Merge pull request #312 from theosanderson/nextstrain

Joint with @amkram (who did most of the heavy lifting)

.all-contributorsrc

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

taxonium_web_client/src/Taxonium.jsx

@@ -12,6 +12,8 @@ import { useMemo, useState } from "react";
 import useBackend from "./hooks/useBackend";
 import useConfig from "./hooks/useConfig";
 import { useSettings } from "./hooks/useSettings";
+import { useEffect } from "react";
+import { useCallback } from "react";
 
 const URL_ON_FAIL = window.location.hostname.includes(".epicov.org")
   ? "https://www.epicov.org/epi3/frontend"
@@ -54,13 +56,29 @@ function Taxonium({
   const colorHook = useColor(colorMapping);
 
   const xType = query.xType;
-  const setxType = (xType) => {
-    updateQuery({ xType });
-  };
+  const setxType = useCallback(
+    (xType) => {
+      updateQuery({ xType });
+    },
+    [updateQuery]
+  );
 
   const { data, boundsForQueries, isCurrentlyOutsideBounds } =
     useGetDynamicData(backend, colorBy, view.viewState, config, xType);
 
+  useEffect(() => {
+    // If there is no distance data, default to time
+    // 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.hasOwnProperty("x_dist")) {
+        setxType("x_time");
+      } else if (!n.hasOwnProperty("x_time")) {
+        setxType("x_dist");
+      }
+    }
+  }, [data.base_data, setxType]);
+
   const search = useSearch({
     data,
     config,

taxonium_web_client/src/components/InputSupplier.jsx

@@ -16,6 +16,8 @@ const prettyTypes = {
   nwk: "Newick tree",
   meta_tsv: "Metadata TSV",
   meta_csv: "Metadata CSV",
+  nextstrain: "Nextstrain JSON",
+  unknown: "Unknown (please select)",
 };
 const fileTypes = Object.keys(prettyTypes);
 

taxonium_web_client/src/hooks/useInputHelper.js

@@ -16,6 +16,7 @@ function guessType(file_object) {
   const file_extension = file_name.split(".").pop();
 
   const tree_extensions = ["nwk", "newick", "tree", "tre", "nh"];
+
   if (tree_extensions.includes(file_extension)) {
     return "nwk";
   }
@@ -27,11 +28,11 @@ function guessType(file_object) {
   }
   if (file_extension === "tsv") {
     return "meta_tsv";
+  }
+  if (file_extension === "json") {
+    return "nextstrain";
   } else {
-    window.alert(
-      "Alert: unrecognised file type, supported types: jsonl (taxonium), nwk (newick), csv, tsv"
-    );
-    return "jsonl";
+    return "unknown";
   }
 }
 
@@ -114,10 +115,14 @@ export const useInputHelper = ({
     if (inputs.filter((input) => input.filetype === "nwk").length > 1) {
       return ["invalid", "You can only use a single tree file"];
     }
+    if (inputs.some((input) => input.filetype === "unknown")) {
+      return ["invalid", "Please select the type of each file"];
+    }
     // must have a tree file or a jsonl
     if (
       inputs.filter((input) => input.filetype === "jsonl").length === 0 &&
-      inputs.filter((input) => input.filetype === "nwk").length === 0
+      inputs.filter((input) => input.filetype === "nwk").length === 0 &&
+      inputs.filter((input) => input.filetype === "nextstrain").length === 0
     ) {
       return [
         "invalid",
@@ -146,10 +151,13 @@ export const useInputHelper = ({
         const meta_file = inputs.find((input) =>
           input.filetype.startsWith("meta_")
         );
-        const tree_file = inputs.find((input) => input.filetype === "nwk");
+        const tree_file = inputs.find(
+          (input) => input.filetype === "nwk" || input.filetype === "nextstrain"
+        );
         const newQuery = {
           treeUrl: tree_file.name,
           ladderizeTree: tree_file.ladderize === true,
+          treeType: tree_file.filetype,
         };
         if (meta_file) {
           newQuery.metaUrl = meta_file.name;
@@ -181,7 +189,10 @@ export const useInputHelper = ({
       }
 
       // if there is a tree file find it
-      const tree_file = inputs.find((input) => input.filetype === "nwk");
+      const tree_file = inputs.find(
+        (input) => input.filetype === "nwk" || input.filetype === "nextstrain"
+      );
+
       upload_obj.filename = tree_file.name;
       upload_obj.data = tree_file.data;
       upload_obj.status =
@@ -221,7 +232,7 @@ export const useInputHelper = ({
         status: "url_supplied",
         filename: query.treeUrl,
         ladderize: query.ladderizeTree === "true",
-        filetype: "nwk",
+        filetype: query.treeType ? query.treeType : "nwk",
         ...extra,
       });
     }

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);
   }
@@ -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;
@@ -275,5 +268,6 @@ export async function processNewickAndMetadata(data, sendStatusMessage) {
       Object.assign(node, blanks);
     }
   });
+
   return tree;
 }