diff --git a/.github/workflows/docker_img.yml b/.github/workflows/docker_img.yml
index 3470644fb386722065358045c226d8989a208b34..76e8788819f6139821b2794a5452ae25ee55d7fe 100644
--- a/.github/workflows/docker_img.yml
+++ b/.github/workflows/docker_img.yml
@@ -24,23 +24,26 @@ jobs:
echo "BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
+ echo "MATOMO_URL=${{ env.MATOMO_URL_PROD }}" >> $GITHUB_ENV
+ echo "MATOMO_ID=${{ env.MATOMO_ID_PROD }}" >> $GITHUB_ENV
+
if [[ "$GITHUB_REF" == 'refs/heads/master' ]]
then
echo "Either master, using prod env..."
- echo "MATOMO_URL=${{ env.MATOMO_URL_PROD }}" >> $GITHUB_ENV
- echo "MATOMO_ID=${{ env.MATOMO_ID_PROD }}" >> $GITHUB_ENV
echo "BS_REST_URL=${{ env.SIIBRA_API_STABLE }}" >> $GITHUB_ENV
elif [[ "$GITHUB_REF" == 'refs/heads/staging' ]]
then
echo "Either staging, using staging env..."
- echo "MATOMO_URL=${{ env.MATOMO_URL_PROD }}" >> $GITHUB_ENV
- echo "MATOMO_ID=${{ env.MATOMO_ID_PROD }}" >> $GITHUB_ENV
echo "BS_REST_URL=${{ env.SIIBRA_API_RC }}" >> $GITHUB_ENV
else
- echo "Using dev env..."
- echo "MATOMO_URL=${{ env.MATOMO_URL_DEV }}" >> $GITHUB_ENV
- echo "MATOMO_ID=${{ env.MATOMO_ID_DEV }}" >> $GITHUB_ENV
- echo "BS_REST_URL=${{ env.SIIBRA_API_LATEST }}" >> $GITHUB_ENV
+ if [[ "$GITHUB_REF" == *hotfix* ]]
+ then
+ echo "Hotfix branch, using prod env..."
+ echo "BS_REST_URL=${{ env.SIIBRA_API_STABLE }}" >> $GITHUB_ENV
+ else
+ echo "Using dev env..."
+ echo "BS_REST_URL=${{ env.SIIBRA_API_LATEST }}" >> $GITHUB_ENV
+ fi
fi
- name: 'Set version variable & expmt feature flag'
diff --git a/Dockerfile b/Dockerfile
index 23dea08fc6aa3b0cbc1e837707d7d6765b761e62..bc614aacaf8dcef73da19f4a59285e6a31e51daf 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,7 +7,7 @@ ARG DATASET_PREVIEW_URL
ENV DATASET_PREVIEW_URL=${DATASET_PREVIEW_URL:-https://hbp-kg-dataset-previewer.apps.hbp.eu/v2}
ARG BS_REST_URL
-ENV BS_REST_URL=${BS_REST_URL:-https://siibra-api-latest.apps-dev.hbp.eu/v1_0}
+ENV BS_REST_URL=${BS_REST_URL:-https://siibra-api-stable.apps.hbp.eu/v1_0}
ARG STRICT_LOCAL
ENV STRICT_LOCAL=${STRICT_LOCAL:-false}
diff --git a/build_env.md b/build_env.md
index 0cb122e3194e0efbf775678d65a0590bdd4f4063..1582bcdb0a487e3a91a88ecdcec45df445a687b9 100644
--- a/build_env.md
+++ b/build_env.md
@@ -7,7 +7,7 @@ As interactive atlas viewer uses [webpack define plugin](https://webpack.js.org/
| `VERSION` | printed in console on viewer startup | `GIT_HASH` \|\| unspecificed hash | v2.2.2 |
| `PRODUCTION` | if the build is for production, toggles optimisations such as minification | `undefined` | true |
| `BACKEND_URL` | backend that the viewer calls to fetch available template spaces, parcellations, plugins, datasets | `null` | https://interactive-viewer.apps.hbp.eu/ |
-| `BS_REST_URL` | [siibra-api](https://github.com/FZJ-INM1-BDA/siibra-api) used to fetch different resources | https://siibra-api-latest.apps-dev.hbp.eu/v1_0 |
+| `BS_REST_URL` | [siibra-api](https://github.com/FZJ-INM1-BDA/siibra-api) used to fetch different resources | https://siibra-api-stable.apps.hbp.eu/v1_0 |
| `DATASET_PREVIEW_URL` | dataset preview url used by component <https://github.com/fzj-inm1-bda/kg-dataset-previewer>. Useful for diagnosing issues with dataset previews.| https://hbp-kg-dataset-previewer.apps.hbp.eu/datasetPreview | http://localhost:1234/datasetPreview |
| `MATOMO_URL` | base url for matomo analytics | `null` | https://example.com/matomo/ |
| `MATOMO_ID` | application id for matomo analytics | `null` | 6 |
diff --git a/common/constants.js b/common/constants.js
index ceeb3d027330bb5167bd469abe812569d8be6da0..a4880c3a454d1d505182126643a24fab6c197a79 100644
--- a/common/constants.js
+++ b/common/constants.js
@@ -22,6 +22,7 @@
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',
+ VIEW_PINNED: `View pinned datasets.`,
BULK_DOWNLOAD: `Download all pinned data`,
NO_BULK_DOWNLOAD: `No datasets pinned`,
@@ -73,7 +74,8 @@
EXIT_ANNOTATION_MODE: 'Exit annotation mode',
// volume tuning specific
- VOLUME_TUNING_EXPAND: 'Expand volume tuning widget'
+ VOLUME_TUNING_EXPAND: 'Expand volume tuning widget',
+ BULK_DELETE_ANNOTATIONS: 'Delete all user annotations',
}
exports.IDS = {
@@ -82,6 +84,8 @@
}
exports.CONST = {
+ LOADING_TXT: `Loading ...`,
+
CANNOT_DECIPHER_HEMISPHERE: 'Cannot decipher region hemisphere.',
DOES_NOT_SUPPORT_MULTI_REGION_SELECTION: `Please only select a single region.`,
MULTI_REGION_SELECTION: `Multi region selection`,
@@ -106,6 +110,9 @@
QUICKTOUR_OK: `Start`,
QUICKTOUR_NEXTTIME: `Not now`,
QUICKTOUR_CANCEL: `Dismiss`,
+
+ DELETE_ALL_ANNOTATION_CONFIRMATION_MSG: `Are you sure you want to delete all annotations?`,
+ LOADING_ANNOTATION_MSG: `Loading annotations... Please wait...`
}
exports.QUICKTOUR_DESC ={
diff --git a/deploy/app.js b/deploy/app.js
index 29d6ab11ead3c319530104720e4708ec1f05986f..0a9aaa02df174ea5d934dddc6c7d998bd647f220 100644
--- a/deploy/app.js
+++ b/deploy/app.js
@@ -7,7 +7,7 @@ const crypto = require('crypto')
const cookieParser = require('cookie-parser')
const bkwdMdl = require('./bkwdCompat')()
-const { router: regionalFeaturesRouter, regionalFeatureIsReady } = require('./regionalFeatures')
+const deprecated = (_req, res) => res.status(410).end()
const LOCAL_CDN_FLAG = !!process.env.PRECOMPUTED_SERVER
@@ -202,11 +202,9 @@ app.use('/logo', require('./logo'))
app.get('/ready', async (req, res) => {
const authIsReady = authReady ? await authReady() : false
- const regionalFeatureReady = await regionalFeatureIsReady()
const allReady = [
authIsReady,
- regionalFeatureReady,
/**
* add other ready endpoints here
* call sig is await fn(): boolean
@@ -234,24 +232,14 @@ const jsonMiddleware = (req, res, next) => {
* resources endpoints
*/
const pluginRouter = require('./plugins')
-const previewRouter = require('./preview')
-
-const setResLocalMiddleWare = routePathname => (req, res, next) => {
- res.locals.routePathname = routePathname
- next()
-}
-
-const deprecated = (req, res) => {
- res.status(404).send(`Route has been removed.`)
-}
app.use('/atlases', deprecated)
app.use('/templates', deprecated)
app.use('/nehubaConfig', deprecated)
app.use('/datasets', deprecated)
-app.use('/regionalFeatures', jsonMiddleware, regionalFeaturesRouter)
+app.use('/regionalFeatures', deprecated)
app.use('/plugins', jsonMiddleware, pluginRouter)
-app.use('/preview', jsonMiddleware, previewRouter)
+app.use('/preview', deprecated)
const catchError = require('./catchError')
app.use(catchError)
diff --git a/deploy/auth/hbp-oidc.js b/deploy/auth/hbp-oidc.js
deleted file mode 100644
index a3dfb823b7e500535da14969f8ea966df5957140..0000000000000000000000000000000000000000
--- a/deploy/auth/hbp-oidc.js
+++ /dev/null
@@ -1,44 +0,0 @@
-const passport = require('passport')
-const { configureAuth } = require('./oidc')
-
-const HOSTNAME = process.env.HOSTNAME || 'http://localhost:3000'
-const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
-const clientId = process.env.HBP_CLIENTID || 'no hbp id'
-const clientSecret = process.env.HBP_CLIENTSECRET || 'no hbp client secret'
-const discoveryUrl = 'https://services.humanbrainproject.eu/oidc'
-const redirectUri = `${HOSTNAME}${HOST_PATHNAME}/hbp-oidc/cb`
-const cb = (tokenset, {sub, given_name, family_name, ...rest}, done) => {
- return done(null, {
- id: `hbp-oidc:${sub}`,
- name: `${given_name} ${family_name}`,
- type: `hbp-oidc`,
- tokenset,
- rest
- })
-}
-
-module.exports = async (app) => {
- try {
- const { oidcStrategy } = await configureAuth({
- clientId,
- clientSecret,
- discoveryUrl,
- redirectUri,
- cb,
- scope: 'openid offline_access',
- clientConfig: {
- redirect_uris: [ redirectUri ],
- response_types: [ 'code' ]
- }
- })
-
- passport.use('hbp-oidc', oidcStrategy)
- app.get('/hbp-oidc/auth', passport.authenticate('hbp-oidc'))
- app.get('/hbp-oidc/cb', passport.authenticate('hbp-oidc', {
- successRedirect: `${HOST_PATHNAME}/`,
- failureRedirect: `${HOST_PATHNAME}/`
- }))
- } catch (e) {
- console.error(e)
- }
-}
diff --git a/deploy/auth/index.js b/deploy/auth/index.js
index ebb1172d85e9abc8b553f2cc0c31f453f238c74f..413afb7088e2cfc62b429c07043a566045461308 100644
--- a/deploy/auth/index.js
+++ b/deploy/auth/index.js
@@ -10,16 +10,12 @@ const ready = async () => isReady
const configureAuth = async (app) => {
console.log('configure Auth')
- const hbpOidc = require('./hbp-oidc')
const { bootstrapApp: boostrapOidcV2 } = require('./hbp-oidc-v2')
const { initPassportJs, objStoreDb } = require('./util')
initPassportJs(app)
- await retry(async () => {
- await hbpOidc(app)
- }, { timeout: 1000, retries: 3 })
await retry(async () => {
await boostrapOidcV2(app)
}, { timeout: 1000, retries: 3 })
diff --git a/deploy/auth/index.spec.js b/deploy/auth/index.spec.js
index a75affe6ffa1c07c4456cb12d61c71d75e090d33..84691ddd6ccae9169f321858453c2eacf0dcb28c 100644
--- a/deploy/auth/index.spec.js
+++ b/deploy/auth/index.spec.js
@@ -1,8 +1,6 @@
const sinon = require('sinon')
const { assert, expect } = require('chai')
const initPassportJsStub = sinon.stub()
-
-const hbpOidcStub = sinon.stub()
const hbpOidcV2Stub = sinon.stub()
const appGetStub = sinon.stub()
@@ -12,9 +10,6 @@ describe('auth/index.js', () => {
require.cache[require.resolve('./util')] = {
exports: { initPassportJs: initPassportJsStub }
}
- require.cache[require.resolve('./hbp-oidc')] = {
- exports: hbpOidcStub
- }
require.cache[require.resolve('./hbp-oidc-v2')] = {
exports: {
bootstrapApp: hbpOidcV2Stub
@@ -24,9 +19,7 @@ describe('auth/index.js', () => {
beforeEach(() => {
delete require.cache[require.resolve('./index.js')]
- hbpOidcStub.returns({})
hbpOidcV2Stub.returns({})
- hbpOidcStub.resetHistory()
hbpOidcV2Stub.resetHistory()
})
@@ -37,11 +30,6 @@ describe('auth/index.js', () => {
const dummyObj = { get: appGetStub }
await configureAuth(dummyObj)
- assert(
- hbpOidcStub.called,
- 'hbpOidc called'
- )
-
assert(
hbpOidcV2Stub.called,
'hbpOidcV2 called'
@@ -58,7 +46,7 @@ describe('auth/index.js', () => {
const { configureAuth } = require('./index.js')
const dummyObj = { get: appGetStub }
- hbpOidcStub.throws(`throw error`)
+ hbpOidcV2Stub.throws(`throw error`)
try {
@@ -76,14 +64,10 @@ describe('auth/index.js', () => {
} catch (e) {
assert(
- hbpOidcStub.calledThrice,
- 'hbpOidc called thrice'
+ hbpOidcV2Stub.calledThrice,
+ 'hbpOidcv2 called thrice'
)
- assert(
- !hbpOidcV2Stub.called,
- 'hbpOidcV2 not called'
- )
}
})
})
@@ -105,7 +89,7 @@ describe('auth/index.js', () => {
const { configureAuth, ready } = require('./index.js')
const dummyObj = { get: appGetStub }
- hbpOidcStub.throws(`throw error`)
+ hbpOidcV2Stub.throws(`throw error`)
try {
await (() => new Promise((rs, rj) => {
diff --git a/deploy/bkwdCompat/urlState.js b/deploy/bkwdCompat/urlState.js
index f902a8a9f32a10dd843a0d0e4e561db18f28c7e3..66f92c3dc4f6b375fcfe0c70f16a685b43c30e0d 100644
--- a/deploy/bkwdCompat/urlState.js
+++ b/deploy/bkwdCompat/urlState.js
@@ -42,7 +42,10 @@ const templateMap = {
id: 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588',
parc: {
'Cytoarchitectonic Maps - v2.4': {
- id: 'juelich/iav/atlas/v1.0.0/7'
+ id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290',
+ },
+ 'Cytoarchitectonic Maps': {
+ id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290',
},
'Cortical Layers Segmentation': {
id: 'juelich/iav/atlas/v1.0.0/3'
@@ -57,13 +60,14 @@ const templateMap = {
id: 'minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2',
parc: {
'Cytoarchitectonic Maps - v2.5.1': {
- id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-26'
+ // redirect julich brain v251 to v290
+ id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290'
},
'Short Fiber Bundles - HCP': {
id: 'juelich/iav/atlas/v1.0.0/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c'
},
'Cytoarchitectonic maps - v1.18': {
- id: 'juelich/iav/atlas/v1.0.0/8'
+ id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
},
'Long Bundle': {
id: 'juelich/iav/atlas/v1.0.0/5'
@@ -93,7 +97,7 @@ const templateMap = {
id: 'minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992',
parc: {
'Cytoarchitectonic Maps - v1.18': {
- id: 'juelich/iav/atlas/v1.0.0/8'
+ id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
}
}
},
@@ -202,8 +206,8 @@ module.exports = (query, _warningCb) => {
// ignore region selected and move on
}
}
-
- let redirectUrl = '/#'
+ const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
+ let redirectUrl = `${HOST_PATHNAME}/#`
if (standaloneVolumes) {
searchParam.set('standaloneVolumes', standaloneVolumes)
if (nav) redirectUrl += nav
@@ -222,7 +226,7 @@ module.exports = (query, _warningCb) => {
}
const { id: p } = parc[parcellationSelected] || {}
if (p) redirectUrl += `/p:${encodeId(p)}`
- if (r) redirectUrl += r
+ if (r && parcellationSelected !== 'Cytoarchitectonic Maps - v2.5.1') redirectUrl += r
if (nav) redirectUrl += nav
if (dsp) redirectUrl += dsp
diff --git a/deploy/csp/index.js b/deploy/csp/index.js
index d745b8d58f0a70422b9d48cb481cf533f01401eb..4deecdda1795ff07c9e6f6f68fcf812c94540432 100644
--- a/deploy/csp/index.js
+++ b/deploy/csp/index.js
@@ -39,12 +39,24 @@ const defaultAllowedSites = [
const connectSrc = [
"'self'",
+
+ // needed by ad hoc generation of URL resources
"blob:",
+
+ // siibra-api endpoints
+ 'siibra-api-latest.apps-dev.hbp.eu',
+ 'siibra-api-rc.apps.hbp.eu',
+ 'siibra-api-stable.apps.hbp.eu',
+
+ // chunk servers
'neuroglancer.humanbrainproject.org',
'neuroglancer.humanbrainproject.eu',
- 'connectivity-query-v1-1-connectivity.apps-dev.hbp.eu',
'object.cscs.ch',
- 'hbp-kg-dataset-previewer.apps.hbp.eu/v2/', // required for dataset previews
+
+ // required for dataset previews
+ 'hbp-kg-dataset-previewer.apps.hbp.eu/v2/',
+
+ // injected by env var
...CSP_CONNECT_SRC
]
@@ -125,6 +137,7 @@ module.exports = {
} else {
console.warn(`CSP Violation: no data received!`)
}
+ res.status(204).end()
})
}
}
diff --git a/deploy/package.json b/deploy/package.json
index 8ac08ced5847f7e9915dabd46bb96e642ad3fcd7..95da8df0bd39afe6c3076fe360260e3b4f81995b 100644
--- a/deploy/package.json
+++ b/deploy/package.json
@@ -5,7 +5,7 @@
"main": "index.js",
"scripts": {
"start": "node server.js",
- "test": "DISABLE_LIMITER=1 node -r dotenv/config ./node_modules/.bin/mocha './**/*.spec.js' --exclude 'node_modules/*' --timeout 60000 --exit",
+ "test": "node -r dotenv/config ./node_modules/.bin/mocha './**/*.spec.js' --exclude 'node_modules/*' --timeout 60000 --exit",
"mocha": "mocha"
},
"keywords": [],
@@ -17,17 +17,15 @@
"connect-redis": "^5.0.0",
"cookie-parser": "^1.4.5",
"express": "^4.16.4",
- "express-rate-limit": "^5.1.1",
"express-session": "^1.15.6",
"got": "^10.5.5",
- "hbp-seafile": "^0.1.0",
+ "hbp-seafile": "^0.2.0",
"helmet-csp": "^2.8.0",
"lru-cache": "^5.1.1",
"memorystore": "^1.6.1",
"nomiseco": "0.0.2",
"openid-client": "^4.4.0",
"passport": "^0.4.0",
- "rate-limit-redis": "^1.7.0",
"redis": "^3.0.2",
"request": "^2.88.0",
"showdown": "^1.9.1",
diff --git a/deploy/preview/index.js b/deploy/preview/index.js
deleted file mode 100644
index 426d04d827b0be5c8305c1466c46f13e071aaaf4..0000000000000000000000000000000000000000
--- a/deploy/preview/index.js
+++ /dev/null
@@ -1,27 +0,0 @@
-const router = require('express').Router()
-const request = require('request')
-const url = require('url')
-const stream = require('stream')
-const { getHandleErrorFn } = require('../util/streamHandleError')
-
-let PROXY_HOSTNAME_WHITELIST
-
-try{
- PROXY_HOSTNAME_WHITELIST = JSON.parse(process.env.PROXY_HOSTNAME_WHITELIST)
-}catch(e){
- PROXY_HOSTNAME_WHITELIST = []
-}
-
-const whiteList = new Set([
- 'object.cscs.ch',
- ...PROXY_HOSTNAME_WHITELIST
-])
-
-router.get('/file', (req, res) => {
- const { fileUrl } = req.query
- const f = url.parse(fileUrl)
- if(f && f.hostname && whiteList.has(f.hostname)) return request(fileUrl).pipe(res).on('error', getHandleErrorFn(req, res))
- else res.status(400).send()
-})
-
-module.exports = router
\ No newline at end of file
diff --git a/deploy/regionalFeatures/index.js b/deploy/regionalFeatures/index.js
deleted file mode 100644
index f642c86afa4b8e1695fde72b9bd600f4c5efbfbc..0000000000000000000000000000000000000000
--- a/deploy/regionalFeatures/index.js
+++ /dev/null
@@ -1,277 +0,0 @@
-const router = require('express').Router()
-const request = require('request')
-
-/**
- * TODO migrate to brainscape in the future
- */
-
-const REGIONAL_FEATURE_ENDPOINT_ARRAY = process.env.REGIONAL_FEATURE_ENDPOINT_ARRAY || []
-
-let arrayToFetch = []
-try {
- arrayToFetch = JSON.parse(REGIONAL_FEATURE_ENDPOINT_ARRAY)
-} catch (e) {
- console.warn(`parsing arrayToFetch parse failed`)
-}
-
-const regionIdToDataIdMap = new Map()
-const datasetIdToDataMap = new Map()
-const datasetIdDetailMap = new Map()
-
-let additionalDatasets = []
-const returnAdditionalDatasets = async () => additionalDatasets
-let isReady = false
-
-const ITERABLE_KEY_SYMBOL = Symbol('ITERABLE_KEY_SYMBOL')
-
-/**
- * this pattern allows all of the special data to be fetched in parallel
- * async await would mean it is fetched one at a time
- */
-
-const processRegionalFeatureObj = ({ regions, data, ['@id']: datasetId, type, name }) => {
-
- datasetIdDetailMap.set(datasetId, {
- ['@id']: datasetId,
- type,
- name
- })
- for (const { status, ['@id']: regionId, name, files } of regions) {
- if (regionIdToDataIdMap.has(regionId)) {
- const existingObj = regionIdToDataIdMap.get(regionId)
- /**
- * existingObj[datasetId] may be undefined
- */
- if (!existingObj[datasetId]) {
- existingObj[datasetId] = {
- type,
- }
- existingObj[ITERABLE_KEY_SYMBOL] = existingObj[ITERABLE_KEY_SYMBOL].concat(datasetId)
- }
- existingObj[datasetId][status] = (existingObj[datasetId][status] || []).concat(files)
- existingObj[datasetId][ITERABLE_KEY_SYMBOL] = (existingObj[datasetId][ITERABLE_KEY_SYMBOL] || []).concat(status)
- } else {
- const datasetObj = {
- [status]: files,
- type,
- }
- datasetObj[ITERABLE_KEY_SYMBOL] = [status]
- const obj = {
- name,
- '@id': regionId,
- [datasetId]: datasetObj
- }
- obj[ITERABLE_KEY_SYMBOL] = [datasetId]
- regionIdToDataIdMap.set(regionId, obj)
- }
- }
-
- const dataIdToDataMap = new Map()
- datasetIdToDataMap.set(datasetId, dataIdToDataMap)
-
- for (const { ['@id']: dataId, contact_points: contactPoints, referenceSpaces, ...rest } of data) {
- dataIdToDataMap.set(dataId, {
- ['@id']: dataId,
- contactPoints,
- referenceSpaces,
- ...rest
- })
- }
-}
-
-Promise.all(
- arrayToFetch.map(url =>
- new Promise((rs, rj) => {
- request.get(url, (err, _resp, body) => {
- if (err) return rj(err)
- const parsedObj = JSON.parse(body)
-
- if (Array.isArray(parsedObj)) {
- parsedObj.map(processRegionalFeatureObj)
- } else {
- processRegionalFeatureObj(parsedObj)
- }
-
- rs()
- })
- })
- )
-).then(() => {
- const map = new Map()
- for (const [regionId, regionObj] of regionIdToDataIdMap.entries()) {
- for (const datasetId of regionObj[ITERABLE_KEY_SYMBOL]) {
- const newArr = (map.get(datasetId) || []).concat(regionId)
- map.set(datasetId, newArr)
- }
- }
-
- for (const [ datasetId, arrRegionIds ] of map.entries()) {
- additionalDatasets = additionalDatasets.concat({
- fullId: `https://nexus.humanbrainproject.org/v0/data/${datasetId}`,
- parcellationRegion: arrRegionIds.map(id => ({ fullId: id })),
- species: [],
- kgReference: [
- `https://kg.ebrains.eu/search/instances/Dataset/${datasetId}`
- ]
- })
- }
-
- isReady = true
-})
-
-const getFeatureMiddleware = (req, res, next) => {
- const { featureFullId } = req.params
- const datasetIdToDataMapToUse = res.locals['overwrite_datasetIdToDataMap'] || datasetIdToDataMap
- if (!datasetIdToDataMapToUse.has(featureFullId)) {
- return res.status(404).send(`Not found. - getFeatureMiddleware -`)
- }
- res.locals['getFeatureMiddleware_cache_0'] = datasetIdToDataMapToUse.get(featureFullId)
- res.locals['getFeatureMiddleware_cache_1'] = datasetIdDetailMap.get(featureFullId)
- next()
-}
-
-const sendFeatureResponse = (req, res) => {
- if (!res.locals['getFeatureMiddleware_cache_0']) return res.status(500).send(`getFeatureMiddleware_cache_0 not populated`)
- const fullIdMap = res.locals['getFeatureMiddleware_cache_0']
- const featureDetail = res.locals['getFeatureMiddleware_cache_1'] || {}
- const dataKeys = Array.from(fullIdMap.keys())
- if (dataKeys.length === 0) return res.status(404).end()
- return res.status(200).json({
- ...featureDetail,
- data: dataKeys.map(dataId => {
- return {
- ['@id']: dataId,
- }
- })
- })
-}
-
-const getFeatureGetDataMiddleware = (req, res, next) => {
- const { dataId } = req.params
- if (!res.locals['getFeatureMiddleware_cache_0']) return res.status(500).send(`getFeatureMiddleware_cache_0 not populated`)
- const map = res.locals['getFeatureMiddleware_cache_0']
- if (!map.has(dataId)) {
- return res.status(404).send(`Not found. - getFeatureGetDataMiddleware -`)
- }
- res.locals['getFeatureGetDataMiddleware_cache_0'] = map.get(dataId)
- next()
-}
-
-const sendFeatureDataResponse = (req, res) => {
- if (!res.locals['getFeatureGetDataMiddleware_cache_0']) return res.stauts(500).send(`getFeatureGetDataMiddleware_cache_0 not populated`)
- const result = res.locals['getFeatureGetDataMiddleware_cache_0']
- res.status(200).json(result)
-}
-
-router.get(
- '/byFeature/:featureFullId',
- getFeatureMiddleware,
- sendFeatureResponse,
-)
-
-router.get(
- '/byFeature/:featureFullId/:dataId',
- getFeatureMiddleware,
- getFeatureGetDataMiddleware,
- sendFeatureDataResponse,
-)
-
-const byRegionMiddleware = (req, res, next) => {
-
- const { regionFullId } = req.params
- const { hemisphere, referenceSpaceId } = req.query
-
- if (!regionIdToDataIdMap.has(regionFullId)) {
- return res.status(404).send(`Not found. - byRegionMiddleware -`)
- }
-
- /**
- * datasetIdToDataMap:
- * datasetId -> dataId -> { ['@id']: string, contactPoints, referenceSpaces }
- */
- const overWriteDatasetIdToMap = new Map()
- res.locals['byRegionMiddleware_cache_0'] = overWriteDatasetIdToMap
- res.locals['overwrite_datasetIdToDataMap'] = overWriteDatasetIdToMap
-
- /**
- * TODO filter by reference spaces
- */
-
- const regionObj = regionIdToDataIdMap.get(regionFullId)
-
- for (const datasetId of regionObj[ITERABLE_KEY_SYMBOL]) {
- const returnMap = new Map()
- overWriteDatasetIdToMap.set(datasetId, returnMap)
- for (const hemisphereKey of regionObj[datasetId][ITERABLE_KEY_SYMBOL]) {
-
- /**
- * if hemisphere is defined, then skip if hemisphereKey does not match
- */
-
- if (!!hemisphere && hemisphereKey !== hemisphere) continue
- for (const { ['@id']: dataId } of regionObj[datasetId][hemisphereKey] || []) {
- try {
- const dataObj = datasetIdToDataMap.get(datasetId).get(dataId)
- if (
- !!referenceSpaceId
- && !! dataObj['referenceSpaces']
- && dataObj['referenceSpaces'].every(rs => rs['fullId'] !== '*' && rs['fullId'] !== referenceSpaceId)
- ) {
- continue
- }
- returnMap.set(
- dataId,
- dataObj
- )
- } catch (e) {
- console.warn(`${datasetId} or ${dataId} could not be found in datasetIdToDataMap`)
- }
- }
- }
- }
-
- next()
-}
-
-router.get(
- '/byRegion/:regionFullId',
- byRegionMiddleware,
- async (req, res) => {
- if (!res.locals['byRegionMiddleware_cache_0']) return res.status(500).send(`byRegionMiddleware_cache_0 not populated`)
-
- const returnMap = res.locals['byRegionMiddleware_cache_0']
- return res.status(200).json({
- features: Array.from(
- returnMap.keys()
- ).filter(id => {
- /**
- * do not return where there are no datas
- */
- return returnMap.get(id).size || 0 > 0
- }).map(id => ({ ['@id']: id }))
- })
- }
-)
-
-router.get(
- '/byRegion/:regionFullId/:featureFullId',
- byRegionMiddleware,
- getFeatureMiddleware,
- sendFeatureResponse,
-)
-
-router.get(
- '/byRegion/:regionFullId/:featureFullId/:dataId',
- byRegionMiddleware,
- getFeatureMiddleware,
- getFeatureGetDataMiddleware,
- sendFeatureDataResponse,
-)
-
-const regionalFeatureIsReady = async () => isReady
-
-module.exports = {
- router,
- regionalFeatureIsReady,
- returnAdditionalDatasets,
-}
diff --git a/deploy/saneUrl/index.js b/deploy/saneUrl/index.js
index b0033f9acefeb56e79bb379cfc0accad09d7b4d6..d6d5caa2ab0ee69c8568a14ee02bd64bf2df7bbd 100644
--- a/deploy/saneUrl/index.js
+++ b/deploy/saneUrl/index.js
@@ -1,41 +1,12 @@
const express = require('express')
const router = express.Router()
-const RateLimit = require('express-rate-limit')
-const RedisStore = require('rate-limit-redis')
const { FallbackStore: Store, NotFoundError } = require('./store')
-const lruStore = require('../lruStore')
const { Store: DepcStore } = require('./depcObjStore')
-const { readUserData, saveUserData } = require('../user/store')
const store = new Store()
const depStore = new DepcStore()
-const { DISABLE_LIMITER, HOSTNAME, HOST_PATHNAME } = process.env
-
-
-let limiter
-const getLimiter = async () => {
- if (DISABLE_LIMITER) return passthrough
-
- if (!!limiter) return limiter
-
- await lruStore._initPr
- if (lruStore.redisURL) {
- limiter = new RateLimit({
- windowMs: 1e3 * 5,
- max: 5,
- store: new RedisStore({ redisURL })
- })
- } else {
- limiter = new RateLimit({
- windowMs: 1e3 * 5,
- max: 5,
- })
- }
- return limiter
-}
-
-const passthrough = (_, __, next) => next()
+const { HOSTNAME, HOST_PATHNAME } = process.env
const acceptHtmlProg = /text\/html/i
@@ -105,52 +76,7 @@ router.get('/:name', async (req, res) => {
})
router.post('/:name',
- getLimiter,
- async (req, res, next) => {
- const { name } = req.params
- try {
- const exist = await getFile(name)
- if (!exist) throw new NotFoundError()
- return res.status(409).send(`filename already exists`)
- } catch (e) {
- if (e instanceof NotFoundError) return next()
- else return res.status(500).send(e)
- }
- },
- express.json(),
- async (req, res) => {
- const { name } = req.params
- const { body, user } = req
-
- try {
- const payload = {
- ...body,
- userId: user && user.id,
- expiry: !user && (Date.now() + 1e3 * 60 * 60 * 72)
- }
-
- await store.set(name, JSON.stringify(payload))
- res.status(200).end()
-
- try {
- if (!user) return
- const { savedCustomLinks = [], ...rest } = await readUserData(user)
- await saveUserData(user, {
- ...rest,
- savedCustomLinks: [
- ...savedCustomLinks,
- name
- ]
- })
- } catch (e) {
- console.error(`reading/writing user data error ${user && user.id}, ${name}`, e)
- }
- } catch (e) {
- console.error(`saneUrl /POST error`, e)
- const { statusCode, statusMessage } = e
- res.status(statusCode || 500).send(statusMessage || 'Error encountered.')
- }
- }
+ (_req, res) => res.status(410).end()
)
router.use((_, res) => {
diff --git a/deploy_env.md b/deploy_env.md
index 7e4a55a80c10ba180399e31f30a9b71b83bddc5b..ca6a5e72c6aa542a6b88471f88eb3174a3b2e05f 100644
--- a/deploy_env.md
+++ b/deploy_env.md
@@ -70,7 +70,6 @@
| `REDIS_PORT` | fall back to `REDIS_RATE_LIMITING_DB_EPHEMERAL_PORT_6379_TCP_PORT` |
| `REDIS_USERNAME` |
| `REDIS_PASSWORD` |
-| `DISABLE_LIMITER` | disable rate limiting (maybe required for automated tests) |
##### SaneUrl
diff --git a/docs/releases/v2.4.1.md b/docs/releases/v2.4.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..4768d30acb00b7b73b5472fbb48c86800739152a
--- /dev/null
+++ b/docs/releases/v2.4.1.md
@@ -0,0 +1,5 @@
+# v2.4.1
+
+## Bugfixes
+
+- fix JulichBrain v2.5.0/v1.18 URL redirection
\ No newline at end of file
diff --git a/docs/releases/v2.4.2.md b/docs/releases/v2.4.2.md
new file mode 100644
index 0000000000000000000000000000000000000000..b2c4a5b8b3fb9b86c60b318067675b3377b00a6e
--- /dev/null
+++ b/docs/releases/v2.4.2.md
@@ -0,0 +1,7 @@
+# v2.4.2
+
+## Bugfixes
+
+- fix template/parcellation selector vertical scroll on small devices
+- fix atlas order (human -> rat -> mouse)
+- fsaverage use pial as default viewing mode (if possible)
diff --git a/docs/releases/v2.4.3.md b/docs/releases/v2.4.3.md
new file mode 100644
index 0000000000000000000000000000000000000000..a91b54fd8df91420a49c0a69415f04782b0a7c12
--- /dev/null
+++ b/docs/releases/v2.4.3.md
@@ -0,0 +1,6 @@
+# v2.4.3
+
+## Bugfixes
+
+- fix some of the big brain maps
+- added UI indication for deprecation/unavailability of functionalities
diff --git a/docs/releases/v2.4.4.md b/docs/releases/v2.4.4.md
new file mode 100644
index 0000000000000000000000000000000000000000..cadb5d9df79de2f9c768008c4a35d1b705a0bb81
--- /dev/null
+++ b/docs/releases/v2.4.4.md
@@ -0,0 +1,13 @@
+# v2.4.4
+
+# Features
+
+- Allow name and description of annotations to be exported
+
+## Bugfixes
+
+- Fix version of connectivity web component
+
+## Under the hood stuff
+
+- Respond in csp violation reports
diff --git a/docs/releases/v2.4.5.md b/docs/releases/v2.4.5.md
new file mode 100644
index 0000000000000000000000000000000000000000..47df26c7f4c10e832a92e0b0e423203bd2aad301
--- /dev/null
+++ b/docs/releases/v2.4.5.md
@@ -0,0 +1,4 @@
+# v2.4.5
+
+## README
+- Modify the readme file with integration into the Siibra naming.
diff --git a/docs/releases/v2.4.6.md b/docs/releases/v2.4.6.md
new file mode 100644
index 0000000000000000000000000000000000000000..7aa58d68364d393a047bbfd87482ef50dfb3f8e5
--- /dev/null
+++ b/docs/releases/v2.4.6.md
@@ -0,0 +1,5 @@
+# v2.4.6
+
+## Bugfixes
+
+- Fix space press issue on full view
diff --git a/docs/releases/v2.4.7.md b/docs/releases/v2.4.7.md
new file mode 100644
index 0000000000000000000000000000000000000000..e5fcfaf6f7acabdd64790c13917249bc7be18669
--- /dev/null
+++ b/docs/releases/v2.4.7.md
@@ -0,0 +1,11 @@
+# v2.4.7
+
+## Bugfixes
+
+- Fix unnamed point landmark naming
+- Fix multiregion legacy links (#1022)
+
+## Under the hood stuff
+
+- Remove unused imports in the backend
+- Use `stable` branch of siibra-api by default (supercedes #997)
diff --git a/docs/releases/v2.4.8.md b/docs/releases/v2.4.8.md
new file mode 100644
index 0000000000000000000000000000000000000000..8ffbb5c55b071438e1fffe6b284b291f7ee77e0b
--- /dev/null
+++ b/docs/releases/v2.4.8.md
@@ -0,0 +1,13 @@
+# v2.4.8
+
+## Enhancements
+
+- Added badges to annotation tab button to show number of annotations added (#1007)
+- Added some feedbacks when annotations are being loaded
+- Added delete all annotation button
+- Added feedbacks when annotation from different reference spaces are added
+
+## Under the hood stuff
+
+- Tweaked space bar capture
+- Allow branches with `hotfix` in its name to target production siibra-api endpoints
diff --git a/mkdocs.yml b/mkdocs.yml
index f504c13ca845a5dd5b2bcb51a01caeadb3f47615..005eb93634ee3d01cea5258c1a22c0673c8c66cc 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -41,6 +41,14 @@ pages:
- Display non-atlas volumes: 'advanced/otherVolumes.md'
- Release notes:
- v2.5.0: 'releases/v2.5.0.md'
+ - v2.4.8: 'releases/v2.4.8.md'
+ - v2.4.7: 'releases/v2.4.7.md'
+ - v2.4.6: 'releases/v2.4.6.md'
+ - v2.4.5: 'releases/v2.4.5.md'
+ - v2.4.4: 'releases/v2.4.4.md'
+ - v2.4.3: 'releases/v2.4.3.md'
+ - v2.4.2: 'releases/v2.4.2.md'
+ - v2.4.1: 'releases/v2.4.1.md'
- v2.4.0: 'releases/v2.4.0.md'
- v2.3.11: 'releases/v2.3.11.md'
- v2.3.10: 'releases/v2.3.10.md'
diff --git a/src/atlasComponents/connectivity/hasConnectivity.directive.ts b/src/atlasComponents/connectivity/hasConnectivity.directive.ts
index b3cf77233d0a1a991722b42876cc38c60c7834ca..8879de8c093488b90acd5fb81d57820f341da36e 100644
--- a/src/atlasComponents/connectivity/hasConnectivity.directive.ts
+++ b/src/atlasComponents/connectivity/hasConnectivity.directive.ts
@@ -26,6 +26,10 @@ export class HasConnectivity implements OnInit, OnDestroy {
}
checkConnectivity(region) {
+ if (!region.context) {
+ this.hasConnectivity = false
+ return
+ }
const {atlas, parcellation, template} = region.context
if (region.name) {
const connectivityUrl = `${this.siibraApiUrl}/atlases/${encodeURIComponent(atlas['@id'])}/parcellations/${encodeURIComponent(parcellation['@id'])}/regions/${encodeURIComponent(region.name)}/features/ConnectivityProfile`
diff --git a/src/atlasComponents/parcellationRegion/region.base.ts b/src/atlasComponents/parcellationRegion/region.base.ts
index a16995b9af3a98b69c44f0577e2f6e1226b087df..b6e234f7bd763d31d851663f5fc147a68a0be883 100644
--- a/src/atlasComponents/parcellationRegion/region.base.ts
+++ b/src/atlasComponents/parcellationRegion/region.base.ts
@@ -34,6 +34,7 @@ export class RegionBase {
set region(val) {
this._region = val
this.region$.next(this._region)
+ this.hasContext$.next(!!this._region.context)
this.position = null
// bug the centroid returned is currently nonsense
@@ -62,6 +63,7 @@ export class RegionBase {
return this._region
}
+ public hasContext$: BehaviorSubject<boolean> = new BehaviorSubject(false)
public region$: BehaviorSubject<any> = new BehaviorSubject(null)
@Input()
@@ -90,7 +92,7 @@ export class RegionBase {
this.regionInOtherTemplates$ = this.region$.pipe(
distinctUntilChanged(),
- filter(v => !!v),
+ filter(v => !!v && !!v.context),
switchMap(region => this.store$.pipe(
select(
regionInOtherTemplateSelector,
@@ -285,7 +287,7 @@ export const regionInOtherTemplateSelector = createSelector(
const otherTemplates = fetchedTemplates
.filter(({ ['@id']: id }) => id !== regionOfInterest.context.template['@id']
&& atlasTemplateSpacesIds.includes(id)
- && regionOfInterest.availableIn.map(ai => ai.id).includes(id))
+ && (regionOfInterest.availableIn || []).map(ai => ai.id).includes(id))
for (const template of otherTemplates) {
const parcellation = template.parcellations.find(p => p['@id'] === regionOfInterest.context.parcellation['@id'])
diff --git a/src/atlasComponents/parcellationRegion/regionMenu/regionMenu.template.html b/src/atlasComponents/parcellationRegion/regionMenu/regionMenu.template.html
index 7f7a0cc5c1aae01b0747185c83b1c4de4c788a09..9717bea444b93fd92fa83b3ed8d1f381c9da79ff 100644
--- a/src/atlasComponents/parcellationRegion/regionMenu/regionMenu.template.html
+++ b/src/atlasComponents/parcellationRegion/regionMenu/regionMenu.template.html
@@ -127,7 +127,7 @@
content: kgRegionalFeatureList,
desc: '',
iconTooltip: 'Regional Features',
- iavNgIf: true
+ iavNgIf: hasContext$ | async
}">
</ng-container>
diff --git a/src/atlasComponents/regionalFeatures/bsFeatures/regionalFeatureWrapper/regionalFeatureWrapper.template.html b/src/atlasComponents/regionalFeatures/bsFeatures/regionalFeatureWrapper/regionalFeatureWrapper.template.html
index 6a62ae958982689268974f1fbfab9047dce5188e..adecf93c84ab9c417168b4588e1aef63e4bb55e0 100644
--- a/src/atlasComponents/regionalFeatures/bsFeatures/regionalFeatureWrapper/regionalFeatureWrapper.template.html
+++ b/src/atlasComponents/regionalFeatures/bsFeatures/regionalFeatureWrapper/regionalFeatureWrapper.template.html
@@ -52,7 +52,7 @@
<!-- feature template -->
<ng-template #itemContainer let-feature>
- <div class="d-inline-block pt-4 cursor-default"
+ <div class="d-block pt-4 cursor-default"
(click)="handleFeatureClick(feature)"
mat-ripple>
diff --git a/src/atlasComponents/uiSelectors/atlasLayerSelector/atlasLayerSelector.style.css b/src/atlasComponents/uiSelectors/atlasLayerSelector/atlasLayerSelector.style.css
index 9d43dc845dcf18755d5326699abaf0ce4139011b..56cfffcf79c4db7ee31690dbe90d44a4016ad97f 100644
--- a/src/atlasComponents/uiSelectors/atlasLayerSelector/atlasLayerSelector.style.css
+++ b/src/atlasComponents/uiSelectors/atlasLayerSelector/atlasLayerSelector.style.css
@@ -38,6 +38,8 @@
.selector-container
{
+ overflow-y:scroll;
+ max-height: 80vh;
width: 21rem;
bottom: 4rem;
z-index: 5;
diff --git a/src/atlasComponents/userAnnotations/annotationList/annotationList.component.ts b/src/atlasComponents/userAnnotations/annotationList/annotationList.component.ts
index 525f5eaa5dad6a2ca706664963bda383d8bef9ac..07eae088ce2154228ecc4df9f2f3779ed3390d5a 100644
--- a/src/atlasComponents/userAnnotations/annotationList/annotationList.component.ts
+++ b/src/atlasComponents/userAnnotations/annotationList/annotationList.component.ts
@@ -1,17 +1,18 @@
-import {Component, ViewChild} from "@angular/core";
-import {ARIA_LABELS} from "common/constants";
+import { Component, Optional, ViewChild } from "@angular/core";
+import { ARIA_LABELS, CONST } from "common/constants";
import { ModularUserAnnotationToolService } from "../tools/service";
import { IAnnotationGeometry, TExportFormats } from "../tools/type";
import { ComponentStore } from "src/viewerModule/componentStore";
-import { map, startWith, tap } from "rxjs/operators";
-import { Observable } from "rxjs";
+import { map, shareReplay, startWith } from "rxjs/operators";
+import { Observable, Subscription } from "rxjs";
import { TZipFileConfig } from "src/zipFilesOutput/type";
import { TFileInputEvent } from "src/getFileInput/type";
import { FileInputDirective } from "src/getFileInput/getFileInput.directive";
import { MatSnackBar } from "@angular/material/snack-bar";
import { unzip } from "src/zipFilesOutput/zipFilesOutput.directive";
+import { DialogService } from "src/services/dialogService.service";
-const README = 'EXAMPLE OF READ ME TEXT'
+const README = `{id}.sands.json file contains the data of annotations. {id}.desc.json contains the metadata of annotations.`
@Component({
selector: 'annotation-list',
@@ -26,11 +27,13 @@ export class AnnotationList {
public ARIA_LABELS = ARIA_LABELS
-
@ViewChild(FileInputDirective)
fileInput: FileInputDirective
+ private subs: Subscription[] = []
+ private managedAnnotations: IAnnotationGeometry[] = []
public managedAnnotations$ = this.annotSvc.spaceFilteredManagedAnnotations$
+ public annotationInOtherSpaces$ = this.annotSvc.otherSpaceManagedAnnotations$
public manAnnExists$ = this.managedAnnotations$.pipe(
map(arr => !!arr && arr.length > 0),
@@ -39,6 +42,7 @@ export class AnnotationList {
public filesExport$: Observable<TZipFileConfig[]> = this.managedAnnotations$.pipe(
startWith([] as IAnnotationGeometry[]),
+ shareReplay(1),
map(manAnns => {
const readme = {
filename: 'README.md',
@@ -50,17 +54,28 @@ export class AnnotationList {
filecontent: JSON.stringify(ann.toSands(), null, 2),
}
})
- return [ readme, ...annotationSands ]
+ const annotationDesc = manAnns.map(ann => {
+ return {
+ filename: `${ann.id}.desc.json`,
+ filecontent: JSON.stringify(this.annotSvc.exportAnnotationMetadata(ann), null, 2)
+ }
+ })
+ return [ readme, ...annotationSands, ...annotationDesc ]
})
)
constructor(
private annotSvc: ModularUserAnnotationToolService,
private snackbar: MatSnackBar,
cStore: ComponentStore<{ useFormat: TExportFormats }>,
+ @Optional() private dialogSvc: DialogService,
) {
cStore.setState({
useFormat: 'sands'
})
+
+ this.subs.push(
+ this.managedAnnotations$.subscribe(anns => this.managedAnnotations = anns)
+ )
}
public hiddenAnnotations$ = this.annotSvc.hiddenAnnotations$
@@ -71,10 +86,15 @@ export class AnnotationList {
private parseAndAddAnnotation(input: string) {
const json = JSON.parse(input)
const annotation = this.annotSvc.parseAnnotationObject(json)
- this.annotSvc.importAnnotation(annotation)
+ if (annotation) this.annotSvc.importAnnotation(annotation)
}
async handleImportEvent(ev: TFileInputEvent<'text' | 'file'>){
+
+ const { abort } = this.dialogSvc.blockUserInteraction({
+ title: CONST.LOADING_TXT,
+ markdown: CONST.LOADING_ANNOTATION_MSG,
+ })
try {
const clearFileInputAndInform = () => {
if (this.fileInput) {
@@ -128,6 +148,31 @@ export class AnnotationList {
this.snackbar.open(`Error importing: ${e.toString()}`, 'Dismiss', {
duration: 3000
})
+ } finally {
+ abort()
+ }
+ }
+
+ async deleteAllAnnotation(){
+ if (this.dialogSvc) {
+ try {
+ await this.dialogSvc.getUserConfirm({
+ markdown: CONST.DELETE_ALL_ANNOTATION_CONFIRMATION_MSG
+ })
+
+ for (const ann of this.managedAnnotations) {
+ ann.remove()
+ }
+ } catch (e) {
+ // aborted
+ }
+ } else {
+ if (window.confirm(CONST.DELETE_ALL_ANNOTATION_CONFIRMATION_MSG)) {
+
+ for (const ann of this.managedAnnotations) {
+ ann.remove()
+ }
+ }
}
}
}
diff --git a/src/atlasComponents/userAnnotations/annotationList/annotationList.style.css b/src/atlasComponents/userAnnotations/annotationList/annotationList.style.css
index 1f57a5f2d7a2155d5fb5c398d7fb079ee9337258..8e3b51c8c14b8e513fa4fb4dd7983b943cc2dc5d 100644
--- a/src/atlasComponents/userAnnotations/annotationList/annotationList.style.css
+++ b/src/atlasComponents/userAnnotations/annotationList/annotationList.style.css
@@ -8,3 +8,11 @@
:host-context([darktheme="false"]) .hovering-header {
background-color: rgb(245, 245, 245);
}
+
+.single-annotation-grid-container
+{
+ display: grid;
+ grid-template-columns: 3em auto;
+ gap: 0px 0px;
+ grid-template-areas: ". .";
+}
diff --git a/src/atlasComponents/userAnnotations/annotationList/annotationList.template.html b/src/atlasComponents/userAnnotations/annotationList/annotationList.template.html
index 17ac890eafc6f4049b039ad7c36147a2d481642d..7543d5d598ce9d77956aa6036636a1ba7b8408c5 100644
--- a/src/atlasComponents/userAnnotations/annotationList/annotationList.template.html
+++ b/src/atlasComponents/userAnnotations/annotationList/annotationList.template.html
@@ -26,13 +26,22 @@
<!-- export -->
<button mat-icon-button
- [zip-files-output]="filesExport$ | async"
+ [zip-files-output]="filesExport$"
zip-files-output-zip-filename="exported_annotations.zip"
[attr.aria-label]="ARIA_LABELS.USER_ANNOTATION_EXPORT"
[matTooltip]="ARIA_LABELS.USER_ANNOTATION_EXPORT"
[disabled]="!(manAnnExists$ | async)">
<i class="fas fa-download"></i>
</button>
+
+ <!-- delete all annotations -->
+ <button mat-icon-button
+ color="warn"
+ (click)="deleteAllAnnotation()"
+ [matTooltip]="ARIA_LABELS.BULK_DELETE_ANNOTATIONS"
+ [disabled]="!(manAnnExists$ | async)">
+ <i class="fas fa-trash"></i>
+ </button>
</mat-card-subtitle>
</div>
@@ -68,13 +77,10 @@
<!-- single annotation edit body -->
<ng-template matExpansionPanelContent>
- <div class="d-flex">
-
+ <div class="single-annotation-grid-container">
<!-- spacer for inset single-annotation-unit -->
- <div class="w-3em flex-grow-0 flex-shrink-0"></div>
-
- <single-annotation-unit [single-annotation-unit-annotation]="managedAnnotation"
- class="flex-grow-1 flex-shrink-1">
+ <div></div>
+ <single-annotation-unit [single-annotation-unit-annotation]="managedAnnotation">
</single-annotation-unit>
</div>
</ng-template>
@@ -82,6 +88,12 @@
</mat-accordion>
</ng-template>
+ <ng-template [ngIf]="annotationInOtherSpaces$ | async" let-annsInOtherSpace>
+ <div *ngIf="annsInOtherSpace.length > 0" class="p-4 text-muted">
+ {{ annsInOtherSpace.length }} annotations found in other reference spaces, and not shown here.
+ </div>
+ </ng-template>
+
<!-- place holder when no annotations exist -->
<ng-template #placeholderTmpl>
<div class="p-4 text-muted">
diff --git a/src/atlasComponents/userAnnotations/annotationMode/annotationMode.component.ts b/src/atlasComponents/userAnnotations/annotationMode/annotationMode.component.ts
index 38eae7e8134c3e7c87fa16722f1a2e248a929718..b316ac2632dd0c6b31cf43bb30345434d7f37941 100644
--- a/src/atlasComponents/userAnnotations/annotationMode/annotationMode.component.ts
+++ b/src/atlasComponents/userAnnotations/annotationMode/annotationMode.component.ts
@@ -11,10 +11,13 @@ import { MatSnackBar } from "@angular/material/snack-bar";
@Component({
selector: 'annotating-tools-panel',
templateUrl: './annotationMode.template.html',
- styleUrls: ['./annotationMode.style.css']
+ styleUrls: ['./annotationMode.style.css'],
+ exportAs: 'annoToolsPanel'
})
export class AnnotationMode implements OnDestroy{
+ public annBadges$ = this.modularToolSvc.badges$
+
public ARIA_LABELS = ARIA_LABELS
public moduleAnnotationTypes: {
diff --git a/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts b/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts
index 69506ed32fd960dbe4da329884fa164d4727469c..fb6500281577a0791f6c82b7d53ce6b7aef636a6 100644
--- a/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts
+++ b/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts
@@ -1,13 +1,20 @@
import { Pipe, PipeTransform } from "@angular/core";
import { IAnnotationGeometry } from "./tools/type";
+type TOpts = {
+ reverse?: boolean
+}
+
@Pipe({
name: 'filterAnnotationsBySpace',
pure: true
})
export class FilterAnnotationsBySpace implements PipeTransform{
- public transform(annotations: IAnnotationGeometry[], space: { '@id': string }): IAnnotationGeometry[]{
- return annotations.filter(ann => ann.space["@id"] === space["@id"])
+ public transform(annotations: IAnnotationGeometry[], space: { '@id': string }, opts?: TOpts): IAnnotationGeometry[]{
+ const { reverse = false } = opts || {}
+ return reverse
+ ? annotations.filter(ann => ann.space["@id"] !== space["@id"])
+ : annotations.filter(ann => ann.space["@id"] === space["@id"])
}
}
\ No newline at end of file
diff --git a/src/atlasComponents/userAnnotations/singleAnnotationUnit/singleAnnotationUnit.component.ts b/src/atlasComponents/userAnnotations/singleAnnotationUnit/singleAnnotationUnit.component.ts
index 299e8ccf558d42e793637ff2a3d95ff3f1e12b77..956f23c080c1929b07fc62159a42024c68334490 100644
--- a/src/atlasComponents/userAnnotations/singleAnnotationUnit/singleAnnotationUnit.component.ts
+++ b/src/atlasComponents/userAnnotations/singleAnnotationUnit/singleAnnotationUnit.component.ts
@@ -115,7 +115,7 @@ export class SingleAnnotationNamePipe implements PipeTransform{
public transform(ann: IAnnotationGeometry, name?: string): string{
if (name) return name
if (ann instanceof Polygon) return `Unnamed Polygon`
- if (ann instanceof Point) return `Unname Point`
+ if (ann instanceof Point) return `Unnamed Point`
if (ann instanceof Line) return `Unnamed Line`
return `Unnamed geometry`
}
@@ -133,4 +133,4 @@ export class SingleAnnotationClsIconPipe implements PipeTransform{
if (ann instanceof Line) return `fas fa-slash`
return `fas fa-mouse-pointer`
}
-}
\ No newline at end of file
+}
diff --git a/src/atlasComponents/userAnnotations/tools/delete.ts b/src/atlasComponents/userAnnotations/tools/delete.ts
index b1658e9cc44f91dc68ed41a5bd1bfe7bd49d0f5c..2e118bcd3dddb46ab2aa8d6ce702b8b14ccdd054 100644
--- a/src/atlasComponents/userAnnotations/tools/delete.ts
+++ b/src/atlasComponents/userAnnotations/tools/delete.ts
@@ -8,6 +8,7 @@ import { AbsToolClass, IAnnotationEvents, IAnnotationGeometry, IAnnotationTools,
export class ToolDelete extends AbsToolClass<Point> implements IAnnotationTools, OnDestroy {
public subs: Subscription[] = []
+ protected managedAnnotations = []
toolType: TToolType = 'deletion'
iconClass = 'fas fa-trash'
name = 'Delete'
diff --git a/src/atlasComponents/userAnnotations/tools/line.ts b/src/atlasComponents/userAnnotations/tools/line.ts
index 644258af23408c6edb3b0c03054ad92c400333d4..606c155f3e995bbf3bba85d6b82cb4040ae7a76e 100644
--- a/src/atlasComponents/userAnnotations/tools/line.ts
+++ b/src/atlasComponents/userAnnotations/tools/line.ts
@@ -193,7 +193,7 @@ export class ToolLine extends AbsToolClass<Line> implements IAnnotationTools, On
subs: Subscription[] = []
- private managedAnnotations: Line[] = []
+ protected managedAnnotations: Line[] = []
public managedAnnotations$ = new Subject<Line[]>()
onMouseMoveRenderPreview(pos: [number, number, number]) {
@@ -312,14 +312,6 @@ export class ToolLine extends AbsToolClass<Line> implements IAnnotationTools, On
this.subs.forEach(s => s.unsubscribe())
}
- addAnnotation(line: Line) {
- const idx = this.managedAnnotations.findIndex(ann => ann.id === line.id)
- if (idx >= 0) throw new Error(`Line annotation has already been added`)
- line.remove = () => this.removeAnnotation(line.id)
- this.managedAnnotations.push(line)
- this.managedAnnotations$.next(this.managedAnnotations)
- }
-
removeAnnotation(id: string){
const idx = this.managedAnnotations.findIndex(ann => ann.id === id)
if (idx < 0) {
diff --git a/src/atlasComponents/userAnnotations/tools/point.ts b/src/atlasComponents/userAnnotations/tools/point.ts
index e6fd9fee4f42d8535bd8998b0ffb471e211e0eec..af1543fed9b100ecabda6373bf4055b685c580f7 100644
--- a/src/atlasComponents/userAnnotations/tools/point.ts
+++ b/src/atlasComponents/userAnnotations/tools/point.ts
@@ -109,7 +109,7 @@ export class ToolPoint extends AbsToolClass<Point> implements IAnnotationTools,
public iconClass = POINT_ICON_CLASS
public subs: Subscription[] = []
- private managedAnnotations: Point[] = []
+ protected managedAnnotations: Point[] = []
public managedAnnotations$ = new Subject<Point[]>()
constructor(
@@ -177,14 +177,6 @@ export class ToolPoint extends AbsToolClass<Point> implements IAnnotationTools,
)
}
- addAnnotation(point: Point){
- const found = this.managedAnnotations.find(p => p.id === point.id)
- if (found) throw new Error(`Point annotation already added`)
- point.remove = () => this.removeAnnotation(point.id)
- this.managedAnnotations.push(point)
- this.managedAnnotations$.next(this.managedAnnotations)
- }
-
/**
* @description remove managed annotation via id
* @param id id of annotation
diff --git a/src/atlasComponents/userAnnotations/tools/poly.ts b/src/atlasComponents/userAnnotations/tools/poly.ts
index d226021de999af7b27ae98815f7fb34176f97ff5..2cd9285b256119f8ec112825b96fc615a6eea407 100644
--- a/src/atlasComponents/userAnnotations/tools/poly.ts
+++ b/src/atlasComponents/userAnnotations/tools/poly.ts
@@ -89,7 +89,7 @@ export class Polygon extends IAnnotationGeometry{
}
toString() {
- return `Points: ${JSON.stringify(this.points.map(p => p.toString()))}, edges: ${JSON.stringify(this.edges)}.`
+ return `Name: ${this.name}, Desc: ${this.desc}, Points: ${JSON.stringify(this.points.map(p => p.toString()))}, edges: ${JSON.stringify(this.edges)}.`
}
toSands(): TSandsPolyLine{
@@ -234,7 +234,7 @@ export class ToolPolygon extends AbsToolClass<Polygon> implements IAnnotationToo
private selectedPoly: Polygon
private lastAddedPoint: Point
- private managedAnnotations: Polygon[] = []
+ protected managedAnnotations: Polygon[] = []
public managedAnnotations$ = new Subject<Polygon[]>()
public subs: Subscription[] = []
@@ -404,14 +404,6 @@ export class ToolPolygon extends AbsToolClass<Polygon> implements IAnnotationToo
)
}
- addAnnotation(poly: Polygon){
- const idx = this.managedAnnotations.findIndex(ann => ann.id === poly.id)
- if (idx >= 0) throw new Error(`Polygon already added.`)
- poly.remove = () => this.removeAnnotation(poly.id)
- this.managedAnnotations.push(poly)
- this.managedAnnotations$.next(this.managedAnnotations)
- }
-
removeAnnotation(id: string) {
const idx = this.managedAnnotations.findIndex(ann => ann.id === id)
if (idx < 0) {
diff --git a/src/atlasComponents/userAnnotations/tools/select.ts b/src/atlasComponents/userAnnotations/tools/select.ts
index fd947eb34e813a956f21349dfd319898ba469fd0..10befd2dfe4b65ade055f2fcc81d57af5e2d4d3b 100644
--- a/src/atlasComponents/userAnnotations/tools/select.ts
+++ b/src/atlasComponents/userAnnotations/tools/select.ts
@@ -11,6 +11,7 @@ export class ToolSelect extends AbsToolClass<Point> implements IAnnotationTools,
toolType: TToolType = 'selecting'
iconClass = 'fas fa-mouse-pointer'
name = 'Select'
+ protected managedAnnotations = []
onMouseMoveRenderPreview(){
return []
diff --git a/src/atlasComponents/userAnnotations/tools/service.ts b/src/atlasComponents/userAnnotations/tools/service.ts
index c5489b5cd4e5edce83a612e209f8a86c1ffa6e6a..f77ec97b490bcb52fb27784b28f1202144a2f96e 100644
--- a/src/atlasComponents/userAnnotations/tools/service.ts
+++ b/src/atlasComponents/userAnnotations/tools/service.ts
@@ -27,6 +27,17 @@ const IAV_VOXEL_SIZES_NM = {
'minds/core/referencespace/v1.0.0/MEBRAINS_T1.masked': [1000000, 1000000, 1000000]
}
+type TAnnotationMetadata = {
+ id: string
+ name: string
+ desc: string
+}
+
+const descType: 'siibra-ex/meta/desc' = 'siibra-ex/meta/desc'
+type TTypedAnnMetadata = {
+ '@type': 'siibra-ex/meta/desc'
+} & TAnnotationMetadata
+
function scanCollapse<T>(){
return (src: Observable<{
tool: string
@@ -93,6 +104,20 @@ export class ModularUserAnnotationToolService implements OnDestroy{
scanCollapse(),
shareReplay(1),
)
+
+ public otherSpaceManagedAnnotations$ = combineLatest([
+ this.selectedTmpl$,
+ this.managedAnnotations$
+ ]).pipe(
+ map(([tmpl, annts]) => {
+ return this.filterAnnotationBySpacePipe.transform(
+ annts,
+ tmpl,
+ { reverse: true }
+ )
+ })
+ )
+
public spaceFilteredManagedAnnotations$ = combineLatest([
this.selectedTmpl$,
this.managedAnnotations$
@@ -105,6 +130,10 @@ export class ModularUserAnnotationToolService implements OnDestroy{
})
)
+ public badges$ = this.spaceFilteredManagedAnnotations$.pipe(
+ map(mann => mann.length > 0 ? mann.length : null)
+ )
+
private registeredTools: {
name: string
iconClass: string
@@ -552,7 +581,7 @@ export class ModularUserAnnotationToolService implements OnDestroy{
const anns: IAnnotationGeometry[] = []
for (const obj of arr) {
const geometry = this.parseAnnotationObject(obj)
- anns.push(geometry)
+ if (geometry) anns.push(geometry)
}
for (const ann of anns) {
@@ -560,6 +589,21 @@ export class ModularUserAnnotationToolService implements OnDestroy{
}
}
+ public exportAnnotationMetadata(ann: IAnnotationGeometry): TAnnotationMetadata & { '@type': 'siibra-ex/meta/desc' } {
+ return {
+ '@type': descType,
+ id: ann.id,
+ name: ann.name,
+ desc: ann.desc,
+ }
+ }
+
+ /**
+ * stop gap measure when exporting/import annotations in sands format
+ * metadata (name/desc) will be saved in a separate metadata file
+ */
+ private metadataMap = new Map<string, TAnnotationMetadata>()
+
private storeAnnotation(anns: IAnnotationGeometry[]){
const arr = []
for (const ann of anns) {
@@ -627,25 +671,49 @@ export class ModularUserAnnotationToolService implements OnDestroy{
})
}
- parseAnnotationObject(json: TSands | TGeometryJson): IAnnotationGeometry{
+ parseAnnotationObject(json: TSands | TGeometryJson | TTypedAnnMetadata): IAnnotationGeometry | null{
+ let returnObj: IAnnotationGeometry
if (json['@type'] === 'tmp/poly') {
- return Polygon.fromSANDS(json)
+ returnObj = Polygon.fromSANDS(json)
}
if (json['@type'] === 'tmp/line') {
- return Line.fromSANDS(json)
+ returnObj = Line.fromSANDS(json)
}
if (json['@type'] === 'https://openminds.ebrains.eu/sands/CoordinatePoint') {
- return Point.fromSANDS(json)
+ returnObj = Point.fromSANDS(json)
}
if (json['@type'] === 'siibra-ex/annotation/point') {
- return Point.fromJSON(json)
+ returnObj = Point.fromJSON(json)
}
if (json['@type'] === 'siibra-ex/annotation/line') {
- return Line.fromJSON(json)
+ returnObj = Line.fromJSON(json)
}
if (json['@type'] === 'siibra-ex/annotation/polyline') {
- return Polygon.fromJSON(json)
+ returnObj = Polygon.fromJSON(json)
+ }
+ if (json['@type'] === descType) {
+ const existingAnn = this.managedAnnotations.find(ann => json.id === ann.id)
+ if (existingAnn) {
+
+ // potentially overwriting existing name and desc...
+ // maybe should show warning?
+ existingAnn.setName(json.name)
+ existingAnn.setDesc(json.desc)
+ return existingAnn
+ } else {
+ const { id, name, desc } = json
+ this.metadataMap.set(id, { id, name, desc })
+ return
+ }
+ } else {
+ const metadata = this.metadataMap.get(returnObj.id)
+ if (returnObj && metadata) {
+ returnObj.setName(metadata?.name || null)
+ returnObj.setDesc(metadata?.desc || null)
+ this.metadataMap.delete(returnObj.id)
+ }
}
+ if (returnObj) return returnObj
throw new Error(`cannot parse annotation object`)
}
diff --git a/src/atlasComponents/userAnnotations/tools/type.ts b/src/atlasComponents/userAnnotations/tools/type.ts
index efb1d9136c74e1f55497efc62b5fda6798b9afbb..e74f0ca8ee389775b93f49836a4f504ab88ccfec 100644
--- a/src/atlasComponents/userAnnotations/tools/type.ts
+++ b/src/atlasComponents/userAnnotations/tools/type.ts
@@ -18,9 +18,9 @@ export abstract class AbsToolClass<T extends IAnnotationGeometry> {
public abstract name: string
public abstract iconClass: string
- public abstract addAnnotation(annotation: T): void
public abstract removeAnnotation(id: string): void
- public abstract managedAnnotations$: Observable<T[]>
+ public abstract managedAnnotations$: Subject<T[]>
+ protected abstract managedAnnotations: T[] = []
abstract subs: Subscription[]
protected space: TBaseAnnotationGeomtrySpec['space']
@@ -154,6 +154,14 @@ export abstract class AbsToolClass<T extends IAnnotationGeometry> {
}),
))
)
+
+ public addAnnotation(geom: T) {
+ const found = this.managedAnnotations.find(ann => ann.id === geom.id)
+ if (found) found.remove()
+ geom.remove = () => this.removeAnnotation(geom.id)
+ this.managedAnnotations.push(geom)
+ this.managedAnnotations$.next(this.managedAnnotations)
+ }
}
export type TToolType = 'selecting' | 'drawing' | 'deletion'
diff --git a/src/auth/auth.service.ts b/src/auth/auth.service.ts
index ae56dcc710806d93c05b0803cc42f0ac656accb1..bb610daceac50e7a2ae11ef8fe0919f025354fa3 100644
--- a/src/auth/auth.service.ts
+++ b/src/auth/auth.service.ts
@@ -32,10 +32,7 @@ export class AuthService implements OnDestroy {
* TODO build it dynamically, or at least possible to configure via env var
*/
public loginMethods: IAuthMethod[] = [{
- name: 'HBP OIDC',
- href: 'hbp-oidc/auth'
- }, {
- name: 'HBP OIDC v2 (beta)',
+ name: 'HBP OIDC v2',
href: 'hbp-oidc-v2/auth'
}]
diff --git a/src/components/confirmDialog/confirmDialog.component.ts b/src/components/confirmDialog/confirmDialog.component.ts
index 5c3d9eb02a50f5847b8ca78a5fabedfd39192f48..ec2e20c9fb6469c9ec26f88c77b73f50a77c57d3 100644
--- a/src/components/confirmDialog/confirmDialog.component.ts
+++ b/src/components/confirmDialog/confirmDialog.component.ts
@@ -25,12 +25,15 @@ export class ConfirmDialogComponent {
@Input()
public markdown: string
+ public hideActionBar = false
+
constructor(@Inject(MAT_DIALOG_DATA) data: any) {
- const { title = null, message = null, markdown, okBtnText, cancelBtnText} = data || {}
+ const { title = null, message = null, markdown, okBtnText, cancelBtnText, hideActionBar} = data || {}
if (title) this.title = title
if (message) this.message = message
if (markdown) this.markdown = markdown
if (okBtnText) this.okBtnText = okBtnText
if (cancelBtnText) this.cancelBtnText = cancelBtnText
+ if (hideActionBar) this.hideActionBar = hideActionBar
}
}
diff --git a/src/components/confirmDialog/confirmDialog.template.html b/src/components/confirmDialog/confirmDialog.template.html
index 401261f1ab1aa9c2324cd8510976e971014db1ea..f5f0549460e034215176f4393e3ea2507c83533d 100644
--- a/src/components/confirmDialog/confirmDialog.template.html
+++ b/src/components/confirmDialog/confirmDialog.template.html
@@ -17,7 +17,7 @@
<mat-divider></mat-divider>
-<mat-dialog-actions class="justify-content-start flex-row-reverse">
+<mat-dialog-actions *ngIf="!hideActionBar" class="justify-content-start flex-row-reverse">
<button [mat-dialog-close]="true" mat-raised-button color="primary">{{ okBtnText }}</button>
<button [mat-dialog-close]="false" mat-button>{{ cancelBtnText }}</button>
</mat-dialog-actions>
diff --git a/src/glue.ts b/src/glue.ts
index 4437da6f1b2f9d35d9423888cb7636b2c0d4976c..027858745e6ac5223431e586aa6bd016e1ff3611 100644
--- a/src/glue.ts
+++ b/src/glue.ts
@@ -238,6 +238,13 @@ export class DatasetPreviewGlue implements IDatasetPreviewGlue, OnDestroy{
shareReplay(1),
)
+ public _volumePreview$ = this.previewingDatasetFiles$.pipe(
+ switchMap(arr => arr.length > 0
+ ? forkJoin(arr.map(v => this.getDatasetPreviewFromId(v)))
+ : of([])),
+ map(arr => arr.filter(v => determinePreviewFileType(v) === EnumPreviewFileTypes.VOLUMES))
+ )
+
private diffPreviewingDatasetFiles$= this.previewingDatasetFiles$.pipe(
debounceTime(100),
startWith([] as IDatasetPreviewData[]),
@@ -326,7 +333,6 @@ export class DatasetPreviewGlue implements IDatasetPreviewGlue, OnDestroy{
distinctUntilChanged(),
))
).subscribe(([ { prvToShow, prvToDismiss }, templateSelected ]) => {
-
const filterdPrvs = prvToShow.filter(prv => DatasetPreviewGlue.PreviewFileIsInCorrectSpace(prv, templateSelected))
for (const prv of filterdPrvs) {
const { volumes } = prv['data']['iav-registered-volumes']
@@ -461,3 +467,28 @@ export class ClickInterceptorService extends RegDeregController<any, boolean>{
// called when the call has not been intercepted
}
}
+
+export type _TPLIVal = {
+ name: string
+ filename: string
+ datasetSchema: string
+ datasetId: string
+ data: {
+ 'iav-registered-volumes': {
+ volumes: {
+ name: string
+ source: string
+ shader: string
+ transform: any
+ opacity: string
+ }[]
+ }
+ }
+ referenceSpaces: {
+ name: string
+ fullId: string
+ }[]
+ mimetype: 'application/json'
+}
+
+export const _PLI_VOLUME_INJ_TOKEN = new InjectionToken<Observable<_TPLIVal[]>>('_PLI_VOLUME_INJ_TOKEN')
diff --git a/src/main.module.ts b/src/main.module.ts
index bfe4020d475c53317d98064505ca26cd3d79ef57..14806e6db813a562e356e7c6e94d47db01d499b5 100644
--- a/src/main.module.ts
+++ b/src/main.module.ts
@@ -39,7 +39,7 @@ import { LoggingModule } from './logging/logging.module';
import { AuthService } from './auth'
import 'src/theme.scss'
-import { DatasetPreviewGlue, datasetPreviewMetaReducer, IDatasetPreviewGlue, GlueEffects, ClickInterceptorService } from './glue';
+import { DatasetPreviewGlue, datasetPreviewMetaReducer, IDatasetPreviewGlue, GlueEffects, ClickInterceptorService, _PLI_VOLUME_INJ_TOKEN } from './glue';
import { viewerStateHelperReducer, viewerStateMetaReducers, ViewerStateHelperEffect } from './services/state/viewerState.store.helper';
import { TOS_OBS_INJECTION_TOKEN } from './ui/kgtos';
import { UiEffects } from './services/state/uiState/ui.effects';
@@ -185,7 +185,11 @@ export function debug(reducer: ActionReducer<any>): ActionReducer<any> {
},
deps: [ UIService ]
},
-
+ {
+ provide: _PLI_VOLUME_INJ_TOKEN,
+ useFactory: (glue: DatasetPreviewGlue) => glue._volumePreview$,
+ deps: [ DatasetPreviewGlue ]
+ },
{
provide: IAV_DATASET_PREVIEW_ACTIVE,
useFactory: (glue: DatasetPreviewGlue) => glue.datasetPreviewDisplayed.bind(glue),
@@ -234,7 +238,7 @@ export function debug(reducer: ActionReducer<any>): ActionReducer<any> {
},
{
provide: BS_ENDPOINT,
- useValue: (environment.BS_REST_URL || `https://siibra-api-latest.apps-dev.hbp.eu/v1_0`).replace(/\/$/, '')
+ useValue: (environment.BS_REST_URL || `https://siibra-api-stable.apps.hbp.eu/v1_0`).replace(/\/$/, '')
},
],
bootstrap : [
diff --git a/src/services/dialogService.service.ts b/src/services/dialogService.service.ts
index ee06d2a91e6a63d5b3e075d6e7cf7a05676108ca..eb0844dd7f3102b921fbe30de7a21a86280fe577 100644
--- a/src/services/dialogService.service.ts
+++ b/src/services/dialogService.service.ts
@@ -3,6 +3,10 @@ import { ConfirmDialogComponent } from "src/components/confirmDialog/confirmDial
import { DialogComponent } from "src/components/dialog/dialog.component";
import {MatDialog, MatDialogRef} from "@angular/material/dialog";
+type TCancellable = {
+ abort: () => void
+}
+
@Injectable({
providedIn: 'root',
})
@@ -16,6 +20,19 @@ export class DialogService {
}
+ public blockUserInteraction(config: Partial<DialogConfig>): TCancellable {
+ const dialogRef = this.dialog.open(ConfirmDialogComponent, {
+ data: {
+ ...config,
+ hideActionBar: true
+ },
+ hasBackdrop: true,
+ disableClose: true
+ })
+ const abort = () => dialogRef.close()
+ return { abort }
+ }
+
public getUserConfirm(config: Partial<DialogConfig> = {}): Promise<string> {
this.confirmDialogRef = this.dialog.open(ConfirmDialogComponent, {
data: config,
diff --git a/src/services/state/ngViewerState.store.ts b/src/services/state/ngViewerState.store.ts
index b028a6be9f12ed69d22a7da64de7df40831c7dc9..f0ad5000d6b1e1e295f38c09a0749d30fdc9f03e 100644
--- a/src/services/state/ngViewerState.store.ts
+++ b/src/services/state/ngViewerState.store.ts
@@ -9,7 +9,7 @@ import { HttpClient } from '@angular/common/http';
import { INgLayerInterface, ngViewerActionAddNgLayer, ngViewerActionRemoveNgLayer, ngViewerActionSetPerspOctantRemoval } from './ngViewerState.store.helper'
import { PureContantService } from 'src/util';
import { PANELS } from './ngViewerState.store.helper'
-import { ngViewerActionToggleMax, ngViewerActionClearView, ngViewerActionSetPanelOrder, ngViewerActionSwitchPanelMode, ngViewerActionForceShowSegment, ngViewerActionNehubaReady } from './ngViewerState/actions';
+import { ngViewerActionToggleMax, ngViewerActionClearView, ngViewerActionSetPanelOrder, ngViewerActionSwitchPanelMode, ngViewerActionForceShowSegment, ngViewerActionNehubaReady, ngViewerActionCycleViews } from './ngViewerState/actions';
import { generalApplyState } from '../stateStore.helper';
import { ngViewerSelectorPanelMode, ngViewerSelectorPanelOrder } from './ngViewerState/selectors';
import { uiActionSnackbarMessage } from './uiState/actions';
@@ -172,9 +172,6 @@ export class NgViewerUseEffect implements OnDestroy {
@Effect()
public cycleViews$: Observable<any>
- @Effect()
- public spacebarListener$: Observable<any>
-
@Effect()
public removeAllNonBaseLayers$: Observable<any>
@@ -255,7 +252,7 @@ export class NgViewerUseEffect implements OnDestroy {
)
this.cycleViews$ = this.actions.pipe(
- ofType(ACTION_TYPES.CYCLE_VIEWS),
+ ofType(ngViewerActionCycleViews.type),
withLatestFrom(this.panelOrder$),
map(([_, panelOrder]) => {
return ngViewerActionSetPanelOrder({
@@ -351,15 +348,6 @@ export class NgViewerUseEffect implements OnDestroy {
})),
)
- this.spacebarListener$ = fromEvent(document.body, 'keydown', { capture: true }).pipe(
- filter((ev: KeyboardEvent) => ev.key === ' '),
- withLatestFrom(this.panelMode$),
- filter(([_ , panelMode]) => panelMode === PANELS.SINGLE_PANEL),
- mapTo({
- type: ACTION_TYPES.CYCLE_VIEWS,
- }),
- )
-
/**
* simplify with layer browser
*/
@@ -427,7 +415,6 @@ export class NgViewerUseEffect implements OnDestroy {
export { INgLayerInterface }
const ACTION_TYPES = {
- CYCLE_VIEWS: 'CYCLE_VIEWS',
REMOVE_ALL_NONBASE_LAYERS: `REMOVE_ALL_NONBASE_LAYERS`,
}
diff --git a/src/services/state/ngViewerState/actions.ts b/src/services/state/ngViewerState/actions.ts
index 7f864defac09d58f556d97d276bd44255a435bc3..c504a085a33cb3a8c67291a3a5c28da57a687838 100644
--- a/src/services/state/ngViewerState/actions.ts
+++ b/src/services/state/ngViewerState/actions.ts
@@ -66,3 +66,7 @@ export const ngViewerActionClearView = createAction(
`[ngViewerAction] clearView`,
props<{ payload: { [key: string]: boolean }}>()
)
+
+export const ngViewerActionCycleViews = createAction(
+ `[ngViewerAction] cycleView`
+)
\ No newline at end of file
diff --git a/src/ui/layerbrowser/layerBrowserComponent/layerbrowser.component.ts b/src/ui/layerbrowser/layerBrowserComponent/layerbrowser.component.ts
index 72a0687e3c67ec3cd078aed5a6bb9d309b9445f4..043e0005a7d84e5a99f7e3acf52a48410df73378 100644
--- a/src/ui/layerbrowser/layerBrowserComponent/layerbrowser.component.ts
+++ b/src/ui/layerbrowser/layerBrowserComponent/layerbrowser.component.ts
@@ -13,6 +13,16 @@ import { ARIA_LABELS } from 'common/constants'
import { INgLayerInterface } from "../index";
+const SHOW_LAYER_NAMES = [
+ 'PLI Fiber Orientation Red Channel',
+ 'PLI Fiber Orientation Green Channel',
+ 'PLI Fiber Orientation Blue Channel',
+ 'Blockface Image',
+ 'PLI Transmittance',
+ 'T2w MRI',
+ 'MRI Labels'
+]
+
@Component({
selector : 'layer-browser',
templateUrl : './layerbrowser.template.html',
@@ -98,7 +108,7 @@ export class LayerBrowser implements OnInit, OnDestroy {
).pipe(
map(([baseNgLayerNames, loadedNgLayers]) => {
const baseNameSet = new Set(baseNgLayerNames)
- return loadedNgLayers.filter(l => !baseNameSet.has(l.name))
+ return loadedNgLayers.filter(l => SHOW_LAYER_NAMES.includes(l.name))
}),
distinctUntilChanged()
)
diff --git a/src/ui/topMenu/topMenuCmp/topMenu.components.ts b/src/ui/topMenu/topMenuCmp/topMenu.components.ts
index 3b4ecb5f4aa8bd0446c5bcf11a5eee79b27c582b..0d464d59a1fe19491977f384eb0a3cb83f61788c 100644
--- a/src/ui/topMenu/topMenuCmp/topMenu.components.ts
+++ b/src/ui/topMenu/topMenuCmp/topMenu.components.ts
@@ -3,13 +3,14 @@ import {
Component,
Input,
TemplateRef,
+ ViewChild,
} from "@angular/core";
import { Observable, of } from "rxjs";
import { map } from "rxjs/operators";
import { AuthService } from "src/auth";
import { MatDialog, MatDialogConfig, MatDialogRef } from "@angular/material/dialog";
import { MatBottomSheet } from "@angular/material/bottom-sheet";
-import { CONST, QUICKTOUR_DESC } from 'common/constants'
+import { CONST, QUICKTOUR_DESC, ARIA_LABELS } from 'common/constants'
import { IQuickTourData } from "src/ui/quickTour/constrants";
import { environment } from 'src/environments/environment'
@@ -26,6 +27,7 @@ export class TopMenuCmp {
public EXPERIMENTAL_FEATURE_FLAG = environment.EXPERIMENTAL_FEATURE_FLAG
+ public ARIA_LABELS = ARIA_LABELS
public PINNED_DATASETS_BADGE_DESC = CONST.PINNED_DATASETS_BADGE_DESC
public matBtnStyle = 'mat-icon-button'
@@ -59,6 +61,14 @@ export class TopMenuCmp {
order: 8,
}
+ public pinnedDsNotAvail = 'We are reworking pinned dataset feature. Please check back later.'
+ @ViewChild('savedDatasets', { read: TemplateRef })
+ private savedDatasetTmpl: TemplateRef<any>
+
+ public openPinnedDatasets(){
+ // this.bottomSheet.open(this.savedDatasetTmpl)
+ }
+
constructor(
private authService: AuthService,
private dialog: MatDialog,
diff --git a/src/ui/topMenu/topMenuCmp/topMenu.template.html b/src/ui/topMenu/topMenuCmp/topMenu.template.html
index dc889adc9b46ee6ddd826bd4c76452d55beb743f..f652afdd663843230c4b712d3f28a35739751dfd 100644
--- a/src/ui/topMenu/topMenuCmp/topMenu.template.html
+++ b/src/ui/topMenu/topMenuCmp/topMenu.template.html
@@ -107,16 +107,19 @@
<!-- pinned dataset btn -->
<ng-template #pinnedDatasetBtnTmpl>
<div class="btnWrapper"
- (click)="bottomSheet.open(savedDatasets)"
+ (click)="openPinnedDatasets()"
[matBadge]="(favDataEntries$ | async)?.length > 0 ? (favDataEntries$ | async)?.length : null "
matBadgeColor="accent"
matBadgePosition="above after"
[matBadgeDescription]="PINNED_DATASETS_BADGE_DESC"
- matTooltip="Pinned datasets">
+ [matTooltip]="pinnedDsNotAvail"
+ aria-disabled="true"
+ role="button">
<iav-dynamic-mat-button
[attr.pinned-datasets-length]="(favDataEntries$ | async)?.length"
[iav-dynamic-mat-button-style]="matBtnStyle"
[iav-dynamic-mat-button-color]="matBtnColor"
+ [iav-dynamic-mat-button-disabled]="true"
iav-dynamic-mat-button-aria-label="Show pinned datasets">
<i class="fas fa-thumbtack"></i>
diff --git a/src/util/directives/keyDownListener.directive.spec.ts b/src/util/directives/keyDownListener.directive.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7be542f0d33d3569569c8415f1e5dfc4fe3a37f2
--- /dev/null
+++ b/src/util/directives/keyDownListener.directive.spec.ts
@@ -0,0 +1,102 @@
+import { DOCUMENT } from "@angular/common"
+import { Component } from "@angular/core"
+import { ComponentFixture, fakeAsync, TestBed, tick } from "@angular/core/testing"
+import { By } from "@angular/platform-browser"
+import { KeyListenerConfig, KeyListner } from "./keyDownListener.directive"
+
+@Component({
+ template: ``
+})
+
+class DummyCmp{
+ public keyConfig: KeyListenerConfig[]=[{
+ type: 'keydown',
+ key: 'a',
+ },{
+ type: 'keyup',
+ key: 'a',
+ },{
+ type: 'keydown',
+ key: 'd',
+ target: 'document',
+ capture: true
+ },{
+ type: 'keydown',
+ key: 'e',
+ target: 'document'
+ }]
+
+ // will get spied on
+ public listener(event: any){
+ console.log('lister called')
+ }
+}
+
+const inputId = `text-input`
+describe('KeyListner', () => {
+ beforeEach(async () => {
+ TestBed.configureTestingModule({
+ imports: [],
+ declarations: [
+ KeyListner,
+ DummyCmp
+ ],
+ }).overrideComponent(DummyCmp, {
+ set: {
+ template: `
+ <div><input id="${inputId}"></div>
+ <div>
+ <div
+ [iav-key-listener]="keyConfig"
+ (iav-key-event)="listener($event)">
+ </div>
+ </div>
+ `
+ }
+ })
+
+ await TestBed.compileComponents()
+ })
+
+ it('> creates component just fine', () => {
+ const fixture = TestBed.createComponent(DummyCmp)
+ expect(fixture).toBeTruthy()
+ })
+ it('> Directive is created', () => {
+ const fixture = TestBed.createComponent(DummyCmp)
+ const keyListenerDirective = fixture.debugElement.query(By.directive(KeyListner))
+ expect(keyListenerDirective).toBeTruthy()
+ })
+
+ describe('> directive working as intended', () => {
+ let eventListSpy: jasmine.Spy
+ let fixture: ComponentFixture<DummyCmp>
+ beforeEach(() => {
+ fixture = TestBed.createComponent(DummyCmp)
+ eventListSpy = spyOn(fixture.componentInstance, 'listener')
+ fixture.detectChanges()
+ })
+ describe('> if dispatch element was host element', () => {
+ it('> should trigger event', () => {
+ const newKeybEv = new KeyboardEvent('keydown', {
+ key: 'd'
+ })
+ const nativeEl = fixture.nativeElement as HTMLElement
+ nativeEl.dispatchEvent(newKeybEv)
+
+ expect(eventListSpy).toHaveBeenCalled()
+ })
+ })
+ describe('> if dispatch element was input', () => {
+ it('> should not trigger event listener', () => {
+ const newKeybEv = new KeyboardEvent('keydown', {
+ key: 'd'
+ })
+ const nativeEl = fixture.debugElement.query(By.css(`#${inputId}`)).nativeElement as HTMLElement
+ nativeEl.dispatchEvent(newKeybEv)
+
+ expect(eventListSpy).not.toHaveBeenCalled()
+ })
+ })
+ })
+})
diff --git a/src/util/directives/keyDownListener.directive.ts b/src/util/directives/keyDownListener.directive.ts
index f3fc055d1ffbb171c5ae2b9a72fa6af3ef12bb80..e400fcea13e3daf14f43aa03d49b578dd330fe2b 100644
--- a/src/util/directives/keyDownListener.directive.ts
+++ b/src/util/directives/keyDownListener.directive.ts
@@ -100,7 +100,7 @@ export interface KeyListenerConfig {
key: string
target?: 'document'
capture?: boolean
- stop: boolean
+ stop?: boolean
// fromEvent seems to be a passive listener, wheather or not { passive: false } flag is set or not
// so preventDefault cannot be called anyway
}
diff --git a/src/util/fn.ts b/src/util/fn.ts
index db3ad47ce6e43a8065bef6acc0459be9a72d5d99..479958c477576d2e34b7cc8f1be6243048024992 100644
--- a/src/util/fn.ts
+++ b/src/util/fn.ts
@@ -246,6 +246,47 @@ const BACKCOMAP_KEY_DICT = {
// fsaverage
"minds/core/referencespace/v1.0.0/tmp-fsaverage": fsAverageKeyVal,
+ },
+ // allen mouse
+ 'juelich/iav/atlas/v1.0.0/2': {
+ // ccf v3
+ "minds/core/referencespace/v1.0.0/265d32a0-3d84-40a5-926f-bf89f68212b9": {
+ // ccf v3 2017
+ "minds/core/parcellationatlas/v1.0.0/05655b58-3b6f-49db-b285-64b5a0276f83": {
+ "whole brain": "v3_2017",
+ "left hemisphere": "v3_2017",
+ "right hemisphere": "v3_2017"
+ },
+ // ccf v3 2015,
+ "minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f": {
+ "whole brain": "atlas",
+ "left hemisphere": "atlas",
+ "right hemisphere": "atlas"
+ }
+ }
+ },
+ // waxholm
+ "minds/core/parcellationatlas/v1.0.0/522b368e-49a3-49fa-88d3-0870a307974a": {
+ "minds/core/referencespace/v1.0.0/d5717c4a-0fa1-46e6-918c-b8003069ade8": {
+ // v1.01
+ "minds/core/parcellationatlas/v1.0.0/11017b35-7056-4593-baad-3934d211daba": {
+ "whole brain": "v1_01",
+ "left hemisphere": "v1_01",
+ "right hemisphere": "v1_01"
+ },
+ // v2
+ "minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d": {
+ "whole brain": "v2",
+ "left hemisphere": "v2",
+ "right hemisphere": "v2"
+ },
+ // v3
+ "minds/core/parcellationatlas/v1.0.0/ebb923ba-b4d5-4b82-8088-fa9215c2e1fe": {
+ "whole brain": "v3",
+ "left hemisphere": "v3",
+ "right hemisphere": "v3"
+ }
+ }
}
}
@@ -287,14 +328,41 @@ export class MultiDimMap{
}
}
-export function recursiveMutate<T>(arr: T[], getChildren: (obj: T) => T[], mutateFn: (obj: T) => void){
+export function mutateDeepMerge(toObj: any, fromObj: any){
+ if (typeof toObj !== 'object') throw new Error(`toObj needs to be object`)
+ if (typeof fromObj !== 'object') throw new Error(`fromObj needs to be object`)
+
+ for (const key in fromObj) {
+ if (!toObj[key]) {
+ toObj[key] = fromObj[key]
+ continue
+ }
+ if (Array.isArray(toObj[key])) {
+ const objToAppend = Array.isArray(fromObj[key])
+ ? fromObj[key]
+ : [fromObj[key]]
+ toObj[key].push(...objToAppend)
+ continue
+ }
+ if (typeof toObj[key] === typeof fromObj[key] && typeof toObj[key] === 'object') {
+ mutateDeepMerge(toObj[key], fromObj[key])
+ continue
+ }
+ throw new Error(`cannot mutate ${key} typeof ${typeof fromObj[key]}`)
+ }
+
+ return toObj
+}
+
+export function recursiveMutate<T>(arr: T[], getChildren: (obj: T) => T[], mutateFn: (obj: T) => void, depthFirst = false){
for (const obj of arr) {
- mutateFn(obj)
+ if (!depthFirst) mutateFn(obj)
recursiveMutate(
getChildren(obj),
getChildren,
mutateFn
)
+ if (depthFirst) mutateFn(obj)
}
}
diff --git a/src/util/patchPureConstants.ts b/src/util/patchPureConstants.ts
new file mode 100644
index 0000000000000000000000000000000000000000..fb1b4ad5b95c613133be272ba8874d39503f6df4
--- /dev/null
+++ b/src/util/patchPureConstants.ts
@@ -0,0 +1,197 @@
+/**
+ * README: the purpose of this file is to monkey patch discrepency between siibra-api
+ * backend and original backend.
+ *
+ * In principle, these should be built into siibra-python, and this file should become obsolete.
+ */
+
+import { IHasId } from "./interfaces";
+import { TRegion } from "./siibraApiConstants/types";
+
+type TAppend = {
+ parent: IHasId | { name: string }
+ '@type': 'julich/siibra/append-region/v0.0.1'
+}
+
+type TPatch = {
+ target: IHasId | { name: string }
+ '@type': 'julich/siibra/patch-region/v0.0.1'
+}
+
+type TPatchRegion = {
+ '@id': string
+ targetSpace: IHasId[] | '*'
+ targetParcellation: IHasId[] | '*'
+ payload: Partial<TRegion>
+} & (TAppend | TPatch)
+
+const encoder = new TextEncoder()
+async function getShaDigest(input: string){
+ const digest = await crypto.subtle.digest('SHA-1', encoder.encode(input))
+ const array = Array.from(new Uint8Array(digest))
+ const hex = array.map(v => v.toString(16)).join('')
+ return hex
+}
+async function getInterpolatedPatchObj(targetName: string, labelIndex: number){
+ const returnObj: TPatchRegion = {
+ '@id': '',
+ "@type": 'julich/siibra/patch-region/v0.0.1',
+ "target": {
+ "name": targetName
+ },
+ "targetParcellation": [{
+ "@id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290'
+ }],
+ "targetSpace": [{
+ '@id': 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588'
+ }],
+ "payload": {
+ "volumeSrc": {
+ 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588': {
+ "collect": [{
+ "@type": "fzj/tmp/volume_type/v0.0.1" as "fzj/tmp/volume_type/v0.0.1",
+ "@id": "fzj/tmp/volume_type/v0.0.1/interpolated",
+ "name": "Julich Brain v2.5 interpolated map",
+ "volume_type": "neuroglancer/precomputed" as "neuroglancer/precomputed",
+ "url": "https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/2019_05_22_interpolated_areas",
+ "detail": {
+ "neuroglancer/precomputed": {
+ "labelIndex": labelIndex,
+ "transform": [[1,0,0,-70677184],[0,1,0,-51990000],[0,0,1,-58788284],[0,0,0,1]]
+ }
+ },
+ "space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
+ map_type: 'labelled'
+ }]
+ }
+ }
+ }
+ }
+ const hex = await getShaDigest(JSON.stringify(returnObj))
+ return {
+ ...returnObj,
+ '@id': hex
+ }
+}
+
+async function getIndividualMap(parentName: string, regionName: string, url: string, transform: number[][], labelIndex: number){
+ const volumeId = await getShaDigest(url)
+ const returnObj: TPatchRegion = {
+ '@id': '',
+ "@type": 'julich/siibra/append-region/v0.0.1',
+ "parent": {
+ "name": parentName
+ },
+ "targetParcellation": [{
+ "@id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290'
+ }],
+ "targetSpace": [{
+ '@id': 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588'
+ }],
+ "payload": {
+ "name": regionName,
+ "volumeSrc": {
+ 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588': {
+ "collect": [{
+ "@type": "fzj/tmp/volume_type/v0.0.1" as "fzj/tmp/volume_type/v0.0.1",
+ "@id": `fzj/tmp/volume_type/v0.0.1/${volumeId}`,
+ "name": "Julich Brain v2.5 detailed map",
+ "volume_type": "neuroglancer/precomputed" as "neuroglancer/precomputed",
+ "url": url,
+ "detail": {
+ "neuroglancer/precomputed": {
+ "labelIndex": labelIndex,
+ "transform": transform
+ }
+ },
+ space_id: 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588',
+ map_type: 'labelled'
+ }]
+ }
+ }
+ }
+ }
+ const hex = await getShaDigest(JSON.stringify(returnObj))
+ return {
+ ...returnObj,
+ '@id': hex
+ }
+}
+
+const bigBrainRegions: Promise<TPatchRegion>[] = [
+ getInterpolatedPatchObj('Area IFJ1 (IFS,PreCS)', 9),
+ getInterpolatedPatchObj('Area IFJ2 (IFS,PreCS)', 10),
+ getInterpolatedPatchObj('Area IFS1 (IFS)', 11),
+ getInterpolatedPatchObj('Area IFS2 (IFS)', 12),
+ getInterpolatedPatchObj('Area IFS3 (IFS)', 13),
+ getInterpolatedPatchObj('Area IFS4 (IFS)', 14),
+
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam1 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam1/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam2 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam2/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam3 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam3/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam4 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam4/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam5 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam5/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam6 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam6/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+
+ getIndividualMap(
+ 'medial geniculate body',
+ "MGB-MGBd (CGM, Metathalamus)",
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2021_04_27_mgb/2021_04_27_MGBd/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'medial geniculate body',
+ "MGB-MGBm (CGM, Metathalamus)",
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2021_04_27_mgb/2021_04_27_MGBm/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'medial geniculate body',
+ "MGB-MGBv (CGM, Metathalamus)",
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2021_04_27_mgb/2021_04_27_MGBv/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+]
+
+export const patchRegions = [
+ ...bigBrainRegions
+]
diff --git a/src/util/pureConstant.service.ts b/src/util/pureConstant.service.ts
index b7962a9fe0ed9622e7237cb2b7cd7245ac9539ad..4c4b83719692c209cb80e2e52a217bec5a38d5fe 100644
--- a/src/util/pureConstant.service.ts
+++ b/src/util/pureConstant.service.ts
@@ -1,6 +1,6 @@
import { Inject, Injectable, OnDestroy } from "@angular/core";
import { Store, select } from "@ngrx/store";
-import { Observable, Subscription, of, forkJoin, combineLatest } from "rxjs";
+import { Observable, Subscription, of, forkJoin, combineLatest, from } from "rxjs";
import { viewerConfigSelectorUseMobileUi } from "src/services/state/viewerConfig.store.helper";
import { shareReplay, tap, scan, catchError, filter, switchMap, map, distinctUntilChanged, mapTo } from "rxjs/operators";
import { HttpClient } from "@angular/common/http";
@@ -10,7 +10,8 @@ import { viewerStateFetchedAtlasesSelector, viewerStateSelectedTemplateSelector
import { BS_ENDPOINT, BACKENDURL } from "src/util/constants";
import { flattenReducer } from 'common/util'
import { IVolumeTypeDetail, TAtlas, TId, TParc, TRegion, TRegionDetail, TSpaceFull, TSpaceSummary, TVolumeSrc } from "./siibraApiConstants/types";
-import { MultiDimMap, recursiveMutate } from "./fn";
+import { MultiDimMap, recursiveMutate, mutateDeepMerge } from "./fn";
+import { patchRegions } from './patchPureConstants'
const validVolumeType = new Set([
@@ -204,6 +205,12 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
)
}
+ private patchRegions$ = forkJoin(
+ patchRegions.map(patch => from(patch))
+ ).pipe(
+ shareReplay(1)
+ )
+
private getRegions(atlasId: string, parcId: string, spaceId: string){
return this.http.get<TRegion[]>(
`${this.bsEndpoint}/atlases/${encodeURIComponent(atlasId)}/parcellations/${encodeURIComponent(parcId)}/regions`,
@@ -213,6 +220,53 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
},
responseType: 'json'
}
+ ).pipe(
+ switchMap(regions => this.patchRegions$.pipe(
+ map(patchRegions => {
+ for (const p of patchRegions) {
+ if (
+ p.targetParcellation !== '*'
+ && Array.isArray(p.targetParcellation)
+ && p.targetParcellation.every(p => p["@id"] !== parcId)
+ ) {
+ continue
+ }
+ if (
+ p.targetSpace !== '*'
+ && Array.isArray(p.targetSpace)
+ && p.targetSpace.every(sp => sp['@id'] !== spaceId)
+ ) {
+ continue
+ }
+
+ recursiveMutate(
+ regions,
+ r => r.children || [],
+ region => {
+
+ if (p["@type"] === 'julich/siibra/append-region/v0.0.1') {
+ if (p.parent['name'] === region.name) {
+ if (!region.children) region.children = []
+ region.children.push(
+ p.payload as TRegion
+ )
+ }
+ }
+ if (p['@type'] === 'julich/siibra/patch-region/v0.0.1') {
+ if (p.target['name'] === region.name) {
+ mutateDeepMerge(
+ region,
+ p.payload
+ )
+ }
+ }
+ },
+ true
+ )
+ }
+ return regions
+ })
+ ))
)
}
@@ -435,7 +489,7 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
}),
catchError((err, obs) => of([])),
tap((arr: any[]) => this.totalAtlasesLength = arr.length),
- scan((acc, curr) => acc.concat(curr).sort((a, b) => (a.order || 1001) - (b.order || 1000)), []),
+ scan((acc, curr) => acc.concat(curr).sort((a, b) => (a.order || 0) - (b.order || 0)), []),
shareReplay(1)
)
diff --git a/src/util/siibraApiConstants/types.ts b/src/util/siibraApiConstants/types.ts
index 677827288aaff99b13332ee6de7559920d64837e..b73781a0242f120fbe78571fd9ae64e06cddc2c4 100644
--- a/src/util/siibraApiConstants/types.ts
+++ b/src/util/siibraApiConstants/types.ts
@@ -18,6 +18,7 @@ export interface IVolumeTypeDetail {
'nii': null
'neuroglancer/precomputed': {
'neuroglancer/precomputed': {
+ 'labelIndex': number
'transform': TNgTransform
}
}
diff --git a/src/viewerModule/module.ts b/src/viewerModule/module.ts
index 53d48a2ecc114144ba740b3f25231f2030882df9..8cd43cf6ace30f25be8afea1cffe58be1c175881 100644
--- a/src/viewerModule/module.ts
+++ b/src/viewerModule/module.ts
@@ -28,6 +28,7 @@ import { API_SERVICE_SET_VIEWER_HANDLE_TOKEN, AtlasViewerAPIServices, setViewerH
import { ILoadMesh, LOAD_MESH_TOKEN } from "src/messaging/types";
import { KeyFrameModule } from "src/keyframesModule/module";
import { ViewerInternalStateSvc } from "./viewerInternalState.service";
+import { LayerBrowserModule } from "src/ui/layerbrowser";
@NgModule({
imports: [
@@ -50,6 +51,7 @@ import { ViewerInternalStateSvc } from "./viewerInternalState.service";
ViewerStateBreadCrumbModule,
KgRegionalFeatureModule,
KeyFrameModule,
+ LayerBrowserModule,
],
declarations: [
ViewerCmp,
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
index 56e87c06579b66207560caf92611ca2ab83b6c39..d3232e3e098d260c3771b95858fb428ea7f1caf0 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
@@ -1,7 +1,7 @@
import { Inject, Injectable, OnDestroy, Optional } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { BehaviorSubject, combineLatest, from, merge, Observable, of, Subject, Subscription } from "rxjs";
-import { debounceTime, distinctUntilChanged, filter, map, shareReplay, switchMap, withLatestFrom } from "rxjs/operators";
+import { BehaviorSubject, combineLatest, from, merge, NEVER, Observable, of, Subject, Subscription } from "rxjs";
+import { debounceTime, distinctUntilChanged, filter, map, shareReplay, startWith, switchMap, withLatestFrom } from "rxjs/operators";
import { viewerStateCustomLandmarkSelector, viewerStateSelectedParcellationSelector, viewerStateSelectedRegionsSelector, viewerStateSelectedTemplateSelector } from "src/services/state/viewerState/selectors";
import { getRgb, IColorMap, INgLayerCtrl, INgLayerInterface, TNgLayerCtrl } from "./layerCtrl.util";
import { getMultiNgIdsRegionsLabelIndexMap } from "../constants";
@@ -12,6 +12,7 @@ import { EnumColorMapName } from "src/util/colorMaps";
import { getShader, PMAP_DEFAULT_CONFIG } from "src/util/constants";
import { ngViewerActionAddNgLayer, ngViewerActionRemoveNgLayer, ngViewerSelectorClearView, ngViewerSelectorLayers } from "src/services/state/ngViewerState.store.helper";
import { serialiseParcellationRegion } from 'common/util'
+import { _PLI_VOLUME_INJ_TOKEN, _TPLIVal } from "src/glue";
export const BACKUP_COLOR = {
red: 255,
@@ -36,7 +37,9 @@ export function getAuxMeshesAndReturnIColor(auxMeshes: IAuxMesh[]): IColorMap{
return returnVal
}
-@Injectable()
+@Injectable({
+ providedIn: 'root'
+})
export class NehubaLayerControlService implements OnDestroy{
static PMAP_LAYER_NAME = 'regional-pmap'
@@ -144,10 +147,25 @@ export class NehubaLayerControlService implements OnDestroy{
while (this.sub.length > 0) this.sub.pop().unsubscribe()
}
+ private pliVol$: Observable<string[]> = this._pliVol$
+ ? this._pliVol$.pipe(
+ map(arr => {
+ const output = []
+ for (const item of arr) {
+ for (const volume of item.data["iav-registered-volumes"].volumes) {
+ output.push(volume.name)
+ }
+ }
+ return output
+ })
+ )
+ : NEVER
constructor(
private store$: Store<any>,
+ @Optional() @Inject(_PLI_VOLUME_INJ_TOKEN) private _pliVol$: Observable<_TPLIVal[]>,
@Optional() @Inject(REGION_OF_INTEREST) roi$: Observable<TRegionDetail>
){
+
if (roi$) {
this.sub.push(
@@ -285,10 +303,10 @@ export class NehubaLayerControlService implements OnDestroy{
shareReplay(1)
)
- public visibleLayer$: Observable<string[]> = combineLatest([
+ public expectedLayerNames$ = combineLatest([
this.selectedTemplateSelector$,
this.auxMeshes$,
- this.selParcNgIdMap$
+ this.selParcNgIdMap$,
]).pipe(
map(([ tmpl, auxMeshes, parcNgIdMap ]) => {
const ngIdSet = new Set<string>()
@@ -305,6 +323,18 @@ export class NehubaLayerControlService implements OnDestroy{
})
)
+ public visibleLayer$: Observable<string[]> = combineLatest([
+ this.expectedLayerNames$,
+ this.pliVol$.pipe(
+ startWith([])
+ ),
+ ]).pipe(
+ map(([ expectedLayerNames, layerNames ]) => {
+ const ngIdSet = new Set<string>([...layerNames, ...expectedLayerNames])
+ return Array.from(ngIdSet)
+ })
+ )
+
/**
* define when shown segments should be updated
*/
diff --git a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
index 6256f6b7e8f02b90e4043e35ee6d0c714a510126..15504851b024378aeb96c8c96ef2f04d73489842 100644
--- a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
@@ -1,7 +1,7 @@
import { AfterViewInit, Component, ElementRef, EventEmitter, Inject, Input, OnChanges, OnDestroy, Optional, Output, SimpleChanges, TemplateRef, ViewChild } from "@angular/core";
import { select, Store } from "@ngrx/store";
import { asyncScheduler, combineLatest, fromEvent, merge, NEVER, Observable, of, Subject } from "rxjs";
-import { ngViewerActionToggleMax } from "src/services/state/ngViewerState/actions";
+import { ngViewerActionCycleViews, ngViewerActionToggleMax } from "src/services/state/ngViewerState/actions";
import { ClickInterceptor, CLICK_INTERCEPTOR_INJECTOR } from "src/util";
import { uiStateMouseOverSegmentsSelector } from "src/services/state/uiState/selectors";
import { debounceTime, distinctUntilChanged, filter, map, mapTo, scan, shareReplay, startWith, switchMap, switchMapTo, take, tap, throttleTime } from "rxjs/operators";
@@ -79,6 +79,8 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnChanges, OnDestroy, A
public ARIA_LABELS = ARIA_LABELS
public IDS = IDS
+ private currentPanelMode: PANELS
+
@ViewChild(NehubaViewerContainerDirective, { static: true })
public nehubaContainerDirective: NehubaViewerContainerDirective
@@ -341,6 +343,9 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnChanges, OnDestroy, A
]).pipe(
switchMap(this.waitForNehuba.bind(this))
).subscribe(([mode, panelOrder]) => {
+
+ this.currentPanelMode = mode
+
const viewPanels = panelOrder.split('').map(v => Number(v)).map(idx => this.viewPanels[idx]) as [HTMLElement, HTMLElement, HTMLElement, HTMLElement]
/**
@@ -652,6 +657,13 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnChanges, OnDestroy, A
this.onDestroyCb.push(() => navSub.unsubscribe())
}
+ handleCycleViewEvent(){
+ if (this.currentPanelMode !== PANELS.SINGLE_PANEL) return
+ this.store$.dispatch(
+ ngViewerActionCycleViews()
+ )
+ }
+
handleViewerLoadedEvent(flag: boolean) {
this.viewerEvent.emit({
type: EnumViewerEvt.VIEWERLOADED,
diff --git a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.template.html b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.template.html
index ba41f41c2cc6d2fc711a0ccb60cee8c8f512ae3f..73aeec9212a1f91a1fa8c16ce1c047e655a0177d 100644
--- a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.template.html
+++ b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.template.html
@@ -11,6 +11,8 @@
iav-nehuba-viewer-container
#iavContainer="iavNehubaViewerContainer"
iav-mouse-hover
+ [iav-key-listener]="[{ type: 'keydown', key: ' ', target: 'document', capture: true }]"
+ (iav-key-event)="handleCycleViewEvent()"
(iavNehubaViewerContainerViewerLoading)="handleViewerLoadedEvent($event)">
</div>
diff --git a/src/viewerModule/nehuba/statusCard/statusCard.component.ts b/src/viewerModule/nehuba/statusCard/statusCard.component.ts
index a6daa233d6acdc5197d19d4a9dbc284c3e26f329..76dfa6bbbdb0288b6755984fa651d71b3e50c5df 100644
--- a/src/viewerModule/nehuba/statusCard/statusCard.component.ts
+++ b/src/viewerModule/nehuba/statusCard/statusCard.component.ts
@@ -57,6 +57,8 @@ export class StatusCardComponent implements OnInit, OnChanges{
order: 6,
}
+ public saneUrlDeprecated = `Custom URL is going away. New custom URLs can no longer be created. Custom URLs you generated in the past will continue to work.`
+
public SHARE_BTN_ARIA_LABEL = ARIA_LABELS.SHARE_BTN
public COPY_URL_TO_CLIPBOARD_ARIA_LABEL = ARIA_LABELS.SHARE_COPY_URL_CLIPBOARD
public SHARE_CUSTOM_URL_ARIA_LABEL = ARIA_LABELS.SHARE_CUSTOM_URL
diff --git a/src/viewerModule/nehuba/statusCard/statusCard.template.html b/src/viewerModule/nehuba/statusCard/statusCard.template.html
index 5e4d793a725e31f41f5bd45406a11b95ef1340a6..5f57d9719055a265dbfb005c5c4d7d3cc46ab1ea 100644
--- a/src/viewerModule/nehuba/statusCard/statusCard.template.html
+++ b/src/viewerModule/nehuba/statusCard/statusCard.template.html
@@ -154,9 +154,11 @@
Copy link to this view
</span>
</mat-list-item>
- <mat-list-item (click)="openDialog(shareSaneUrl, { ariaLabel: SHARE_CUSTOM_URL_DIALOG_ARIA_LABEL })"
+ <mat-list-item
[attr.aria-label]="SHARE_CUSTOM_URL_ARIA_LABEL"
- [attr.tab-index]="10">
+ [attr.tab-index]="10"
+ [matTooltip]="saneUrlDeprecated"
+ class="text-muted">
<mat-icon
class="mr-4"
fontSet="fas"
diff --git a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
index 551bec7a55fc14645db6470dc3920ddaef092a8c..a00b376604e92ed7e4328b4289c227813f475836 100644
--- a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
+++ b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
@@ -28,6 +28,7 @@ type TInternalState = {
hemisphere: 'left' | 'right' | 'both'
}
const pZoomFactor = 5e3
+const preferredFsMode = 'pial'
type THandlingCustomEv = {
regions: ({ name?: string, error?: string })[]
@@ -534,8 +535,9 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, OnChanges, Af
}
}
- // load mode0 by default
- this.loadMode(this.config.modes[0])
+ // load preferredFsMode or mode0 by default
+ const loadMode = this.config.modes.find(m => m.name === preferredFsMode) || this.config.modes[0]
+ this.loadMode(loadMode)
this.viewerEvent.emit({
type: EnumViewerEvt.VIEWERLOADED,
diff --git a/src/viewerModule/viewerCmp/viewerCmp.component.ts b/src/viewerModule/viewerCmp/viewerCmp.component.ts
index 1426fc874577952974e87f3ecc347ee632004db2..bb0c20a548bf82504019a4fe307c180d6d498d4b 100644
--- a/src/viewerModule/viewerCmp/viewerCmp.component.ts
+++ b/src/viewerModule/viewerCmp/viewerCmp.component.ts
@@ -1,6 +1,6 @@
import { Component, ComponentFactory, ComponentFactoryResolver, ElementRef, Inject, Injector, Input, OnDestroy, Optional, TemplateRef, ViewChild, ViewContainerRef } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import {combineLatest, merge, Observable, of, Subject, Subscription} from "rxjs";
+import {combineLatest, merge, NEVER, Observable, of, Subject, Subscription} from "rxjs";
import {catchError, distinctUntilChanged, filter, map, shareReplay, startWith, switchMap } from "rxjs/operators";
import { viewerStateSetSelectedRegions } from "src/services/state/viewerState/actions";
import {
@@ -23,6 +23,8 @@ import { ContextMenuService, TContextMenuReg } from "src/contextMenuModule";
import { ComponentStore } from "../componentStore";
import { MAT_DIALOG_DATA } from "@angular/material/dialog";
import { GenericInfoCmp } from "src/atlasComponents/regionalFeatures/bsFeatures/genericInfo";
+import { _PLI_VOLUME_INJ_TOKEN, _TPLIVal } from "src/glue";
+import { uiActionSetPreviewingDatasetFiles } from "src/services/state/uiState.store.helper";
type TCStoreViewerCmp = {
overlaySideNav: any
@@ -115,7 +117,10 @@ export function ROIFactory(store: Store<any>, svc: PureContantService){
})
export class ViewerCmp implements OnDestroy {
-
+ public _pliTitle = "Fiber structures of a human hippocampus based on joint DMRI, 3D-PLI, and TPFM acquisitions"
+ public _pliDesc = "The collected datasets provide real multimodal, multiscale structural connectivity insights into the human hippocampus. One post mortem hippocampus was scanned with Anatomical and Diffusion MRI (dMRI) [1], 3D Polarized Light Imaging (3D-PLI) [2], and Two-Photon Fluorescence Microscopy (TPFM) [3] using protocols specifically developed during SGA1 and SGA2, rendering joint tissue imaging possible. MRI scanning was performed with a 11.7 T Preclinical MRI system (gradients: 760 mT/m, slew rate: 9500 T/m/s) yielding T1-w and T2-w maps at 200 µm and dMRI-based maps at 300 µm resolution. During tissue sectioning (60 µm thickness) blockface (en-face) images were acquired from the surface of the frozen brain block, serving as reference for data integration/co-alignment. 530 brain sections were scanned with 3D-PLI. HPC-based image analysis provided transmittance, retardation, and fiber orientation maps at 1.3 µm in-plane resolution. TPFM was finally applied to selected brain sections utilizing autofluorescence properties of the fibrous tissue which appears after PBS washing (MAGIC protocol). The TPFM measurements provide a resolution of 0.44 µm x 0.44 µm x 1 µm."
+ public _pliLink = "https://doi.org/10.25493/JQ30-E08"
+
public CONST = CONST
public ARIA_LABELS = ARIA_LABELS
@@ -215,17 +220,36 @@ export class ViewerCmp implements OnDestroy {
private getRegionFromlabelIndexId: (arg: {labelIndexId: string}) => any
private genericInfoCF: ComponentFactory<GenericInfoCmp>
+
+ public pliVol$ = this._pliVol$ || NEVER
+ public clearVoi(){
+ this.store$.dispatch(
+ uiActionSetPreviewingDatasetFiles({
+ previewingDatasetFiles: []
+ })
+ )
+ }
constructor(
private store$: Store<any>,
private viewerModuleSvc: ContextMenuService<TContextArg<'threeSurfer' | 'nehuba'>>,
private cStore: ComponentStore<TCStoreViewerCmp>,
cfr: ComponentFactoryResolver,
+ @Optional() @Inject(_PLI_VOLUME_INJ_TOKEN) private _pliVol$: Observable<_TPLIVal[]>,
@Optional() @Inject(REGION_OF_INTEREST) public regionOfInterest$: Observable<any>
){
this.genericInfoCF = cfr.resolveComponentFactory(GenericInfoCmp)
this.subscriptions.push(
+ this.pliVol$.subscribe(val => {
+ if (val.length > 0) {
+ this.sidenavTopSwitch && this.sidenavTopSwitch.open()
+ this.sidenavLeftSwitch && this.sidenavLeftSwitch.open()
+ } else {
+ this.sidenavTopSwitch && this.sidenavTopSwitch.close()
+ this.sidenavLeftSwitch && this.sidenavLeftSwitch.close()
+ }
+ }),
this.selectedRegions$.subscribe(() => {
this.clearPreviewingDataset()
}),
diff --git a/src/viewerModule/viewerCmp/viewerCmp.template.html b/src/viewerModule/viewerCmp/viewerCmp.template.html
index 30d2c0411ce039d73beba463374fe6a3e2bed884..b77622c13103c80c4ccc5e2c938ccd1bca2a97d1 100644
--- a/src/viewerModule/viewerCmp/viewerCmp.template.html
+++ b/src/viewerModule/viewerCmp/viewerCmp.template.html
@@ -39,11 +39,13 @@
matColor: 'primary',
fontIcon: 'fa-list',
tooltip: 'Annotation list',
- click: viewerModeDrawer.toggle.bind(viewerModeDrawer)
+ click: viewerModeDrawer.toggle.bind(viewerModeDrawer),
+ badge: toolPanel?.annBadges$ | async
}">
</ng-container>
- <annotating-tools-panel class="z-index-10">
+ <annotating-tools-panel class="z-index-10"
+ #toolPanel="annoToolsPanel">
</annotating-tools-panel>
</div>
@@ -97,7 +99,6 @@
</mat-drawer-container>
-
<!-- top drawer -->
<mat-drawer-container
[hidden]="viewerMode$ | async"
@@ -250,9 +251,14 @@
'invisible overflow-hidden h-0': overlaySidenav$ | async,
'h-100': !(overlaySidenav$ | async)
}" class="position-relative d-flex flex-column">
+
+ <ng-template let-pliVol [ngIf]="pliVol$ | async" [ngIfElse]="sidenavRegionTmpl">
+ <ng-template [ngIf]="pliVol.length > 0" [ngIfElse]="sidenavRegionTmpl">
+ <ng-template [ngTemplateOutlet]="voiTmpl">
- <ng-container *ngTemplateOutlet="sidenavRegionTmpl">
- </ng-container>
+ </ng-template>
+ </ng-template>
+ </ng-template>
<!-- TODO dataset preview will become deprecated in the future.
Regional feature/data feature will replace it -->
@@ -422,6 +428,8 @@
let-customColor="customColor"
let-customColorDarkmode="customColorDarkmode"
let-tooltip="tooltip"
+ let-badge="badge"
+ let-badgeColor="badgeColor"
let-click="click">
<!-- (click)="sideNavMasterSwitch.toggle()" -->
<button mat-raised-button
@@ -434,7 +442,9 @@
}"
(click)="click && click()"
[style.backgroundColor]="customColor"
- [color]="(!customColor && matColor) ? matColor : null">
+ [color]="(!customColor && matColor) ? matColor : null"
+ [matBadge]="badge"
+ [matBadgeColor]="badgeColor || 'warn'">
<span [ngClass]="{'iv-custom-comp text': !!customColor}">
<i class="fas" [ngClass]="fontIcon || 'fa-question'"></i>
@@ -442,6 +452,59 @@
</button>
</ng-template>
+<!-- VOI sidenav tmpl -->
+<ng-template #voiTmpl>
+
+ <!-- back btn -->
+ <button mat-button
+ (click)="clearVoi()"
+ [attr.aria-label]="ARIA_LABELS.CLOSE"
+ class="position-absolute z-index-10 m-2">
+ <i class="fas fa-chevron-left"></i>
+ <span class="ml-1">
+ Back
+ </span>
+ </button>
+
+ <mat-card class="sidenav-cover-header-container">
+ <div class="sidenav-cover-header-container">
+ <mat-card-title>
+ {{ _pliTitle }}
+ </mat-card-title>
+
+ <mat-card-subtitle class="d-inline-flex align-items-center flex-wrap">
+ <mat-icon fontSet="fas" fontIcon="fa-database"></mat-icon>
+ <span>
+ Dataset preview
+ </span>
+
+ <mat-divider vertical="true" class="ml-2 h-2rem"></mat-divider>
+
+ <a [href]="_pliLink"
+ mat-icon-button
+ matTooltip="Explore in EBRAINS Knowledge Graph"
+ target="_blank">
+ <i class="fas fa-external-link-alt"></i>
+ </a>
+
+ </mat-card-subtitle>
+ </div>
+
+ <small class="text-muted iv-custom-comp darker-bg">
+ {{ _pliDesc }}
+ </small>
+
+ <mat-expansion-panel class="sidenav-cover-header-container">
+ <mat-expansion-panel-header>
+ <mat-panel-title>
+ Registered Volumes
+ </mat-panel-title>
+ </mat-expansion-panel-header>
+ <layer-browser></layer-browser>
+ </mat-expansion-panel>
+ </mat-card>
+</ng-template>
+
<!-- region sidenav tmpl -->
<ng-template #sidenavRegionTmpl>
@@ -572,21 +635,21 @@
<!-- Multi regions include -->
<ng-template #multiRegionInclTmpl>
- <mat-chip-list>
- <mat-chip *ngFor="let r of regions"
- iav-region
- [region]="r"
- [ngClass]="{
- 'darktheme':regionDirective.rgbDarkmode === true,
- 'lighttheme': regionDirective.rgbDarkmode === false
- }"
- [style.backgroundColor]="regionDirective.rgbString"
- #regionDirective="iavRegion">
- <span class="iv-custom-comp text text-truncate d-inline pl-4">
- {{ r.name }}
- </span>
- </mat-chip>
- </mat-chip-list>
+
+ <mat-chip *ngFor="let r of regions"
+ iav-region
+ [region]="r"
+ class="m-1"
+ [ngClass]="{
+ 'darktheme':regionDirective.rgbDarkmode === true,
+ 'lighttheme': regionDirective.rgbDarkmode === false
+ }"
+ [style.backgroundColor]="regionDirective.rgbString"
+ #regionDirective="iavRegion">
+ <span class="iv-custom-comp text text-truncate d-inline">
+ {{ r.name }}
+ </span>
+ </mat-chip>
</ng-template>
<ng-container *ngTemplateOutlet="ngMatAccordionTmpl; context: {
diff --git a/src/zipFilesOutput/zipFilesOutput.directive.ts b/src/zipFilesOutput/zipFilesOutput.directive.ts
index bcf70bddfaf8e3e84ab97f887ae93ae8e95fcfc6..dc980728cfd8675ecfaaf57eb1c4317f74556ba0 100644
--- a/src/zipFilesOutput/zipFilesOutput.directive.ts
+++ b/src/zipFilesOutput/zipFilesOutput.directive.ts
@@ -2,6 +2,8 @@ import { Directive, HostListener, Inject, Input } from "@angular/core";
import { TZipFileConfig } from "./type";
import * as JSZip from "jszip";
import { DOCUMENT } from "@angular/common";
+import { isObservable, Observable } from "rxjs";
+import { take } from "rxjs/operators";
@Directive({
selector: '[zip-files-output]',
@@ -10,15 +12,15 @@ import { DOCUMENT } from "@angular/common";
export class ZipFilesOutput {
@Input('zip-files-output')
- zipFiles: TZipFileConfig[] = []
+ zipFiles: Observable<TZipFileConfig[]> | TZipFileConfig[] = []
@Input('zip-files-output-zip-filename')
zipFilename = 'archive.zip'
- @HostListener('click')
- async onClick(){
+ private async zipArray(arrZipConfig: TZipFileConfig[]){
+
const zip = new JSZip()
- for (const zipFile of this.zipFiles) {
+ for (const zipFile of arrZipConfig) {
const { filecontent, filename, base64 } = zipFile
zip.file(filename, filecontent, { base64 })
}
@@ -32,6 +34,21 @@ export class ZipFilesOutput {
this.doc.body.removeChild(anchor)
URL.revokeObjectURL(anchor.href)
}
+
+ @HostListener('click')
+ async onClick(){
+ if (Array.isArray(this.zipFiles)) {
+ await this.zipArray(this.zipFiles)
+ return
+ }
+ if (isObservable(this.zipFiles)) {
+ const zipFiles = await this.zipFiles.pipe(
+ take(1)
+ ).toPromise()
+ await this.zipArray(zipFiles)
+ return
+ }
+ }
constructor(
@Inject(DOCUMENT) private doc: Document
){