Merge pull request #1197 from ScilifelabDataCentre/develop

Deploying to Production

.github/sitemap.xml

@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<urlset
-      xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"
-      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-      xsi:schemaLocation="http://www.sitemaps.org/schemas/sitemap/0.9
-            http://www.sitemaps.org/schemas/sitemap/0.9/sitemap.xsd">
-<!-- created with Free Online Sitemap Generator www.xml-sitemaps.com -->
-
+<?xml version="1.0" encoding="UTF-8"?>
+<urlset
+      xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"
+      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+      xsi:schemaLocation="http://www.sitemaps.org/schemas/sitemap/0.9
+            http://www.sitemaps.org/schemas/sitemap/0.9/sitemap.xsd">
+<!-- created with Free Online Sitemap Generator www.xml-sitemaps.com -->
+
 
 <url>
   <loc>https://www.pathogens.se/</loc>
@@ -298,7 +298,7 @@
   <priority>0.80</priority>
 </url>
 <url>
-  <loc>https://www.pathogens.se/partners/</loc>
+  <loc>https://www.pathogens.se/other_national_portals/</loc>
   <lastmod>2024-08-13T11:14:57+00:00</lastmod>
   <priority>0.80</priority>
 </url>
@@ -423,7 +423,7 @@
   <priority>0.64</priority>
 </url>
 <url>
-  <loc>https://www.pathogens.se/sv/partners/</loc>
+  <loc>https://www.pathogens.se/sv/other_national_portals/</loc>
   <lastmod>2024-08-13T11:14:58+00:00</lastmod>
   <priority>0.64</priority>
 </url>
@@ -1376,7 +1376,7 @@
   <loc>https://www.pathogens.se/wastewater/map_orebro.pdf</loc>
   <lastmod>2024-08-13T11:14:49+00:00</lastmod>
   <priority>0.33</priority>
-</url>
-
-
+</url>
+
+
 </urlset>

.github/workflows/dockerhub.yml

@@ -41,15 +41,15 @@ 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: |
@@ -58,7 +58,7 @@ 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: '25 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

@@ -36,7 +36,7 @@ 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

content/english/about/_index.md

@@ -24,7 +24,7 @@ This website is built using [Hugo](https://gohugo.io/) in combination with [Boot
 
 #### History of the Portal
 
-The Swedish Pathogens Portal was originally launched as the 'Swedish COVID-19 Data Portal' in June 2020 on assignment and with funding from the Swedish Research Council a.k.a. Vetenskapsrådet (more details [here](https://www.vr.se/english/just-now/news/news-archive/2020-06-03-new-national-portal-makes-research-data-on-covid-19-accessible.html)). The Portal was actually the first national node of the [European COVID-19 Data Platform](https://covid19dataportal.eu/), which was initiated and funded by the European Commission (more details [here](https://www.embl.org/news/science/embl-ebi-launches-covid-19-data-portal/)) and you can find an overview of other national nodes [here](/partners/). The Portal focused on SARS-CoV-2 and COVID-19 research data exclusively until the end of 2021. We released a [news item](/updates/first_year/) summarising our activities in 2021.
+The Swedish Pathogens Portal was originally launched as the 'Swedish COVID-19 Data Portal' in June 2020 on assignment and with funding from the Swedish Research Council a.k.a. Vetenskapsrådet (more details [here](https://www.vr.se/english/just-now/news/news-archive/2020-06-03-new-national-portal-makes-research-data-on-covid-19-accessible.html)). The Portal was actually the first national node of the [European COVID-19 Data Platform](https://covid19dataportal.eu/), which was initiated and funded by the European Commission (more details [here](https://www.embl.org/news/science/embl-ebi-launches-covid-19-data-portal/)) and you can find an overview of other national nodes [here](/other_national_portals/). The Portal focused on SARS-CoV-2 and COVID-19 research data exclusively until the end of 2021. We released a [news item](/updates/first_year/) summarising our activities in 2021.
 
 From 2022, the Portal expanded to cover other research relevant to pandemic preparedness and became a part of the [SciLifeLab Pandemic Laboratory Preparedness programme](https://www.scilifelab.se/pandemic-response/pandemic-laboratory-preparedness/). The SciLifeLab Pandemic Laboratory Preparedness Programme is funded by the earmarked governmental funding to SciLifeLab ([Research proposition Prop. 202/21:60](https://www.regeringen.se/rattsliga-dokument/proposition/2020/12/forskning-frihet-framtid--kunskap-och-innovation-for-sverige/)).
 

content/english/about/partner_organisations.md

@@ -15,7 +15,7 @@ layout: about_navbar
   </div>
   <div class="col-12 col-md-8 col-lg-9">
   <h6>Pathogens Portal</h6>
-    <p>The <a href="https://www.pathogensportal.org/" target="_blank">Pathogens Portal</a>, maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (<a href="https://www.ebi.ac.uk/" target="_blank">EMBL-EBI</a>) and partners, was launched in July 2023. The Pathogens Portal is a resource for e.g. researchers, clinicians, and policymakers. Its aim is  to facilitate access to the latest and most comprehensive datasets on pathogens. The COVID-19 pandemic put a  spotlight on the importance of data sharing and for focused access to relevant datasets. Therefore, the Pathogens Portal was developed as a centralised platform for  data sharing and accessing data on key pathogens. These pathogens include both pathogens affecting humans and animals, and on vectors and hosts. Bringing together data from a number of sources, and linking data contributes to a better understand Pathogen ́s Biology. Funded through five European Union projects funded under the Horizon 2020 and Horizon Europe programmes: <a href="https://recodid.eu/" target="_blank">RECODID</a>, <a href="https://www.veo-europe.eu/" target="_blank">VEO</a>, <a href="https://www.eosc-life.eu/" target="_blank">EOSC-Life</a>, <a href="https://elixir-europe.org/about-us/how-funded/eu-projects/converge" target="_blank">CONVERGE</a> and <a href="https://by-covid.org/" target="_blank">BY-COVID</a>. Moving forward, national nodes of the Pathogens Portal will be added, the Swedish Pathogens Portal is the first to launch in Sept 2023. </p>
+    <p>The <a href="https://www.pathogensportal.org/" target="_blank">Pathogens Portal</a>, maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (<a href="https://www.ebi.ac.uk/" target="_blank">EMBL-EBI</a>) and partners, was launched in July 2023. The Pathogens Portal is a resource for e.g. researchers, clinicians, and policymakers. Its aim is  to facilitate access to the latest and most comprehensive datasets on pathogens. The COVID-19 pandemic put a  spotlight on the importance of data sharing and for focused access to relevant datasets. Therefore, the Pathogens Portal was developed as a centralised platform for  data sharing and accessing data on key pathogens. These pathogens include both pathogens affecting humans and animals, and on vectors and hosts. Bringing together data from a number of sources, and linking data contributes to a better understand Pathogen ́s Biology. Funded through five European Union projects funded under the Horizon 2020 and Horizon Europe programmes: <a href="https://recodid.eu/" target="_blank">RECODID</a>, <a href="https://www.veo-europe.eu/" target="_blank">VEO</a>, <a href="https://www.eosc-life.eu/" target="_blank">EOSC-Life</a>, <a href="https://elixir-europe.org/about-us/how-funded/eu-projects/converge" target="_blank">CONVERGE</a> and <a href="https://by-covid.org/" target="_blank">BY-COVID</a>. Moving forward, national nodes of the Pathogens Portal will be added, the Swedish Pathogens Portal is the first to launch in Sept 2023. An overview of other national nodes <a href="/other_national_portals/">can be found here</a>.</p>
   </div>
 </div>
 <hr class="faded" />
@@ -28,7 +28,7 @@ layout: about_navbar
   </div>
   <div class="col-12 col-md-8 col-lg-9">
   <h6>European COVID-19 Data Platform</h6>
-    <p>The Swedish Pathogens Portal was originally launched as the ‘Swedish COVID-19 Data Portal’ and it was a national node of the <a href="https://www.covid19dataportal.org/" target="_blank">European COVID-19 Data Platform</a>. The European COVID-19 Data Platform is operated by the <a href="https://ebi.ac.uk" target="_blank">European Bioinformatics Institute</a> (a part of the <a href="https://www.embl.org/" target="_blank">European Molecular Biology Laboratory</a> (EMBL-EBI)), together with the European Commission, and other research partners, such as ELIXIR. An overview of other national nodes <a href="/partners/">can be found here</a>.</p>
+    <p>The Swedish Pathogens Portal was originally launched as the ‘Swedish COVID-19 Data Portal’ and it was a national node of the <a href="https://www.covid19dataportal.org/" target="_blank">European COVID-19 Data Platform</a>. The European COVID-19 Data Platform is operated by the <a href="https://ebi.ac.uk" target="_blank">European Bioinformatics Institute</a> (a part of the <a href="https://www.embl.org/" target="_blank">European Molecular Biology Laboratory</a> (EMBL-EBI)), together with the European Commission, and other research partners, such as ELIXIR. An overview of other national nodes <a href="/other_national_portals/">can be found here</a>.</p>
     <p>The European COVID-19 Data Platform aims to facilitate data sharing and analysis in order to accelerate coronavirus research. It enables researchers to upload, access and analyse reference data and specialist datasets related to COVID-19. It is synchronised with COVID-19-related data and scientific literature held in EMBL-EBI's data resources, including ENA, UniProt, PDBe, EMDB, Expression Atlas and Europe PMC. The data continues to grow in diversity and volume, but include sequences, structures, expression data, compound screens, biochemistries and scientific publications.</p>
   </div>
 </div>