reorganise files

.eslintrc

@@ -16,6 +16,7 @@ rules:
   dot-notation: off # allows someObject["a"] as well as someObject.a
   comma-dangle: ["error", "never"]
   padded-blocks: off
+  no-plusplus: off # we are old enought to use i++
   arrow-body-style: off
   arrow-parens: ["error", "always"] # use brackets always, (a) => body // () => body // (a, b) => body
   no-case-declarations: off # we don't surround case blocks with { } in our switch statements as we use fallthroughs deliberately

src/actions/colors.js

@@ -1,6 +1,6 @@
 import { parseGenotype } from "../util/getGenotype";
 import getColorScale from "../util/getColorScale";
-import { calcNodeColor } from "../util/treeHelpers";
+import { calcNodeColor } from "../components/tree/treeHelpers";
 import * as types from "./types";
 
 export const updateColors = function (providedColorBy = undefined) {

src/actions/filesDropped.js

@@ -1,8 +1,7 @@
-/*eslint max-len: 0*/
-import { infoNotification, errorNotification, successNotification, warningNotification } from "./notifications";
 import Papa from "papaparse";
+import { errorNotification, successNotification, warningNotification } from "./notifications";
 import { ADD_COLOR_BYS } from "./types";
-import { turnAttrsIntoHeaderArray } from "../util/downloadDataFunctions";
+import { turnAttrsIntoHeaderArray } from "../components/download/helperFunctions";
 
 const csvCompleteCallback = (dispatch, getState, results, file) => {
   const { tree } = getState();

src/actions/treeProperties.js

@@ -2,7 +2,7 @@ import { calcVisibility,
   calcTipRadii,
   calcTipCounts,
   identifyPathToTip,
-  calcBranchThickness } from "../util/treeHelpers";
+  calcBranchThickness } from "../components/tree/treeHelpers";
 import * as types from "./types";
 
 const calculateVisiblityAndBranchThickness = (tree, controls, dates, {idxOfInViewRootNode = 0, tipSelectedIdx = 0} = {}) => {

src/components/app.js

@@ -15,7 +15,7 @@ import TreeView from "./tree/treeView";
 import { controlsHiddenWidth } from "../util/globals";
 import TitleBar from "./framework/title-bar";
 import Footer from "./framework/footer";
-import DownloadModal from "./controls/downloadModal";
+import DownloadModal from "./download/downloadModal";
 import { analyticsNewPage } from "../util/googleAnalytics";
 import filesDropped from "../actions/filesDropped";
 

src/components/controls/downloadModal.js → src/components/download/downloadModal.js

@@ -5,32 +5,9 @@ import { DISMISS_DOWNLOAD_MODAL } from "../../actions/types";
 import { materialButton, medGrey, infoPanelStyles } from "../../globalStyles";
 import { stopProp } from "../tree/tipSelectedPanel";
 import { authorString, formatURLString } from "../../util/stringHelpers";
-import * as download from "../../util/downloadDataFunctions";
+import * as helpers from "./helperFunctions";
 import * as icons from "../framework/svg-icons";
 
-export const isPaperURLValid = (d) => {
-  return (
-    Object.prototype.hasOwnProperty.call(d, "paper_url") &&
-    !d.paper_url.endsWith('/') &&
-    d.paper_url !== "?"
-  );
-};
-
-export const getAuthor = (info, k) => {
-  if (info === undefined || k === undefined) {
-    return (
-      <span>Not Available</span>
-    );
-  }
-  if (isPaperURLValid(info[k])) {
-    return (
-      <a href={formatURLString(info[k].paper_url)} target="_blank">
-        {authorString(k)}
-      </a>
-    );
-  }
-  return authorString(k);
-};
 
 @connect((state) => ({
   browserDimensions: state.browserDimensions.browserDimensions,
@@ -99,11 +76,11 @@ class DownloadModal extends React.Component {
     const iconWidth = 25;
     const iconStroke = medGrey;
     const buttons = [
-      ["Tree (newick)", (<icons.RectangularTree width={iconWidth} stroke={iconStroke} />), () => download.newick(this.props.dispatch, dataset, this.props.tree.nodes[0], false)],
-      ["TimeTree (newick)", (<icons.RectangularTree width={iconWidth} stroke={iconStroke} />), () => download.newick(this.props.dispatch, dataset, this.props.tree.nodes[0], true)],
-      ["Strain Metadata (CSV)", (<icons.Meta width={iconWidth} stroke={iconStroke} />), () => download.strainCSV(this.props.dispatch, dataset, this.props.tree.nodes, this.props.tree.attrs)],
-      ["Author Metadata (CSV)", (<icons.Meta width={iconWidth} stroke={iconStroke} />), () => download.authorCSV(this.props.dispatch, dataset, this.props.metadata.metadata)],
-      ["Screenshot (SGV)", (<icons.Panels width={iconWidth} stroke={iconStroke} />), () => download.SVG(this.props.dispatch, dataset)]
+      ["Tree (newick)", (<icons.RectangularTree width={iconWidth} stroke={iconStroke} />), () => helpers.newick(this.props.dispatch, dataset, this.props.tree.nodes[0], false)],
+      ["TimeTree (newick)", (<icons.RectangularTree width={iconWidth} stroke={iconStroke} />), () => helpers.newick(this.props.dispatch, dataset, this.props.tree.nodes[0], true)],
+      ["Strain Metadata (CSV)", (<icons.Meta width={iconWidth} stroke={iconStroke} />), () => helpers.strainCSV(this.props.dispatch, dataset, this.props.tree.nodes, this.props.tree.attrs)],
+      ["Author Metadata (CSV)", (<icons.Meta width={iconWidth} stroke={iconStroke} />), () => helpers.authorCSV(this.props.dispatch, dataset, this.props.metadata.metadata)],
+      ["Screenshot (SGV)", (<icons.Panels width={iconWidth} stroke={iconStroke} />), () => helpers.SVG(this.props.dispatch, dataset)]
     ];
     return (
       <div className="row">
@@ -151,7 +128,7 @@ class DownloadModal extends React.Component {
                 return meta.author_info[a].n > meta.author_info[b].n ? -1 : 1;
               }).map((k) => (
                 <span key={k}>
-                  {getAuthor(meta.author_info, k)}
+                  {helpers.getAuthor(meta.author_info, k)}
                   {" (n = " + meta.author_info[k].n + "), "}
                 </span>
               ))}

src/util/downloadDataFunctions.js → src/components/download/helperFunctions.js

@@ -1,7 +1,31 @@
 /* eslint no-restricted-syntax: 0 */
-import { infoNotification, errorNotification, successNotification, warningNotification } from "../actions/notifications";
-import { prettyString, formatURLString } from "./stringHelpers";
-import { isPaperURLValid } from "../components/controls/downloadModal";
+import React from "react";
+import { infoNotification, errorNotification, successNotification, warningNotification } from "../../actions/notifications";
+import { prettyString, formatURLString, authorString } from "../../util/stringHelpers";
+
+export const isPaperURLValid = (d) => {
+  return (
+    Object.prototype.hasOwnProperty.call(d, "paper_url") &&
+    !d.paper_url.endsWith('/') &&
+    d.paper_url !== "?"
+  );
+};
+
+export const getAuthor = (info, k) => {
+  if (info === undefined || k === undefined) {
+    return (
+      <span>Not Available</span>
+    );
+  }
+  if (isPaperURLValid(info[k])) {
+    return (
+      <a href={formatURLString(info[k].paper_url)} target="_blank">
+        {authorString(k)}
+      </a>
+    );
+  }
+  return authorString(k);
+};
 
 /* this function based on https://github.com/daviddao/biojs-io-newick/blob/master/src/newick.js */
 const treeToNewick = (root, temporal) => {

src/components/map/map.js

@@ -8,18 +8,18 @@ import { select } from "d3-selection";
 import leafletImage from "leaflet-image";
 import Card from "../framework/card";
 import { numericToCalendar, calendarToNumeric } from "../../util/dateHelpers";
-import { drawDemesAndTransmissions, updateOnMoveEnd, updateVisibility } from "../../util/mapHelpers";
+import { drawDemesAndTransmissions, updateOnMoveEnd, updateVisibility } from "./mapHelpers";
 import { enableAnimationDisplay, animationWindowWidth, animationTick, twoColumnBreakpoint, enableAnimationPerfTesting } from "../../util/globals";
 import computeResponsive from "../../util/computeResponsive";
 import { modifyURLquery } from "../../util/urlHelpers";
 import {
   createDemeAndTransmissionData,
   updateDemeAndTransmissionDataColAndVis,
   updateDemeAndTransmissionDataLatLong
-} from "../../util/mapHelpersLatLong";
+} from "./mapHelpersLatLong";
 import { changeDateFilter } from "../../actions/treeProperties";
 import { MAP_ANIMATION_PLAY_PAUSE_BUTTON } from "../../actions/types";
-import { incommingMapPNG } from "../../util/downloadDataFunctions";
+import { incommingMapPNG } from "../download/helperFunctions";
 
 /* global L */
 // L is global in scope and placed by leaflet()

src/util/mapHelpersLatLong.js → src/components/map/mapHelpersLatLong.js

@@ -2,7 +2,7 @@ import _forOwn from "lodash/forOwn";
 import _map from "lodash/map";
 import _minBy from "lodash/minBy";
 import { interpolateNumber } from "d3-interpolate";
-import { averageColors } from "./colorHelpers";
+import { averageColors } from "../../util/colorHelpers";
 import { computeMidpoint, Bezier } from "./transmissionBezier";
 
 /* global L */