diff --git a/.github/workflows/docker_img.yml b/.github/workflows/docker_img.yml
index 928c13769d4d699156888a04ee5cad19f0519a1b..daa098e920be68ce850beb81fd1450505dbfc1cd 100644
--- a/.github/workflows/docker_img.yml
+++ b/.github/workflows/docker_img.yml
@@ -48,22 +48,26 @@ jobs:
- name: 'Set version variable & expmt feature flag'
run: |
+ GIT_HASH=$(git rev-parse --short HEAD)
+ echo "Setting GIT_HASH: $GIT_HASH"
+ echo "GIT_HASH=$GIT_HASH" >> $GITHUB_ENV
+
+ VERSION=$(jq -r '.version' package.json)
+ echo "Setting VERSION: $VERSION"
+ echo "VERSION=$VERSION" >> $GITHUB_ENV
if [[ "$GITHUB_REF" == 'refs/heads/master' ]] || [[ "$GITHUB_REF" == 'refs/heads/staging' ]]
then
- echo "Either master or staging, using package.json"
- VERSION=$(jq -r '.version' package.json)
+ echo "prod/staging build, do not enable experimental features"
else
- echo "Using git hash"
- VERSION=$(git rev-parse --short HEAD)
+ echo "dev bulid, enable experimental features"
echo "EXPERIMENTAL_FEATURE_FLAG=true" >> $GITHUB_ENV
fi
- echo "Setting VERSION: $VERSION"
- echo "VERSION=$VERSION" >> $GITHUB_ENV
- name: 'Build docker image'
run: |
DOCKER_BUILT_TAG=${{ env.DOCKER_REGISTRY }}siibra-explorer:$BRANCH_NAME
echo "Building $DOCKER_BUILT_TAG"
docker build \
+ --build-arg GIT_HASH=$GIT_HASH \
--build-arg VERSION=$VERSION \
--build-arg MATOMO_URL=$MATOMO_URL \
--build-arg MATOMO_ID=$MATOMO_ID \
diff --git a/Dockerfile b/Dockerfile
index bc614aacaf8dcef73da19f4a59285e6a31e51daf..3b017144535e201d255259c3b28ec4833d965e0c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -24,6 +24,12 @@ ENV MATOMO_ID=${MATOMO_ID}
ARG EXPERIMENTAL_FEATURE_FLAG
ENV EXPERIMENTAL_FEATURE_FLAG=${EXPERIMENTAL_FEATURE_FLAG:-false}
+ARG GIT_HASH
+ENV GIT_HASH=${GIT_HASH:-unknownhash}
+
+ARG VERSION
+ENV VERSION=${VERSION:-unknownversion}
+
COPY . /iv
WORKDIR /iv
@@ -33,8 +39,6 @@ RUN node ./src/environments/parseEnv.js
# When building in local, where node_module already exist, prebuilt binary may throw an error
RUN rm -rf ./node_modules
-ARG VERSION
-ENV VERSION=${VERSION}
RUN npm i
RUN npm run build-aot
diff --git a/angular.json b/angular.json
index 381d8126cb58142d0ab49b4dabda5cd8ad15124d..8e887675e54154cb46b0eac5e871ce64c6079695 100644
--- a/angular.json
+++ b/angular.json
@@ -34,9 +34,43 @@
"src/overwrite.scss",
"src/extra_styles.css"
],
- "scripts": [
- "worker/worker.js"
- ]
+ "scripts": [{
+ "input": "worker/worker.js",
+ "inject": false,
+ "bundleName": "worker"
+ },{
+ "input": "worker/worker-plotly.js",
+ "inject": false,
+ "bundleName": "worker-plotly"
+ },{
+ "input": "worker/worker-nifti.js",
+ "inject": false,
+ "bundleName": "worker-nifti"
+ },
+
+ {
+ "input": "third_party/catchSyntaxError.js",
+ "inject": false,
+ "bundleName": "catchSyntaxError"
+ },{
+ "input": "third_party/syntaxError.js",
+ "inject": false,
+ "bundleName": "syntaxError"
+ },
+
+ {
+ "input": "third_party/vanilla_nehuba.js",
+ "inject": false,
+ "bundleName": "vanilla_nehuba"
+ },{
+ "input": "export-nehuba/dist/min/main.bundle.js",
+ "inject": false,
+ "bundleName": "main.bundle"
+ },{
+ "input": "export-nehuba/dist/min/chunk_worker.bundle.js",
+ "inject": false,
+ "bundleName": "chunk_worker.bundle"
+ }]
},
"configurations": {
"production": {
@@ -47,7 +81,14 @@
}
],
"buildOptimizer": true,
- "optimization": false,
+ "optimization": {
+ "scripts": true,
+ "fonts": true,
+ "styles": {
+ "inlineCritical": false,
+ "minify": true
+ }
+ },
"vendorChunk": true,
"extractLicenses": false,
"sourceMap": false,
diff --git a/deploy/csp/index.js b/deploy/csp/index.js
index 4deecdda1795ff07c9e6f6f68fcf812c94540432..b7e07519626b1a0b3cf8f8f86728a1c6d7d333fd 100644
--- a/deploy/csp/index.js
+++ b/deploy/csp/index.js
@@ -116,8 +116,8 @@ module.exports = {
'unpkg.com/kg-dataset-previewer@1.2.0/', // preview component
'cdnjs.cloudflare.com/ajax/libs/mathjax/', // math jax
'https://unpkg.com/three-surfer@0.0.10/dist/bundle.js', // for threeSurfer (freesurfer support in browser)
- 'https://unpkg.com/ng-layer-tune@0.0.2/dist/ng-layer-tune/ng-layer-tune.esm.js', // needed for ng layer control
- (req, res) => res.locals.nonce ? `'nonce-${res.locals.nonce}'` : null,
+ 'https://unpkg.com/ng-layer-tune@0.0.2/dist/ng-layer-tune/', // needed for ng layer control
+ (req, res) => res.locals.nonce ? [`'nonce-${res.locals.nonce}'`] : [],
...SCRIPT_SRC,
...WHITE_LIST_SRC,
...defaultAllowedSites
diff --git a/deploy/package-lock.json b/deploy/package-lock.json
index 5d707a769ac807f9c1473f3940fe0464dba4657b..3a8058b86a578efd909ca7b5d28a32edd93e5492 100644
--- a/deploy/package-lock.json
+++ b/deploy/package-lock.json
@@ -379,11 +379,6 @@
}
}
},
- "bowser": {
- "version": "2.5.4",
- "resolved": "https://registry.npmjs.org/bowser/-/bowser-2.5.4.tgz",
- "integrity": "sha512-74GGwfc2nzYD19JCiA0RwCxdq7IY5jHeEaSrrgm/5kusEuK+7UK0qDG3gyzN47c4ViNyO4osaKtZE+aSV6nlpQ=="
- },
"brace-expansion": {
"version": "1.1.11",
"resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz",
@@ -436,11 +431,6 @@
"resolved": "https://registry.npmjs.org/camelcase/-/camelcase-5.3.1.tgz",
"integrity": "sha512-L28STB170nwWS63UjtlEOE3dldQApaJXZkOI1uMFfzf3rRuPegHaHesyee+YxQ+W6SvRDQV6UrdOdRiR153wJg=="
},
- "camelize": {
- "version": "1.0.0",
- "resolved": "https://registry.npmjs.org/camelize/-/camelize-1.0.0.tgz",
- "integrity": "sha1-FkpUg+Yw+kMh5a8HAg5TGDGyYJs="
- },
"caseless": {
"version": "0.12.0",
"resolved": "https://registry.npmjs.org/caseless/-/caseless-0.12.0.tgz",
@@ -581,11 +571,6 @@
"resolved": "https://registry.npmjs.org/content-disposition/-/content-disposition-0.5.2.tgz",
"integrity": "sha1-DPaLud318r55YcOoUXjLhdunjLQ="
},
- "content-security-policy-builder": {
- "version": "2.1.0",
- "resolved": "https://registry.npmjs.org/content-security-policy-builder/-/content-security-policy-builder-2.1.0.tgz",
- "integrity": "sha512-/MtLWhJVvJNkA9dVLAp6fg9LxD2gfI6R2Fi1hPmfjYXSahJJzcfvoeDOxSyp4NvxMuwWv3WMssE9o31DoULHrQ=="
- },
"content-type": {
"version": "1.0.4",
"resolved": "https://registry.npmjs.org/content-type/-/content-type-1.0.4.tgz",
@@ -680,11 +665,6 @@
"assert-plus": "^1.0.0"
}
},
- "dasherize": {
- "version": "2.0.0",
- "resolved": "https://registry.npmjs.org/dasherize/-/dasherize-2.0.0.tgz",
- "integrity": "sha1-bYCcnNDPe7iVLYD8hPoT1H3bEwg="
- },
"debug": {
"version": "2.6.9",
"resolved": "https://registry.npmjs.org/debug/-/debug-2.6.9.tgz",
@@ -1195,15 +1175,9 @@
"dev": true
},
"helmet-csp": {
- "version": "2.9.1",
- "resolved": "https://registry.npmjs.org/helmet-csp/-/helmet-csp-2.9.1.tgz",
- "integrity": "sha512-HgdXSJ6AVyXiy5ohVGpK6L7DhjI9KVdKVB1xRoixxYKsFXFwoVqtLKgDnfe3u8FGGKf9Ml9k//C9rnncIIAmyA==",
- "requires": {
- "bowser": "2.5.4",
- "camelize": "1.0.0",
- "content-security-policy-builder": "2.1.0",
- "dasherize": "2.0.0"
- }
+ "version": "3.4.0",
+ "resolved": "https://registry.npmjs.org/helmet-csp/-/helmet-csp-3.4.0.tgz",
+ "integrity": "sha512-a+YgzWw6dajqhQfb6ktxil0FsQuWTKzrLSUfy55dxS8fuvl1jidTIMPZ2udN15mjjcpBPgTHNHGF5tyWKYyR8w=="
},
"http-cache-semantics": {
"version": "4.0.4",
diff --git a/deploy/package.json b/deploy/package.json
index 8a165a87192525bf0b6bcd9ba86df86fe5ddb30c..a8b5d1488439346a9c7b6adc2322a57a482f218e 100644
--- a/deploy/package.json
+++ b/deploy/package.json
@@ -20,7 +20,7 @@
"express-session": "^1.15.6",
"got": "^10.5.5",
"hbp-seafile": "^0.2.0",
- "helmet-csp": "^2.8.0",
+ "helmet-csp": "^3.4.0",
"lru-cache": "^5.1.1",
"memorystore": "^1.6.1",
"nomiseco": "0.0.2",
diff --git a/deploy/saneUrl/index.js b/deploy/saneUrl/index.js
index 06659fa88748f40db5d57459c43c896b03e7babb..09fe10b25a57e336b25118d57f4b5849c1f8234d 100644
--- a/deploy/saneUrl/index.js
+++ b/deploy/saneUrl/index.js
@@ -36,7 +36,9 @@ const getFile = async name => {
}
const hardCodedMap = new Map([
+ ['bigbrainGreyWhite', '#/a:juelich:iav:atlas:v1.0.0:1/t:minds:core:referencespace:v1.0.0:a1655b99-82f1-420f-a3c2-fe80fd4c8588/p:juelich:iav:atlas:v1.0.0:4/@:0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..7LIx..gIW~.10AwC.B1KK~..1LSm'],
['whs4', '#/a:minds:core:parcellationatlas:v1.0.0:522b368e-49a3-49fa-88d3-0870a307974a/t:minds:core:referencespace:v1.0.0:d5717c4a-0fa1-46e6-918c-b8003069ade8/p:minds:core:parcellationatlas:v1.0.0:ebb923ba-b4d5-4b82-8088-fa9215c2e1fe-v4/@:0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..kxV..0.0.0..8Yu'],
+ ['allen2017', '#/a:juelich:iav:atlas:v1.0.0:2/t:minds:core:referencespace:v1.0.0:265d32a0-3d84-40a5-926f-bf89f68212b9/p:minds:core:parcellationatlas:v1.0.0:05655b58-3b6f-49db-b285-64b5a0276f83/@:0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..kxV..0.0.0..8Yu'],
['mebrains', '#/a:juelich:iav:atlas:v1.0.0:monkey/t:minds:core:referencespace:v1.0.0:MEBRAINS_T1.masked/p:minds:core:parcellationatlas:v1.0.0:mebrains-tmp-id/@:0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..7LIx..0.0.0..1LSm']
])
diff --git a/docs/releases/v2.5.7.md b/docs/releases/v2.5.7.md
index 9aaabad886b2affba5f2747f71b3021ade63ddf6..5e6a2ef22cad04a1190c4fe5691eb45e870086a1 100644
--- a/docs/releases/v2.5.7.md
+++ b/docs/releases/v2.5.7.md
@@ -1,5 +1,16 @@
# v2.5.7
+## Bugfix
+
+- fixed version in console
+
## Feature
- Add menu to change perspective orientation by coronal/sagittal/axial views.
+
+## Under the hood
+
+- added saneurl for bigbrain isocortex, allen CCFv3 2017
+- fixed csp issues
+- optimised build (assets should be smaller)
+- added git hash in console
diff --git a/package.json b/package.json
index c87724a7533539c7f37e81b9be6f2b089996675e..1b8c4de04b3f608d8cba63b6abc8f96120f17696 100644
--- a/package.json
+++ b/package.json
@@ -3,7 +3,7 @@
"version": "2.5.7",
"description": "HBP interactive atlas viewer. Integrating KG query, dataset previews & more. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular",
"scripts": {
- "build-aot": "VERSION=`node -e 'console.log(require(\"./package.json\").version)'` ng build --prod && node ./third_party/matomo/processMatomo.js",
+ "build-aot": "ng build && node ./third_party/matomo/processMatomo.js",
"dev-server-aot": "ng serve",
"e2e": "echo NYI && exit 1",
"wd": "webdriver-manager",
@@ -11,7 +11,7 @@
"eslint": "eslint",
"ng": "ng",
"start": "ng serve",
- "build": "ng build --prod",
+ "build": "ng build",
"watch": "ng build --watch --configuration development",
"test": "ng test",
"test-ci": "ng test --progress false --watch false --browsers=ChromeHeadless"
diff --git a/src/atlasViewer/atlasViewer.workerService.service.ts b/src/atlasViewer/atlasViewer.workerService.service.ts
index 62395463088ed3939c419ec61329c18e68865993..653764d97a7670d16ca8805c1033f09775de0cb0 100644
--- a/src/atlasViewer/atlasViewer.workerService.service.ts
+++ b/src/atlasViewer/atlasViewer.workerService.service.ts
@@ -3,15 +3,7 @@ import { fromEvent } from "rxjs";
import { filter, take } from "rxjs/operators";
import { getUuid } from "src/util/fn";
-/* telling webpack to pack the worker file */
-
-import '!!file-loader?name=worker.js!worker/worker.js'
-import '!!file-loader?name=worker-plotly.js!worker/worker-plotly.js'
-import '!!file-loader?name=worker-nifti.js!worker/worker-nifti.js'
-
-/**
- * export the worker, so that services that does not require dependency injection can import the worker
- */
+// worker is now exported in angular.json file
export const worker = new Worker('worker.js')
interface IWorkerMessage {
diff --git a/src/environments/environment.common.ts b/src/environments/environment.common.ts
index 52bdf0c70442a366f643e161bca3502346b756c4..85a5e68ae63408c740790bd514fb6ad3fdbe8bb2 100644
--- a/src/environments/environment.common.ts
+++ b/src/environments/environment.common.ts
@@ -1,6 +1,7 @@
export const environment = {
- VERSION: 'unspecificied hash',
+ GIT_HASH: 'unknown hash',
+ VERSION: 'unknown version',
PRODUCTION: true,
BACKEND_URL: null,
DATASET_PREVIEW_URL: 'https://hbp-kg-dataset-previewer.apps.hbp.eu/v2',
diff --git a/src/environments/parseEnv.js b/src/environments/parseEnv.js
index 2b3052d932dd2be8ca0f738ec2f4e26c91ef1801..84c95658b5b7466938de4d8c8f675950662b1162 100644
--- a/src/environments/parseEnv.js
+++ b/src/environments/parseEnv.js
@@ -13,17 +13,21 @@ const main = async () => {
MATOMO_ID,
BS_REST_URL,
VERSION,
- GIT_HASH,
+ GIT_HASH = 'unknown hash',
EXPERIMENTAL_FEATURE_FLAG
} = process.env
const version = JSON.stringify(
- VERSION || GIT_HASH || 'unspecificied hash'
- )
+ VERSION || 'unknown version'
+ )
+ const gitHash = JSON.stringify(
+ GIT_HASH || 'unknown hash'
+ )
const outputTxt = `
import { environment as commonEnv } from './environment.common'
export const environment = {
...commonEnv,
+ GIT_HASH: ${gitHash},
VERSION: ${version},
BS_REST_URL: ${JSON.stringify(BS_REST_URL)},
BACKEND_URL: ${JSON.stringify(BACKEND_URL)},
diff --git a/src/main-common.ts b/src/main-common.ts
index 3afe8d0ad8e5dd329f4392e4e7de3aff1228fe00..c3f3f5ee2d1f07260b1932bbe9152d65c7e81dc7 100644
--- a/src/main-common.ts
+++ b/src/main-common.ts
@@ -1,17 +1,19 @@
// Included to include a copy of vanilla nehuba
import '!!file-loader?context=third_party&name=vanilla.html!third_party/vanilla.html'
import '!!file-loader?context=third_party&name=vanilla_styles.css!third_party/styles.css'
-import '!!file-loader?context=third_party&name=vanilla_nehuba.js!third_party/vanilla_nehuba.js'
import '!!file-loader?context=third_party&name=preinit_vanilla.html!third_party/preinit_vanilla.html'
/**
* Catching Safari 10 bug:
*
* https://bugs.webkit.org/show_bug.cgi?id=171041
-*
+*
+* moved to angular.json
+* look for
+* - third_party/catchSyntaxError.js
+* - third_party/syntaxError.js
*/
-import '!!file-loader?context=third_party&name=catchSyntaxError.js!third_party/catchSyntaxError.js'
-import '!!file-loader?context=third_party&name=syntaxError.js!third_party/syntaxError.js'
+
import '!!file-loader?context=src/res&name=icons/iav-icons.css!src/res/icons/iav-icons.css'
import '!!file-loader?context=src/res&name=icons/iav-icons.ttf!src/res/icons/iav-icons.ttf'
@@ -36,9 +38,9 @@ import { platformBrowserDynamic } from '@angular/platform-browser-dynamic'
import { MainModule } from './main.module';
import { environment } from 'src/environments/environment'
-const { PRODUCTION, VERSION } = environment
+const { PRODUCTION, VERSION, GIT_HASH } = environment
if (PRODUCTION) enableProdMode()
-if (PRODUCTION) { console.log(`Interactive Atlas Viewer: ${VERSION}`) }
+if (PRODUCTION) { console.log(`Siibra Explorer: ${VERSION}::${GIT_HASH}`) }
platformBrowserDynamic().bootstrapModule(MainModule)
diff --git a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
index 1d27731f97714e8000e71027ac174ab5473fb6de..84621341979625d6ee5c4b866f405e940b886fbc 100644
--- a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
@@ -10,8 +10,9 @@ import { deserialiseParcRegionId } from 'common/util'
import { IMeshesToLoad, SET_MESHES_TO_LOAD } from "../constants";
import { IColorMap, SET_COLORMAP_OBS, SET_LAYER_VISIBILITY } from "../layerCtrl.service";
-import '!!file-loader?context=third_party&name=main.bundle.js!export-nehuba/dist/min/main.bundle.js'
-import '!!file-loader?context=third_party&name=chunk_worker.bundle.js!export-nehuba/dist/min/chunk_worker.bundle.js'
+/**
+ * import of nehuba js files moved to angular.json
+ */
import { INgLayerCtrl, NG_LAYER_CONTROL, SET_SEGMENT_VISIBILITY, TNgLayerCtrl } from "../layerCtrl.service/layerCtrl.util";
const NG_LANDMARK_LAYER_NAME = 'spatial landmark layer'