diff --git a/Dockerfile b/Dockerfile
index 4f02923a5ee7b504d9d9f57f0d3ebbad4a90d72f..a20f2d36324fee46ce3a90f029ba9361839ab550 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -18,7 +18,6 @@ FROM node:8-alpine
ARG PORT
ENV PORT=$PORT
ENV NODE_ENV=production
-ENV DOCKER_BUILD=true
RUN apk --no-cache add ca-certificates
RUN mkdir /iv-app
diff --git a/deploy/datasets/index.js b/deploy/datasets/index.js
index 70d2d38bc516f8b71f4015d7cf0211b3c7894dce..1d9ac9c01a25faba6f28e75a1bc519f04fe71922 100644
--- a/deploy/datasets/index.js
+++ b/deploy/datasets/index.js
@@ -1,111 +1,37 @@
const express = require('express')
-const fs = require('fs')
-const path = require('path')
const datasetsRouter = express.Router()
+const { init, getDatasets } = require('./query')
-const cachedFilePath = path.join(__dirname, '..', 'res', 'cachedKgDS.20190225.json')
-let cachedData = null
-let cachedSpaces = null
+init()
-fs.readFile(cachedFilePath, 'utf-8', (err, data) => {
- if (err)
- throw err
- const json = JSON.parse(data)
- cachedData = json.results.filter(ds => ds.embargoStatus.some(s => s === 'Free'))
-
- const allPNames = cachedData.filter(v => v.parcellationRegion.length > 0).map(v => v.parcellationRegion[0].name)
- const noPNameNoRefSpace = cachedData.filter(v => v.parcellationRegion.length === 0 && v.referenceSpaces.length === 0)
-})
-
-datasetsRouter.get('/templateName/:templateName', (req, res) => {
+datasetsRouter.get('/templateName/:templateName', (req, res, next) => {
const { templateName } = req.params
- /**
- * temporary use cached data. in future, live fetch data and/or apply caching
- */
- const filteredData = cachedData.filter(ds => {
- return templateName === 'undefined'
- ? ds.referenceSpaces.length === 0
- : ds.referenceSpaces.some(rs => rs.name === templateName)
- })
- res.status(200).send(JSON.stringify(filteredData))
-})
-
-
-const readConfigFile = (filename) => new Promise((resolve, reject) => {
- const filepath = path.join(__dirname, '..', 'res', filename)
- fs.readFile(filepath, 'utf-8', (err, data) => {
- if(err) reject(err)
- resolve(data)
- })
+ getDatasets({ templateName })
+ .then(ds => {
+ res.status(200).send(JSON.stringify(ds))
+ })
+ .catch(error => {
+ next({
+ code: 500,
+ error
+ })
+ })
})
-const flattenArray = (array) => {
- return array.filter(item => item.children.length === 0).concat(
- ...array.filter(item => item.children.length > 0).map(item => flattenArray(item.children))
- )
-}
-
-let juBrain = null
-let shortBundle = null
-let longBundle = null
-
-readConfigFile('colin.json')
- .then(data => JSON.parse(data))
- .then(json => {
- juBrain = flattenArray(json.parcellations[0].regions)
- })
- .catch(console.error)
-readConfigFile('MNI152.json')
- .then(data => JSON.parse(data))
- .then(json => {
- longBundle = flattenArray(json.parcellations[0].regions)
- shortBundle = flattenArray(json.parcellations[1].regions)
- })
- .catch(console.error)
datasetsRouter.get('/parcellationName/:parcellationName', (req, res) => {
const { parcellationName } = req.params
- let returnArr
- switch (parcellationName) {
- case 'JuBrain Cytoarchitectonic Atlas':
- returnArr = juBrain
- ? cachedData
- .filter(ds => !/infant/i.test(ds.name))
- .filter(ds =>
- ds.parcellationRegion.length > 0 &&
- ds.parcellationRegion.some(pr => {
- const regex = new RegExp(pr.name)
- return juBrain.some(juBR => regex.test(juBR.name))
- }))
- : []
- break;
- case 'Fibre Bundle Atlas - Long Bundle':
- returnArr = longBundle
- ? cachedData
- .filter(ds =>
- ds.parcellationRegion.length > 0 &&
- ds.parcellationRegion.some(pr => {
- const regex = new RegExp(pr.name)
- return longBundle.some(lbr => regex.test(lbr.name))
- }))
- : []
- break;
- case 'Fibre Bundle Atlas - Short Bundle':
- returnArr = shortBundle
- ? cachedData
- .filter(ds =>
- ds.parcellationRegion.length > 0 &&
- ds.parcellationRegion.some(pr => {
- const regex = new RegExp(pr.name)
- return shortBundle.some(sbr => regex.test(sbr.name))
- }))
- : []
- break;
- default:
- returnArr = []
- }
- res.status(200).send(JSON.stringify(returnArr))
+ getDatasets({ parcellationName })
+ .then(ds => {
+ res.status(200).send(JSON.stringify(ds))
+ })
+ .catch(error => {
+ next({
+ code: 500,
+ error
+ })
+ })
})
module.exports = datasetsRouter
\ No newline at end of file
diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
new file mode 100644
index 0000000000000000000000000000000000000000..213dee9b3972bc847524d62dda91329c12ea56a4
--- /dev/null
+++ b/deploy/datasets/query.js
@@ -0,0 +1,118 @@
+const fs = require('fs')
+const request = require('request')
+const path = require('path')
+
+let cachedData = null
+let otherQueryResult = null
+const queryUrl = process.env.KG_DATASET_QUERY_URL || `https://kg-int.humanbrainproject.org/query/minds/core/dataset/v1.0.0/interactiveViewerKgQuery/instances/public?size=450&vocab=https%3A%2F%2Fschema.hbp.eu%2FmyQuery%2F`
+const timeout = process.env.TIMEOUT || 5000
+
+const fetchDatasetFromKg = () => new Promise((resolve, reject) => {
+ request(queryUrl, (err, resp, body) => {
+ if (err)
+ return reject(err)
+ const json = JSON.parse(body)
+ resolve(json)
+ })
+})
+
+const getDs = () => Promise.race([
+ new Promise((rs, rj) => {
+ setTimeout(() => {
+ if (cachedData) {
+ rs(cachedData)
+ } else {
+ /**
+ * cached data not available, have to wait
+ */
+ }
+ }, timeout)
+ }),
+ fetchDatasetFromKg()
+ .then(({results, ...rest}) => {
+ cachedData = results
+ otherQueryResult = rest
+ return cachedData
+ })
+])
+
+/**
+ * Needed by filter by parcellation
+ */
+
+const flattenArray = (array) => {
+ return array.filter(item => item.children.length === 0).concat(
+ ...array.filter(item => item.children.length > 0).map(item => flattenArray(item.children))
+ )
+}
+
+const readConfigFile = (filename) => new Promise((resolve, reject) => {
+ const filepath = path.join(__dirname, '..', 'res', filename)
+ fs.readFile(filepath, 'utf-8', (err, data) => {
+ if(err) reject(err)
+ resolve(data)
+ })
+})
+
+let juBrain = null
+let shortBundle = null
+let longBundle = null
+
+readConfigFile('colin.json')
+ .then(data => JSON.parse(data))
+ .then(json => {
+ juBrain = flattenArray(json.parcellations[0].regions)
+ })
+ .catch(console.error)
+
+readConfigFile('MNI152.json')
+ .then(data => JSON.parse(data))
+ .then(json => {
+ longBundle = flattenArray(json.parcellations[0].regions)
+ shortBundle = flattenArray(json.parcellations[1].regions)
+ })
+ .catch(console.error)
+
+const filterByPRs = (prs, atlasPr) => atlasPr
+ ? prs.some(pr => {
+ const regex = new RegExp((pr.name))
+ return atlasPr.some(aPr => regex.test(aPr.name))
+ })
+ : false
+
+const filter = (datasets, {templateName, parcellationName}) => datasets.filter(ds => {
+ if (templateName) {
+ return templateName === 'undefined'
+ ? ds.referenceSpaces.length === 0
+ : ds.referenceSpaces.some(rs => rs.name === templateName)
+ }
+ if (parcellationName) {
+ return ds.parcellationRegion.length > 0
+ ? filterByPRs(
+ ds.parcellationRegion,
+ parcellationName === 'JuBrain Cytoarchitectonic Atlas' && juBrain && !/infant/.test(ds.name)
+ ? juBrain
+ : parcellationName === 'Fibre Bundle Atlas - Long Bundle' && longBundle
+ ? longBundle
+ : parcellationName === 'Fibre Bundle Atlas - Short Bundle' && shortBundle
+ ? shortBundle
+ : null
+ )
+ : false
+ }
+
+ return false
+})
+
+/**
+ * on init, populate the cached data
+ */
+exports.init = () => fetchDatasetFromKg()
+ .then(json => {
+ cachedData = json
+ })
+
+exports.getDatasets = ({ templateName, parcellationName }) => getDs()
+ .then(json => filter(json, {templateName, parcellationName}))
+
+
diff --git a/deploy/package.json b/deploy/package.json
index fe22fd3a98bad52e51abf25f7763a6e9105293f0..0dfc574576eb6939f44b3e00b6c5d6bd91e17603 100644
--- a/deploy/package.json
+++ b/deploy/package.json
@@ -11,7 +11,8 @@
"license": "ISC",
"dependencies": {
"express": "^4.16.4",
- "openid-client": "^2.4.5"
+ "openid-client": "^2.4.5",
+ "request": "^2.88.0"
},
"devDependencies": {
"cors": "^2.8.5",
diff --git a/deploy/server.js b/deploy/server.js
index 6dd4b914fbb81239e450c1561a6219cc44eb0f18..d740f148761158f4dbb514b61a30e2a82b0295b0 100644
--- a/deploy/server.js
+++ b/deploy/server.js
@@ -14,7 +14,7 @@ const nehubaConfigRouter = require('./nehubaConfig')
const datasetRouter = require('./datasets')
const catchError = require('./catchError')
-const publicPath = process.env.DOCKER_BUILD
+const publicPath = process.env.NODE_ENV === 'production'
? path.join(__dirname, 'public')
: path.join(__dirname, '..', 'dist', 'aot')
diff --git a/src/components/pagination/pagination.component.ts b/src/components/pagination/pagination.component.ts
index fc962a2ae61f8423b9b898a7ad40bca1e7e5de0d..1723d4540cef7683c09f8ca7f5e81986c6003f80 100644
--- a/src/components/pagination/pagination.component.ts
+++ b/src/components/pagination/pagination.component.ts
@@ -8,12 +8,13 @@ import { Component, Input, Output, EventEmitter } from '@angular/core'
]
})
-export class PaginationComponent{
+export class PaginationComponent {
@Input() total : number = 0
@Input() hitsPerPage : number = 15
@Input() currentPage : number = 0
@Output() paginationChange : EventEmitter<number> = new EventEmitter()
+ @Output() outOfBound: EventEmitter<number> = new EventEmitter()
goto(pgnum:number){
const emitValue = pgnum < 0 ?
diff --git a/src/ui/databrowser/databrowser.component.ts b/src/ui/databrowser/databrowser.component.ts
index bee9c53cf554c960d200b4d33d0e0dc657572ef5..aa889e93b111861b12ee659466452047d9653cec 100644
--- a/src/ui/databrowser/databrowser.component.ts
+++ b/src/ui/databrowser/databrowser.component.ts
@@ -3,7 +3,7 @@ import { Store, select } from "@ngrx/store";
import { DataStateInterface, Property, safeFilter, DataEntry, File, SELECT_REGIONS, getLabelIndexMap, isDefined, SPATIAL_GOTO_PAGE, CHANGE_NAVIGATION, UPDATE_SPATIAL_DATA_VISIBLE, DESELECT_REGIONS, DESELECT_LANDMARKS, SELECT_LANDMARKS } from "../../services/stateStore.service";
import { map, filter, distinctUntilChanged } from "rxjs/operators";
import { HasPathProperty } from "../../util/pipes/pathToNestedChildren.pipe";
-import { Observable, Subscription, combineLatest } from "rxjs";
+import { Observable, Subscription, combineLatest, Subject } from "rxjs";
import { FileViewer } from "../fileviewer/fileviewer.component";
import { WidgetServices } from "../../atlasViewer/widgetUnit/widgetService.service";
import { AtlasViewerConstantsServices } from "../../atlasViewer/atlasViewer.constantService.service";
@@ -47,6 +47,12 @@ export class DataBrowserUI implements OnDestroy,OnInit{
private spatialDataEntries$ : Observable<any[]>
private spatialPagination$ : Observable<{spatialSearchPagination:number,spatialSearchTotalResults:number}>
+ /**
+ * TODO filter types
+ */
+ public filterApplied$: Observable<any>
+ private typeVisibility$: Subject<Set<String>> = new Subject()
+
private subscriptions : Subscription[] = []
get showDataTypes(){
@@ -86,6 +92,10 @@ export class DataBrowserUI implements OnDestroy,OnInit{
map(results => [...results[0], ...results[1]])
)
+ this.filterApplied$ = combineLatest(
+ this.selectedRegions$,
+ this.typeVisibility$
+ )
this.metadataMap$ = this.store.pipe(
select('dataStore'),
@@ -150,6 +160,10 @@ export class DataBrowserUI implements OnDestroy,OnInit{
this.subscriptions.push(
this.spatialPagination$.subscribe(this.handleSpatialPaginationChange.bind(this))
)
+
+ this.subscriptions.push(
+ this.filterApplied$.subscribe(() => this.currentPage = 0)
+ )
}
ngOnDestroy(){
@@ -285,6 +299,8 @@ export class DataBrowserUI implements OnDestroy,OnInit{
this.hideDataTypes = new Set(
[...this.hideDataTypes]
)
+
+ this.typeVisibility$.next(new Set([...this.hideDataTypes]))
}
gothere(event:MouseEvent,position:any){
diff --git a/src/util/pipes/filterDataEntriesByRegion.pipe.ts b/src/util/pipes/filterDataEntriesByRegion.pipe.ts
index 9236d20bd695bc7e59e55a52cc3265febe7122d7..1924a87ccae557fbf348092dad369e1c7e67ce68 100644
--- a/src/util/pipes/filterDataEntriesByRegion.pipe.ts
+++ b/src/util/pipes/filterDataEntriesByRegion.pipe.ts
@@ -14,10 +14,11 @@ export class FilterDataEntriesByRegion implements PipeTransform{
/**
* TODO: temporary hack, some dataset region name is not exactly the same as region
*/
- const regex = new RegExp(pr.name)
+ /* https://stackoverflow.com/a/9310752/6059235 */
+ const regex = new RegExp(pr.name.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, '\\$&'))
return selectedRegions.some(sr => regex.test(sr.name))
/**
- * more correct
+ * more correct, but probably should use UUID in the future
*/
return selectedRegions.some(sr => sr.name === pr.name)
})