Merge branch 'master' into nextstrain-export

.all-contributorsrc

@@ -77,7 +77,6 @@
         "infra"
       ]
     }
-
   ],
   "contributorsPerLine": 7,
   "projectName": "taxonium",

taxonium_web_client/src/Taxonium.jsx

@@ -71,9 +71,9 @@ function Taxonium({
     // This can happen with e.g. nextstrain json
     if (data.base_data && data.base_data.nodes) {
       const n = data.base_data.nodes[0];
-      if (!n.x_dist) {
+      if (!n.hasOwnProperty("x_dist")) {
         setxType("x_time");
-      } else if (!n.x_time) {
+      } else if (!n.hasOwnProperty("x_time")) {
         setxType("x_dist");
       }
     }

taxonium_web_client/src/hooks/useInputHelper.js

@@ -156,7 +156,7 @@ export const useInputHelper = ({
         );
         const newQuery = {
           treeUrl: tree_file.name,
-          ladderizeTree: tree_file.ladderize === "true",
+          ladderizeTree: tree_file.ladderize === true,
           treeType: tree_file.filetype,
         };
         if (meta_file) {

taxonium_web_client/src/utils/processNewick.js

@@ -98,15 +98,13 @@ async function cleanup(tree) {
 
   const scale_x = 450 / ref_x;
 
-  console.log(scale_y, "scale_y");
   tree.node.forEach((node) => {
     node.x_dist = node.x_dist * scale_x;
     node.y = node.y * scale_y;
   });
 }
 
 export async function processNewick(data, sendStatusMessage) {
-  console.log("got data", data);
   let the_data;
 
   the_data = await fetch_or_extract(data, sendStatusMessage, "tree");
@@ -139,11 +137,8 @@ export async function processNewick(data, sendStatusMessage) {
   }
   assignNumTips(tree.root);
   const total_tips = tree.root.num_tips;
-  console.log("tree.root.num_tips", tree.root.num_tips);
 
   if (data.ladderize) {
-    console.log("ladderizing");
-
     sortWithNumTips(tree.root);
     tree.node = kn_expand_node(tree.root);
   }
@@ -186,7 +181,7 @@ export async function processNewick(data, sendStatusMessage) {
     rootId: 0,
     overwrite_config: { num_tips: total_tips },
   };
-  console.log(JSON.stringify(output));
+
   return output;
 }
 
@@ -198,8 +193,6 @@ export async function processMetadataFile(data, sendStatusMessage) {
 
   the_data = await fetch_or_extract(data, logStatusToConsole, "metadata");
 
-  console.log("Got metadata file");
-
   const lines = the_data.split("\n");
   const output = {};
   let separator;
@@ -275,6 +268,6 @@ export async function processNewickAndMetadata(data, sendStatusMessage) {
       Object.assign(node, blanks);
     }
   });
-  console.log(tree);
+
   return tree;
 }

taxonium_web_client/src/utils/processNextstrain.js

@@ -5,6 +5,85 @@ import { kn_expand_node, kn_calxy } from "./jstree";
 
 const emptyList = [];
 
+const nodeMutationsFromNextStrainToTaxonium = (
+  mutations,
+  unique_mutations,
+  mutation_lookup
+) => {
+  //console.log("mutations", mutations);
+  const keys = Object.keys(mutations);
+  const nuc_muts = mutations["nuc"] ? mutations["nuc"] : [];
+
+  const genes = keys.filter((key) => key !== "nuc");
+  const taxonium_muts = [];
+  nuc_muts.forEach((nuc_mut) => {
+    // input format is like "C123T", we want to break this into old_residue, position and new_residue
+    // use regex to match the position
+    const position = nuc_mut.match(/\d+/g);
+    const index_of_position = nuc_mut.indexOf(position[0]);
+    const previous_residue = nuc_mut.substring(0, index_of_position);
+    const new_residue = nuc_mut.substring(
+      index_of_position + position[0].length
+    );
+    const tax_format = {
+      type: "nt",
+      gene: "nt",
+      previous_residue,
+      new_residue,
+      residue_pos: parseInt(position[0]),
+    };
+    const jsonned = JSON.stringify(tax_format);
+    //console.log("jsonned", jsonned);
+    if (mutation_lookup[jsonned]) {
+      taxonium_muts.push(mutation_lookup[jsonned]);
+    } else {
+      unique_mutations.push({
+        ...tax_format,
+        mutation_id: unique_mutations.length,
+      });
+      const this_index = unique_mutations.length - 1;
+      mutation_lookup[jsonned] = this_index;
+      taxonium_muts.push(this_index);
+    }
+  });
+
+  genes.forEach((gene) => {
+    const gene_muts = mutations[gene];
+    gene_muts.forEach((gene_mut) => {
+      // input format is like "Q123F", we want to break this into old_residue, position and new_residue
+      // use regex to match the position
+      const position = gene_mut.match(/\d+/g);
+      const index_of_position = gene_mut.indexOf(position[0]);
+      const previous_residue = gene_mut.substring(0, index_of_position);
+      const new_residue = gene_mut.substring(
+        index_of_position + position[0].length
+      );
+      const tax_format = {
+        type: "aa",
+        gene,
+        previous_residue,
+        new_residue,
+        residue_pos: parseInt(position[0]),
+      };
+      const jsonned = JSON.stringify(tax_format);
+      //console.log("jsonned", jsonned);
+      if (mutation_lookup[jsonned]) {
+        taxonium_muts.push(mutation_lookup[jsonned]);
+      } else {
+        unique_mutations.push({
+          ...tax_format,
+          mutation_id: unique_mutations.length,
+        });
+        const this_index = unique_mutations.length - 1;
+        mutation_lookup[jsonned] = this_index;
+        taxonium_muts.push(this_index);
+      }
+    });
+  });
+
+  return taxonium_muts;
+};
+
 async function do_fetch(url, sendStatusMessage, whatIsBeingDownloaded) {
   if (!sendStatusMessage) {
     sendStatusMessage = () => {};
@@ -81,7 +160,7 @@ async function cleanup(tree) {
     const cleaned = {
       name: node.name.replace(/'/g, ""),
       parent_id: node.parent ? node.parent.node_id : node.node_id,
-      mutations: emptyList,
+      mutations: node.mutations ? node.mutations : emptyList,
       y: node.y,
       num_tips: node.num_tips,
       is_tip: node.child.length === 0,
@@ -129,7 +208,7 @@ async function cleanup(tree) {
   });
 }
 
-async function processJsTree(tree, data, sendStatusMessage) {
+async function processJsTree(tree, data, config, sendStatusMessage) {
   function assignNumTips(node) {
     if (node.child.length === 0) {
       node.num_tips = 1;
@@ -169,6 +248,7 @@ async function processJsTree(tree, data, sendStatusMessage) {
     tree.node.forEach((node) => {
       node.d = node.pre_x_dist;
     });
+
     kn_calxy(tree, true);
     // kn_calxy sets x -> move x to x_dist
     tree.node.forEach((node) => {
@@ -218,16 +298,22 @@ async function processJsTree(tree, data, sendStatusMessage) {
     node_to_mut: {},
     rootMutations: [],
     rootId: 0,
-    overwrite_config: { num_tips: total_tips },
+    overwrite_config: { ...config, num_tips: total_tips },
   };
+
   return output;
 }
 
 function json_preorder(root) {
+  let n_tips = 0;
   const parents = {};
   parents[root.name] = null;
   const path = [];
   const stack = [root];
+
+  const unique_mutations = [];
+
+  const mutation_lookup = {};
   while (stack.length > 0) {
     const nodeJson = stack.pop();
     let div = null;
@@ -238,14 +324,22 @@ function json_preorder(root) {
     if (nodeJson.node_attrs.num_date) {
       time = nodeJson.node_attrs.num_date.value;
     }
-
+    //console.log(nodeJson);
     // this is the node format for downstream processing
     const parsedNode = {
       name: nodeJson.name,
       child: [],
       meta: "",
       hl: false,
       hidden: false,
+      mutations:
+        nodeJson.branch_attrs && nodeJson.branch_attrs.mutations
+          ? nodeMutationsFromNextStrainToTaxonium(
+              nodeJson.branch_attrs.mutations,
+              unique_mutations,
+              mutation_lookup
+            )
+          : [],
     };
 
     // assign distance
@@ -273,15 +367,22 @@ function json_preorder(root) {
         parents[childJson.name] = parsedNode;
         stack.push(childJson);
       }
+    } else {
+      n_tips += 1;
     }
   }
-  return [path, parents];
+  return { path, parents, n_tips, unique_mutations };
 }
 
 async function json_to_tree(json) {
   const rootJson = json.tree;
-  const [preorder, parents] = json_preorder(rootJson);
-  let n_tips = 0;
+  const {
+    path: preorder,
+    parents,
+    n_tips,
+    unique_mutations,
+  } = json_preorder(rootJson);
+
   const nodes = [];
   let root;
   for (const node of preorder) {
@@ -303,32 +404,46 @@ async function json_to_tree(json) {
     nodes.push(node);
   }
 
-  return {
+  const jsTree = {
     // tree in jstree.js format
     node: nodes,
     error: 0,
     n_tips: n_tips,
     root: root,
   };
-}
 
-export async function processNextstrain(data, sendStatusMessage) {
-  console.log("got data", data);
-  let the_data;
+  const config = {};
+
+  console.log("META", json.meta);
+  config.title = json.meta.title;
+  console.log("META PROV", json.meta.data_provenance);
+  config.source =
+    json.meta.data_provenance.map((source) => source.name).join(" & ") +
+    " on " +
+    json.meta.updated +
+    " in a build maintained by " +
+    json.meta.maintainers.map((source) => source.name).join(" & ");
+  config.overlay = `<p>This is a tree generated from a <a href='//nextstrain.org'>NextStrain</a> JSON file, being visualised in Taxonium.</p>.`;
+  if (json.meta.build_url) {
+    config.overlay += `<p>The NextStrain build is available <a class='underline' href='${json.meta.build_url}'>here</a>.</p>`;
+  }
 
-  the_data = await fetch_or_extract(data, sendStatusMessage, "tree");
+  return { jsTree, config, unique_mutations };
+}
 
-  console.log("the_data", the_data);
+export async function processNextstrain(data, sendStatusMessage) {
+  const the_data = await fetch_or_extract(data, sendStatusMessage, "tree");
 
   sendStatusMessage({
     message: "Parsing NS file",
   });
 
-  const input_string = the_data;
-
-  const jsTree = await json_to_tree(JSON.parse(input_string));
+  const { jsTree, config, unique_mutations } = await json_to_tree(
+    JSON.parse(the_data)
+  );
 
-  const output = await processJsTree(jsTree, data, sendStatusMessage);
+  const output = await processJsTree(jsTree, data, config, sendStatusMessage);
+  const node_to_mut = output.nodes.map((x) => x.mutations);
 
-  return output;
+  return { ...output, mutations: unique_mutations, node_to_mut: node_to_mut };
 }

taxonium_web_client/src/webworkers/localBackendWorker.js

@@ -333,7 +333,6 @@ onmessage = async (event) => {
   //Process uploaded data:
   console.log("Worker onmessage");
   const { data } = event;
-  console.log(data, "data");
   if (
     data.type === "upload" &&
     data.data &&
@@ -360,8 +359,6 @@ onmessage = async (event) => {
     data.data.filename &&
     data.data.filetype === "nextstrain"
   ) {
-    console.log("got nextstrain file", data.data);
-
     processedUploadedData = await processNextstrain(
       data.data,
       sendStatusMessage