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

for more information, see https://pre-commit.ci
theosanderson · Feb 25, 2025 · def419e · def419e
1 parent 24cf702
commit def419e
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Showing 3 changed files with 38 additions and 17 deletions.
diff --git a/taxonium_component/src/webworkers/treenomeWorker.js b/taxonium_component/src/webworkers/treenomeWorker.js
@@ -97,7 +97,7 @@ const computeVariationData = async (data, type, ntBounds, jobId) => {
 
   const preorder_nodes = pre_order(nodes);
   const root = preorder_nodes.find((id) => id === lookup[id].parent_id);
-  
+
   // Use rootSequences from config
   if (data.data && data.data.config && data.data.config.rootSequences) {
     ref = data.data.config.rootSequences;

diff --git a/taxonium_data_handling/filtering.js b/taxonium_data_handling/filtering.js
@@ -22,10 +22,15 @@ const getNumericFilterFunction = (number_method, number_value) => {
   throw new Error("Invalid number_method: " + number_method);
 };
 
-const getRevertantMutationsSet = (all_data, node_to_mut, mutations, rootSequences) => {
+const getRevertantMutationsSet = (
+  all_data,
+  node_to_mut,
+  mutations,
+  rootSequences
+) => {
   // Initialize gene_sequence - preferably from rootSequences, fallback to rootMutations
   let gene_sequence;
-  
+
   if (rootSequences && rootSequences.aa) {
     // Use rootSequences if available
     gene_sequence = rootSequences.aa;
@@ -41,7 +46,7 @@ const getRevertantMutationsSet = (all_data, node_to_mut, mutations, rootSequence
       gene_sequence[m.gene][m.residue_pos] = m.new_residue;
     });
   }
-  
+
   const revertant_mutations = mutations.filter(
     (m) =>
       m.gene in gene_sequence &&
@@ -397,7 +402,14 @@ function searchFilteringIfUncached({
       position: spec.position,
       new_residue: spec.new_residue,
     };
-    return filterByGenotype(data, genotype, mutations, node_to_mut, all_data, rootSequences);
+    return filterByGenotype(
+      data,
+      genotype,
+      mutations,
+      node_to_mut,
+      all_data,
+      rootSequences
+    );
   } else if (spec.method === "number") {
     if (spec.number == "") {
       return [];
@@ -550,7 +562,14 @@ const getTipAtts = (input, node_id, attribute) => {
   return allAtts;
 };
 
-const filterByGenotype = (data, genotype, mutations, node_to_mut, all_data, rootSequences) => {
+const filterByGenotype = (
+  data,
+  genotype,
+  mutations,
+  node_to_mut,
+  all_data,
+  rootSequences
+) => {
   const genotype_cache = {};
   const { gene, position, new_residue } = genotype;
 
@@ -613,11 +632,13 @@ const filterByGenotype = (data, genotype, mutations, node_to_mut, all_data, root
       if (cur_node.parent_id === cur_node.node_id) {
         // We've reached the root node
         // Check if we have rootSequences data
-        if (rootSequences &&
-            rootSequences.aa && 
-            rootSequences.aa[gene] && 
-            rootSequences.aa[gene][position] === new_residue) {
-          to_label.forEach(node_id => {
+        if (
+          rootSequences &&
+          rootSequences.aa &&
+          rootSequences.aa[gene] &&
+          rootSequences.aa[gene][position] === new_residue
+        ) {
+          to_label.forEach((node_id) => {
             genotype_cache[node_id] = true;
           });
           return true;

diff --git a/taxonium_data_handling/importing.js b/taxonium_data_handling/importing.js
@@ -302,13 +302,13 @@ export const processJsonl = async (
   const rootSequences = { nt: {}, aa: {} };
   if (rootMutations && rootMutations.length > 0) {
     // Group mutations by gene
-    rootMutations.forEach(mutIndex => {
-      const mut = new_data.header.mutations ? 
-        new_data.header.mutations[mutIndex] : 
-        new_data.header.aa_mutations[mutIndex];
-      
+    rootMutations.forEach((mutIndex) => {
+      const mut = new_data.header.mutations
+        ? new_data.header.mutations[mutIndex]
+        : new_data.header.aa_mutations[mutIndex];
+
       if (!mut) return;
-      
+
       if (mut.gene === "nt") {
         rootSequences.nt[mut.residue_pos] = mut.new_residue;
       } else {