From 359d855e11223a89aaa9233862a0be3309c0f7af Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Wed, 14 Oct 2020 21:17:42 +0200
Subject: [PATCH] bugfix: dataset retrieval on regionId basis
---
common/constants.js | 7 +
common/util.js | 6 +
deploy/datasets/index.js | 9 +-
deploy/datasets/query.js | 14 +-
deploy/datasets/util.js | 93 ++++++++++-
deploy/datasets/util.spec.js | 71 ++++++++-
e2e/src/util.js | 148 +++++++++++++++---
.../atlasLayerSelector.component.ts | 9 +-
.../atlasLayerSelector.template.html | 2 +-
.../databrowserModule/databrowser.service.ts | 25 ++-
.../databrowser/databrowser.base.ts | 8 +-
.../databrowser/databrowser.template.html | 3 +-
.../util/filterDataEntriesByRegion.pipe.ts | 19 ++-
.../nehubaContainer.component.ts | 3 +-
.../nehubaContainer.template.html | 8 +-
.../regionSearch/regionSearch.component.ts | 5 +-
.../regionSearch/regionSearch.template.html | 1 +
17 files changed, 375 insertions(+), 56 deletions(-)
diff --git a/common/constants.js b/common/constants.js
index 3c00fdf2c..d94ab3a30 100644
--- a/common/constants.js
+++ b/common/constants.js
@@ -17,6 +17,8 @@
DOWNLOAD_PREVIEW_CSV: `Download CSV`,
DATASET_FILE_PREVIEW: `Preview of dataset`,
PIN_DATASET: 'Toggle pinning dataset',
+ TEXT_INPUT_SEARCH_REGION: 'Search for any region of interest in the atlas selected',
+ CLEAR_SELECTED_REGION: 'Clear selected region',
// overlay/layout specific
SELECT_ATLAS: 'Select a different atlas',
@@ -29,6 +31,7 @@
SHOW_FULL_STATUS_PANEL: 'Show full status panel',
HIDE_FULL_STATUS_PANEL: 'Hide full status panel',
TOGGLE_SIDE_PANEL: 'Toggle side panel',
+ TOGGLE_ATLAS_LAYER_SELECTOR: 'Toggle atlas layer selector',
// sharing module
SHARE_BTN: `Share this view`,
@@ -52,4 +55,8 @@
// mesh loading status
MESH_LOADING_STATUS: 'mesh-loading-status'
}
+
+ exports.CONST = {
+ REGIONAL_FEATURES: 'Regional features'
+ }
})(typeof exports === 'undefined' ? module.exports : exports)
diff --git a/common/util.js b/common/util.js
index cb1004eef..de5efde33 100644
--- a/common/util.js
+++ b/common/util.js
@@ -34,6 +34,12 @@
return returnV
}
+ exports.getUniqueRegionId = (template, parcellation, region) => {
+ const templateId = template['@id'] || template['name']
+ const parcId = parcellation['@id'] || parcellation['name']
+ return `${templateId}/${parcId}/${region['name']}`
+ }
+
exports.getIdObj = getIdObj
exports.getIdFromFullId = fullId => {
diff --git a/deploy/datasets/index.js b/deploy/datasets/index.js
index dc98c0bae..502a4c350 100644
--- a/deploy/datasets/index.js
+++ b/deploy/datasets/index.js
@@ -2,7 +2,7 @@ const express = require('express')
const path = require('path')
const fs = require('fs')
const datasetsRouter = express.Router()
-const { init, getDatasets, getPreview, getDatasetFromId, getExternalSchemaDatasets, getDatasetFileAsZip, getTos, hasPreview } = require('./query')
+const { init, getDatasets, getPreview, getDatasetFromId, getExternalSchemaDatasets, getDatasetFileAsZip, getTos, hasPreview, getDatasetsByRegion } = require('./query')
const { retry } = require('./util')
const url = require('url')
const qs = require('querystring')
@@ -72,6 +72,13 @@ datasetsRouter.get('/templateNameParcellationName/:templateName/:parcellationNam
})
})
+datasetsRouter.get('/byRegion/:regionId', noCacheMiddleWare, async (req, res) => {
+ const { regionId } = req.params
+ const { user } = req
+ const ds = await getDatasetsByRegion({ regionId, user })
+ res.status(200).json(ds)
+})
+
const deprecatedNotice = (_req, res) => {
res.status(400).send(`querying datasets with /templateName or /parcellationName separately have been deprecated. Please use /templateNameParcellationName/:templateName/:parcellationName instead`)
}
diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
index c1a11c28d..091bc7fcd 100644
--- a/deploy/datasets/query.js
+++ b/deploy/datasets/query.js
@@ -4,7 +4,7 @@ const URL = require('url')
const path = require('path')
const archiver = require('archiver')
const { getPreviewFile, hasPreview } = require('./supplements/previewFile')
-const { constants, init: kgQueryUtilInit, getUserKGRequestParam, filterDatasets } = require('./util')
+const { constants, init: kgQueryUtilInit, getUserKGRequestParam, filterDatasets, filterDatasetsByRegion } = require('./util')
const ibc = require('./importIBS')
let cachedData = null
@@ -126,6 +126,14 @@ const init = async () => {
return await getPublicDs()
}
+const getDatasetsByRegion = async ({ regionId, user }) => {
+ /**
+ * potentially add other sources of datasets
+ */
+ const kgDatasets = await getDs({ user })
+ return filterDatasetsByRegion(kgDatasets, regionId)
+}
+
const getDatasets = ({ templateName, parcellationName, user }) => {
// Get Local datasets
const localDatasets = [
@@ -136,7 +144,6 @@ const getDatasets = ({ templateName, parcellationName, user }) => {
// Get all datasets and merge local ones
return getDs({ user })
.then(json => {
- // console.log(json.map(j=> j.parcellationRegion))
json = [...json, ...localDatasets]
return filterDatasets(json, { templateName, parcellationName })
})
@@ -233,6 +240,7 @@ module.exports = {
getPreview,
hasPreview,
getTos,
- getExternalSchemaDatasets
+ getExternalSchemaDatasets,
+ getDatasetsByRegion,
}
diff --git a/deploy/datasets/util.js b/deploy/datasets/util.js
index eea0c8f74..ae9a088df 100644
--- a/deploy/datasets/util.js
+++ b/deploy/datasets/util.js
@@ -3,7 +3,7 @@ const { getCommonSenseDsFilter } = require('./supplements/commonSense')
const { hasPreview } = require('./supplements/previewFile')
const path = require('path')
const fs = require('fs')
-const { getIdFromFullId, retry, flattenRegions } = require('../../common/util')
+const { getIdFromFullId, retry, flattenRegions, getUniqueRegionId } = require('../../common/util')
let getPublicAccessToken
@@ -79,6 +79,57 @@ const populateSet = (flattenedRegions, set = new Set()) => {
const initPrArray = []
+/**
+ * regionMap maps schema/id to { parent, children }
+ */
+const regionMap = new Map()
+
+const getParseRegion = (template, parcellation) => {
+
+ const getRegionIdFromRegion = region => {
+ return region.fullId
+ ? getIdFromFullId(region.fullId)
+ : getUniqueRegionId(template, parcellation, region)
+ }
+
+ const parseRegion = (region, parent) => {
+ const regionId = getRegionIdFromRegion(region)
+ const { children, relatedAreas } = region
+ const childrenIds = [
+ ...(children || []).map(getRegionIdFromRegion)
+ ]
+
+ const alternateIds = [
+ ...(relatedAreas || []).map(getRegionIdFromRegion)
+ ]
+
+ regionMap.set(regionId, {
+ parent,
+ self: [ regionId, ...alternateIds ],
+ children: childrenIds
+ })
+ for (const altId of alternateIds) {
+ regionMap.set(altId, {
+ parent,
+ self: [ regionId, ...alternateIds ],
+ children: childrenIds
+ })
+ }
+ for (const c of (children || [])) {
+ parseRegion(c, regionId)
+ }
+ }
+ return parseRegion
+}
+
+const processParc = (t, p) => {
+ const parseRegion = getParseRegion(t, p)
+ const { regions } = p
+ for (const r of regions) {
+ parseRegion(r)
+ }
+}
+
let juBrainSet = new Set(),
bigbrainCytoSet = new Set()
shortBundleSet = new Set(),
@@ -93,6 +144,9 @@ initPrArray.push(
readConfigFile('bigbrain.json')
.then(data => JSON.parse(data))
.then(json => {
+ for (const p of json.parcellations) {
+ processParc(json, p)
+ }
const bigbrainCyto = flattenRegions(json.parcellations.find(({ name }) => name === 'Cytoarchitectonic Maps').regions)
bigbrainCytoSet = populateSet(bigbrainCyto)
})
@@ -103,6 +157,9 @@ initPrArray.push(
readConfigFile('MNI152.json')
.then(data => JSON.parse(data))
.then(json => {
+ for (const p of json.parcellations) {
+ processParc(json, p)
+ }
const longBundle = flattenRegions(json.parcellations.find(({ ['@id']: id }) => id === KG_IDS.PARCELLATIONS.LONG_BUNDLE).regions)
const shortBundle = flattenRegions(json.parcellations.find(({ ['@id']: id }) => id === KG_IDS.PARCELLATIONS.SHORT_BUNDLE).regions)
const jubrain = flattenRegions(json.parcellations.find(({ ['@id']: id }) => id === KG_IDS.PARCELLATIONS.JULICH_BRAIN).regions)
@@ -117,6 +174,9 @@ initPrArray.push(
readConfigFile('waxholmRatV2_0.json')
.then(data => JSON.parse(data))
.then(json => {
+ for (const p of json.parcellations) {
+ processParc(json, p)
+ }
const waxholm3 = flattenRegions(json.parcellations[0].regions)
const waxholm2 = flattenRegions(json.parcellations[1].regions)
const waxholm1 = flattenRegions(json.parcellations[2].regions)
@@ -132,6 +192,9 @@ initPrArray.push(
readConfigFile('allenMouse.json')
.then(data => JSON.parse(data))
.then(json => {
+ for (const p of json.parcellations) {
+ processParc(json, p)
+ }
const flattenedAllen2017 = flattenRegions(json.parcellations[0].regions)
allen2017Set = populateSet(flattenedAllen2017)
@@ -197,6 +260,33 @@ const datasetBelongToParcellation = ({ parcellationName = null, dataset = {parce
? true
: (dataset.parcellationAtlas || []).some(({ name }) => name === parcellationName)
+const relatedRegionsCache = new Map()
+const traverseRegionMap = regionSchemaId => {
+ if (relatedRegionsCache.has(regionSchemaId)) return relatedRegionsCache.get(regionSchemaId)
+ const out = regionMap.get(regionSchemaId)
+ if (!out) {
+ return []
+ }
+ const { parent, self, children } = out
+
+ /**
+ * how to determine how to traverse the tree to determine related regions?
+ * for now, will traverse towards the parents
+ * ie, when selecting a leaf node, all nodes up to the root will be considered important
+ */
+
+ const relatedSchemaIds = self.concat(
+ parent ? traverseRegionMap(parent) : []
+ )
+ relatedRegionsCache.set(regionSchemaId, relatedSchemaIds)
+ return relatedSchemaIds
+}
+
+const filterDatasetsByRegion = async (datasets = [], regionSchemaId) => {
+ const allRelevantSchemaSet = new Set(traverseRegionMap(regionSchemaId))
+ return datasets.filter(ds => ds['parcellationRegion'].some(pr => allRelevantSchemaSet.has(getIdFromFullId(pr.fullId))))
+}
+
/**
* NB: if changed, also change ~/docs/advanced/dataset.md
* @param {*} dataset
@@ -309,6 +399,7 @@ module.exports = {
datasetBelongToParcellation,
datasetRegionExistsInParcellationRegion,
datasetBelongsInTemplate,
+ filterDatasetsByRegion,
_getParcellations: async () => {
await Promise.all(initPrArray)
return {
diff --git a/deploy/datasets/util.spec.js b/deploy/datasets/util.spec.js
index aadd7283f..802edd662 100644
--- a/deploy/datasets/util.spec.js
+++ b/deploy/datasets/util.spec.js
@@ -1,4 +1,4 @@
-const { populateSet, datasetBelongToParcellation, retry, datasetBelongsInTemplate, filterDatasets, datasetRegionExistsInParcellationRegion, _getParcellations } = require('./util')
+const { populateSet, datasetBelongToParcellation, retry, datasetBelongsInTemplate, filterDatasets, datasetRegionExistsInParcellationRegion, _getParcellations, filterDatasetsByRegion } = require('./util')
const { fake } = require('sinon')
const { assert, expect } = require('chai')
const waxholmv2 = require('./testData/waxholmv2')
@@ -289,4 +289,73 @@ describe('datasets/util.js', () => {
])
})
})
+
+ describe('filterDatasetsByRegion', () => {
+
+ const idHumanArea7ASPL = 'minds/core/parcellationregion/v1.0.0/e26e999f-77ad-4934-9569-8290ed05ebda'
+ const idHumanArea7A = `minds/core/parcellationregion/v1.0.0/811f4adb-4a7c-45c1-8034-4afa9edf586a`
+ const idMouseWholeBrain = `minds/core/parcellationregion/v1.0.0/be45bc91-8db5-419f-9471-73a320f44e06`
+ const idMousePrimaryMotor = `minds/core/parcellationregion/v1.0.0/a07b4390-62db-451b-b211-a45f67c6b18e`
+ const idMousePrimarySomatosensory = `minds/core/parcellationregion/v1.0.0/f99995b6-a3d0-42be-88c3-eff8a83e60ea`
+
+ const dataHumanArea7ASPL = {
+ name: 'dataHumanArea7ASPL',
+ parcellationRegion: [{
+ fullId: idHumanArea7ASPL
+ }]
+ }
+ const dataMouseWholeBrain = {
+ name: 'dataMouseWholeBrain',
+ parcellationRegion: [{
+ fullId: idMouseWholeBrain
+ }]
+ }
+
+ const dataMousePrimaryMotor = {
+ name: 'dataMousePrimaryMotor',
+ parcellationRegion: [{
+ // Mouse Primary motor area (2017)
+ fullId: idMousePrimaryMotor
+ }]
+ }
+
+ describe('human parc regions', () => {
+ it('should leave in data with matching reference space', async () => {
+ const result = await filterDatasetsByRegion([dataHumanArea7ASPL], idHumanArea7ASPL)
+ expect(result).to.deep.equal([dataHumanArea7ASPL])
+ })
+ it('should filter out data with no matching reference space', async () => {
+ const result = await filterDatasetsByRegion([dataMouseWholeBrain], idHumanArea7ASPL)
+ expect(result).to.deep.equal([])
+ })
+ it('if query region is relatedAreas, should also leave in dataset', async () => {
+ const result = await filterDatasetsByRegion([dataHumanArea7ASPL], idHumanArea7A)
+ expect(result).to.deep.equal([dataHumanArea7ASPL])
+ })
+ })
+
+ describe('mouse parc regions', () => {
+
+ it('should leave in data with matchin reference space', async () => {
+ const result = await filterDatasetsByRegion([dataMouseWholeBrain], idMouseWholeBrain)
+ expect(result).to.deep.equal([dataMouseWholeBrain])
+
+ const result2 = await filterDatasetsByRegion([dataMousePrimaryMotor], idMousePrimaryMotor)
+ expect(result2).to.deep.equal([dataMousePrimaryMotor])
+ })
+ it('should filter out data with no matching referene space', async () => {
+ const result = await filterDatasetsByRegion([dataHumanArea7ASPL], idMouseWholeBrain)
+ expect(result).to.deep.equal([])
+ })
+ it('should filter out data if sup region is selected', async () => {
+ // example: whole brain is selected, but dataset in primary motor area will be FILTERED OUT
+ const result = await filterDatasetsByRegion([dataMousePrimaryMotor], idMouseWholeBrain)
+ expect(result).to.deep.equal([])
+ })
+ it('should leave in data when sub region is selected', async () => {
+ const result = await filterDatasetsByRegion([dataMouseWholeBrain], idMousePrimaryMotor)
+ expect(result).to.deep.equal([dataMouseWholeBrain])
+ })
+ })
+ })
})
diff --git a/e2e/src/util.js b/e2e/src/util.js
index 5d9884acf..7b536b72e 100644
--- a/e2e/src/util.js
+++ b/e2e/src/util.js
@@ -8,7 +8,7 @@ const { By, Key, until } = require('selenium-webdriver')
const CITRUS_LIGHT_URL = `https://unpkg.com/citruslight@0.1.0/citruslight.js`
const { polyFillClick } = require('./material-util')
-const { ARIA_LABELS } = require('../../common/constants')
+const { ARIA_LABELS, CONST } = require('../../common/constants')
const { retry } = require('../../common/util')
function getActualUrl(url) {
@@ -26,8 +26,6 @@ async function _getIndexFromArrayOfWebElements(search, webElements) {
return texts.findIndex(text => text.indexOf(search) >= 0)
}
-const regionSearchAriaLabelText = 'Search for any region of interest in the atlas selected'
-
const verifyPosition = position => {
if (!position) throw new Error(`cursorGoto: position must be defined!`)
@@ -550,8 +548,8 @@ class WdLayoutPage extends WdBase{
async _findTitleCard(title) {
const titleCards = await this._browser
- .findElement( By.tagName('ui-splashscreen') )
- .findElements( By.tagName('mat-card') )
+ .findElement( By.css('ui-splashscreen') )
+ .findElements( By.css('mat-card') )
const idx = await _getIndexFromArrayOfWebElements(title, titleCards)
if (idx >= 0) return titleCards[idx]
else throw new Error(`${title} does not fit any titleCards`)
@@ -563,17 +561,106 @@ class WdLayoutPage extends WdBase{
}
async selectTitleTemplateParcellation(templateName, parcellationName){
- const titleCard = await this._findTitleCard(templateName)
- const parcellations = await titleCard
- .findElement( By.css('mat-card-content.available-parcellations-container') )
- .findElements( By.tagName('button') )
- const idx = await _getIndexFromArrayOfWebElements( parcellationName, parcellations )
- if (idx >= 0) await parcellations[idx].click()
- else throw new Error(`parcellationName ${parcellationName} does not exist`)
+ throw new Error(`selectTitleTemplateParcellation has been deprecated. use selectAtlasTemplateParcellation`)
+ }
+
+ /**
+ * _setAtlasSelectorExpanded
+ * toggle/set the open state of the atlas-layer-selector element
+ * If the only argument (flag) is not provided, it will toggle the atlas-layer-selector
+ *
+ * Will throw if atlas-layer-selector is not in the DOM
+ *
+ * @param {boolean} flag
+ *
+ */
+ async _setAtlasSelectorExpanded(flag) {
+ const atlasLayerSelectorEl = this._browser.findElement(
+ By.css('atlas-layer-selector')
+ )
+ const openedFlag = (await atlasLayerSelectorEl.getAttribute('data-opened')) === 'true'
+ if (typeof flag === 'undefined' || flag !== openedFlag) {
+ await atlasLayerSelectorEl.findElement(By.css(`button[aria-label="${ARIA_LABELS.TOGGLE_ATLAS_LAYER_SELECTOR}"]`)).click()
+ }
}
+ async changeTemplate(templateName){
+ if (!templateName) throw new Error(`templateName needs to be provided`)
+ await this._setAtlasSelectorExpanded(true)
+ await this.wait(1000)
+ const allTiles = await this._browser
+ .findElement( By.css('atlas-layer-selector') )
+ .findElements( By.css(`mat-grid-tile`) )
+
+ const idx = await _getIndexFromArrayOfWebElements(templateName, allTiles)
+ if (idx >= 0) await allTiles[idx].click()
+ else throw new Error(`#changeTemplate: templateName ${templateName} cannot be found.`)
+ }
+
+ async changeParc(parcName) {
+ throw new Error(`changeParc NYI`)
+ }
+
+ async selectAtlasTemplateParcellation(atlasName, templateName, parcellationName, parcVersion) {
+ if (!atlasName) throw new Error(`atlasName needs to be provided`)
+ try {
+ /**
+ * if at title screen
+ */
+ await (await this._findTitleCard(atlasName)).click()
+ } catch (e) {
+ /**
+ * if not at title screen
+ * select from dropdown
+ */
+ }
+
+ if (templateName) {
+ await this.wait(1000)
+ await this.waitUntilAllChunksLoaded()
+ await this.changeTemplate(templateName)
+ }
+
+ if (parcellationName) {
+ await this.wait(1000)
+ await this.waitUntilAllChunksLoaded()
+ await this.changeParc(parcellationName)
+ }
+
+ await this._setAtlasSelectorExpanded(false)
+ }
// SideNav
+ _getSideNavPrimary(){
+ return this._browser.findElement(
+ By.css('mat-drawer[data-mat-drawer-primary-open]')
+ )
+ }
+
+ async _getSideNavPrimaryExpanded(){
+ return (await this._getSideNavPrimary()
+ .getAttribute('data-mat-drawer-primary-open')) === 'true'
+ }
+
+ _getSideNavSecondary(){
+ return this._browser.findElement(
+ By.css('mat-drawer[data-mat-drawer-secondary-open]')
+ )
+ }
+
+ async _getSideNavSecondaryExpanded(){
+ return (await this._getSideNavSecondary()
+ .getAttribute('data-mat-drawer-secondary-open')) === 'true'
+ }
+
+ async _setSideNavPrimaryExpanded(flag) {
+ const matDrawerPrimaryEl = this._getSideNavPrimary()
+ const openedFlag = await this._getSideNavPrimaryExpanded()
+ if (typeof flag === 'undefined' || flag !== openedFlag) {
+ await this._browser.findElement(By.css(`button[aria-label="${ARIA_LABELS.TOGGLE_SIDE_PANEL}"]`)).click()
+ }
+ }
+
_getSideNav() {
throw new Error(`side bar no longer exist`)
}
@@ -787,7 +874,7 @@ class WdIavPage extends WdLayoutPage{
async clearAllSelectedRegions() {
const clearAllRegionBtn = await this._browser.findElement(
- By.css('[aria-label="Clear all regions"]')
+ By.css(`[aria-label="${ARIA_LABELS.CLEAR_SELECTED_REGION}"]`)
)
await clearAllRegionBtn.click()
await this.wait(500)
@@ -834,9 +921,15 @@ class WdIavPage extends WdLayoutPage{
else throw new Error(`${title} is not found as one of the dropdown templates`)
}
- _getSearchRegionInput(){
- return this._getSideNav()
- .findElement( By.css(`[aria-label="${regionSearchAriaLabelText}"]`) )
+ async _getSearchRegionInput(){
+ await this._setSideNavPrimaryExpanded(true)
+ await this.wait(500)
+ const secondaryOpen = await this._getSideNavSecondaryExpanded()
+ if (secondaryOpen) {
+ return this._getSideNavSecondary().findElement( By.css(`[aria-label="${ARIA_LABELS.TEXT_INPUT_SEARCH_REGION}"]`) )
+ } else {
+ return this._getSideNavPrimary().findElement( By.css(`[aria-label="${ARIA_LABELS.TEXT_INPUT_SEARCH_REGION}"]`) )
+ }
}
async searchRegionWithText(text=''){
@@ -888,8 +981,8 @@ class WdIavPage extends WdLayoutPage{
_getModalityListView(){
return this._browser
- .findElement( By.tagName('modality-picker') )
- .findElements( By.tagName('mat-checkbox') )
+ .findElement( By.css('modality-picker') )
+ .findElements( By.css('mat-checkbox') )
}
async getModalities(){
@@ -905,9 +998,22 @@ class WdIavPage extends WdLayoutPage{
_getSingleDatasetListView(){
return this._browser
- .findElement( By.tagName('data-browser') )
- .findElement( By.css('div.cdk-virtual-scroll-content-wrapper') )
- .findElements( By.tagName('single-dataset-list-view') )
+ .findElement( By.css('data-browser') )
+ .findElements( By.css('single-dataset-list-view') )
+ }
+
+ _getRegionalFeatureEl(){
+ return this._getSideNavSecondary().findElement(
+ By.css(`mat-expansion-panel[data-mat-expansion-title="${CONST.REGIONAL_FEATURES}"]`)
+ )
+ }
+
+ async _setRegionalFeaturesExpanded(flag){
+ const regionFeatureExpEl = this._getRegionalFeatureEl()
+ const openedFlag = (await regionFeatureExpEl.getAttribute('data-opened')) === 'true'
+ if (typeof flag === 'undefined' || flag !== openedFlag) {
+ await regionFeatureExpEl.findElement(By.css(`mat-expansion-panel-header`)).click()
+ }
}
async getVisibleDatasets() {
diff --git a/src/ui/atlasLayerSelector/atlasLayerSelector.component.ts b/src/ui/atlasLayerSelector/atlasLayerSelector.component.ts
index af2558291..fe54b4608 100644
--- a/src/ui/atlasLayerSelector/atlasLayerSelector.component.ts
+++ b/src/ui/atlasLayerSelector/atlasLayerSelector.component.ts
@@ -1,12 +1,12 @@
-import {Component, OnInit, ViewChildren, QueryList, Output, EventEmitter} from "@angular/core";
+import { Component, OnInit, ViewChildren, QueryList, HostBinding } from "@angular/core";
import { select, Store } from "@ngrx/store";
import { safeFilter } from "src/services/stateStore.service";
-import { distinctUntilChanged, map, withLatestFrom, shareReplay, groupBy, mergeMap, toArray, switchMap, scan, tap, filter } from "rxjs/operators";
+import { distinctUntilChanged, map, withLatestFrom, shareReplay, groupBy, mergeMap, toArray, switchMap, scan, filter } from "rxjs/operators";
import { Observable, Subscription, from, zip, of, combineLatest } from "rxjs";
import { viewerStateSelectTemplateWithId, viewerStateToggleLayer } from "src/services/state/viewerState.store.helper";
import { MatMenuTrigger } from "@angular/material/menu";
import { viewerStateGetSelectedAtlas, viewerStateAtlasLatestParcellationSelector } from "src/services/state/viewerState/selectors";
-import {CLEAR_CONNECTIVITY_REGION, SET_CONNECTIVITY_VISIBLE} from "src/services/state/viewerState.store";
+import { ARIA_LABELS } from 'common/constants'
@Component({
selector: 'atlas-layer-selector',
@@ -16,6 +16,8 @@ import {CLEAR_CONNECTIVITY_REGION, SET_CONNECTIVITY_VISIBLE} from "src/services/
})
export class AtlasLayerSelector implements OnInit {
+ public TOGGLE_ATLAS_LAYER_SELECTOR = ARIA_LABELS.TOGGLE_ATLAS_LAYER_SELECTOR
+
@ViewChildren(MatMenuTrigger) matMenuTriggers: QueryList<MatMenuTrigger>
public atlas: any
@@ -30,6 +32,7 @@ export class AtlasLayerSelector implements OnInit {
public selectedAtlas$: Observable<any>
private subscriptions: Subscription[] = []
+ @HostBinding('attr.data-opened')
public selectorExpanded: boolean = false
public selectedTemplatePreviewUrl: string = ''
diff --git a/src/ui/atlasLayerSelector/atlasLayerSelector.template.html b/src/ui/atlasLayerSelector/atlasLayerSelector.template.html
index fa3219cf9..2398853b0 100644
--- a/src/ui/atlasLayerSelector/atlasLayerSelector.template.html
+++ b/src/ui/atlasLayerSelector/atlasLayerSelector.template.html
@@ -65,7 +65,7 @@
matTooltip="Select layer"
mat-mini-fab
*ngIf="((availableTemplates$ | async).length > 1) || ((groupedLayers$ | async).length + (nonGroupedLayers$ | async).length > 1)"
- aria-label="Layer selector expand button"
+ [attr.aria-label]="TOGGLE_ATLAS_LAYER_SELECTOR"
(click)="selectorExpanded = !selectorExpanded">
<i class="fas fa-layer-group"></i>
</button>
diff --git a/src/ui/databrowserModule/databrowser.service.ts b/src/ui/databrowserModule/databrowser.service.ts
index 3f9c3245c..8d3828f0b 100644
--- a/src/ui/databrowserModule/databrowser.service.ts
+++ b/src/ui/databrowserModule/databrowser.service.ts
@@ -1,7 +1,7 @@
import { HttpClient } from "@angular/common/http";
import {ComponentRef, Injectable, OnDestroy} from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { BehaviorSubject, combineLatest, from, fromEvent, Observable, of, Subscription } from "rxjs";
+import { BehaviorSubject, combineLatest, forkJoin, from, fromEvent, Observable, of, Subscription } from "rxjs";
import { catchError, debounceTime, distinctUntilChanged, filter, map, shareReplay, switchMap, tap, withLatestFrom } from "rxjs/operators";
import { AtlasViewerConstantsServices } from "src/atlasViewer/atlasViewer.constantService.service";
import { AtlasWorkerService } from "src/atlasViewer/atlasViewer.workerService.service";
@@ -12,12 +12,13 @@ import { WidgetUnit } from "src/widget";
import { LoggingService } from "src/logging";
import { SHOW_KG_TOS } from "src/services/state/uiState.store";
import { FETCHED_DATAENTRIES, FETCHED_SPATIAL_DATA, IavRootStoreInterface, IDataEntry, safeFilter } from "src/services/stateStore.service";
-import { regionFlattener } from "src/util/regionFlattener";
import { DataBrowser } from "./databrowser/databrowser.component";
import { NO_METHODS } from "./util/filterDataEntriesByMethods.pipe";
import { FilterDataEntriesByRegion } from "./util/filterDataEntriesByRegion.pipe";
import { datastateActionToggleFav, datastateActionUnfavDataset, datastateActionFavDataset } from "src/services/state/dataState/actions";
+import { getIdFromFullId } from 'common/util'
+
const noMethodDisplayName = 'No methods described'
/**
@@ -62,12 +63,10 @@ export class DatabrowserService implements OnDestroy {
})
}
public createDatabrowser: (arg: {regions: any[], template: any, parcellation: any}) => {dataBrowser: ComponentRef<DataBrowser>, widgetUnit: ComponentRef<WidgetUnit>}
- public getDataByRegion: ({regions, parcellation, template}: {regions: any[], parcellation: any, template: any}) => Promise<IDataEntry[]> = ({regions, parcellation, template}) => new Promise((resolve, reject) => {
- this.lowLevelQuery(template.name, parcellation.name)
- .then(de => this.filterDEByRegion.transform(de, regions, parcellation.regions.map(regionFlattener).reduce((acc, item) => acc.concat(item), [])))
- .then(resolve)
- .catch(reject)
- })
+ public getDataByRegion: ({ regions, parcellation, template }: {regions: any[], parcellation: any, template: any}) => Promise<IDataEntry[]> = ({regions, parcellation, template}) =>
+ forkJoin(regions.map(this.getDatasetsByRegion.bind(this))).pipe(
+ map((arrOfArr: IDataEntry[][]) => arrOfArr.reduce((acc, curr) => acc.concat(curr), []))
+ ).toPromise()
private filterDEByRegion: FilterDataEntriesByRegion = new FilterDataEntriesByRegion()
private dataentries: IDataEntry[] = []
@@ -258,6 +257,16 @@ export class DatabrowserService implements OnDestroy {
public fetchingFlag: boolean = false
private mostRecentFetchToken: any
+ private getDatasetsByRegion(region: { fullId: string }){
+ return this.http.get<IDataEntry>(
+ `${this.constantService.backendUrl}datasets/byRegion/${encodeURIComponent(getIdFromFullId(region.fullId))}`,
+ {
+ headers: this.constantService.getHttpHeader(),
+ responseType: 'json'
+ }
+ )
+ }
+
private lowLevelQuery(templateName: string, parcellationName: string): Promise<IDataEntry[]> {
const encodedTemplateName = encodeURIComponent(templateName)
const encodedParcellationName = encodeURIComponent(parcellationName)
diff --git a/src/ui/databrowserModule/databrowser/databrowser.base.ts b/src/ui/databrowserModule/databrowser/databrowser.base.ts
index ce800d094..04b10b309 100644
--- a/src/ui/databrowserModule/databrowser/databrowser.base.ts
+++ b/src/ui/databrowserModule/databrowser/databrowser.base.ts
@@ -3,6 +3,7 @@ import { LoggingService } from "src/logging"
import { DatabrowserService } from "../singleDataset/singleDataset.base"
import { Observable } from "rxjs"
import { IDataEntry } from "src/services/stateStore.service"
+import { getUniqueRegionId } from 'common/util'
export class DatabrowserBase{
@@ -35,17 +36,18 @@ export class DatabrowserBase{
ngOnChanges(){
-
+ const { regions, parcellation, template } = this
this.regions = this.regions.map(r => {
/**
* TODO to be replaced with properly region UUIDs from KG
*/
+ const uniqueRegionId = getUniqueRegionId(template, parcellation, r)
return {
- id: `${this.parcellation?.name || 'untitled_parcellation'}/${r.name}`,
+ fullId: uniqueRegionId,
+ id: uniqueRegionId,
...r,
}
})
- const { regions, parcellation, template } = this
this.fetchingFlag = true
// input may be undefined/null
diff --git a/src/ui/databrowserModule/databrowser/databrowser.template.html b/src/ui/databrowserModule/databrowser/databrowser.template.html
index 27e4efbc0..0621b5e53 100644
--- a/src/ui/databrowserModule/databrowser/databrowser.template.html
+++ b/src/ui/databrowserModule/databrowser/databrowser.template.html
@@ -72,7 +72,8 @@
minBufferPx="200"
maxBufferPx="400"
itemSize="50">
- <div class="virtual-scroll-element overflow-hidden" *cdkVirtualFor="let dataset of filteredDataEntry; trackBy: trackByFn; templateCacheSize: 20; let index = index">
+ <div *cdkVirtualFor="let dataset of filteredDataEntry; trackBy: trackByFn; templateCacheSize: 20; let index = index"
+ class="virtual-scroll-element overflow-hidden">
<!-- divider, show if not first -->
<mat-divider *ngIf="index !== 0"></mat-divider>
diff --git a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
index d976cba7a..cea115981 100644
--- a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
+++ b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
@@ -12,13 +12,17 @@ export const regionsEqual = (r1, r2) => {
}
const isSubRegion = (high, low) => regionsEqual(high, low)
- ? true
- : high.children && Array.isArray(high.children)
- ? high.children.some(r => isSubRegion(r, low))
- : false
+ || (
+ high.children
+ && Array.isArray(high.children)
+ && high.children.some(r => isSubRegion(r, low))
+ )
+
-const filterSubSelect = (dataEntry, selectedRegions) =>
- dataEntry.parcellationRegion.some(pr => selectedRegions.some(sr => isSubRegion(pr, sr)))
+const filterSubSelect = (dataEntry, selectedRegions) => {
+ if (dataEntry.name === 'Density measurements of different receptors for Area 7A (SPL) [human, v1.0]') console.log(dataEntry)
+ return dataEntry.parcellationRegion.some(pr => selectedRegions.some(sr => isSubRegion(pr, sr)))
+}
@Pipe({
name: 'filterDataEntriesByRegion',
@@ -27,8 +31,7 @@ const filterSubSelect = (dataEntry, selectedRegions) =>
export class FilterDataEntriesByRegion implements PipeTransform {
public transform(dataentries: IDataEntry[], selectedRegions: any[], flattenedAllRegions: any[]) {
return dataentries && selectedRegions && selectedRegions.length > 0
- ? dataentries
- .filter(de => filterSubSelect(de, selectedRegions))
+ ? dataentries.filter(de => filterSubSelect(de, selectedRegions))
: dataentries
}
}
diff --git a/src/ui/nehubaContainer/nehubaContainer.component.ts b/src/ui/nehubaContainer/nehubaContainer.component.ts
index 6a80e1fb4..7f0e469ac 100644
--- a/src/ui/nehubaContainer/nehubaContainer.component.ts
+++ b/src/ui/nehubaContainer/nehubaContainer.component.ts
@@ -25,7 +25,7 @@ import { AtlasViewerAPIServices, IUserLandmark } from "src/atlasViewer/atlasView
import { NehubaViewerUnit } from "./nehubaViewer/nehubaViewer.component";
import { compareLandmarksChanged } from "src/util/constants";
import { PureContantService } from "src/util";
-import { ARIA_LABELS, IDS } from 'common/constants'
+import { ARIA_LABELS, IDS, CONST } from 'common/constants'
import { ngViewerActionSetPerspOctantRemoval, PANELS, ngViewerActionToggleMax, ngViewerActionAddNgLayer, ngViewerActionRemoveNgLayer } from "src/services/state/ngViewerState.store.helper";
import { viewerStateSelectRegionWithIdDeprecated, viewerStateAddUserLandmarks, viewreStateRemoveUserLandmarks, viewerStateCustomLandmarkSelector, viewerStateSelectedParcellationSelector, viewerStateSelectedTemplateSelector } from 'src/services/state/viewerState.store.helper'
import { SwitchDirective } from "src/util/directives/switch.directive";
@@ -146,6 +146,7 @@ const {
export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
+ public CONST = CONST
public ARIA_LABEL_ZOOM_IN = ZOOM_IN
public ARIA_LABEL_ZOOM_OUT = ZOOM_OUT
public ARIA_LABEL_TOGGLE_SIDE_PANEL = TOGGLE_SIDE_PANEL
diff --git a/src/ui/nehubaContainer/nehubaContainer.template.html b/src/ui/nehubaContainer/nehubaContainer.template.html
index bde6da235..68a7f3450 100644
--- a/src/ui/nehubaContainer/nehubaContainer.template.html
+++ b/src/ui/nehubaContainer/nehubaContainer.template.html
@@ -48,7 +48,7 @@
<!-- sidenav-content -->
<mat-drawer class="box-shadow-none border-0 pe-none bg-none col-10 col-sm-10 col-md-5 col-lg-4 col-xl-3 col-xxl-2"
mode="side"
- [attr.data-mat-drawer-open]="matDrawerMaster.opened"
+ [attr.data-mat-drawer-primary-open]="matDrawerMaster.opened"
[opened]="sideNavMasterSwitch.switchState"
[autoFocus]="false"
(closedStart)="sideNavSwitch.switchState && matDrawerMinor.close()"
@@ -121,7 +121,7 @@
<!-- sidenav-content -->
<mat-drawer class="darker-bg iv-custom-comp visible col-10 col-sm-10 col-md-5 col-lg-4 col-xl-3 col-xxl-2 d-flex flex-column pe-all"
mode="push"
- [attr.data-mat-drawer-open]="matDrawerMinor.opened"
+ [attr.data-mat-drawer-secondary-open]="matDrawerMinor.opened"
[autoFocus]="false"
#matDrawerMinor="matDrawer"
(openedChange)="$event && sideNavSwitch.open()"
@@ -309,6 +309,8 @@
let-iavNgIf="iavNgIf"
let-content="content">
<mat-expansion-panel class="mt-1 mb-1"
+ [attr.data-opened]="expansionPanel.expanded"
+ [attr.data-mat-expansion-title]="title"
hideToggle
*ngIf="iavNgIf"
#expansionPanel="matExpansionPanel">
@@ -389,7 +391,7 @@
</ng-template>
<ng-container *ngTemplateOutlet="ngMatAccordionTmpl; context: {
- title: 'Regional features',
+ title: CONST.REGIONAL_FEATURES,
desc: iavDbDirective?.dataentries?.length,
iconClass: 'fas fa-database',
iconTooltip: iavDbDirective?.dataentries?.length | regionAccordionTooltipTextPipe : 'regionalFeatures',
diff --git a/src/ui/viewerStateController/regionSearch/regionSearch.component.ts b/src/ui/viewerStateController/regionSearch/regionSearch.component.ts
index 2d6acd658..43fbe5722 100644
--- a/src/ui/viewerStateController/regionSearch/regionSearch.component.ts
+++ b/src/ui/viewerStateController/regionSearch/regionSearch.component.ts
@@ -11,6 +11,7 @@ import { MatDialog } from "@angular/material/dialog";
import { MatAutocompleteSelectedEvent } from "@angular/material/autocomplete";
import { PureContantService } from "src/util";
import { viewerStateToggleRegionSelect, viewerStateNavigateToRegion, viewerStateSetSelectedRegions, viewerStateSetSelectedRegionsWithIds } from "src/services/state/viewerState.store.helper";
+import { ARIA_LABELS } from 'common/constants'
const filterRegionBasedOnText = searchTerm => region => region.name.toLowerCase().includes(searchTerm.toLowerCase())
|| (region.relatedAreas && region.relatedAreas.some(relatedArea => relatedArea.name && relatedArea.name.toLowerCase().includes(searchTerm.toLowerCase())))
@@ -36,7 +37,9 @@ export class RegionTextSearchAutocomplete {
public compareFn = compareFn
- @Input() public ariaLabel: string = `Search for any region of interest in the atlas selected`
+ public CLEAR_SELECTED_REGION = ARIA_LABELS.CLEAR_SELECTED_REGION
+
+ @Input() public ariaLabel: string = ARIA_LABELS.TEXT_INPUT_SEARCH_REGION
@Input() public showBadge: boolean = false
@Input() public showAutoComplete: boolean = true
diff --git a/src/ui/viewerStateController/regionSearch/regionSearch.template.html b/src/ui/viewerStateController/regionSearch/regionSearch.template.html
index 42ddf8f77..b2f543412 100644
--- a/src/ui/viewerStateController/regionSearch/regionSearch.template.html
+++ b/src/ui/viewerStateController/regionSearch/regionSearch.template.html
@@ -17,6 +17,7 @@
<!-- close region selection -->
<button *ngIf="(regionsSelected$ | async)?.length > 0"
mat-icon-button
+ [attr.aria-label]="CLEAR_SELECTED_REGION"
(click)="optionSelected()"
matSuffix>
<i class="fas fa-times"></i>
--
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