From 0ca50a6934747ae74124c4703f5d390592782b6d Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Thu, 4 Aug 2022 14:48:45 +0000
Subject: [PATCH] updates

---
 docs/taxoniumtools.md                         |  2 -
 .../src/components/AboutOverlay.jsx           |  4 +-
 .../src/components/SearchPanel.jsx            | 64 +++++++++----------
 .../src/hooks/usePerNodeFunctions.js          | 15 ++++-
 4 files changed, 47 insertions(+), 38 deletions(-)

diff --git a/docs/taxoniumtools.md b/docs/taxoniumtools.md
index 5eb6912d..0179b85a 100644
--- a/docs/taxoniumtools.md
+++ b/docs/taxoniumtools.md
@@ -35,12 +35,10 @@ You can then open that `tfci-taxonium.jsonl.gz` file at [taxonium.org](http://ta
 Right now Taxoniumtools is limited in the types of genome annotations it can support, for SARS-CoV-2 we recommend using the exact [modified .gb file we use in the example](https://raw.githubusercontent.com/theosanderson/taxonium/master/taxoniumtools/test_data/hu1.gb), which splits ORF1ab into ORF1a and ORF1b to avoid the need to model ribosome slippage.
 ```
 
-
 ```{note}
 Some people ask what the "L" in JSONL is for. JSONL means "JSON Lines". Each line of the file is a separate JSON object. In the case of Taxonium JSONL format, the very first line contains a lot of metadata about the tree as a whole, and then each additional line contains information about a single node. It's important to use the "jsonl" extension instead of "json" as otherwise the interface may try to parse your tree as a NextStrain JSON file.
 ```
 
-
 ##### usher_to_taxonium
 
 ```{eval-rst}
diff --git a/taxonium_web_client/src/components/AboutOverlay.jsx b/taxonium_web_client/src/components/AboutOverlay.jsx
index 64f52bd8..70b81346 100644
--- a/taxonium_web_client/src/components/AboutOverlay.jsx
+++ b/taxonium_web_client/src/components/AboutOverlay.jsx
@@ -15,8 +15,8 @@ function AboutOverlay({ enabled, setEnabled, overlayContent }) {
         <div className="m-5">
           <h2 className="font-bold mb-3">Welcome to Taxonium</h2>
           <p className="mb-1">
-            Taxonium is a web application for exploring phylogenetic trees.
-            Find out more at our{" "}
+            Taxonium is a web application for exploring phylogenetic trees. Find
+            out more at our{" "}
             <a
               className="text-blue underline"
               href="https://github.com/theosanderson/taxodium"
diff --git a/taxonium_web_client/src/components/SearchPanel.jsx b/taxonium_web_client/src/components/SearchPanel.jsx
index 56a18b5e..de678a76 100644
--- a/taxonium_web_client/src/components/SearchPanel.jsx
+++ b/taxonium_web_client/src/components/SearchPanel.jsx
@@ -168,39 +168,39 @@ function SearchPanel({
                   </div>
 
                   {config.enable_ns_download &&
-                        selectedDetails.nodeDetails[key] < 1000000 &&  (
-                    <>
-                      <div className="mb-3">
-                        <Button className="" onClick={handleDownloadJson}>
-                          Download Nextstrain JSON
-                        </Button>
-                      </div>
+                    selectedDetails.nodeDetails[key] < 1000000 && (
+                      <>
+                        <div className="mb-3">
+                          <Button className="" onClick={handleDownloadJson}>
+                            Download Nextstrain JSON
+                          </Button>
+                        </div>
 
-                      {backend.type === "server" &&
-                        selectedDetails.nodeDetails[key] < 20000 && (
-                          <>
-                            <div className="mb-3">
-                              <Button
-                                className=""
-                                href={
-                                  "https://nextstrain.org/fetch/" +
-                                  backend
-                                    .getNextstrainJsonUrl(
-                                      selectedDetails.nodeDetails.node_id,
-                                      config
-                                    )
-                                    .replace("https://", "")
-                                    .replace("http://", "")
-                                }
-                                target="_blank"
-                              >
-                                View clade in Nextstrain
-                              </Button>
-                            </div>
-                          </>
-                        )}
-                    </>
-                  )}
+                        {backend.type === "server" &&
+                          selectedDetails.nodeDetails[key] < 20000 && (
+                            <>
+                              <div className="mb-3">
+                                <Button
+                                  className=""
+                                  href={
+                                    "https://nextstrain.org/fetch/" +
+                                    backend
+                                      .getNextstrainJsonUrl(
+                                        selectedDetails.nodeDetails.node_id,
+                                        config
+                                      )
+                                      .replace("https://", "")
+                                      .replace("http://", "")
+                                  }
+                                  target="_blank"
+                                >
+                                  View clade in Nextstrain
+                                </Button>
+                              </div>
+                            </>
+                          )}
+                      </>
+                    )}
 
                   {config.covspectrum_links && (
                     <div className="mb-3">
diff --git a/taxonium_web_client/src/hooks/usePerNodeFunctions.js b/taxonium_web_client/src/hooks/usePerNodeFunctions.js
index d351b98a..915cb0da 100644
--- a/taxonium_web_client/src/hooks/usePerNodeFunctions.js
+++ b/taxonium_web_client/src/hooks/usePerNodeFunctions.js
@@ -3,7 +3,18 @@ import { useMemo } from "react";
 function usePerNodeFunctions(data, config) {
   const getNodeGenotype = (node_id) => {
     console.log("data", data);
-    let cur_node = data.data.nodeLookup[node_id];
+
+    let data_to_use;
+    if (data.data.nodeLookup[node_id]) {
+      data_to_use = data.data;
+    } else if (data.base_data.nodeLookup[node_id]) {
+      data_to_use = data.base_data;
+    } else {
+      console.log("UNEXPECTED ERROR: node not found", node_id);
+      return null;
+    }
+    let cur_node = data_to_use.nodeLookup[node_id];
+
     const assembled_mutations = [];
 
     while (cur_node.parent_id !== cur_node.node_id) {
@@ -17,7 +28,7 @@ function usePerNodeFunctions(data, config) {
           )
       );
       assembled_mutations.push(...filtered_nt_mutations);
-      cur_node = data.data.nodeLookup[cur_node.parent_id];
+      cur_node = data_to_use.nodeLookup[cur_node.parent_id];
     }
     return assembled_mutations;
   };