diff --git a/.travis.yml b/.travis.yml
index e9d1d40d26897d755b439e0d8b1f70d76d32aa64..6e5c0d5b25d8b0008aa359d3e984d3bc96b4b2c4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -42,6 +42,50 @@ jobs:
- NODE_ENV=test
- PORT=12234
+ - stage: Check version numbers and release notes
+ name: Check version number advanced (package.json)
+ if: |
+ (type = pull_request AND branch = staging) OR \
+ (type = pull_request AND branch = master AND NOT head_branch = staging)
+ script:
+ - MASTER_VERSION=$(git show origin/master:package.json | jq '.version')
+ - THIS_VERSION=$(jq '.version' < package.json)
+ - test "$MASTER_VERSION" == "$THIS_VERSION" && exit 1 || exit 0
+
+ - name: Check release notes authored (docs/releases/v?.?.?.md)
+ if: |
+ (type = pull_request AND branch = staging) OR \
+ (type = pull_request AND branch = master AND NOT head_branch = staging)
+ script:
+ - |
+ VERSION_NUM=$(jq '.version' < package.json) && \
+ VERSION_NUM=${VERSION_NUM#\"} && \
+ VERSION_NUM=${VERSION_NUM%\"} && \
+ test -f docs/releases/v$VERSION_NUM.md && exit 0 || exit 1
+
+ - name: Release notes linked in mkdocs.yml
+ if: |
+ (type = pull_request AND branch = staging) OR \
+ (type = pull_request AND branch = master AND NOT head_branch = staging)
+ script:
+ - VERSION_NUM=$(jq '.version' < package.json)
+ - VERSION_NUM=${VERSION_NUM#\"}
+ - VERSION_NUM=${VERSION_NUM%\"}
+ - 'echo "VERSION_NUM: $VERSION_NUM"'
+ - cat mkdocs.yml
+ - GREP_VERSION_NUM=$(cat mkdocs.yml | grep $VERSION_NUM)
+ - 'echo GREP_VERSION_NUM: $GREP_VERSION_NUM'
+ - test -z "$GREP_VERSION_NUM" && exit 1 || exit 0
+
+ - stage: Create github release
+ if: |
+ type = push AND \
+ branch = master
+ before_script:
+ - chmod ugo+x ./release.sh
+ script: ./release.sh
+ env:
+ - secure: "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"
# Temporarily disabling browserstack e2e tests. They seem to fail without any reason
@@ -58,12 +102,6 @@ jobs:
# - BROWSERSTACK_USERNAME=xiao33
# - secure: "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"
-env:
- global:
- - CHROMIUM_VERSION=80.0.3987.106
- - PPTR_VERSION=2.1.0
- - PROTRACTOR_SPECS=./src/navigating/*.e2e-spec.js
-
# addons:
# browserstack:
# username: "xiao33"
diff --git a/Dockerfile b/Dockerfile
index f13fff01bd1405023b5479bf74c9d55dde5774f6..62d83bb2de3faa969d4d4f86c782517cb6bbce9e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,7 +7,7 @@ ARG USE_LOGO
ENV USE_LOGO=${USE_LOGO:-hbp}
ARG DATASET_PREVIEW_URL
-ENV DATASET_PREVIEW_URL=${DATASET_PREVIEW_URL:-https://hbp-kg-dataset-previewer.apps.hbp.eu/datasetPreview}
+ENV DATASET_PREVIEW_URL=${DATASET_PREVIEW_URL:-https://hbp-kg-dataset-previewer.apps.hbp.eu/v2}
ARG USE_LOGO
ENV USE_LOGO=${USE_LOGO:-hbp}
diff --git a/deploy/csp/index.js b/deploy/csp/index.js
index 7eebf7be2f84b32c2a7c454a5f608d9963f9f49d..eb071a225d65ddec4b5c9f2f3fc9d1cb315a831d 100644
--- a/deploy/csp/index.js
+++ b/deploy/csp/index.js
@@ -87,12 +87,10 @@ module.exports = (app) => {
'unpkg.com',
'*.unpkg.com',
'*.jsdelivr.net',
-
- // Catching Safari 10 bug unsafe-eval
- "'sha256-yEVCaeeaeg6koloXfx+6DuFnP7SnjOwYZiWBTRFurJw='",
(req, res) => res.locals.nonce ? `'nonce-${res.locals.nonce}'` : null,
...SCRIPT_SRC,
- ...WHITE_LIST_SRC
+ ...WHITE_LIST_SRC,
+ ...defaultAllowedSites
],
reportUri: CSP_REPORT_URI || '/report-violation'
},
diff --git a/deploy/datasets/testData/mni152JuBrain.js b/deploy/datasets/testData/mni152JuBrain.js
index 788d622c47c85e9318868752bd2c14686df37f7e..4cfe826de11c69cc3d16018564f11f4a53c43601 100644
--- a/deploy/datasets/testData/mni152JuBrain.js
+++ b/deploy/datasets/testData/mni152JuBrain.js
@@ -185,9 +185,9 @@ module.exports = [
"parcellationRegion": [
{
"species": [],
- "name": "Area hOc1",
+ "name": "Area hOc1 (V1, 17, CalcS)",
"alias": null,
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/b851eb9d-9502-45e9-8dd8-2861f0e6da3f"
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/5151ab8f-d8cb-4e67-a449-afe2a41fb007"
}
],
"species": [
@@ -297,9 +297,9 @@ module.exports = [
"parcellationRegion": [
{
"species": [],
- "name": "Area 44d",
+ "name": "Area 44 (IFG)",
"alias": null,
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/8aeae833-81c8-4e27-a8d6-deee339d6052"
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/8a6be82c-5947-4fff-8348-cf9bf73e4f40"
}
],
"species": [
diff --git a/deploy/datasets/util.js b/deploy/datasets/util.js
index 508e884817e7ac4a480f497e4cbd2116f61011f0..d7835269ed744b76392571424ef3ef5a080d9ce4 100644
--- a/deploy/datasets/util.js
+++ b/deploy/datasets/util.js
@@ -97,7 +97,7 @@ initPrArray.push(
.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 jubrain = flattenRegions(json.parcellations.find(({ name }) => 'Cytoarchitectonic Maps' === name).regions)
longBundleSet = populateSet(longBundle)
shortBundleSet = populateSet(shortBundle)
juBrainSet = populateSet(jubrain)
diff --git a/docs/releases/v2.2.6.md b/docs/releases/v2.2.6.md
new file mode 100644
index 0000000000000000000000000000000000000000..717faaf5a20dab8896bfaea6da9e9d4ca6577969
--- /dev/null
+++ b/docs/releases/v2.2.6.md
@@ -0,0 +1,14 @@
+# v2.2.6
+
+## Feat
+
+- Added Julich Brain v2.4 to the supported atlases
+
+## Bugfixes
+
+- Fixed matomo CSP issues
+- Updated kg dataset previewer URL
+
+# Under the hood
+
+- CI/CD: auto tag releases on github
diff --git a/mkdocs.yml b/mkdocs.yml
index 84be99658419b3b6f6776a860578fdb2b42c4ba6..0897e824b6399dacd8e474d2b88c38f67042a4f9 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -41,6 +41,7 @@ pages:
- Display non-atlas volumes: 'advanced/otherVolumes.md'
- Release notes:
- v2.2.7: 'releases/v2.2.7.md'
+ - v2.2.6: 'releases/v2.2.6.md'
- v2.2.5: 'releases/v2.2.5.md'
- v2.2.4: 'releases/v2.2.4.md'
- v2.2.3: 'releases/v2.2.3.md'
diff --git a/package.json b/package.json
index f3a7aff77be89c8a6a737042e84839ec3829d5b8..83e92595c694c3c9029f0ca866f0c35f29d716cc 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "interactive-viewer",
- "version": "2.2.2",
+ "version": "2.2.6",
"description": "HBP interactive atlas viewer. Integrating KG query, dataset previews & more. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular.io",
"scripts": {
"dev-server-export": "webpack-dev-server --config webpack.export.js",
diff --git a/release.sh b/release.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2eb23818ae9e75d207b874bbaa1b924d9b83dccf
--- /dev/null
+++ b/release.sh
@@ -0,0 +1,70 @@
+#! /bin/bash
+
+# This is an automated script for TravisCI
+# It is triggered on push to master
+# It will create a release and publish to the github repo
+
+OWNER=HumanBrainProject
+REPO=interactive-viewer
+USER=xgui3783
+EMAIL=xgui3783@gmail.com
+#GITHUB_TOKEN should be populated by CI
+
+test -z "$GITHUB_TOKEN" && exit 1
+
+TAG=$(jq '.version' < package.json)
+TAG=${TAG#\"}
+TAG=v${TAG%\"}
+OBJECT=$(git rev-parse HEAD)
+DATE=$(date --iso-8601=seconds)
+BODY='{
+ "tag": "'$TAG'",
+ "message": "Annotated release for '$TAG'",
+ "object": "'$OBJECT'",
+ "type": "commit",
+ "tagger": {
+ "name": "'$USER'",
+ "email": "'$EMAIL'",
+ "date": "'$DATE'"
+ }
+}'
+
+# Create annotated tag
+
+echo curl -XPOST \
+ -H "Accept: application/vnd.github.v3+json" \
+ -u "$USER:$GITHUB_TOKEN"\
+ -d "$BODY" \
+ https://api.github.com/repos/$OWNER/$REPO/git/tags
+
+# Push tag to remote
+
+CREATE_REF_BODY='{
+ "ref":"refs/tags/'$TAG'",
+ "sha":"'$OBJECT'"
+}'
+
+echo curl -XPOST\
+ -u "$USER:$GITHUB_TOKEN"\
+ -H "Accept: application/vnd.github.v3+json" \
+ -d "$CREATE_REF_BODY"\
+ https://api.github.com/repos/$OWNER/$REPO/git/refs
+
+# Create release
+
+RELEASE_NOTES=$(sed -e 's/$/\\n/' docs/releases/$TAG.md)
+
+RELEASE_BODY='{
+ "tag_name":"'$TAG'",
+ "name":"'$TAG'",
+ "body":"'$(echo $RELEASE_NOTES)'",
+ "target_commitish": "master",
+ "draft":false,
+ "prerelease":false
+}'
+
+echo curl -XPOST\
+ -u "$USER:$GITHUB_TOKEN"\
+ -H "Accept: application/vnd.github.v3+json" \
+ -d "$RELEASE_BODY" \
+ https://api.github.com/repos/$OWNER/$REPO/releases
diff --git a/src/glue.spec.ts b/src/glue.spec.ts
index f5ee1d2f46b0321c522dab6f574b6fcd6edc378f..f53f7a4fc88a2966de4d42d45f736d6081fb9f68 100644
--- a/src/glue.spec.ts
+++ b/src/glue.spec.ts
@@ -5,7 +5,6 @@ import { provideMockStore, MockStore } from "@ngrx/store/testing"
import { getRandomHex } from 'common/util'
import { EnumWidgetTypes, TypeOpenedWidget, uiActionSetPreviewingDatasetFiles } from "./services/state/uiState.store.helper"
import { hot } from "jasmine-marbles"
-import * as DATABROWSER_MODULE_EXPORTS from 'src/ui/databrowserModule'
import { HttpClientTestingModule, HttpTestingController } from "@angular/common/http/testing"
import { glueActionToggleDatasetPreview } from './glue'
import { getIdObj } from 'common/util'
@@ -244,7 +243,7 @@ describe('> glue.ts', () => {
// debounce at 100ms
tick(200)
- const req = ctrl.expectOne(`${DS_PREVIEW_URL}/${datasetId}/${encodeURIComponent(filename)}`)
+ const req = ctrl.expectOne(`${DS_PREVIEW_URL}/${encodeURIComponent('minds/core/dataset/v1.0.0')}/${datasetId}/${encodeURIComponent(filename)}`)
req.flush(nifti)
}))
})
diff --git a/src/glue.ts b/src/glue.ts
index bf94ffeb1133885acbdbff350ad7f9691d1df6a8..c107f92a97d2c3f0d881aa00c268bd87335c20fb 100644
--- a/src/glue.ts
+++ b/src/glue.ts
@@ -145,20 +145,21 @@ export class DatasetPreviewGlue implements IDatasetPreviewGlue, OnDestroy{
}
private fetchedDatasetPreviewCache: Map<string, any> = new Map()
- private getDatasetPreviewFromId({ datasetId, filename }: IDatasetPreviewData){
+ private getDatasetPreviewFromId({ datasetId, filename, datasetSchema = 'minds/core/dataset/v1.0.0' }: IDatasetPreviewData){
const dsPrvId = DatasetPreviewGlue.GetDatasetPreviewId({ datasetId, filename })
- const cachedPrv = this.fetchedDatasetPreviewCache.get(dsPrvId)
+ const cachedPrv = this.fetchedDatasetPreviewCache.get(`${datasetSchema}/${dsPrvId}`)
const filteredDsId = /[a-f0-9-]+$/.exec(datasetId)
if (cachedPrv) return of(cachedPrv)
- return this.http.get(`${DS_PREVIEW_URL}/${filteredDsId}/${encodeURIComponent(filename)}`, { responseType: 'json' }).pipe(
+ return this.http.get(`${DS_PREVIEW_URL}/${encodeURIComponent(datasetSchema)}/${filteredDsId}/${encodeURIComponent(filename)}`, { responseType: 'json' }).pipe(
map(json => {
return {
...json,
filename,
- datasetId
+ datasetId,
+ datasetSchema
}
}),
- tap(val => this.fetchedDatasetPreviewCache.set(dsPrvId, val))
+ tap(val => this.fetchedDatasetPreviewCache.set(`${datasetSchema}/${dsPrvId}`, val))
)
}
@@ -313,6 +314,7 @@ export class DatasetPreviewGlue implements IDatasetPreviewGlue, OnDestroy{
}
private openDatasetPreviewWidget(data: IDatasetPreviewData) {
+ console.log({ data })
const { datasetId: kgId, filename } = data
if (!!this.actionOnWidget) {
@@ -369,9 +371,10 @@ export class DatasetPreviewGlue implements IDatasetPreviewGlue, OnDestroy{
public displayDatasetPreview(previewFile: DatasetPreview, dataset: IKgDataEntry){
const { filename, datasetId } = previewFile
const { fullId } = dataset
- const { kgId } = getIdObj(fullId)
+ const { kgId, kgSchema } = getIdObj(fullId)
const datasetPreviewFile = {
+ datasetSchema: kgSchema,
datasetId: datasetId || kgId,
filename
}
diff --git a/src/index.html b/src/index.html
index db01a3a08a97a7ef99a8e796f554141df7466496..4c6e55195c1ba02d70354a8f9e50cbd3feaaa116 100644
--- a/src/index.html
+++ b/src/index.html
@@ -11,7 +11,7 @@
<link rel="stylesheet" href="theme.css">
<link rel="stylesheet" href="version.css">
- <script src="https://unpkg.com/kg-dataset-previewer@0.0.19/dist/kg-dataset-previewer/kg-dataset-previewer.js" defer>
+ <script src="https://unpkg.com/kg-dataset-previewer@1.0.6/dist/kg-dataset-previewer/kg-dataset-previewer.js" defer>
</script>
<title>Interactive Atlas Viewer</title>
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index 1d7876bee0c9e0d46989e1cd52f37df23e64e3a0..dd0aca9af3f8096dd23c839585d4fd2ab2fa52e8 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -6,10 +6,17 @@
"useTheme": "dark",
"ngId": "mni152",
"nehubaConfigURL": "nehubaConfig/MNI152NehubaConfig",
+ "otherNgIds": [
+ "jubrain mni152 v18 left",
+ "jubrain mni152 v18 right",
+ "julich brain mni152 v22 left",
+ "julich brain mni152 v22 right"
+ ],
"parcellations": [
{
- "name": "JuBrain Cytoarchitectonic Atlas",
- "ngId": "jubrain mni152 v18 left",
+ "fullId": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "name": "Cytoarchitectonic Maps",
"auxillaryMeshIndices": [
65535
],
@@ -19,12 +26,11 @@
"originDatasets": [
{
"kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce"
+ "kgId": "5249afa7-5e04-4ffd-8039-c3a9231f717c"
}
],
"properties": {
- "version": "1.0",
- "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI ICBM 2009c Asymmetric as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
"publications": [
{
"doi": "https://doi.org/10.1038/nrn2776",
@@ -44,8072 +50,12551 @@
{
"name": "telencephalon",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "cerebral nuclei",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "basal forebrain",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "magnocellular group within septum",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "Ch 123 (Basal Forebrain)",
- "arealabel": "Ch-123",
"status": "publicP",
- "labelIndex": null,
- "synonyms": [],
- "rgb": [
- 124,
- 233,
- 167
- ],
"children": [
{
- "name": "Ch 123 (Basal Forebrain) - left hemisphere",
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "left hemisphere",
+ "labelIndex": 76,
"rgb": [
- 124,
- 233,
- 167
+ 200,
+ 200,
+ 200
+ ],
+ "ngId": "ICBM152_V24_LEFT_NG",
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
],
- "labelIndex": 286,
- "ngId": "jubrain mni152 v18 left",
- "children": [],
- "position": [
- -3648265,
- 3367508,
- -8957413
- ]
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ },
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "id": "286",
+ "grayvalue": "76"
+ },
+ "dat": {
+ "colors": false,
+ "names": false
+ }
+ }
},
{
- "name": "Ch 123 (Basal Forebrain) - right hemisphere",
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "right hemisphere",
+ "labelIndex": 76,
"rgb": [
- 124,
- 233,
- 167
+ 200,
+ 200,
+ 200
+ ],
+ "ngId": "ICBM152_V24_RIGHT_NG",
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
],
- "ngId": "jubrain mni152 v18 right",
- "labelIndex": 286,
- "children": [],
- "position": [
- 1687097,
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+ }
},
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"ngId": "fibre bundle long",
diff --git a/src/res/ext/MNI152NehubaConfig.json b/src/res/ext/MNI152NehubaConfig.json
index 69dd2a1de6769d5637c4641baf9097e68c49d69e..13084b6ed79d8998eea03e1331ddcada26f2d0c4 100644
--- a/src/res/ext/MNI152NehubaConfig.json
+++ b/src/res/ext/MNI152NehubaConfig.json
@@ -95,7 +95,7 @@
},
"jubrain mni152 v18 left": {
"type": "segmentation",
- "visible": true,
+ "visible": false,
"source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/icbm152casym/left",
"transform": [
[
@@ -126,7 +126,7 @@
},
"jubrain mni152 v18 right": {
"type": "segmentation",
- "visible": true,
+ "visible": false,
"source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/icbm152casym/right",
"transform": [
[
@@ -155,6 +155,136 @@
]
]
},
+ "julich brain mni152 v22 left": {
+ "type": "segmentation",
+ "visible": false,
+ "source": "precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/data-repo/20200807_julich_brain_v2_mni152_left/precomputed",
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+ "julich brain mni152 v22 right": {
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+ "visible": false,
+ "source": "precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/data-repo/20200807_julich_brain_v2_mni152_right/precomputed",
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+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201002_JulichBrain-V2_4-ICBM152_MPM_mesh/precomputed/left",
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+ "ICBM152_V24_RIGHT_NG": {
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+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201002_JulichBrain-V2_4-ICBM152_MPM_mesh/precomputed/right",
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+ },
"fibre bundle long": {
"type": "segmentation",
"source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/Fiber_Bundle/long-bundles_maxprob",
diff --git a/src/res/ext/colin.json b/src/res/ext/colin.json
index 0bfba5ad72b835a7937719b0942b0ef39477aa21..9a1badde70653ffd7a9a362a67baa4abb80fbcbe 100644
--- a/src/res/ext/colin.json
+++ b/src/res/ext/colin.json
@@ -8,8 +8,9 @@
"nehubaConfigURL": "nehubaConfig/colinNehubaConfig",
"parcellations": [
{
- "name": "JuBrain Cytoarchitectonic Atlas",
- "ngId": "jubrain colin v18 left",
+ "fullId": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "name": "Cytoarchitectonic Maps",
"auxillaryMeshIndices": [
65535
],
@@ -19,11 +20,10 @@
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{
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- "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce"
+ "kgId": "5249afa7-5e04-4ffd-8039-c3a9231f717c"
}
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"description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
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@@ -44,8516 +44,12555 @@
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- "synonyms": [],
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"children": [
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+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
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{
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+ "name": "Ch 123 (Basal Forebrain)",
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+ "ngId": "COLIN_V24_RIGHT_NG",
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+ "kgHref": "https://kg.ebrains.eu/instances/Dataset/147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
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"name": "sublenticular part of basal forebrain",
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+ ],
+ "_": {
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+ }
}
],
"properties": {
"name": "MNI Colin 27",
"description": "A stereotaxic average of 27 T1-weighted MRI scans of the same individual. (Holmes et al., 1998), mapped to fit the MNI305 space. Although not capturing brain variability, it is well established in neuroscience due to its high definition. HBP provides the JuBrain probabilistic cytoarchitectonic atlas (Amunts et al.) in this space."
}
-}
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/res/ext/colinNehubaConfig.json b/src/res/ext/colinNehubaConfig.json
index a8b1d29df406129bb0f5623ad1acb3f4324fb2de..eaccca12dbb17e43c4f2268f8acdd66a57b41c3b 100644
--- a/src/res/ext/colinNehubaConfig.json
+++ b/src/res/ext/colinNehubaConfig.json
@@ -23,7 +23,7 @@
"mesh": {
"removeBasedOnNavigation": true,
"flipRemovedOctant": true,
- "surfaceParcellation": false
+ "surfaceParcellation": true
},
"removePerspectiveSlicesBackground": {
"mode": "=="
@@ -87,10 +87,10 @@
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]
},
- "jubrain colin v18 left": {
+ "COLIN_V24_LEFT_NG": {
"type": "segmentation",
"visible": true,
- "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/colin27/left",
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20200926_JulichBrain-V2_4-Colin_MPM_mesh/precomputed/left",
"transform": [
[
1,
@@ -116,12 +116,15 @@
0,
1
]
- ]
+ ],
+ "_": {
+ "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20200926_JulichBrain-V2_4-Colin_MPM_mesh/raw/745a37f64b6995a661f5a61287b4067df01687cb/output/nehuba-ui/left_config.json"
+ }
},
- "jubrain colin v18 right": {
+ "COLIN_V24_RIGHT_NG": {
"type": "segmentation",
"visible": true,
- "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/colin27/right",
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20200926_JulichBrain-V2_4-Colin_MPM_mesh/precomputed/right",
"transform": [
[
1,
@@ -147,7 +150,10 @@
0,
1
]
- ]
+ ],
+ "_": {
+ "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20200926_JulichBrain-V2_4-Colin_MPM_mesh/raw/745a37f64b6995a661f5a61287b4067df01687cb/output/nehuba-ui/right_config.json"
+ }
}
},
"navigation": {
diff --git a/src/services/effect/effect.spec.ts b/src/services/effect/effect.spec.ts
index d62f8d8b0efb499858aa10443d92809c34b94ba1..3ca67f80459bfe76a2ffa296d3829d7d84434f91 100644
--- a/src/services/effect/effect.spec.ts
+++ b/src/services/effect/effect.spec.ts
@@ -10,31 +10,7 @@ import { defaultRootState } from '../stateStore.service'
const colinsJson = require('!json-loader!../../res/ext/colin.json')
-
-const hoc1 = {
- name: "Area hOc1 (V1, 17, CalcS) - left hemisphere",
- rgb: [
- 190,
- 132,
- 147,
- ],
- labelIndex: 8,
- ngId: "jubrain colin v18 left",
- children: [],
- status: "publicP",
- position: [
- -8533787,
- -84646549,
- 1855106,
- ],
- originDatasets: [
- {
- kgSchema: "minds/core/dataset/v1.0.0",
- kgId: "5c669b77-c981-424a-858d-fe9f527dbc07",
- filename: "Area hOc1 (V1, 17, CalcS) [v2.4, Colin 27, left hemisphere]"
- }
- ],
-}
+const COLIN_JULICHBRAIN_LAYER_NAME = `COLIN_V24_LEFT_NG`
describe('effect.ts', () => {
describe('getGetRegionFromLabelIndexId', () => {
@@ -46,8 +22,10 @@ describe('effect.ts', () => {
updated: true,
},
})
- const fetchedRegion = getRegionFromlabelIndexId({ labelIndexId: 'jubrain colin v18 left#8' })
- expect(fetchedRegion).toEqual(hoc1)
+ const fetchedRegion = getRegionFromlabelIndexId({ labelIndexId: `${COLIN_JULICHBRAIN_LAYER_NAME}#116` })
+ expect(fetchedRegion).toBeTruthy()
+ expect(fetchedRegion.fullId.kg.kgId).toEqual('b09aaa77-f41b-4008-b8b9-f984b0417cf3')
+
})
})
diff --git a/src/services/state/uiState.store.helper.ts b/src/services/state/uiState.store.helper.ts
index 8f3ead0a17d7911b8bafedec1612cfc3a2cfa451..176e86c145f8db13b6d16b1932c6f50b22019553 100644
--- a/src/services/state/uiState.store.helper.ts
+++ b/src/services/state/uiState.store.helper.ts
@@ -41,6 +41,7 @@ export enum EnumWidgetTypes{
export interface IDatasetPreviewData{
datasetId: string
filename: string
+ datasetSchema?: string
}
export type TypeOpenedWidget = {
diff --git a/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.component.ts b/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.component.ts
index 5161a4ed7c52d03b989f800e42d25cc57ffbd041..04d5130a5f9e67fc1e64ca90b02d54b4389f2f02 100644
--- a/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.component.ts
+++ b/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.component.ts
@@ -5,6 +5,7 @@ import { Observable, fromEvent, Subscription, of, throwError } from "rxjs";
import { switchMapTo, catchError, take, concatMap, map, retryWhen, delay } from "rxjs/operators";
import { DomSanitizer, SafeResourceUrl } from "@angular/platform-browser";
import { ARIA_LABELS } from 'common/constants'
+import { DS_PREVIEW_URL } from 'src/util/constants'
const {
DOWNLOAD_PREVIEW,
@@ -78,6 +79,8 @@ export class PreviewComponentWrapper{
this.backendUrl = backendUrl
this.datasetName = datasetName
}
+
+ this.backendUrl = this.backendUrl || DS_PREVIEW_URL
}
public downloadHref: SafeResourceUrl
diff --git a/src/ui/nehubaContainer/splashScreen/splashScreen.template.html b/src/ui/nehubaContainer/splashScreen/splashScreen.template.html
index 9e4ddfcf883cad44de3a0d6f2bbc623292b31a38..1881ab9d96cf3c02a733c5ed50c1960b56f68e95 100644
--- a/src/ui/nehubaContainer/splashScreen/splashScreen.template.html
+++ b/src/ui/nehubaContainer/splashScreen/splashScreen.template.html
@@ -34,7 +34,7 @@
*ngFor="let parcellation of template.parcellations"
mat-button
color="primary">
- {{ parcellation.name | tmpParcNamePipe }}
+ {{ (parcellation.displayName || parcellation.name) | tmpParcNamePipe }}
</button>
</mat-card-content>
diff --git a/src/ui/parcellationRegion/regionMenu/regionMenu.template.html b/src/ui/parcellationRegion/regionMenu/regionMenu.template.html
index 714b6e70af6d1c12eb02122b4c0a8a2148bd1149..56f05d9b1abcb0690e1221b90d34b899739c9cbd 100644
--- a/src/ui/parcellationRegion/regionMenu/regionMenu.template.html
+++ b/src/ui/parcellationRegion/regionMenu/regionMenu.template.html
@@ -52,6 +52,7 @@
iav-dataset-preview-dataset-file
[iav-dataset-preview-dataset-file-kgid]="originDataset.kgId"
[iav-dataset-preview-dataset-file-filename]="originDataset.filename"
+ [iav-dataset-preview-dataset-file-kgschema]="originDataset.kgSchema"
#previewDirective="iavDatasetPreviewDatasetFile"
iv-custom-comp
[attr.primary]="previewDirective.active || null"
diff --git a/src/ui/viewerStateController/viewerStateCFull/viewerState.template.html b/src/ui/viewerStateController/viewerStateCFull/viewerState.template.html
index 6a341997d00442b6bc64b0bf594222b80256777d..1a1cbc903564885f09a99c3bbc6bb7f7832d6fce 100644
--- a/src/ui/viewerStateController/viewerStateCFull/viewerState.template.html
+++ b/src/ui/viewerStateController/viewerStateCFull/viewerState.template.html
@@ -86,7 +86,7 @@
<mat-option
*ngFor="let parcellation of (templateSelected.parcellations | appendTooltipTextPipe)"
[value]="parcellation.name">
- {{ parcellation.name | tmpParcNamePipe }}
+ {{ (parcellation.displayName || parcellation.name) | tmpParcNamePipe }}
</mat-option>
</mat-select>
</mat-form-field>
diff --git a/src/ui/viewerStateController/viewerStateCMini/viewerStateMini.template.html b/src/ui/viewerStateController/viewerStateCMini/viewerStateMini.template.html
index 40ac0c2afaac85eb6e4647933aea9ae1b8b58083..2604321cb2f7ec6f857ab83acaff064338a19284 100644
--- a/src/ui/viewerStateController/viewerStateCMini/viewerStateMini.template.html
+++ b/src/ui/viewerStateController/viewerStateCMini/viewerStateMini.template.html
@@ -3,7 +3,7 @@
{{ templateSelected.name }}
</div>
<div *ngIf="parcellationSelected$ | async as parcellationSelected">
- {{ parcellationSelected.name | tmpParcNamePipe }}
+ {{ (parcellationSelected.displayName || parcellationSelected.name) | tmpParcNamePipe }}
</div>
<!-- selected parcellation regions -->
diff --git a/webpack.staticassets.js b/webpack.staticassets.js
index 163b00926ab96d02e90a6cdad81ba97ccf9a66f9..9175274b0c76c85fe74ac0db54aad8b4e49ca55f 100644
--- a/webpack.staticassets.js
+++ b/webpack.staticassets.js
@@ -71,7 +71,7 @@ module.exports = {
: JSON.stringify('unspecificied hash'),
PRODUCTION: !!process.env.PRODUCTION,
BACKEND_URL: (process.env.BACKEND_URL && JSON.stringify(process.env.BACKEND_URL)) || 'null',
- DATASET_PREVIEW_URL: JSON.stringify(process.env.DATASET_PREVIEW_URL || 'https://hbp-kg-dataset-previewer.apps.hbp.eu/datasetPreview'),
+ DATASET_PREVIEW_URL: JSON.stringify(process.env.DATASET_PREVIEW_URL || 'https://hbp-kg-dataset-previewer.apps.hbp.eu/v2'),
SPATIAL_TRANSFORM_BACKEND: JSON.stringify(process.env.SPATIAL_TRANSFORM_BACKEND || 'https://hbp-spatial-backend.apps.hbp.eu'),
MATOMO_URL: JSON.stringify(process.env.MATOMO_URL || null),
MATOMO_ID: JSON.stringify(process.env.MATOMO_ID || null),