higlass 1.12.1 → 1.12.3

package/app/scripts/BedLikeTrack.js

@@ -5,6 +5,7 @@ import classifyPoint from 'robust-point-in-polygon';
 import { zoomIdentity } from 'd3-zoom';
 
 import HorizontalTiled1DPixiTrack from './HorizontalTiled1DPixiTrack';
+import trackUtils from './track-utils';
 
 // Services
 import { tileProxy } from './services';
@@ -13,7 +14,6 @@ import {
   colorDomainToRgbaArray,
   colorToHex,
   segmentsToRows,
-  trackUtils,
   valueToColor,
 } from './utils';
 

package/app/scripts/CenterTrack.jsx

@@ -8,10 +8,7 @@ import clsx from 'clsx';
 import TrackControl from './TrackControl';
 
 // Utils
-import { or, resetD3BrushStyle } from './utils';
-
-// Configs
-import { IS_TRACK_RANGE_SELECTABLE } from './configs';
+import { or, resetD3BrushStyle, IS_TRACK_RANGE_SELECTABLE } from './utils';
 
 // Styles
 import styles from '../styles/CenterTrack.module.scss'; // eslint-disable-line no-unused-vars

package/app/scripts/ConfigViewMenu.jsx

@@ -9,7 +9,8 @@ import NestedContextMenu from './NestedContextMenu';
 // Styles
 import classes from '../styles/ContextMenu.module.scss';
 
-import { OPTIONS_INFO, THEME_DARK } from './configs';
+import { THEME_DARK } from './configs';
+import OPTIONS_INFO from './options-info';
 
 class ConfigViewMenu extends ContextMenuContainer {
   constructor(props) {

package/app/scripts/GenomePositionSearchBox.jsx

@@ -795,11 +795,7 @@ class GenomePositionSearchBox extends React.Component {
             className={styles['genome-position-search-bar-button']}
             id={this.uid}
             onChange={this.handleAssemblySelectEvt.bind(this)}
-            title={
-              this.state.selectedAssembly
-                ? this.state.selectedAssembly
-                : '(none)'
-            }
+            value={this.state.selectedAssembly || undefined}
           >
             {assemblyMenuItems}
           </select>
@@ -839,7 +835,11 @@ class GenomePositionSearchBox extends React.Component {
             </div>
           )}
           renderMenu={this.handleRenderMenu.bind(this)}
-          value={this.positionText}
+          value={
+            this.state.selectedAssembly
+              ? this.positionText
+              : 'No valid assembly selected'
+          }
           wrapperStyle={{ width: '100%' }}
         />
 

package/app/scripts/HeatmapTiledPixiTrack.js

@@ -23,9 +23,11 @@ import AxisPixi from './AxisPixi';
 // Services
 import { tileProxy } from './services';
 
-import { GLOBALS, HEATED_OBJECT_MAP } from './configs';
-
-import { NUM_PRECOMP_SUBSETS_PER_2D_TTILE } from './configs/dense-data-extrema-config';
+import {
+  GLOBALS,
+  HEATED_OBJECT_MAP,
+  NUM_PRECOMP_SUBSETS_PER_2D_TTILE,
+} from './configs';
 
 const COLORBAR_MAX_HEIGHT = 200;
 const COLORBAR_WIDTH = 10;

package/app/scripts/HorizontalGeneAnnotationsTrack.js

@@ -11,7 +11,8 @@ import HorizontalTiled1DPixiTrack from './HorizontalTiled1DPixiTrack';
 import { tileProxy } from './services';
 
 // Utils
-import { colorToHex, trackUtils } from './utils';
+import { colorToHex } from './utils';
+import trackUtils from './track-utils';
 
 // these are default values that are overwritten by the track's options
 const FONT_SIZE = 11;

package/app/scripts/HorizontalTiledPlot.jsx

@@ -10,10 +10,7 @@ import HorizontalItem from './HorizontalItem';
 import SortableList from './SortableList';
 
 // Utils
-import { or, resetD3BrushStyle, sum } from './utils';
-
-// Configs
-import { IS_TRACK_RANGE_SELECTABLE } from './configs';
+import { or, resetD3BrushStyle, sum, IS_TRACK_RANGE_SELECTABLE } from './utils';
 
 // Styles
 import styles from '../styles/HorizontalTiledPlot.module.scss'; // eslint-disable-line no-unused-vars

package/app/scripts/SearchField.js

@@ -1,6 +1,6 @@
 import { bisector } from 'd3-array';
 import { format } from 'd3-format';
-import absToChr from './utils/abs-to-chr';
+import { absToChr } from './utils';
 
 class SearchField {
   constructor(chromInfo) {

package/app/scripts/SeriesListMenu.jsx

@@ -6,7 +6,8 @@ import ContextMenuItem from './ContextMenuItem';
 import NestedContextMenu from './NestedContextMenu';
 
 // Configs
-import { OPTIONS_INFO, THEME_DARK, TRACKS_INFO_BY_TYPE } from './configs';
+import { THEME_DARK, TRACKS_INFO_BY_TYPE } from './configs';
+import OPTIONS_INFO from './options-info';
 
 // Styles
 import classes from '../styles/ContextMenu.module.scss';

package/app/scripts/TiledPixiTrack.js

@@ -2,7 +2,7 @@ import { scaleLinear, scaleLog, scaleQuantile } from 'd3-scale';
 import { median, range, ticks } from 'd3-array';
 import slugid from 'slugid';
 
-import DataFetcher from './DataFetcher';
+import { DataFetcher } from './data-fetchers';
 import PixiTrack from './PixiTrack';
 
 // Utils

package/app/scripts/TrackRenderer.jsx

@@ -61,7 +61,6 @@ import SVGTrack from './SVGTrack';
 
 // Higher-order components
 import withPubSub from './hocs/with-pub-sub';
-import getDataFetcher from './data-fetchers/get-data-fetcher';
 import withTheme from './hocs/with-theme';
 
 // Utils
@@ -74,16 +73,16 @@ import {
 } from './utils';
 
 // Configs
-import {
-  AVAILABLE_FOR_PLUGINS,
-  GLOBALS,
-  THEME_DARK,
-  TRACKS_INFO_BY_TYPE,
-} from './configs';
+import { GLOBALS, THEME_DARK, TRACKS_INFO_BY_TYPE } from './configs';
+
+// Plugins
+import { AVAILABLE_FOR_PLUGINS } from './plugins';
 
 // Styles
 import classes from '../styles/TrackRenderer.module.scss';
 
+const { getDataFetcher } = AVAILABLE_FOR_PLUGINS.dataFetchers;
+
 const SCROLL_TIMEOUT = 100;
 
 class TrackRenderer extends React.Component {

package/app/scripts/VerticalTiledPlot.jsx

@@ -12,10 +12,7 @@ import VerticalItem from './VerticalItem';
 import SortableList from './SortableList';
 
 // Utils
-import { or, resetD3BrushStyle, sum } from './utils';
-
-// Configs
-import { IS_TRACK_RANGE_SELECTABLE } from './configs';
+import { or, resetD3BrushStyle, sum, IS_TRACK_RANGE_SELECTABLE } from './utils';
 
 // Styles
 import styles from '../styles/VerticalTiledPlot.module.scss'; // eslint-disable-line no-unused-vars

package/app/scripts/configs/README.md

@@ -0,0 +1,3 @@
+# configs
+
+This folder contains constant values that determine the visual parameters and options of HiGlass tracks and views.

package/app/scripts/configs/available-track-types.js

@@ -1,4 +1,4 @@
-import { DATATYPE_TO_TRACK_TYPE } from '.';
+import { DATATYPE_TO_TRACK_TYPE } from './datatype-to-track-type';
 
 /**
  * Return a list of the available track types, given a set of data types

package/app/scripts/configs/datatype-to-track-type.js

@@ -1,4 +1,4 @@
-import { TRACKS_INFO } from '.';
+import { TRACKS_INFO } from './tracks-info';
 
 export const DATATYPE_TO_TRACK_TYPE = (orientation) => {
   const localDatatypeToTrackType = {};

package/app/scripts/configs/index.js

@@ -11,11 +11,12 @@ export { THEME_LIGHT, THEME_DARK, THEME_DEFAULT } from './themes';
 export { default as GLOBALS } from './globals';
 export { default as DATATYPE_TO_TRACK_TYPE } from './datatype-to-track-type';
 export { default as HEATED_OBJECT_MAP } from './colormaps';
-export { default as IS_TRACK_RANGE_SELECTABLE } from './is-track-range-selectable';
-export { default as OPTIONS_INFO } from './options-info';
 export { default as TRACKS_INFO } from './tracks-info';
 export { default as TRACKS_INFO_BY_TYPE } from './tracks-info-by-type';
 export { default as POSITIONS_BY_DATATYPE } from './positions-by-datatype';
 export { default as DEFAULT_TRACKS_FOR_DATATYPE } from './default-tracks-for-datatype';
-export { default as AVAILABLE_FOR_PLUGINS } from './available-for-plugins';
 export { default as AVAILABLE_TRACK_TYPES } from './available-track-types';
+export {
+  NUM_PRECOMP_SUBSETS_PER_1D_TTILE,
+  NUM_PRECOMP_SUBSETS_PER_2D_TTILE,
+} from './dense-data-extrema-config';

package/app/scripts/configs/positions-by-datatype.js

@@ -1,4 +1,4 @@
-import { TRACKS_INFO } from '.';
+import { TRACKS_INFO } from './tracks-info';
 
 export const POSITIONS_BY_DATATYPE = TRACKS_INFO.reduce(
   (positionsByDatatype, track) => {

package/app/scripts/configs/tracks-info-by-type.js

@@ -1,4 +1,4 @@
-import { TRACKS_INFO } from '.';
+import { TRACKS_INFO } from './tracks-info';
 
 export const TRACKS_INFO_BY_TYPE = TRACKS_INFO.reduce((tracksByType, track) => {
   tracksByType[track.type] = track;

package/app/scripts/{DataFetcher.js → data-fetchers/DataFetcher.js}

@@ -5,13 +5,12 @@ import {
   dictValues,
   minNonZero,
   maxNonZero,
-} from './utils';
-
-import DenseDataExtrema1D from './utils/DenseDataExtrema1D';
-import DenseDataExtrema2D from './utils/DenseDataExtrema2D';
+  DenseDataExtrema1D,
+  DenseDataExtrema2D,
+} from '../utils';
 
 // Services
-import { tileProxy } from './services';
+import { tileProxy } from '../services';
 
 export default class DataFetcher {
   constructor(dataConfig, pubSub) {

package/app/scripts/data-fetchers/README.md

@@ -0,0 +1,3 @@
+# data-fetchers
+
+This folder contains code related to HiGlass data fetchers.

package/app/scripts/data-fetchers/index.js

@@ -0,0 +1,3 @@
+export { default as DataFetcher } from './DataFetcher';
+export { default as GBKDataFetcher } from './genbank-fetcher';
+export { default as LocalDataFetcher } from './local-tile-fetcher';

package/app/scripts/data-fetchers/local-tile-fetcher.js

@@ -1,4 +1,4 @@
-import { tileResponseToData } from '../worker';
+import { tileResponseToData } from '../services';
 
 class LocalTileDataFetcher {
   constructor(dataConfig) {

package/app/scripts/hglib.jsx

@@ -29,8 +29,9 @@ export {
   waitForTilesLoaded,
   waitForTransitionsFinished,
   mountHGComponent,
-  getTrackObjectFromHGC,
-} from './utils';
+} from './test-helpers';
+
+export { getTrackObjectFromHGC } from './utils';
 
 export { version } from '../../package.json';
 

package/app/scripts/hocs/with-modal.jsx

@@ -1,6 +1,6 @@
 import React from 'react';
 
-import toVoid from '../utils/to-void';
+import { toVoid } from '../utils';
 
 const { Provider, Consumer } = React.createContext({
   close: toVoid,

package/app/scripts/hocs/with-pub-sub.jsx

@@ -1,6 +1,6 @@
 import React from 'react';
 
-import toVoid from '../utils/to-void';
+import { toVoid } from '../utils';
 
 const fake = {
   __fake__: true,

package/app/scripts/hocs/with-theme.jsx

@@ -1,6 +1,6 @@
 import React from 'react';
 
-import toVoid from '../utils/to-void';
+import { toVoid } from '../utils';
 
 const { Provider, Consumer } = React.createContext({
   close: toVoid,

package/app/scripts/{configs/options-info.js → options-info.js}

@@ -1,6 +1,10 @@
+// A better position of this file would be under \configs,
+// but this file imports HeatmapOptions that contains React
+// components, so having this file near track implementations
+
 import { formatPrefix, precisionPrefix } from 'd3-format';
 
-import HeatmapOptions from '../HeatmapOptions';
+import HeatmapOptions from './HeatmapOptions';
 
 const valueColumnOptions = (track) => {
   if (!track.header) return [];
@@ -59,7 +63,7 @@ const OPACITY_OPTIONS_NO_ZERO = sizesInPx([0.2, 0.4, 0.6, 0.8, 1.0], '%', 100);
 
 // these values define the options that are visible in the track config
 // menu
-export const OPTIONS_INFO = {
+const OPTIONS_INFO = {
   axisLabelFormatting: {
     name: 'Axis Label Formatting',
     inlineOptions: {

package/app/scripts/plugins/README.md

@@ -0,0 +1,3 @@
+# plugins
+
+This folder contains code that are used by plugin tracks and data fetchers.

package/app/scripts/{configs → plugins}/available-for-plugins.js

@@ -22,7 +22,7 @@ import slugid from 'slugid';
 import { mix } from '../mixwith';
 
 // Configs
-import * as configs from '.';
+import * as configs from '../configs';
 
 // Utils
 import * as utils from '../utils';
@@ -81,8 +81,7 @@ import ViewportTrackerVertical from '../ViewportTrackerVertical';
 
 // Factories
 import ContextMenuItem from '../ContextMenuItem';
-import DataFetcher from '../DataFetcher';
-import LruCache from '../factories/LruCache';
+import LruCache from '../utils/LruCache';
 
 // Services
 import * as services from '../services';
@@ -92,9 +91,12 @@ import ChromosomeInfo from '../ChromosomeInfo';
 import SearchField from '../SearchField';
 
 // Data Fetchers
-import GBKDataFetcher from '../data-fetchers/genbank-fetcher';
-import LocalDataFetcher from '../data-fetchers/local-tile-fetcher';
-import getDataFetcher from '../data-fetchers/get-data-fetcher';
+import {
+  DataFetcher,
+  GBKDataFetcher,
+  LocalDataFetcher,
+} from '../data-fetchers';
+import getDataFetcher from './get-data-fetcher';
 
 import { version } from '../../../package.json';
 

package/app/scripts/{data-fetchers → plugins}/get-data-fetcher.js

@@ -1,7 +1,10 @@
-import GBKDataFetcher from './genbank-fetcher';
-import LocalDataFetcher from './local-tile-fetcher';
-import DataFetcher from '../DataFetcher';
-import { AVAILABLE_FOR_PLUGINS } from '../configs';
+import {
+  DataFetcher,
+  GBKDataFetcher,
+  LocalDataFetcher,
+} from '../data-fetchers';
+// TODO: we need to address this cyclic dependency
+import { AVAILABLE_FOR_PLUGINS } from '.';
 
 const getDataFetcher = (
   dataConfig,

package/app/scripts/plugins/index.js

@@ -0,0 +1,2 @@
+export { default as getDataFetcher } from './get-data-fetcher';
+export { default as AVAILABLE_FOR_PLUGINS } from './available-for-plugins';

package/app/scripts/services/README.md

@@ -0,0 +1 @@
+# services

package/app/scripts/services/element-resize-listener.js

@@ -1,4 +1,4 @@
-import getXylofon from '../utils/get-xylofon';
+import { getXylofon } from '../utils';
 
 let isInit = false;
 

package/app/scripts/services/index.js

@@ -8,3 +8,4 @@ export {
   getTileProxyAuthHeader,
   authHeader,
 } from './tile-proxy';
+export { tileResponseToData } from './worker';

package/app/scripts/services/tile-proxy.js

@@ -1,7 +1,7 @@
 import { range } from 'd3-array';
 import slugid from 'slugid';
 
-import { workerGetTiles, workerSetPix } from '../worker';
+import { workerGetTiles, workerSetPix } from './worker';
 
 import { trimTrailingSlash as tts, timeout as sleep } from '../utils';
 

package/app/scripts/{worker.js → services/worker.js}

@@ -1,8 +1,10 @@
 import { scaleLog, scaleLinear } from 'd3-scale';
-import getAggregationFunction from './utils/get-aggregation-function';
-import selectedItemsToSize from './utils/selected-items-to-size';
-import DenseDataExtrema1D from './utils/DenseDataExtrema1D';
-import DenseDataExtrema2D from './utils/DenseDataExtrema2D';
+import {
+  DenseDataExtrema1D,
+  DenseDataExtrema2D,
+  getAggregationFunction,
+  selectedItemsToSize,
+} from '../utils';
 
 /*
 function countTransform(count) {

package/app/scripts/test-helpers/README.md

@@ -0,0 +1,3 @@
+# test-helpers
+
+Several useful methods for running tests. In this project, these methods are only used in tests, but plugin tracks also make use of them, so not really extraneous.

package/app/scripts/test-helpers/index.js

@@ -0,0 +1,9 @@
+export {
+  changeOptions,
+  waitForJsonComplete,
+  waitForTilesLoaded,
+  waitForTransitionsFinished,
+  mountHGComponent,
+  mountHGComponentAsync,
+  removeHGComponent,
+} from './test-helpers';

package/app/scripts/{utils → test-helpers}/test-helpers.jsx

@@ -1,6 +1,3 @@
-// In this project, these methods are only used in tests,
-// but plugin tracks also make use of them... so not really extraneous.
-
 import React from 'react';
 import ReactDOM from 'react-dom';
 
@@ -9,10 +6,7 @@ import { mount } from 'enzyme';
 
 import { requestsInFlight } from '../services';
 
-import {
-  getTrackObjectFromHGC,
-  getTrackRenderer,
-} from './get-higlass-components';
+import { getTrackObjectFromHGC, getTrackRenderer } from '../utils';
 
 import HiGlassComponent from '../HiGlassComponent';
 

package/app/scripts/{utils/track-utils.js → track-utils.js}

@@ -1,5 +1,5 @@
 import { zoomIdentity } from 'd3-zoom';
-import AxisPixi from '../AxisPixi';
+import AxisPixi from './AxisPixi';
 
 /**
  * The d3.range and python range functinons. Returns

package/app/scripts/utils/DenseDataExtrema1D.js

@@ -1,4 +1,4 @@
-import { NUM_PRECOMP_SUBSETS_PER_1D_TTILE } from '../configs/dense-data-extrema-config';
+import { NUM_PRECOMP_SUBSETS_PER_1D_TTILE } from '../configs';
 
 class DenseDataExtrema1D {
   /**

package/app/scripts/utils/DenseDataExtrema2D.js

@@ -1,6 +1,6 @@
 import ndarray from 'ndarray';
 
-import { NUM_PRECOMP_SUBSETS_PER_2D_TTILE } from '../configs/dense-data-extrema-config';
+import { NUM_PRECOMP_SUBSETS_PER_2D_TTILE } from '../configs';
 
 class DenseDataExtrema2D {
   /**

package/app/scripts/utils/README.md

@@ -0,0 +1,3 @@
+# utils
+
+This folder contains helpful functions that are commonly used.

package/app/scripts/utils/color-to-hex.js

@@ -1,7 +1,7 @@
 import { color } from 'd3-color';
 
 // Configs
-import GLOBALS from '../configs/globals';
+import { GLOBALS } from '../configs';
 
 /**
  * Convert a regular color value (e.g. 'red', '#FF0000', 'rgb(255,0,0)') to a

package/app/scripts/utils/data-to-genomic-loci.js

@@ -1,4 +1,4 @@
-import { absToChr } from '.';
+import absToChr from './abs-to-chr';
 
 const dataToGenomicLoci = (x0, x1, chromInfo) => {
   const gX0 = absToChr(x0, chromInfo);

package/app/scripts/utils/genome-loci-to-pixels.js

@@ -1,4 +1,4 @@
-import { chrToAbs } from '.';
+import chrToAbs from './chr-to-abs';
 
 const genomeLociToPixels = (genomeLoci, chromInfo) => [
   chrToAbs(genomeLoci[0], genomeLoci[1], chromInfo),

package/app/scripts/utils/get-element-dim.js

@@ -1,4 +1,4 @@
-import ElementResizeListener from '../services/element-resize-listener';
+import { ElementResizeListener } from '../services';
 
 const getElementDim = (element) => {
   ElementResizeListener.listen();

package/app/scripts/utils/index.js

@@ -78,21 +78,14 @@ export { default as expandCombinedTracks } from './expand-combined-tracks';
 export { default as segmentsToRows } from './segments-to-rows';
 export { default as visitPositionedTracks } from './visit-positioned-tracks';
 export { default as visitTracks } from './visit-tracks';
-export { default as trackUtils } from './track-utils';
 export { default as DenseDataExtrema1D } from './DenseDataExtrema1D';
 export { default as DenseDataExtrema2D } from './DenseDataExtrema2D';
+export { default as getAggregationFunction } from './get-aggregation-function';
+export { default as selectedItemsToSize } from './selected-items-to-size';
+export { default as IS_TRACK_RANGE_SELECTABLE } from './is-track-range-selectable';
 
 export {
   getTrackObjectFromHGC,
   getTrackRenderer,
   getTiledPlot,
 } from './get-higlass-components';
-export {
-  changeOptions,
-  waitForJsonComplete,
-  waitForTilesLoaded,
-  waitForTransitionsFinished,
-  mountHGComponent,
-  mountHGComponentAsync,
-  removeHGComponent,
-} from './test-helpers';

package/app/scripts/{configs → utils}/is-track-range-selectable.js

@@ -1,4 +1,4 @@
-import { or } from '../utils';
+import or from './or';
 
 export const IS_TRACK_RANGE_SELECTABLE = (track) => {
   switch (track.type) {

package/app/scripts/utils/load-chrom-infos.js

@@ -1,6 +1,6 @@
 import { chromInfo } from '../services';
 
-import { objVals } from '.';
+import objVals from './obj-vals';
 
 const loadChromInfos = (views) =>
   objVals(views)

package/app/scripts/utils/obj-vals.js

@@ -1,4 +1,4 @@
-import { map } from '.';
+import map from './map';
 
 /**
  * Convert an object into array which entries are the prop values of the object

package/app/scripts/utils/show-mouse-position.js

@@ -1,6 +1,6 @@
 import { globalPubSub } from 'pub-sub-es';
 
-import { hexStrToInt } from '.';
+import hexStrToInt from './hex-string-to-int';
 
 // Configs
 import { GLOBALS } from '../configs';