Merge pull request #345 from ScilifelabDataCentre/develop

New data centre section

.github/workflows/dockerhub.yml

@@ -40,15 +40,15 @@ jobs:
         uses: actions/checkout@v4
       # only needed when publishing to Github (ghcr.io)
       - name: Log in to Github Container Repository
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           # will run as the user who triggered the action, using its token
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Docker Meta
         id: meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           images: ${{ matrix.images }}
           tags: |
@@ -57,7 +57,7 @@ jobs:
             type=semver,pattern={{major}}.{{minor}}
             type=semver,pattern={{major}}
       - name: Build and Publish
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           file: ${{ matrix.dockerfile }}
           context: .

.github/workflows/link-checker.yml

@@ -4,8 +4,6 @@
 name: Check broken links (htmltest)
 on:
   workflow_dispatch:
-    branches:
-      - develop
   schedule:
     - cron: '15 8 1-7 * 3'
 
@@ -17,7 +15,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Hugo
-        uses: peaceiris/actions-hugo@v2
+        uses: peaceiris/actions-hugo@v3
         with:
           hugo-version: "latest"
 
@@ -32,7 +30,7 @@ jobs:
           config: .github/htmltest-config.yml
 
       - name: Archive htmltest results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: htmltest-report
           path: tmp/.htmltest/htmltest.log

.github/workflows/trivy-branch.yaml

@@ -30,7 +30,7 @@ jobs:
           severity: 'CRITICAL,HIGH'
 
       - name: Upload Trivy scan results to GitHub Security tab
-        uses: github/codeql-action/upload-sarif@v2
+        uses: github/codeql-action/upload-sarif@v3
         with:
           sarif_file: 'trivy-results.sarif'
           category: trivy-branch

.github/workflows/trivy-scheduled.yaml

@@ -38,7 +38,7 @@ jobs:
           severity: 'CRITICAL,HIGH'
 
       - name: Upload Trivy scan results to GitHub Security tab
-        uses: github/codeql-action/upload-sarif@v2
+        uses: github/codeql-action/upload-sarif@v3
         with:
           sarif_file: 'trivy-results.sarif'
           category: trivy-cron

Dockerfiles/Dockerfile

@@ -16,7 +16,7 @@ RUN wget --quiet "https://github.com/gohugoio/hugo/releases/download/v${HUGO_VER
 # Serve the generated html using nginx
 FROM nginxinc/nginx-unprivileged:alpine
 RUN sed -i '3 a\    absolute_redirect off;' /etc/nginx/conf.d/default.conf && \
-    sed -i '4 a\    add_header X-Frame-Options DENY always;' /etc/nginx/conf.d/default.conf && \
+    sed -i '4 a\    add_header X-Frame-Options SAMEORIGIN always;' /etc/nginx/conf.d/default.conf && \
     sed -i 's/#error_page  404/error_page  404/' /etc/nginx/conf.d/default.conf
 COPY --from=build /target /usr/share/nginx/html
 

content/data_centre/_index.md

@@ -0,0 +1,7 @@
+---
+title: Data Centre
+---
+
+SciLifeLab sees data as one of the most valuable and long-lasting products of research. SciLifeLab Data Centre is a central SciLifeLab unit responsible for IT- and data management issues, with a particular focus on making data as Open and FAIR as possible. It creates multiple services designed to assist the life science research community with data management at every part of the data lifecycle.
+
+Click on the cards below to find out more about different aspects of the work of SciLifeLab Data Centre.

content/data_centre/find_service.md

@@ -0,0 +1,16 @@
+---
+Title: Find services
+---
+
+The Service Finder tool will prompt you to answer a flowchart of funnelled questions and suggest a suitable service based on your specific requirements.
+
+<!-- The flowchart is only shown in bigger screens -->
+<div class="text-center d-none d-lg-block">
+    <embed src="/misc/onboarding_schema.pdf#toolbar=0" type="application/pdf" frameBorder="0" scrolling="auto" width="950" height="1100">
+</div>
+
+<!-- Flowchart link is displayed on smaller screens -->
+<div class="d-lg-none">
+    The flowchart is not displayed in smaller screens, instead the PDF file can be viewed/downloaded
+    <a href="/misc/onboarding_schema.pdf">here</a>
+</div>

content/data_centre/onboarding.md

@@ -0,0 +1,12 @@
+---
+title: Onboarding for Fellows
+description: SciLifeLab Data Centre looks forward to engaging, supporting, and collaborating with you and your research group.
+thumbnail: /img/dc_thumbnails/fellows_onboarding.jpeg
+layout: onboarding
+---
+
+## Welcome to SciLifeLab Data Centre information package for fellows
+
+SciLifeLab Data Centre looks forward to engaging, supporting, and collaborating with you and your research group. In this new section of the SciLifeLab Data Platform, you will find comprehensive information, services, and support for digital infrastructure, computing, storage, hosting, AI, Research Data Management, Open Science, FAIR data, and more. Find out specific information grouped under the tabs below.
+
+<a href="/contact/" class="btn btn-aqua mb-2">Click for support</a>

data/services.json

@@ -98,12 +98,12 @@
       "Data Centre"
     ],
     "name": "SciLifeLab Serve",
-    "description": "Platform for sharing machine learning models and data science applications, such as Shiny and Dash apps.",
+    "description": "SciLifeLab Serve is a platform offering machine learning model serving, data science app hosting (Shiny, Gradio, Streamlit, Dash, etc.).",
     "url": "https://serve.scilifelab.se/",
     "maintained_by": "SciLifeLab Data Centre",
     "maintained_by_url": "https://scilifelab.se/data",
     "support_email": "[email protected]",
-    "support_website": "https://serve.scilifelab.se/user_guide",
+    "support_website": "https://serve.scilifelab.se/docs/",
     "support_status": "https://status.dc.scilifelab.se/795925203"
   },
   {

layouts/data_centre/list.html

@@ -0,0 +1,27 @@
+{{ define "main" }}
+
+{{ .Content }}
+
+<!-- Collect the available pages and list as cards -->
+<div class="row g-3">
+  {{ range .Pages.ByTitle }}
+    {{ if ne .Title "Find services" }}
+      <div class="col-md-6 col-lg-4">
+        <div class="card-teal-25">
+          <div {{ if .Params.thumbnail_border }}class="p-1" {{ end }}>
+            <a target="_self" href="{{ .RelPermalink }}"><img class="img-fluid"
+              src="{{ with .Params.thumbnail }}{{ . }}{{ else }}{{ "/img/logos/scilifelab_thumbnail.jpg" }}{{ end }}"
+              alt="{{ .Title }}"></a>
+          </div>
+          <div class="p-2 card-teal-title">
+            <h5><a href="{{ .RelPermalink }}" target="_self">{{ .Title }}</a></h5>
+          </div>
+          <div class="p-2">
+            {{ .Params.description }}
+          </div>
+      </div>
+    {{ end }}
+  {{ end }}
+</div>
+
+{{ end }}