SpectraMax: Parse wavelengths as an array; truncate wavelength badges with hover tooltip

lambda/src/data_hub_lambda/spectramax_plate_reader/utils.py

@@ -183,17 +183,20 @@ def _parse_column_layout(col_header_line: str) -> _ColumnLayout:
     raise ValueError("Could not determine column layout from header row")
 
 
-def parse_metadata(file_path: Path) -> dict[str, str]:
+def parse_metadata(file_path: Path) -> dict[str, object]:
     """Extract measurement metadata from a SpectraMax `.xls` file.
 
     Returns:
         A dict with keys `measurement_mode`, `measurement_type`, and
-        `wavelength`.  Example::
+        `wavelengths`.  Wavelengths are returned as a list of numeric
+        strings (without the ``nm`` suffix) to mirror the shape used by
+        other multi-wavelength instruments (e.g. Azure 600 Gel Doc) and
+        let the UI layer own display formatting.  Example::
 
             {
                 "measurement_mode": "Absorbance",
                 "measurement_type": "Endpoint",
-                "wavelength": "750 nm",
+                "wavelengths": ["750", "700", "650", "600"],
             }
 
     Raises:
@@ -223,7 +226,7 @@ def parse_metadata(file_path: Path) -> dict[str, str]:
         return {
             "measurement_mode": header.measurement_mode,
             "measurement_type": header.measurement_type,
-            "wavelength": ", ".join(f"{w} nm" for w in wavelengths),
+            "wavelengths": [str(w) for w in wavelengths],
         }
 
     raise ValueError(f"No 'Plate:' header line found in {file_path}")

lambda/tests/integration/test_lambda_api.py

@@ -111,7 +111,7 @@ class TestSpectraMaxHappyPath:
                 {
                     "measurement_mode": "Absorbance",
                     "measurement_type": "Endpoint",
-                    "wavelength": "750 nm",
+                    "wavelengths": ["750"],
                 },
                 id="endpoint",
             ),
@@ -121,7 +121,7 @@ class TestSpectraMaxHappyPath:
                 {
                     "measurement_mode": "Absorbance",
                     "measurement_type": "Well Scan",
-                    "wavelength": "595 nm",
+                    "wavelengths": ["595"],
                 },
                 id="well-scan",
             ),
@@ -131,7 +131,7 @@ class TestSpectraMaxHappyPath:
                 {
                     "measurement_mode": "Absorbance",
                     "measurement_type": "Kinetic",
-                    "wavelength": "595 nm",
+                    "wavelengths": ["595"],
                 },
                 id="kinetic",
             ),
@@ -147,7 +147,7 @@ def test_xls_completes_with_processed_csv(
         mock_s3_upload: MagicMock,
         fixture_file: str,
         run_id: str,
-        expected_metadata: dict[str, str],
+        expected_metadata: dict[str, object],
     ) -> None:
         filename = f"{run_id}.xls"
         s3_key = f"spectramax-id3-plate-reader/{run_id}/{filename}"

lambda/tests/spectramax_plate_reader/test_parse_metadata.py

@@ -77,47 +77,47 @@ def test_endpoint_absorbance(self) -> None:
         assert result == {
             "measurement_mode": "Absorbance",
             "measurement_type": "Endpoint",
-            "wavelength": "750 nm",
+            "wavelengths": ["750"],
         }
 
     def test_well_scan_absorbance(self) -> None:
         result = parse_metadata(_FIXTURES_DIR / "spectramax_plate_reader_well_scan.xls")
         assert result == {
             "measurement_mode": "Absorbance",
             "measurement_type": "Well Scan",
-            "wavelength": "595 nm",
+            "wavelengths": ["595"],
         }
 
     def test_endpoint_fluorescence(self) -> None:
         result = parse_metadata(_FIXTURES_DIR / "spectramax_plate_reader_fluorescence.xls")
         assert result == {
             "measurement_mode": "Fluorescence",
             "measurement_type": "Endpoint",
-            "wavelength": "512 nm",
+            "wavelengths": ["512"],
         }
 
     def test_endpoint_sparse_absorbance(self) -> None:
         result = parse_metadata(_FIXTURES_DIR / "spectramax_plate_reader_endpoint_sparse.xls")
         assert result == {
             "measurement_mode": "Absorbance",
             "measurement_type": "Endpoint",
-            "wavelength": "600 nm",
+            "wavelengths": ["600"],
         }
 
     def test_kinetic_absorbance(self) -> None:
         result = parse_metadata(_FIXTURES_DIR / "spectramax_plate_reader_kinetic.xls")
         assert result == {
             "measurement_mode": "Absorbance",
             "measurement_type": "Kinetic",
-            "wavelength": "595 nm",
+            "wavelengths": ["595"],
         }
 
     def test_endpoint_flat(self) -> None:
         result = parse_metadata(_FIXTURES_DIR / "spectramax_plate_reader_endpoint_flat.xls")
         assert result == {
             "measurement_mode": "Absorbance",
             "measurement_type": "Endpoint",
-            "wavelength": "595 nm",
+            "wavelengths": ["595"],
         }
 
 
@@ -138,7 +138,7 @@ def test_absorbance_endpoint(self, tmp_path: Path) -> None:
         assert result == {
             "measurement_mode": "Absorbance",
             "measurement_type": "Endpoint",
-            "wavelength": "750 nm",
+            "wavelengths": ["750"],
         }
 
     def test_fluorescence_kinetic(self, tmp_path: Path) -> None:
@@ -152,7 +152,7 @@ def test_fluorescence_kinetic(self, tmp_path: Path) -> None:
         assert result == {
             "measurement_mode": "Fluorescence",
             "measurement_type": "Kinetic",
-            "wavelength": "488 nm",
+            "wavelengths": ["488"],
         }
 
     def test_reduced_anchor(self, tmp_path: Path) -> None:
@@ -167,7 +167,7 @@ def test_reduced_anchor(self, tmp_path: Path) -> None:
         assert result == {
             "measurement_mode": "Absorbance",
             "measurement_type": "Endpoint",
-            "wavelength": "600 nm",
+            "wavelengths": ["600"],
         }
 
 
@@ -198,7 +198,16 @@ def test_dual_wavelength(self, tmp_path: Path) -> None:
         assert result == {
             "measurement_mode": "Absorbance",
             "measurement_type": "Endpoint",
-            "wavelength": "750 nm, 600 nm",
+            "wavelengths": ["750", "600"],
+        }
+
+    def test_four_wavelengths(self, tmp_path: Path) -> None:
+        path = _build_xls(tmp_path, wavelength="750 700 650 600")
+        result = parse_metadata(path)
+        assert result == {
+            "measurement_mode": "Absorbance",
+            "measurement_type": "Endpoint",
+            "wavelengths": ["750", "700", "650", "600"],
         }
 
     def test_missing_plate_header(self, tmp_path: Path) -> None:

web-app/components/instruments/runs-table/gel-doc-runs-table.tsx

@@ -21,10 +21,11 @@ import type { RunRow } from ".";
 import { ClickableRow } from "./clickable-row";
 import { FilterableColumnHeader } from "./filterable-column-header";
 import {
-  MetadataArrayBadges,
   MetadataFieldBadge,
+  TruncatedBadges,
   getMetadataArray,
   getMetadataField,
+  sortWavelengths,
 } from "./metadata-utils";
 import { RanByCell } from "./ran-by-cell";
 import { RunSelectAllCheckbox, RunSelectCheckbox } from "./run-select-checkbox";
@@ -46,6 +47,7 @@ export function GelDocRunsTable({
     getMetadataArray(row.metadata, "wavelengths")
   );
   const wavelengthColors = buildWavelengthColorMap(allWavelengths);
+  const sortedWavelengthOptions = sortWavelengths(filterOptions.wavelengths);
   const runRefs: RunRef[] = data.map((row) => ({
     id: row.id,
     instrumentId: row.instrument_id,
@@ -80,7 +82,7 @@ export function GelDocRunsTable({
             <FilterableColumnHeader
               label="Wavelengths"
               paramKey="gel_wavelength"
-              options={filterOptions.wavelengths}
+              options={sortedWavelengthOptions}
             />
           </TableHead>
           <TableHead>
@@ -105,7 +107,9 @@ export function GelDocRunsTable({
           const isDeleted = row.deleted_at !== null;
           const captureType = getMetadataField(row.metadata, "capture_type");
           const imagingMode = getMetadataField(row.metadata, "imaging_mode");
-          const wavelengths = getMetadataArray(row.metadata, "wavelengths");
+          const wavelengths = sortWavelengths(
+            getMetadataArray(row.metadata, "wavelengths")
+          );
           const wavelengthColorLabels = getMetadataArray(
             row.metadata,
             "colors"
@@ -166,15 +170,17 @@ export function GelDocRunsTable({
                 />
               </TableCell>
               <TableCell>
-                <MetadataArrayBadges
+                <TruncatedBadges
                   values={wavelengths}
                   colorMap={wavelengthColors}
+                  maxVisible={1}
                 />
               </TableCell>
               <TableCell>
-                <MetadataArrayBadges
+                <TruncatedBadges
                   values={wavelengthColorLabels}
                   colorMap={CHANNEL_COLOR_STYLES}
+                  maxVisible={2}
                 />
               </TableCell>
               <TableCell>

web-app/components/instruments/runs-table/metadata-utils.tsx

@@ -1,6 +1,8 @@
 export {
   MetadataArrayBadges,
   MetadataFieldBadge,
+  TruncatedBadges,
   getMetadataArray,
   getMetadataField,
+  sortWavelengths,
 } from "@/components/runs/metadata-badges";

web-app/components/instruments/runs-table/plate-reader-runs-table.tsx

@@ -19,7 +19,13 @@ import { cn, formatBytes } from "@/lib/utils";
 import type { RunRow } from ".";
 import { ClickableRow } from "./clickable-row";
 import { FilterableColumnHeader } from "./filterable-column-header";
-import { MetadataFieldBadge, getMetadataField } from "./metadata-utils";
+import {
+  MetadataFieldBadge,
+  TruncatedBadges,
+  getMetadataArray,
+  getMetadataField,
+  sortWavelengths,
+} from "./metadata-utils";
 import { RanByCell } from "./ran-by-cell";
 import { RunSelectAllCheckbox, RunSelectCheckbox } from "./run-select-checkbox";
 import type { RunRef } from "./run-selection-provider";
@@ -37,6 +43,7 @@ export function PlateReaderRunsTable({
   ranByOptions: { value: string; label: string }[];
 }) {
   const wavelengthColors = buildWavelengthColorMap(filterOptions.wavelengths);
+  const sortedWavelengthOptions = sortWavelengths(filterOptions.wavelengths);
   const runRefs: RunRef[] = data.map((row) => ({
     id: row.id,
     instrumentId: row.instrument_id,
@@ -55,9 +62,9 @@ export function PlateReaderRunsTable({
           <TableHead className="text-right">Total Size</TableHead>
           <TableHead>
             <FilterableColumnHeader
-              label="Wavelength"
+              label="Wavelengths"
               paramKey="wavelength"
-              options={filterOptions.wavelengths}
+              options={sortedWavelengthOptions}
             />
           </TableHead>
           <TableHead>
@@ -87,7 +94,9 @@ export function PlateReaderRunsTable({
       <TableBody>
         {data.map((row) => {
           const isDeleted = row.deleted_at !== null;
-          const wavelength = getMetadataField(row.metadata, "wavelength");
+          const wavelengths = sortWavelengths(
+            getMetadataArray(row.metadata, "wavelengths")
+          );
           const mode = getMetadataField(row.metadata, "measurement_mode");
           const type = getMetadataField(row.metadata, "measurement_type");
           return (
@@ -130,11 +139,10 @@ export function PlateReaderRunsTable({
                 {formatBytes(row.total_size_bytes)}
               </TableCell>
               <TableCell>
-                <MetadataFieldBadge
-                  value={wavelength}
-                  colorClass={
-                    wavelength ? wavelengthColors[wavelength] : undefined
-                  }
+                <TruncatedBadges
+                  values={wavelengths}
+                  colorMap={wavelengthColors}
+                  maxVisible={1}
                 />
               </TableCell>
               <TableCell>