Release/1.3

.env.template

@@ -3,6 +3,10 @@
 USER_ID=<user id of system user>
 GROUP_ID=<group id of system user>
 
+# GitHub OAuth variables. Only required if using GitHub as an OAuth provider.
+GITHUB_OAUTH_CLIENT_ID=<Client ID of GitHub OAuth app.>
+GITHUB_OAUTH_CLIENT_SECRET=<Client Secret of GitHub Oauth app.>
+
 ORCID_SANDBOX_AUTHENTICATION=<true or false; true=>use the Sandbox Orcid, false=>use the Production Orcid.  Defaults to false.>
 
 # Authentication variables
@@ -37,6 +41,7 @@ CACHE_BRAPI_FETCH_PAGE_SIZE=65000
 
 # BrAPI Server Variables
 BRAPI_SERVER_PORT=8083
+BRAPI_DOCKER_IMAGE=breedinginsight/brapi-java-server:develop
 
 # Brapi Server Variables
 BRAPI_DEFAULT_URL=http://localhost:8083
@@ -73,4 +78,4 @@ STUDY_START_DELAY=10s
 TRIAL_START_DELAY=15s
 TRAIT_START_DELAY=20s
 OBSERVATION_START_DELAY=25s
-OBSERVATION_UNIT_START_DELAY=30s
+OBSERVATION_UNIT_START_DELAY=30s

.github/pull_request_template.md

@@ -16,8 +16,6 @@ _Please include any details needed for reviewers to test this code_
 
 - [ ] I have performed a self-review of my own code
 - [ ] I have tested my code and ensured it meets the acceptance criteria of the story
-- [ ] I have tested that my code works with both the brapi-java-server and BreedBase
-- [ ] I have create/modified unit tests to cover this change
+- [ ] I have create/modified unit and/or integration tests to cover this change or tests are not applicable
 - [ ] I have commented my code, particularly in hard-to-understand areas
-- [ ] I have made corresponding changes to documentation
-- [ ] I have run TAF: _\<please include a link to TAF run>_
+- [ ] I have either updated the source of truth or arranged for update with product owner if needed https://breedinginsight.atlassian.net/wiki/spaces/BI/pages/1559953409/Source+of+Truth

.github/workflows/build.yml

@@ -19,12 +19,22 @@ name: maven build
 
 on:
   pull_request:
-    type: [opened, edited]
+    types: [opened, synchronize, edited]
+  workflow_dispatch:
+    inputs:
+      brapi_server_image:
+        description: 'BrAPI Server Docker Image'
+        required: false
+        default: 'breedinginsight/brapi-java-server:develop'
+      bi_api_branch:
+        description: 'BI API Branch'
+        required: false
+        default: 'develop'
 
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     services:
       postgres:
@@ -38,11 +48,15 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
 
     steps:
-      - uses: actions/checkout@v2
+      - name: Checkout BI API
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.bi_api_branch || github.ref }}
       - name: Set up JDK 13
-        uses: actions/setup-java@v1.4.3
+        uses: actions/setup-java@v4
         with:
           java-version: 13
+          distribution: 'zulu'
 
       - name: Build with Maven
         run: mvn validate -B flyway:migrate clean install --file pom.xml --settings settings.xml
@@ -59,4 +73,7 @@ jobs:
           JWT_SECRET: ${{ secrets.JWT_SECRET }}
           OAUTH_CLIENT_ID: 123abc
           OAUTH_CLIENT_SECRET: asdfljkhalkbaldsfjasdfi238497098asdf
-          BRAPI_REFERENCE_SOURCE: breedinginsight.org
+          GITHUB_OAUTH_CLIENT_ID: 12345678901234567890
+          GITHUB_OAUTH_CLIENT_SECRET: 1234567890123456789012345678901234567890
+          BRAPI_REFERENCE_SOURCE: breedinginsight.org
+          BRAPI_DOCKER_IMAGE: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.brapi_server_image || 'breedinginsight/brapi-java-server:develop' }}

.github/workflows/release.yml

@@ -66,6 +66,8 @@ jobs:
           JWT_SECRET: ${{ secrets.JWT_SECRET }}
           OAUTH_CLIENT_ID: 123abc
           OAUTH_CLIENT_SECRET: asdfljkhalkbaldsfjasdfi238497098asdf
+          GITHUB_OAUTH_CLIENT_ID: 12345678901234567890
+          GITHUB_OAUTH_CLIENT_SECRET: 1234567890123456789012345678901234567890
           BRAPI_REFERENCE_SOURCE: breedinginsight.org
       - name: Login to Docker Hub
         uses: docker/login-action@v1

.github/workflows/versioner-develop.yml

@@ -80,6 +80,8 @@ jobs:
           JWT_SECRET: ${{ secrets.JWT_SECRET }}
           OAUTH_CLIENT_ID: 123abc
           OAUTH_CLIENT_SECRET: asdfljkhalkbaldsfjasdfi238497098asdf
+          GITHUB_OAUTH_CLIENT_ID: 12345678901234567890
+          GITHUB_OAUTH_CLIENT_SECRET: 1234567890123456789012345678901234567890
           BRAPI_REFERENCE_SOURCE: breedinginsight.org
       - name: Login to Docker Hub
         uses: docker/login-action@v1

AGENTS.md

@@ -0,0 +1,75 @@
+# AGENTS.md
+
+## Scope
+- These instructions apply to the whole repository.
+- If a subdirectory contains its own `AGENTS.md`, the more specific file wins for that subtree.
+
+## Repository Overview
+- Java 13 Maven backend using Micronaut.
+- Main application code: `src/main/java/org/breedinginsight`
+- Tests: `src/test/java/org/breedinginsight`
+- DB migrations: `src/main/resources/db/migration`
+- API docs and related materials: `docs`
+- Build config: `pom.xml`
+- Docker and local setup: `README.md`, `docker-compose.yml`
+
+## Working Rules
+- Keep changes narrow and task-focused.
+- Prefer fixing root causes over adding one-off workarounds.
+- Do not edit `.env`, `.env.test`, `.env.template`, or other secret-bearing config files unless explicitly asked.
+- Do not modify `target/`, `.idea/`, or the large SQL dump files unless the task is specifically about them.
+- Scope searches to relevant directories instead of scanning the entire repository when possible.
+- Do not edit historical Flyway migrations unless explicitly requested. Add a new migration instead.
+
+## Files To Ignore By Default
+- `target/`
+- `.idea/`
+
+## Validation
+- Use Maven for validation.
+- Source envs from `.env` when running `mvn` commands by using `set -a`, `source .env`, and `set +a`.
+- Preferred targeted test command:
+  ```sh
+  set -a
+  source .env
+  set +a
+  mvn -Dtest=ClassName test --settings settings.xml
+  ```
+- Full test command:
+  ```sh
+  set -a
+  source .env
+  set +a
+  mvn test --settings settings.xml
+  ```
+- Full build without tests:
+  ```sh
+  set -a
+  source .env
+  set +a
+  mvn clean validate install -D maven.test.skip=true --settings settings.xml
+  ```
+- Tests may require Docker, Testcontainers, and local services. If validation cannot run, say exactly what blocked it.
+
+## API Change Rules
+- If endpoint behavior changes, do not update the relevant API docs or spec files in `docs`, they are no longer being maintained.
+- If API code changes, add or update endpoint or integration tests.
+
+## Database Rules
+- Schema changes belong in a new Flyway migration under `src/main/resources/db/migration`.
+- If schema changes affect generated jOOQ code, run the documented generation flow.
+
+## Testing Guidance
+- Prefer targeted tests for the changed area before suggesting a full test run.
+- Prefer high-signal tests over broad or repetitive test coverage.
+- Do not add unit tests by default for straightforward changes.
+- Add unit tests selectively for hard-to-reproduce bugs, complex logic regressions, or behavior that is difficult or expensive to validate through integration tests.
+- Prefer integration or endpoint tests for user-facing and API behavior changes.
+- Avoid tests that mainly lock in implementation details or create disproportionate maintenance burden.
+- When adding regression coverage, prefer the smallest number of tests that gives confidence in the fix.
+- For controller or API changes, look first under `src/test/java/org/breedinginsight/api` and `src/test/java/org/breedinginsight/brapi`.
+- For importer work, check `src/test/java/org/breedinginsight/brapps/importer`.
+
+## Response Expectations
+- Summarize changed files, validation performed, and any remaining risks.
+- If tests or docs updates were skipped, explain why.

docker-compose.yml

@@ -40,6 +40,8 @@ services:
       - API_INTERNAL_PORT=${API_INTERNAL_PORT}
       - API_INTERNAL_TEST_PORT=${API_INTERNAL_TEST_PORT}
       - OAUTH_CLIENT_ID=${OAUTH_CLIENT_ID}
+      - GITHUB_OAUTH_CLIENT_ID=${GITHUB_OAUTH_CLIENT_ID}
+      - GITHUB_OAUTH_CLIENT_SECRET=${GITHUB_OAUTH_CLIENT_SECRET}
       - JWT_DOMAIN=${JWT_DOMAIN}
       - DB_SERVER=${DB_SERVER}
       - DB_NAME=${DB_NAME}

pom.xml

@@ -83,13 +83,13 @@
         <geojson-jackson.version>1.14</geojson-jackson.version>
         <apache-commons-csv.version>1.9.0</apache-commons-csv.version>
         <apache-commons-lang.version>3.12.0</apache-commons-lang.version>
-        <testcontainers.version>1.16.3</testcontainers.version>
+        <testcontainers.version>1.21.4</testcontainers.version>
         <!-- Version of flyway dependent on version of micronaut -->
         <flyway.version>7.7.3</flyway.version>
         <guava.version>31.0.1-jre</guava.version>
         <okhttp.version>4.9.3</okhttp.version>
         <mockito.version>4.3.1</mockito.version>
-        <brapi-java-client.version>2.1-SNAPSHOT</brapi-java-client.version>
+        <brapi-java-client.version>2.2.0</brapi-java-client.version>
         <commons-io.version>2.11.0</commons-io.version>
         <tika-app.version>2.2.1</tika-app.version>
         <!-- Version of apache-poi depends on version of tika. Tika uses these. -->
@@ -192,6 +192,11 @@
             <artifactId>micronaut-inject</artifactId>
             <scope>compile</scope>
         </dependency>
+        <dependency>
+            <groupId>io.micronaut</groupId>
+            <artifactId>micronaut-http-client</artifactId>
+            <scope>compile</scope>
+        </dependency>
         <dependency>
             <groupId>io.micronaut</groupId>
             <artifactId>micronaut-validation</artifactId>
@@ -536,6 +541,16 @@
                     <target>${maven.compiler.target}</target>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <configuration>
+                    <!-- Temporary: skip Gigwa IT until the Gigwa image issue is resolved -->
+                    <excludes>
+                        <exclude>**/GigwaGenotypeServiceImplIntegrationTest.java</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
             <plugin>
                 <groupId>org.jooq</groupId>
                 <artifactId>jooq-codegen-maven</artifactId>
@@ -619,6 +634,10 @@
                     <url>jdbc:postgresql://${DB_SERVER}/${DB_NAME}</url>
                     <user>${DB_USER}</user>
                     <password>${DB_PASSWORD}</password>
+                    <locations>
+                        <location>filesystem:src/main/java/org/breedinginsight/db/migration</location>
+                        <location>filesystem:src/main/resources/db/migration</location>
+                    </locations>
                 </configuration>
                 <dependencies>
                     <dependency>

settings.xml

@@ -52,7 +52,7 @@
                 <repository>
                     <id>github-fannypack</id>
                     <name>FannyPack github repository</name>
-                    <url>https://maven.pkg.github.com/Kowalski-IO/fannypack</url>
+                    <url>https://maven.pkg.github.com/BrandonKowalski/fannypack</url>
                     <releases><enabled>true</enabled></releases>
                     <snapshots><enabled>true</enabled></snapshots>
                 </repository>

src/main/java/org/breedinginsight/api/auth/AuthServiceLoginHandler.java

@@ -30,7 +30,6 @@
 import io.micronaut.security.token.jwt.cookie.JwtCookieLoginHandler;
 import io.micronaut.security.token.jwt.generator.AccessRefreshTokenGenerator;
 import io.micronaut.security.token.jwt.generator.AccessTokenConfiguration;
-import io.micronaut.security.token.jwt.generator.JwtGeneratorConfiguration;
 import lombok.extern.slf4j.Slf4j;
 import org.breedinginsight.api.model.v1.auth.SignUpJWT;
 import org.breedinginsight.model.ProgramUser;
@@ -83,7 +82,7 @@ public AuthServiceLoginHandler(JwtCookieConfiguration jwtCookieConfiguration,
 
     @Override
     public MutableHttpResponse<?> loginSuccess(UserDetails userDetails, HttpRequest<?> request) {
-        // Called when login to orcid is successful.
+        // Called when login to OAuth provider is successful.
         // Check if our login to our system is successful.
         if (request.getCookies().contains(accountTokenCookieName)) {
             Cookie accountTokenCookie = request.getCookies().get(accountTokenCookieName);
@@ -124,7 +123,7 @@ public MutableHttpResponse<?> loginSuccess(UserDetails userDetails, HttpRequest<
 
     private AuthenticatedUser getUserCredentials(UserDetails userDetails) throws AuthenticationException {
 
-        Optional<User> user = userService.getByOrcid(userDetails.getUsername());
+        Optional<User> user = userService.getByOAuthId(userDetails.getUsername());
 
         if (user.isPresent()) {
             if (user.get().getActive()) {
@@ -159,9 +158,20 @@ public MutableHttpResponse<?> loginFailed(AuthenticationResponse authenticationF
         }
     }
 
+    private String parseOAuthProvider(HttpRequest request) {
+        // The request path will be something like "/sso/success/github".
+        if (request.getPath().toLowerCase().contains("github")) {
+            return "github";
+        } else {
+            // Default to ORCID.
+            return "orcid";
+        }
+    }
+
     private MutableHttpResponse newAccountCreationResponse(UserDetails userDetails, String accountToken, HttpRequest request) {
 
-        String orcid = userDetails.getUsername();
+        String oAuthId = userDetails.getUsername();
+        String oAuthProvider = parseOAuthProvider(request);
         SignUpJWT signUpJWT;
         try {
             signUpJWT = signUpJwtService.validateAndParseAccountSignUpJwt(accountToken);
@@ -185,9 +195,9 @@ private MutableHttpResponse newAccountCreationResponse(UserDetails userDetails,
         }
 
         if (newUser.getAccountToken().equals(signUpJWT.getJwtId().toString())) {
-            // Assign orcid to that user
+            // Assign OAuth Id and provider to that user.
             try {
-                userService.updateOrcid(newUser.getId(), orcid);
+                userService.updateOAuthInfo(newUser.getId(), oAuthId, oAuthProvider);
             } catch (DoesNotExistException e) {
                 MutableHttpResponse resp = HttpResponse.seeOther(URI.create(newAccountErrorUrl));
                 return resp;

src/main/java/org/breedinginsight/api/auth/GithubApiClient.java

@@ -0,0 +1,32 @@
+/*
+ * 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.
+ */
+
+package org.breedinginsight.api.auth;
+
+import io.micronaut.http.annotation.Get;
+import io.micronaut.http.annotation.Header;
+import io.micronaut.http.client.annotation.Client;
+import io.reactivex.Flowable;
+
+@Header(name = "User-Agent", value = "Micronaut")
+@Client("https://api.github.com")
+public interface GithubApiClient {
+
+    @Get("/user")
+    Flowable<GithubUser> getUser(@Header("Authorization") String authorization);
+}
+

src/main/java/org/breedinginsight/api/auth/GithubUser.java

@@ -0,0 +1,37 @@
+/*
+ * 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.
+ */
+
+package org.breedinginsight.api.auth;
+
+import com.fasterxml.jackson.databind.PropertyNamingStrategy;
+import com.fasterxml.jackson.databind.annotation.JsonNaming;
+import io.micronaut.core.annotation.Introspected;
+import lombok.Getter;
+
+@Introspected
+@JsonNaming(PropertyNamingStrategy.SnakeCaseStrategy.class)
+@Getter
+public class GithubUser {
+
+    private String id;
+    // The login will be the unique GitHub username.
+    private String login;
+    private String name;
+    private String email;
+
+}
+