diff --git a/lambda/src/data_hub_lambda/epson_v700_scanner/image_processing.py b/lambda/src/data_hub_lambda/epson_v700_scanner/image_processing.py index 8fbad989..bffa601c 100644 --- a/lambda/src/data_hub_lambda/epson_v700_scanner/image_processing.py +++ b/lambda/src/data_hub_lambda/epson_v700_scanner/image_processing.py @@ -16,6 +16,34 @@ _TIFF_SUFFIXES = {".tif", ".tiff"} +# PhotometricInterpretation values: 2 = RGB, others (0, 1, 3) are grayscale or +# palette and are treated as B&W for our display purposes. +_PHOTOMETRIC_RGB = 2 + + +def _derive_dpi(x_resolution: Any) -> int | None: + """Compute integer DPI from a TIFF ``XResolution`` rational tuple.""" + if not isinstance(x_resolution, (list, tuple)) or len(x_resolution) != 2: + return None + numerator, denominator = x_resolution + if not isinstance(numerator, (int, float)) or not isinstance(denominator, (int, float)): + return None + if denominator == 0: + return None + return int(numerator / denominator) + + +def _derive_color_mode(samples_per_pixel: Any, photometric_interpretation: Any) -> str | None: + """Infer ``rgb`` vs ``bw`` from TIFF tags, preferring SamplesPerPixel.""" + if isinstance(samples_per_pixel, (list, tuple)): + samples_per_pixel = samples_per_pixel[0] if samples_per_pixel else None + if isinstance(samples_per_pixel, int): + return "rgb" if samples_per_pixel >= 3 else "bw" + if isinstance(photometric_interpretation, int): + return "rgb" if photometric_interpretation == _PHOTOMETRIC_RGB else "bw" + return None + + _METADATA_TAG_NAMES = { "ImageWidth", "ImageLength", @@ -66,7 +94,16 @@ def export_jpg(self) -> Path: return jpg_path def parse_metadata(self) -> dict[str, Any]: - """Extract TIFF tags as a flat string-keyed dict.""" + """Extract TIFF tags as a flat string-keyed dict. + + In addition to the raw TIFF tags, this also emits two derived + scalar fields used by the web UI for filtering and display: + + - ``dpi``: integer DPI computed from ``XResolution`` (a (numerator, + denominator) rational). For Epson V700 scans this is 300 or 600. + - ``color_mode``: ``"rgb"`` or ``"bw"``, inferred from + ``SamplesPerPixel`` (preferred) or ``PhotometricInterpretation``. + """ metadata: dict[str, Any] = {} with tifffile.TiffFile(self.path) as tif: page = tif.pages.first @@ -80,6 +117,18 @@ def parse_metadata(self) -> dict[str, Any]: h, w = self.intensities.shape[:2] metadata["OriginalHeight"] = int(h) metadata["OriginalWidth"] = int(w) + + dpi = _derive_dpi(metadata.get("XResolution")) + if dpi is not None: + metadata["dpi"] = dpi + + color_mode = _derive_color_mode( + metadata.get("SamplesPerPixel"), + metadata.get("PhotometricInterpretation"), + ) + if color_mode is not None: + metadata["color_mode"] = color_mode + return metadata # ------------------------------------------------------------------ diff --git a/lambda/tests/epson_v700_scanner/test_image_processing.py b/lambda/tests/epson_v700_scanner/test_image_processing.py index dbc558f5..b76c8c76 100644 --- a/lambda/tests/epson_v700_scanner/test_image_processing.py +++ b/lambda/tests/epson_v700_scanner/test_image_processing.py @@ -11,6 +11,8 @@ from data_hub_lambda.epson_v700_scanner.image_processing import ( MAX_DIMENSION, TIFFToJPEGConverter, + _derive_color_mode, + _derive_dpi, ) @@ -119,6 +121,71 @@ def test_returns_standard_tiff_tags(self, tmp_path: Path) -> None: assert "BitsPerSample" in metadata +class TestDeriveDpi: + def test_returns_300_dpi(self) -> None: + # 300 dpi = 300 * 2^22 / 2^22; the V700 stores it as 1258291200/4194304 + assert _derive_dpi([1258291200, 4194304]) == 300 + + def test_returns_600_dpi(self) -> None: + assert _derive_dpi([1258291200, 2097152]) == 600 + + def test_handles_tuple(self) -> None: + assert _derive_dpi((600, 1)) == 600 + + def test_returns_none_for_missing(self) -> None: + assert _derive_dpi(None) is None + + def test_returns_none_for_zero_denominator(self) -> None: + assert _derive_dpi([300, 0]) is None + + def test_returns_none_for_malformed(self) -> None: + assert _derive_dpi([300]) is None + assert _derive_dpi("not a list") is None + + +class TestDeriveColorMode: + def test_samples_per_pixel_3_is_rgb(self) -> None: + assert _derive_color_mode(3, None) == "rgb" + + def test_samples_per_pixel_1_is_bw(self) -> None: + assert _derive_color_mode(1, None) == "bw" + + def test_falls_back_to_photometric_rgb(self) -> None: + assert _derive_color_mode(None, 2) == "rgb" + + def test_falls_back_to_photometric_bw(self) -> None: + assert _derive_color_mode(None, 1) == "bw" + + def test_returns_none_when_both_missing(self) -> None: + assert _derive_color_mode(None, None) is None + + +class TestParseMetadataDerivedFields: + def test_emits_dpi_and_rgb_color_mode(self, tmp_path: Path) -> None: + img = np.random.randint(0, 255, (100, 100, 3), dtype=np.uint8) + tif_path = tmp_path / "scan.tif" + tifffile.imwrite(str(tif_path), img, resolution=(300, 300)) + + converter = TIFFToJPEGConverter(tif_path) + converter.load() + metadata = converter.parse_metadata() + + assert metadata["dpi"] == 300 + assert metadata["color_mode"] == "rgb" + + def test_emits_bw_color_mode_for_grayscale(self, tmp_path: Path) -> None: + img = np.random.randint(0, 255, (100, 100), dtype=np.uint8) + tif_path = tmp_path / "gray.tif" + tifffile.imwrite(str(tif_path), img, resolution=(600, 600)) + + converter = TIFFToJPEGConverter(tif_path) + converter.load() + metadata = converter.parse_metadata() + + assert metadata["dpi"] == 600 + assert metadata["color_mode"] == "bw" + + class TestValidation: def test_rejects_missing_file(self, tmp_path: Path) -> None: converter = TIFFToJPEGConverter(tmp_path / "nonexistent.tif") diff --git a/web-app/app/api/v1/instruments/[instrumentId]/runs/route.ts b/web-app/app/api/v1/instruments/[instrumentId]/runs/route.ts index 1be66f77..640a8409 100644 --- a/web-app/app/api/v1/instruments/[instrumentId]/runs/route.ts +++ b/web-app/app/api/v1/instruments/[instrumentId]/runs/route.ts @@ -172,7 +172,7 @@ export async function POST(request: NextRequest, { params }: RouteContext) { const origin = new URL(request.url).origin; await sendSlackMessage( `*${instrument.displayName}*\n` + - `New run \`${runId}\` created (source: ${source}).\n` + + `New instrument run reported: \`${runId}\`.\n` + `<${origin}/instruments/${instrumentId}/runs/${encodeURIComponent(runId)}|View in Data Hub>` ); } diff --git a/web-app/app/instruments/[instrumentId]/page.tsx b/web-app/app/instruments/[instrumentId]/page.tsx index 5225a0ea..d68178cb 100644 --- a/web-app/app/instruments/[instrumentId]/page.tsx +++ b/web-app/app/instruments/[instrumentId]/page.tsx @@ -6,6 +6,7 @@ import { type RunRow, } from "@/components/instruments/runs-table"; import { DefaultRunsTable } from "@/components/instruments/runs-table/default-runs-table"; +import { EpsonScannerRunsTable } from "@/components/instruments/runs-table/epson-scanner-runs-table"; import { GelDocRunsTable } from "@/components/instruments/runs-table/gel-doc-runs-table"; import { HinaRunsTable } from "@/components/instruments/runs-table/hina-runs-table"; import { PlateReaderRunsTable } from "@/components/instruments/runs-table/plate-reader-runs-table"; @@ -90,6 +91,15 @@ function renderRunsTableVariant( ranByOptions={ranByOptions} /> ); + case "epson_v700_scanner": + return ( + + ); case "default": return ( = { qpcr: "qPCR", tape_station: "TapeStation", hina_microscope: "Hina Microscope", + epson_v700_scanner: "Epson V700 Scanner", }; const INSTRUMENT_TYPE_OPTIONS = VALID_INSTRUMENT_TYPES.map((value) => ({ diff --git a/web-app/components/instruments/runs-table/epson-scanner-runs-table.tsx b/web-app/components/instruments/runs-table/epson-scanner-runs-table.tsx new file mode 100644 index 00000000..0d11278b --- /dev/null +++ b/web-app/components/instruments/runs-table/epson-scanner-runs-table.tsx @@ -0,0 +1,172 @@ +import { RelativeTime } from "@/components/dashboard/relative-time"; +import { Badge } from "@/components/ui/badge"; +import { + Table, + TableBody, + TableCell, + TableHead, + TableHeader, + TableRow, +} from "@/components/ui/table"; +import type { EpsonScannerFilterOptions } from "@/lib/api/instrument-runs"; +import { + COLOR_MODE_COLORS, + DPI_COLORS, + formatColorMode, +} from "@/lib/instrument-colors"; +import { runRowToRef } from "@/lib/runs/row-actions"; +import { cn, formatBytes } from "@/lib/utils"; + +import type { RunRow } from "."; +import { FilterableColumnHeader } from "./filterable-column-header"; +import { MetadataFieldBadge, getMetadataField } from "./metadata-utils"; +import { RanByCell } from "./ran-by-cell"; +import { RawFileColumnHeader } from "./raw-file-column-header"; +import { RunIdLabel } from "./run-id-label"; +import { RunRowActions } from "./run-row-actions"; +import { RunSelectAllCheckbox, RunSelectCheckbox } from "./run-select-checkbox"; +import type { RunRef } from "./run-selection-provider"; +import { RunStatusIcon } from "./run-status-icon"; + +// DPI is a numeric scalar; sort ascending so "300" < "600" rather than +// lexicographic order. +function sortDpiOptions(dpis: string[]): string[] { + return [...dpis].sort((a, b) => Number(a) - Number(b)); +} + +function colorModeOption(value: string): { value: string; label: string } { + return { value, label: formatColorMode(value) }; +} + +export function EpsonScannerRunsTable({ + data, + instrumentId, + filterOptions, + ranByOptions, +}: { + data: RunRow[]; + instrumentId: string; + filterOptions: EpsonScannerFilterOptions; + ranByOptions: { value: string; label: string }[]; +}) { + const runRefs: RunRef[] = data.map(runRowToRef); + const dpiOptions = sortDpiOptions(filterOptions.dpis); + const colorModeOptions = filterOptions.colorModes.map(colorModeOption); + + return ( + + + + + + + Run ID + + + + + + + + + + + + + + + + Created + + Actions + + + + + {data.map((row) => { + const isDeleted = row.deleted_at !== null; + const dpi = getMetadataField(row.metadata, "dpi"); + const colorMode = getMetadataField(row.metadata, "color_mode"); + return ( + + + + + +
+ + + {isDeleted && ( + + deleted + + )} +
+ + + {row.file_count} + + + {formatBytes(row.total_size_bytes)} + + + + + + + + + + + + + + + + + + ); + })} + +
+ ); +} diff --git a/web-app/components/runs/run-metadata-badges.tsx b/web-app/components/runs/run-metadata-badges.tsx index 70a8c942..82722e16 100644 --- a/web-app/components/runs/run-metadata-badges.tsx +++ b/web-app/components/runs/run-metadata-badges.tsx @@ -7,10 +7,13 @@ import { import { CAPTURE_TYPE_COLORS, CHANNEL_COLOR_STYLES, + COLOR_MODE_COLORS, + DPI_COLORS, IMAGING_MODE_COLORS, MEASUREMENT_MODE_COLORS, MEASUREMENT_TYPE_COLORS, buildWavelengthColorMap, + formatColorMode, getDyeChannelColor, } from "@/lib/instrument-colors"; import { cn } from "@/lib/utils"; @@ -228,6 +231,46 @@ export function TapeStationRunBadges({ ); } +// --------------------------------------------------------------------------- +// Epson V700 Scanner +// --------------------------------------------------------------------------- + +export function hasEpsonScannerMetadata(metadata: Record) { + return Boolean( + getMetadataField(metadata, "dpi") || + getMetadataField(metadata, "color_mode") + ); +} + +export function EpsonScannerRunBadges({ + metadata, +}: { + metadata: Record; +}) { + const dpi = getMetadataField(metadata, "dpi"); + const colorMode = getMetadataField(metadata, "color_mode"); + + if (!dpi && !colorMode) return null; + + return ( + <> + {dpi && ( + + + + )} + {colorMode && ( + + + + )} + + ); +} + // --------------------------------------------------------------------------- // Hina microscope // --------------------------------------------------------------------------- diff --git a/web-app/components/runs/variants/epson-scanner-run-detail.tsx b/web-app/components/runs/variants/epson-scanner-run-detail.tsx new file mode 100644 index 00000000..7ed443fe --- /dev/null +++ b/web-app/components/runs/variants/epson-scanner-run-detail.tsx @@ -0,0 +1,58 @@ +import { DeleteRunDialog } from "@/components/runs/delete-run-dialog"; +import { RestoreRunButton } from "@/components/runs/restore-run-button"; +import type { RunDetailProps } from "@/components/runs/run-detail"; +import { RunDetail } from "@/components/runs/run-detail"; +import { + EpsonScannerRunBadges, + hasEpsonScannerMetadata, +} from "@/components/runs/run-metadata-badges"; + +export function EpsonScannerRunDetail({ + run, + files, + instrumentId, + runId, + attributionsSlot, +}: RunDetailProps) { + const isDeleted = run.deletedAt !== null; + const activeFileCount = files.filter((f) => f.deletedAt === null).length; + const hasProcessedFiles = + files.filter((f) => f.category === "processed" && f.deletedAt === null) + .length > 0; + + return ( + <> + + {!isDeleted && ( + + )} + {isDeleted && ( + + )} + + + + {hasEpsonScannerMetadata(run.metadata as Record) && ( + + } + /> + + )} + + + + + + ); +} diff --git a/web-app/components/runs/variants/index.tsx b/web-app/components/runs/variants/index.tsx index b2b78a27..01ffc89b 100644 --- a/web-app/components/runs/variants/index.tsx +++ b/web-app/components/runs/variants/index.tsx @@ -1,6 +1,7 @@ import type { RunDetailProps } from "@/components/runs/run-detail"; import { DefaultRunDetail } from "./default-run-detail"; +import { EpsonScannerRunDetail } from "./epson-scanner-run-detail"; import { GelDocRunDetail } from "./gel-doc-run-detail"; import { HinaMicroscopeRunDetail } from "./hina-microscope-run-detail"; import { PlateReaderRunDetail } from "./plate-reader-run-detail"; @@ -21,6 +22,8 @@ export function RunDetailVariant(props: RunDetailVariantProps) { return ; case "hina_microscope": return ; + case "epson_v700_scanner": + return ; default: return ; } diff --git a/web-app/drizzle/0018_epson_v700_scanner_type.sql b/web-app/drizzle/0018_epson_v700_scanner_type.sql new file mode 100644 index 00000000..71730163 --- /dev/null +++ b/web-app/drizzle/0018_epson_v700_scanner_type.sql @@ -0,0 +1 @@ +ALTER TYPE "public"."instrument_type" ADD VALUE 'epson_v700_scanner'; \ No newline at end of file diff --git a/web-app/drizzle/0019_set_epson_scanner_type.sql b/web-app/drizzle/0019_set_epson_scanner_type.sql new file mode 100644 index 00000000..e5ad88f0 --- /dev/null +++ b/web-app/drizzle/0019_set_epson_scanner_type.sql @@ -0,0 +1,3 @@ +UPDATE "instruments" +SET "instrument_type" = 'epson_v700_scanner' +WHERE "id" = 'epson-v700-scanner'; diff --git a/web-app/drizzle/meta/0018_snapshot.json b/web-app/drizzle/meta/0018_snapshot.json new file mode 100644 index 00000000..eac41b3d --- /dev/null +++ b/web-app/drizzle/meta/0018_snapshot.json @@ -0,0 +1,1676 @@ +{ + "id": "9e23f9d3-eab3-4b1e-a80d-31913aa5c3a0", + "prevId": "57e13a3d-135f-4b02-a507-323cf2d64140", + "version": "7", + "dialect": "postgresql", + "tables": { + "public.account": { + "name": "account", + "schema": "", + "columns": { + "userId": { + "name": "userId", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "type": { + "name": "type", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "provider": { + "name": "provider", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "providerAccountId": { + "name": "providerAccountId", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "refresh_token": { + "name": "refresh_token", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "access_token": { + "name": "access_token", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "expires_at": { + "name": "expires_at", + "type": "integer", + "primaryKey": false, + "notNull": false + }, + "token_type": { + "name": "token_type", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "scope": { + "name": "scope", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "id_token": { + "name": "id_token", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "session_state": { + "name": "session_state", + "type": "text", + "primaryKey": false, + "notNull": false + } + }, + "indexes": { + "idx_accounts_user_id": { + "name": "idx_accounts_user_id", + "columns": [ + { + "expression": "userId", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + } + }, + "foreignKeys": { + "account_userId_user_id_fk": { + "name": "account_userId_user_id_fk", + "tableFrom": "account", + "tableTo": "user", + "columnsFrom": [ + "userId" + ], + "columnsTo": [ + "id" + ], + "onDelete": "cascade", + "onUpdate": "no action" + } + }, + "compositePrimaryKeys": { + "account_provider_providerAccountId_pk": { + "name": "account_provider_providerAccountId_pk", + "columns": [ + "provider", + "providerAccountId" + ] + } + }, + "uniqueConstraints": {}, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.archive_jobs": { + "name": "archive_jobs", + "schema": "", + "columns": { + "id": { + "name": "id", + "type": "uuid", + "primaryKey": true, + "notNull": true, + "default": "gen_random_uuid()" + }, + "instrument_run_id": { + "name": "instrument_run_id", + "type": "uuid", + "primaryKey": false, + "notNull": true + }, + "fingerprint": { + "name": "fingerprint", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "archive_bucket": { + "name": "archive_bucket", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "archive_key": { + "name": "archive_key", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "size_bytes": { + "name": "size_bytes", + "type": "bigint", + "primaryKey": false, + "notNull": false + }, + "status": { + "name": "status", + "type": "archive_job_status", + "typeSchema": "public", + "primaryKey": false, + "notNull": true, + "default": "'pending'" + }, + "error_message": { + "name": "error_message", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "created_by": { + "name": "created_by", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "created_at": { + "name": "created_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": true, + "default": "now()" + }, + "completed_at": { + "name": "completed_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + } + }, + "indexes": { + "uq_archive_jobs_inflight": { + "name": "uq_archive_jobs_inflight", + "columns": [ + { + "expression": "instrument_run_id", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "fingerprint", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": true, + "where": "\"archive_jobs\".\"status\" in ('pending', 'building')", + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_archive_jobs_run_fingerprint_status": { + "name": "idx_archive_jobs_run_fingerprint_status", + "columns": [ + { + "expression": "instrument_run_id", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "fingerprint", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "status", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + } + }, + "foreignKeys": { + "archive_jobs_instrument_run_id_instrument_runs_id_fk": { + "name": "archive_jobs_instrument_run_id_instrument_runs_id_fk", + "tableFrom": "archive_jobs", + "tableTo": "instrument_runs", + "columnsFrom": [ + "instrument_run_id" + ], + "columnsTo": [ + "id" + ], + "onDelete": "cascade", + "onUpdate": "no action" + }, + "archive_jobs_created_by_user_id_fk": { + "name": "archive_jobs_created_by_user_id_fk", + "tableFrom": "archive_jobs", + "tableTo": "user", + "columnsFrom": [ + "created_by" + ], + "columnsTo": [ + "id" + ], + "onDelete": "set null", + "onUpdate": "no action" + } + }, + "compositePrimaryKeys": {}, + "uniqueConstraints": {}, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.files": { + "name": "files", + "schema": "", + "columns": { + "id": { + "name": "id", + "type": "bigserial", + "primaryKey": true, + "notNull": true + }, + "instrument_run_id": { + "name": "instrument_run_id", + "type": "uuid", + "primaryKey": false, + "notNull": true + }, + "relative_path": { + "name": "relative_path", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "s3_bucket": { + "name": "s3_bucket", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "s3_key": { + "name": "s3_key", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "filename": { + "name": "filename", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "content_type": { + "name": "content_type", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "size_bytes": { + "name": "size_bytes", + "type": "bigint", + "primaryKey": false, + "notNull": false + }, + "category": { + "name": "category", + "type": "file_category", + "typeSchema": "public", + "primaryKey": false, + "notNull": true, + "default": "'raw'" + }, + "status": { + "name": "status", + "type": "file_status", + "typeSchema": "public", 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"isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + } + }, + "foreignKeys": { + "run_attributions_run_id_instrument_runs_id_fk": { + "name": "run_attributions_run_id_instrument_runs_id_fk", + "tableFrom": "run_attributions", + "tableTo": "instrument_runs", + "columnsFrom": [ + "run_id" + ], + "columnsTo": [ + "id" + ], + "onDelete": "cascade", + "onUpdate": "no action" + }, + "run_attributions_user_id_user_id_fk": { + "name": "run_attributions_user_id_user_id_fk", + "tableFrom": "run_attributions", + "tableTo": "user", + "columnsFrom": [ + "user_id" + ], + "columnsTo": [ + "id" + ], + "onDelete": "cascade", + "onUpdate": "no action" + } + }, + "compositePrimaryKeys": { + "run_attributions_run_id_user_id_pk": { + "name": "run_attributions_run_id_user_id_pk", + "columns": [ + "run_id", + "user_id" + ] + } + }, + "uniqueConstraints": {}, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.run_comments": { + "name": "run_comments", + "schema": "", + "columns": { + "id": { + "name": "id", + "type": "uuid", + "primaryKey": true, + "notNull": true, + "default": "gen_random_uuid()" + }, + "run_id": { + "name": "run_id", + "type": "uuid", + "primaryKey": false, + "notNull": true + }, + "user_id": { + "name": "user_id", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "body": { + "name": "body", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "created_at": { + "name": "created_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": true, + "default": "now()" + }, + "updated_at": { + "name": "updated_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": true, + "default": "now()" + }, + "edited_at": { + "name": "edited_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + }, + "deleted_at": { + "name": "deleted_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + } + }, + "indexes": { + "idx_run_comments_run_id_created_at": { + "name": "idx_run_comments_run_id_created_at", + "columns": [ + { + "expression": "run_id", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "created_at", + "isExpression": false, + "asc": false, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_run_comments_user_id": { + "name": "idx_run_comments_user_id", + "columns": [ + { + "expression": "user_id", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + } + }, + "foreignKeys": { + "run_comments_run_id_instrument_runs_id_fk": { + "name": "run_comments_run_id_instrument_runs_id_fk", + "tableFrom": "run_comments", + "tableTo": "instrument_runs", + "columnsFrom": [ + "run_id" + ], + "columnsTo": [ + "id" + ], + "onDelete": "cascade", + "onUpdate": "no action" + }, + "run_comments_user_id_user_id_fk": { + "name": "run_comments_user_id_user_id_fk", + "tableFrom": "run_comments", + "tableTo": "user", + "columnsFrom": [ + "user_id" + ], + "columnsTo": [ + "id" + ], + "onDelete": "cascade", + "onUpdate": "no action" + } + }, + "compositePrimaryKeys": {}, + "uniqueConstraints": {}, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.session": { + "name": "session", + "schema": "", + "columns": { + "sessionToken": { + "name": "sessionToken", + "type": "text", + "primaryKey": true, + "notNull": true + }, + "userId": { + "name": "userId", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "expires": { + "name": "expires", + "type": "timestamp", + "primaryKey": false, + "notNull": true + } + }, + "indexes": { + "idx_sessions_user_id": { + "name": "idx_sessions_user_id", + "columns": [ + { + "expression": "userId", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + } + }, + "foreignKeys": { + "session_userId_user_id_fk": { + "name": "session_userId_user_id_fk", + "tableFrom": "session", + "tableTo": "user", + "columnsFrom": [ + "userId" + ], + "columnsTo": [ + "id" + ], + "onDelete": "cascade", + "onUpdate": "no action" + } + }, + "compositePrimaryKeys": {}, + "uniqueConstraints": {}, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.user": { + "name": "user", + "schema": "", + "columns": { + "id": { + "name": "id", + "type": "text", + "primaryKey": true, + "notNull": true + }, + "name": { + "name": "name", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "email": { + "name": "email", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "emailVerified": { + "name": "emailVerified", + "type": "timestamp", + "primaryKey": false, + "notNull": false + }, + "image": { + "name": "image", + "type": "text", + "primaryKey": false, + "notNull": false + } + }, + "indexes": {}, + "foreignKeys": {}, + "compositePrimaryKeys": {}, + "uniqueConstraints": { + "user_email_unique": { + "name": "user_email_unique", + "nullsNotDistinct": false, + "columns": [ + "email" + ] + } + }, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.watcher_events": { + "name": "watcher_events", + "schema": "", + "columns": { + "id": { + "name": "id", + "type": "bigserial", + "primaryKey": true, + "notNull": true + }, + "watcher_id": { + "name": "watcher_id", + "type": "uuid", + "primaryKey": false, + "notNull": true + }, + "event_type": { + "name": "event_type", + "type": "watcher_event_type", + "typeSchema": "public", + "primaryKey": false, + "notNull": true + }, + "message": { + "name": "message", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "details": { + "name": "details", + "type": "jsonb", + "primaryKey": false, + "notNull": false + }, + "timestamp": { + "name": "timestamp", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": true + }, + "created_at": { + "name": "created_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": true, + "default": "now()" + } + }, + "indexes": { + "idx_watcher_events_watcher_id_timestamp": { + "name": "idx_watcher_events_watcher_id_timestamp", + "columns": [ + { + "expression": "watcher_id", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "timestamp", + "isExpression": false, + "asc": false, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_watcher_events_watcher_id_event_type": { + "name": "idx_watcher_events_watcher_id_event_type", + "columns": [ + { + "expression": "watcher_id", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "event_type", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + } + }, + "foreignKeys": { + "watcher_events_watcher_id_watchers_id_fk": { + "name": "watcher_events_watcher_id_watchers_id_fk", + "tableFrom": "watcher_events", + "tableTo": "watchers", + "columnsFrom": [ + "watcher_id" + ], + "columnsTo": [ + "id" + ], + "onDelete": "no action", + "onUpdate": "no action" + } + }, + "compositePrimaryKeys": {}, + "uniqueConstraints": {}, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.watcher_heartbeats": { + "name": "watcher_heartbeats", + "schema": "", + "columns": { + "id": { + "name": "id", + "type": "bigserial", + "primaryKey": true, + "notNull": true + }, + "watcher_id": { + "name": "watcher_id", + "type": "uuid", + "primaryKey": false, + "notNull": true + }, + "timestamp": { + "name": "timestamp", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": true + }, + "status": { + "name": "status", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "upload_mode": { + "name": "upload_mode", + "type": "upload_mode", + "typeSchema": "public", + "primaryKey": false, + "notNull": false + }, + "files_uploaded_since_last": { + "name": "files_uploaded_since_last", + "type": "integer", + "primaryKey": false, + "notNull": false, + "default": 0 + }, + "runs_reported_since_last": { + "name": "runs_reported_since_last", + "type": "integer", + "primaryKey": false, + "notNull": false, + "default": 0 + }, + "errors_since_last": { + "name": "errors_since_last", + "type": "integer", + "primaryKey": false, + "notNull": false, + "default": 0 + }, + "uptime_seconds": { + "name": "uptime_seconds", + "type": "integer", + "primaryKey": false, + "notNull": false + }, + "created_at": { + "name": "created_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": true, + "default": "now()" + } + }, + "indexes": { + "idx_watcher_heartbeats_watcher_id_timestamp": { + "name": "idx_watcher_heartbeats_watcher_id_timestamp", + "columns": [ + { + "expression": "watcher_id", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "timestamp", + "isExpression": false, + "asc": false, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + } + }, + "foreignKeys": { + "watcher_heartbeats_watcher_id_watchers_id_fk": { + "name": "watcher_heartbeats_watcher_id_watchers_id_fk", + "tableFrom": "watcher_heartbeats", + "tableTo": "watchers", + "columnsFrom": [ + "watcher_id" + ], + "columnsTo": [ + "id" + ], + "onDelete": "no action", + "onUpdate": "no action" + } + }, + "compositePrimaryKeys": {}, + "uniqueConstraints": {}, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.watchers": { + "name": "watchers", + "schema": "", + "columns": { + "id": { + "name": "id", + "type": "uuid", + "primaryKey": true, + "notNull": true, + "default": "gen_random_uuid()" + }, + "instrument_id": { + "name": "instrument_id", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "hostname": { + "name": "hostname", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "os_info": { + "name": "os_info", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "watcher_version": { + "name": "watcher_version", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "config_checksum": { + "name": "config_checksum", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "config_yaml": { + "name": "config_yaml", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "last_heartbeat_at": { + "name": "last_heartbeat_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + }, + "status": { + "name": "status", + "type": "watcher_status", + "typeSchema": "public", + "primaryKey": false, + "notNull": true, + "default": "'registered'" + }, + "created_at": { + "name": "created_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": true, + "default": "now()" + }, + "updated_at": { + "name": "updated_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": true, + "default": "now()" + }, + "deleted_at": { + "name": "deleted_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + } + }, + "indexes": { + "uq_watchers_active_instrument_id": { + "name": "uq_watchers_active_instrument_id", + "columns": [ + { + "expression": "instrument_id", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": true, + "where": "\"watchers\".\"deleted_at\" is null", + "concurrently": false, + "method": "btree", + "with": {} + } + }, + "foreignKeys": { + "watchers_instrument_id_instruments_id_fk": { + "name": "watchers_instrument_id_instruments_id_fk", + "tableFrom": "watchers", + "tableTo": "instruments", + "columnsFrom": [ + "instrument_id" + ], + "columnsTo": [ + "id" + ], + "onDelete": "no action", + "onUpdate": "no action" + } + }, + "compositePrimaryKeys": {}, + "uniqueConstraints": {}, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + } + }, + "enums": { + "public.archive_job_status": { + "name": "archive_job_status", + "schema": "public", + "values": [ + "pending", + "building", + "ready", + "failed" + ] + }, + "public.file_category": { + "name": "file_category", + "schema": "public", + "values": [ + "raw", + "processed" + ] + }, + "public.file_status": { + "name": "file_status", + "schema": "public", + "values": [ + "detected", + "upload_requested", + "uploaded", + "processing", + "completed", + "failed" + ] + }, + "public.instrument_run_source": { + "name": "instrument_run_source", + "schema": "public", + "values": [ + "lambda", + "watcher" + ] + }, + "public.instrument_status": { + "name": "instrument_status", + "schema": "public", + "values": [ + "pending", + "active", + "inactive" + ] + }, + "public.instrument_type": { + "name": "instrument_type", + "schema": "public", + "values": [ + "generic", + "plate_reader", + "gel_doc", + "qpcr", + "tape_station", + "hina_microscope", + "epson_v700_scanner" + ] + }, + "public.upload_mode": { + "name": "upload_mode", + "schema": "public", + "values": [ + "auto", + "manual" + ] + }, + "public.watcher_event_type": { + "name": "watcher_event_type", + "schema": "public", + "values": [ + "watcher_started", + "watcher_stopped", + "file_uploaded", + "upload_failed", + "run_reported", + "config_synced", + "error", + "update_started", + "update_succeeded", + "update_failed" + ] + }, + "public.watcher_status": { + "name": "watcher_status", + "schema": "public", + "values": [ + "registered", + "watching", + "stopped" + ] + } + }, + "schemas": {}, + "sequences": {}, + "roles": {}, + "policies": {}, + "views": {}, + "_meta": { + "columns": {}, + "schemas": {}, + "tables": {} + } +} \ No newline at end of file diff --git a/web-app/drizzle/meta/_journal.json b/web-app/drizzle/meta/_journal.json index 4aead99b..a2058a08 100644 --- a/web-app/drizzle/meta/_journal.json +++ b/web-app/drizzle/meta/_journal.json @@ -127,6 +127,20 @@ "when": 1778177006266, "tag": "0017_drop_files_purged_at", "breakpoints": true + }, + { + "idx": 18, + "version": "7", + "when": 1778207440654, + "tag": "0018_epson_v700_scanner_type", + "breakpoints": true + }, + { + "idx": 19, + "version": "7", + "when": 1778207440655, + "tag": "0019_set_epson_scanner_type", + "breakpoints": true } ] } \ No newline at end of file diff --git a/web-app/lib/api/instrument-runs.ts b/web-app/lib/api/instrument-runs.ts index 2c6ed2c2..b336a7e1 100644 --- a/web-app/lib/api/instrument-runs.ts +++ b/web-app/lib/api/instrument-runs.ts @@ -151,6 +151,11 @@ type RunListFilters = { // so key ordering differences between client serialization and stored value // don't matter. hinaSize?: string; + // Epson V700 Scanner derived metadata. `dpi` is a numeric string (e.g. "300", + // "600") and `colorMode` is the canonical "rgb"/"bw" string written by the + // Lambda's TIFF metadata parser. + dpi?: string; + colorMode?: string; // Either a userId (match runs attributed to that user) or the reserved // sentinel "unattributed" (match runs with no attributions). ranBy?: string; @@ -275,6 +280,21 @@ export async function buildRunListQuery(filters: RunListFilters) { ); } + // Epson V700 Scanner metadata column filters. Both use the `->>` text + // accessor for scalar equality, which is *not* covered by the default + // jsonb_ops GIN index — these conditions piggyback on + // `idx_instrument_runs_active(instrument_id, …)` and re-evaluate per row, + // which is fine on instrument-scoped pages but worth a dedicated + // expression index if it ever becomes a hot path. + if (filters.dpi) { + conditions.push(sql`${instrumentRuns.metadata}->>'dpi' = ${filters.dpi}`); + } + if (filters.colorMode) { + conditions.push( + sql`${instrumentRuns.metadata}->>'color_mode' = ${filters.colorMode}` + ); + } + // Attribution filter — correlated (NOT) EXISTS against run_attributions. if (filters.ranBy === UNATTRIBUTED_SENTINEL) { conditions.push( @@ -493,6 +513,8 @@ const ALLOWED_METADATA_KEYS = new Set([ "measurement_type", "capture_type", "imaging_mode", + "dpi", + "color_mode", ]); async function distinctMetadataValues( @@ -667,6 +689,25 @@ export async function getHinaFilterOptions( return { channels, dimensions, sizes }; } +// --------------------------------------------------------------------------- +// Distinct metadata values for Epson V700 Scanner column filters. +// --------------------------------------------------------------------------- + +export type EpsonScannerFilterOptions = { + dpis: string[]; + colorModes: string[]; +}; + +export async function getEpsonScannerFilterOptions( + instrumentId: string +): Promise { + const [dpis, colorModes] = await Promise.all([ + distinctMetadataValues(instrumentId, "dpi"), + distinctMetadataValues(instrumentId, "color_mode"), + ]); + return { dpis, colorModes }; +} + // --------------------------------------------------------------------------- // Dispatcher: fetch whichever per-instrument filter options apply to this // instrument type. The discriminated return shape lets the caller narrow to @@ -680,6 +721,7 @@ export type InstrumentFilterOptionsByType = | { kind: "gel_doc"; options: GelDocFilterOptions } | { kind: "qpcr"; options: QpcrFilterOptions } | { kind: "hina_microscope"; options: HinaFilterOptions } + | { kind: "epson_v700_scanner"; options: EpsonScannerFilterOptions } | { kind: "default" }; export async function getInstrumentFilterOptions( @@ -707,6 +749,11 @@ export async function getInstrumentFilterOptions( kind: "hina_microscope", options: await getHinaFilterOptions(instrumentId), }; + case "epson_v700_scanner": + return { + kind: "epson_v700_scanner", + options: await getEpsonScannerFilterOptions(instrumentId), + }; case "generic": case "tape_station": return { kind: "default" }; diff --git a/web-app/lib/db/schema.ts b/web-app/lib/db/schema.ts index d86ea9af..1bf5859a 100644 --- a/web-app/lib/db/schema.ts +++ b/web-app/lib/db/schema.ts @@ -57,6 +57,7 @@ export const instrumentTypeEnum = pgEnum("instrument_type", [ "qpcr", "tape_station", "hina_microscope", + "epson_v700_scanner", ]); export const VALID_INSTRUMENT_TYPES = instrumentTypeEnum.enumValues; diff --git a/web-app/lib/instrument-colors.ts b/web-app/lib/instrument-colors.ts index c34d9c9d..44c16da2 100644 --- a/web-app/lib/instrument-colors.ts +++ b/web-app/lib/instrument-colors.ts @@ -38,6 +38,36 @@ export const CHANNEL_COLOR_STYLES: Record = { "border-rose-200 bg-rose-50 text-rose-700 dark:border-rose-800 dark:bg-rose-950 dark:text-rose-300", }; +// ---------- Epson V700 Scanner ---------- + +export const DPI_COLORS: Record = { + "300": + "border-sky-200 bg-sky-50 text-sky-700 dark:border-sky-800 dark:bg-sky-950 dark:text-sky-300", + "600": + "border-indigo-200 bg-indigo-50 text-indigo-700 dark:border-indigo-800 dark:bg-indigo-950 dark:text-indigo-300", +}; + +// Stored values are the canonical strings written by the Lambda +// (`"rgb"` / `"bw"`); the human label is computed at the call site. +export const COLOR_MODE_COLORS: Record = { + rgb: "border-fuchsia-200 bg-fuchsia-50 text-fuchsia-700 dark:border-fuchsia-800 dark:bg-fuchsia-950 dark:text-fuchsia-300", + bw: "border-stone-200 bg-stone-50 text-stone-700 dark:border-stone-800 dark:bg-stone-950 dark:text-stone-300", +}; + +export const COLOR_MODE_LABELS: Record = { + rgb: "RGB", + bw: "B&W", +}; + +/** + * Map a stored color-mode value (`"rgb"` / `"bw"`) to its display label, + * falling back to the raw value for forward-compatibility with any future + * values the Lambda might emit before this map is updated. + */ +export function formatColorMode(value: string): string { + return COLOR_MODE_LABELS[value] ?? value; +} + // ---------- Plate reader ---------- export const MEASUREMENT_TYPE_COLORS: Record = { diff --git a/web-app/lib/search-params.ts b/web-app/lib/search-params.ts index 5cc50df3..ddf40296 100644 --- a/web-app/lib/search-params.ts +++ b/web-app/lib/search-params.ts @@ -49,6 +49,10 @@ export const instrumentDetailSearchParams = { hina_channel: parseAsString, hina_dimension: parseAsString, hina_size: parseAsString, + // Epson V700 Scanner metadata column filters. `dpi` is a numeric string + // ("300", "600"); `color_mode` is "rgb" or "bw". + dpi: parseAsString, + color_mode: parseAsString, // Attribution filter: either a userId or the reserved sentinel "unattributed". ran_by: parseAsString, };