From f158f4364889394e72d6bd54b7e079abf2dcb2b7 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 30 Sep 2024 21:41:08 +0000 Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- taxonium_component/src/components/Key.jsx | 2 +- .../src/webworkers/localBackendWorker.js | 2 +- taxonium_data_handling/importing.js | 57 +++++++++++++------ 3 files changed, 42 insertions(+), 19 deletions(-) diff --git a/taxonium_component/src/components/Key.jsx b/taxonium_component/src/components/Key.jsx index 189dfef0..edcdf050 100644 --- a/taxonium_component/src/components/Key.jsx +++ b/taxonium_component/src/components/Key.jsx @@ -149,7 +149,7 @@ const Key = ({ {!collapsed && - ((colorRamps && colorByField in colorRamps) ? ( + (colorRamps && colorByField in colorRamps ? ( ) : ( { +export const setUpStream = ( + the_stream, + data, + sendStatusMessage, + jsonlParser +) => { const pipeline = the_stream.pipe(jsonlParser()); let line_number = 0; - pipeline.on('data', decoded => { + pipeline.on("data", (decoded) => { if ((line_number % 10000 === 0 && line_number > 0) || line_number == 500) { console.log(`Processed ${formatNumber(line_number)} lines`); if (data.header.total_nodes) { @@ -63,11 +67,11 @@ export const setUpStream = (the_stream, data, sendStatusMessage, jsonlParser) => line_number++; }); - pipeline.on('error', function (err) { + pipeline.on("error", function (err) { console.log(err); }); - pipeline.on('end', function () { + pipeline.on("end", function () { console.log("end"); }); }; @@ -76,7 +80,7 @@ export const processJsonl = async ( jsonl, sendStatusMessage, ReadableWebToNodeStream, - jsonlParser, + jsonlParser ) => { console.log("Worker processJsonl"); const data = jsonl.data; @@ -126,12 +130,16 @@ export const processJsonl = async ( // Wait for the stream to finish await new Promise((resolve, reject) => { - the_stream.on('end', resolve); - the_stream.on('error', reject); + the_stream.on("end", resolve); + the_stream.on("error", reject); }); console.log("done with stream"); - const scale_y = 24e2 / (new_data.nodes.length > 10e3 ? new_data.nodes.length : new_data.nodes.length * 0.6666); + const scale_y = + 24e2 / + (new_data.nodes.length > 10e3 + ? new_data.nodes.length + : new_data.nodes.length * 0.6666); console.log("Scaling"); for (const node of new_data.nodes) { node.y = roundToDp(node.y * scale_y, 6); @@ -143,8 +151,16 @@ export const processJsonl = async ( const overallMaxY = reduceMaxOrMin(new_data.nodes, (node) => node.y, "max"); const overallMinY = reduceMaxOrMin(new_data.nodes, (node) => node.y, "min"); - const overallMaxX = reduceMaxOrMin(new_data.nodes, (node) => node.x_dist, "max"); - const overallMinX = reduceMaxOrMin(new_data.nodes, (node) => node.x_dist, "min"); + const overallMaxX = reduceMaxOrMin( + new_data.nodes, + (node) => node.x_dist, + "max" + ); + const overallMinX = reduceMaxOrMin( + new_data.nodes, + (node) => node.x_dist, + "min" + ); const root = new_data.nodes.find((node) => node.parent_id === node.node_id); const rootMutations = root.mutations; @@ -162,7 +178,9 @@ export const processJsonl = async ( overallMinX, overallMinY, y_positions, - mutations: new_data.header.mutations ? new_data.header.mutations : new_data.header.aa_mutations, + mutations: new_data.header.mutations + ? new_data.header.mutations + : new_data.header.aa_mutations, node_to_mut: new_data.node_to_mut, rootMutations: rootMutations, rootId: root.node_id, @@ -174,10 +192,14 @@ export const processJsonl = async ( export const generateConfig = (config, processedUploadedData) => { config.num_nodes = processedUploadedData.nodes.length; - config.initial_x = (processedUploadedData.overallMaxX + processedUploadedData.overallMinX) / 2; - config.initial_y = (processedUploadedData.overallMaxY + processedUploadedData.overallMinY) / 2; + config.initial_x = + (processedUploadedData.overallMaxX + processedUploadedData.overallMinX) / 2; + config.initial_y = + (processedUploadedData.overallMaxY + processedUploadedData.overallMinY) / 2; config.initial_zoom = config.initial_zoom ? config.initial_zoom : -2; - config.genes = [...new Set(processedUploadedData.mutations.map((x) => (x ? x.gene : null)))] + config.genes = [ + ...new Set(processedUploadedData.mutations.map((x) => (x ? x.gene : null))), + ] .filter((x) => x) .sort(); @@ -216,7 +238,8 @@ export const generateConfig = (config, processedUploadedData) => { const prettyName = (x) => { if (x.startsWith("meta_")) { const bit = x.substring(5); - const capitalised_first_letter = bit.charAt(0).toUpperCase() + bit.slice(1); + const capitalised_first_letter = + bit.charAt(0).toUpperCase() + bit.slice(1); return capitalised_first_letter; } if (x === "mutation") { @@ -296,4 +319,4 @@ export const generateConfig = (config, processedUploadedData) => { : colorByOptions[0]; }; -export default { processJsonl, generateConfig }; \ No newline at end of file +export default { processJsonl, generateConfig };