From 912f0f6c7c1bca204926d0c70ba8740ca7b242ce Mon Sep 17 00:00:00 2001 From: Alexis Lucattini Date: Sun, 10 Nov 2024 19:17:54 +1100 Subject: [PATCH] Sanitise subject id for oncoanalyser / sash / nf workflows --- .../lambdas/generate_dna_payload_py/generate_dna_payload.py | 2 +- .../lambdas/generate_rna_payload_py/generate_rna_payload.py | 2 +- .../lambdas/generate_sash_payload_py/generate_sash_payload.py | 2 +- .../get_oncoanalyser_dna_rna_payload.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/handy-pal/part_3/launch-oncoanalyser-ready-events/lambdas/generate_dna_payload_py/generate_dna_payload.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/handy-pal/part_3/launch-oncoanalyser-ready-events/lambdas/generate_dna_payload_py/generate_dna_payload.py index 43976f858..e01f98d03 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/handy-pal/part_3/launch-oncoanalyser-ready-events/lambdas/generate_dna_payload_py/generate_dna_payload.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/handy-pal/part_3/launch-oncoanalyser-ready-events/lambdas/generate_dna_payload_py/generate_dna_payload.py @@ -89,7 +89,7 @@ def handler(event, context) -> Dict: "input_event_data": { "mode": MODE, "analysisType": ANALYSIS_TYPE, - "subjectId": subject_id, + "subjectId": subject_id.replace(" ", "_"), "tumorDnaSampleId": tumor_library_id, "normalDnaSampleId": normal_library_id, "tumorDnaBamUri": join_url_paths(dragen_somatic_output_s3_uri, tumor_library_id + "_tumor.bam"), diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/handy-pal/part_3/launch-oncoanalyser-ready-events/lambdas/generate_rna_payload_py/generate_rna_payload.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/handy-pal/part_3/launch-oncoanalyser-ready-events/lambdas/generate_rna_payload_py/generate_rna_payload.py index 8fc1a9dc6..2c6c3fa5b 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/handy-pal/part_3/launch-oncoanalyser-ready-events/lambdas/generate_rna_payload_py/generate_rna_payload.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/handy-pal/part_3/launch-oncoanalyser-ready-events/lambdas/generate_rna_payload_py/generate_rna_payload.py @@ -47,7 +47,7 @@ def handler(event, context) -> Dict: "input_event_data": { "mode": MODE, "analysisType": ANALYSIS_TYPE, - "subjectId": subject_id, + "subjectId": subject_id.replace(" ", "_"), "tumorRnaSampleId": tumor_library_id, "tumorRnaFastqListRows": tumor_fastq_list_rows, }, diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/t-rex/part_2/oncoanalyser-dna-complete-to-sash-ready/lambdas/generate_sash_payload_py/generate_sash_payload.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/t-rex/part_2/oncoanalyser-dna-complete-to-sash-ready/lambdas/generate_sash_payload_py/generate_sash_payload.py index f72e596b1..f842ffc1c 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/t-rex/part_2/oncoanalyser-dna-complete-to-sash-ready/lambdas/generate_sash_payload_py/generate_sash_payload.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/t-rex/part_2/oncoanalyser-dna-complete-to-sash-ready/lambdas/generate_sash_payload_py/generate_sash_payload.py @@ -80,7 +80,7 @@ def handler(event, context) -> Dict: # Get the bam uris by taking the library ids return { "input_event_data": { - "subjectId": subject_id, + "subjectId": subject_id.replace(" ", "_"), "tumorDnaSampleId": tumor_library_id, "normalDnaSampleId": normal_library_id, "dragenSomaticUri": dragen_somatic_output_s3_uri, diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/t-rex/part_3/oncoanalyser-dna-or-rna-to-oncoanalyser-both-ready/lambdas/get_oncoanalyser_dna_rna_payload_py/get_oncoanalyser_dna_rna_payload.py b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/t-rex/part_3/oncoanalyser-dna-or-rna-to-oncoanalyser-both-ready/lambdas/get_oncoanalyser_dna_rna_payload_py/get_oncoanalyser_dna_rna_payload.py index 07351a47a..afcb4a92c 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/t-rex/part_3/oncoanalyser-dna-or-rna-to-oncoanalyser-both-ready/lambdas/get_oncoanalyser_dna_rna_payload_py/get_oncoanalyser_dna_rna_payload.py +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/t-rex/part_3/oncoanalyser-dna-or-rna-to-oncoanalyser-both-ready/lambdas/get_oncoanalyser_dna_rna_payload_py/get_oncoanalyser_dna_rna_payload.py @@ -49,7 +49,7 @@ def handler(event, context) -> Dict: "input_event_data": { "mode": MODE, "analysisType": ANALYSIS_TYPE, - "subjectId": subject_id, + "subjectId": subject_id.replace(" ", "_"), "tumorDnaSampleId": tumor_dna_library_id, "normalDnaSampleId": normal_dna_library_id, "tumorRnaSampleId": tumor_rna_library_id,