Fix merge-rgids step

umccr · Nov 20, 2024 · 177d4cf · 177d4cf
1 parent 4a928bd
commit 177d4cf
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Showing 3 changed files with 7 additions and 8 deletions.
diff --git a/...n-manager/lambdas/merge_rgids_with_fastq_list_rows_py/merge_rgids_with_fastq_list_rows.py b/...n-manager/lambdas/merge_rgids_with_fastq_list_rows_py/merge_rgids_with_fastq_list_rows.py
@@ -14,27 +14,24 @@
 ]
 """
 
-
+# Imports
 import typing
 from io import StringIO
-
 import boto3
 from os import environ
 import re
 import pandas as pd
 
 from wrapica.project_data import (
-    find_project_data_bulk,
     convert_uri_to_project_data_obj,
-    ProjectData, convert_project_data_obj_to_uri, read_icav2_file_contents, list_project_data_non_recursively
+    ProjectData, read_icav2_file_contents, list_project_data_non_recursively
 )
-from wrapica.enums import DataType, UriType
+from wrapica.enums import DataType
 
 if typing.TYPE_CHECKING:
     from mypy_boto3_ssm import SSMClient
     from mypy_boto3_secretsmanager import SecretsManagerClient
 
-
 # Constants
 # index.index2.lane.rgsm.instrument_run_id
 RGID_PARTIAL_REGEX = re.compile(r"\w+\.\w+\.(\d+.\w+).\w+")

diff --git a/...acks/ora-compression-manager/lambdas/merge_rgids_with_fastq_list_rows_py/requirements.txt b/...acks/ora-compression-manager/lambdas/merge_rgids_with_fastq_list_rows_py/requirements.txt
@@ -0,0 +1,2 @@
+pandas==2.2.3
+wrapica==2.27.1.post20240830140737
diff --git a/.../stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json b/.../stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json
@@ -92,8 +92,8 @@
       "Parameters": {
         "FunctionName": "${__merge_fastq_list_csv_with_rgid_lambda_function_arn__}",
         "Payload": {
-          "rgids.$": "$.get_rgids_from_db_step.rgids",
-          "output_dir_uri.$": "$.analysis_outputs_step.output_json.instrumentRunOraOutputUri"
+          "rgids_list.$": "$.get_rgids_from_db_step.rgids",
+          "instrument_run_folder_uri.$": "$.analysis_outputs_step.output_json.instrumentRunOraOutputUri"
         }
       },
       "Retry": [
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		pandas==2.2.3
		wrapica==2.27.1.post20240830140737