nextstrain json download works (loads in auspice.us) with dist/metada…

…ta/mutations
theosanderson · Jul 29, 2022 · 7c5a000 · 7c5a000
1 parent 2923de5
commit 7c5a000
Show file tree

Hide file tree

Showing 5 changed files with 76 additions and 12 deletions.
diff --git a/taxonium_data_handling/exporting.js b/taxonium_data_handling/exporting.js
@@ -1,5 +1,9 @@
 // can be called by local or server backend
-export const getNextstrainSubtreeJson = async (subtree_root_id, nodes) => {
+export const getNextstrainSubtreeJson = async (
+  subtree_root_id,
+  nodes,
+  config
+) => {
   const subtree_root = nodes.find((node) => node.node_id === subtree_root_id);
 
   const childMap = {};
@@ -15,49 +19,105 @@ export const getNextstrainSubtreeJson = async (subtree_root_id, nodes) => {
     }
   }
 
+  let muts = subtree_root.mutations.map((m) => config.mutations[m]);
+  const nucMuts = muts.filter((m) => m.type === "nt");
+  const aaMuts = muts.filter((m) => m.type === "aa");
+
   const treeJson = {
     name: subtree_root.name,
     node_id: subtree_root.node_id,
-    node_attrs: {},
+    node_attrs: { div: 0 },
+    branch_attrs: {
+      mutations: {
+        nuc: nucMuts.map(
+          (m) => `${m.previous_residue}${m.residue_pos}${m.new_residue}`
+        ),
+      },
+    },
   };
+  const alreadyIn = [];
+  aaMuts.forEach((m) => {
+    if (alreadyIn.includes(m.gene)) {
+      treeJson.branch_attrs.mutations[m.gene].push(
+        `${m.previous_residue}${m.residue_pos}${m.new_residue}`
+      );
+    } else {
+      treeJson.branch_attrs.mutations[m.gene] = [
+        `${m.previous_residue}${m.residue_pos}${m.new_residue}`,
+      ];
+      alreadyIn.push(m.gene);
+    }
+  });
+
   Object.keys(subtree_root)
     .filter((v) => v.startsWith("meta_"))
     .map((v) => ({ [v.slice(5)]: { value: subtree_root[v] } }))
-    .forEach((v) => Object.assign(treeJson.node_attrs, v));
+    .forEach((v) => {
+      Object.assign(treeJson.node_attrs, v);
+    });
 
   const stack = [treeJson];
+  const metadataSet = new Set();
 
   while (stack.length > 0) {
     const currNodeJson = stack.pop();
+    const currNodeDiv = currNodeJson.node_attrs.div;
     const children = childMap[currNodeJson.node_id];
     const childrenJson = [];
     if (children !== undefined) {
       for (const child_id of children) {
         const child_node = lookup[child_id];
+        let muts = child_node.mutations.map((m) => config.mutations[m]);
+        const nucMuts = muts.filter((m) => m.type === "nt");
+        const aaMuts = muts.filter((m) => m.type === "aa");
+        console.log(nucMuts, aaMuts);
+        const nucMutsNoAmb = nucMuts.filter(
+          (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
+        // many thousands of ambiguous mutations which throws off display
         const childJson = {
           name: child_node.name,
           node_id: child_node.node_id,
-          node_attrs: {},
+          node_attrs: {
+            div: currNodeDiv + nucMutsNoAmb.length,
+          },
+          branch_attrs: {},
         };
 
         // TODO add div key for genetic distance
 
         Object.keys(child_node)
           .filter((v) => v.startsWith("meta_"))
           .map((v) => ({ [v.slice(5)]: { value: child_node[v] } }))
-          .forEach((v) => Object.assign(childJson.node_attrs, v));
-
+          .forEach((v) => {
+            metadataSet.add(Object.keys(v)[0]);
+            Object.assign(childJson.node_attrs, v);
+          });
         childrenJson.push(childJson);
         stack.push(childJson);
       }
     }
-    currNodeJson.children = childrenJson;
+    if (childrenJson.length > 0) {
+      currNodeJson.children = childrenJson;
+    }
   }
   let json = {
     meta: {
       description: "JSON exported from Taxonium.",
       panels: ["tree"],
-      title: "Taxonium JSON",
+      title: config.title,
+      description: "Source: " + config.source,
+      display_defaults: {
+        distance_measure: "div",
+        color_by: metadataSet[0],
+      },
+      colorings: Array.from(metadataSet).map((v) => ({
+        key: v,
+        title: v,
+        type: "categorical",
+      })),
     },
     tree: treeJson,
     version: "v2",

diff --git a/taxonium_web_client/src/Taxonium.jsx b/taxonium_web_client/src/Taxonium.jsx
@@ -56,6 +56,9 @@ function Taxonium({
   }, [config.colorMapping]);
   const colorHook = useColor(colorMapping);
 
+  //TODO: this is always true for now
+  config.enable_ns_download = true;
+
   const xType = query.xType;
   const setxType = useCallback(
     (xType) => {

diff --git a/taxonium_web_client/src/components/SearchPanel.jsx b/taxonium_web_client/src/components/SearchPanel.jsx
@@ -65,8 +65,7 @@ function SearchPanel({
   const handleDownloadJson = () => {
     if (selectedDetails.nodeDetails) {
       const node_id = selectedDetails.nodeDetails.node_id;
-      console.log("json for node", selectedDetails.nodeDetails);
-      backend.getNextstrainJson(node_id);
+      backend.getNextstrainJson(node_id, config);
     }
   };
 

diff --git a/taxonium_web_client/src/hooks/useLocalBackend.js b/taxonium_web_client/src/hooks/useLocalBackend.js
@@ -190,11 +190,12 @@ function useLocalBackend(uploaded_data, proto) {
     };
   }, []);
 
-  const getNextstrainJson = useCallback((nodeId) => {
+  const getNextstrainJson = useCallback((nodeId, config) => {
     console.log("getNextstrainJson", nodeId);
     worker.postMessage({
       type: "nextstrain",
       node_id: nodeId,
+      config: config,
     });
   }, []);
 

diff --git a/taxonium_web_client/src/webworkers/localBackendWorker.js b/taxonium_web_client/src/webworkers/localBackendWorker.js
@@ -396,7 +396,8 @@ onmessage = async (event) => {
     if (data.type === "nextstrain") {
       const result = await getNextstrainSubtreeJson(
         data.node_id,
-        processedUploadedData.nodes
+        processedUploadedData.nodes,
+        data.config
       );
       postMessage({ type: "nextstrain", data: result });
     }