From 201bef413871bb20b438d07723e4a59c615be91b Mon Sep 17 00:00:00 2001 From: Wasim Sandhu Date: Thu, 23 Apr 2026 16:06:07 -0700 Subject: [PATCH 1/7] =?UTF-8?q?feat:=20Add=20Hina=20microscope=20(`hina-mi?= =?UTF-8?q?croscope`)=20ND2=20=E2=86=92=20JPG=20processor?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Converts uploaded .nd2 files into composite RGB JPG overlays using arcadia-microscopy-tools. Per-channel intensities are percentile stretched (1st–99th) and blended via `overlay_channels`; Z-stacks collapse to a max-intensity projection, and T/P axes fall back to the first index. Run-level metadata (sizes, channels, dimensions) is parsed once per run via a best-effort `if run.metadata` gate after `ensure_run`, so the first file to arrive wins while every file still produces its own JPG. Also adds the `hina` subcommand to `data-hub-process`, an S3 trigger for `hina-microscope/*.nd2`, and unit tests covering metadata serialization, axis reduction, percentile rescale, and the single-shot metadata gate. --- docs/lambda.md | 3 + infra/template.yaml | 9 + lambda/pyproject.toml | 1 + lambda/src/data_hub_lambda/cli.py | 40 ++ lambda/src/data_hub_lambda/handler.py | 7 + .../hina_microscope/__init__.py | 3 + .../hina_microscope/image_processing.py | 159 ++++++++ .../hina_microscope/parse_metadata.py | 40 ++ .../hina_microscope/process_file.py | 100 +++++ .../hina_microscope/test_image_processing.py | 96 +++++ .../hina_microscope/test_parse_metadata.py | 161 ++++++++ .../hina_microscope/test_process_file.py | 190 ++++++++++ lambda/tests/integration/conftest.py | 1 + .../shared/src/data_hub_shared/constants.py | 1 + packages/shared/src/data_hub_shared/enums.py | 1 + uv.lock | 354 ++++++++++++++---- 16 files changed, 1098 insertions(+), 68 deletions(-) create mode 100644 lambda/src/data_hub_lambda/hina_microscope/__init__.py create mode 100644 lambda/src/data_hub_lambda/hina_microscope/image_processing.py create mode 100644 lambda/src/data_hub_lambda/hina_microscope/parse_metadata.py create mode 100644 lambda/src/data_hub_lambda/hina_microscope/process_file.py create mode 100644 lambda/tests/hina_microscope/test_image_processing.py create mode 100644 lambda/tests/hina_microscope/test_parse_metadata.py create mode 100644 lambda/tests/hina_microscope/test_process_file.py diff --git a/docs/lambda.md b/docs/lambda.md index af034564..338bae22 100644 --- a/docs/lambda.md +++ b/docs/lambda.md @@ -33,6 +33,7 @@ When a file fails processing (or needs to be re-run), users can trigger reproces | Akta FPLC | `akta_fplc` | `akta-fplc` | | Azure 600 Gel Doc | `azure_600_gel_doc` | `azure-600-gel-doc` | | Azure Cielo qPCR | `azure_cielo_qpcr` | `azure-cielo-qpcr` | +| Hina Microscope | `hina_microscope` | `hina-microscope` | | SpectraMax iD3 Plate Reader | `spectramax_plate_reader` | `spectramax-id3-plate-reader` | | SpectraMax iD5 Plate Reader | `spectramax_plate_reader` | `spectramax-id5-plate-reader` | @@ -67,6 +68,7 @@ Available commands: | Command | Description | | --- | --- | | `gel-doc` | Process an Azure 600 Gel Doc TIFF (contrast-enhanced PNG + metadata) | +| `hina` | Convert a Hina microscope ND2 file to a JPG overlay + metadata | | `qpcr` | Parse dye channels from an Azure Cielo qPCR Cq Values CSV | | `spectramax` | Parse metadata and raw well data from a SpectraMax `.xls` export | | `tapestation` | Extract the tape type from a TapeStation CSV filename | @@ -102,6 +104,7 @@ The Lambda function depends on a scientific Python stack: - `matplotlib` — plotting - `scikit-image` — image processing - `tifffile` — TIFF file reading +- `arcadia-microscopy-tools` — ND2 reading, channel handling, and multi-channel compositing for the Hina microscope - `pydantic` — data validation - `requests` — HTTP client for the Data Hub API - `aws-lambda-typing` — type stubs for Lambda events/context diff --git a/infra/template.yaml b/infra/template.yaml index 784c8f63..a0fd3cff 100644 --- a/infra/template.yaml +++ b/infra/template.yaml @@ -107,6 +107,15 @@ Resources: # with `+` — this matches keys ending in `_Cq Values.csv`. Value: _Cq+Values.csv Function: !GetAtt DataHubFunction.Arn + - Event: s3:ObjectCreated:* + Filter: + S3Key: + Rules: + - Name: prefix + Value: hina-microscope/ + - Name: suffix + Value: .nd2 + Function: !GetAtt DataHubFunction.Arn - Event: s3:ObjectCreated:* Filter: S3Key: diff --git a/lambda/pyproject.toml b/lambda/pyproject.toml index 8a05bda6..7b148b26 100644 --- a/lambda/pyproject.toml +++ b/lambda/pyproject.toml @@ -4,6 +4,7 @@ version = "0.2.0" requires-python = ">=3.12" dependencies = [ "data-hub-shared", + "arcadia-microscopy-tools>=0.3.2", "aws-lambda-typing>=2.20.0", "click>=8.1", "matplotlib>=3.8", diff --git a/lambda/src/data_hub_lambda/cli.py b/lambda/src/data_hub_lambda/cli.py index bfb77d0b..528d8e3b 100644 --- a/lambda/src/data_hub_lambda/cli.py +++ b/lambda/src/data_hub_lambda/cli.py @@ -51,6 +51,46 @@ def gel_doc(file: Path, output_dir: Path | None) -> None: click.echo(json.dumps(metadata, indent=2)) +# --------------------------------------------------------------------------- +# Hina microscope (Nikon ND2) +# --------------------------------------------------------------------------- + + +@cli.command("hina") +@click.argument("file", type=click.Path(exists=True, dir_okay=False, path_type=Path)) +@click.option( + "--output-dir", + type=click.Path(file_okay=False, path_type=Path), + default=None, + help="Directory for the exported JPG (default: same directory as FILE).", +) +def hina(file: Path, output_dir: Path | None) -> None: + """Convert a Hina microscope ND2 file to a JPG overlay. + + Loads the ND2 via `arcadia-microscopy-tools`, produces a composite + JPG overlay (per-channel percentile-stretched intensities blended onto + a brightfield/zero background using each channel's native color), and + prints the parsed run-level metadata. + """ + from data_hub_lambda.hina_microscope.image_processing import ND2Processor + from data_hub_lambda.hina_microscope.parse_metadata import parse_metadata + + processor = ND2Processor(file) + processor.load() + jpg_path = processor.export_jpg() + + if output_dir is not None: + output_dir.mkdir(parents=True, exist_ok=True) + dest = output_dir / jpg_path.name + shutil.move(str(jpg_path), str(dest)) + jpg_path = dest + + click.echo(f"Exported JPG: {jpg_path}") + + metadata = parse_metadata(processor.image) + click.echo(json.dumps(metadata, indent=2)) + + # --------------------------------------------------------------------------- # Azure Cielo qPCR # --------------------------------------------------------------------------- diff --git a/lambda/src/data_hub_lambda/handler.py b/lambda/src/data_hub_lambda/handler.py index f6bbe957..a5e866c4 100644 --- a/lambda/src/data_hub_lambda/handler.py +++ b/lambda/src/data_hub_lambda/handler.py @@ -17,6 +17,7 @@ akta_fplc, azure_600_gel_doc, azure_cielo_qpcr, + hina_microscope, spectramax_plate_reader, ) from data_hub_shared import slack @@ -215,6 +216,12 @@ def lambda_handler(event: dict[str, Any], context: Context) -> dict[str, Any] | filename=event_info.filename, ) + elif instrument_id == Instrument.HINA_MICROSCOPE.value: + result_url = hina_microscope.process_file( + run_id=event_info.run_id, + filename=event_info.filename, + ) + elif instrument_id in ( Instrument.SPECTRAMAX_ID3_PLATE_READER.value, Instrument.SPECTRAMAX_ID5_PLATE_READER.value, diff --git a/lambda/src/data_hub_lambda/hina_microscope/__init__.py b/lambda/src/data_hub_lambda/hina_microscope/__init__.py new file mode 100644 index 00000000..a4427588 --- /dev/null +++ b/lambda/src/data_hub_lambda/hina_microscope/__init__.py @@ -0,0 +1,3 @@ +from data_hub_lambda.hina_microscope.process_file import ( + process_file, # noqa: F401 +) diff --git a/lambda/src/data_hub_lambda/hina_microscope/image_processing.py b/lambda/src/data_hub_lambda/hina_microscope/image_processing.py new file mode 100644 index 00000000..4ff17f53 --- /dev/null +++ b/lambda/src/data_hub_lambda/hina_microscope/image_processing.py @@ -0,0 +1,159 @@ +from __future__ import annotations +import logging +from pathlib import Path + +import numpy as np +import skimage as ski +from arcadia_microscopy_tools import MicroscopyImage +from arcadia_microscopy_tools.blending import overlay_channels +from arcadia_microscopy_tools.channels import BRIGHTFIELD, Channel +from numpy.typing import NDArray +from PIL import Image + +logger = logging.getLogger(__name__) + +ND2_SUFFIXES = (".nd2",) + +# Percentile range for per-channel contrast stretching before overlay. +# 1st-99th percentile clips hot pixels / rare noise peaks while keeping the +# bulk of the dynamic range visible. +CONTRAST_PERCENTILES: tuple[float, float] = (1.0, 99.0) + +# JPEG quality for the exported composite. +JPEG_QUALITY = 90 + + +class ND2Processor: + """Convert a Nikon ND2 file into a per-run JPG preview. + + The pipeline uses `arcadia_microscopy_tools.MicroscopyImage` to load the + ND2, reduces each channel down to a single 2D frame (max-projection over + Z, first index over T / P), percentile-stretches intensities, and then + composites the channels into an RGB overlay using each channel's native + fluorophore color via `overlay_channels`. + """ + + def __init__(self, path: Path) -> None: + self.path = path + self._image: MicroscopyImage | None = None + + def load(self) -> None: + if not self.path.exists(): + raise FileNotFoundError(f"ND2 file not found: {self.path}") + if self.path.suffix.lower() not in ND2_SUFFIXES: + raise ValueError(f"Expected ND2 file (.nd2), got: {self.path.suffix}") + + self._image = MicroscopyImage.from_nd2_path(self.path) + + @property + def image(self) -> MicroscopyImage: + if self._image is None: + raise RuntimeError("Call load() first.") + return self._image + + def export_jpg(self) -> Path: + """Render the composite overlay and write it as a JPG next to the source.""" + rgb = self._render_rgb() + rgb_uint8 = (np.clip(rgb, 0.0, 1.0) * 255).astype(np.uint8) + + jpg_path = self.path.parent / f"{self.path.stem}.jpg" + Image.fromarray(rgb_uint8, mode="RGB").save(jpg_path, format="JPEG", quality=JPEG_QUALITY) + return jpg_path + + def _render_rgb(self) -> NDArray[np.float64]: + """Produce the RGB overlay for the loaded image.""" + per_channel_2d: dict[Channel, NDArray[np.float64]] = {} + for channel in self.image.channels: + intensities = self.image.get_intensities_from_channel(channel) + reduced = self._reduce_to_2d(intensities, self._non_channel_axes()) + per_channel_2d[channel] = _rescale_percentile(reduced, CONTRAST_PERCENTILES) + + background = self._pick_background(per_channel_2d) + + # Fluorescence channels are overlaid on top of the grayscale background. + # Skip the background channel (if it was picked from the image) so it + # isn't blended onto itself. + overlay_inputs = { + ch: arr for ch, arr in per_channel_2d.items() if ch.name != BRIGHTFIELD.name + } + if not overlay_inputs: + # Single-channel brightfield (or equivalent): return the background + # as an RGB image so the caller still gets a valid overlay. + return ski.color.gray2rgb(background) + + return overlay_channels(background, overlay_inputs) + + def _non_channel_axes(self) -> list[str]: + """Ordered axis labels for the per-channel array (C dropped).""" + return [axis for axis in self.image.sizes.keys() if axis != "C"] + + @staticmethod + def _reduce_to_2d( + intensities: NDArray, # type: ignore[type-arg] + axis_labels: list[str], + ) -> NDArray[np.float64]: + """Collapse leading axes down to a (Y, X) frame. + + Z axes are max-projected; T and P axes fall back to the first index. + Any unknown leading axis is also reduced by taking the first index, + with a warning logged. + """ + arr = intensities + labels = list(axis_labels) + while len(labels) > 2: + label = labels[0] + if label == "Z": + arr = arr.max(axis=0) + elif label in ("T", "P"): + logger.info( + "Reducing axis %s (size %d) by taking first index only.", + label, + arr.shape[0], + ) + arr = arr[0] + else: + logger.warning( + "Unknown leading axis %s (size %d); taking first index.", + label, + arr.shape[0], + ) + arr = arr[0] + labels = labels[1:] + return arr + + @staticmethod + def _pick_background( + per_channel: dict[Channel, NDArray[np.float64]], + ) -> NDArray[np.float64]: + """Pick a grayscale [0, 1] background for the overlay. + + Prefers an existing BRIGHTFIELD channel (gives a natural context + image); falls back to zeros with the same 2D shape as the first + channel so fluorescence alone still renders correctly. + """ + for channel, arr in per_channel.items(): + if channel.name == BRIGHTFIELD.name: + return arr + + first = next(iter(per_channel.values())) + return np.zeros_like(first, dtype=np.float64) + + +def _rescale_percentile( + intensities: NDArray, # type: ignore[type-arg] + percentiles: tuple[float, float], +) -> NDArray[np.float64]: + """Percentile-based contrast stretching into [0, 1].""" + if intensities.size == 0: + return np.zeros_like(intensities, dtype=np.float64) + + lo, hi = np.percentile(intensities, percentiles) + if lo == hi: + return np.zeros_like(intensities, dtype=np.float64) + + rescaled = ski.exposure.rescale_intensity( + intensities, + in_range=(lo, hi), # type: ignore[arg-type] + out_range=(0.0, 1.0), # type: ignore[arg-type] + ) + return rescaled.astype(np.float64) diff --git a/lambda/src/data_hub_lambda/hina_microscope/parse_metadata.py b/lambda/src/data_hub_lambda/hina_microscope/parse_metadata.py new file mode 100644 index 00000000..a2fa506b --- /dev/null +++ b/lambda/src/data_hub_lambda/hina_microscope/parse_metadata.py @@ -0,0 +1,40 @@ +from __future__ import annotations +from typing import Any + +from arcadia_microscopy_tools import MicroscopyImage +from arcadia_microscopy_tools.channels import Channel +from arcadia_microscopy_tools.metadata_structures import DimensionFlags + + +def parse_metadata(image: MicroscopyImage) -> dict[str, Any]: + """Extract run-level metadata from a loaded Nikon ND2 image. + + Returns a JSON-serializable dict with three keys: + + - `sizes`: the full dimension map, e.g. `{"C": 4, "Y": 256, "X": 256}`. + - `channels`: a list of `{name, excitation_nm, emission_nm, color}` dicts. + - `dimensions`: a list of `DimensionFlags` member names set on the image. + + The function operates on the already-loaded `MicroscopyImage` so the + caller does not need to re-open the ND2 file for the metadata step. + """ + return { + "sizes": dict(image.sizes), + "channels": [_channel_to_dict(channel) for channel in image.channels], + "dimensions": _dimension_names(image.dimensions), + } + + +def _channel_to_dict(channel: Channel) -> dict[str, Any]: + color = channel.color.hex_code if channel.color is not None else None + return { + "name": channel.name, + "excitation_nm": channel.excitation_nm, + "emission_nm": channel.emission_nm, + "color": color, + } + + +def _dimension_names(dimensions: DimensionFlags) -> list[str]: + """Serialize a `DimensionFlags` IntFlag as a list of member names.""" + return [flag.name for flag in DimensionFlags if flag in dimensions and flag.name] diff --git a/lambda/src/data_hub_lambda/hina_microscope/process_file.py b/lambda/src/data_hub_lambda/hina_microscope/process_file.py new file mode 100644 index 00000000..37cf2fec --- /dev/null +++ b/lambda/src/data_hub_lambda/hina_microscope/process_file.py @@ -0,0 +1,100 @@ +from __future__ import annotations +import logging + +from data_hub_lambda.api_client import get_client +from data_hub_lambda.constants import DATA_HUB_WEB_URL +from data_hub_lambda.hina_microscope.image_processing import ND2Processor +from data_hub_lambda.hina_microscope.parse_metadata import parse_metadata +from data_hub_shared import s3_utils +from data_hub_shared.config import config +from data_hub_shared.enums import Instrument + +logger = logging.getLogger(__name__) + +INSTRUMENT_ID = Instrument.HINA_MICROSCOPE.value + + +def process_file(run_id: str, filename: str) -> str: + """Process a single Hina microscope ND2 file through the Data Hub API. + + Downloads the raw ND2, runs it through the image processing pipeline to + produce a composite JPG overlay, uploads the JPG to the processed bucket, + and registers both files via the API. Run-level metadata (sizes, + channels, dimensions) is parsed and stored once per run — the first file + to arrive wins. Subsequent files in the same run still get a JPG but + skip the metadata step. + + Args: + run_id: The run ID (grouping key for files in a single imaging session). + filename: The original filename (e.g. `well_A1_xy01.nd2`). + + Returns: + The web app URL for the instrument run. + """ + logger.info("Processing Hina microscope file: %s (run: %s)", filename, run_id) + + client = get_client() + s3_bucket = config.AWS_S3_RAW_DATA_BUCKET + s3_key = f"{INSTRUMENT_ID}/{run_id}/{filename}" + + run = client.ensure_run(INSTRUMENT_ID, run_id) + + file_record = client.create_file( + instrument_id=INSTRUMENT_ID, + run_id=run_id, + s3_bucket=s3_bucket or "", + s3_key=s3_key, + filename=filename, + ) + file_id = file_record.id + + try: + client.update_file(file_id, status="processing") + + raw_data_dir = config.LOCAL_RAW_DATA_DIRPATH / INSTRUMENT_ID / run_id + local_file_path = raw_data_dir / filename + s3_utils.download_file(f"s3://{s3_bucket}/{s3_key}", local_file_path) + logger.info("Downloaded %s to %s", filename, local_file_path) + + processor = ND2Processor(local_file_path) + processor.load() + jpg_file_path = processor.export_jpg() + + processed_bucket = config.AWS_S3_PROCESSED_DATA_BUCKET + jpg_s3_key = f"{INSTRUMENT_ID}/{run_id}/{jpg_file_path.name}" + s3_utils.upload_file(jpg_file_path, f"s3://{processed_bucket}/{jpg_s3_key}") + logger.info("Uploaded processed image to s3://%s/%s", processed_bucket, jpg_s3_key) + + processed_file = client.create_file( + instrument_id=INSTRUMENT_ID, + run_id=run_id, + s3_bucket=processed_bucket or "", + s3_key=jpg_s3_key, + filename=jpg_file_path.name, + category="processed", + ) + client.update_file( + processed_file.id, + size_bytes=jpg_file_path.stat().st_size, + content_type="image/jpeg", + ) + + # Run-level metadata is deterministic for a Hina run (same channels, + # sizes, dimensions across every .nd2 file in the run) so we only + # parse and store it once — on the first file to arrive. + if not run.metadata: + metadata = parse_metadata(processor.image) + client.update_run(INSTRUMENT_ID, run_id, metadata=metadata) + logger.info("Parsed and stored run-level metadata for %s", run_id) + else: + logger.info("Run %s already has metadata; skipping metadata step.", run_id) + + client.update_file(file_id, status="completed") + logger.info("File %s marked as completed.", filename) + + except Exception as e: + logger.error("Error processing file: %s", e) + client.update_file(file_id, status="failed", error_message=str(e)) + raise + + return f"{DATA_HUB_WEB_URL}/instruments/{INSTRUMENT_ID}/runs/{run_id}" diff --git a/lambda/tests/hina_microscope/test_image_processing.py b/lambda/tests/hina_microscope/test_image_processing.py new file mode 100644 index 00000000..800997d8 --- /dev/null +++ b/lambda/tests/hina_microscope/test_image_processing.py @@ -0,0 +1,96 @@ +"""Unit tests for `hina_microscope.image_processing`. + +Covers the deterministic helper functions (`_reduce_to_2d`, +`_rescale_percentile`) without requiring a real ND2 fixture. +""" + +from __future__ import annotations + +import numpy as np +import pytest + +from data_hub_lambda.hina_microscope.image_processing import ( + ND2Processor, + _rescale_percentile, +) + + +class TestReduceTo2D: + def test_2d_input_passes_through(self) -> None: + arr = np.arange(16, dtype=np.float64).reshape(4, 4) + + out = ND2Processor._reduce_to_2d(arr, ["Y", "X"]) + + np.testing.assert_array_equal(out, arr) + + def test_z_axis_takes_max_projection(self) -> None: + # Z-stack with a per-plane max at z=2 in every pixel. + stack = np.stack( + [ + np.full((3, 3), 1, dtype=np.float64), + np.full((3, 3), 5, dtype=np.float64), + np.full((3, 3), 9, dtype=np.float64), + ] + ) + + out = ND2Processor._reduce_to_2d(stack, ["Z", "Y", "X"]) + + assert out.shape == (3, 3) + assert np.all(out == 9) + + def test_t_axis_takes_first_frame(self) -> None: + series = np.stack( + [ + np.full((2, 2), 1, dtype=np.float64), + np.full((2, 2), 2, dtype=np.float64), + ] + ) + + out = ND2Processor._reduce_to_2d(series, ["T", "Y", "X"]) + + assert np.all(out == 1) + + def test_p_axis_takes_first_point(self) -> None: + positions = np.stack( + [ + np.full((2, 2), 7, dtype=np.float64), + np.full((2, 2), 8, dtype=np.float64), + ] + ) + + out = ND2Processor._reduce_to_2d(positions, ["P", "Y", "X"]) + + assert np.all(out == 7) + + def test_tz_combined_reduces_in_order(self) -> None: + # shape: (T=2, Z=3, Y=2, X=2). First T is a Z-stack with max=9. + arr = np.arange(24, dtype=np.float64).reshape(2, 3, 2, 2) + + out = ND2Processor._reduce_to_2d(arr, ["T", "Z", "Y", "X"]) + + # T=0 slice is arr[0] (shape 3,2,2). Max over Z=0 axis gives arr[0][2]. + np.testing.assert_array_equal(out, arr[0].max(axis=0)) + + +class TestRescalePercentile: + def test_range_maps_to_0_1(self) -> None: + arr = np.linspace(100, 200, 100, dtype=np.float64) + + out = _rescale_percentile(arr, (1, 99)) + + assert out.min() == pytest.approx(0.0, abs=1e-6) + assert out.max() == pytest.approx(1.0, abs=1e-6) + + def test_constant_array_returns_zeros(self) -> None: + arr = np.full((4, 4), 42.0, dtype=np.float64) + + out = _rescale_percentile(arr, (1, 99)) + + np.testing.assert_array_equal(out, np.zeros_like(arr)) + + def test_empty_array_returns_empty_array(self) -> None: + arr = np.array([], dtype=np.float64) + + out = _rescale_percentile(arr, (1, 99)) + + assert out.shape == (0,) diff --git a/lambda/tests/hina_microscope/test_parse_metadata.py b/lambda/tests/hina_microscope/test_parse_metadata.py new file mode 100644 index 00000000..a287fd1e --- /dev/null +++ b/lambda/tests/hina_microscope/test_parse_metadata.py @@ -0,0 +1,161 @@ +from __future__ import annotations +from types import SimpleNamespace +from typing import cast + +import pytest +from arcadia_microscopy_tools import MicroscopyImage +from arcadia_microscopy_tools.channels import BRIGHTFIELD, DAPI, FITC +from arcadia_microscopy_tools.metadata_structures import DimensionFlags + +from data_hub_lambda.hina_microscope.parse_metadata import ( + _channel_to_dict, + _dimension_names, + parse_metadata, +) + + +def _make_image( + sizes: dict[str, int], + channels: list, + dimensions: DimensionFlags, +) -> MicroscopyImage: + """Build a minimal MicroscopyImage-shaped stub for metadata tests.""" + return cast( + MicroscopyImage, + SimpleNamespace(sizes=sizes, channels=channels, dimensions=dimensions), + ) + + +class TestParseMetadata: + def test_returns_expected_keys(self) -> None: + image = _make_image({"C": 1, "Y": 2, "X": 2}, [DAPI], DimensionFlags(0)) + + result = parse_metadata(image) + + assert set(result.keys()) == {"sizes", "channels", "dimensions"} + + def test_preserves_sizes_mapping(self) -> None: + image = _make_image({"C": 4, "Y": 256, "X": 256}, [DAPI, FITC], DimensionFlags(0)) + + result = parse_metadata(image) + + assert result["sizes"] == {"C": 4, "Y": 256, "X": 256} + + def test_channels_serialized_as_dicts(self) -> None: + image = _make_image( + {"C": 3, "Y": 8, "X": 8}, + [BRIGHTFIELD, DAPI, FITC], + DimensionFlags.MULTICHANNEL, + ) + + result = parse_metadata(image) + + assert result["channels"] == [ + { + "name": "BRIGHTFIELD", + "excitation_nm": None, + "emission_nm": None, + "color": "#ffffff", + }, + { + "name": "DAPI", + "excitation_nm": 405, + "emission_nm": 450, + "color": "#0033ff", + }, + { + "name": "FITC", + "excitation_nm": 488, + "emission_nm": 512, + "color": "#07ff00", + }, + ] + + def test_dimensions_serialized_as_names(self) -> None: + image = _make_image( + {"C": 2, "Z": 5, "Y": 8, "X": 8}, + [DAPI, FITC], + DimensionFlags.MULTICHANNEL | DimensionFlags.Z_STACK, + ) + + result = parse_metadata(image) + + assert sorted(result["dimensions"]) == ["MULTICHANNEL", "Z_STACK"] + + def test_empty_dimensions_serializes_to_empty_list(self) -> None: + image = _make_image({"C": 1, "Y": 8, "X": 8}, [DAPI], DimensionFlags(0)) + + result = parse_metadata(image) + + assert result["dimensions"] == [] + + def test_result_is_json_serializable(self) -> None: + import json + + image = _make_image( + {"C": 2, "T": 10, "Y": 32, "X": 32}, + [DAPI, FITC], + DimensionFlags.MULTICHANNEL | DimensionFlags.TIMELAPSE, + ) + + result = parse_metadata(image) + + # Round-trip through JSON to verify everything is serializable. + round_tripped = json.loads(json.dumps(result)) + assert round_tripped == result + + +class TestChannelToDict: + def test_channel_with_all_fields(self) -> None: + result = _channel_to_dict(DAPI) + assert result == { + "name": "DAPI", + "excitation_nm": 405, + "emission_nm": 450, + "color": "#0033ff", + } + + def test_channel_without_wavelengths(self) -> None: + result = _channel_to_dict(BRIGHTFIELD) + assert result["excitation_nm"] is None + assert result["emission_nm"] is None + assert result["color"] == "#ffffff" + + def test_channel_with_none_color(self) -> None: + from arcadia_microscopy_tools.channels import Channel + + bare = Channel(name="CUSTOM", excitation_nm=500, emission_nm=520, color=None) + + result = _channel_to_dict(bare) + + assert result == { + "name": "CUSTOM", + "excitation_nm": 500, + "emission_nm": 520, + "color": None, + } + + +class TestDimensionNames: + def test_single_flag(self) -> None: + assert _dimension_names(DimensionFlags.MULTICHANNEL) == ["MULTICHANNEL"] + + def test_combined_flags_preserves_all_members(self) -> None: + combined = DimensionFlags.MULTICHANNEL | DimensionFlags.Z_STACK | DimensionFlags.TIMELAPSE + + result = _dimension_names(combined) + + assert set(result) == {"MULTICHANNEL", "Z_STACK", "TIMELAPSE"} + + def test_no_flags(self) -> None: + assert _dimension_names(DimensionFlags(0)) == [] + + +@pytest.fixture(autouse=True) +def _no_warnings_leak(): + """Keep tests quiet regardless of upstream deprecation warnings.""" + import warnings + + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + yield diff --git a/lambda/tests/hina_microscope/test_process_file.py b/lambda/tests/hina_microscope/test_process_file.py new file mode 100644 index 00000000..d2a7d619 --- /dev/null +++ b/lambda/tests/hina_microscope/test_process_file.py @@ -0,0 +1,190 @@ +"""Unit tests for `hina_microscope.process_file`. + +These verify the orchestration logic — specifically that run-level metadata +is parsed and stored only on the first file to arrive in a given run — by +mocking S3 I/O, the API client, the ND2 processor, and the metadata parser. +""" + +from __future__ import annotations +from pathlib import Path +from typing import Any +from unittest.mock import MagicMock, patch + +import pytest + +from data_hub_lambda.models import FileResponse, RunResponse + + +@pytest.fixture(autouse=True) +def _reset_api_client() -> Any: + """Ensure `get_client()` returns a fresh mock per test.""" + import data_hub_lambda.api_client as api_module + + original = api_module._client + api_module._client = None + try: + yield + finally: + api_module._client = original + + +def _run_response(metadata: dict | None = None) -> RunResponse: + return RunResponse( + id="run-uuid", + instrument_id="hina-microscope", + run_id="run-xyz", + source="lambda", + metadata=metadata or {}, + ) + + +def _file_response(file_id: int = 123) -> FileResponse: + return FileResponse( + id=file_id, + instrument_run_id="run-uuid", + filename="sample.nd2", + s3_bucket="raw", + s3_key="hina-microscope/run-xyz/sample.nd2", + category="raw", + status="uploaded", + ) + + +def _build_client_mock(run_metadata: dict | None) -> MagicMock: + client = MagicMock() + client.ensure_run.return_value = _run_response(metadata=run_metadata) + # `create_file` is called twice (raw, processed); give each a distinct id. + client.create_file.side_effect = [ + _file_response(file_id=10), + _file_response(file_id=11), + ] + return client + + +@pytest.fixture +def patched_jpg_path(tmp_path: Path) -> Path: + """A fake JPG output path that actually exists on disk (for stat()).""" + jpg = tmp_path / "sample.jpg" + jpg.write_bytes(b"fake-jpg-bytes") + return jpg + + +@pytest.fixture +def patched_processor(patched_jpg_path: Path) -> MagicMock: + """A stand-in `ND2Processor` whose `export_jpg` returns a real tmp file.""" + processor = MagicMock() + processor.image = MagicMock() + processor.load.return_value = None + processor.export_jpg.return_value = patched_jpg_path + return processor + + +class TestProcessFileRunMetadataGate: + """Verifies the single-shot-metadata behavior of `process_file`.""" + + def test_first_file_parses_metadata_and_updates_run( + self, + patched_processor: MagicMock, + ) -> None: + client = _build_client_mock(run_metadata=None) # empty = first file + + with ( + patch("data_hub_lambda.hina_microscope.process_file.get_client", return_value=client), + patch("data_hub_lambda.hina_microscope.process_file.s3_utils") as s3_mock, + patch( + "data_hub_lambda.hina_microscope.process_file.ND2Processor", + return_value=patched_processor, + ), + patch( + "data_hub_lambda.hina_microscope.process_file.parse_metadata", + return_value={"sizes": {"C": 1}, "channels": [], "dimensions": []}, + ) as parse_mock, + ): + from data_hub_lambda.hina_microscope.process_file import process_file + + process_file(run_id="run-xyz", filename="sample.nd2") + + # First file → metadata is parsed and persisted. + parse_mock.assert_called_once_with(patched_processor.image) + client.update_run.assert_called_once() + _, kwargs = client.update_run.call_args + assert kwargs == { + "metadata": {"sizes": {"C": 1}, "channels": [], "dimensions": []}, + } + + # JPG is generated and uploaded regardless. + patched_processor.export_jpg.assert_called_once() + s3_mock.upload_file.assert_called_once() + + def test_later_file_skips_metadata_but_still_generates_jpg( + self, + patched_processor: MagicMock, + ) -> None: + existing_metadata = { + "sizes": {"C": 2, "Y": 8, "X": 8}, + "channels": [{"name": "DAPI"}], + "dimensions": ["MULTICHANNEL"], + } + client = _build_client_mock(run_metadata=existing_metadata) + + with ( + patch("data_hub_lambda.hina_microscope.process_file.get_client", return_value=client), + patch("data_hub_lambda.hina_microscope.process_file.s3_utils") as s3_mock, + patch( + "data_hub_lambda.hina_microscope.process_file.ND2Processor", + return_value=patched_processor, + ), + patch( + "data_hub_lambda.hina_microscope.process_file.parse_metadata", + ) as parse_mock, + ): + from data_hub_lambda.hina_microscope.process_file import process_file + + process_file(run_id="run-xyz", filename="sample-2.nd2") + + # Second file → metadata step is skipped. + parse_mock.assert_not_called() + client.update_run.assert_not_called() + + # JPG is still generated and uploaded. + patched_processor.export_jpg.assert_called_once() + s3_mock.upload_file.assert_called_once() + + +class TestProcessFileFailure: + """On exception, the raw file status is marked `failed` with an error message.""" + + def test_marks_raw_file_failed_on_exception(self, tmp_path: Path) -> None: + client = _build_client_mock(run_metadata=None) + + failing_processor = MagicMock() + failing_processor.load.side_effect = RuntimeError("boom") + + with ( + patch("data_hub_lambda.hina_microscope.process_file.get_client", return_value=client), + patch("data_hub_lambda.hina_microscope.process_file.s3_utils"), + patch( + "data_hub_lambda.hina_microscope.process_file.ND2Processor", + return_value=failing_processor, + ), + ): + from data_hub_lambda.hina_microscope.process_file import process_file + + with pytest.raises(RuntimeError, match="boom"): + process_file(run_id="run-xyz", filename="broken.nd2") + + # File should be transitioned through processing → failed with the error message. + statuses = [ + call.kwargs.get("status") + for call in client.update_file.call_args_list + if "status" in call.kwargs + ] + assert "processing" in statuses + assert "failed" in statuses + + failed_call = next( + call + for call in client.update_file.call_args_list + if call.kwargs.get("status") == "failed" + ) + assert failed_call.kwargs["error_message"] == "boom" diff --git a/lambda/tests/integration/conftest.py b/lambda/tests/integration/conftest.py index 0cc2371a..d96dd26d 100644 --- a/lambda/tests/integration/conftest.py +++ b/lambda/tests/integration/conftest.py @@ -33,6 +33,7 @@ _INSTRUMENTS: dict[str, str] = { "azure-cielo-qpcr": "Azure Cielo qPCR", "azure-600-gel-doc": "Azure 600 Gel Doc", + "hina-microscope": "Hina Microscope", "spectramax-id3-plate-reader": "SpectraMax iD3 Plate Reader", "spectramax-id5-plate-reader": "SpectraMax iD5 Plate Reader", } diff --git a/packages/shared/src/data_hub_shared/constants.py b/packages/shared/src/data_hub_shared/constants.py index eb48cc5a..9d103394 100644 --- a/packages/shared/src/data_hub_shared/constants.py +++ b/packages/shared/src/data_hub_shared/constants.py @@ -7,6 +7,7 @@ Instrument.AKTA_FPLC.value: "Akta FPLC", Instrument.AZURE_600_GEL_DOC.value: "Azure 600 Gel Doc", Instrument.AZURE_CIELO_QPCR.value: "Azure Cielo qPCR", + Instrument.HINA_MICROSCOPE.value: "Hina Microscope", Instrument.SPECTRAMAX_ID3_PLATE_READER.value: "SpectraMax iD3 Plate Reader", Instrument.SPECTRAMAX_ID5_PLATE_READER.value: "SpectraMax iD5 Plate Reader", } diff --git a/packages/shared/src/data_hub_shared/enums.py b/packages/shared/src/data_hub_shared/enums.py index a2eb91a1..c4e3eea1 100644 --- a/packages/shared/src/data_hub_shared/enums.py +++ b/packages/shared/src/data_hub_shared/enums.py @@ -12,5 +12,6 @@ class Instrument(Enum): AKTA_FPLC = "akta-fplc" AZURE_600_GEL_DOC = "azure-600-gel-doc" AZURE_CIELO_QPCR = "azure-cielo-qpcr" + HINA_MICROSCOPE = "hina-microscope" 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metadata the Lambda writes from parse_metadata.py (channel name + hex swatch, dimension flags, formatted size string) - New `HinaMicroscopeRunDetail` variant whose Report section is an image carousel (shadcn/ui + embla) over the processed JPGs produced per ND2 file - Shared helpers `getMetadataRecord` and `getMetadataObjectArray` to safely read the nested `sizes` dict and `channels` array-of-dicts --- .../instruments/edit-instrument-dialog.tsx | 1 + .../runs-table/hina-runs-table.tsx | 173 +++ .../instruments/runs-table/index.tsx | 10 + .../instruments/runs-table/metadata-utils.tsx | 2 + .../components/runs/hina-report-section.tsx | 144 ++ web-app/components/runs/metadata-badges.tsx | 25 + .../components/runs/run-metadata-badges.tsx | 141 ++ .../variants/hina-microscope-run-detail.tsx | 60 + web-app/components/runs/variants/index.tsx | 3 + web-app/components/ui/carousel.tsx | 242 +++ .../drizzle/0008_chilly_princess_powerful.sql | 1 + web-app/drizzle/meta/0008_snapshot.json | 1362 +++++++++++++++++ web-app/drizzle/meta/_journal.json | 7 + web-app/lib/db/schema.ts | 1 + web-app/package-lock.json | 29 + web-app/package.json | 1 + 16 files changed, 2202 insertions(+) create mode 100644 web-app/components/instruments/runs-table/hina-runs-table.tsx create mode 100644 web-app/components/runs/hina-report-section.tsx create mode 100644 web-app/components/runs/variants/hina-microscope-run-detail.tsx create mode 100644 web-app/components/ui/carousel.tsx create mode 100644 web-app/drizzle/0008_chilly_princess_powerful.sql create mode 100644 web-app/drizzle/meta/0008_snapshot.json diff --git a/web-app/components/instruments/edit-instrument-dialog.tsx b/web-app/components/instruments/edit-instrument-dialog.tsx index 75f9f1ef..ad3ef57b 100644 --- a/web-app/components/instruments/edit-instrument-dialog.tsx +++ b/web-app/components/instruments/edit-instrument-dialog.tsx @@ -31,6 +31,7 @@ const TYPE_LABELS: Record = { gel_doc: "Gel Doc", qpcr: "qPCR", tape_station: "TapeStation", + hina_microscope: "Hina Microscope", }; const INSTRUMENT_TYPE_OPTIONS = VALID_INSTRUMENT_TYPES.map((value) => ({ diff --git a/web-app/components/instruments/runs-table/hina-runs-table.tsx b/web-app/components/instruments/runs-table/hina-runs-table.tsx new file mode 100644 index 00000000..7950c94a --- /dev/null +++ b/web-app/components/instruments/runs-table/hina-runs-table.tsx @@ -0,0 +1,173 @@ +import { RelativeTime } from "@/components/dashboard/relative-time"; +import { + extractHinaChannels, + formatHinaSizes, +} from "@/components/runs/run-metadata-badges"; +import { Badge } from "@/components/ui/badge"; +import { + Table, + TableBody, + TableCell, + TableHead, + TableHeader, + TableRow, +} from "@/components/ui/table"; +import { runRowToRef } from "@/lib/runs/row-actions"; +import { cn, formatBytes } from "@/lib/utils"; + +import type { RunsTableProps } from "."; +import { ClickableRow } from "./clickable-row"; +import { FilterableColumnHeader } from "./filterable-column-header"; +import { + MetadataArrayBadges, + getMetadataArray, + getMetadataRecord, +} 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"; + +export function HinaRunsTable({ + data, + instrumentId, + ranByOptions, +}: RunsTableProps) { + const runRefs: RunRef[] = data.map(runRowToRef); + + return ( + + + + + + + Run ID + + + + + + + Channels + Dimensions + Sizes + + + + Created + + Actions + + + + + {data.map((row) => { + const isDeleted = row.deleted_at !== null; + const channels = extractHinaChannels(row.metadata); + const dimensions = getMetadataArray(row.metadata, "dimensions"); + const sizes = getMetadataRecord(row.metadata, "sizes"); + const sizesLabel = sizes ? formatHinaSizes(sizes) : ""; + return ( + + + + + +
+ + + {isDeleted && ( + + deleted + + )} +
+ + + {row.file_count} + + + {formatBytes(row.total_size_bytes)} + + + {channels.length === 0 ? ( + — + ) : ( +
+ {channels.map((c) => { + const style = c.color + ? { borderColor: c.color, color: c.color } + : undefined; + return ( + + {c.color && ( + + ); + })} +
+ )} + + + + + + {sizesLabel ? ( + + {sizesLabel} + + ) : ( + — + )} + + + + + + + + + + + + ); + })} + +
+ ); +} diff --git a/web-app/components/instruments/runs-table/index.tsx b/web-app/components/instruments/runs-table/index.tsx index 6f2f7953..0c51790d 100644 --- a/web-app/components/instruments/runs-table/index.tsx +++ b/web-app/components/instruments/runs-table/index.tsx @@ -9,6 +9,7 @@ import { SearchX } from "lucide-react"; import { DefaultRunsTable } from "./default-runs-table"; import { GelDocRunsTable } from "./gel-doc-runs-table"; +import { HinaRunsTable } from "./hina-runs-table"; import { PlateReaderRunsTable } from "./plate-reader-runs-table"; import { QpcrRunsTable } from "./qpcr-runs-table"; import { RunsTableFooter } from "./runs-table-footer"; @@ -98,6 +99,15 @@ export function InstrumentRunsTable({ /> ); break; + case "hina_microscope": + table = ( + + ); + break; default: table = ( + files + .filter( + (f) => + f.category === "processed" && f.deletedAt === null && isImageFile(f) + ) + .sort(sortByFilename), + [files] + ); + + const [api, setApi] = useState(null); + const [currentIndex, setCurrentIndex] = useState(0); + + useEffect(() => { + if (!api) return; + // Subscribe to Embla's own "select" and "reInit" events — no synchronous + // state sync needed on mount since Embla defaults to snap 0 which matches + // our initial state. `reInit` covers the case where the carousel recalcs + // after images load and potentially lands on a different snap. + const onSelect = () => setCurrentIndex(api.selectedScrollSnap()); + api.on("select", onSelect); + api.on("reInit", onSelect); + return () => { + api.off("select", onSelect); + api.off("reInit", onSelect); + }; + }, [api]); + + if (processedImages.length === 0) { + return ( +
+

Report Data

+ + +

+ No report data has been generated for this run. +

+ + +
+ ); + } + + const currentFile = + processedImages[Math.min(currentIndex, processedImages.length - 1)]; + const currentDownloadUrl = `/api/v1/files/${currentFile.id}/download`; + + return ( +
+

+ Report Data{" "} + + {processedImages.length} image(s) + +

+ + +
+
+

+ {currentFile.filename} +

+ + {currentIndex + 1} / {processedImages.length} + +
+ +
+ + + {processedImages.map((file, i) => { + const url = `/api/v1/files/${file.id}/download`; + return ( + +
+ {/* eslint-disable-next-line @next/next/no-img-element */} + {file.filename} +
+ + ); + })} + + {processedImages.length > 1 && ( + <> + + + + )} + + + +
+ ); +} diff --git a/web-app/components/runs/metadata-badges.tsx b/web-app/components/runs/metadata-badges.tsx index 4d105185..e02d0ec2 100644 --- a/web-app/components/runs/metadata-badges.tsx +++ b/web-app/components/runs/metadata-badges.tsx @@ -23,6 +23,31 @@ export function getMetadataArray(metadata: unknown, key: string): string[] { return []; } +export function getMetadataRecord( + metadata: unknown, + key: string +): Record | null { + if (!metadata || typeof metadata !== "object") return null; + const value = (metadata as Record)[key]; + if (value && typeof value === "object" && !Array.isArray(value)) { + return value as Record; + } + return null; +} + +export function getMetadataObjectArray( + metadata: unknown, + key: string +): Record[] { + if (!metadata || typeof metadata !== "object") return []; + const value = (metadata as Record)[key]; + if (!Array.isArray(value)) return []; + return value.filter( + (v): v is Record => + v !== null && typeof v === "object" && !Array.isArray(v) + ); +} + /** * Sort a list of wavelength strings (e.g. `"750"`) in ascending numerical * order. Non-numeric entries are pushed to the end, preserving their diff --git a/web-app/components/runs/run-metadata-badges.tsx b/web-app/components/runs/run-metadata-badges.tsx index 4ced7c50..5b7478c1 100644 --- a/web-app/components/runs/run-metadata-badges.tsx +++ b/web-app/components/runs/run-metadata-badges.tsx @@ -13,6 +13,8 @@ import { cn } from "@/lib/utils"; import { getMetadataArray, getMetadataField, + getMetadataObjectArray, + getMetadataRecord, sortWavelengths, } from "@/components/runs/metadata-badges"; @@ -221,6 +223,145 @@ export function TapeStationRunBadges({ ); } +// --------------------------------------------------------------------------- +// Hina microscope +// --------------------------------------------------------------------------- + +export type HinaChannel = { + name: string; + color: string | null; +}; + +// Preferred dimension order for the `sizes` badge. ND2 files commonly include +// C (channels), Z (z-slices), T (time), Y (height), X (width); we render them +// in this order when present and append any unrecognised keys at the end so +// unknown dimensions still surface rather than being silently dropped. +const SIZE_DIMENSION_ORDER = ["T", "Z", "C", "Y", "X"]; + +export function extractHinaChannels(metadata: unknown): HinaChannel[] { + const raw = getMetadataObjectArray(metadata, "channels"); + return raw + .map((c) => { + const name = c.name != null ? String(c.name) : ""; + const color = typeof c.color === "string" ? c.color : null; + return { name, color }; + }) + .filter((c) => c.name.length > 0); +} + +export function formatHinaSizes(sizes: Record): string { + const entries = Object.entries(sizes).filter( + ([, v]) => typeof v === "number" || typeof v === "string" + ); + if (entries.length === 0) return ""; + + const known = SIZE_DIMENSION_ORDER.filter((k) => + entries.some(([ek]) => ek === k) + ); + const unknown = entries + .map(([k]) => k) + .filter((k) => !SIZE_DIMENSION_ORDER.includes(k)) + .sort(); + const orderedKeys = [...known, ...unknown]; + + const sizeMap = Object.fromEntries(entries) as Record< + string, + number | string + >; + + // Separate spatial dimensions (Y x X) into a compact "HxW" group so the + // badge reads like "C=4 · 256x256" rather than "C=4 · Y=256 · X=256". + const spatial: string[] = []; + if (sizeMap.Y != null) spatial.push(String(sizeMap.Y)); + if (sizeMap.X != null) spatial.push(String(sizeMap.X)); + + const scalar = orderedKeys + .filter((k) => k !== "X" && k !== "Y") + .map((k) => `${k}=${sizeMap[k]}`); + + const parts = [...scalar]; + if (spatial.length > 0) parts.push(spatial.join("\u00d7")); + return parts.join(" \u00b7 "); +} + +export function hasHinaMetadata(metadata: Record) { + return Boolean( + extractHinaChannels(metadata).length || + getMetadataArray(metadata, "dimensions").length || + (getMetadataRecord(metadata, "sizes") && + Object.keys(getMetadataRecord(metadata, "sizes") ?? {}).length > 0) + ); +} + +// Inline-styled badge using an arbitrary hex color for the border + text. +// Used for Hina channels since channel color is run-specific and can't be +// baked into a static Tailwind palette. +function ChannelBadge({ name, color }: HinaChannel) { + const style = color ? { borderColor: color, color } : undefined; + return ( + + {color && ( + + ); +} + +export function HinaChannelBadges({ channels }: { channels: HinaChannel[] }) { + if (channels.length === 0) + return —; + return ( +
+ {channels.map((c) => ( + + ))} +
+ ); +} + +export function HinaRunBadges({ + metadata, +}: { + metadata: Record; +}) { + const channels = extractHinaChannels(metadata); + const dimensions = getMetadataArray(metadata, "dimensions"); + const sizes = getMetadataRecord(metadata, "sizes"); + const sizesLabel = sizes ? formatHinaSizes(sizes) : ""; + + if (channels.length === 0 && dimensions.length === 0 && !sizesLabel) + return null; + + return ( + <> + {channels.length > 0 && ( + + {channels.map((c) => ( + + ))} + + )} + {dimensions.length > 0 && ( + + {dimensions.map((d) => ( + + ))} + + )} + {sizesLabel && ( + + + + )} + + ); +} + // --------------------------------------------------------------------------- // Default / generic — each key gets a row with outline badge value(s) // --------------------------------------------------------------------------- diff --git a/web-app/components/runs/variants/hina-microscope-run-detail.tsx b/web-app/components/runs/variants/hina-microscope-run-detail.tsx new file mode 100644 index 00000000..f04f9e9d --- /dev/null +++ b/web-app/components/runs/variants/hina-microscope-run-detail.tsx @@ -0,0 +1,60 @@ +import { DeleteRunDialog } from "@/components/runs/delete-run-dialog"; +import { HinaReportSection } from "@/components/runs/hina-report-section"; +import { RestoreRunButton } from "@/components/runs/restore-run-button"; +import type { RunDetailProps } from "@/components/runs/run-detail"; +import { RunDetail } from "@/components/runs/run-detail"; +import { + HinaRunBadges, + hasHinaMetadata, +} from "@/components/runs/run-metadata-badges"; + +export function HinaMicroscopeRunDetail({ + run, + files, + instrumentId, + runId, + attributionsSlot, +}: RunDetailProps) { + const isDeleted = run.deletedAt !== null; + const canRestore = isDeleted && run.filesPurgedAt === 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 && ( + + )} + {canRestore && ( + + )} + + + + {hasHinaMetadata(run.metadata as Record) && ( + + } /> + + )} + + + + + + + + ); +} diff --git a/web-app/components/runs/variants/index.tsx b/web-app/components/runs/variants/index.tsx index 77990cb3..b2b78a27 100644 --- a/web-app/components/runs/variants/index.tsx +++ b/web-app/components/runs/variants/index.tsx @@ -2,6 +2,7 @@ import type { RunDetailProps } from "@/components/runs/run-detail"; import { DefaultRunDetail } from "./default-run-detail"; import { GelDocRunDetail } from "./gel-doc-run-detail"; +import { HinaMicroscopeRunDetail } from "./hina-microscope-run-detail"; import { PlateReaderRunDetail } from "./plate-reader-run-detail"; import { QpcrRunDetail } from "./qpcr-run-detail"; import { TapeStationRunDetail } from "./tape-station-run-detail"; @@ -18,6 +19,8 @@ export function RunDetailVariant(props: RunDetailVariantProps) { return ; case "tape_station": return ; + case "hina_microscope": + return ; default: return ; } diff --git a/web-app/components/ui/carousel.tsx b/web-app/components/ui/carousel.tsx new file mode 100644 index 00000000..12316ca0 --- /dev/null +++ b/web-app/components/ui/carousel.tsx @@ -0,0 +1,242 @@ +"use client"; + +import useEmblaCarousel, { + type UseEmblaCarouselType, +} from "embla-carousel-react"; +import * as React from "react"; + +import { Button } from "@/components/ui/button"; +import { cn } from "@/lib/utils"; +import { ChevronLeftIcon, ChevronRightIcon } from "lucide-react"; + +type CarouselApi = UseEmblaCarouselType[1]; +type UseCarouselParameters = Parameters; +type CarouselOptions = UseCarouselParameters[0]; +type CarouselPlugin = UseCarouselParameters[1]; + +type CarouselProps = { + opts?: CarouselOptions; + plugins?: CarouselPlugin; + orientation?: "horizontal" | "vertical"; + setApi?: (api: CarouselApi) => void; +}; + +type CarouselContextProps = { + carouselRef: ReturnType[0]; + api: ReturnType[1]; + scrollPrev: () => void; + scrollNext: () => void; + canScrollPrev: boolean; + canScrollNext: boolean; +} & CarouselProps; + +const CarouselContext = React.createContext(null); + +function useCarousel() { + const context = React.useContext(CarouselContext); + + if (!context) { + throw new Error("useCarousel must be used within a "); + } + + return context; +} + +function Carousel({ + orientation = "horizontal", + opts, + setApi, + plugins, + className, + children, + ...props +}: React.ComponentProps<"div"> & CarouselProps) { + const [carouselRef, api] = useEmblaCarousel( + { + ...opts, + axis: orientation === "horizontal" ? "x" : "y", + }, + plugins + ); + const [canScrollPrev, setCanScrollPrev] = React.useState(false); + const [canScrollNext, setCanScrollNext] = React.useState(false); + + const onSelect = React.useCallback((api: CarouselApi) => { + if (!api) return; + setCanScrollPrev(api.canScrollPrev()); + setCanScrollNext(api.canScrollNext()); + }, []); + + const scrollPrev = React.useCallback(() => { + api?.scrollPrev(); + }, [api]); + + const scrollNext = React.useCallback(() => { + api?.scrollNext(); + }, [api]); + + const handleKeyDown = React.useCallback( + (event: React.KeyboardEvent) => { + if (event.key === "ArrowLeft") { + event.preventDefault(); + scrollPrev(); + } else if (event.key === "ArrowRight") { + event.preventDefault(); + scrollNext(); + } + }, + [scrollPrev, scrollNext] + ); + + React.useEffect(() => { + if (!api || !setApi) return; + setApi(api); + }, [api, setApi]); + + React.useEffect(() => { + if (!api) return; + onSelect(api); + api.on("reInit", onSelect); + api.on("select", onSelect); + + return () => { + api?.off("select", onSelect); + }; + }, [api, onSelect]); + + return ( + +
+ {children} +
+ + ); +} + +function CarouselContent({ className, ...props }: React.ComponentProps<"div">) { + const { carouselRef, orientation } = useCarousel(); + + return ( +
+
+
+ ); +} + +function CarouselItem({ className, ...props }: React.ComponentProps<"div">) { + const { orientation } = useCarousel(); + + return ( +
+ ); +} + +function CarouselPrevious({ + className, + variant = "outline", + size = "icon-sm", + ...props +}: React.ComponentProps) { + const { orientation, scrollPrev, canScrollPrev } = useCarousel(); + + return ( + + ); +} + +function CarouselNext({ + className, + variant = "outline", + size = "icon-sm", + ...props +}: React.ComponentProps) { + const { orientation, scrollNext, canScrollNext } = useCarousel(); + + return ( + + ); +} + +export { + Carousel, + CarouselContent, + CarouselItem, + CarouselNext, + CarouselPrevious, + useCarousel, + type CarouselApi, +}; diff --git a/web-app/drizzle/0008_chilly_princess_powerful.sql b/web-app/drizzle/0008_chilly_princess_powerful.sql new file mode 100644 index 00000000..a373cea5 --- /dev/null +++ b/web-app/drizzle/0008_chilly_princess_powerful.sql @@ -0,0 +1 @@ +ALTER TYPE "public"."instrument_type" ADD VALUE 'hina_microscope'; \ No newline at end of file diff --git a/web-app/drizzle/meta/0008_snapshot.json b/web-app/drizzle/meta/0008_snapshot.json new file mode 100644 index 00000000..76833cf3 --- /dev/null +++ b/web-app/drizzle/meta/0008_snapshot.json @@ -0,0 +1,1362 @@ +{ + "id": "c2b6ce60-ef03-4243-b22b-989c7dc2e1bd", + "prevId": "5ed571bb-c4c1-4f0b-a8fa-7f1a16e2c57b", + "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.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", + "primaryKey": false, + "notNull": true, + "default": "'detected'" + }, + "metadata": { + "name": "metadata", + "type": "jsonb", + "primaryKey": false, + "notNull": true, + "default": "'{}'::jsonb" + }, + "error_message": { + "name": "error_message", + "type": "text", + "primaryKey": false, + "notNull": false + }, + "detected_at": { + "name": "detected_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + }, + "upload_requested_at": { + "name": "upload_requested_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + }, + "uploaded_at": { + "name": "uploaded_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + }, + "processed_at": { + "name": "processed_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + }, + "created_at": { + "name": "created_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_files_instrument_run_id_relative_path": { + "name": "uq_files_instrument_run_id_relative_path", + "columns": [ + { + "expression": "instrument_run_id", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "relative_path", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": true, + "where": "\"files\".\"relative_path\" is not null", + "concurrently": false, + "method": "btree", + "with": {} + }, + "uq_files_s3_key": { + "name": "uq_files_s3_key", + "columns": [ + { + "expression": "s3_key", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": true, + "where": "\"files\".\"s3_key\" is not null", + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_files_instrument_run_id": { + "name": "idx_files_instrument_run_id", + "columns": [ + { + "expression": "instrument_run_id", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_files_status_instrument_run_id": { + "name": "idx_files_status_instrument_run_id", + "columns": [ + { + "expression": "status", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "instrument_run_id", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_files_active": { + "name": "idx_files_active", + "columns": [ + { + "expression": "instrument_run_id", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "where": "\"files\".\"deleted_at\" is null", + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_files_upload_queue": { + "name": "idx_files_upload_queue", + "columns": [ + { + "expression": "upload_requested_at", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "where": "\"files\".\"upload_requested_at\" is not null and \"files\".\"uploaded_at\" is null and \"files\".\"deleted_at\" is null", + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_files_metadata_gin": { + "name": "idx_files_metadata_gin", + "columns": [ + { + "expression": "metadata", + "isExpression": false, + "asc": true, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "gin", + "with": {} + } + }, + "foreignKeys": { + "files_instrument_run_id_instrument_runs_id_fk": { + "name": "files_instrument_run_id_instrument_runs_id_fk", + "tableFrom": "files", + "tableTo": "instrument_runs", + "columnsFrom": [ + "instrument_run_id" + ], + "columnsTo": [ + "id" + ], + "onDelete": "no action", + "onUpdate": "no action" + } + }, + "compositePrimaryKeys": {}, + "uniqueConstraints": {}, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.instrument_runs": { + "name": "instrument_runs", + "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 + }, + "run_id": { + "name": "run_id", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "source": { + "name": "source", + "type": "instrument_run_source", + "typeSchema": "public", + "primaryKey": false, + "notNull": true, + "default": "'lambda'" + }, + "watcher_id": { + "name": "watcher_id", + "type": "uuid", + "primaryKey": false, + "notNull": false + }, + "metadata": { + "name": "metadata", + "type": "jsonb", + "primaryKey": false, + "notNull": true, + "default": "'{}'::jsonb" + }, + "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 + }, + "files_purged_at": { + "name": "files_purged_at", + "type": "timestamp with time zone", + "primaryKey": false, + "notNull": false + } + }, + "indexes": { + "idx_instrument_runs_instrument_id_created_at": { + "name": "idx_instrument_runs_instrument_id_created_at", + "columns": [ + { + "expression": "instrument_id", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "created_at", + "isExpression": false, + "asc": false, + "nulls": "last" + } + ], + "isUnique": false, + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_instrument_runs_active": { + "name": "idx_instrument_runs_active", + "columns": [ + { + "expression": "instrument_id", + "isExpression": false, + "asc": true, + "nulls": "last" + }, + { + "expression": "created_at", + "isExpression": false, + "asc": false, + "nulls": "last" + } + ], + "isUnique": false, + "where": "\"instrument_runs\".\"deleted_at\" is null", + "concurrently": false, + "method": "btree", + "with": {} + }, + "idx_instrument_runs_metadata_gin": { + "name": "idx_instrument_runs_metadata_gin", + "columns": [ + { + "expression": 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"instrument_id", + "run_id" + ] + } + }, + "policies": {}, + "checkConstraints": {}, + "isRLSEnabled": false + }, + "public.instruments": { + "name": "instruments", + "schema": "", + "columns": { + "id": { + "name": "id", + "type": "text", + "primaryKey": true, + "notNull": true + }, + "display_name": { + "name": "display_name", + "type": "text", + "primaryKey": false, + "notNull": true + }, + "status": { + "name": "status", + "type": "instrument_status", + "typeSchema": "public", + "primaryKey": false, + "notNull": true, + "default": "'active'" + }, + "instrument_type": { + "name": "instrument_type", + "type": "instrument_type", + "typeSchema": "public", + "primaryKey": false, + "notNull": true, + "default": "'generic'" + }, + "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": 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"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" + ] + }, + "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" + ] + }, + "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 2fe2e63e..18af47d4 100644 --- a/web-app/drizzle/meta/_journal.json +++ b/web-app/drizzle/meta/_journal.json @@ -57,6 +57,13 @@ "when": 1776804297734, "tag": "0007_dazzling_hercules", "breakpoints": true + }, + { + "idx": 8, + "version": "7", + "when": 1776986418967, + "tag": "0008_chilly_princess_powerful", + "breakpoints": true } ] } \ No newline at end of file diff --git a/web-app/lib/db/schema.ts b/web-app/lib/db/schema.ts index 3f4cc30e..61644494 100644 --- a/web-app/lib/db/schema.ts +++ b/web-app/lib/db/schema.ts @@ -51,6 +51,7 @@ export const instrumentTypeEnum = pgEnum("instrument_type", [ "gel_doc", "qpcr", "tape_station", + "hina_microscope", ]); export const VALID_INSTRUMENT_TYPES = instrumentTypeEnum.enumValues; diff --git a/web-app/package-lock.json b/web-app/package-lock.json index 3d132ef6..9672843d 100644 --- a/web-app/package-lock.json +++ b/web-app/package-lock.json @@ -21,6 +21,7 @@ "date-fns": "^4.1.0", "date-fns-tz": "^3.2.0", "drizzle-orm": "^0.45.2", + "embla-carousel-react": "^8.6.0", "lucide-react": "^1.7.0", "mcp-handler": "^1.1.0", "next": "^16.2.4", @@ -9677,6 +9678,34 @@ "integrity": "sha512-/4t+AS1l4S3ZC0Ja7PHFIWeBIxGA3QGqV8/yKsP36v7NcyUCl+bIcmw6s5zVuMIECWwBrAK/6QLzTmbJChBboQ==", "license": "ISC" }, + "node_modules/embla-carousel": { + "version": "8.6.0", + "resolved": "https://registry.npmjs.org/embla-carousel/-/embla-carousel-8.6.0.tgz", + "integrity": "sha512-SjWyZBHJPbqxHOzckOfo8lHisEaJWmwd23XppYFYVh10bU66/Pn5tkVkbkCMZVdbUE5eTCI2nD8OyIP4Z+uwkA==", + "license": "MIT" + }, + "node_modules/embla-carousel-react": { + "version": "8.6.0", + "resolved": "https://registry.npmjs.org/embla-carousel-react/-/embla-carousel-react-8.6.0.tgz", + "integrity": "sha512-0/PjqU7geVmo6F734pmPqpyHqiM99olvyecY7zdweCw+6tKEXnrE90pBiBbMMU8s5tICemzpQ3hi5EpxzGW+JA==", + "license": "MIT", + "dependencies": { + "embla-carousel": "8.6.0", + "embla-carousel-reactive-utils": "8.6.0" + }, + "peerDependencies": { + "react": "^16.8.0 || ^17.0.1 || ^18.0.0 || ^19.0.0 || ^19.0.0-rc" + } + }, + "node_modules/embla-carousel-reactive-utils": { + "version": "8.6.0", + "resolved": "https://registry.npmjs.org/embla-carousel-reactive-utils/-/embla-carousel-reactive-utils-8.6.0.tgz", + "integrity": "sha512-fMVUDUEx0/uIEDM0Mz3dHznDhfX+znCCDCeIophYb1QGVM7YThSWX+wz11zlYwWFOr74b4QLGg0hrGPJeG2s4A==", + "license": "MIT", + "peerDependencies": { + "embla-carousel": "8.6.0" + } + }, "node_modules/emoji-regex": { "version": "9.2.2", "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-9.2.2.tgz", diff --git a/web-app/package.json b/web-app/package.json index e958e682..b337e97f 100644 --- a/web-app/package.json +++ b/web-app/package.json @@ -36,6 +36,7 @@ "date-fns": "^4.1.0", "date-fns-tz": "^3.2.0", "drizzle-orm": "^0.45.2", + "embla-carousel-react": "^8.6.0", "lucide-react": "^1.7.0", "mcp-handler": "^1.1.0", "next": "^16.2.4", From 0fef702dc702147bf5717c8ddd1cce95667a0b1c Mon Sep 17 00:00:00 2001 From: Wasim Sandhu Date: Thu, 23 Apr 2026 16:42:54 -0700 Subject: [PATCH 3/7] Lambda: Bump ephemeral storage, memory, and timeout for large ND2 files MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Hina microscope uploads can be 3-4 GB, which immediately exhausts the previous 512 MB /tmp and 1 GB RAM limits (decoded ND2 arrays are even larger than the compressed file). Raise EphemeralStorage to 10 GB, MemorySize to 10 GB, and Timeout to 900 s — all Lambda hard maxes. Also add a pre-cleanup call at the top of `lambda_handler`: the existing `finally: _cleanup_tmp()` doesn't run when the runtime SIGKILLs the process (OOM / timeout), so a warm container can start a new invocation with stale downloads still occupying /tmp. --- infra/template.yaml | 12 +++++++++--- lambda/src/data_hub_lambda/handler.py | 5 +++++ 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/infra/template.yaml b/infra/template.yaml index a0fd3cff..eca1dac8 100644 --- a/infra/template.yaml +++ b/infra/template.yaml @@ -52,8 +52,12 @@ Parameters: Globals: Function: - Timeout: 300 - MemorySize: 1024 + # Large files (e.g. 3-4 GB Hina microscope ND2s) force us near Lambda's + # hard limits: 10 GB RAM to hold the decoded image array, 900 s to + # download + process, and 10 GB of /tmp (set per-function below) to + # land the raw file plus the generated JPG. + Timeout: 900 + MemorySize: 10240 Resources: # ---- S3 buckets ---- @@ -159,7 +163,9 @@ Resources: PackageType: Image ImageUri: !Ref EcrImageUri EphemeralStorage: - Size: 512 + # 10 GB (the Lambda max) — large Hina ND2 uploads need room for the + # raw download, the decoded working copy, and the generated JPG. + Size: 10240 Role: !GetAtt LambdaExecutionRole.Arn FunctionUrlConfig: AuthType: NONE diff --git a/lambda/src/data_hub_lambda/handler.py b/lambda/src/data_hub_lambda/handler.py index a5e866c4..d4551d02 100644 --- a/lambda/src/data_hub_lambda/handler.py +++ b/lambda/src/data_hub_lambda/handler.py @@ -189,6 +189,11 @@ def lambda_handler(event: dict[str, Any], context: Context) -> dict[str, Any] | logger.info("Run ID: '%s'", run_id) instrument_name = INSTRUMENT_ID_TO_NAME_MAP[instrument_id] + # Pre-cleanup: if the previous invocation on this warm container was + # SIGKILL'd (e.g. OOM), the `finally` block below didn't run and stale + # downloads may still be sitting in /tmp. Wipe them before we start. + _cleanup_tmp() + try: logger.info("Processing file %s...", event_info.filename) From 865b437663f62781b6eaa34fa6f25e19bdfacc1b Mon Sep 17 00:00:00 2001 From: Wasim Sandhu Date: Thu, 23 Apr 2026 16:49:28 -0700 Subject: [PATCH 4/7] fix: Update Drizzle config --- web-app/drizzle.config.ts | 2 ++ 1 file changed, 2 insertions(+) diff --git a/web-app/drizzle.config.ts b/web-app/drizzle.config.ts index 8408f240..5f90ddda 100644 --- a/web-app/drizzle.config.ts +++ b/web-app/drizzle.config.ts @@ -7,4 +7,6 @@ export default defineConfig({ dbCredentials: { url: process.env.DATABASE_URL!, }, + schemaFilter: ["public"], + tablesFilter: ["!pg_stat_statements", "!pg_stat_statements_info"], }); From c76bbc9d5b96da67cd1815404266f0de33679e93 Mon Sep 17 00:00:00 2001 From: Wasim Sandhu Date: Fri, 24 Apr 2026 11:53:27 -0700 Subject: [PATCH 5/7] feat(runs): disable upload actions when watcher is offline Requesting an upload transitions a file to `upload_requested`, which only resolves if a watcher is online to push the file to S3. When no watcher is heartbeating, the UI now disables both per-row and bulk Upload buttons and shows a tooltip explaining why, preventing files from getting stuck in `upload_requested` with no agent to action them. The run detail page fetches the instrument (cached) alongside run files and threads an `isWatcherOnline` flag through `RunDetailProps` and each variant into `RunFilesSection` and `RunFilesTable`. Made-with: Cursor --- .../[instrumentId]/runs/[runId]/page.tsx | 10 ++- web-app/components/runs/run-detail.ts | 4 ++ web-app/components/runs/run-files-section.tsx | 62 ++++++++++++++----- web-app/components/runs/run-files-table.tsx | 50 ++++++++++++--- .../runs/variants/default-run-detail.tsx | 2 + .../runs/variants/gel-doc-run-detail.tsx | 2 + .../variants/hina-microscope-run-detail.tsx | 2 + .../runs/variants/plate-reader-run-detail.tsx | 2 + .../runs/variants/qpcr-run-detail.tsx | 2 + .../runs/variants/tape-station-run-detail.tsx | 2 + 10 files changed, 113 insertions(+), 25 deletions(-) diff --git a/web-app/app/instruments/[instrumentId]/runs/[runId]/page.tsx b/web-app/app/instruments/[instrumentId]/runs/[runId]/page.tsx index f171e635..8cd7c7a7 100644 --- a/web-app/app/instruments/[instrumentId]/runs/[runId]/page.tsx +++ b/web-app/app/instruments/[instrumentId]/runs/[runId]/page.tsx @@ -5,6 +5,7 @@ import { getRunFiles, lookupRunByNaturalKey, } from "@/lib/api/instrument-runs"; +import { getInstrumentById } from "@/lib/api/instruments"; import { auth } from "@/lib/auth"; import { notFound, redirect } from "next/navigation"; import type { Metadata } from "next/types"; @@ -31,8 +32,14 @@ export default async function RunDetailPage({ params }: Props) { const run = await lookupRunByNaturalKey(instrumentId, runId); if (!run) notFound(); - const runFiles = await getRunFiles(run.id); + const [runFiles, instrument] = await Promise.all([ + getRunFiles(run.id), + getInstrumentById(instrumentId), + ]); const wellData = await getProcessedCsvData(runFiles); + // Gate client-side upload actions on watcher availability — a queued + // upload request is a no-op if no agent is around to action it. + const isWatcherOnline = (instrument?.watchersOnline ?? 0) > 0; return (
@@ -42,6 +49,7 @@ export default async function RunDetailPage({ params }: Props) { wellData={wellData} instrumentId={instrumentId} runId={runId} + isWatcherOnline={isWatcherOnline} attributionsSlot={
- + {isWatcherOnline ? ( + + ) : ( + + + {/* Wrapping span keeps the tooltip reachable while the + underlying button is disabled. */} + + + + + + {WATCHER_OFFLINE_UPLOAD_TOOLTIP} + + + )} + {isWatcherOnline ? ( + + ) : ( + + + {/* Wrapping span keeps the tooltip reachable while + the underlying button is disabled. */} + + + + + + {WATCHER_OFFLINE_UPLOAD_TOOLTIP} + + + )}
); } diff --git a/web-app/components/instruments/runs-table/filterable-column-header.tsx b/web-app/components/instruments/runs-table/filterable-column-header.tsx index 5e09e3d4..558245d4 100644 --- a/web-app/components/instruments/runs-table/filterable-column-header.tsx +++ b/web-app/components/instruments/runs-table/filterable-column-header.tsx @@ -14,20 +14,25 @@ import { instrumentDetailSearchParams } from "@/lib/search-params"; import { cn } from "@/lib/utils"; import { ChevronsUpDown, ListFilter } from "lucide-react"; import { useQueryStates } from "nuqs"; +import type { inferParserType } from "nuqs/server"; -type FilterParamKey = - | "wavelength" - | "measurement_mode" - | "measurement_type" - | "capture_type" - | "imaging_mode" - | "gel_wavelength" - | "gel_color" - | "dye_channel" - | "hina_channel" - | "hina_dimension" - | "hina_size" - | "ran_by"; +type InstrumentDetailFilters = inferParserType< + typeof instrumentDetailSearchParams +>; + +// Filter-column params are the nullable-string entries in the nuqs map +// (`parseAsString` without a default). Keys whose parser carries a default +// — page/per_page/search/include_deleted — aren't column filters and get +// excluded automatically here. Adding a new `parseAsString` filter to +// `instrumentDetailSearchParams` makes it a valid `paramKey` with no +// hand-maintenance needed at this boundary. +export type FilterParamKey = { + [K in keyof InstrumentDetailFilters]: null extends InstrumentDetailFilters[K] + ? InstrumentDetailFilters[K] extends string | null + ? K + : never + : never; +}[keyof InstrumentDetailFilters]; // Options accept either plain strings (value == label) or { value, label } // pairs for cases where the URL-stable value and the display label differ diff --git a/web-app/components/instruments/runs-table/hina-runs-table.tsx b/web-app/components/instruments/runs-table/hina-runs-table.tsx index ed1b7966..9fb73b50 100644 --- a/web-app/components/instruments/runs-table/hina-runs-table.tsx +++ b/web-app/components/instruments/runs-table/hina-runs-table.tsx @@ -2,7 +2,7 @@ import { RelativeTime } from "@/components/dashboard/relative-time"; import { extractHinaChannels, formatHinaSizes, - getHinaChannelBadgeStyle, + HinaChannelBadges, } from "@/components/runs/run-metadata-badges"; import { Badge } from "@/components/ui/badge"; import { @@ -21,9 +21,9 @@ import type { RunRow } from "."; import { ClickableRow } from "./clickable-row"; import { FilterableColumnHeader } from "./filterable-column-header"; import { - MetadataArrayBadges, getMetadataArray, getMetadataRecord, + MetadataArrayBadges, } from "./metadata-utils"; import { RanByCell } from "./ran-by-cell"; import { RawFileColumnHeader } from "./raw-file-column-header"; @@ -136,32 +136,7 @@ export function HinaRunsTable({ {formatBytes(row.total_size_bytes)} - {channels.length === 0 ? ( - — - ) : ( -
- {channels.map((c) => { - const { badge, dot } = getHinaChannelBadgeStyle(c.color); - return ( - - {c.color && ( - - ); - })} -
- )} + diff --git a/web-app/components/instruments/runs-table/index.tsx b/web-app/components/instruments/runs-table/index.tsx index 41e3343f..6e30fa45 100644 --- a/web-app/components/instruments/runs-table/index.tsx +++ b/web-app/components/instruments/runs-table/index.tsx @@ -1,23 +1,11 @@ -import type { - GelDocFilterOptions, - HinaFilterOptions, - PlateReaderFilterOptions, - QpcrFilterOptions, - RunListRow, -} from "@/lib/api/instrument-runs"; -import type { InstrumentType } from "@/lib/db/schema"; +import type { RunListRow } from "@/lib/api/instrument-runs"; import { SearchX } from "lucide-react"; -import { DefaultRunsTable } from "./default-runs-table"; -import { GelDocRunsTable } from "./gel-doc-runs-table"; -import { HinaRunsTable } from "./hina-runs-table"; -import { PlateReaderRunsTable } from "./plate-reader-runs-table"; -import { QpcrRunsTable } from "./qpcr-runs-table"; import { RunsTableFooter } from "./runs-table-footer"; // Re-export under the historical name so imports like // `import type { RunRow } from "@/components/instruments/runs-table"` -// keep working. The type itself is now derived server-side. +// keep working. The type itself is derived server-side. export type RunRow = RunListRow; export type RanByOption = { value: string; label: string }; @@ -28,36 +16,40 @@ export type RunsTableProps = { ranByOptions: RanByOption[]; }; -export function InstrumentRunsTable({ - data, - instrumentId, - instrumentType, +/** + * Thin wrapper around the per-instrument table variants. + * + * Previously this component owned a big `switch (instrumentType)` with one + * optional `filterOptions` prop per instrument type (plus a non-null assertion + * at every call site). That scaled poorly — every new instrument forced a new + * optional prop here and a new `!` in the caller. + * + * The shell is now purely structural: the empty-state card when there are no + * rows, otherwise the bordered frame + footer around whichever table variant + * the caller chose to render as `children`. Picking the variant is the + * caller's job, which lets each page compose the right discriminated + * filter-options narrowing without routing them through this shell. + */ +export function InstrumentRunsTableShell({ + isEmpty, hasFilters, - filterOptions, - gelDocFilterOptions, - qpcrFilterOptions, - hinaFilterOptions, - ranByOptions, + shownCount, totalCount, pendingUploadCount, unattributedCount, ranByYouCount, + children, }: { - data: RunRow[]; - instrumentId: string; - instrumentType: InstrumentType; + isEmpty: boolean; hasFilters: boolean; - filterOptions?: PlateReaderFilterOptions; - gelDocFilterOptions?: GelDocFilterOptions; - qpcrFilterOptions?: QpcrFilterOptions; - hinaFilterOptions?: HinaFilterOptions; - ranByOptions: RanByOption[]; + shownCount: number; totalCount: number; pendingUploadCount: number; unattributedCount: number; ranByYouCount: number; + children: React.ReactNode; }) { - if (data.length === 0) { + if (isEmpty) { return (
@@ -70,63 +62,11 @@ export function InstrumentRunsTable({ ); } - let table; - switch (instrumentType) { - case "plate_reader": - table = ( - - ); - break; - case "gel_doc": - table = ( - - ); - break; - case "qpcr": - table = ( - - ); - break; - case "hina_microscope": - table = ( - - ); - break; - default: - table = ( - - ); - } - return (
- {table} + {children}
- {isWatcherOnline ? ( - - ) : ( - - - {/* Wrapping span keeps the tooltip reachable while the - underlying button is disabled. */} - - - - - - {WATCHER_OFFLINE_UPLOAD_TOOLTIP} - - - )} + + {isPending ? ( + + ) : ( + + )} + Upload {selectedDetectedIds.length} + + + + + Reprocess file? + + {file.filename} will be sent + to the Lambda function for reprocessing. Any existing report data + for this file will be cleared. + + + + Cancel + onReprocess(file.id)}> + Reprocess + + + + + ); +} + +function UploadDismissActions({ + file, + isPending, + onUpload, + onDismiss, +}: { + file: RunFile; + isPending: boolean; + onUpload: (id: number) => void; + onDismiss: (id: number) => void; +}) { + return ( + <> + onUpload(file.id)} + disabled={isPending} + > + + Upload + + + + + + + + Dismiss file? + + {file.filename} will be + soft-deleted. The watcher will skip it on future scans. + + + + Cancel + onDismiss(file.id)}> + Dismiss + + + + + + ); +} + +function canReprocess(file: RunFile): boolean { + return ( + file.deletedAt === null && + REPROCESSABLE_STATUSES.has(file.status) && + file.s3Key !== null + ); +} + +// --------------------------------------------------------------------------- +// Read-only variant: no selection column, no upload/dismiss. Reprocessing is +// still allowed for completed/failed files so operators can recover report +// data without restoring the run. +// --------------------------------------------------------------------------- + +export type ReadOnlyRunFilesTableProps = { + files: RunFile[]; + isPending: boolean; + onReprocess: (id: number) => void; +}; + +export function ReadOnlyRunFilesTable({ + files, + isPending, + onReprocess, +}: ReadOnlyRunFilesTableProps) { + return ( + + + + + + + + + {files.map((file) => { + const isDismissed = file.deletedAt !== null; + return ( + + + + {canReprocess(file) && ( +
+ +
+ )} + + + ); + })} + +
+ ); +} + +// --------------------------------------------------------------------------- +// Editable variant: adds a selection column (for bulk upload/dismiss flows) +// and per-row upload/dismiss buttons on detected files. Falls back to the +// reprocess action for completed/failed files, matching the read-only table. +// --------------------------------------------------------------------------- + export type RunFilesTableSelection = { selectedIds: Set; visibleSelectableIds: Set; @@ -140,32 +369,23 @@ export type RunFilesTableSelection = { onToggleAll: () => void; }; -export type RunFilesTableProps = { +export type EditableRunFilesTableProps = { files: RunFile[]; - isDeleted: boolean; isPending: boolean; - // When false, per-row "Upload" actions are disabled so users can't queue - // a transition to `upload_requested` that no agent would pick up. - isWatcherOnline: boolean; selection: RunFilesTableSelection; onUpload: (id: number) => void; onDismiss: (id: number) => void; onReprocess: (id: number) => void; }; -const WATCHER_OFFLINE_UPLOAD_TOOLTIP = - "Watcher is offline. Bring the watcher online before requesting uploads — otherwise nothing will transfer this file to S3."; - -export function RunFilesTable({ +export function EditableRunFilesTable({ files, - isDeleted, isPending, - isWatcherOnline, selection, onUpload, onDismiss, onReprocess, -}: RunFilesTableProps) { +}: EditableRunFilesTableProps) { const { selectedIds, visibleSelectableIds, @@ -176,7 +396,7 @@ export function RunFilesTable({ onToggleAll, } = selection; - const showSelectionColumn = !isDeleted && visibleSelectableIds.size > 0; + const showSelectionColumn = visibleSelectableIds.size > 0; return ( @@ -196,35 +416,17 @@ export function RunFilesTable({ /> )} - - File name - - - Type - - - Size - - - Created - - - Status - + {files.map((file) => { const isDismissed = file.deletedAt !== null; - const isSelectable = - !isDeleted && file.status === "detected" && !isDismissed; + const isSelectable = file.status === "detected" && !isDismissed; const isSelected = selectedIds.has(file.id); - const showRowActions = - !isDeleted && - !isDismissed && - file.status === "detected" && - !hasBulkSelection; + const showUploadDismiss = + !isDismissed && file.status === "detected" && !hasBulkSelection; return ( )} - - - {file.filename} - {DOWNLOADABLE_STATUSES.has(file.status) && ( - - - - )} - - - - - {file.category} - - - - {formatBytes(file.sizeBytes)} - - - {file.createdAt ? formatDateTime(file.createdAt) : "—"} - - - - + - {showRowActions ? ( + {showUploadDismiss ? (
- {isWatcherOnline ? ( - - ) : ( - - - {/* Wrapping span keeps the tooltip reachable while - the underlying button is disabled. */} - - - - - - {WATCHER_OFFLINE_UPLOAD_TOOLTIP} - - - )} - - - - - - - Dismiss file? - - - {file.filename} - {" "} - will be soft-deleted. The watcher will skip it on - future scans. - - - - Cancel - onDismiss(file.id)}> - Dismiss - - - - +
) : ( - !isDismissed && - REPROCESSABLE_STATUSES.has(file.status) && - file.s3Key !== null && ( + canReprocess(file) && (
- - - - - - - Reprocess file? - - - {file.filename} - {" "} - will be sent to the Lambda function for - reprocessing. Any existing report data for this - file will be cleared. - - - - Cancel - onReprocess(file.id)} - > - Reprocess - - - - +
) )} diff --git a/web-app/components/runs/run-metadata-badges.tsx b/web-app/components/runs/run-metadata-badges.tsx index 690cd8dd..bb894b06 100644 --- a/web-app/components/runs/run-metadata-badges.tsx +++ b/web-app/components/runs/run-metadata-badges.tsx @@ -279,10 +279,12 @@ function relativeLuminance({ return 0.2126 * linear(r) + 0.7152 * linear(g) + 0.0722 * linear(b); } -// Channel colors come straight from instrument metadata, so any value is -// possible — including white, which disappears against the light theme's -// white surface. For near-white colors we blend with `--foreground` so the -// border/text remain visible in light mode while staying vivid in dark mode. +// Channel colors come straight from instrument metadata. To keep channel +// badges visually consistent with the other metadata badges, we always use +// the default outline border and carry the channel's identity on the dot and +// text color alone. Near-white colors are blended with `--foreground` so the +// text remains readable on light surfaces while staying vivid on dark ones, +// and the dot is ringed with `--border` so a white swatch is still visible. const NEAR_WHITE_LUMINANCE = 0.85; export type ChannelBadgeStyle = { @@ -297,21 +299,15 @@ export function getHinaChannelBadgeStyle( const rgb = parseColorToRgb(color); const isNearWhite = rgb !== null && relativeLuminance(rgb) > NEAR_WHITE_LUMINANCE; - if (isNearWhite) { - const adapted = `color-mix(in oklab, ${color}, var(--foreground) 45%)`; - return { - badge: { borderColor: adapted, color: adapted }, - // Keep the true channel color on the dot so the swatch still reads as - // "white", but ring it with the theme border so it stays visible. - dot: { - backgroundColor: color, - boxShadow: "inset 0 0 0 1px var(--border)", - }, - }; - } + const textColor = isNearWhite ? "text-foreground" : color; return { - badge: { borderColor: color, color }, - dot: { backgroundColor: color }, + badge: { color: textColor }, + dot: isNearWhite + ? { + backgroundColor: color, + boxShadow: "inset 0 0 0 1px var(--border)", + } + : { backgroundColor: color }, }; } @@ -397,7 +393,7 @@ function ChannelBadge({ name, color }: HinaChannel) { export function HinaChannelBadges({ channels }: { channels: HinaChannel[] }) { if (channels.length === 0) - return —; + return —; return (
{channels.map((c) => ( diff --git a/web-app/components/runs/variants/default-run-detail.tsx b/web-app/components/runs/variants/default-run-detail.tsx index d97ab1e3..0c4b32c7 100644 --- a/web-app/components/runs/variants/default-run-detail.tsx +++ b/web-app/components/runs/variants/default-run-detail.tsx @@ -12,7 +12,6 @@ export function DefaultRunDetail({ files, instrumentId, runId, - isWatcherOnline, attributionsSlot, }: RunDetailProps) { const isDeleted = run.deletedAt !== null; @@ -51,7 +50,6 @@ export function DefaultRunDetail({ instrumentId={instrumentId} runId={runId} isDeleted={isDeleted} - isWatcherOnline={isWatcherOnline} /> diff --git a/web-app/components/runs/variants/gel-doc-run-detail.tsx b/web-app/components/runs/variants/gel-doc-run-detail.tsx index 8243fab5..a0828c01 100644 --- a/web-app/components/runs/variants/gel-doc-run-detail.tsx +++ b/web-app/components/runs/variants/gel-doc-run-detail.tsx @@ -12,7 +12,6 @@ export function GelDocRunDetail({ files, instrumentId, runId, - isWatcherOnline, attributionsSlot, }: RunDetailProps) { const isDeleted = run.deletedAt !== null; @@ -51,7 +50,6 @@ export function GelDocRunDetail({ instrumentId={instrumentId} runId={runId} isDeleted={isDeleted} - isWatcherOnline={isWatcherOnline} /> diff --git a/web-app/components/runs/variants/hina-microscope-run-detail.tsx b/web-app/components/runs/variants/hina-microscope-run-detail.tsx index 0f877a25..f04f9e9d 100644 --- a/web-app/components/runs/variants/hina-microscope-run-detail.tsx +++ b/web-app/components/runs/variants/hina-microscope-run-detail.tsx @@ -13,7 +13,6 @@ export function HinaMicroscopeRunDetail({ files, instrumentId, runId, - isWatcherOnline, attributionsSlot, }: RunDetailProps) { const isDeleted = run.deletedAt !== null; @@ -50,7 +49,6 @@ export function HinaMicroscopeRunDetail({ instrumentId={instrumentId} runId={runId} isDeleted={isDeleted} - isWatcherOnline={isWatcherOnline} /> diff --git a/web-app/components/runs/variants/plate-reader-run-detail.tsx b/web-app/components/runs/variants/plate-reader-run-detail.tsx index fec5ca3d..eff9bf14 100644 --- a/web-app/components/runs/variants/plate-reader-run-detail.tsx +++ b/web-app/components/runs/variants/plate-reader-run-detail.tsx @@ -263,7 +263,6 @@ export function PlateReaderRunDetail({ wellData, instrumentId, runId, - isWatcherOnline, attributionsSlot, }: RunDetailProps) { const isDeleted = run.deletedAt !== null; @@ -314,7 +313,6 @@ export function PlateReaderRunDetail({ instrumentId={instrumentId} runId={runId} isDeleted={isDeleted} - isWatcherOnline={isWatcherOnline} /> diff --git a/web-app/components/runs/variants/qpcr-run-detail.tsx b/web-app/components/runs/variants/qpcr-run-detail.tsx index b45ec187..63ee1d8d 100644 --- a/web-app/components/runs/variants/qpcr-run-detail.tsx +++ b/web-app/components/runs/variants/qpcr-run-detail.tsx @@ -12,7 +12,6 @@ export function QpcrRunDetail({ files, instrumentId, runId, - isWatcherOnline, attributionsSlot, }: RunDetailProps) { const isDeleted = run.deletedAt !== null; @@ -49,7 +48,6 @@ export function QpcrRunDetail({ instrumentId={instrumentId} runId={runId} isDeleted={isDeleted} - isWatcherOnline={isWatcherOnline} /> diff --git a/web-app/components/runs/variants/tape-station-run-detail.tsx b/web-app/components/runs/variants/tape-station-run-detail.tsx index da2e063f..40fba943 100644 --- a/web-app/components/runs/variants/tape-station-run-detail.tsx +++ b/web-app/components/runs/variants/tape-station-run-detail.tsx @@ -12,7 +12,6 @@ export function TapeStationRunDetail({ files, instrumentId, runId, - isWatcherOnline, attributionsSlot, }: RunDetailProps) { const isDeleted = run.deletedAt !== null; @@ -51,7 +50,6 @@ export function TapeStationRunDetail({ instrumentId={instrumentId} runId={runId} isDeleted={isDeleted} - isWatcherOnline={isWatcherOnline} /> diff --git a/web-app/components/runs/watcher-gated-upload-button.tsx b/web-app/components/runs/watcher-gated-upload-button.tsx new file mode 100644 index 00000000..192f96da --- /dev/null +++ b/web-app/components/runs/watcher-gated-upload-button.tsx @@ -0,0 +1,65 @@ +"use client"; + +import { Button } from "@/components/ui/button"; +import { + Tooltip, + TooltipContent, + TooltipTrigger, +} from "@/components/ui/tooltip"; +import { cn } from "@/lib/utils"; +import type * as React from "react"; + +import { useWatcherStatus } from "./watcher-status-provider"; + +const DEFAULT_OFFLINE_TOOLTIP = + "Watcher is offline. Bring the watcher online before requesting uploads — otherwise nothing will transfer to S3."; + +/** + * Renders an upload-style `Button` that is fully interactive when the + * instrument's watcher is online, and a disabled button wrapped in an + * explanatory tooltip when it is offline. + * + * Watcher status is read from the nearest `WatcherStatusProvider`, so + * callers don't need to thread `isWatcherOnline` down through the tree. + * + * The offline path intentionally wraps the disabled button in a + * `tabIndex={0}` span so the tooltip remains reachable via hover and + * keyboard focus even though the underlying ` + ); + } + + return ( + + + + + + + + {offlineTooltip} + + + ); +} diff --git a/web-app/components/runs/watcher-status-provider.tsx b/web-app/components/runs/watcher-status-provider.tsx new file mode 100644 index 00000000..753a84d5 --- /dev/null +++ b/web-app/components/runs/watcher-status-provider.tsx @@ -0,0 +1,41 @@ +"use client"; + +import { createContext, use, type ReactNode } from "react"; + +/** + * Describes whether the instrument's watcher is actively heartbeating. + * + * Downstream upload-style controls read this to decide between the + * enabled button and the disabled-with-tooltip variant (see + * `watcher-gated-upload-button.tsx`). Centralizing the flag here keeps + * the run-detail variants free of `isWatcherOnline` prop drilling. + */ +export type WatcherStatus = { + isWatcherOnline: boolean; +}; + +const WatcherStatusContext = createContext(null); + +export function WatcherStatusProvider({ + isWatcherOnline, + children, +}: { + isWatcherOnline: boolean; + children: ReactNode; +}) { + return ( + + {children} + + ); +} + +export function useWatcherStatus(): WatcherStatus { + const context = use(WatcherStatusContext); + if (!context) { + throw new Error( + "useWatcherStatus must be used within a " + ); + } + return context; +} diff --git a/web-app/components/ui/carousel.tsx b/web-app/components/ui/carousel.tsx index 12316ca0..cf58d601 100644 --- a/web-app/components/ui/carousel.tsx +++ b/web-app/components/ui/carousel.tsx @@ -33,7 +33,7 @@ type CarouselContextProps = { const CarouselContext = React.createContext(null); function useCarousel() { - const context = React.useContext(CarouselContext); + const context = React.use(CarouselContext); if (!context) { throw new Error("useCarousel must be used within a "); diff --git a/web-app/lib/api/instrument-runs.ts b/web-app/lib/api/instrument-runs.ts index aaff8a1f..bf9ccb82 100644 --- a/web-app/lib/api/instrument-runs.ts +++ b/web-app/lib/api/instrument-runs.ts @@ -2,6 +2,7 @@ import { parse } from "csv-parse/sync"; import { formatHinaSizes } from "@/components/runs/run-metadata-badges"; import { db } from "@/lib/db"; +import type { InstrumentType } from "@/lib/db/schema"; import { files, instrumentRuns, @@ -667,6 +668,52 @@ export async function getHinaFilterOptions( return { channels, dimensions, sizes }; } +// --------------------------------------------------------------------------- +// Dispatcher: fetch whichever per-instrument filter options apply to this +// instrument type. The discriminated return shape lets the caller narrow to +// the correct variant component without non-null assertions, and TS +// exhaustiveness-checks the switch so a newly added `InstrumentType` won't +// compile until it's handled here. +// --------------------------------------------------------------------------- + +export type InstrumentFilterOptionsByType = + | { kind: "plate_reader"; options: PlateReaderFilterOptions } + | { kind: "gel_doc"; options: GelDocFilterOptions } + | { kind: "qpcr"; options: QpcrFilterOptions } + | { kind: "hina_microscope"; options: HinaFilterOptions } + | { kind: "default" }; + +export async function getInstrumentFilterOptions( + instrumentType: InstrumentType, + instrumentId: string +): Promise { + switch (instrumentType) { + case "plate_reader": + return { + kind: "plate_reader", + options: await getPlateReaderFilterOptions(instrumentId), + }; + case "gel_doc": + return { + kind: "gel_doc", + options: await getGelDocFilterOptions(instrumentId), + }; + case "qpcr": + return { + kind: "qpcr", + options: await getQpcrFilterOptions(instrumentId), + }; + case "hina_microscope": + return { + kind: "hina_microscope", + options: await getHinaFilterOptions(instrumentId), + }; + case "generic": + case "tape_station": + return { kind: "default" }; + } +} + // --------------------------------------------------------------------------- // Distinct users who have attributed any (non-deleted) run for this // instrument — used to populate the "Ran By" column filter dropdown.