tidy

aws/ec2/userdata_annotate_riis.sh

@@ -1,19 +1,14 @@
 #!/bin/bash
 # This is the user data script to be executed on an EC2 instance.
-
-aws configure set default.region us-east-1 && \
-aws configure set default.output json
-
 sudo apt update
-#sudo apt install apache2 certbot plocate unzip
 sudo apt install docker.io
 sudo apt install docker-compose-v2
 
 # TODO: change this to pull a Docker image
 git clone https://github.com/lifemapper/bison.git
 
 cd bison
-sudo docker compose -f docker-compose.task.yml up -d
-#sudo docker compose -f docker-compose.development.yml -f docker-compose.yml  up
+sudo docker compose -f compose.annotate_riis.yml up -d
+#sudo docker compose -f compose.development.yml -f compose.yml  up
 # Executes from /home/bison directory, which contains bison code
-sudo docker exec bison-bison-1 venv/bin/python -m bison.tools.annotate_riis
+sudo docker exec bison-bison-1 venv/bin/python -m bison.task.annotate_riis

aws/events/bison_s0_resolve_riis_lambda.py

@@ -16,8 +16,7 @@
 timeout = 900
 waittime = 1
 EC2_TASK_INSTANCE_ID = "i-0c7e54e257d5c8574"
-EC2_KEY = bison_task_key
-# bison_task_ec2 = "arn:aws:ec2:us-east-1:321942852011:instance/i-0595bfd381e64d2c9"
+# EC2_TASK_INSTANCE_ARN = "arn:aws:ec2:us-east-1:321942852011:instance/i-0595bfd381e64d2c9"
 
 # Initialize Botocore session
 session = boto3.session.Session()
@@ -29,7 +28,7 @@
 client_ssm = session.client("ssm", config=config)
 
 # Bison command
-bison_script = "venv/bin/python -m bison.tools.annotate_riis"
+bison_script = "venv/bin/python -m bison.task.annotate_riis"
 
 
 # --------------------------------------------------------------------------------------
@@ -56,9 +55,9 @@ def lambda_handler(event, context):
     try:
         instance_meta = response["StartingInstances"][0]
     except KeyError:
-        raise Exception(f"Invalid response returned {instance_meta}")
+        raise Exception(f"Invalid response returned {response}")
     except ValueError:
-        raise Exception(f"No instances returned in {instance_meta}")
+        raise Exception(f"No instances returned in {response}")
     except Exception:
         raise
 
@@ -68,10 +67,10 @@ def lambda_handler(event, context):
     print(f"Started instance {instance_meta['InstanceId']}. ")
     print(f"Moved from {curr_state} to {prev_state}")
 
-    # sudo docker compose -f docker-compose.task.yml up
+    # sudo docker compose -f compose.annotate_riis.yml up
     response = client_ssm.send_command(
         DocumentName='AWS-RunShellScript',
         Parameters={'commands': [bison_script]},
-        InstanceIds=[bison_task_instance_id]
+        InstanceIds=[EC2_TASK_INSTANCE_ID]
     )
     return instance_id

aws/permissions/role/bison_ec2_s3_role_trust_relationships.json

@@ -15,4 +15,4 @@
 			]
 		}
 	]
-}
+}

aws/permissions/role/bison_redshift_lambda_role_trust_relationships.json

@@ -24,4 +24,4 @@
             "Action": "sts:AssumeRole"
         }
     ]
-}
+}

aws_scripts/bison_matrix_stats.py

@@ -7,7 +7,7 @@
 from bison.common.log import Logger
 from bison.common.aws_util import S3
 from bison.common.constants import (
-    PROJECT, S3_BUCKET, S3_OUT_DIR, TMP_PATH, WORKFLOW_ROLE, S3_LOG_DIR
+    REGION, S3_BUCKET, S3_OUT_DIR, TMP_PATH, S3_LOG_DIR
 )
 
 n = DT.datetime.now()
@@ -398,7 +398,7 @@ def write_to_csv(self, filename):
     script_name = os.path.splitext(os.path.basename(__file__))[0]
     logger = Logger(script_name)
 
-    s3 = S3(PROJECT, WORKFLOW_ROLE)
+    s3 = S3(region=REGION)
 
     # Read directly into DataFrame
     orig_df = s3.get_dataframe_from_parquet(