fix: Map missing fields in Chromeleon parser for adapter migration (#1207)

## Summary

- Fixes crash when `device_information` is `null` in raw JSON (Glycans
sequence)
- Maps `analyst` and `submitter` per LC document from injection-level
fields
- Maps `injection name` → `sample document.written name`
- Uses `signal name` as `device type` instead of hardcoded "HPLC"
- Uses `sampler model number` as `asset management identifier` when
available
- Merges non-null custom variables into injection custom info

## Context

The Chromeleon adapter is migrating from producing ASM directly to
producing a raw JSON dump parsed by the allotropy `BENCHLING_CHROMELEON`
parser. The raw JSON contains all the data but several critical fields
were not being mapped into ASM output. This PR closes all mapping gaps
so the new pipeline produces equivalent output to the old adapter.

## Test plan

- [x] All 8 production sequences from output.zip parse successfully
(including previously-crashing Glycans)
- [x] No data loss in existing test output (verified via DeepDiff)
- [x] New test cases added: null device_information + custom variables +
non-UV signals, and multi-signal + valid sampler model
- [x] Other parsers using same schema mapper (cytiva_unicorn,
benchling_empower, agilent_openlab_cds) still pass
- [x] Vendor discovery tests pass (313 tests)
- [x] Lint passes

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: nathan-stender

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
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}