Merge pull request #991 from ScilifelabDataCentre/develop

Updates W22
ScilifelabDataCentre · Jun 2, 2023 · ba78082 · ba78082
2 parents 460c86b + a444152
commit ba78082
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diff --git a/.github/workflows/dockerhub.yml b/.github/workflows/dockerhub.yml
@@ -1,7 +1,7 @@
 ---
-# Build and publish docker image(s)
-# Publishing to Dockerhub requires a username and token
-# as the secrets DOCKERHUB_USERNAME and DOCKERHUB_TOKEN
+# Build and publish image(s) to GitHub (ghcr.io)
+# Publishing to GitHub requires a username (who triggered the action)
+# and password (as the secrets GITHUB_TOKEN)
 # remember to change repo-name and set dockerfile(s)/image name(s) in the matrix
 
 name: Publish Docker Image
@@ -32,22 +32,13 @@ jobs:
       matrix:
         include:
           - dockerfile: Dockerfiles/Dockerfile
-            images: |
-              docker.io/scilifelabdatacentre/covid-portal
-              ghcr.io/scilifelabdatacentre/covid-portal
+            images: ghcr.io/scilifelabdatacentre/covid-portal
     permissions:
       contents: read
       packages: write
     steps:
       - name: Check out the repo
         uses: actions/checkout@v3
-      # only needed when publishing to Dockerhub
-      - name: Log in to Docker Hub
-        uses: docker/login-action@v2
-        with:
-          # available in scilifelabdatacentre, ask admin for help
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
       # only needed when publishing to Github (ghcr.io)
       - name: Log in to Github Container Repository
         uses: docker/login-action@v2

diff --git a/config.yaml b/config.yaml
@@ -83,6 +83,8 @@ caches:
 taxonomies:
   highlights_topic: highlights_topics
   highlights_voc: highlights_vocs
+  dashboards_topic: dashboards_topics
 permalinks:
   highlights_topics: "/highlights/topics/:slug/"
   highlights_vocs: "/highlights/vocs/:slug/"
+  dashboards_topics: "/dashboards/topics/:slug/"
diff --git a/content/english/dashboards/RECOVAC.md b/content/english/dashboards/RECOVAC.md
diff --git a/content/english/dashboards/_index.md b/content/english/dashboards/_index.md
@@ -7,4 +7,10 @@ menu:
         name: Dashboards
         identifier: dashboards
         post: Dashboards are pages describing research done on a given subject. They include visualisations of and links to data from the research groups(s) involved. <a href="/dashboards/">See all dashboards <i class="bi bi-arrow-right-circle-fill"></i></a>
+aliases:
+      - /dashboards
+      - /visualisations
+      - /dashboards_topics/
 ---
+
+The *Dashboards* section describes research done on a given subject relevant to pandemic preparedness research by researchers affiliated with a Swedish research institute. Specifically, in our case we write about COVID-19 and SARS-CoV-2, infectious diseases in general, antibiotic resistance, and Mpox. The goal is to highlight and visualise openly shared data that can potentially be used by many other researchers to make further discoveries.
diff --git a/content/english/dashboards/covid_publications.md b/content/english/dashboards/covid_publications.md
@@ -10,6 +10,7 @@ menu:
         name: "COVID-19 publication overview"
 aliases:
     - /projects/dashboard/
+dashboards_topics: [COVID-19, Infectious diseases]
 ---
 The visualisations on this page evaluate the development of COVID-19 and SARS-CoV-2 research across Sweden by assessing publication output. Specifically, we consider multiple aspects of journal publications and preprints where at least one author has an affiliation with a Swedish research institute. The database containing the publications themselves [can be found on this page](/publications/). Note that our database is manually curated and, as such, may not be exhaustive. The full database is available for download and use for other purposes, please see [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014) for details.
 
@@ -41,13 +42,13 @@ These wordclouds display the words and two word phrases that appear most frequen
 
 #### All publications
 
-<div class="row my-4"><div class="col-md-8"><img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-titles_all.png"></div></div>
+<div class="row my-4"><div class="col-md-8"><img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-titles_all.png"></div></div>
 
 #### Publications attributed to particular research funders
 
 Wordclouds are displayed for each funder that we identified as having been associated with at least 20 publications in the database.
 
-<div class="container"> <div class="row mt-2"> <div class="col-md mr-4"> <div class="row"> <h5>Swedish Research Council:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-titles_vr.png"> </div> </div> <div class="col-md mr-4"> <div class="row"> <h5>SciLifeLab/KAW:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-titles_kaw.png"> </div> </div> <div class="col-md"> <div class="row"> <h5>Horizon 2020:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-titles_h2020.png"> </div> </div> </div> </div>
+<div class="container"> <div class="row mt-2"> <div class="col-md mr-4"> <div class="row"> <h5>Swedish Research Council:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-titles_vr.png"> </div> </div> <div class="col-md mr-4"> <div class="row"> <h5>SciLifeLab/KAW:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-titles_kaw.png"> </div> </div> <div class="col-md"> <div class="row"> <h5>Horizon 2020:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-titles_h2020.png"> </div> </div> </div> </div>
 
 ## Most frequent words or two word phrases in the abstracts
 
@@ -57,10 +58,10 @@ These wordclouds display the words and two word phrases that appear most frequen
 
 #### All publications
 
-<div class="row my-4"><div class="col-md-8"><img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-abstracts_all.png"></div></div>
+<div class="row my-4"><div class="col-md-8"><img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-abstracts_all.png"></div></div>
 
 #### Publications attributed to particular research funders
 
 Wordclouds are displayed for each funder that we identified as having been associated with at least 20 publications in the database.
 
-<div class="container"> <div class="row mt-2"> <div class="col-md mr-4"> <div class="row"> <h5>Swedish Research Council:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-abstracts_vr.png"> </div> </div> <div class="col-md mr-4"> <div class="row"> <h5>SciLifeLab/KAW:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-abstracts_kaw.png"> </div> </div> <div class="col-md"> <div class="row"> <h5>Horizon 2020:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-abstracts_h2020.png"> </div> </div> </div> </div>
+<div class="container"> <div class="row mt-2"> <div class="col-md mr-4"> <div class="row"> <h5>Swedish Research Council:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-abstracts_vr.png"> </div> </div> <div class="col-md mr-4"> <div class="row"> <h5>SciLifeLab/KAW:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-abstracts_kaw.png"> </div> </div> <div class="col-md"> <div class="row"> <h5>Horizon 2020:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-abstracts_h2020.png"> </div> </div> </div> </div>
diff --git a/content/english/dashboards/crush_covid.md b/content/english/dashboards/crush_covid.md
@@ -4,25 +4,40 @@ description: CRUSH Covid maps outbreaks in Uppsala County by visualising the num
 banner: /dashboard_thumbs/CRUSH.png
 toc: false
 menu:
-    dashboard_menu:
-        identifier: crush_covid
-        name: "CRUSH Covid Uppsala (Partner)"
+  dashboard_menu:
+    identifier: crush_covid
+    name: "CRUSH Covid Uppsala (Partner)"
 aliases:
-    - /data_types/health_data/crush_covid/
+  - /data_types/health_data/crush_covid/
+dashboards_topics: [COVID-19, Infectious diseases]
 ---
 
-<div class="containter"><div class="row mr-2 mt-2"><div class="col-lg-9"><p><b>CRUSH Covid</b> is a collaboration between the Region Uppsala and researchers from five different departments at Uppsala University. The purpose of the project is to map outbreaks of COVID-19 in Uppsala County and attempt to mitigate their impact by keeping the public informed. Information on the CRUSH Covid dashboard was originally updated weekly, but the update schedule changed in autumn 2022. The dashboard will now be <b>updated every 1-2 months.</b></p>
-<p>CRUSH Covid is led by Mats Martinell (senior lecturer at the Department of Public Health and Caring Sciences, General Medicine and Preventive Medicine, Uppsala University) and Tove Fall (professor of Molecular Epidemiology at the Department of Medical Sciences, Molecular Epidemiology, Uppsala University). Sewage analysis is supported by SciLifeLab and Uppsala Vatten. Modelling work is supported by Vinnova.</p>
-<p>For questions and feedback, please contact Georgios Varotsis (<a href="mailto:georgios.varotsis@medsci.uu.se">georgios.varotsis@medsci.uu.se</a>).</p><p>CRUSH Covid has received ethical approval from the Swedish Ethical Review Authority (ref. no. 2020-04210, 2020-06315 and 2020-06501).</p>
-</div><div class="col-lg-3"><div class="d-flex justify-content-center mb-3"><img src="/img/logos/crush_covid_logo.png" alt="CRUSH Covid" height="30"></div><div class="d-flex justify-content-center mb-3"><img src="/img/logos/uu_logo.png" alt="Uppsala University" height="100"></div>
-<div class="d-flex justify-content-center mb-3"><img src="/img/logos/regionuppsala_logo.png" alt="Region Uppsala" height="40"></div></div></div></div>
+<div class="containter">
+<div class="row mr-2 mt-2">
+<div class="col-lg-9">
+<p>CRUSH Covid Uppsala is a research project in which <b>Region Uppsala</b> collaborates with researchers from five different research departments at <b>Uppsala University</b>. The purpose of the project is to map outbreaks of COVID-19 in Uppsala County and to try to mitigate the impact of outbreaks by informing the public.</p>
+
+<p>CRUSH Covid is led by <b>Mats Martinell</b> (senior lecturer at the Department of Public Health and Caring Sciences, General Medicine and Preventive Medicine, Uppsala University) and <b>Tove Fall</b> (professor of Molecular Epidemiology at the Department of Medical Sciences, Molecular Epidemiology, Uppsala University). Sewage analysis is supported by SciLifeLab and Uppsala Vatten. Modelling work is supported by Vinnova.</p>
+
+<p>For questions and feedback, please contact <b>Georgios Varotsis</b> (<a href="mailto:georgios.varotsis@medsci.uu.se">georgios.varotsis@medsci.uu.se</a>).</p>
+
+<p>CRUSH Covid has received ethical approval from the Swedish Ethical Review Authority (ref. no. 2020-04210, 2020-06315 and 2020-06501).</p>
+
+<p>The CRUSH Covid team has released data and information about the project in two places. The primary source of data and information was their <a target="_blank" href="https://crush-covid.shinyapps.io/crush_covid/">custom shiny app, named the CRUSH Covid dashboard</a>, which contained data visualisations as well as reports. As of September 2022, updates to the app ceased. The Portal's dashboard (i.e. this webpage) is the secondary source of data and information for this project. The data generated from CRUSH Covid between 2020-2022 can be downloaded directly below.</p>
+</div>
+<div class="col-lg-3">
+<div class="d-flex justify-content-center mb-3"><img src="/img/logos/crush_covid_logo.png" alt="CRUSH Covid" height="30"></div>
+<div class="d-flex justify-content-center mb-3"><img src="/img/logos/uu_logo.png" alt="Uppsala University" height="100"></div>
+<div class="d-flex justify-content-center mb-3"><img src="/img/logos/regionuppsala_logo.png" alt="Region Uppsala" height="40"></div>
+</div>
+</div>
+</div>
 
 #### Download CRUSH Covid data
 
-<div class="alert alert-info">Last updated: {{% crush_covid_modified %}}.</div>
+<div class="alert alert-info">Last updated: 2022-09-15</div>
 
-* [Number of tests and % positivity by postal code in Uppsala County, .csv file](https://blobserver.dckube.scilifelab.se/blob/CRUSH_Covid_data.csv) (updated every 1-2 months from September 2022).
-    For each postal code which is found within the Uppsala län, the dataset contains weekly data on cases per capita, tests per capita and % positivity. Our estimates are calculated based on the adult population of each postal code (individuals 15 years of age and older). For reference, both the total population and the adult population are included.
+- [Number of tests and % positivity by postal code in Uppsala County, .csv file](https://blobserver.dc.scilifelab.se/blob/CRUSH_Covid_data.csv). For each postal code which is found within the Uppsala län, the dataset contains weekly data on cases per capita, tests per capita and % positivity. The estimates are calculated based on the adult population of each postal code (individuals 15 years of age and older). For reference, both the total population and the adult population are included.
 
 #### Interactive dashboard and reports
 

diff --git a/content/english/dashboards/npc-statistics.md b/content/english/dashboards/npc-statistics.md
@@ -9,6 +9,7 @@ menu:
 toc: false
 aliases:
     - /data_types/health_data/npc-statistics/
+dashboards_topics: [COVID-19, Infectious diseases]
 ---
 
 <div class="alert alert-info small">