omnibioai-tool-runtime 0.1.0
Portable tool runtime for OmniBioAI TES (RESULT_URI uploader for s3:// and azureblob://)
License: MIT
Requires Python: >=3.10
Keywords: omnibioai, tes, bioinformatics, batch, azure, aws

# Omni Tool Runtime

**Portable, cloud-agnostic execution runtime for OmniBioAI tools**

---

## Overview

`omnibioai-tool-runtime` is a **minimal, deterministic execution runtime** used by
OmniBioAI’s Tool Execution Service (TES) to run individual tools across **multiple execution backends**, including:

* Local Docker execution
* AWS Batch
* Azure Batch
* (future) Kubernetes Jobs
* (future) TES-compatible HPC schedulers

The runtime provides a **strict execution contract** so that:

* TES adapters stay thin and backend-specific
* Tool containers remain portable and backend-agnostic
* Results are uploaded consistently (S3 / Azure Blob / future backends)

This mirrors the design philosophy used throughout OmniBioAI:
**separate orchestration from execution, and execution from logic.**

---

## What This Runtime Is (and Is Not)

### ✅ This runtime **is**

* A **containerized tool launcher**
* Responsible for:

  * Reading tool inputs from environment variables
  * Executing tool logic
  * Writing `results.json`
  * Uploading results to cloud storage
* Cloud-agnostic (AWS / Azure supported today)

### ❌ This runtime is **not**

* A workflow engine
* A scheduler
* An LLM executor
* A UI layer

Those responsibilities live elsewhere in OmniBioAI.

---

## Execution Contract (Critical)

All tools executed via `omnibioai-tool-runtime` **must** follow this contract.

### Environment Variables (Injected by TES Adapter)

| Variable         | Description                                        |
| ---------------- | -------------------------------------------------- |
| `TOOL_ID`        | Tool identifier (`echo_test`, `blastn`, etc.)      |
| `RUN_ID`         | Unique run ID (generated by adapter)               |
| `INPUTS_JSON`    | JSON-encoded tool inputs                           |
| `RESOURCES_JSON` | JSON-encoded resource request                      |
| `S3_RESULT_URI`  | (AWS Batch) S3 URI to upload results               |
| `RESULT_URI`     | (Azure Batch) `azureblob://` URI to upload results |

Only **one** of `S3_RESULT_URI` or `RESULT_URI` is expected per run.

---

## Repository Structure

```text
omnibioai-tool-runtime/
├── Dockerfile
├── README.md
├── pyproject.toml
├── omni_tool_runtime/
│   ├── __init__.py
│   ├── result_uri.py          # URI parsing & dispatch
│   ├── upload_result.py       # Unified upload logic
│   └── uploaders/
│       ├── s3_uploader.py
│       └── azureblob_uploader.py
├── tools/
│   └── echo_test/
│       ├── __init__.py
│       └── run.py
└── tests/
```

---

## Example Tool: `echo_test`

This is the **reference implementation** for all future tools.

### Behavior

* Reads `INPUTS_JSON`
* Echoes a value
* Writes `results.json`
* Uploads results to configured storage backend

### Minimal tool implementation

```python
# tools/echo_test/run.py
import json
import os
from omni_tool_runtime.upload_result import upload_result

def main():
    tool_id = os.environ["TOOL_ID"]
    run_id = os.environ["RUN_ID"]
    inputs = json.loads(os.environ.get("INPUTS_JSON", "{}"))

    text = inputs.get("text", "")

    result = {
        "ok": True,
        "tool_id": tool_id,
        "run_id": run_id,
        "results": {"echo": text},
    }

    upload_result(result)

if __name__ == "__main__":
    main()
```

---

## How Results Upload Works

`upload_result()` automatically detects the backend:

| Backend | URI Example                                       |
| ------- | ------------------------------------------------- |
| AWS     | `s3://bucket/prefix/run_id/results.json`          |
| Azure   | `azureblob://account/container/path/results.json` |

The runtime:

1. Serializes result as JSON
2. Uploads to correct backend
3. Prints result to stdout (for debugging)

Adapters **never upload results themselves**.

---

## Building the Docker Image

From repository root:

```bash
docker build -t man4ish/omnibioai-tool-runtime:latest .
```

Verify:

```bash
docker images | grep omnibioai-tool-runtime
```

---

## Running a Tool Locally (No Cloud)

```bash
docker run --rm \
  -e TOOL_ID=echo_test \
  -e RUN_ID=local-test-1 \
  -e INPUTS_JSON='{"text":"hello world"}' \
  -e RESOURCES_JSON='{}' \
  man4ish/omnibioai-tool-runtime:latest
```

Expected:

* JSON output printed to stdout
* No upload attempted if no result URI is provided

---

## AWS Batch Usage

### Job Definition

* Image: `man4ish/omnibioai-tool-runtime:latest`
* Command override:

```json
["python", "-m", "tools.echo_test.run"]
```

### Injected Environment

* `S3_RESULT_URI` provided by `AwsBatchAdapter`
* IAM Role handles S3 auth

---

## Azure Batch Usage

### Task Settings

* Image: `man4ish/omnibioai-tool-runtime:latest`
* Command:

```bash
python -m tools.echo_test.run
```

### Injected Environment

* `RESULT_URI=azureblob://...`
* Managed Identity handles Blob auth

---

## Pushing the Image

### Docker Hub

```bash
docker push man4ish/omnibioai-tool-runtime:latest
```

### Azure Container Registry

```bash
az acr login --name YOUR_ACR
docker tag man4ish/omnibioai-tool-runtime:latest YOUR_ACR.azurecr.io/omnibioai-tool-runtime:latest
docker push YOUR_ACR.azurecr.io/omnibioai-tool-runtime:latest
```

---

## Adding a New Tool

### Step 1: Create tool folder

```bash
mkdir tools/my_new_tool
touch tools/my_new_tool/__init__.py
touch tools/my_new_tool/run.py
```

### Step 2: Implement `run.py`

Rules:

* Must read env vars
* Must write result via `upload_result()`
* Must be deterministic

### Step 3: Register tool in adapter config

**AWS Batch**

```yaml
job_definition_map:
  my_new_tool: "omnibioai-my-new-tool:1"
```

**Azure Batch**

```yaml
tools:
  my_new_tool:
    image: "man4ish/omnibioai-tool-runtime:latest"
    command: ["python", "-m", "tools.my_new_tool.run"]
```

---

## Current State

### Implemented

* Unified runtime image
* AWS Batch support
* Azure Batch support
* S3 + Azure Blob uploads
* Deterministic execution contract
* Reference `echo_test` tool

### Intentionally Missing (by design)

* No workflow orchestration
* No retry logic
* No state machine
* No scheduling policy

---

## Planned Future Enhancements

### Short-term

* Tool generator CLI (`omnibioai tool new`)
* Structured logging
* Result size validation
* Runtime version pinning

### Medium-term

* Kubernetes Job adapter support
* Streaming stdout to object storage
* Tool-level resource enforcement
* Tool metadata introspection

### Long-term

* Signed result manifests
* Provenance hashing
* Deterministic replay support
* Cross-cloud artifact mirroring

---

## Design Philosophy (Important)

This runtime is intentionally **boring**.

That’s a feature.

* No magic
* No backend assumptions
* No hidden orchestration
* One job → one tool → one result

Everything complex belongs **above** this layer.

---

## Final Note

If this runtime feels similar to:

* CWL CommandLineTool
* TES task containers
* AWS Batch single-purpose images

That’s intentional.

You’re building the **correct abstraction boundary**.