mcp-agentic-pipelines 1.0.1

package/.env.example

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+# ═══════════════════════════════════════════════════════════════
+# Unified MCP Server — Environment Configuration
+# Generated for jinan-kordab | Date: 2026-06-21
+# ═══════════════════════════════════════════════════════════════
+#
+# === LLM PROVIDER CONFIGURATION (unified multi-provider) =======
+#
+# Each component can use a different LLM provider or inherit the default.
+# Supported providers: openai | anthropic | google | deepseek |
+#                       groq | ollama | openrouter | azure | custom
+#
+# Provider auto-configuration (base URL + default model):
+#   openai      → https://api.openai.com/v1              | gpt-4o-mini
+#   anthropic   → https://api.anthropic.com/v1            | claude-3-haiku-20240307
+#   google      → https://generativelanguage.googleapis.com/v1beta | gemini-2.0-flash
+#   deepseek    → https://api.deepseek.com                | deepseek-chat
+#   groq        → https://api.groq.com/openai/v1          | llama-3.3-70b-versatile
+#   ollama      → http://localhost:11434/v1               | llama3.2
+#   openrouter  → https://openrouter.ai/api/v1            | openai/gpt-4o-mini
+#   azure       → (requires AZURE_* vars below)            | (requires deployment)
+#   custom      → (requires LLM_DEFAULT_BASE_URL + LLM_DEFAULT_MODEL)
+#
+# ═══════════════════════════════════════════════════════════════
+
+# --- Default LLM (used when per-component override is not set) ---
+LLM_DEFAULT_PROVIDER=openai
+LLM_DEFAULT_API_KEY=sk-your-key-here
+LLM_DEFAULT_BASE_URL=               # Override auto-detected base URL
+LLM_DEFAULT_MODEL=                  # Override auto-detected model
+
+# --- Azure OpenAI (only needed when provider=azure) ---
+AZURE_OPENAI_ENDPOINT=https://your-resource.openai.azure.com
+AZURE_OPENAI_API_KEY=
+AZURE_OPENAI_DEPLOYMENT=gpt-4o-mini
+AZURE_OPENAI_API_VERSION=2024-08-01-preview
+
+# --- Anthropic-specific (auto-set, override here) ---
+# ANTHROPIC_API_KEY=                # Falls back to LLM_DEFAULT_API_KEY if provider=anthropic
+# ANTHROPIC_BASE_URL=               # Default: https://api.anthropic.com/v1
+
+# --- Google-specific ---
+# GOOGLE_API_KEY=                   # Falls back to LLM_DEFAULT_API_KEY if provider=google
+
+# --- Ollama-specific ---
+# OLLAMA_HOST=http://localhost:11434
+
+# ═══════════════════════════════════════════════════════════════
+
+# --- DeepPipe Engine ---
+DEEPPIPE_INDEX_PATH=./data/deeppipe.db
+DEEPPIPE_LLM_PROVIDER=              # Falls back to LLM_DEFAULT_PROVIDER
+DEEPPIPE_LLM_API_KEY=               # Falls back to LLM_DEFAULT_API_KEY
+DEEPPIPE_LLM_MODEL=                 # Falls back to provider default
+
+# --- Piste (Fact-Checking) ---
+# Piste uses DSPy over LiteLLM — supports 100+ models natively
+PISTE_API_URL=http://localhost:8000
+PISTE_LLM_PROVIDER=deepseek         # LiteLLM model string, e.g. deepseek/deepseek-chat
+PISTE_LLM_API_KEY=                  # Falls back to LLM_DEFAULT_API_KEY
+TAVILY_API_KEY=                     # At least one search provider required
+SERPER_API_KEY=
+GOOGLE_CSE_API_KEY=                 # Optional fallback
+GOOGLE_CSE_ID=
+
+# --- Precis (RAG Pipeline) ---
+# Precis supports: deepseek, openai, anthropic, google, ollama
+PRECIS_API_URL=http://localhost:8001
+PRECIS_LLM_PROVIDER=deepseek        # Provider name for Precis backend
+PRECIS_LLM_API_KEY=                 # Falls back to LLM_DEFAULT_API_KEY
+
+# --- Clinical Intake ---
+# LLM for clinical reasoning
+CLINICAL_LLM_PROVIDER=deepseek      # Falls back to LLM_DEFAULT_PROVIDER
+CLINICAL_LLM_API_KEY=               # Falls back to LLM_DEFAULT_API_KEY
+CLINICAL_LLM_MODEL=                 # Falls back to provider default
+# STT (Speech-to-Text)
+CLINICAL_STT_PROVIDER=groq          # Currently: groq (whisper-large-v3)
+GROQ_API_KEY=
+# TTS (Text-to-Speech)
+CLINICAL_TTS_PROVIDER=elevenlabs    # Currently: elevenlabs
+ELEVENLABS_API_KEY=
+ELEVENLABS_VOICE_ID=21m00Tcm4TlvDq8ikWAM
+
+# ═══════════════════════════════════════════════════════════════
+
+# --- MCP Server ---
+MCP_SERVER_NAME=unified-jk-mcp
+MCP_SERVER_VERSION=0.1.0
+MCP_TRANSPORT=stdio                 # stdio | sse
+MCP_SSE_PORT=3100
+MCP_LOG_LEVEL=info                  # debug | info | warn | error
+MCP_RATE_LIMIT_ENABLED=true
+MCP_RATE_LIMIT_MAX_RPS=10

package/README.md

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+# mcp-agentic-pipelines
+
+> **One MCP server. Five AI pipelines. Thirty-one tools. Zero manual setup.**
+
+[![npm](https://img.shields.io/npm/v/mcp-agentic-pipelines)](https://www.npmjs.com/package/mcp-agentic-pipelines)
+
+Composable, agentic AI pipelines for Anthropic's Model Context Protocol. Fact-check claims with DSPy, search documents with hybrid RAG, extract intelligence with DeepPipe, and run clinical voice intake — all from a single MCP server. Designed for Claude Desktop, VS Code, Cursor, and any MCP-compatible client.
+
+---
+
+## All 31 Tools
+
+### 🔍 DeepPipe — Document Intelligence (10 tools)
+| Tool | What it does |
+|---|---|
+| `deeppipe_search` | Full-text + vector hybrid search across all documents |
+| `deeppipe_ingest` | Ingest raw text/JSON documents for indexing |
+| `deeppipe_ingest_file` | Ingest documents directly from file paths |
+| `deeppipe_chat_context` | RAG-style Q&A with source citations |
+| `deeppipe_extractive_answer` | Extract a precise answer from documents |
+| `deeppipe_list_documents` | List all indexed documents with metadata |
+| `deeppipe_get_document` | Retrieve a specific document by ID |
+| `deeppipe_get_text` | Get the full text content of a document |
+| `deeppipe_remove_document` | Remove a document from the index |
+| `deeppipe_stats` | View index statistics and document count |
+
+### 🧠 Piste — Fact-Checking (6 tools)
+| Tool | What it does |
+|---|---|
+| `piste_fact_check` | Run a claim through the full 4-stage DSPy pipeline (retrieval → verification → aggregation → verdict) |
+| `piste_list_verdicts` | Browse all past fact-check verdicts |
+| `piste_replay` | Replay the audit trail of any fact-check run |
+| `piste_get_audit` | Get the detailed reasoning chain for a verdict |
+| `piste_get_verdict` | Retrieve a specific verdict by claim ID |
+| `piste_submit_feedback` | Submit human feedback to improve future checks |
+
+### 📚 Precis — RAG Pipeline (8 tools)
+| Tool | What it does |
+|---|---|
+| `precis_query` | Full RAG query — hybrid search + LLM answer generation |
+| `precis_list_documents` | List all documents in the RAG corpus |
+| `precis_debug_stem` | Inspect how the stemmer processes a query |
+| `precis_debug_search` | See raw hybrid search results (before LLM) |
+| `precis_upload_document` | Upload a document to the RAG corpus |
+| `precis_upload_batch` | Batch-upload multiple documents at once |
+| `precis_extract_work_order` | Extract structured work orders from documents |
+| `precis_list_work_orders` | Browse all extracted work orders |
+
+### 🎙️ Clinical — Voice Intake (5 tools)
+| Tool | What it does |
+|---|---|
+| `clinical_start_session` | Start a new voice intake session (returns session ID) |
+| `clinical_process_audio` | Send audio → STT transcription → SOAP notes |
+| `clinical_generate_podcast` | Generate a clinical podcast from session notes |
+| `clinical_list_sessions` | List all voice intake sessions |
+| `clinical_get_session` | Get full details of a specific session |
+
+### ⚙️ Built-in (2 tools)
+| Tool | What it does |
+|---|---|
+| `mcp_health` | Server health, tool count, provider status |
+| `mcp_list_providers` | List all 9 supported LLM providers |
+
+---
+
+## Compose Pipelines Together
+
+These tools are designed to be chained. Here's a real workflow:
+
+```
+1. deeppipe_ingest           → Load a research paper into the index
+2. precis_upload_document    → Add it to the RAG corpus
+3. deeppipe_search           → Find relevant passages
+4. piste_fact_check          → Verify claims found in those passages
+5. precis_query              → Generate a RAG answer from verified context
+6. clinical_start_session    → Start voice notes on the findings
+7. clinical_generate_podcast → Turn it all into a shareable podcast
+```
+
+**In Claude Desktop, this is a conversation:**
+> *"Search my documents for claims about climate policy, fact-check each one,
+> then generate a clinical podcast summarizing the verified findings."*
+
+Claude orchestrates the tool calls — your server provides the pipelines.
+
+---
+
+## Architecture
+
+```mermaid
+graph LR
+    subgraph Top[" "]
+        direction LR
+        CL[Claude Desktop]
+        VS[VS Code]
+        CU[Cursor]
+    end
+
+    subgraph Core["MCP Server Core"]
+        direction LR
+        ROUTER[Request Router<br/>6 handlers]
+        RATE[Rate Limiter]
+        GUARD[Dep Guard]
+    end
+
+    subgraph DP["DeepPipe<br/>10 tools · TS"]
+        D1[search] --> D2[ingest] --> D3[chat]
+    end
+
+    subgraph PS["Piste<br/>6 tools · Python"]
+        P1[fact_check] --> PY1[DSPy Pipeline]
+    end
+
+    subgraph PR["Precis<br/>8 tools · Python"]
+        R1[query] --> PY2[RAG Engine]
+    end
+
+    subgraph CLN["Clinical<br/>5 tools · TS"]
+        C1[session] --> C2[audio] --> C3[podcast]
+    end
+
+    subgraph Bottom[" "]
+        direction LR
+        LLM[9 LLM Providers<br/>DeepSeek · OpenAI · Anthropic · Groq · Ollama · Google · Azure · OpenRouter · Custom]
+        EXT[Tavily · Serper · ElevenLabs]
+        DEP[uv · 10 pip pkgs · 6 npm pkgs]
+    end
+
+    Top --> Core
+    Core --> DP & PS & PR & CLN
+    DP & PS & PR & CLN --> Bottom
+
+    style Top fill:#f8f9fa,color:#333
+    style Core fill:#e8f4fd,color:#333
+    style DP fill:#f0f8ff,color:#1a5276,stroke:#aed6f1
+    style PS fill:#fef9e7,color:#7d6608,stroke:#f9e79f
+    style PR fill:#eafaf1,color:#1e8449,stroke:#a9dfbf
+    style CLN fill:#fdedec,color:#922b21,stroke:#f5b7b1
+    style Bottom fill:#f8f9fa,color:#333
+```
+
+---
+
+## Quick Start
+
+```bash
+# 1. Install (npm + Python deps handled automatically)
+npx mcp-agentic-pipelines setup
+
+# 2. Start the server
+npx mcp-agentic-pipelines
+
+# 3. Or run the test suite
+npx mcp-agentic-pipelines test
+```
+
+### MCP Client Configuration
+
+Add to your MCP client config:
+
+```json
+{
+  "mcpServers": {
+    "mcp-agentic-pipelines": {
+      "command": "npx",
+      "args": ["mcp-agentic-pipelines"]
+    }
+  }
+}
+```
+
+### Environment Variables
+
+Copy `.env.example` to `.env` and set your keys:
+
+| Key | Purpose |
+|---|---|
+| `DEEPSEEK_API_KEY` | Default LLM (DeepSeek) |
+| `OPENAI_API_KEY` | Fallback LLM |
+| `GROQ_API_KEY` | Clinical voice (STT) |
+| `ELEVENLABS_API_KEY` | Clinical voice (TTS) |
+| `TAVILY_API_KEY` | Piste web search |
+| `SERPER_API_KEY` | Piste web search |
+
+*Server starts with any subset — missing keys skip their tools gracefully.*
+
+---
+
+## Requirements
+
+- **Node.js ≥ 18**
+- **Python 3.11+** (automatically managed via `uv` — no manual Python install needed on Linux/macOS)
+- **API keys** for the tools you want to use (DeepSeek, Groq, ElevenLabs, Tavily, etc.)
+
+---
+
+## Development
+
+```bash
+git clone https://github.com/jinan-kordab/mcp-agentic-pipelines.git
+cd mcp-agentic-pipelines
+npm install
+node setup.mjs        # one-time — installs all Python deps
+node test.mjs         # runs all 31 tool tests
+```
+
+---
+
+## Architecture (Directory)
+
+```
+packages/
+├── core/          Shared types, config, logging, Python bridge
+├── server/        MCP entry point, request routing
+├── deeppipe/      10 document intelligence tools
+├── piste/         6 fact-checking tools (Python bridge → DSPy)
+├── precis/        8 RAG tools (Python bridge → hybrid search)
+├── clinical/      5 voice intake tools (native TypeScript)
+vendors/
+├── piste/         DSPy pipeline modules + stdin/stdout bridge
+├── precis/        RAG backend modules + stdin/stdout bridge
+├── clinical-intake/  Voice pipeline (npm workspace)
+setup.mjs          One-time setup (uv, npm, pip)
+test.mjs           Complete test suite (31 tools)
+```
+
+---
+
+## License
+
+MIT © [Jinan Kordab](https://github.com/jinan-kordab)
+
+
+---
+
+## Architecture
+
+```
+packages/
+├── core/          Shared types, config, logging, Python bridge
+├── server/        MCP entry point, request routing
+├── deeppipe/      10 document intelligence tools
+├── piste/         6 fact-checking tools (Python bridge → DSPy)
+├── precis/        8 RAG tools (Python bridge → hybrid search)
+├── clinical/      5 voice intake tools (native TypeScript)
+vendors/
+├── piste/         DSPy pipeline modules + stdin/stdout bridge
+├── precis/        RAG backend modules + stdin/stdout bridge
+├── clinical-intake/  Voice pipeline (npm workspace)
+setup.mjs          One-time setup (uv, npm, pip)
+test.mjs           Complete test suite (31 tools)
+```
+
+---
+
+## License
+
+MIT © [Jinan Kordab](https://github.com/jinan-kordab)

package/package.json

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+{
+  "name": "mcp-agentic-pipelines",
+  "version": "1.0.1",
+  "description": "Composable, agentic pipelines for MCP — fact-checking (DSPy), RAG (hybrid search), document intelligence (DeepPipe), and clinical voice (Groq/ElevenLabs). 31 AI tools, one command, zero manual setup.",
+  "author": "Jinan Kordab <https://github.com/jinan-kordab>",
+  "license": "MIT",
+  "repository": "github:jinan-kordab/mcp-agentic-pipelines",
+  "homepage": "https://github.com/jinan-kordab/mcp-agentic-pipelines#readme",
+  "bugs": "https://github.com/jinan-kordab/mcp-agentic-pipelines/issues",
+  "keywords": [
+    "mcp",
+    "modelcontextprotocol",
+    "ai",
+    "llm",
+    "fact-checking",
+    "dspy",
+    "rag",
+    "document-intelligence",
+    "voice-ai",
+    "agentic",
+    "pipelines",
+    "claude",
+    "anthropic"
+  ],
+  "bin": {
+    "mcp-agentic-pipelines": "./packages/server/src/index.ts"
+  },
+  "files": [
+    "packages/",
+    "vendors/",
+    "setup.mjs",
+    "test.mjs",
+    ".env.example",
+    "README.md"
+  ],
+  "workspaces": [
+    "packages/core",
+    "packages/deeppipe",
+    "packages/piste",
+    "packages/precis",
+    "packages/clinical",
+    "packages/server"
+  ],
+  "scripts": {
+    "setup": "node setup.mjs",
+    "start": "node --import tsx packages/server/src/index.ts",
+    "dev": "node --import tsx packages/server/src/index.ts",
+    "test": "node test.mjs",
+    "typecheck": "tsc --noEmit",
+    "clean": "rimraf packages/*/dist"
+  },
+  "devDependencies": {
+    "@types/node": "^22.0.0",
+    "rimraf": "^6.0.0",
+    "tsx": "^4.0.0",
+    "typescript": "^5.6.0",
+    "vitest": "^2.0.0"
+  },
+  "dependencies": {
+    "@kordabjinan/deeppipe": "^0.1.0",
+    "@modelcontextprotocol/sdk": "^1.0.0",
+    "dotenv": "^16.4.5",
+    "groq-sdk": "^0.8.0",
+    "openai": "^4.73.0",
+    "zod": "^3.23.0"
+  },
+  "engines": {
+    "node": ">=18.0.0"
+  }
+}

package/packages/clinical/package.json

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+{
+  "name": "@unified-mcp/clinical",
+  "version": "0.1.0",
+  "description": "Clinical Intake integration for unified MCP server — AI pre-consultation voice agent with multi-provider LLM support",
+  "type": "module",
+  "main": "./src/index.ts",
+  "types": "./src/index.ts",
+  "scripts": {
+    "build": "tsc -p tsconfig.json",
+    "typecheck": "tsc -p tsconfig.json --noEmit",
+    "test": "vitest run",
+    "test:watch": "vitest"
+  },
+  "dependencies": {
+    "@unified-mcp/core": "^0.1.0",
+    "openai": "^4.73.0",
+    "groq-sdk": "^0.8.0"
+  },
+  "devDependencies": {
+    "vitest": "^2.0.0"
+  }
+}