BI-1945 - Store AdditionalInfo as JSONB in BrAPI Java TestServer

docker-compose.yml

@@ -100,7 +100,7 @@ services:
       - ${BRAPI_SERVER_PORT}:8080
     volumes:
       - ./src/main/resources/brapi/properties/application.properties:/home/brapi/properties/application.properties
-      - ./src/main/resources/brapi/sql/:/home/brapi/sql/
+      - ./src/main/resources/brapi/sql/:/home/brapi/db/sql/
     networks:
       backend:
         aliases:

src/main/resources/brapi/properties/application.properties

@@ -15,20 +15,24 @@
 #    limitations under the License.
 #
 
-application.properties.templateserver.port = 8080
+server.port = 8080
 server.servlet.context-path=/brapi/v2
 
 spring.datasource.url=jdbc:postgresql://${BRAPI_DB_SERVER}/${BRAPI_DB}
+spring.datasource.hikari.data-source-properties.stringtype=unspecified
 spring.datasource.username=${BRAPI_DB_USER}
 spring.datasource.password=${BRAPI_DB_PASSWORD}
 
 spring.datasource.driver-class-name=org.postgresql.Driver
 
-spring.jpa.hibernate.ddl-auto=create-only
+spring.flyway.locations=classpath:db/migration,classpath:db/sql,classpath:org/brapi/test/BrAPITestServer/db/migration
+spring.flyway.schemas=public
+spring.flyway.baselineOnMigrate=true
+
+spring.jpa.hibernate.ddl-auto=validate
 spring.jpa.show-sql=false
-spring.jpa.properties.hibernate.hbm2ddl.import_files=sql/species.sql, sql/create_indexes.sql
 
 spring.mvc.dispatch-options-request=true
 
 security.oidc_discovery_url=https://example.com/auth/.well-known/openid-configuration
-security.enabled=false
+security.enabled=false

src/main/resources/brapi/sql/create_indexes.sql → src/main/resources/brapi/sql/R__create_indexes.sql

@@ -19,10 +19,8 @@ CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_edge_connected_node_id" ON ped
 CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_edge_edge_type" ON pedigree_edge (edge_type);
 CREATE INDEX CONCURRENTLY IF NOT EXISTS "program_external_references_program_entity_id" ON program_external_references (program_entity_id);
 CREATE INDEX CONCURRENTLY IF NOT EXISTS "external_reference_composite" ON external_reference (external_reference_source, external_reference_id);
-CREATE INDEX CONCURRENTLY IF NOT EXISTS "program_additional_info_composite" ON program_additional_info (additional_info_id, program_entity_id);
 CREATE INDEX CONCURRENTLY IF NOT EXISTS "list_list_name" ON list (list_name);
 CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_node_germplasm_id" ON pedigree_node (germplasm_id);
-CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_additional_info_germplasm_entity_id" ON germplasm_additional_info (germplasm_entity_id);
 CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_external_references_germplasm_entity_id" ON germplasm_external_references (germplasm_entity_id);
 CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_synonym_germplasm_id" ON germplasm_synonym (germplasm_id);
 CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_taxon_germplasm_id" ON germplasm_taxon (germplasm_id);

src/main/resources/brapi/sql/R__species.sql

@@ -0,0 +1,34 @@
+-- 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.
+
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '4', 'Blueberry') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '5', 'Salmon') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '6', 'Grape') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '7', 'Alfalfa') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '8', 'Sweet Potato') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '9', 'Trout') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '10', 'Soybean') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '11', 'Cranberry') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '12', 'Cucumber') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '13', 'Oat') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '14', 'Citrus') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '15', 'Sugar Cane') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '16', 'Strawberry') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '17', 'Honey') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '18', 'Pecan') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '19', 'Lettuce') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '20', 'Cotton') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '21', 'Sorghum') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '22', 'Hemp') ON CONFLICT DO NOTHING;

src/test/java/org/breedinginsight/BrAPITest.java

@@ -60,6 +60,7 @@ public BrAPITest() {
                 .withEnv("BRAPI_DB", "postgres")
                 .withEnv("BRAPI_DB_USER", "postgres")
                 .withEnv("BRAPI_DB_PASSWORD", "postgres")
+                .withClasspathResourceMapping("sql/brapi/mount", "/home/brapi/db/sql", BindMode.READ_WRITE)  // HACK - READ_WRITE forces testcontainers to use a bind mount (which overwrites) instead of copying files.
                 .withClasspathResourceMapping("brapi/properties/application.properties", "/home/brapi/properties/application.properties", BindMode.READ_ONLY)
                 .waitingFor(Wait.forLogMessage(".*Started BrapiTestServer in \\d*.\\d* seconds.*", 1).withStartupTimeout(Duration.ofMinutes(1)));
 

src/test/resources/brapi/properties/application.properties

@@ -15,18 +15,22 @@
 #    limitations under the License.
 #
 
-application.properties.templateserver.port = 8080
+server.port = 8080
 server.servlet.context-path=/brapi/v2
 
 spring.datasource.url=jdbc:postgresql://${BRAPI_DB_SERVER}/${BRAPI_DB}
+spring.datasource.hikari.data-source-properties.stringtype=unspecified
 spring.datasource.username=${BRAPI_DB_USER}
 spring.datasource.password=${BRAPI_DB_PASSWORD}
 
 spring.datasource.driver-class-name=org.postgresql.Driver
 
-spring.jpa.hibernate.ddl-auto=create-drop
+spring.flyway.locations=classpath:db/migration,classpath:db/sql,classpath:org/brapi/test/BrAPITestServer/db/migration
+spring.flyway.schemas=public
+spring.flyway.baselineOnMigrate=true
+
+spring.jpa.hibernate.ddl-auto=validate
 spring.jpa.show-sql=false
-#spring.jpa.properties.hibernate.hbm2ddl.import_files=sql/species.sql
 
 spring.mvc.dispatch-options-request=true
 

src/test/resources/sql/brapi/mount/R__create_indexes.sql

@@ -0,0 +1,26 @@
+-- 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.
+
+-- Indexes to improve read performance of Germplasm operations.
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_edge_this_node_id" ON pedigree_edge (this_node_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_edge_connected_node_id" ON pedigree_edge (connceted_node_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_edge_edge_type" ON pedigree_edge (edge_type);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "program_external_references_program_entity_id" ON program_external_references (program_entity_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "external_reference_composite" ON external_reference (external_reference_source, external_reference_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "list_list_name" ON list (list_name);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_node_germplasm_id" ON pedigree_node (germplasm_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_external_references_germplasm_entity_id" ON germplasm_external_references (germplasm_entity_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_synonym_germplasm_id" ON germplasm_synonym (germplasm_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_taxon_germplasm_id" ON germplasm_taxon (germplasm_id);

src/test/resources/sql/brapi/species.sql

@@ -17,9 +17,22 @@
  */
 
 -- name: InsertSpecies
-INSERT INTO crop (id, crop_name) VALUES ('1', 'Blueberry');
-INSERT INTO crop (id, crop_name) VALUES ('2', 'Salmon');
-INSERT INTO crop (id, crop_name) VALUES ('3', 'Grape');
-INSERT INTO crop (id, crop_name) VALUES ('4', 'Alfalfa');
-INSERT INTO crop (id, crop_name) VALUES ('5', 'Sweet Potato');
-INSERT INTO crop (id, crop_name) VALUES ('6', 'Trout');
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '4', 'Blueberry') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '5', 'Salmon') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '6', 'Grape') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '7', 'Alfalfa') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '8', 'Sweet Potato') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '9', 'Trout') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '10', 'Soybean') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '11', 'Cranberry') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '12', 'Cucumber') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '13', 'Oat') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '14', 'Citrus') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '15', 'Sugar Cane') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '16', 'Strawberry') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '17', 'Honey') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '18', 'Pecan') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '19', 'Lettuce') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '20', 'Cotton') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '21', 'Sorghum') ON CONFLICT DO NOTHING;
+INSERT INTO crop (auth_user_id, id, crop_name) VALUES ('anonymousUser', '22', 'Hemp') ON CONFLICT DO NOTHING;