Increase tw-cli to v0.9.2

Dockerfile

@@ -4,9 +4,9 @@ ARG LAMBDA_TASK_ROOT=/var/task
 
 RUN apt-get update && apt-get upgrade -y && \
     apt-get install --no-install-recommends --yes wget ca-certificates && \
-    wget https://github.com/seqeralabs/tower-cli/releases/download/v0.5/tw-0.5-linux-x86_64 && \
-    chmod +x ./tw-0.5-linux-x86_64 && \
-    mv ./tw-0.5-linux-x86_64 /usr/local/bin/tw && \
+    wget https://github.com/seqeralabs/tower-cli/releases/download/v0.9.2/tw-linux-x86_64 && \
+    chmod +x ./tw-linux-x86_64 && \
+    mv ./tw-linux-x86_64 /usr/local/bin/tw && \
     rm -rf /var/lib/apt/lists/*
 
 WORKDIR ${LAMBDA_TASK_ROOT}

app.py

@@ -107,7 +107,7 @@ def get_parameters(session=None, params_to_retrieve=None):
         underlying image or Lambda function code.
 
         Example: {'Parameter': 
-            {'Name': '/lambda_tutorial/workspace_id', 
+            {'Name': '/lambda_tutorial_adrian/workspace_id', 
             'Type': 'String', 
             'Value': '34830707738561', 
             'Version': 3, 
@@ -124,7 +124,7 @@ def get_parameters(session=None, params_to_retrieve=None):
             logger.debug(tw_params[param])
 
             # Update logging_level based on logging_level key.
-            if param == '/lambda_tutorial/logging_level':
+            if param == '/lambda_tutorial_adrian/logging_level':
                 desired_level = tw_params[param]
                 if desired_level.upper() != "DEBUG":
                     update_logging_level(desired_level=desired_level)
@@ -148,13 +148,13 @@ def get_secrets(session=None):
         for a simpler implementation.
 
         Example: {'tower_PAT': 
-            {'ARN': 'arn:aws:secretsmanager:YOUR_REGION:YOUR_ACCOUNT:secret:lambda_tutorial/tower_PAT-Abcdef', 
-            'Name': 'lambda_tutorial/tower_PAT', 
+            {'ARN': 'arn:aws:secretsmanager:YOUR_REGION:YOUR_ACCOUNT:secret:lambda_tutorial_adrian/tower_PAT-Abcdef', 
+            'Name': 'lambda_tutorial_adrian/tower_PAT', 
             'SecretString': 'eyJ0.....', 
            ...
     '''
     tw_secrets = {}
-    secret_name = "lambda_tutorial/tower_PAT"
+    secret_name = "lambda_tutorial_adrian/tower_PAT"
     secrets_client: SecretsManagerClient = session.client('secretsmanager')
 
     try:
@@ -205,7 +205,7 @@ def set_environment_variables(tw_params=None, tw_secrets=None):
         Set this before running tw transactions.
     '''
     os.environ['TOWER_ACCESS_TOKEN'] = tw_secrets['tower_PAT']
-    os.environ['TOWER_API_ENDPOINT'] = tw_params['/lambda_tutorial/tower_api_endpoint']
+    os.environ['TOWER_API_ENDPOINT'] = tw_params['/lambda_tutorial_adrian/tower_api_endpoint']
 
 
 def check_if_event_in_scope(event=None, tw_params=None):
@@ -216,23 +216,23 @@ def check_if_event_in_scope(event=None, tw_params=None):
             2) Boto3 S3 client list_objects requires the Prefix parameter to have a '/' at the end
                 so we add this back in since the split function removes it
         Example of object key:
-            "lambda_tutorial/samplesheet_full.csv"
+            "lambda_tutorial_adrian/samplesheet_full.csv"
     '''
     # Check if event should be processed or ignored. Cease processing if:
     #   1) Notification isn't from designated prefix.
     #   2) Notification doesn't match file type trigger.
     event_key = event['Records'][0]['s3']['object']['key']
     filetype = event_key.rsplit('.', 1)[1]
 
-    if not event_key.startswith(tw_params['/lambda_tutorial/s3_root_prefix']):
+    if not event_key.startswith(tw_params['/lambda_tutorial_adrian/s3_root_prefix']):
         # Event is out of scope and should not be retried.
         log_error_and_raise_exception(
             errorstring=f"Event key: {event_key} does not match designated prefix. Cease processing.",
             e=None,
             retry_transaction=False
         )
 
-    if filetype not in tw_params['/lambda_tutorial/samplesheet_file_types'].split(','):
+    if filetype not in tw_params['/lambda_tutorial_adrian/samplesheet_file_types'].split(','):
         # Event is out of scope and should not be retried.
         log_error_and_raise_exception(
             errorstring=f"Event key: {event_key} not a trigger file type. Cease processing.",
@@ -253,7 +253,7 @@ def download_samplesheet(session=None, event=None):
     try:
         s3bucket = event['Records'][0]['s3']['bucket']['name']
         s3key = event['Records'][0]['s3']['object']['key']
-        # Example of key: "lambda_tutorial/complete.txt"
+        # Example of key: "lambda_tutorial_adrian/complete.txt"
         samplesheet_filename = s3key.rsplit('/')[1]
         dataset_name = samplesheet_filename.split('.')[0]
 
@@ -296,7 +296,7 @@ def create_tower_dataset(local_samplesheet=None, dataset_name=None, event=None,
     s3key = event['Records'][0]['s3']['object']['key']
     s3source = f"s3://{s3bucket}/{s3key}"
 
-    workspace_id = tw_params['/lambda_tutorial/workspace_id']
+    workspace_id = tw_params['/lambda_tutorial_adrian/workspace_id']
     description = f"Generated by Lambda {datetime.datetime.now().strftime('%Y-%m-%d %H:%M')} from {s3source}"
 
     # Python subprocess module works best with command split into array. 
@@ -340,8 +340,8 @@ def launch_tower_pipeline(datasetid=None, tw_params=None):
             3) Invoke the target pipeline passing the parameter file with the defined input source.
     '''
     # Extract parameters for inclusion in tw commands
-    workspace_id = tw_params['/lambda_tutorial/workspace_id']
-    target_pipeline_name = tw_params['/lambda_tutorial/target_pipeline_name']
+    workspace_id = tw_params['/lambda_tutorial_adrian/workspace_id']
+    target_pipeline_name = tw_params['/lambda_tutorial_adrian/target_pipeline_name']
 
     # Generate command for dataset URL retrieval (required for subsequent pipeline launch comand)
     command = f"tw -o json datasets url --workspace={workspace_id} --id={datasetid}"
@@ -469,7 +469,7 @@ def update_logging_level(desired_level=None):
         logger.warning(f"Modified logging level to {desired_level}")
     else:
         # Create logger alert and stick with default DEBUG
-        logger.error(f"SSM parameter 'lambda_tutorial/logging_level' value {desired_level} is not a valid logging level. Continuing with DEBUG.")
+        logger.error(f"SSM parameter 'lambda_tutorial_adrian/logging_level' value {desired_level} is not a valid logging level. Continuing with DEBUG.")
 
 
 def handler(event, context):
@@ -490,12 +490,12 @@ def handler(event, context):
         #   Keynames are odd for a Python dictionary, but it works and aligns with required AWS set-up commands.
         #   Keep logging_level as first entry to control logging behaviour of other values when retrieved.
         params_to_retrieve = [
-            '/lambda_tutorial/logging_level',
-            '/lambda_tutorial/workspace_id',
-            '/lambda_tutorial/s3_root_prefix',
-            '/lambda_tutorial/samplesheet_file_types',
-            '/lambda_tutorial/target_pipeline_name',
-            "/lambda_tutorial/tower_api_endpoint"
+            '/lambda_tutorial_adrian/logging_level',
+            '/lambda_tutorial_adrian/workspace_id',
+            '/lambda_tutorial_adrian/s3_root_prefix',
+            '/lambda_tutorial_adrian/samplesheet_file_types',
+            '/lambda_tutorial_adrian/target_pipeline_name',
+            "/lambda_tutorial_adrian/tower_api_endpoint"
         ]
         tw_params = get_parameters(session=session, params_to_retrieve=params_to_retrieve)
         logger.debug(f"Parameters are: {tw_params}")

entry_script.sh

@@ -2,7 +2,7 @@
 
 # Reference: https://docs.aws.amazon.com/lambda/latest/dg/images-test.html
 if [ -z "${AWS_LAMBDA_RUNTIME_API}" ]; then
-  exec /usr/local/bin/aws-lambda-rie-x86_64 /usr/bin/python3 -m awslambdaric "$@"
+  exec /usr/local/bin/aws-lambda-rie-x86_64 /usr/local/bin/python -m awslambdaric "$@"
 else
-  exec /usr/bin/python3 -m awslambdaric "$@"
+  exec /usr/local/bin/python -m awslambdaric "$@"
 fi

samplesheet_full.csv

@@ -0,0 +1,9 @@
+sample,fastq_1,fastq_2,strandedness
+GM12878_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603629_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603629_T1_2.fastq.gz,reverse
+GM12878_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603630_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603630_T1_2.fastq.gz,reverse
+K562_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603392_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603392_T1_2.fastq.gz,reverse
+K562_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603393_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603393_T1_2.fastq.gz,reverse
+MCF7_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370490_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370490_T1_2.fastq.gz,reverse
+MCF7_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370491_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370491_T1_2.fastq.gz,reverse
+H1_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370468_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370468_T1_2.fastq.gz,reverse
+H1_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370469_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370469_T1_2.fastq.gz,reverse

testing/test_event_good.json

@@ -3,7 +3,7 @@
       {
         "eventVersion": "2.0",
         "eventSource": "aws:s3",
-        "awsRegion": "YOUR_AWS_REGION",
+        "awsRegion": "us-east-1",
         "eventTime": "1970-01-01T00:00:00.000Z",
         "eventName": "ObjectCreated:Put",
         "userIdentity": {
@@ -20,14 +20,14 @@
           "s3SchemaVersion": "1.0",
           "configurationId": "testConfigRule",
           "bucket": {
-            "name": "YOUR_S3_BUCKET",
+            "name": "adrian-navarro-test",
             "ownerIdentity": {
               "principalId": "EXAMPLE"
             },
-            "arn": "arn:aws:s3:::example-bucket"
+            "arn": "arn:aws:s3:::adrian-navarro-test"
           },
           "object": {
-            "key": "lambda_tutorial/samplesheet_full.csv",
+            "key": "lambda_tutorial/adrian/samplesheet_full.csv",
             "size": 1024,
             "eTag": "0123456789abcdef0123456789abcdef",
             "sequencer": "0A1B2C3D4E5F678901"