From dd5e3019ff89b29c0f65569e0cf440a3a3c59297 Mon Sep 17 00:00:00 2001
From: Alexis Lucattini <Alexis.Lucattini@umccr.org>
Date: Tue, 5 Nov 2024 21:30:15 +1100
Subject: [PATCH] fix-ora-compression-manager

---
 .../ora-compression-manager/deploy/index.ts   |   3 +-
 .../merge_file_sizes_for_fastq_list_rows.py   | 515 ++++++++++++++++--
 .../fastq_list_row_compression_event.asl.json |   4 +-
 .../set_compression_outputs.asl.json          |   2 +-
 4 files changed, 483 insertions(+), 41 deletions(-)

diff --git a/lib/workload/stateless/stacks/ora-compression-manager/deploy/index.ts b/lib/workload/stateless/stacks/ora-compression-manager/deploy/index.ts
index ff8e9f1e2..553802e0d 100644
--- a/lib/workload/stateless/stacks/ora-compression-manager/deploy/index.ts
+++ b/lib/workload/stateless/stacks/ora-compression-manager/deploy/index.ts
@@ -228,6 +228,7 @@ export class OraCompressionIcav2PipelineManagerStack extends cdk.Stack {
         ICAV2_ACCESS_TOKEN_SECRET_ID: icav2AccessTokenSecretObj.secretName,
       },
       timeout: Duration.seconds(60),
+      memorySize: 1024,
     });
     // Give the lambda function access to the secret
     icav2AccessTokenSecretObj.grantRead(setMergeSizesLambdaObj.currentVersion);
@@ -270,7 +271,7 @@ export class OraCompressionIcav2PipelineManagerStack extends cdk.Stack {
           detailType: [props.detailType],
           detail: {
             workflowName: [{ 'equals-ignore-case': props.workflowName }],
-            state: [{ 'equals-ignore-case': 'SUCCEEDED' }],
+            status: [{ 'equals-ignore-case': 'SUCCEEDED' }],
           },
         },
       }
diff --git a/lib/workload/stateless/stacks/ora-compression-manager/lambdas/merge_file_sizes_for_fastq_list_rows_py/merge_file_sizes_for_fastq_list_rows.py b/lib/workload/stateless/stacks/ora-compression-manager/lambdas/merge_file_sizes_for_fastq_list_rows_py/merge_file_sizes_for_fastq_list_rows.py
index a8f57f850..a6844d78b 100644
--- a/lib/workload/stateless/stacks/ora-compression-manager/lambdas/merge_file_sizes_for_fastq_list_rows_py/merge_file_sizes_for_fastq_list_rows.py
+++ b/lib/workload/stateless/stacks/ora-compression-manager/lambdas/merge_file_sizes_for_fastq_list_rows_py/merge_file_sizes_for_fastq_list_rows.py
@@ -28,7 +28,6 @@
     read_icav2_file_contents
 )
 
-
 # Type checking
 if typing.TYPE_CHECKING:
     from mypy_boto3_ssm import SSMClient
@@ -37,6 +36,7 @@
 # Globals
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
+
 # AWS things
 def get_ssm_client() -> 'SSMClient':
     """
@@ -86,20 +86,20 @@ def read_md5sum(project_data: ProjectData) -> pd.DataFrame:
     :param project_data:
     :return:
     """
-    with read_icav2_file_contents(project_data.project_id, project_data.data.id) as file_contents:
+    with StringIO(read_icav2_file_contents(project_data.project_id, project_data.data.id)) as file_contents:
         return pd.read_csv(
-            StringIO(file_contents),
+            file_contents,
             header=None,
-            names=["md5sum", "file_name"],
+            names=["md5sum", "fastqPath"],
             sep="  ",
             engine="python"
         )
 
 
 def read_file_sizes(project_data: ProjectData) -> pd.DataFrame:
-    with read_icav2_file_contents(project_data.project_id, project_data.data.id) as file_contents:
+    with StringIO(read_icav2_file_contents(project_data.project_id, project_data.data.id)) as file_contents:
         return pd.read_csv(
-            StringIO(file_contents),
+            file_contents,
             sep="\t"
         )
 
@@ -110,8 +110,17 @@ def read_fastq_list_csv(project_data: ProjectData) -> pd.DataFrame:
     :param project_data:
     :return:
     """
-    with read_icav2_file_contents(project_data.project_id, project_data.data.id) as file_contents:
-        return pd.read_csv(StringIO(file_contents))
+    with StringIO(read_icav2_file_contents(project_data.project_id, project_data.data.id)) as file_contents:
+        return pd.read_csv(file_contents).rename(
+            columns={
+                "RGID": "rgid",
+                "RGLB": "rglb",
+                "RGSM": "rgsm",
+                "Lane": "lane",
+                "Read1File": "read1File",
+                "Read2File": "read2File"
+            }
+        )
 
 
 def get_icav2_file_from_folder(project_data_list: typing.List[ProjectData], file_name: str) -> ProjectData:
@@ -125,8 +134,8 @@ def get_icav2_file_from_folder(project_data_list: typing.List[ProjectData], file
         return next(
             filter(
                 lambda project_data_iter: (
-                    project_data_iter.data.details.name == file_name and
-                    DataType[project_data_iter.data.details.data_type] == DataType.FILE
+                        project_data_iter.data.details.name == file_name and
+                        DataType[project_data_iter.data.details.data_type] == DataType.FILE
                 ),
                 project_data_list
             )
@@ -153,21 +162,25 @@ def merge_fastq_list_rows_with_md5sums_and_filesizes(
     """
     # Extend the gzipped md5s to the fastq list rows
     fastq_list_ora_df = fastq_list_ora_df.merge(
-        fastq_gzipped_md5_df,
+        fastq_gzipped_md5_df.assign(
+            fastqPath=lambda row_iter_: row_iter_.fastqPath.str.rstrip(".gz") + ".ora"
+        ),
         how="left",
         left_on="read1File",
-        right_on="fileName"
+        right_on="fastqPath"
     ).drop(
-        columns='fileName'
+        columns='fastqPath'
     ).rename(
         columns={"md5sum": "read1FileGzippedMd5sum"}
     ).merge(
-        fastq_gzipped_md5_df,
+        fastq_gzipped_md5_df.assign(
+            fastqPath=lambda row_iter_: row_iter_.fastqPath.str.rstrip(".gz") + ".ora"
+        ),
         how="left",
         left_on="read2File",
-        right_on="fileName"
+        right_on="fastqPath"
     ).drop(
-        columns='fileName'
+        columns='fastqPath'
     ).rename(
         columns={"md5sum": "read2FileGzippedMd5sum"}
     )
@@ -177,61 +190,65 @@ def merge_fastq_list_rows_with_md5sums_and_filesizes(
         fastq_ora_md5_df,
         how="left",
         left_on="read1File",
-        right_on="fileName"
+        right_on="fastqPath"
     ).drop(
-        columns='fileName'
+        columns='fastqPath'
     ).rename(
         columns={"md5sum": "read1FileOraMd5sum"}
     ).merge(
         fastq_ora_md5_df,
         how="left",
         left_on="read2File",
-        right_on="fileName"
+        right_on="fastqPath"
     ).drop(
-        columns='fileName'
+        columns='fastqPath'
     ).rename(
         columns={"md5sum": "read2FileOraMd5sum"}
     )
 
     # Extend the gzipped file sizes to the fastq list rows
     fastq_list_ora_df = fastq_list_ora_df.merge(
-        fastq_gzipped_filesizes_df,
+        fastq_gzipped_filesizes_df.assign(
+            fastqPath=lambda row_iter_: row_iter_.fastqPath.str.rstrip(".gz") + ".ora"
+        ),
         how="left",
         left_on="read1File",
-        right_on="fileName"
+        right_on="fastqPath"
     ).drop(
-        columns='fileName'
+        columns='fastqPath'
     ).rename(
-        columns={"fileSize": "read1GzippedFileSize"}
+        columns={"fileSizeInBytes": "read1GzippedFileSizeInBytes"}
     ).merge(
-        fastq_gzipped_filesizes_df,
+        fastq_gzipped_filesizes_df.assign(
+            fastqPath=lambda row_iter_: row_iter_.fastqPath.str.rstrip(".gz") + ".ora"
+        ),
         how="left",
         left_on="read2File",
-        right_on="fileName"
+        right_on="fastqPath"
     ).drop(
-        columns='fileName'
+        columns='fastqPath'
     ).rename(
-        columns={"fileSize": "read2GzippedFileSize"}
+        columns={"fileSizeInBytes": "read2GzippedFileSizeInBytes"}
     )
 
     fastq_list_ora_df = fastq_list_ora_df.merge(
         fastq_ora_filesizes_df,
         how="left",
         left_on="read1File",
-        right_on="fileName"
+        right_on="fastqPath"
     ).drop(
-        columns='fileName'
+        columns='fastqPath'
     ).rename(
-        columns={"fileSize": "read1OraFileSize"}
+        columns={"fileSizeInBytes": "read1OraFileSizeInBytes"}
     ).merge(
         fastq_ora_filesizes_df,
         how="left",
         left_on="read2File",
-        right_on="fileName"
+        right_on="fastqPath"
     ).drop(
-        columns='fileName'
+        columns='fastqPath'
     ).rename(
-        columns={"fileSize": "read2OraFileSize"}
+        columns={"fileSizeInBytes": "read2OraFileSizeInBytes"}
     )
 
     # Return the fastq files
@@ -296,21 +313,21 @@ def handler(event, context):
     fastq_gzipped_md5_file_obj = read_md5sum(
         get_icav2_file_from_folder(
             output_dir_project_data_list,
-            "fastq_gzipped_md5.txt")
+            "fastq_gzipped.md5.txt")
     )
 
     # Get the file sizes for the new ora compressed tsv
     fastq_ora_md5_file_obj = read_md5sum(
         get_icav2_file_from_folder(
             output_dir_project_data_list,
-            "fastq_ora_md5.txt")
+            "fastq_ora.md5.txt")
     )
 
     # Get the original gzipped tsv file size
     fastq_gzipped_filesizes_file_obj = read_file_sizes(
         get_icav2_file_from_folder(
             output_dir_project_data_list,
-    "fastq_gzipped_filesizes.tsv"
+            "fastq_gzipped.filesizes.tsv"
         )
     )
 
@@ -318,7 +335,7 @@ def handler(event, context):
     fastq_ora_filesizes_file_obj = read_file_sizes(
         get_icav2_file_from_folder(
             output_dir_project_data_list,
-            "fastq_ora_filesizes.tsv"
+            "fastq_ora.filesizes.tsv"
         )
     )
 
@@ -345,5 +362,427 @@ def handler(event, context):
         inplace=True
     )
 
+    # FIXME Drop rgid and rglb since we don't
+    # FIXME accurately have these values yet
+    # FIXME this will be possible once the fastq manager exists
+    fastq_list_ora_df.drop(
+        columns=["rgid", "rglb"],
+        inplace=True
+    )
+
     # Return the merged file as a json list
     return fastq_list_ora_df.to_dict(orient="records")
+
+
+# if __name__ == "__main__":
+#     import json
+#
+#     environ['AWS_PROFILE'] = 'umccr-development'
+#     environ['AWS_REGION'] = 'ap-southeast-2'
+#     environ['ICAV2_ACCESS_TOKEN_SECRET_ID'] = "ICAv2JWTKey-umccr-prod-service-dev"
+#     print(
+#         json.dumps(
+#             handler(
+#                 {
+#                     "output_dir_uri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/"
+#                 },
+#                 None
+#             ),
+#             indent=4
+#         )
+#     )
+#
+#     # [
+#     #     {
+#     #         "rgsm": "L2401526",
+#     #         "lane": 1,
+#     #         "read1FileGzippedMd5sum": "ff9f75053fd5dfe34ac011fd679c62dd",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "18a267c2c5ca2f71e272815cd7508fd8",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "bb26321f461de85419c95131ce73f0a5",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "986ef94789f76d7a5e510d34b465033b",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 42630072057,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 43902595265,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 8647052933,
+#     #         "read2OraFileSizeInBytes": 9265337812,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401526/L2401526_S1_L001_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401526/L2401526_S1_L001_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401532",
+#     #         "lane": 1,
+#     #         "read1FileGzippedMd5sum": "7ec0a49be2a3c0a049b7593d00474cdb",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "af902803801285d3475ef1c8776ad611",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "6e2c5ce6e3014fd5f8be78bf9d769b26",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "54c5a6787ab80f07c25fc4abd5eb6bbc",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 4870,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 5969,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 4189,
+#     #         "read2OraFileSizeInBytes": 4914,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401532/L2401532_S7_L001_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401532/L2401532_S7_L001_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401528",
+#     #         "lane": 1,
+#     #         "read1FileGzippedMd5sum": "6de45d4c93afcf310d45c0edb0361427",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "c9a3dfed465b4053e1bacbc9e1b6bc70",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "1b947ed0f912f5dc0d5246cf0cbe63b9",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "16e8dc8d559dd8dd9515946c5112021c",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 43357314992,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 44092409731,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 8541275179,
+#     #         "read2OraFileSizeInBytes": 8863424337,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401528/L2401528_S3_L001_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401528/L2401528_S3_L001_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401531",
+#     #         "lane": 1,
+#     #         "read1FileGzippedMd5sum": "6dd394650558c4a93e2e2dd0322eaf08",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "f8ccf03414fc374903b1a2a5302ac517",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "1c61d4cca313a29dab5a05c2b9173a93",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "14583d8caca26fda8fac0701c0588292",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 43818023110,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 44844382192,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 8589773627,
+#     #         "read2OraFileSizeInBytes": 9065337736,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401531/L2401531_S6_L001_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401531/L2401531_S6_L001_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401527",
+#     #         "lane": 1,
+#     #         "read1FileGzippedMd5sum": "0953e17b02574f3167abbaba37dcd4ef",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "4d7f065b4ba5f7a702a469d566403bc6",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "70e9b68355b87e6fc3d96871def6e881",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "f3d0b90486c6f77fd78832777972b1be",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 37685523375,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 39255037633,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 7599984647,
+#     #         "read2OraFileSizeInBytes": 8409290279,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401527/L2401527_S2_L001_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401527/L2401527_S2_L001_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401530",
+#     #         "lane": 1,
+#     #         "read1FileGzippedMd5sum": "cd9e0018d17f119871e3b34ee5c6cf78",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "b4d9ab7d12e752eef790f27dd7d68aa5",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "9f2eb09791defb77c40e54693301d327",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "81434c21c81358e2d454750d428912ac",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 40837628477,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 41771419794,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 8127751530,
+#     #         "read2OraFileSizeInBytes": 8567645785,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401530/L2401530_S5_L001_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401530/L2401530_S5_L001_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401529",
+#     #         "lane": 1,
+#     #         "read1FileGzippedMd5sum": "69b4f91a0c87e52a5f02186d61f58f5d",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "5c42766421250fcbb97944d7e0920cc0",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "26cd69ff20668ca692f4fbc043bbfba6",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "09442fbd28bbf53778b71eeed1223027",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 40964945004,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 41736727855,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 8158884285,
+#     #         "read2OraFileSizeInBytes": 8535009518,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401529/L2401529_S4_L001_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_1/L2401529/L2401529_S4_L001_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401539",
+#     #         "lane": 2,
+#     #         "read1FileGzippedMd5sum": "1cf861134c39c7a1fe885396de951fd9",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "8f97bf9c1fcbb364d7779d9bdaba7e12",  # pragma: allowlist secret
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+#     #         "read2GzippedFileSizeInBytes": 6065388584,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 1209397423,
+#     #         "read2OraFileSizeInBytes": 1129072555,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401533/L2401533_S18_L004_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401533/L2401533_S18_L004_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401552",
+#     #         "lane": 4,
+#     #         "read1FileGzippedMd5sum": "a32f53cd103868e9000d105a6e907cde",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "15963cfcd84d2ee0326a10ada72e204c",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "69c89690e2a0a7c5585b3967c8cb6bca",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "611bd48574d9e684031d09b94dc21a15",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 33237582408,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 36766116815,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 6123700775,
+#     #         "read2OraFileSizeInBytes": 8612068652,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401552/L2401552_S26_L004_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401552/L2401552_S26_L004_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401536",
+#     #         "lane": 4,
+#     #         "read1FileGzippedMd5sum": "d278e8dc93355cceb54e38e128075989",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "bc5a290c4cdd223abde54714c9c16245",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "76ca92e1017fad3c2d372e2199a333a8",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "1d0460fa288bbc3e9230b94f6ff0e664",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 501994324,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 501436393,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 108705055,
+#     #         "read2OraFileSizeInBytes": 106336466,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401536/L2401536_S21_L004_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401536/L2401536_S21_L004_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401545",
+#     #         "lane": 4,
+#     #         "read1FileGzippedMd5sum": "68efe19804293a725fd41bd94878d378",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "9006f2e7db1b0cf9e640d3f60c20d6d3",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "cf9e7482431174d17f710fd94e3ae972",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "acc3bf20a8b03283fb66edc41fd65c7a",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 1717017,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 2075979,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 796634,
+#     #         "read2OraFileSizeInBytes": 1165743,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401545/L2401545_S23_L004_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401545/L2401545_S23_L004_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401535",
+#     #         "lane": 4,
+#     #         "read1FileGzippedMd5sum": "313a6608fba6b5fd7fdd830eace645c1",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "4260bd94f0e2f2e961bc3aaf3e0e9851",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "624e816beb856153d35e8a71478277ea",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "201607c4b04536c07e0b5514d961e56e",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 4592850293,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 4532211687,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 912733086,
+#     #         "read2OraFileSizeInBytes": 863814241,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401535/L2401535_S20_L004_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401535/L2401535_S20_L004_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401548",
+#     #         "lane": 4,
+#     #         "read1FileGzippedMd5sum": "c32a0f8a097796431462a4942106159f",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "3ab0eb6b307b0138a3c086b0ddd395dd",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "39dff48606c97a86deb048a9c3a367ee",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "3020cb923c39f0a75fa26030b88c3ade",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 40344869450,  # pragma: allowlist secret
+#     #         "read2GzippedFileSizeInBytes": 43831721872,  # pragma: allowlist secret
+#     #         "read1OraFileSizeInBytes": 7394266403,
+#     #         "read2OraFileSizeInBytes": 9748368514,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401548/L2401548_S24_L004_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401548/L2401548_S24_L004_R2_001.fastq.ora"
+#     #     },
+#     #     {
+#     #         "rgsm": "L2401499",
+#     #         "lane": 4,
+#     #         "read1FileGzippedMd5sum": "dbf0cdca626f00e95f327e377f25e3d4",  # pragma: allowlist secret
+#     #         "read2FileGzippedMd5sum": "d4fae1544cb032110dc02c5c1a676eed",  # pragma: allowlist secret
+#     #         "read1FileOraMd5sum": "47987c5ea8fa2aa8d73af6ca0719e587",  # pragma: allowlist secret
+#     #         "read2FileOraMd5sum": "2fb0307a88b882e0bdd29b16e5367cb6",  # pragma: allowlist secret
+#     #         "read1GzippedFileSizeInBytes": 31601361740,
+#     #         "read2GzippedFileSizeInBytes": 32500865849,
+#     #         "read1OraFileSizeInBytes": 5680732076,
+#     #         "read2OraFileSizeInBytes": 6122244909,
+#     #         "read1FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401499/L2401499_S17_L004_R1_001.fastq.ora",
+#     #         "read2FileUri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/ora-compression/202411046290aa4g/241024_A00130_0336_BHW7MVDSXC/Samples/Lane_4/L2401499/L2401499_S17_L004_R2_001.fastq.ora"
+#     #     }
+#     # ]
\ No newline at end of file
diff --git a/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/fastq_list_row_compression_event.asl.json b/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/fastq_list_row_compression_event.asl.json
index 6450c5a49..52f34f2ec 100644
--- a/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/fastq_list_row_compression_event.asl.json
+++ b/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/fastq_list_row_compression_event.asl.json
@@ -7,7 +7,9 @@
       "Resource": "arn:aws:states:::lambda:invoke",
       "OutputPath": "$.Payload",
       "Parameters": {
-        "Payload.$": "$",
+        "Payload": {
+          "output_dir_uri.$": "$.payload.data.outputs.instrumentRunOraOutputUri"
+        },
         "FunctionName": "${__merge_sizes_lambda_function_arn__}"
       },
       "Retry": [
diff --git a/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json b/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json
index 492c8fb85..fb11e337a 100644
--- a/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json
+++ b/lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json
@@ -25,7 +25,7 @@
       "Parameters": {
         "FunctionName": "${__set_outputs_json_lambda_function_arn__}",
         "Payload": {
-          "instrument_run_id.$": "$.ready_event_data_inputs.instrumentRunId",
+          "instrument_run_id.$": "$.get_db_attributes_step.ready_event_data_inputs.instrumentRunId",
           "analysis_output_uri.$": "$.get_db_attributes_step.analysis_output_uri"
         }
       },