nextstrain#1055: add selected metadata button; filter out unselected …

…nodes when metadata generated via this method

src/components/download/downloadModal.js

@@ -163,7 +163,8 @@ class DownloadModal extends React.Component {
     const buttons = [
       ["Tree (newick)", (<RectangularTreeIcon width={iconWidth} selected />), () => helpers.newick(this.props.dispatch, filePrefix, this.props.nodes[0], false)],
       ["TimeTree (newick)", (<RectangularTreeIcon width={iconWidth} selected />), () => helpers.newick(this.props.dispatch, filePrefix, this.props.nodes[0], true)],
-      ["Strain Metadata (TSV)", (<MetaIcon width={iconWidth} selected />), () => helpers.strainTSV(this.props.dispatch, filePrefix, this.props.nodes, this.props.metadata.colorings)]
+      ["All Metadata (TSV)", (<MetaIcon width={iconWidth} selected />), () => helpers.strainTSV(this.props.dispatch, filePrefix, this.props.nodes, this.props.metadata.colorings, false, null)],
+      ["Selected Metadata (TSV)", (<MetaIcon width={iconWidth} selected />), () => helpers.strainTSV(this.props.dispatch, filePrefix, this.props.nodes, this.props.metadata.colorings, true, this.props.tree.visibility)]
     ];
     if (helpers.areAuthorsPresent(this.props.tree)) {
       buttons.push(["Author Metadata (TSV)", (<MetaIcon width={iconWidth} selected />), () => helpers.authorTSV(this.props.dispatch, filePrefix, this.props.tree)]);

src/components/download/helperFunctions.js

@@ -3,6 +3,8 @@ import { infoNotification, warningNotification } from "../../actions/notificatio
 import { spaceBetweenTrees } from "../tree/tree";
 import { getTraitFromNode, getDivFromNode, getFullAuthorInfoFromNode, getVaccineFromNode, getAccessionFromNode } from "../../util/treeMiscHelpers";
 import { numericToCalendar } from "../../util/dateHelpers";
+import { NODE_VISIBLE } from "../../util/globals";
+import { calcVisiblity } from "../../util/treeVisibilityHelpers";
 
 export const isPaperURLValid = (d) => {
   return (
@@ -105,15 +107,20 @@ export const authorTSV = (dispatch, filePrefix, tree) => {
  * Create & write a TSV file where each row is a strain in the tree,
  * with the relevent information (accession, traits, etcetera)
  */
-export const strainTSV = (dispatch, filePrefix, nodes, colorings) => {
+export const strainTSV = (dispatch, filePrefix, nodes, colorings, selectedNodesOnly, nodeVisibilities) => {
 
   /* traverse the tree & store tip information. We cannot write this out as we go as we don't know
   exactly which header fields we want until the tree has been traversed. */
   const tipTraitValues = {};
   const headerFields = ["Strain"];
 
-  for (const node of nodes) {
+  for (const [i, node] of nodes.entries()) {
     if (node.hasChildren) continue; /* we only consider tips */
+
+    if (selectedNodesOnly && nodeVisibilities
+      && (nodeVisibilities[i] !== NODE_VISIBLE || !node.inView)) 
+        continue; /* skip unselected nodes if requested */
+
     tipTraitValues[node.name] = {Strain: node.name};
     if (!node.node_attrs) continue; /* if this is not set then we don't have any node info! */
 
@@ -189,6 +196,7 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings) => {
   }
 
   /* write out information we've collected */
+  // todo: filename for selected only
   const filename = `${filePrefix}_metadata.tsv`;
   write(filename, MIME.tsv, linesToWrite.join("\n"));
   dispatch(infoNotification({message: `Metadata exported to ${filename}`}));

src/util/treeVisibilityHelpers.js

@@ -131,7 +131,7 @@ FILTERS:
  - filters (in this code) is a list of filters to apply
    e.g. [{trait: "country", values: [...]}, ...]
 */
-const calcVisibility = (tree, controls, dates) => {
+export const calcVisibility = (tree, controls, dates) => {
   if (tree.nodes) {
     /* inView represents nodes that are within the current view window (i.e. not off the screen) */
     let inView;