From ecd930d7baae1c7fe2f8b466383cb8cff878a105 Mon Sep 17 00:00:00 2001 From: Alexis Lucattini Date: Sun, 3 Nov 2024 20:20:14 +1100 Subject: [PATCH] Standardise loggers in python lambda functions Resolves https://github.com/umccr/orcabus/issues/644 --- .../check_or_launch_job_lambda.py | 8 ++++++-- .../fastq_list_rows_to_cwl_input.py | 6 +++++- .../get_metadata_objects_from_samplesheet.py | 6 +++++- .../icav2_launch_pipeline_lambda.py | 6 +++++- .../lambdas/check_success_py/check_success.py | 8 ++++++-- .../lambdas/compress_icav2_vcf/compress_icav2_vcf.py | 10 +++++++--- .../lambdas/delete_cache_uri_py/delete_cache_uri.py | 6 +++++- .../generate_copy_manifest_dict.py | 6 +++++- .../lambdas/set_outputs_json_py/set_outputs_json.py | 6 +++++- .../generate_pieriandx_objects.py | 8 ++++++-- .../generate_samplesheet_py/generate_samplesheet.py | 7 +++++-- .../get_informaticsjob_and_report_status.py | 8 ++++++-- .../get_demultiplex_stats_py/get_demultiplex_stats.py | 6 +++++- .../lambdas/get_fastqc_stats/run_fastqc.py | 7 +++++-- .../lambdas/get_sequali_stats/get_sequali_stats.py | 6 +++++- .../build_cttso_v2_samplesheet.py | 8 ++++++-- .../collect_qc_metrics_from_alignment_directory.py | 6 +++++- .../generate_event_data_objects.py | 6 +++++- .../get_data_from_redcap_py/get_data_from_redcap.py | 7 +++++-- .../get_deidentified_case_metadata.py | 8 ++++++-- .../get_identified_case_metadata.py | 8 ++++++-- .../get_pieriandx_data_files.py | 7 +++++-- .../lambdas/set_outputs_json_py/set_outputs_json.py | 6 +++++- .../lambdas/set_outputs_json_py/set_outputs_json.py | 6 +++++- .../lambdas/set_outputs_json_py/set_outputs_json.py | 6 +++++- 25 files changed, 134 insertions(+), 38 deletions(-) diff --git a/lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/check_or_launch_job_lambda.py b/lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/check_or_launch_job_lambda.py index 74d10c778..8ba38daf4 100644 --- a/lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/check_or_launch_job_lambda.py +++ b/lib/workload/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/lib/workload/components/python-lambda-fastq-list-rows-to-cwl-input/fastq_list_rows_to_cwl_input_py/fastq_list_rows_to_cwl_input.py b/lib/workload/components/python-lambda-fastq-list-rows-to-cwl-input/fastq_list_rows_to_cwl_input_py/fastq_list_rows_to_cwl_input.py index e2a22464a..7051169b9 100644 --- a/lib/workload/components/python-lambda-fastq-list-rows-to-cwl-input/fastq_list_rows_to_cwl_input_py/fastq_list_rows_to_cwl_input.py +++ b/lib/workload/components/python-lambda-fastq-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/lib/workload/components/python-lambda-get-metadata-objects-from-samplesheet/get_metadata_objects_from_samplesheet_py/get_metadata_objects_from_samplesheet.py b/lib/workload/components/python-lambda-get-metadata-objects-from-samplesheet/get_metadata_objects_from_samplesheet_py/get_metadata_objects_from_samplesheet.py index 11d20f6a7..8471324c7 100644 --- a/lib/workload/components/python-lambda-get-metadata-objects-from-samplesheet/get_metadata_objects_from_samplesheet_py/get_metadata_objects_from_samplesheet.py +++ b/lib/workload/components/python-lambda-get-metadata-objects-from-samplesheet/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/lib/workload/components/sfn-icav2-ready-event-handler/icav2_launch_pipeline_lambda_py/icav2_launch_pipeline_lambda.py b/lib/workload/components/sfn-icav2-ready-event-handler/icav2_launch_pipeline_lambda_py/icav2_launch_pipeline_lambda.py index 877b5eced..827d10cfd 100644 --- a/lib/workload/components/sfn-icav2-ready-event-handler/icav2_launch_pipeline_lambda_py/icav2_launch_pipeline_lambda.py +++ b/lib/workload/components/sfn-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/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/check_success_py/check_success.py b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/check_success_py/check_success.py index df1104361..5d66cab04 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/check_success_py/check_success.py +++ b/lib/workload/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/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/compress_icav2_vcf/compress_icav2_vcf.py b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/compress_icav2_vcf/compress_icav2_vcf.py index 2dc450bf3..7d4ac959e 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/compress_icav2_vcf/compress_icav2_vcf.py +++ b/lib/workload/stateless/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/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/delete_cache_uri.py b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/delete_cache_uri.py index d38f0857f..35787fb6c 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/delete_cache_uri.py +++ b/lib/workload/stateless/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/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/generate_copy_manifest_dict_py/generate_copy_manifest_dict.py b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/generate_copy_manifest_dict_py/generate_copy_manifest_dict.py index 1da66023b..70226cdb7 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/generate_copy_manifest_dict_py/generate_copy_manifest_dict.py +++ b/lib/workload/stateless/stacks/cttso-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/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py index 1fbf2ad5a..1d2982b06 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py +++ b/lib/workload/stateless/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/lib/workload/stateless/stacks/pieriandx-pipeline-manager/lambdas/generate_pieriandx_objects_py/generate_pieriandx_objects.py b/lib/workload/stateless/stacks/pieriandx-pipeline-manager/lambdas/generate_pieriandx_objects_py/generate_pieriandx_objects.py index 064600506..e73f44166 100644 --- a/lib/workload/stateless/stacks/pieriandx-pipeline-manager/lambdas/generate_pieriandx_objects_py/generate_pieriandx_objects.py +++ b/lib/workload/stateless/stacks/pieriandx-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/lib/workload/stateless/stacks/pieriandx-pipeline-manager/lambdas/generate_samplesheet_py/generate_samplesheet.py b/lib/workload/stateless/stacks/pieriandx-pipeline-manager/lambdas/generate_samplesheet_py/generate_samplesheet.py index 573866520..7f1f6f05a 100644 --- a/lib/workload/stateless/stacks/pieriandx-pipeline-manager/lambdas/generate_samplesheet_py/generate_samplesheet.py +++ b/lib/workload/stateless/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/lib/workload/stateless/stacks/pieriandx-pipeline-manager/lambdas/get_informaticsjob_and_report_status_py/get_informaticsjob_and_report_status.py b/lib/workload/stateless/stacks/pieriandx-pipeline-manager/lambdas/get_informaticsjob_and_report_status_py/get_informaticsjob_and_report_status.py index 640507ec4..eb40298cd 100644 --- a/lib/workload/stateless/stacks/pieriandx-pipeline-manager/lambdas/get_informaticsjob_and_report_status_py/get_informaticsjob_and_report_status.py +++ b/lib/workload/stateless/stacks/pieriandx-pipeline-manager/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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_demultiplex_stats_py/get_demultiplex_stats.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_demultiplex_stats_py/get_demultiplex_stats.py index 12fe6c70f..e0775aca4 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_demultiplex_stats_py/get_demultiplex_stats.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_fastqc_stats/run_fastqc.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_fastqc_stats/run_fastqc.py index df379e699..7da64269d 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_fastqc_stats/run_fastqc.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_sequali_stats/get_sequali_stats.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_sequali_stats/get_sequali_stats.py index 2b92069a3..02af82f94 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/clag/part_2/fastq-list-rows-event-shower/lambdas/get_sequali_stats/get_sequali_stats.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_3/fastq-list-row-event-shower-complete-to-cttsov2-ready/lambdas/build_cttsov2_samplesheet_py/build_cttso_v2_samplesheet.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_3/fastq-list-row-event-shower-complete-to-cttsov2-ready/lambdas/build_cttsov2_samplesheet_py/build_cttso_v2_samplesheet.py index 522fb637d..3ae841a48 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_3/fastq-list-row-event-shower-complete-to-cttsov2-ready/lambdas/build_cttsov2_samplesheet_py/build_cttso_v2_samplesheet.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_3/fastq-list-row-event-shower-complete-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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/push-fastq-list-row-qc-complete-event/lambdas/collect_qc_metrics_from_alignment_directory_py/collect_qc_metrics_from_alignment_directory.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/push-fastq-list-row-qc-complete-event/lambdas/collect_qc_metrics_from_alignment_directory_py/collect_qc_metrics_from_alignment_directory.py index aa1e979fc..12b51b685 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/push-fastq-list-row-qc-complete-event/lambdas/collect_qc_metrics_from_alignment_directory_py/collect_qc_metrics_from_alignment_directory.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/push-fastq-list-row-qc-complete-event/lambdas/collect_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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/push-fastq-list-row-qc-complete-event/lambdas/generate_event_data_objects_py/generate_event_data_objects.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/push-fastq-list-row-qc-complete-event/lambdas/generate_event_data_objects_py/generate_event_data_objects.py index bf281a42b..53eeb1d9b 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/push-fastq-list-row-qc-complete-event/lambdas/generate_event_data_objects_py/generate_event_data_objects.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/push-fastq-list-row-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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_data_from_redcap_py/get_data_from_redcap.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_data_from_redcap_py/get_data_from_redcap.py index 93ba97ac6..1f65e8e3c 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_data_from_redcap_py/get_data_from_redcap.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_deidentified_case_metadata_py/get_deidentified_case_metadata.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_deidentified_case_metadata_py/get_deidentified_case_metadata.py index 8fd513f6e..92d9e2b8c 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_deidentified_case_metadata_py/get_deidentified_case_metadata.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_identified_case_metadata_py/get_identified_case_metadata.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_identified_case_metadata_py/get_identified_case_metadata.py index 40b07d516..a146478bd 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_identified_case_metadata_py/get_identified_case_metadata.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-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/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_pieriandx_data_files_py/get_pieriandx_data_files.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_pieriandx_data_files_py/get_pieriandx_data_files.py index 078bea0ab..04cc8fa41 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-to-pieriandx-ready-event/lambdas/get_pieriandx_data_files_py/get_pieriandx_data_files.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_2/cttso-v2-output-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/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py b/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py index bbcc1e5d8..7ea20b089 100644 --- a/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py +++ b/lib/workload/stateless/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/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py b/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py index 3c1fc765f..3171b2a8c 100644 --- a/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py +++ b/lib/workload/stateless/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/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py b/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py index 27f9abc73..a853074bc 100644 --- a/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py +++ b/lib/workload/stateless/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':