add script for triggering remote job, reading logs, and opening simul…

…arium website

batch_test.py

@@ -0,0 +1,79 @@
+import boto3
+import time
+import webbrowser
+import uuid
+import argparse
+
+client = boto3.client('batch')
+cloudwatch = boto3.client('logs')
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-r", type=str, default="examples/recipes/v2/one_sphere.json", help="recipe")
+parser.add_argument("-c", type=str, default="examples/packing-configs/run.json", help="config")
+args = parser.parse_args()
+
+# Submit Job to AWS batch using config and recipe from commandline
+response = client.submit_job(
+    jobName=str(uuid.uuid4()),
+    jobQueue='arn:aws:batch:us-west-2:771753870375:job-queue/alli-ruge-job-queue',
+    jobDefinition='cellpack-test-job-definition',
+    parameters={},
+    containerOverrides={
+        'command': [
+            'echo',
+            'hello world',
+        ],
+        'environment': [
+            {
+                'name': 'config',
+                'value': args.c
+            },
+            {
+                'name': 'recipe',
+                'value': args.r
+            },
+        ],
+        'resourceRequirements': []
+    },
+)
+
+if response and response.get('jobId'):
+    jobId = response.get('jobId')
+    jobStatus = "N/A"
+    while jobStatus not in ["SUCCEEDED", "FAILED"]:
+        # While the job is processing, check job status every 2 seconds and
+        # print the status when it changes
+        time.sleep(2)
+        descriptionResponse = client.describe_jobs(
+            jobs=[
+                jobId,
+            ]
+        )
+        if descriptionResponse and descriptionResponse.get('jobs') and len(descriptionResponse.get('jobs')) > 0:
+            newStatus = descriptionResponse.get('jobs')[0].get("status")
+            if newStatus != jobStatus:
+                print(newStatus)
+                jobStatus = newStatus
+                logStreamName = descriptionResponse.get('jobs')[0].get("container", {}).get("logStreamName")
+        else:
+            print("something went wrong, leaving!")
+            continue
+
+    # Using logStreamName provided while checking status, get all of the logs from the job run
+    cloudwatchResponse = cloudwatch.get_log_events(
+        logStreamName=logStreamName,
+        logGroupIdentifier="/aws/batch/job"
+    )
+
+    print(f"\nLogs from AWS Batch Run:")
+    for event in cloudwatchResponse.get("events", {}):
+        message = event.get("message")
+        if message.startswith("View in Simularium:"):
+            # We found the log with the simularium url!
+            url = message[20:]
+            webbrowser.open_new_tab(url)
+        else:
+            print(message)
+else:
+    print("Error: response didn't have jobId")
+

cellpack/autopack/upy/simularium/simularium_helper.py

@@ -1403,6 +1403,7 @@ def post_and_open_file(self, file_name, open_results_in_browser=True):
         )
         if file_name and url:
             simulariumHelper.store_metadata(file_name, url, db="firebase")
+            print(f"View in Simularium: https://simularium.allencell.org/viewer?trajUrl={url}")
             if open_results_in_browser:
                 simulariumHelper.open_in_simularium(url)
 
@@ -1411,7 +1412,7 @@ def store_result_file(file_path, storage=None):
         if storage == "aws":
             handler = DATABASE_IDS.handlers().get(storage)
             initialized_handler = handler(
-                bucket_name="cellpack-results",
+                bucket_name="cellpack-demo",
                 sub_folder_name="simularium",
                 region_name="us-west-2",
             )