run task on ec2; not working

lifemapper · Oct 16, 2024 · a64dce2 · a64dce2
1 parent 6771781
commit a64dce2
Show file tree

Hide file tree

Showing 4 changed files with 10 additions and 7 deletions.
diff --git a/aws/events/bison_s0_resolve_riis_lambda.py b/aws/events/bison_s0_resolve_riis_lambda.py
@@ -15,7 +15,8 @@
 external_schema = "redshift_spectrum"
 timeout = 900
 waittime = 1
-bison_task_instance_id = "i-0595bfd381e64d2c9"
+EC2_TASK_INSTANCE_ID = "i-0c7e54e257d5c8574"
+EC2_KEY = bison_task_key
 # bison_task_ec2 = "arn:aws:ec2:us-east-1:321942852011:instance/i-0595bfd381e64d2c9"
 
 # Initialize Botocore session
@@ -28,7 +29,8 @@
 client_ssm = session.client("ssm", config=config)
 
 # Bison command
-bison_script = "~/bison/bison/tools/annotate_riis.py"
+bison_script = "venv/bin/python -m bison.tools.annotate_riis"
+
 
 # --------------------------------------------------------------------------------------
 def lambda_handler(event, context):
@@ -47,7 +49,7 @@ def lambda_handler(event, context):
         Exception: on unknown error.
     """
     response = client_ec2.start_instances(
-        InstanceIds=[bison_task_instance_id],
+        InstanceIds=[EC2_TASK_INSTANCE_ID],
         AdditionalInfo="Task initiated by Lambda",
         DryRun=False
     )
@@ -69,7 +71,7 @@ def lambda_handler(event, context):
     # sudo docker compose -f docker-compose.task.yml up
     response = client_ssm.send_command(
         DocumentName='AWS-RunShellScript',
-        Parameters={'commands': [script]},
-        InstanceIds=exec_list
+        Parameters={'commands': [bison_script]},
+        InstanceIds=[bison_task_instance_id]
     )
     return instance_id
diff --git a/aws/permissions/policy/bison_create_run_ec2_policy.json b/aws/permissions/policy/bison_create_run_ec2_policy.json
@@ -12,4 +12,4 @@
 			"Resource": "arn:aws:ec2:us-east-1:321942852011:instance/i-0595bfd381e64d2c9"
 		}
 	]
-}
+}
diff --git a/bison/common/constants.py b/bison/common/constants.py
@@ -13,7 +13,7 @@
 GBIF_ODR_FNAME = "occurrence.parquet"
 
 TMP_PATH = "/tmp"
-
+EC2_TASK_INSTANCE_ID = "i-0c7e54e257d5c8574"
 S3_BUCKET = f"{PROJECT}-{AWS_ACCOUNT}-{REGION}"
 S3_IN_DIR = "input"
 S3_OUT_DIR = "output"

diff --git a/flask_app/task/routes.py b/flask_app/task/routes.py
@@ -22,6 +22,7 @@ def index():
     """
     return render_template("task.index.html")
 
+
 # .....................................................................................
 # .....................................................................................
 if __name__ == "__main__":
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,4 +12,4 @@ @@
     			"Resource": "arn:aws:ec2:us-east-1:321942852011:instance/i-0595bfd381e64d2c9"
     		}
     	]
-    }
+    }