Merge pull request #39 from Breeding-Insight/release/1.0

Merge for Release/1.0

Author: mlm483

docker-compose.yaml

@@ -4,39 +4,34 @@ services:
   brapi-java-server-v1:
     image: brapicoordinatorselby/brapi-java-server:v1
     restart: unless-stopped
-    depends_on: 
+    depends_on:
       - postgres
     volumes:
       - /home/jenkins/brapi.org/brapi-test-server/properties/v1/application.properties:/home/brapi/properties/application.properties
   brapi-java-server-v2:
     image: brapicoordinatorselby/brapi-java-server:v2
     restart: unless-stopped
-    depends_on: 
+    depends_on:
       - postgres
     volumes:
       - /home/jenkins/brapi.org/brapi-test-server/properties/v2/application.properties:/home/brapi/properties/application.properties
   keycloak-brapi:
-    image: jboss/keycloak:12.0.1
+    image: brapicoordinatorselby/brapi-keycloak:latest
     restart: unless-stopped
-    depends_on: 
+    entrypoint: /opt/keycloak/bin/kc.sh start --optimized --proxy edge
+    depends_on:
       - postgres
-    volumes:
-      - /home/jenkins/brapi.org/brapi-test-server/keycloak/standalone.xml:/opt/jboss/keycloak/standalone/configuration/standalone.xml
     environment:
       - KEYCLOAK_USER
       - KEYCLOAK_PASSWORD
-      - DB_VENDOR
-      - DB_ADDR
-      - DB_DATABASE
-      - DB_USER
-      - DB_PASSWORD
-      - PROXY_ADDRESS_FORWARDING=true
+      - KC_HOSTNAME=auth.brapi.org
+      - KC_DB
+      - KC_DB_URL
+      - KC_DB_USERNAME
+      - KC_DB_PASSWORD
   postgres:
-    image: postgres
+    image: postgres:13
     restart: unless-stopped
-    environment:
-      - POSTGRES_USER
-      - POSTGRES_PASSWORD
     volumes:
       - /home/jenkins/brapi.org/brapi-test-server/data:/var/lib/postgresql/data
 networks:

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/ListEntity.java

@@ -30,6 +30,7 @@ public class ListEntity extends BrAPIPrimaryEntity {
 	@ManyToOne(fetch = FetchType.LAZY)
 	private PersonEntity listOwnerPerson;
 	@OneToMany(mappedBy="list", cascade = CascadeType.ALL)
+	@OrderColumn(name = "position")
 	private List<ListItemEntity> data;
 
 	public PersonEntity getListOwnerPerson() {

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/ListItemEntity.java

@@ -11,6 +11,8 @@ public class ListItemEntity extends BrAPIBaseEntity {
 	private ListEntity list;
 	@Column
 	private String item;
+	@Column
+	private Integer position;
 
 	public ListEntity getList() {
 		return list;
@@ -24,6 +26,10 @@ public String getItem() {
 	public void setItem(String item) {
 		this.item = item;
 	}
-	
-	
+	public Integer getPosition() {
+		return position;
+	}
+	public void setPosition(Integer position) {
+		this.position = position;
+	}
 }

src/main/java/org/brapi/test/BrAPITestServer/service/core/ListService.java

@@ -1,9 +1,6 @@
 package org.brapi.test.BrAPITestServer.service.core;
 
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.Optional;
+import java.util.*;
 import java.util.stream.Collectors;
 
 import jakarta.validation.Valid;
@@ -237,12 +234,19 @@ private void updateEntity(ListEntity entity, @Valid ListNewRequest list) throws
 		}
 
 		if (list.getData() != null) {
-			entity.setData(list.getData().stream().map((item) -> {
-				ListItemEntity itemEntity = new ListItemEntity();
-				itemEntity.setItem(item);
-				itemEntity.setList(entity);
-				return itemEntity;
-			}).collect(Collectors.toList()));
+			List<ListItemEntity> items = new ArrayList<>();
+			ListIterator<String> iter = list.getData().listIterator();
+			while (iter.hasNext()) {
+				String item = iter.next();
+				if (item != null) {
+					ListItemEntity itemEntity = new ListItemEntity();
+					itemEntity.setPosition(iter.nextIndex());
+					itemEntity.setItem(item);
+					itemEntity.setList(entity);
+					items.add(itemEntity);
+				}
+			}
+			entity.setData(items);
 		} else {
 			entity.setData(new ArrayList<>());
 		}

src/main/resources/db/migration/V001.001__datasets_array.sql

@@ -0,0 +1,39 @@
+-- See the NOTICE file distributed with this work for additional information
+-- regarding copyright ownership.
+--
+-- 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.
+
+-- Updates trial.additional_info to have a datasets array instead of just observationDatasetId.
+-- Leaves observationDatasetId in place out of an abundance of caution.
+-- Only updates rows that don't already have datasets key (just in case the code was updated prematurely).
+DO
+$$
+BEGIN
+    UPDATE
+        trial
+    SET
+        additional_info = additional_info
+            || JSONB_BUILD_OBJECT(
+                'datasets',
+                JSONB_BUILD_ARRAY(
+                    JSONB_BUILD_OBJECT(
+                        'id', additional_info->'observationDatasetId',
+                        'name', additional_info->'defaultObservationLevel',
+                        'level', '0'
+                    )
+                )
+            )
+    WHERE
+        additional_info->'datasets' IS NULL;
+END
+$$;

src/main/resources/db/migration/V002.001__update_list_positions.sql

@@ -0,0 +1,68 @@
+
+-- This migration updates existing list_item records based on DeltaBreed (Breeding Insight) specific fields.
+--
+-- These are the list types, the BJTS uses Java enums and stores ints in the database.
+-- 0: germplasm
+-- 1: markers
+-- 2: programs
+-- 3: trials
+-- 4: studies
+-- 5: observationUnits
+-- 6: observations
+-- 7: observationVariables
+-- 8: samples
+
+DO
+$$
+BEGIN
+    -- Update germplasm list items, the goal is to use the order defined by the listEntryNumbers.
+    UPDATE
+        list_item
+    SET
+        position = subquery.position
+    FROM
+        (
+            SELECT
+                -- Subtract 1 from row_number to get zero indexing.
+                row_number() OVER (PARTITION BY li.list_id ORDER BY (g.additional_info->'listEntryNumbers'->>xr.external_reference_id)::int) - 1 AS position,
+                li.id AS list_item_id
+            FROM
+                list_item li
+                    JOIN list l ON li.list_id = l.id
+                    JOIN list_external_references ler ON l.id = ler.list_entity_id
+                    JOIN external_reference xr ON xr.id = ler.external_references_id AND xr.external_reference_source = 'breedinginsight.org/lists'
+                    JOIN germplasm g ON li.item = g.germplasm_name
+            WHERE
+                l.list_type = 0  -- 0 is germplasm
+            ORDER BY
+                l.id
+        ) AS subquery
+    WHERE
+        list_item.id = subquery.list_item_id
+    ;
+
+    -- Update all non-germplasm list items. There is no existing order to preserve, assign sequential position values arbitrarily.
+    UPDATE
+        list_item
+    SET
+        position = subquery.position
+    FROM
+        (
+            SELECT
+                -- Subtract 1 from row_number to get zero indexing.
+                row_number() OVER (PARTITION BY li.list_id) - 1 AS position,
+                li.id AS list_item_id
+            FROM
+                list_item li
+                JOIN list l ON li.list_id = l.id
+            WHERE
+                l.list_type != 0  -- 0 is germplasm, here we are addressing non-germplasm lists.
+            ORDER BY
+                l.id
+        ) AS subquery
+    WHERE
+        list_item.id = subquery.list_item_id
+    ;
+
+END;
+$$;

src/main/resources/db/migration/V002__add_list_position.sql

@@ -0,0 +1,9 @@
+-- This migration adds a position field to list_item so that lists can be explicitly ordered.
+
+-- Add position to list_item.
+ALTER TABLE list_item
+ADD COLUMN position INT NOT NULL DEFAULT 0;
+-- Add an index on the position column
+CREATE INDEX idx_list_item_position ON list_item(position);
+-- Add a composite index on list_id and position for better performance when querying items within a specific list
+CREATE INDEX idx_list_item_list_position ON list_item(list_id, position);