diff --git a/.all-contributorsrc b/.all-contributorsrc
index 7a3ba708..ef7e1780 100644
--- a/.all-contributorsrc
+++ b/.all-contributorsrc
@@ -77,7 +77,6 @@
"infra"
]
}
-
],
"contributorsPerLine": 7,
"projectName": "taxonium",
diff --git a/taxonium_web_client/src/Taxonium.jsx b/taxonium_web_client/src/Taxonium.jsx
index b0d86f62..f5e2f5c3 100644
--- a/taxonium_web_client/src/Taxonium.jsx
+++ b/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");
}
}
diff --git a/taxonium_web_client/src/hooks/useInputHelper.js b/taxonium_web_client/src/hooks/useInputHelper.js
index 43dadfa1..9c1d8ea2 100644
--- a/taxonium_web_client/src/hooks/useInputHelper.js
+++ b/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) {
diff --git a/taxonium_web_client/src/utils/processNewick.js b/taxonium_web_client/src/utils/processNewick.js
index b1598ece..227291b9 100644
--- a/taxonium_web_client/src/utils/processNewick.js
+++ b/taxonium_web_client/src/utils/processNewick.js
@@ -98,7 +98,6 @@ 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;
@@ -106,7 +105,6 @@ async function cleanup(tree) {
}
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;
}
diff --git a/taxonium_web_client/src/utils/processNextstrain.js b/taxonium_web_client/src/utils/processNextstrain.js
index 265677c8..6434cd3c 100644
--- a/taxonium_web_client/src/utils/processNextstrain.js
+++ b/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;
@@ -238,7 +324,7 @@ 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,
@@ -246,6 +332,14 @@ function json_preorder(root) {
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 = `This is a tree generated from a NextStrain JSON file, being visualised in Taxonium.
.`;
+ if (json.meta.build_url) {
+ config.overlay += `The NextStrain build is available here.
`;
+ }
- 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 };
}
diff --git a/taxonium_web_client/src/webworkers/localBackendWorker.js b/taxonium_web_client/src/webworkers/localBackendWorker.js
index 9a179d18..0c488594 100644
--- a/taxonium_web_client/src/webworkers/localBackendWorker.js
+++ b/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