Add lane to bclconvert samplesheet if it doesn't exist

lib/workload/stateless/stacks/bclconvert-manager/translator_service/helper/icav2_analysis/analysis_helper.py

@@ -197,7 +197,8 @@ def collect_analysis_objects(project_id: str, analysis_id: str) -> Dict:
     logger.info("Reading in the samplesheet")
     samplesheet_dict = read_v2_samplesheet(
         project_id=project_id,
-        data_id=samplesheet_file_id
+        samplesheet_data_id=samplesheet_file_id,
+        runinfo_data_id=run_info_file_id
     )
 
     return {

lib/workload/stateless/stacks/bclconvert-manager/translator_service/helper/runinfo/__init__.py

@@ -1,5 +1,6 @@
-from .runinfo_helper import get_run_id_from_run_info
+from .runinfo_helper import get_run_id_from_run_info, get_num_lanes_from_run_info
 
 __all__ = [
+    'get_num_lanes_from_run_info',
     'get_run_id_from_run_info'
 ]

lib/workload/stateless/stacks/bclconvert-manager/translator_service/helper/runinfo/runinfo_helper.py

@@ -100,3 +100,12 @@ def get_run_id_from_run_info(project_id: str, data_id: str) -> str:
     """
     return read_runinfo_xml(project_id, data_id)['RunInfo']['Run']['@Id']
 
+
+def get_num_lanes_from_run_info(project_id: str, data_id: str) -> int:
+    """
+    Get the number of lanes in a run info object
+    :param project_id:
+    :param data_id:
+    :return:
+    """
+    return int(read_runinfo_xml(project_id, data_id)['RunInfo']['Run']['FlowcellLayout']['@LaneCount'])

lib/workload/stateless/stacks/bclconvert-manager/translator_service/helper/samplesheet/samplesheet_helper.py

@@ -7,6 +7,7 @@
 from io import StringIO
 from typing import Dict
 
+from more_itertools import flatten
 # UMCCR Libraries
 from v2_samplesheet_maker.functions.v2_samplesheet_reader import v2_samplesheet_reader
 from wrapica.project_data import read_icav2_file_contents_to_string
@@ -19,12 +20,17 @@
 logger.setLevel(logging.INFO)
 
 
-def read_v2_samplesheet(project_id: str, data_id: str) -> Dict:
+def read_v2_samplesheet(
+        project_id: str,
+        samplesheet_data_id: str,
+        runinfo_data_id: str
+) -> Dict:
     """
     Given a v2 samplesheet path, read in the file as a v2 samplesheet (we first convert to json)
 
     :param project_id:
-    :param data_id:
+    :param samplesheet_data_id:
+    :param runinfo_data_id
 
     :return: A dictionary
 
@@ -90,12 +96,43 @@ def read_v2_samplesheet(project_id: str, data_id: str) -> Dict:
         ]
     }
     """
+    from ..runinfo import get_num_lanes_from_run_info
 
-    return v2_samplesheet_reader(
+    v2_samplesheet_dict = v2_samplesheet_reader(
         StringIO(
             read_icav2_file_contents_to_string(
                 project_id=project_id,
-                data_id=data_id
+                data_id=samplesheet_data_id
             )
         )
     )
+
+    # Get bclconvert data from the v2 samplesheet dict
+    # And confirm that the lane column is present
+    if 'lane' in v2_samplesheet_dict['bclconvert_data'][0].keys():
+        # Return the samplesheet as is
+        return v2_samplesheet_dict
+
+    # Otherwise we read the runinfo file
+    num_lanes = get_num_lanes_from_run_info(
+        project_id=project_id,
+        data_id=runinfo_data_id
+    )
+
+    # And now append the lane attribute to every
+    v2_samplesheet_dict['bclconvert_data'] = flatten(
+        map(
+            lambda bclconvert_data_row_iter: list(
+                map(
+                    lambda lane_iter: {
+                        **bclconvert_data_row_iter,
+                        **{"lane": lane_iter + 1}
+                    },
+                    range(num_lanes)
+                )
+            ),
+            v2_samplesheet_dict['bclconvert_data']
+        ),
+    )
+
+    return v2_samplesheet_dict

lib/workload/stateless/stacks/bclconvert-manager/translator_service/icav2_event_translator.py

@@ -499,3 +499,5 @@ def parse_event_code(event_code):
 #     #   "statusCode": 200,
 #     #   "body": "\"Internal event sent to the event bus and both msg stored in the DynamoDB table.\""
 #     # }
+
+