From 37bd45d1c533416e21c0f8b1fa4ffa5c23aedd08 Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Wed, 5 Jun 2024 16:16:48 -0700
Subject: [PATCH 01/33] AG-1471: install synapseclient, download release data
 from Synpase

---
 .github/workflows/e2e.yml | 74 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100644 .github/workflows/e2e.yml

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
new file mode 100644
index 00000000..83e8f49a
--- /dev/null
+++ b/.github/workflows/e2e.yml
@@ -0,0 +1,74 @@
+on:
+  push:
+    branches:
+      - AG-1471_AG-1473_AG-1474
+
+jobs:
+  e2e:
+    runs-on: ubuntu-20.04
+    environment: e2e
+    env:
+      CI: true
+      LOCAL_DATA_PATH: './local/data'
+      LOCAL_TEAM_IMAGES_DIR: './local/data/team_images'
+      LOCAL_COLLECTIONS_PATH: './scripts/collections.csv'
+      LOCAL_IMPORT_SCRIPT_PATH: './docker/import-data.sh'
+      LOCAL_CREATE_INDEXES_PATH: './scripts/mongo-create-Indexes.js'
+      DOCKER_COMPOSE_PATH: './docker/docker-compose.yml'
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: get data image tag, data manifest id, and data version
+        env:
+          PACKAGE_JSON_PATH: 'package.json'
+          DATA_IMAGE_NAME: '${{ vars.DB_NAME }}/data'
+        run: |
+          DATA_MANIFEST_ID=$(jq -r '."data-file"' "${{ env.PACKAGE_JSON_PATH }}")
+          echo "DATA_MANIFEST_ID=${DATA_MANIFEST_ID}" >> "$GITHUB_ENV"
+
+          DATA_VERSION=$(jq -r '."data-version"' "${{ env.PACKAGE_JSON_PATH }}")
+          echo "DATA_VERSION=${DATA_VERSION}" >> "$GITHUB_ENV"
+
+          DATA_IMAGE_TAG="${{ env.DATA_IMAGE_NAME }}:${DATA_MANIFEST_ID}-v${DATA_VERSION}"
+          echo "DATA_IMAGE_TAG=${DATA_IMAGE_TAG}" >> "$GITHUB_ENV"
+
+      # TODO - check remote repository
+      - name: check whether image exists
+        id: image-exists
+        run: |
+          echo "==> data image tag: ${{ env.DATA_IMAGE_TAG }}"
+          echo "IMAGE_EXISTS=false" >> "$GITHUB_ENV"
+
+          # TODO - move into job which conditionally runs based on IMAGE_EXISTS
+      # https://github.com/actions/setup-python/issues/807
+      - name: create placeholder requirements.txt file
+        run: touch ./requirements.txt
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+
+      - name: install synapseclient
+        run: |
+          pip install --upgrade synapseclient
+
+      - name: download data from synapse
+        timeout-minutes: 10
+        env:
+          SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }}
+        run: |
+          echo "==> make directory for team images"
+          mkdir -p "${{ env.LOCAL_TEAM_IMAGES_DIR }}"
+
+          echo "==> download manifest file from Synapse"
+          synapse get --downloadLocation "${{ env.LOCAL_DATA_PATH }}" -v "${{ env.DATA_VERSION }}" "${{ env.DATA_MANIFEST_ID }}"
+
+          echo "==> download all files referenced in manifest from Synapse"
+          cat "${{ env.LOCAL_DATA_PATH }}"/data_manifest.csv | tail -n +2 | while IFS=, read -r id version; do
+              echo "===> Downloading ${id}.${version}"
+              synapse get --downloadLocation "${{ env.LOCAL_DATA_PATH }}" -v "${version}" "${id}"
+            done
+
+          echo "==> download team images"
+          synapse get -r --downloadLocation "${{ env.LOCAL_TEAM_IMAGES_DIR }}/" "${{ vars.TEAM_IMAGES_ID }}"

From 841db259b510c856fcc38af54926930ce45bb947 Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Wed, 5 Jun 2024 16:19:16 -0700
Subject: [PATCH 02/33] AG-1473: create mongo image containing release data

---
 .github/workflows/e2e.yml | 14 +++++++++++++
 docker/Dockerfile         | 27 +++++++++++++++++++++++++
 docker/docker-compose.yml | 20 +++++++++++++++++++
 docker/import-data.sh     | 42 +++++++++++++++++++++++++++++++++++++++
 scripts/collections.csv   | 16 +++++++++++++++
 5 files changed, 119 insertions(+)
 create mode 100644 docker/Dockerfile
 create mode 100644 docker/docker-compose.yml
 create mode 100644 docker/import-data.sh
 create mode 100644 scripts/collections.csv

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index 83e8f49a..531e798a 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -72,3 +72,17 @@ jobs:
 
           echo "==> download team images"
           synapse get -r --downloadLocation "${{ env.LOCAL_TEAM_IMAGES_DIR }}/" "${{ vars.TEAM_IMAGES_ID }}"
+
+      - name: build image
+        env:
+          DOCKERFILE_PATH: './docker/Dockerfile'
+        run: |
+          docker build \
+          -t "${{ env.DATA_IMAGE_TAG }}" \
+          -f "${{ env.DOCKERFILE_PATH }}" \
+          --build-arg LOCAL_DATA_PATH="${{ env.LOCAL_DATA_PATH }}" \
+          --build-arg LOCAL_COLLECTIONS_PATH="${{ env.LOCAL_COLLECTIONS_PATH }}" \
+          --build-arg LOCAL_IMPORT_SCRIPT_PATH="${{ env.LOCAL_IMPORT_SCRIPT_PATH }}" \
+          --build-arg LOCAL_CREATE_INDEXES_PATH="${{ env.LOCAL_CREATE_INDEXES_PATH }}" \
+          .
+      # TODO - push image to remote repository
diff --git a/docker/Dockerfile b/docker/Dockerfile
new file mode 100644
index 00000000..b25d7970
--- /dev/null
+++ b/docker/Dockerfile
@@ -0,0 +1,27 @@
+FROM mongo:latest
+
+# Paths on local machine - may be overwritten at build time
+ARG LOCAL_DATA_PATH="./local/data" 
+ARG LOCAL_COLLECTIONS_PATH="./scripts/collections.csv"
+ARG LOCAL_IMPORT_SCRIPT_PATH="./docker/import-data.sh"
+ARG LOCAL_CREATE_INDEXES_PATH="./scripts/mongo-create-Indexes.js"
+
+# Paths within the image
+ENV DATA_DIR="input_data"
+ENV TEAM_IMAGES_DIR="${DATA_DIR}/team_images"
+ENV COLLECTIONS_FILE="collections.csv"
+ENV IMPORT_DATA_FILE="import-data.sh"
+ENV CREATE_INDEXES_FILE="create-indexes.js"
+
+# Copy data and scripts to image
+COPY "${LOCAL_DATA_PATH}" "${DATA_DIR}"
+COPY "${LOCAL_COLLECTIONS_PATH}" "${COLLECTIONS_FILE}"
+COPY "${LOCAL_IMPORT_SCRIPT_PATH}" "${IMPORT_DATA_FILE}"
+COPY "${LOCAL_CREATE_INDEXES_PATH}" "${CREATE_INDEXES_FILE}"
+
+# Make scripts executable
+RUN chmod +x "${IMPORT_DATA_FILE}"
+RUN chmod +x "${CREATE_INDEXES_FILE}"
+
+# On container startup, import data into mongodb
+CMD ["/bin/bash", "import-data.sh"]
\ No newline at end of file
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
new file mode 100644
index 00000000..51d8c00d
--- /dev/null
+++ b/docker/docker-compose.yml
@@ -0,0 +1,20 @@
+services:
+  mongodb:
+    image: mongo
+    ports:
+      - "${DB_PORT}:27017"
+    expose:
+      - "${DB_PORT}"
+    environment:
+      - MONGO_INITDB_ROOT_USERNAME=${DB_USER}
+      - MONGO_INITDB_ROOT_PASSWORD=${DB_PASS}
+      - MONGO_INITDB_DATABASE=${DB_NAME}
+  mongo-seed:
+    image: ${DATA_IMAGE_TAG}
+    depends_on: 
+      - mongodb
+    environment:
+      - DB_HOST=mongodb # must match mongo service name
+      - DB_USER=${DB_USER}
+      - DB_PASS=${DB_PASS}
+      - DB_NAME=${DB_NAME}
diff --git a/docker/import-data.sh b/docker/import-data.sh
new file mode 100644
index 00000000..5eb1ba38
--- /dev/null
+++ b/docker/import-data.sh
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+# Expects the following environment variables to be set: 
+# - DB_HOST - mongo db host
+# - DB_USER - mongo db root username
+# - DB_PASS - mongo db root password
+# - DB_NAME - mongo db name
+# - COLLECTIONS_FILE - path to file that maps collection names to file names
+# - DATA_DIR - path to directory that contains collections data
+# - TEAM_IMAGES_DIR - path to directory that contains team images files
+# - CREATE_INDEXES_FILE - path to file that creates mongo db indexes
+
+# Abort on error: https://bertvv.github.io/cheat-sheets/Bash.html#writing-robust-scripts-and-debugging
+set -o errexit   # abort on nonzero exitstatus
+set -o nounset   # abort on unbound variable
+set -o pipefail  # don't hide errors within pipes
+
+# Import collections into mongodb
+echo "importing collections"
+while IFS=',' read -r collection filename
+do
+    echo "importing ${collection} from ${filename}"
+    mongoimport \
+      -h "${DB_HOST}" -d "${DB_NAME}" -u "${DB_USER}" -p "${DB_PASS}" \
+      --authenticationDatabase admin \
+      --collection "${collection}" \
+      --jsonArray --drop \
+      --file "${DATA_DIR}/${filename}"
+done < "${COLLECTIONS_FILE}"
+
+# Create indexes
+echo "creating indexes"
+mongosh \
+  --host "${DB_HOST}" -u "${DB_USER}" -p "${DB_PASS}" \
+  --authenticationDatabase admin \
+  "${CREATE_INDEXES_FILE}"
+
+# Import images
+echo "importing images"
+pushd "${TEAM_IMAGES_DIR}"
+ls -1r *.{jpg,jpeg,png} | while read x; do mongofiles -h "${DB_HOST}" -d "${DB_NAME}" -u "${DB_USER}" -p "${DB_PASS}" --authenticationDatabase admin -v put $x; echo $x; done
+popd
\ No newline at end of file
diff --git a/scripts/collections.csv b/scripts/collections.csv
new file mode 100644
index 00000000..1ac9a11a
--- /dev/null
+++ b/scripts/collections.csv
@@ -0,0 +1,16 @@
+genes,rnaseq_differential_expression.json
+geneslinks,network.json
+geneinfo,gene_info.json
+teaminfo,team_info.json
+genesproteomics,proteomics.json
+genesmetabolomics,metabolomics.json
+genesneuropathcorr,neuropath_corr.json
+geneexpvalidation,target_exp_validation_harmonized.json
+genescoredistribution,distribution_data.json
+genesoverallscores,overall_scores.json
+rnaboxdistribution,rna_distribution_data.json
+proteomicsboxdistribution,proteomics_distribution_data.json
+proteomicstmt,proteomics_tmt.json
+proteomicssrm,proteomics_srm.json
+genesbiodomains,genes_biodomains.json
+biodomaininfo,biodomain_info.json
\ No newline at end of file

From e95715492994a3324141e32ca32fff7d40dca24f Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Wed, 5 Jun 2024 16:19:51 -0700
Subject: [PATCH 03/33] AG-1474: run e2e tests

---
 .github/workflows/e2e.yml | 65 +++++++++++++++++++++++++++++++++++++--
 docker/README.md          | 26 ++++++++++++++++
 playwright.config.ts      | 14 +++++----
 src/server/api.ts         | 35 ++++++++++++---------
 4 files changed, 117 insertions(+), 23 deletions(-)
 create mode 100644 docker/README.md

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index 531e798a..58790e32 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -1,10 +1,14 @@
+name: Build Data Image and Run End-to-end Tests
+
 on:
   push:
-    branches:
-      - AG-1471_AG-1473_AG-1474
+    branches: [ develop, main ]
+  pull_request:
+    branches: [ develop, main ]
 
 jobs:
   e2e:
+    timeout-minutes: 60
     runs-on: ubuntu-20.04
     environment: e2e
     env:
@@ -39,7 +43,7 @@ jobs:
           echo "==> data image tag: ${{ env.DATA_IMAGE_TAG }}"
           echo "IMAGE_EXISTS=false" >> "$GITHUB_ENV"
 
-          # TODO - move into job which conditionally runs based on IMAGE_EXISTS
+      # TODO - move into job which conditionally runs based on IMAGE_EXISTS
       # https://github.com/actions/setup-python/issues/807
       - name: create placeholder requirements.txt file
         run: touch ./requirements.txt
@@ -86,3 +90,58 @@ jobs:
           --build-arg LOCAL_CREATE_INDEXES_PATH="${{ env.LOCAL_CREATE_INDEXES_PATH }}" \
           .
       # TODO - push image to remote repository
+
+      # TODO - move into job that pulls image from remote repository
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 16
+
+      - name: install dependencies
+        run: npm install
+
+      - name: install Playwright Browsers
+        run: npx playwright install --with-deps
+
+      - name: start database, server, and app
+        env:
+          DB_USER: ${{ secrets.DB_USER }}
+          DB_PASS: ${{ secrets.DB_PASS }}
+          DB_PORT: ${{ vars.DB_PORT }}
+          DB_NAME: ${{ vars.DB_NAME }}
+        run: |
+          echo "==> start database and data containers"
+          docker-compose -f "${{ env.DOCKER_COMPOSE_PATH }}" up -d
+
+          echo "==> wait for data container to finish seeding database container"
+          DATA_CONTAINER=$(docker compose -f "${{ env.DOCKER_COMPOSE_PATH }}" ps -a --format '{{.Name}}' mongo-seed)
+          docker wait "${DATA_CONTAINER}"
+
+          echo "==> start server and app in background and wait for server to grab port"
+          MONGODB_HOST="localhost" MONGODB_PORT="${{ env.DB_PORT }}" APP_ENV="e2e" npm run dev >/dev/null 2>&1 &
+          sleep 5
+
+      - name: run e2e tests
+        run: npx playwright test
+
+      - name: clean up database, server, and app
+        env:
+          DB_USER: ${{ secrets.DB_USER }}
+          DB_PASS: ${{ secrets.DB_PASS }}
+          DB_PORT: ${{ vars.DB_PORT }}
+          DB_NAME: ${{ vars.DB_NAME }}
+        run: |
+          echo "==> stop app"
+          pid=$(lsof -i :3000 -t) && kill ${pid}
+
+          echo "==> stop server"
+          pid=$(lsof -i :8080 -t) && kill ${pid}
+
+          echo "==> stop database"
+          docker-compose -f "${{ env.DOCKER_COMPOSE_PATH }}" down
+
+      - uses: actions/upload-artifact@v4
+        if: ${{ !cancelled() }}
+        with:
+          name: playwright-report
+          path: playwright-report/
+          retention-days: 5
diff --git a/docker/README.md b/docker/README.md
new file mode 100644
index 00000000..b832dd85
--- /dev/null
+++ b/docker/README.md
@@ -0,0 +1,26 @@
+# Agora Docker Image
+
+Files in this directory:
+
+- `Dockerfile`: creates the `agora/data` docker image, which contains data for a particular Agora data release (manifest synId + version) and team images and will seed a mongodb at start up using `import-data.sh`
+- `docker-compose.yml`: spins up `mongo` and `agora/data` docker containers
+
+## Workflow Setup
+
+The following secrets and variables need to be set up in GitHub for the `e2e.yml` workflow to create the `agora/data` Docker image:
+
+e2e Environment secrets:
+
+| Variable           | Description                                | Example           |
+| ------------------ | ------------------------------------------ | ----------------- |
+| DB_USER            | The database user                          | dbuser            |
+| DB_PASS            | The database password                      | supersecret       |
+| SYNAPSE_AUTH_TOKEN | The Synapse service user view/download PAT | token-string-here |
+
+e2e Environment variables:
+
+| Variable       | Description                         | Example |
+| -------------- | ----------------------------------- | ------- |
+| DB_NAME        | The database name                   | agora   |
+| DB_PORT        | The database port                   | 27017   |
+| TEAM_IMAGES_ID | The synId of the team images folder | syn123  |
diff --git a/playwright.config.ts b/playwright.config.ts
index 9c6e531a..4e87eb67 100644
--- a/playwright.config.ts
+++ b/playwright.config.ts
@@ -1,6 +1,7 @@
 import { defineConfig, devices } from '@playwright/test';
 
-export const baseURL = 'http://localhost:8080';
+const port = 8080;
+export const baseURL = `http://127.0.0.1:${port}`;
 
 /**
  * Read environment variables from file.
@@ -14,7 +15,7 @@ export const baseURL = 'http://localhost:8080';
 export default defineConfig({
   testDir: './tests',
   // timeout for every test
-  timeout: 25 * 60 * 1000,
+  timeout: 3 * 60 * 1000,
   /* Run tests in files in parallel */
   fullyParallel: true,
   /* Fail the build on CI if you accidentally left test.only in the source code. */
@@ -22,9 +23,9 @@ export default defineConfig({
   /* Retry on CI only */
   retries: process.env.CI ? 2 : 0,
   /* Opt out of parallel tests on CI. */
-  workers: process.env.CI ? 1 : undefined,
+  workers: process.env.CI ? 2 : undefined,
   /* Reporter to use. See https://playwright.dev/docs/test-reporters */
-  reporter: 'html',
+  reporter: process.env.CI ? [['list'], ['html']] : 'html',
   /* Shared settings for all the projects below. See https://playwright.dev/docs/api/class-testoptions. */
   use: {
     /* Base URL to use in actions like `await page.goto('/')`. */
@@ -75,7 +76,8 @@ export default defineConfig({
   /* Run your local dev server before starting the tests */
   webServer: {
     command: 'npm run start',
-    url: baseURL,
-    reuseExistingServer: !process.env.CI,
+    port,
+    reuseExistingServer: true,
+    timeout: 120 * 1000,
   },
 });
diff --git a/src/server/api.ts b/src/server/api.ts
index b37be822..fc47c37c 100644
--- a/src/server/api.ts
+++ b/src/server/api.ts
@@ -38,30 +38,37 @@ const database = { url: '' };
         doc && ('doc => ' + util.inspect(doc)), '\n');
 }); */
 
-console.log(process.env);
-console.log(process.env.MONGODB_HOST);
-console.log(process.env.MONGODB_PORT);
-
 // Set the database url
 if (
   process.env.MONGODB_HOST &&
   process.env.MONGODB_PORT &&
   process.env.APP_ENV
 ) {
-  const results = awsParamStore.getParametersSync(
-    [
-      '/agora-' + process.env.APP_ENV + '/MongodbUsername',
-      '/agora-' + process.env.APP_ENV + '/MongodbPassword',
-    ],
-    { region: 'us-east-1' }
-  );
+  let dbUser: string | undefined;
+  let dbPass: string | undefined;
+  if (process.env.APP_ENV === 'e2e') {
+    dbUser = process.env.DB_USER;
+    dbPass = process.env.DB_PASS;
+  } else {
+    const results = awsParamStore.getParametersSync(
+      [
+        '/agora-' + process.env.APP_ENV + '/MongodbUsername',
+        '/agora-' + process.env.APP_ENV + '/MongodbPassword',
+      ],
+      { region: 'us-east-1' }
+    );
+    if (results && results.Parameters) {
+      dbUser = results.Parameters[1]['Value'];
+      dbPass = results.Parameters[0]['Value'];
+    }
+  }
   
-  if (results && results.Parameters) {
+  if (dbUser && dbPass) {
     database.url =
       'mongodb://' +
-      results.Parameters[1]['Value'] +
+      dbUser +
       ':' +
-      results.Parameters[0]['Value'] +
+      dbPass +
       '@' +
       process.env.MONGODB_HOST +
       ':' +

From 7e281259904142132353f376936cdb60ddb7e7ca Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Thu, 6 Jun 2024 08:53:29 -0700
Subject: [PATCH 04/33] AG-1471: do not run job on pull_request trigger since
 forks do not have access to secrets

---
 .github/workflows/e2e.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index 58790e32..3053ba76 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -1,13 +1,12 @@
 name: Build Data Image and Run End-to-end Tests
 
-on:
-  push:
-    branches: [ develop, main ]
-  pull_request:
-    branches: [ develop, main ]
+on: push
 
 jobs:
   e2e:
+    # Run in Sage repo on develop or main branches
+    # and on all branches in user-owned forks
+    if: ${{ github.ref_name == 'develop' || github.ref_name == 'main' || github.actor == github.repository_owner }}
     timeout-minutes: 60
     runs-on: ubuntu-20.04
     environment: e2e

From 66cece35ae64a00b4b13a04d6549fde07ac5fe67 Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Thu, 13 Jun 2024 11:49:25 -0700
Subject: [PATCH 05/33] AG-1472: check if image exists in GHCR, then build/push
 image if needed

---
 .github/workflows/e2e.yml | 49 +++++++++++++++++++++++++++++++++------
 docker/Dockerfile         |  8 +++++++
 docker/docker-compose.yml |  2 +-
 3 files changed, 51 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index 3053ba76..c3ef6d4a 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -9,9 +9,14 @@ jobs:
     if: ${{ github.ref_name == 'develop' || github.ref_name == 'main' || github.actor == github.repository_owner }}
     timeout-minutes: 60
     runs-on: ubuntu-20.04
+    permissions:
+      packages: write
     environment: e2e
     env:
       CI: true
+      ORG_NAME: 'Sage-Bionetworks'
+      NAMESPACE: ${{ github.repository_owner }}
+      DATA_IMAGE_NAME: '${{ vars.DB_NAME }}/data'
       LOCAL_DATA_PATH: './local/data'
       LOCAL_TEAM_IMAGES_DIR: './local/data/team_images'
       LOCAL_COLLECTIONS_PATH: './scripts/collections.csv'
@@ -24,7 +29,6 @@ jobs:
       - name: get data image tag, data manifest id, and data version
         env:
           PACKAGE_JSON_PATH: 'package.json'
-          DATA_IMAGE_NAME: '${{ vars.DB_NAME }}/data'
         run: |
           DATA_MANIFEST_ID=$(jq -r '."data-file"' "${{ env.PACKAGE_JSON_PATH }}")
           echo "DATA_MANIFEST_ID=${DATA_MANIFEST_ID}" >> "$GITHUB_ENV"
@@ -32,31 +36,52 @@ jobs:
           DATA_VERSION=$(jq -r '."data-version"' "${{ env.PACKAGE_JSON_PATH }}")
           echo "DATA_VERSION=${DATA_VERSION}" >> "$GITHUB_ENV"
 
-          DATA_IMAGE_TAG="${{ env.DATA_IMAGE_NAME }}:${DATA_MANIFEST_ID}-v${DATA_VERSION}"
+          DATA_IMAGE_TAG="${DATA_MANIFEST_ID}.${DATA_VERSION}"
           echo "DATA_IMAGE_TAG=${DATA_IMAGE_TAG}" >> "$GITHUB_ENV"
 
-      # TODO - check remote repository
+          DATA_IMAGE_PATH="ghcr.io/${{ env.NAMESPACE }}/${{ env.DATA_IMAGE_NAME }}:${DATA_IMAGE_TAG}"
+          echo "DATA_IMAGE_PATH=${DATA_IMAGE_PATH}" >> "$GITHUB_ENV"
+
+      - name: login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: check whether image exists
         id: image-exists
+        env:
+          # https://docs.github.com/en/rest/packages/packages?apiVersion=2022-11-28#list-package-versions-for-a-package-owned-by-an-organization
+          ORG_PATH: '/orgs/${{ env.ORG_NAME }}/packages/container/${{ env.DATA_IMAGE_NAME }}/versions'
+          # https://docs.github.com/en/rest/packages/packages?apiVersion=2022-11-28#list-package-versions-for-a-package-owned-by-the-authenticated-user
+          USER_PATH: '/user/packages/container/${{ env.DATA_IMAGE_NAME }}/versions'
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          echo "==> data image tag: ${{ env.DATA_IMAGE_TAG }}"
-          echo "IMAGE_EXISTS=false" >> "$GITHUB_ENV"
+          GH_PATH=$( [[ "${{ env.NAMESPACE }}" == "${{ env.ORG_NAME }}" ]] && echo "${{ env.ORG_PATH }}" || echo "${{ env.USER_PATH }}" )
+          IMAGE_VERSIONS=$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" "${GH_PATH}")
+          IMAGE_EXISTS=$(echo "${IMAGE_VERSIONS}" | jq '[.[] | select(any(.metadata.container.tags[]; . == "${{ env.DATA_IMAGE_TAG }}"))] | length > 0')
+          echo "IMAGE_EXISTS=${IMAGE_EXISTS}" >> "$GITHUB_ENV"
 
       # TODO - move into job which conditionally runs based on IMAGE_EXISTS
       # https://github.com/actions/setup-python/issues/807
       - name: create placeholder requirements.txt file
+        if: ${{ env.IMAGE_EXISTS == 'false'}}
         run: touch ./requirements.txt
 
       - uses: actions/setup-python@v5
+        if: ${{ env.IMAGE_EXISTS == 'false'}}
         with:
           python-version: '3.9'
           cache: 'pip'
 
       - name: install synapseclient
+        if: ${{ env.IMAGE_EXISTS == 'false'}}
         run: |
           pip install --upgrade synapseclient
 
       - name: download data from synapse
+        if: ${{ env.IMAGE_EXISTS == 'false'}}
         timeout-minutes: 10
         env:
           SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }}
@@ -77,18 +102,28 @@ jobs:
           synapse get -r --downloadLocation "${{ env.LOCAL_TEAM_IMAGES_DIR }}/" "${{ vars.TEAM_IMAGES_ID }}"
 
       - name: build image
+        if: ${{ env.IMAGE_EXISTS == 'false'}}
         env:
           DOCKERFILE_PATH: './docker/Dockerfile'
         run: |
           docker build \
-          -t "${{ env.DATA_IMAGE_TAG }}" \
+          -t "${{ env.DATA_IMAGE_PATH }}" \
           -f "${{ env.DOCKERFILE_PATH }}" \
+          --build-arg SOURCE_REPO="https://github.com/${{ env.NAMESPACE }}/${{ vars.DB_NAME }}" \
+          --build-arg DESCRIPTION="${GITHUB_SHA::7}" \
           --build-arg LOCAL_DATA_PATH="${{ env.LOCAL_DATA_PATH }}" \
           --build-arg LOCAL_COLLECTIONS_PATH="${{ env.LOCAL_COLLECTIONS_PATH }}" \
           --build-arg LOCAL_IMPORT_SCRIPT_PATH="${{ env.LOCAL_IMPORT_SCRIPT_PATH }}" \
           --build-arg LOCAL_CREATE_INDEXES_PATH="${{ env.LOCAL_CREATE_INDEXES_PATH }}" \
           .
-      # TODO - push image to remote repository
+
+      # Note: if a new package is created using this workflow, then the package
+      # visibility will default to the source repository visbility. For example,
+      # a package created by a workflow in a public repo will also be public.
+      # Publicly visible container packages are anonymously downloadable.
+      - name: push to GitHub Container Registry
+        if: ${{ env.IMAGE_EXISTS == 'false' }}
+        run: docker push "${{ env.DATA_IMAGE_PATH }}"
 
       # TODO - move into job that pulls image from remote repository
       - uses: actions/setup-node@v4
diff --git a/docker/Dockerfile b/docker/Dockerfile
index b25d7970..365f23f5 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,5 +1,9 @@
 FROM mongo:latest
 
+# GHCR labels
+ARG SOURCE_REPO="https://github.com/Sage-Bionetworks/agora"
+ARG DESCRIPTION=""
+
 # Paths on local machine - may be overwritten at build time
 ARG LOCAL_DATA_PATH="./local/data" 
 ARG LOCAL_COLLECTIONS_PATH="./scripts/collections.csv"
@@ -23,5 +27,9 @@ COPY "${LOCAL_CREATE_INDEXES_PATH}" "${CREATE_INDEXES_FILE}"
 RUN chmod +x "${IMPORT_DATA_FILE}"
 RUN chmod +x "${CREATE_INDEXES_FILE}"
 
+# Add label for GHCR source repo
+LABEL org.opencontainers.image.source="${SOURCE_REPO}"
+LABEL org.opencontainers.image.description="${DESCRIPTION}"
+
 # On container startup, import data into mongodb
 CMD ["/bin/bash", "import-data.sh"]
\ No newline at end of file
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
index 51d8c00d..a1c1afc2 100644
--- a/docker/docker-compose.yml
+++ b/docker/docker-compose.yml
@@ -10,7 +10,7 @@ services:
       - MONGO_INITDB_ROOT_PASSWORD=${DB_PASS}
       - MONGO_INITDB_DATABASE=${DB_NAME}
   mongo-seed:
-    image: ${DATA_IMAGE_TAG}
+    image: ${DATA_IMAGE_PATH}
     depends_on: 
       - mongodb
     environment:

From 3b527b7e739f196441d769cf98301b7a9952111a Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Thu, 13 Jun 2024 13:30:27 -0700
Subject: [PATCH 06/33] AG-1472: split workflow into three jobs

---
 .github/workflows/e2e.yml | 110 +++++++++++++++++++++++++-------------
 docker/Dockerfile         |   2 +-
 2 files changed, 75 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index c3ef6d4a..56fa11e6 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -1,46 +1,46 @@
 name: Build Data Image and Run End-to-end Tests
 
 on: push
+env:
+  ORG_NAME: 'Sage-Bionetworks'
+  NAMESPACE: ${{ github.repository_owner }}
 
 jobs:
-  e2e:
+  check-for-image:
     # Run in Sage repo on develop or main branches
     # and on all branches in user-owned forks
     if: ${{ github.ref_name == 'develop' || github.ref_name == 'main' || github.actor == github.repository_owner }}
-    timeout-minutes: 60
+    timeout-minutes: 5
     runs-on: ubuntu-20.04
     permissions:
-      packages: write
+      packages: read
     environment: e2e
     env:
-      CI: true
-      ORG_NAME: 'Sage-Bionetworks'
-      NAMESPACE: ${{ github.repository_owner }}
       DATA_IMAGE_NAME: '${{ vars.DB_NAME }}/data'
-      LOCAL_DATA_PATH: './local/data'
-      LOCAL_TEAM_IMAGES_DIR: './local/data/team_images'
-      LOCAL_COLLECTIONS_PATH: './scripts/collections.csv'
-      LOCAL_IMPORT_SCRIPT_PATH: './docker/import-data.sh'
-      LOCAL_CREATE_INDEXES_PATH: './scripts/mongo-create-Indexes.js'
-      DOCKER_COMPOSE_PATH: './docker/docker-compose.yml'
+    outputs:
+      DATA_MANIFEST_ID: ${{ steps.get-ids-from-package-json.outputs.DATA_MANIFEST_ID }}
+      DATA_VERSION: ${{ steps.get-ids-from-package-json.outputs.DATA_VERSION }}
+      DATA_IMAGE_PATH: ${{ steps.get-ids-from-package-json.outputs.DATA_IMAGE_PATH }}
+      IMAGE_EXISTS: ${{ steps.check-container-repo.outputs.IMAGE_EXISTS }}
     steps:
       - uses: actions/checkout@v4
 
       - name: get data image tag, data manifest id, and data version
+        id: get-ids-from-package-json
         env:
           PACKAGE_JSON_PATH: 'package.json'
         run: |
           DATA_MANIFEST_ID=$(jq -r '."data-file"' "${{ env.PACKAGE_JSON_PATH }}")
-          echo "DATA_MANIFEST_ID=${DATA_MANIFEST_ID}" >> "$GITHUB_ENV"
+          echo "DATA_MANIFEST_ID=${DATA_MANIFEST_ID}" >> "$GITHUB_OUTPUT"
 
           DATA_VERSION=$(jq -r '."data-version"' "${{ env.PACKAGE_JSON_PATH }}")
-          echo "DATA_VERSION=${DATA_VERSION}" >> "$GITHUB_ENV"
+          echo "DATA_VERSION=${DATA_VERSION}" >> "$GITHUB_OUTPUT"
 
           DATA_IMAGE_TAG="${DATA_MANIFEST_ID}.${DATA_VERSION}"
-          echo "DATA_IMAGE_TAG=${DATA_IMAGE_TAG}" >> "$GITHUB_ENV"
+          echo "DATA_IMAGE_TAG=${DATA_IMAGE_TAG}" >> "$GITHUB_OUTPUT"
 
           DATA_IMAGE_PATH="ghcr.io/${{ env.NAMESPACE }}/${{ env.DATA_IMAGE_NAME }}:${DATA_IMAGE_TAG}"
-          echo "DATA_IMAGE_PATH=${DATA_IMAGE_PATH}" >> "$GITHUB_ENV"
+          echo "DATA_IMAGE_PATH=${DATA_IMAGE_PATH}" >> "$GITHUB_OUTPUT"
 
       - name: login to GitHub Container Registry
         uses: docker/login-action@v3
@@ -50,38 +50,54 @@ jobs:
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: check whether image exists
-        id: image-exists
+        id: check-container-repo
         env:
           # https://docs.github.com/en/rest/packages/packages?apiVersion=2022-11-28#list-package-versions-for-a-package-owned-by-an-organization
           ORG_PATH: '/orgs/${{ env.ORG_NAME }}/packages/container/${{ env.DATA_IMAGE_NAME }}/versions'
           # https://docs.github.com/en/rest/packages/packages?apiVersion=2022-11-28#list-package-versions-for-a-package-owned-by-the-authenticated-user
           USER_PATH: '/user/packages/container/${{ env.DATA_IMAGE_NAME }}/versions'
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DATA_IMAGE_TAG: ${{ steps.get-ids-from-package-json.outputs.DATA_IMAGE_TAG }}
         run: |
           GH_PATH=$( [[ "${{ env.NAMESPACE }}" == "${{ env.ORG_NAME }}" ]] && echo "${{ env.ORG_PATH }}" || echo "${{ env.USER_PATH }}" )
           IMAGE_VERSIONS=$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" "${GH_PATH}")
           IMAGE_EXISTS=$(echo "${IMAGE_VERSIONS}" | jq '[.[] | select(any(.metadata.container.tags[]; . == "${{ env.DATA_IMAGE_TAG }}"))] | length > 0')
-          echo "IMAGE_EXISTS=${IMAGE_EXISTS}" >> "$GITHUB_ENV"
+          echo "IMAGE_EXISTS=${IMAGE_EXISTS}" >> "$GITHUB_OUTPUT"
+
+  build-image:
+    needs: check-for-image
+    if: ${{ needs.check-for-image.result == 'success' && needs.check-for-image.outputs.IMAGE_EXISTS == 'false' }}
+    timeout-minutes: 60
+    runs-on: ubuntu-20.04
+    permissions:
+      packages: write
+    environment: e2e
+    env:
+      LOCAL_DATA_PATH: './local/data'
+      LOCAL_TEAM_IMAGES_DIR: './local/data/team_images'
+      LOCAL_COLLECTIONS_PATH: './scripts/collections.csv'
+      LOCAL_IMPORT_SCRIPT_PATH: './docker/import-data.sh'
+      LOCAL_CREATE_INDEXES_PATH: './scripts/mongo-create-Indexes.js'
+      DATA_VERSION: ${{ needs.check-for-image.outputs.DATA_VERSION }}
+      DATA_MANIFEST_ID: ${{ needs.check-for-image.outputs.DATA_MANIFEST_ID }}
+      DATA_IMAGE_PATH: ${{ needs.check-for-image.outputs.DATA_IMAGE_PATH }}
+    steps:
+      - uses: actions/checkout@v4
 
-      # TODO - move into job which conditionally runs based on IMAGE_EXISTS
       # https://github.com/actions/setup-python/issues/807
       - name: create placeholder requirements.txt file
-        if: ${{ env.IMAGE_EXISTS == 'false'}}
         run: touch ./requirements.txt
 
       - uses: actions/setup-python@v5
-        if: ${{ env.IMAGE_EXISTS == 'false'}}
         with:
           python-version: '3.9'
           cache: 'pip'
 
       - name: install synapseclient
-        if: ${{ env.IMAGE_EXISTS == 'false'}}
         run: |
           pip install --upgrade synapseclient
 
       - name: download data from synapse
-        if: ${{ env.IMAGE_EXISTS == 'false'}}
         timeout-minutes: 10
         env:
           SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }}
@@ -102,7 +118,6 @@ jobs:
           synapse get -r --downloadLocation "${{ env.LOCAL_TEAM_IMAGES_DIR }}/" "${{ vars.TEAM_IMAGES_ID }}"
 
       - name: build image
-        if: ${{ env.IMAGE_EXISTS == 'false'}}
         env:
           DOCKERFILE_PATH: './docker/Dockerfile'
         run: |
@@ -117,15 +132,41 @@ jobs:
           --build-arg LOCAL_CREATE_INDEXES_PATH="${{ env.LOCAL_CREATE_INDEXES_PATH }}" \
           .
 
+      - name: login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       # Note: if a new package is created using this workflow, then the package
       # visibility will default to the source repository visbility. For example,
       # a package created by a workflow in a public repo will also be public.
       # Publicly visible container packages are anonymously downloadable.
       - name: push to GitHub Container Registry
-        if: ${{ env.IMAGE_EXISTS == 'false' }}
         run: docker push "${{ env.DATA_IMAGE_PATH }}"
 
-      # TODO - move into job that pulls image from remote repository
+  run-e2e-tests:
+    needs:
+      - check-for-image
+      - build-image
+    if: ${{ needs.check-for-image.result == 'success' && (needs.build-image.result == 'success' || needs.build-image.result == 'skipped')}}
+    timeout-minutes: 60
+    runs-on: ubuntu-20.04
+    permissions:
+      packages: read
+    environment: e2e
+    env:
+      CI: true
+      DOCKER_COMPOSE_PATH: './docker/docker-compose.yml'
+      DATA_IMAGE_PATH: ${{ needs.check-for-image.outputs.DATA_IMAGE_PATH }}
+      DB_USER: ${{ secrets.DB_USER }}
+      DB_PASS: ${{ secrets.DB_PASS }}
+      DB_PORT: ${{ vars.DB_PORT }}
+      DB_NAME: ${{ vars.DB_NAME }}
+    steps:
+      - uses: actions/checkout@v4
+
       - uses: actions/setup-node@v4
         with:
           node-version: 16
@@ -136,12 +177,14 @@ jobs:
       - name: install Playwright Browsers
         run: npx playwright install --with-deps
 
+      - name: login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: start database, server, and app
-        env:
-          DB_USER: ${{ secrets.DB_USER }}
-          DB_PASS: ${{ secrets.DB_PASS }}
-          DB_PORT: ${{ vars.DB_PORT }}
-          DB_NAME: ${{ vars.DB_NAME }}
         run: |
           echo "==> start database and data containers"
           docker-compose -f "${{ env.DOCKER_COMPOSE_PATH }}" up -d
@@ -158,11 +201,6 @@ jobs:
         run: npx playwright test
 
       - name: clean up database, server, and app
-        env:
-          DB_USER: ${{ secrets.DB_USER }}
-          DB_PASS: ${{ secrets.DB_PASS }}
-          DB_PORT: ${{ vars.DB_PORT }}
-          DB_NAME: ${{ vars.DB_NAME }}
         run: |
           echo "==> stop app"
           pid=$(lsof -i :3000 -t) && kill ${pid}
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 365f23f5..41ba0461 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -27,7 +27,7 @@ COPY "${LOCAL_CREATE_INDEXES_PATH}" "${CREATE_INDEXES_FILE}"
 RUN chmod +x "${IMPORT_DATA_FILE}"
 RUN chmod +x "${CREATE_INDEXES_FILE}"
 
-# Add label for GHCR source repo
+# Add GHCR labels
 LABEL org.opencontainers.image.source="${SOURCE_REPO}"
 LABEL org.opencontainers.image.description="${DESCRIPTION}"
 

From 71d831670de810d99115a40ac5e84cda77b9e129 Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Thu, 13 Jun 2024 14:15:46 -0700
Subject: [PATCH 07/33] AG-1472: handle case where package has not yet been
 created

---
 .github/workflows/e2e.yml | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index 56fa11e6..891cbac6 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -60,8 +60,19 @@ jobs:
           DATA_IMAGE_TAG: ${{ steps.get-ids-from-package-json.outputs.DATA_IMAGE_TAG }}
         run: |
           GH_PATH=$( [[ "${{ env.NAMESPACE }}" == "${{ env.ORG_NAME }}" ]] && echo "${{ env.ORG_PATH }}" || echo "${{ env.USER_PATH }}" )
+
+          # allow errror to handle case where gh throws an error when package has not yet been created
+          set +e
           IMAGE_VERSIONS=$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" "${GH_PATH}")
-          IMAGE_EXISTS=$(echo "${IMAGE_VERSIONS}" | jq '[.[] | select(any(.metadata.container.tags[]; . == "${{ env.DATA_IMAGE_TAG }}"))] | length > 0')
+          set -e
+
+          PACKAGE_NOT_FOUND=$(echo "${IMAGE_VERSIONS}" | jq '.message? == "Not Found"')
+          if [[ "${PACKAGE_NOT_FOUND}" == "true" ]]; then 
+            IMAGE_EXISTS="false"
+          else
+            IMAGE_EXISTS=$(echo "${IMAGE_VERSIONS}" | jq '[.[] | select(any(.metadata.container.tags[]; . == "${{ env.DATA_IMAGE_TAG }}"))] | length > 0')
+          fi
+
           echo "IMAGE_EXISTS=${IMAGE_EXISTS}" >> "$GITHUB_OUTPUT"
 
   build-image:

From 072d0fcbc1dc44fd19f1a40be82ee393c73bf14c Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Thu, 13 Jun 2024 14:39:45 -0700
Subject: [PATCH 08/33] AG-1472: remove forward slash from package name so gh
 call works

---
 .github/workflows/e2e.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index 891cbac6..2f335c4a 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -16,7 +16,7 @@ jobs:
       packages: read
     environment: e2e
     env:
-      DATA_IMAGE_NAME: '${{ vars.DB_NAME }}/data'
+      DATA_IMAGE_NAME: '${{ vars.DB_NAME }}-data'
     outputs:
       DATA_MANIFEST_ID: ${{ steps.get-ids-from-package-json.outputs.DATA_MANIFEST_ID }}
       DATA_VERSION: ${{ steps.get-ids-from-package-json.outputs.DATA_VERSION }}
@@ -66,7 +66,7 @@ jobs:
           IMAGE_VERSIONS=$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" "${GH_PATH}")
           set -e
 
-          PACKAGE_NOT_FOUND=$(echo "${IMAGE_VERSIONS}" | jq '.message? == "Not Found"')
+          PACKAGE_NOT_FOUND=$(echo "${IMAGE_VERSIONS}" | jq '.message? == "Package not found."')
           if [[ "${PACKAGE_NOT_FOUND}" == "true" ]]; then 
             IMAGE_EXISTS="false"
           else

From 48b4d5a33892756af126c13e8838486cf9c9a87d Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Thu, 13 Jun 2024 16:36:32 -0700
Subject: [PATCH 09/33] AG-1472: ensure e2e tests are run when image has
 already been built

---
 .github/workflows/e2e.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index 2f335c4a..a3f14900 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -161,7 +161,9 @@ jobs:
     needs:
       - check-for-image
       - build-image
-    if: ${{ needs.check-for-image.result == 'success' && (needs.build-image.result == 'success' || needs.build-image.result == 'skipped')}}
+    # always() prevents skipping this job when build-image was skipped
+    # see https://github.com/actions/runner/issues/491
+    if: ${{ always() && needs.check-for-image.result == 'success' && (needs.build-image.result == 'success' || needs.build-image.result == 'skipped')}}
     timeout-minutes: 60
     runs-on: ubuntu-20.04
     permissions:

From ca3242fd1a73d87cec96dd4b8d429dfc127e41d0 Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Fri, 14 Jun 2024 11:34:13 -0700
Subject: [PATCH 10/33] AG-1472: improvements from code review

---
 .github/workflows/e2e.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index a3f14900..10eceabd 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -1,9 +1,6 @@
 name: Build Data Image and Run End-to-end Tests
 
 on: push
-env:
-  ORG_NAME: 'Sage-Bionetworks'
-  NAMESPACE: ${{ github.repository_owner }}
 
 jobs:
   check-for-image:
@@ -16,6 +13,8 @@ jobs:
       packages: read
     environment: e2e
     env:
+      ORG_NAME: 'Sage-Bionetworks'
+      NAMESPACE: ${{ github.repository_owner }}
       DATA_IMAGE_NAME: '${{ vars.DB_NAME }}-data'
     outputs:
       DATA_MANIFEST_ID: ${{ steps.get-ids-from-package-json.outputs.DATA_MANIFEST_ID }}
@@ -61,7 +60,7 @@ jobs:
         run: |
           GH_PATH=$( [[ "${{ env.NAMESPACE }}" == "${{ env.ORG_NAME }}" ]] && echo "${{ env.ORG_PATH }}" || echo "${{ env.USER_PATH }}" )
 
-          # allow errror to handle case where gh throws an error when package has not yet been created
+          # allow error to handle case where gh throws an error when package has not yet been created
           set +e
           IMAGE_VERSIONS=$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" "${GH_PATH}")
           set -e
@@ -135,7 +134,7 @@ jobs:
           docker build \
           -t "${{ env.DATA_IMAGE_PATH }}" \
           -f "${{ env.DOCKERFILE_PATH }}" \
-          --build-arg SOURCE_REPO="https://github.com/${{ env.NAMESPACE }}/${{ vars.DB_NAME }}" \
+          --build-arg SOURCE_REPO="https://github.com/${{ github.repository }}" \
           --build-arg DESCRIPTION="${GITHUB_SHA::7}" \
           --build-arg LOCAL_DATA_PATH="${{ env.LOCAL_DATA_PATH }}" \
           --build-arg LOCAL_COLLECTIONS_PATH="${{ env.LOCAL_COLLECTIONS_PATH }}" \
@@ -151,7 +150,7 @@ jobs:
           password: ${{ secrets.GITHUB_TOKEN }}
 
       # Note: if a new package is created using this workflow, then the package
-      # visibility will default to the source repository visbility. For example,
+      # visibility will default to the source repository visibility. For example,
       # a package created by a workflow in a public repo will also be public.
       # Publicly visible container packages are anonymously downloadable.
       - name: push to GitHub Container Registry

From ec54f2db6e7f4b35f0704e82bb40a31f0d106695 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 14 Jun 2024 19:56:13 +0000
Subject: [PATCH 11/33] Bump braces from 3.0.2 to 3.0.3

Bumps [braces](https://github.com/micromatch/braces) from 3.0.2 to 3.0.3.
- [Changelog](https://github.com/micromatch/braces/blob/master/CHANGELOG.md)
- [Commits](https://github.com/micromatch/braces/compare/3.0.2...3.0.3)

---
updated-dependencies:
- dependency-name: braces
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 package-lock.json | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 56d6ebd7..bd50cc38 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -7076,11 +7076,11 @@
       }
     },
     "node_modules/braces": {
-      "version": "3.0.2",
-      "resolved": "https://registry.npmjs.org/braces/-/braces-3.0.2.tgz",
-      "integrity": "sha512-b8um+L1RzM3WDSzvhm6gIz1yfTbBt6YTlcEKAvsmqCZZFw46z626lVj9j1yEPW33H5H+lBQpZMP1k8l+78Ha0A==",
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/braces/-/braces-3.0.3.tgz",
+      "integrity": "sha512-yQbXgO/OSZVD2IsiLlro+7Hf6Q18EJrKSEsdoMzKePKXct3gvD8oLcOQdIzGupr5Fj+EDe8gO/lxc1BzfMpxvA==",
       "dependencies": {
-        "fill-range": "^7.0.1"
+        "fill-range": "^7.1.1"
       },
       "engines": {
         "node": ">=8"
@@ -11512,9 +11512,9 @@
       "integrity": "sha512-P9bmyZ3h/PRG+Nzga+rbdI4OEpNDzAVyy74uVO9ATgzLK6VtAsYybF/+TOCvrc0MO793d6+42lLyZTw7/ArVzA=="
     },
     "node_modules/fill-range": {
-      "version": "7.0.1",
-      "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.0.1.tgz",
-      "integrity": "sha512-qOo9F+dMUmC2Lcb4BbVvnKJxTPjCm+RRpe4gDuGrzkL7mEVl/djYSu2OdQ2Pa302N4oqkSg9ir6jaLWJ2USVpQ==",
+      "version": "7.1.1",
+      "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.1.1.tgz",
+      "integrity": "sha512-YsGpe3WHLK8ZYi4tWDg2Jy3ebRz2rXowDxnld4bkQB00cc/1Zw9AWnC0i9ztDJitivtQvaI9KaLyKrc+hBW0yg==",
       "dependencies": {
         "to-regex-range": "^5.0.1"
       },
@@ -27995,11 +27995,11 @@
       }
     },
     "braces": {
-      "version": "3.0.2",
-      "resolved": "https://registry.npmjs.org/braces/-/braces-3.0.2.tgz",
-      "integrity": "sha512-b8um+L1RzM3WDSzvhm6gIz1yfTbBt6YTlcEKAvsmqCZZFw46z626lVj9j1yEPW33H5H+lBQpZMP1k8l+78Ha0A==",
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/braces/-/braces-3.0.3.tgz",
+      "integrity": "sha512-yQbXgO/OSZVD2IsiLlro+7Hf6Q18EJrKSEsdoMzKePKXct3gvD8oLcOQdIzGupr5Fj+EDe8gO/lxc1BzfMpxvA==",
       "requires": {
-        "fill-range": "^7.0.1"
+        "fill-range": "^7.1.1"
       }
     },
     "brorand": {
@@ -31344,9 +31344,9 @@
       "integrity": "sha512-P9bmyZ3h/PRG+Nzga+rbdI4OEpNDzAVyy74uVO9ATgzLK6VtAsYybF/+TOCvrc0MO793d6+42lLyZTw7/ArVzA=="
     },
     "fill-range": {
-      "version": "7.0.1",
-      "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.0.1.tgz",
-      "integrity": "sha512-qOo9F+dMUmC2Lcb4BbVvnKJxTPjCm+RRpe4gDuGrzkL7mEVl/djYSu2OdQ2Pa302N4oqkSg9ir6jaLWJ2USVpQ==",
+      "version": "7.1.1",
+      "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.1.1.tgz",
+      "integrity": "sha512-YsGpe3WHLK8ZYi4tWDg2Jy3ebRz2rXowDxnld4bkQB00cc/1Zw9AWnC0i9ztDJitivtQvaI9KaLyKrc+hBW0yg==",
       "requires": {
         "to-regex-range": "^5.0.1"
       }

From faac5943f037fb222c43264059bcae122852b051 Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Fri, 14 Jun 2024 13:08:46 -0700
Subject: [PATCH 12/33] AG-1472: ensure org package is lowercase

---
 .github/workflows/e2e.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index 10eceabd..e5bebde0 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -38,7 +38,9 @@ jobs:
           DATA_IMAGE_TAG="${DATA_MANIFEST_ID}.${DATA_VERSION}"
           echo "DATA_IMAGE_TAG=${DATA_IMAGE_TAG}" >> "$GITHUB_OUTPUT"
 
-          DATA_IMAGE_PATH="ghcr.io/${{ env.NAMESPACE }}/${{ env.DATA_IMAGE_NAME }}:${DATA_IMAGE_TAG}"
+          # GHCR requires image names to be lowercase: https://github.com/orgs/community/discussions/27086
+          NAMESPACE_LOWERCASE=$(echo "${{ env.NAMESPACE }}" | tr '[:upper:]' '[:lower:]')
+          DATA_IMAGE_PATH="ghcr.io/${NAMESPACE_LOWERCASE}/${{ env.DATA_IMAGE_NAME }}:${DATA_IMAGE_TAG}"
           echo "DATA_IMAGE_PATH=${DATA_IMAGE_PATH}" >> "$GITHUB_OUTPUT"
 
       - name: login to GitHub Container Registry

From 194503281aeeab84f3f585138ce04ee49d001d68 Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Fri, 14 Jun 2024 14:59:33 -0700
Subject: [PATCH 13/33] AG-1498: support use of containerized data image in
 local development [skip ci]

---
 .env.example              |  5 +++++
 .gitignore                |  4 ++++
 README.md                 | 42 +++++++++++++++++++++++++++++++++------
 docker/README.md          |  4 ++--
 docker/docker-compose.yml |  1 +
 package.json              |  8 +++++++-
 6 files changed, 55 insertions(+), 9 deletions(-)
 create mode 100644 .env.example

diff --git a/.env.example b/.env.example
new file mode 100644
index 00000000..6f395adf
--- /dev/null
+++ b/.env.example
@@ -0,0 +1,5 @@
+DB_USER="root"
+DB_PASS="${DB_PASS}"
+DB_PORT="27015"
+DB_NAME="agora"
+DATA_IMAGE_PATH="ghcr.io/sage-bionetworks/agora-data:${DATA_IMAGE_TAG}"
diff --git a/.gitignore b/.gitignore
index dc4ac05b..38f0ccaf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -48,3 +48,7 @@ testem.log
 # System files
 .DS_Store
 Thumbs.db
+
+# Environment file
+.env
+
diff --git a/README.md b/README.md
index e867757c..1ff11469 100644
--- a/README.md
+++ b/README.md
@@ -35,7 +35,11 @@ cd Agora
 npm install
 ```
 
-### 2 - Create database
+The next sections focus on setting up a mongo database loaded with Agora's data. There are two options: 
+ - Use a local mongo database that you manually create and populate with data (steps 2-5) 
+ - Use a containerized mongo database that is pre-populated with data (step 6)
+
+### 2 - Create local database
 
 You will need to create a MongoDB database and name it `agora`. 
 
@@ -53,7 +57,7 @@ npm run mongo:start
 npm run mongo:start:windows
 ```
 
-### 3 - Populate database
+### 3 - Populate local database
 
 Agora's data is stored in json files in the [Agora Synapse project](https://www.synapse.org/#!Synapse:syn11850457/files/), in the following subfolders:
 * [Agora Live Data](https://www.synapse.org/#!Synapse:syn12177492) - This folder contains all production data releases, as well as data releases that were never released to production
@@ -148,14 +152,14 @@ npm run mongo:create:indexes
 
 You'll need `Linux` to run the previous scripts. If you need to do this in `Windows`, you can get any `Linux` distribution at the `Windows Store` (e.g. `Ubuntu`).
 
-### 4 - Build
+### 4 - Build using local database
 
 ```bash
 # Build the server and app
 npm run dev
 ```
 
-### 5 - Start
+### 5 - Start using local database
 
 ```bash
 # Start the server and app
@@ -164,6 +168,32 @@ npm run start
 
 Go to [http://localhost:8080](http://localhost:8080)
 
+### 6 - Use containerized database
+
+1. Install Docker, if necessary.
+2. Update `data-file` and `data-version` in `package.json` to reflect the desired data release version, if necessary.
+3. Create an environment file: `npm run create-env`. 
+4. Start the containerized database: `npm run docker:db:start`. The necessary images will be pulled from GHCR. If you would like to use a different image, update DATA_IMAGE_PATH in .env. If the desired image does not exist, see steps below to create the desired image.
+5. Run the server and app against the containerized database: `npm run docker:dev`.
+6. Stop the containerized database: `npm run docker:db:stop`.
+
+#### Creating an image for a new data release
+
+A "data release" is defined in the `package.json` by the `data-file` and `data-version` values. Images pre-loaded with data from the data release are created when the `e2e.yml` GitHub Action workflow runs and are pushed to the GitHub Container Registry (GHCR) package for that namespace -- the `sage-bionetworks` organization namespace when the workflow runs in the base repo or in the user's namespace (e.g. `hallieswan`) when running in a forked repo.
+
+The `sage-bionetworks` package will contain images for data releases that have been specified in `package.json` on `develop` or `main`. The user's package will contain images for data releases that have been specified in `package.json` in branches pushed to their fork. 
+
+If a dev needs to create an image for a data release that does not yet exist in the Sage-Bionetworks package, they should follow these steps: 
+
+1. Create a new branch.
+2. Update the `package.json` to reflect the appropriate `data-file` and `data-version` files.
+3. If necessary, update `./scripts/collections.csv` to specify new collections and `./scripts/mongo-create-Indexes.js` to specify new indexes.
+4. Commit the changes.
+5. Push the changes to your remote fork to trigger a run of the `e2e.yml` workflow. 
+6. The new image will be available in your user namespaced GHCR package, e.g. `https://github.com/hallieswan/Agora/pkgs/container/agora-data`.
+7. Update your local `.env` file so `DATA_IMAGE_PATH` points to the newly created image, e.g. `ghcr.io/hallieswan/agora-data:syn13363290.68`.
+8. Start the containerized database: `npm run docker:db:start`.
+
 # Development
 
 ```bash
@@ -183,7 +213,7 @@ npm run test
 npm run test:watch
 
 # Run end-to-end tests (requires build)
-npm run test:e2e
+npm run e2e
 ```
 
 # Deployment
@@ -206,7 +236,7 @@ npm run test
 npm run build
 
 # Run end-to-end tests
-npm run test:e2e
+npm run e2e
 
 # Go to localhost:8080 and verify the app is running without errors
 npm run start
diff --git a/docker/README.md b/docker/README.md
index b832dd85..2ef4cf2b 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -2,8 +2,8 @@
 
 Files in this directory:
 
-- `Dockerfile`: creates the `agora/data` docker image, which contains data for a particular Agora data release (manifest synId + version) and team images and will seed a mongodb at start up using `import-data.sh`
-- `docker-compose.yml`: spins up `mongo` and `agora/data` docker containers
+- `Dockerfile`: creates the `agora-data` docker image, which contains data for a particular Agora data release (manifest synId + version) and team images and will seed a mongodb at start up using `import-data.sh`
+- `docker-compose.yml`: spins up `mongo` and `agora-data` docker containers
 
 ## Workflow Setup
 
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
index a1c1afc2..0a7aae29 100644
--- a/docker/docker-compose.yml
+++ b/docker/docker-compose.yml
@@ -11,6 +11,7 @@ services:
       - MONGO_INITDB_DATABASE=${DB_NAME}
   mongo-seed:
     image: ${DATA_IMAGE_PATH}
+    platform: linux/amd64
     depends_on: 
       - mongodb
     environment:
diff --git a/package.json b/package.json
index a92ebd8d..bee07c33 100644
--- a/package.json
+++ b/package.json
@@ -40,7 +40,13 @@
     "data:local": "npm run clean:data && sh ./scripts/get-data-local.sh",
     "e2e": "playwright test --trace on",
     "e2e:ui": "playwright test --ui",
-    "e2e:update": "npm install -D @playwright/test@latest; npx playwright install --with-deps; npx playwright --version"
+    "e2e:update": "npm install -D @playwright/test@latest; npx playwright install --with-deps; npx playwright --version",
+    "create-env": "DB_PASS=$(openssl rand -base64 12) DATA_IMAGE_TAG=$(npm run docker:data-image-tag -s) envsubst < .env.example > .env",
+    "docker:data-image-tag": "jq -r '.\"data-file\" + \".\" + .\"data-version\"' package.json",
+    "docker:db:seed-complete": "echo 'Waiting for docker db to finish loading data (~30s)....'; DATA_CONTAINER=$(docker compose --env-file .env -f ./docker/docker-compose.yml ps -a --format '{{.Name}}' mongo-seed); docker wait ${DATA_CONTAINER}",
+    "docker:db:start": "docker-compose --env-file .env -f ./docker/docker-compose.yml up -d; npm run docker:db:seed-complete",
+    "docker:db:stop": "docker-compose --env-file .env -f ./docker/docker-compose.yml down",
+    "docker:dev": "set -a; source .env; set +a; MONGODB_HOST=\"localhost\" MONGODB_PORT=\"${DB_PORT}\" APP_ENV=\"e2e\" npm run dev"
   },
   "pre-commit": [
     "test"

From 70595259522e7e13370ce0953f3df6c6f59a7cd8 Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Mon, 17 Jun 2024 14:04:29 -0700
Subject: [PATCH 14/33] AG-1330: combine workflows into one workflow with
 multiple jobs

---
 .github/workflows/{e2e.yml => ci.yml} | 18 ++++++++-
 .github/workflows/node.js.yml         | 55 ---------------------------
 2 files changed, 16 insertions(+), 57 deletions(-)
 rename .github/workflows/{e2e.yml => ci.yml} (95%)
 delete mode 100644 .github/workflows/node.js.yml

diff --git a/.github/workflows/e2e.yml b/.github/workflows/ci.yml
similarity index 95%
rename from .github/workflows/e2e.yml
rename to .github/workflows/ci.yml
index e5bebde0..bf85cac5 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/ci.yml
@@ -1,8 +1,21 @@
-name: Build Data Image and Run End-to-end Tests
+name: Build and run unit tests, build data image and run e2e tests
 
 on: push
 
 jobs:
+  build-and-run-unit-tests:
+    timeout-minutes: 60
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 16
+          cache: 'npm'
+      - run: npm ci
+      - run: APP_ENV=develop npm run ci:build:develop
+      - run: npm test
+
   check-for-image:
     # Run in Sage repo on develop or main branches
     # and on all branches in user-owned forks
@@ -184,9 +197,10 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version: 16
+          cache: 'npm'
 
       - name: install dependencies
-        run: npm install
+        run: npm ci
 
       - name: install Playwright Browsers
         run: npx playwright install --with-deps
diff --git a/.github/workflows/node.js.yml b/.github/workflows/node.js.yml
deleted file mode 100644
index d8172629..00000000
--- a/.github/workflows/node.js.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-nodejs
-
-name: Node.js CI
-
-on:
-  push:
-    branches: [ develop, main ]
-  pull_request:
-    branches: [ develop, main ]
-
-jobs:
-  build:
-    timeout-minutes: 60
-    
-    runs-on: ubuntu-latest
-
-    strategy:
-      matrix:
-        node-version: [16.x]
-        # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
-    # Allow OIDC Integration (so we can assume the AWS role to deploy)
-    # permissions:
-    #   id-token: write
-    #   contents: read
-    steps:
-    - uses: actions/checkout@v3
-    - name: Use Node.js ${{ matrix.node-version }}
-      uses: actions/setup-node@v3
-      with:
-        node-version: ${{ matrix.node-version }}
-        cache: 'npm'
-    - run: npm ci
-    - run: APP_ENV=develop npm run ci:build:develop
-    # Background dev server
-    # - run: npm run dev &
-    - run: npm test
-
-    # - name: Configure AWS Credentials
-    #   uses: aws-actions/configure-aws-credentials@v4
-    #   with:
-    #     aws-region: "us-east-1"
-    #     role-to-assume: "arn:aws:iam::607346494281:role/sagebase-github-oidc-agora-eb-deploy"
-    #     role-session-name: GitHubActions-${{ github.repository_owner }}-${{ github.event.repository.name }}-${{ github.run_id }}
-    #     role-duration-seconds: 1200
-    # - name: Install Playwright Browsers
-    #   run: npx playwright install --with-deps
-    # - name: Run Playwright tests
-    #   run: npx playwright test
-    # - uses: actions/upload-artifact@v3
-    #   if: always()
-    #   with:
-    #     name: playwright-report
-    #     path: playwright-report/
-    #     retention-days: 30

From 24cc20d7bbfa44b6bbd92494059550a18bf25c83 Mon Sep 17 00:00:00 2001
From: Hallie Swan <26949006+hallieswan@users.noreply.github.com>
Date: Thu, 27 Jun 2024 09:18:34 -0700
Subject: [PATCH 15/33] AG-1518: rename data release image to distinguish from
 sage-monorepo image

---
 .env.example             | 2 +-
 .github/workflows/ci.yml | 2 +-
 README.md                | 8 ++++----
 docker/README.md         | 6 +++---
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.env.example b/.env.example
index 6f395adf..c0dc0e5b 100644
--- a/.env.example
+++ b/.env.example
@@ -2,4 +2,4 @@ DB_USER="root"
 DB_PASS="${DB_PASS}"
 DB_PORT="27015"
 DB_NAME="agora"
-DATA_IMAGE_PATH="ghcr.io/sage-bionetworks/agora-data:${DATA_IMAGE_TAG}"
+DATA_IMAGE_PATH="ghcr.io/sage-bionetworks/agora-data-nonmonorepo:${DATA_IMAGE_TAG}"
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bf85cac5..f077db93 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
     env:
       ORG_NAME: 'Sage-Bionetworks'
       NAMESPACE: ${{ github.repository_owner }}
-      DATA_IMAGE_NAME: '${{ vars.DB_NAME }}-data'
+      DATA_IMAGE_NAME: '${{ vars.DB_NAME }}-data-nonmonorepo'
     outputs:
       DATA_MANIFEST_ID: ${{ steps.get-ids-from-package-json.outputs.DATA_MANIFEST_ID }}
       DATA_VERSION: ${{ steps.get-ids-from-package-json.outputs.DATA_VERSION }}
diff --git a/README.md b/README.md
index 1ff11469..1ac18756 100644
--- a/README.md
+++ b/README.md
@@ -179,7 +179,7 @@ Go to [http://localhost:8080](http://localhost:8080)
 
 #### Creating an image for a new data release
 
-A "data release" is defined in the `package.json` by the `data-file` and `data-version` values. Images pre-loaded with data from the data release are created when the `e2e.yml` GitHub Action workflow runs and are pushed to the GitHub Container Registry (GHCR) package for that namespace -- the `sage-bionetworks` organization namespace when the workflow runs in the base repo or in the user's namespace (e.g. `hallieswan`) when running in a forked repo.
+A "data release" is defined in the `package.json` by the `data-file` and `data-version` values. Images pre-loaded with data from the data release are created when the `ci.yml` GitHub Action workflow runs and are pushed to the GitHub Container Registry (GHCR) package for that namespace -- the `sage-bionetworks` organization namespace when the workflow runs in the base repo or in the user's namespace (e.g. `hallieswan`) when running in a forked repo.
 
 The `sage-bionetworks` package will contain images for data releases that have been specified in `package.json` on `develop` or `main`. The user's package will contain images for data releases that have been specified in `package.json` in branches pushed to their fork. 
 
@@ -189,9 +189,9 @@ If a dev needs to create an image for a data release that does not yet exist in
 2. Update the `package.json` to reflect the appropriate `data-file` and `data-version` files.
 3. If necessary, update `./scripts/collections.csv` to specify new collections and `./scripts/mongo-create-Indexes.js` to specify new indexes.
 4. Commit the changes.
-5. Push the changes to your remote fork to trigger a run of the `e2e.yml` workflow. 
-6. The new image will be available in your user namespaced GHCR package, e.g. `https://github.com/hallieswan/Agora/pkgs/container/agora-data`.
-7. Update your local `.env` file so `DATA_IMAGE_PATH` points to the newly created image, e.g. `ghcr.io/hallieswan/agora-data:syn13363290.68`.
+5. Push the changes to your remote fork to trigger a run of the `ci.yml` workflow. 
+6. The new image will be available in your user namespaced GHCR package, e.g. `https://github.com/hallieswan/Agora/pkgs/container/agora-data-nonmonorepo`.
+7. Update your local `.env` file so `DATA_IMAGE_PATH` points to the newly created image, e.g. `ghcr.io/hallieswan/agora-data-nonmonorepo:syn13363290.68`.
 8. Start the containerized database: `npm run docker:db:start`.
 
 # Development
diff --git a/docker/README.md b/docker/README.md
index 2ef4cf2b..78416d8b 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -2,12 +2,12 @@
 
 Files in this directory:
 
-- `Dockerfile`: creates the `agora-data` docker image, which contains data for a particular Agora data release (manifest synId + version) and team images and will seed a mongodb at start up using `import-data.sh`
-- `docker-compose.yml`: spins up `mongo` and `agora-data` docker containers
+- `Dockerfile`: creates the `agora-data-nonmonorepo` docker image, which contains data for a particular Agora data release (manifest synId + version) and team images and will seed a mongodb at start up using `import-data.sh`
+- `docker-compose.yml`: spins up `mongo` and `agora-data-nonmonorepo` docker containers
 
 ## Workflow Setup
 
-The following secrets and variables need to be set up in GitHub for the `e2e.yml` workflow to create the `agora/data` Docker image:
+The following secrets and variables need to be set up in GitHub for the `ci.yml` workflow to create the `agora-data-nonmonorepo` Docker image:
 
 e2e Environment secrets:
 

From b4392b501c5e17b2978454692f18023277bd3230 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 7 Aug 2024 21:14:54 +0000
Subject: [PATCH 16/33] Bump fast-xml-parser and @aws-sdk/credential-providers

Bumps [fast-xml-parser](https://github.com/NaturalIntelligence/fast-xml-parser) and [@aws-sdk/credential-providers](https://github.com/aws/aws-sdk-js-v3/tree/HEAD/packages/credential-providers). These dependencies needed to be updated together.

Updates `fast-xml-parser` from 4.2.5 to 4.4.1
- [Release notes](https://github.com/NaturalIntelligence/fast-xml-parser/releases)
- [Changelog](https://github.com/NaturalIntelligence/fast-xml-parser/blob/master/CHANGELOG.md)
- [Commits](https://github.com/NaturalIntelligence/fast-xml-parser/compare/v4.2.5...v4.4.1)

Updates `@aws-sdk/credential-providers` from 3.398.0 to 3.624.0
- [Release notes](https://github.com/aws/aws-sdk-js-v3/releases)
- [Changelog](https://github.com/aws/aws-sdk-js-v3/blob/main/packages/credential-providers/CHANGELOG.md)
- [Commits](https://github.com/aws/aws-sdk-js-v3/commits/v3.624.0/packages/credential-providers)

---
updated-dependencies:
- dependency-name: fast-xml-parser
  dependency-type: indirect
- dependency-name: "@aws-sdk/credential-providers"
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 package-lock.json | 3642 ++++++++++++++++++++++++---------------------
 1 file changed, 1975 insertions(+), 1667 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index bd50cc38..251c0982 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1181,455 +1181,634 @@
       "integrity": "sha512-H71nDOOL8Y7kWRLqf6Sums+01Q5msqBW2KhDUTemh1tvY04eSkSXrK0uj/4mmY0Xr16/3zyZmsrxN7CKuRbNRg==",
       "dev": true
     },
-    "node_modules/@aws-crypto/crc32": {
-      "version": "3.0.0",
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+          "version": "2.6.3",
+          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.3.tgz",
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           "optional": true
         }
       }
     },
     "@smithy/util-middleware": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/@smithy/util-middleware/-/util-middleware-2.0.0.tgz",
-      "integrity": "sha512-eCWX4ECuDHn1wuyyDdGdUWnT4OGyIzV0LN1xRttBFMPI9Ff/4heSHVxneyiMtOB//zpXWCha1/SWHJOZstG7kA==",
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+      "resolved": "https://registry.npmjs.org/@smithy/util-middleware/-/util-middleware-3.0.3.tgz",
+      "integrity": "sha512-l+StyYYK/eO3DlVPbU+4Bi06Jjal+PFLSMmlWM1BEwyLxZ3aKkf1ROnoIakfaA7mC6uw3ny7JBkau4Yc+5zfWw==",
       "optional": true,
       "requires": {
-        "tslib": "^2.5.0"
+        "@smithy/types": "^3.3.0",
+        "tslib": "^2.6.2"
       },
       "dependencies": {
         "tslib": {
-          "version": "2.6.2",
-          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.2.tgz",
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+          "version": "2.6.3",
+          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.3.tgz",
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           "optional": true
         }
       }
     },
     "@smithy/util-retry": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/@smithy/util-retry/-/util-retry-2.0.0.tgz",
-      "integrity": "sha512-/dvJ8afrElasuiiIttRJeoS2sy8YXpksQwiM/TcepqdRVp7u4ejd9C4IQURHNjlfPUT7Y6lCDSa2zQJbdHhVTg==",
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/@smithy/util-retry/-/util-retry-3.0.3.tgz",
+      "integrity": "sha512-AFw+hjpbtVApzpNDhbjNG5NA3kyoMs7vx0gsgmlJF4s+yz1Zlepde7J58zpIRIsdjc+emhpAITxA88qLkPF26w==",
       "optional": true,
       "requires": {
-        "@smithy/service-error-classification": "^2.0.0",
-        "tslib": "^2.5.0"
+        "@smithy/service-error-classification": "^3.0.3",
+        "@smithy/types": "^3.3.0",
+        "tslib": "^2.6.2"
       },
       "dependencies": {
         "tslib": {
-          "version": "2.6.2",
-          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.2.tgz",
-          "integrity": "sha512-AEYxH93jGFPn/a2iVAwW87VuUIkR1FVUKB77NwMF7nBTDkDrrT/Hpt/IrCJ0QXhW27jTBDcf5ZY7w6RiqTMw2Q==",
+          "version": "2.6.3",
+          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.3.tgz",
+          "integrity": "sha512-xNvxJEOUiWPGhUuUdQgAJPKOOJfGnIyKySOc09XkKsgdUV/3E2zvwZYdejjmRgPCgcym1juLH3226yA7sEFJKQ==",
           "optional": true
         }
       }
     },
     "@smithy/util-stream": {
-      "version": "2.0.5",
-      "resolved": "https://registry.npmjs.org/@smithy/util-stream/-/util-stream-2.0.5.tgz",
-      "integrity": "sha512-ylx27GwI05xLpYQ4hDIfS15vm+wYjNN0Sc2P0FxuzgRe8v0BOLHppGIQ+Bezcynk8C9nUzsUue3TmtRhjut43g==",
+      "version": "3.1.3",
+      "resolved": "https://registry.npmjs.org/@smithy/util-stream/-/util-stream-3.1.3.tgz",
+      "integrity": "sha512-FIv/bRhIlAxC0U7xM1BCnF2aDRPq0UaelqBHkM2lsCp26mcBbgI0tCVTv+jGdsQLUmAMybua/bjDsSu8RQHbmw==",
       "optional": true,
       "requires": {
-        "@smithy/fetch-http-handler": "^2.0.5",
-        "@smithy/node-http-handler": "^2.0.5",
-        "@smithy/types": "^2.2.2",
-        "@smithy/util-base64": "^2.0.0",
-        "@smithy/util-buffer-from": "^2.0.0",
-        "@smithy/util-hex-encoding": "^2.0.0",
-        "@smithy/util-utf8": "^2.0.0",
-        "tslib": "^2.5.0"
+        "@smithy/fetch-http-handler": "^3.2.4",
+        "@smithy/node-http-handler": "^3.1.4",
+        "@smithy/types": "^3.3.0",
+        "@smithy/util-base64": "^3.0.0",
+        "@smithy/util-buffer-from": "^3.0.0",
+        "@smithy/util-hex-encoding": "^3.0.0",
+        "@smithy/util-utf8": "^3.0.0",
+        "tslib": "^2.6.2"
       },
       "dependencies": {
         "tslib": {
-          "version": "2.6.2",
-          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.2.tgz",
-          "integrity": "sha512-AEYxH93jGFPn/a2iVAwW87VuUIkR1FVUKB77NwMF7nBTDkDrrT/Hpt/IrCJ0QXhW27jTBDcf5ZY7w6RiqTMw2Q==",
+          "version": "2.6.3",
+          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.3.tgz",
+          "integrity": "sha512-xNvxJEOUiWPGhUuUdQgAJPKOOJfGnIyKySOc09XkKsgdUV/3E2zvwZYdejjmRgPCgcym1juLH3226yA7sEFJKQ==",
           "optional": true
         }
       }
     },
     "@smithy/util-uri-escape": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/@smithy/util-uri-escape/-/util-uri-escape-2.0.0.tgz",
-      "integrity": "sha512-ebkxsqinSdEooQduuk9CbKcI+wheijxEb3utGXkCoYQkJnwTnLbH1JXGimJtUkQwNQbsbuYwG2+aFVyZf5TLaw==",
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/@smithy/util-uri-escape/-/util-uri-escape-3.0.0.tgz",
+      "integrity": "sha512-LqR7qYLgZTD7nWLBecUi4aqolw8Mhza9ArpNEQ881MJJIU2sE5iHCK6TdyqqzcDLy0OPe10IY4T8ctVdtynubg==",
       "optional": true,
       "requires": {
-        "tslib": "^2.5.0"
+        "tslib": "^2.6.2"
       },
       "dependencies": {
         "tslib": {
-          "version": "2.6.2",
-          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.2.tgz",
-          "integrity": "sha512-AEYxH93jGFPn/a2iVAwW87VuUIkR1FVUKB77NwMF7nBTDkDrrT/Hpt/IrCJ0QXhW27jTBDcf5ZY7w6RiqTMw2Q==",
+          "version": "2.6.3",
+          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.3.tgz",
+          "integrity": "sha512-xNvxJEOUiWPGhUuUdQgAJPKOOJfGnIyKySOc09XkKsgdUV/3E2zvwZYdejjmRgPCgcym1juLH3226yA7sEFJKQ==",
           "optional": true
         }
       }
     },
     "@smithy/util-utf8": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/@smithy/util-utf8/-/util-utf8-2.0.0.tgz",
-      "integrity": "sha512-rctU1VkziY84n5OXe3bPNpKR001ZCME2JCaBBFgtiM2hfKbHFudc/BkMuPab8hRbLd0j3vbnBTTZ1igBf0wgiQ==",
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/@smithy/util-utf8/-/util-utf8-3.0.0.tgz",
+      "integrity": "sha512-rUeT12bxFnplYDe815GXbq/oixEGHfRFFtcTF3YdDi/JaENIM6aSYYLJydG83UNzLXeRI5K8abYd/8Sp/QM0kA==",
       "optional": true,
       "requires": {
-        "@smithy/util-buffer-from": "^2.0.0",
-        "tslib": "^2.5.0"
+        "@smithy/util-buffer-from": "^3.0.0",
+        "tslib": "^2.6.2"
       },
       "dependencies": {
         "tslib": {
-          "version": "2.6.2",
-          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.2.tgz",
-          "integrity": "sha512-AEYxH93jGFPn/a2iVAwW87VuUIkR1FVUKB77NwMF7nBTDkDrrT/Hpt/IrCJ0QXhW27jTBDcf5ZY7w6RiqTMw2Q==",
+          "version": "2.6.3",
+          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.6.3.tgz",
+          "integrity": "sha512-xNvxJEOUiWPGhUuUdQgAJPKOOJfGnIyKySOc09XkKsgdUV/3E2zvwZYdejjmRgPCgcym1juLH3226yA7sEFJKQ==",
           "optional": true
         }
       }
@@ -31279,9 +31587,9 @@
       "dev": true
     },
     "fast-xml-parser": {
-      "version": "4.2.5",
-      "resolved": "https://registry.npmjs.org/fast-xml-parser/-/fast-xml-parser-4.2.5.tgz",
-      "integrity": "sha512-B9/wizE4WngqQftFPmdaMYlXoJlJOYxGQOanC77fq9k8+Z0v5dDSVh+3glErdIROP//s/jgb7ZuxKfB8nVyo0g==",
+      "version": "4.4.1",
+      "resolved": "https://registry.npmjs.org/fast-xml-parser/-/fast-xml-parser-4.4.1.tgz",
+      "integrity": "sha512-xkjOecfnKGkSsOwtZ5Pz7Us/T6mrbPQrq0nh+aCO5V9nk5NLWmasAHumTKjiPJPWANe+kAZ84Jc8ooJkzZ88Sw==",
       "optional": true,
       "requires": {
         "strnum": "^1.0.5"
@@ -38710,7 +39018,7 @@
       "version": "8.3.2",
       "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
       "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
-      "devOptional": true
+      "dev": true
     },
     "v8-compile-cache": {
       "version": "2.3.0",

From fd775f926e49ab1b2b4a6e39a85f07a58a9fe4d5 Mon Sep 17 00:00:00 2001
From: Jessica Britton <jessica.britton@sagebase.org>
Date: Fri, 1 Nov 2024 17:18:18 -0700
Subject: [PATCH 17/33] Bump to mv70 (display) in dev

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index bee07c33..a85258d2 100644
--- a/package.json
+++ b/package.json
@@ -2,7 +2,7 @@
   "name": "agora",
   "version": "3.4.0",
   "data-file": "syn13363290",
-  "data-version": "68",
+  "data-version": "79",
   "private": true,
   "scripts": {
     "dev": "concurrently --kill-others \"npm:dev:server\" \"npm:dev:app\"",

From 51b2d4d98ad21f9719023a6822d5c69df9906d2e Mon Sep 17 00:00:00 2001
From: Jessica Britton <jessica.britton@sagebase.org>
Date: Wed, 6 Nov 2024 11:14:55 -0800
Subject: [PATCH 18/33] AG-1395: Fix typo in manifest version value

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index a85258d2..d310d92a 100644
--- a/package.json
+++ b/package.json
@@ -2,7 +2,7 @@
   "name": "agora",
   "version": "3.4.0",
   "data-file": "syn13363290",
-  "data-version": "79",
+  "data-version": "70",
   "private": true,
   "scripts": {
     "dev": "concurrently --kill-others \"npm:dev:server\" \"npm:dev:app\"",

From 38963af3f20f5079c50862e09b99bb640ed7f660 Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Mon, 25 Nov 2024 11:52:32 -0800
Subject: [PATCH 19/33] removed druggability section in gene details resources
 tab

---
 .../gene-resources.component.html             | 28 -------------------
 1 file changed, 28 deletions(-)

diff --git a/src/app/features/genes/components/gene-resources/gene-resources.component.html b/src/app/features/genes/components/gene-resources/gene-resources.component.html
index a3b06208..4f9081be 100644
--- a/src/app/features/genes/components/gene-resources/gene-resources.component.html
+++ b/src/app/features/genes/components/gene-resources/gene-resources.component.html
@@ -1,31 +1,3 @@
-<div *ngIf="gene" class="section">
-  <div class="section-inner pb-0">
-    <div class="container-sm">
-      <div>
-        <h2>
-          Druggability of {{ gene.hgnc_symbol || gene.ensembl_gene_id }}
-        </h2>
-        <p class="druggability-description">
-          AMP-AD pharmaceutical partners scored the tractability of targets
-          using publicly-available resources and have generated ratings of
-          small-molecule druggability, therapeutic antibody feasibility, and
-          safety.
-        </p>
-        <modal-link
-          text="Learn more about the analysis"
-          header="Druggability/Ligandability Information"
-          wikiId="612874"
-        >
-        </modal-link>
-
-        <hr class="separator separator-md" />
-
-        <gene-druggability *ngIf="gene" [gene]="gene"></gene-druggability>
-      </div>
-    </div>
-  </div>
-</div>
-
 <ng-container *ngIf="gene">
   <div *ngIf="gene.is_tep === true || gene.is_adi === true" class="section">
     <div class="section-inner">

From 8ff797841877948bde6de0de46e134a8ae009abf Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Tue, 26 Nov 2024 16:18:31 -0800
Subject: [PATCH 20/33] added new resource cards in Resources tab

---
 .../gene-resources.component.html             |  41 ++++---
 .../gene-resources.component.ts               | 107 ++++++++++++++----
 ...{AdditionalResource.ts => ResourceCard.ts} |   2 +-
 src/app/models/index.ts                       |   2 +-
 4 files changed, 109 insertions(+), 43 deletions(-)
 rename src/app/models/{AdditionalResource.ts => ResourceCard.ts} (69%)

diff --git a/src/app/features/genes/components/gene-resources/gene-resources.component.html b/src/app/features/genes/components/gene-resources/gene-resources.component.html
index a3b06208..f7cf5fca 100644
--- a/src/app/features/genes/components/gene-resources/gene-resources.component.html
+++ b/src/app/features/genes/components/gene-resources/gene-resources.component.html
@@ -1,26 +1,25 @@
 <div *ngIf="gene" class="section">
-  <div class="section-inner pb-0">
+  <div class="section-inner">
     <div class="container-sm">
-      <div>
-        <h2>
-          Druggability of {{ gene.hgnc_symbol || gene.ensembl_gene_id }}
-        </h2>
-        <p class="druggability-description">
-          AMP-AD pharmaceutical partners scored the tractability of targets
-          using publicly-available resources and have generated ratings of
-          small-molecule druggability, therapeutic antibody feasibility, and
-          safety.
-        </p>
-        <modal-link
-          text="Learn more about the analysis"
-          header="Druggability/Ligandability Information"
-          wikiId="612874"
-        >
-        </modal-link>
-
-        <hr class="separator separator-md" />
-
-        <gene-druggability *ngIf="gene" [gene]="gene"></gene-druggability>
+      <h2>
+        Drug Development Resources
+      </h2>
+      <p class="druggability-description">
+        These external sites provide drug development resources.
+      </p>
+      <div 
+        *ngFor="let r of drugDevelopmentResources; let i = index" 
+        class="row tab-row last-row"
+      >
+        <div class="col-md-3 col-sm-8 col-8 header-title">{{ r.title }}</div>
+        <div class="col-md-3 col-sm-4 col-4 text-center header-link">
+          <a class="additional-resource-links link no-bold" href="{{ r.link }}" target="_blank">{{
+            r.linkText
+          }}</a>
+        </div>
+        <div class="col-md-6 col-sm-12 col-12 header-description">
+          {{ r.description }}
+        </div>
       </div>
     </div>
   </div>
diff --git a/src/app/features/genes/components/gene-resources/gene-resources.component.ts b/src/app/features/genes/components/gene-resources/gene-resources.component.ts
index 7af7bff5..0fa53683 100644
--- a/src/app/features/genes/components/gene-resources/gene-resources.component.ts
+++ b/src/app/features/genes/components/gene-resources/gene-resources.component.ts
@@ -1,6 +1,6 @@
 import { Component, Input, OnInit } from '@angular/core';
 
-import { Gene, AdditionalResource } from '../../../../models';
+import { Gene, ResourceCard } from '../../../../models';
 
 @Component({
   selector: 'gene-resources',
@@ -10,7 +10,8 @@ import { Gene, AdditionalResource } from '../../../../models';
 export class GeneResourcesComponent implements OnInit {
   @Input() gene: Gene | undefined;
   
-  additionalResources: AdditionalResource[] = [];
+  additionalResources: ResourceCard[] = [];
+  drugDevelopmentResources: ResourceCard[] = [];
 
   ngOnInit(): void {
     this.init();
@@ -29,7 +30,14 @@ export class GeneResourcesComponent implements OnInit {
       return;
     }
 
-    this.additionalResources = [
+    this.drugDevelopmentResources = [
+      {
+        title: 'Chemical Probes',
+        description:
+          'View expert reviews and evaluations of chemical probes.',
+        linkText: 'Visit Chemical Probes',
+        link: `https://www.chemicalprobes.org/?q=${this.gene?.hgnc_symbol}`,
+      },
       {
         title: 'Open Targets',
         description:
@@ -37,6 +45,13 @@ export class GeneResourcesComponent implements OnInit {
         linkText: 'Visit Open Targets',
         link: `https://platform.opentargets.org/target/${this.gene?.ensembl_gene_id}`,
       },
+      {
+        title: 'PharmGKB',
+        description:
+          'Search PharmGKB for information on gene-drug and gene-phenotype relationships.',
+        linkText: 'Visit PharmGKB',
+        link: 'https://www.pharmgkb.org',
+      },
       {
         title: 'Pharos',
         description:
@@ -45,19 +60,22 @@ export class GeneResourcesComponent implements OnInit {
         link: `https://pharos.nih.gov/targets?q=${this.gene?.ensembl_gene_id}`,
       },
       {
-        title: 'Brain RNAseq',
+        title: 'Probe Miner',
         description:
-          'Search for this gene on the Brain RNAseq site, which hosts single-cell RNAseq data.',
-        linkText: 'Visit BrainRNAseq',
-        link: 'http://www.brainrnaseq.org/',
+          'Search Probe Miner for information on chemical probes for this gene.',
+        linkText: 'Visit Probe Miner',
+        link: 'https://probeminer.icr.ac.uk/#/',
       },
       {
-        title: 'Genomics DB',
+        title: 'Protein Data Bank',
         description:
-          'View this gene on the National Institute on Aging Genetics of Alzheimer\'s Disease Data Storage Site (NIAGADS) Genomics Database.',
-        linkText: 'Visit Genomics DB',
-        link: `https://www.niagads.org/genomics/app/record/gene/${this.gene?.ensembl_gene_id}`,
+          'Search PDB for experimental and computed protin structure information.',
+        linkText: 'Search PDB',
+        link: 'https://www.rcsb.org',
       },
+    ];
+
+    this.additionalResources = [
       {
         title: 'AD Atlas',
         description:
@@ -66,11 +84,31 @@ export class GeneResourcesComponent implements OnInit {
         link: `https://adatlas.org/?geneID=${this.gene?.ensembl_gene_id}`,
       },
       {
-        title: 'Pub AD',
+        title: 'Allen Institute Transcriptomics',
         description:
-          'View dementia-related publication information for this gene on PubAD.',
-        linkText: 'Visit PubAD',
-        link: `${ this.getPubADLink() }`,
+          'View single nucleus RNAseq data for this gene using the Allen Institute’s Transcriptomics Comparative Viewer.',
+        linkText: 'Visit AD Transcriptomics Viewer',
+        link: `https://knowledge.brain-map.org/data/5IU4U8BP711TR6KZ843/2CD0HDC5PS6A58T0P6E/compare?geneOption=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
+      },
+      {
+        title: 'Alzforum',
+        description:
+          'Visit Alzforum for news and information resources about AD and related disorders.',
+        linkText: 'Visit Alzforum',
+        link: 'https://www.alzforum.org',
+      },
+      {
+        title: 'AlzPED',
+        description:
+          'Search AlzPED for information on preclinical efficacy studies of candidate AD therapeutics.',
+        linkText: 'Visit AlzPED',
+        link: 'https://alzped.nia.nih.gov',
+      },
+      {
+        title: 'AMP-PD Target Explorer', 
+        description: 'View this gene in the AMP-PD Target Explorer, a resource that hosts evidence about whether genes are associated with Parkinson\'s Disease.', 
+        linkText: 'Visit AMP-PD',
+        link: `https://target-explorer.amp-pd.org/genes/target-search?gene=${this.gene?.ensembl_gene_id}`
       },
       {
         title: 'Gene Ontology',
@@ -79,6 +117,27 @@ export class GeneResourcesComponent implements OnInit {
         linkText: 'Visit Ensembl',
         link: `https://www.ensembl.org/Homo_sapiens/Gene/Ontologies/molecular_function?g=${this.gene?.ensembl_gene_id}`,
       },
+      {
+        title: 'GeneCards',
+        description:
+          'Visit GeneCards to view integrated information about this gene.',
+        linkText: 'Visit GeneCards',
+        link: `https://www.genecards.org/Search/Keyword?queryString=${this.gene?.ensembl_gene_id}`,
+      },
+      {
+        title: 'Genomics DB',
+        description:
+          'View this gene on the National Institute on Aging Genetics of Alzheimer\'s Disease Data Storage Site (NIAGADS) Genomics Database.',
+        linkText: 'Visit Genomics DB',
+        link: `https://www.niagads.org/genomics/app/record/gene/${this.gene?.ensembl_gene_id}`,
+      },
+      {
+        title: 'Pub AD',
+        description:
+          'View dementia-related publication information for this gene on PubAD.',
+        linkText: 'Visit PubAD',
+        link: `${ this.getPubADLink() }`,
+      },
       {
         title: 'Reactome Pathways',
         description:
@@ -87,11 +146,19 @@ export class GeneResourcesComponent implements OnInit {
         link: `https://www.ensembl.org/Homo_sapiens/Gene/Pathway?g=${this.gene?.ensembl_gene_id}`,
       },
       {
-        title: 'AMP-PD Target Explorer', 
-        description: 'View this gene in the AMP-PD Target Explorer, a resource that hosts evidence about whether genes are associated with Parkinson\'s Disease.', 
-        linkText: 'Visit AMP-PD',
-        link: `https://target-explorer.amp-pd.org/genes/target-search?gene=${this.gene?.ensembl_gene_id}`
-      }
+        title: 'SEA-AD',
+        description:
+          'Explore the Seattle Alzheimer’s Disease Brain Cell Atlas resources.',
+        linkText: 'Visit SEA-AD',
+        link: 'https://portal.brain-map.org/explore/seattle-alzheimers-disease',
+      },
+      {
+        title: 'UniProtKB',
+        description:
+          'View sequence and functional information about the protein(s) encoded by this gene.',
+        linkText: 'Visit UniProtKB',
+        link: `https://www.uniprot.org/uniprotkb?query=${this.gene?.ensembl_gene_id}`,
+      },
     ];
   }
 }
diff --git a/src/app/models/AdditionalResource.ts b/src/app/models/ResourceCard.ts
similarity index 69%
rename from src/app/models/AdditionalResource.ts
rename to src/app/models/ResourceCard.ts
index 35d2aa82..f6f76cab 100644
--- a/src/app/models/AdditionalResource.ts
+++ b/src/app/models/ResourceCard.ts
@@ -1,4 +1,4 @@
-export interface AdditionalResource {
+export interface ResourceCard {
     title: string;
     description: string;
     linkText: string;
diff --git a/src/app/models/index.ts b/src/app/models/index.ts
index 06fdfa87..3c411cf3 100644
--- a/src/app/models/index.ts
+++ b/src/app/models/index.ts
@@ -15,4 +15,4 @@ export * from './charts';
 export * from './scores';
 export * from './GCTColumn';
 export * from './biodomains';
-export * from './AdditionalResource';
\ No newline at end of file
+export * from './ResourceCard';
\ No newline at end of file

From 95312a555c66c03d0ca0b7fc5f10063f22a1c9c2 Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Tue, 26 Nov 2024 16:54:38 -0800
Subject: [PATCH 21/33] adding pharos class to hero

---
 .../genes/components/gene-hero/gene-hero.component.html       | 4 ++++
 .../genes/components/gene-hero/gene-hero.component.scss       | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.html b/src/app/features/genes/components/gene-hero/gene-hero.component.html
index 78fef743..63d581e6 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.html
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.html
@@ -22,6 +22,10 @@ <h4 class="gene-hero-biodomains-heading">Biological Domains</h4>
             {{ getBiodomains() }}
           </p>
         </div>
+        <div *ngIf="gene.druggability[0].pharos_class">
+          <h4 class="gene-hero-pharos-heading">PHAROS</h4>
+          <p>{{ gene.druggability[0].pharos_class }}</p>
+        </div>
         <div class="gene-hero-aliases">
           <h4 class="gene-hero-aliases-heading">Also known as</h4>
           <ng-container *ngIf="getEnsemblUrl() !== ''">
diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.scss b/src/app/features/genes/components/gene-hero/gene-hero.component.scss
index f2c8c354..46cedd97 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.scss
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.scss
@@ -49,7 +49,7 @@ hr {
   font-style: italic;
 }
 
-.gene-hero-aliases-heading, .gene-hero-biodomains-heading {
+.gene-hero-aliases-heading, .gene-hero-biodomains-heading, .gene-hero-pharos-heading {
   text-transform: uppercase;
   margin-bottom: 15px;
 }

From 6f5e7127008e91c6416e7ec6635413657e99815a Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Tue, 26 Nov 2024 16:57:48 -0800
Subject: [PATCH 22/33] updated section title from PHAROS to PHAROS CLASS

---
 .../genes/components/gene-hero/gene-hero.component.html         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.html b/src/app/features/genes/components/gene-hero/gene-hero.component.html
index 63d581e6..cb2b483c 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.html
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.html
@@ -23,7 +23,7 @@ <h4 class="gene-hero-biodomains-heading">Biological Domains</h4>
           </p>
         </div>
         <div *ngIf="gene.druggability[0].pharos_class">
-          <h4 class="gene-hero-pharos-heading">PHAROS</h4>
+          <h4 class="gene-hero-pharos-heading">Pharos Class</h4>
           <p>{{ gene.druggability[0].pharos_class }}</p>
         </div>
         <div class="gene-hero-aliases">

From b6e7ed1ae7d1910b168ac2479279f05f57e195db Mon Sep 17 00:00:00 2001
From: JessterB <89862046+JessterB@users.noreply.github.com>
Date: Wed, 27 Nov 2024 11:39:03 -0800
Subject: [PATCH 23/33] Adjust ordering of resource sections

---
 .../gene-resources.component.html             | 56 +++++++++----------
 1 file changed, 28 insertions(+), 28 deletions(-)

diff --git a/src/app/features/genes/components/gene-resources/gene-resources.component.html b/src/app/features/genes/components/gene-resources/gene-resources.component.html
index f7cf5fca..fd82817e 100644
--- a/src/app/features/genes/components/gene-resources/gene-resources.component.html
+++ b/src/app/features/genes/components/gene-resources/gene-resources.component.html
@@ -1,30 +1,3 @@
-<div *ngIf="gene" class="section">
-  <div class="section-inner">
-    <div class="container-sm">
-      <h2>
-        Drug Development Resources
-      </h2>
-      <p class="druggability-description">
-        These external sites provide drug development resources.
-      </p>
-      <div 
-        *ngFor="let r of drugDevelopmentResources; let i = index" 
-        class="row tab-row last-row"
-      >
-        <div class="col-md-3 col-sm-8 col-8 header-title">{{ r.title }}</div>
-        <div class="col-md-3 col-sm-4 col-4 text-center header-link">
-          <a class="additional-resource-links link no-bold" href="{{ r.link }}" target="_blank">{{
-            r.linkText
-          }}</a>
-        </div>
-        <div class="col-md-6 col-sm-12 col-12 header-description">
-          {{ r.description }}
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-
 <ng-container *ngIf="gene">
   <div *ngIf="gene.is_tep === true || gene.is_adi === true" class="section">
     <div class="section-inner">
@@ -57,12 +30,39 @@ <h2 id="target-enabling-resources-header">Target Enabling Resources</h2>
   </div>
 </ng-container>
 
+<div *ngIf="gene" class="section">
+  <div class="section-inner">
+    <div class="container-sm">
+      <h2>
+        Drug Development Resources
+      </h2>
+      <p class="druggability-description">
+        These external sites provide information and resources related to drug development.
+      </p>
+      <div
+        *ngFor="let r of drugDevelopmentResources; let i = index"
+        class="row tab-row last-row"
+      >
+        <div class="col-md-3 col-sm-8 col-8 header-title">{{ r.title }}</div>
+        <div class="col-md-3 col-sm-4 col-4 text-center header-link">
+          <a class="additional-resource-links link no-bold" href="{{ r.link }}" target="_blank">{{
+              r.linkText
+            }}</a>
+        </div>
+        <div class="col-md-6 col-sm-12 col-12 header-description">
+          {{ r.description }}
+        </div>
+      </div>
+    </div>
+  </div>
+</div>
+
 <div *ngIf="additionalResources" class="section">
   <div class="section-inner">
     <div class="container-sm">
       <h2>Additional Resources</h2>
       <p>
-        These external sites provide additional useful information for exploring AD targets.
+        These external sites provide additional information about therapeutic targets for AD and related dementias.
       </p>
       <div
         *ngFor="let r of additionalResources; let i = index"

From 02629884a50cc5f1aa93afab8714df7e7f9aa963 Mon Sep 17 00:00:00 2001
From: JessterB <89862046+JessterB@users.noreply.github.com>
Date: Wed, 27 Nov 2024 11:39:35 -0800
Subject: [PATCH 24/33] Update resource strings and URLs

---
 .../gene-resources.component.ts               | 60 +++++++++----------
 1 file changed, 30 insertions(+), 30 deletions(-)

diff --git a/src/app/features/genes/components/gene-resources/gene-resources.component.ts b/src/app/features/genes/components/gene-resources/gene-resources.component.ts
index 0fa53683..b7b0905b 100644
--- a/src/app/features/genes/components/gene-resources/gene-resources.component.ts
+++ b/src/app/features/genes/components/gene-resources/gene-resources.component.ts
@@ -9,7 +9,7 @@ import { Gene, ResourceCard } from '../../../../models';
 })
 export class GeneResourcesComponent implements OnInit {
   @Input() gene: Gene | undefined;
-  
+
   additionalResources: ResourceCard[] = [];
   drugDevelopmentResources: ResourceCard[] = [];
 
@@ -34,43 +34,43 @@ export class GeneResourcesComponent implements OnInit {
       {
         title: 'Chemical Probes',
         description:
-          'View expert reviews and evaluations of chemical probes.',
+          'View expert reviews and evaluations of any chemical probes that are available for this target.',
         linkText: 'Visit Chemical Probes',
         link: `https://www.chemicalprobes.org/?q=${this.gene?.hgnc_symbol}`,
       },
       {
         title: 'Open Targets',
         description:
-          'View this gene on Open Targets, a resource that provides evidence on the validity of therapeutic targets based on genome-scale experiments and analysis.',
+          'View evidence on the validity of this therapeutic target based on genome-scale experiments and analysis.',
         linkText: 'Visit Open Targets',
         link: `https://platform.opentargets.org/target/${this.gene?.ensembl_gene_id}`,
       },
       {
         title: 'PharmGKB',
         description:
-          'Search PharmGKB for information on gene-drug and gene-phenotype relationships.',
+          'Search for information on gene-drug and gene-phenotype relationships.',
         linkText: 'Visit PharmGKB',
         link: 'https://www.pharmgkb.org',
       },
       {
         title: 'Pharos',
         description:
-          'View this gene on Pharos, a resource that provides access to the integrated knowledge-base from the Illuminating the Druggable Genome program.',
+          'View information about this target in the Knowledge Management Center for the Illuminating the Druggable Genome program.',
         linkText: 'Visit Pharos',
         link: `https://pharos.nih.gov/targets?q=${this.gene?.ensembl_gene_id}`,
       },
       {
         title: 'Probe Miner',
         description:
-          'Search Probe Miner for information on chemical probes for this gene.',
+          'Search for information on chemical probes based on large-scale, publicly available, medicinal chemistry data.',
         linkText: 'Visit Probe Miner',
         link: 'https://probeminer.icr.ac.uk/#/',
       },
       {
         title: 'Protein Data Bank',
         description:
-          'Search PDB for experimental and computed protin structure information.',
-        linkText: 'Search PDB',
+          'Search for experimental and computed 3D protein structure information.',
+        linkText: 'Visit PDB',
         link: 'https://www.rcsb.org',
       },
     ];
@@ -79,16 +79,9 @@ export class GeneResourcesComponent implements OnInit {
       {
         title: 'AD Atlas',
         description:
-          'View this gene on the AD Atlas site, a network-based resource for investigating AD in a multi-omic context.',
+          'Perform interactive network and enrichment analyses on this target using a heterogenous network of multiomic, association, and endophenotypic data.',
         linkText: 'Visit AD Atlas',
-        link: `https://adatlas.org/?geneID=${this.gene?.ensembl_gene_id}`,
-      },
-      {
-        title: 'Allen Institute Transcriptomics',
-        description:
-          'View single nucleus RNAseq data for this gene using the Allen Institute’s Transcriptomics Comparative Viewer.',
-        linkText: 'Visit AD Transcriptomics Viewer',
-        link: `https://knowledge.brain-map.org/data/5IU4U8BP711TR6KZ843/2CD0HDC5PS6A58T0P6E/compare?geneOption=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
+        link: `https://adatlas.org/?type=geneEnsembl&ids=${this.gene?.ensembl_gene_id}`,
       },
       {
         title: 'Alzforum',
@@ -100,62 +93,69 @@ export class GeneResourcesComponent implements OnInit {
       {
         title: 'AlzPED',
         description:
-          'Search AlzPED for information on preclinical efficacy studies of candidate AD therapeutics.',
+          'Search for information on preclinical efficacy studies of candidate AD therapeutics.',
         linkText: 'Visit AlzPED',
         link: 'https://alzped.nia.nih.gov',
       },
       {
-        title: 'AMP-PD Target Explorer', 
-        description: 'View this gene in the AMP-PD Target Explorer, a resource that hosts evidence about whether genes are associated with Parkinson\'s Disease.', 
+        title: 'AMP-PD Target Explorer',
+        description: 'View evidence about whether this target is associated with Parkinson\'s Disease.',
         linkText: 'Visit AMP-PD',
         link: `https://target-explorer.amp-pd.org/genes/target-search?gene=${this.gene?.ensembl_gene_id}`
       },
+      {
+        title: 'Brain Knowledge Platform',
+        description:
+          'View single nucleus RNAseq results for this target using the Allen Institute SEA-AD Comparative Viewer.',
+        linkText: 'Visit Brain Knowledge Platform',
+        link: `https://knowledge.brain-map.org/data/5IU4U8BP711TR6KZ843/2CD0HDC5PS6A58T0P6E/compare?geneOption=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
+      },
       {
         title: 'Gene Ontology',
         description:
-          'View the gene ontology information for this gene on Ensembl.',
-        linkText: 'Visit Ensembl',
-        link: `https://www.ensembl.org/Homo_sapiens/Gene/Ontologies/molecular_function?g=${this.gene?.ensembl_gene_id}`,
+          'View the GO terms associated with this target and explore ontology-related tools.',
+        linkText: 'Visit AmiGO 2',
+        link: `https://amigo.geneontology.org/amigo/search/annotation?q=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
       },
       {
         title: 'GeneCards',
         description:
-          'Visit GeneCards to view integrated information about this gene.',
+          'View integrated information about this target gathered from a comprehensive collection of public sources.',
         linkText: 'Visit GeneCards',
-        link: `https://www.genecards.org/Search/Keyword?queryString=${this.gene?.ensembl_gene_id}`,
+        link: `https://www.genecards.org/cgi-bin/carddisp.pl?gene=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
       },
       {
         title: 'Genomics DB',
         description:
-          'View this gene on the National Institute on Aging Genetics of Alzheimer\'s Disease Data Storage Site (NIAGADS) Genomics Database.',
+          'View information about this target on the National Institute on Aging Genetics of Alzheimer\'s Disease Data Storage Site (NIAGADS) Genomics Database.',
         linkText: 'Visit Genomics DB',
         link: `https://www.niagads.org/genomics/app/record/gene/${this.gene?.ensembl_gene_id}`,
       },
       {
         title: 'Pub AD',
         description:
-          'View dementia-related publication information for this gene on PubAD.',
+          'View dementia-related publication information for this target.',
         linkText: 'Visit PubAD',
         link: `${ this.getPubADLink() }`,
       },
       {
         title: 'Reactome Pathways',
         description:
-          'View the reactome pathway information for this gene on Ensembl.',
+          'View the reactome pathway information for this target on Ensembl.',
         linkText: 'Visit Ensembl',
         link: `https://www.ensembl.org/Homo_sapiens/Gene/Pathway?g=${this.gene?.ensembl_gene_id}`,
       },
       {
         title: 'SEA-AD',
         description:
-          'Explore the Seattle Alzheimer’s Disease Brain Cell Atlas resources.',
+          'Explore the Seattle Alzheimer’s Disease Brain Cell Atlas resources from the Allen Institute.',
         linkText: 'Visit SEA-AD',
         link: 'https://portal.brain-map.org/explore/seattle-alzheimers-disease',
       },
       {
         title: 'UniProtKB',
         description:
-          'View sequence and functional information about the protein(s) encoded by this gene.',
+          'View protein sequence and functional information about this target.',
         linkText: 'Visit UniProtKB',
         link: `https://www.uniprot.org/uniprotkb?query=${this.gene?.ensembl_gene_id}`,
       },

From 91a8bb722d7493475af6b6e4b216a2dd7495dfe7 Mon Sep 17 00:00:00 2001
From: JessterB <89862046+JessterB@users.noreply.github.com>
Date: Wed, 27 Nov 2024 11:40:15 -0800
Subject: [PATCH 25/33] Update mongoDB install URLs in README

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 1ac18756..e4c67d16 100644
--- a/README.md
+++ b/README.md
@@ -43,8 +43,8 @@ The next sections focus on setting up a mongo database loaded with Agora's data.
 
 You will need to create a MongoDB database and name it `agora`. 
 
-- [Using the MongoDB Shell](https://www.mongodb.com/basics/create-database#option-2)
-- [Using MongoDB Compass](https://www.mongodb.com/basics/create-database#option-3)
+- [Using the MongoDB Shell](https://www.mongodb.com/resources/products/fundamentals/create-database#using-the-mongodb-shell)
+- [Using MongoDB Compass](https://www.mongodb.com/resources/products/fundamentals/create-database#using-the-mongodb-compass)
 - [Using Studio3T](https://studio3t.com/knowledge-base/articles/common-mongodb-commands/#1-mongodb-create-database)
 
 Note: You can use the following scripts to start the database:

From d78f439c0f9d468d8ba5cc9f799c389823ff8a81 Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Wed, 27 Nov 2024 13:39:19 -0800
Subject: [PATCH 26/33] adding uniprotkb_accessions links

---
 .../gene-hero/gene-hero.component.html        | 28 +++++++++++--------
 .../gene-hero/gene-hero.component.scss        |  4 +++
 .../gene-hero/gene-hero.component.ts          |  9 +++++-
 src/app/models/genes.ts                       |  1 +
 src/server/models/genes.ts                    |  1 +
 5 files changed, 31 insertions(+), 12 deletions(-)

diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.html b/src/app/features/genes/components/gene-hero/gene-hero.component.html
index 78fef743..ed60ff50 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.html
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.html
@@ -14,33 +14,39 @@ <h2 class="gene-hero-name">
       <p class="gene-hero-provider">
         {{ getSummary() }}
       </p>
-      <ng-container *ngIf="gene.bio_domains || getAlias() || getEnsemblUrl() !== ''">
+      <ng-container *ngIf="gene.bio_domains || getAliases() || getEnsemblUrl() !== ''">
         <hr />
         <div *ngIf="gene.bio_domains" class="gene-hero-biodomains">
           <h4 class="gene-hero-biodomains-heading">Biological Domains</h4>
           <p>
-            {{ getBiodomains() }}
+            &nbsp; {{ getBiodomains() }}
           </p>
         </div>
         <div class="gene-hero-aliases">
           <h4 class="gene-hero-aliases-heading">Also known as</h4>
           <ng-container *ngIf="getEnsemblUrl() !== ''">
-            <p>
-              <a [href]="getEnsemblUrl()" target="_blank">{{ gene.ensembl_gene_id }}</a>
+            <p class="aliases">
+              &nbsp;  <a [href]="getEnsemblUrl()" target="_blank">{{ gene.ensembl_gene_id }}</a>
               <span *ngIf="gene.ensembl_info.ensembl_release">
                 (Ensembl Release {{ gene.ensembl_info.ensembl_release }})
               </span>
             </p>
           </ng-container>
-          <ng-container *ngIf="getEnsemblUrl() === ''">
-            <span *ngIf="getEnsemblUrl() === ''">{{ gene.ensembl_gene_id }}</span>
-          </ng-container>
-          <p *ngIf="gene.ensembl_info.ensembl_possible_replacements.length > 0">
-            <a [href]="getPossibleReplacementsURL()">Possible replacement value<span *ngIf="gene.ensembl_info.ensembl_possible_replacements.length > 1">s</span></a>:
+          <p *ngIf="getEnsemblUrl() === ''">
+            &nbsp; <span *ngIf="getEnsemblUrl() === ''">{{ gene.ensembl_gene_id }}</span>
+          </p>
+          <p *ngIf="gene.ensembl_info.ensembl_possible_replacements.length > 0" class="aliases">
+            &nbsp; <a [href]="getPossibleReplacementsURL()">Possible replacement value<span *ngIf="gene.ensembl_info.ensembl_possible_replacements.length > 1">s</span></a>:
             {{ gene.ensembl_info.ensembl_possible_replacements.join(', ')}}
           </p>
-          <p *ngIf="getAlias() !== ''">
-            {{ getAlias() }}
+          <p *ngIf="gene.uniprotkb_accessions" class="aliases">
+            &nbsp; UNIPROTKB 
+            <ng-container *ngFor="let accession of gene.uniprotkb_accessions; let isLast = last" class="aliases">
+              <a [href]="getUniProtKBLink(accession)" target="_blank">{{ accession }}</a><span *ngIf="!isLast">, </span>
+            </ng-container>
+          </p>
+          <p *ngIf="gene.alias.length > 0" class="aliases">
+            &nbsp; {{ getAliases() }}
           </p>
         </div>
       </ng-container>
diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.scss b/src/app/features/genes/components/gene-hero/gene-hero.component.scss
index f2c8c354..0532e164 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.scss
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.scss
@@ -54,6 +54,10 @@ hr {
   margin-bottom: 15px;
 }
 
+.aliases {
+  margin-bottom: 0;
+}
+
 .possible-replacements {
   margin-bottom: 15px;
 }
\ No newline at end of file
diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.ts b/src/app/features/genes/components/gene-hero/gene-hero.component.ts
index dd47d840..8d56fabb 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.ts
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.ts
@@ -85,13 +85,20 @@ export class GeneHeroComponent {
     }
   }
 
-  getAlias(): string {
+  getAliases(): string {
     if (this.gene?.alias && this.gene.alias.length > 0) {
       return this.gene.alias.join(', ');
     }
     return '';
   }
 
+  getUniProtKBLink(uniProtId: string) {
+    if (uniProtId) {
+      return `https://www.uniprot.org/uniprotkb/${uniProtId}/entry`;
+    }
+    return '';
+  }
+
   getBiodomains(): string {
     if (!this.gene || !this.gene.bio_domains)
       return '';
diff --git a/src/app/models/genes.ts b/src/app/models/genes.ts
index 6f8e5939..f153a8a5 100644
--- a/src/app/models/genes.ts
+++ b/src/app/models/genes.ts
@@ -55,6 +55,7 @@ export interface Gene {
   summary: string;
   hgnc_symbol: string;
   alias: string[];
+  uniprotkb_accessions: string[];
   is_igap: boolean;
   is_eqtl: boolean;
   is_any_rna_changed_in_ad_brain: boolean;
diff --git a/src/server/models/genes.ts b/src/server/models/genes.ts
index a4fe82b2..aea8b9e3 100644
--- a/src/server/models/genes.ts
+++ b/src/server/models/genes.ts
@@ -67,6 +67,7 @@ const GeneSchema = new Schema<Gene>(
     summary: { type: String, required: true },
     hgnc_symbol: { type: String, required: true },
     alias: [{ type: String, required: true }],
+    uniprotkb_accessions: [{ type: String, required: true }],
     is_igap: { type: Boolean, required: true },
     is_eqtl: { type: Boolean, required: true },
     is_any_rna_changed_in_ad_brain: { type: Boolean, required: true },

From dab1ac8f7225bcf4b933b1ea37e4a6e21e047a4e Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Wed, 27 Nov 2024 15:33:47 -0800
Subject: [PATCH 27/33] applied a margin under subheadings biodomains and
 pharos class

---
 .../components/gene-hero/gene-hero.component.html    |  2 +-
 .../components/gene-hero/gene-hero.component.scss    | 12 +++++++++++-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.html b/src/app/features/genes/components/gene-hero/gene-hero.component.html
index cb2b483c..81728ab3 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.html
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.html
@@ -22,7 +22,7 @@ <h4 class="gene-hero-biodomains-heading">Biological Domains</h4>
             {{ getBiodomains() }}
           </p>
         </div>
-        <div *ngIf="gene.druggability[0].pharos_class">
+        <div *ngIf="gene.druggability[0].pharos_class" class="gene-hero-pharos">
           <h4 class="gene-hero-pharos-heading">Pharos Class</h4>
           <p>{{ gene.druggability[0].pharos_class }}</p>
         </div>
diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.scss b/src/app/features/genes/components/gene-hero/gene-hero.component.scss
index 46cedd97..332c004f 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.scss
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.scss
@@ -38,7 +38,17 @@ hr {
 }
 
 .gene-hero-biodomains {
-  margin-bottom: 30px;
+  margin-bottom: 15px;
+  
+  p {
+    margin-left: 10px;
+  }
+}
+
+.gene-hero-pharos {
+  p {
+    margin-left: 10px;
+  }
 }
 
 .gene-hero-summary {

From b0e062407acfb22b8d28fc8aac696a038a3ead3f Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Wed, 27 Nov 2024 17:05:16 -0800
Subject: [PATCH 28/33] adding margin to subitems in hero

---
 .../gene-hero/gene-hero.component.html           | 16 ++++++++--------
 .../gene-hero/gene-hero.component.scss           |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.html b/src/app/features/genes/components/gene-hero/gene-hero.component.html
index ed60ff50..468e9f06 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.html
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.html
@@ -18,35 +18,35 @@ <h2 class="gene-hero-name">
         <hr />
         <div *ngIf="gene.bio_domains" class="gene-hero-biodomains">
           <h4 class="gene-hero-biodomains-heading">Biological Domains</h4>
-          <p>
-            &nbsp; {{ getBiodomains() }}
+          <p class="aliases">
+            {{ getBiodomains() }}
           </p>
         </div>
         <div class="gene-hero-aliases">
           <h4 class="gene-hero-aliases-heading">Also known as</h4>
           <ng-container *ngIf="getEnsemblUrl() !== ''">
             <p class="aliases">
-              &nbsp;  <a [href]="getEnsemblUrl()" target="_blank">{{ gene.ensembl_gene_id }}</a>
+              <a [href]="getEnsemblUrl()" target="_blank">{{ gene.ensembl_gene_id }}</a>
               <span *ngIf="gene.ensembl_info.ensembl_release">
                 (Ensembl Release {{ gene.ensembl_info.ensembl_release }})
               </span>
             </p>
           </ng-container>
-          <p *ngIf="getEnsemblUrl() === ''">
-            &nbsp; <span *ngIf="getEnsemblUrl() === ''">{{ gene.ensembl_gene_id }}</span>
+          <p *ngIf="getEnsemblUrl() === ''" class="aliases">
+            <span *ngIf="getEnsemblUrl() === ''">{{ gene.ensembl_gene_id }}</span>
           </p>
           <p *ngIf="gene.ensembl_info.ensembl_possible_replacements.length > 0" class="aliases">
-            &nbsp; <a [href]="getPossibleReplacementsURL()">Possible replacement value<span *ngIf="gene.ensembl_info.ensembl_possible_replacements.length > 1">s</span></a>:
+            <a [href]="getPossibleReplacementsURL()">Possible replacement value<span *ngIf="gene.ensembl_info.ensembl_possible_replacements.length > 1">s</span></a>:
             {{ gene.ensembl_info.ensembl_possible_replacements.join(', ')}}
           </p>
           <p *ngIf="gene.uniprotkb_accessions" class="aliases">
-            &nbsp; UNIPROTKB 
+            UNIPROTKB 
             <ng-container *ngFor="let accession of gene.uniprotkb_accessions; let isLast = last" class="aliases">
               <a [href]="getUniProtKBLink(accession)" target="_blank">{{ accession }}</a><span *ngIf="!isLast">, </span>
             </ng-container>
           </p>
           <p *ngIf="gene.alias.length > 0" class="aliases">
-            &nbsp; {{ getAliases() }}
+            {{ getAliases() }}
           </p>
         </div>
       </ng-container>
diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.scss b/src/app/features/genes/components/gene-hero/gene-hero.component.scss
index 0532e164..1afc9a95 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.scss
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.scss
@@ -55,7 +55,7 @@ hr {
 }
 
 .aliases {
-  margin-bottom: 0;
+  margin: 0 0 0 10px;
 }
 
 .possible-replacements {

From a2ff72b6f467c03d1642656f00629ddf92b7bbfa Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Wed, 27 Nov 2024 17:39:34 -0800
Subject: [PATCH 29/33] added new uniprotkb_accessions property to mocks

---
 src/app/testing/gene-mocks.ts | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/app/testing/gene-mocks.ts b/src/app/testing/gene-mocks.ts
index c26bdea0..3ba576d3 100644
--- a/src/app/testing/gene-mocks.ts
+++ b/src/app/testing/gene-mocks.ts
@@ -28,6 +28,7 @@ export const geneMock1: Gene = {
     'Moesin (for membrane-organizing extension spike protein) is a member of the ERM family which includes ezrin and radixin. ERM proteins appear to function as cross-linkers between plasma membranes and actin-based cytoskeletons. Moesin is localized to filopodia and other membranous protrusions that are important for cell-cell recognition and signaling and for cell movement. [provided by RefSeq, Jul 2008].',
   hgnc_symbol: 'MSN',
   alias: ['HEL70', 'IMD50'],
+  uniprotkb_accessions: [],
   is_igap: false,
   is_eqtl: false,
   is_any_rna_changed_in_ad_brain: true,
@@ -2986,6 +2987,7 @@ export const geneMock2: Gene = {
     'PLEC1b',
     'PLTN',
   ],
+  uniprotkb_accessions: [],
   is_igap: false,
   is_eqtl: true,
   is_any_rna_changed_in_ad_brain: true,
@@ -3164,6 +3166,7 @@ export const geneMock3: Gene = {
     'p59Hck',
     'p61Hck',
   ],
+  uniprotkb_accessions: [],
   is_igap: false,
   is_eqtl: true,
   is_any_rna_changed_in_ad_brain: true,
@@ -3372,6 +3375,7 @@ export const nominatedGeneMock1: Gene = {
   summary: '',
   hgnc_symbol: 'MSN',
   alias: [],
+  uniprotkb_accessions: [],
   is_igap: false,
   is_eqtl: false,
   is_any_rna_changed_in_ad_brain: false,
@@ -3469,6 +3473,7 @@ export const noHGNCgeneMock: Gene = {
   summary: '',
   hgnc_symbol: '',
   alias: [],
+  uniprotkb_accessions: [],
   is_igap: false,
   is_eqtl: false,
   is_any_rna_changed_in_ad_brain: false,

From 2da975a63ef1b3531e74b34c08a03cf7608c10f4 Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Tue, 3 Dec 2024 14:35:13 -0800
Subject: [PATCH 30/33] Update ci.yml

updating docker-compose to docker compose
---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f077db93..175622d4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -215,7 +215,7 @@ jobs:
       - name: start database, server, and app
         run: |
           echo "==> start database and data containers"
-          docker-compose -f "${{ env.DOCKER_COMPOSE_PATH }}" up -d
+          docker compose -f "${{ env.DOCKER_COMPOSE_PATH }}" up -d
 
           echo "==> wait for data container to finish seeding database container"
           DATA_CONTAINER=$(docker compose -f "${{ env.DOCKER_COMPOSE_PATH }}" ps -a --format '{{.Name}}' mongo-seed)
@@ -237,7 +237,7 @@ jobs:
           pid=$(lsof -i :8080 -t) && kill ${pid}
 
           echo "==> stop database"
-          docker-compose -f "${{ env.DOCKER_COMPOSE_PATH }}" down
+          docker compose -f "${{ env.DOCKER_COMPOSE_PATH }}" down
 
       - uses: actions/upload-artifact@v4
         if: ${{ !cancelled() }}

From 57fa18ac51b10e12a8978f0ab22579e4a5494a12 Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Mon, 16 Dec 2024 10:20:17 -0800
Subject: [PATCH 31/33] AG-1565 remove druggability columns

---
 package.json                                  |  4 +-
 .../gene-nominated-targets.component.ts       | 30 -----------
 .../gene-similar/gene-similar.component.ts    | 21 --------
 .../gene-table/gene-table.component.ts        | 15 +-----
 src/app/models/genes.ts                       |  3 --
 tests/nominated-targets.spec.ts               | 53 -------------------
 tests/similar-genes.spec.ts                   |  7 ---
 7 files changed, 3 insertions(+), 130 deletions(-)

diff --git a/package.json b/package.json
index d310d92a..638b6ba1 100644
--- a/package.json
+++ b/package.json
@@ -1,8 +1,8 @@
 {
   "name": "agora",
-  "version": "3.4.0",
+  "version": "3.5.0",
   "data-file": "syn13363290",
-  "data-version": "70",
+  "data-version": "71",
   "private": true,
   "scripts": {
     "dev": "concurrently --kill-others \"npm:dev:server\" \"npm:dev:app\"",
diff --git a/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts b/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
index 7db6dccb..8ba8aebb 100644
--- a/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
+++ b/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
@@ -56,21 +56,6 @@ export class GeneNominatedTargetsComponent implements OnInit {
       header: 'Pharos Class',
       selected: false,
     },
-    {
-      field: 'sm_druggability_display_value',
-      header: 'Small Molecule Druggability',
-      selected: false,
-    },
-    {
-      field: 'safety_rating_display_value',
-      header: 'Safety Rating',
-      selected: false,
-    },
-    {
-      field: 'ab_modality_display_value',
-      header: 'Antibody Modality',
-      selected: false,
-    },
   ];
 
   constructor(private apiService: ApiService) {}
@@ -138,23 +123,8 @@ export class GeneNominatedTargetsComponent implements OnInit {
           de.pharos_class_display_value = de.druggability[0].pharos_class
             ? de.druggability[0].pharos_class
             : 'No value';
-          de.sm_druggability_display_value =
-            de.druggability[0].sm_druggability_bucket +
-            ': ' +
-            de.druggability[0].classification;
-          de.safety_rating_display_value =
-            de.druggability[0].safety_bucket +
-            ': ' +
-            de.druggability[0].safety_bucket_definition;
-          de.ab_modality_display_value =
-            de.druggability[0].abability_bucket +
-            ': ' +
-            de.druggability[0].abability_bucket_definition;
         } else {
           de.pharos_class_display_value = 'No value';
-          de.sm_druggability_display_value = 'No value';
-          de.safety_rating_display_value = 'No value';
-          de.ab_modality_display_value = 'No value';
         }
       });
 
diff --git a/src/app/features/genes/components/gene-similar/gene-similar.component.ts b/src/app/features/genes/components/gene-similar/gene-similar.component.ts
index 1d475610..3bcb4159 100644
--- a/src/app/features/genes/components/gene-similar/gene-similar.component.ts
+++ b/src/app/features/genes/components/gene-similar/gene-similar.component.ts
@@ -45,12 +45,6 @@ export class GeneSimilarComponent implements OnInit {
       header: 'Protein Expression Change',
     },
     { field: 'pharos_class_display_value', header: 'Pharos Class' },
-    {
-      field: 'sm_druggability_display_value',
-      header: 'Small Molecule Druggability',
-    },
-    { field: 'safety_rating_display_value', header: 'Safety Rating' },
-    { field: 'ab_modality_display_value', header: 'Antibody Modality' },
   ];
 
   gctLink: { [key: string]: string } | undefined;
@@ -117,23 +111,8 @@ export class GeneSimilarComponent implements OnInit {
           de.pharos_class_display_value = de.druggability[0].pharos_class
             ? de.druggability[0].pharos_class
             : 'No value';
-          de.sm_druggability_display_value =
-            de.druggability[0].sm_druggability_bucket +
-            ': ' +
-            de.druggability[0].classification;
-          de.safety_rating_display_value =
-            de.druggability[0].safety_bucket +
-            ': ' +
-            de.druggability[0].safety_bucket_definition;
-          de.ab_modality_display_value =
-            de.druggability[0].abability_bucket +
-            ': ' +
-            de.druggability[0].abability_bucket_definition;
         } else {
           de.pharos_class_display_value = 'No value';
-          de.sm_druggability_display_value = 'No value';
-          de.safety_rating_display_value = 'No value';
-          de.ab_modality_display_value = 'No value';
         }
       });
 
diff --git a/src/app/features/genes/components/gene-table/gene-table.component.ts b/src/app/features/genes/components/gene-table/gene-table.component.ts
index fc80a076..452622c3 100644
--- a/src/app/features/genes/components/gene-table/gene-table.component.ts
+++ b/src/app/features/genes/components/gene-table/gene-table.component.ts
@@ -116,20 +116,7 @@ export class GeneTableComponent implements OnInit {
       } else if (a == null && b == null) {
         result = 0;
       } else if (typeof a === 'string' && typeof b === 'string') {
-        // Natural sorting for this score type, which can be >= 10
-        if (event.field === 'sm_druggability_display_value'
-          || event.field === 'safety_rating_display_value'
-          || event.field === 'ab_modality_display_value') {
-          let nA = parseInt(a.split(':')[0], 10);
-          let nB = parseInt(b.split(':')[0], 10);
-
-          nA = !isNaN(nA) ? nA : 999 * event.order;
-          nB = !isNaN(nB) ? nB : 999 * event.order;
-
-          result = nA < nB ? -1 : nA > nB ? 1 : 0;
-        } else {
-          result = a.localeCompare(b);
-        }
+        result = a.localeCompare(b);
       } else {
         result = a < b ? -1 : a > b ? 1 : 0;
       }
diff --git a/src/app/models/genes.ts b/src/app/models/genes.ts
index f153a8a5..f7ea1958 100644
--- a/src/app/models/genes.ts
+++ b/src/app/models/genes.ts
@@ -85,9 +85,6 @@ export interface Gene {
   similar_genes_network?: SimilarGenesNetwork;
 
   // Similar table (not in mongo document)
-  ab_modality_display_value?: string;
-  safety_rating_display_value?: string;
-  sm_druggability_display_value?: string;
   pharos_class_display_value?: string;
   is_any_rna_changed_in_ad_brain_display_value?: string;
   is_any_protein_changed_in_ad_brain_display_value?: string;
diff --git a/tests/nominated-targets.spec.ts b/tests/nominated-targets.spec.ts
index d350f668..757c8a80 100644
--- a/tests/nominated-targets.spec.ts
+++ b/tests/nominated-targets.spec.ts
@@ -9,57 +9,4 @@ test.describe('specific viewport block', () => {
     // Expect a title "to contain" a substring.
     await expect(page).toHaveTitle('Nominated Targets | Candidate genes for AD treatment or prevention');
   });
-
-  test('has correct sort on druggability columns', async ({ page }) => {
-    await page.goto('/genes/nominated-targets');
-
-    await expect(page.locator('table')).toBeVisible();
-  
-    await page.locator('#pr_id_3 span').click();
-
-    await page.getByLabel('Nominations').click();
-    await page.getByLabel('Year First Nominated').click();
-    await page.getByLabel('Nominating Teams').click();
-    await page.getByLabel('Cohort Study').click();
-    await page.getByLabel('Small Molecule Druggability').click();
-    await page.getByLabel('Safety Rating').click();
-    await page.getByLabel('Antibody Modality').click();
-
-    // sort forward on small molecule druggability
-    await page.getByRole('cell', { name: 'Small Molecule Druggability' }).click();
-
-    const row = page.locator('table tr:nth-child(2)');
-    let cell = row.getByRole('cell').nth(1);
-    await expect(cell).not.toContainText('No Value');
-    
-    // sort reverse on small molecule druggability
-    await page.getByRole('cell', { name: 'Small Molecule Druggability' }).click();
-    
-    cell = row.getByRole('cell').nth(1); 
-    await expect(cell).not.toContainText('No Value');
-
-    // sort forward on safety rating
-    await page.getByRole('cell', { name: 'Safety Rating' }).click();
-
-    cell = row.getByRole('cell').nth(2);
-    await expect(cell).not.toContainText('No Value');
-    
-    // sort reverse on safety rating
-    await page.getByRole('cell', { name: 'Safety Rating' }).click();
-    
-    cell = row.getByRole('cell').nth(2); 
-    await expect(cell).not.toContainText('No Value');
-
-    // sort forward on antibody modality
-    await page.getByRole('cell', { name: 'Antibody Modality' }).click();
-
-    cell = row.getByRole('cell').nth(3);
-    await expect(cell).not.toContainText('No Value');
-    
-    // sort reverse on antibody modality
-    await page.getByRole('cell', { name: 'Antibody Modality' }).click();
-    
-    cell = row.getByRole('cell').nth(3); 
-    await expect(cell).not.toContainText('No Value');
-  });
 });
\ No newline at end of file
diff --git a/tests/similar-genes.spec.ts b/tests/similar-genes.spec.ts
index c0292a09..4796e075 100644
--- a/tests/similar-genes.spec.ts
+++ b/tests/similar-genes.spec.ts
@@ -20,12 +20,5 @@ test.describe('specific viewport block', () => {
 
     const cell = await page.getByRole('row').nth(1).getByRole('cell').nth(1).innerText();
     expect(cell).not.toBe('');
-
-    
-    // sort reverse on small molecule druggability
-    await page.getByRole('cell', { name: 'Nominated Target' }).click();
-    
-    const cell2 = await page.getByRole('row').nth(1).getByRole('cell').nth(1).innerText();
-    expect(cell2).not.toBe('');
   });
 });
\ No newline at end of file

From 3adca17e79c0839c98baea0beda97eda43376cb6 Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Tue, 17 Dec 2024 02:36:10 -0800
Subject: [PATCH 32/33] AG-1599 remove pharos class

---
 .../gene-druggability.component.ts            |  31 ++---
 .../gene-hero/gene-hero.component.html        |   4 +-
 .../gene-nominated-targets.component.ts       |   8 +-
 .../gene-similar/gene-similar.component.ts    |   8 +-
 src/app/models/genes.ts                       |   7 +-
 src/app/testing/gene-mocks.ts                 | 130 ++++++++----------
 src/server/models/genes.ts                    |   4 +-
 7 files changed, 82 insertions(+), 110 deletions(-)

diff --git a/src/app/features/genes/components/gene-druggability/gene-druggability.component.ts b/src/app/features/genes/components/gene-druggability/gene-druggability.component.ts
index 5a5cfd9f..65e2e2df 100644
--- a/src/app/features/genes/components/gene-druggability/gene-druggability.component.ts
+++ b/src/app/features/genes/components/gene-druggability/gene-druggability.component.ts
@@ -1,4 +1,4 @@
-import { Component, OnInit, Input } from '@angular/core';
+import { Component, Input } from '@angular/core';
 import { ActivatedRoute } from '@angular/router';
 
 import { Gene, Druggability } from '../../../../models';
@@ -18,7 +18,7 @@ export interface GeneResourceType {
   templateUrl: './gene-druggability.component.html',
   styleUrls: ['./gene-druggability.component.scss'],
 })
-export class GeneDruggabilityComponent implements OnInit {
+export class GeneDruggabilityComponent {
   _gene: Gene | undefined;
   get gene(): Gene | undefined {
     return this._gene;
@@ -43,28 +43,23 @@ export class GeneDruggabilityComponent implements OnInit {
     private geneService: GeneService
   ) {}
 
-  ngOnInit() {
-    //
-  }
-
   init() {
     // Update the initial buckets
     if (this.gene) {
       if (!this.gene.druggability) {
-        this.gene.druggability = [
-          {
-            sm_druggability_bucket: this.getDefaultBucketNumber(),
-            safety_bucket: this.getDefaultBucketNumber(),
-            abability_bucket: this.getDefaultBucketNumber(),
-            pharos_class: '',
-            classification: this.getDefaultText(),
-            safety_bucket_definition: this.getDefaultText(),
-            abability_bucket_definition: this.getDefaultText(),
-          },
-        ];
+        this.gene.druggability =
+        {
+          sm_druggability_bucket: this.getDefaultBucketNumber(),
+          safety_bucket: this.getDefaultBucketNumber(),
+          abability_bucket: this.getDefaultBucketNumber(),
+          pharos_class: [],
+          classification: this.getDefaultText(),
+          safety_bucket_definition: this.getDefaultText(),
+          abability_bucket_definition: this.getDefaultText(),
+        };
       }
 
-      this.druggability = this.gene.druggability[0];
+      this.druggability = this.gene.druggability;
       this.currentBucketSM = this.druggability.sm_druggability_bucket;
       this.currentBucketAB = this.druggability.abability_bucket;
       this.currentBucketSF = this.druggability.safety_bucket;
diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.html b/src/app/features/genes/components/gene-hero/gene-hero.component.html
index fdd55361..49773c20 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.html
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.html
@@ -22,9 +22,9 @@ <h4 class="gene-hero-biodomains-heading">Biological Domains</h4>
             {{ getBiodomains() }}
           </p>
         </div>
-        <div *ngIf="gene.druggability[0].pharos_class" class="gene-hero-pharos">
+        <div *ngIf="gene.druggability && gene.druggability.pharos_class" class="gene-hero-pharos">
           <h4 class="gene-hero-pharos-heading">Pharos Class</h4>
-          <p>{{ gene.druggability[0].pharos_class }}</p>
+          <p>{{ gene.druggability.pharos_class.join(', ') }}</p>
         </div>
         <div class="gene-hero-aliases">
           <h4 class="gene-hero-aliases-heading">Also known as</h4>
diff --git a/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts b/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
index 8ba8aebb..d50d9e36 100644
--- a/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
+++ b/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
@@ -119,13 +119,7 @@ export class GeneNominatedTargetsComponent implements OnInit {
           : undefined;
 
         // Populate Druggability display fields
-        if (de.druggability && de.druggability.length) {
-          de.pharos_class_display_value = de.druggability[0].pharos_class
-            ? de.druggability[0].pharos_class
-            : 'No value';
-        } else {
-          de.pharos_class_display_value = 'No value';
-        }
+        de.pharos_class_display_value = de.druggability.pharos_class;
       });
 
       this.genes = genes;
diff --git a/src/app/features/genes/components/gene-similar/gene-similar.component.ts b/src/app/features/genes/components/gene-similar/gene-similar.component.ts
index 3bcb4159..4135149f 100644
--- a/src/app/features/genes/components/gene-similar/gene-similar.component.ts
+++ b/src/app/features/genes/components/gene-similar/gene-similar.component.ts
@@ -107,13 +107,7 @@ export class GeneSimilarComponent implements OnInit {
           de.nominated_target_display_value = false;
 
         // Populate Druggability display fields
-        if (de.druggability && de.druggability.length) {
-          de.pharos_class_display_value = de.druggability[0].pharos_class
-            ? de.druggability[0].pharos_class
-            : 'No value';
-        } else {
-          de.pharos_class_display_value = 'No value';
-        }
+        de.pharos_class_display_value = de.druggability.pharos_class;
       });
 
       this.genes = genes;
diff --git a/src/app/models/genes.ts b/src/app/models/genes.ts
index f7ea1958..f7ba2e8f 100644
--- a/src/app/models/genes.ts
+++ b/src/app/models/genes.ts
@@ -23,7 +23,6 @@ export interface TargetNomination {
   input_data: string;
   validation_study_details: string;
   initial_nomination: number;
-  //
   team_data?: Team;
 }
 
@@ -41,7 +40,7 @@ export interface Druggability {
   sm_druggability_bucket: number;
   safety_bucket: number;
   abability_bucket: number;
-  pharos_class: string;
+  pharos_class: string[];
   // classification should really be named sm_druggability_bucket_definition
   classification: string;
   safety_bucket_definition: string;
@@ -64,7 +63,7 @@ export interface Gene {
   protein_brain_change_studied: boolean;
   target_nominations: TargetNomination[] | null;
   median_expression: MedianExpression[];
-  druggability: Druggability[];
+  druggability: Druggability;
   total_nominations: number | null;
   is_adi: boolean;
   is_tep: boolean;
@@ -85,7 +84,7 @@ export interface Gene {
   similar_genes_network?: SimilarGenesNetwork;
 
   // Similar table (not in mongo document)
-  pharos_class_display_value?: string;
+  pharos_class_display_value?: string[];
   is_any_rna_changed_in_ad_brain_display_value?: string;
   is_any_protein_changed_in_ad_brain_display_value?: string;
   nominated_target_display_value?: boolean;
diff --git a/src/app/testing/gene-mocks.ts b/src/app/testing/gene-mocks.ts
index 3ba576d3..0edc07b0 100644
--- a/src/app/testing/gene-mocks.ts
+++ b/src/app/testing/gene-mocks.ts
@@ -205,20 +205,18 @@ export const geneMock1: Gene = {
       tissue: 'STG',
     },
   ],
-  druggability: [
-    {
-      sm_druggability_bucket: 3,
-      safety_bucket: 4,
-      abability_bucket: 3,
-      pharos_class: 'Tbio',
-      classification:
-        'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
-      safety_bucket_definition:
-        'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
-      abability_bucket_definition:
-        'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
-    },
-  ],
+  druggability: {
+    sm_druggability_bucket: 3,
+    safety_bucket: 4,
+    abability_bucket: 3,
+    pharos_class: ['Tbio'],
+    classification:
+      'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+    safety_bucket_definition:
+      'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+    abability_bucket_definition:
+      'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+  },
   total_nominations: 5,
   rna_differential_expression: [
     {
@@ -3129,20 +3127,18 @@ export const geneMock2: Gene = {
       tissue: 'STG',
     },
   ],
-  druggability: [
-    {
-      sm_druggability_bucket: 3,
-      safety_bucket: 4,
-      abability_bucket: 3,
-      pharos_class: 'Tbio',
-      classification:
-        'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
-      safety_bucket_definition:
-        'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
-      abability_bucket_definition:
-        'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
-    },
-  ],
+  druggability: {
+    sm_druggability_bucket: 3,
+    safety_bucket: 4,
+    abability_bucket: 3,
+    pharos_class: ['Tbio'],
+    classification:
+      'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+    safety_bucket_definition:
+      'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+    abability_bucket_definition:
+      'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+  },
   total_nominations: 3,
   is_adi: false,
   is_tep: true,
@@ -3257,20 +3253,18 @@ export const geneMock3: Gene = {
       tissue: 'STG',
     },
   ],
-  druggability: [
-    {
-      sm_druggability_bucket: 3,
-      safety_bucket: 4,
-      abability_bucket: 3,
-      pharos_class: 'Tbio',
-      classification:
-        'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
-      safety_bucket_definition:
-        'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
-      abability_bucket_definition:
-        'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
-    },
-  ],
+  druggability: {
+    sm_druggability_bucket: 3,
+    safety_bucket: 4,
+    abability_bucket: 3,
+    pharos_class: ['Tbio'],
+    classification:
+      'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+    safety_bucket_definition:
+      'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+    abability_bucket_definition:
+      'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+  },
   total_nominations: null,
   is_adi: false,
   is_tep: true,
@@ -3441,20 +3435,18 @@ export const nominatedGeneMock1: Gene = {
     },
   ],
   median_expression: [],
-  druggability: [
-    {
-      sm_druggability_bucket: 3,
-      safety_bucket: 4,
-      abability_bucket: 3,
-      pharos_class: 'Tbio',
-      classification:
-        'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
-      safety_bucket_definition:
-        'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
-      abability_bucket_definition:
-        'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
-    },
-  ],
+  druggability: {
+    sm_druggability_bucket: 3,
+    safety_bucket: 4,
+    abability_bucket: 3,
+    pharos_class: ['Tbio'],
+    classification:
+      'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+    safety_bucket_definition:
+      'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+    abability_bucket_definition:
+      'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+  },
   total_nominations: 4,
   is_adi: false,
   is_tep: false,
@@ -3544,20 +3536,18 @@ export const noHGNCgeneMock: Gene = {
     },
   ],
   median_expression: [],
-  druggability: [
-    {
-      sm_druggability_bucket: 3,
-      safety_bucket: 4,
-      abability_bucket: 3,
-      pharos_class: 'Tbio',
-      classification:
-        'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
-      safety_bucket_definition:
-        'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
-      abability_bucket_definition:
-        'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
-    },
-  ],
+  druggability: {
+    sm_druggability_bucket: 3,
+    safety_bucket: 4,
+    abability_bucket: 3,
+    pharos_class: ['Tbio'],
+    classification:
+      'Targetable by structure: Structurally druggable protein, based on the presence of a druggable pocket in the protein (DrugEBIlity/CanSAR).',
+    safety_bucket_definition:
+      'More than two of: high off target gene expression, cancer driver, essential gene, associated deleterious genetic disorder, HPO phenotype associated gene, or black box warning on clinically used drug.',
+    abability_bucket_definition:
+      'Cell membrane-bound proteins. Highly accessible to antibody-based therapies, but potentially less so than secreted proteins or ECM components.',
+  },
   total_nominations: 4,
   is_adi: false,
   is_tep: false,
diff --git a/src/server/models/genes.ts b/src/server/models/genes.ts
index aea8b9e3..e714e078 100644
--- a/src/server/models/genes.ts
+++ b/src/server/models/genes.ts
@@ -53,7 +53,7 @@ const DruggabilitySchema = new Schema<Druggability>({
   sm_druggability_bucket: { type: Number, required: true },
   safety_bucket: { type: Number, required: true },
   abability_bucket: { type: Number, required: true },
-  pharos_class: { type: String, required: true },
+  pharos_class: { type: [String], required: true },
   classification: { type: String, required: true },
   safety_bucket_definition: { type: String, required: true },
   abability_bucket_definition: { type: String, required: true },
@@ -76,7 +76,7 @@ const GeneSchema = new Schema<Gene>(
     protein_brain_change_studied: { type: Boolean, required: true },
     target_nominations: { type: [TargetNominationSchema], required: true },
     median_expression: { type: [MedianExpressionSchema], required: true },
-    druggability: { type: [DruggabilitySchema], required: true },
+    druggability: { type: DruggabilitySchema, required: true },
     total_nominations: { type: Number, required: true },
     ensembl_info: { type: EnsemblInfoSchema, required: true }
   },

From 4a9d8d41ebae38fdaef0a9fea9bee6732d825e43 Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Tue, 17 Dec 2024 16:16:02 -0800
Subject: [PATCH 33/33] fix pharos class schema bug

---
 .../gene-nominated-targets/gene-nominated-targets.component.ts | 3 ++-
 .../genes/components/gene-similar/gene-similar.component.ts    | 3 ++-
 src/app/models/genes.ts                                        | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts b/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
index d50d9e36..4934dd58 100644
--- a/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
+++ b/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
@@ -119,7 +119,8 @@ export class GeneNominatedTargetsComponent implements OnInit {
           : undefined;
 
         // Populate Druggability display fields
-        de.pharos_class_display_value = de.druggability.pharos_class;
+        if (de.druggability)
+          de.pharos_class_display_value = de.druggability.pharos_class;
       });
 
       this.genes = genes;
diff --git a/src/app/features/genes/components/gene-similar/gene-similar.component.ts b/src/app/features/genes/components/gene-similar/gene-similar.component.ts
index 4135149f..bf8744fa 100644
--- a/src/app/features/genes/components/gene-similar/gene-similar.component.ts
+++ b/src/app/features/genes/components/gene-similar/gene-similar.component.ts
@@ -107,7 +107,8 @@ export class GeneSimilarComponent implements OnInit {
           de.nominated_target_display_value = false;
 
         // Populate Druggability display fields
-        de.pharos_class_display_value = de.druggability.pharos_class;
+        if (de.druggability)
+          de.pharos_class_display_value = de.druggability.pharos_class;
       });
 
       this.genes = genes;
diff --git a/src/app/models/genes.ts b/src/app/models/genes.ts
index f7ba2e8f..7f11a466 100644
--- a/src/app/models/genes.ts
+++ b/src/app/models/genes.ts
@@ -40,7 +40,7 @@ export interface Druggability {
   sm_druggability_bucket: number;
   safety_bucket: number;
   abability_bucket: number;
-  pharos_class: string[];
+  pharos_class?: string[];
   // classification should really be named sm_druggability_bucket_definition
   classification: string;
   safety_bucket_definition: string;