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 01/34] 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 }}/" "${{ vars.TEAM_IMAGES_ID }}" From 841db259b510c856fcc38af54926930ce45bb947 Mon Sep 17 00:00:00 2001 From: Hallie Swan <26949006+hallieswan@users.noreply.github.com> Date: Wed, 5 Jun 2024 16:19:16 -0700 Subject: [PATCH 02/34] AG-1473: create mongo image containing release data --- .github/workflows/e2e.yml | 14 +++++++++++++ docker/Dockerfile | 27 +++++++++++++++++++++++++ docker/docker-compose.yml | 20 +++++++++++++++++++ docker/import-data.sh | 42 +++++++++++++++++++++++++++++++++++++++ scripts/collections.csv | 16 +++++++++++++++ 5 files changed, 119 insertions(+) create mode 100644 docker/Dockerfile create mode 100644 docker/docker-compose.yml create mode 100644 docker/import-data.sh create mode 100644 scripts/collections.csv diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml index 83e8f49a..531e798a 100644 --- a/.github/workflows/e2e.yml +++ b/.github/workflows/e2e.yml @@ -72,3 +72,17 @@ jobs: echo "==> download team images" synapse get -r --downloadLocation "${{ 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 03/34] 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 04/34] 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 05/34] 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 06/34] 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 07/34] 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}" >> "$GITHUB_OUTPUT" build-image: From 072d0fcbc1dc44fd19f1a40be82ee393c73bf14c Mon Sep 17 00:00:00 2001 From: Hallie Swan <26949006+hallieswan@users.noreply.github.com> Date: Thu, 13 Jun 2024 14:39:45 -0700 Subject: [PATCH 08/34] AG-1472: remove forward slash from package name so gh call works --- .github/workflows/e2e.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml index 891cbac6..2f335c4a 100644 --- a/.github/workflows/e2e.yml +++ b/.github/workflows/e2e.yml @@ -16,7 +16,7 @@ jobs: packages: read environment: e2e env: - DATA_IMAGE_NAME: '${{ 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 09/34] 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 10/34] 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 11/34] 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] --- 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 12/34] 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}" >> "$GITHUB_OUTPUT" - name: login to GitHub Container Registry From 194503281aeeab84f3f585138ce04ee49d001d68 Mon Sep 17 00:00:00 2001 From: Hallie Swan <26949006+hallieswan@users.noreply.github.com> Date: Fri, 14 Jun 2024 14:59:33 -0700 Subject: [PATCH 13/34] AG-1498: support use of containerized data image in local development [skip ci] --- .env.example | 5 +++++ .gitignore | 4 ++++ README.md | 42 +++++++++++++++++++++++++++++++++------ docker/README.md | 4 ++-- docker/docker-compose.yml | 1 + package.json | 8 +++++++- 6 files changed, 55 insertions(+), 9 deletions(-) create mode 100644 .env.example diff --git a/.env.example b/.env.example new file mode 100644 index 00000000..6f395adf --- /dev/null +++ b/.env.example @@ -0,0 +1,5 @@ +DB_USER="root" +DB_PASS="${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 14/34] 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 15/34] 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 16/34] 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 ... 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"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 Date: Fri, 1 Nov 2024 17:18:18 -0700 Subject: [PATCH 17/34] 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 Date: Wed, 6 Nov 2024 11:14:55 -0800 Subject: [PATCH 18/34] 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 19/34] 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 @@ -
-
-
-
-

- Druggability of {{ gene.hgnc_symbol || gene.ensembl_gene_id }} -

-

- 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. -

- - - -
- - -
-
-
-
-
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 20/34] 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 @@
-
+
-
-

- Druggability of {{ gene.hgnc_symbol || gene.ensembl_gene_id }} -

-

- 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. -

- - - -
- - +

+ Drug Development Resources +

+

+ These external sites provide drug development resources. +

+
+
{{ r.title }}
+ +
+ {{ r.description }} +
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 21/34] 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 @@

Biological Domains

{{ getBiodomains() }}

+
+

PHAROS

+

{{ gene.druggability[0].pharos_class }}

+

Also known as

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 22/34] 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 @@

Biological Domains

-

PHAROS

+

Pharos Class

{{ gene.druggability[0].pharos_class }}

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 23/34] 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 @@ -
-
-
-

- Drug Development Resources -

-

- These external sites provide drug development resources. -

-
-
{{ r.title }}
- -
- {{ r.description }} -
-
-
-
-
-
@@ -57,12 +30,39 @@

Target Enabling Resources

+
+
+
+

+ Drug Development Resources +

+

+ These external sites provide information and resources related to drug development. +

+
+
{{ r.title }}
+ +
+ {{ r.description }} +
+
+
+
+
+

Additional Resources

- 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.

Date: Wed, 27 Nov 2024 11:39:35 -0800 Subject: [PATCH 24/34] 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 25/34] 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 26/34] 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 @@

{{ getSummary() }}

- +

Biological Domains

- {{ getBiodomains() }} +   {{ getBiodomains() }}

Also known as

-

- {{ gene.ensembl_gene_id }} +

+   {{ gene.ensembl_gene_id }} (Ensembl Release {{ gene.ensembl_info.ensembl_release }})

- - {{ gene.ensembl_gene_id }} - -

- Possible replacement values: +

+   {{ gene.ensembl_gene_id }} +

+

+   Possible replacement values: {{ gene.ensembl_info.ensembl_possible_replacements.join(', ')}}

-

- {{ getAlias() }} +

+   UNIPROTKB + + {{ accession }}, + +

+

+   {{ getAliases() }}

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( 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 27/34] 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 @@

Biological Domains

{{ getBiodomains() }}

-
+

Pharos Class

{{ gene.druggability[0].pharos_class }}

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 28/34] 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 @@


Biological Domains

-

-   {{ getBiodomains() }} +

+ {{ getBiodomains() }}

Also known as

-   {{ gene.ensembl_gene_id }} + {{ gene.ensembl_gene_id }} (Ensembl Release {{ gene.ensembl_info.ensembl_release }})

-

-   {{ gene.ensembl_gene_id }} +

+ {{ gene.ensembl_gene_id }}

-   Possible replacement values: + Possible replacement values: {{ gene.ensembl_info.ensembl_possible_replacements.join(', ')}}

-   UNIPROTKB + UNIPROTKB {{ accession }},

-   {{ getAliases() }} + {{ getAliases() }}

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 29/34] 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 30/34] 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 31/34] 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 32/34] 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 @@

Biological Domains

{{ getBiodomains() }}

-
+

Pharos Class

-

{{ gene.druggability[0].pharos_class }}

+

{{ gene.druggability.pharos_class.join(', ') }}

Also known as

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({ 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( 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 33/34] 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; From 9a45720ed9914ffc52335ec1e644537231ea72ba Mon Sep 17 00:00:00 2001 From: Beatriz Saldana <37123591+beatrizsaldana@users.noreply.github.com> Date: Wed, 18 Dec 2024 10:33:46 -0800 Subject: [PATCH 34/34] Dev to Staging: Agora 3.5.0 and Data mv71 (#1343) * AG-1471: install synapseclient, download release data from Synpase * AG-1473: create mongo image containing release data * AG-1474: run e2e tests * AG-1471: do not run job on pull_request trigger since forks do not have access to secrets * AG-1472: check if image exists in GHCR, then build/push image if needed * AG-1472: split workflow into three jobs * AG-1472: handle case where package has not yet been created * AG-1472: remove forward slash from package name so gh call works * AG-1472: ensure e2e tests are run when image has already been built * AG-1472: improvements from code review * 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] * AG-1472: ensure org package is lowercase * AG-1498: support use of containerized data image in local development [skip ci] * AG-1330: combine workflows into one workflow with multiple jobs * AG-1518: rename data release image to distinguish from sage-monorepo image * 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] * Bump to mv70 (display) in dev * AG-1395: Fix typo in manifest version value * removed druggability section in gene details resources tab * added new resource cards in Resources tab * adding pharos class to hero * updated section title from PHAROS to PHAROS CLASS * Adjust ordering of resource sections * Update resource strings and URLs * Update mongoDB install URLs in README * adding uniprotkb_accessions links * applied a margin under subheadings biodomains and pharos class * adding margin to subitems in hero * added new uniprotkb_accessions property to mocks * Update ci.yml updating docker-compose to docker compose * AG-1565 remove druggability columns * AG-1599 remove pharos class * fix pharos class schema bug --------- Signed-off-by: dependabot[bot] Co-authored-by: Hallie Swan <26949006+hallieswan@users.noreply.github.com> Co-authored-by: sagely1 <114952739+sagely1@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jessica Britton Co-authored-by: JessterB <89862046+JessterB@users.noreply.github.com> --- .env.example | 5 + .github/workflows/ci.yml | 247 ++ .github/workflows/node.js.yml | 55 - .gitignore | 4 + README.md | 46 +- docker/Dockerfile | 35 + docker/README.md | 26 + docker/docker-compose.yml | 21 + docker/import-data.sh | 42 + package-lock.json | 3670 +++++++++-------- package.json | 12 +- playwright.config.ts | 14 +- scripts/collections.csv | 16 + .../gene-druggability.component.ts | 31 +- .../gene-hero/gene-hero.component.html | 26 +- .../gene-hero/gene-hero.component.scss | 18 +- .../gene-hero/gene-hero.component.ts | 9 +- .../gene-nominated-targets.component.ts | 39 +- .../gene-resources.component.html | 57 +- .../gene-resources.component.ts | 125 +- .../gene-similar/gene-similar.component.ts | 30 +- .../gene-table/gene-table.component.ts | 15 +- ...{AdditionalResource.ts => ResourceCard.ts} | 2 +- src/app/models/genes.ts | 11 +- src/app/models/index.ts | 2 +- src/app/testing/gene-mocks.ts | 135 +- src/server/api.ts | 35 +- src/server/models/genes.ts | 5 +- tests/nominated-targets.spec.ts | 53 - tests/similar-genes.spec.ts | 7 - 30 files changed, 2719 insertions(+), 2074 deletions(-) create mode 100644 .env.example create mode 100644 .github/workflows/ci.yml delete mode 100644 .github/workflows/node.js.yml create mode 100644 docker/Dockerfile create mode 100644 docker/README.md create mode 100644 docker/docker-compose.yml create mode 100644 docker/import-data.sh create mode 100644 scripts/collections.csv rename src/app/models/{AdditionalResource.ts => ResourceCard.ts} (69%) diff --git a/.env.example b/.env.example new file mode 100644 index 00000000..c0dc0e5b --- /dev/null +++ b/.env.example @@ -0,0 +1,5 @@ +DB_USER="root" +DB_PASS="${DB_PASS}" +DB_PORT="27015" +DB_NAME="agora" +DATA_IMAGE_PATH="ghcr.io/sage-bionetworks/agora-data-nonmonorepo:${DATA_IMAGE_TAG}" diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 00000000..175622d4 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,247 @@ +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 + if: ${{ github.ref_name == 'develop' || github.ref_name == 'main' || github.actor == github.repository_owner }} + timeout-minutes: 5 + runs-on: ubuntu-20.04 + permissions: + packages: read + environment: e2e + env: + ORG_NAME: 'Sage-Bionetworks' + NAMESPACE: ${{ github.repository_owner }} + DATA_IMAGE_NAME: '${{ 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 }} + 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}" >> "$GITHUB_OUTPUT" + + DATA_VERSION=$(jq -r '."data-version"' "${{ env.PACKAGE_JSON_PATH }}") + echo "DATA_VERSION=${DATA_VERSION}" >> "$GITHUB_OUTPUT" + + DATA_IMAGE_TAG="${DATA_MANIFEST_ID}.${DATA_VERSION}" + echo "DATA_IMAGE_TAG=${DATA_IMAGE_TAG}" >> "$GITHUB_OUTPUT" + + # GHCR requires image names to be lowercase: https://github.com/orgs/community/discussions/27086 + NAMESPACE_LOWERCASE=$(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 + uses: docker/login-action@v3 + with: + registry: ghcr.io + username: ${{ github.repository_owner }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: check whether image exists + id: check-container-repo + env: + # https://docs.github.com/en/rest/packages/packages?apiVersion=2022-11-28#list-package-versions-for-a-package-owned-by-an-organization + ORG_PATH: '/orgs/${{ 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 }}" ) + + # 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 + + PACKAGE_NOT_FOUND=$(echo "${IMAGE_VERSIONS}" | jq '.message? == "Package 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: + 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 + + # 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 }}/" "${{ vars.TEAM_IMAGES_ID }}" + + - name: build image + env: + DOCKERFILE_PATH: './docker/Dockerfile' + run: | + docker build \ + -t "${{ env.DATA_IMAGE_PATH }}" \ + -f "${{ env.DOCKERFILE_PATH }}" \ + --build-arg SOURCE_REPO="https://github.com/${{ github.repository }}" \ + --build-arg DESCRIPTION="${GITHUB_SHA::7}" \ + --build-arg LOCAL_DATA_PATH="${{ env.LOCAL_DATA_PATH }}" \ + --build-arg LOCAL_COLLECTIONS_PATH="${{ env.LOCAL_COLLECTIONS_PATH }}" \ + --build-arg LOCAL_IMPORT_SCRIPT_PATH="${{ env.LOCAL_IMPORT_SCRIPT_PATH }}" \ + --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: ${{ secrets.GITHUB_TOKEN }} + + # Note: if a new package is created using this workflow, then the package + # visibility will default to the source repository visibility. For example, + # a package created by a workflow in a public repo will also be public. + # Publicly visible container packages are anonymously downloadable. + - name: push to GitHub Container Registry + run: docker push "${{ env.DATA_IMAGE_PATH }}" + + run-e2e-tests: + needs: + - check-for-image + - build-image + # 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: + 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 + cache: 'npm' + + - name: install dependencies + run: npm ci + + - 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: ${{ secrets.GITHUB_TOKEN }} + + - name: start database, server, and app + run: | + echo "==> start database and data containers" + docker compose -f "${{ 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 + 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/.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 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..e4c67d16 100644 --- a/README.md +++ b/README.md @@ -35,12 +35,16 @@ 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`. -- [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: @@ -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 `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. + +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 `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 ```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/Dockerfile b/docker/Dockerfile new file mode 100644 index 00000000..41ba0461 --- /dev/null +++ b/docker/Dockerfile @@ -0,0 +1,35 @@ +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" +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 "${CREATE_INDEXES_FILE}" + +# Add GHCR labels +LABEL org.opencontainers.image.source="${SOURCE_REPO}" +LABEL org.opencontainers.image.description="${DESCRIPTION}" + +# On container startup, import data into mongodb +CMD ["/bin/bash", "import-data.sh"] \ No newline at end of file diff --git a/docker/README.md b/docker/README.md new file mode 100644 index 00000000..78416d8b --- /dev/null +++ b/docker/README.md @@ -0,0 +1,26 @@ +# Agora Docker Image + +Files in this directory: + +- `Dockerfile`: creates the `agora-data-nonmonorepo` docker image, which contains data for a particular Agora data release (manifest synId + version) and team images and will seed a mongodb at start up using `import-data.sh` +- `docker-compose.yml`: spins up `mongo` and `agora-data-nonmonorepo` docker containers + +## Workflow Setup + +The following secrets and variables need to be set up in GitHub for the `ci.yml` workflow to create the `agora-data-nonmonorepo` Docker image: + +e2e Environment secrets: + +| Variable | Description | Example | +| ------------------ | ------------------------------------------ | ----------------- | +| DB_USER | The database user | dbuser | +| DB_PASS | The database password | supersecret | +| SYNAPSE_AUTH_TOKEN | The Synapse service user view/download PAT | token-string-here | + +e2e Environment variables: + +| Variable | Description | Example | +| -------------- | ----------------------------------- | ------- | +| DB_NAME | The database name | agora | +| DB_PORT | The database port | 27017 | +| TEAM_IMAGES_ID | The synId of the team images folder | syn123 | diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml new file mode 100644 index 00000000..0a7aae29 --- /dev/null +++ b/docker/docker-compose.yml @@ -0,0 +1,21 @@ +services: + mongodb: + image: mongo + ports: + - "${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: ${DATA_IMAGE_PATH} + platform: linux/amd64 + depends_on: + - mongodb + environment: + - DB_HOST=mongodb # must match mongo service name + - DB_USER=${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/package-lock.json b/package-lock.json index 56d6ebd7..251c0982 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1181,455 +1181,634 @@ "integrity": "sha512-H71nDOOL8Y7kWRLqf6Sums+01Q5msqBW2KhDUTemh1tvY04eSkSXrK0uj/4mmY0Xr16/3zyZmsrxN7CKuRbNRg==", "dev": true }, - 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"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" @@ -31344,9 +31652,9 @@ "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" } @@ -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", diff --git a/package.json b/package.json index a92ebd8d..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": "68", + "data-version": "71", "private": true, "scripts": { "dev": "concurrently --kill-others \"npm:dev:server\" \"npm:dev:app\"", @@ -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" 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/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 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 78fef743..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 @@ -14,33 +14,43 @@

{{ getSummary() }}

- +

Biological Domains

-

+

{{ getBiodomains() }}

+
+

Pharos Class

+

{{ gene.druggability.pharos_class.join(', ') }}

+

Also known as

-

+

{{ gene.ensembl_gene_id }} (Ensembl Release {{ gene.ensembl_info.ensembl_release }})

- +

{{ gene.ensembl_gene_id }} - -

+

+

Possible replacement values: {{ gene.ensembl_info.ensembl_possible_replacements.join(', ')}}

-

- {{ getAlias() }} +

+ UNIPROTKB + + {{ accession }}, + +

+

+ {{ getAliases() }}

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..579aee65 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 { @@ -49,11 +59,15 @@ 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; } +.aliases { + margin: 0 0 0 10px; +} + .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/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..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 @@ -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) {} @@ -134,28 +119,8 @@ 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'; - 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'; - } + if (de.druggability) + de.pharos_class_display_value = de.druggability.pharos_class; }); this.genes = genes; 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..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 @@ -1,31 +1,3 @@ -
-
-
-
-

- Druggability of {{ gene.hgnc_symbol || gene.ensembl_gene_id }} -

-

- 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. -

- - - -
- - -
-
-
-
-
@@ -58,12 +30,39 @@

Target Enabling Resources

+
+
+
+

+ Drug Development Resources +

+

+ These external sites provide information and resources related to drug development. +

+
+
{{ r.title }}
+ +
+ {{ r.description }} +
+
+
+
+
+

Additional Resources

- 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.

= 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/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/genes.ts b/src/app/models/genes.ts index 6f8e5939..7f11a466 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; @@ -55,6 +54,7 @@ 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; @@ -63,7 +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; @@ -84,10 +84,7 @@ 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; + 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/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 diff --git a/src/app/testing/gene-mocks.ts b/src/app/testing/gene-mocks.ts index c26bdea0..0edc07b0 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, @@ -204,20 +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: [ { @@ -2986,6 +2985,7 @@ export const geneMock2: Gene = { 'PLEC1b', 'PLTN', ], + uniprotkb_accessions: [], is_igap: false, is_eqtl: true, is_any_rna_changed_in_ad_brain: true, @@ -3127,20 +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, @@ -3164,6 +3162,7 @@ export const geneMock3: Gene = { 'p59Hck', 'p61Hck', ], + uniprotkb_accessions: [], is_igap: false, is_eqtl: true, is_any_rna_changed_in_ad_brain: true, @@ -3254,20 +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, @@ -3372,6 +3369,7 @@ 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, @@ -3437,20 +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, @@ -3469,6 +3465,7 @@ export const noHGNCgeneMock: Gene = { summary: '', hgnc_symbol: '', alias: [], + uniprotkb_accessions: [], is_igap: false, is_eqtl: false, is_any_rna_changed_in_ad_brain: false, @@ -3539,20 +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/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 + ':' + diff --git a/src/server/models/genes.ts b/src/server/models/genes.ts index a4fe82b2..e714e078 100644 --- a/src/server/models/genes.ts +++ b/src/server/models/genes.ts @@ -53,7 +53,7 @@ const DruggabilitySchema = new Schema({ 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 }, @@ -67,6 +67,7 @@ const GeneSchema = new Schema( 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 }, @@ -75,7 +76,7 @@ const GeneSchema = new Schema( 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 } }, 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