fix: Map missing fields in Chromeleon parser for adapter migration

src/allotropy/allotrope/schema_mappers/adm/liquid_chromatography/benchling/_2023/_09/liquid_chromatography.py

@@ -244,6 +244,8 @@ class Measurement:
 @dataclass(frozen=True)
 class MeasurementGroup:
     measurements: list[Measurement]
+    analyst: str | None = None
+    submitter: str | None = None
     fractions: list[Fraction] | None = None
     logs: list[Log] | None = None
     measurement_aggregate_custom_info: dict[str, Any] | None = None
@@ -317,7 +319,8 @@ def _get_technique_document(
         self, group: MeasurementGroup, metadata: Metadata
     ) -> LiquidChromatographyDocumentItem:
         return LiquidChromatographyDocumentItem(
-            analyst=metadata.analyst,
+            analyst=group.analyst or metadata.analyst,
+            submitter=group.submitter,
             measurement_aggregate_document=add_custom_information_document(
                 MeasurementAggregateDocument(
                     measurement_document=[

src/allotropy/parsers/benchling_chromeleon/benchling_chromeleon_reader.py

@@ -14,7 +14,9 @@ class BenchlingChromeleonReader:
     def __init__(self, named_file_contents: NamedFileContents) -> None:
         contents: dict[str, Any] = json.load(named_file_contents.contents)
         self.sequence: dict[str, Any] = contents.get("sequence", {})
-        self.device_information: dict[str, Any] = contents.get("device information", {})
+        self.device_information: dict[str, Any] = (
+            contents.get("device information") or {}
+        )
         self.injections: list[dict[str, Any]] = assert_not_none(
             contents.get("injections"), "injections"
         )

src/allotropy/parsers/benchling_chromeleon/benchling_chromeleon_structure.py

@@ -28,8 +28,10 @@
 
 
 def _create_device_documents(
-    device_information: dict[str, Any]
+    device_information: dict[str, Any] | None,
 ) -> list[DeviceDocument] | None:
+    if not device_information:
+        return None
     return [
         DeviceDocument(
             device_type="pump",
@@ -51,12 +53,15 @@ def create_metadata(
     first_injection: dict[str, Any],
     sequence: dict[str, Any],
     file_path: str,
-    device_information: dict[str, Any],
+    device_information: dict[str, Any] | None,
 ) -> Metadata:
+    asset_management_identifier = (
+        (device_information.get("sampler model number") if device_information else None)
+        or first_injection.get("precondition system instrument name")
+        or NOT_APPLICABLE
+    )
     return Metadata(
-        asset_management_identifier=first_injection.get(
-            "precondition system instrument name", NOT_APPLICABLE
-        ),
+        asset_management_identifier=asset_management_identifier,
         software_name=constants.SOFTWARE_NAME,
         file_name=Path(file_path).name,
         unc_path=file_path,
@@ -223,6 +228,7 @@ def _create_measurements(injection: dict[str, Any]) -> list[Measurement] | None:
             measurement_identifier=random_uuid_str(),
             description=injection.get("description"),
             sample_identifier=injection["sample identifier"],
+            written_name=injection.get("injection name"),
             location_identifier=injection.get("location identifier"),
             well_location_identifier=injection.get("custom variables", {}).get("Well"),
             observation=injection.get("custom variables", {}).get("Observation"),
@@ -239,7 +245,7 @@ def _create_measurements(injection: dict[str, Any]) -> list[Measurement] | None:
             },
             device_control_docs=[
                 DeviceControlDoc(
-                    device_type=constants.DEVICE_TYPE,
+                    device_type=signal.get("signal name", constants.DEVICE_TYPE),
                     detection_type=signal.get("detection type"),
                     detector_offset_setting=val
                     if (val := signal.get("detector offset setting")) != "unknown"
@@ -271,6 +277,11 @@ def _create_measurements(injection: dict[str, Any]) -> list[Measurement] | None:
                 "creation user name": injection.get("creation user name"),
                 "injection program": injection.get("injection program"),
                 "injection method": injection.get("injection method"),
+                **{
+                    k: v
+                    for k, v in injection.get("custom variables", {}).items()
+                    if v is not None
+                },
             },
             chromatography_serial_num=NOT_APPLICABLE,
             chromatogram_data_cube=_get_chromatogram(signal) if signal else None,
@@ -284,7 +295,11 @@ def create_measurement_groups(
     injections: list[dict[str, Any]]
 ) -> list[MeasurementGroup]:
     return [
-        MeasurementGroup(measurements=measurements)
-        for sample_injections in injections
-        if (measurements := _create_measurements(sample_injections)) is not None
+        MeasurementGroup(
+            measurements=measurements,
+            analyst=injection.get("last update user name"),
+            submitter=injection.get("creation user name"),
+        )
+        for injection in injections
+        if (measurements := _create_measurements(injection)) is not None
     ]

tests/parsers/benchling_chromeleon/benchling_chromeleon_structure_test.py

@@ -117,7 +117,7 @@ def test_create_metadata(mock_data: dict[str, Any]) -> None:
     )
 
     assert isinstance(metadata, Metadata)
-    assert metadata.asset_management_identifier == "Instrument123"
+    assert metadata.asset_management_identifier == "WPS-3000RS"
     assert metadata.software_name == constants.SOFTWARE_NAME
     assert metadata.file_name == "test_file.json"
     assert metadata.unc_path == "/data/test_file.json"
@@ -173,7 +173,7 @@ def test_create_measurement_groups(mock_data: dict[str, Any]) -> None:
 
     device_control_doc = measurement.device_control_docs[0]
     assert device_control_doc is not None
-    assert device_control_doc.device_type == constants.DEVICE_TYPE
+    assert device_control_doc.device_type == "UV_VIS_1"
     assert device_control_doc.detection_type == "single channel"
     assert device_control_doc.electronic_absorbance_reference_bandwidth_setting == 1.0
     assert device_control_doc.electronic_absorbance_reference_wavelength_setting == 0.0

tests/parsers/benchling_chromeleon/testdata/input/chromeleon_example_multi_signal.json

@@ -0,0 +1,123 @@
+{
+  "device information": {
+    "pump model number": "VF-P10-A",
+    "uv model number": "VF-D40-A",
+    "sampler model number": "VF-A10-A"
+  },
+  "sequence": {
+    "sequence creation time": "2026-02-13T10:00:00+01:00",
+    "sequence directory": "ChromeleonLocal",
+    "sequence name": "Test_MultiSignal",
+    "sequence update operator": "operator1",
+    "sequence update time": "2026-02-14T15:00:00+01:00",
+    "custom formulas": []
+  },
+  "injections": [
+    {
+      "injection number": 1,
+      "injection name": "MQW",
+      "injection identifier": "99999999-8888-7777-6666-555555555555",
+      "injection time": "2026-02-14T21:52:50+01:00",
+      "injection position": "B:A1",
+      "injection status": "Finished",
+      "injection type": "Unknown",
+      "description": "",
+      "sample identifier": "",
+      "location identifier": "B:A1",
+      "last update user name": "Instrument Controller",
+      "creation user name": "PD01",
+      "detection type": "single channel",
+      "injection volume setting": 4.0,
+      "injection volume setting unit": "uL",
+      "custom variables": {
+        "ColumnValvePosition": 1.0
+      },
+      "signals": [
+        {
+          "signal name": "UV_VIS_1",
+          "detection type": "single channel",
+          "detector sampling rate setting": "unknown",
+          "detector offset setting": "unknown",
+          "bandwidth setting": 4.0,
+          "wavelength setting": 220.0,
+          "reference bandwidth setting": null,
+          "reference wavelength setting": null,
+          "chromatogram": {
+            "x": [
+              0.0,
+              0.5,
+              1.0,
+              1.5,
+              2.0
+            ],
+            "y": [
+              0.0,
+              0.5,
+              1.0,
+              0.5,
+              0.0
+            ]
+          },
+          "peaks": []
+        },
+        {
+          "signal name": "UV_VIS_2",
+          "detection type": "single channel",
+          "detector sampling rate setting": "unknown",
+          "detector offset setting": "unknown",
+          "bandwidth setting": 4.0,
+          "wavelength setting": 280.0,
+          "reference bandwidth setting": null,
+          "reference wavelength setting": null,
+          "chromatogram": {
+            "x": [
+              0.0,
+              0.5,
+              1.0,
+              1.5,
+              2.0
+            ],
+            "y": [
+              0.0,
+              0.3,
+              0.8,
+              0.3,
+              0.0
+            ]
+          },
+          "peaks": [
+            {
+              "identifier": "1",
+              "name": "Peak1",
+              "start time": 0.4,
+              "end time": 1.6,
+              "retention time": 1.0,
+              "area": 8000.0,
+              "height": 800.0,
+              "relative peak area": 100.0,
+              "relative peak height": 100.0,
+              "peak width at half height": 0.6,
+              "peak width at 5 % of height": null,
+              "peak width at 10 % of height": null,
+              "peak width at baseline": null,
+              "amount": null,
+              "relative retention time": null,
+              "capacity factor": null,
+              "chromatographic peak resolution": null,
+              "number of theoretical plates by peak width at half height": null,
+              "asymmetry factor measured at 5 % height": null,
+              "start value baseline": null,
+              "stop value baseline": null,
+              "peak right width at 10 % of height": null,
+              "peak left width at 10 % of height": null,
+              "group area": null,
+              "rel ce area total": null,
+              "chromatographic peak resolution (USP)": null,
+              "asymmetry aia": null
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}