers.version>1.19.8</testcontainers.version>
<testcontainers.version>1.20.3</testcontainers.version>
<mockito-inline.version>5.2.0</mockito-inline.version>
<sonar.organization>dissco</sonar.organization>
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
Expand Down Expand Up @@ -190,13 +189,13 @@
<configuration>
<mainClass>eu.dissco.orchestration.backend.maven.MavenRunner</mainClass>
<arguments>
<argument>https://schemas.dissco.tech/schemas/fdo-type/data-mapping/0.3.0/data-mapping.json</argument>
<argument>https://schemas.dissco.tech/schemas/developer-schema/data-mapping/0.3.0/data-mapping-request.json</argument>
<argument>https://schemas.dissco.tech/schemas/fdo-type/machine-annotation-service/0.3.0/machine-annotation-service.json</argument>
<argument>https://schemas.dissco.tech/schemas/developer-schema/machine-annotation-service/0.3.0/machine-annotation-service-request.json</argument>
<argument>https://schemas.dissco.tech/schemas/fdo-type/source-system/0.3.0/source-system.json</argument>
<argument>https://schemas.dissco.tech/schemas/developer-schema/source-system/0.3.0/source-system-request.json</argument>
<argument>https://schemas.dissco.tech/schemas/fdo-type/create-update-tombstone-event/0.3.0/create-update-tombstone-event.json</argument>
<argument>https://schemas.dissco.tech/schemas/fdo-type/data-mapping/0.4.0/data-mapping.json</argument>
<argument>https://schemas.dissco.tech/schemas/developer-schema/data-mapping/0.4.0/data-mapping-request.json</argument>
<argument>https://schemas.dissco.tech/schemas/fdo-type/machine-annotation-service/0.4.0/machine-annotation-service.json</argument>
<argument>https://schemas.dissco.tech/schemas/developer-schema/machine-annotation-service/0.4.0/machine-annotation-service-request.json</argument>
<argument>https://schemas.dissco.tech/schemas/fdo-type/source-system/0.4.0/source-system.json</argument>
<argument>https://schemas.dissco.tech/schemas/developer-schema/source-system/0.4.0/source-system-request.json</argument>
<argument>https://schemas.dissco.tech/schemas/fdo-type/create-update-tombstone-event/0.4.0/create-update-tombstone-event.json</argument>
</arguments>
</configuration>
</plugin>
Expand Down
23 changes: 14 additions & 9 deletions src/main/java/eu/dissco/orchestration/backend/controller/DataMappingController.java
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package eu.dissco.orchestration.backend.controller;

import static eu.dissco.orchestration.backend.domain.AgentRoleType.CREATOR;
import static eu.dissco.orchestration.backend.domain.AgentRoleType.TOMBSTONER;
import static eu.dissco.orchestration.backend.utils.ControllerUtils.getAgent;

import com.fasterxml.jackson.core.JsonProcessingException;
Expand Down Expand Up @@ -47,10 +49,11 @@ public ResponseEntity<JsonApiWrapper> createDataMapping(Authentication authentic
@RequestBody JsonApiRequestWrapper requestBody, HttpServletRequest servletRequest)
throws JsonProcessingException, ProcessingFailedException, ForbiddenException {
var dataMapping = getDataMappingRequestFromRequest(requestBody);
var user = getAgent(authentication);
log.info("Received create request for data mapping: {} from user: {}", dataMapping, user.getId());
var agent = getAgent(authentication, CREATOR);
log.info("Received create request for data mapping: {} from agent: {}", dataMapping,
agent.getId());
String path = appProperties.getBaseUrl() + servletRequest.getRequestURI();
var result = service.createDataMapping(dataMapping, user, path);
var result = service.createDataMapping(dataMapping, agent, path);
return ResponseEntity.status(HttpStatus.CREATED).body(result);
}

Expand All @@ -61,10 +64,11 @@ public ResponseEntity<JsonApiWrapper> updateDataMapping(Authentication authentic
throws JsonProcessingException, NotFoundException, ProcessingFailedException, ForbiddenException {
var dataMapping = getDataMappingRequestFromRequest(requestBody);
var id = prefix + '/' + suffix;
var user = getAgent(authentication);
log.info("Received update request for data mapping: {} from user: {}", dataMapping, user.getId());
var agent = getAgent(authentication, CREATOR);
log.info("Received update request for data mapping: {} from agent: {}", dataMapping,
agent.getId());
String path = appProperties.getBaseUrl() + servletRequest.getRequestURI();
var result = service.updateDataMapping(id, dataMapping, user, path);
var result = service.updateDataMapping(id, dataMapping, agent, path);
if (result == null) {
return ResponseEntity.status(HttpStatus.NO_CONTENT).build();
} else {
Expand All @@ -78,8 +82,8 @@ public ResponseEntity<Void> tombstoneDataMapping(Authentication authentication,
@PathVariable("prefix") String prefix, @PathVariable("suffix") String suffix)
throws NotFoundException, ProcessingFailedException, ForbiddenException {
String id = prefix + "/" + suffix;
var agent = getAgent(authentication);
log.info("Received delete request for mapping: {} from user: {}", id, agent.getId());
var agent = getAgent(authentication, TOMBSTONER);
log.info("Received delete request for mapping: {} from agent: {}", id, agent.getId());
service.tombstoneDataMapping(id, agent);
return ResponseEntity.status(HttpStatus.NO_CONTENT).build();
}
Expand All @@ -103,7 +107,8 @@ public ResponseEntity<JsonApiListWrapper> getDataMappings(
log.info("Received get request for mappings with pageNumber: {} and pageSzie: {}: ", pageNum,
pageSize);
String path = appProperties.getBaseUrl() + servletRequest.getRequestURI();
return ResponseEntity.status(HttpStatus.OK).body(service.getDataMappings(pageNum, pageSize, path));
return ResponseEntity.status(HttpStatus.OK)
.body(service.getDataMappings(pageNum, pageSize, path));
}

private DataMappingRequest getDataMappingRequestFromRequest(JsonApiRequestWrapper requestBody)
Expand Down
22 changes: 12 additions & 10 deletions ...n/java/eu/dissco/orchestration/backend/controller/MachineAnnotationServiceController.java
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package eu.dissco.orchestration.backend.controller;

import static eu.dissco.orchestration.backend.domain.AgentRoleType.CREATOR;
import static eu.dissco.orchestration.backend.domain.AgentRoleType.TOMBSTONER;
import static eu.dissco.orchestration.backend.utils.ControllerUtils.getAgent;

import com.fasterxml.jackson.core.JsonProcessingException;
Expand Down Expand Up @@ -48,11 +50,11 @@ public ResponseEntity<JsonApiWrapper> createMachineAnnotationService(
@RequestBody JsonApiRequestWrapper requestBody, HttpServletRequest servletRequest)
throws JsonProcessingException, ProcessingFailedException, ForbiddenException {
var machineAnnotationService = getMachineAnnotation(requestBody);
var user = getAgent(authentication);
log.info("Received create request for machine annotation service: {} from user: {}",
machineAnnotationService, user.getId());
var agent = getAgent(authentication, CREATOR);
log.info("Received create request for machine annotation service: {} from agent: {}",
machineAnnotationService, agent.getId());
String path = appProperties.getBaseUrl() + servletRequest.getRequestURI();
var result = service.createMachineAnnotationService(machineAnnotationService, user, path);
var result = service.createMachineAnnotationService(machineAnnotationService, agent, path);
return ResponseEntity.status(HttpStatus.CREATED).body(result);
}

Expand All @@ -63,12 +65,12 @@ public ResponseEntity<JsonApiWrapper> updateMachineAnnotationService(
@RequestBody JsonApiRequestWrapper requestBody, HttpServletRequest servletRequest)
throws JsonProcessingException, NotFoundException, ProcessingFailedException, ForbiddenException {
var machineAnnotationService = getMachineAnnotation(requestBody);
var user = getAgent(authentication);
var agent = getAgent(authentication, CREATOR);
var id = prefix + '/' + suffix;
log.info("Received update request for machine annotation service: {} from user: {}", id,
user.getId());
log.info("Received update request for machine annotation service: {} from agent: {}", id,
agent.getId());
String path = appProperties.getBaseUrl() + servletRequest.getRequestURI();
var result = service.updateMachineAnnotationService(id, machineAnnotationService, user, path);
var result = service.updateMachineAnnotationService(id, machineAnnotationService, agent, path);
if (result == null) {
return ResponseEntity.status(HttpStatus.NO_CONTENT).build();
} else {
Expand All @@ -82,8 +84,8 @@ public ResponseEntity<Void> tombstoneMachineAnnotationService(Authentication aut
@PathVariable("prefix") String prefix, @PathVariable("suffix") String suffix)
throws NotFoundException, ProcessingFailedException, ForbiddenException {
String id = prefix + "/" + suffix;
var agent = getAgent(authentication);
log.info("Received delete request for machine annotation service: {} from user: {}", id,
var agent = getAgent(authentication, TOMBSTONER);
log.info("Received delete request for machine annotation service: {} from agent: {}", id,
agent.getId());
service.tombstoneMachineAnnotationService(id, agent);
return ResponseEntity.status(HttpStatus.NO_CONTENT).build();
Expand Down
20 changes: 11 additions & 9 deletions src/main/java/eu/dissco/orchestration/backend/controller/SourceSystemController.java
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package eu.dissco.orchestration.backend.controller;

import static eu.dissco.orchestration.backend.domain.AgentRoleType.CREATOR;
import static eu.dissco.orchestration.backend.domain.AgentRoleType.TOMBSTONER;
import static eu.dissco.orchestration.backend.utils.ControllerUtils.getAgent;

import com.fasterxml.jackson.core.JsonProcessingException;
Expand Down Expand Up @@ -49,10 +51,10 @@ public ResponseEntity<JsonApiWrapper> createSourceSystem(Authentication authenti
throws IOException, NotFoundException, ProcessingFailedException, ForbiddenException {
var sourceSystemRequest = getSourceSystemFromRequest(requestBody);
String path = appProperties.getBaseUrl() + servletRequest.getRequestURI();
var user = getAgent(authentication);
log.info("Received create request for source system: {} from user: {}", sourceSystemRequest,
user.getId());
var result = service.createSourceSystem(sourceSystemRequest, user, path);
var agent = getAgent(authentication, CREATOR);
log.info("Received create request for source system: {} from agent: {}", sourceSystemRequest,
agent.getId());
var result = service.createSourceSystem(sourceSystemRequest, agent, path);
return ResponseEntity.status(HttpStatus.CREATED).body(result);
}

Expand All @@ -64,10 +66,10 @@ public ResponseEntity<JsonApiWrapper> updateSourceSystem(Authentication authenti
throws IOException, NotFoundException, ProcessingFailedException, ForbiddenException {
var sourceSystemRequest = getSourceSystemFromRequest(requestBody);
var id = prefix + '/' + suffix;
var user = getAgent(authentication);
log.info("Received update request for source system: {} from user: {}", id, user.getId());
var agent = getAgent(authentication, CREATOR);
log.info("Received update request for source system: {} from agent: {}", id, agent.getId());
String path = appProperties.getBaseUrl() + servletRequest.getRequestURI();
var result = service.updateSourceSystem(id, sourceSystemRequest, user, path, trigger);
var result = service.updateSourceSystem(id, sourceSystemRequest, agent, path, trigger);
if (result == null) {
return ResponseEntity.status(HttpStatus.NO_CONTENT).build();
} else {
Expand All @@ -81,8 +83,8 @@ public ResponseEntity<Void> tombstoneSourceSystem(Authentication authentication,
@PathVariable("prefix") String prefix, @PathVariable("suffix") String suffix)
throws NotFoundException, ProcessingFailedException, ForbiddenException {
String id = prefix + "/" + suffix;
var agent = getAgent(authentication);
log.info("Received delete request for mapping: {} from user: {}", id, agent.getId());
var agent = getAgent(authentication, TOMBSTONER);
log.info("Received delete request for mapping: {} from agent: {}", id, agent.getId());
service.tombstoneSourceSystem(id, agent);
return ResponseEntity.status(HttpStatus.NO_CONTENT).build();
}
Expand Down
23 changes: 23 additions & 0 deletions src/main/java/eu/dissco/orchestration/backend/domain/AgentRoleType.java
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package eu.dissco.orchestration.backend.domain;

import lombok.Getter;

@Getter
public enum AgentRoleType {

COLLECTOR("collector"),
DATA_TRANSLATOR("data-translator"),
CREATOR("creator"),
IDENTIFIER("identifier"),
GEOREFERENCER("georeferencer"),
RIGHTS_OWNER("rights-owner"),
PROCESSING_SERVICE("processing-service"),
SOURCE_SYSTEM("source-system"),
TOMBSTONER("tombstoner");

private final String name;

AgentRoleType(String name) {
this.name = name;
}
}
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