From ccc2f7eee804ee4ec4e22b6cd32e46f2f1dfc2a8 Mon Sep 17 00:00:00 2001 From: Kyle Ellrott Date: Sun, 18 Jan 2026 23:59:56 -0800 Subject: [PATCH 01/14] Adding web view subcommand to sifter --- cmd/root.go | 2 + cmd/web/main.go | 88 ++++++++++++++++++++++++++++++++++++++ cmd/web/static/app.js | 33 +++++++++++++++ cmd/web/static/index.html | 29 +++++++++++++ cmd/web/static/style.css | 89 +++++++++++++++++++++++++++++++++++++++ web/static/index.html | 25 +++++++++++ 6 files changed, 266 insertions(+) create mode 100644 cmd/web/main.go create mode 100644 cmd/web/static/app.js create mode 100644 cmd/web/static/index.html create mode 100644 cmd/web/static/style.css create mode 100644 web/static/index.html diff --git a/cmd/root.go b/cmd/root.go index 2e889eb..0204651 100644 --- a/cmd/root.go +++ b/cmd/root.go @@ -7,6 +7,7 @@ import ( "github.com/bmeg/sifter/cmd/inspect" "github.com/bmeg/sifter/cmd/run" "github.com/bmeg/sifter/cmd/scan" + "github.com/bmeg/sifter/cmd/web" "github.com/spf13/cobra" ) @@ -22,6 +23,7 @@ func init() { RootCmd.AddCommand(inspect.Cmd) RootCmd.AddCommand(graphplan.Cmd) RootCmd.AddCommand(scan.Cmd) + RootCmd.AddCommand(web.Cmd) } var genBashCompletionCmd = &cobra.Command{ diff --git a/cmd/web/main.go b/cmd/web/main.go new file mode 100644 index 0000000..ff0ffb8 --- /dev/null +++ b/cmd/web/main.go @@ -0,0 +1,88 @@ +package web + +import ( + "embed" + "encoding/json" + "fmt" + "io/fs" + "log" + "net/http" + "os" + "path/filepath" + "strings" + + "github.com/spf13/cobra" +) + +//go:embed static/* +var staticFS embed.FS + +var playbookDir string + +// Cmd is the declaration of the command line +var Cmd = &cobra.Command{ + Use: "web + + + + +
+ +
+
+
+
+ + + + + \ No newline at end of file diff --git a/cmd/web/static/style.css b/cmd/web/static/style.css new file mode 100644 index 0000000..5312646 --- /dev/null +++ b/cmd/web/static/style.css @@ -0,0 +1,89 @@ +/* Premium dark theme with glassmorphism and smooth gradients */ +:root { + --font-family: 'Inter', sans-serif; + --bg-gradient: linear-gradient(135deg, #1e1e2f, #2a2a3d); + --sidebar-bg: rgba(255, 255, 255, 0.08); + --content-bg: rgba(255, 255, 255, 0.04); + --text-color: #e0e0e0; + --accent-color: #4f9bff; +} + +* { + box-sizing: border-box; + margin: 0; + padding: 0; +} + +body { + font-family: var(--font-family); + background: var(--bg-gradient); + color: var(--text-color); + height: 100vh; + display: flex; + align-items: center; + justify-content: center; +} + +.container { + display: flex; + width: 90vw; + height: 80vh; + backdrop-filter: blur(12px); + border-radius: 12px; + overflow: hidden; + box-shadow: 0 8px 32px rgba(0,0,0,0.6); +} + +.sidebar { + flex: 0 0 250px; + background: var(--sidebar-bg); + padding: 20px; + overflow-y: auto; +} + +.sidebar h1 { + font-size: 1.4rem; + margin-bottom: 1rem; + color: var(--accent-color); +} + +.sidebar ul { + list-style: none; +} + +.sidebar li { + margin: 8px 0; + cursor: pointer; + padding: 6px 10px; + border-radius: 6px; + transition: background 0.2s, transform 0.1s; +} + +.sidebar li:hover { + background: rgba(255,255,255,0.1); + transform: translateX(4px); +} + +.content { + flex: 1; + background: var(--content-bg); + padding: 20px; + overflow-y: auto; +} + +pre { + margin: 0; + height: 100%; + overflow: auto; +} + +code { + font-family: 'Source Code Pro', monospace; + font-size: 0.9rem; +} + +@media (max-width: 768px) { + .container { flex-direction: column; height: auto; } + .sidebar { flex: none; width: 100%; } + .content { flex: none; height: 60vh; } +} diff --git a/web/static/index.html b/web/static/index.html new file mode 100644 index 0000000..ebe026c --- /dev/null +++ b/web/static/index.html @@ -0,0 +1,25 @@ + + + + + + Sifter Playbook Viewer + + + + + + +
+ +
+
+
+
+ + + + From 136b16f50fff96d193f8799d66a58245b153f58d Mon Sep 17 00:00:00 2001 From: Kyle Ellrott Date: Sat, 24 Jan 2026 23:38:37 -0800 Subject: [PATCH 02/14] Starting to work on webapp --- sifter-view/.gitignore | 41 + sifter-view/README.md | 36 + sifter-view/app/favicon.ico | Bin 0 -> 25931 bytes sifter-view/app/globals.css | 26 + sifter-view/app/layout.tsx | 34 + sifter-view/app/page.tsx | 16 + sifter-view/components/PlaybookFlow.tsx | 50 + sifter-view/components/PlaybookViewer.tsx | 79 + sifter-view/eslint.config.mjs | 18 + sifter-view/next.config.ts | 10 + sifter-view/package-lock.json | 5366 +++++++++++++++++++++ sifter-view/package.json | 29 + sifter-view/postcss.config.mjs | 7 + sifter-view/public/file.svg | 1 + sifter-view/public/globe.svg | 1 + sifter-view/public/next.svg | 1 + sifter-view/public/vercel.svg | 1 + sifter-view/public/window.svg | 1 + sifter-view/tsconfig.json | 34 + 19 files changed, 5751 insertions(+) create mode 100644 sifter-view/.gitignore create mode 100644 sifter-view/README.md create mode 100644 sifter-view/app/favicon.ico create mode 100644 sifter-view/app/globals.css create mode 100644 sifter-view/app/layout.tsx create mode 100644 sifter-view/app/page.tsx create mode 100644 sifter-view/components/PlaybookFlow.tsx create mode 100644 sifter-view/components/PlaybookViewer.tsx create mode 100644 sifter-view/eslint.config.mjs create mode 100644 sifter-view/next.config.ts create mode 100644 sifter-view/package-lock.json create mode 100644 sifter-view/package.json create mode 100644 sifter-view/postcss.config.mjs create mode 100644 sifter-view/public/file.svg create mode 100644 sifter-view/public/globe.svg create mode 100644 sifter-view/public/next.svg create mode 100644 sifter-view/public/vercel.svg create mode 100644 sifter-view/public/window.svg create mode 100644 sifter-view/tsconfig.json diff --git a/sifter-view/.gitignore b/sifter-view/.gitignore new file mode 100644 index 0000000..5ef6a52 --- /dev/null +++ b/sifter-view/.gitignore @@ -0,0 +1,41 @@ +# See https://help.github.com/articles/ignoring-files/ for more about ignoring files. + +# dependencies +/node_modules +/.pnp +.pnp.* +.yarn/* +!.yarn/patches +!.yarn/plugins +!.yarn/releases +!.yarn/versions + +# testing +/coverage + +# next.js +/.next/ +/out/ + +# production +/build + +# misc +.DS_Store +*.pem + +# debug +npm-debug.log* +yarn-debug.log* +yarn-error.log* +.pnpm-debug.log* + +# env files (can opt-in for committing if needed) +.env* + +# vercel +.vercel + +# typescript +*.tsbuildinfo +next-env.d.ts diff --git a/sifter-view/README.md b/sifter-view/README.md new file mode 100644 index 0000000..e215bc4 --- /dev/null +++ b/sifter-view/README.md @@ -0,0 +1,36 @@ +This is a [Next.js](https://nextjs.org) project bootstrapped with [`create-next-app`](https://nextjs.org/docs/app/api-reference/cli/create-next-app). + +## Getting Started + +First, run the development server: + +```bash +npm run dev +# or +yarn dev +# or +pnpm dev +# or +bun dev +``` + +Open [http://localhost:3000](http://localhost:3000) with your browser to see the result. + +You can start editing the page by modifying `app/page.tsx`. The page auto-updates as you edit the file. + +This project uses [`next/font`](https://nextjs.org/docs/app/building-your-application/optimizing/fonts) to automatically optimize and load [Geist](https://vercel.com/font), a new font family for Vercel. + +## Learn More + +To learn more about Next.js, take a look at the following resources: + +- [Next.js Documentation](https://nextjs.org/docs) - learn about Next.js features and API. +- [Learn Next.js](https://nextjs.org/learn) - an interactive Next.js tutorial. + +You can check out [the Next.js GitHub repository](https://github.com/vercel/next.js) - your feedback and contributions are welcome! + +## Deploy on Vercel + +The easiest way to deploy your Next.js app is to use the [Vercel Platform](https://vercel.com/new?utm_medium=default-template&filter=next.js&utm_source=create-next-app&utm_campaign=create-next-app-readme) from the creators of Next.js. + +Check out our [Next.js deployment 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a/sifter-view/app/layout.tsx b/sifter-view/app/layout.tsx new file mode 100644 index 0000000..f7fa87e --- /dev/null +++ b/sifter-view/app/layout.tsx @@ -0,0 +1,34 @@ +import type { Metadata } from "next"; +import { Geist, Geist_Mono } from "next/font/google"; +import "./globals.css"; + +const geistSans = Geist({ + variable: "--font-geist-sans", + subsets: ["latin"], +}); + +const geistMono = Geist_Mono({ + variable: "--font-geist-mono", + subsets: ["latin"], +}); + +export const metadata: Metadata = { + title: "Create Next App", + description: "Generated by create next app", +}; + +export default function RootLayout({ + children, +}: Readonly<{ + children: React.ReactNode; +}>) { + return ( + + + {children} + + + ); +} diff --git a/sifter-view/app/page.tsx b/sifter-view/app/page.tsx new file mode 100644 index 0000000..85a5576 --- /dev/null +++ b/sifter-view/app/page.tsx @@ -0,0 +1,16 @@ + +'use client' + +import PlaybookViewer from "@/components/PlaybookViewer"; +import PlaybookFlow from "@/components/PlaybookFlow" +import Image from "next/image"; + +export default function Home() { + return ( +
+
+ +
+
+ ); +} diff --git a/sifter-view/components/PlaybookFlow.tsx b/sifter-view/components/PlaybookFlow.tsx new file mode 100644 index 0000000..bb40013 --- /dev/null +++ b/sifter-view/components/PlaybookFlow.tsx @@ -0,0 +1,50 @@ +'use client'; + +import React, { useCallback } from 'react'; + +import { + ReactFlow, + useNodesState, + useEdgesState, + addEdge, + Background, + Controls, + OnConnect, + Connection +} from "@xyflow/react"; + +// Import the necessary styles +import "@xyflow/react/dist/style.css"; + +const initialNodes = [ + { id: '1', position: { x: 0, y: 0 }, data: { label: 'Start Node' } }, + { id: '2', position: { x: 0, y: 100 }, data: { label: 'End Node' } }, +]; + +const initialEdges = [{ id: 'e1-2', source: '1', target: '2', animated: true }]; + +export default function PlaybookFlow() { + const [nodes, setNodes, onNodesChange] = useNodesState(initialNodes); + const [edges, setEdges, onEdgesChange] = useEdgesState(initialEdges); + + const onConnect: OnConnect = useCallback( + (connection: Connection) => setEdges((edges) => addEdge(connection, edges)), + [setEdges] + ); + + return ( +
+ + + + +
+ ); +} \ No newline at end of file diff --git a/sifter-view/components/PlaybookViewer.tsx b/sifter-view/components/PlaybookViewer.tsx new file mode 100644 index 0000000..f6eafd4 --- /dev/null +++ b/sifter-view/components/PlaybookViewer.tsx @@ -0,0 +1,79 @@ +import React, { useEffect, useState } from "react"; +import hljs from "highlight.js"; +import "highlight.js/styles/github-dark.css"; + +// Types for API responses +type PlaybookList = string[]; + +type PlaybookViewerProps = {}; + +export default function PlaybookViewer(_: PlaybookViewerProps) { + const [playbooks, setPlaybooks] = useState([]); + const [selected, setSelected] = useState(null); + const [content, setContent] = useState(""); + + // Load list of playbooks on mount + useEffect(() => { + fetch("/api/playbooks") + .then((res) => { + if (!res.ok) throw new Error("Failed to fetch playbook list"); + return res.json(); + }) + .then((data: PlaybookList) => setPlaybooks(data)) + .catch((err) => console.error(err)); + }, []); + + // Load selected playbook content + const loadPlaybook = (name: string) => { + setSelected(name); + fetch(`/api/playbook?name=${encodeURIComponent(name)}`) + .then((res) => { + if (!res.ok) throw new Error("Playbook not found"); + return res.text(); + }) + .then((txt) => setContent(txt)) + .catch((err) => console.error(err)); + }; + + // Highlight content after it changes + useEffect(() => { + if (content) { + // Using highlight.js to highlight the content as YAML + const block = document.getElementById("playbook-content"); + if (block) { + hljs.highlightElement(block); + } + } + }, [content]); + + return ( +
+ {/* Sidebar */} + + + {/* Content */} +
+
+          
+            {content || "Select a playbook to view its content"}
+          
+        
+
+
+ ); +} diff --git a/sifter-view/eslint.config.mjs b/sifter-view/eslint.config.mjs new file mode 100644 index 0000000..05e726d --- /dev/null +++ b/sifter-view/eslint.config.mjs @@ -0,0 +1,18 @@ +import { defineConfig, globalIgnores } from "eslint/config"; +import nextVitals from "eslint-config-next/core-web-vitals"; +import nextTs from "eslint-config-next/typescript"; + +const eslintConfig = defineConfig([ + ...nextVitals, + ...nextTs, + // Override default ignores of eslint-config-next. + globalIgnores([ + // Default ignores of eslint-config-next: + ".next/**", + "out/**", + "build/**", + "next-env.d.ts", + ]), +]); + +export default eslintConfig; diff --git a/sifter-view/next.config.ts b/sifter-view/next.config.ts new file mode 100644 index 0000000..650ca82 --- /dev/null +++ b/sifter-view/next.config.ts @@ -0,0 +1,10 @@ +import type { NextConfig } from "next"; + +const nextConfig: NextConfig = { + /* config options here */ + output: 'export', + // Optional: Change the output directory from 'out' to 'dist' + distDir: 'dist', +}; + +export default nextConfig; diff --git a/sifter-view/package-lock.json b/sifter-view/package-lock.json new file mode 100644 index 0000000..32b6f84 --- /dev/null +++ b/sifter-view/package-lock.json @@ -0,0 +1,5366 @@ +{ + "name": "sifter-view", + "version": "0.1.0", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "sifter-view", + "version": "0.1.0", + "dependencies": { + "@xyflow/react": "^12.10.0", + "dagre": "^0.8.5", + "highlight.js": "^11.11.1", + "next": "16.1.4", + "react": "19.2.3", + "react-dom": "19.2.3" + }, + "devDependencies": { + "@tailwindcss/postcss": "^4", + "@types/node": "^20", + "@types/react": "^19", + "@types/react-dom": "^19", + "eslint": "^9", + "eslint-config-next": "16.1.4", + "tailwindcss": "^4", + "typescript": "^5" + } + }, + "node_modules/@alloc/quick-lru": { + "version": "5.2.0", + "resolved": "https://registry.npmjs.org/@alloc/quick-lru/-/quick-lru-5.2.0.tgz", + 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"react": ">=16.8" + }, + "peerDependenciesMeta": { + "@types/react": { + "optional": true + }, + "immer": { + "optional": true + }, + "react": { + "optional": true + } + } + } + } +} diff --git a/sifter-view/package.json b/sifter-view/package.json new file mode 100644 index 0000000..c8d5692 --- /dev/null +++ b/sifter-view/package.json @@ -0,0 +1,29 @@ +{ + "name": "sifter-view", + "version": "0.1.0", + "private": true, + "scripts": { + "dev": "next dev", + "build": "next build", + "start": "next start", + "lint": "eslint" + }, + "dependencies": { + "@xyflow/react": "^12.10.0", + "dagre": "^0.8.5", + "highlight.js": "^11.11.1", + "next": "16.1.4", + "react": "19.2.3", + "react-dom": "19.2.3" + }, + "devDependencies": { + "@tailwindcss/postcss": "^4", + "@types/node": "^20", + "@types/react": "^19", + "@types/react-dom": "^19", + "eslint": "^9", + "eslint-config-next": "16.1.4", + "tailwindcss": "^4", + "typescript": "^5" + } +} diff --git a/sifter-view/postcss.config.mjs b/sifter-view/postcss.config.mjs new file mode 100644 index 0000000..61e3684 --- /dev/null +++ b/sifter-view/postcss.config.mjs @@ -0,0 +1,7 @@ +const config = { + plugins: { + "@tailwindcss/postcss": {}, + }, +}; + +export default config; diff --git a/sifter-view/public/file.svg b/sifter-view/public/file.svg new file mode 100644 index 0000000..004145c --- /dev/null +++ b/sifter-view/public/file.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/sifter-view/public/globe.svg b/sifter-view/public/globe.svg new file mode 100644 index 0000000..567f17b --- /dev/null +++ b/sifter-view/public/globe.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/sifter-view/public/next.svg b/sifter-view/public/next.svg new file mode 100644 index 0000000..5174b28 --- /dev/null +++ b/sifter-view/public/next.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/sifter-view/public/vercel.svg b/sifter-view/public/vercel.svg new file mode 100644 index 0000000..7705396 --- /dev/null +++ b/sifter-view/public/vercel.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/sifter-view/public/window.svg b/sifter-view/public/window.svg new file mode 100644 index 0000000..b2b2a44 --- /dev/null +++ b/sifter-view/public/window.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/sifter-view/tsconfig.json b/sifter-view/tsconfig.json new file mode 100644 index 0000000..3a13f90 --- /dev/null +++ b/sifter-view/tsconfig.json @@ -0,0 +1,34 @@ +{ + "compilerOptions": { + "target": "ES2017", + "lib": ["dom", "dom.iterable", "esnext"], + "allowJs": true, + "skipLibCheck": true, + "strict": true, + "noEmit": true, + "esModuleInterop": true, + "module": "esnext", + "moduleResolution": "bundler", + "resolveJsonModule": true, + "isolatedModules": true, + "jsx": "react-jsx", + "incremental": true, + "plugins": [ + { + "name": "next" + } + ], + "paths": { + "@/*": ["./*"] + } + }, + "include": [ + "next-env.d.ts", + "**/*.ts", + "**/*.tsx", + ".next/types/**/*.ts", + ".next/dev/types/**/*.ts", + "**/*.mts" + ], + "exclude": ["node_modules"] +} From e11bd7ec4ed2903703b2d43b6c81d34ebf3f0f60 Mon Sep 17 00:00:00 2001 From: Kyle Ellrott Date: Sun, 25 Jan 2026 19:34:16 -0800 Subject: [PATCH 03/14] dagre layout for playbook prototype --- cmd/web/main.go | 35 ++- sifter-view/components/PlaybookFlow.tsx | 305 +++++++++++++++++++++++- sifter-view/package-lock.json | 7 + sifter-view/package.json | 1 + sifter-view/tsconfig.json | 18 +- web/static/index.html | 25 -- 6 files changed, 350 insertions(+), 41 deletions(-) delete mode 100644 web/static/index.html diff --git a/cmd/web/main.go b/cmd/web/main.go index ff0ffb8..735bfba 100644 --- a/cmd/web/main.go +++ b/cmd/web/main.go @@ -9,6 +9,7 @@ import ( "net/http" "os" "path/filepath" + "sigs.k8s.io/yaml" "strings" "github.com/spf13/cobra" @@ -18,6 +19,7 @@ import ( var staticFS embed.FS var playbookDir string +var siteDir string // Cmd is the declaration of the command line var Cmd = &cobra.Command{ @@ -27,13 +29,18 @@ var Cmd = &cobra.Command{ RunE: func(cmd *cobra.Command, args []string) error { playbookDir = args[0] - // Serve embedded static files - staticFiles, err := fs.Sub(staticFS, "static") - if err != nil { - log.Fatalf("failed to create sub FS: %v", err) - } - http.Handle("/", http.FileServer(http.FS(staticFiles))) + if siteDir == "" { + // Serve embedded static files + staticFiles, err := fs.Sub(staticFS, "static") + if err != nil { + log.Fatalf("failed to create sub FS: %v", err) + } + http.Handle("/", http.FileServer(http.FS(staticFiles))) + } else { + http.Handle("/", http.FileServer(http.Dir(siteDir))) + + } // API endpoints http.HandleFunc("/api/playbooks", listPlaybooksHandler) http.HandleFunc("/api/playbook", getPlaybookHandler) @@ -83,6 +90,22 @@ func getPlaybookHandler(w http.ResponseWriter, r *http.Request) { http.Error(w, "playbook not found", http.StatusNotFound) return } + format := r.URL.Query().Get("format") + if format == "json" { + jsonBytes, err := yaml.YAMLToJSON(content) + if err != nil { + http.Error(w, "failed to convert yaml to json", http.StatusInternalServerError) + return + } + w.Header().Set("Content-Type", "application/json") + w.Write(jsonBytes) + return + } w.Header().Set("Content-Type", "text/plain") w.Write(content) } + +func init() { + flags := Cmd.Flags() + flags.StringVarP(&siteDir, "site-dir", "s", siteDir, "Serve Custom site dir") +} diff --git a/sifter-view/components/PlaybookFlow.tsx b/sifter-view/components/PlaybookFlow.tsx index bb40013..f419dc6 100644 --- a/sifter-view/components/PlaybookFlow.tsx +++ b/sifter-view/components/PlaybookFlow.tsx @@ -1,6 +1,6 @@ 'use client'; -import React, { useCallback } from 'react'; +import React, { useCallback, useEffect } from 'react'; import { ReactFlow, @@ -16,14 +16,307 @@ import { // Import the necessary styles import "@xyflow/react/dist/style.css"; -const initialNodes = [ - { id: '1', position: { x: 0, y: 0 }, data: { label: 'Start Node' } }, - { id: '2', position: { x: 0, y: 100 }, data: { label: 'End Node' } }, -]; +import dagre from 'dagre'; +import type { Node, Edge } from '@xyflow/react'; + + +// ------------------------------------------------------------------- +// Types for the Sifter playbook JSON (imported as a static module) +// ------------------------------------------------------------------- +interface Playbook { + class: string; + name?: string; + inputs: Record; + outputs?: Record; + pipelines: Record; + params?: any; +} + +type PipelineStep = Record; // each step is a single‑key object + + + +var playbook : Playbook = { + "class": "sifter", + "inputs": { + "cases_data": { + "jsonLoad": { + "input": "out.case.json" + } + }, + "cases_scrape": { + "plugin": { + "commandLine": "docker run --rm bmeg/sifter-gdc-scan /opt/gdc-scan.py cases" + } + }, + "projects_data": { + "jsonLoad": { + "input": "out.projects.json" + } + }, + "projects_scrape": { + "plugin": { + "commandLine": "docker run --rm bmeg/sifter-gdc-scan /opt/gdc-scan.py projects" + } + } + }, + "name": "GDCConvert", + "params": { + "schema": { + "default": "bmeg-dictionary/gdcdictionary/schemas", + "type": "path" + } + }, + "pipelines": { + "aliquots": [ + { + "from": "cases_data" + }, + { + "fieldProcess": { + "field": "samples" + } + }, + { + "fieldProcess": { + "field": "portions" + } + }, + { + "fieldProcess": { + "field": "analytes" + } + }, + { + "fieldProcess": { + "field": "aliquots" + } + }, + { + "project": { + "mapping": { + "id": "{{row.aliquot_id}}", + "type": "aliquot" + } + } + }, + { + "objectValidate": { + "schema": "{{params.schema}}", + "title": "aliquot" + } + }, + { + "emit": { + "name": "aliquot" + } + } + ], + "cases": [ + { + "from": "cases_data" + }, + { + "project": { + "mapping": { + "experiments": "exp:{{row.project.project_id}}", + "studies": "{{row.project.project_id}}", + "type": "case" + } + } + }, + { + "objectValidate": { + "schema": "{{params.schema}}", + "title": "case" + } + }, + { + "emit": { + "name": "case" + } + } + ], + "experiments": [ + { + "from": "projects_data" + }, + { + "project": { + "mapping": { + "code": "{{row.project_id}}", + "programs": "{{row.program.name}}", + "projects": "{{row.project_id}}", + "submitter_id": "{{row.program.name}}", + "type": "experiment" + } + } + }, + { + "objectValidate": { + "schema": "{{params.schema}}", + "title": "experiment" + } + }, + { + "emit": { + "name": "experiment" + } + } + ], + "projects": [ + { + "from": "projects_data" + }, + { + "project": { + "mapping": { + "code": "{{row.project_id}}", + "programs": "{{row.program.name}}" + } + } + }, + { + "objectValidate": { + "schema": "{{params.schema}}", + "title": "project" + } + }, + { + "emit": { + "name": "project" + } + } + ], + "samples": [ + { + "from": "cases_data" + }, + { + "fieldProcess": { + "field": "samples" + } + }, + { + "project": { + "mapping": { + "id": "{{row.sample_id}}", + "type": "sample" + } + } + }, + { + "objectValidate": { + "schema": "{{params.schema}}", + "title": "sample" + } + }, + { + "emit": { + "name": "sample" + } + } + ] + } +} + + +// ------------------------------------------------------------------- +// Build a React‑Flow graph from a Playbook, using Dagre for layout +// ------------------------------------------------------------------- + +const NODE_WIDTH = 150; +const NODE_HEIGHT = 40; + +function buildGraph(pb: Playbook): { nodes: Node[]; edges: Edge[] } { + // Create a directed Dagre graph + const g = new dagre.graphlib.Graph({ directed: true }); + //g.setGraph({ rankdir: 'LR', nodesep: 80, ranksep: 120 }); + g.setGraph({}); + + g.setDefaultEdgeLabel(function() { return {}; }); + + // ---- INPUT NODES --------------------------------------------------- + Object.keys(pb.inputs).forEach((name) => { + const id = `input-${name}`; + g.setNode(id, { label: name, width: NODE_WIDTH, height: NODE_HEIGHT }); + }); + + // ---- OUTPUT NODES --------------------------------------------------- + if (pb.outputs) { + Object.keys(pb.outputs).forEach((name) => { + const id = `output-${name}`; + g.setNode(id, { label: name, width: NODE_WIDTH, height: NODE_HEIGHT }); + }); + } + + // ---- PIPELINE STEP NODES & EDGES ----------------------------------- + Object.entries(pb.pipelines).forEach(([pipelineName, steps]) => { + steps.forEach((stepObj, idx) => { + const stepKey = Object.keys(stepObj)[0]; // e.g. "from", "fieldProcess", "emit", … + const nodeId = `${pipelineName}-${idx}`; + g.setNode(nodeId, { label: stepKey, width: NODE_WIDTH, height: NODE_HEIGHT }); + + // Edge from previous step (if any) + if (idx > 0) { + const prevId = `${pipelineName}-${idx - 1}`; + g.setEdge(prevId, nodeId); + } else { + // First step – connect to the input referenced by the "from" field + const fromName = (stepObj as any).from; + if (fromName) { + g.setEdge(`input-${fromName}`, nodeId); + } + } + + // If this step is an emit and an explicit output exists, connect to it + if (stepKey === 'emit' && pb.outputs) { + const emitName = (stepObj as any).emit?.name; + if (emitName && pb.outputs[emitName]) { + g.setEdge(nodeId, `output-${emitName}`); + } + } + }); + }); + + // Run the layout algorithm + dagre.layout(g); + + // Convert Dagre nodes/edges to React‑Flow structures + const nodes: Node[] = g.nodes().map((id) => { + const { x, y, label } = g.node(id); + return { + id, + position: { x, y }, + data: { label }, + // Optional: give each node a consistent size for the UI + style: { width: NODE_WIDTH, height: NODE_HEIGHT }, + } as Node; + }); + + const edges: Edge[] = g.edges().map((e) => ({ + id: `e-${e.v}-${e.w}`, + source: e.v, + target: e.w, + animated: true, + })); + + return { nodes, edges }; +} + +// ------------------------------------------------------------------- +// React component – PlaybookFlow +// ------------------------------------------------------------------- -const initialEdges = [{ id: 'e1-2', source: '1', target: '2', animated: true }]; export default function PlaybookFlow() { + + + var initialGraph = buildGraph(playbook); + + var initialEdges: Edge[] = initialGraph.edges; + var initialNodes: Node[] = initialGraph.nodes; + const [nodes, setNodes, onNodesChange] = useNodesState(initialNodes); const [edges, setEdges, onEdgesChange] = useEdgesState(initialEdges); diff --git a/sifter-view/package-lock.json b/sifter-view/package-lock.json index 32b6f84..fc437f4 100644 --- a/sifter-view/package-lock.json +++ b/sifter-view/package-lock.json @@ -17,6 +17,7 @@ }, "devDependencies": { "@tailwindcss/postcss": "^4", + "@types/dagre": "^0.7.53", "@types/node": "^20", "@types/react": "^19", "@types/react-dom": "^19", @@ -888,6 +889,12 @@ "@types/d3-selection": "*" } }, + "node_modules/@types/dagre": { + "version": "0.7.53", + "resolved": "https://registry.npmjs.org/@types/dagre/-/dagre-0.7.53.tgz", + "integrity": "sha512-f4gkWqzPZvYmKhOsDnhq/R8mO4UMcKdxZo+i5SCkOU1wvGeHJeUXGIHeE9pnwGyPMDof1Vx5ZQo4nxpeg2TTVQ==", + "dev": true + }, "node_modules/@types/estree": { "version": "1.0.8", "resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.8.tgz", diff --git a/sifter-view/package.json b/sifter-view/package.json index c8d5692..9b4eced 100644 --- a/sifter-view/package.json +++ b/sifter-view/package.json @@ -18,6 +18,7 @@ }, "devDependencies": { "@tailwindcss/postcss": "^4", + "@types/dagre": "^0.7.53", "@types/node": "^20", "@types/react": "^19", "@types/react-dom": "^19", diff --git a/sifter-view/tsconfig.json b/sifter-view/tsconfig.json index 3a13f90..0400cf0 100644 --- a/sifter-view/tsconfig.json +++ b/sifter-view/tsconfig.json @@ -1,7 +1,11 @@ { "compilerOptions": { "target": "ES2017", - "lib": ["dom", "dom.iterable", "esnext"], + "lib": [ + "dom", + "dom.iterable", + "esnext" + ], "allowJs": true, "skipLibCheck": true, "strict": true, @@ -19,7 +23,9 @@ } ], "paths": { - "@/*": ["./*"] + "@/*": [ + "./*" + ] } }, "include": [ @@ -28,7 +34,11 @@ "**/*.tsx", ".next/types/**/*.ts", ".next/dev/types/**/*.ts", - "**/*.mts" + "**/*.mts", + "dist/types/**/*.ts", + "dist/dev/types/**/*.ts" ], - "exclude": ["node_modules"] + "exclude": [ + "node_modules" + ] } diff --git a/web/static/index.html b/web/static/index.html deleted file mode 100644 index ebe026c..0000000 --- a/web/static/index.html +++ /dev/null @@ -1,25 +0,0 @@ - - - - - - Sifter Playbook Viewer - - - - - - -
- -
-
-
-
- - - - From f3020bc9dd393081e8736f2258669b21f5764a82 Mon Sep 17 00:00:00 2001 From: Kyle Ellrott Date: Sun, 25 Jan 2026 23:41:08 -0800 Subject: [PATCH 04/14] Removing some invalid old examples --- .gitmodules | 3 - cmd/web/main.go | 29 ++-- examples/Makefile | 10 -- examples/bmeg-dictionary | 1 - examples/cbio.yaml | 144 ------------------ examples/gdc-convert.yaml | 98 ------------- examples/gdc-scan-docker/Dockerfile | 4 - examples/gdc-scan-docker/gdc-scan.py | 134 ----------------- examples/gene-table.yaml | 31 ---- examples/genome.yaml | 92 ------------ examples/hugo-ensembl.yaml | 25 ---- sifter-view/components/PlaybookFlow.tsx | 185 +++++------------------- test/resources/xml_load.yaml | 11 +- 13 files changed, 58 insertions(+), 709 deletions(-) delete mode 100644 examples/Makefile delete mode 160000 examples/bmeg-dictionary delete mode 100644 examples/cbio.yaml delete mode 100644 examples/gdc-convert.yaml delete mode 100644 examples/gdc-scan-docker/Dockerfile delete mode 100755 examples/gdc-scan-docker/gdc-scan.py delete mode 100644 examples/gene-table.yaml delete mode 100644 examples/genome.yaml delete mode 100644 examples/hugo-ensembl.yaml diff --git a/.gitmodules b/.gitmodules index cfa2b86..e69de29 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +0,0 @@ -[submodule "examples/bmeg-dictionary"] - path = examples/bmeg-dictionary - url = https://github.com/bmeg/bmeg-dictionary.git diff --git a/cmd/web/main.go b/cmd/web/main.go index 735bfba..abad2c8 100644 --- a/cmd/web/main.go +++ b/cmd/web/main.go @@ -9,9 +9,10 @@ import ( "net/http" "os" "path/filepath" - "sigs.k8s.io/yaml" "strings" + "sigs.k8s.io/yaml" + "github.com/spf13/cobra" ) @@ -30,20 +31,24 @@ var Cmd = &cobra.Command{ playbookDir = args[0] + var httpFS http.FileSystem + if siteDir == "" { // Serve embedded static files staticFiles, err := fs.Sub(staticFS, "static") if err != nil { log.Fatalf("failed to create sub FS: %v", err) } - http.Handle("/", http.FileServer(http.FS(staticFiles))) + httpFS = http.FS(staticFiles) } else { - http.Handle("/", http.FileServer(http.Dir(siteDir))) - + httpFS = http.Dir(siteDir) } + http.Handle("/", http.FileServer(httpFS)) + // API endpoints - http.HandleFunc("/api/playbooks", listPlaybooksHandler) - http.HandleFunc("/api/playbook", getPlaybookHandler) + ph := playbookHandler{playbookDir} + http.HandleFunc("/api/playbooks", ph.listPlaybooksHandler) + http.HandleFunc("/api/playbook", ph.getPlaybookHandler) port := "8081" fmt.Printf("Server listening on http://localhost:%s\n", port) @@ -53,8 +58,12 @@ var Cmd = &cobra.Command{ }, } -func listPlaybooksHandler(w http.ResponseWriter, r *http.Request) { - entries, err := os.ReadDir(playbookDir) +type playbookHandler struct { + baseDir string +} + +func (ph *playbookHandler) listPlaybooksHandler(w http.ResponseWriter, r *http.Request) { + entries, err := os.ReadDir(ph.baseDir) if err != nil { http.Error(w, "failed to read playbook directory", http.StatusInternalServerError) return @@ -73,7 +82,7 @@ func listPlaybooksHandler(w http.ResponseWriter, r *http.Request) { json.NewEncoder(w).Encode(names) } -func getPlaybookHandler(w http.ResponseWriter, r *http.Request) { +func (ph *playbookHandler) getPlaybookHandler(w http.ResponseWriter, r *http.Request) { name := r.URL.Query().Get("name") if name == "" { http.Error(w, "missing name parameter", http.StatusBadRequest) @@ -84,7 +93,7 @@ func getPlaybookHandler(w http.ResponseWriter, r *http.Request) { http.Error(w, "invalid playbook name", http.StatusBadRequest) return } - path := filepath.Join("examples", name) + path := filepath.Join(ph.baseDir, name) content, err := os.ReadFile(path) if err != nil { http.Error(w, "playbook not found", http.StatusNotFound) diff --git a/examples/Makefile b/examples/Makefile deleted file mode 100644 index b9128fd..0000000 --- a/examples/Makefile +++ /dev/null @@ -1,10 +0,0 @@ - -cbio-example: out/gene.table.table.gz - sifter run cbio.yaml --inputs tar=chol_tcga_pan_can_atlas_2018.tar.gz,geneTable=out/gene.table.table.gz - -out/gene.table.table.gz: - sifter run gene-table.yaml - - -chol_tcga_pan_can_atlas_2018.tar.gz: - curl -O http://download.cbioportal.org/chol_tcga_pan_can_atlas_2018.tar.gz diff --git a/examples/bmeg-dictionary b/examples/bmeg-dictionary deleted file mode 160000 index 6edc8d8..0000000 --- a/examples/bmeg-dictionary +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 6edc8d805d08f3230d63660a7cbb1166410c6377 diff --git a/examples/cbio.yaml b/examples/cbio.yaml deleted file mode 100644 index ea36b31..0000000 --- a/examples/cbio.yaml +++ /dev/null @@ -1,144 +0,0 @@ - -class: sifter -name: CBioPortal - -params: - tar: "" - geneTable: "" - schema: bmeg-dictionary/gdcdictionary/schemas - -inputs: - untar: - plugin: - commandLine: tar -xzf {{params.tar}} - - patientReader: - tableLoad: - input: data_clinical_patient.txt - - sampleReader: - tableLoad: - input: data_clinical_sample.txt - - rnaReader: - transposeLoad: - input: data_RNA_Seq_expression_median.txt - rowSkip: 1 - - mutationReader: - tableLoad: - input: data_mutations_extended.txt - -pipelines: - cases: - - from: patientReader - - project: - mapping: - id: "{{row.PATIENT_ID}}" - submitter_id: "{{row.PATIENT_ID}}" - type: "case" - experiments: - submitter_id: "TCGA" - - objectValidate: - title: Case - schema: "{{params.schema}}" - - emit: - name: case - - samples: - - from: sampleReader - - project: - mapping: - id: "{{row.SAMPLE_ID}}" - submitter_id: "{{row.SAMPLE_ID}}" - cases: - submitter_id: "{{row.PATIENT_ID}}" - type: "sample" - - objectValidate: - title: Sample - schema: "{{params.schema}}" - - emit: - name: sample - - aliquots: - - from: sampleReader - - project: - mapping: - id: "{{row.SAMPLE_ID}}-0000" - submitter_id: "{{row.SAMPLE_ID}}-0000" - samples: - submitter_id: "{{row.SAMPLE_ID}}" - type: "aliquot" - - objectValidate: - title: Aliquot - schema: "{{params.schema}}" - - emit: - name: aliquot - - gene_expression: - - from: rnaReader - - project: - mapping: - id: "gexp:{{row.Entrez_Gene_Id}}" - aliquot_id: "{{row.Entrez_Gene_Id}}-0000" - - lookup: - tsv: - input: "{{params.geneTable}}" - lookup: "{{row.Entrez_Gene_Id}}" - - map: - method: nodeMap - python: | - def nodeMap(x): - values = {} - for k, v in x.items(): - if k not in ["id", "aliquot_id", "Entrez_Gene_Id"]: - values[k] = v - return { - "id": x["id"], - "aliquot_id": x["aliquot_id"], - "metric": "OTHER", - "values": values - } - - emit: - name: gene_expression - - mutations: - - from: mutationReader - - map: - method: alleleID - python: | - import hashlib - def alleleID(row): - s = "GRCh37" + row["Chromosome"] + str(row["Start_Position"]) + str(row["End_Position"]) + row["Reference_Allele"] + row["Tumor_Seq_Allele1"] - row["allele_id"] = "Allele:" + hashlib.sha1(s.encode()).hexdigest() - return row - - project: - mapping: - aliquot: "{{row.Tumor_Sample_Barcode}}-0000" - ref: "{{row.Reference_Allele}}" - alt: "{{row.Tumor_Seq_Allele1}}" - ensembl_transcript: "{{row.Transcript_ID}}" - - objectValidate: - title: SomaticVariant - schema: "{{params.schema}}" - - emit: - name: somatic_variant - - alleles: - - from: mutationReader - - project: - mapping: - genome: "{{row.NCBI_Build}}" - chromosome: "{{row.Chromosome}}" - start: "{{row.Start_Position}}" - end: "{{row.End_Position}}" - strand: "{{row.Strand}}" - reference_bases: "{{row.Reference_Allele}}" - alternate_bases: "{{row.Tumor_Seq_Allele1}}" - hugo_symbol: "{{row.Hugo_Symbol}}" - effect: "{{row.Variant_Classification}}" - - objectValidate: - title: Allele - schema: "{{params.schema}}" - - emit: - name: allele diff --git a/examples/gdc-convert.yaml b/examples/gdc-convert.yaml deleted file mode 100644 index c5c16ee..0000000 --- a/examples/gdc-convert.yaml +++ /dev/null @@ -1,98 +0,0 @@ - - -class: sifter -name: GDCConvert - -params: - schema: - type: path - default: bmeg-dictionary/gdcdictionary/schemas - -inputs: - projects_scrape: - plugin: - commandLine: docker run --rm bmeg/sifter-gdc-scan /opt/gdc-scan.py projects - cases_scrape: - plugin: - commandLine: docker run --rm bmeg/sifter-gdc-scan /opt/gdc-scan.py cases - projects_data: - jsonLoad: - input: out.projects.json - cases_data: - jsonLoad: - input: out.case.json - -pipelines: - projects: - - from: projects_data - - project: - mapping: - code: "{{row.project_id}}" - programs: "{{row.program.name}}" - - objectValidate: - title: project - schema: "{{params.schema}}" - - emit: - name: project - - experiments: - - from: projects_data - - project: - mapping: - code: "{{row.project_id}}" - programs: "{{row.program.name}}" - submitter_id: "{{row.program.name}}" - projects: "{{row.project_id}}" - type: experiment - - objectValidate: - title: experiment - schema: "{{params.schema}}" - - emit: - name: experiment - - cases: - - from: cases_data - - project: - mapping: - studies: "{{row.project.project_id}}" - experiments: "exp:{{row.project.project_id}}" - type: case - - objectValidate: - title: case - schema: "{{params.schema}}" - - emit: - name: case - - samples: - - from: cases_data - - fieldProcess: - field: samples - - project: - mapping: - type: sample - id: "{{row.sample_id}}" - - objectValidate: - title: sample - schema: "{{params.schema}}" - - emit: - name: sample - - aliquots: - - from: cases_data - - fieldProcess: - field: samples - - fieldProcess: - field: portions - - fieldProcess: - field: analytes - - fieldProcess: - field: aliquots - - project: - mapping: - type: aliquot - id: "{{row.aliquot_id}}" - - objectValidate: - title: aliquot - schema: "{{params.schema}}" - - emit: - name: aliquot diff --git a/examples/gdc-scan-docker/Dockerfile b/examples/gdc-scan-docker/Dockerfile deleted file mode 100644 index 39236f7..0000000 --- a/examples/gdc-scan-docker/Dockerfile +++ /dev/null @@ -1,4 +0,0 @@ -FROM python:3.7 - -RUN pip install requests -ADD gdc-scan.py /opt/ diff --git a/examples/gdc-scan-docker/gdc-scan.py b/examples/gdc-scan-docker/gdc-scan.py deleted file mode 100755 index b9a4cf2..0000000 --- a/examples/gdc-scan-docker/gdc-scan.py +++ /dev/null @@ -1,134 +0,0 @@ -#!/usr/bin/env python - -import json -import logging -import os -import sys - -import requests - -URL_BASE = "https://api.gdc.cancer.gov/" - -client = requests - -def query_gdc(endpoint, params): - """ - query_gdc makes a query to the GDC API while handling common issues - like pagination, retries, etc. - - The return value is an iterator. - """ - # Copy input params to avoid modification. - params = dict(params) - page_size = 100 - params['size'] = page_size - # With a GET request, the filters parameter needs to be converted - # from a dictionary to JSON-formatted string - if 'filters' in params: - params['filters'] = json.dumps(params['filters']) - - # Iterate through all the pages. - while True: - try: - req = client.get(URL_BASE + endpoint, params=params) - data = req.json() - data = data['data'] - - hits = data.get("hits", []) - if len(hits) == 0: - return - - for hit in hits: - yield hit - - # Get the next page. - params['from'] = data['pagination']['from'] + page_size - except Exception as e: - logging.warning(str(e)) - logging.warning(json.dumps(params)) - raise - - -# The GDC API requires you to request that nested fields be expanded. -# https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_A_Available_Fields/#cases-field-groups -# -# Note that (as of this writing) we are expanding most but -# not all possible fields. Mostly we're skipping "files" data. -expand_case_fields = ",".join(""" -demographic -diagnoses -diagnoses.treatments -exposures -family_histories -project -project.program -samples -samples.annotations -samples.portions -samples.portions.analytes -samples.portions.analytes.aliquots -samples.portions.analytes.aliquots.annotations -samples.portions.analytes.aliquots.center -samples.portions.analytes.annotations -samples.portions.annotations -samples.portions.center -samples.portions.slides -samples.portions.slides.annotations -summary -summary.data_categories -summary.experimental_strategies -tissue_source_site -type -""".strip().split()) - -# These are the fields we want to keep from the GDC Case (BMEG Case). -keep_case_fields = """ -diagnoses -demographic -disease_type -primary_site -summary -project -""".strip().split() - -expand_project_fields = ",".join(""" -dbgap_accession_number -disease_type -name -primary_site -project_id -released -state -program -summary -""".strip().split()) - - -def scrapeProjects(): - projectOut = open("out.projects.json", "w") - for row in query_gdc("projects", {"expand": expand_project_fields}): - projectOut.write(json.dumps(row)) - projectOut.write("\n") - projectOut.close() - - -def scrapeCases(): - # Crawl all cases, samples, aliquots to generate - # BMEG Cases, Samples, and Aliquots. - parameters={} - parameters['expand'] = expand_case_fields - case_gids = [] - caseOut = open("out.case.json", "w") - - for row in query_gdc("cases", parameters): - caseOut.write(json.dumps(row)) - caseOut.write("\n") - - caseOut.close() - - -if __name__ == "__main__": - if sys.argv[1] == "projects": - scrapeProjects() - if sys.argv[1] == "cases": - scrapeCases() diff --git a/examples/gene-table.yaml b/examples/gene-table.yaml deleted file mode 100644 index 5126308..0000000 --- a/examples/gene-table.yaml +++ /dev/null @@ -1,31 +0,0 @@ - -class: sifter -name: gene-table - -params: - geneTSV: ftp://ftp.ncbi.nih.gov/gene/DATA/gene2ensembl.gz - -inputs: - geneReader: - tableLoad: - input: "{{params.geneTSV}}" - columns: - - tax_id - - GeneID - - Ensembl_gene_identifier - - RNA_nucleotide_accession.version - - Ensembl_rna_identifier - - protein_accession.version - - Ensembl_protein_identifier - -pipelines: - transform: - - from: geneReader - - filter: - field: tax_id - match: "9606" - - tableWrite: - output: gene.table - columns: - - GeneID - - Ensembl_gene_identifier diff --git a/examples/genome.yaml b/examples/genome.yaml deleted file mode 100644 index 510ee81..0000000 --- a/examples/genome.yaml +++ /dev/null @@ -1,92 +0,0 @@ - -class: sifter -name: RefGenome - -params: - gtfPath: ftp://ftp.ensembl.org/pub/grch37/release-96/gff3/homo_sapiens/Homo_sapiens.GRCh37.87.gff3.gz - schema: ./bmeg-dictionary/gdcdictionary/schemas - -inputs: - gtfReader: - tableLoad: - input: "{{params.gtfPath}}" - columns: - - seqid - - source - - type - - start - - end - - score - - strand - - phase - - attributes - -pipelines: - transform: - - from: gtfReader - - fieldParse: - field: attributes - sep: ";" - - fieldType: - start: integer - end: integer - - exons: - - from: transform - - filter: - field: type - match: exon - - regexReplace: - field: Parent - regex: "^transcript:" - replace: "" - dst: transcript_id - - project: - mapping: - exon_id: "{{row.exon_id}}" - transcript_id: ["{{row.transcript_id}}"] - - reduce: - field: exon_id - method: merge - python: | - def merge(x, y): - x['transcript_id'] = x['transcript_id'] + y['transcript_id'] - return x - - objectValidate: - title: exon - schema: "{{params.schema}}" - - emit: - name: exon - - genes: - - from: transform - - filter: - field: type - match: gene - - project: - mapping: - gene_id: "{{row.gene_id}}" - - objectValidate: - title: gene - schema: "{{params.schema}}" - - emit: - name: gene - - transcripts: - - from: transform - - filter: - field: type - match: mRNA - - regexReplace: - field: Parent - regex: "^gene:" - replace: "" - dst: gene_id - - project: - mapping: - transcript_id: "{{row.transcript_id}}" - - objectValidate: - title: transcript - schema: "{{params.schema}}" - - emit: - name: transcript diff --git a/examples/hugo-ensembl.yaml b/examples/hugo-ensembl.yaml deleted file mode 100644 index 295f68d..0000000 --- a/examples/hugo-ensembl.yaml +++ /dev/null @@ -1,25 +0,0 @@ - -class: sifter -name: hugo-ensembl - -params: - hugoJSON: ftp://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/locus_types/gene_with_protein_product.json - -inputs: - hugoReader: - jsonLoad: - input: "{{params.hugoJSON}}" - -pipelines: - transform: - - from: hugoReader - - fieldProcess: - field: response.docs - - filter: - field: ensembl_gene_id - check: exists - - tableWrite: - output: hugo-ensembl.table - columns: - - symbol - - ensembl_gene_id diff --git a/sifter-view/components/PlaybookFlow.tsx b/sifter-view/components/PlaybookFlow.tsx index f419dc6..da0f613 100644 --- a/sifter-view/components/PlaybookFlow.tsx +++ b/sifter-view/components/PlaybookFlow.tsx @@ -24,8 +24,9 @@ import type { Node, Edge } from '@xyflow/react'; // Types for the Sifter playbook JSON (imported as a static module) // ------------------------------------------------------------------- interface Playbook { - class: string; + class?: string; name?: string; + outdir: string; inputs: Record; outputs?: Record; pipelines: Record; @@ -37,84 +38,51 @@ type PipelineStep = Record; // each step is a single‑key object var playbook : Playbook = { - "class": "sifter", "inputs": { - "cases_data": { - "jsonLoad": { - "input": "out.case.json" + "caseData": { + "json": { + "path": "{{params.cases}}" } - }, - "cases_scrape": { - "plugin": { - "commandLine": "docker run --rm bmeg/sifter-gdc-scan /opt/gdc-scan.py cases" - } - }, - "projects_data": { - "jsonLoad": { - "input": "out.projects.json" + } + }, + "name": "gdc", + "outdir": "output/", + "outputs": { + "caseFile": { + "json": { + "from": "caseObject", + "path": "gdc.caseObject.case.json.gz" } }, - "projects_scrape": { - "plugin": { - "commandLine": "docker run --rm bmeg/sifter-gdc-scan /opt/gdc-scan.py projects" + "caseGraph": { + "graph": { + "EdgeFix": { + "gpython": { + "$ref": "test.py" + }, + "method": "test" + }, + "from": "caseObject", + "path": "gdc.caseGraph", + "schema": "{{params.schema}}", + "title": "Case" } } }, - "name": "GDCConvert", "params": { + "cases": { + "default": "../../resources/gdc-case.json.gz", + "type": "file" + }, "schema": { - "default": "bmeg-dictionary/gdcdictionary/schemas", + "default": "../../resources/schemas", "type": "path" } }, "pipelines": { - "aliquots": [ - { - "from": "cases_data" - }, - { - "fieldProcess": { - "field": "samples" - } - }, - { - "fieldProcess": { - "field": "portions" - } - }, - { - "fieldProcess": { - "field": "analytes" - } - }, - { - "fieldProcess": { - "field": "aliquots" - } - }, - { - "project": { - "mapping": { - "id": "{{row.aliquot_id}}", - "type": "aliquot" - } - } - }, - { - "objectValidate": { - "schema": "{{params.schema}}", - "title": "aliquot" - } - }, - { - "emit": { - "name": "aliquot" - } - } - ], - "cases": [ + "caseObject": [ { - "from": "cases_data" + "from": "caseData" }, { "project": { @@ -128,92 +96,7 @@ var playbook : Playbook = { { "objectValidate": { "schema": "{{params.schema}}", - "title": "case" - } - }, - { - "emit": { - "name": "case" - } - } - ], - "experiments": [ - { - "from": "projects_data" - }, - { - "project": { - "mapping": { - "code": "{{row.project_id}}", - "programs": "{{row.program.name}}", - "projects": "{{row.project_id}}", - "submitter_id": "{{row.program.name}}", - "type": "experiment" - } - } - }, - { - "objectValidate": { - "schema": "{{params.schema}}", - "title": "experiment" - } - }, - { - "emit": { - "name": "experiment" - } - } - ], - "projects": [ - { - "from": "projects_data" - }, - { - "project": { - "mapping": { - "code": "{{row.project_id}}", - "programs": "{{row.program.name}}" - } - } - }, - { - "objectValidate": { - "schema": "{{params.schema}}", - "title": "project" - } - }, - { - "emit": { - "name": "project" - } - } - ], - "samples": [ - { - "from": "cases_data" - }, - { - "fieldProcess": { - "field": "samples" - } - }, - { - "project": { - "mapping": { - "id": "{{row.sample_id}}", - "type": "sample" - } - } - }, - { - "objectValidate": { - "schema": "{{params.schema}}", - "title": "sample" - } - }, - { - "emit": { - "name": "sample" + "title": "Case" } } ] diff --git a/test/resources/xml_load.yaml b/test/resources/xml_load.yaml index e162d2c..9683d67 100644 --- a/test/resources/xml_load.yaml +++ b/test/resources/xml_load.yaml @@ -6,9 +6,8 @@ inputs: type: File default: test.xml -steps: - - xmlLoad: - input: "{{inputs.xml}}" - transform: - - emit: - name: output \ No newline at end of file +outputs: + jsonXml: + json: + from: xml + From 7646081d3c41f86eec6efc7bffacb3f6b8a0425c Mon Sep 17 00:00:00 2001 From: Kyle Ellrott Date: Thu, 19 Feb 2026 13:05:56 -0800 Subject: [PATCH 05/14] Working on display of pipelines --- sifter-view/app/globals.css | 12 + sifter-view/components/PlaybookFlow.tsx | 326 +++--- sifter-view/components/PlaybookViewer.tsx | 19 +- sifter-view/lib/playbookApi.ts | 279 +++++ sifter-view/package-lock.json | 1224 +++++++++++++++++++-- 5 files changed, 1638 insertions(+), 222 deletions(-) create mode 100644 sifter-view/lib/playbookApi.ts diff --git a/sifter-view/app/globals.css b/sifter-view/app/globals.css index a2dc41e..2e8d4fd 100644 --- a/sifter-view/app/globals.css +++ b/sifter-view/app/globals.css @@ -24,3 +24,15 @@ body { color: var(--foreground); font-family: Arial, Helvetica, sans-serif; } + +.react-flow { + --xy-node-color: #000; + --xy-node-color-default: #000; +} + +.react-flow__node-input, +.react-flow__node-default, +.react-flow__node-output, +.react-flow__node-group { + color: #000; +} diff --git a/sifter-view/components/PlaybookFlow.tsx b/sifter-view/components/PlaybookFlow.tsx index da0f613..d9e0902 100644 --- a/sifter-view/components/PlaybookFlow.tsx +++ b/sifter-view/components/PlaybookFlow.tsx @@ -1,6 +1,6 @@ 'use client'; -import React, { useCallback, useEffect } from 'react'; +import React, { memo, useCallback, useEffect, useMemo, useState } from 'react'; import { ReactFlow, @@ -9,6 +9,7 @@ import { addEdge, Background, Controls, + NodeProps, OnConnect, Connection } from "@xyflow/react"; @@ -18,162 +19,195 @@ import "@xyflow/react/dist/style.css"; import dagre from 'dagre'; import type { Node, Edge } from '@xyflow/react'; +import { getPlaybook, type Playbook } from '@/lib/playbookApi'; -// ------------------------------------------------------------------- -// Types for the Sifter playbook JSON (imported as a static module) -// ------------------------------------------------------------------- -interface Playbook { - class?: string; - name?: string; - outdir: string; - inputs: Record; - outputs?: Record; - pipelines: Record; - params?: any; -} - -type PipelineStep = Record; // each step is a single‑key object +type PipelineNodeData = { + label: string; + steps: string[]; +}; +const BASE_NODE_WIDTH = 170; +const BASE_NODE_HEIGHT = 44; +const PIPELINE_NODE_WIDTH = 260; +const PIPELINE_CELL_HEIGHT = 34; +const PIPELINE_HEADER_HEIGHT = 36; +const PipelineStackNode = memo(function PipelineStackNode({ data }: NodeProps) { + const typedData = data as PipelineNodeData; + const steps = typedData?.steps ?? []; -var playbook : Playbook = { - "inputs": { - "caseData": { - "json": { - "path": "{{params.cases}}" - } - } - }, - "name": "gdc", - "outdir": "output/", - "outputs": { - "caseFile": { - "json": { - "from": "caseObject", - "path": "gdc.caseObject.case.json.gz" - } - }, - "caseGraph": { - "graph": { - "EdgeFix": { - "gpython": { - "$ref": "test.py" - }, - "method": "test" - }, - "from": "caseObject", - "path": "gdc.caseGraph", - "schema": "{{params.schema}}", - "title": "Case" - } - } - }, - "params": { - "cases": { - "default": "../../resources/gdc-case.json.gz", - "type": "file" - }, - "schema": { - "default": "../../resources/schemas", - "type": "path" - } - }, - "pipelines": { - "caseObject": [ - { - "from": "caseData" - }, - { - "project": { - "mapping": { - "experiments": "exp:{{row.project.project_id}}", - "studies": "{{row.project.project_id}}", - "type": "case" - } - } - }, - { - "objectValidate": { - "schema": "{{params.schema}}", - "title": "Case" - } - } - ] - } -} - + return ( +
+
+ {typedData.label} +
+ {steps.map((step: string, index: number) => ( +
+ {index + 1}. {step} +
+ ))} +
+ ); +}); // ------------------------------------------------------------------- // Build a React‑Flow graph from a Playbook, using Dagre for layout // ------------------------------------------------------------------- -const NODE_WIDTH = 150; -const NODE_HEIGHT = 40; +function getOutputSourcePipeline(outputDefinition: Record): string | undefined { + for (const value of Object.values(outputDefinition)) { + if (value && typeof value === 'object' && typeof value.from === 'string') { + return value.from; + } + } + return undefined; +} function buildGraph(pb: Playbook): { nodes: Node[]; edges: Edge[] } { // Create a directed Dagre graph const g = new dagre.graphlib.Graph({ directed: true }); - //g.setGraph({ rankdir: 'LR', nodesep: 80, ranksep: 120 }); - g.setGraph({}); + g.setGraph({ rankdir: 'LR', nodesep: 60, ranksep: 100 }); g.setDefaultEdgeLabel(function() { return {}; }); // ---- INPUT NODES --------------------------------------------------- Object.keys(pb.inputs).forEach((name) => { const id = `input-${name}`; - g.setNode(id, { label: name, width: NODE_WIDTH, height: NODE_HEIGHT }); + g.setNode(id, { + label: name, + width: BASE_NODE_WIDTH, + height: BASE_NODE_HEIGHT, + nodeType: 'default', + nodeData: { label: `INPUT · ${name}` }, + }); }); // ---- OUTPUT NODES --------------------------------------------------- if (pb.outputs) { Object.keys(pb.outputs).forEach((name) => { const id = `output-${name}`; - g.setNode(id, { label: name, width: NODE_WIDTH, height: NODE_HEIGHT }); + g.setNode(id, { + label: name, + width: BASE_NODE_WIDTH, + height: BASE_NODE_HEIGHT, + nodeType: 'default', + nodeData: { label: `OUTPUT · ${name}` }, + }); }); } - // ---- PIPELINE STEP NODES & EDGES ----------------------------------- + // ---- PIPELINE NODES -------------------------------------------------- Object.entries(pb.pipelines).forEach(([pipelineName, steps]) => { - steps.forEach((stepObj, idx) => { - const stepKey = Object.keys(stepObj)[0]; // e.g. "from", "fieldProcess", "emit", … - const nodeId = `${pipelineName}-${idx}`; - g.setNode(nodeId, { label: stepKey, width: NODE_WIDTH, height: NODE_HEIGHT }); - - // Edge from previous step (if any) - if (idx > 0) { - const prevId = `${pipelineName}-${idx - 1}`; - g.setEdge(prevId, nodeId); - } else { - // First step – connect to the input referenced by the "from" field - const fromName = (stepObj as any).from; - if (fromName) { - g.setEdge(`input-${fromName}`, nodeId); - } + const stepLabels = steps.map((stepObj) => Object.keys(stepObj)[0]); + const nodeHeight = PIPELINE_HEADER_HEIGHT + Math.max(1, stepLabels.length) * PIPELINE_CELL_HEIGHT; + + g.setNode(pipelineName, { + label: pipelineName, + width: PIPELINE_NODE_WIDTH, + height: nodeHeight, + nodeType: 'pipeline', + nodeData: { label: pipelineName, steps: stepLabels }, + }); + + const firstStep = steps[0] as any; + const fromName = firstStep?.from; + if (fromName) { + if (pb.inputs?.[fromName]) { + g.setEdge(`input-${fromName}`, pipelineName); + } else if (pb.pipelines?.[fromName]) { + g.setEdge(fromName, pipelineName); } + } - // If this step is an emit and an explicit output exists, connect to it - if (stepKey === 'emit' && pb.outputs) { - const emitName = (stepObj as any).emit?.name; - if (emitName && pb.outputs[emitName]) { - g.setEdge(nodeId, `output-${emitName}`); + if (pb.outputs) { + steps.forEach((stepObj) => { + const stepKey = Object.keys(stepObj)[0]; + if (stepKey === 'emit') { + const emitName = (stepObj as any).emit?.name; + if (emitName && pb.outputs?.[emitName]) { + g.setEdge(pipelineName, `output-${emitName}`); + } } + }); + } + }); + + if (pb.outputs) { + Object.entries(pb.outputs).forEach(([outputName, outputDefinition]) => { + const sourcePipeline = getOutputSourcePipeline(outputDefinition); + if (sourcePipeline && pb.pipelines?.[sourcePipeline]) { + g.setEdge(sourcePipeline, `output-${outputName}`); } }); - }); + } // Run the layout algorithm dagre.layout(g); // Convert Dagre nodes/edges to React‑Flow structures const nodes: Node[] = g.nodes().map((id) => { - const { x, y, label } = g.node(id); + const nodeDefinition = g.node(id) as { + x: number; + y: number; + width: number; + height: number; + label?: string; + nodeType?: string; + nodeData?: Record; + }; + + const { x, y, label, width, height, nodeType, nodeData } = nodeDefinition; + const isInputNode = id.startsWith('input-'); + const isOutputNode = id.startsWith('output-'); + return { id, - position: { x, y }, - data: { label }, - // Optional: give each node a consistent size for the UI - style: { width: NODE_WIDTH, height: NODE_HEIGHT }, + position: { x: x - width / 2, y: y - height / 2 }, + data: nodeData ?? { label }, + type: nodeType ?? 'default', + style: nodeType === 'pipeline' + ? undefined + : { + width: BASE_NODE_WIDTH, + height: BASE_NODE_HEIGHT, + color: '#000', + fontWeight: 600, + borderWidth: 2, + borderStyle: 'solid', + borderColor: isInputNode ? '#3b82f6' : isOutputNode ? '#16a34a' : '#999', + backgroundColor: isInputNode ? '#eff6ff' : isOutputNode ? '#f0fdf4' : '#fff', + }, } as Node; }); @@ -193,26 +227,72 @@ function buildGraph(pb: Playbook): { nodes: Node[]; edges: Edge[] } { export default function PlaybookFlow() { + const [nodes, setNodes, onNodesChange] = useNodesState([]); + const [edges, setEdges, onEdgesChange] = useEdgesState([]); + const [isLoading, setIsLoading] = useState(true); + const [loadError, setLoadError] = useState(null); + const nodeTypes = useMemo(() => ({ pipeline: PipelineStackNode }), []); - - var initialGraph = buildGraph(playbook); + useEffect(() => { + let isMounted = true; + + const loadPlaybook = async () => { + try { + setLoadError(null); + setIsLoading(true); + const playbook = await getPlaybook(); + const graph = buildGraph(playbook); + if (!isMounted) { + return; + } + setNodes(graph.nodes); + setEdges(graph.edges); + } catch (error) { + if (!isMounted) { + return; + } + setLoadError(error instanceof Error ? error.message : 'Failed to load playbook'); + } finally { + if (isMounted) { + setIsLoading(false); + } + } + }; - var initialEdges: Edge[] = initialGraph.edges; - var initialNodes: Node[] = initialGraph.nodes; + void loadPlaybook(); - const [nodes, setNodes, onNodesChange] = useNodesState(initialNodes); - const [edges, setEdges, onEdgesChange] = useEdgesState(initialEdges); + return () => { + isMounted = false; + }; + }, [setEdges, setNodes]); - const onConnect: OnConnect = useCallback( - (connection: Connection) => setEdges((edges) => addEdge(connection, edges)), - [setEdges] + const onConnect: OnConnect = useCallback( + (connection: Connection) => setEdges((currentEdges) => addEdge(connection, currentEdges)), + [setEdges] + ); + + if (loadError) { + return ( +
+ Failed to load playbook: {loadError} +
+ ); + } + + if (isLoading) { + return ( +
+ Loading playbook... +
); + } return (
{ - fetch("/api/playbooks") - .then((res) => { - if (!res.ok) throw new Error("Failed to fetch playbook list"); - return res.json(); - }) + getPlaybooks() .then((data: PlaybookList) => setPlaybooks(data)) .catch((err) => console.error(err)); }, []); @@ -26,12 +25,8 @@ export default function PlaybookViewer(_: PlaybookViewerProps) { // Load selected playbook content const loadPlaybook = (name: string) => { setSelected(name); - fetch(`/api/playbook?name=${encodeURIComponent(name)}`) - .then((res) => { - if (!res.ok) throw new Error("Playbook not found"); - return res.text(); - }) - .then((txt) => setContent(txt)) + getPlaybook(name) + .then((playbook) => setContent(JSON.stringify(playbook, null, 2))) .catch((err) => console.error(err)); }; @@ -69,7 +64,7 @@ export default function PlaybookViewer(_: PlaybookViewerProps) { {/* Content */}
-          
+          
             {content || "Select a playbook to view its content"}
           
         
diff --git a/sifter-view/lib/playbookApi.ts b/sifter-view/lib/playbookApi.ts new file mode 100644 index 0000000..84be7bc --- /dev/null +++ b/sifter-view/lib/playbookApi.ts @@ -0,0 +1,279 @@ +type PipelineStep = Record; + +export interface Playbook { + class?: string; + name?: string; + outdir?: string; + inputs: Record; + outputs?: Record; + pipelines: Record; + params?: any; +} + +const STUB_PLAYBOOK: Playbook = { + class: 'sifter', + inputs: { + caseData: { + jsonLoad: { + input: '{{params.cases}}', + }, + }, + }, + name: 'gdc', + outputs: { + aliquot: { + json: { + from: 'aliquotObject', + path: 'aliquot.json', + }, + }, + case: { + json: { + from: 'caseObject', + path: 'case.json', + }, + }, + project: { + json: { + from: 'projectObject', + path: 'project.json', + }, + }, + sample: { + json: { + from: 'sampleObject', + path: 'sample.json', + }, + }, + table: { + csv: { + from: 'aliquotAlias', + path: 'aliquot.table.csv', + }, + }, + }, + params: { + cases: { + default: 'cases.json', + type: 'path', + }, + schema: { + default: 'schema', + type: 'path', + }, + }, + pipelines: { + aliquotAlias: [ + { + from: 'aliquotData', + }, + { + clean: { + fields: ['aliquot_id', 'submitter_id', 'project_id'], + }, + }, + ], + aliquotData: [ + { + from: 'sampleData', + }, + { + fieldProcess: { + field: 'portions', + mapping: { + project_id: '{{row.project_id}}', + sample: '{{row.sample_id}}', + }, + }, + }, + { + fieldProcess: { + field: 'analytes', + mapping: { + project_id: '{{row.project_id}}', + sample: '{{row.sample}}', + }, + }, + }, + { + fieldProcess: { + field: 'aliquots', + mapping: { + project_id: '{{row.project_id}}', + sample: '{{row.sample}}', + }, + }, + }, + { + project: { + mapping: { + id: '{{row.aliquot_id}}', + type: 'aliquot', + }, + }, + }, + ], + aliquotObject: [ + { + from: 'aliquotData', + }, + { + project: { + mapping: { + sample: [{ id: '{{row.sample}}' }], + }, + }, + }, + { + objectValidate: { + schema: '{{params.schema}}', + title: 'Aliquot', + }, + }, + ], + caseObject: [ + { + from: 'caseData', + }, + { + project: { + mapping: { + experiments: 'exp:{{row.project.project_id}}', + project_id: '{{row.project.project_id}}', + projects: [{ id: 'project/{{row.project.project_id}}' }], + studies: '{{row.project.project_id}}', + type: 'case', + }, + }, + }, + { + map: { + gpython: + '\ndef fix(x):\n samples = []\n for s in x.get(\'samples\', []):\n samples.append({"id":s["sample_id"]})\n x[\'samples\'] = samples\n return x\n', + method: 'fix', + }, + }, + { + objectValidate: { + schema: '{{params.schema}}', + title: 'Case', + }, + }, + ], + projectObject: [ + { + from: 'caseObject', + }, + { + distinct: { + value: '{{row.project_id}}', + }, + }, + { + project: { + mapping: { + id: '{{row.project_id}}', + submitter_id: '{{row.project_id}}', + type: 'project', + }, + }, + }, + { + clean: { + fields: ['id', 'project_id', 'submitter_id', 'type'], + }, + }, + { + objectValidate: { + schema: '{{params.schema}}', + title: 'Project', + }, + }, + ], + sampleData: [ + { + from: 'caseData', + }, + { + fieldProcess: { + field: 'samples', + mapping: { + case: '{{row.id}}', + project_id: '{{row.project.project_id}}', + }, + }, + }, + ], + sampleObject: [ + { + from: 'sampleData', + }, + { + project: { + mapping: { + id: '{{row.sample_id}}', + type: 'sample', + }, + }, + }, + { + project: { + mapping: { + case: [{ id: '{{row.case}}' }], + }, + }, + }, + { + objectValidate: { + schema: '{{params.schema}}', + title: 'Sample', + }, + }, + ], + }, +}; + +const STUB_PLAYBOOKS: Record = { + gdc: STUB_PLAYBOOK, + demo: { + ...STUB_PLAYBOOK, + name: 'demo', + }, +}; + +const DEFAULT_PLAYBOOK_NAME = 'gdc'; +const DEFAULT_STUB_LATENCY_MS = 250; + +function getStubLatencyMs(): number { + // Configure stub delay with NEXT_PUBLIC_PLAYBOOK_STUB_LATENCY_MS (defaults to 250ms). + const rawValue = process.env.NEXT_PUBLIC_PLAYBOOK_STUB_LATENCY_MS; + if (!rawValue) { + return DEFAULT_STUB_LATENCY_MS; + } + + const parsedValue = Number(rawValue); + if (!Number.isFinite(parsedValue) || parsedValue < 0) { + return DEFAULT_STUB_LATENCY_MS; + } + + return parsedValue; +} + +async function sleep(ms: number): Promise { + await new Promise((resolve) => setTimeout(resolve, ms)); +} + +export async function getPlaybooks(): Promise { + await sleep(getStubLatencyMs()); + return Object.keys(STUB_PLAYBOOKS); +} + +export async function getPlaybook(name: string = DEFAULT_PLAYBOOK_NAME): Promise { + await sleep(getStubLatencyMs()); + const playbook = STUB_PLAYBOOKS[name]; + if (!playbook) { + throw new Error(`Playbook not found: ${name}`); + } + + return structuredClone(playbook); +} diff --git a/sifter-view/package-lock.json b/sifter-view/package-lock.json index fc437f4..6926b3c 100644 --- a/sifter-view/package-lock.json +++ b/sifter-view/package-lock.json @@ -263,6 +263,39 @@ "node": ">=6.9.0" } }, + "node_modules/@emnapi/core": { + "version": "1.8.1", + "resolved": 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"version": "1.30.2", + "resolved": "https://registry.npmjs.org/lightningcss-win32-x64-msvc/-/lightningcss-win32-x64-msvc-1.30.2.tgz", + "integrity": "sha512-5g1yc73p+iAkid5phb4oVFMB45417DkRevRbt/El/gKXJk4jid+vPFF/AXbxn05Aky8PapwzZrdJShv5C0avjw==", + "cpu": [ + "x64" + ], + "dev": true, + "license": "MPL-2.0", + "optional": true, + "os": [ + "win32" + ], + "engines": { + "node": ">= 12.0.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/parcel" + } + }, "node_modules/locate-path": { "version": "6.0.0", "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-6.0.0.tgz", From 02021a8379ff003df92fe9596579d7c54e75caf2 Mon Sep 17 00:00:00 2001 From: Kyle Ellrott Date: Thu, 19 Feb 2026 13:21:58 -0800 Subject: [PATCH 06/14] Working on making the UI represent the playbook correctly --- sifter-view/components/PlaybookFlow.tsx | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/sifter-view/components/PlaybookFlow.tsx b/sifter-view/components/PlaybookFlow.tsx index d9e0902..c843278 100644 --- a/sifter-view/components/PlaybookFlow.tsx +++ b/sifter-view/components/PlaybookFlow.tsx @@ -9,6 +9,8 @@ import { addEdge, Background, Controls, + Handle, + Position, NodeProps, OnConnect, Connection @@ -40,6 +42,7 @@ const PipelineStackNode = memo(function PipelineStackNode({ data }: NodeProps + +
{ - const stepKey = Object.keys(stepObj)[0]; - if (stepKey === 'emit') { - const emitName = (stepObj as any).emit?.name; - if (emitName && pb.outputs?.[emitName]) { - g.setEdge(pipelineName, `output-${emitName}`); - } - } - }); - } }); if (pb.outputs) { @@ -196,6 +189,8 @@ function buildGraph(pb: Playbook): { nodes: Node[]; edges: Edge[] } { position: { x: x - width / 2, y: y - height / 2 }, data: nodeData ?? { label }, type: nodeType ?? 'default', + targetPosition: Position.Left, + sourcePosition: Position.Right, style: nodeType === 'pipeline' ? undefined : { @@ -216,6 +211,10 @@ function buildGraph(pb: Playbook): { nodes: Node[]; edges: Edge[] } { source: e.v, target: e.w, animated: true, + style: { + stroke: '#64748b', + strokeWidth: 2.5, + }, })); return { nodes, edges }; @@ -288,7 +287,7 @@ export default function PlaybookFlow() { } return ( -
+
Date: Thu, 19 Feb 2026 14:04:16 -0800 Subject: [PATCH 07/14] Adding framework for custom rendering of pipeline steps in graph view --- sifter-view/components/PlaybookFlow.tsx | 40 +++++------ .../playbook-steps/cells/BaseStepCell.tsx | 45 ++++++++++++ .../cells/FieldProcessStepCell.tsx | 10 +++ .../playbook-steps/cells/FromStepCell.tsx | 13 ++++ .../playbook-steps/cells/GenericStepCell.tsx | 7 ++ .../playbook-steps/cells/MapStepCell.tsx | 10 +++ .../cells/ObjectValidateStepCell.tsx | 10 +++ .../playbook-steps/cells/ProjectStepCell.tsx | 10 +++ .../components/playbook-steps/cells/index.ts | 6 ++ .../components/playbook-steps/cells/utils.ts | 22 ++++++ .../components/playbook-steps/registry.tsx | 72 +++++++++++++++++++ .../components/playbook-steps/types.ts | 10 +++ 12 files changed, 235 insertions(+), 20 deletions(-) create mode 100644 sifter-view/components/playbook-steps/cells/BaseStepCell.tsx create mode 100644 sifter-view/components/playbook-steps/cells/FieldProcessStepCell.tsx create mode 100644 sifter-view/components/playbook-steps/cells/FromStepCell.tsx create mode 100644 sifter-view/components/playbook-steps/cells/GenericStepCell.tsx create mode 100644 sifter-view/components/playbook-steps/cells/MapStepCell.tsx create mode 100644 sifter-view/components/playbook-steps/cells/ObjectValidateStepCell.tsx create mode 100644 sifter-view/components/playbook-steps/cells/ProjectStepCell.tsx create mode 100644 sifter-view/components/playbook-steps/cells/index.ts create mode 100644 sifter-view/components/playbook-steps/cells/utils.ts create mode 100644 sifter-view/components/playbook-steps/registry.tsx create mode 100644 sifter-view/components/playbook-steps/types.ts diff --git a/sifter-view/components/PlaybookFlow.tsx b/sifter-view/components/PlaybookFlow.tsx index c843278..4747fa2 100644 --- a/sifter-view/components/PlaybookFlow.tsx +++ b/sifter-view/components/PlaybookFlow.tsx @@ -22,11 +22,13 @@ import "@xyflow/react/dist/style.css"; import dagre from 'dagre'; import type { Node, Edge } from '@xyflow/react'; import { getPlaybook, type Playbook } from '@/lib/playbookApi'; +import { getStepCellComponent } from './playbook-steps/registry'; +import type { PipelineStep } from './playbook-steps/types'; type PipelineNodeData = { label: string; - steps: string[]; + steps: PipelineStep[]; }; const BASE_NODE_WIDTH = 170; @@ -66,22 +68,17 @@ const PipelineStackNode = memo(function PipelineStackNode({ data }: NodeProps {typedData.label}
- {steps.map((step: string, index: number) => ( -
- {index + 1}. {step} -
- ))} + {steps.map((step: PipelineStep, index: number) => { + const CellComponent = getStepCellComponent(step.operation); + return ( + + ); + })}
); }); @@ -134,15 +131,18 @@ function buildGraph(pb: Playbook): { nodes: Node[]; edges: Edge[] } { // ---- PIPELINE NODES -------------------------------------------------- Object.entries(pb.pipelines).forEach(([pipelineName, steps]) => { - const stepLabels = steps.map((stepObj) => Object.keys(stepObj)[0]); - const nodeHeight = PIPELINE_HEADER_HEIGHT + Math.max(1, stepLabels.length) * PIPELINE_CELL_HEIGHT; + const stepData: PipelineStep[] = steps.map((stepObj) => { + const [operation, config] = Object.entries(stepObj)[0] ?? ['unknown', undefined]; + return { operation, config }; + }); + const nodeHeight = PIPELINE_HEADER_HEIGHT + Math.max(1, stepData.length) * PIPELINE_CELL_HEIGHT; g.setNode(pipelineName, { label: pipelineName, width: PIPELINE_NODE_WIDTH, height: nodeHeight, nodeType: 'pipeline', - nodeData: { label: pipelineName, steps: stepLabels }, + nodeData: { label: pipelineName, steps: stepData }, }); const firstStep = steps[0] as any; diff --git a/sifter-view/components/playbook-steps/cells/BaseStepCell.tsx b/sifter-view/components/playbook-steps/cells/BaseStepCell.tsx new file mode 100644 index 0000000..206908e --- /dev/null +++ b/sifter-view/components/playbook-steps/cells/BaseStepCell.tsx @@ -0,0 +1,45 @@ +import type { StepCellProps } from '../types'; +import { toStepLabel } from './utils'; + +const PIPELINE_CELL_HEIGHT = 34; + +type BaseStepCellProps = StepCellProps & { + secondaryText?: string; +}; + +export function BaseStepCell({ step, index, isLast, secondaryText }: BaseStepCellProps) { + return ( +
+
+ {index + 1}. + {step.operation} +
+ {secondaryText ? ( + + {secondaryText} + + ) : null} +
+ ); +} diff --git a/sifter-view/components/playbook-steps/cells/FieldProcessStepCell.tsx b/sifter-view/components/playbook-steps/cells/FieldProcessStepCell.tsx new file mode 100644 index 0000000..59cffca --- /dev/null +++ b/sifter-view/components/playbook-steps/cells/FieldProcessStepCell.tsx @@ -0,0 +1,10 @@ +import type { StepCellProps } from '../types'; +import { isRecord } from './utils'; +import { BaseStepCell } from './BaseStepCell'; + +export function FieldProcessStepCell(props: StepCellProps) { + const config = props.step.config; + const field = isRecord(config) && typeof config.field === 'string' ? config.field : undefined; + + return ; +} diff --git a/sifter-view/components/playbook-steps/cells/FromStepCell.tsx b/sifter-view/components/playbook-steps/cells/FromStepCell.tsx new file mode 100644 index 0000000..cea69fe --- /dev/null +++ b/sifter-view/components/playbook-steps/cells/FromStepCell.tsx @@ -0,0 +1,13 @@ +import type { StepCellProps } from '../types'; +import { isRecord } from './utils'; +import { BaseStepCell } from './BaseStepCell'; + +export function FromStepCell(props: StepCellProps) { + const source = typeof props.step.config === 'string' + ? props.step.config + : isRecord(props.step.config) && typeof props.step.config.from === 'string' + ? props.step.config.from + : undefined; + + return ; +} diff --git a/sifter-view/components/playbook-steps/cells/GenericStepCell.tsx b/sifter-view/components/playbook-steps/cells/GenericStepCell.tsx new file mode 100644 index 0000000..b587fdd --- /dev/null +++ b/sifter-view/components/playbook-steps/cells/GenericStepCell.tsx @@ -0,0 +1,7 @@ +import type { StepCellProps } from '../types'; +import { getStepSummaryValue } from './utils'; +import { BaseStepCell } from './BaseStepCell'; + +export function GenericStepCell(props: StepCellProps) { + return ; +} diff --git a/sifter-view/components/playbook-steps/cells/MapStepCell.tsx b/sifter-view/components/playbook-steps/cells/MapStepCell.tsx new file mode 100644 index 0000000..6fbfcb5 --- /dev/null +++ b/sifter-view/components/playbook-steps/cells/MapStepCell.tsx @@ -0,0 +1,10 @@ +import type { StepCellProps } from '../types'; +import { isRecord } from './utils'; +import { BaseStepCell } from './BaseStepCell'; + +export function MapStepCell(props: StepCellProps) { + const config = props.step.config; + const engine = isRecord(config) && typeof config.engine === 'string' ? config.engine : undefined; + + return ; +} diff --git a/sifter-view/components/playbook-steps/cells/ObjectValidateStepCell.tsx b/sifter-view/components/playbook-steps/cells/ObjectValidateStepCell.tsx new file mode 100644 index 0000000..a649b82 --- /dev/null +++ b/sifter-view/components/playbook-steps/cells/ObjectValidateStepCell.tsx @@ -0,0 +1,10 @@ +import type { StepCellProps } from '../types'; +import { isRecord } from './utils'; +import { BaseStepCell } from './BaseStepCell'; + +export function ObjectValidateStepCell(props: StepCellProps) { + const config = props.step.config; + const schema = isRecord(config) && typeof config.schema === 'string' ? config.schema : undefined; + + return ; +} diff --git a/sifter-view/components/playbook-steps/cells/ProjectStepCell.tsx b/sifter-view/components/playbook-steps/cells/ProjectStepCell.tsx new file mode 100644 index 0000000..3d6d034 --- /dev/null +++ b/sifter-view/components/playbook-steps/cells/ProjectStepCell.tsx @@ -0,0 +1,10 @@ +import type { StepCellProps } from '../types'; +import { isRecord } from './utils'; +import { BaseStepCell } from './BaseStepCell'; + +export function ProjectStepCell(props: StepCellProps) { + const config = props.step.config; + const projectionCount = isRecord(config) ? Object.keys(config).length : undefined; + + return ; +} diff --git a/sifter-view/components/playbook-steps/cells/index.ts b/sifter-view/components/playbook-steps/cells/index.ts new file mode 100644 index 0000000..f6d02dc --- /dev/null +++ b/sifter-view/components/playbook-steps/cells/index.ts @@ -0,0 +1,6 @@ +export { GenericStepCell } from './GenericStepCell'; +export { FromStepCell } from './FromStepCell'; +export { ProjectStepCell } from './ProjectStepCell'; +export { MapStepCell } from './MapStepCell'; +export { FieldProcessStepCell } from './FieldProcessStepCell'; +export { ObjectValidateStepCell } from './ObjectValidateStepCell'; diff --git a/sifter-view/components/playbook-steps/cells/utils.ts b/sifter-view/components/playbook-steps/cells/utils.ts new file mode 100644 index 0000000..d4ba609 --- /dev/null +++ b/sifter-view/components/playbook-steps/cells/utils.ts @@ -0,0 +1,22 @@ +export function isRecord(value: unknown): value is Record { + return value !== null && typeof value === 'object' && !Array.isArray(value); +} + +export function toStepLabel(operation: string): string { + return operation + .replace(/([a-z0-9])([A-Z])/g, '$1 $2') + .replace(/^./, (x) => x.toUpperCase()); +} + +export function getStepSummaryValue(config: unknown): string | undefined { + if (typeof config === 'string' || typeof config === 'number' || typeof config === 'boolean') { + return String(config); + } + if (Array.isArray(config)) { + return `${config.length} items`; + } + if (isRecord(config)) { + return `${Object.keys(config).length} fields`; + } + return undefined; +} \ No newline at end of file diff --git a/sifter-view/components/playbook-steps/registry.tsx b/sifter-view/components/playbook-steps/registry.tsx new file mode 100644 index 0000000..9ef555b --- /dev/null +++ b/sifter-view/components/playbook-steps/registry.tsx @@ -0,0 +1,72 @@ +import type { ComponentType } from 'react'; + +import type { StepCellProps } from './types'; +import { + FieldProcessStepCell, + FromStepCell, + GenericStepCell, + MapStepCell, + ObjectValidateStepCell, + ProjectStepCell, +} from './cells'; + +export type StepCellComponent = ComponentType; + +const STEP_OPERATIONS = [ + 'from', + 'split', + 'fieldParse', + 'fieldType', + 'objectValidate', + 'filter', + 'clean', + 'debug', + 'regexReplace', + 'project', + 'map', + 'plugin', + 'flatmap', + 'reduce', + 'distinct', + 'fieldProcess', + 'dropNull', + 'lookup', + 'intervalIntersect', + 'hash', + 'accumulate', + 'uuid', +] as const; + +type StepOperation = (typeof STEP_OPERATIONS)[number]; + +const OPERATION_CELL_COMPONENTS: Record = { + from: FromStepCell, + split: GenericStepCell, + fieldParse: GenericStepCell, + fieldType: GenericStepCell, + objectValidate: ObjectValidateStepCell, + filter: GenericStepCell, + clean: GenericStepCell, + debug: GenericStepCell, + regexReplace: GenericStepCell, + project: ProjectStepCell, + map: MapStepCell, + plugin: GenericStepCell, + flatmap: GenericStepCell, + reduce: GenericStepCell, + distinct: GenericStepCell, + fieldProcess: FieldProcessStepCell, + dropNull: GenericStepCell, + lookup: GenericStepCell, + intervalIntersect: GenericStepCell, + hash: GenericStepCell, + accumulate: GenericStepCell, + uuid: GenericStepCell, +}; + +export function getStepCellComponent(operation: string): StepCellComponent { + if ((STEP_OPERATIONS as readonly string[]).includes(operation)) { + return OPERATION_CELL_COMPONENTS[operation as StepOperation]; + } + return GenericStepCell; +} diff --git a/sifter-view/components/playbook-steps/types.ts b/sifter-view/components/playbook-steps/types.ts new file mode 100644 index 0000000..cf70e36 --- /dev/null +++ b/sifter-view/components/playbook-steps/types.ts @@ -0,0 +1,10 @@ +export type PipelineStep = { + operation: string; + config: unknown; +}; + +export type StepCellProps = { + step: PipelineStep; + index: number; + isLast: boolean; +}; From 432f9e01302eb46ffea39eeddf27f491cc1aa2f6 Mon Sep 17 00:00:00 2001 From: Kyle Ellrott Date: Thu, 19 Feb 2026 14:53:49 -0800 Subject: [PATCH 08/14] Adding an inspection panel --- sifter-view/app/page.tsx | 2 +- sifter-view/components/PlaybookFlow.tsx | 377 +++++++++++++++++- sifter-view/components/PlaybookViewer.tsx | 11 +- .../components/playbook-steps/registry.tsx | 2 +- 4 files changed, 366 insertions(+), 26 deletions(-) diff --git a/sifter-view/app/page.tsx b/sifter-view/app/page.tsx index 85a5576..be317a4 100644 --- a/sifter-view/app/page.tsx +++ b/sifter-view/app/page.tsx @@ -9,7 +9,7 @@ export default function Home() { return (
- +
); diff --git a/sifter-view/components/PlaybookFlow.tsx b/sifter-view/components/PlaybookFlow.tsx index 4747fa2..e10a938 100644 --- a/sifter-view/components/PlaybookFlow.tsx +++ b/sifter-view/components/PlaybookFlow.tsx @@ -22,7 +22,7 @@ import "@xyflow/react/dist/style.css"; import dagre from 'dagre'; import type { Node, Edge } from '@xyflow/react'; import { getPlaybook, type Playbook } from '@/lib/playbookApi'; -import { getStepCellComponent } from './playbook-steps/registry'; +import { getStepCellComponent, STEP_OPERATIONS } from './playbook-steps/registry'; import type { PipelineStep } from './playbook-steps/types'; @@ -31,6 +31,8 @@ type PipelineNodeData = { steps: PipelineStep[]; }; +type RawPipelineStep = Record; + const BASE_NODE_WIDTH = 170; const BASE_NODE_HEIGHT = 44; const PIPELINE_NODE_WIDTH = 260; @@ -220,6 +222,15 @@ function buildGraph(pb: Playbook): { nodes: Node[]; edges: Edge[] } { return { nodes, edges }; } +function parsePipelineStep(stepObj: RawPipelineStep): PipelineStep { + const [operation, config] = Object.entries(stepObj)[0] ?? ['unknown', null]; + return { operation, config }; +} + +function serializePipelineStep(step: PipelineStep): RawPipelineStep { + return { [step.operation]: step.config }; +} + // ------------------------------------------------------------------- // React component – PlaybookFlow // ------------------------------------------------------------------- @@ -228,10 +239,79 @@ function buildGraph(pb: Playbook): { nodes: Node[]; edges: Edge[] } { export default function PlaybookFlow() { const [nodes, setNodes, onNodesChange] = useNodesState([]); const [edges, setEdges, onEdgesChange] = useEdgesState([]); + const [playbook, setPlaybook] = useState(null); + const [selectedNodeId, setSelectedNodeId] = useState(null); + const [configDrafts, setConfigDrafts] = useState>({}); + const [configErrors, setConfigErrors] = useState>({}); + const [draggingStepIndex, setDraggingStepIndex] = useState(null); + const [dragOverStepIndex, setDragOverStepIndex] = useState(null); const [isLoading, setIsLoading] = useState(true); const [loadError, setLoadError] = useState(null); const nodeTypes = useMemo(() => ({ pipeline: PipelineStackNode }), []); + const selectedNode = useMemo( + () => nodes.find((node) => node.id === selectedNodeId) ?? null, + [nodes, selectedNodeId] + ); + + const selectedPipelineName = useMemo(() => { + if (!selectedNodeId || !playbook) { + return null; + } + return playbook.pipelines[selectedNodeId] ? selectedNodeId : null; + }, [playbook, selectedNodeId]); + + const selectedPipelineSteps = useMemo(() => { + if (!selectedPipelineName || !playbook) { + return [] as PipelineStep[]; + } + return (playbook.pipelines[selectedPipelineName] ?? []).map((stepObj) => + parsePipelineStep(stepObj as RawPipelineStep) + ); + }, [playbook, selectedPipelineName]); + + const updateSelectedPipelineSteps = useCallback( + (updater: (currentSteps: PipelineStep[]) => PipelineStep[]) => { + if (!selectedPipelineName) { + return; + } + + setPlaybook((currentPlaybook) => { + if (!currentPlaybook) { + return currentPlaybook; + } + + const currentPipelineSteps = (currentPlaybook.pipelines[selectedPipelineName] ?? []).map((stepObj) => + parsePipelineStep(stepObj as RawPipelineStep) + ); + const updatedPipelineSteps = updater(currentPipelineSteps); + + return { + ...currentPlaybook, + pipelines: { + ...currentPlaybook.pipelines, + [selectedPipelineName]: updatedPipelineSteps.map(serializePipelineStep), + }, + }; + }); + }, + [selectedPipelineName] + ); + + const updateStepAtIndex = useCallback( + (index: number, updater: (step: PipelineStep) => PipelineStep) => { + updateSelectedPipelineSteps((currentSteps) => + currentSteps.map((step, stepIndex) => (stepIndex === index ? updater(step) : step)) + ); + }, + [updateSelectedPipelineSteps] + ); + + const clearConfigUiState = useCallback(() => { + setConfigDrafts({}); + setConfigErrors({}); + }, []); + useEffect(() => { let isMounted = true; @@ -239,13 +319,11 @@ export default function PlaybookFlow() { try { setLoadError(null); setIsLoading(true); - const playbook = await getPlaybook(); - const graph = buildGraph(playbook); + const loadedPlaybook = await getPlaybook(); if (!isMounted) { return; } - setNodes(graph.nodes); - setEdges(graph.edges); + setPlaybook(loadedPlaybook); } catch (error) { if (!isMounted) { return; @@ -265,11 +343,94 @@ export default function PlaybookFlow() { }; }, [setEdges, setNodes]); + useEffect(() => { + if (!playbook) { + return; + } + + const graph = buildGraph(playbook); + setNodes(graph.nodes); + setEdges(graph.edges); + }, [playbook, setEdges, setNodes]); + + useEffect(() => { + clearConfigUiState(); + }, [clearConfigUiState, selectedPipelineName]); + const onConnect: OnConnect = useCallback( (connection: Connection) => setEdges((currentEdges) => addEdge(connection, currentEdges)), [setEdges] ); + const handleConfigDraftChange = useCallback((stepIndex: number, draftValue: string) => { + setConfigDrafts((currentDrafts) => ({ + ...currentDrafts, + [stepIndex]: draftValue, + })); + + try { + JSON.parse(draftValue); + setConfigErrors((currentErrors) => { + const { [stepIndex]: _, ...remainingErrors } = currentErrors; + return remainingErrors; + }); + } catch { + setConfigErrors((currentErrors) => ({ + ...currentErrors, + [stepIndex]: 'Invalid JSON', + })); + } + }, []); + + const commitConfigDraft = useCallback( + (stepIndex: number) => { + const draftValue = configDrafts[stepIndex]; + if (draftValue === undefined) { + return; + } + + let parsedConfig: unknown; + try { + parsedConfig = JSON.parse(draftValue); + } catch { + return; + } + + updateStepAtIndex(stepIndex, (step) => ({ + ...step, + config: parsedConfig, + })); + }, + [configDrafts, updateStepAtIndex] + ); + + const reorderSelectedPipelineSteps = useCallback( + (fromIndex: number, toIndex: number) => { + if (fromIndex === toIndex) { + return; + } + + updateSelectedPipelineSteps((currentSteps) => { + if ( + fromIndex < 0 || + toIndex < 0 || + fromIndex >= currentSteps.length || + toIndex >= currentSteps.length + ) { + return currentSteps; + } + + const reorderedSteps = [...currentSteps]; + const [movedStep] = reorderedSteps.splice(fromIndex, 1); + reorderedSteps.splice(toIndex, 0, movedStep); + return reorderedSteps; + }); + + clearConfigUiState(); + }, + [clearConfigUiState, updateSelectedPipelineSteps] + ); + if (loadError) { return (
@@ -287,19 +448,201 @@ export default function PlaybookFlow() { } return ( -
- +
+ setSelectedNodeId(node.id)} + onPaneClick={() => setSelectedNodeId(null)} + fitView + > + + + +
+