Merge pull request #680 from umccr/bugfix/sanitise-subject-id-for-orc…

…abus Sanitise subject id for oncoanalyser / sash / nf workflows
umccr · Nov 10, 2024 · 80491d0 · 80491d0
2 parents c2f1418 + 912f0f6
commit 80491d0
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/.../launch-oncoanalyser-ready-events/lambdas/generate_dna_payload_py/generate_dna_payload.py b/.../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/.../launch-oncoanalyser-ready-events/lambdas/generate_rna_payload_py/generate_rna_payload.py b/.../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/...yser-dna-complete-to-sash-ready/lambdas/generate_sash_payload_py/generate_sash_payload.py b/...yser-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/...oth-ready/lambdas/get_oncoanalyser_dna_rna_payload_py/get_oncoanalyser_dna_rna_payload.py b/...oth-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,