Merge pull request #1143 from ScilifelabDataCentre/develop

Sending latest changes live.

CONTRIBUTING/adding_editing_information.md

@@ -7,6 +7,7 @@ Contributions are welcomed for all sections of the portal. This page describes h
 - [Making contributions via GitHub](#making-contributions-via-github)
 - [How to add a new page](#how-to-add-a-new-page)
 - [Adding available data](#adding-available-data)
+- [Best practices for images](#best-practices-for-images)
 - [Dashboard pages](#dashboard-pages)
 - [Data highlights](#data-highlights)
 - [Editorials](#editorials)
@@ -120,6 +121,14 @@ In order to add entries in the dataset, you should edit the `available_datasets.
     },
 ```
 
+## Best practices for images
+
+The Swedish Pathogens Portal uses images in many different kinds of pages (see e.g. [data highlights](#data-highlights) and [editorials](#editorials)). In order to ensure that the size and speed of the site is not negatively affected by the addition of images, please follow this guidance when uploading images.
+
+- Use appropriate image dimensions - the dimensions of the images (in terms of height and width) should be the minimum possible without compromising the appearance of the image on the site. [Testing locally](https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md) can help to determine which dimensions to use. As a general rule, thumbnail images should be twice as wide as they are high. We recommend that thumbnail images are `500px` in width and `250px` if they are also to be used as images within a page (e.g. as an illustration in an editorial). Many tools can be used to resize an image, including Macbook's inbuilt 'Preview' tool. See the _"Change an image’s dimensions"_ section in their [official documentation](https://support.apple.com/en-in/guide/preview/prvw2015/mac) for instructions.
+
+- Minimise image file size - minimising the dimensions of an image will reduce the overall size of the image file (in terms of memory e.g. MB). However, compression can be used to further reduce the file size in some cases. This can be done with online compression tools like [tinypng](https://tinypng.com/) or [tinyjpg](https://tinyjpg.com/).
+
 ## Dashboard pages
 
 **Data dashboards** are pages that include data from either research groups or public data sources. They include custom, dynamic visualisations of the data alongside relevant information about the background of the study, the methods used to collect data, and the research groups involved, among other things.
@@ -153,15 +162,15 @@ Under the metadata, you can write information about the research and the data. T
 
 ### Illustrations
 
-Links to dashboard pages are typically shown in cards e.g. in <https://pathogens.se/dashboards/>. These cards show a small image that is representative of that dashboard. The size of the image should be 250 px high and 500 px wide. The portal team can help with resizing/editing images. Images should be placed in the `/static/dashboard_thumbs` folder.
+Links to dashboard pages are typically shown in cards e.g. in <https://pathogens.se/dashboards/>. These cards show a small image (thumbnail) that is representative of that dashboard. Follow our guidance on [best practices for images](#best-practices-for-images) when uploading images. The portal team can also help with resizing/editing images. Images should be placed in the `/static/dashboard_thumbs` folder.
 
 ## Data highlights
 
 **Data highlights** are short, data-centric articles focusing on recent research that openly shares data, code, or other research outputs
 
 ### Illustrations
 
-Each highlight can have two illustrations. One is used as a thumbnail image on the pages showing multiple highlights e.g. <https://pathogens.se/highlights/>. The other can be shown on the page. Only the first is required, and should be 250 px high and 500 px wide. The portal team can help with resizing/editing images. The illustrations should be placed in the `/static/highlights/banners` folder. The images can be in .png or .jpg format.
+Each highlight can have two illustrations. One is used as a thumbnail image on the pages showing multiple highlights e.g. <https://pathogens.se/highlights/>. The other can be shown on the page. Only the first is required. Follow our guidance on [best practices for images](#best-practices-for-images) when uploading images. The portal team can also help with resizing/editing images. The illustrations should be placed in the `/static/highlights/banners` folder. The images can be in .png or .jpg format.
 
 ### Data highlight files
 
@@ -217,7 +226,7 @@ Information about any infrastruture used to complete the study.
 
 ### Illustrations
 
-Each editorial has an illustation that should be 250 px high and 500 px wide. The portal team can help with resizing/editing images. The illustrations should be placed in the `/static/editorials` folder. The images can be in .png or .jpg format.
+Each editorial has a thumbnail and image to be included in the article. This can be the same image. Follow our guidance on [best practices for images](#best-practices-for-images) when uploading images. The portal team can also help with resizing/editing images. The illustrations should be placed in the `/static/editorials` folder. The images can be in .png or .jpg format.
 
 ### Editorial files
 
@@ -267,11 +276,11 @@ News items about the portal are published under `/updates/`. The news items are
 
 ### Illustrations
 
-Each news item can have two illustrations. One is used as a thumbnail image on the [portal news page](http://pathogens.se/updates/). The other can be shown on the page. Only the first is required, and should be 250 px high and 500 px wide. The portal team can help with resizing/editing images. The illustrations should be placed in the `/static//updates/banners/` folder. The images can be in .png or .jpg format.
+Each news item can have two illustrations. One is used as a thumbnail image on the [portal news page](http://pathogens.se/updates/). The other can be shown on the page. Only the first is required. Follow our guidance on [best practices for images](#best-practices-for-images) when uploading images. The portal team can also help with resizing/editing images. The illustrations should be placed in the `/static//updates/banners/` folder. The images can be in .png or .jpg format.
 
 ### News files
 
-The news items can be added in the folder `/content/english/updates/`. Each news item is a file with extension **.md**. The file name used here will also be the URL of the news item (e.g., `test-news.md` will become `https://pathogens.se/updates/test-news/`).
+The news items can be added in the folder `/content/english/updates/`. Each news item is a file with extension **.md**. The file name used here will also be the URL of the news item (e.g. `test-news.md` will become `https://pathogens.se/updates/test-news/`).
 
 ### Content of the news files
 

Dockerfiles/Dockerfile

@@ -2,15 +2,16 @@
 FROM alpine:3.19.1 AS build
 RUN apk add --no-cache wget=1.21.4-r0
 ARG HUGO_VERSION="0.123.7"
+ARG HUGO_ENV_ARG
+WORKDIR /src
+COPY ./ /src
 RUN wget --quiet "https://github.com/gohugoio/hugo/releases/download/v${HUGO_VERSION}/hugo_${HUGO_VERSION}_Linux-64bit.tar.gz" && \
     tar xzf hugo_${HUGO_VERSION}_Linux-64bit.tar.gz && \
     rm -r hugo_${HUGO_VERSION}_Linux-64bit.tar.gz && \
     mv hugo /usr/bin && \
-    chmod 755 /usr/bin/hugo
-WORKDIR /src
-COPY ./ /src
-RUN mkdir /target && \
-    hugo -d /target
+    chmod 755 /usr/bin/hugo && \
+    mkdir /target && \
+    hugo -d /target -e "${HUGO_ENV_ARG}"
 
 # Serve the generated html using nginx
 FROM nginxinc/nginx-unprivileged:alpine

content/english/dashboards/_index.md

@@ -7,6 +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>
+    dashboard_menu:
+        identifier: all_dashboards
+        name: "All dashboards"
+        weight: 1
 aliases:
       - /dashboards
       - /visualisations

content/english/dashboards/covid_publications.md

@@ -51,13 +51,44 @@ 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.dc.scilifelab.se/blob/covid-portal-titles_all.png"></div></div>
+<div class="row my-4">
+  <div class="col-md-8">
+    <img alt="Wordcloud image from all titles" 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.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>
+<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 alt="Wordcloud image from VR publication titles" 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 alt="Wordcloud image from KAW publication titles" 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 alt="Wordcloud image from Horizon 2020 publication titles" 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
 
@@ -67,10 +98,41 @@ 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.dc.scilifelab.se/blob/covid-portal-abstracts_all.png"></div></div>
+<div class="row my-4">
+  <div class="col-md-8">
+    <img alt="Wordcloud image from all publication abstract" 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.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>
+<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 alt="Wordcloud image from VR publication abstract" 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 alt="Wordcloud image from KAW publication abstract" 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 alt="Wordcloud image from Horizon 2020 publication abstract" src="https://blobserver.dc.scilifelab.se/blob/covid-portal-abstracts_h2020.png">
+      </div>
+    </div>
+  </div>
+</div>

content/english/dashboards/npc-statistics.md

@@ -16,7 +16,7 @@ dashboards_topics: [COVID-19, Infectious diseases]
 <div class="alert alert-info small">
   <p><i class="bi bi-exclamation-triangle-fill"></i>The National Pandemic Centre (NPC) at Karolinska Institute ceased operations of high throughput PCR diagnostics on 2020-12-21.</p>
   <p><span class="font-weight-bold">The data presented here is no longer updated</span> but is kept for historical reference.</p>
-  <a href="https://nyheter.ki.se/covid-19-tester-ki-atergar-till-ordinarie-laboratorieverksamhet-men-har-fortsatt-beredskap">KI Press Release</a>
+  <a class="dark-blue" href="https://nyheter.ki.se/covid-19-tester-ki-atergar-till-ordinarie-laboratorieverksamhet-men-har-fortsatt-beredskap">KI Press Release</a>
 </div>
 
 The dataset visualised in the graphs on this page is available [here](https://datagraphics.dc.scilifelab.se/dataset/bbbaf64a25a1452287a8630503f07418).  The numbers reported here were compiled automatically and, as such, might not correspond to

content/english/dashboards/post_covid.md

@@ -179,7 +179,7 @@ Below is a list of pre-prints and published scientific journal articles on _Post
 
 {{< postcovid_publications >}}
 
-<a id="background"><h2> </h2></a>
+<a id="background"></a>
 
 ## Background Information
 

content/english/dashboards/serology-statistics.md

@@ -18,13 +18,13 @@ dashboards_topics: [COVID-19, Infectious diseases]
 
 <div class="alert alert-info">
   <i class="bi bi-exclamation-triangle-fill"></i>
-  <span>The data on this page are largely historic, though they may be updated occasionally. The Autoimmunity and Serology Profiling unit has now expanded their pandemic preparedness efforts to include tests for multiple other viruses. Information about that work can be found on the <a href="/dashboards/serology_multidisease/"> multi-disease serology dashboard</a>.</span>
+  <span>The data on this page are largely historic, though they may be updated occasionally. The Autoimmunity and Serology Profiling unit has now expanded their pandemic preparedness efforts to include tests for multiple other viruses. Information about that work can be found on the <a class="dark-blue" href="/dashboards/serology_multidisease/"> multi-disease serology dashboard</a>.</span>
 </div>
 
 Serology tests involve testing bodily fluids for the presence of antibodies or other substances. Since the beginning of the pandemic, the SciLifeLab Autoimmunity and Serology Profiling unit has conducted serology tests for antibodies targeting SARS-CoV-2 proteins. The unit has continuously provided the latest data to the Swedish Pathogens Portal. In each of the below sections, we show the numbers of samples that were **positive**, **negative** or **research and development (R&D)**.
 
-- **Positive tests**: Serology tests indicating the _presence_ of immunoglobulin G (IgG) antibodies targetting SARS-CoV-2 proteins.
-- **Negative tests**: Serology tests indicating the _absence_ of immunoglobulin G (IgG) antibodies targetting SARS-CoV-2 proteins.
+- **Positive tests**: Serology tests indicating the _presence_ of immunoglobulin G (IgG) antibodies targeting SARS-CoV-2 proteins.
+- **Negative tests**: Serology tests indicating the _absence_ of immunoglobulin G (IgG) antibodies targeting SARS-CoV-2 proteins.
 - **R&D tests**: All of the remaining serum, plasma, and saliva samples that were completed to test the levels IgG, IgM, or IgA antibodies targeting SARS-CoV-2 proteins. This includes all of the positive and negative controls, all replicated and re-ran samples and assays, all samples analysed during the continuous development and optimisation of the tests, technically failed samples, and all research associated projects.
 
 <div class="alert alert-info">Data last updated: {{% serology_date_modified %}}.</div>

content/english/dashboards/vaccines.md

@@ -15,7 +15,7 @@ dashboards_topics: [COVID-19, Infectious diseases]
 
 <div class="alert alert-info">
   <i class="bi bi-exclamation-triangle-fill"></i>
-  <span>The data on this page is no longer updated at the data source. We are currently assessing the use of other data sources for vaccine data. Please see our <a href="/dashboards/recovac/">RECOVAC dashboard</a> for information on vaccine effectiveness and safety.</span>
+  <span>The data on this page is no longer updated at the data source. We are currently assessing the use of other data sources for vaccine data. Please see our <a class="dark-blue" href="/dashboards/recovac/">RECOVAC dashboard</a> for information on vaccine effectiveness and safety.</span>
 </div>
 
 ## General information on COVID-19 vaccines
@@ -40,7 +40,7 @@ On this page, we explore publicly available data for COVID-19 vaccination in Swe
 This page also displays information about [ongoing research projects](/dashboards/vaccines/#ongoing-research-projects) across Sweden related to COVID-19 vaccines. The list includes different kinds of projects, including life science projects, registry-based projects, and public health projects. We also [display a subset of publications](/dashboards/vaccines/#publications) related to vaccine research by researchers affiliated with a Swedish university or research institute.
 
 <div class="alert alert-info">
-    <i class="bi bi-info-circle-fill"></i> We invite researchers affiliated with a Swedish research institute to <a href="https://www.covid19dataportal.se/contact/">contact us</a> about adding information, data, and/or visualisations related to their own vaccine research to this Portal.
+    <i class="bi bi-info-circle-fill"></i> We invite researchers affiliated with a Swedish research institute to <a class="dark-blue" href="https://www.covid19dataportal.se/contact/">contact us</a> about adding information, data, and/or visualisations related to their own vaccine research to this Portal.
 </div>
 
 For more information on vaccination in Sweden, please also see the [RECOVAC dashboard on this portal](/dashboards/recovac/). The dashboard contains information and data visualisations related to the register-based large-scale national population study to monitor COVID-19 vaccination effectiveness and safety [(RECOVAC)](https://www.gu.se/en/research/recovac).

content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md

@@ -5,7 +5,7 @@ aliases:
   - /dashboards/wastewater/covid_quant_kth/
 ---
 
-<div class="alert alert-info">As of June 2023, the SARS-CoV-2 data will no longer be updated by SEEC-KTH. Data from after June 2023 is <a href="/dashboards/wastewater/covid_quantification/covid_quant_slu/">available from other research groups.</a></div>
+<div class="alert alert-info">As of June 2023, the SARS-CoV-2 data will no longer be updated by SEEC-KTH. Data from after June 2023 is <a class="dark-blue" href="/dashboards/wastewater/covid_quantification/covid_quant_slu/">available from other research groups.</a></div>
 
 <div class="mt-3">
   <a href="/dashboards/wastewater/covid_quantification/"><i class="bi bi-arrow-left-circle-fill"></i> Go back to SARS-CoV-2 quantification within the wastewater epidemiology dashboard</a>