diff --git a/explorer/.env b/.env similarity index 100% rename from explorer/.env rename to .env diff --git a/.eslintignore b/.eslintignore new file mode 100644 index 000000000..fb4fd631f --- /dev/null +++ b/.eslintignore @@ -0,0 +1,10 @@ +**/node_modules/* +**/out/* +**/.next/* + +build + +/analytics +/.gitlab +/reports +/meta-scripts diff --git a/explorer/.eslintrc.json b/.eslintrc.json similarity index 100% rename from explorer/.eslintrc.json rename to .eslintrc.json diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 4e14a66eb..eb3d33ed6 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -9,4 +9,4 @@ updates: interval: "daily" assignees: - "noopdog" - open-pull-requests-limit: 50 \ No newline at end of file + open-pull-requests-limit: 50 diff --git a/.github/workflows/label.yml b/.github/workflows/label.yml index b1cf14a47..39d219332 100644 --- a/.github/workflows/label.yml +++ b/.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 diff --git a/.github/workflows/run-checks.yml b/.github/workflows/run-checks.yml index b5b6a1cfe..1d2b72718 100644 --- a/.github/workflows/run-checks.yml +++ b/.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 diff --git a/.github/workflows/run-playwright-tests-anvil-catalog.yml b/.github/workflows/run-playwright-tests-anvil-catalog.yml index a46060008..23f7109c0 100644 --- a/.github/workflows/run-playwright-tests-anvil-catalog.yml +++ b/.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 \ No newline at end of file + path: playwright-report/ + retention-days: 30 diff --git a/.github/workflows/run-playwright-tests-anvil-cmg.yml b/.github/workflows/run-playwright-tests-anvil-cmg.yml index 20bc651b1..d7e83eca1 100644 --- a/.github/workflows/run-playwright-tests-anvil-cmg.yml +++ b/.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 \ No newline at end of file + path: playwright-report/ + retention-days: 30 diff --git a/.gitignore b/.gitignore index 39cb7e21b..1e1895ac0 100644 --- a/.gitignore +++ b/.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 diff --git a/.gitlab/fragments/explorer/build.yaml b/.gitlab/fragments/explorer/build.yaml index bc5c6ad27..8e032d914 100644 --- a/.gitlab/fragments/explorer/build.yaml +++ b/.gitlab/fragments/explorer/build.yaml @@ -1,7 +1,6 @@ script: - - cd explorer - (cd files && npm ci) - npm ci - rm -rf out - npm run "$data_browser_build_script" - - tar -cvj -f ../.gitlab/distribution.tar.bz2 out + - tar -cvj -f .gitlab/distribution.tar.bz2 out diff --git a/explorer/.husky/commit-msg b/.husky/commit-msg similarity index 97% rename from explorer/.husky/commit-msg rename to .husky/commit-msg index 1726b4279..d2c2a8cf2 100755 --- a/explorer/.husky/commit-msg +++ b/.husky/commit-msg @@ -13,8 +13,6 @@ if ! grep -iqE "$commit_regex" "$1"; then exit 1 fi -cd explorer - # Check for Conventional Commits format npx commitlint --config ./commitlint.config.js --edit $1 diff --git a/explorer/.husky/pre-commit b/.husky/pre-commit similarity index 97% rename from explorer/.husky/pre-commit rename to .husky/pre-commit index 8a9c08280..46e198e01 100755 --- a/explorer/.husky/pre-commit +++ b/.husky/pre-commit @@ -1,8 +1,6 @@ #!/bin/sh . "$(dirname "$0")/_/husky.sh" -cd explorer - echo '🏗️👷 Checking your project before committing' # Check Prettier diff --git a/explorer/.prettierignore b/.prettierignore similarity index 81% rename from explorer/.prettierignore rename to .prettierignore index efa39da96..1cd2a3cf7 100644 --- a/explorer/.prettierignore +++ b/.prettierignore @@ -1,6 +1,9 @@ # general README.md /CHANGELOG.md +/analytics +/.gitlab +/reports # testing coverage diff --git a/explorer/.prettierrc.json b/.prettierrc.json similarity index 100% rename from explorer/.prettierrc.json rename to .prettierrc.json diff --git a/explorer/.storybook/main.js b/.storybook/main.js similarity index 100% rename from explorer/.storybook/main.js rename to .storybook/main.js diff --git a/explorer/.storybook/preview-head.html b/.storybook/preview-head.html similarity index 100% rename from explorer/.storybook/preview-head.html rename to .storybook/preview-head.html diff --git a/explorer/.storybook/preview.js b/.storybook/preview.js similarity index 100% rename from explorer/.storybook/preview.js rename to .storybook/preview.js diff --git a/explorer/@types/global.d.ts b/@types/global.d.ts similarity index 100% rename from explorer/@types/global.d.ts rename to @types/global.d.ts diff --git a/explorer/__tests__/project-matrix-mapper.test.ts b/__tests__/project-matrix-mapper.test.ts similarity index 100% rename from explorer/__tests__/project-matrix-mapper.test.ts rename to __tests__/project-matrix-mapper.test.ts diff --git a/explorer/app/apis/azul/anvil-cmg/common/aggregatedEntities.ts b/app/apis/azul/anvil-cmg/common/aggregatedEntities.ts similarity index 100% rename from explorer/app/apis/azul/anvil-cmg/common/aggregatedEntities.ts rename to app/apis/azul/anvil-cmg/common/aggregatedEntities.ts diff --git a/explorer/app/apis/azul/anvil-cmg/common/constants.ts b/app/apis/azul/anvil-cmg/common/constants.ts similarity index 100% rename from explorer/app/apis/azul/anvil-cmg/common/constants.ts rename to app/apis/azul/anvil-cmg/common/constants.ts diff --git a/explorer/app/apis/azul/anvil-cmg/common/entities.ts b/app/apis/azul/anvil-cmg/common/entities.ts similarity index 100% rename from explorer/app/apis/azul/anvil-cmg/common/entities.ts rename to app/apis/azul/anvil-cmg/common/entities.ts diff --git a/explorer/app/apis/azul/anvil-cmg/common/responses.ts b/app/apis/azul/anvil-cmg/common/responses.ts similarity index 100% rename from explorer/app/apis/azul/anvil-cmg/common/responses.ts rename to app/apis/azul/anvil-cmg/common/responses.ts diff --git a/explorer/app/apis/azul/anvil-cmg/common/transformers.ts b/app/apis/azul/anvil-cmg/common/transformers.ts similarity index 100% rename from explorer/app/apis/azul/anvil-cmg/common/transformers.ts rename to app/apis/azul/anvil-cmg/common/transformers.ts diff --git a/explorer/app/apis/azul/anvil-cmg/common/utils.ts b/app/apis/azul/anvil-cmg/common/utils.ts similarity index 100% rename from explorer/app/apis/azul/anvil-cmg/common/utils.ts rename to app/apis/azul/anvil-cmg/common/utils.ts diff --git a/explorer/app/apis/azul/anvil/common/aggregatedEntities.ts b/app/apis/azul/anvil/common/aggregatedEntities.ts similarity index 100% rename from explorer/app/apis/azul/anvil/common/aggregatedEntities.ts rename to app/apis/azul/anvil/common/aggregatedEntities.ts diff --git a/explorer/app/apis/azul/anvil/common/constants.ts b/app/apis/azul/anvil/common/constants.ts similarity index 100% rename from explorer/app/apis/azul/anvil/common/constants.ts rename to app/apis/azul/anvil/common/constants.ts diff --git a/explorer/app/apis/azul/anvil/common/entities.ts b/app/apis/azul/anvil/common/entities.ts similarity index 100% rename from explorer/app/apis/azul/anvil/common/entities.ts rename to app/apis/azul/anvil/common/entities.ts diff --git a/explorer/app/apis/azul/anvil/common/responses.ts b/app/apis/azul/anvil/common/responses.ts similarity index 100% rename from explorer/app/apis/azul/anvil/common/responses.ts rename to app/apis/azul/anvil/common/responses.ts diff --git a/explorer/app/apis/azul/anvil/common/transformers.ts b/app/apis/azul/anvil/common/transformers.ts similarity index 100% rename from explorer/app/apis/azul/anvil/common/transformers.ts rename to app/apis/azul/anvil/common/transformers.ts diff --git a/explorer/app/apis/azul/common/entities.ts b/app/apis/azul/common/entities.ts similarity index 100% rename from explorer/app/apis/azul/common/entities.ts rename to app/apis/azul/common/entities.ts diff --git a/explorer/app/apis/azul/common/utils.ts b/app/apis/azul/common/utils.ts similarity index 100% rename from explorer/app/apis/azul/common/utils.ts rename to app/apis/azul/common/utils.ts diff --git a/explorer/app/apis/azul/hca-dcp/archivePreview/archivePreview.ts b/app/apis/azul/hca-dcp/archivePreview/archivePreview.ts similarity index 100% rename from explorer/app/apis/azul/hca-dcp/archivePreview/archivePreview.ts rename to app/apis/azul/hca-dcp/archivePreview/archivePreview.ts diff --git a/explorer/app/apis/azul/hca-dcp/archivePreview/constants.ts b/app/apis/azul/hca-dcp/archivePreview/constants.ts similarity index 100% rename from explorer/app/apis/azul/hca-dcp/archivePreview/constants.ts rename to app/apis/azul/hca-dcp/archivePreview/constants.ts diff --git a/explorer/app/apis/azul/hca-dcp/common/aggregatedEntities.ts b/app/apis/azul/hca-dcp/common/aggregatedEntities.ts similarity index 100% rename from explorer/app/apis/azul/hca-dcp/common/aggregatedEntities.ts rename to app/apis/azul/hca-dcp/common/aggregatedEntities.ts diff --git a/explorer/app/apis/azul/hca-dcp/common/entities.ts b/app/apis/azul/hca-dcp/common/entities.ts similarity index 100% rename from explorer/app/apis/azul/hca-dcp/common/entities.ts rename to app/apis/azul/hca-dcp/common/entities.ts diff --git a/explorer/app/apis/azul/hca-dcp/common/responses.ts b/app/apis/azul/hca-dcp/common/responses.ts similarity index 100% rename from explorer/app/apis/azul/hca-dcp/common/responses.ts rename to app/apis/azul/hca-dcp/common/responses.ts diff --git a/explorer/app/apis/azul/hca-dcp/common/utils.ts b/app/apis/azul/hca-dcp/common/utils.ts similarity index 100% rename from explorer/app/apis/azul/hca-dcp/common/utils.ts rename to app/apis/azul/hca-dcp/common/utils.ts diff --git a/explorer/app/apis/catalog/anvil-catalog/common/entities.ts b/app/apis/catalog/anvil-catalog/common/entities.ts similarity index 100% rename from explorer/app/apis/catalog/anvil-catalog/common/entities.ts rename to app/apis/catalog/anvil-catalog/common/entities.ts diff --git a/explorer/app/apis/catalog/anvil-catalog/common/utils.ts b/app/apis/catalog/anvil-catalog/common/utils.ts similarity index 100% rename from explorer/app/apis/catalog/anvil-catalog/common/utils.ts rename to app/apis/catalog/anvil-catalog/common/utils.ts diff --git a/explorer/app/apis/catalog/common/entities.ts b/app/apis/catalog/common/entities.ts similarity index 100% rename from explorer/app/apis/catalog/common/entities.ts rename to app/apis/catalog/common/entities.ts diff --git a/explorer/app/apis/catalog/common/utils.ts b/app/apis/catalog/common/utils.ts similarity index 100% rename from explorer/app/apis/catalog/common/utils.ts rename to app/apis/catalog/common/utils.ts diff --git a/explorer/app/apis/catalog/ncpi-catalog/common/entities.ts b/app/apis/catalog/ncpi-catalog/common/entities.ts similarity index 100% rename from explorer/app/apis/catalog/ncpi-catalog/common/entities.ts rename to app/apis/catalog/ncpi-catalog/common/entities.ts diff --git a/explorer/app/apis/catalog/ncpi-catalog/common/utils.ts b/app/apis/catalog/ncpi-catalog/common/utils.ts similarity index 100% rename from explorer/app/apis/catalog/ncpi-catalog/common/utils.ts rename to app/apis/catalog/ncpi-catalog/common/utils.ts diff --git a/explorer/app/common/types.ts b/app/common/types.ts similarity index 100% rename from explorer/app/common/types.ts rename to app/common/types.ts diff --git a/explorer/app/components/Detail/components/AccessibilityBadge/accessibilityBadge.styles.ts b/app/components/Detail/components/AccessibilityBadge/accessibilityBadge.styles.ts similarity index 100% rename from explorer/app/components/Detail/components/AccessibilityBadge/accessibilityBadge.styles.ts rename to app/components/Detail/components/AccessibilityBadge/accessibilityBadge.styles.ts diff --git a/explorer/app/components/Detail/components/AccessibilityBadge/accessibilityBadge.tsx b/app/components/Detail/components/AccessibilityBadge/accessibilityBadge.tsx similarity index 100% rename from explorer/app/components/Detail/components/AccessibilityBadge/accessibilityBadge.tsx rename to app/components/Detail/components/AccessibilityBadge/accessibilityBadge.tsx diff --git a/explorer/app/components/Detail/components/AccessibilityBadge/components/Stack/stack.tsx b/app/components/Detail/components/AccessibilityBadge/components/Stack/stack.tsx similarity index 100% rename from explorer/app/components/Detail/components/AccessibilityBadge/components/Stack/stack.tsx rename to app/components/Detail/components/AccessibilityBadge/components/Stack/stack.tsx diff --git a/explorer/app/components/Detail/components/ConsentCodeList/consentCodeList.tsx b/app/components/Detail/components/ConsentCodeList/consentCodeList.tsx similarity index 100% rename from explorer/app/components/Detail/components/ConsentCodeList/consentCodeList.tsx rename to app/components/Detail/components/ConsentCodeList/consentCodeList.tsx diff --git a/explorer/app/components/Detail/components/ConsentTooltip/consentTooltip.tsx b/app/components/Detail/components/ConsentTooltip/consentTooltip.tsx similarity index 100% rename from explorer/app/components/Detail/components/ConsentTooltip/consentTooltip.tsx rename to app/components/Detail/components/ConsentTooltip/consentTooltip.tsx diff --git a/explorer/app/components/Detail/components/Consortium/components/ConsortiumDescription/components/ConsortiumDescriptionFallback/consortiumDescriptionFallback.tsx b/app/components/Detail/components/Consortium/components/ConsortiumDescription/components/ConsortiumDescriptionFallback/consortiumDescriptionFallback.tsx similarity index 100% rename from explorer/app/components/Detail/components/Consortium/components/ConsortiumDescription/components/ConsortiumDescriptionFallback/consortiumDescriptionFallback.tsx rename to app/components/Detail/components/Consortium/components/ConsortiumDescription/components/ConsortiumDescriptionFallback/consortiumDescriptionFallback.tsx diff --git a/explorer/app/components/Detail/components/Consortium/components/ConsortiumDescription/consortiumDescription.styles.ts b/app/components/Detail/components/Consortium/components/ConsortiumDescription/consortiumDescription.styles.ts similarity index 100% rename from explorer/app/components/Detail/components/Consortium/components/ConsortiumDescription/consortiumDescription.styles.ts rename to app/components/Detail/components/Consortium/components/ConsortiumDescription/consortiumDescription.styles.ts diff --git a/explorer/app/components/Detail/components/Consortium/components/ConsortiumDescription/consortiumDescription.tsx b/app/components/Detail/components/Consortium/components/ConsortiumDescription/consortiumDescription.tsx similarity index 100% rename from explorer/app/components/Detail/components/Consortium/components/ConsortiumDescription/consortiumDescription.tsx rename to app/components/Detail/components/Consortium/components/ConsortiumDescription/consortiumDescription.tsx diff --git a/explorer/app/components/Detail/components/EntityGuard/common/entities.ts b/app/components/Detail/components/EntityGuard/common/entities.ts similarity index 100% rename from explorer/app/components/Detail/components/EntityGuard/common/entities.ts rename to app/components/Detail/components/EntityGuard/common/entities.ts diff --git a/explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx b/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx similarity index 100% rename from explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx rename to app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx diff --git a/explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx b/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx similarity index 100% rename from explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx rename to app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx diff --git a/explorer/app/components/Detail/components/EntityGuard/entityGuard.styles.ts b/app/components/Detail/components/EntityGuard/entityGuard.styles.ts similarity index 100% rename from explorer/app/components/Detail/components/EntityGuard/entityGuard.styles.ts rename to app/components/Detail/components/EntityGuard/entityGuard.styles.ts diff --git a/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx b/app/components/Detail/components/EntityGuard/entityGuard.tsx similarity index 100% rename from explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx rename to app/components/Detail/components/EntityGuard/entityGuard.tsx diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/archivePreviewDialog.styles.ts b/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/archivePreviewDialog.styles.ts similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/archivePreviewDialog.styles.ts rename to app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/archivePreviewDialog.styles.ts diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/archivePreviewDialog.tsx b/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/archivePreviewDialog.tsx similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/archivePreviewDialog.tsx rename to app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/archivePreviewDialog.tsx diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/components/ArchivePreviewTable/archivePreviewTable.styles.ts b/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/components/ArchivePreviewTable/archivePreviewTable.styles.ts similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/components/ArchivePreviewTable/archivePreviewTable.styles.ts rename to app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/components/ArchivePreviewTable/archivePreviewTable.styles.ts diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/components/ArchivePreviewTable/archivePreviewTable.tsx b/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/components/ArchivePreviewTable/archivePreviewTable.tsx similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/components/ArchivePreviewTable/archivePreviewTable.tsx rename to app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/components/ArchivePreviewTable/archivePreviewTable.tsx diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationArchivePreview/fileLocationArchivePreview.styles.ts b/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationArchivePreview/fileLocationArchivePreview.styles.ts similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationArchivePreview/fileLocationArchivePreview.styles.ts rename to app/components/Detail/components/GeneratedMatricesTables/components/FileLocationArchivePreview/fileLocationArchivePreview.styles.ts diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationArchivePreview/fileLocationArchivePreview.tsx b/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationArchivePreview/fileLocationArchivePreview.tsx similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationArchivePreview/fileLocationArchivePreview.tsx rename to app/components/Detail/components/GeneratedMatricesTables/components/FileLocationArchivePreview/fileLocationArchivePreview.tsx diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationCopy/fileLocationCopy.tsx b/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationCopy/fileLocationCopy.tsx similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationCopy/fileLocationCopy.tsx rename to app/components/Detail/components/GeneratedMatricesTables/components/FileLocationCopy/fileLocationCopy.tsx diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationDownload/fileLocationDownload.tsx b/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationDownload/fileLocationDownload.tsx similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileLocationDownload/fileLocationDownload.tsx rename to app/components/Detail/components/GeneratedMatricesTables/components/FileLocationDownload/fileLocationDownload.tsx diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileNameCell/fileNameCell.styles.ts b/app/components/Detail/components/GeneratedMatricesTables/components/FileNameCell/fileNameCell.styles.ts similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileNameCell/fileNameCell.styles.ts rename to app/components/Detail/components/GeneratedMatricesTables/components/FileNameCell/fileNameCell.styles.ts diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileNameCell/fileNameCell.tsx b/app/components/Detail/components/GeneratedMatricesTables/components/FileNameCell/fileNameCell.tsx similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/components/FileNameCell/fileNameCell.tsx rename to app/components/Detail/components/GeneratedMatricesTables/components/FileNameCell/fileNameCell.tsx diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/generatedMatricesTables.styles.ts b/app/components/Detail/components/GeneratedMatricesTables/generatedMatricesTables.styles.ts similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/generatedMatricesTables.styles.ts rename to app/components/Detail/components/GeneratedMatricesTables/generatedMatricesTables.styles.ts diff --git a/explorer/app/components/Detail/components/GeneratedMatricesTables/generatedMatricesTables.tsx b/app/components/Detail/components/GeneratedMatricesTables/generatedMatricesTables.tsx similarity index 100% rename from explorer/app/components/Detail/components/GeneratedMatricesTables/generatedMatricesTables.tsx rename to app/components/Detail/components/GeneratedMatricesTables/generatedMatricesTables.tsx diff --git a/explorer/app/components/Detail/components/Section/components/AtlasSection/atlasSection.styles.ts b/app/components/Detail/components/Section/components/AtlasSection/atlasSection.styles.ts similarity index 100% rename from explorer/app/components/Detail/components/Section/components/AtlasSection/atlasSection.styles.ts rename to app/components/Detail/components/Section/components/AtlasSection/atlasSection.styles.ts diff --git a/explorer/app/components/Detail/components/Section/components/AtlasSection/atlasSection.tsx b/app/components/Detail/components/Section/components/AtlasSection/atlasSection.tsx similarity index 100% rename from explorer/app/components/Detail/components/Section/components/AtlasSection/atlasSection.tsx rename to app/components/Detail/components/Section/components/AtlasSection/atlasSection.tsx diff --git a/explorer/app/components/Detail/components/Section/components/AtlasSection/constants.ts b/app/components/Detail/components/Section/components/AtlasSection/constants.ts similarity index 100% rename from explorer/app/components/Detail/components/Section/components/AtlasSection/constants.ts rename to app/components/Detail/components/Section/components/AtlasSection/constants.ts diff --git a/explorer/app/components/Detail/components/Section/components/AtlasSection/types.ts b/app/components/Detail/components/Section/components/AtlasSection/types.ts similarity index 100% rename from explorer/app/components/Detail/components/Section/components/AtlasSection/types.ts rename to app/components/Detail/components/Section/components/AtlasSection/types.ts diff --git a/explorer/app/components/Export/components/AnVILExplorer/ExportMethod/exportMethod.tsx b/app/components/Export/components/AnVILExplorer/ExportMethod/exportMethod.tsx similarity index 100% rename from explorer/app/components/Export/components/AnVILExplorer/ExportMethod/exportMethod.tsx rename to app/components/Export/components/AnVILExplorer/ExportMethod/exportMethod.tsx diff --git a/explorer/app/components/Export/components/AnVILExplorer/components/ManifestDownload/components/ManifestDownloadEntity/manifestDownloadEntity.tsx b/app/components/Export/components/AnVILExplorer/components/ManifestDownload/components/ManifestDownloadEntity/manifestDownloadEntity.tsx similarity index 100% rename from explorer/app/components/Export/components/AnVILExplorer/components/ManifestDownload/components/ManifestDownloadEntity/manifestDownloadEntity.tsx rename to app/components/Export/components/AnVILExplorer/components/ManifestDownload/components/ManifestDownloadEntity/manifestDownloadEntity.tsx diff --git a/explorer/app/components/Index/common/constants.ts b/app/components/Index/common/constants.ts similarity index 100% rename from explorer/app/components/Index/common/constants.ts rename to app/components/Index/common/constants.ts diff --git a/explorer/app/components/Index/common/entities.ts b/app/components/Index/common/entities.ts similarity index 100% rename from explorer/app/components/Index/common/entities.ts rename to app/components/Index/common/entities.ts diff --git a/explorer/app/components/Index/common/indexTransformer.ts b/app/components/Index/common/indexTransformer.ts similarity index 100% rename from explorer/app/components/Index/common/indexTransformer.ts rename to app/components/Index/common/indexTransformer.ts diff --git a/explorer/app/components/Index/common/utils.ts b/app/components/Index/common/utils.ts similarity index 100% rename from explorer/app/components/Index/common/utils.ts rename to app/components/Index/common/utils.ts diff --git a/explorer/app/components/Index/components/BioNetworkCell/bioNetworkCell.styles.ts b/app/components/Index/components/BioNetworkCell/bioNetworkCell.styles.ts similarity index 100% rename from explorer/app/components/Index/components/BioNetworkCell/bioNetworkCell.styles.ts rename to app/components/Index/components/BioNetworkCell/bioNetworkCell.styles.ts diff --git a/explorer/app/components/Index/components/BioNetworkCell/bioNetworkCell.tsx b/app/components/Index/components/BioNetworkCell/bioNetworkCell.tsx similarity index 100% rename from explorer/app/components/Index/components/BioNetworkCell/bioNetworkCell.tsx rename to app/components/Index/components/BioNetworkCell/bioNetworkCell.tsx diff --git a/explorer/app/components/Index/components/ConsentCodesCell/consentCodesCell.tsx b/app/components/Index/components/ConsentCodesCell/consentCodesCell.tsx similarity index 100% rename from explorer/app/components/Index/components/ConsentCodesCell/consentCodesCell.tsx rename to app/components/Index/components/ConsentCodesCell/consentCodesCell.tsx diff --git a/explorer/app/components/Index/components/CopyCell/copyCell.styles.ts b/app/components/Index/components/CopyCell/copyCell.styles.ts similarity index 100% rename from explorer/app/components/Index/components/CopyCell/copyCell.styles.ts rename to app/components/Index/components/CopyCell/copyCell.styles.ts diff --git a/explorer/app/components/Index/components/CopyCell/copyCell.tsx b/app/components/Index/components/CopyCell/copyCell.tsx similarity index 100% rename from explorer/app/components/Index/components/CopyCell/copyCell.tsx rename to app/components/Index/components/CopyCell/copyCell.tsx diff --git a/explorer/app/components/Layout/components/BackPage/components/BackPageHero/components/BackPageHeroActions/backPageHeroActions.styles.ts b/app/components/Layout/components/BackPage/components/BackPageHero/components/BackPageHeroActions/backPageHeroActions.styles.ts similarity index 100% rename from explorer/app/components/Layout/components/BackPage/components/BackPageHero/components/BackPageHeroActions/backPageHeroActions.styles.ts rename to app/components/Layout/components/BackPage/components/BackPageHero/components/BackPageHeroActions/backPageHeroActions.styles.ts diff --git a/explorer/app/components/Layout/components/BackPage/components/BackPageHero/components/BackPageHeroActions/backPageHeroActions.tsx b/app/components/Layout/components/BackPage/components/BackPageHero/components/BackPageHeroActions/backPageHeroActions.tsx similarity index 100% rename from explorer/app/components/Layout/components/BackPage/components/BackPageHero/components/BackPageHeroActions/backPageHeroActions.tsx rename to app/components/Layout/components/BackPage/components/BackPageHero/components/BackPageHeroActions/backPageHeroActions.tsx diff --git a/explorer/app/components/Layout/components/Content/components/HelpIconButton/helpIconButton.tsx b/app/components/Layout/components/Content/components/HelpIconButton/helpIconButton.tsx similarity index 100% rename from explorer/app/components/Layout/components/Content/components/HelpIconButton/helpIconButton.tsx rename to app/components/Layout/components/Content/components/HelpIconButton/helpIconButton.tsx diff --git a/explorer/app/components/Layout/components/Content/components/Link/link.tsx b/app/components/Layout/components/Content/components/Link/link.tsx similarity index 100% rename from explorer/app/components/Layout/components/Content/components/Link/link.tsx rename to app/components/Layout/components/Content/components/Link/link.tsx diff --git a/explorer/app/components/Layout/components/Content/content.styles.ts b/app/components/Layout/components/Content/content.styles.ts similarity index 100% rename from explorer/app/components/Layout/components/Content/content.styles.ts rename to app/components/Layout/components/Content/content.styles.ts diff --git a/explorer/app/components/Layout/components/Content/content.tsx b/app/components/Layout/components/Content/content.tsx similarity index 100% rename from explorer/app/components/Layout/components/Content/content.tsx rename to app/components/Layout/components/Content/content.tsx diff --git a/explorer/app/components/Layout/components/Footer/components/Branding/components/ANVILBranding/anvilBranding.styles.ts b/app/components/Layout/components/Footer/components/Branding/components/ANVILBranding/anvilBranding.styles.ts similarity index 100% rename from explorer/app/components/Layout/components/Footer/components/Branding/components/ANVILBranding/anvilBranding.styles.ts rename to app/components/Layout/components/Footer/components/Branding/components/ANVILBranding/anvilBranding.styles.ts diff --git a/explorer/app/components/Layout/components/Footer/components/Branding/components/ANVILBranding/anvilBranding.tsx b/app/components/Layout/components/Footer/components/Branding/components/ANVILBranding/anvilBranding.tsx similarity index 100% rename from explorer/app/components/Layout/components/Footer/components/Branding/components/ANVILBranding/anvilBranding.tsx rename to app/components/Layout/components/Footer/components/Branding/components/ANVILBranding/anvilBranding.tsx diff --git a/explorer/app/components/Layout/components/Footer/components/Branding/components/HCABranding/hcaBranding.styles.ts b/app/components/Layout/components/Footer/components/Branding/components/HCABranding/hcaBranding.styles.ts similarity index 100% rename from explorer/app/components/Layout/components/Footer/components/Branding/components/HCABranding/hcaBranding.styles.ts rename to app/components/Layout/components/Footer/components/Branding/components/HCABranding/hcaBranding.styles.ts diff --git a/explorer/app/components/Layout/components/Footer/components/Branding/components/HCABranding/hcaBranding.tsx b/app/components/Layout/components/Footer/components/Branding/components/HCABranding/hcaBranding.tsx similarity index 100% rename from explorer/app/components/Layout/components/Footer/components/Branding/components/HCABranding/hcaBranding.tsx rename to app/components/Layout/components/Footer/components/Branding/components/HCABranding/hcaBranding.tsx diff --git a/explorer/app/components/Layout/components/Header/components/Content/components/Logo/components/LogoExplorer/components/ANVILExplorer/ANVILExplorer.tsx b/app/components/Layout/components/Header/components/Content/components/Logo/components/LogoExplorer/components/ANVILExplorer/ANVILExplorer.tsx similarity index 100% rename from explorer/app/components/Layout/components/Header/components/Content/components/Logo/components/LogoExplorer/components/ANVILExplorer/ANVILExplorer.tsx rename to app/components/Layout/components/Header/components/Content/components/Logo/components/LogoExplorer/components/ANVILExplorer/ANVILExplorer.tsx diff --git a/explorer/app/components/Layout/components/Header/components/Content/components/Logo/components/LogoExplorer/logoExplorer.tsx b/app/components/Layout/components/Header/components/Content/components/Logo/components/LogoExplorer/logoExplorer.tsx similarity index 100% rename from explorer/app/components/Layout/components/Header/components/Content/components/Logo/components/LogoExplorer/logoExplorer.tsx rename to app/components/Layout/components/Header/components/Content/components/Logo/components/LogoExplorer/logoExplorer.tsx diff --git a/explorer/app/components/Layout/components/Header/components/Content/components/Navigation/components/NavigationMenuItems/components/LabelIconMenuItem/labelIconMenuItem.styles.ts b/app/components/Layout/components/Header/components/Content/components/Navigation/components/NavigationMenuItems/components/LabelIconMenuItem/labelIconMenuItem.styles.ts similarity index 100% rename from explorer/app/components/Layout/components/Header/components/Content/components/Navigation/components/NavigationMenuItems/components/LabelIconMenuItem/labelIconMenuItem.styles.ts rename to app/components/Layout/components/Header/components/Content/components/Navigation/components/NavigationMenuItems/components/LabelIconMenuItem/labelIconMenuItem.styles.ts diff --git a/explorer/app/components/Layout/components/Header/components/Content/components/Navigation/components/NavigationMenuItems/components/LabelIconMenuItem/labelIconMenuItem.tsx b/app/components/Layout/components/Header/components/Content/components/Navigation/components/NavigationMenuItems/components/LabelIconMenuItem/labelIconMenuItem.tsx similarity index 100% rename from explorer/app/components/Layout/components/Header/components/Content/components/Navigation/components/NavigationMenuItems/components/LabelIconMenuItem/labelIconMenuItem.tsx rename to app/components/Layout/components/Header/components/Content/components/Navigation/components/NavigationMenuItems/components/LabelIconMenuItem/labelIconMenuItem.tsx diff --git a/explorer/app/components/common/Banner/components/Announcements/announcements.tsx b/app/components/common/Banner/components/Announcements/announcements.tsx similarity index 100% rename from explorer/app/components/common/Banner/components/Announcements/announcements.tsx rename to app/components/common/Banner/components/Announcements/announcements.tsx diff --git a/explorer/app/components/common/Banner/components/Announcements/components/BetaAnnouncement/betaAnnouncement.styles.ts b/app/components/common/Banner/components/Announcements/components/BetaAnnouncement/betaAnnouncement.styles.ts similarity index 100% rename from explorer/app/components/common/Banner/components/Announcements/components/BetaAnnouncement/betaAnnouncement.styles.ts rename to app/components/common/Banner/components/Announcements/components/BetaAnnouncement/betaAnnouncement.styles.ts diff --git a/explorer/app/components/common/Banner/components/Announcements/components/BetaAnnouncement/betaAnnouncement.tsx b/app/components/common/Banner/components/Announcements/components/BetaAnnouncement/betaAnnouncement.tsx similarity index 100% rename from explorer/app/components/common/Banner/components/Announcements/components/BetaAnnouncement/betaAnnouncement.tsx rename to app/components/common/Banner/components/Announcements/components/BetaAnnouncement/betaAnnouncement.tsx diff --git a/explorer/app/components/common/Banner/components/Announcements/components/SessionTimeout/sessionTimeout.tsx b/app/components/common/Banner/components/Announcements/components/SessionTimeout/sessionTimeout.tsx similarity index 100% rename from explorer/app/components/common/Banner/components/Announcements/components/SessionTimeout/sessionTimeout.tsx rename to app/components/common/Banner/components/Announcements/components/SessionTimeout/sessionTimeout.tsx diff --git a/explorer/app/components/common/Banner/components/Announcements/components/SystemIndexing/systemIndexing.tsx b/app/components/common/Banner/components/Announcements/components/SystemIndexing/systemIndexing.tsx similarity index 100% rename from explorer/app/components/common/Banner/components/Announcements/components/SystemIndexing/systemIndexing.tsx rename to app/components/common/Banner/components/Announcements/components/SystemIndexing/systemIndexing.tsx diff --git a/explorer/app/components/common/Banner/components/Announcements/components/SystemStatus/systemStatus.tsx b/app/components/common/Banner/components/Announcements/components/SystemStatus/systemStatus.tsx similarity index 100% rename from explorer/app/components/common/Banner/components/Announcements/components/SystemStatus/systemStatus.tsx rename to app/components/common/Banner/components/Announcements/components/SystemStatus/systemStatus.tsx diff --git a/explorer/app/components/common/Button/components/ButtonOutline/buttonOutline.tsx b/app/components/common/Button/components/ButtonOutline/buttonOutline.tsx similarity index 100% rename from explorer/app/components/common/Button/components/ButtonOutline/buttonOutline.tsx rename to app/components/common/Button/components/ButtonOutline/buttonOutline.tsx diff --git a/explorer/app/components/common/Figure/figure.styles.ts b/app/components/common/Figure/figure.styles.ts similarity index 100% rename from explorer/app/components/common/Figure/figure.styles.ts rename to app/components/common/Figure/figure.styles.ts diff --git a/explorer/app/components/common/Figure/figure.tsx b/app/components/common/Figure/figure.tsx similarity index 100% rename from explorer/app/components/common/Figure/figure.tsx rename to app/components/common/Figure/figure.tsx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/betaAnnouncement.mdx b/app/components/common/MDXContent/anvil-cmg/betaAnnouncement.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/betaAnnouncement.mdx rename to app/components/common/MDXContent/anvil-cmg/betaAnnouncement.mdx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/dataReleasePolicy.mdx b/app/components/common/MDXContent/anvil-cmg/dataReleasePolicy.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/dataReleasePolicy.mdx rename to app/components/common/MDXContent/anvil-cmg/dataReleasePolicy.mdx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/exportWarning.mdx b/app/components/common/MDXContent/anvil-cmg/exportWarning.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/exportWarning.mdx rename to app/components/common/MDXContent/anvil-cmg/exportWarning.mdx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/index.tsx b/app/components/common/MDXContent/anvil-cmg/index.tsx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/index.tsx rename to app/components/common/MDXContent/anvil-cmg/index.tsx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/loginReminder.mdx b/app/components/common/MDXContent/anvil-cmg/loginReminder.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/loginReminder.mdx rename to app/components/common/MDXContent/anvil-cmg/loginReminder.mdx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/loginTermsOfService.mdx b/app/components/common/MDXContent/anvil-cmg/loginTermsOfService.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/loginTermsOfService.mdx rename to app/components/common/MDXContent/anvil-cmg/loginTermsOfService.mdx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/loginText.mdx b/app/components/common/MDXContent/anvil-cmg/loginText.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/loginText.mdx rename to app/components/common/MDXContent/anvil-cmg/loginText.mdx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/loginWarning.mdx b/app/components/common/MDXContent/anvil-cmg/loginWarning.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/loginWarning.mdx rename to app/components/common/MDXContent/anvil-cmg/loginWarning.mdx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/manifestDownloadStart.mdx b/app/components/common/MDXContent/anvil-cmg/manifestDownloadStart.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/manifestDownloadStart.mdx rename to app/components/common/MDXContent/anvil-cmg/manifestDownloadStart.mdx diff --git a/explorer/app/components/common/MDXContent/anvil-cmg/manifestDownloadSuccess.mdx b/app/components/common/MDXContent/anvil-cmg/manifestDownloadSuccess.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/anvil-cmg/manifestDownloadSuccess.mdx rename to app/components/common/MDXContent/anvil-cmg/manifestDownloadSuccess.mdx diff --git a/explorer/app/components/common/MDXContent/common/exportToTerraStart.mdx b/app/components/common/MDXContent/common/exportToTerraStart.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/common/exportToTerraStart.mdx rename to app/components/common/MDXContent/common/exportToTerraStart.mdx diff --git a/explorer/app/components/common/MDXContent/common/exportToTerraSuccess.mdx b/app/components/common/MDXContent/common/exportToTerraSuccess.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/common/exportToTerraSuccess.mdx rename to app/components/common/MDXContent/common/exportToTerraSuccess.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/batchCorrectionWarning.mdx b/app/components/common/MDXContent/hca-dcp/batchCorrectionWarning.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/batchCorrectionWarning.mdx rename to app/components/common/MDXContent/hca-dcp/batchCorrectionWarning.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/contributorGeneratedMatrices.mdx b/app/components/common/MDXContent/hca-dcp/contributorGeneratedMatrices.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/contributorGeneratedMatrices.mdx rename to app/components/common/MDXContent/hca-dcp/contributorGeneratedMatrices.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/dataReleasePolicy.mdx b/app/components/common/MDXContent/hca-dcp/dataReleasePolicy.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/dataReleasePolicy.mdx rename to app/components/common/MDXContent/hca-dcp/dataReleasePolicy.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/dcpGeneratedMatrices.mdx b/app/components/common/MDXContent/hca-dcp/dcpGeneratedMatrices.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/dcpGeneratedMatrices.mdx rename to app/components/common/MDXContent/hca-dcp/dcpGeneratedMatrices.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/downloadBatchCorrectionWarning.mdx b/app/components/common/MDXContent/hca-dcp/downloadBatchCorrectionWarning.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/downloadBatchCorrectionWarning.mdx rename to app/components/common/MDXContent/hca-dcp/downloadBatchCorrectionWarning.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/downloadCurlCommandStart.mdx b/app/components/common/MDXContent/hca-dcp/downloadCurlCommandStart.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/downloadCurlCommandStart.mdx rename to app/components/common/MDXContent/hca-dcp/downloadCurlCommandStart.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/downloadCurlCommandSuccess.mdx b/app/components/common/MDXContent/hca-dcp/downloadCurlCommandSuccess.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/downloadCurlCommandSuccess.mdx rename to app/components/common/MDXContent/hca-dcp/downloadCurlCommandSuccess.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/exportToTerraStart.mdx b/app/components/common/MDXContent/hca-dcp/exportToTerraStart.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/exportToTerraStart.mdx rename to app/components/common/MDXContent/hca-dcp/exportToTerraStart.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/exportToTerraSuccessWithWarning.mdx b/app/components/common/MDXContent/hca-dcp/exportToTerraSuccessWithWarning.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/exportToTerraSuccessWithWarning.mdx rename to app/components/common/MDXContent/hca-dcp/exportToTerraSuccessWithWarning.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/exportWarning.mdx b/app/components/common/MDXContent/hca-dcp/exportWarning.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/exportWarning.mdx rename to app/components/common/MDXContent/hca-dcp/exportWarning.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/index.tsx b/app/components/common/MDXContent/hca-dcp/index.tsx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/index.tsx rename to app/components/common/MDXContent/hca-dcp/index.tsx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/loginReminder.mdx b/app/components/common/MDXContent/hca-dcp/loginReminder.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/hca-dcp/loginReminder.mdx rename to app/components/common/MDXContent/hca-dcp/loginReminder.mdx diff --git a/explorer/app/components/common/MDXContent/hca-dcp/loginTermsOfService.mdx b/app/components/common/MDXContent/hca-dcp/loginTermsOfService.mdx similarity index 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from explorer/app/components/common/MDXContent/hca-dcp/manifestDownloadSuccess.mdx rename to app/components/common/MDXContent/hca-dcp/manifestDownloadSuccess.mdx diff --git a/explorer/app/components/common/MDXContent/lungmap/batchCorrectionWarning.mdx b/app/components/common/MDXContent/lungmap/batchCorrectionWarning.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/lungmap/batchCorrectionWarning.mdx rename to app/components/common/MDXContent/lungmap/batchCorrectionWarning.mdx diff --git a/explorer/app/components/common/MDXContent/lungmap/dataReleasePolicy.mdx b/app/components/common/MDXContent/lungmap/dataReleasePolicy.mdx similarity index 100% rename from explorer/app/components/common/MDXContent/lungmap/dataReleasePolicy.mdx rename to app/components/common/MDXContent/lungmap/dataReleasePolicy.mdx diff --git a/explorer/app/components/common/MDXContent/lungmap/downloadBatchCorrectionWarning.mdx 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a/docs/configuration-guide.md b/docs/configuration-guide.md index f42d6bd44..a1faa07bb 100644 --- a/docs/configuration-guide.md +++ b/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}/${env}/index`. -* Entity list configuration implements `EntityConfig` where `T` is the response model defined above in step 1. -* Once configured, the entity list configuration must be specified in the `entities` array in the site config. + +- Naming convention: `entityNameEntityConfig.ts`. +- Location: `/site-config/${site}/${env}/index`. +- Entity list configuration implements `EntityConfig` where `T` is the response model defined above in step 1. +- Once configured, the entity list configuration must be specified in the `entities` array in the site config. ### 3. Create a View Builder -A view builder contains functions that build the component props required for displaying a value in an entity list. Each function takes at least a response model (either from an API endpoint or a row in a TSV), is parameterized by the type of component it builds props for and uses transformers to convert the response value into prop-specific values. -* Naming convention: `viewModelBuilders.ts`. A view builder is API-specific. -* Location: `/viewModelBuilders/${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. diff --git a/explorer/e2e/anvil-catalog/anvilcatalog-filters.spec.ts b/e2e/anvil-catalog/anvilcatalog-filters.spec.ts similarity index 100% rename from explorer/e2e/anvil-catalog/anvilcatalog-filters.spec.ts rename to e2e/anvil-catalog/anvilcatalog-filters.spec.ts diff --git a/explorer/e2e/anvil-catalog/anvilcatalog-select-tabs.spec.ts b/e2e/anvil-catalog/anvilcatalog-select-tabs.spec.ts similarity index 100% rename from explorer/e2e/anvil-catalog/anvilcatalog-select-tabs.spec.ts rename to e2e/anvil-catalog/anvilcatalog-select-tabs.spec.ts diff --git a/explorer/e2e/anvil-catalog/anvilcatalog-sort.spec.ts b/e2e/anvil-catalog/anvilcatalog-sort.spec.ts similarity index 100% rename from explorer/e2e/anvil-catalog/anvilcatalog-sort.spec.ts rename to e2e/anvil-catalog/anvilcatalog-sort.spec.ts diff --git a/explorer/e2e/anvil-catalog/anvilcatalog-tabs-buttons.spec.ts b/e2e/anvil-catalog/anvilcatalog-tabs-buttons.spec.ts similarity index 100% rename from explorer/e2e/anvil-catalog/anvilcatalog-tabs-buttons.spec.ts rename to e2e/anvil-catalog/anvilcatalog-tabs-buttons.spec.ts diff --git a/explorer/e2e/anvil-catalog/anvilcatalog-tabs.ts b/e2e/anvil-catalog/anvilcatalog-tabs.ts similarity index 100% rename from explorer/e2e/anvil-catalog/anvilcatalog-tabs.ts rename to e2e/anvil-catalog/anvilcatalog-tabs.ts diff --git a/explorer/e2e/anvil-catalog/anvilcatalog-url.spec.ts b/e2e/anvil-catalog/anvilcatalog-url.spec.ts similarity index 100% rename from explorer/e2e/anvil-catalog/anvilcatalog-url.spec.ts rename to e2e/anvil-catalog/anvilcatalog-url.spec.ts diff --git a/explorer/e2e/anvil-catalog/constants.ts b/e2e/anvil-catalog/constants.ts similarity index 100% rename from explorer/e2e/anvil-catalog/constants.ts rename to e2e/anvil-catalog/constants.ts diff --git a/explorer/e2e/anvil/anvil-backpages.spec.ts b/e2e/anvil/anvil-backpages.spec.ts similarity index 100% rename from explorer/e2e/anvil/anvil-backpages.spec.ts rename to e2e/anvil/anvil-backpages.spec.ts diff --git a/explorer/e2e/anvil/anvil-check-system-status.ts b/e2e/anvil/anvil-check-system-status.ts similarity index 100% rename from explorer/e2e/anvil/anvil-check-system-status.ts rename to e2e/anvil/anvil-check-system-status.ts diff --git a/explorer/e2e/anvil/anvil-filters.spec.ts b/e2e/anvil/anvil-filters.spec.ts similarity index 100% rename from explorer/e2e/anvil/anvil-filters.spec.ts rename to e2e/anvil/anvil-filters.spec.ts diff --git a/explorer/e2e/anvil/anvil-index-export-button.spec.ts b/e2e/anvil/anvil-index-export-button.spec.ts similarity index 100% rename from explorer/e2e/anvil/anvil-index-export-button.spec.ts rename to e2e/anvil/anvil-index-export-button.spec.ts diff --git a/explorer/e2e/anvil/anvil-pagination.spec.ts b/e2e/anvil/anvil-pagination.spec.ts similarity index 100% rename from explorer/e2e/anvil/anvil-pagination.spec.ts rename to e2e/anvil/anvil-pagination.spec.ts diff --git a/explorer/e2e/anvil/anvil-sort.spec.ts b/e2e/anvil/anvil-sort.spec.ts similarity index 100% rename from explorer/e2e/anvil/anvil-sort.spec.ts rename to e2e/anvil/anvil-sort.spec.ts diff --git a/explorer/e2e/anvil/anvil-tabs-buttons.spec.ts b/e2e/anvil/anvil-tabs-buttons.spec.ts similarity index 100% rename from explorer/e2e/anvil/anvil-tabs-buttons.spec.ts rename to e2e/anvil/anvil-tabs-buttons.spec.ts diff --git a/explorer/e2e/anvil/anvil-tabs.ts b/e2e/anvil/anvil-tabs.ts similarity index 100% rename from explorer/e2e/anvil/anvil-tabs.ts rename to e2e/anvil/anvil-tabs.ts diff --git a/explorer/e2e/anvil/anvil-urls.spec.ts b/e2e/anvil/anvil-urls.spec.ts similarity index 100% rename from explorer/e2e/anvil/anvil-urls.spec.ts rename to e2e/anvil/anvil-urls.spec.ts diff --git a/explorer/e2e/anvil/constants.ts b/e2e/anvil/constants.ts similarity index 100% rename from explorer/e2e/anvil/constants.ts rename to e2e/anvil/constants.ts diff --git a/explorer/e2e/checkIsIndexing.ts b/e2e/checkIsIndexing.ts similarity index 100% rename from explorer/e2e/checkIsIndexing.ts rename to e2e/checkIsIndexing.ts diff --git a/explorer/e2e/testFunctions.ts b/e2e/testFunctions.ts similarity index 100% rename from explorer/e2e/testFunctions.ts rename to e2e/testFunctions.ts diff --git a/explorer/e2e/testInterfaces.ts b/e2e/testInterfaces.ts similarity index 100% rename from explorer/e2e/testInterfaces.ts rename to e2e/testInterfaces.ts diff --git a/explorer/e2e/testReadme.md b/e2e/testReadme.md similarity index 100% rename from explorer/e2e/testReadme.md rename to e2e/testReadme.md diff --git a/explorer/.eslintignore b/explorer/.eslintignore deleted file mode 100644 index 6dde21733..000000000 --- a/explorer/.eslintignore +++ /dev/null @@ -1,5 +0,0 @@ -**/node_modules/* -**/out/* -**/.next/* - -build \ No newline at end of file diff --git a/explorer/.gitignore b/explorer/.gitignore deleted file mode 100644 index e9f80fc38..000000000 --- a/explorer/.gitignore +++ /dev/null @@ -1,53 +0,0 @@ -# See https://help.github.com/articles/ignoring-files/ for more about ignoring files. - -# dependencies -/node_modules -/.pnp -.pnp.js - -# testing -/coverage -/test-results/* - -# next.js -/.next/ -/out/ - -# production -/build - -# misc -.DS_Store -*.pem - -# debug -npm-debug.log* -yarn-debug.log* -yarn-error.log* -.pnpm-debug.log* - -# env files -/.env*.local -/.env.development -/.env.production - -# vercel -.vercel - -# typescript -*.tsbuildinfo - -# vscode -/.vscode - -# hygen -_templates - -# nvm -.nvmrc - -# favicons -/public/favicons/* - -/files/anvil-catalog/out/ -/files/ncpi-catalog/out/ diff --git a/explorer/files/anvil-catalog/build-anvil-catalog.ts b/files/anvil-catalog/build-anvil-catalog.ts similarity index 100% rename from explorer/files/anvil-catalog/build-anvil-catalog.ts rename to files/anvil-catalog/build-anvil-catalog.ts diff --git a/explorer/files/anvil-catalog/build-consortia.ts b/files/anvil-catalog/build-consortia.ts similarity index 100% rename from explorer/files/anvil-catalog/build-consortia.ts rename to files/anvil-catalog/build-consortia.ts diff --git a/explorer/files/anvil-catalog/build-studies.ts b/files/anvil-catalog/build-studies.ts similarity index 100% rename from explorer/files/anvil-catalog/build-studies.ts rename to files/anvil-catalog/build-studies.ts diff --git a/explorer/files/anvil-catalog/build-workspaces.ts b/files/anvil-catalog/build-workspaces.ts similarity index 100% rename from explorer/files/anvil-catalog/build-workspaces.ts rename to files/anvil-catalog/build-workspaces.ts diff --git a/explorer/files/anvil-catalog/constants.ts b/files/anvil-catalog/constants.ts similarity index 100% rename from explorer/files/anvil-catalog/constants.ts rename to files/anvil-catalog/constants.ts diff --git a/explorer/files/anvil-catalog/files/consortia/1000g.mdx b/files/anvil-catalog/files/consortia/1000g.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/1000g.mdx rename to files/anvil-catalog/files/consortia/1000g.mdx diff --git a/explorer/files/anvil-catalog/files/consortia/ccdg.mdx b/files/anvil-catalog/files/consortia/ccdg.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/ccdg.mdx rename to files/anvil-catalog/files/consortia/ccdg.mdx diff --git a/explorer/files/anvil-catalog/files/consortia/cmg.mdx b/files/anvil-catalog/files/consortia/cmg.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/cmg.mdx rename to files/anvil-catalog/files/consortia/cmg.mdx diff --git a/explorer/files/anvil-catalog/files/consortia/cser.mdx b/files/anvil-catalog/files/consortia/cser.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/cser.mdx rename to files/anvil-catalog/files/consortia/cser.mdx diff --git a/explorer/files/anvil-catalog/files/consortia/emerge.mdx b/files/anvil-catalog/files/consortia/emerge.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/emerge.mdx rename to files/anvil-catalog/files/consortia/emerge.mdx diff --git a/explorer/files/anvil-catalog/files/consortia/gregor.mdx b/files/anvil-catalog/files/consortia/gregor.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/gregor.mdx rename to files/anvil-catalog/files/consortia/gregor.mdx diff --git a/explorer/files/anvil-catalog/files/consortia/gtex.mdx b/files/anvil-catalog/files/consortia/gtex.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/gtex.mdx rename to files/anvil-catalog/files/consortia/gtex.mdx diff --git a/explorer/files/anvil-catalog/files/consortia/hprc.mdx b/files/anvil-catalog/files/consortia/hprc.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/hprc.mdx rename to files/anvil-catalog/files/consortia/hprc.mdx diff --git a/explorer/files/anvil-catalog/files/consortia/page.mdx b/files/anvil-catalog/files/consortia/page.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/page.mdx rename to files/anvil-catalog/files/consortia/page.mdx diff --git a/explorer/files/anvil-catalog/files/consortia/t2t.mdx b/files/anvil-catalog/files/consortia/t2t.mdx similarity index 100% rename from explorer/files/anvil-catalog/files/consortia/t2t.mdx rename to files/anvil-catalog/files/consortia/t2t.mdx diff --git a/explorer/files/anvil-catalog/files/dashboard-source-anvil.tsv b/files/anvil-catalog/files/dashboard-source-anvil.tsv similarity index 100% rename from explorer/files/anvil-catalog/files/dashboard-source-anvil.tsv rename to files/anvil-catalog/files/dashboard-source-anvil.tsv diff --git a/explorer/files/common/consent-codes.ts b/files/common/consent-codes.ts similarity index 100% rename from explorer/files/common/consent-codes.ts rename to files/common/consent-codes.ts diff --git a/explorer/files/common/dbGaP.ts b/files/common/dbGaP.ts similarity index 100% rename from explorer/files/common/dbGaP.ts rename to files/common/dbGaP.ts diff --git a/explorer/files/common/disease_abbrev_mapping.tsv b/files/common/disease_abbrev_mapping.tsv similarity index 100% rename from explorer/files/common/disease_abbrev_mapping.tsv rename to files/common/disease_abbrev_mapping.tsv diff --git a/explorer/files/common/utils.ts b/files/common/utils.ts similarity index 100% rename from explorer/files/common/utils.ts rename to files/common/utils.ts diff --git a/explorer/files/ncpi-catalog-dug/out/ncpi-dug-studies.json b/files/ncpi-catalog-dug/out/ncpi-dug-studies.json similarity index 100% rename from explorer/files/ncpi-catalog-dug/out/ncpi-dug-studies.json rename to files/ncpi-catalog-dug/out/ncpi-dug-studies.json diff --git a/explorer/files/ncpi-catalog/build-ncpi-catalog.ts b/files/ncpi-catalog/build-ncpi-catalog.ts similarity index 100% rename from explorer/files/ncpi-catalog/build-ncpi-catalog.ts rename to files/ncpi-catalog/build-ncpi-catalog.ts diff --git a/explorer/files/ncpi-catalog/build-plaftorms.ts b/files/ncpi-catalog/build-plaftorms.ts similarity index 100% rename from explorer/files/ncpi-catalog/build-plaftorms.ts rename to files/ncpi-catalog/build-plaftorms.ts diff --git a/explorer/files/ncpi-catalog/build-platform-studies.ts b/files/ncpi-catalog/build-platform-studies.ts similarity index 100% rename from explorer/files/ncpi-catalog/build-platform-studies.ts rename to files/ncpi-catalog/build-platform-studies.ts diff --git a/explorer/files/ncpi-catalog/constants.ts b/files/ncpi-catalog/constants.ts similarity index 100% rename from explorer/files/ncpi-catalog/constants.ts rename to files/ncpi-catalog/constants.ts diff --git a/explorer/files/ncpi-catalog/files/dashboard-source-ncpi.tsv b/files/ncpi-catalog/files/dashboard-source-ncpi.tsv similarity index 100% rename from explorer/files/ncpi-catalog/files/dashboard-source-ncpi.tsv rename to files/ncpi-catalog/files/dashboard-source-ncpi.tsv diff --git a/explorer/files/ncpi-catalog/ncpi-update-README.md b/files/ncpi-catalog/ncpi-update-README.md similarity index 100% rename from explorer/files/ncpi-catalog/ncpi-update-README.md rename to files/ncpi-catalog/ncpi-update-README.md diff --git a/explorer/files/ncpi-catalog/update-anvil-source.ts b/files/ncpi-catalog/update-anvil-source.ts similarity index 100% rename from explorer/files/ncpi-catalog/update-anvil-source.ts rename to files/ncpi-catalog/update-anvil-source.ts diff --git a/explorer/files/ncpi-catalog/update-bdc-source.ts b/files/ncpi-catalog/update-bdc-source.ts similarity index 100% rename from explorer/files/ncpi-catalog/update-bdc-source.ts rename to files/ncpi-catalog/update-bdc-source.ts diff --git a/explorer/files/ncpi-catalog/update-crdc-source.ts b/files/ncpi-catalog/update-crdc-source.ts similarity index 100% rename from explorer/files/ncpi-catalog/update-crdc-source.ts rename to files/ncpi-catalog/update-crdc-source.ts diff --git a/explorer/files/ncpi-catalog/update-kfdrc-source.ts b/files/ncpi-catalog/update-kfdrc-source.ts similarity index 100% rename from explorer/files/ncpi-catalog/update-kfdrc-source.ts rename to files/ncpi-catalog/update-kfdrc-source.ts diff --git a/explorer/files/ncpi-catalog/utils.ts b/files/ncpi-catalog/utils.ts similarity index 100% rename from explorer/files/ncpi-catalog/utils.ts rename to files/ncpi-catalog/utils.ts diff --git a/explorer/files/package-lock.json b/files/package-lock.json similarity index 100% rename from explorer/files/package-lock.json rename to files/package-lock.json diff --git a/explorer/files/package.json b/files/package.json similarity index 100% rename from explorer/files/package.json rename to files/package.json diff --git a/explorer/files/tsconfig.json b/files/tsconfig.json similarity index 100% rename from explorer/files/tsconfig.json rename to files/tsconfig.json diff --git a/explorer/jest.config.js b/jest.config.js similarity index 92% rename from explorer/jest.config.js rename to jest.config.js index c812141ed..e7c876133 100644 --- a/explorer/jest.config.js +++ b/jest.config.js @@ -15,7 +15,7 @@ const customJestConfig = { // if using TypeScript with a baseUrl set to the root directory then you need the below for alias' to work moduleDirectories: ["node_modules", "/"], testEnvironment: "jest-environment-jsdom", - testPathIgnorePatterns: ["/node_modules/", "/e2e/"], + testPathIgnorePatterns: ["/node_modules/", "/e2e/", "/analytics/"], }; // createJestConfig is exported this way to ensure that next/jest can load the Next.js config which is async diff --git a/explorer/mdx-components.tsx b/mdx-components.tsx similarity index 100% rename from explorer/mdx-components.tsx rename to mdx-components.tsx diff --git a/explorer/next-env.d.ts b/next-env.d.ts similarity index 100% rename from explorer/next-env.d.ts rename to next-env.d.ts diff --git a/explorer/next-sitemap.config.mjs b/next-sitemap.config.mjs similarity index 100% rename from explorer/next-sitemap.config.mjs rename to next-sitemap.config.mjs diff --git a/explorer/next.config.mjs b/next.config.mjs similarity index 100% rename from explorer/next.config.mjs rename to next.config.mjs diff --git a/explorer/package-lock.json b/package-lock.json similarity index 100% rename from explorer/package-lock.json rename to package-lock.json diff --git a/explorer/package.json b/package.json similarity index 98% rename from explorer/package.json rename to package.json index 34dbeba9d..321b10c5b 100644 --- a/explorer/package.json +++ b/package.json @@ -26,7 +26,7 @@ "start": "npx serve out", "lint": "next lint --dir .", "check-format": "prettier --check .", - "prepare": "cd .. && husky install explorer/.husky", + "prepare": "husky install ./.husky", "storybook": "storybook dev -s images,.next -p 6006", "build-storybook": "storybook build", "test": "jest --watch", diff --git a/explorer/pages/404.tsx b/pages/404.tsx similarity index 100% rename from explorer/pages/404.tsx rename to pages/404.tsx diff --git a/explorer/pages/[entityListType]/[...params].tsx b/pages/[entityListType]/[...params].tsx similarity index 100% rename from explorer/pages/[entityListType]/[...params].tsx rename to pages/[entityListType]/[...params].tsx diff --git a/explorer/pages/[entityListType]/index.tsx b/pages/[entityListType]/index.tsx similarity index 100% rename from explorer/pages/[entityListType]/index.tsx rename to pages/[entityListType]/index.tsx diff --git a/explorer/pages/_app.tsx b/pages/_app.tsx similarity index 100% rename from explorer/pages/_app.tsx rename to pages/_app.tsx diff --git a/explorer/pages/_document.tsx b/pages/_document.tsx similarity index 100% rename from explorer/pages/_document.tsx rename to pages/_document.tsx diff --git a/explorer/pages/_error.tsx b/pages/_error.tsx similarity index 100% rename from explorer/pages/_error.tsx rename to pages/_error.tsx diff --git a/explorer/pages/apis/index.tsx b/pages/apis/index.tsx similarity index 100% rename from explorer/pages/apis/index.tsx rename to pages/apis/index.tsx diff --git a/explorer/pages/beta-announcement/index.tsx b/pages/beta-announcement/index.tsx similarity index 100% rename from explorer/pages/beta-announcement/index.tsx rename to pages/beta-announcement/index.tsx diff --git a/explorer/pages/export/download-manifest.tsx b/pages/export/download-manifest.tsx similarity index 100% rename from explorer/pages/export/download-manifest.tsx rename to pages/export/download-manifest.tsx diff --git a/explorer/pages/export/export-to-terra.tsx b/pages/export/export-to-terra.tsx similarity index 100% rename from explorer/pages/export/export-to-terra.tsx rename to pages/export/export-to-terra.tsx diff --git a/explorer/pages/export/get-curl-command.tsx b/pages/export/get-curl-command.tsx similarity index 100% rename from explorer/pages/export/get-curl-command.tsx rename to pages/export/get-curl-command.tsx diff --git a/explorer/pages/export/index.tsx b/pages/export/index.tsx similarity index 100% rename from explorer/pages/export/index.tsx rename to pages/export/index.tsx diff --git a/explorer/pages/guides/index.tsx b/pages/guides/index.tsx similarity index 100% rename from explorer/pages/guides/index.tsx rename to pages/guides/index.tsx diff --git a/explorer/pages/index.tsx b/pages/index.tsx similarity index 100% rename from explorer/pages/index.tsx rename to pages/index.tsx diff --git a/explorer/pages/login/index.tsx b/pages/login/index.tsx similarity index 100% rename from explorer/pages/login/index.tsx rename to pages/login/index.tsx diff --git a/explorer/pages/metadata/index.tsx b/pages/metadata/index.tsx similarity index 100% rename from explorer/pages/metadata/index.tsx rename to pages/metadata/index.tsx diff --git a/explorer/pages/privacy/index.tsx b/pages/privacy/index.tsx similarity index 100% rename from explorer/pages/privacy/index.tsx rename to pages/privacy/index.tsx diff --git a/explorer/pages/terms-of-service/index.tsx b/pages/terms-of-service/index.tsx similarity index 100% rename from explorer/pages/terms-of-service/index.tsx rename to pages/terms-of-service/index.tsx diff --git a/explorer/playwright-report/.gitkeep b/playwright-report/.gitkeep similarity index 100% rename from explorer/playwright-report/.gitkeep rename to playwright-report/.gitkeep diff --git a/explorer/playwright.config.ts b/playwright.config.ts similarity index 100% rename from explorer/playwright.config.ts rename to playwright.config.ts diff --git a/explorer/playwright_anvil-catalog.config.ts b/playwright_anvil-catalog.config.ts similarity index 100% rename from explorer/playwright_anvil-catalog.config.ts rename to playwright_anvil-catalog.config.ts diff --git a/explorer/playwright_anvil.config.ts b/playwright_anvil.config.ts similarity index 100% rename from explorer/playwright_anvil.config.ts rename to playwright_anvil.config.ts diff --git a/explorer/public/guides/copy-notebook.png b/public/guides/copy-notebook.png similarity index 100% rename from explorer/public/guides/copy-notebook.png rename to public/guides/copy-notebook.png diff --git a/explorer/public/guides/create-new-workspace.png b/public/guides/create-new-workspace.png similarity index 100% rename from explorer/public/guides/create-new-workspace.png rename to public/guides/create-new-workspace.png diff --git a/explorer/public/guides/existing-workspace.png b/public/guides/existing-workspace.png similarity index 100% rename from explorer/public/guides/existing-workspace.png rename to public/guides/existing-workspace.png diff --git a/explorer/public/guides/exploring-studies.png b/public/guides/exploring-studies.png similarity index 100% rename from explorer/public/guides/exploring-studies.png rename to public/guides/exploring-studies.png diff --git a/explorer/public/guides/export-to-terra1.png b/public/guides/export-to-terra1.png similarity index 100% rename from explorer/public/guides/export-to-terra1.png rename to public/guides/export-to-terra1.png diff --git a/explorer/public/guides/export-to-terra2.png b/public/guides/export-to-terra2.png similarity index 100% rename from explorer/public/guides/export-to-terra2.png rename to public/guides/export-to-terra2.png diff --git a/explorer/public/guides/exporting-method.png b/public/guides/exporting-method.png similarity index 100% rename from explorer/public/guides/exporting-method.png rename to public/guides/exporting-method.png diff --git a/explorer/public/guides/exporting-with-terra.png b/public/guides/exporting-with-terra.png similarity index 100% rename from explorer/public/guides/exporting-with-terra.png rename to public/guides/exporting-with-terra.png diff --git a/explorer/public/guides/find-the-explorer.png b/public/guides/find-the-explorer.png similarity index 100% rename from explorer/public/guides/find-the-explorer.png rename to public/guides/find-the-explorer.png diff --git a/explorer/public/guides/run-notebook.png b/public/guides/run-notebook.png similarity index 100% rename from explorer/public/guides/run-notebook.png rename to public/guides/run-notebook.png diff --git a/explorer/public/guides/search-and-filter.png b/public/guides/search-and-filter.png similarity index 100% rename from explorer/public/guides/search-and-filter.png rename to public/guides/search-and-filter.png diff --git a/explorer/public/guides/select-filter.png b/public/guides/select-filter.png similarity index 100% rename from explorer/public/guides/select-filter.png rename to public/guides/select-filter.png diff --git a/explorer/public/guides/selecting-workspace.png b/public/guides/selecting-workspace.png similarity index 100% rename from explorer/public/guides/selecting-workspace.png rename to public/guides/selecting-workspace.png diff --git a/explorer/public/guides/working-with-data.png b/public/guides/working-with-data.png similarity index 100% rename from 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explorer/public/images/hcaPortal.png rename to public/images/hcaPortal.png diff --git a/explorer/public/images/hhs.svg b/public/images/hhs.svg similarity index 100% rename from explorer/public/images/hhs.svg rename to public/images/hhs.svg diff --git a/explorer/public/images/icons/cellxgene.svg b/public/images/icons/cellxgene.svg similarity index 100% rename from explorer/public/images/icons/cellxgene.svg rename to public/images/icons/cellxgene.svg diff --git a/explorer/public/images/icons/cxg.png b/public/images/icons/cxg.png similarity index 100% rename from explorer/public/images/icons/cxg.png rename to public/images/icons/cxg.png diff --git a/explorer/public/images/icons/hca-bio-networks/adipose.png b/public/images/icons/hca-bio-networks/adipose.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/adipose.png rename to public/images/icons/hca-bio-networks/adipose.png diff --git a/explorer/public/images/icons/hca-bio-networks/breast.png b/public/images/icons/hca-bio-networks/breast.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/breast.png rename to public/images/icons/hca-bio-networks/breast.png diff --git a/explorer/public/images/icons/hca-bio-networks/development.png b/public/images/icons/hca-bio-networks/development.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/development.png rename to public/images/icons/hca-bio-networks/development.png diff --git a/explorer/public/images/icons/hca-bio-networks/eye.png b/public/images/icons/hca-bio-networks/eye.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/eye.png rename to public/images/icons/hca-bio-networks/eye.png diff --git a/explorer/public/images/icons/hca-bio-networks/genetic-diversity.png b/public/images/icons/hca-bio-networks/genetic-diversity.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/genetic-diversity.png rename to public/images/icons/hca-bio-networks/genetic-diversity.png diff --git a/explorer/public/images/icons/hca-bio-networks/gut.png b/public/images/icons/hca-bio-networks/gut.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/gut.png rename to public/images/icons/hca-bio-networks/gut.png diff --git a/explorer/public/images/icons/hca-bio-networks/heart.png b/public/images/icons/hca-bio-networks/heart.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/heart.png rename to public/images/icons/hca-bio-networks/heart.png diff --git a/explorer/public/images/icons/hca-bio-networks/immune.png b/public/images/icons/hca-bio-networks/immune.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/immune.png rename to public/images/icons/hca-bio-networks/immune.png diff --git a/explorer/public/images/icons/hca-bio-networks/kidney.png b/public/images/icons/hca-bio-networks/kidney.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/kidney.png rename to public/images/icons/hca-bio-networks/kidney.png diff --git a/explorer/public/images/icons/hca-bio-networks/liver.png b/public/images/icons/hca-bio-networks/liver.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/liver.png rename to public/images/icons/hca-bio-networks/liver.png diff --git a/explorer/public/images/icons/hca-bio-networks/lung.png b/public/images/icons/hca-bio-networks/lung.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/lung.png rename to public/images/icons/hca-bio-networks/lung.png diff --git a/explorer/public/images/icons/hca-bio-networks/musculoskeletal.png b/public/images/icons/hca-bio-networks/musculoskeletal.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/musculoskeletal.png rename to public/images/icons/hca-bio-networks/musculoskeletal.png diff --git a/explorer/public/images/icons/hca-bio-networks/nervous-system.png b/public/images/icons/hca-bio-networks/nervous-system.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/nervous-system.png rename to public/images/icons/hca-bio-networks/nervous-system.png diff --git a/explorer/public/images/icons/hca-bio-networks/oral-and-craniofacial.png b/public/images/icons/hca-bio-networks/oral-and-craniofacial.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/oral-and-craniofacial.png rename to public/images/icons/hca-bio-networks/oral-and-craniofacial.png diff --git a/explorer/public/images/icons/hca-bio-networks/organoid.png b/public/images/icons/hca-bio-networks/organoid.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/organoid.png rename to public/images/icons/hca-bio-networks/organoid.png diff --git a/explorer/public/images/icons/hca-bio-networks/pancreas.png b/public/images/icons/hca-bio-networks/pancreas.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/pancreas.png rename to public/images/icons/hca-bio-networks/pancreas.png diff --git a/explorer/public/images/icons/hca-bio-networks/reproduction.png b/public/images/icons/hca-bio-networks/reproduction.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/reproduction.png rename to public/images/icons/hca-bio-networks/reproduction.png diff --git a/explorer/public/images/icons/hca-bio-networks/skin.png b/public/images/icons/hca-bio-networks/skin.png similarity index 100% rename from explorer/public/images/icons/hca-bio-networks/skin.png rename to public/images/icons/hca-bio-networks/skin.png diff --git a/explorer/public/images/icons/lgea.png b/public/images/icons/lgea.png similarity index 100% rename from explorer/public/images/icons/lgea.png rename to public/images/icons/lgea.png diff --git a/explorer/public/images/icons/lungmap.svg b/public/images/icons/lungmap.svg similarity index 100% rename from explorer/public/images/icons/lungmap.svg rename to public/images/icons/lungmap.svg diff --git a/explorer/public/images/icons/shiny.png b/public/images/icons/shiny.png similarity index 100% rename from explorer/public/images/icons/shiny.png rename to public/images/icons/shiny.png diff --git a/explorer/public/images/icons/single-cell.png b/public/images/icons/single-cell.png similarity index 100% rename from explorer/public/images/icons/single-cell.png rename to public/images/icons/single-cell.png diff --git a/explorer/public/images/icons/stem.svg b/public/images/icons/stem.svg similarity index 100% rename from explorer/public/images/icons/stem.svg rename to public/images/icons/stem.svg diff --git a/explorer/public/images/icons/toppcell.png b/public/images/icons/toppcell.png similarity index 100% rename from explorer/public/images/icons/toppcell.png rename to public/images/icons/toppcell.png diff --git a/explorer/public/images/icons/ucsc-cell.svg b/public/images/icons/ucsc-cell.svg similarity index 100% rename from explorer/public/images/icons/ucsc-cell.svg rename to public/images/icons/ucsc-cell.svg diff --git a/explorer/public/images/icons/ucsc-genome.svg b/public/images/icons/ucsc-genome.svg similarity index 100% rename from explorer/public/images/icons/ucsc-genome.svg rename to public/images/icons/ucsc-genome.svg diff --git a/explorer/public/images/logoAnvil.png b/public/images/logoAnvil.png similarity index 100% rename from explorer/public/images/logoAnvil.png rename to public/images/logoAnvil.png diff --git a/explorer/public/images/logoHumanCellAtlas.png b/public/images/logoHumanCellAtlas.png similarity index 100% rename from explorer/public/images/logoHumanCellAtlas.png rename to public/images/logoHumanCellAtlas.png diff --git a/explorer/public/images/logoLungmap.png b/public/images/logoLungmap.png similarity index 100% rename from explorer/public/images/logoLungmap.png rename to public/images/logoLungmap.png diff --git a/explorer/public/images/logoNCPI.png b/public/images/logoNCPI.png similarity index 100% rename from explorer/public/images/logoNCPI.png rename to public/images/logoNCPI.png diff --git a/explorer/public/images/nhgri.svg b/public/images/nhgri.svg similarity index 100% rename from explorer/public/images/nhgri.svg rename to public/images/nhgri.svg diff --git a/explorer/public/images/nih.svg b/public/images/nih.svg similarity index 100% rename from explorer/public/images/nih.svg rename to public/images/nih.svg diff --git a/explorer/public/images/usagov.png b/public/images/usagov.png similarity index 100% rename from explorer/public/images/usagov.png rename to public/images/usagov.png diff --git a/pull_request_template.md b/pull_request_template.md index fc67186d3..57788f349 100644 --- a/pull_request_template.md +++ b/pull_request_template.md @@ -1,10 +1,13 @@ ### Ticket + Closes #. ### Reviewers + @. ### Changes + - Added - Removed - Modified diff --git a/explorer/scripts/browserconfig.xml b/scripts/browserconfig.xml similarity index 100% rename from explorer/scripts/browserconfig.xml rename to scripts/browserconfig.xml diff --git a/explorer/scripts/build.sh b/scripts/build.sh similarity index 100% rename from explorer/scripts/build.sh rename to scripts/build.sh diff --git a/explorer/scripts/common-build.sh b/scripts/common-build.sh similarity index 100% rename from explorer/scripts/common-build.sh rename to scripts/common-build.sh diff --git a/explorer/scripts/dev.sh b/scripts/dev.sh similarity index 100% rename from explorer/scripts/dev.sh rename to scripts/dev.sh diff --git a/scripts/package-lock.json b/scripts/package-lock.json deleted file mode 100644 index d414d50e5..000000000 --- a/scripts/package-lock.json +++ /dev/null @@ -1,3646 +0,0 @@ -{ - "name": "scripts", - "lockfileVersion": 2, - "requires": true, - "packages": { - "": { - "name": "scripts", - "devDependencies": { - 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"module", - "scripts": { - "update-archive-previews": "node update-archive-previews.js", - "update-sitemap": "node update-sitemap.js" - }, - "devDependencies": { - "@aws-sdk/client-s3": "^3.56.0", - "@aws-sdk/credential-providers": "^3.56.0", - "got": "^12.0.3", - "sitemap": "^7.1.1" - } -} diff --git a/explorer/scripts/site.webmanifest b/scripts/site.webmanifest similarity index 100% rename from explorer/scripts/site.webmanifest rename to scripts/site.webmanifest diff --git a/scripts/update-archive-previews.js b/scripts/update-archive-previews.js deleted file mode 100644 index 6113ce113..000000000 --- a/scripts/update-archive-previews.js +++ /dev/null @@ -1,289 +0,0 @@ -import { promisify } from "util"; -import fs, { promises as fsPromises } from "fs"; -import path from "path"; -import got from "got"; -import { - S3Client, - PutObjectCommand, - HeadObjectCommand, -} from "@aws-sdk/client-s3"; - -import { fromIni } from "@aws-sdk/credential-providers"; - -import { pipeline as callbackPipeline } from "stream"; -import { exec as callbackExec } from "child_process"; - -const pipeline = promisify(callbackPipeline); -const exec = promisify(callbackExec); - -const outPath = path.resolve("../downloads"); - -const scriptArgs = {}; - -process.argv.slice(2).forEach((arg) => { - const [key, value] = arg.split("="); - scriptArgs[key] = value; -}); - -const env = scriptArgs.env; - -let hcaApiUrl; -let bucketName; -let client; - -(function () { - if (env === "dev") { - hcaApiUrl = - "https://service.dev.singlecell.gi.ucsc.edu/index/files?filters=%7B%22fileFormat%22%3A%7B%22is%22%3A%5B%22zip%22%2C%22zip.gz%22%2C%22tar%22%2C%22tar.gz%22%5D%7D%7D&size=500&catalog=dcp2"; - bucketName = "dev.archive-preview.singlecell.gi.ucsc.edu"; - client = new S3Client({ - region: "us-east-1", - credentials: fromIni({ - profile: "platform-hca-dev", - mfaCodeProvider: async (mfaSerial) => { - return "864992"; - }, - }), - }); - } else { - hcaApiUrl = - "https://service.azul.data.humancellatlas.org/index/files?filters=%7B%22fileFormat%22%3A%7B%22is%22%3A%5B%22zip%22%2C%22zip.gz%22%2C%22tar%22%2C%22tar.gz%22%5D%7D%7D&size=500&catalog=dcp39"; - if (env === "test") { - bucketName = "cc-archive-preview-test"; - client = new S3Client({ region: "us-east-1" }); - } else if (env === "prod") { - //wve-data.humancellatlas.org.archive-preview - bucketName = "archive-preview.humancellatlas.org"; - client = new S3Client({ - region: "us-east-1", - credentials: fromIni({ - profile: "platform-hca-prod", - mfaCodeProvider: async (mfaSerial) => { - return "997196"; - }, - }), - }); - } else { - console.log("Missing or invalid environment argument"); - console.log( - "USAGE: npm run-script update-archive-previews -- env={test|dev|prod}" - ); - return; - } - } - - //TODO: Delete downloads content on startup... - - (async function () { - try { - await fsPromises.mkdir(outPath); - } catch (e) { - // ignoring the error under the assumption that the folder already exists - } - - const hits = await getSearchResults(); - - for (let entry of hits) { - for (let file of entry.files) { - try { - await processFile(file); - } catch (e) { - console.log(e); - continue; - } - } - } - - console.log("Done"); - })(); -})(); - -async function getSearchResults() { - // make a request using the hcaApiUrl, paginate through the results, and return a combined results array - - const allHits = []; - let url = hcaApiUrl; - - while (url) { - const { hits, pagination } = await got(url).json(); - allHits.push(...hits); - url = pagination.next; - } - - return allHits; -} - -async function processFile(file) { - // if the archive file doesn't already have a json manifest, generate one and upload it - - console.log(file.url); - - // determine if the json already exists: - - const jsonName = - "archive-preview/" + - file.uuid + - "-" + - file.version.replace(/:/g, "_") + - ".json"; - - const headCommand = new HeadObjectCommand({ - Bucket: bucketName, - Key: jsonName, - }); - - let jsonExists = true; - - try { - await client.send(headCommand); - } catch (e) { - jsonExists = false; - } - - if (!jsonExists) { - // download the archive: - - const fetchUrl = file.url.replace( - "repository/files/", - "fetch/repository/files/" - ); - - const { Location: fileUrl } = await got(fetchUrl).json(); - - const fileDlName = file.name || file.uuid + "." + file.format; - const fileDlPath = path.resolve(outPath, fileDlName); - - if (fileDlPath.substring(0, outPath.length + 1) !== outPath + path.sep) { - throw new Error("Invalid archive name"); - } - - await pipeline(got.stream(fileUrl), fs.createWriteStream(fileDlPath)); - - // generate the json, upload it, and clean up the downloaded file: - - const manifest = await generateManifest( - file.uuid, - file.version, - fileDlName - ); - - const putCommand = new PutObjectCommand({ - Bucket: bucketName, - Key: jsonName, - Body: JSON.stringify(manifest), //await fsPromises.readFile(jsonPath) - }); - - const results = await client.send(putCommand); - - await fsPromises.rm(fileDlPath); - - console.log("Processed file"); - } else { - console.log("JSON exists"); - } -} - -async function generateManifest(uuid, version, fileName) { - // generate json manifest for an archive file - - // set up paths and temp directory: - - const filePath = path.resolve(outPath, fileName); - - const filesDirName = `TEMP_${fileName}_extracted`.replace(/ /g, "_"); - const filesDirPath = path.resolve(outPath, filesDirName); - - await fsPromises.mkdir(filesDirPath); - - // get string listing files in the archive and extract the files to the file system: - - let filesString; - - if (/\.zip(?:$|\.)/i.test(fileName)) { - let zipName; - - if (/\.gz$/i.test(fileName)) { - zipName = `TEMP_${fileName}_ungz.zip`; - await exec( - `gzip -dc ${formatBashString(fileName)} > ${formatBashString(zipName)}`, - { cwd: outPath } - ); - } else { - zipName = fileName; - } - - // get file list: - const { stdout } = await exec(`unzip -Z1 ${formatBashString(zipName)}`, { - cwd: outPath, - }); - filesString = stdout; - // extract files: - await exec( - `unzip -q -d ${formatBashString(filesDirName)} ${formatBashString( - zipName - )}`, - { cwd: outPath } - ); - - if (zipName !== fileName) { - await fsPromises.rm(path.resolve(outPath, zipName)); - } - } else { - // get file list: - const { stdout } = await exec(`tar -tf ${formatBashString(fileName)}`, { - cwd: outPath, - }); - filesString = stdout; - // extract files: - await exec( - `tar -xf ${formatBashString(fileName)} -C ${formatBashString( - filesDirName - )}`, - { cwd: outPath } - ); - } - - // iterate over file list and get files' info: - - const filesArr = filesString - .split("\n") - .map((line) => line.trim()) - .filter((line) => line); - - const filesInfo = []; - - for (const name of filesArr) { - try { - const { size, mtime } = await fsPromises.stat( - path.resolve(filesDirPath, name) - ); - filesInfo.push({ - name, - size, - modified: mtime.toISOString(), - }); - } catch (e) { - console.log(e); - continue; - } - } - - // clean up files and return json: - - await fsPromises.rm(filesDirPath, { recursive: true }); - - return { - archive: { - name: fileName, - size: (await fsPromises.stat(filePath)).size, - uuid, - version, - }, - files: filesInfo, - }; -} - -function formatBashString(str) { - // add quotes and escape sequences so that the string can be safely used in a bash command - return '"' + str.replace(/[$`"\\\n!]/g, "\\$&") + '"'; -} diff --git a/scripts/update-sitemap.js b/scripts/update-sitemap.js deleted file mode 100644 index aba42af74..000000000 --- a/scripts/update-sitemap.js +++ /dev/null @@ -1,65 +0,0 @@ - - -import { promisify } from "util"; -import fs from "fs"; -import got from "got"; -import { SitemapStream } from "sitemap"; -import { pipeline as callbackPipeline } from "stream"; - -const pipeline = promisify(callbackPipeline); - -const pageSize = 50; -const sitemapOutPath = "../dist/explore/projects-sitemap.xml"; - -const scriptArgs = {}; - -process.argv.slice(2).forEach((arg) => { - const [key, value] = arg.split("="); - scriptArgs[key] = value; -}); - -var hcaApiUrl; - -// TODO: add stuff for the "env" argument - -if (!scriptArgs.catalog) { - console.log("Missing/invalid arguments"); - console.log("Usage: npm run-script update-sitemap -- catalog= env={dev|prod}"); -} else (async function() { - hcaApiUrl = "https://service.azul.data.humancellatlas.org/index/projects?catalog=" + scriptArgs.catalog + "&size=" + pageSize; - - const stream = new SitemapStream({ hostname: "https://data.humancellatlas.org/" }); - const lastmod = new Date().toISOString(); - - for (let entry of await getSearchResults(hcaApiUrl)) { - for (let project of entry.projects) { - stream.write({ - url: "/explore/projects/" + project.projectId, - lastmod, - changefreq: "monthly" - }); - } - } - - const pl = pipeline(stream, fs.createWriteStream(sitemapOutPath)); - stream.end(); - await pl; - - console.log("Done"); -})(); - - -async function getSearchResults(url) { - // make a request using the url, paginate through the results, and return a combined results array - - const allHits = []; - - while (url) { - const { hits, pagination } = await got(url).json(); - allHits.push(...hits); - url = pagination.next; - } - - return allHits; -} - diff --git a/explorer/site-config/anvil-catalog/category.ts b/site-config/anvil-catalog/category.ts similarity index 100% rename from explorer/site-config/anvil-catalog/category.ts rename to site-config/anvil-catalog/category.ts diff --git a/explorer/site-config/anvil-catalog/dev/.env b/site-config/anvil-catalog/dev/.env similarity index 100% rename from explorer/site-config/anvil-catalog/dev/.env rename to site-config/anvil-catalog/dev/.env diff --git a/explorer/site-config/anvil-catalog/dev/common/constants.ts b/site-config/anvil-catalog/dev/common/constants.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/common/constants.ts rename to site-config/anvil-catalog/dev/common/constants.ts diff --git a/explorer/site-config/anvil-catalog/dev/common/utils.ts b/site-config/anvil-catalog/dev/common/utils.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/common/utils.ts rename to site-config/anvil-catalog/dev/common/utils.ts diff --git a/explorer/site-config/anvil-catalog/dev/config.ts b/site-config/anvil-catalog/dev/config.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/config.ts rename to site-config/anvil-catalog/dev/config.ts diff --git a/explorer/site-config/anvil-catalog/dev/detail/consortium/overviewMainColumn.ts b/site-config/anvil-catalog/dev/detail/consortium/overviewMainColumn.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/detail/consortium/overviewMainColumn.ts rename to site-config/anvil-catalog/dev/detail/consortium/overviewMainColumn.ts diff --git a/explorer/site-config/anvil-catalog/dev/detail/consortium/overviewSideColumn.ts b/site-config/anvil-catalog/dev/detail/consortium/overviewSideColumn.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/detail/consortium/overviewSideColumn.ts rename to site-config/anvil-catalog/dev/detail/consortium/overviewSideColumn.ts diff --git a/explorer/site-config/anvil-catalog/dev/detail/consortium/studiesMainColumn.ts b/site-config/anvil-catalog/dev/detail/consortium/studiesMainColumn.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/detail/consortium/studiesMainColumn.ts rename to site-config/anvil-catalog/dev/detail/consortium/studiesMainColumn.ts diff --git a/explorer/site-config/anvil-catalog/dev/detail/consortium/top.ts b/site-config/anvil-catalog/dev/detail/consortium/top.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/detail/consortium/top.ts rename to site-config/anvil-catalog/dev/detail/consortium/top.ts diff --git a/explorer/site-config/anvil-catalog/dev/detail/consortium/workspacesMainColumn.ts b/site-config/anvil-catalog/dev/detail/consortium/workspacesMainColumn.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/detail/consortium/workspacesMainColumn.ts rename to site-config/anvil-catalog/dev/detail/consortium/workspacesMainColumn.ts diff --git a/explorer/site-config/anvil-catalog/dev/detail/study/overviewMainColumn.ts b/site-config/anvil-catalog/dev/detail/study/overviewMainColumn.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/detail/study/overviewMainColumn.ts rename to site-config/anvil-catalog/dev/detail/study/overviewMainColumn.ts diff --git a/explorer/site-config/anvil-catalog/dev/detail/study/overviewSideColumn.ts b/site-config/anvil-catalog/dev/detail/study/overviewSideColumn.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/detail/study/overviewSideColumn.ts rename to site-config/anvil-catalog/dev/detail/study/overviewSideColumn.ts diff --git a/explorer/site-config/anvil-catalog/dev/detail/study/top.ts b/site-config/anvil-catalog/dev/detail/study/top.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/detail/study/top.ts rename to site-config/anvil-catalog/dev/detail/study/top.ts diff --git a/explorer/site-config/anvil-catalog/dev/detail/study/workspacesMainColumn.ts b/site-config/anvil-catalog/dev/detail/study/workspacesMainColumn.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/detail/study/workspacesMainColumn.ts rename to site-config/anvil-catalog/dev/detail/study/workspacesMainColumn.ts diff --git a/explorer/site-config/anvil-catalog/dev/export/export.ts b/site-config/anvil-catalog/dev/export/export.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/export/export.ts rename to site-config/anvil-catalog/dev/export/export.ts diff --git a/explorer/site-config/anvil-catalog/dev/index/common/constants.ts b/site-config/anvil-catalog/dev/index/common/constants.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/index/common/constants.ts rename to site-config/anvil-catalog/dev/index/common/constants.ts diff --git a/explorer/site-config/anvil-catalog/dev/index/consortiaEntityConfig.ts b/site-config/anvil-catalog/dev/index/consortiaEntityConfig.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/index/consortiaEntityConfig.ts rename to site-config/anvil-catalog/dev/index/consortiaEntityConfig.ts diff --git a/explorer/site-config/anvil-catalog/dev/index/studiesEntityConfig.ts b/site-config/anvil-catalog/dev/index/studiesEntityConfig.ts similarity index 100% rename from explorer/site-config/anvil-catalog/dev/index/studiesEntityConfig.ts rename to site-config/anvil-catalog/dev/index/studiesEntityConfig.ts diff --git 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explorer/site-config/hca-dcp/ma-prod/config.ts rename to site-config/hca-dcp/ma-prod/config.ts diff --git a/explorer/site-config/hca-dcp/prod/.env b/site-config/hca-dcp/prod/.env similarity index 100% rename from explorer/site-config/hca-dcp/prod/.env rename to site-config/hca-dcp/prod/.env diff --git a/explorer/site-config/hca-dcp/prod/config.ts b/site-config/hca-dcp/prod/config.ts similarity index 100% rename from explorer/site-config/hca-dcp/prod/config.ts rename to site-config/hca-dcp/prod/config.ts diff --git a/explorer/site-config/lungmap/dev/.env b/site-config/lungmap/dev/.env similarity index 100% rename from explorer/site-config/lungmap/dev/.env rename to site-config/lungmap/dev/.env diff --git a/explorer/site-config/lungmap/dev/config.ts b/site-config/lungmap/dev/config.ts similarity index 100% rename from explorer/site-config/lungmap/dev/config.ts rename to site-config/lungmap/dev/config.ts diff --git a/explorer/site-config/lungmap/dev/detail/project/exportMainColumn.ts b/site-config/lungmap/dev/detail/project/exportMainColumn.ts similarity index 100% rename from explorer/site-config/lungmap/dev/detail/project/exportMainColumn.ts rename to site-config/lungmap/dev/detail/project/exportMainColumn.ts diff --git a/explorer/site-config/lungmap/dev/detail/project/exportSideColumn.ts b/site-config/lungmap/dev/detail/project/exportSideColumn.ts similarity index 100% rename from explorer/site-config/lungmap/dev/detail/project/exportSideColumn.ts rename to site-config/lungmap/dev/detail/project/exportSideColumn.ts diff --git a/explorer/site-config/lungmap/dev/detail/project/mainColumn.ts b/site-config/lungmap/dev/detail/project/mainColumn.ts similarity index 100% rename from explorer/site-config/lungmap/dev/detail/project/mainColumn.ts rename to site-config/lungmap/dev/detail/project/mainColumn.ts diff --git a/explorer/site-config/lungmap/dev/detail/project/matricesMainColumn.ts b/site-config/lungmap/dev/detail/project/matricesMainColumn.ts similarity index 100% rename from explorer/site-config/lungmap/dev/detail/project/matricesMainColumn.ts rename to site-config/lungmap/dev/detail/project/matricesMainColumn.ts diff --git a/explorer/site-config/lungmap/dev/detail/project/metadataSideColumn.ts b/site-config/lungmap/dev/detail/project/metadataSideColumn.ts similarity index 100% rename from explorer/site-config/lungmap/dev/detail/project/metadataSideColumn.ts rename to site-config/lungmap/dev/detail/project/metadataSideColumn.ts diff --git a/explorer/site-config/lungmap/dev/detail/project/projectFilesMainColumn.ts b/site-config/lungmap/dev/detail/project/projectFilesMainColumn.ts similarity index 100% rename from explorer/site-config/lungmap/dev/detail/project/projectFilesMainColumn.ts rename to site-config/lungmap/dev/detail/project/projectFilesMainColumn.ts diff --git a/explorer/site-config/lungmap/dev/detail/project/projectFilesSideColumn.ts b/site-config/lungmap/dev/detail/project/projectFilesSideColumn.ts similarity index 100% rename from explorer/site-config/lungmap/dev/detail/project/projectFilesSideColumn.ts rename to site-config/lungmap/dev/detail/project/projectFilesSideColumn.ts diff --git a/explorer/site-config/lungmap/dev/export/exportConfig.ts b/site-config/lungmap/dev/export/exportConfig.ts similarity index 100% rename from explorer/site-config/lungmap/dev/export/exportConfig.ts rename to site-config/lungmap/dev/export/exportConfig.ts diff --git a/explorer/site-config/lungmap/dev/export/sideColumn.ts b/site-config/lungmap/dev/export/sideColumn.ts similarity index 100% rename from explorer/site-config/lungmap/dev/export/sideColumn.ts rename to site-config/lungmap/dev/export/sideColumn.ts diff --git a/explorer/site-config/lungmap/dev/index/common/constants.ts b/site-config/lungmap/dev/index/common/constants.ts similarity index 100% rename from explorer/site-config/lungmap/dev/index/common/constants.ts rename to site-config/lungmap/dev/index/common/constants.ts diff --git a/explorer/site-config/lungmap/dev/index/projectsEntityConfig.ts b/site-config/lungmap/dev/index/projectsEntityConfig.ts similarity index 100% rename from explorer/site-config/lungmap/dev/index/projectsEntityConfig.ts rename to site-config/lungmap/dev/index/projectsEntityConfig.ts diff --git a/explorer/site-config/lungmap/dev/index/summary.ts b/site-config/lungmap/dev/index/summary.ts similarity index 100% rename from explorer/site-config/lungmap/dev/index/summary.ts rename to site-config/lungmap/dev/index/summary.ts diff --git a/explorer/site-config/lungmap/dev/index/summaryViewModelBuilder.ts b/site-config/lungmap/dev/index/summaryViewModelBuilder.ts similarity index 100% rename from explorer/site-config/lungmap/dev/index/summaryViewModelBuilder.ts rename to site-config/lungmap/dev/index/summaryViewModelBuilder.ts diff --git a/explorer/site-config/lungmap/dev/socialMedia.ts b/site-config/lungmap/dev/socialMedia.ts similarity index 100% rename from explorer/site-config/lungmap/dev/socialMedia.ts rename to site-config/lungmap/dev/socialMedia.ts diff --git a/explorer/site-config/lungmap/images/favicons/android-chrome-192x192.png b/site-config/lungmap/images/favicons/android-chrome-192x192.png similarity index 100% rename from explorer/site-config/lungmap/images/favicons/android-chrome-192x192.png rename to site-config/lungmap/images/favicons/android-chrome-192x192.png diff --git a/explorer/site-config/lungmap/images/favicons/android-chrome-256x256.png b/site-config/lungmap/images/favicons/android-chrome-256x256.png similarity index 100% rename from explorer/site-config/lungmap/images/favicons/android-chrome-256x256.png rename to site-config/lungmap/images/favicons/android-chrome-256x256.png diff --git a/explorer/site-config/lungmap/images/favicons/apple-touch-icon.png b/site-config/lungmap/images/favicons/apple-touch-icon.png similarity index 100% rename from explorer/site-config/lungmap/images/favicons/apple-touch-icon.png rename to site-config/lungmap/images/favicons/apple-touch-icon.png diff --git a/explorer/site-config/lungmap/images/favicons/favicon-16x16.png b/site-config/lungmap/images/favicons/favicon-16x16.png similarity index 100% rename from explorer/site-config/lungmap/images/favicons/favicon-16x16.png rename to site-config/lungmap/images/favicons/favicon-16x16.png diff --git a/explorer/site-config/lungmap/images/favicons/favicon-32x32.png b/site-config/lungmap/images/favicons/favicon-32x32.png similarity index 100% rename from explorer/site-config/lungmap/images/favicons/favicon-32x32.png rename to site-config/lungmap/images/favicons/favicon-32x32.png diff --git a/explorer/site-config/lungmap/images/favicons/favicon.ico b/site-config/lungmap/images/favicons/favicon.ico similarity index 100% rename from explorer/site-config/lungmap/images/favicons/favicon.ico rename to site-config/lungmap/images/favicons/favicon.ico diff --git a/explorer/site-config/lungmap/images/favicons/mstile-150x150.png b/site-config/lungmap/images/favicons/mstile-150x150.png similarity index 100% rename from explorer/site-config/lungmap/images/favicons/mstile-150x150.png rename to site-config/lungmap/images/favicons/mstile-150x150.png diff --git a/explorer/site-config/lungmap/images/favicons/safari-pinned-tab.svg b/site-config/lungmap/images/favicons/safari-pinned-tab.svg similarity index 100% rename from explorer/site-config/lungmap/images/favicons/safari-pinned-tab.svg rename to site-config/lungmap/images/favicons/safari-pinned-tab.svg diff --git a/explorer/site-config/lungmap/prod/.env b/site-config/lungmap/prod/.env similarity index 100% rename from explorer/site-config/lungmap/prod/.env rename to site-config/lungmap/prod/.env diff --git a/explorer/site-config/lungmap/prod/config.ts b/site-config/lungmap/prod/config.ts similarity index 100% rename from explorer/site-config/lungmap/prod/config.ts rename to site-config/lungmap/prod/config.ts diff --git a/explorer/site-config/ncpi-catalog/category.ts b/site-config/ncpi-catalog/category.ts similarity index 100% rename from explorer/site-config/ncpi-catalog/category.ts rename to site-config/ncpi-catalog/category.ts diff --git a/explorer/site-config/ncpi-catalog/dev/.env b/site-config/ncpi-catalog/dev/.env similarity index 100% rename from explorer/site-config/ncpi-catalog/dev/.env rename to site-config/ncpi-catalog/dev/.env diff --git a/explorer/site-config/ncpi-catalog/dev/config.ts b/site-config/ncpi-catalog/dev/config.ts similarity index 100% rename from explorer/site-config/ncpi-catalog/dev/config.ts rename to site-config/ncpi-catalog/dev/config.ts diff --git a/explorer/site-config/ncpi-catalog/dev/detail/study/overviewMainColumn.ts b/site-config/ncpi-catalog/dev/detail/study/overviewMainColumn.ts similarity index 100% rename from explorer/site-config/ncpi-catalog/dev/detail/study/overviewMainColumn.ts rename to site-config/ncpi-catalog/dev/detail/study/overviewMainColumn.ts diff --git a/explorer/site-config/ncpi-catalog/dev/detail/study/overviewSideColumn.ts b/site-config/ncpi-catalog/dev/detail/study/overviewSideColumn.ts similarity index 100% rename from explorer/site-config/ncpi-catalog/dev/detail/study/overviewSideColumn.ts rename to site-config/ncpi-catalog/dev/detail/study/overviewSideColumn.ts diff --git a/explorer/site-config/ncpi-catalog/dev/detail/study/top.ts b/site-config/ncpi-catalog/dev/detail/study/top.ts similarity index 100% rename from explorer/site-config/ncpi-catalog/dev/detail/study/top.ts rename to site-config/ncpi-catalog/dev/detail/study/top.ts diff --git a/explorer/site-config/ncpi-catalog/dev/index/platformsEntityConfig.ts b/site-config/ncpi-catalog/dev/index/platformsEntityConfig.ts similarity index 100% rename from explorer/site-config/ncpi-catalog/dev/index/platformsEntityConfig.ts rename to site-config/ncpi-catalog/dev/index/platformsEntityConfig.ts diff --git a/explorer/site-config/ncpi-catalog/dev/index/studiesEntityConfig.ts b/site-config/ncpi-catalog/dev/index/studiesEntityConfig.ts similarity index 100% rename from explorer/site-config/ncpi-catalog/dev/index/studiesEntityConfig.ts rename to site-config/ncpi-catalog/dev/index/studiesEntityConfig.ts diff --git a/explorer/site-config/ncpi-catalog/prod/.env b/site-config/ncpi-catalog/prod/.env similarity index 100% rename from explorer/site-config/ncpi-catalog/prod/.env rename to site-config/ncpi-catalog/prod/.env diff --git a/explorer/site-config/ncpi-catalog/prod/config.ts b/site-config/ncpi-catalog/prod/config.ts similarity index 100% rename from explorer/site-config/ncpi-catalog/prod/config.ts rename to site-config/ncpi-catalog/prod/config.ts diff --git a/trufflehog-rules.json b/trufflehog-rules.json index 4b5296811..ce42aa0e9 100644 --- a/trufflehog-rules.json +++ b/trufflehog-rules.json @@ -17,4 +17,4 @@ "Google (GCP) Service-account": "\"type\": \"service_account\"", "Twilio API Key": "SK[a-z0-9]{32}", "AWS Secret": "(?:\"|')?(?:AWS|aws|Aws)?_?(?:SECRET|secret|Secret)?_?(?:ACCESS|access|Access)?_?(?:KEY|key|Key)(?:\"|')?\\s*(?:\\:|=>|=)\\s*(?:\"|')?[A-Za-z0-9/\\+=]{40}(?:\"|')?" -} \ No newline at end of file +} diff --git a/explorer/tsconfig.json b/tsconfig.json similarity index 92% rename from explorer/tsconfig.json rename to tsconfig.json index 1421c1774..bf7695c31 100644 --- a/explorer/tsconfig.json +++ b/tsconfig.json @@ -26,5 +26,5 @@ ] }, "include": ["next-env.d.ts", "**/*.ts", "**/*.tsx", ".next/types/**/*.ts"], - "exclude": ["node_modules", "./files"] + "exclude": ["node_modules", "./files", "./analytics"] }