From 4162ac259817e00283dd005b8b879d5f78b07c84 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Mon, 30 Jun 2025 10:55:27 -0400
Subject: [PATCH 1/5] [BI-2539] - added variable with default

---
 docker-compose.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker-compose.yml b/docker-compose.yml
index 6fce914..c415b66 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -13,6 +13,7 @@ services:
       - SANDBOX_MODE=${SANDBOX_MODE}
       - BRAPI_REFERENCE_SOURCE=${BRAPI_REFERENCE_SOURCE}
       - BRAPI_VENDOR_SUBMISSION_ENABLED=${BRAPI_VENDOR_SUBMISSION_ENABLED:-false}
+      - VUE_APP_ALTERNATE_AUTHENTICATION_ENABLED=${VUE_APP_ALTERNATE_AUTHENTICATION_ENABLED:-false}
     networks:
       upstream:
   biapi:

From 18a21b1b8e67a8c3739e12b82bf628120d965d87 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Mon, 30 Jun 2025 14:28:21 -0400
Subject: [PATCH 2/5] Update docker-compose.yml

---
 docker-compose.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index c415b66..9fd9ffd 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -13,7 +13,7 @@ services:
       - SANDBOX_MODE=${SANDBOX_MODE}
       - BRAPI_REFERENCE_SOURCE=${BRAPI_REFERENCE_SOURCE}
       - BRAPI_VENDOR_SUBMISSION_ENABLED=${BRAPI_VENDOR_SUBMISSION_ENABLED:-false}
-      - VUE_APP_ALTERNATE_AUTHENTICATION_ENABLED=${VUE_APP_ALTERNATE_AUTHENTICATION_ENABLED:-false}
+      - ALTERNATE_AUTHENTICATION_ENABLED=${ALTERNATE_AUTHENTICATION_ENABLED:-false}
     networks:
       upstream:
   biapi:

From c2179a0516e89ad30b3cda7eded6ff7c46186dfe Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Tue, 1 Jul 2025 15:37:36 -0400
Subject: [PATCH 3/5] [BI-2539] - added GitHub OAuth variables

---
 .env.template      | 4 ++++
 docker-compose.yml | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/.env.template b/.env.template
index debcfe3..871f599 100644
--- a/.env.template
+++ b/.env.template
@@ -7,6 +7,10 @@ OAUTH_CLIENT_SECRET=<ouath_client_secret goes here>
 JWT_SECRET=<jwt secret goes here>
 JWT_DOMAIN=<jwt domain ex. localhost>
 
+# GitHub OAuth variables. Only required if using GitHub as an alternative to ORCID.
+GITHUB_OAUTH_CLIENT_ID=<Client ID of GitHub OAuth app.>
+GITHUB_OAUTH_CLIENT_SECRET=<Client Secret of GitHub Oauth app.>
+
 # Database variables
 DB_PASSWORD=<database password goes here>
 DB_SERVER=<database server path (ex. localhost:5432)>
diff --git a/docker-compose.yml b/docker-compose.yml
index 9fd9ffd..e473af6 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -38,6 +38,8 @@ services:
       - OAUTH_OPENID_ISSUER=${OAUTH_OPENID_ISSUER:-https://sandbox.orcid.org}
       - OAUTH_OPENID_JWKSURI=${OAUTH_OPENID_JWKSURI:-https://sandbox.orcid.org/oauth/jwks}
       - OAUTH_OPENID_USERINFOURL=${OAUTH_OPENID_USERINFOURL:-https://sandbox.orcid.org/oauth/userinfo}
+      - GITHUB_OAUTH_CLIENT_ID=${GITHUB_OAUTH_CLIENT_ID}
+      - GITHUB_OAUTH_CLIENT_SECRET=${GITHUB_OAUTH_CLIENT_SECRET}
       - BRAPI_DEFAULT_URL=${BRAPI_DEFAULT_URL}
       - BRAPI_REFERENCE_SOURCE=${BRAPI_REFERENCE_SOURCE}
       - BRAPI_READ_TIMEOUT=${BRAPI_READ_TIMEOUT:-10m}

From da3ede3d2e4c28f772f806d6262550a90fae010f Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Thu, 10 Jul 2025 15:04:00 -0400
Subject: [PATCH 4/5] [BI-2539] - added flyway location variables

---
 .env.template      | 3 +++
 docker-compose.yml | 1 +
 2 files changed, 4 insertions(+)

diff --git a/.env.template b/.env.template
index 871f599..408d39e 100644
--- a/.env.template
+++ b/.env.template
@@ -78,3 +78,6 @@ AWS_S3_ENDPOINT=<s3 endpoint, default https://s3.us-east-1.amazonaws.com
 
 # feature flags
 BRAPI_VENDOR_SUBMISSION_ENABLED=false # allow sample submissions to be transmitted to a vendor via BrAPI
+
+# Migration locations for both maven flyway plugin (configured in pom.xml) and micronaut flyway library (configured in application.yml).
+FLYWAY_LOCATIONS=classpath:org/breedinginsight/db/migration,classpath:db/migration
\ No newline at end of file
diff --git a/docker-compose.yml b/docker-compose.yml
index e473af6..1f2be7b 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -63,6 +63,7 @@ services:
       - BRAPI_VENDOR_SUBMISSION_ENABLED=${BRAPI_VENDOR_SUBMISSION_ENABLED:-false}
       - CACHE_PAGINATE_GERMPLASM=${CACHE_PAGINATE_GERMPLASM:-false}
       - CACHE_BRAPI_FETCH_PAGE_SIZE=${CACHE_BRAPI_FETCH_PAGE_SIZE:-65000}
+      - FLYWAY_LOCATIONS=${FLYWAY_LOCATIONS:-classpath:org/breedinginsight/db/migration,classpath:db/migration}
     networks:
       backend:
       protected:

From ffae97878daba476eb0a588436003ba8d6ce8b7b Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Wed, 20 Aug 2025 12:54:38 -0400
Subject: [PATCH 5/5] [BI-2539] - removed unused variable

---
 docker-compose.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index 1f2be7b..e473af6 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -63,7 +63,6 @@ services:
       - BRAPI_VENDOR_SUBMISSION_ENABLED=${BRAPI_VENDOR_SUBMISSION_ENABLED:-false}
       - CACHE_PAGINATE_GERMPLASM=${CACHE_PAGINATE_GERMPLASM:-false}
       - CACHE_BRAPI_FETCH_PAGE_SIZE=${CACHE_BRAPI_FETCH_PAGE_SIZE:-65000}
-      - FLYWAY_LOCATIONS=${FLYWAY_LOCATIONS:-classpath:org/breedinginsight/db/migration,classpath:db/migration}
     networks:
       backend:
       protected: