diff --git a/public/zarr_samples.csv b/public/zarr_samples.csv index db078c6..3ac6024 100644 --- a/public/zarr_samples.csv +++ b/public/zarr_samples.csv @@ -1,91 +1,91 @@ -OME-NGFF version,URL,SizeX,SizeY,SizeZ,SizeC,SizeT,Axes,Wells,Fields,Keywords,License,Study,DOI,Date added,Representative Image ID -0.1,https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/12689244.zarr,4992,4255,401,3,1,XYZCT,,,,CC BY 4.0,idr0106,,2020-11-04,12689244 -0.1,https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/179706.zarr,1344,1024,1,2,329,XYZCT,,,,CC BY 4.0,idr0002,,2020-11-04,179706 -0.1,https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/1884807.zarr,256,256,1,3,1,XYZCT,,,,CC BY 4.0,idr0021,,2020-11-04,1884807 -0.1,https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/1885619.zarr,30,30,571,1,1,XYZCT,,,,CC BY 4.0,idr0023,,2020-11-04,1885619 -0.1,https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/4007801.zarr,2169,2048,988,2,532,XYZCT,,,,CC BY 4.0,idr0044,,2020-11-04,4007801 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newline at end of file diff --git a/src/App.jsx b/src/App.jsx index da51769..14e574d 100644 --- a/src/App.jsx +++ b/src/App.jsx @@ -4,51 +4,78 @@ import React from "react"; import Papa from "papaparse"; import ImageItem from "./ImageItem"; +import ZarrUrl from "./ZarrUrl"; + +const supportedColumns = [ + "Version", + "Axes", + "shape", + "chunks", + "Wells", + "Fields", + "Keywords", + "Thumbnail", +]; + +const defaultColumns = [ + "Thumbnail" +] export default function App() { const [tableData, setTableData] = React.useState([]); + const [tableColumns, setTableColumns] = React.useState([]); + + + // check for ?csv=url + const params = new URLSearchParams(location.search); + let csvUrl = params.get("csv"); + // columns=Version,Axes,shape,chunks,Wells,Fields,Keywords,Thumbnail, + let cols = params.get("columns"); + console.log("cols", cols); + let zarr_columns = []; + if (cols) { + zarr_columns = cols.split(",").filter(col => supportedColumns.includes(col)); + } else { + zarr_columns = defaultColumns; + } + console.log("zarr_columsn", zarr_columns) + try { + new URL(csvUrl); + } catch (error) { + csvUrl = "/zarr_samples.csv"; + } + React.useEffect(() => { - const params = new URLSearchParams(location.search); - let csvUrl = params.get("csv"); - try { - new URL(csvUrl); - } catch (error) { - csvUrl = "/zarr_samples.csv"; - } Papa.parse(csvUrl, { header: true, download: true, complete: function (results) { setTableData(results.data); + setTableColumns(results.meta.fields); }, }); }, []); - let zarr_columns = [ - "URL", - "Version", - "Axes", - "shape, chunks", - "Wells", - "Fields", - "Keywords", - "Thumbnail", - ]; - - let custom_columns = ["License", "Study", "DOI", "Date added"]; function renderRow(rowdata) { return - {custom_columns.map((col_name) => {rowdata[col_name]})} + {tableColumns.map((col_name) => { + if (col_name == "URL") { + return + } else { + return {rowdata[col_name]} + } + })} } const validRows = tableData.filter(rowdata => rowdata.URL?.length > 0); const table_rows = validRows.map((rowdata) => { + // Each row is a combination of custom table data and NGFF Image data return ( {renderRow(rowdata)} - {custom_columns.map((name) => ( + {tableColumns.map((name) => ( {name} ))} {zarr_columns.map((name) => ( diff --git a/src/ImageItem.jsx b/src/ImageItem.jsx index 624a8a6..341a405 100644 --- a/src/ImageItem.jsx +++ b/src/ImageItem.jsx @@ -2,8 +2,6 @@ import React from "react"; import Thumbnail from "./Thumbnail"; // import Viewer from "./Viewer"; -import OpenWith from "./OpenWith"; -import CopyButton from "./CopyButton"; import { loadOmeroMultiscales, open, getNgffAxes } from "./util"; import { openArray } from "zarr"; @@ -78,15 +76,14 @@ export default function ImageItem({ source, zarr_columns }) { // setLayers([layerData]); - // ["URL", "Version", "Axes", "shape, chunks", "Wells", "Fields", "Keywords", "Thumbnail"]; setImageInfo({ attrs, "Axes": axes.map((axis) => axis.name).join(""), "Version": attrs.multiscales?.[0]?.version, "Keywords": keywords, "Wells": wells, - "shape": shape.join(", "), - "chunks": chunks.join(", "), + "shape": "(" + shape.join(", ") + ")", + "chunks": "(" + chunks.join(", ") + ")", "Fields": fields, // use this source for to handle plate -> Image update source @@ -102,34 +99,14 @@ export default function ImageItem({ source, zarr_columns }) { position: "relative", }; - let link_style = { - maxWidth: 150, - display: "block", - textOverflow: "ellipsis", - direction: "rtl", - whiteSpace: "nowrap", - overflow: "hidden" - } - - // ["URL", "Version", "Axes", "shape, chunks", "Wells", "Fields", "Keywords", "Thumbnail"]; - function renderColumn(col_name) { - if (col_name == "URL") { - return ( - {source} - - - - ) - } else if (col_name == "Thumbnail") { + if (col_name == "Thumbnail") { return (
{imgInfo.attrs && }
) - } else if (col_name == "shape, chunks") { - return ({imgInfo.shape})
({imgInfo.chunks}) } else { return imgInfo[col_name]; } diff --git a/src/ZarrUrl.jsx b/src/ZarrUrl.jsx new file mode 100644 index 0000000..1f2f219 --- /dev/null +++ b/src/ZarrUrl.jsx @@ -0,0 +1,25 @@ +import React from "react"; + +import CopyButton from "./CopyButton"; +import OpenWith from "./OpenWith"; + +export default function ZarrUrl({ source }) { + let link_style = { + maxWidth: 150, + display: "block", + textOverflow: "ellipsis", + direction: "rtl", + whiteSpace: "nowrap", + overflow: "hidden", + }; + + return ( + + + {source} + + + + + ); +}