From 1f73526c9ebde652f92849fb853ace7c06fd6381 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Mon, 22 Jan 2024 15:02:54 +0000
Subject: [PATCH 01/27] Moved GH workflow reporting into separate job

---
 .github/workflows/PR-validation.yml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index 69e1ada3..b94fc734 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -5,9 +5,7 @@ on:
     branches:
       - master
 jobs:
-  test-api:
-    permissions:
-      id-token: write # Required for authentication through OIDC to AWS
+  reporting:
     runs-on: ubuntu-22.04
     steps:
       - name: Report workflow details
@@ -20,6 +18,13 @@ jobs:
         run: |
           git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
           git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
+  test-api:
+    permissions:
+      id-token: write # Required for authentication through OIDC to AWS
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
       - name: Set up JDK 8
         uses: actions/setup-java@v3
         with:

From b6dd3099ead7192f52ef6adf8336473ced38c7f2 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Mon, 22 Jan 2024 17:32:36 +0000
Subject: [PATCH 02/27] Moved Dockerfile to repo root and API jar build
 artefact to dedicated build directory

---
 .gitignore                      |  2 +-
 docker/Dockerfile => Dockerfile |  0
 Makefile                        | 14 ++++++++------
 scripts/build-appjar.sh         |  2 +-
 4 files changed, 10 insertions(+), 8 deletions(-)
 rename docker/Dockerfile => Dockerfile (100%)

diff --git a/.gitignore b/.gitignore
index 30698a5b..8386fb7f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -32,7 +32,7 @@ target/
 !.elasticbeanstalk/*.cfg.yml
 !.elasticbeanstalk/*.global.yml
 Dockerrun.aws.json
-/docker/app.jar
+build/*
 /.dockerignore
 
 #Local docker-compose env-variable files
diff --git a/docker/Dockerfile b/Dockerfile
similarity index 100%
rename from docker/Dockerfile
rename to Dockerfile
diff --git a/Makefile b/Makefile
index 27c3ae62..08e0bf41 100644
--- a/Makefile
+++ b/Makefile
@@ -67,13 +67,15 @@ show-version: \
               Show the current application version.)
 	@echo "${VERSION_TAG}"
 
+build/:
+	mkdir build/
+
 .PHONY: build
-build: clean ui-build docker/${DEPLOY_JAR} \
+build: clean build/ ui-build build/${DEPLOY_JAR} \
        $(call print-help,build,\
        Build the docker images from using the current git revision.)
 	@docker build -t ${ECR_REPO_NAME}:${VERSION_TAG} \
-		--build-arg uberjar_path=${DEPLOY_JAR} \
-		./docker/
+		--build-arg uberjar_path=build/${DEPLOY_JAR} .
 
 .PHONY: ui-build
 ui-build: google-oauth2-secrets \
@@ -87,10 +89,10 @@ ui-build: google-oauth2-secrets \
 clean: \
        $(call print-help,clean,\
        Remove the locally built JAR file.)
-	@rm -f ./docker/${DEPLOY_JAR}
+	@rm -f ./build/${DEPLOY_JAR}
 
-docker/${DEPLOY_JAR}: \
-                      $(call print-help,docker/${DEPLOY_JAR},\
+build/${DEPLOY_JAR}: \
+                      $(call print-help,build/${DEPLOY_JAR},\
                       Build the jar file.)
 	@./scripts/build-appjar.sh
 
diff --git a/scripts/build-appjar.sh b/scripts/build-appjar.sh
index 8fbdd2de..d4576157 100755
--- a/scripts/build-appjar.sh
+++ b/scripts/build-appjar.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-ARTEFACT="docker/app.jar"
+ARTEFACT="build/app.jar"
 LATEST_TAG=$(git describe --abbrev=0)
 RELEASE_NAME="wormbase-names-${LATEST_TAG}"
 DEPLOY_JAR="target/${RELEASE_NAME}.jar"

From 68744da50f14a83a5d53f3d53ec391d1f27ba542 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Tue, 23 Jan 2024 15:15:25 +0000
Subject: [PATCH 03/27] Moved git version retrieval to separate target (to
 enable target calling without)

---
 Makefile | 68 ++++++++++++++++++++++++++++++++++----------------------
 1 file changed, 42 insertions(+), 26 deletions(-)

diff --git a/Makefile b/Makefile
index 08e0bf41..7d299ece 100644
--- a/Makefile
+++ b/Makefile
@@ -21,21 +21,9 @@ DEPLOY_JAR := app.jar
 PORT := 3000
 WB_ACC_NUM := 357210185381
 
-REVISION_NAME_CMD := git describe --tags
-# If REF_NAME is defined, convert provided ref in matching name
-# (ref could be a tagname, a reference like "HEAD", branch-names...)
-ifneq (${REF_NAME},)
-	REVISION_NAME := $(shell ${REVISION_NAME_CMD} ${REF_NAME})
-# Else, assume working-directory deployment
-else
-	REVISION_NAME := $(shell ${REVISION_NAME_CMD} --dirty=-DIRTY)
-endif
-
-VERSION_TAG ?= $(shell echo "${REVISION_NAME}" | sed 's/^wormbase-names-//')
-
 ECR_URI := ${WB_ACC_NUM}.dkr.ecr.us-east-1.amazonaws.com
 ECR_REPO_URI := ${ECR_URI}/${ECR_REPO_NAME}
-ECR_IMAGE_URI := ${ECR_REPO_URI}:${VERSION_TAG}
+ECR_IMAGE_URI = ${ECR_REPO_URI}:${VERSION_TAG}
 # Set AWS (EB) profile env vars if undefined
 ifneq (${AWS_PROFILE},)
 	AWS_EB_PROFILE ?= ${AWS_PROFILE}
@@ -61,8 +49,30 @@ need-help := $(filter help,$(MAKECMDGOALS))
 help: ; @echo $(if $(need-help),,\
 	Type \'$(MAKE)$(dash-f) help\' to get help)
 
+.PHONY: ENV.VERSION_TAG
+ENV.VERSION_TAG: \
+	$(call print-help,ENV.VERSION_TAG,\
+	Extract the VERSION_TAG env variables for make targets from git tags if undefined.)
+	$(eval REVISION_NAME_CMD = git describe --tags)
+ifeq (${VERSION_TAG},)
+# If REF_NAME is defined, convert provided ref in matching name
+# (ref could be a tagname, a reference like "HEAD", branch-names...)
+ifneq (${REF_NAME},)
+	$(eval REVISION_NAME_CMD = ${REVISION_NAME_CMD} ${REF_NAME})
+# Else, assume working-directory deployment
+else
+	$(eval REVISION_NAME_CMD = ${REVISION_NAME_CMD} --dirty=-DIRTY)
+endif
+	$(eval VERSION_TAG = $(shell ${REVISION_NAME_CMD} | sed 's/^wormbase-names-//'))
+	$(call check_defined, VERSION_TAG, Ensure your working directory is a\
+	                                   git clone of the repository)
+	@echo "Retrieved VERSION_TAG '${VERSION_TAG}' from git tags."
+else
+	@echo "Using predefined VERSION_TAG '${VERSION_TAG}'."
+endif
+
 .PHONY: show-version
-show-version: \
+show-version: ENV.VERSION_TAG \
               $(call print-help,show-version,\
               Show the current application version.)
 	@echo "${VERSION_TAG}"
@@ -71,7 +81,7 @@ build/:
 	mkdir build/
 
 .PHONY: build
-build: clean build/ ui-build build/${DEPLOY_JAR} \
+build: ENV.VERSION_TAG clean build/ ui-build build/${DEPLOY_JAR} \
        $(call print-help,build,\
        Build the docker images from using the current git revision.)
 	@docker build -t ${ECR_REPO_NAME}:${VERSION_TAG} \
@@ -114,14 +124,14 @@ docker-push-ecr: docker-ecr-login \
 	@docker push ${ECR_IMAGE_URI}
 
 .PHONY: docker-tag
-docker-tag: \
+docker-tag: ENV.VERSION_TAG \
             $(call print-help,docker-tag,\
             Tag the image with current git revision and ':latest' alias.)
 	@docker tag ${ECR_REPO_NAME}:${VERSION_TAG} ${ECR_IMAGE_URI}
 	@docker tag ${ECR_REPO_NAME}:${VERSION_TAG} ${ECR_REPO_URI}
 
 .PHONY: eb-def-app-env
-eb-def-app-env: google-oauth2-secrets \
+eb-def-app-env: google-oauth2-secrets ENV.VERSION_TAG \
                 $(call print-help,eb-def-app-env \
 				[WB_DB_URI=<datomic-db-uri>] [GOOGLE_REDIRECT_URI=<google-redirect-uri>],\
                 Define the ElasticBeanStalk app-environment config file.)
@@ -188,7 +198,7 @@ eb-local: docker-ecr-login \
 	@eb local run --envvars PORT=${PORT},WB_DB_URI=${WB_DB_URI},GOOGLE_REDIRECT_URI=${GOOGLE_REDIRECT_URI}
 
 .PHONY: run
-run: \
+run: ENV.VERSION_TAG \
      $(call print-help,run [PORT=<port>] [PROJ_NAME=<docker-project-name>] \
 	 [WB_DB_URI=<datomic-uri>] [GOOGLE_REDIRECT_URI=<google-redirect-uri>],\
      Run the application in docker (locally).)
@@ -217,16 +227,15 @@ deploy-ecr: docker-build docker-tag docker-push-ecr
             Deploy the application to the AWS container registry.)
 
 .PHONY: vc-release
-vc-release: export VERSION_TAG := ${VERSION_TAG}
-vc-release: $(call print-help,vc-release LEVEL=<major|minor|patch>,\
+vc-release: ENV.VERSION_TAG \
+            $(call print-help,vc-release LEVEL=<major|minor|patch>,\
             Perform the Version Control tasks to release the applicaton.)
 	clj -A:release --without-sign ${LEVEL}
 	@echo "Edit version of application in pom.xml to match wormbase-names-* version reported above (version number only)."
 
 
 .PHONY: release
-release: export VERSION_TAG := ${VERSION_TAG}
-release: deploy-ecr \
+release: ENV.VERSION_TAG deploy-ecr \
          $(call print-help,release [AWS_PROFILE=<profile_name>] [REF_NAME=<tag-or-gitref>],\
          Release the applicaton.)
 
@@ -266,15 +275,22 @@ google-oauth2-secrets: \
                        $(call print-help,google-oauth2-secrets,\
                        Store the Google oauth2 client details as env variables.)
 	$(eval GOOGLE_OAUTH_CLIENT_ID = $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-id" --query "Parameter.Value" --output text --with-decryption))
-	$(call check_defined, GOOGLE_OAUTH_CLIENT_ID)
+	$(call check_defined, GOOGLE_OAUTH_CLIENT_ID, Check the defined GOOGLE_APP_PROFILE value\
+	 and ensure the AWS_PROFILE variable is appropriately defined)
 	$(eval GOOGLE_OAUTH_CLIENT_SECRET = $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-secret" --query "Parameter.Value" --output text --with-decryption))
-	$(call check_defined, GOOGLE_OAUTH_CLIENT_SECRET)
+	$(call check_defined, GOOGLE_OAUTH_CLIENT_SECRET, Check the defined GOOGLE_APP_PROFILE value\
+	 and ensure the AWS_PROFILE variable is appropriately defined)
 	@echo "Retrieved google-oauth2-secrets for GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}'."
 
+# Check that given variables are set and all have non-empty values,
+# die with an error otherwise.
+#
+# Params:
+#   1. Variable name(s) to test.
+#   2. (optional) Error message to print.
 check_defined = \
     $(strip $(foreach 1,$1, \
         $(call __check_defined,$1,$(strip $(value 2)))))
 __check_defined = \
     $(if $(value $1),, \
-      $(error Failed to retrieve $1. Check the defined GOOGLE_APP_PROFILE value\
-	and ensure the AWS_PROFILE variable is appropriately defined) )
+      $(error Failed to define $1. $(if $2, $2)))

From 593601c7a698f307ba51cfe7381e1b671a8f8cca Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Wed, 24 Jan 2024 10:07:26 +0000
Subject: [PATCH 04/27] Split google secret retrieval into independent ENV
 targets

---
 Makefile | 31 +++++++++++++++++++++++++------
 1 file changed, 25 insertions(+), 6 deletions(-)

diff --git a/Makefile b/Makefile
index 7d299ece..d24d18e3 100644
--- a/Makefile
+++ b/Makefile
@@ -88,7 +88,7 @@ build: ENV.VERSION_TAG clean build/ ui-build build/${DEPLOY_JAR} \
 		--build-arg uberjar_path=build/${DEPLOY_JAR} .
 
 .PHONY: ui-build
-ui-build: google-oauth2-secrets \
+ui-build: ENV.GOOGLE_OAUTH_CLIENT_ID \
           $(call print-help,ui-build,\
           Build JS and CSS file for release.)
 	@ export REACT_APP_GOOGLE_OAUTH_CLIENT_ID=${GOOGLE_OAUTH_CLIENT_ID} && \
@@ -270,17 +270,36 @@ run-dev-ui: google-oauth2-secrets\
 	 npm install && \
 	 npm run start
 
-.PHONY: google-oauth2-secrets
-google-oauth2-secrets: \
-                       $(call print-help,google-oauth2-secrets,\
-                       Store the Google oauth2 client details as env variables.)
+.PHONY: ENV.GOOGLE_OAUTH_CLIENT_ID
+ENV.GOOGLE_OAUTH_CLIENT_ID: \
+	$(call print-help,ENV.GOOGLE_OAUTH_CLIENT_ID,\
+	Retrieve the GOOGLE_OAUTH_CLIENT_ID env variable for make targets from aws ssm if undefined.)
+ifeq (${GOOGLE_OAUTH_CLIENT_ID},)
 	$(eval GOOGLE_OAUTH_CLIENT_ID = $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-id" --query "Parameter.Value" --output text --with-decryption))
 	$(call check_defined, GOOGLE_OAUTH_CLIENT_ID, Check the defined GOOGLE_APP_PROFILE value\
 	 and ensure the AWS_PROFILE variable is appropriately defined)
+	@echo "Retrieved GOOGLE_OAUTH_CLIENT_ID from AWS SSM (GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}')."
+else
+	@echo "Using predefined GOOGLE_OAUTH_CLIENT_ID."
+endif
+
+.PHONY: ENV.GOOGLE_OAUTH_CLIENT_SECRET
+ENV.GOOGLE_OAUTH_CLIENT_SECRET: \
+	$(call print-help,ENV.GOOGLE_OAUTH_CLIENT_SECRET,\
+	Retrieve the GOOGLE_OAUTH_CLIENT_SECRET env variable for make targets from aws ssm if undefined.)
+ifeq (${GOOGLE_OAUTH_CLIENT_SECRET},)
 	$(eval GOOGLE_OAUTH_CLIENT_SECRET = $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-secret" --query "Parameter.Value" --output text --with-decryption))
 	$(call check_defined, GOOGLE_OAUTH_CLIENT_SECRET, Check the defined GOOGLE_APP_PROFILE value\
 	 and ensure the AWS_PROFILE variable is appropriately defined)
-	@echo "Retrieved google-oauth2-secrets for GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}'."
+	@echo "Retrieved GOOGLE_OAUTH_CLIENT_SECRET from AWS SSM (GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}')."
+else
+	@echo "Using predefined GOOGLE_OAUTH_CLIENT_SECRET."
+endif
+
+.PHONY: google-oauth2-secrets
+google-oauth2-secrets: ENV.GOOGLE_OAUTH_CLIENT_ID ENV.GOOGLE_OAUTH_CLIENT_SECRET \
+                       $(call print-help,google-oauth2-secrets,\
+                       Store the Google oauth2 client details as env variables.)
 
 # Check that given variables are set and all have non-empty values,
 # die with an error otherwise.

From f241ca09a6a58052ecb3141fc524ec2efc93a540 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Wed, 24 Jan 2024 16:16:16 +0000
Subject: [PATCH 05/27] Enabled (google) secrets storage and sourcing in
 Makefile

---
 Makefile | 39 ++++++++++++++++++++++++---------------
 1 file changed, 24 insertions(+), 15 deletions(-)

diff --git a/Makefile b/Makefile
index d24d18e3..e36d7d62 100644
--- a/Makefile
+++ b/Makefile
@@ -17,6 +17,9 @@ else
 	GOOGLE_REDIRECT_URI ?= ${LOCAL_GOOGLE_REDIRECT_URI}
 	GOOGLE_APP_PROFILE ?= "dev"
 endif
+
+STORE_SECRETS_FILE = secrets.makedef
+
 DEPLOY_JAR := app.jar
 PORT := 3000
 WB_ACC_NUM := 357210185381
@@ -49,6 +52,13 @@ need-help := $(filter help,$(MAKECMDGOALS))
 help: ; @echo $(if $(need-help),,\
 	Type \'$(MAKE)$(dash-f) help\' to get help)
 
+source-secrets:
+ifneq ($(SECRETS_SRC), )
+	@echo "Sourcing secrets file ${SECRETS_SRC}"
+	$(eval SECRETS_CONTENT := $(shell cat "${SECRETS_SRC}"))
+	$(foreach secret,${SECRETS_CONTENT},$(eval ${secret}))
+endif
+
 .PHONY: ENV.VERSION_TAG
 ENV.VERSION_TAG: \
 	$(call print-help,ENV.VERSION_TAG,\
@@ -271,36 +281,35 @@ run-dev-ui: google-oauth2-secrets\
 	 npm run start
 
 .PHONY: ENV.GOOGLE_OAUTH_CLIENT_ID
-ENV.GOOGLE_OAUTH_CLIENT_ID: \
+ENV.GOOGLE_OAUTH_CLIENT_ID: source-secrets \
 	$(call print-help,ENV.GOOGLE_OAUTH_CLIENT_ID,\
 	Retrieve the GOOGLE_OAUTH_CLIENT_ID env variable for make targets from aws ssm if undefined.)
-ifeq (${GOOGLE_OAUTH_CLIENT_ID},)
-	$(eval GOOGLE_OAUTH_CLIENT_ID = $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-id" --query "Parameter.Value" --output text --with-decryption))
+	$(eval ACTION_MSG := $(if ${GOOGLE_OAUTH_CLIENT_ID},"Using predefined GOOGLE_OAUTH_CLIENT_ID.","Retrieving GOOGLE_OAUTH_CLIENT_ID from AWS SSM (GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}')."))
+	@echo ${ACTION_MSG}
+	$(if ${GOOGLE_OAUTH_CLIENT_ID},,$(eval GOOGLE_OAUTH_CLIENT_ID := $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-id" --query "Parameter.Value" --output text --with-decryption)))
 	$(call check_defined, GOOGLE_OAUTH_CLIENT_ID, Check the defined GOOGLE_APP_PROFILE value\
 	 and ensure the AWS_PROFILE variable is appropriately defined)
-	@echo "Retrieved GOOGLE_OAUTH_CLIENT_ID from AWS SSM (GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}')."
-else
-	@echo "Using predefined GOOGLE_OAUTH_CLIENT_ID."
-endif
 
 .PHONY: ENV.GOOGLE_OAUTH_CLIENT_SECRET
-ENV.GOOGLE_OAUTH_CLIENT_SECRET: \
+ENV.GOOGLE_OAUTH_CLIENT_SECRET: source-secrets \
 	$(call print-help,ENV.GOOGLE_OAUTH_CLIENT_SECRET,\
 	Retrieve the GOOGLE_OAUTH_CLIENT_SECRET env variable for make targets from aws ssm if undefined.)
-ifeq (${GOOGLE_OAUTH_CLIENT_SECRET},)
-	$(eval GOOGLE_OAUTH_CLIENT_SECRET = $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-secret" --query "Parameter.Value" --output text --with-decryption))
+	$(eval ACTION_MSG := $(if ${GOOGLE_OAUTH_CLIENT_SECRET},"Using predefined GOOGLE_OAUTH_CLIENT_SECRET.","Retrieving GOOGLE_OAUTH_CLIENT_SECRET from AWS SSM (GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}')."))
+	@echo ${ACTION_MSG}
+	$(if ${GOOGLE_OAUTH_CLIENT_SECRET},,$(eval GOOGLE_OAUTH_CLIENT_SECRET := $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-secret" --query "Parameter.Value" --output text --with-decryption)))
 	$(call check_defined, GOOGLE_OAUTH_CLIENT_SECRET, Check the defined GOOGLE_APP_PROFILE value\
 	 and ensure the AWS_PROFILE variable is appropriately defined)
-	@echo "Retrieved GOOGLE_OAUTH_CLIENT_SECRET from AWS SSM (GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}')."
-else
-	@echo "Using predefined GOOGLE_OAUTH_CLIENT_SECRET."
-endif
 
 .PHONY: google-oauth2-secrets
-google-oauth2-secrets: ENV.GOOGLE_OAUTH_CLIENT_ID ENV.GOOGLE_OAUTH_CLIENT_SECRET \
+google-oauth2-secrets: source-secrets ENV.GOOGLE_OAUTH_CLIENT_ID ENV.GOOGLE_OAUTH_CLIENT_SECRET \
                        $(call print-help,google-oauth2-secrets,\
                        Store the Google oauth2 client details as env variables.)
 
+${STORE_SECRETS_FILE}: google-oauth2-secrets
+	@install -m 600 /dev/null ${STORE_SECRETS_FILE}
+	@echo "GOOGLE_OAUTH_CLIENT_ID:=${GOOGLE_OAUTH_CLIENT_ID}" >> ${STORE_SECRETS_FILE}
+	@echo "GOOGLE_OAUTH_CLIENT_SECRET:=${GOOGLE_OAUTH_CLIENT_SECRET}" >> ${STORE_SECRETS_FILE}
+
 # Check that given variables are set and all have non-empty values,
 # die with an error otherwise.
 #

From 4ea0c50afd431d31e964b5c9dd057c965cd8aafd Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Thu, 25 Jan 2024 11:42:47 +0000
Subject: [PATCH 06/27] Enabled building ui without nvm usage (for CI/docker
 context)

---
 .github/workflows/PR-validation.yml |  2 +-
 Makefile                            | 22 +++++++++++-----------
 README.md                           |  4 ++--
 scripts/build-ui.sh                 | 19 +++++++++++++------
 4 files changed, 27 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index 69e1ada3..c09227a2 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -50,5 +50,5 @@ jobs:
           clojure -Spom
       - name: Run Integration tests
         run: |
-          make run-tests GOOGLE_APP_PROFILE=dev
+          make run-tests APP_PROFILE=dev
   #TODO: add UI and API build and container packaging test
diff --git a/Makefile b/Makefile
index e36d7d62..0439c98b 100644
--- a/Makefile
+++ b/Makefile
@@ -5,17 +5,17 @@ LOCAL_GOOGLE_REDIRECT_URI := "http://lvh.me:3000"
 ifeq ($(PROJ_NAME), wormbase-names)
 	WB_DB_URI ?= "datomic:ddb://us-east-1/WSNames/wormbase"
 	GOOGLE_REDIRECT_URI ?= "https://names.wormbase.org"
-	GOOGLE_APP_PROFILE ?= "prod"
+	APP_PROFILE ?= "prod"
 else ifeq ($(PROJ_NAME), wormbase-names-test)
 	WB_DB_URI ?= "datomic:ddb://us-east-1/WSNames-test-14/wormbase"
 	GOOGLE_REDIRECT_URI ?= "https://test-names.wormbase.org"
-	GOOGLE_APP_PROFILE ?= "prod"
+	APP_PROFILE ?= "prod"
 else
 	WB_DB_URI ?= "datomic:ddb-local://localhost:8000/WBNames_local/wormbase"
 #   Ensure GOOGLE_REDIRECT_URI is defined appropriately as an env variable or CLI argument
 #   if intended for AWS deployment (default is set for local execution)
 	GOOGLE_REDIRECT_URI ?= ${LOCAL_GOOGLE_REDIRECT_URI}
-	GOOGLE_APP_PROFILE ?= "dev"
+	APP_PROFILE ?= "dev"
 endif
 
 STORE_SECRETS_FILE = secrets.makedef
@@ -102,8 +102,8 @@ ui-build: ENV.GOOGLE_OAUTH_CLIENT_ID \
           $(call print-help,ui-build,\
           Build JS and CSS file for release.)
 	@ export REACT_APP_GOOGLE_OAUTH_CLIENT_ID=${GOOGLE_OAUTH_CLIENT_ID} && \
-	  echo "Building UI using GOOGLE_APP_PROFILE: '${GOOGLE_APP_PROFILE}'" && \
-	  ./scripts/build-ui.sh
+	  echo "Building UI using APP_PROFILE: '${APP_PROFILE}'" && \
+	  ./scripts/build-ui.sh ${APP_PROFILE}
 
 .PHONY: clean
 clean: \
@@ -284,20 +284,20 @@ run-dev-ui: google-oauth2-secrets\
 ENV.GOOGLE_OAUTH_CLIENT_ID: source-secrets \
 	$(call print-help,ENV.GOOGLE_OAUTH_CLIENT_ID,\
 	Retrieve the GOOGLE_OAUTH_CLIENT_ID env variable for make targets from aws ssm if undefined.)
-	$(eval ACTION_MSG := $(if ${GOOGLE_OAUTH_CLIENT_ID},"Using predefined GOOGLE_OAUTH_CLIENT_ID.","Retrieving GOOGLE_OAUTH_CLIENT_ID from AWS SSM (GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}')."))
+	$(eval ACTION_MSG := $(if ${GOOGLE_OAUTH_CLIENT_ID},"Using predefined GOOGLE_OAUTH_CLIENT_ID.","Retrieving GOOGLE_OAUTH_CLIENT_ID from AWS SSM (APP_PROFILE '${APP_PROFILE}')."))
 	@echo ${ACTION_MSG}
-	$(if ${GOOGLE_OAUTH_CLIENT_ID},,$(eval GOOGLE_OAUTH_CLIENT_ID := $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-id" --query "Parameter.Value" --output text --with-decryption)))
-	$(call check_defined, GOOGLE_OAUTH_CLIENT_ID, Check the defined GOOGLE_APP_PROFILE value\
+	$(if ${GOOGLE_OAUTH_CLIENT_ID},,$(eval GOOGLE_OAUTH_CLIENT_ID := $(shell aws ssm get-parameter --name "/name-service/${APP_PROFILE}/google-oauth2-app-config/client-id" --query "Parameter.Value" --output text --with-decryption)))
+	$(call check_defined, GOOGLE_OAUTH_CLIENT_ID, Check the defined APP_PROFILE value\
 	 and ensure the AWS_PROFILE variable is appropriately defined)
 
 .PHONY: ENV.GOOGLE_OAUTH_CLIENT_SECRET
 ENV.GOOGLE_OAUTH_CLIENT_SECRET: source-secrets \
 	$(call print-help,ENV.GOOGLE_OAUTH_CLIENT_SECRET,\
 	Retrieve the GOOGLE_OAUTH_CLIENT_SECRET env variable for make targets from aws ssm if undefined.)
-	$(eval ACTION_MSG := $(if ${GOOGLE_OAUTH_CLIENT_SECRET},"Using predefined GOOGLE_OAUTH_CLIENT_SECRET.","Retrieving GOOGLE_OAUTH_CLIENT_SECRET from AWS SSM (GOOGLE_APP_PROFILE '${GOOGLE_APP_PROFILE}')."))
+	$(eval ACTION_MSG := $(if ${GOOGLE_OAUTH_CLIENT_SECRET},"Using predefined GOOGLE_OAUTH_CLIENT_SECRET.","Retrieving GOOGLE_OAUTH_CLIENT_SECRET from AWS SSM (APP_PROFILE '${APP_PROFILE}')."))
 	@echo ${ACTION_MSG}
-	$(if ${GOOGLE_OAUTH_CLIENT_SECRET},,$(eval GOOGLE_OAUTH_CLIENT_SECRET := $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-secret" --query "Parameter.Value" --output text --with-decryption)))
-	$(call check_defined, GOOGLE_OAUTH_CLIENT_SECRET, Check the defined GOOGLE_APP_PROFILE value\
+	$(if ${GOOGLE_OAUTH_CLIENT_SECRET},,$(eval GOOGLE_OAUTH_CLIENT_SECRET := $(shell aws ssm get-parameter --name "/name-service/${APP_PROFILE}/google-oauth2-app-config/client-secret" --query "Parameter.Value" --output text --with-decryption)))
+	$(call check_defined, GOOGLE_OAUTH_CLIENT_SECRET, Check the defined APP_PROFILE value\
 	 and ensure the AWS_PROFILE variable is appropriately defined)
 
 .PHONY: google-oauth2-secrets
diff --git a/README.md b/README.md
index c3aa6a57..efb013a1 100644
--- a/README.md
+++ b/README.md
@@ -299,7 +299,7 @@ To deploy an update for the main application, change your working dir
 to the repository root dir and execute the following commands (bash):
 ```bash
 # Build the client application to ensure no errors occur.
-make ui-build GOOGLE_APP_PROFILE=prod
+make ui-build APP_PROFILE=prod
 
 # Generate the pom.xml file (not version-controlled)
 # to ensure no errors occur (in API code)
@@ -332,7 +332,7 @@ sudo service docker start
 # NOTE: To deploy a tagged or branched codeversion that does not equal your (potentially dirty) working-dir content,
 #       use the additional argument REF_NAME=<ref-name>
 #       E.g. make release AWS_PROFILE=wormbase REF_NAME=wormbase-names-1.4.7
-make release [AWS_PROFILE=<profile_name>] GOOGLE_APP_PROFILE=prod
+make release [AWS_PROFILE=<profile_name>] APP_PROFILE=prod
 
 # Deploy the application to an EB environmnent.
 # Before execution:
diff --git a/scripts/build-ui.sh b/scripts/build-ui.sh
index 5f4401c2..b1fc439b 100755
--- a/scripts/build-ui.sh
+++ b/scripts/build-ui.sh
@@ -1,9 +1,16 @@
 #!/bin/bash
+APP_PROFILE=$1
 
-export NVM_DIR="$HOME/.nvm"
-
-[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"  # This loads nvm
-[ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion"  # This loads nvm bash_completion
 cd client/
-nvm exec npm ci
-nvm exec npm run build
+
+if [ "${APP_PROFILE}" == "dev" ]; then
+    echo "Activating nvm"
+    export NVM_DIR="$HOME/.nvm"
+
+    [ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"  # This loads nvm
+    [ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion"  # This loads nvm bash_completion
+    nvm use
+fi
+
+npm ci
+npm run build

From 069ff778c49f98e43d438401a611e05f5c2ca65e Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Thu, 25 Jan 2024 17:45:24 +0000
Subject: [PATCH 07/27] Support building app jar to custom path

---
 Makefile                | 14 +++++++++-----
 scripts/build-appjar.sh | 12 +++++-------
 2 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/Makefile b/Makefile
index 0439c98b..a9522c8b 100644
--- a/Makefile
+++ b/Makefile
@@ -20,7 +20,7 @@ endif
 
 STORE_SECRETS_FILE = secrets.makedef
 
-DEPLOY_JAR := app.jar
+APP_JAR_PATH ?= build/app.jar
 PORT := 3000
 WB_ACC_NUM := 357210185381
 
@@ -109,12 +109,16 @@ ui-build: ENV.GOOGLE_OAUTH_CLIENT_ID \
 clean: \
        $(call print-help,clean,\
        Remove the locally built JAR file.)
-	@rm -f ./build/${DEPLOY_JAR}
+	@rm -f ${APP_JAR_PATH}
 
-build/${DEPLOY_JAR}: \
-                      $(call print-help,build/${DEPLOY_JAR},\
+${APP_JAR_PATH}: build/ \
+                      $(call print-help,${APP_JAR_PATH},\
                       Build the jar file.)
-	@./scripts/build-appjar.sh
+	@./scripts/build-appjar.sh ${APP_JAR_PATH}
+
+build-app-jar: ${APP_JAR_PATH} \
+               $(call print-help,build-app-jar,\
+               Build the jar file.)
 
 .PHONY: docker-build
 docker-build: clean build \
diff --git a/scripts/build-appjar.sh b/scripts/build-appjar.sh
index d4576157..af79b3c0 100755
--- a/scripts/build-appjar.sh
+++ b/scripts/build-appjar.sh
@@ -1,19 +1,17 @@
 #!/bin/bash
 
-ARTEFACT="build/app.jar"
-LATEST_TAG=$(git describe --abbrev=0)
-RELEASE_NAME="wormbase-names-${LATEST_TAG}"
-DEPLOY_JAR="target/${RELEASE_NAME}.jar"
+ARTEFACT=$1
+TMP_JAR=$(mktemp --dry-run target/wb-names-app-XXXXXXXXXX.jar)
 
 rm -rf target
 mkdir -p target
 clj -Spom
-clj -A:logging:prod:datomic-pro:webassets:depstar -m hf.depstar.uberjar "${DEPLOY_JAR}"
+clj -A:logging:prod:datomic-pro:webassets:depstar -m hf.depstar.uberjar "${TMP_JAR}"
 if [ $? -eq 0 ]; then
-    mv "${DEPLOY_JAR}" "${ARTEFACT}"
-    echo "${ARTEFACT}"
+    mv "${TMP_JAR}" "${ARTEFACT}"
     exit 0
 else
+    echo >&2 "Failed to build jar '${TMP_JAR}'"
     exit 1
 fi
 

From 8a7d6b55590eef8bf6e31fdc7b2349b8d4f1b27a Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Thu, 25 Jan 2024 17:49:11 +0000
Subject: [PATCH 08/27] Make build target naming consistent

---
 Makefile  | 6 +++---
 README.md | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index a9522c8b..eb8bf0c6 100644
--- a/Makefile
+++ b/Makefile
@@ -97,9 +97,9 @@ build: ENV.VERSION_TAG clean build/ ui-build build/${DEPLOY_JAR} \
 	@docker build -t ${ECR_REPO_NAME}:${VERSION_TAG} \
 		--build-arg uberjar_path=build/${DEPLOY_JAR} .
 
-.PHONY: ui-build
-ui-build: ENV.GOOGLE_OAUTH_CLIENT_ID \
-          $(call print-help,ui-build,\
+.PHONY: build-ui
+build-ui: ENV.GOOGLE_OAUTH_CLIENT_ID \
+          $(call print-help,build-ui,\
           Build JS and CSS file for release.)
 	@ export REACT_APP_GOOGLE_OAUTH_CLIENT_ID=${GOOGLE_OAUTH_CLIENT_ID} && \
 	  echo "Building UI using APP_PROFILE: '${APP_PROFILE}'" && \
diff --git a/README.md b/README.md
index efb013a1..77070453 100644
--- a/README.md
+++ b/README.md
@@ -181,7 +181,7 @@ Correct functionality of the client app can be tested in two ways:
 - Making a production build of the client app. Failure during this process means fixes will be needed before deployment.
 ```bash
 # performs a npm clean install of dependencies based on package-lock.json
-make ui-build
+make build-ui
 ```
 
 To start up a local client development server:<a id="local-rest"></a>
@@ -299,7 +299,7 @@ To deploy an update for the main application, change your working dir
 to the repository root dir and execute the following commands (bash):
 ```bash
 # Build the client application to ensure no errors occur.
-make ui-build APP_PROFILE=prod
+make build-ui APP_PROFILE=prod
 
 # Generate the pom.xml file (not version-controlled)
 # to ensure no errors occur (in API code)

From bb678e9d8621ba74b84c187fcac9b4c863f97c80 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 15:00:22 +0000
Subject: [PATCH 09/27] Build complete application in Dockerfile.

This ensures container building process is build-environment agnostic.
---
 Dockerfile | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++----
 Makefile   |  9 ++++++---
 2 files changed, 56 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index cc6732dd..60f299c6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,9 +1,55 @@
-FROM openjdk:8-jre-alpine
+ARG WORKDIR=/wb_names
+ARG APPJAR_BUILDPATH=build/wb-names-app.jar
 
-ARG uberjar_path=
-ADD $uberjar_path /srv/app.jar
+### Stage 1: build UI
+FROM node:12 AS BUILD_UI_STAGE
+
+ARG WORKDIR
+
+WORKDIR $WORKDIR
+COPY Makefile ./
+COPY client/ ./client/
+COPY scripts/ ./scripts/
+
+RUN --mount=type=secret,id=make-secrets-file,required=true \
+    make build-ui SECRETS_SRC=/run/secrets/make-secrets-file APP_PROFILE=prod
+
+### Stage 2: build API (and include UI components)
+FROM clojure:temurin-8-tools-deps-jammy as BUILD_API_STAGE
+
+ARG WORKDIR
+ARG APPJAR_BUILDPATH
+
+RUN apt update && apt upgrade -y && apt install -y maven unzip
+
+#Install clojure manually (com.datomic/datomic-pro 1.0.6165 is not stored on maven central)
+COPY build/datomic-pro-1.0.6165.zip datomic-pro-1.0.6165.zip
+RUN unzip datomic-pro-1.0.6165.zip \
+     && cd datomic-pro-1.0.6165/ \
+     && bin/maven-install
+
+WORKDIR $WORKDIR
+COPY Makefile ./
+COPY src/wormbase/ src/wormbase/
+COPY resources/ ./resources/
+COPY deps.edn ./
+COPY project.clj ./
+COPY scripts/ ./scripts/
+COPY --from=BUILD_UI_STAGE $WORKDIR/client/ $WORKDIR/client/
+
+RUN make build-app-jar APP_JAR_PATH=$APPJAR_BUILDPATH
+
+### Stage 3: build final application image
+FROM openjdk:8-jre-alpine as APPLICATION_IMAGE_STAGE
+
+ARG WORKDIR
+ARG APPJAR_BUILDPATH
+
+RUN apk update && apk upgrade
+
+COPY --from=BUILD_API_STAGE $WORKDIR/$APPJAR_BUILDPATH /srv/wb-names-app.jar
 
 # Expose necessary ports
 EXPOSE 3000
 
-CMD ["java", "-cp", "/srv/app.jar", "clojure.main", "-m", "wormbase.names.service"]
+CMD ["java", "-cp", "/srv/wb-names-app.jar", "clojure.main", "-m", "wormbase.names.service"]
diff --git a/Makefile b/Makefile
index eb8bf0c6..11759b5e 100644
--- a/Makefile
+++ b/Makefile
@@ -91,11 +91,14 @@ build/:
 	mkdir build/
 
 .PHONY: build
-build: ENV.VERSION_TAG clean build/ ui-build build/${DEPLOY_JAR} \
+build: build/ ENV.VERSION_TAG ${STORE_SECRETS_FILE} \
        $(call print-help,build,\
-       Build the docker images from using the current git revision.)
+       Build the docker images from the current git revision.)
+	@aws s3 cp s3://wormbase/datomic-pro/distro/datomic-pro-1.0.6165.zip build/
 	@docker build -t ${ECR_REPO_NAME}:${VERSION_TAG} \
-		--build-arg uberjar_path=build/${DEPLOY_JAR} .
+		--secret id=make-secrets-file,src=${STORE_SECRETS_FILE} \
+		.
+	@rm ${STORE_SECRETS_FILE}
 
 .PHONY: build-ui
 build-ui: ENV.GOOGLE_OAUTH_CLIENT_ID \

From 1a0ca06eb649df6b69b882392547b9dab9a726e4 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 15:04:24 +0000
Subject: [PATCH 10/27] Enable make run using AWS_PROFILE for AWS
 authentication (DB access)

---
 Makefile | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index 11759b5e..e855073a 100644
--- a/Makefile
+++ b/Makefile
@@ -219,17 +219,30 @@ run: ENV.VERSION_TAG \
      $(call print-help,run [PORT=<port>] [PROJ_NAME=<docker-project-name>] \
 	 [WB_DB_URI=<datomic-uri>] [GOOGLE_REDIRECT_URI=<google-redirect-uri>],\
      Run the application in docker (locally).)
-	@docker run \
+	
+	$(eval RUN_CMD = docker run \
 		--name ${PROJ_NAME} \
 		--publish-all=true \
 		--publish ${PORT}:${PORT} \
 		--detach \
-		-e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \
-		-e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \
 		-e WB_DB_URI=${WB_DB_URI} \
 		-e GOOGLE_REDIRECT_URI=${GOOGLE_REDIRECT_URI} \
-		-e PORT=${PORT} \
-		${ECR_REPO_NAME}:${VERSION_TAG}
+		-e PORT=${PORT})
+ifneq (${AWS_ACCESS_KEY_ID},)
+ifneq (${AWS_SECRET_ACCESS_KEY},)
+	$(eval RUN_CMD = ${RUN_CMD} -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY})
+	$(eval RUN_CMD = ${RUN_CMD} -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID})
+else
+	@echo 'ENV var "AWS_ACCESS_KEY_ID" is defined but "AWS_SECRET_ACCESS_KEY" is not. Either define both or none.' >&2
+	@exit 1
+endif
+else
+ifneq (${AWS_PROFILE},)
+	$(eval RUN_CMD = ${RUN_CMD} -e AWS_PROFILE=${AWS_PROFILE} -v ~/.aws:/root/.aws)
+endif
+endif
+
+	${RUN_CMD} ${ECR_REPO_NAME}:${VERSION_TAG}
 
 .PHONY: docker-clean
 docker-clean: \

From 1ecec25b0f6c5a25f69a05f9c467ad787bb1bae3 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 15:04:47 +0000
Subject: [PATCH 11/27] Minor cleanup

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index e855073a..70271548 100644
--- a/Makefile
+++ b/Makefile
@@ -321,7 +321,7 @@ ENV.GOOGLE_OAUTH_CLIENT_SECRET: source-secrets \
 	 and ensure the AWS_PROFILE variable is appropriately defined)
 
 .PHONY: google-oauth2-secrets
-google-oauth2-secrets: source-secrets ENV.GOOGLE_OAUTH_CLIENT_ID ENV.GOOGLE_OAUTH_CLIENT_SECRET \
+google-oauth2-secrets: ENV.GOOGLE_OAUTH_CLIENT_ID ENV.GOOGLE_OAUTH_CLIENT_SECRET \
                        $(call print-help,google-oauth2-secrets,\
                        Store the Google oauth2 client details as env variables.)
 

From 9037191a7380ac4710ec6161b20110e2422b6073 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 16:22:22 +0000
Subject: [PATCH 12/27] Run target naming cleanup

---
 Makefile | 37 +++++++++++++++++++------------------
 1 file changed, 19 insertions(+), 18 deletions(-)

diff --git a/Makefile b/Makefile
index 70271548..dc675855 100644
--- a/Makefile
+++ b/Makefile
@@ -90,10 +90,10 @@ show-version: ENV.VERSION_TAG \
 build/:
 	mkdir build/
 
-.PHONY: build
-build: build/ ENV.VERSION_TAG ${STORE_SECRETS_FILE} \
-       $(call print-help,build,\
-       Build the docker images from the current git revision.)
+.PHONY: build-docker-image
+build-docker-image: build/ ENV.VERSION_TAG ${STORE_SECRETS_FILE} \
+                       $(call print-help,build,\
+                       Build the docker image from the current git revision.)
 	@aws s3 cp s3://wormbase/datomic-pro/distro/datomic-pro-1.0.6165.zip build/
 	@docker build -t ${ECR_REPO_NAME}:${VERSION_TAG} \
 		--secret id=make-secrets-file,src=${STORE_SECRETS_FILE} \
@@ -111,8 +111,9 @@ build-ui: ENV.GOOGLE_OAUTH_CLIENT_ID \
 .PHONY: clean
 clean: \
        $(call print-help,clean,\
-       Remove the locally built JAR file.)
+       Remove the locally built UI and API artefacts.)
 	@rm -f ${APP_JAR_PATH}
+	@rm -rf client/build/*
 
 ${APP_JAR_PATH}: build/ \
                       $(call print-help,${APP_JAR_PATH},\
@@ -123,10 +124,10 @@ build-app-jar: ${APP_JAR_PATH} \
                $(call print-help,build-app-jar,\
                Build the jar file.)
 
-.PHONY: docker-build
-docker-build: clean build \
-              $(call print-help,docker-build,\
-              Create docker container.)
+.PHONY: build-local
+build-local: clean build-ui build-app-jar \
+              $(call print-help,build-local,\
+              Build UI and app JAR (locally).)
 
 .PHONY: docker-ecr-login
 docker-ecr-login: \
@@ -214,11 +215,11 @@ eb-local: docker-ecr-login \
           Runs the ElasticBeanStalk/docker build and run locally.)
 	@eb local run --envvars PORT=${PORT},WB_DB_URI=${WB_DB_URI},GOOGLE_REDIRECT_URI=${GOOGLE_REDIRECT_URI}
 
-.PHONY: run
-run: ENV.VERSION_TAG \
-     $(call print-help,run [PORT=<port>] [PROJ_NAME=<docker-project-name>] \
-	 [WB_DB_URI=<datomic-uri>] [GOOGLE_REDIRECT_URI=<google-redirect-uri>],\
-     Run the application in docker (locally).)
+.PHONY: run-docker
+run-docker: ENV.VERSION_TAG clean-docker-run \
+            $(call print-help,run [PORT=<port>] [PROJ_NAME=<docker-project-name>] \
+	        [WB_DB_URI=<datomic-uri>] [GOOGLE_REDIRECT_URI=<google-redirect-uri>],\
+            Run the application docker container (locally).)
 	
 	$(eval RUN_CMD = docker run \
 		--name ${PROJ_NAME} \
@@ -244,9 +245,9 @@ endif
 
 	${RUN_CMD} ${ECR_REPO_NAME}:${VERSION_TAG}
 
-.PHONY: docker-clean
-docker-clean: \
-              $(call print-help,docker-clean [PROJ_NAME=<docker-project-name>],\
+.PHONY: clean-docker-run
+clean-docker-run: \
+              $(call print-help,clean-docker-run [PROJ_NAME=<docker-project-name>],\
               Stop and remove the docker container (if running).)
 	@docker stop ${PROJ_NAME}
 	@docker rm ${PROJ_NAME}
@@ -278,7 +279,7 @@ run-tests: google-oauth2-secrets \
 	  export GOOGLE_REDIRECT_URI=${LOCAL_GOOGLE_REDIRECT_URI} && \
 	  clojure -A:datomic-pro:logging:webassets:dev:test:run-tests
 
-.PHONY: run-dev-server
+.PHONY: run-dev-webserver
 run-dev-webserver: PORT := 4010
 run-dev-webserver: google-oauth2-secrets \
                    $(call print-help,run-dev-webserver PORT=<port> WB_DB_URI=<datomic-uri> \

From c2fe52af6c2b23380022fc812c1813c44da56e2a Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 16:26:25 +0000
Subject: [PATCH 13/27] Added .dockerIgnore to reduce docker image build-time
 and size

---
 .dockerignore | 6 ++++++
 .gitignore    | 1 -
 2 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 .dockerignore

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 00000000..a7bfaf60
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,6 @@
+client/node_modules/
+client/build/
+target/
+.github/
+.ebextensions/
+.elasticbeanstalk/
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 8386fb7f..9d9861ae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -33,7 +33,6 @@ target/
 !.elasticbeanstalk/*.global.yml
 Dockerrun.aws.json
 build/*
-/.dockerignore
 
 #Local docker-compose env-variable files
 .env

From ffee94ec8755cb1a36f3e3b0998c51fe0eb18ea5 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 16:32:45 +0000
Subject: [PATCH 14/27] Moved datomic bundle download into separate target (for
 improved repeat-performance)

---
 Makefile | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index dc675855..79c5262c 100644
--- a/Makefile
+++ b/Makefile
@@ -90,11 +90,14 @@ show-version: ENV.VERSION_TAG \
 build/:
 	mkdir build/
 
+build/datomic-pro-1.0.6165.zip:
+	@echo "Downloading datomic bundle from S3."
+	@aws s3 cp s3://wormbase/datomic-pro/distro/datomic-pro-1.0.6165.zip build/
+
 .PHONY: build-docker-image
-build-docker-image: build/ ENV.VERSION_TAG ${STORE_SECRETS_FILE} \
+build-docker-image: build/ ENV.VERSION_TAG ${STORE_SECRETS_FILE} build/datomic-pro-1.0.6165.zip \
                        $(call print-help,build,\
                        Build the docker image from the current git revision.)
-	@aws s3 cp s3://wormbase/datomic-pro/distro/datomic-pro-1.0.6165.zip build/
 	@docker build -t ${ECR_REPO_NAME}:${VERSION_TAG} \
 		--secret id=make-secrets-file,src=${STORE_SECRETS_FILE} \
 		.

From a7652b424d14c9ceebf9e0e55cabfbb7bd937395 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 16:33:59 +0000
Subject: [PATCH 15/27] Prevent accidental secrets leakage

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 9d9861ae..fc9aa6bf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -39,6 +39,7 @@ build/*
 
 # secrets
 /resources/secrets/
+secrets.makedef
 
 # Generated assets
 /resources/client_build

From a4945219b4cb10b4a5e42b4c6cf8db35d52ce3a2 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 16:43:52 +0000
Subject: [PATCH 16/27] Added note to document current issues running
 run-docker using local DB

---
 Makefile | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/Makefile b/Makefile
index 79c5262c..6bf0d9bd 100644
--- a/Makefile
+++ b/Makefile
@@ -218,6 +218,14 @@ eb-local: docker-ecr-login \
           Runs the ElasticBeanStalk/docker build and run locally.)
 	@eb local run --envvars PORT=${PORT},WB_DB_URI=${WB_DB_URI},GOOGLE_REDIRECT_URI=${GOOGLE_REDIRECT_URI}
 
+#Note: the run-docker command can currently only be used with non-local WB_DB_URI value.
+# Current setup fails to connect to local datomic DB (on host, outside of container)
+# from within the application container.
+# Making the host's "localhost" accessible within the container as "host.docker.internal"
+# through the following options in the `docker run` command makes the DB URI accessible
+# from within the container, but the transactor still fails to be accessible.
+#     -e WB_DB_URI=datomic:ddb-local://host.docker.internal:8000/WBNames_local/wormbase
+#     --add-host=host.docker.internal:host-gateway
 .PHONY: run-docker
 run-docker: ENV.VERSION_TAG clean-docker-run \
             $(call print-help,run [PORT=<port>] [PROJ_NAME=<docker-project-name>] \

From 90e15d9aa00e5ab9d57520a8f604fa5c2ec79bca Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 17:00:52 +0000
Subject: [PATCH 17/27] Added container build and run testing to PR validation

---
 .github/workflows/PR-validation.yml | 36 ++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index f107cd19..97516ffc 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -56,4 +56,38 @@ jobs:
       - name: Run Integration tests
         run: |
           make run-tests APP_PROFILE=dev
-  #TODO: add UI and API build and container packaging test
+  build-and-run-container:
+    permissions:
+      id-token: write # Required for authentication through OIDC to AWS
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: AWS credentials configuration
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
+          role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-test-api
+          aws-region: us-east-1
+          mask-aws-account-id: true
+      - name: Build container image
+        run: |
+          make build-docker-imagedock
+      - name: Launch test instance of container (connecting to test env DB)
+        run: |
+          make run-docker PROJ_NAME=wormbase-names-test
+          sleep 60
+      - name: Test API accessability
+        id: test-api-accessability
+        continue-on-error: true
+        run: |
+          curl -I http://localhost:3000/api/auth/identity
+      - name: Test UI accessability
+        id: test-ui-accessability
+        continue-on-error: true
+        run: |
+          curl -I http://localhost:3000/
+      - name: Report container logs if either accessibility test fails
+        if: ${{ steps.test-ui-accessability.outcome == 'failure' || steps.test-api-accessability.outcome == 'failure' }}
+        run: |
+          docker logs wormbase-names-test

From b7d1f797193cfffcf1a30c81bdb0560df99f345c Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 17:06:59 +0000
Subject: [PATCH 18/27] Fixed editor mishap

---
 .github/workflows/PR-validation.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index 97516ffc..15fb312e 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -72,7 +72,7 @@ jobs:
           mask-aws-account-id: true
       - name: Build container image
         run: |
-          make build-docker-imagedock
+          make build-docker-image
       - name: Launch test instance of container (connecting to test env DB)
         run: |
           make run-docker PROJ_NAME=wormbase-names-test

From 70e0451a1bcf7811caf38b5a0139d660832a3b8c Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 17:10:27 +0000
Subject: [PATCH 19/27] Allow retrieval of tags for image building in GH
 actions

---
 .github/workflows/PR-validation.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index 15fb312e..0ea1f719 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -63,6 +63,8 @@ jobs:
     steps:
       - name: Check out repository code
         uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - name: AWS credentials configuration
         uses: aws-actions/configure-aws-credentials@v4
         with:

From d7ccfd7ac40ad0672e78708b827197af4dbfc93f Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 19:36:54 +0000
Subject: [PATCH 20/27] Prevent errors on cleanup of non-existing containers

---
 Makefile | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 6bf0d9bd..1d996d88 100644
--- a/Makefile
+++ b/Makefile
@@ -260,8 +260,10 @@ endif
 clean-docker-run: \
               $(call print-help,clean-docker-run [PROJ_NAME=<docker-project-name>],\
               Stop and remove the docker container (if running).)
-	@docker stop ${PROJ_NAME}
-	@docker rm ${PROJ_NAME}
+# Stop if running container found
+	@echo $(if $(shell docker ps -q --filter name=${PROJ_NAME}),$(shell docker stop ${PROJ_NAME})) > /dev/null
+# Remove if stopped container found
+	@echo $(if $(shell docker ps -a -q --filter name=${PROJ_NAME}),$(shell docker rm ${PROJ_NAME})) > /dev/null
 
 .PHONY: deploy-ecr
 deploy-ecr: docker-build docker-tag docker-push-ecr

From 8d5eac98e7d4fbe743f8c3cdcaf575032ea3c2c9 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 19:52:31 +0000
Subject: [PATCH 21/27] Ensure container run tests cause correct job failure
 reporting on step failure

---
 .github/workflows/PR-validation.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index 0ea1f719..02e14bae 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -81,12 +81,10 @@ jobs:
           sleep 60
       - name: Test API accessability
         id: test-api-accessability
-        continue-on-error: true
         run: |
           curl -I http://localhost:3000/api/auth/identity
       - name: Test UI accessability
         id: test-ui-accessability
-        continue-on-error: true
         run: |
           curl -I http://localhost:3000/
       - name: Report container logs if either accessibility test fails

From 4ea84b138ee69f93bffd9c5cbd387c5b4f38fb8a Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 20:12:21 +0000
Subject: [PATCH 22/27] Fix 2 to ensure container accessability tests cause
 correct job failure reporting on step failure

---
 .github/workflows/PR-validation.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index 02e14bae..d588d409 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -81,13 +81,19 @@ jobs:
           sleep 60
       - name: Test API accessability
         id: test-api-accessability
+        continue-on-error: true
         run: |
           curl -I http://localhost:3000/api/auth/identity
       - name: Test UI accessability
         id: test-ui-accessability
+        continue-on-error: true
         run: |
           curl -I http://localhost:3000/
       - name: Report container logs if either accessibility test fails
         if: ${{ steps.test-ui-accessability.outcome == 'failure' || steps.test-api-accessability.outcome == 'failure' }}
         run: |
           docker logs wormbase-names-test
+      - name: Report accessibility test failures
+        if: ${{ steps.test-ui-accessability.outcome == 'failure' || steps.test-api-accessability.outcome == 'failure' }}
+        run: |
+          echo "::setFailed title=Accessability tests failed::UI and/or API accessability tests failed."

From 9522c4927337073a7246643e0b6dad7dd55dc95a Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 20:18:52 +0000
Subject: [PATCH 23/27] Attempt 3 to fix correct job failure reporting on
 run-accessability testing step failures

---
 .github/workflows/PR-validation.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index d588d409..74d5f080 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -95,5 +95,4 @@ jobs:
           docker logs wormbase-names-test
       - name: Report accessibility test failures
         if: ${{ steps.test-ui-accessability.outcome == 'failure' || steps.test-api-accessability.outcome == 'failure' }}
-        run: |
-          echo "::setFailed title=Accessability tests failed::UI and/or API accessability tests failed."
+        run: echo "::setFailed title=Accessability tests failed::UI and/or API accessability tests failed."

From ae20125be17beadc260a3651d3d4c1295c54498f Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 20:30:11 +0000
Subject: [PATCH 24/27] Attempt 4 to fix correct job failure reporting on
 run-accessability testing step failures

---
 .github/workflows/PR-validation.yml | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index 74d5f080..3a387cd9 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -93,6 +93,15 @@ jobs:
         if: ${{ steps.test-ui-accessability.outcome == 'failure' || steps.test-api-accessability.outcome == 'failure' }}
         run: |
           docker logs wormbase-names-test
-      - name: Report accessibility test failures
+      - name: Report UI accessibility test failures
+        if: ${{ steps.test-ui-accessability.outcome == 'failure' }}
+        run: |
+          echo "UI accessability test step failed."
+      - name: Report API accessibility test failures
+        if: ${{ steps.test-api-accessability.outcome == 'failure' }}
+        run: |
+          echo "API accessability test step failed."
+      - name: Fail if either accessibility test fails
         if: ${{ steps.test-ui-accessability.outcome == 'failure' || steps.test-api-accessability.outcome == 'failure' }}
-        run: echo "::setFailed title=Accessability tests failed::UI and/or API accessability tests failed."
+        run: |
+          exit 1

From cdf92ab6ea7e6d964a1a15dba44e7c358af57327 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 21:03:12 +0000
Subject: [PATCH 25/27] Define default AWS_DEFAULT_REGION value and pass
 through to container at runtime

---
 Makefile | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index 1d996d88..9c465b2f 100644
--- a/Makefile
+++ b/Makefile
@@ -2,12 +2,13 @@ ECR_REPO_NAME := wormbase/names
 EB_APP_ENV_FILE := app-env.config
 PROJ_NAME ?= wormbase-names-dev
 LOCAL_GOOGLE_REDIRECT_URI := "http://lvh.me:3000"
+AWS_DEFAULT_REGION ?= us-east-1
 ifeq ($(PROJ_NAME), wormbase-names)
-	WB_DB_URI ?= "datomic:ddb://us-east-1/WSNames/wormbase"
+	WB_DB_URI ?= "datomic:ddb://${AWS_DEFAULT_REGION}/WSNames/wormbase"
 	GOOGLE_REDIRECT_URI ?= "https://names.wormbase.org"
 	APP_PROFILE ?= "prod"
 else ifeq ($(PROJ_NAME), wormbase-names-test)
-	WB_DB_URI ?= "datomic:ddb://us-east-1/WSNames-test-14/wormbase"
+	WB_DB_URI ?= "datomic:ddb://${AWS_DEFAULT_REGION}/WSNames-test-14/wormbase"
 	GOOGLE_REDIRECT_URI ?= "https://test-names.wormbase.org"
 	APP_PROFILE ?= "prod"
 else
@@ -24,7 +25,7 @@ APP_JAR_PATH ?= build/app.jar
 PORT := 3000
 WB_ACC_NUM := 357210185381
 
-ECR_URI := ${WB_ACC_NUM}.dkr.ecr.us-east-1.amazonaws.com
+ECR_URI := ${WB_ACC_NUM}.dkr.ecr.${AWS_DEFAULT_REGION}.amazonaws.com
 ECR_REPO_URI := ${ECR_URI}/${ECR_REPO_NAME}
 ECR_IMAGE_URI = ${ECR_REPO_URI}:${VERSION_TAG}
 # Set AWS (EB) profile env vars if undefined
@@ -182,7 +183,7 @@ eb-create: eb-def-app-env \
 		&& exit 1 \
 	)
 	@eb create ${PROJ_NAME} \
-	        --region=us-east-1 \
+	        --region=${AWS_DEFAULT_REGION} \
 	        --tags="CreatedBy=${AWS_IAM_UNAME},Role=RestAPI" \
 	        --cname="${PROJ_NAME}" \
 	        -p docker \
@@ -209,6 +210,7 @@ eb-setenv: \
 		_JAVA_OPTIONS="-Xmx14g" \
 		AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
 		AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
+		AWS_DEFAULT_REGION="${AWS_DEFAULT_REGION}" \
 		-e "${PROJ_NAME}"
 
 .PHONY: eb-local
@@ -239,7 +241,8 @@ run-docker: ENV.VERSION_TAG clean-docker-run \
 		--detach \
 		-e WB_DB_URI=${WB_DB_URI} \
 		-e GOOGLE_REDIRECT_URI=${GOOGLE_REDIRECT_URI} \
-		-e PORT=${PORT})
+		-e PORT=${PORT} \
+		-e AWS_DEFAULT_REGION=${AWS_DEFAULT_REGION})
 ifneq (${AWS_ACCESS_KEY_ID},)
 ifneq (${AWS_SECRET_ACCESS_KEY},)
 	$(eval RUN_CMD = ${RUN_CMD} -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY})

From af9a7ac4210fb9fa01a7167cff145769bd33b2cf Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 21:25:40 +0000
Subject: [PATCH 26/27] Attempt to pass through temporary AWS credentials
 retrieved through roles to application container

---
 Makefile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/Makefile b/Makefile
index 9c465b2f..8f6653dd 100644
--- a/Makefile
+++ b/Makefile
@@ -247,6 +247,9 @@ ifneq (${AWS_ACCESS_KEY_ID},)
 ifneq (${AWS_SECRET_ACCESS_KEY},)
 	$(eval RUN_CMD = ${RUN_CMD} -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY})
 	$(eval RUN_CMD = ${RUN_CMD} -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID})
+ifneq (${AWS_SESSION_TOKEN},)
+	$(eval RUN_CMD = ${RUN_CMD} -e AWS_SESSION_TOKEN=${AWS_SESSION_TOKEN})
+endif
 else
 	@echo 'ENV var "AWS_ACCESS_KEY_ID" is defined but "AWS_SECRET_ACCESS_KEY" is not. Either define both or none.' >&2
 	@exit 1

From 82b7ca3cea8bb1765a79ce73df8e93c4067fd3a8 Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Fri, 26 Jan 2024 22:10:33 +0000
Subject: [PATCH 27/27] Allow more time for application to start up + silenced
 curl progress reporting

---
 .github/workflows/PR-validation.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/PR-validation.yml b/.github/workflows/PR-validation.yml
index 3a387cd9..e61d1b1a 100644
--- a/.github/workflows/PR-validation.yml
+++ b/.github/workflows/PR-validation.yml
@@ -78,17 +78,17 @@ jobs:
       - name: Launch test instance of container (connecting to test env DB)
         run: |
           make run-docker PROJ_NAME=wormbase-names-test
-          sleep 60
+          sleep 120
       - name: Test API accessability
         id: test-api-accessability
         continue-on-error: true
         run: |
-          curl -I http://localhost:3000/api/auth/identity
+          curl --no-progress-meter -I http://localhost:3000/api/auth/identity
       - name: Test UI accessability
         id: test-ui-accessability
         continue-on-error: true
         run: |
-          curl -I http://localhost:3000/
+          curl --no-progress-meter -I http://localhost:3000/
       - name: Report container logs if either accessibility test fails
         if: ${{ steps.test-ui-accessability.outcome == 'failure' || steps.test-api-accessability.outcome == 'failure' }}
         run: |