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Merged
jloux-brapi merged 6 commits into from
Dec 16, 2024
Merged

Migrate Java Test Server to Java 21, Postgres 17.2 #76

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c72591e
Migrate javax to jakarta, ditch WebSecurityConfigurerAdapter
jloux-brapi Dec 13, 2024
8f23684
Java 21 Upgrade (First Pass)
jloux-brapi Dec 13, 2024
5306e44
Make default string type varchar(255) in DB, change init schema
jloux-brapi Dec 13, 2024
4019f1d
Merge branch 'keycloak-dev-docker' into java-21-upgrade
jloux-brapi Dec 16, 2024
303b265
Upgrade docker containers to latest postgres
jloux-brapi Dec 16, 2024
82588ed
Update prerequisites in README
jloux-brapi Dec 16, 2024
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -2,7 +2,7 @@
# 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
FROM amazoncorretto:21

# 8080 - brapi app port | 5005 - brapi app debug port | 8008 - keycloak app port
EXPOSE 8080 5005 8008
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -10,8 +10,8 @@ Use [/calls](https://test-server.brapi.org/brapi/v1/call) (V1) or [/serverinfo](

## Prerequisites
* Maven 3.9
* Java 8
* Postgres 13
* Java 21
* Postgres 17.2

## Auth Configuration
BrAPI has provided a [sample central authentication service for the test server](https://brapi.org/oauth).
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2 changes: 1 addition & 1 deletion docker-compose-dev.yaml
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Expand Up @@ -11,7 +11,7 @@ services:
volumes:
- .\src\main\resources\properties\application.properties:/home/brapi/properties/application.properties
brapi-db:
image: postgres:13
image: postgres:17.2
environment:
POSTGRES_USER: brapi
POSTGRES_PASSWORD: password
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4 changes: 2 additions & 2 deletions docker-compose-local-auth.yaml
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Expand Up @@ -39,7 +39,7 @@ services:
ports:
- "8008:8008"
brapi-db:
image: postgres:13
image: postgres:17.2
environment:
POSTGRES_USER: brapi
POSTGRES_PASSWORD: password
Expand All @@ -48,7 +48,7 @@ services:
ports:
- "5433:5432"
keycloak-db:
image: postgres:13
image: postgres:17.2
volumes:
- keycloak-data:/var/lib/postgresql/data
environment:
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4 changes: 2 additions & 2 deletions docker-compose.yaml
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Expand Up @@ -30,10 +30,10 @@ services:
- KC_DB_USERNAME
- KC_DB_PASSWORD
postgres:
image: postgres:13
image: postgres:17.2
volumes:
# Update this path with the path your pipeline tool expects
- /home/jenkins/brapi.org/brapi-test-server/data:/var/lib/postgresql/data
- /home/jenkins/brapi.org/brapi-test-server/17-2:/var/lib/postgresql/data
networks:
default:
external:
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41 changes: 34 additions & 7 deletions pom.xml
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<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<java.version>1.8</java.version>
<spring.version>2.5.12</spring.version>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<java.version>21</java.version>
<spring.version>3.4.0</spring.version>
<maven.compiler.source>21</maven.compiler.source>
<maven.compiler.target>21</maven.compiler.target>
<springfox-version>2.10.0</springfox-version>
<slf4j-version>2.0.16</slf4j-version>
</properties>

<dependencies>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>7.7.3</version>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>11.0.1</version>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-database-postgresql</artifactId>
<version>11.0.1</version>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
Expand Down Expand Up @@ -58,6 +64,11 @@
<artifactId>spring-boot-starter-security</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-validation</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt</artifactId>
Expand Down Expand Up @@ -100,6 +111,11 @@
<artifactId>jackson-datatype-threetenbp</artifactId>
<version>2.8.4</version>
</dependency>
<dependency>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
<version>3.0.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
Expand All @@ -115,13 +131,24 @@
<artifactId>java-jwt</artifactId>
<version>3.14.0</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j-version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>${slf4j-version}</version>
</dependency>
</dependencies>

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.4.1</version>
<configuration>
<archive>
<manifest>
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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/CommonCropNamesApi.java
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import org.springframework.web.bind.annotation.RequestParam;


@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "commoncropnames", description = "the commoncropnames API")
public interface CommonCropNamesApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/ListsApi.java
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import java.util.ArrayList;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "lists", description = "the lists API")
public interface ListsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/LocationsApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "locations", description = "the locations API")
public interface LocationsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/PeopleApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "people", description = "the people API")
public interface PeopleApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/ProgramsApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "programs", description = "the programs API")
public interface ProgramsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/SeasonsApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "seasons", description = "the seasons API")
public interface SeasonsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/ServerInfoApi.java
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Expand Up @@ -18,7 +18,7 @@

import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "serverinfo", description = "the serverinfo API")
public interface ServerInfoApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/StudiesApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "studies", description = "the studies API")
public interface StudiesApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/StudytypesApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "studytypes", description = "the studytypes API")
public interface StudytypesApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/core/TrialsApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
@Api(value = "trials", description = "the trials API")
public interface TrialsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/AlleleMatrixApi.java
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import io.swagger.model.geno.AlleleMatrixSearchRequest;
import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2022-06-17T15:45:22.167Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2022-06-17T15:45:22.167Z[GMT]")
@Validated
public interface AlleleMatrixApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/CallSetsApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "callsets", description = "the callsets API")
public interface CallSetsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/CallsApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "calls", description = "the calls API")
public interface CallsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/MapsApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "maps", description = "the maps API")
public interface MapsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/MarkerPositionsApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "markerpositions", description = "the markerpositions API")
public interface MarkerPositionsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/PlatesApi.java
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import java.util.List;
import java.util.Map;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2022-06-02T18:30:00.206Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2022-06-02T18:30:00.206Z[GMT]")
@Validated
public interface PlatesApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/ReferenceSetsApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "referencesets", description = "the referencesets API")
public interface ReferenceSetsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/ReferencesApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "references", description = "the references API")
public interface ReferencesApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/SamplesApi.java
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import java.util.List;
import java.util.Map;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "samples", description = "the samples API")
public interface SamplesApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/VariantSetsApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "variantsets", description = "the variantsets API")
public interface VariantSetsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/VariantsApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "variants", description = "the variants API")
public interface VariantsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/geno/VendorApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:53.794Z[GMT]")
@Api(value = "vendor", description = "the vendor API")
public interface VendorApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/germ/AttributeValuesApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@Api(value = "attributevalues", description = "the attributevalues API")
public interface AttributeValuesApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/germ/AttributesApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@Api(value = "attributes", description = "the attributes API")
public interface AttributesApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/germ/BreedingMethodsApi.java
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import jakarta.validation.Valid;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@Api(value = "breedingmethods", description = "the breedingmethods API")
public interface BreedingMethodsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/germ/CrossesApi.java
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import java.util.List;
import java.util.Map;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@Api(value = "crosses", description = "the crosses API")
public interface CrossesApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/germ/CrossingProjectsApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@Api(value = "crossingprojects", description = "the crossingprojects API")
public interface CrossingProjectsApi {

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2 changes: 1 addition & 1 deletion src/main/java/io/swagger/api/germ/GermplasmApi.java
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import jakarta.validation.Valid;
import java.util.List;

@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:33:36.513Z[GMT]")
@Api(value = "germplasm", description = "the germplasm API")
public interface GermplasmApi {

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