- {summary.map((d, i) =>
- (i + 1 !== summary.length ?
- {preambleText}
- {" A full list of sequence authors is available via the CSV files below."}
-
- {getAcknowledgments({})}
-
Data usage policy
- {dataUsage}
+ {summary.map((d, i) =>
+ (i + 1 !== summary.length ?
{`${d}, `} :
{`${d}. `})
+ )}
+
+ {" A full list of sequence authors is available via the TSV files below."}
+
+ {getAcknowledgments({}, {preamble: {fontWeight: 300}, acknowledgments: {fontWeight: 300}})}
-
The current data analysis relies on
- {this.relevantPublications()}
+
+ Data usage policy
+
+ {dataUsage.join(" ")}
+
+
+ Please cite the authors who contributed genomic data (where relevant), as well as:
+
+ {this.formatPublications(this.getRelevantPublications())}
-
Download data as
- {this.downloadButtons()}
-
- (click outside this box to return to the app)
-
-
+
+ Download data:
+ {this.downloadButtons()}
+
);
diff --git a/src/components/download/helperFunctions.js b/src/components/download/helperFunctions.js
index fa61eb35b..29f8f11f3 100644
--- a/src/components/download/helperFunctions.js
+++ b/src/components/download/helperFunctions.js
@@ -1,6 +1,6 @@
/* eslint no-restricted-syntax: 0 */
import React from "react";
-import { infoNotification, errorNotification, successNotification, warningNotification } from "../../actions/notifications";
+import { infoNotification, warningNotification } from "../../actions/notifications";
import { prettyString, formatURLString, authorString } from "../../util/stringHelpers";
export const isPaperURLValid = (d) => {
@@ -53,6 +53,7 @@ const treeToNewick = (root, temporal) => {
const MIME = {
text: "text/plain;charset=utf-8;",
csv: 'text/csv;charset=utf-8;',
+ tsv: `text/tab-separated-values;charset=utf-8;`,
svg: "image/svg+xml;charset=utf-8"
};
@@ -70,9 +71,9 @@ const write = (filename, type, content) => {
document.body.removeChild(link);
};
-export const authorCSV = (dispatch, filePrefix, metadata, tree) => {
- const lineArray = [["Author", "n (strains)", "publication title", "journal", "publication URL", "strains"]];
- const filename = filePrefix + "_authors.csv";
+export const authorTSV = (dispatch, filePrefix, metadata, tree) => {
+ const lineArray = [["Author", "n (strains)", "publication title", "journal", "publication URL", "strains"].join("\t")];
+ const filename = filePrefix + "_authors.tsv";
const authors = {};
tree.nodes.filter((n) => !n.hasChildren && n.attr.authors).forEach((n) => {
@@ -90,12 +91,12 @@ export const authorCSV = (dispatch, filePrefix, metadata, tree) => {
prettyString(metadata.author_info[author].title, {removeComma: true}),
prettyString(metadata.author_info[author].journal, {removeComma: true}),
isPaperURLValid(metadata.author_info[author]) ? formatURLString(metadata.author_info[author].paper_url) : "unknown",
- authors[author].join(" ")
+ authors[author].join(",")
]);
}
- body.forEach((line) => { lineArray.push(line.join(",")); });
- write(filename, MIME.csv, lineArray.join("\n"));
+ body.forEach((line) => { lineArray.push(line.join("\t")); });
+ write(filename, MIME.tsv, lineArray.join("\n"));
dispatch(infoNotification({message: "Author metadata exported", details: filename}));
};
@@ -103,9 +104,9 @@ export const turnAttrsIntoHeaderArray = (attrs) => {
return ["Strain"].concat(attrs.map((v) => prettyString(v)));
};
-export const strainCSV = (dispatch, filePrefix, nodes, rawAttrs) => {
+export const strainTSV = (dispatch, filePrefix, nodes, rawAttrs) => {
// dont need to traverse the tree - can just loop the nodes
- const filename = filePrefix + "_metadata.csv";
+ const filename = filePrefix + "_metadata.tsv";
const data = [];
const includeAttr = (v) => (!(v.includes("entropy") || v.includes("confidence") || v === "div" || v === "paper_url"));
const attrs = ["accession", "date", "region", "country", "division", "authors", "journal", "title", "url"];
@@ -157,104 +158,231 @@ export const strainCSV = (dispatch, filePrefix, nodes, rawAttrs) => {
}
data.push(line);
}
- const lineArray = [turnAttrsIntoHeaderArray(attrs)];
+ const lineArray = [turnAttrsIntoHeaderArray(attrs).join("\t")];
data.forEach((line) => {
- const lineString = line.join(",");
+ const lineString = line.join("\t");
lineArray.push(lineString);
});
- const csvContent = lineArray.join("\n");
- write(filename, MIME.csv, csvContent);
+ const tsvContent = lineArray.join("\n");
+ write(filename, MIME.tsv, tsvContent);
dispatch(infoNotification({message: "Metadata exported to " + filename}));
};
export const newick = (dispatch, filePrefix, root, temporal) => {
- const fName = temporal ? filePrefix + "_timetree.new" : filePrefix + "_tree.new";
+ const fName = temporal ? filePrefix + "_timetree.nwk" : filePrefix + "_tree.nwk";
const message = temporal ? "TimeTree" : "Tree";
write(fName, MIME.text, treeToNewick(root, temporal));
dispatch(infoNotification({message: message + " written to " + fName}));
};
-export const incommingMapPNG = (data) => {
- let svg = '';
- svg += `
";
- write(data.fileName, "image/svg", svg);
+const processXMLString = (input) => {
+ /* split into bounding
(or ');
+/* take the panels (see processXMLString for struct) and calculate the overall size of the SVG
+as well as the offsets (x, y) to position panels appropriately within this */
+const createBoundingDimensionsAndPositionPanels = (panels, panelLayout, numLinesOfText) => {
+ const padding = 50;
+ let width = 0;
+ let height = 0;
+ if (panels.tree && panels.mapD3 && panels.mapTiles) {
+ if (panelLayout === "grid") {
+ width = panels.tree.width + padding + panels.mapTiles.width;
+ height = Math.max(panels.tree.height, panels.mapTiles.height);
+ panels.mapD3.x = panels.tree.width + padding;
+ } else {
+ width = Math.max(panels.tree.width, panels.mapTiles.width);
+ height = panels.tree.height + padding + panels.mapTiles.height;
+ panels.mapD3.y = panels.tree.height + padding;
+ }
+ panels.mapTiles.x = panels.mapD3.x;
+ panels.mapTiles.y = panels.mapD3.y;
+ } else if (panels.tree) {
+ width = panels.tree.width;
+ height = panels.tree.height;
+ } else if (panels.mapD3 && panels.mapTiles) {
+ width = panels.mapTiles.width;
+ height = panels.mapTiles.height;
}
- svgFixed = svgFixed.replace("cursor: pointer;", "");
- /* https://stackoverflow.com/questions/23218174/how-do-i-save-export-an-svg-file-after-creating-an-svg-with-d3-js-ie-safari-an */
- if (!svgFixed.match(/^]+xmlns="http\:\/\/www\.w3\.org\/2000\/svg"/)) {
- svgFixed = svgFixed.replace(/^
@@ -376,6 +382,6 @@ class Footer extends React.Component {
}
// {dot}
-// {this.downloadDataButton()}
+//
export default Footer;
diff --git a/src/components/frequencies/index.js b/src/components/frequencies/index.js
index 128d09fce..5cb3dd885 100644
--- a/src/components/frequencies/index.js
+++ b/src/components/frequencies/index.js
@@ -107,7 +107,7 @@ export class Frequencies extends React.Component {
fontSize: "14px"
}}
/>
-