[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
theosanderson · Oct 8, 2024 · 87e5d71 · 87e5d71
1 parent 2fb64d7
commit 87e5d71
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Showing 2 changed files with 21 additions and 16 deletions.
diff --git a/taxonium_component/src/webworkers/localBackendWorker.js b/taxonium_component/src/webworkers/localBackendWorker.js
@@ -7,8 +7,8 @@ import {
 import { processNewickAndMetadata } from "../utils/processNewick.js";
 import { processNextstrain } from "../utils/processNextstrain.js";
 import { ReadableWebToNodeStream } from "readable-web-to-node-stream";
-import {parser } from "stream-json";
-import {streamValues } from "stream-json/streamers/StreamValues";
+import { parser } from "stream-json";
+import { streamValues } from "stream-json/streamers/StreamValues";
 
 console.log("worker starting");
 postMessage({ data: "Worker starting" });
@@ -214,9 +214,10 @@ onmessage = async (event) => {
       data.data,
       sendStatusMessage,
       ReadableWebToNodeStream,
-      parser,streamValues
+      parser,
+      streamValues
     );
-    
+
     console.log("processedUploadedData created");
   } else if (
     data.type === "upload" &&

diff --git a/taxonium_data_handling/importing.js b/taxonium_data_handling/importing.js
@@ -20,7 +20,6 @@ class StreamSplitter extends stream.Transform {
         const headerData = data.slice(0, newlineIndex);
         const restData = data.slice(newlineIndex + 1);
 
-
         // Write header data to headerParser
         this.headerParser.write(headerData);
         this.headerParser.end();
@@ -33,7 +32,7 @@ class StreamSplitter extends stream.Transform {
         this.firstPart = false;
       } else {
         // No newline found, store data in buffer
-       this.headerParser.write(data);
+        this.headerParser.write(data);
       }
     } else {
       // After header is processed, pass data to dataParser
@@ -55,7 +54,6 @@ class StreamSplitter extends stream.Transform {
   }
 }
 
-
 const roundToDp = (number, dp) => {
   return Math.round(number * Math.pow(10, dp)) / Math.pow(10, dp);
 };
@@ -92,21 +90,24 @@ export const setUpStream = (
   // Header parser
   const headerParser = parser({ jsonStreaming: true });
   const headerPipeline = headerParser.pipe(streamValues());
-  
+
   let headerBytesProcessed = 0;
   const HEADER_PROGRESS_INTERVAL = 1024 * 1024; // 1MB
 
-  headerParser.on('data', (chunk) => {
+  headerParser.on("data", (chunk) => {
     headerBytesProcessed += chunk.length;
     if (headerBytesProcessed >= HEADER_PROGRESS_INTERVAL) {
       sendStatusMessage({
-        message: `Processing header: ${(headerBytesProcessed / (1024 * 1024)).toFixed(2)} MB processed`,
+        message: `Processing header: ${(
+          headerBytesProcessed /
+          (1024 * 1024)
+        ).toFixed(2)} MB processed`,
       });
       headerBytesProcessed = 0; // Reset the counter
     }
   });
 
-  headerPipeline.on('data', (chunk) => {
+  headerPipeline.on("data", (chunk) => {
     data.header = chunk.value;
     data.nodes = [];
     data.node_to_mut = {};
@@ -115,7 +116,7 @@ export const setUpStream = (
     });
   });
 
-  headerPipeline.on('error', (err) => {
+  headerPipeline.on("error", (err) => {
     console.error("Header parser error:", err);
     sendStatusMessage({
       error: `Header parser error: ${err.message}`,
@@ -177,19 +178,22 @@ export const setUpStream = (
   const splitter = new StreamSplitter(headerParser, dataParser);
 
   // Pipe the input stream through the splitter
-  the_stream.pipe(splitter).on("error", (err) => console.error("Splitter error:", err));
+  the_stream
+    .pipe(splitter)
+    .on("error", (err) => console.error("Splitter error:", err));
 
   // Handle the completion of the dataParser
   dataParser.on("finish", () => {
     console.log("Finished processing the stream");
   });
 };
 
-
 export const processJsonl = async (
   jsonl,
   sendStatusMessage,
-  ReadableWebToNodeStream, parser, streamValues
+  ReadableWebToNodeStream,
+  parser,
+  streamValues
 ) => {
   console.log(
     "Worker processJsonl" //, jsonl
@@ -205,7 +209,7 @@ export const processJsonl = async (
     the_stream = new stream.PassThrough();
   }
   let new_data = {};
-  setUpStream(the_stream, new_data, sendStatusMessage,parser, streamValues);
+  setUpStream(the_stream, new_data, sendStatusMessage, parser, streamValues);
 
   if (status === "loaded") {
     const dataAsArrayBuffer = data;