diff --git a/.travis.yml b/.travis.yml
index e9d1d40d26897d755b439e0d8b1f70d76d32aa64..8bb9b983c6dc51d942b8e050a0145afed95d32c5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -64,6 +64,7 @@ env:
- PPTR_VERSION=2.1.0
- PROTRACTOR_SPECS=./src/navigating/*.e2e-spec.js
+
# addons:
# browserstack:
# username: "xiao33"
diff --git a/deploy/atlas/index.js b/deploy/atlas/index.js
index 24fde48792abae55803d31156ed06dab05d69cf1..92ff4f851d80f5762ad6b9a8bdc045bb9738afb9 100644
--- a/deploy/atlas/index.js
+++ b/deploy/atlas/index.js
@@ -99,8 +99,7 @@ router.get('/:atlasId', async (req, res) => {
const lastPathPreview = `preview?${searchParam.toString()}`
return {
...tmpl,
- previewUrl: getPreviewFn({ res, lastpart: lastPathPreview }),
- url: getPreviewFn({ res, lastpart: lastTemplatePath })
+ previewUrl: getPreviewFn({ res, lastpart: lastPathPreview })
}
})
})
diff --git a/deploy/atlas/index.spec.js b/deploy/atlas/index.spec.js
index 9762c9a2076477435fdefe22488cdce0eb06e984..727ae6e55a48746943df2cfe7a59375ae5cf57da 100644
--- a/deploy/atlas/index.spec.js
+++ b/deploy/atlas/index.spec.js
@@ -1,12 +1,12 @@
const { expect, assert } = require('chai')
const express = require('express')
-const router = require('./index')
const { retry } = require('../../common/util')
const got = require('got')
let server, atlases, templates = []
const PORT = 12345
const baseUrl = `http://localhost:${PORT}`
+process.env.HOSTNAME = baseUrl
let routePathname
describe('atlas/index.js', () => {
before(async () => {
@@ -19,7 +19,7 @@ describe('atlas/index.js', () => {
next()
})
- app.use(router)
+ app.use(require('./index'))
server = app.listen(PORT)
@@ -52,28 +52,18 @@ describe('atlas/index.js', () => {
const { body } = await got(`${baseUrl}/`, { responseType: 'json' })
expect(body.length).to.equal(3)
assert(
- body.every(({ url }) => /^marshmellow/.test(url)),
+ body.every(({ url }) => /marshmellow/.test(url)),
'url pathname should be as set'
)
})
it('> every end point works', async () => {
for (const { url } of atlases) {
expect(!!url).to.be.true
- const { body } = await got(`${baseUrl}/${url}`, {responseType: 'json'})
- expect(body.templateSpaces.length).to.be.greaterThan(0)
- templates.push(
- body.templateSpaces
+ const { body } = await got(
+ /^http/.test(url) ? url : `${baseUrl}/${url}`,
+ {responseType: 'json'}
)
- }
- })
-
- it('> templates resolves fine', async () => {
- for (const arrTmpl of templates) {
- for (const { url } of arrTmpl) {
- expect(!!url).to.equal(true)
- const { body } = await got(`${baseUrl}/${url}`, { responseType: 'json' })
- expect(body.parcellations.length).to.be.greaterThan(0)
- }
+ expect(body.templateSpaces.length).to.be.greaterThan(0)
}
})
})
\ No newline at end of file
diff --git a/deploy/datasets/util.js b/deploy/datasets/util.js
index 25953080f60a025c8d321ee976dd50cf894cc4f3..eea0c8f742b4d1cdfb8142168c09ff0892f171e8 100644
--- a/deploy/datasets/util.js
+++ b/deploy/datasets/util.js
@@ -7,6 +7,14 @@ const { getIdFromFullId, retry, flattenRegions } = require('../../common/util')
let getPublicAccessToken
+const KG_IDS = {
+ PARCELLATIONS: {
+ LONG_BUNDLE: 'juelich/iav/atlas/v1.0.0/5',
+ SHORT_BUNDLE: 'juelich/iav/atlas/v1.0.0/6',
+ JULICH_BRAIN: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
+ }
+}
+
const getUserKGRequestParam = async ({ user }) => {
let publicAccessToken
/**
@@ -95,9 +103,9 @@ initPrArray.push(
readConfigFile('MNI152.json')
.then(data => JSON.parse(data))
.then(json => {
- const longBundle = flattenRegions(json.parcellations.find(({ name }) => name === 'Fibre Bundle Atlas - Long Bundle').regions)
- const shortBundle = flattenRegions(json.parcellations.find(({ name }) => name === 'Fibre Bundle Atlas - Short Bundle').regions)
- const jubrain = flattenRegions(json.parcellations.find(({ name }) => 'JuBrain Cytoarchitectonic Atlas' === name).regions)
+ const longBundle = flattenRegions(json.parcellations.find(({ ['@id']: id }) => id === KG_IDS.PARCELLATIONS.LONG_BUNDLE).regions)
+ const shortBundle = flattenRegions(json.parcellations.find(({ ['@id']: id }) => id === KG_IDS.PARCELLATIONS.SHORT_BUNDLE).regions)
+ const jubrain = flattenRegions(json.parcellations.find(({ ['@id']: id }) => id === KG_IDS.PARCELLATIONS.JULICH_BRAIN).regions)
longBundleSet = populateSet(longBundle)
shortBundleSet = populateSet(shortBundle)
juBrainSet = populateSet(jubrain)
diff --git a/src/atlasViewer/atlasViewer.urlUtil.spec.ts b/src/atlasViewer/atlasViewer.urlUtil.spec.ts
index 74966bd4b9e4e02c8397d2cc150a1260d02f0cc8..2aff96c2df6af1d1a02b27b2f12d3710399a78d0 100644
--- a/src/atlasViewer/atlasViewer.urlUtil.spec.ts
+++ b/src/atlasViewer/atlasViewer.urlUtil.spec.ts
@@ -10,6 +10,9 @@ const mni152 = require('!json-loader!src/res/ext/MNI152.json')
const mni152Nehubaconfig = require('!json-loader!src/res/ext/MNI152NehubaConfig.json')
const allen = require('!json-loader!src/res/ext/allenMouse.json')
const waxholm = require('!json-loader!src/res/ext/waxholmRatV2_0.json')
+const atlasHumanMultilevel = require('!json-loader!src/res/ext/atlas/atlas_multiLevelHuman.json')
+
+const { defaultState: viewerHelperDefaultState,viewerStateHelperStoreName } = require('src/services/state/viewerState.store.helper')
const { viewerState, ...rest } = defaultRootState
const fetchedTemplateRootState = {
@@ -18,24 +21,63 @@ const fetchedTemplateRootState = {
...viewerState,
fetchedTemplates: [ bigbrainJson, colin, mni152, allen, waxholm ],
},
+ [viewerStateHelperStoreName]: {
+ ...viewerHelperDefaultState,
+ fetchedAtlases: [ atlasHumanMultilevel ]
+ }
}
// TODO finish writing tests
describe('atlasViewer.urlService.service.ts', () => {
describe('cvtSearchParamToState', () => {
- it('parses template into atlasId properly', () => {
- /**
- * TODO finish test
- */
- expect(true).toBe(false)
- })
- it('convert empty search param to empty state', () => {
+ it('> convert empty search param to empty state', () => {
const searchparam = new URLSearchParams()
expect(() => cvtSearchParamToState(searchparam, defaultRootState)).toThrow()
})
- it('successfully converts with only template defined', () => {
+ it('> parses template into atlasId properly', () => {
+ const searchparam = new URLSearchParams()
+ searchparam.set('templateSelected', bigbrainJson.name)
+
+ const newState = cvtSearchParamToState(searchparam, fetchedTemplateRootState)
+ expect(
+ newState[viewerStateHelperStoreName]['selectedAtlasId']
+ ).toEqual(
+ atlasHumanMultilevel['@id']
+ )
+ })
+
+ describe('> parses parcellation selected into overlayingAdditionalParcellations properly', () => {
+ it('> if the selected layer is base layer, it should not populate overlayingAdditionalParcellations', () => {
+ const searchparam = new URLSearchParams()
+
+ searchparam.set('templateSelected', bigbrainJson.name)
+ searchparam.set('parcellationSelected', bigbrainJson.parcellations[0].name)
+
+ const newState = cvtSearchParamToState(searchparam, fetchedTemplateRootState)
+ expect(
+ newState[viewerStateHelperStoreName]['overlayingAdditionalParcellations']
+ ).toEqual([])
+ })
+
+ it('> if the selected layer is non base layer, it should be populated', () => {
+ const searchparam = new URLSearchParams()
+
+ searchparam.set('templateSelected', bigbrainJson.name)
+ searchparam.set('parcellationSelected', bigbrainJson.parcellations[1].name)
+
+ const newState = cvtSearchParamToState(searchparam, fetchedTemplateRootState)
+ expect(
+ newState[viewerStateHelperStoreName]['overlayingAdditionalParcellations'].length
+ ).toEqual(1)
+ expect(
+ newState[viewerStateHelperStoreName]['overlayingAdditionalParcellations'][0]['@id']
+ ).toEqual(bigbrainJson.parcellations[1]['@id'])
+ })
+ })
+
+ it('> successfully converts with only template defined', () => {
const searchparam = new URLSearchParams('?templateSelected=Big+Brain+%28Histology%29')
const newState = cvtSearchParamToState(searchparam, fetchedTemplateRootState)
diff --git a/src/atlasViewer/atlasViewer.urlUtil.ts b/src/atlasViewer/atlasViewer.urlUtil.ts
index 6184b130722f96a04d8c9cb2e284476762a189f2..9697231b36839dac9afa766651cdb4e00d52446f 100644
--- a/src/atlasViewer/atlasViewer.urlUtil.ts
+++ b/src/atlasViewer/atlasViewer.urlUtil.ts
@@ -315,13 +315,14 @@ export const cvtSearchParamToState = (searchparams: URLSearchParams, state: IavR
const viewreHelperState = returnState[viewerStateHelperStoreName]
const { templateSelected, parcellationSelected } = returnState['viewerState']
const { fetchedAtlases, ...rest } = viewreHelperState
- parcellationSelected['@id']
- const selectedAtlas = fetchedAtlases.find(a => a['templateSpaces'].find(t => t['@id'] === templateSelected['@id']))
- const overlayLayer = selectedAtlas['parcellations'].find(p => p['@id'] === parcellationSelected['@id'])
+
+ const selectedAtlas = fetchedAtlases.find(a => a['templateSpaces'].find(t => t['@id'] === (templateSelected && templateSelected['@id'])))
+
+ const overlayLayer = selectedAtlas && selectedAtlas['parcellations'].find(p => p['@id'] === (parcellationSelected && parcellationSelected['@id']))
returnState[viewerStateHelperStoreName] = {
...viewreHelperState,
- selectedAtlasId: selectedAtlas['@id'],
- overlayingAdditionalParcellations: !overlayLayer['baseLayer']
+ selectedAtlasId: selectedAtlas && selectedAtlas['@id'],
+ overlayingAdditionalParcellations: (overlayLayer && !overlayLayer['baseLayer'])
? [ overlayLayer ]
: []
}
diff --git a/src/services/state/viewerState.store.helper.ts b/src/services/state/viewerState.store.helper.ts
index ff34382e6938a70fc3b317de36dc2949ed360d93..21f3f715941b3f16d69a8aa15f215a6a2a28a97c 100644
--- a/src/services/state/viewerState.store.helper.ts
+++ b/src/services/state/viewerState.store.helper.ts
@@ -185,3 +185,4 @@ export function viewerStateFleshOutDetail(reducer: ActionReducer<any>): ActionRe
}
}
+export const defaultState = initialState
\ No newline at end of file
diff --git a/src/services/stateStore.service.ts b/src/services/stateStore.service.ts
index 83981d12f1bd436ada7cc052d49a8260124eb031..1aba9e107022f5b0a0ec793a791f985c706969bd 100644
--- a/src/services/stateStore.service.ts
+++ b/src/services/stateStore.service.ts
@@ -35,6 +35,11 @@ import {
stateStore as viewerState,
} from './state/viewerState.store'
+import {
+ defaultState as defaultViewerHelperState,
+ viewerStateHelperStoreName
+} from './state/viewerState.store.helper'
+
export { pluginState }
export { viewerConfigState }
export { NgViewerStateInterface, NgViewerActionInterface, ngViewerState }
@@ -198,9 +203,8 @@ export interface IavRootStoreInterface {
}
import { DATASTORE_DEFAULT_STATE } from 'src/ui/databrowserModule'
-import { createAction, props } from '@ngrx/store';
-export const defaultRootState: IavRootStoreInterface = {
+export const defaultRootState: any = {
pluginState: pluginDefaultState,
dataStore: DATASTORE_DEFAULT_STATE,
ngViewerState: ngViewerDefaultState,
@@ -208,4 +212,5 @@ export const defaultRootState: IavRootStoreInterface = {
userConfigState: userConfigDefaultState,
viewerConfigState: viewerConfigDefaultState,
viewerState: viewerDefaultState,
+ [viewerStateHelperStoreName]: defaultViewerHelperState
}
diff --git a/src/ui/viewerStateController/viewerState.useEffect.spec.ts b/src/ui/viewerStateController/viewerState.useEffect.spec.ts
index dd055354b4e04fa8d05b06321f4f41c7dc9ffaee..513854f6703aa76d6b5b3c2f79b9fd574c8a13d6 100644
--- a/src/ui/viewerStateController/viewerState.useEffect.spec.ts
+++ b/src/ui/viewerStateController/viewerState.useEffect.spec.ts
@@ -85,45 +85,42 @@ describe('viewerState.useEffect.ts', () => {
}).compileComponents()
}))
- describe('selectTemplateWithName$', () => {
+ describe('selectTemplate$', () => {
it('if coordXform returns error', () => {
- expect(false).toBe(true)
const viewerStateCtrlEffect = TestBed.inject(ViewerStateControllerUseEffect)
- // expect(
- // viewerStateCtrlEffect.selectTemplateWithName$
- // ).toBeObservable(
- // hot(
- // 'a',
- // {
- // a: {
- // type: NEWVIEWER,
- // selectTemplate: reconstitutedColin,
- // selectParcellation: reconstitutedColin.parcellations[0]
- // }
- // }
- // )
- // )
+ expect(
+ viewerStateCtrlEffect.selectTemplate$
+ ).toBeObservable(
+ hot(
+ 'a',
+ {
+ a: {
+ type: NEWVIEWER,
+ selectTemplate: reconstitutedColin,
+ selectParcellation: reconstitutedColin.parcellations[0]
+ }
+ }
+ )
+ )
})
it('calls with correct param', () => {
- expect(false).toBe(true)
- // necessary for observable to fire
const viewerStateCtrlEffect = TestBed.inject(ViewerStateControllerUseEffect)
- // expect(
- // viewerStateCtrlEffect.selectTemplateWithName$
- // ).toBeObservable(
- // hot(
- // 'a',
- // {
- // a: {
- // type: NEWVIEWER,
- // selectTemplate: reconstitutedColin,
- // selectParcellation: reconstitutedColin.parcellations[0]
- // }
- // }
- // )
- // )
+ expect(
+ viewerStateCtrlEffect.selectTemplate$
+ ).toBeObservable(
+ hot(
+ 'a',
+ {
+ a: {
+ type: NEWVIEWER,
+ selectTemplate: reconstitutedColin,
+ selectParcellation: reconstitutedColin.parcellations[0]
+ }
+ }
+ )
+ )
expect(spy).toHaveBeenCalledWith(
bigbrainJson.name,
reconstitutedColin.name,
@@ -145,21 +142,21 @@ describe('viewerState.useEffect.ts', () => {
}
updatedColinNavigation.zoomFactor = zoom
updatedColinNavigation.pose.orientation = orientation
- expect(false).toBe(true)
- // expect(
- // viewerStateCtrlEffect.selectTemplateWithName$
- // ).toBeObservable(
- // hot(
- // 'a',
- // {
- // a: {
- // type: NEWVIEWER,
- // selectTemplate: updatedColin,
- // selectParcellation: updatedColin.parcellations[0]
- // }
- // }
- // )
- // )
+
+ expect(
+ viewerStateCtrlEffect.selectTemplate$
+ ).toBeObservable(
+ hot(
+ 'a',
+ {
+ a: {
+ type: NEWVIEWER,
+ selectTemplate: updatedColin,
+ selectParcellation: updatedColin.parcellations[0]
+ }
+ }
+ )
+ )
})
})
})