From 74fee3b464e0c85f677c60728eea40db5dde24d6 Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Mon, 28 Jul 2025 08:31:38 -0400
Subject: [PATCH 1/8] [BI-2700] Improve Technical Documentation For DeltaBreed
 Paper

---
 README.md                  | 56 +++++++++++++++++++++++++++++++++++++-
 docker-compose-mailhog.yml | 12 ++++++++
 2 files changed, 67 insertions(+), 1 deletion(-)
 create mode 100644 docker-compose-mailhog.yml

diff --git a/README.md b/README.md
index 48a9037..856e63a 100644
--- a/README.md
+++ b/README.md
@@ -6,9 +6,63 @@
     This repo contains the docker-compose configurations used to run DeltaBreed.
 </h2>
 
-# Prereqs
+# <a id="get_started"></a>Getting Started
+## Outline
+<ul>
+<li>Download prereqs</li>
+<li>Set up OAuth with ORCID</li>
+<li>Set up environmental variables</li>
+<li>Run docker-compose</li>
+<li>Get ORCID credentials into database</li>
+<li>Access DeltaBreed on web</li>
+</ul>
+
+## Download Prereqs
 Docker and Docker-compose are both required.
 
+## Set up OAuth with ORCID
+Running DeltaBreed requires setting up OAuth with ORCID (Open Researcher and Contributor ID), --this is what orcid is--
+
+TODO steps
+
+## Set up environmental variables
+To set necessary private environmental variables for DeltaBreed to run, at the root level of the repo locally create a file called `.env`.
+
+(a template exists named `.env.template` todo check if .env.quicktemplate might be better alternative)
+
+The containers are not run by the root user but by a new user and group called
+'host'.  The user and group ids for host are both set to 1001 by default.  If
+you wish to change these to your own user and group ids, add the following
+contents to .env:
+```
+USER_ID=1001
+GROUP_ID=1001
+```
+Change 1001 to your own id values.  You can find at the console your user and group ids using the id command:
+for user id
+```
+id -u
+```
+and for group id
+```
+id -g
+```
+
+todo remaining variables that need extra guidance
+
+## Run docker-compose
+Run the following in the bi-docker-stack repository
+
+```
+docker-compose -f docker-compose.yml -f docker-compose-redis.yml -f docker-compose-gigwa.yml -f docker-compose-mailhog.yml up -d
+```
+
+## Get ORCID credentials into database
+Run this shell script (TODO)
+
+## Access DeltaBreed on web
+DeltaBreed can then be accessed via the url entered for ```WEB_BASE_URL``` in the .env file.
+
 # Architecture
 The primary components of DeltaBreed are the Web UI (Breeding-Insight/bi-web) and the API (Breeding-Insight/bi-api).
 The [BrAPI Java Server](https://github.com/plantbreeding/brapi-Java-TestServer) is used for phenotypic data storage, [Gigwa](https://github.com/SouthGreenPlatform/Gigwa2) is used for genotypic data storage, and interoperability with external applications such as [Field Book](https://github.com/PhenoApps/Field-Book/) is enabled by [BrAPI](https://brapi.org/).
diff --git a/docker-compose-mailhog.yml b/docker-compose-mailhog.yml
new file mode 100644
index 0000000..ad81bf3
--- /dev/null
+++ b/docker-compose-mailhog.yml
@@ -0,0 +1,12 @@
+version: "3.7"
+
+services:
+  mailhog:
+    image: mailhog/mailhog:latest
+    container_name: mailhog
+    restart: always
+    ports:
+      - ${MAILHOG_WEB_PORT:-8025}:8025
+      - ${MAILHOG_PORT:-1025}:1025
+    networks:
+      backend:

From b08df7b36295e9da27fcf36da6181a9034a7d6b7 Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Mon, 28 Jul 2025 16:45:19 -0400
Subject: [PATCH 2/8] [BI-2700] Add scripts and further readme changes

---
 README.md   | 87 ++++++++++++++++++++++++-----------------------------
 addUser.ps1 |  8 +++++
 addUser.sh  |  8 +++++
 3 files changed, 56 insertions(+), 47 deletions(-)
 create mode 100644 addUser.ps1
 create mode 100644 addUser.sh

diff --git a/README.md b/README.md
index 856e63a..641494d 100644
--- a/README.md
+++ b/README.md
@@ -6,6 +6,13 @@
     This repo contains the docker-compose configurations used to run DeltaBreed.
 </h2>
 
+# Table of Contents
+<p align="center">
+  <a href="#get_started">Getting Started</a> |
+  <a href="#architecture">Architecture</a> |
+  <a href="#other-envs">Setting Up Other Environments</a>
+</p>
+
 # <a id="get_started"></a>Getting Started
 ## Outline
 <ul>
@@ -21,14 +28,28 @@
 Docker and Docker-compose are both required.
 
 ## Set up OAuth with ORCID
-Running DeltaBreed requires setting up OAuth with ORCID (Open Researcher and Contributor ID), --this is what orcid is--
+Running DeltaBreed requires setting up OAuth with [ORCID](https://info.orcid.org/what-is-orcid/) (Open Researcher and Contributor ID).
+
+<ol>
+<li><a href="https://orcid.org/register">Create an ORCID account</a></li>
+<li>Sign into ORCID</li>
+<li>Go to "Developer Tools"</li>
+<li>Agree to Terms of Service and register for ORCID public API credentials</li>
+<li>Enter application name and description (todo check if any requirements)</li>
+<li>Enter application URL <code>http://test.localhost:8080</code> (todo check this can work)</li>
+<li>Add Redirect URI <code>http://test.localhost:8081/sso/success/orcid</code></li>
+<li>Select "Save application" at the bottom of the page</li>
+<li>Copy the generated Client ID and Client Secret to add to the .env file (see <a href="env_vars">Set up environmental variables</a>)</li>
+</ol>
 
-TODO steps
+## <a id="env_vars"></a>Set up environmental variables
+To set necessary private environmental variables for DeltaBreed to run, at the root level of the repo locally create a file called `.env`. 
+A template exists named `.env.quicktemplate` that has most environmental variables already filled. 
+If a user wants to customize services in more depth (not covered in this quick start guide), they can instead base their `.env` off of `.env.template`.
 
-## Set up environmental variables
-To set necessary private environmental variables for DeltaBreed to run, at the root level of the repo locally create a file called `.env`.
+The following is guidance for filling out remaining parts of `.env.quicktemplate`.
 
-(a template exists named `.env.template` todo check if .env.quicktemplate might be better alternative)
+(TODO remaining vars)
 
 The containers are not run by the root user but by a new user and group called
 'host'.  The user and group ids for host are both set to 1001 by default.  If
@@ -48,8 +69,6 @@ and for group id
 id -g
 ```
 
-todo remaining variables that need extra guidance
-
 ## Run docker-compose
 Run the following in the bi-docker-stack repository
 
@@ -58,45 +77,34 @@ docker-compose -f docker-compose.yml -f docker-compose-redis.yml -f docker-compo
 ```
 
 ## Get ORCID credentials into database
-Run this shell script (TODO)
+For Mac/Linux, run `addUser.sh`
+
+For Windows, run `addUser.ps1`
 
 ## Access DeltaBreed on web
 DeltaBreed can then be accessed via the url entered for ```WEB_BASE_URL``` in the .env file.
 
-# Architecture
+# <a id="architecture"></a> Architecture
 The primary components of DeltaBreed are the Web UI (Breeding-Insight/bi-web) and the API (Breeding-Insight/bi-api).
 The [BrAPI Java Server](https://github.com/plantbreeding/brapi-Java-TestServer) is used for phenotypic data storage, [Gigwa](https://github.com/SouthGreenPlatform/Gigwa2) is used for genotypic data storage, and interoperability with external applications such as [Field Book](https://github.com/PhenoApps/Field-Book/) is enabled by [BrAPI](https://brapi.org/).
 DeltaBreed uses [ORCID](https://orcid.org/) for authentication.
 
 ![DeltaBreed v1.0 architecture diagram.](./images/architecture.1.0.png)
 
-# Configuration
-The containers are not run by the root user but by a new user and group called
-'host'.  The user and group ids for host are both set to 1001 by default.  If
-you wish to change these to your own user and group ids, add the following
-contents to .env:
-```
-USER_ID=1001
-GROUP_ID=1001
-```
-Change 1001 to your own id values.  You can find at the console your user and group ids using the id command:
-for user id
-```
-id -u
-```
-and for group id
+# <a id="other_envs"></a>Setting up Other Environments
+## Development Environment
+
+To run a development environment, you will need to initialize the git submodules that exist within this repository:
+
 ```
-id -g
+git submodule update --init --recursive
 ```
 
-## Configure Services
-
-Private values used in each environment are stored in Lastpass and are never
-placed in docker-compose.yml and never committed to the repo.  At the root level
-of the repo locally create a file called `.env` (a template exists named `.env.template`) 
-and save the Lastpass contents for "bi-api secrets" in this file.
+Then run:
 
-# Run
+```
+docker-compose -f docker-compose.yml -f docker-compose-redis.yml -f docker-compose-gigwa.yml -f docker-compose-dev.yml up -d
+```
 
 ## Production Environment
 
@@ -157,18 +165,3 @@ The Dockerfile for the reverse proxy contains the nginx rules used to direct
 traffic to the appropriate upstream server. Any new features added to bi-api
 that use an endpoint not in the /v1/ or /sso/ name spaces must have a rule added
 to the proxy config in order to send these requests upstream.
-
-
-# Development Environment
-
-To run a development environment, you will need to initialize the git submodules that exist within this repository:
-
-```
-git submodule update --init --recursive
-```
-
-Then run:
-
-```
-docker-compose -f docker-compose.yml -f docker-compose-redis.yml -f docker-compose-gigwa.yml -f docker-compose-dev.yml up -d
-```
diff --git a/addUser.ps1 b/addUser.ps1
new file mode 100644
index 0000000..e4e04a6
--- /dev/null
+++ b/addUser.ps1
@@ -0,0 +1,8 @@
+$oauth_id = Read-Host "Enter ORCID (e.g. 0000-1111-2222-3333)"
+$email = Read-Host "Enter email (must be the email used with ORCID)"
+
+$insertUser = "INSERT INTO bi_user (orcid, name, email, created_by, updated_by, active) VALUES ('${oauth_id}', 'admin', '${email}', '00000000-0000-0000-0000-000000000000', '00000000-0000-0000-0000-000000000000', true);"
+$insertRole = "INSERT INTO system_user_role (bi_user_id, system_role_id, created_by, updated_by) VALUES ((SELECT id FROM bi_user WHERE email='${email}'), (SELECT id FROM system_role WHERE domain = 'System Administrator'), '00000000-0000-0000-0000-000000000000', '00000000-0000-0000-0000-000000000000');"
+
+docker exec -it bidb psql -U postgres -d bidb -c $insertUser
+docker exec -it bidb psql -U postgres -d bidb -c $insertRole
\ No newline at end of file
diff --git a/addUser.sh b/addUser.sh
new file mode 100644
index 0000000..1d68bac
--- /dev/null
+++ b/addUser.sh
@@ -0,0 +1,8 @@
+read -p "Enter ORCID (e.g. 0000-1111-2222-3333):" oauth_id
+read -p "Enter email (must be the email used with ORCID):" email
+
+insertUser="INSERT INTO bi_user (orcid, name, email, created_by, updated_by, active) VALUES ('${oauth_id}', 'admin', '${email}', '00000000-0000-0000-0000-000000000000', '00000000-0000-0000-0000-000000000000', true);"
+docker exec -it bidb psql -U postgres -d bidb -c "${insertUser}"
+
+insertRole="INSERT INTO system_user_role (bi_user_id, system_role_id, created_by, updated_by) VALUES ((SELECT id FROM bi_user WHERE email='${email}'), (SELECT id FROM system_role WHERE domain = 'System Administrator'), '00000000-0000-0000-0000-000000000000', '00000000-0000-0000-0000-000000000000');"
+docker exec -it bidb psql -U postgres -d bidb -c "${insertRole}"
\ No newline at end of file

From 15539ee8a816d02646ee5daf036c203e701b96b3 Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Tue, 29 Jul 2025 11:12:43 -0400
Subject: [PATCH 3/8] [BI-2700] Added .env.quicktemplate and README
 improvements

---
 .env.quicktemplate | 79 ++++++++++++++++++++++++++++++++++++++++++++++
 README.md          |  4 +--
 2 files changed, 81 insertions(+), 2 deletions(-)
 create mode 100644 .env.quicktemplate

diff --git a/.env.quicktemplate b/.env.quicktemplate
new file mode 100644
index 0000000..a892e3d
--- /dev/null
+++ b/.env.quicktemplate
@@ -0,0 +1,79 @@
+##Variables for user to set
+USER_ID=<user id of system user>
+GROUP_ID=<group id of system user>
+#todo test run without user_id and group_id
+
+#Values from ORCID
+# Authentication variables
+OAUTH_CLIENT_ID=<oauth app client id>
+OAUTH_CLIENT_SECRET=<oauth_client_secret goes here>
+ADMIN_ORCID=<orcid for admin account goes here>
+
+# Build variables needed to pull down JAR files from Github Packages
+GITHUB_ACTOR=<github user name>
+GITHUB_TOKEN=<github personal access token>
+#todo unclear if we actually need github actor and token
+
+##Variables already set
+
+JWT_SECRET=<json web token secret> #default insecure value? not secure but find for local, prepend with insecure if possible todo
+JWT_DOMAIN=localhost
+
+# Database variables
+DB_PASSWORD=postgres
+DB_SERVER=dbserver:5432
+DB_NAME=bidb
+DB_USER=postgres
+
+# Micronaut variables
+API_INTERNAL_PORT=8081
+API_INTERNAL_TEST_PORT=8082
+
+BRAPI_READ_TIMEOUT=60m
+
+# Max number of records to POST to the BrAPI service per request
+POST_CHUNK_SIZE=1000
+
+# Request cache records paginating through available records per program by CACHE_BRAPI_FETCH_PAGE_SIZE
+CACHE_PAGINATE_GERMPLASM=false
+CACHE_BRAPI_FETCH_PAGE_SIZE=65000
+
+# BrAPI Server Variables
+BRAPI_SERVER_PORT=8080
+
+BRAPI_DEFAULT_URL=http://brapiserver:8080
+BRAPI_REFERENCE_SOURCE=breedinginsight.org
+
+BRAPI_DB_SERVER=dbserver:5432
+BRAPI_DB=postgres
+BRAPI_DB_USER=postgres
+BRAPI_DB_PASSWORD=postgres
+
+WEB_BASE_URL=http://localhost
+API_BASE_URL=http://localhost
+
+# Public domain name
+REGISTERED_DOMAIN=localhost
+
+# Email relay information
+EMAIL_RELAY_HOST=mailhog
+EMAIL_RELAY_PORT=1025
+EMAIL_FROM=bidevteam@cornell.edu
+
+REDIS_URL=redis://localhost:6379
+
+GIGWA_PORT=6060
+GIGWA_HOST=http://gigwa:8080/
+GIGWA_USER=gigwadmin
+GIGWA_PASSWORD=nimda
+GIGWA_MONGO_USER=mongo
+GIGWA_MONGO_PASSWORD=mongo
+
+AWS_REGION=us-east-1
+AWS_ACCESS_KEY_ID=test
+AWS_SECRET_KEY=test
+AWS_GENO_BUCKET=breedinginsight.org-dev-bucket
+AWS_S3_ENDPOINT=http://localstack:4566
+
+# feature flags
+BRAPI_VENDOR_SUBMISSION_ENABLED=false # allow sample submissions to be transmitted to a vendor via BrAPI
\ No newline at end of file
diff --git a/README.md b/README.md
index 641494d..b90ac76 100644
--- a/README.md
+++ b/README.md
@@ -35,7 +35,7 @@ Running DeltaBreed requires setting up OAuth with [ORCID](https://info.orcid.org
 <li>Sign into ORCID</li>
 <li>Go to "Developer Tools"</li>
 <li>Agree to Terms of Service and register for ORCID public API credentials</li>
-<li>Enter application name and description (todo check if any requirements)</li>
+<li>Enter application name and description (no particular requirements)</li>
 <li>Enter application URL <code>http://test.localhost:8080</code> (todo check this can work)</li>
 <li>Add Redirect URI <code>http://test.localhost:8081/sso/success/orcid</code></li>
 <li>Select "Save application" at the bottom of the page</li>
@@ -73,7 +73,7 @@ id -g
 Run the following in the bi-docker-stack repository
 
 ```
-docker-compose -f docker-compose.yml -f docker-compose-redis.yml -f docker-compose-gigwa.yml -f docker-compose-mailhog.yml up -d
+docker-compose -f docker-compose.yml -f docker-compose-redis.yml -f docker-compose-gigwa.yml -f docker-compose-localstack.yml -f docker-compose-mailhog.yml -f docker-compose-qa.yml up -d --build
 ```
 
 ## Get ORCID credentials into database

From 55a64f13e3d7d9f208ca7d2b9d1e316da6f3fbac Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Tue, 29 Jul 2025 12:16:32 -0400
Subject: [PATCH 4/8] [BI-2700] Added default secret

---
 .env.quicktemplate | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.env.quicktemplate b/.env.quicktemplate
index a892e3d..fcddeed 100644
--- a/.env.quicktemplate
+++ b/.env.quicktemplate
@@ -16,7 +16,7 @@ GITHUB_TOKEN=<github personal access token>
 
 ##Variables already set
 
-JWT_SECRET=<json web token secret> #default insecure value? not secure but find for local, prepend with insecure if possible todo
+JWT_SECRET=insecure2520f59b2bccc64ce155482bc413f6b9ede5c6d418ab529d1b2051baa6f0849e
 JWT_DOMAIN=localhost
 
 # Database variables

From 812bfde85043b01393acf1744202b98816a00aa7 Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Wed, 30 Jul 2025 17:52:21 -0400
Subject: [PATCH 5/8] [BI-2700] Updates

---
 .env.quicktemplate | 15 +--------------
 README.md          | 47 +++++++++++++++++++++++-----------------------
 2 files changed, 24 insertions(+), 38 deletions(-)

diff --git a/.env.quicktemplate b/.env.quicktemplate
index fcddeed..bf0233d 100644
--- a/.env.quicktemplate
+++ b/.env.quicktemplate
@@ -1,21 +1,8 @@
-##Variables for user to set
-USER_ID=<user id of system user>
-GROUP_ID=<group id of system user>
-#todo test run without user_id and group_id
-
-#Values from ORCID
-# Authentication variables
+##ORCID Variables for user to set
 OAUTH_CLIENT_ID=<oauth app client id>
 OAUTH_CLIENT_SECRET=<oauth_client_secret goes here>
-ADMIN_ORCID=<orcid for admin account goes here>
-
-# Build variables needed to pull down JAR files from Github Packages
-GITHUB_ACTOR=<github user name>
-GITHUB_TOKEN=<github personal access token>
-#todo unclear if we actually need github actor and token
 
 ##Variables already set
-
 JWT_SECRET=insecure2520f59b2bccc64ce155482bc413f6b9ede5c6d418ab529d1b2051baa6f0849e
 JWT_DOMAIN=localhost
 
diff --git a/README.md b/README.md
index b90ac76..5b73dd9 100644
--- a/README.md
+++ b/README.md
@@ -36,8 +36,8 @@ Running DeltaBreed requires setting up OAuth with [ORCID](https://info.orcid.org
 <li>Go to "Developer Tools"</li>
 <li>Agree to Terms of Service and register for ORCID public API credentials</li>
 <li>Enter application name and description (no particular requirements)</li>
-<li>Enter application URL <code>http://test.localhost:8080</code> (todo check this can work)</li>
-<li>Add Redirect URI <code>http://test.localhost:8081/sso/success/orcid</code></li>
+<li>Enter application URL <code>http://test.localhost:8080</code></li>
+<li>Add Redirect URI <code>http://test.localhost/sso/success/orcid</code></li>
 <li>Select "Save application" at the bottom of the page</li>
 <li>Copy the generated Client ID and Client Secret to add to the .env file (see <a href="env_vars">Set up environmental variables</a>)</li>
 </ol>
@@ -47,27 +47,7 @@ To set necessary private environmental variables for DeltaBreed to run, at the r
 A template exists named `.env.quicktemplate` that has most environmental variables already filled. 
 If a user wants to customize services in more depth (not covered in this quick start guide), they can instead base their `.env` off of `.env.template`.
 
-The following is guidance for filling out remaining parts of `.env.quicktemplate`.
-
-(TODO remaining vars)
-
-The containers are not run by the root user but by a new user and group called
-'host'.  The user and group ids for host are both set to 1001 by default.  If
-you wish to change these to your own user and group ids, add the following
-contents to .env:
-```
-USER_ID=1001
-GROUP_ID=1001
-```
-Change 1001 to your own id values.  You can find at the console your user and group ids using the id command:
-for user id
-```
-id -u
-```
-and for group id
-```
-id -g
-```
+In this new `.env` based off the template, set `OAUTH_CLIENT_ID` and `OAUTH_CLIENT_SECRET` to the generated Client ID and Client Secret copied in the previous step
 
 ## Run docker-compose
 Run the following in the bi-docker-stack repository
@@ -82,7 +62,7 @@ For Mac/Linux, run `addUser.sh`
 For Windows, run `addUser.ps1`
 
 ## Access DeltaBreed on web
-DeltaBreed can then be accessed via the url entered for ```WEB_BASE_URL``` in the .env file.
+DeltaBreed can then be accessed via `http://localhost:8080`. 
 
 # <a id="architecture"></a> Architecture
 The primary components of DeltaBreed are the Web UI (Breeding-Insight/bi-web) and the API (Breeding-Insight/bi-api).
@@ -165,3 +145,22 @@ The Dockerfile for the reverse proxy contains the nginx rules used to direct
 traffic to the appropriate upstream server. Any new features added to bi-api
 that use an endpoint not in the /v1/ or /sso/ name spaces must have a rule added
 to the proxy config in order to send these requests upstream.
+
+## User Configuration
+The containers are not run by the root user but by a new user and group called
+'host'.  The user and group ids for host are both set to 1001 by default.  If
+you wish to change these to your own user and group ids, add the following
+contents to .env:
+```
+USER_ID=1001
+GROUP_ID=1001
+```
+Change 1001 to your own id values.  You can find at the console your user and group ids using the id command:
+for user id
+```
+id -u
+```
+and for group id
+```
+id -g
+```
\ No newline at end of file

From a5a7247dee6f1e7ba1fa73f7082e5043cc56f37d Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Thu, 31 Jul 2025 14:33:08 -0400
Subject: [PATCH 6/8] [BI-2700] Code review fixes part 1

---
 .env.quicktemplate            | 10 +++++-----
 README.md                     | 18 ++++++++++--------
 docker-compose-localstack.yml |  1 +
 3 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/.env.quicktemplate b/.env.quicktemplate
index bf0233d..c34f4c5 100644
--- a/.env.quicktemplate
+++ b/.env.quicktemplate
@@ -4,7 +4,7 @@ OAUTH_CLIENT_SECRET=<oauth_client_secret goes here>
 
 ##Variables already set
 JWT_SECRET=insecure2520f59b2bccc64ce155482bc413f6b9ede5c6d418ab529d1b2051baa6f0849e
-JWT_DOMAIN=localhost
+JWT_DOMAIN=deltabreed.localhost
 
 # Database variables
 DB_PASSWORD=postgres
@@ -36,18 +36,18 @@ BRAPI_DB=postgres
 BRAPI_DB_USER=postgres
 BRAPI_DB_PASSWORD=postgres
 
-WEB_BASE_URL=http://localhost
-API_BASE_URL=http://localhost
+WEB_BASE_URL=http://deltabreed.localhost
+API_BASE_URL=http://deltabreed.localhost
 
 # Public domain name
-REGISTERED_DOMAIN=localhost
+REGISTERED_DOMAIN=deltabreed.localhost
 
 # Email relay information
 EMAIL_RELAY_HOST=mailhog
 EMAIL_RELAY_PORT=1025
 EMAIL_FROM=bidevteam@cornell.edu
 
-REDIS_URL=redis://localhost:6379
+REDIS_URL=redis://redis:6379
 
 GIGWA_PORT=6060
 GIGWA_HOST=http://gigwa:8080/
diff --git a/README.md b/README.md
index 5b73dd9..094f0d1 100644
--- a/README.md
+++ b/README.md
@@ -18,7 +18,7 @@
 <ul>
 <li>Download prereqs</li>
 <li>Set up OAuth with ORCID</li>
-<li>Set up environmental variables</li>
+<li>Set up environment variables</li>
 <li>Run docker-compose</li>
 <li>Get ORCID credentials into database</li>
 <li>Access DeltaBreed on web</li>
@@ -36,15 +36,15 @@ Running DeltaBreed requires setting up OAuth with [ORCID](https://info.orcid.org
 <li>Go to "Developer Tools"</li>
 <li>Agree to Terms of Service and register for ORCID public API credentials</li>
 <li>Enter application name and description (no particular requirements)</li>
-<li>Enter application URL <code>http://test.localhost:8080</code></li>
-<li>Add Redirect URI <code>http://test.localhost/sso/success/orcid</code></li>
+<li>Enter application URL <code>http://deltabreed.localhost:8080</code></li>
+<li>Add Redirect URI <code>http://deltabreed.localhost/sso/success/orcid</code></li>
 <li>Select "Save application" at the bottom of the page</li>
-<li>Copy the generated Client ID and Client Secret to add to the .env file (see <a href="env_vars">Set up environmental variables</a>)</li>
+<li>Copy the generated Client ID and Client Secret to add to the .env file (see <a href="env_vars">Set up environment variables</a>)</li>
 </ol>
 
-## <a id="env_vars"></a>Set up environmental variables
-To set necessary private environmental variables for DeltaBreed to run, at the root level of the repo locally create a file called `.env`. 
-A template exists named `.env.quicktemplate` that has most environmental variables already filled. 
+## <a id="env_vars"></a>Set up environment variables
+To set necessary private environment variables for DeltaBreed to run, at the root level of the repo locally create a file called `.env`. 
+A template exists named `.env.quicktemplate` that has most environment variables already filled. 
 If a user wants to customize services in more depth (not covered in this quick start guide), they can instead base their `.env` off of `.env.template`.
 
 In this new `.env` based off the template, set `OAUTH_CLIENT_ID` and `OAUTH_CLIENT_SECRET` to the generated Client ID and Client Secret copied in the previous step
@@ -57,12 +57,14 @@ docker-compose -f docker-compose.yml -f docker-compose-redis.yml -f docker-compo
 ```
 
 ## Get ORCID credentials into database
+To get ORCID credentials into the database, an interactive script must be run that prompts the user to input their ORCID and email.
+
 For Mac/Linux, run `addUser.sh`
 
 For Windows, run `addUser.ps1`
 
 ## Access DeltaBreed on web
-DeltaBreed can then be accessed via `http://localhost:8080`. 
+DeltaBreed can then be accessed via `http://deltabreed.localhost:8080`. 
 
 # <a id="architecture"></a> Architecture
 The primary components of DeltaBreed are the Web UI (Breeding-Insight/bi-web) and the API (Breeding-Insight/bi-api).
diff --git a/docker-compose-localstack.yml b/docker-compose-localstack.yml
index c552570..7e152e7 100644
--- a/docker-compose-localstack.yml
+++ b/docker-compose-localstack.yml
@@ -6,6 +6,7 @@ services:
     image: localstack/localstack:3.0.2
     ports:
       - "4566:4566"
+    restart: always
     networks:
       backend:
         aliases:

From 5e78dd6165e9023d8a98566465bd9f8fbd98750e Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Thu, 31 Jul 2025 16:21:38 -0400
Subject: [PATCH 7/8] [BI-2700] Code review, merging env templates

---
 .env.quicktemplate | 66 -------------------------------
 .env.template      | 96 ++++++++++++++++++++++++----------------------
 README.md          |  3 +-
 3 files changed, 52 insertions(+), 113 deletions(-)
 delete mode 100644 .env.quicktemplate

diff --git a/.env.quicktemplate b/.env.quicktemplate
deleted file mode 100644
index c34f4c5..0000000
--- a/.env.quicktemplate
+++ /dev/null
@@ -1,66 +0,0 @@
-##ORCID Variables for user to set
-OAUTH_CLIENT_ID=<oauth app client id>
-OAUTH_CLIENT_SECRET=<oauth_client_secret goes here>
-
-##Variables already set
-JWT_SECRET=insecure2520f59b2bccc64ce155482bc413f6b9ede5c6d418ab529d1b2051baa6f0849e
-JWT_DOMAIN=deltabreed.localhost
-
-# Database variables
-DB_PASSWORD=postgres
-DB_SERVER=dbserver:5432
-DB_NAME=bidb
-DB_USER=postgres
-
-# Micronaut variables
-API_INTERNAL_PORT=8081
-API_INTERNAL_TEST_PORT=8082
-
-BRAPI_READ_TIMEOUT=60m
-
-# Max number of records to POST to the BrAPI service per request
-POST_CHUNK_SIZE=1000
-
-# Request cache records paginating through available records per program by CACHE_BRAPI_FETCH_PAGE_SIZE
-CACHE_PAGINATE_GERMPLASM=false
-CACHE_BRAPI_FETCH_PAGE_SIZE=65000
-
-# BrAPI Server Variables
-BRAPI_SERVER_PORT=8080
-
-BRAPI_DEFAULT_URL=http://brapiserver:8080
-BRAPI_REFERENCE_SOURCE=breedinginsight.org
-
-BRAPI_DB_SERVER=dbserver:5432
-BRAPI_DB=postgres
-BRAPI_DB_USER=postgres
-BRAPI_DB_PASSWORD=postgres
-
-WEB_BASE_URL=http://deltabreed.localhost
-API_BASE_URL=http://deltabreed.localhost
-
-# Public domain name
-REGISTERED_DOMAIN=deltabreed.localhost
-
-# Email relay information
-EMAIL_RELAY_HOST=mailhog
-EMAIL_RELAY_PORT=1025
-EMAIL_FROM=bidevteam@cornell.edu
-
-REDIS_URL=redis://redis:6379
-
-GIGWA_PORT=6060
-GIGWA_HOST=http://gigwa:8080/
-GIGWA_USER=gigwadmin
-GIGWA_PASSWORD=nimda
-GIGWA_MONGO_USER=mongo
-GIGWA_MONGO_PASSWORD=mongo
-
-AWS_REGION=us-east-1
-AWS_ACCESS_KEY_ID=test
-AWS_SECRET_KEY=test
-AWS_GENO_BUCKET=breedinginsight.org-dev-bucket
-AWS_S3_ENDPOINT=http://localstack:4566
-
-# feature flags
-BRAPI_VENDOR_SUBMISSION_ENABLED=false # allow sample submissions to be transmitted to a vendor via BrAPI
\ No newline at end of file
diff --git a/.env.template b/.env.template
index debcfe3..1aaa714 100644
--- a/.env.template
+++ b/.env.template
@@ -1,22 +1,17 @@
-USER_ID=<user id of system user>
-GROUP_ID=<group id of system user>
-
-# Authentication variables
+##ORCID Authentication Variables for user to set
 OAUTH_CLIENT_ID=<oauth app client id>
-OAUTH_CLIENT_SECRET=<ouath_client_secret goes here>
-JWT_SECRET=<jwt secret goes here>
-JWT_DOMAIN=<jwt domain ex. localhost>
+OAUTH_CLIENT_SECRET=<oauth_client_secret goes here>
 
-# Database variables
-DB_PASSWORD=<database password goes here>
-DB_SERVER=<database server path (ex. localhost:5432)>
-DB_NAME=<database name>
-DB_USER=<database user>
-ADMIN_ORCID=<orcid for admin account goes here>
+##Variables already set
+#Authentication variables
+JWT_SECRET=insecure2520f59b2bccc64ce155482bc413f6b9ede5c6d418ab529d1b2051baa6f0849e
+JWT_DOMAIN=deltabreed.localhost
 
-# Build variables needed to pull down JAR files from Github Packages
-GITHUB_ACTOR=<github user name>
-GITHUB_TOKEN=<github personal access token>
+# Database variables
+DB_PASSWORD=postgres
+DB_SERVER=dbserver:5432
+DB_NAME=bidb
+DB_USER=postgres
 
 # Micronaut variables
 API_INTERNAL_PORT=8081
@@ -37,40 +32,51 @@ BRAPI_SERVER_PORT=8080
 BRAPI_DEFAULT_URL=http://brapiserver:8080
 BRAPI_REFERENCE_SOURCE=breedinginsight.org
 
-BRAPI_DB_SERVER=<brapi database server (ex. dbserver:5432)>
-BRAPI_DB=<brapi database name>
-BRAPI_DB_USER=<brapi database user>
-BRAPI_DB_PASSWORD=<brapi database password>
+#BrAPI database variables
+BRAPI_DB_SERVER=dbserver:5432
+BRAPI_DB=postgres
+BRAPI_DB_USER=postgres
+BRAPI_DB_PASSWORD=postgres
 
-WEB_BASE_URL=http://localhost
-API_BASE_URL=http://localhost
-ANALYTICS_GTAG_ID=<Google analytics gtag id>
+WEB_BASE_URL=http://deltabreed.localhost
+API_BASE_URL=http://deltabreed.localhost
 
 # Public domain name
-REGISTERED_DOMAIN=localhost
+REGISTERED_DOMAIN=deltabreed.localhost
 
 # Email relay information
-EMAIL_RELAY_HOST=<mailhog for development, email-smtp.us-east-1.amazonaws.com for production>
-EMAIL_RELAY_PORT=<1025 for development, 2587 for production>
-EMAIL_FROM=noreply@breedinginsight.org
-#EMAIL_RELAY_LOGIN=<blank for development>
-#EMAIL_RELAY_PASSWORD=<blank for development>
-
-REDIS_URL=<redis url, ex redis://localhost:6379>
-REDIS_TIMEOUT=<timeout, default 30s>
-REDIS_SSL=<enable ssl, default false>
-
-GIGWA_HOST=<gigwa host (including port), ex http://localhost:8080>
-GIGWA_USER=<username>
-GIGWA_PASSWORD=<password>
-GIGWA_MONGO_USER=<gigwa mongodb username>
-GIGWA_MONGO_PASSWORD=<gigwa mongodb password>
-
-AWS_REGION=<aws region, default us-east-1>
-AWS_ACCESS_KEY_ID=<access key>
-AWS_SECRET_KEY=<secret>
-AWS_GENO_BUCKET=<s3 bucket for genotypic data uploads>
-AWS_S3_ENDPOINT=<s3 endpoint, default https://s3.us-east-1.amazonaws.com
+EMAIL_RELAY_HOST=mailhog
+EMAIL_RELAY_PORT=1025
+EMAIL_FROM=bidevteam@cornell.edu
+
+REDIS_URL=redis://redis:6379
+
+GIGWA_PORT=6060
+GIGWA_HOST=http://gigwa:8080/
+GIGWA_USER=gigwadmin
+GIGWA_PASSWORD=nimda
+GIGWA_MONGO_USER=mongo
+GIGWA_MONGO_PASSWORD=mongo
+
+AWS_REGION=us-east-1
+AWS_ACCESS_KEY_ID=test
+AWS_SECRET_KEY=test
+#s3 bucket for genotypic data uploads
+AWS_GENO_BUCKET=breedinginsight.org-dev-bucket
+AWS_S3_ENDPOINT=http://localstack:4566
 
 # feature flags
 BRAPI_VENDOR_SUBMISSION_ENABLED=false # allow sample submissions to be transmitted to a vendor via BrAPI
+
+#Change if want to override defaults
+
+#REDIS_TIMEOUT=<timeout, default 30s>
+#REDIS_SSL=<enable ssl, default false>
+#USER_ID=<user id of system user, default 1001>
+#GROUP_ID=<group id of system user, default 1001>
+
+#Optional Variables
+#ANALYTICS_GTAG_ID=<Google analytics gtag id>
+#ADMIN_ORCID=<orcid for admin account goes here>
+#EMAIL_RELAY_LOGIN=
+#EMAIL_RELAY_PASSWORD=
\ No newline at end of file
diff --git a/README.md b/README.md
index 094f0d1..7199f78 100644
--- a/README.md
+++ b/README.md
@@ -44,8 +44,7 @@ Running DeltaBreed requires setting up OAuth with [ORCID](https://info.orcid.org
 
 ## <a id="env_vars"></a>Set up environment variables
 To set necessary private environment variables for DeltaBreed to run, at the root level of the repo locally create a file called `.env`. 
-A template exists named `.env.quicktemplate` that has most environment variables already filled. 
-If a user wants to customize services in more depth (not covered in this quick start guide), they can instead base their `.env` off of `.env.template`.
+A template exists named `.env.template` that has most environment variables already filled. 
 
 In this new `.env` based off the template, set `OAUTH_CLIENT_ID` and `OAUTH_CLIENT_SECRET` to the generated Client ID and Client Secret copied in the previous step
 

From 08b69a5601e51524fd9fc800b6c9bce434d7cf0f Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Thu, 31 Jul 2025 16:48:43 -0400
Subject: [PATCH 8/8] [BI-2700] removed unneeded var

---
 .env.template | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.env.template b/.env.template
index 1aaa714..ecea0b0 100644
--- a/.env.template
+++ b/.env.template
@@ -77,6 +77,5 @@ BRAPI_VENDOR_SUBMISSION_ENABLED=false # allow sample submissions to be transmitt
 
 #Optional Variables
 #ANALYTICS_GTAG_ID=<Google analytics gtag id>
-#ADMIN_ORCID=<orcid for admin account goes here>
 #EMAIL_RELAY_LOGIN=
 #EMAIL_RELAY_PASSWORD=
\ No newline at end of file