chore: move contents of explorer to top level (#4230)

.eslintignore

@@ -0,0 +1,10 @@
+**/node_modules/*
+**/out/*
+**/.next/*
+
+build
+
+/analytics
+/.gitlab
+/reports
+/meta-scripts

.github/dependabot.yml

@@ -9,4 +9,4 @@ updates:
       interval: "daily"
     assignees:
       - "noopdog"
-    open-pull-requests-limit: 50
+    open-pull-requests-limit: 50

.github/workflows/label.yml

@@ -7,7 +7,7 @@ jobs:
       pull-requests: write
     runs-on: ubuntu-latest
     steps:
-    - uses: DataBiosphere/azul-github-labeler-action@releases/v5
-      with:
-        repo-token: "${{secrets.GITHUB_TOKEN}}"
-        label: canary
+      - uses: DataBiosphere/azul-github-labeler-action@releases/v5
+        with:
+          repo-token: "${{secrets.GITHUB_TOKEN}}"
+          label: canary

.github/workflows/run-checks.yml

@@ -1,5 +1,5 @@
 name: Run checks
-on: [ pull_request ]
+on: [pull_request]
 
 jobs:
   build:
@@ -10,7 +10,6 @@ jobs:
         with:
           node-version: "20.10.0"
       - run: |
-          cd explorer
           npm ci
           npm run check-format
           npm run lint

.github/workflows/run-playwright-tests-anvil-catalog.yml

@@ -1,9 +1,9 @@
 name: Playwright Tests anvil-catalog
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
 jobs:
   test:
     timeout-minutes: 60
@@ -15,25 +15,22 @@ jobs:
           node-version: "20.10.0"
       - name: Install dependencies
         run: |
-            cd explorer
-            npm ci
+          npm ci
       - name: Install Playwright Browsers
         run: |
-            cd explorer
-            npx playwright install --with-deps
+          npx playwright install --with-deps
       - name: Build AnVIL-catalog database
         run: |
-            cd ./explorer/files
-            npm ci
-            mkdir ./anvil-catalog/out
-            npm run build-anvil-db
+          cd ./files
+          npm ci
+          mkdir ./anvil-catalog/out
+          npm run build-anvil-db
       - name: Run Playwright tests
         run: |
-          cd explorer
           npm run test:anvil-catalog
       - uses: actions/upload-artifact@v3
         if: always()
         with:
           name: playwright-report
-          path: explorer/playwright-report/
-          retention-days: 30
+          path: playwright-report/
+          retention-days: 30

.github/workflows/run-playwright-tests-anvil-cmg.yml

@@ -1,9 +1,9 @@
 name: Playwright Tests anvil-cmg
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
 jobs:
   test:
     timeout-minutes: 60
@@ -15,27 +15,22 @@ jobs:
           node-version: "20.10.0"
       - name: Install dependencies
         run: |
-            cd explorer
-            npm ci
+          npm ci
       - name: Check Backend System Status - TEST RESULTS ARE NOT VALID IF THIS FAILS
         run: |
-            cd explorer
-            npm run check-system-status:anvil-cmg
+          npm run check-system-status:anvil-cmg
       - name: Install Playwright Browsers
         run: |
-            cd explorer
-            npx playwright install --with-deps
+          npx playwright install --with-deps
       - name: Run Playwright tests
         run: |
-          cd explorer
           npm run test:anvil-cmg
       - name: Check backend status again - TEST RESULTS ARE NOT VALID IF THIS FAILS
         run: |
-          cd explorer
           npm run check-system-status:anvil-cmg
       - uses: actions/upload-artifact@v3
         if: always()
         with:
           name: playwright-report
-          path: explorer/playwright-report/
-          retention-days: 30
+          path: playwright-report/
+          retention-days: 30

.gitignore

@@ -1,21 +1,64 @@
+# See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
+
+# dependencies
 node_modules
-node_modules_bak
-.tmp
+/.pnp
+.pnp.js
 
-# IDEs and editors
-.idea
+# testing
+/coverage
+/test-results/*
+
+# next.js
+/.next/
+/out/
 
-#Typescript
-typings
+# production
+/build
 
 # misc
-npm-debug.log
-downloads/*
+.DS_Store
+*.pem
+.tmp
+/downloads/*
+
+# debug
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+.pnpm-debug.log*
 
 #System Files
 .DS_Store
 Thumbs.db
 
+# env files
+/.env*.local
+/.env.development
+/.env.production
+
+# vercel
+.vercel
+
+# typescript
+*.tsbuildinfo
+
+# IDEs and editors
+.idea
+/.vscode
+
+# hygen
+_templates
+
+# nvm
+.nvmrc
+
+# favicons
+/public/favicons/*
+
+/files/anvil-catalog/out/
+/files/ncpi-catalog/out/
+
 #Python
 __pycache__/
 /analytics/**/_build

.gitlab/fragments/explorer/build.yaml

@@ -1,7 +1,6 @@
 script:
-  - cd explorer
   - (cd files && npm ci)
   - npm ci
   - rm -rf out
   - npm run "$data_browser_build_script"
-  - tar -cvj -f ../.gitlab/distribution.tar.bz2 out
+  - tar -cvj -f ./.gitlab/distribution.tar.bz2 out

explorer/.husky/commit-msg → .husky/commit-msg

@@ -13,8 +13,6 @@ if ! grep -iqE "$commit_regex" "$1"; then
     exit 1
 fi
 
-cd explorer
-
 # Check for Conventional Commits format
 
 npx commitlint --config ./commitlint.config.js --edit $1

explorer/.husky/pre-commit → .husky/pre-commit

@@ -1,8 +1,6 @@
 #!/bin/sh
 . "$(dirname "$0")/_/husky.sh"
 
-cd explorer
-
 echo '🏗️👷 Checking your project before committing'
 
 # Check Prettier

explorer/.prettierignore → .prettierignore

@@ -1,6 +1,9 @@
 # general
 README.md
 /CHANGELOG.md
+/analytics
+/.gitlab
+/reports
 
 # testing
 coverage

docs/configuration-guide.md

@@ -1,6 +1,7 @@
 # Configuration Guide
 
 ## Configuring an Entity List
+
 Entity lists display result sets from either an API endpoint or a TSV and can be statically built or dynamically requested. To configure an entity list:
 
 ### 1. Add Response Model
@@ -9,50 +10,59 @@ Entity lists display result sets from either an API endpoint or a TSV and can be
 
 The Azul entity list API endpoint returns entities (`hits`) in a format that can be modeled as a response object containing a core entity and multiple aggregated entities. For example:
 
-* A `hits` value returned from the `/index/files` endpoint contains:
+- A `hits` value returned from the `/index/files` endpoint contains:
 
   1. File entity
   2. Aggregated projects
   3. Aggregated samples
   4. Aggregated values for all other entities...
 
-* A `hits` value returned from the `/index/projects` endpoint contains:
+- A `hits` value returned from the `/index/projects` endpoint contains:
+
   1. Project entity
   2. Aggregated files
   3. Aggregated samples
   4. Aggregated values for all other entities...
 
-* A `hits` value returned from the `/index/samples` endpoint contains:
+- A `hits` value returned from the `/index/samples` endpoint contains:
   1. Sample entity
   2. Aggregated files
   3. Aggregated projects
   4. Aggregated values for all other entities...
 
 An Azul entities endpoint requires the following models:
-* `XEntity` - the core entity returned from the endpoint (e.g. the single element contained in the `files` array value returned in `/index/files`). Core entity models are added to `/apis/azul/${site}/common/entities`.
-* `XEntityResponse` - a model of the singleton array containing the core entity, returned from the endpoint (e.g. the `files` array value returned in `/index/files`). Entity response models are added to `/apis/azul/${site}/common/entities`.
-* `AggregatedY` - an aggregated entity returned from the endpoint (e.g. the `projects` or `files` values returned in `/index/files`).  Aggregated entities are added to `/apis/azul/${site}/common/aggregatedEntities`.
-* `XsResponse` - a model of the full response returned from the endpoint. Response models are added to `/apis/azul/${site}/common/responses`.
+
+- `XEntity` - the core entity returned from the endpoint (e.g. the single element contained in the `files` array value returned in `/index/files`). Core entity models are added to `/apis/azul/${site}/common/entities`.
+- `XEntityResponse` - a model of the singleton array containing the core entity, returned from the endpoint (e.g. the `files` array value returned in `/index/files`). Entity response models are added to `/apis/azul/${site}/common/entities`.
+- `AggregatedY` - an aggregated entity returned from the endpoint (e.g. the `projects` or `files` values returned in `/index/files`). Aggregated entities are added to `/apis/azul/${site}/common/aggregatedEntities`.
+- `XsResponse` - a model of the full response returned from the endpoint. Response models are added to `/apis/azul/${site}/common/responses`.
 
 #### 1.2 TSV Response Model
+
 Add an interface matching the response model expected from the API endpoint or TSV row.
-* Naming convention: `entities.ts`.
-* Location: `/apis/${apiName}/common`.
+
+- Naming convention: `entities.ts`.
+- Location: `/apis/${apiName}/common`.
 
 ### 2. Create Entity List-Specific Configuration
-* Naming convention: `entityNameEntityConfig.ts`.
-* Location: `/site-config/${site}/${env}/index`.
-* Entity list configuration implements `EntityConfig<T>` where `T` is the response model defined above in step 1.
-* Once configured, the entity list configuration must be specified in the `entities` array in the site config.
+
+- Naming convention: `entityNameEntityConfig.ts`.
+- Location: `/site-config/${site}/${env}/index`.
+- Entity list configuration implements `EntityConfig<T>` where `T` is the response model defined above in step 1.
+- Once configured, the entity list configuration must be specified in the `entities` array in the site config.
 
 ### 3. Create a View Builder
-A view builder contains functions that build the component props required for displaying a value in an entity list. Each function takes at least a response model (either from an API endpoint or a row in a TSV), is parameterized by the type of component it builds props for and uses transformers to convert the response value into prop-specific values. 
-* Naming convention: `viewModelBuilders.ts`. A view builder is API-specific.
-* Location: `/viewModelBuilders/${apiName}/common/`.
-* Function naming convention: `buildX` where `X` is the response value to display.
+
+A view builder contains functions that build the component props required for displaying a value in an entity list. Each function takes at least a response model (either from an API endpoint or a row in a TSV), is parameterized by the type of component it builds props for and uses transformers to convert the response value into prop-specific values.
+
+- Naming convention: `viewModelBuilders.ts`. A view builder is API-specific.
+- Location: `/viewModelBuilders/${apiName}/common/`.
+- Function naming convention: `buildX` where `X` is the response value to display.
 
 ### 4. Create a Response Transformer
+
 A transformer contains functions that map a response model (either from an API endpoint or a row in a TSV) to a view model that is optimized for display.
-* Naming convention: `transformers.ts`. A transformer is API-specific.
-* Location: `/apis/${apiName}/common/`.
-* Function naming convention: `getX` where `X` is the response value to transform.
+
+- Naming convention: `transformers.ts`. A transformer is API-specific.
+- Location: `/apis/${apiName}/common/`.
+- Function naming convention: `getX` where `X` is the response value to transform.