Merge from BI Server

.github/pull.yml

@@ -0,0 +1,11 @@
+version: "1"
+rules:
+  - base: develop
+    upstream: plantbreeding:brapi-server-v2
+    mergeMethod: merge
+    assignees:
+      - nickpalladino
+      - mlm483
+      - dmeidlin
+      - davedrp
+label: "upstream-merge"

Dockerfile

@@ -1,13 +1,15 @@
-# build image : `docker build -t brapicoordinatorselby/brapi-java-server ./`
-# run container (dev): `docker run --name=brapi-test-server --network=bridge -p 8081:8081 -d brapicoordinatorselby/brapi-java-server`
-# run container (prod): `docker run --name=brapi-test-server --restart always --network=brapi_net -d brapicoordinatorselby/brapi-java-server`
+# build image stack: `docker build -t docker-username/image-stack-name ./`
+# run container (dev): `docker run --name=brapi-test-server --network=bridge -p 8081:8081 -d docker-username/image-stack-name`
+# run container (prod): `docker run --name=brapi-test-server --restart always --network=brapi_net -d docker-username/image-stack-name`
 
 FROM adoptopenjdk/openjdk8
 
-EXPOSE 8080
+# 8080 - brapi app port | 5005 - brapi app debug port | 8008 - keycloak app port
+EXPOSE 8080 5005 8008
 
 RUN mkdir /home/brapi
 
 COPY target/brapi-Java-TestServer-0.1.0.jar src/main/resources/ /home/brapi/
 
-CMD java -cp "/home/brapi/:/home/brapi/brapi-Java-TestServer-0.1.0.jar" org.springframework.boot.loader.JarLauncher
+# Open up debug port on JVM
+CMD java -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=0.0.0.0:5005 -cp "/home/brapi/:/home/brapi/brapi-Java-TestServer-0.1.0.jar" org.springframework.boot.loader.JarLauncher

docker-compose-dev.yaml

@@ -0,0 +1,21 @@
+services:
+  brapi-java-server-v2:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    ports:
+      - "8080:8080"
+      - "5005:5005"
+    depends_on:
+      - brapi-db
+    volumes:
+      - .\src\main\resources\properties\application.properties:/home/brapi/properties/application.properties
+  brapi-db:
+    image: postgres:13
+    environment:
+      POSTGRES_USER: brapi
+      POSTGRES_PASSWORD: password
+    volumes:
+      - /var/lib/postgresql/data
+    ports:
+      - "5433:5432"

docker-compose-local-auth.yaml

@@ -0,0 +1,61 @@
+services:
+  brapi-java-server-v2:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    ports:
+      - "8080:8080"
+      - "5005:5005"
+    depends_on:
+      - brapi-db
+    volumes:
+      - .\src\main\resources\properties\application.properties:/home/brapi/properties/application.properties
+  keycloak-brapi:
+    image: quay.io/keycloak/keycloak:latest
+    entrypoint: /opt/keycloak/bin/kc.sh start-dev
+    depends_on:
+      - keycloak-db
+    environment:
+      - KEYCLOAK_USER=admin
+      - KEYCLOAK_PASSWORD=admin
+      # The KC_HOSTNAME needs to be the same as the defined keycloak-brapi service in the compose file for a local setup.
+      # This allows the brapi app to talk to the keycloak container via the service name in the url, and sets up keycloak
+      # url defaults so that when brapi gets auth urls from keycloak it can still talk to it.
+      - KC_HOSTNAME=keycloak-brapi
+      - KC_DB=postgres
+      - KC_DB_URL=jdbc:postgresql://keycloak-db:5432/keycloak
+      - KC_DB_SCHEMA=public
+      - KC_DB_USERNAME=keycloak
+      - KC_DB_PASSWORD=password
+      - KC_HOSTNAME_STRICT=false
+      - KC_HOSTNAME_STRICT_HTTPS=false
+      - KC_HTTP_PORT=8008
+
+      - KC_LOG_LEVEL=info
+      - KC_METRICS_ENABLED=true
+      - KC_HEALTH_ENABLED=true
+      - KEYCLOAK_ADMIN=admin
+      - KEYCLOAK_ADMIN_PASSWORD=admin
+    ports:
+      - "8008:8008"
+  brapi-db:
+    image: postgres:13
+    environment:
+      POSTGRES_USER: brapi
+      POSTGRES_PASSWORD: password
+    volumes:
+      - brapi-data:/var/lib/postgresql/data
+    ports:
+      - "5433:5432"
+  keycloak-db:
+    image: postgres:13
+    volumes:
+      - keycloak-data:/var/lib/postgresql/data
+    environment:
+      POSTGRES_USER: keycloak
+      POSTGRES_PASSWORD: password
+    ports:
+      - "5434:5432"
+volumes:
+  keycloak-data:
+  brapi-data:

docker-compose.yaml

@@ -1,27 +1,27 @@
-version: '3'
-
 services:
+  # Update this image with whatever image you have access to
   brapi-java-server-v1:
     image: brapicoordinatorselby/brapi-java-server:v1
-    restart: unless-stopped
     depends_on:
       - postgres
     volumes:
       - /home/jenkins/brapi.org/brapi-test-server/properties/v1/application.properties:/home/brapi/properties/application.properties
   brapi-java-server-v2:
+    # Update this image with whatever image you have access to
     image: brapicoordinatorselby/brapi-java-server:v2
-    restart: unless-stopped
     depends_on:
       - postgres
     volumes:
+      # Update this path with the path your pipeline tool expects
       - /home/jenkins/brapi.org/brapi-test-server/properties/v2/application.properties:/home/brapi/properties/application.properties
   keycloak-brapi:
+    # Update this image with whatever keycloak image you have access to
     image: brapicoordinatorselby/brapi-keycloak:latest
-    restart: unless-stopped
     entrypoint: /opt/keycloak/bin/kc.sh start --optimized --proxy edge
     depends_on:
       - postgres
     environment:
+      # These vars will change depending on how you have configured your keycloak DB
       - KEYCLOAK_USER
       - KEYCLOAK_PASSWORD
       - KC_HOSTNAME=auth.brapi.org
@@ -31,8 +31,8 @@ services:
       - KC_DB_PASSWORD
   postgres:
     image: postgres:13
-    restart: unless-stopped
     volumes:
+      # Update this path with the path your pipeline tool expects
       - /home/jenkins/brapi.org/brapi-test-server/data:/var/lib/postgresql/data
 networks:
     default:

src/main/java/io/swagger/api/core/BatchDeletesApi.java

@@ -0,0 +1,129 @@
+/**
+ * NOTE: This class is auto generated by the swagger code generator program (3.0.18).
+ * https://github.com/swagger-api/swagger-codegen
+ * Do not edit the class manually.
+ */
+package io.swagger.api.core;
+
+import io.swagger.model.BrAPIResponse;
+import io.swagger.model.Model202AcceptedSearchResponse;
+import io.swagger.model.core.*;
+import io.swagger.annotations.*;
+
+import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestHeader;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+
+import jakarta.validation.Valid;
+
+import java.util.ArrayList;
+
+@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
+@Api(value = "batchDeletes", description = "the batch deletes API")
+public interface BatchDeletesApi {
+
+    @ApiOperation(value = "Get the details of a specific Batch Delete", nickname = "batchDeletesBatchDbIdGet", notes = "Get a specific generic batch delete", response = BatchDeletesSingleResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "BatchDeletes", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = BatchDeletesSingleResponse.class),
+            @ApiResponse(code = 400, message = "Bad Request", response = String.class),
+            @ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+            @ApiResponse(code = 403, message = "Forbidden", response = String.class),
+            @ApiResponse(code = 404, message = "Not Found", response = String.class) })
+    @RequestMapping(value = "/batchDeletes/{batchDeleteDbId}", produces = { "application/json" }, method = RequestMethod.GET)
+    ResponseEntity<BatchDeletesSingleResponse> batchDeletesBatchDbIdGet(
+            @ApiParam(value = "The unique ID of this generic batch", required = true) @PathVariable("batchDeletDbId") String batchDbId,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+
+    @ApiOperation(value = "Add Items to a specific Batch Delete", nickname = "batchDeletesBatchDbIdItemsPost", notes = "Add new data to a specific generic batch delete", response = BatchDeleteResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "BatchDeletes", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = BatchDeleteResponse.class),
+            @ApiResponse(code = 400, message = "Bad Request", response = String.class),
+            @ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+            @ApiResponse(code = 403, message = "Forbidden", response = String.class),
+            @ApiResponse(code = 404, message = "Not Found", response = String.class) })
+    @RequestMapping(value = "/batchDeletes/{batchDeleteDbId}/items", produces = { "application/json" }, consumes = {
+            "application/json" }, method = RequestMethod.POST)
+    ResponseEntity<BatchDeleteResponse> batchDeletesBatchDbIdItemsPost(
+            @ApiParam(value = "The unique ID of this generic batch", required = true) @PathVariable("batchDeleteDbId") String batchDeleteDbId,
+            @ApiParam(value = "") @Valid @RequestBody ArrayList<String> body,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+
+    @ApiOperation(value = "Add Items to a specific Batch Delete", nickname = "batchDeletesBatchDbIdDataPost", notes = "Add new data to a specific generic batch delete", response = BatchDeleteResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "BatchDeletes", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = BatchDeleteResponse.class),
+            @ApiResponse(code = 400, message = "Bad Request", response = String.class),
+            @ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+            @ApiResponse(code = 403, message = "Forbidden", response = String.class),
+            @ApiResponse(code = 404, message = "Not Found", response = String.class) })
+    @RequestMapping(value = "/batchDeletes/{batchDeleteDbId}/data", produces = { "application/json" }, consumes = {
+            "application/json" }, method = RequestMethod.POST)
+    ResponseEntity<BatchDeleteResponse> batchDeletesBatchDbIdDataPost(
+            @ApiParam(value = "The unique ID of this generic batch", required = true) @PathVariable("batchDeleteDbId") String batchDbId,
+            @ApiParam(value = "") @Valid @RequestBody ArrayList<String> body,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+
+    @ApiOperation(value = "Update an existing generic batch delete", nickname = "batchDeletesBatchDbIdPut", notes = "Update an existing generic batch delete", response = BatchDeletesSingleResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "BatchDeletes", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = BatchDeletesSingleResponse.class),
+            @ApiResponse(code = 400, message = "Bad Request", response = String.class),
+            @ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+            @ApiResponse(code = 403, message = "Forbidden", response = String.class),
+            @ApiResponse(code = 404, message = "Not Found", response = String.class) })
+    @RequestMapping(value = "/batchDeletes/{batchDeleteDbId}", produces = { "application/json" }, consumes = {
+            "application/json" }, method = RequestMethod.PUT)
+    ResponseEntity<BatchDeletesSingleResponse> batchDeletesBatchDbIdPut(
+            @ApiParam(value = "The unique ID of this generic batch", required = true) @PathVariable("batchDeleteDbId") String batchDbId,
+            @ApiParam(value = "") @Valid @RequestBody BatchDeleteNewRequest body,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+
+    @ApiOperation(value = "Create a New Batch Delete", nickname = "batchDeletesPost", notes = "Create a new batch delete", response = BatchDeletesListResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "BatchDeletes", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = BatchDeletesListResponse.class),
+            @ApiResponse(code = 400, message = "Bad Request", response = String.class),
+            @ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+            @ApiResponse(code = 403, message = "Forbidden", response = String.class) })
+    @RequestMapping(value = "/batchDeletes", produces = { "application/json" }, consumes = {
+            "application/json" }, method = RequestMethod.POST)
+    ResponseEntity<? extends BrAPIResponse> batchDeletesPost(@ApiParam(value = "") @Valid @RequestBody BatchDeleteSearchRequest body,
+                                                             @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+
+    @ApiOperation(value = "Get the results of a Batch Delete search request", nickname = "searchBatchDeletesSearchResultsDbIdGet", notes = "Advanced searching for the batch delete resource. See Search Services for additional implementation details.", response = BatchDeletesListResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "BatchDeletes", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = BatchDeletesListResponse.class),
+            @ApiResponse(code = 202, message = "Accepted", response = Model202AcceptedSearchResponse.class),
+            @ApiResponse(code = 400, message = "Bad Request", response = String.class),
+            @ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+            @ApiResponse(code = 403, message = "Forbidden", response = String.class) })
+    @RequestMapping(value = "/search/batchDeletes/{searchResultsDbId}", produces = {
+            "application/json" }, method = RequestMethod.GET)
+    ResponseEntity<? extends BrAPIResponse> searchBatchDeletesSearchResultsDbIdGet(
+            @ApiParam(value = "Permanent unique identifier which references the search results", required = true) @PathVariable("searchResultsDbId") String searchResultsDbId,
+            @ApiParam(value = "page") @Valid @RequestParam(value = "page", required = false) Integer page,
+            @ApiParam(value = "pageSize") @Valid @RequestParam(value = "pageSize", required = false) Integer pageSize,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization) throws BrAPIServerException;
+
+    @ApiOperation(value = "Delete a specific Batch Delete", nickname = "batchDeletesBatchDbIdDelete", notes = "Delete a specific generic batch delete", response = BatchDeletesSingleResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "BatchDeletes", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = BatchDeletesSingleResponse.class),
+            @ApiResponse(code = 400, message = "Bad Request", response = String.class),
+            @ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+            @ApiResponse(code = 403, message = "Forbidden", response = String.class),
+            @ApiResponse(code = 404, message = "Not Found", response = String.class) })
+    @RequestMapping(value = "/batchDeletes/{batchDeleteDbId}", produces = { "application/json" }, method = RequestMethod.DELETE)
+    ResponseEntity<BatchDeletesSingleResponse> batchDeletesBatchDbIdDelete(
+            @ApiParam(value = "The unique ID of this generic batch", required = true) @PathVariable("batchDeleteDbId") String batchDbId,
+            @ApiParam(value = "hard") @Valid @RequestParam(value = "hardDelete", defaultValue = "false", required = false) boolean hardDelete,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+
+}

src/main/java/io/swagger/api/core/ListsApi.java

@@ -40,6 +40,7 @@ public interface ListsApi {
 			@ApiResponse(code = 403, message = "Forbidden", response = String.class) })
 	@RequestMapping(value = "/lists", produces = { "application/json" }, method = RequestMethod.GET)
 	ResponseEntity<ListsListResponse> listsGet(
+			@ApiParam(value = "batchDeleteDbId") @Valid @RequestParam(value = "batchDeleteDbId", required = false) String batchDelete,
 			@ApiParam(value = "listType") @Valid @RequestParam(value = "listType", required = false) String listType,
 			@ApiParam(value = "listName") @Valid @RequestParam(value = "listName", required = false) String listName,
 			@ApiParam(value = "listDbId") @Valid @RequestParam(value = "listDbId", required = false) String listDbId,
@@ -67,6 +68,20 @@ ResponseEntity<ListsSingleResponse> listsListDbIdGet(
 			@ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
 			throws BrAPIServerException;
 
+	@ApiOperation(value = "Delete an existing generic list", nickname = "listsListDbIdDelete", notes = "Delete an existing generic list", response = ListsListResponse.class, authorizations = {
+			@Authorization(value = "AuthorizationToken") }, tags = { "Lists", })
+	@ApiResponses(value = { @ApiResponse(code = 204, message = "OK", response = ListsSingleResponse.class),
+			@ApiResponse(code = 400, message = "Bad Request", response = String.class),
+			@ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+			@ApiResponse(code = 403, message = "Forbidden", response = String.class),
+			@ApiResponse(code = 404, message = "Not Found", response = String.class) })
+	@RequestMapping(value = "/lists/{listDbId}", produces = { "application/json" }, method = RequestMethod.DELETE)
+	ResponseEntity<ListsSingleResponse> listsListDbIdDelete(
+			@ApiParam(value = "The unique ID of this generic list", required = true) @PathVariable("listDbId") String listDbId,
+			@ApiParam(value = "hardDelete") @Valid @RequestParam(value = "hardDelete", defaultValue = "false", required = false) boolean hardDelete,
+			@ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException;
+
 	@ApiOperation(value = "Add Items to a specific List", nickname = "listsListDbIdItemsPost", notes = "Add new data to a specific generic lists", response = ListResponse.class, authorizations = {
 			@Authorization(value = "AuthorizationToken") }, tags = { "Lists", })
 	@ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = ListResponse.class),