From 377ac338bb5f97dcf4d122791b84aef18a8365ec Mon Sep 17 00:00:00 2001 From: Matt Watson Date: Fri, 19 Jun 2026 14:18:30 -0400 Subject: [PATCH] set up deterministic GitBook-driven docs deployment ...with build-time sync and no content churn in repo. - Added build-time GitBook sync pipeline in apps/docs/scripts/sync-gitbook.mjs to clone pinned content, transform GitBook markdown syntax, copy assets, generate sidebar, and emit manifest. - Runtime/build to generated navigation and sync-first flow: - apps/docs/astro.config.mjs now uses generated sidebar and disables default Starlight 404 route. - apps/docs/package.json now has sync:content, dev:sync, and sync-before-build behavior, with plain dev for fast local iteration. - Added safety/consistency controls: - Overwrite guard via GITBOOK_ALLOW_OVERWRITE=1. - Frontmatter title injection when missing. - Duplicate H1 removal when it matches frontmatter title. - Sidebar generation cleanup to avoid duplicate parent-as-child labels and prefer Overview. - Introduced pinned source-of-truth lock file: - Added apps/docs/gitbook.lock.json with GitBook repo + ref SHA. - Sync script now defaults to lock file repo/ref (env overrides still supported), including SHA checkout support. - Generated-artifact model: - Added apps/docs/.gitignore entries for synced docs content/assets and generated sidebar/manifest so content syncs are local/build artifacts. - Removed manual tracked sidebar and updated tests to validate generated sidebar (apps/docs/src/config/sidebar.test.ts; deleted apps/docs/src/config/sidebar.ts). - Added scheduled auto-sync CI in bdc-web: - New workflow .github/workflows/docs-gitbook-sync.yml checks GitBook main every 30 minutes (plus manual trigger), updates lock when changed, validates docs build, and commits only lock updates on success. - Trigger on schedule-only and workflow_dispatch only. etc. - avoid node 20 - organize imports and formatting - shift action timing - add docs site readme --- .github/workflows/docs-gitbook-sync.yml | 111 ++++ apps/docs/.gitignore | 5 + apps/docs/README.md | 71 ++ apps/docs/astro.config.mjs | 3 +- apps/docs/gitbook.lock.json | 4 + apps/docs/package.json | 4 +- apps/docs/scripts/sync-gitbook.mjs | 615 ++++++++++++++++++ apps/docs/src/config/sidebar.test.ts | 29 +- apps/docs/src/config/sidebar.ts | 411 ------------ apps/docs/src/content/docs/404.md | 13 - .../src/content/docs/analyze-data/index.md | 6 - .../seven-bridges/analysis-tips.md | 6 - .../seven-bridges/annotation-explorer.md | 6 - .../seven-bridges/getting-started.md | 6 - .../seven-bridges/gwas-genesis.md | 6 - .../docs/analyze-data/seven-bridges/index.md | 6 - .../seven-bridges/knowledge-center.md | 6 - .../seven-bridges/troubleshooting-tasks.md | 6 - .../docs/analyze-data/terra/account-setup.md | 6 - .../analyze-data/terra/batch-workflows.md | 6 - .../docs/analyze-data/terra/billing.md | 6 - .../docs/analyze-data/terra/bring-data.md | 6 - 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- .../bring-your-own-tool/wdl-workflows.md | 6 - .../src/content/docs/community-tools/index.md | 6 - .../community/citation-and-acknowledgement.md | 6 - .../community/contributing-user-resources.md | 6 - .../src/content/docs/community/glossary.md | 6 - apps/docs/src/content/docs/community/index.md | 6 - .../dicom-de-identification.md | 6 - .../ecosystem-security-statement.md | 6 - .../community/request-for-comments/index.md | 6 - .../docs/community/strategic-planning.md | 6 - .../docs/community/video-content-guidance.md | 6 - .../docs/data-access/checking-access.md | 6 - .../docs/data-access/data-interoperability.md | 6 - .../src/content/docs/data-access/index.md | 6 - .../data-access/submitting-dbgap-request.md | 6 - .../docs/data-access/understanding-access.md | 6 - .../docs/data-management/data-submission.md | 6 - .../data-management/dbgap-configuration.md | 6 - .../docs/data-management/de-identification.md | 6 - .../src/content/docs/data-management/index.md | 6 - 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Read current locked SHA + id: lock + run: | + node - <<'NODE' + const fs = require('node:fs'); + const path = 'apps/docs/gitbook.lock.json'; + let ref = ''; + + if (fs.existsSync(path)) { + try { + const parsed = JSON.parse(fs.readFileSync(path, 'utf8')); + if (parsed && typeof parsed.ref === 'string') ref = parsed.ref; + } catch { + ref = ''; + } + } + + fs.appendFileSync(process.env.GITHUB_OUTPUT, `ref=${ref}\n`); + NODE + + - name: Update lock file + if: steps.gitbook.outputs.sha != steps.lock.outputs.ref + run: | + node - <<'NODE' + const fs = require('node:fs'); + const path = 'apps/docs/gitbook.lock.json'; + const sha = process.env.GITBOOK_SHA; + + const lock = { + repo: 'https://github.com/stagecc/bdc-gitbook.git', + ref: sha, + }; + + fs.writeFileSync(path, `${JSON.stringify(lock, null, 2)}\n`); + NODE + env: + GITBOOK_SHA: ${{ steps.gitbook.outputs.sha }} + + - name: Setup Node + if: steps.gitbook.outputs.sha != steps.lock.outputs.ref + uses: actions/setup-node@v5 + with: + node-version: '22' + cache: npm + + - name: Install dependencies + if: steps.gitbook.outputs.sha != steps.lock.outputs.ref + run: npm ci + + - name: Validate docs build + if: steps.gitbook.outputs.sha != steps.lock.outputs.ref + run: npm run build --workspace=@bdc/docs + env: + GITBOOK_REF: ${{ steps.gitbook.outputs.sha }} + + - name: Commit updated lock + if: steps.gitbook.outputs.sha != steps.lock.outputs.ref + run: | + git config user.name "github-actions[bot]" + git config user.email "41898282+github-actions[bot]@users.noreply.github.com" + + git add "apps/docs/gitbook.lock.json" + + if git diff --cached --quiet; then + echo "No lock changes to commit." + exit 0 + fi + + short_sha="${GITBOOK_SHA:0:12}" + git commit -m "chore(docs): sync GitBook lock to ${short_sha}" + git push + env: + GITBOOK_SHA: ${{ steps.gitbook.outputs.sha }} + + - name: No content changes detected + if: steps.gitbook.outputs.sha == steps.lock.outputs.ref + run: echo "GitBook is already in sync at ${{ steps.lock.outputs.ref }}" diff --git a/apps/docs/.gitignore b/apps/docs/.gitignore new file mode 100644 index 00000000..fe60bb4b --- /dev/null +++ b/apps/docs/.gitignore @@ -0,0 +1,5 @@ +# Build-time synced GitBook content +src/content/docs/ +public/gitbook-assets/ +src/config/sidebar.generated.ts +src/generated/gitbook-manifest.json diff --git a/apps/docs/README.md b/apps/docs/README.md new file mode 100644 index 00000000..f0b905c9 --- /dev/null +++ b/apps/docs/README.md @@ -0,0 +1,71 @@ +# BDC Documentation App Overview + +This app (`@bdc/docs`) is an Astro + Starlight documentation site. + +Content is sourced from GitBook via the `stagecc/bdc-gitbook` repository, which is in-sync with the [BDC GitBook](https://bdcatalyst.gitbook.io/), and fetched at build time. + +## Source of truth + +- GitBook content repo: `https://github.com/stagecc/bdc-gitbook` +- Lock file in this repo: `apps/docs/gitbook.lock.json` + - `repo`: Git URL to clone + - `ref`: pinned commit SHA to sync + +The lock file provides deterministic builds and deployment traceability. + +## How sync works + +Sync is handled by `apps/docs/scripts/sync-gitbook.mjs`. + +At a high level, the script: + +1. resolves source repo/ref from env vars, then lock file; +2. clones GitBook content into a temporary directory; +3. rebuilds generated docs content and assets from scratch; +4. converts GitBook markdown syntax into Starlight-compatible markdown; +5. generates sidebar config from `SUMMARY.md`; and +6. writes a sync manifest (source repo/ref/sha and counts). + +Generated outputs (ignored by git): + +- `apps/docs/src/content/docs/` +- `apps/docs/public/gitbook-assets/` +- `apps/docs/src/config/sidebar.generated.ts` +- `apps/docs/src/generated/gitbook-manifest.json` + +## Local commands + +From repo root: + +- Build docs (sync first): + - `npm run build --workspace=@bdc/docs` +- Dev server only (fast loop, no sync): + - `npm run dev --workspace=@bdc/docs` +- Sync then run dev server: + - `npm run dev:sync --workspace=@bdc/docs` +- Sync content only (supporting local dev): + - `npm run sync:content --workspace=@bdc/docs` + +Notes: + +- The sync script requires `GITBOOK_ALLOW_OVERWRITE=1` to prevent accidental destructive writes. +- Package scripts set this automatically for normal usage. + +## CI / deployment flow + +Workflow: `.github/workflows/docs-gitbook-sync.yml` + +- Runs on schedule and manual dispatch +- Checks latest `stagecc/bdc-gitbook` `main` commit +- Compares to `apps/docs/gitbook.lock.json` +- If changed: + - updates lock file + - validates docs build + - commits lock update + +Amplify listens to this repository and deploys `apps/docs` from resulting commits. + +## Operational guidance + +- To pin docs to a specific GitBook commit manually, update `apps/docs/gitbook.lock.json` and commit. +- To test against a different ref temporarily, set `GITBOOK_REF` when running `sync-gitbook.mjs`. diff --git a/apps/docs/astro.config.mjs b/apps/docs/astro.config.mjs index feced0a0..13cd331d 100644 --- a/apps/docs/astro.config.mjs +++ b/apps/docs/astro.config.mjs @@ -2,7 +2,7 @@ import { dirname, join } from 'node:path'; import { fileURLToPath } from 'node:url'; import starlight from '@astrojs/starlight'; import { defineConfig } from 'astro/config'; -import { sidebar } from './src/config/sidebar.ts'; +import { sidebar } from './src/config/sidebar.generated.ts'; const rootDir = dirname(fileURLToPath(import.meta.url)); const uswdsPackages = join(rootDir, '../../node_modules/@uswds/uswds/packages'); @@ -26,6 +26,7 @@ export default defineConfig({ }, ], customCss: ['./src/styles/custom.scss'], + disable404Route: true, sidebar, }), ], diff --git a/apps/docs/gitbook.lock.json b/apps/docs/gitbook.lock.json new file mode 100644 index 00000000..ac11415b --- /dev/null +++ b/apps/docs/gitbook.lock.json @@ -0,0 +1,4 @@ +{ + "repo": "https://github.com/stagecc/bdc-gitbook.git", + "ref": "e9780d21ef367b15d45bf45ad1a1c24f9e007f83" +} diff --git a/apps/docs/package.json b/apps/docs/package.json index 6117964d..f680a373 100644 --- a/apps/docs/package.json +++ b/apps/docs/package.json @@ -5,7 +5,9 @@ "type": "module", "scripts": { "dev": "astro dev", - "build": "astro build", + "dev:sync": "npm run sync:content && astro dev", + "sync:content": "GITBOOK_ALLOW_OVERWRITE=1 node ./scripts/sync-gitbook.mjs", + "build": "npm run sync:content && astro build", "preview": "astro preview" }, "dependencies": { diff --git a/apps/docs/scripts/sync-gitbook.mjs b/apps/docs/scripts/sync-gitbook.mjs new file mode 100644 index 00000000..a41a9eab --- /dev/null +++ b/apps/docs/scripts/sync-gitbook.mjs @@ -0,0 +1,615 @@ +import { execFileSync } from 'node:child_process'; +import { + cp, + mkdir, + mkdtemp, + readdir, + readFile, + rm, + stat, + writeFile, +} from 'node:fs/promises'; +import { tmpdir } from 'node:os'; +import { basename, dirname, extname, join, relative, resolve } from 'node:path'; +import { fileURLToPath } from 'node:url'; + +// Build-time GitBook sync pipeline: +// 1. Resolve source repo/ref (env -> lock file -> defaults) +// 2. Clone source into a temp dir +// 3. Regenerate docs content + assets from source +// 4. Derive sidebar from SUMMARY.md +// 5. Emit manifest for traceability +const scriptDir = dirname(fileURLToPath(import.meta.url)); +const docsRoot = resolve(scriptDir, '..'); +const lockFilePath = resolve(docsRoot, 'gitbook.lock.json'); +const defaultRepoUrl = 'https://github.com/stagecc/bdc-gitbook.git'; + +const lockConfig = await readLockConfig(lockFilePath); + +const repoUrl = process.env.GITBOOK_REPO ?? lockConfig.repo ?? defaultRepoUrl; +const repoRef = process.env.GITBOOK_REF ?? lockConfig.ref ?? 'main'; +const skipSync = process.env.SKIP_CONTENT_SYNC === '1'; +const allowOverwrite = process.env.GITBOOK_ALLOW_OVERWRITE === '1'; +const outputDocsDir = resolve( + docsRoot, + process.env.GITBOOK_OUTPUT_DOCS_DIR ?? 'src/content/docs', +); +const outputAssetsDir = resolve( + docsRoot, + process.env.GITBOOK_OUTPUT_ASSETS_DIR ?? 'public/gitbook-assets', +); +const outputSidebarFile = resolve( + docsRoot, + process.env.GITBOOK_OUTPUT_SIDEBAR_FILE ?? 'src/config/sidebar.generated.ts', +); +const outputManifestFile = resolve( + docsRoot, + process.env.GITBOOK_OUTPUT_MANIFEST_FILE ?? + 'src/generated/gitbook-manifest.json', +); + +if (skipSync) { + console.log('Skipping GitBook sync because SKIP_CONTENT_SYNC=1'); + process.exit(0); +} + +if (!allowOverwrite) { + throw new Error( + 'Refusing to overwrite docs content without GITBOOK_ALLOW_OVERWRITE=1. ' + + 'Use npm scripts (sync:content, build, dev:sync) or set the variable explicitly.', + ); +} + +const tempRoot = await mkdtemp(join(tmpdir(), 'bdc-gitbook-sync-')); + +try { + const sourceDir = join(tempRoot, 'source'); + console.log(`Cloning ${repoUrl}#${repoRef} ...`); + await cloneSourceRepo(sourceDir, repoUrl, repoRef); + + const summaryPath = join(sourceDir, 'SUMMARY.md'); + const summaryText = await readFile(summaryPath, 'utf8'); + + await cleanDir(outputDocsDir); + await cleanDir(outputAssetsDir); + + await copyMarkdownFiles(sourceDir, outputDocsDir); + await ensureDefault404Doc(outputDocsDir); + await copyGitbookAssets(sourceDir, outputAssetsDir); + + const sidebar = buildSidebarFromSummary(summaryText); + await writeSidebarFile(outputSidebarFile, sidebar); + + const sha = execFileSync('git', ['-C', sourceDir, 'rev-parse', 'HEAD'], { + encoding: 'utf8', + }).trim(); + + const stats = await countGeneratedFiles(outputDocsDir, outputAssetsDir); + await writeManifest(outputManifestFile, { + repoUrl, + repoRef, + sha, + syncedAt: new Date().toISOString(), + docsFiles: stats.docsFiles, + assetFiles: stats.assetFiles, + }); + + console.log( + `Synced GitBook content: ${stats.docsFiles} docs, ${stats.assetFiles} assets`, + ); +} finally { + await rm(tempRoot, { recursive: true, force: true }); +} + +async function cleanDir(dirPath) { + // Always fully replace generated outputs to prevent stale artifacts. + await rm(dirPath, { recursive: true, force: true }); + await mkdir(dirPath, { recursive: true }); +} + +async function copyMarkdownFiles(sourceDir, destinationDir) { + const allFiles = await walkFiles(sourceDir); + + for (const absPath of allFiles) { + const relPath = relative(sourceDir, absPath); + if (shouldSkipSourceFile(relPath)) continue; + if (extname(relPath).toLowerCase() !== '.md') continue; + + const content = await readFile(absPath, 'utf8'); + const transformed = transformMarkdown(content, relPath); + + const outRelPath = mapContentOutputPath(relPath); + const outAbsPath = join(destinationDir, outRelPath); + await mkdir(dirname(outAbsPath), { recursive: true }); + await writeFile(outAbsPath, transformed, 'utf8'); + } +} + +async function copyGitbookAssets(sourceDir, destinationDir) { + const sourceAssets = join(sourceDir, '.gitbook/assets'); + try { + const info = await stat(sourceAssets); + if (!info.isDirectory()) return; + } catch { + return; + } + + await cp(sourceAssets, destinationDir, { recursive: true }); +} + +async function ensureDefault404Doc(docsDir) { + const filePath = join(docsDir, '404.md'); + const content = [ + '---', + 'title: "Page Not Found"', + 'template: splash', + '---', + '', + '# Page Not Found', + '', + 'The page you requested does not exist in this documentation set.', + '', + ].join('\n'); + await writeFile(filePath, content, 'utf8'); +} + +function shouldSkipSourceFile(relPath) { + if (relPath.startsWith('.git/')) return true; + if (relPath.startsWith('.github/')) return true; + if (relPath.startsWith('.gitbook/')) return true; + if (relPath === 'SUMMARY.md') return true; + return false; +} + +function mapContentOutputPath(relPath) { + const normalized = relPath.replace(/\\/g, '/'); + if (normalized === 'README.md') return 'index.md'; + return normalized.replace(/\/README\.md$/, '/index.md'); +} + +function transformMarkdown(input, fileRelPath) { + // Order matters: convert GitBook syntax first, then normalize frontmatter/headings. + let content = input; + + content = transformHintBlocks(content); + content = transformFileBlocks(content, fileRelPath); + content = transformIncludeBlocks(content); + content = transformEmbedBlocks(content); + content = rewriteGitbookAssetPaths(content); + content = rewriteInternalMarkdownLinks(content, fileRelPath); + content = ensureFrontmatter(content, fileRelPath); + content = removeDuplicateTopHeading(content); + + return content; +} + +function transformHintBlocks(content) { + const styleMap = { + info: 'note', + warning: 'caution', + danger: 'danger', + success: 'tip', + }; + + let next = content.replace( + /\{%\s*hint\s+style="([a-z]+)"\s*%\}/g, + (_match, style) => { + const callout = styleMap[style] ?? 'note'; + return `:::${callout}`; + }, + ); + + next = next.replace(/\{%\s*endhint\s*%\}/g, ':::'); + return next; +} + +function transformFileBlocks(content, fileRelPath) { + // Existing block form: + // {% file src="..." %}Label{% endfile %} + let next = content.replace( + /\{%\s*file\s+src="([^"]+)"\s*%\}([\s\S]*?)\{%\s*endfile\s*%\}/g, + (_match, src, inner) => { + const text = inner + .split('\n') + .map((line) => line.trim()) + .filter(Boolean) + .join(' ') + .trim(); + const label = text || basename(src); + const target = rewriteLinkTarget(src, fileRelPath); + return `[${label}](${target})`; + }, + ); + + // {% file src="..." %} + next = next.replace(/\{%\s*file\s+src="([^"]+)"\s*%\}/g, (_match, src) => { + const label = basename(src); + const target = rewriteLinkTarget(src, fileRelPath); + return `[${label}](${target})`; + }); + + return next; +} + +function transformIncludeBlocks(content) { + return content.replace( + /\{%\s*include\s+"([^"]+)"\s*%\}/g, + (_match, includePath) => { + return `> Included content: ${includePath}`; + }, + ); +} + +function transformEmbedBlocks(content) { + return content.replace( + /\{%\s*embed\s+url="([^"]+)"\s*%\}/g, + (_match, url) => { + return `[Embedded content](${url})`; + }, + ); +} + +function rewriteGitbookAssetPaths(content) { + return content.replace( + /(?:\.\.\/|\.\/)*\.gitbook\/assets\//g, + '/gitbook-assets/', + ); +} + +function rewriteInternalMarkdownLinks(content, fileRelPath) { + return content.replace(/\]\(([^)]+)\)/g, (match, rawTarget) => { + const trimmed = rawTarget.trim().replace(/^<|>$/g, ''); + if (!trimmed) return match; + + const rewritten = rewriteLinkTarget(trimmed, fileRelPath); + if (!rewritten) return match; + return `](${rewritten})`; + }); +} + +function rewriteLinkTarget(target, fileRelPath) { + if (target.startsWith('http://') || target.startsWith('https://')) + return target; + if (target.startsWith('mailto:')) return target; + if (target.startsWith('#')) return target; + + const anchorIndex = target.indexOf('#'); + const rawPath = anchorIndex === -1 ? target : target.slice(0, anchorIndex); + const anchor = anchorIndex === -1 ? '' : target.slice(anchorIndex); + + if (!rawPath) return target; + + if (rawPath.includes('.gitbook/assets/')) { + return rewriteGitbookAssetPaths(rawPath) + anchor; + } + + if (!rawPath.toLowerCase().endsWith('.md')) return target; + + // Convert file-relative markdown links to site slugs. + const currentDir = dirname(fileRelPath); + const resolvedPath = normalizePosixPath(resolvePosix(currentDir, rawPath)); + const slug = slugFromSourcePath(resolvedPath); + const normalizedSlug = slug ? `/${slug}` : '/'; + + return `${normalizedSlug}${anchor}`; +} + +function ensureFrontmatter(content, fileRelPath) { + const title = inferTitle(content, fileRelPath); + const parsed = parseFrontmatter(content); + + if (!parsed) { + return `---\ntitle: ${JSON.stringify(title)}\n---\n\n${content}`; + } + + if (/^title\s*:/m.test(parsed.frontmatter)) { + return content; + } + + const frontmatterWithTitle = `title: ${JSON.stringify(title)}\n${parsed.frontmatter}`; + return `---\n${frontmatterWithTitle}\n---${parsed.body}`; +} + +function removeDuplicateTopHeading(content) { + // Starlight renders `title` from frontmatter. Drop duplicate top-level headings when equal. + const parsed = parseFrontmatter(content); + if (!parsed) return content; + + const titleMatch = parsed.frontmatter.match(/^title\s*:\s*(.+)$/m); + if (!titleMatch) return content; + + const frontmatterTitle = stripYamlString(titleMatch[1]); + const headingMatch = parsed.body.match(/^\s*\n?#\s+(.+)\n?/); + if (!headingMatch) return content; + + const headingTitle = headingMatch[1].trim(); + if (normalizeTitle(frontmatterTitle) !== normalizeTitle(headingTitle)) { + return content; + } + + const bodyWithoutHeading = parsed.body.replace(/^\s*\n?#\s+(.+)\n+/, '\n'); + return `---\n${parsed.frontmatter}\n---${bodyWithoutHeading}`; +} + +function inferTitle(content, fileRelPath) { + const match = content.match(/^#\s+(.+)$/m); + if (match?.[1]) return match[1].trim(); + + const noExt = basename(fileRelPath, '.md'); + if (noExt.toLowerCase() === 'readme') { + const parent = basename(dirname(fileRelPath)); + return titleCase(parent || 'Overview'); + } + return titleCase(noExt); +} + +function parseFrontmatter(content) { + const match = content.match(/^---\r?\n([\s\S]*?)\r?\n---([\s\S]*)$/); + if (!match) return null; + return { + frontmatter: match[1], + body: match[2], + }; +} + +function stripYamlString(rawValue) { + return rawValue.trim().replace(/^['"]|['"]$/g, ''); +} + +function normalizeTitle(value) { + return value + .replace(/<[^>]+>/g, '') + .replace(/\s+/g, ' ') + .trim() + .toLowerCase(); +} + +function buildSidebarFromSummary(summaryText) { + // SUMMARY.md is treated as the canonical nav tree from GitBook. + const lines = summaryText.split(/\r?\n/); + const sections = []; + let currentSection = null; + let stack = []; + + for (const line of lines) { + const heading = line.match(/^##\s+(.+)$/); + if (heading) { + currentSection = { label: heading[1].trim(), items: [] }; + sections.push(currentSection); + stack = []; + continue; + } + + const itemMatch = line.match(/^(\s*)\*\s+\[([^\]]+)\]\(([^)]+)\)/); + if (!itemMatch || !currentSection) continue; + + const indent = itemMatch[1].length; + const level = Math.floor(indent / 2); + const node = { + label: itemMatch[2].trim(), + target: itemMatch[3].trim(), + children: [], + }; + + if (level === 0) { + currentSection.items.push(node); + stack = [node]; + continue; + } + + const parent = stack[level - 1]; + if (!parent) { + currentSection.items.push(node); + stack = [node]; + continue; + } + + parent.children.push(node); + stack[level] = node; + stack.length = level + 1; + } + + return sections + .map((section) => ({ + label: section.label, + items: section.items.map(convertSummaryNodeToSidebar).filter(Boolean), + })) + .filter((section) => section.items.length > 0); +} + +function convertSummaryNodeToSidebar(node) { + const linkItem = convertSummaryLink(node.label, node.target); + const children = node.children + .map(convertSummaryNodeToSidebar) + .filter(Boolean); + + if (children.length > 0) { + const overviewItem = linkItem ? { ...linkItem, label: 'Overview' } : null; + const hasDuplicateOverview = + overviewItem !== null && + children.some( + (item) => sidebarItemKey(item) === sidebarItemKey(overviewItem), + ); + const items = + overviewItem && !hasDuplicateOverview + ? [overviewItem, ...children] + : children; + + return { + label: node.label, + collapsed: true, + items, + }; + } + + return linkItem; +} + +function convertSummaryLink(label, target) { + if (target.startsWith('http://') || target.startsWith('https://')) { + return { label, link: target }; + } + + if (!target.toLowerCase().endsWith('.md')) { + return { label, link: target }; + } + + const normalized = normalizePosixPath(target); + const slug = slugFromSourcePath(normalized); + if (!slug) { + return { label, link: '/' }; + } + + return { label, slug }; +} + +function slugFromSourcePath(sourcePath) { + const noExt = sourcePath.replace(/\.md$/i, ''); + if (noExt === 'README') return ''; + return noExt + .replace(/\/README$/i, '') + .replace(/^\/+/, '') + .replace(/\/+$/, ''); +} + +function sidebarItemKey(item) { + if (!item || typeof item !== 'object') return null; + if ('slug' in item && item.slug) return `slug:${item.slug}`; + if ('link' in item && item.link) return `link:${item.link}`; + return null; +} + +async function writeSidebarFile(filePath, sidebar) { + const content = [ + "import type { StarlightUserConfig } from '@astrojs/starlight/types';", + '', + "type Sidebar = NonNullable;", + '', + '// This file is auto-generated by scripts/sync-gitbook.mjs.', + `export const sidebar: Sidebar = ${JSON.stringify(sidebar, null, 2)};`, + '', + ].join('\n'); + + await mkdir(dirname(filePath), { recursive: true }); + await writeFile(filePath, content, 'utf8'); +} + +async function writeManifest(filePath, manifest) { + await mkdir(dirname(filePath), { recursive: true }); + await writeFile(filePath, `${JSON.stringify(manifest, null, 2)}\n`, 'utf8'); +} + +async function countGeneratedFiles(docsDir, assetsDir) { + const docsFiles = (await walkFiles(docsDir)).filter((file) => + file.endsWith('.md'), + ).length; + const assetFiles = (await walkFiles(assetsDir)).length; + return { docsFiles, assetFiles }; +} + +async function walkFiles(startDir) { + const files = []; + const entries = await readdir(startDir, { withFileTypes: true }); + + for (const entry of entries) { + const absPath = join(startDir, entry.name); + if (entry.isDirectory()) { + files.push(...(await walkFiles(absPath))); + } else if (entry.isFile()) { + files.push(absPath); + } + } + + return files; +} + +function normalizePosixPath(pathValue) { + return pathValue.replace(/\\/g, '/').replace(/^\.\//, ''); +} + +function resolvePosix(fromDir, targetPath) { + const from = fromDir.split('/').filter(Boolean); + const target = targetPath.split('/').filter(Boolean); + + if (targetPath.startsWith('/')) { + return target.join('/'); + } + + const stack = [...from]; + for (const part of target) { + if (part === '.') continue; + if (part === '..') { + stack.pop(); + continue; + } + stack.push(part); + } + return stack.join('/'); +} + +function titleCase(input) { + return input + .replace(/[-_]+/g, ' ') + .replace(/\s+/g, ' ') + .trim() + .replace(/\b\w/g, (ch) => ch.toUpperCase()); +} + +async function readLockConfig(filePath) { + try { + const contents = await readFile(filePath, 'utf8'); + const parsed = JSON.parse(contents); + if (!parsed || typeof parsed !== 'object') return {}; + + const repo = typeof parsed.repo === 'string' ? parsed.repo : undefined; + const ref = typeof parsed.ref === 'string' ? parsed.ref : undefined; + return { repo, ref }; + } catch { + return {}; + } +} + +async function cloneSourceRepo(sourceDir, url, ref) { + // `git clone --branch` cannot target arbitrary commit SHAs. + // Branch/tag refs use clone --branch; SHA refs use clone + detached checkout. + if (!isCommitSha(ref)) { + execFileSync( + 'git', + ['clone', '--depth', '1', '--branch', ref, url, sourceDir], + { + stdio: 'inherit', + }, + ); + return; + } + + execFileSync('git', ['clone', '--depth', '1', url, sourceDir], { + stdio: 'inherit', + }); + + try { + execFileSync('git', ['-C', sourceDir, 'checkout', '--detach', ref], { + stdio: 'inherit', + }); + return; + } catch { + execFileSync( + 'git', + ['-C', sourceDir, 'fetch', '--depth', '1', 'origin', ref], + { + stdio: 'inherit', + }, + ); + execFileSync( + 'git', + ['-C', sourceDir, 'checkout', '--detach', 'FETCH_HEAD'], + { + stdio: 'inherit', + }, + ); + } +} + +function isCommitSha(value) { + return /^[0-9a-f]{40}$/i.test(value); +} diff --git a/apps/docs/src/config/sidebar.test.ts b/apps/docs/src/config/sidebar.test.ts index 02c9586c..1e0c60a6 100644 --- a/apps/docs/src/config/sidebar.test.ts +++ b/apps/docs/src/config/sidebar.test.ts @@ -1,7 +1,22 @@ -import { describe, expect, it } from 'vitest'; -import { sidebar } from './sidebar'; +import { existsSync } from 'node:fs'; +import { dirname, join } from 'node:path'; +import { fileURLToPath } from 'node:url'; +import type { StarlightUserConfig } from '@astrojs/starlight/types'; +import { beforeAll, describe, expect, it } from 'vitest'; -type SidebarItem = (typeof sidebar)[number]; +type Sidebar = NonNullable; +type SidebarItem = Sidebar[number]; + +const configDir = dirname(fileURLToPath(import.meta.url)); +const generatedSidebarPath = join(configDir, 'sidebar.generated.ts'); +const describeGeneratedSidebar = existsSync(generatedSidebarPath) + ? describe + : describe.skip; + +async function loadSidebar(): Promise { + const generated = await import('./sidebar.generated'); + return generated.sidebar; +} function collectSlugs(items: SidebarItem[]): string[] { const slugs: string[] = []; @@ -25,7 +40,13 @@ function collectLabels(items: SidebarItem[]): string[] { return labels; } -describe('sidebar', () => { +describeGeneratedSidebar('sidebar.generated', () => { + let sidebar: Sidebar = []; + + beforeAll(async () => { + sidebar = await loadSidebar(); + }); + it('every item has a label', () => { const labels = collectLabels(sidebar); for (const label of labels) { diff --git a/apps/docs/src/config/sidebar.ts b/apps/docs/src/config/sidebar.ts deleted file mode 100644 index cfd729d5..00000000 --- a/apps/docs/src/config/sidebar.ts +++ /dev/null @@ -1,411 +0,0 @@ -import type { StarlightUserConfig } from '@astrojs/starlight/types'; - -type Sidebar = NonNullable; - -export const sidebar: Sidebar = [ - { - label: 'Guides', - items: [ - { label: 'Introduction', slug: 'guides/intro' }, - { label: 'Quick Start', slug: 'guides/quick-start' }, - ], - }, - { - label: 'Reference', - autogenerate: { directory: 'reference' }, - }, - { label: 'Getting Started', slug: 'getting-started' }, - { - label: 'Community', - items: [ - { label: 'Who We Are', slug: 'community' }, - { label: 'BDC Glossary', slug: 'community/glossary' }, - { - label: 'Citation and Acknowledgement', - slug: 'community/citation-and-acknowledgement', - }, - { - label: 'Strategic Planning', - slug: 'community/strategic-planning', - }, - { - label: 'Request for Comments', - items: [ - { label: 'Overview', slug: 'community/request-for-comments' }, - { - label: 'Ecosystem Security Statement', - slug: 'community/request-for-comments/ecosystem-security-statement', - }, - { - label: 'DICOM De-Identification', - slug: 'community/request-for-comments/dicom-de-identification', - }, - ], - collapsed: true, - }, - { - label: 'Video Content Guidance', - slug: 'community/video-content-guidance', - }, - { - label: 'Contributing User Resources', - slug: 'community/contributing-user-resources', - }, - ], - }, - { - label: 'Data Access', - items: [ - { label: 'Overview', slug: 'data-access' }, - { - label: 'Data Interoperability', - slug: 'data-access/data-interoperability', - }, - { - label: 'Understanding Access', - slug: 'data-access/understanding-access', - }, - { - label: 'Submitting a dbGaP Request', - slug: 'data-access/submitting-dbgap-request', - }, - { label: 'Checking Access', slug: 'data-access/checking-access' }, - ], - }, - { - label: 'Explore Available Data', - items: [ - { label: 'Overview', slug: 'explore-available-data' }, - { - label: 'Dug Semantic Search', - items: [ - { - label: 'Overview', - slug: 'explore-available-data/dug-semantic-search', - }, - { - label: 'Search and Results', - slug: 'explore-available-data/dug-semantic-search/search-and-results', - }, - ], - collapsed: true, - }, - { - label: 'PIC-SURE', - items: [ - { - label: 'User Guide', - slug: 'explore-available-data/pic-sure', - }, - { - label: 'Getting Started', - slug: 'explore-available-data/pic-sure/getting-started', - }, - { - label: 'Requirements and Login', - slug: 'explore-available-data/pic-sure/requirements-and-login', - }, - { - label: 'Available Data', - slug: 'explore-available-data/pic-sure/available-data', - }, - { - label: 'TOPMed Datasets', - slug: 'explore-available-data/pic-sure/topmed-datasets', - }, - { - label: 'BioLINCC Datasets', - slug: 'explore-available-data/pic-sure/biolincc-datasets', - }, - { - label: 'CONNECTS Dataset', - slug: 'explore-available-data/pic-sure/connects-dataset', - }, - { - label: 'Data Organization', - slug: 'explore-available-data/pic-sure/data-organization', - }, - { - label: 'Features and Layout', - slug: 'explore-available-data/pic-sure/features-and-layout', - }, - { - label: 'Open vs. Authorized Access', - slug: 'explore-available-data/pic-sure/open-vs-authorized-access', - }, - { - label: 'Open Access', - slug: 'explore-available-data/pic-sure/open-access', - }, - { - label: 'Authorized Access', - slug: 'explore-available-data/pic-sure/authorized-access', - }, - { - label: 'API Analysis', - slug: 'explore-available-data/pic-sure/api-analysis', - }, - { - label: 'Additional Resources', - slug: 'explore-available-data/pic-sure/additional-resources', - }, - { - label: 'API Documentation', - slug: 'explore-available-data/pic-sure/api-documentation', - }, - { - label: 'Appendix 1: Identifiers', - slug: 'explore-available-data/pic-sure/appendix-1-identifiers', - }, - { - label: 'Appendix 2: Harmonized Variables', - slug: 'explore-available-data/pic-sure/appendix-2-harmonized-variables', - }, - ], - collapsed: true, - }, - { - label: 'Gen3', - items: [ - { label: 'Overview', slug: 'explore-available-data/gen3' }, - { - label: 'Dictionary', - slug: 'explore-available-data/gen3/dictionary', - }, - { - label: 'Exploration', - slug: 'explore-available-data/gen3/exploration', - }, - { label: 'Query', slug: 'explore-available-data/gen3/query' }, - { - label: 'Workspace', - slug: 'explore-available-data/gen3/workspace', - }, - { - label: 'Profile', - slug: 'explore-available-data/gen3/profile', - }, - { - label: 'PFB Files', - slug: 'explore-available-data/gen3/pfb-files', - }, - { - label: 'Current Projects', - slug: 'explore-available-data/gen3/current-projects', - }, - ], - collapsed: true, - }, - ], - }, - { - label: 'Analyze Data', - items: [ - { label: 'Overview', slug: 'analyze-data' }, - { - label: 'Transferring Files', - slug: 'analyze-data/transferring-files', - }, - { - label: 'Seven Bridges', - items: [ - { label: 'Overview', slug: 'analyze-data/seven-bridges' }, - { - label: 'Knowledge Center', - slug: 'analyze-data/seven-bridges/knowledge-center', - }, - { - label: 'Getting Started', - slug: 'analyze-data/seven-bridges/getting-started', - }, - { - label: 'Analysis Tips', - slug: 'analyze-data/seven-bridges/analysis-tips', - }, - { - label: 'Troubleshooting Tasks', - slug: 'analyze-data/seven-bridges/troubleshooting-tasks', - }, - { - label: 'GWAS with GENESIS', - slug: 'analyze-data/seven-bridges/gwas-genesis', - }, - { - label: 'Annotation Explorer', - slug: 'analyze-data/seven-bridges/annotation-explorer', - }, - ], - collapsed: true, - }, - { - label: 'Terra', - items: [ - { label: 'Overview', slug: 'analyze-data/terra' }, - { - label: 'Account Setup', - slug: 'analyze-data/terra/account-setup', - }, - { label: 'Billing', slug: 'analyze-data/terra/billing' }, - { - label: 'Managing Costs', - slug: 'analyze-data/terra/managing-costs', - }, - { - label: 'Workspace Setup', - slug: 'analyze-data/terra/workspace-setup', - }, - { - label: 'Data Storage', - slug: 'analyze-data/terra/data-storage', - }, - { - label: 'Collaboration', - slug: 'analyze-data/terra/collaboration', - }, - { label: 'Security', slug: 'analyze-data/terra/security' }, - { label: 'Bring Data', slug: 'analyze-data/terra/bring-data' }, - { - label: 'Data from Gen3', - slug: 'analyze-data/terra/data-from-gen3', - }, - { - label: 'Data from Library', - slug: 'analyze-data/terra/data-from-library', - }, - { - label: 'Use Own Data', - slug: 'analyze-data/terra/use-own-data', - }, - { - label: 'Run Analyses', - slug: 'analyze-data/terra/run-analyses', - }, - { - label: 'Batch Workflows', - slug: 'analyze-data/terra/batch-workflows', - }, - { - label: 'Interactive Analysis', - slug: 'analyze-data/terra/interactive-analysis', - }, - { label: 'GWAS', slug: 'analyze-data/terra/gwas' }, - { - label: 'Troubleshooting', - slug: 'analyze-data/terra/troubleshooting', - }, - ], - collapsed: true, - }, - ], - }, - { - label: 'Community Tools & Integration', - items: [ - { label: 'Overview', slug: 'community-tools' }, - { - label: 'Bring Your Own Tool', - items: [ - { - label: 'Overview', - slug: 'community-tools/bring-your-own-tool', - }, - { - label: 'BYOT Glossary', - slug: 'community-tools/bring-your-own-tool/glossary', - }, - { - label: 'Working with Docker', - slug: 'community-tools/bring-your-own-tool/docker', - }, - { - label: 'WDL Workflows', - slug: 'community-tools/bring-your-own-tool/wdl-workflows', - }, - { - label: 'CWL Workflows', - slug: 'community-tools/bring-your-own-tool/cwl-workflows', - }, - { - label: 'Version Control', - slug: 'community-tools/bring-your-own-tool/version-control', - }, - { - label: 'Advanced Topics', - slug: 'community-tools/bring-your-own-tool/advanced-topics', - }, - ], - collapsed: true, - }, - ], - }, - { label: 'Grant Proposals', slug: 'grant-proposals' }, - { label: 'Cloud Costs', slug: 'cloud-costs' }, - { - label: 'Release Notes', - collapsed: true, - autogenerate: { directory: 'release-notes' }, - }, - { - label: 'Tutorials', - items: [ - { label: 'Overview', slug: 'tutorials' }, - { - label: 'Seven Bridges', - items: [ - { label: 'Overview', slug: 'tutorials/seven-bridges' }, - { - label: 'GENESIS Workflows', - slug: 'tutorials/seven-bridges/genesis-workflows', - }, - { - label: 'Cloud Costs', - slug: 'tutorials/seven-bridges/cloud-costs', - }, - ], - collapsed: true, - }, - { - label: 'Terra', - items: [ - { label: 'Overview', slug: 'tutorials/terra' }, - { - label: 'Gen3 Data on Terra', - slug: 'tutorials/terra/gen3-data-on-terra', - }, - { - label: 'GWAS 1000 Genomes', - slug: 'tutorials/terra/gwas-1000-genomes', - }, - { label: 'GWAS TOPMed', slug: 'tutorials/terra/gwas-topmed' }, - { - label: 'TOPMed Aligner', - slug: 'tutorials/terra/topmed-aligner', - }, - ], - collapsed: true, - }, - ], - }, - { - label: 'Data Management', - items: [ - { label: 'Strategy', slug: 'data-management' }, - { - label: 'Data Submission', - slug: 'data-management/data-submission', - }, - { - label: 'De-identification', - slug: 'data-management/de-identification', - }, - { - label: 'Submission FAQs', - slug: 'data-management/submission-faqs', - }, - { - label: 'dbGaP Configuration', - slug: 'data-management/dbgap-configuration', - }, - ], - }, -]; diff --git a/apps/docs/src/content/docs/404.md b/apps/docs/src/content/docs/404.md deleted file mode 100644 index ec27cb00..00000000 --- a/apps/docs/src/content/docs/404.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: "404" -template: splash -editUrl: false -hero: - title: "404" - tagline: Page not found. Check the URL or try using the search bar. - actions: - - text: Go home - icon: right-arrow - link: / - variant: primary ---- diff --git a/apps/docs/src/content/docs/analyze-data/index.md b/apps/docs/src/content/docs/analyze-data/index.md deleted file mode 100644 index 2bc028ee..00000000 --- a/apps/docs/src/content/docs/analyze-data/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Analyze Data" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/seven-bridges/analysis-tips.md b/apps/docs/src/content/docs/analyze-data/seven-bridges/analysis-tips.md deleted file mode 100644 index 2b72eb5b..00000000 --- a/apps/docs/src/content/docs/analyze-data/seven-bridges/analysis-tips.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Comprehensive Analysis Tips" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/seven-bridges/annotation-explorer.md b/apps/docs/src/content/docs/analyze-data/seven-bridges/annotation-explorer.md deleted file mode 100644 index c0cffb9c..00000000 --- a/apps/docs/src/content/docs/analyze-data/seven-bridges/annotation-explorer.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Annotation Explorer" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/seven-bridges/getting-started.md b/apps/docs/src/content/docs/analyze-data/seven-bridges/getting-started.md deleted file mode 100644 index dcce9ab3..00000000 --- a/apps/docs/src/content/docs/analyze-data/seven-bridges/getting-started.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Getting Started Guide" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/seven-bridges/gwas-genesis.md b/apps/docs/src/content/docs/analyze-data/seven-bridges/gwas-genesis.md deleted file mode 100644 index ddf24bbf..00000000 --- a/apps/docs/src/content/docs/analyze-data/seven-bridges/gwas-genesis.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "GWAS with GENESIS Workflows" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/seven-bridges/index.md b/apps/docs/src/content/docs/analyze-data/seven-bridges/index.md deleted file mode 100644 index 00ffb051..00000000 --- a/apps/docs/src/content/docs/analyze-data/seven-bridges/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "BDC-Seven Bridges" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/seven-bridges/knowledge-center.md b/apps/docs/src/content/docs/analyze-data/seven-bridges/knowledge-center.md deleted file mode 100644 index 7ef4b843..00000000 --- a/apps/docs/src/content/docs/analyze-data/seven-bridges/knowledge-center.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Knowledge Center" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/seven-bridges/troubleshooting-tasks.md b/apps/docs/src/content/docs/analyze-data/seven-bridges/troubleshooting-tasks.md deleted file mode 100644 index 6c4789b0..00000000 --- a/apps/docs/src/content/docs/analyze-data/seven-bridges/troubleshooting-tasks.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Troubleshooting Tasks" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/account-setup.md b/apps/docs/src/content/docs/analyze-data/terra/account-setup.md deleted file mode 100644 index a336b0ab..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/account-setup.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Account Setup" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/batch-workflows.md b/apps/docs/src/content/docs/analyze-data/terra/batch-workflows.md deleted file mode 100644 index a324fb09..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/batch-workflows.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Batch Processing with Workflows" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/billing.md b/apps/docs/src/content/docs/analyze-data/terra/billing.md deleted file mode 100644 index a4e7ac39..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/billing.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Billing" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/bring-data.md b/apps/docs/src/content/docs/analyze-data/terra/bring-data.md deleted file mode 100644 index cb828558..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/bring-data.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Bring Data into a Workspace" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/collaboration.md b/apps/docs/src/content/docs/analyze-data/terra/collaboration.md deleted file mode 100644 index 4fcbe72c..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/collaboration.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Collaboration" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/data-from-gen3.md b/apps/docs/src/content/docs/analyze-data/terra/data-from-gen3.md deleted file mode 100644 index c8a2e6bb..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/data-from-gen3.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Bring in Data from Gen3" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/data-from-library.md b/apps/docs/src/content/docs/analyze-data/terra/data-from-library.md deleted file mode 100644 index dfb6ed13..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/data-from-library.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "From Terra's Data Library" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/data-storage.md b/apps/docs/src/content/docs/analyze-data/terra/data-storage.md deleted file mode 100644 index 87a867a8..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/data-storage.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Data Storage & Management" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/gwas.md b/apps/docs/src/content/docs/analyze-data/terra/gwas.md deleted file mode 100644 index f98a79d9..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/gwas.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Genome-Wide Association Studies" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/index.md b/apps/docs/src/content/docs/analyze-data/terra/index.md deleted file mode 100644 index ab2e2256..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "BDC-Terra" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/interactive-analysis.md b/apps/docs/src/content/docs/analyze-data/terra/interactive-analysis.md deleted file mode 100644 index 12c83363..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/interactive-analysis.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Interactive Analysis" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/managing-costs.md b/apps/docs/src/content/docs/analyze-data/terra/managing-costs.md deleted file mode 100644 index e711df06..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/managing-costs.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Managing Costs" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/run-analyses.md b/apps/docs/src/content/docs/analyze-data/terra/run-analyses.md deleted file mode 100644 index 3df3d835..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/run-analyses.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Run Analyses" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/security.md b/apps/docs/src/content/docs/analyze-data/terra/security.md deleted file mode 100644 index 10ceeb4b..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/security.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Security" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/troubleshooting.md b/apps/docs/src/content/docs/analyze-data/terra/troubleshooting.md deleted file mode 100644 index 51933bc3..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/troubleshooting.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Troubleshooting & Support" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/use-own-data.md b/apps/docs/src/content/docs/analyze-data/terra/use-own-data.md deleted file mode 100644 index d761fc86..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/use-own-data.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Use Your Own Data with Terra" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/terra/workspace-setup.md b/apps/docs/src/content/docs/analyze-data/terra/workspace-setup.md deleted file mode 100644 index a98a310e..00000000 --- a/apps/docs/src/content/docs/analyze-data/terra/workspace-setup.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Workspace Setup" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/analyze-data/transferring-files.md b/apps/docs/src/content/docs/analyze-data/transferring-files.md deleted file mode 100644 index 43eee9ff..00000000 --- a/apps/docs/src/content/docs/analyze-data/transferring-files.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Transferring Files Between Seven Bridges and Terra" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/cloud-costs.md b/apps/docs/src/content/docs/cloud-costs.md deleted file mode 100644 index 6df56ab4..00000000 --- a/apps/docs/src/content/docs/cloud-costs.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Incurring Cloud Costs" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/advanced-topics.md b/apps/docs/src/content/docs/community-tools/bring-your-own-tool/advanced-topics.md deleted file mode 100644 index 75fb58ae..00000000 --- a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/advanced-topics.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Advanced Topics" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/cwl-workflows.md b/apps/docs/src/content/docs/community-tools/bring-your-own-tool/cwl-workflows.md deleted file mode 100644 index e5ea55fc..00000000 --- a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/cwl-workflows.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Creating, Testing & Scaling CWL Workflows" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/docker.md b/apps/docs/src/content/docs/community-tools/bring-your-own-tool/docker.md deleted file mode 100644 index efd76584..00000000 --- a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/docker.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Working with Docker" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/glossary.md b/apps/docs/src/content/docs/community-tools/bring-your-own-tool/glossary.md deleted file mode 100644 index 7c62b1f7..00000000 --- a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/glossary.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "BYOT Glossary" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/index.md b/apps/docs/src/content/docs/community-tools/bring-your-own-tool/index.md deleted file mode 100644 index e1f9d509..00000000 --- a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Bring Your Own Tool(s)" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/version-control.md b/apps/docs/src/content/docs/community-tools/bring-your-own-tool/version-control.md deleted file mode 100644 index 311f96e4..00000000 --- a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/version-control.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Version Control, Publishing & Validation of Workflows" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/wdl-workflows.md b/apps/docs/src/content/docs/community-tools/bring-your-own-tool/wdl-workflows.md deleted file mode 100644 index 22b0894c..00000000 --- a/apps/docs/src/content/docs/community-tools/bring-your-own-tool/wdl-workflows.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Creating, Testing & Scaling WDL Workflows" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community-tools/index.md b/apps/docs/src/content/docs/community-tools/index.md deleted file mode 100644 index 2647e425..00000000 --- a/apps/docs/src/content/docs/community-tools/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Community Tools & Integration" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community/citation-and-acknowledgement.md b/apps/docs/src/content/docs/community/citation-and-acknowledgement.md deleted file mode 100644 index 51d08604..00000000 --- a/apps/docs/src/content/docs/community/citation-and-acknowledgement.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Citation and Acknowledgement" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community/contributing-user-resources.md b/apps/docs/src/content/docs/community/contributing-user-resources.md deleted file mode 100644 index 879077a0..00000000 --- a/apps/docs/src/content/docs/community/contributing-user-resources.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Contributing User Resources to BDC" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community/glossary.md b/apps/docs/src/content/docs/community/glossary.md deleted file mode 100644 index 51bb9e90..00000000 --- a/apps/docs/src/content/docs/community/glossary.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "BDC Glossary" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community/index.md b/apps/docs/src/content/docs/community/index.md deleted file mode 100644 index 765e592d..00000000 --- a/apps/docs/src/content/docs/community/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Who We Are" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community/request-for-comments/dicom-de-identification.md b/apps/docs/src/content/docs/community/request-for-comments/dicom-de-identification.md deleted file mode 100644 index e9847055..00000000 --- a/apps/docs/src/content/docs/community/request-for-comments/dicom-de-identification.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "NHLBI DICOM Medical Image De-Identification Baseline Protocol" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community/request-for-comments/ecosystem-security-statement.md b/apps/docs/src/content/docs/community/request-for-comments/ecosystem-security-statement.md deleted file mode 100644 index 3805e7e7..00000000 --- a/apps/docs/src/content/docs/community/request-for-comments/ecosystem-security-statement.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "NHLBI BioData Catalyst Ecosystem Security Statement" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community/request-for-comments/index.md b/apps/docs/src/content/docs/community/request-for-comments/index.md deleted file mode 100644 index d41e5a3e..00000000 --- a/apps/docs/src/content/docs/community/request-for-comments/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Request for Comments" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community/strategic-planning.md b/apps/docs/src/content/docs/community/strategic-planning.md deleted file mode 100644 index 3f46dc2a..00000000 --- a/apps/docs/src/content/docs/community/strategic-planning.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Strategic Planning" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/community/video-content-guidance.md b/apps/docs/src/content/docs/community/video-content-guidance.md deleted file mode 100644 index 8b0436f9..00000000 --- a/apps/docs/src/content/docs/community/video-content-guidance.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "BDC Video Content Guidance" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-access/checking-access.md b/apps/docs/src/content/docs/data-access/checking-access.md deleted file mode 100644 index 08351f84..00000000 --- a/apps/docs/src/content/docs/data-access/checking-access.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Checking Access" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-access/data-interoperability.md b/apps/docs/src/content/docs/data-access/data-interoperability.md deleted file mode 100644 index 2e85ca50..00000000 --- a/apps/docs/src/content/docs/data-access/data-interoperability.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Data Interoperability" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-access/index.md b/apps/docs/src/content/docs/data-access/index.md deleted file mode 100644 index 2fd6a69d..00000000 --- a/apps/docs/src/content/docs/data-access/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Data Access" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-access/submitting-dbgap-request.md b/apps/docs/src/content/docs/data-access/submitting-dbgap-request.md deleted file mode 100644 index 6a8cc801..00000000 --- a/apps/docs/src/content/docs/data-access/submitting-dbgap-request.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Submitting a dbGaP Data Access Request" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-access/understanding-access.md b/apps/docs/src/content/docs/data-access/understanding-access.md deleted file mode 100644 index 8e1aa95b..00000000 --- a/apps/docs/src/content/docs/data-access/understanding-access.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Understanding Access" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-management/data-submission.md b/apps/docs/src/content/docs/data-management/data-submission.md deleted file mode 100644 index 795cdeb2..00000000 --- a/apps/docs/src/content/docs/data-management/data-submission.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Instructions for Data Submission to BDC" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-management/dbgap-configuration.md b/apps/docs/src/content/docs/data-management/dbgap-configuration.md deleted file mode 100644 index f2b077a3..00000000 --- a/apps/docs/src/content/docs/data-management/dbgap-configuration.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "dbGaP Study Configuration Process" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-management/de-identification.md b/apps/docs/src/content/docs/data-management/de-identification.md deleted file mode 100644 index 0ce57303..00000000 --- a/apps/docs/src/content/docs/data-management/de-identification.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "De-identification Readme" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-management/index.md b/apps/docs/src/content/docs/data-management/index.md deleted file mode 100644 index 17ffac41..00000000 --- a/apps/docs/src/content/docs/data-management/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Data Management Strategy" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/data-management/submission-faqs.md b/apps/docs/src/content/docs/data-management/submission-faqs.md deleted file mode 100644 index a986edb9..00000000 --- a/apps/docs/src/content/docs/data-management/submission-faqs.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Data Submission FAQs" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/dug-semantic-search/index.md b/apps/docs/src/content/docs/explore-available-data/dug-semantic-search/index.md deleted file mode 100644 index 31abbfeb..00000000 --- a/apps/docs/src/content/docs/explore-available-data/dug-semantic-search/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Dug Semantic Search" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/dug-semantic-search/search-and-results.md b/apps/docs/src/content/docs/explore-available-data/dug-semantic-search/search-and-results.md deleted file mode 100644 index 1807bf12..00000000 --- a/apps/docs/src/content/docs/explore-available-data/dug-semantic-search/search-and-results.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Search and Results" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/gen3/current-projects.md b/apps/docs/src/content/docs/explore-available-data/gen3/current-projects.md deleted file mode 100644 index a889c1b3..00000000 --- a/apps/docs/src/content/docs/explore-available-data/gen3/current-projects.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Current Projects" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/gen3/dictionary.md b/apps/docs/src/content/docs/explore-available-data/gen3/dictionary.md deleted file mode 100644 index 89f85f8e..00000000 --- a/apps/docs/src/content/docs/explore-available-data/gen3/dictionary.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Dictionary" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/gen3/exploration.md b/apps/docs/src/content/docs/explore-available-data/gen3/exploration.md deleted file mode 100644 index 65103b60..00000000 --- a/apps/docs/src/content/docs/explore-available-data/gen3/exploration.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Exploration" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/gen3/index.md b/apps/docs/src/content/docs/explore-available-data/gen3/index.md deleted file mode 100644 index e4d0066c..00000000 --- a/apps/docs/src/content/docs/explore-available-data/gen3/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Discovering Data Using Gen3" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/gen3/pfb-files.md b/apps/docs/src/content/docs/explore-available-data/gen3/pfb-files.md deleted file mode 100644 index 444bfda0..00000000 --- a/apps/docs/src/content/docs/explore-available-data/gen3/pfb-files.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "PFB Files" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/gen3/profile.md b/apps/docs/src/content/docs/explore-available-data/gen3/profile.md deleted file mode 100644 index 6619e390..00000000 --- a/apps/docs/src/content/docs/explore-available-data/gen3/profile.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Profile" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/gen3/query.md b/apps/docs/src/content/docs/explore-available-data/gen3/query.md deleted file mode 100644 index 7e550bd9..00000000 --- a/apps/docs/src/content/docs/explore-available-data/gen3/query.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Query" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/gen3/workspace.md b/apps/docs/src/content/docs/explore-available-data/gen3/workspace.md deleted file mode 100644 index 89c31351..00000000 --- a/apps/docs/src/content/docs/explore-available-data/gen3/workspace.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Workspace" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/index.md b/apps/docs/src/content/docs/explore-available-data/index.md deleted file mode 100644 index 27b8682c..00000000 --- a/apps/docs/src/content/docs/explore-available-data/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Explore Available Data" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/additional-resources.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/additional-resources.md deleted file mode 100644 index 68f1624c..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/additional-resources.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Additional Resources" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/api-analysis.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/api-analysis.md deleted file mode 100644 index 9ebe0a7c..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/api-analysis.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Data Analysis Using the PIC-SURE API" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/api-documentation.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/api-documentation.md deleted file mode 100644 index 0caa1c5f..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/api-documentation.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "PIC-SURE API Documentation" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/appendix-1-identifiers.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/appendix-1-identifiers.md deleted file mode 100644 index 0715735c..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/appendix-1-identifiers.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Appendix 1: BDC Identifiers" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/appendix-2-harmonized-variables.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/appendix-2-harmonized-variables.md deleted file mode 100644 index 5f3b9ef4..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/appendix-2-harmonized-variables.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Appendix 2: Table of Harmonized Variables" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/authorized-access.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/authorized-access.md deleted file mode 100644 index a632baa9..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/authorized-access.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "PIC-SURE Authorized Access" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/available-data.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/available-data.md deleted file mode 100644 index 305a67d9..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/available-data.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Available Data and Managing Data Access" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/biolincc-datasets.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/biolincc-datasets.md deleted file mode 100644 index 2f4130e2..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/biolincc-datasets.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "BioLINCC Datasets" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/connects-dataset.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/connects-dataset.md deleted file mode 100644 index 10a4b38f..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/connects-dataset.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "CONNECTS Dataset" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/data-organization.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/data-organization.md deleted file mode 100644 index 2114636f..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/data-organization.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Data Organization in PIC-SURE" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/features-and-layout.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/features-and-layout.md deleted file mode 100644 index d423c1ce..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/features-and-layout.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "PIC-SURE Features and General Layout" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/getting-started.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/getting-started.md deleted file mode 100644 index 23168cbd..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/getting-started.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Getting Started with PIC-SURE" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/index.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/index.md deleted file mode 100644 index f046849e..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "PIC-SURE User Guide" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/open-access.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/open-access.md deleted file mode 100644 index 55705c3f..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/open-access.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "PIC-SURE Open Access" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/open-vs-authorized-access.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/open-vs-authorized-access.md deleted file mode 100644 index 0ff0ae57..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/open-vs-authorized-access.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "PIC-SURE Open Access vs. Authorized Access" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/requirements-and-login.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/requirements-and-login.md deleted file mode 100644 index 88dbf955..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/requirements-and-login.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Requirements and Login" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/explore-available-data/pic-sure/topmed-datasets.md b/apps/docs/src/content/docs/explore-available-data/pic-sure/topmed-datasets.md deleted file mode 100644 index 21bf0d31..00000000 --- a/apps/docs/src/content/docs/explore-available-data/pic-sure/topmed-datasets.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "TOPMed and TOPMed Related Datasets" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/getting-started.md b/apps/docs/src/content/docs/getting-started.md deleted file mode 100644 index d1df4c7d..00000000 --- a/apps/docs/src/content/docs/getting-started.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Getting Started" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/grant-proposals.md b/apps/docs/src/content/docs/grant-proposals.md deleted file mode 100644 index 43899a32..00000000 --- a/apps/docs/src/content/docs/grant-proposals.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Writing BDC into a Grant Proposal" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/guides/intro.md b/apps/docs/src/content/docs/guides/intro.md deleted file mode 100644 index 11813399..00000000 --- a/apps/docs/src/content/docs/guides/intro.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -title: Introduction -description: A guide in my new Starlight docs site. ---- - -Guides lead a user through a specific task they want to accomplish. - -## Further reading - -- Read [about guides](https://starlight.astro.build/guides/authoring-content/) in the Starlight docs. diff --git a/apps/docs/src/content/docs/guides/quick-start.md b/apps/docs/src/content/docs/guides/quick-start.md deleted file mode 100644 index ee4dbb54..00000000 --- a/apps/docs/src/content/docs/guides/quick-start.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: Quick Start Guide -description: A guide to getting started with BDC ---- - -Enim id occaecat laboris commodo dolore non dolore commodo qui proident exercitation deserunt dolor incididunt. Lorem ipsum magna excepteur qui do do est do in ea fugiat deserunt ut enim commodo do labore irure incididunt aliquip. Non commodo officia cillum mollit id cupidatat id ut in enim nostrud sit labore aute in. - -Dolor aliquip non minim adipisicing velit anim nulla incididunt esse nisi officia magna nulla consectetur ut pariatur ut deserunt. Nostrud proident enim ad ad et aliquip duis sit ex anim consequat in eiusmod ex exercitation reprehenderit. - -## Further reading - -- Read [this](https://example.com/) resource. -- Check out [that](https://example.com/) resource. diff --git a/apps/docs/src/content/docs/index.mdx b/apps/docs/src/content/docs/index.mdx deleted file mode 100644 index a0097cd8..00000000 --- a/apps/docs/src/content/docs/index.mdx +++ /dev/null @@ -1,37 +0,0 @@ ---- -title: NHLBI BioData Catalyst® (BDC) Documentation -description: This is a repository for documentation related to the platforms and services that are part of the BDC ecosystem. -template: splash -hero: - tagline: Welcome to NHLBI BioData Catalyst® (BDC) - image: - file: https://picsum.photos/300/300 - actions: - - text: Quick Start Guide - link: /guides/quick-start/ - icon: right-arrow - - text: Read the BDC docs - link: /reference/ - icon: external - variant: minimal ---- - -import { Card, CardGrid, LinkButton } from '@astrojs/starlight/components'; - -## Next steps - - - - Edit `src/content/docs/index.md` to change this page. - - - Add Markdown or MDX files to `src/content/docs` to create new pages. - - - Edit your `sidebar` and other config in `astro.config.mjs`. - - - Learn more in [the Starlight Docs](https://starlight.astro.build/). - Tester - - diff --git a/apps/docs/src/content/docs/release-notes/2020-04-02.md b/apps/docs/src/content/docs/release-notes/2020-04-02.md deleted file mode 100644 index 424e0498..00000000 --- a/apps/docs/src/content/docs/release-notes/2020-04-02.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2020-04-02 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2020-08-24.md b/apps/docs/src/content/docs/release-notes/2020-08-24.md deleted file mode 100644 index 993ee923..00000000 --- a/apps/docs/src/content/docs/release-notes/2020-08-24.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2020-08-24 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2020-10-23.md b/apps/docs/src/content/docs/release-notes/2020-10-23.md deleted file mode 100644 index 81d05e29..00000000 --- a/apps/docs/src/content/docs/release-notes/2020-10-23.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2020-10-23 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2021-01-15.md b/apps/docs/src/content/docs/release-notes/2021-01-15.md deleted file mode 100644 index 288858b7..00000000 --- a/apps/docs/src/content/docs/release-notes/2021-01-15.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2021-01-15 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2021-04-02.md b/apps/docs/src/content/docs/release-notes/2021-04-02.md deleted file mode 100644 index 2b348341..00000000 --- a/apps/docs/src/content/docs/release-notes/2021-04-02.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2021-04-02 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2021-07-09.md b/apps/docs/src/content/docs/release-notes/2021-07-09.md deleted file mode 100644 index e095a224..00000000 --- a/apps/docs/src/content/docs/release-notes/2021-07-09.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2021-07-09 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2021-10-04.md b/apps/docs/src/content/docs/release-notes/2021-10-04.md deleted file mode 100644 index 86f0e308..00000000 --- a/apps/docs/src/content/docs/release-notes/2021-10-04.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2021-10-04 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2022-01-24.md b/apps/docs/src/content/docs/release-notes/2022-01-24.md deleted file mode 100644 index f23f285e..00000000 --- a/apps/docs/src/content/docs/release-notes/2022-01-24.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2022-01-24 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2022-04-04.md b/apps/docs/src/content/docs/release-notes/2022-04-04.md deleted file mode 100644 index 70d3f21f..00000000 --- a/apps/docs/src/content/docs/release-notes/2022-04-04.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2022-04-04 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2022-07-11.md b/apps/docs/src/content/docs/release-notes/2022-07-11.md deleted file mode 100644 index 9ee70794..00000000 --- a/apps/docs/src/content/docs/release-notes/2022-07-11.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2022-07-11 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2022-10-03.md b/apps/docs/src/content/docs/release-notes/2022-10-03.md deleted file mode 100644 index b85e9c44..00000000 --- a/apps/docs/src/content/docs/release-notes/2022-10-03.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2022-10-03 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2023-01-09.md b/apps/docs/src/content/docs/release-notes/2023-01-09.md deleted file mode 100644 index a1c6b1d6..00000000 --- a/apps/docs/src/content/docs/release-notes/2023-01-09.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2023-01-09 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2023-04-04.md b/apps/docs/src/content/docs/release-notes/2023-04-04.md deleted file mode 100644 index 47b73eb6..00000000 --- a/apps/docs/src/content/docs/release-notes/2023-04-04.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2023-04-04 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2023-07-11.md b/apps/docs/src/content/docs/release-notes/2023-07-11.md deleted file mode 100644 index 04416e59..00000000 --- a/apps/docs/src/content/docs/release-notes/2023-07-11.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2023-07-11 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2023-10-04.md b/apps/docs/src/content/docs/release-notes/2023-10-04.md deleted file mode 100644 index 224a61da..00000000 --- a/apps/docs/src/content/docs/release-notes/2023-10-04.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2023-10-04 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2024-01-08.md b/apps/docs/src/content/docs/release-notes/2024-01-08.md deleted file mode 100644 index 66d73bc4..00000000 --- a/apps/docs/src/content/docs/release-notes/2024-01-08.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2024-01-08 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2024-04-01.md b/apps/docs/src/content/docs/release-notes/2024-04-01.md deleted file mode 100644 index df20711a..00000000 --- a/apps/docs/src/content/docs/release-notes/2024-04-01.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2024-04-01 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2024-07-02.md b/apps/docs/src/content/docs/release-notes/2024-07-02.md deleted file mode 100644 index 03eded2c..00000000 --- a/apps/docs/src/content/docs/release-notes/2024-07-02.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2024-07-02 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2024-10-21.md b/apps/docs/src/content/docs/release-notes/2024-10-21.md deleted file mode 100644 index 93df07b7..00000000 --- a/apps/docs/src/content/docs/release-notes/2024-10-21.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2024-10-21 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2025-01-15.md b/apps/docs/src/content/docs/release-notes/2025-01-15.md deleted file mode 100644 index 4c932631..00000000 --- a/apps/docs/src/content/docs/release-notes/2025-01-15.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2025-01-15 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2025-04-15.md b/apps/docs/src/content/docs/release-notes/2025-04-15.md deleted file mode 100644 index eeb97d10..00000000 --- a/apps/docs/src/content/docs/release-notes/2025-04-15.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2025-04-15 BDC Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2025-07-15.md b/apps/docs/src/content/docs/release-notes/2025-07-15.md deleted file mode 100644 index b3eb2e3b..00000000 --- a/apps/docs/src/content/docs/release-notes/2025-07-15.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2025-07-15 BDC Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/2025-11-15.md b/apps/docs/src/content/docs/release-notes/2025-11-15.md deleted file mode 100644 index 7c3f5645..00000000 --- a/apps/docs/src/content/docs/release-notes/2025-11-15.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "2025-11-15 BDC Ecosystem Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/data-versioning.md b/apps/docs/src/content/docs/release-notes/data-versioning.md deleted file mode 100644 index 13f34d79..00000000 --- a/apps/docs/src/content/docs/release-notes/data-versioning.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Data Versioning Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/index.md b/apps/docs/src/content/docs/release-notes/index.md deleted file mode 100644 index e866f3fc..00000000 --- a/apps/docs/src/content/docs/release-notes/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/release-notes/nih-recover.md b/apps/docs/src/content/docs/release-notes/nih-recover.md deleted file mode 100644 index bca04fe6..00000000 --- a/apps/docs/src/content/docs/release-notes/nih-recover.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "NIH RECOVER Release Notes" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/tutorials/index.md b/apps/docs/src/content/docs/tutorials/index.md deleted file mode 100644 index 7cd922db..00000000 --- a/apps/docs/src/content/docs/tutorials/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Tutorials: Videos & Modules" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/tutorials/seven-bridges/cloud-costs.md b/apps/docs/src/content/docs/tutorials/seven-bridges/cloud-costs.md deleted file mode 100644 index d14dbedc..00000000 --- a/apps/docs/src/content/docs/tutorials/seven-bridges/cloud-costs.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Estimating and Managing Your Cloud Costs" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/tutorials/seven-bridges/genesis-workflows.md b/apps/docs/src/content/docs/tutorials/seven-bridges/genesis-workflows.md deleted file mode 100644 index b3a366c5..00000000 --- a/apps/docs/src/content/docs/tutorials/seven-bridges/genesis-workflows.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Genetic Association Testing using GENESIS Workflows" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/tutorials/seven-bridges/index.md b/apps/docs/src/content/docs/tutorials/seven-bridges/index.md deleted file mode 100644 index 87642df3..00000000 --- a/apps/docs/src/content/docs/tutorials/seven-bridges/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "BDC-Seven Bridges Tutorials" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/tutorials/terra/gen3-data-on-terra.md b/apps/docs/src/content/docs/tutorials/terra/gen3-data-on-terra.md deleted file mode 100644 index c6034318..00000000 --- a/apps/docs/src/content/docs/tutorials/terra/gen3-data-on-terra.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Getting Started with Gen3 Data on Terra" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/tutorials/terra/gwas-1000-genomes.md b/apps/docs/src/content/docs/tutorials/terra/gwas-1000-genomes.md deleted file mode 100644 index abd157ac..00000000 --- a/apps/docs/src/content/docs/tutorials/terra/gwas-1000-genomes.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "GWAS with 1000 Genomes Data" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/tutorials/terra/gwas-topmed.md b/apps/docs/src/content/docs/tutorials/terra/gwas-topmed.md deleted file mode 100644 index 48773fbd..00000000 --- a/apps/docs/src/content/docs/tutorials/terra/gwas-topmed.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "GWAS with TOPMed Data" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/tutorials/terra/index.md b/apps/docs/src/content/docs/tutorials/terra/index.md deleted file mode 100644 index 9afc16b1..00000000 --- a/apps/docs/src/content/docs/tutorials/terra/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "BDC-Terra Tutorials" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook). diff --git a/apps/docs/src/content/docs/tutorials/terra/topmed-aligner.md b/apps/docs/src/content/docs/tutorials/terra/topmed-aligner.md deleted file mode 100644 index da73a9ac..00000000 --- a/apps/docs/src/content/docs/tutorials/terra/topmed-aligner.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "TOPMed Aligner: Import Data From Gen3 into Terra" -description: "TODO: migrate from GitBook" ---- - -Content to be migrated from [GitBook](https://github.com/stagecc/bdc-gitbook).