feat: Update adapters using 2024/06 Plate Reader schema to include ASM file identifier

src/allotropy/parsers/agilent_gen5/agilent_gen5_structure.py

@@ -4,6 +4,7 @@
 from dataclasses import dataclass
 from io import StringIO
 import math
+from pathlib import Path
 import re
 
 import pandas as pd
@@ -773,14 +774,15 @@ def _get_sources(
 
 
 def create_metadata(header_data: HeaderData) -> Metadata:
+    asm_file_identifier = Path(header_data.file_name).with_suffix(".json")
     return Metadata(
         device_identifier=NOT_APPLICABLE,
         model_number=header_data.model_number or NOT_APPLICABLE,
         equipment_serial_number=header_data.equipment_serial_number,
         software_name=DEFAULT_SOFTWARE_NAME,
         software_version=header_data.software_version,
         file_name=header_data.file_name,
-        asm_file_identifier=NOT_APPLICABLE,
+        asm_file_identifier=asm_file_identifier.name,
         data_system_instance_id=NOT_APPLICABLE,
         unc_path=NOT_APPLICABLE,
     )

src/allotropy/parsers/bmg_mars/bmg_mars_structure.py

@@ -2,6 +2,7 @@
 
 from dataclasses import dataclass
 from enum import Enum
+from pathlib import Path
 import re
 
 import pandas as pd
@@ -97,9 +98,10 @@ def create(data: SeriesData, header_content: str) -> Header:
 
 
 def create_metadata(header: Header, file_name: str) -> Metadata:
+    asm_file_identifier = Path(file_name).with_suffix(".json")
     return Metadata(
         file_name=file_name,
-        asm_file_identifier=NOT_APPLICABLE,
+        asm_file_identifier=asm_file_identifier.name,
         unc_path=header.path,
         device_identifier=NOT_APPLICABLE,
         model_number=NOT_APPLICABLE,

src/allotropy/parsers/methodical_mind/methodical_mind_parser.py

@@ -30,7 +30,10 @@ class MethodicalMindParser(VendorParser[Data, Model]):
     def create_data(self, named_file_contents: NamedFileContents) -> Data:
         reader = MethodicalMindReader(named_file_contents)
         return Data(
-            create_metadata(Header.create(reader.plate_headers[0])),
+            create_metadata(
+                Header.create(reader.plate_headers[0]),
+                named_file_contents.original_file_name,
+            ),
             create_measurement_groups(
                 [PlateData.create(header, data) for header, data in reader]
             ),

src/allotropy/parsers/methodical_mind/methodical_mind_structure.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
+from pathlib import Path
 
 import pandas as pd
 
@@ -84,7 +85,8 @@ def create(luminescence: int, location_id: str, well_plate_id: str) -> WellData:
         )
 
 
-def create_metadata(header: Header) -> Metadata:
+def create_metadata(header: Header, file_name: str) -> Metadata:
+    asm_file_identifier = Path(file_name).with_suffix(".json")
     return Metadata(
         file_name=header.file_name.rsplit("\\", 1)[-1],
         unc_path=header.file_name,
@@ -93,7 +95,7 @@ def create_metadata(header: Header) -> Metadata:
         device_identifier=NOT_APPLICABLE,
         model_number=header.model,
         equipment_serial_number=header.serial_number,
-        asm_file_identifier=NOT_APPLICABLE,
+        asm_file_identifier=asm_file_identifier.name,
         data_system_instance_id=NOT_APPLICABLE,
     )
 

src/allotropy/parsers/perkin_elmer_envision/perkin_elmer_envision_structure.py

@@ -20,6 +20,7 @@
 from collections.abc import Iterator
 from dataclasses import dataclass
 from enum import Enum
+from pathlib import Path
 from re import search
 
 import numpy as np
@@ -693,9 +694,10 @@ def create(reader: CsvReader) -> Data:
 def create_metadata(
     software: Software, instrument: Instrument, file_name: str
 ) -> Metadata:
+    asm_file_identifier = Path(file_name).with_suffix(".json")
     return Metadata(
         file_name=file_name,
-        asm_file_identifier=NOT_APPLICABLE,
+        asm_file_identifier=asm_file_identifier.name,
         unc_path=NOT_APPLICABLE,
         software_name=software.software_name,
         software_version=software.software_version,

tests/parsers/agilent_gen5/testdata/absorbance/010307_114129_BNCH654563_stdcurve_singleplate01.json

@@ -7208,7 +7208,7 @@
             ]
         },
         "data system document": {
-            "ASM file identifier": "N/A",
+            "ASM file identifier": "010307_114129_BNCH654563_stdcurve_singleplate01.json",
             "data system instance identifier": "N/A",
             "file name": "010307_114129_BNCH654563_stdcurve_singleplate01.txt",
             "UNC path": "N/A",

tests/parsers/agilent_gen5/testdata/absorbance/240411_172731_BNCH2345883_abs450_96well_non_numeric_values.json

@@ -4236,7 +4236,7 @@
             }
         ],
         "data system document": {
-            "ASM file identifier": "N/A",
+            "ASM file identifier": "240411_172731_BNCH2345883_abs450_96well_non_numeric_values.json",
             "data system instance identifier": "N/A",
             "file name": "240411_172731_BNCH2345883_abs450_96well_non_numeric_values.txt",
             "UNC path": "N/A",

tests/parsers/agilent_gen5/testdata/absorbance/Kinetic_Analysis_Mean_Slope_and_Standard_Curve_tab.json

@@ -21720,12 +21720,12 @@
             ]
         },
         "data system document": {
-            "ASM file identifier": "N/A",
+            "ASM file identifier": "Kinetic_Analysis_Mean_Slope_and_Standard_Curve_tab.json",
             "data system instance identifier": "N/A",
             "file name": "Kinetic_Analysis_Mean_Slope_and_Standard_Curve_tab.txt",
             "UNC path": "N/A",
             "ASM converter name": "allotropy_agilent_gen5",
-            "ASM converter version": "0.1.53",
+            "ASM converter version": "0.1.56",
             "software name": "Gen5",
             "software version": "3.12.08"
         },

tests/parsers/agilent_gen5/testdata/absorbance/endpoint_pathlength_correct_singleplate.json

@@ -37544,7 +37544,7 @@
             ]
         },
         "data system document": {
-            "ASM file identifier": "N/A",
+            "ASM file identifier": "endpoint_pathlength_correct_singleplate.json",
             "data system instance identifier": "N/A",
             "file name": "endpoint_pathlength_correct_singleplate.txt",
             "UNC path": "N/A",