GA4GH WES Implementation of PAML::Platform class

docs/wes_platform.md

@@ -0,0 +1,126 @@
+# GA4GH WES Platform Implementation
+
+This document describes the GA4GH Workflow Execution Service (WES) platform implementation for the PAML library.
+
+## Overview
+
+The GA4GH WES API provides a standard way to submit and manage workflows across different workflow execution systems. 
+This implementation allows you to use the PAML library to submit workflows to any WES-compatible service.
+
+The WES platform implementation (`GA4GHWESPlatform`) inherits from the `Platform` abstract base class and implements all the required methods to interact with a WES API endpoint.
+
+## Features
+
+- Connect to any WES API endpoint
+- Submit CWL workflows
+- Monitor workflow execution status
+- Retrieve workflow outputs
+
+## Limitations
+
+Since the WES API is focused on workflow execution and doesn't include concepts like projects, folders, or file management, some features of the Platform API are not fully supported:
+
+- File operations (upload, download, copy) are limited
+- Project management is simulated using virtual projects
+- User management is not supported
+
+## Usage
+
+### Initialization and Connection
+
+```python
+from src.cwl_platform import PlatformFactory
+
+# Initialize the platform factory
+factory = PlatformFactory()
+
+# Get the WES platform
+platform = factory.get_platform('GA4GHWESPlatform')
+
+# Connect to the WES API
+platform.connect(
+    api_endpoint="https://wes.example.com/ga4gh/wes/v1",
+    auth_token="your_auth_token"  # Optional
+)
+```
+
+### Submitting a Workflow
+
+```python
+
+# Create a virtual project (not used by WES but required by the API)
+project = {
+    project_name = 'GA4GH WES Example Project'
+}
+#project = platform.create_project('wes-example', 'WES Example Project')
+
+# Define workflow parameters
+workflow_parameters = {
+    "input_file": {
+        "class": "File",
+        "path": "platform-specific id"
+    },
+    "output_filename": "output.txt"
+}
+
+# Submit the workflow
+task = platform.submit_task(
+    name="My Workflow",
+    project=project,
+    workflow="platform://<platform-specific workflow id",  # URL or local file path
+    parameters=workflow_parameters
+    execution_settings={
+        'workflow_engine': 'Arvados'
+    }
+)
+
+# Get the run ID
+run_id = task.run_id
+```
+
+### Monitoring Workflow Execution
+
+```python
+# Check the workflow state
+state = platform.get_task_state(task)
+print(f"Workflow state: {state}")
+
+# Refresh the state from the server
+state = platform.get_task_state(task, refresh=True)
+print(f"Updated workflow state: {state}")
+
+# Monitor until completion
+import time
+while True:
+    state = platform.get_task_state(task, refresh=True)
+    print(f"Workflow state: {state}")
+
+    if state in ['Complete', 'Failed', 'Cancelled']:
+        break
+
+    time.sleep(10)  # Check every 10 seconds
+```
+
+### Retrieving Workflow Outputs
+
+```python
+# Get all outputs
+outputs = platform.get_task_outputs(task)
+print(f"Outputs: {outputs}")
+
+# Get a specific output
+output_file = platform.get_task_output(task, "output_file")
+print(f"Output file: {output_file}")
+```
+
+## Example Script
+
+See the `examples/wes_platform_example.py` script for a complete example of using the WES platform implementation.
+
+## Configuration
+
+The WES platform can be configured using the following environment variables:
+
+- `WES_API_ENDPOINT`: The URL of the WES API endpoint
+- `WES_AUTH_TOKEN`: Authentication token for the WES API
+

examples/wes_platform_example.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python3
+'''
+Example script demonstrating how to use the WES Platform implementation
+'''
+import json
+import sys
+import time
+import logging
+import argparse
+
+from cwl_platform import PlatformFactory
+
+def main():
+    '''
+    Main function
+    '''
+    # Set up logging
+    logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+    logger = logging.getLogger(__name__)
+
+    # Parse command line arguments
+    parser = argparse.ArgumentParser(description='WES Platform Example')
+    parser.add_argument('--api-endpoint', required=True, help='WES API endpoint URL')
+    parser.add_argument('--auth-token', help='Authentication token for the WES API')
+    parser.add_argument('--workflow', required=True, help='Path to workflow file or URL')
+    parser.add_argument('--params', required=True, help='Path to workflow parameters JSON file')
+    args = parser.parse_args()
+
+    # Initialize the platform factory
+    factory = PlatformFactory()
+
+    try:
+        # Get the WES platform
+        platform = factory.get_platform('WES')
+        logger.info("Initialized WES platform")
+
+        # Connect to the WES API
+        connected = platform.connect(
+            api_endpoint=args.api_endpoint,
+            auth_token=args.auth_token
+        )
+
+        if not connected:
+            logger.error("Failed to connect to WES API")
+            return 1
+
+        logger.info("Connected to WES API")
+
+        # Create a virtual project (not used by WES but required by the API)
+        project = platform.create_project('wes-example', 'WES Example Project')
+        logger.info("Created virtual project: %s", project['name'])
+
+        # Load workflow parameters
+        with open(args.params, 'r', encoding='utf-8') as f:
+            parameters = json.load(f)
+
+        # Submit the workflow
+        task = platform.submit_task(
+            name="WES Example Task",
+            project=project,
+            workflow=args.workflow,
+            parameters=parameters
+        )
+
+        if not task:
+            logger.error("Failed to submit workflow")
+            return 1
+
+        logger.info("Submitted workflow with run ID: %s", task.run_id)
+
+        # Monitor the workflow execution
+        while True:
+            state = platform.get_task_state(task, refresh=True)
+            logger.info("Workflow state: %s", state)
+
+            if state in ['Complete', 'Failed', 'Cancelled']:
+                break
+
+            time.sleep(10)  # Check every 10 seconds
+
+        # Get the workflow outputs
+        if state == 'Complete':
+            outputs = platform.get_task_outputs(task)
+            logger.info("Workflow completed successfully")
+            logger.info("Outputs: %s", outputs)
+            return 0
+
+        logger.error("Workflow failed or was cancelled")
+        return 1
+
+    except Exception as e: # pylint: disable=broad-except
+        logger.exception("Error: %s", e)
+        return 1
+
+if __name__ == '__main__':
+    sys.exit(main())

src/cwl_platform/__init__.py

@@ -6,13 +6,15 @@
 
 from .arvados_platform import ArvadosPlatform
 from .sevenbridges_platform import SevenBridgesPlatform
+from .ngs360_platform import NGS360Platform
 #from .omics_platform import OmicsPlatform
 
 # Move this for a config file
 SUPPORTED_PLATFORMS = {
     'Arvados': ArvadosPlatform,
 #    'Omics': OmicsPlatform,
-    'SevenBridges': SevenBridgesPlatform
+    'SevenBridges': SevenBridgesPlatform,
+    'NGS360': NGS360Platform
 }
 
 class PlatformFactory():