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Merge pull request #1136 from ScilifelabDataCentre/accessibilty_2
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Accessibility fixes
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@Ziip-dev
Ziip-dev committed May 17, 2024
2 parents 7f13f8c + 54a68e3 commit aee9e79
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70 changes: 66 additions & 4 deletions content/english/dashboards/covid_publications.md
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Expand Up @@ -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

Expand All @@ -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>
2 changes: 1 addition & 1 deletion content/english/dashboards/npc-statistics.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion content/english/dashboards/post_covid.md
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion content/english/dashboards/serology-statistics.md
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Expand Up @@ -18,7 +18,7 @@ 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 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)**.
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4 changes: 2 additions & 2 deletions content/english/dashboards/vaccines.md
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Expand Up @@ -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
Expand All @@ -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).
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2 changes: 1 addition & 1 deletion content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md
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Expand Up @@ -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>
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10 changes: 6 additions & 4 deletions content/english/share-data.md
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Expand Up @@ -40,10 +40,12 @@ Before submission of raw sequence data (e.g. shotgun sequencing) it is necessary
- [SciLifeLab Data Repository for metadata records of sequence data with restricted access](https://scilifelab.se/data/repository)

<div class="container mb-4 ena_tutorial_banner">
<a href="/support_services/tutorial_ena/tutorial_ena_intro/"><img height="30px"
src="/img/ena_tutorial/ENA_logo_2021.png"></a> <a
href="/support_services/tutorial_ena/tutorial_ena_intro/">Tutorial for SARS-CoV-2 genome data submission to
ENA</a>
<a href="/support_services/tutorial_ena/tutorial_ena_intro/" aria-hidden="true">
<img height="30px" alt="ENA logo" src="/img/ena_tutorial/ENA_logo_2021.png">
</a>
<a href="/support_services/tutorial_ena/tutorial_ena_intro/">
Tutorial for SARS-CoV-2 genome data submission to ENA
</a>
</div>

---
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4 changes: 2 additions & 2 deletions content/english/support.md
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Expand Up @@ -30,7 +30,7 @@ You are welcome to send both general questions about best approaches to research

<div class="col-12 col-md-4 col-lg-3 d-none d-md-block">
<figure class="figure">
<img width="200" src="/img/logos/nbislogo-orange-txt.svg#floatright">
<img width="200" alt="NBIS logo" src="/img/logos/nbislogo-orange-txt.svg#floatright">
</figure>
</div>

Expand All @@ -53,7 +53,7 @@ You can read more about [each of these support services on NBIS website](https:/

<div class="col-12 col-md-4 col-lg-3 d-none d-md-block">
<figure class="figure">
<img width="250" src="/img/logos/SND_logo_eng.png#floatright">
<img width="250" alt="SND logo" src="/img/logos/SND_logo_eng.png#floatright">
</figure>
</div>
If you are not working within the life sciences, you will need to turn to the research institute or university where you are working for with your data-related questions. Many of the research institutes in Sweden have a local data support service as part of the [Swedish National Data Service network](https://snd.gu.se/en/about-us/snd-network).
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10 changes: 7 additions & 3 deletions layouts/contact/list.html
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Expand Up @@ -47,8 +47,8 @@ <h2>{{ if eq $.Site.Language.LanguageName "Svenska" }}Kontakta oss{{ else }}Cont
</div>
</div>
<div class="g-recaptcha" data-sitekey="6LesV0gaAAAAAGFjazG7Hd_hN72cpeYm2woivBT3"></div>
<input type="url" id="originUrl" name="originUrl" value="" hidden />
<input type='hidden' name='origin' value='general_contact'>
<input type="url" id="originUrl" name="originUrl" value="" hidden aria-label="form-origin-url" />
<input type='hidden' name='origin' value='general_contact' hidden aria-label="form-name" />
<div class="form-group row">
<div class="col-sm-9">
<button type="submit" class="btn btn-secondary mt-3">{{ if eq $.Site.Language.LanguageName "Svenska" }}Skicka in formuläret{{ else }}Submit the form{{ end }}</button>
Expand Down Expand Up @@ -82,7 +82,7 @@ <h3>Personal data policy</h3>
event.preventDefault();
alert("{{ if eq $.Site.Language.LanguageName "Svenska" }}Vänligen markera 'I'm not a robot' ovanför 'Skicka' -knappen.{{ else }}Please tick 'I'm not a robot' above the 'Submit' button.{{ end }}");
}
})
});

document.getElementById('originUrl').value = location.href;

Expand All @@ -97,6 +97,10 @@ <h3>Personal data policy</h3>
});
});

window.addEventListener("load", function () {
$('textarea#g-recaptcha-response').attr('aria-label', "The recaptcha response will appear here");
});

</script>

{{ end }}
10 changes: 7 additions & 3 deletions layouts/events/list.html
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Expand Up @@ -103,8 +103,8 @@ <h5 class="modal-title" id="suggestionModalLabel">Events & training suggestion</
(your email will not be displayed in the event information).</div>
</div>
<div class="g-recaptcha" data-sitekey="6LesV0gaAAAAAGFjazG7Hd_hN72cpeYm2woivBT3"></div>
<input type="url" id="originUrl" name="originUrl" value="" hidden />
<input type='hidden' name='origin' value='event_training_suggestion'>
<input type="url" id="originUrl" name="originUrl" value="" hidden aria-label="form-origin-url" />
<input type='hidden' name='origin' value='event_training_suggestion' hidden aria-label="form-name" />
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
Expand Down Expand Up @@ -226,7 +226,7 @@ <h5><a class="" role="button" data-bs-toggle="modal"
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="descriptionModalLabel">${event.title}</h5>
<h5 class="modal-title" id="descriptionModalLabel${ind}">${event.title}</h5>
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
</div>
<div class="modal-body">
Expand Down Expand Up @@ -327,6 +327,10 @@ <h5 class="modal-title" id="descriptionModalLabel">${event.title}</h5>
}
}); // Forms validation block ends here

window.addEventListener("load", function () {
$('textarea#g-recaptcha-response').attr('aria-label', "The recaptcha response will appear here");
});

}); // Document "DOMContentLoaded" trigger ends here
</script>

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14 changes: 7 additions & 7 deletions layouts/index.html
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Expand Up @@ -161,7 +161,7 @@ <h5>Biobanks</h5>
and data stored in various biobanks across Sweden in their research. The database allows to find sample
collections matching their needs using various filters.
</div>
<a class="mb-1" href="/biobanks/">Read more <i class="bi bi-arrow-right-square-fill"></i></a>
<a class="mb-1 dark-blue" href="/biobanks/">Read more <i class="bi bi-arrow-right-square-fill"></i></a>
{{ end }}
</div>
</div>
Expand All @@ -181,7 +181,7 @@ <h5>Biobanks</h5>
<!-- Topics box -->
<div class="bg-home-topics mb-4">
<h4 class="mt-0 mb-1">Pandemic preparedness topics</h4>
<p class="mb-2 small">Click on one of the <b><a href="/topics/">topics</a></b> below to see only the content that is related to that topic.</p>
<p class="mb-2 small">Click on one of the <b><a class="dark-blue" href="/topics/">topics</a></b> below to see only the content that is related to that topic.</p>
{{ range .Site.Menus.topics_menu }}
<a href="{{ .Page.RelPermalink }}"><span class="bg-home-topics-btn">{{ .Name }}</span></a>
{{ end }}
Expand All @@ -207,7 +207,7 @@ <h4 class="mb-1">What's new?</h4>
</div> {{ end }}
{{ end }}
<div class="mt-3 bg-see-all-link">
<a href="/updates/">See all Portal news <i class="bi bi-arrow-right-square-fill"></i></a>
<a class="dark-blue" href="/updates/">See all Portal news <i class="bi bi-arrow-right-square-fill"></i></a>
</div>
</div>
</div>
Expand All @@ -230,20 +230,20 @@ <h4>Om portalen</h4>

<!-- Share your data ad -->
<div class="row mt-4 pt-2 px-2">
<div class="share-new-data text-white py-2 px-3">
<div class="share-new-data py-2 px-3">
<h4 class="my-1">{{ if eq $.Site.Language.LanguageName "Svenska" }}Dela nya data{{ else }}Share new data{{ end }}</h4>
{{ if eq $.Site.Language.LanguageName "Svenska" }}Teamet som arbetar med portalen hjälper dig
gärna dela dina forskningsdata i öppna databaser och svarar på frågor om datahantering.{{ else }}The portal
team is happy to assist you with submitting your data to open repositories or answer any questions about data
management.{{ end }}
<div class="row">
<div class="col-auto">
<h6><a class="btn-white-teal"
<h6><a class="btn-white-black"
href="{{ if eq $.Site.Language.LanguageName "Svenska" }}/sv{{ end }}/share-data/">{{ if eq $.Site.Language.LanguageName "Svenska" }}Riktlinjer{{ else }}Guidelines{{ end }}
<i class="bi bi-arrow-right"></i></a></h6>
</div>
<div class="col-auto">
<h6><a class="btn-white-teal"
<h6><a class="btn-white-black"
href="{{ if eq $.Site.Language.LanguageName "Svenska" }}/sv{{ end }}/support/">{{ if eq $.Site.Language.LanguageName "Svenska" }}Stödtjänster{{ else }}Support
request{{ end }} <i class="bi bi-arrow-right"></i></a></h6>
</div>
Expand Down Expand Up @@ -312,7 +312,7 @@ <h4 class="mb-1">Events</h4>
}); // for each events iteration to create html ends here

eventsHTML += ` <div class="mt-3 bg-see-all-link">
<a href="/events/">See all events <i class="bi bi-arrow-right-square-fill"></i></a>
<a class="dark-blue" href="/events/">See all events <i class="bi bi-arrow-right-square-fill"></i></a>
</div>
</div>`;
var eventsSection = document.getElementById('events-section');
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9 changes: 5 additions & 4 deletions layouts/partials/dashboards.html
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Expand Up @@ -25,10 +25,11 @@
<div class="col p-2">
<div class="bg-dashboard">
<!-- div {{ if .Page.Params.banner_border }}class="px-1 pt-1" {{ end }} -->
<div>
<a href="{{ .Page.RelPermalink }}">
<img class="img-fluid" src="{{ with .Page.Params.banner }}{{ . }}{{ else }}{{ "/img/plp_default2.png" }}{{ end }}">
</a>
<div aria-hidden="true">
<a href="{{ .Page.RelPermalink }}">
<img class="img-fluid" src="{{ with .Page.Params.banner }}{{ . }}{{ else }}{{ "/img/plp_default2.png" }}{{ end }}"
alt="Thumbnail for {{ .Name }}">
</a>
</div>
<div class="p-2 bg-dashboard-title">
<h6><a href="{{ .Page.RelPermalink }}">{{ .Name }}</a></h6>
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