omnibioai-tool-runtime 0.1.0__tar.gz

omnibioai_tool_runtime-0.1.0/PKG-INFO

@@ -0,0 +1,371 @@
+Metadata-Version: 2.4
+Name: omnibioai-tool-runtime
+Version: 0.1.0
+Summary: Portable tool runtime for OmniBioAI TES (RESULT_URI uploader for s3:// and azureblob://)
+Author: Manish Kumar
+License: MIT
+Keywords: omnibioai,tes,bioinformatics,batch,azure,aws
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: pydantic>=2.0
+Provides-Extra: aws
+Requires-Dist: boto3>=1.26; extra == "aws"
+Provides-Extra: azure
+Requires-Dist: azure-identity>=1.15; extra == "azure"
+Requires-Dist: azure-storage-blob>=12.19; extra == "azure"
+
+# 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**.
+

omnibioai_tool_runtime-0.1.0/README.md

@@ -0,0 +1,352 @@
+# 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**.
+

omnibioai_tool_runtime-0.1.0/omnibioai_tool_runtime.egg-info/PKG-INFO

@@ -0,0 +1,371 @@
+Metadata-Version: 2.4
+Name: omnibioai-tool-runtime
+Version: 0.1.0
+Summary: Portable tool runtime for OmniBioAI TES (RESULT_URI uploader for s3:// and azureblob://)
+Author: Manish Kumar
+License: MIT
+Keywords: omnibioai,tes,bioinformatics,batch,azure,aws
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: pydantic>=2.0
+Provides-Extra: aws
+Requires-Dist: boto3>=1.26; extra == "aws"
+Provides-Extra: azure
+Requires-Dist: azure-identity>=1.15; extra == "azure"
+Requires-Dist: azure-storage-blob>=12.19; extra == "azure"
+
+# 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**.
+

omnibioai_tool_runtime-0.1.0/omnibioai_tool_runtime.egg-info/SOURCES.txt

@@ -0,0 +1,13 @@
+README.md
+pyproject.toml
+omnibioai_tool_runtime.egg-info/PKG-INFO
+omnibioai_tool_runtime.egg-info/SOURCES.txt
+omnibioai_tool_runtime.egg-info/dependency_links.txt
+omnibioai_tool_runtime.egg-info/requires.txt
+omnibioai_tool_runtime.egg-info/top_level.txt
+tests/test_result_uri_parse.py
+tests/test_tools_echo_test.py
+tests/test_upload_dispatch.py
+tools/__init__.py
+tools/echo_test/__init__.py
+tools/echo_test/run.py

omnibioai_tool_runtime-0.1.0/omnibioai_tool_runtime.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

omnibioai_tool_runtime-0.1.0/omnibioai_tool_runtime.egg-info/requires.txt

@@ -0,0 +1,8 @@
+pydantic>=2.0
+
+[aws]
+boto3>=1.26
+
+[azure]
+azure-identity>=1.15
+azure-storage-blob>=12.19

omnibioai_tool_runtime-0.1.0/omnibioai_tool_runtime.egg-info/top_level.txt

@@ -0,0 +1 @@
+tools

omnibioai_tool_runtime-0.1.0/pyproject.toml

@@ -0,0 +1,30 @@
+[build-system]
+requires = ["setuptools>=65", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "omnibioai-tool-runtime"
+version = "0.1.0"
+description = "Portable tool runtime for OmniBioAI TES (RESULT_URI uploader for s3:// and azureblob://)"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "MIT" }
+authors = [{ name = "Manish Kumar" }]
+keywords = ["omnibioai", "tes", "bioinformatics", "batch", "azure", "aws"]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: OS Independent",
+]
+
+dependencies = [
+  "pydantic>=2.0"
+]
+
+[project.optional-dependencies]
+aws = ["boto3>=1.26"]
+azure = ["azure-identity>=1.15", "azure-storage-blob>=12.19"]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["omnibioai_tool_runtime*", "tools*"]

omnibioai_tool_runtime-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

omnibioai_tool_runtime-0.1.0/tests/test_result_uri_parse.py

@@ -0,0 +1,50 @@
+# tests/test_result_uri_parse.py
+from __future__ import annotations
+
+import pytest
+
+from omni_tool_runtime.result_uri import parse_result_uri
+
+
+def test_parse_s3_uri_ok():
+    p = parse_result_uri("s3://my-bucket/some/prefix/results.json")
+    assert p.scheme == "s3"
+    assert p.account_or_bucket == "my-bucket"
+    assert p.container is None
+    assert p.path == "some/prefix/results.json"
+
+
+def test_parse_s3_uri_requires_bucket_and_key():
+    with pytest.raises(ValueError):
+        parse_result_uri("s3://")
+    with pytest.raises(ValueError):
+        parse_result_uri("s3://bucket-only")
+    with pytest.raises(ValueError):
+        parse_result_uri("s3://bucket/")
+
+
+def test_parse_azureblob_uri_ok():
+    p = parse_result_uri("azureblob://acct/container/path/to/results.json")
+    assert p.scheme == "azureblob"
+    assert p.account_or_bucket == "acct"
+    assert p.container == "container"
+    assert p.path == "path/to/results.json"
+
+
+def test_parse_azureblob_uri_requires_container_and_path():
+    with pytest.raises(ValueError):
+        parse_result_uri("azureblob://acct/")
+    with pytest.raises(ValueError):
+        parse_result_uri("azureblob://acct/container")
+    with pytest.raises(ValueError):
+        parse_result_uri("azureblob://acct/container/")
+
+
+def test_parse_rejects_unknown_scheme():
+    with pytest.raises(ValueError, match="Unsupported"):
+        parse_result_uri("gs://bucket/key")  # not supported yet
+
+
+def test_parse_rejects_missing_scheme():
+    with pytest.raises(ValueError, match="missing scheme"):
+        parse_result_uri("bucket/key")

omnibioai_tool_runtime-0.1.0/tests/test_tools_echo_test.py

@@ -0,0 +1,24 @@
+import json
+import os
+import subprocess
+import sys
+
+
+def test_echo_test_local_mode_no_result_uri():
+    env = dict(os.environ)
+    env["TOOL_ID"] = "echo_test"
+    env["RUN_ID"] = "local123"
+    env["INPUTS_JSON"] = json.dumps({"text": "hello"})
+    env["RESOURCES_JSON"] = json.dumps({"cpu": 1})
+    env["RESULT_URI"] = ""  # local mode
+
+    p = subprocess.run(
+        [sys.executable, "-m", "tools.echo_test.run"],
+        env=env,
+        capture_output=True,
+        text=True,
+    )
+    assert p.returncode == 0
+    out = json.loads(p.stdout)
+    assert out["ok"] is True
+    assert out["results"]["echo"] == "hello"

omnibioai_tool_runtime-0.1.0/tests/test_upload_dispatch.py

@@ -0,0 +1,103 @@
+# tests/test_upload_dispatch.py
+from __future__ import annotations
+
+import pytest
+
+import omni_tool_runtime.upload_result as mod
+
+
+class _S3Spy:
+    def __init__(self, aws_profile=None):
+        self.aws_profile = aws_profile
+        self.calls = []
+
+    def upload_bytes(self, *, bucket: str, key: str, data: bytes, content_type: str) -> None:
+        self.calls.append(
+            {"bucket": bucket, "key": key, "data": data, "content_type": content_type, "aws_profile": self.aws_profile}
+        )
+
+
+class _AzureSpy:
+    def __init__(self, account_name: str, auth: str = "managed_identity", connection_string=None):
+        self.account_name = account_name
+        self.auth = auth
+        self.connection_string = connection_string
+        self.calls = []
+
+    def upload_bytes(self, *, container: str, blob_path: str, data: bytes, content_type: str) -> None:
+        self.calls.append(
+            {
+                "account_name": self.account_name,
+                "auth": self.auth,
+                "connection_string": self.connection_string,
+                "container": container,
+                "blob_path": blob_path,
+                "data": data,
+                "content_type": content_type,
+            }
+        )
+
+
+def test_upload_dispatch_to_s3(monkeypatch: pytest.MonkeyPatch):
+    s3_spy = _S3Spy(aws_profile="prof1")
+
+    # Patch constructor used inside upload_to_result_uri
+    monkeypatch.setattr(mod, "S3Uploader", lambda aws_profile=None: _S3Spy(aws_profile=aws_profile))
+    # But we need the created instance to inspect calls. So patch with closure:
+    created = {}
+
+    def _ctor(aws_profile=None):
+        created["inst"] = _S3Spy(aws_profile=aws_profile)
+        return created["inst"]
+
+    monkeypatch.setattr(mod, "S3Uploader", _ctor)
+
+    uri = "s3://bkt/prefix/run1/results.json"
+    payload = b'{"ok": true}'
+    mod.upload_to_result_uri(result_uri=uri, data=payload, content_type="application/json", aws_profile="prof1")
+
+    inst = created["inst"]
+    assert len(inst.calls) == 1
+    c = inst.calls[0]
+    assert c["bucket"] == "bkt"
+    assert c["key"] == "prefix/run1/results.json"
+    assert c["data"] == payload
+    assert c["content_type"] == "application/json"
+    assert c["aws_profile"] == "prof1"
+
+
+def test_upload_dispatch_to_azureblob(monkeypatch: pytest.MonkeyPatch):
+    created = {}
+
+    def _ctor(account_name: str, auth: str = "managed_identity", connection_string=None):
+        created["inst"] = _AzureSpy(account_name=account_name, auth=auth, connection_string=connection_string)
+        return created["inst"]
+
+    monkeypatch.setattr(mod, "AzureBlobUploader", _ctor)
+
+    uri = "azureblob://acct1/contA/tes-runs/r1/tools/echo_test/results.json"
+    payload = b'{"ok": true}'
+
+    mod.upload_to_result_uri(
+        result_uri=uri,
+        data=payload,
+        content_type="application/json",
+        azure_auth="connection_string",
+        azure_connection_string="UseDevelopmentStorage=true",
+    )
+
+    inst = created["inst"]
+    assert len(inst.calls) == 1
+    c = inst.calls[0]
+    assert c["account_name"] == "acct1"
+    assert c["auth"] == "connection_string"
+    assert c["connection_string"] == "UseDevelopmentStorage=true"
+    assert c["container"] == "contA"
+    assert c["blob_path"] == "tes-runs/r1/tools/echo_test/results.json"
+    assert c["data"] == payload
+    assert c["content_type"] == "application/json"
+
+
+def test_upload_unsupported_scheme_raises():
+    with pytest.raises(ValueError):
+        mod.upload_to_result_uri(result_uri="gs://bucket/key", data=b"x")

omnibioai_tool_runtime-0.1.0/tools/__init__.py

@@ -0,0 +1,2 @@
+# tools/__init__.py
+from __future__ import annotations

omnibioai_tool_runtime-0.1.0/tools/echo_test/__init__.py

@@ -0,0 +1,2 @@
+# tools/echo_test/__init__.py
+from __future__ import annotations

omnibioai_tool_runtime-0.1.0/tools/echo_test/run.py

@@ -0,0 +1,56 @@
+# tools/echo_test/run.py
+from __future__ import annotations
+
+import json
+import os
+import sys
+
+from omni_tool_runtime.upload_result import upload_to_result_uri
+
+
+def main() -> int:
+    tool_id = os.getenv("TOOL_ID", "")
+    run_id = os.getenv("RUN_ID", "")
+    result_uri = (os.getenv("RESULT_URI", "") or "").strip()
+
+    inputs_json = os.getenv("INPUTS_JSON", "{}")
+    try:
+        inputs = json.loads(inputs_json)
+    except Exception as e:
+        out = {"ok": False, "error": f"bad INPUTS_JSON: {e}", "tool_id": tool_id, "run_id": run_id}
+        print(json.dumps(out))
+        return 2
+
+    text = inputs.get("text")  # keep strict contract (or: inputs.get("text") or inputs.get("msg"))
+    if text is None:
+        result_obj = {
+            "ok": False,
+            "error": "missing inputs.text",
+            "tool_id": tool_id,
+            "run_id": run_id,
+            "inputs": inputs,
+        }
+    else:
+        result_obj = {
+            "ok": True,
+            "tool_id": tool_id,
+            "run_id": run_id,
+            "results": {"echo": text},
+        }
+
+    body = json.dumps(result_obj, indent=2)
+
+    # Always print for logs/debug
+    print(body)
+
+    # If RESULT_URI not set -> local mode: succeed
+    if not result_uri:
+        return 0
+
+    # Cloud mode: upload
+    upload_to_result_uri(result_uri=result_uri, content=body.encode("utf-8"))
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())