From 311919956f84ad1d4a027ec4f6608ddf44ad75be Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Wed, 14 Aug 2024 12:06:06 +0200
Subject: [PATCH] fix: statistical map
---
.github/workflows/_screenshot.yml | 73 ++++++++++++
.github/workflows/docker_img.yml | 182 ++++++++++++++----------------
docs/releases/v2.14.8.md | 9 ++
mkdocs.yml | 1 +
package-lock.json | 12 +-
package.json | 4 +-
6 files changed, 175 insertions(+), 106 deletions(-)
create mode 100644 .github/workflows/_screenshot.yml
create mode 100644 docs/releases/v2.14.8.md
diff --git a/.github/workflows/_screenshot.yml b/.github/workflows/_screenshot.yml
new file mode 100644
index 000000000..146e54d3f
--- /dev/null
+++ b/.github/workflows/_screenshot.yml
@@ -0,0 +1,73 @@
+name: "[e2e] screenshot"
+on:
+ workflow_call:
+ inputs:
+ os:
+ required: false
+ type: string
+ default: ubuntu-latest
+ browser:
+ required: false
+ type: string
+ default: chrome
+ url:
+ required: true
+ type: string
+ screenshot-filename:
+ required: true
+ type: string
+ description: "desired filename *without* extension. .png will *always* be appended"
+ secrets:
+ client-id:
+ required: false
+ client-secret:
+ required: false
+
+jobs:
+ screenshot:
+ runs-on: ${{ inputs.os }}
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-node@v4
+ with:
+ node-version: 20
+ - name: Set variables
+ run: |
+ GIT_DIGEST=${{ github.sha }}
+ GIT_DIGEST=$(echo $GIT_DIGEST | head -c 6)
+
+ echo "mkdir -p $(dirname ${{ inputs.screenshot-filename }})"
+ mkdir -p $(dirname ${{ inputs.screenshot-filename }})
+
+ SCREENSHOT_URL=${{ inputs.url }}
+ SCREENSHOT_PATH=${{ inputs.screenshot-filename }}
+
+ echo "SCREENSHOT_URL: $SCREENSHOT_URL"
+ echo "SCREENSHOT_PATH: $SCREENSHOT_PATH"
+
+ echo "SCREENSHOT_URL=$SCREENSHOT_URL" >> $GITHUB_ENV
+ echo "SCREENSHOT_PATH=$SCREENSHOT_PATH" >> $GITHUB_ENV
+
+ - name: Install dependency
+ run: npm install cypress
+
+ - name: Run Cypress
+ uses: cypress-io/github-action@v6
+ with:
+ spec: cypress/e2e/screenshot.cy.js
+ browser: ${{ inputs.browser }}
+
+ - uses: actions/upload-artifact@v4
+ with:
+ name: ${{ env.SCREENSHOT_PATH }}
+ path: cypress/screenshots/screenshot.cy.js/*.png
+ retention-days: 5
+
+ - continue-on-error: true
+ uses: FZJ-INM1-BDA/iav-dep-test/.github/actions/upload_dataproxy@master
+ with:
+ upload-file: cypress/screenshots/screenshot.cy.js/${{ inputs.screenshot-filename }}.png
+ bucket-name: reference-atlas-data
+ dest-path: viewere2e/${{ inputs.screenshot-filename }}.png
+ client-id: ${{ secrets.client-id }}
+ client-secret: ${{ secrets.client-secret }}
diff --git a/.github/workflows/docker_img.yml b/.github/workflows/docker_img.yml
index acd0d525a..fbb54a653 100644
--- a/.github/workflows/docker_img.yml
+++ b/.github/workflows/docker_img.yml
@@ -13,8 +13,51 @@ on:
- 'docs/**/*'
jobs:
+ set-vars:
+ runs-on: ubuntu-latest
+ outputs:
+ GIT_DIGEST: ${{ steps.set-vars-step.outputs.GIT_DIGEST }}
+ BRANCH_NAME: ${{ steps.set-vars-step.outputs.BRANCH_NAME }}
+ BUILD_TEXT: ${{ steps.set-vars-step.outputs.BUILD_TEXT }}
+ DEPLOY_ID: ${{ steps.set-vars-step.outputs.DEPLOY_ID }}
+ SXPLR_VERSION: ${{ steps.set-vars-step.outputs.SXPLR_VERSION }}
+ steps:
+ - uses: actions/checkout@v4
+ - id: 'set-vars-step'
+ name: Set variables
+ run: |
+ GIT_DIGEST=${{ github.sha }}
+ echo "Git digest: $GIT_DIGEST"
+ GIT_DIGEST=$(echo $GIT_DIGEST | grep -oP '^.{6}')
+ echo "Using first 6 chars of hash: $GIT_DIGEST"
+ echo "GIT_DIGEST=$GIT_DIGEST" >> $GITHUB_OUTPUT
+
+ echo "Using github.ref: $GITHUB_REF"
+
+ BRANCH_NAME=${GITHUB_REF#refs/heads/}
+ echo "BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_OUTPUT
+
+ echo "Branch is $BRANCH_NAME ."
+
+ if [[ "$BRANCH_NAME" == 'master' ]]
+ then
+ echo "BUILD_TEXT=" >> $GITHUB_OUTPUT
+ else
+ echo "BUILD_TEXT=$BRANCH_NAME" >> $GITHUB_OUTPUT
+ fi
+
+ # DEPLOY_ID == remove _ / and lowercase everything from branch
+ DEPLOY_ID=$(echo ${BRANCH_NAME//[_\/]/} | awk '{ print tolower($0) }')
+ echo "DEPLOY_ID=$DEPLOY_ID" >> $GITHUB_OUTPUT
+
+ SXPLR_VERSION=$(jq -r '.version' package.json)
+ echo "SXPLR_VERSION=$SXPLR_VERSION"
+ echo "SXPLR_VERSION=$SXPLR_VERSION" >> $GITHUB_OUTPUT
+
build-docker-img:
runs-on: ubuntu-latest
+ needs:
+ - set-vars
env:
MATOMO_ID_PROD: '12'
MATOMO_URL_PROD: 'https://stats.humanbrainproject.eu/'
@@ -25,9 +68,6 @@ jobs:
SIIBRA_API_RC: 'https://siibra-api-rc.apps.hbp.eu/v3_0'
SIIBRA_API_LATEST: 'https://siibra-api-latest.apps-dev.hbp.eu/v3_0'
- outputs:
- GIT_DIGEST: ${{ steps.build-docker-image.outputs.GIT_DIGEST }}
-
steps:
- uses: actions/checkout@v4
with:
@@ -65,14 +105,9 @@ jobs:
- id: 'build-docker-image'
name: 'Build docker image'
run: |
- GIT_DIGEST=${{ github.sha }}
+ GIT_DIGEST=${{ needs.set-vars.outputs.GIT_DIGEST }}
echo "Git digest: $GIT_DIGEST"
- # 62 char limit in label
- GIT_DIGEST=$(echo $GIT_DIGEST | grep -oP '^.{6}')
- echo "Using first 6 chars of hash: $GIT_DIGEST"
- echo "GIT_DIGEST=$GIT_DIGEST" >> $GITHUB_OUTPUT
-
DOCKER_BUILT_TAG=${{ env.DOCKER_REGISTRY }}siibra-explorer:$BRANCH_NAME
echo "Building $DOCKER_BUILT_TAG"
docker build \
@@ -106,59 +141,24 @@ jobs:
docker tag $DOCKER_BUILT_TAG $VERSIONED_DOCKER_BUILT_TAG
docker push $VERSIONED_DOCKER_BUILT_TAG
- setting-vars:
- if: success()
- runs-on: ubuntu-latest
- outputs:
- BRANCH_NAME: ${{ steps.set-vars.outputs.BRANCH_NAME }}
- BUILD_TEXT: ${{ steps.set-vars.outputs.BUILD_TEXT }}
- DEPLOY_ID: ${{ steps.set-vars.outputs.DEPLOY_ID }}
- SXPLR_VERSION: ${{ steps.set-vars.outputs.SXPLR_VERSION }}
- steps:
- - uses: actions/checkout@v4
- - id: set-vars
- name: Set vars
- run: |
- echo "Using github.ref: $GITHUB_REF"
-
- BRANCH_NAME=${GITHUB_REF#refs/heads/}
- echo "BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_OUTPUT
-
- echo "Branch is $BRANCH_NAME ."
-
- if [[ "$BRANCH_NAME" == 'master' ]]
- then
- echo "BUILD_TEXT=" >> $GITHUB_OUTPUT
- else
- echo "BUILD_TEXT=$BRANCH_NAME" >> $GITHUB_OUTPUT
- fi
-
- # DEPLOY_ID == remove _ / and lowercase everything from branch
- DEPLOY_ID=$(echo ${BRANCH_NAME//[_\/]/} | awk '{ print tolower($0) }')
- echo "DEPLOY_ID=$DEPLOY_ID" >> $GITHUB_OUTPUT
-
- SXPLR_VERSION=$(jq -r '.version' package.json)
- echo "SXPLR_VERSION=$SXPLR_VERSION"
- echo "SXPLR_VERSION=$SXPLR_VERSION" >> $GITHUB_OUTPUT
-
-
trigger-deploy-rc-rancher:
- if: ${{ needs.setting-vars.outputs.BRANCH_NAME == 'staging' && success() }}
+ if: ${{ needs.set-vars.outputs.BRANCH_NAME == 'staging' && success() }}
needs:
- build-docker-img
- - setting-vars
+ - set-vars
uses: ./.github/workflows/deploy-helm.yml
with:
DEPLOYMENT_NAME: rc
IMAGE_TAG: staging
- IMAGE_DIGEST: ${{ needs.build-docker-img.outputs.GIT_DIGEST }}
+ IMAGE_DIGEST: ${{ needs.set-vars.outputs.GIT_DIGEST }}
secrets:
KUBECONFIG: ${{ secrets.KUBECONFIG }}
- cypress-staging:
+ cypress-staging-viewer:
+
needs:
- trigger-deploy-rc-rancher
- runs-on: ${{ matrix.os }}
+ - set-vars
strategy:
fail-fast: false
matrix:
@@ -174,78 +174,64 @@ jobs:
- webkit
include:
- viewer: ng
- url: https://atlases.ebrains.eu/viewer-staging/go/human
+ saneurl: human
- viewer: fsa
- url: https://atlases.ebrains.eu/viewer-staging/go/fsaverage
+ saneurl: fsaverage
exclude:
- os: ubuntu-latest
browser: webkit
# - os: windows-latest
# browser: webkit
+ uses: ./.github/workflows/_screenshot.yml
+ with:
+ url: https://atlases.ebrains.eu/viewer-staging/go/${{ matrix.saneurl }}
+ screenshot-filename: ${{ needs.set-vars.outputs.GIT_DIGEST }}/viewer-preview/${{ matrix.viewer }}_${{ matrix.os }}_${{ matrix.browser }}
+ secrets:
+ client-id: ${{ secrets.EBRAINS_SIIBRA_EXPLORER_OIDC_CLIENTID}}
+ client-secret: ${{ secrets.EBRAINS_SIIBRA_EXPLORER_OIDC_CLIENTSECRET}}
- steps:
- - uses: actions/checkout@v4
- - uses: actions/setup-node@v4
- with:
- node-version: 20
- - name: Set variables
- run: |
- GIT_DIGEST=${{ github.sha }}
- GIT_DIGEST=$(echo $GIT_DIGEST | head -c 6)
-
- SCREENSHOT_URL=${{ matrix.url }}
- SCREENSHOT_PATH=screenshot_"$GIT_DIGEST"_${{ matrix.viewer }}_${{ matrix.os }}_${{ matrix.browser }}
-
- echo "SCREENSHOT_URL: $SCREENSHOT_URL"
- echo "SCREENSHOT_PATH: $SCREENSHOT_PATH"
-
- echo "SCREENSHOT_URL=$SCREENSHOT_URL" >> $GITHUB_ENV
- echo "SCREENSHOT_PATH=$SCREENSHOT_PATH" >> $GITHUB_ENV
-
- - name: Install dependency
- run: npm install cypress
-
- - name: Install optional dependency
- if: ${{ matrix.browser == 'webkit' }}
- run: |
- npm install --save-dev playwright-webkit
- echo "USE_SAFARI=1" >> $GITHUB_ENV
-
- - name: Run Cypress
- uses: cypress-io/github-action@v6
- with:
- spec: cypress/e2e/screenshot.cy.js
- browser: ${{ matrix.browser }}
-
- - uses: actions/upload-artifact@v4
- with:
- name: ${{ env.SCREENSHOT_PATH }}
- path: cypress/screenshots/screenshot.cy.js/*.png
- retention-days: 5
+ cypress-staging-url:
+ needs:
+ - trigger-deploy-rc-rancher
+ - set-vars
+ strategy:
+ fail-fast: false
+ matrix:
+ saneurl:
+ - siibra_paper_2023_2A
+ - siibra_paper_2023_2B
+ - siibra_paper_2023_2C
+ - siibra_paper_2023_2D
+ - siibra_paper_2023_2E
+ - siibra_paper_2023_2F
+ uses: ./.github/workflows/_screenshot.yml
+ with:
+ url: https://atlases.ebrains.eu/viewer-staging/go/${{ matrix.saneurl }}
+ screenshot-filename: ${{ needs.set-vars.outputs.GIT_DIGEST }}/url-preview/${{ matrix.saneurl }}
trigger-deploy-expmt-rancher:
- if: ${{ needs.setting-vars.outputs.BRANCH_NAME == 'staging' && success() }}
+ if: ${{ needs.set-vars.outputs.BRANCH_NAME == 'staging' && success() }}
needs:
- build-docker-img
- - setting-vars
+ - set-vars
uses: ./.github/workflows/deploy-helm.yml
with:
DEPLOYMENT_NAME: expmt
IMAGE_TAG: staging
- IMAGE_DIGEST: ${{ needs.build-docker-img.outputs.GIT_DIGEST }}
+ IMAGE_DIGEST: ${{ needs.set-vars.outputs.GIT_DIGEST }}
secrets:
KUBECONFIG: ${{ secrets.KUBECONFIG }}
trigger-deploy-master-rancher:
- if: ${{ needs.setting-vars.outputs.BRANCH_NAME == 'master' && success() }}
+ if: ${{ needs.set-vars.outputs.BRANCH_NAME == 'master' && success() }}
needs:
- build-docker-img
- - setting-vars
+ - set-vars
uses: ./.github/workflows/deploy-helm.yml
with:
DEPLOYMENT_NAME: prod
- IMAGE_TAG: ${{ needs.setting-vars.outputs.SXPLR_VERSION }}
- IMAGE_DIGEST: ${{ needs.build-docker-img.outputs.GIT_DIGEST }}
+ IMAGE_TAG: ${{ needs.set-vars.outputs.SXPLR_VERSION }}
+ IMAGE_DIGEST: ${{ needs.set-vars.outputs.GIT_DIGEST }}
secrets:
KUBECONFIG: ${{ secrets.KUBECONFIG }}
diff --git a/docs/releases/v2.14.8.md b/docs/releases/v2.14.8.md
new file mode 100644
index 000000000..07aaa2eb2
--- /dev/null
+++ b/docs/releases/v2.14.8.md
@@ -0,0 +1,9 @@
+# v2.14.8
+
+## Bugfix
+
+- fixed issue of displaying statistical maps
+
+## Behind the Scenes
+
+- Minor tweak on e2e screenshots
diff --git a/mkdocs.yml b/mkdocs.yml
index d1561a776..c4814abb7 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -45,6 +45,7 @@ nav:
- Differential gene expression analysis: "advanced/differential_gene_expression_analysis.md"
- Release notes:
+ - v2.14.8: 'releases/v2.14.8.md'
- v2.14.7: 'releases/v2.14.7.md'
- v2.14.6: 'releases/v2.14.6.md'
- v2.14.5: 'releases/v2.14.5.md'
diff --git a/package-lock.json b/package-lock.json
index 1f5725874..7f9aadb06 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
{
"name": "siibra-explorer",
- "version": "2.14.6",
+ "version": "2.14.7",
"lockfileVersion": 3,
"requires": true,
"packages": {
"": {
"name": "siibra-explorer",
- "version": "2.14.6",
+ "version": "2.14.7",
"license": "apache-2.0",
"dependencies": {
"@angular/animations": "^15.2.10",
@@ -23,7 +23,7 @@
"@ngrx/effects": "^15.4.0",
"@ngrx/store": "^15.4.0",
"acorn": "^8.4.1",
- "export-nehuba": "^0.1.9",
+ "export-nehuba": "^0.1.10",
"file-loader": "^6.2.0",
"jszip": "^3.6.0",
"postcss": "^8.3.6",
@@ -7646,9 +7646,9 @@
"dev": true
},
"node_modules/export-nehuba": {
- "version": "0.1.9",
- "resolved": "https://registry.npmjs.org/export-nehuba/-/export-nehuba-0.1.9.tgz",
- "integrity": "sha512-59vm+BlB1zuD2ftDWUGUv6Jt0WGHjzB6egGGuD+JRR9oW4D7m9DNuOwheymSvlUxJ2GEOjMBe3I460T51m6W/A==",
+ "version": "0.1.10",
+ "resolved": "https://registry.npmjs.org/export-nehuba/-/export-nehuba-0.1.10.tgz",
+ "integrity": "sha512-CC4KnFtdtfbST4LKVxZO3DQ1p6jkmJHf9PPVaRyUrdD0UAM/Oh1Hita2vdnabsEPkAiJ0UMK1bLZ7KQ+5HLhHQ==",
"dependencies": {
"pako": "^1.0.6"
}
diff --git a/package.json b/package.json
index 4654168af..356214b9b 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "siibra-explorer",
- "version": "2.14.7",
+ "version": "2.14.8",
"description": "siibra-explorer - explore brain atlases. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular",
"scripts": {
"lint": "eslint src --ext .ts",
@@ -52,7 +52,7 @@
"@ngrx/effects": "^15.4.0",
"@ngrx/store": "^15.4.0",
"acorn": "^8.4.1",
- "export-nehuba": "^0.1.9",
+ "export-nehuba": "^0.1.10",
"file-loader": "^6.2.0",
"jszip": "^3.6.0",
"postcss": "^8.3.6",
--
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