Standardise loggers in python lambda functions

Resolves #644
umccr · Nov 3, 2024 · ecd930d · ecd930d
1 parent ed92fcf
commit ecd930d
Show file tree

Hide file tree

Showing 25 changed files with 134 additions and 38 deletions.
diff --git a/...d/components/icav2-copy-files/check_or_launch_job_lambda_py/check_or_launch_job_lambda.py b/...d/components/icav2-copy-files/check_or_launch_job_lambda_py/check_or_launch_job_lambda.py
@@ -50,8 +50,12 @@
     from mypy_boto3_secretsmanager import SecretsManagerClient
 
 # Set logging
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
+logger = logging.getLogger()
 
 # Globals
 SUCCESS_STATES = [

diff --git a/...tq-list-rows-to-cwl-input/fastq_list_rows_to_cwl_input_py/fastq_list_rows_to_cwl_input.py b/...tq-list-rows-to-cwl-input/fastq_list_rows_to_cwl_input_py/fastq_list_rows_to_cwl_input.py
@@ -13,8 +13,12 @@
 from typing import Dict, Union
 
 # Set logger
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def pascal_case_to_snake_case(pascal_case_str: str) -> str:

diff --git a/...lesheet/get_metadata_objects_from_samplesheet_py/get_metadata_objects_from_samplesheet.py b/...lesheet/get_metadata_objects_from_samplesheet_py/get_metadata_objects_from_samplesheet.py
@@ -12,8 +12,12 @@
 from metadata_tools import get_all_libraries
 
 # Logger
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_library_objs(library_id_list: List[str]) -> List[Dict]:

diff --git a/...icav2-ready-event-handler/icav2_launch_pipeline_lambda_py/icav2_launch_pipeline_lambda.py b/...icav2-ready-event-handler/icav2_launch_pipeline_lambda_py/icav2_launch_pipeline_lambda.py
@@ -154,8 +154,12 @@
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 # Set loggers
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':

diff --git a/...load/stateless/stacks/cttso-v2-pipeline-manager/lambdas/check_success_py/check_success.py b/...load/stateless/stacks/cttso-v2-pipeline-manager/lambdas/check_success_py/check_success.py
@@ -28,8 +28,12 @@
 from wrapica.enums import DataType
 
 # Set logger
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
+logger = logging.getLogger()
 
 if typing.TYPE_CHECKING:
     from mypy_boto3_secretsmanager.client import SecretsManagerClient

diff --git a/...ateless/stacks/cttso-v2-pipeline-manager/lambdas/compress_icav2_vcf/compress_icav2_vcf.py b/...ateless/stacks/cttso-v2-pipeline-manager/lambdas/compress_icav2_vcf/compress_icav2_vcf.py
@@ -25,9 +25,13 @@
     from mypy_boto3_ssm import SSMClient
     from mypy_boto3_secretsmanager import SecretsManagerClient
 
-logger = logging.getLogger(__name__)
-
-logging.basicConfig(level=logging.INFO)
+# Set logger
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
+logger = logging.getLogger()
 
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 

diff --git a/...tateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/delete_cache_uri.py b/...tateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/delete_cache_uri.py
@@ -33,8 +33,12 @@
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 # Set loggers
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':

diff --git a/...v2-pipeline-manager/lambdas/generate_copy_manifest_dict_py/generate_copy_manifest_dict.py b/...v2-pipeline-manager/lambdas/generate_copy_manifest_dict_py/generate_copy_manifest_dict.py
@@ -50,8 +50,12 @@
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 # Set loggers
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':

diff --git a/...tateless/stacks/cttso-v2-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py b/...tateless/stacks/cttso-v2-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py
@@ -46,8 +46,12 @@
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 # Set loggers
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':

diff --git a/...andx-pipeline-manager/lambdas/generate_pieriandx_objects_py/generate_pieriandx_objects.py b/...andx-pipeline-manager/lambdas/generate_pieriandx_objects_py/generate_pieriandx_objects.py
@@ -102,8 +102,12 @@
 ]
 
 # Set basic logger
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
+logger = logging.getLogger()
 
 
 

diff --git a/...stacks/pieriandx-pipeline-manager/lambdas/generate_samplesheet_py/generate_samplesheet.py b/...stacks/pieriandx-pipeline-manager/lambdas/generate_samplesheet_py/generate_samplesheet.py
@@ -31,9 +31,12 @@
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 # Set loggers
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
-
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':
     """

diff --git a/...r/lambdas/get_informaticsjob_and_report_status_py/get_informaticsjob_and_report_status.py b/...r/lambdas/get_informaticsjob_and_report_status_py/get_informaticsjob_and_report_status.py
@@ -38,8 +38,12 @@
 from pieriandx_pipeline_tools.utils.secretsmanager_helpers import set_pieriandx_env_vars
 
 # Set logger
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
+logger = logging.getLogger()
 
 
 JOB_STATUS_BOOL = {

diff --git a/..._2/fastq-list-rows-event-shower/lambdas/get_demultiplex_stats_py/get_demultiplex_stats.py b/..._2/fastq-list-rows-event-shower/lambdas/get_demultiplex_stats_py/get_demultiplex_stats.py
@@ -56,8 +56,12 @@
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 # Set loggers
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':

diff --git a/...onstructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_fastqc_stats/run_fastqc.py b/...onstructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_fastqc_stats/run_fastqc.py
@@ -64,9 +64,12 @@
 """
 
 # Set loggers
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
-
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':
     """

diff --git a/...s/clag/part_2/fastq-list-rows-event-shower/lambdas/get_sequali_stats/get_sequali_stats.py b/...s/clag/part_2/fastq-list-rows-event-shower/lambdas/get_sequali_stats/get_sequali_stats.py
@@ -75,8 +75,12 @@
 """
 
 # Set loggers
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':

diff --git a/...plete-to-cttsov2-ready/lambdas/build_cttsov2_samplesheet_py/build_cttso_v2_samplesheet.py b/...plete-to-cttsov2-ready/lambdas/build_cttsov2_samplesheet_py/build_cttso_v2_samplesheet.py
@@ -11,8 +11,12 @@
 from typing import Optional
 import logging
 
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.INFO)
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
+logger = logging.getLogger()
 
 # Globals
 HEADER = {

diff --git a/...ect_qc_metrics_from_alignment_directory_py/collect_qc_metrics_from_alignment_directory.py b/...ect_qc_metrics_from_alignment_directory_py/collect_qc_metrics_from_alignment_directory.py
@@ -59,8 +59,12 @@
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 # Set logger
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':

diff --git a/...w-qc-complete-event/lambdas/generate_event_data_objects_py/generate_event_data_objects.py b/...w-qc-complete-event/lambdas/generate_event_data_objects_py/generate_event_data_objects.py
@@ -28,8 +28,12 @@
 from typing import Dict
 
 # Set log level
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def handler(event, context) -> Dict[str, Dict[str, str]]:

diff --git a/...2-output-to-pieriandx-ready-event/lambdas/get_data_from_redcap_py/get_data_from_redcap.py b/...2-output-to-pieriandx-ready-event/lambdas/get_data_from_redcap_py/get_data_from_redcap.py
@@ -24,9 +24,12 @@
     from mypy_boto3_lambda import LambdaClient
 
 # Set logger
-logging.basicConfig(level=logging.INFO)
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(level=logging.INFO)
 
 # Globals
 AUS_TIMEZONE = pytz.timezone("Australia/Melbourne")

diff --git a/...x-ready-event/lambdas/get_deidentified_case_metadata_py/get_deidentified_case_metadata.py b/...x-ready-event/lambdas/get_deidentified_case_metadata_py/get_deidentified_case_metadata.py
@@ -36,8 +36,12 @@
 
 
 # Set logger
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
+logger = logging.getLogger()
 
 # Globals
 AUS_TIMEZONE = pytz.timezone("Australia/Melbourne")

diff --git a/...iandx-ready-event/lambdas/get_identified_case_metadata_py/get_identified_case_metadata.py b/...iandx-ready-event/lambdas/get_identified_case_metadata_py/get_identified_case_metadata.py
@@ -49,8 +49,12 @@
 import logging
 
 # Set logger
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
+logger = logging.getLogger()
 
 # Globals
 AUS_TIMEZONE = pytz.timezone("Australia/Melbourne")

diff --git a/...-to-pieriandx-ready-event/lambdas/get_pieriandx_data_files_py/get_pieriandx_data_files.py b/...-to-pieriandx-ready-event/lambdas/get_pieriandx_data_files_py/get_pieriandx_data_files.py
@@ -52,9 +52,12 @@
 }
 
 # Set loggers
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
-
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':
     """

diff --git a/...ess/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py b/...ess/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py
@@ -44,8 +44,12 @@
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 # Set logger
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':

diff --git a/...less/stacks/tumor-normal-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py b/...less/stacks/tumor-normal-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py
@@ -45,8 +45,12 @@
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 # Set logger
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':

diff --git a/...stacks/wgts-alignment-qc-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py b/...stacks/wgts-alignment-qc-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py
@@ -48,8 +48,12 @@
 
 
 # Set logger
+logging.basicConfig(
+    level=logging.INFO,
+    force=True,
+    format='%(asctime)s %(message)s'
+)
 logger = logging.getLogger()
-logger.setLevel(logging.INFO)
 
 
 def get_secrets_manager_client() -> 'SecretsManagerClient':