Merge pull request #819 from nextstrain/include-strain-metadata-acces…

…sion

Correctly handle a strain's accession & url data

cli/server/convertJsonSchemas.js

@@ -305,8 +305,8 @@ const setNodeBranchAttrs = (v2) => {
   traverseTree(v2.tree, (node) => {
 
     if (node.attr) {
-      if (node.attr.url) node.url = node.node_attrs.url;
-      if (node.attr.accession) node.accession = node.node_attrs.accession;
+      if (node.attr.url) node.node_attrs.url = node.attr.url;
+      if (node.attr.accession) node.node_attrs.accession = node.attr.accession;
     }
 
 

src/components/download/helperFunctions.js

@@ -2,7 +2,7 @@
 import React from "react";
 import { infoNotification, warningNotification } from "../../actions/notifications";
 import { spaceBetweenTrees } from "../tree/tree";
-import { getTraitFromNode, getDivFromNode, getFullAuthorInfoFromNode, getVaccineFromNode } from "../../util/treeMiscHelpers";
+import { getTraitFromNode, getDivFromNode, getFullAuthorInfoFromNode, getVaccineFromNode, getAccessionFromNode } from "../../util/treeMiscHelpers";
 import { numericToCalendar } from "../../util/dateHelpers";
 
 export const isPaperURLValid = (d) => {
@@ -111,7 +111,7 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings) => {
 
     /* collect values (as writable strings) of the same "traits" as can be viewed by the modal displayed
     when clicking on tips. Note that "num_date", "author" and "vaccine" are considered seperately below */
-    const nodeAttrsToIgnore = ["author", "div", "num_date", "vaccine"];
+    const nodeAttrsToIgnore = ["author", "div", "num_date", "vaccine", "accession"];
     const traits = Object.keys(node.node_attrs).filter((k) => !nodeAttrsToIgnore.includes(k));
     for (const trait of traits) {
       if (!headerFields.includes(trait)) headerFields.push(trait);
@@ -156,6 +156,14 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings) => {
       if (!headerFields.includes(traitName)) headerFields.push(traitName);
       tipTraitValues[node.name][traitName] = vaccine.selection_date;
     }
+
+    /* handle `accession` specially */
+    const accession = getAccessionFromNode(node);
+    if (accession) {
+      const traitName = "Accession";
+      if (!headerFields.includes(traitName)) headerFields.push(traitName);
+      tipTraitValues[node.name][traitName] = accession;
+    }
   }
 
   /* turn the information into a string to be written */

src/components/tree/infoPanels/click.js

@@ -2,7 +2,7 @@ import React from "react";
 import { isValueValid } from "../../../util/globals";
 import { infoPanelStyles } from "../../../globalStyles";
 import { numericToCalendar } from "../../../util/dateHelpers";
-import { getTraitFromNode, getFullAuthorInfoFromNode, getVaccineFromNode } from "../../../util/treeMiscHelpers";
+import { getTraitFromNode, getFullAuthorInfoFromNode, getVaccineFromNode, getAccessionFromNode, getUrlFromNode } from "../../../util/treeMiscHelpers";
 
 export const styles = {
   container: {
@@ -51,8 +51,9 @@ const formatURL = (url) => {
 };
 
 const AccessionAndUrl = ({node}) => {
-  const accession = getTraitFromNode(node, "accession");
-  const url = getTraitFromNode(node, "url");
+  const accession = getAccessionFromNode(node);
+  const url = getUrlFromNode(node);
+
 
   if (isValueValid(accession) && isValueValid(url)) {
     return (
@@ -70,7 +71,7 @@ const AccessionAndUrl = ({node}) => {
   } else if (isValueValid(url)) {
     return (
       <tr>
-        <th style={infoPanelStyles.item}>URL</th>
+        <th style={infoPanelStyles.item}>Strain URL</th>
         <td style={infoPanelStyles.item}>
           <a href={formatURL(url)} target="_blank"><em>click here</em></a>
         </td>

src/util/treeMiscHelpers.js

@@ -1,6 +1,14 @@
-
 import { isValueValid } from "./globals";
 
+/* --- TO IMPROVE -----
+These "getter" functions for node-related data require knowledge of
+the semantics of how data is stored on a node. For instance, you need
+to know that `num_date` is stored in a different structure to `div`.
+This logic should be encapsulated within `getTraitFromNode` so we
+don't need separate `getDivFromNode` functions etc.
+james hadfield, nov 2019.
+*/
+
 /**
  * Given a coloring key or a geographic resolution key
  * (sometimes referred to as a "trait")
@@ -18,7 +26,6 @@ import { isValueValid } from "./globals";
  * which don't share the same structure as traits. See the JSON spec for more details.
  */
 export const getTraitFromNode = (node, trait, {entropy=false, confidence=false}={}) => {
-
   if (!node.node_attrs) return undefined;
 
   if (!entropy && !confidence) {
@@ -36,13 +43,15 @@ export const getTraitFromNode = (node, trait, {entropy=false, confidence=false}=
 };
 
 export const getDivFromNode = (node) => {
+  /* see comment at top of this file */
   if (node.node_attrs && node.node_attrs.div !== undefined) {
     return node.node_attrs.div;
   }
   return undefined;
 };
 
 export const getVaccineFromNode = (node) => {
+  /* see comment at top of this file */
   if (node.node_attrs && node.node_attrs.vaccine) {
     return node.node_attrs.vaccine;
   }
@@ -53,3 +62,15 @@ export const getFullAuthorInfoFromNode = (node) =>
   (node.node_attrs && node.node_attrs.author && node.node_attrs.author.value) ?
     node.node_attrs.author :
     undefined;
+
+export const getAccessionFromNode = (node) => {
+  /* see comment at top of this file */
+  if (node.node_attrs && node.node_attrs.accession) {
+    return node.node_attrs.accession;
+  }
+  return undefined;
+};
+
+/* see comment at top of this file */
+export const getUrlFromNode = (node) =>
+  (node.node_attrs && node.node_attrs.url) ? node.node_attrs.url : undefined;