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

for more information, see https://pre-commit.ci

taxonium_backend/server.js

@@ -25,7 +25,7 @@ program
   .option("--data_url <data url>", "data url")
   .option(
     "--data_file <data file>",
-    "local data file, as alternative to data url"
+    "local data file, as alternative to data url",
   );
 
 program.parse();
@@ -153,7 +153,7 @@ app.get("/search", function (req, res) {
       result.data.length +
       " results in " +
       (Date.now() - start_time) +
-      "ms"
+      "ms",
   );
   console.log("Result type was " + result.type);
 });
@@ -255,7 +255,7 @@ app.get("/nodes/", function (req, res) {
       max_y,
       min_x,
       max_x,
-      req.query.xType
+      req.query.xType,
     );
   }
   console.log("Ready to send after " + (Date.now() - start_time) + "ms.");
@@ -267,19 +267,19 @@ app.get("/nodes/", function (req, res) {
       (Date.now() - start_time) +
       "ms, and output " +
       result.length +
-      " nodes."
+      " nodes.",
   );
 });
 
 function startListening() {
   if (command_options.ssl) {
     options = {
       key: fs.readFileSync(
-        "/etc/letsencrypt/live/api.taxonium.org/privkey.pem"
+        "/etc/letsencrypt/live/api.taxonium.org/privkey.pem",
       ),
       ca: fs.readFileSync("/etc/letsencrypt/live/api.taxonium.org/chain.pem"),
       cert: fs.readFileSync(
-        "/etc/letsencrypt/live/api.taxonium.org/fullchain.pem"
+        "/etc/letsencrypt/live/api.taxonium.org/fullchain.pem",
       ),
     };
     https.createServer(options, app).listen(command_options.port, "0.0.0.0");
@@ -451,7 +451,7 @@ app.get("/node_details/", async (req, res) => {
   }
   validateSIDandSend(detailed_node, req.query.sid, res);
   console.log(
-    "Request took " + (Date.now() - start_time) + "ms, and output " + node
+    "Request took " + (Date.now() - start_time) + "ms, and output " + node,
   );
 });
 
@@ -462,7 +462,7 @@ app.get("/tip_atts", async (req, res) => {
   const atts = filtering.getTipAtts(processedData.nodes, node_id, att);
   validateSIDandSend(atts, req.query.sid, res);
   console.log(
-    "Request took " + (Date.now() - start_time) + "ms, and output " + atts
+    "Request took " + (Date.now() - start_time) + "ms, and output " + atts,
   );
 });
 
@@ -473,11 +473,11 @@ app.get("/nextstrain_json/:root_id", async (req, res) => {
     root_id,
     processedData.nodes,
     config,
-    processedData.mutations
+    processedData.mutations,
   );
   res.setHeader(
     "Content-Disposition",
-    "attachment; " + "filename=" + root_id + ".nextstrain.json"
+    "attachment; " + "filename=" + root_id + ".nextstrain.json",
   );
   res.send(json);
 });
@@ -503,7 +503,7 @@ const loadData = async () => {
 
   processedData = await importing.processJsonl(
     supplied_object,
-    logStatusMessage
+    logStatusMessage,
   );
 
   logStatusMessage({
@@ -515,7 +515,7 @@ const loadData = async () => {
   }
 
   processedData.genes = new Set(
-    processedData.mutations.map((mutation) => mutation.gene)
+    processedData.mutations.map((mutation) => mutation.gene),
   );
   // as array
   processedData.genes = Array.from(processedData.genes);
@@ -528,7 +528,7 @@ const loadData = async () => {
     processedData.overallMaxY,
     processedData.overallMinX,
     processedData.overallMaxX,
-    "x_dist"
+    "x_dist",
   );
 
   cached_starting_values = result;

taxonium_data_handling/exporting.js

@@ -3,7 +3,7 @@ const addAAmuts = (aaMuts, node) => {
   aaMuts.forEach((m) => {
     if (alreadyIn.includes(m.gene)) {
       node.branch_attrs.mutations[m.gene].push(
-        `${m.previous_residue}${m.residue_pos}${m.new_residue}`
+        `${m.previous_residue}${m.residue_pos}${m.new_residue}`,
       );
     } else {
       node.branch_attrs.mutations[m.gene] = [
@@ -16,7 +16,7 @@ const addAAmuts = (aaMuts, node) => {
 
 const addNucMuts = (nucMuts, node) => {
   node.branch_attrs.mutations["nuc"] = nucMuts.map(
-    (m) => `${m.previous_residue}${m.residue_pos}${m.new_residue}`
+    (m) => `${m.previous_residue}${m.residue_pos}${m.new_residue}`,
   );
 };
 
@@ -25,7 +25,7 @@ export const getNextstrainSubtreeJson = async (
   subtree_root_id,
   nodes,
   config,
-  mutations
+  mutations,
 ) => {
   const subtree_root = nodes.find((node) => node.node_id === subtree_root_id);
 
@@ -81,7 +81,7 @@ export const getNextstrainSubtreeJson = async (
         const aaMuts = muts.filter((m) => m.type === "aa");
 
         const nucMutsNoAmb = nucMuts.filter(
-          (m) => m.new_residue != "-" && m.previous_residue != "-"
+          (m) => m.new_residue != "-" && m.previous_residue != "-",
         );
         // TODO: Above discards ambiguities from distance calculation.
         // Do we want to do this? In mpx e.g. there are nodes with

taxonium_data_handling/filtering.js

@@ -39,7 +39,7 @@ const getRevertantMutationsSet = (all_data, node_to_mut, mutations) => {
     (m) =>
       m.gene in gene_sequence &&
       gene_sequence[m.gene][m.residue_pos] === m.new_residue &&
-      m.new_residue !== m.previous_residue
+      m.new_residue !== m.previous_residue,
   );
   return new Set(revertant_mutations.map((m) => m.mutation_id));
 };
@@ -53,7 +53,7 @@ const reduceOverPlotting = (input, precisionX, precisionY, xType) => {
     "precisionX:",
     precisionX,
     "precisionY:",
-    precisionY
+    precisionY,
   );
 
   const filtered = input.filter((node) => {
@@ -126,7 +126,7 @@ const addParents = (data, filtered) => {
     }
   }
   const with_parents = data.filter((node) =>
-    selected_node_ids_set.has(node.node_id)
+    selected_node_ids_set.has(node.node_id),
   );
   const final_size = with_parents.length;
   console.log("Adding parents took " + (Date.now() - start_time) + "ms.");
@@ -154,7 +154,7 @@ function getNodes(data, y_positions, min_y, max_y, min_x, max_x, xType) {
     filtered.filter((node) => node.num_tips == 1),
     getPrecision(min_x, max_x),
     getPrecision(min_y, max_y),
-    xType
+    xType,
   );
   const time3 = Date.now();
   console.log("Reducing took " + (time3 - time2) + "ms.");
@@ -197,7 +197,7 @@ function searchFiltering({
   if (cache_helper && cache_helper.store_in_cache) {
     cache_helper.store_in_cache(
       hash_spec,
-      result.map((node) => node.node_id)
+      result.map((node) => node.node_id),
     );
   }
   return result;
@@ -226,7 +226,7 @@ function searchFilteringIfUncached({
             node_to_mut: node_to_mut,
             all_data: all_data,
             cache_helper: cache_helper,
-          })
+          }),
         );
         workingData = workingData.filter((n) => new_results.has(n));
       });
@@ -280,14 +280,14 @@ function searchFilteringIfUncached({
     spec.text = spec.text.toLowerCase();
     filtered = data.filter(
       (node) =>
-        node[spec.type] && node[spec.type].toLowerCase().includes(spec.text)
+        node[spec.type] && node[spec.type].toLowerCase().includes(spec.text),
     );
     return filtered;
   } else if (spec.method === "text_exact") {
     // case insensitive
     spec.text = spec.text.toLowerCase();
     filtered = data.filter(
-      (node) => node[spec.type] && node[spec.type].toLowerCase() === spec.text
+      (node) => node[spec.type] && node[spec.type].toLowerCase() === spec.text,
     );
     return filtered;
   } else if (spec.method === "text_per_line") {
@@ -299,7 +299,7 @@ function searchFilteringIfUncached({
         .map((line) => {
           return line.trim();
         })
-        .filter((line) => line !== "")
+        .filter((line) => line !== ""),
     );
 
     filtered = data.filter((node) => {
@@ -333,8 +333,8 @@ function searchFilteringIfUncached({
     filtered = data.filter(
       (node) =>
         node_to_mut[node.node_id].some((mutation_id) =>
-          relevant_mutations_set.has(mutation_id)
-        ) && node.num_tips > spec.min_tips
+          relevant_mutations_set.has(mutation_id),
+        ) && node.num_tips > spec.min_tips,
     );
     //console.log("filtered:", filtered);
     return filtered;
@@ -346,16 +346,16 @@ function searchFilteringIfUncached({
       revertant_mutations_set = getRevertantMutationsSet(
         all_data,
         node_to_mut,
-        mutations
+        mutations,
       );
     }
 
     filtered = data.filter(
       (node) =>
         node.num_tips > spec.min_tips &&
         node_to_mut[node.node_id].some((mutation_id) =>
-          revertant_mutations_set.has(mutation_id)
-        )
+          revertant_mutations_set.has(mutation_id),
+        ),
     );
     //console.log("filtered:", filtered);
     return filtered;
@@ -374,7 +374,7 @@ function searchFilteringIfUncached({
     const number_value = parseFloat(spec.number);
     const filterFunc = getNumericFilterFunction(
       spec.number_method,
-      number_value
+      number_value,
     );
 
     filtered = data.filter((node) => filterFunc(node[spec.type]));
@@ -430,7 +430,7 @@ function singleSearch({
 
     // TODO if we ensured all searches maintained order we could use binary search here
     const filtered_cut = filtered.filter(
-      (node) => node.y < max_y && node.y > min_y
+      (node) => node.y < max_y && node.y > min_y,
     );
 
     console.log("length of filtered_cut:", filtered_cut.length);
@@ -442,7 +442,7 @@ function singleSearch({
       filtered_cut,
       getPrecision(min_x, max_x),
       getPrecision(min_y, max_y),
-      xType
+      xType,
     );
     result = {
       type: "filtered",
@@ -530,7 +530,7 @@ const filterByGenotype = (data, genotype, mutations, node_to_mut, all_data) => {
   const positive_mutations = new Set(
     relevant_mutations
       .filter((mutation) => mutation.new_residue === new_residue)
-      .map((m) => m.mutation_id)
+      .map((m) => m.mutation_id),
   );
 
   // if no positive mutations then return empty array
@@ -541,7 +541,7 @@ const filterByGenotype = (data, genotype, mutations, node_to_mut, all_data) => {
   const negative_mutations = new Set(
     relevant_mutations
       .filter((mutation) => mutation.new_residue !== new_residue)
-      .map((m) => m.mutation_id)
+      .map((m) => m.mutation_id),
   );
   const output = data.filter((node) => {
     //   console.log("node:",node);
@@ -556,7 +556,7 @@ const filterByGenotype = (data, genotype, mutations, node_to_mut, all_data) => {
       const is_positive =
         cache_value === true ||
         node_to_mut[cur_node.node_id].some((mutation_id) =>
-          positive_mutations.has(mutation_id)
+          positive_mutations.has(mutation_id),
         );
       if (is_positive) {
         // console.log("positive");
@@ -568,7 +568,7 @@ const filterByGenotype = (data, genotype, mutations, node_to_mut, all_data) => {
       const is_negative =
         cache_value === false ||
         node_to_mut[cur_node.node_id].some((mutation_id) =>
-          negative_mutations.has(mutation_id)
+          negative_mutations.has(mutation_id),
         );
       if (is_negative) {
         // console.log("negative");

taxonium_data_handling/importing.js

@@ -20,13 +20,13 @@ function reduceMaxOrMin(array, accessFunction, maxOrMin) {
     return accessFunction(
       array.reduce(function (max, item) {
         return accessFunction(item) > accessFunction(max) ? item : max;
-      })
+      }),
     );
   } else if (maxOrMin === "min") {
     return accessFunction(
       array.reduce(function (min, item) {
         return accessFunction(item) < accessFunction(min) ? item : min;
-      })
+      }),
     );
   }
 }
@@ -84,7 +84,7 @@ export const setUpStream = (the_stream, data, sendStatusMessage) => {
 
 export const processJsonl = async (jsonl, sendStatusMessage) => {
   console.log(
-    "Worker processJsonl" //, jsonl
+    "Worker processJsonl", //, jsonl
   );
   const data = jsonl.data;
   const status = jsonl.status;
@@ -164,12 +164,12 @@ export const processJsonl = async (jsonl, sendStatusMessage) => {
   const overallMaxX = reduceMaxOrMin(
     new_data.nodes,
     (node) => node.x_dist,
-    "max"
+    "max",
   );
   const overallMinX = reduceMaxOrMin(
     new_data.nodes,
     (node) => node.x_dist,
-    "min"
+    "min",
   );
 
   const root = new_data.nodes.find((node) => node.parent_id === node.node_id);
@@ -242,7 +242,7 @@ export const generateConfig = (config, processedUploadedData) => {
       : ["x_time"];
 
   config.keys_to_display = Object.keys(processedUploadedData.nodes[0]).filter(
-    (x) => !to_remove.includes(x)
+    (x) => !to_remove.includes(x),
   );
 
   /*config.search_types = [

taxonium_electron/index.html

@@ -1,4 +1,4 @@
-<!DOCTYPE html>
+<!doctype html>
 <html>
   <head>
     <meta charset="UTF-8" />

taxonium_electron/src/main.js

@@ -61,7 +61,7 @@ const setup = (mainWindow, args) => {
   binaryPath = path.join(binaryDirectory, binaryFilename);
   scriptPath = path.join(
     __dirname,
-    "../node_modules/taxonium_backend/server.js"
+    "../node_modules/taxonium_backend/server.js",
   );
 
   max_old_space_arg = "--max-old-space-size=" + bytesToMb(maxMemory);

taxonium_web_client/public/index.html

@@ -1,4 +1,4 @@
-<!DOCTYPE html>
+<!doctype html>
 <html lang="en">
   <head>
     <!-- Global site tag (gtag.js) - Google Analytics -->