Merge pull request #1069 from ScilifelabDataCentre/develop

send latest Portal changes live ahead of release

.github/workflows/dockerhub.yml

@@ -65,3 +65,4 @@ jobs:
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          build-args: HUGO_ENV_ARG=${{ github.ref_name == 'main' && 'production' || github.event_name == 'release' && 'production' || 'development' }}

config.yaml

@@ -3,7 +3,7 @@ title: "The Swedish Pathogens Portal"
 buildFuture: true
 params:
   title: "The Swedish Pathogens Portal"
-  description: The Swedish Pathogens Portal
+  description: "The Swedish Pathogens Portal provides information about available datasets, resources, tools, and services related to pandemic preparedness in Sweden. We offer support to all those involved in pandemic preparedness research that are affiliated with a Swedish research institution or university."
   images:
     - /img/swe_pathogens_social_media.png
 
@@ -68,7 +68,7 @@ languages:
     languageName: Svenska
     contentDir: content/svenska
     weight: 2
-    description: Svenska Pathogens Portalen
+    description: "Den Patogens Portal Sverige tillhandahåller information, riktlinjer, verktyg och tjänster för att stödja forskare vid svenska lärosäten verksamma inom forskningsfältet pandemisk beredskap med datarelaterade frågor."
 
 markup:
   goldmark:

content/english/dashboards/RECOVAC.md

@@ -25,8 +25,7 @@ EPN Nr 2020-01800, 2020-05829, 2021-00267, 2021-00829, 2021-02106, 2021-04098, 2
 
 ## Data visualisations
 
-<!-- <div class="alert alert-info">All data last updated: {{% RECOVAC_date_modified %}}</div> -->
-<div class="alert alert-info">All data last updated: 08-11-2023</div>
+<div class="alert alert-info">All data last updated: {{% RECOVAC_date_modified %}}</div>
 
 _All code used to produce the visualisations on this page is available on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/RECOVAC). The particular scripts used in each case are linked below the plots._
 
@@ -94,11 +93,8 @@ When hovering over the plot with the cursor, additional grey icons appear in the
   Rotating your phone may improve graph layout
 </div>
 
-<!-- <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/swedishpop_subplot_button.json" height="800px" >}}</div>
-</div> -->
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="/img/swedishpop_subplot_button.json" height="800px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/swedishpop_subplot_button.json" height="800px" >}}</div>
 </div>
 
 **Code used to produce plots:** [Preparation for vaccine coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_dataprep.py), [Graph of vaccine coverage](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_plotwbuttons.py), [Graph and data preparation for ICU admissions data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_ICU_plotwbuttons.py).
@@ -152,8 +148,7 @@ When hovering over the plot with the cursor, additional grey icons appear in the
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="/img/comorbs_subplot_button.json" height="800px" >}}</div>
-    <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}</div> -->
+    <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}</div>
 </div>
 
 **Code used to produce plots:** [Preparation of COVID-19 case data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_cases_dataprep.py), [Preparation of vaccination coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_vaccinecov_dataprep.py), [Graph containing subplots](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_subplots_wbuttons.py).

content/english/dashboards/post_covid.md

@@ -27,8 +27,7 @@ For more information on _Post COVID-19 condition_ in Sweden, please see [this se
 
 ### Data
 
-<div class="alert alert-info">All data last updated: 2023-11-10</div>
-<!-- {{% postcovid_date_modified %}} -->
+<div class="alert alert-info">All data last updated: {{% postcovid_date_modified %}}</div>
 
 The data underlying the visualisations on this page are from [The Swedish Board of Health and Welfare](https://www.socialstyrelsen.se/statistik-och-data/statistik/statistik-om-covid-19/) and comprise of data from both the [Patient Register](https://www.socialstyrelsen.se/statistik-och-data/register/alla-register/patientregistret/) and the [‘Cause of Death’ Register](https://www.socialstyrelsen.se/statistik-och-data/register/alla-register/dodsorsaksregistret/). The data are updated monthly, on the second Wednesday of the month, and are available for download [here](https://www.socialstyrelsen.se/statistik-och-data/statistik/statistik-om-covid-19/). Additional data about COVID-19 can be requested from the corresponding registers by any researchers fulfilling the requirements for access, the guidelines for access via the RUT (Register Utiliser Tool) are available [here](https://bestalladata.socialstyrelsen.se/data-for-forskning/).
 
@@ -51,17 +50,15 @@ These plots display the number of times that patients were assigned the diagnose
 #### Diagnosis U09.9
 
 <div class="plot_wrapper mb-3">
-  <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_agesex_casedist.json" height="500px" >}}</div> -->
-    <div class="table-responsive">{{< plotly json="/img/postcov_plots/U099_agesex_casedist.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_agesex_casedist.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py).
 
 #### Diagnosis Z86.1A/U08.9
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="/img/postcov_plots/U089_agesex_casedist.json" height="500px" >}}</div>
-    <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_agesex_casedist.json" height="500px" >}}</div> -->
+    <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_agesex_casedist.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py).
@@ -73,17 +70,15 @@ The maps below show the number of people that received the diagnoses of interest
 #### Diagnosis U09.9
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="/img/postcov_plots/map_postcovid_percent_of_population_U099.json" height="500px" >}}</div>
-    <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U099.json" height="500px" >}}</div> -->
+    <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U099.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U099.py).
 
 #### Diagnosis Z86.1A/U08.9
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="/img/postcov_plots/map_postcovid_percent_of_population_U089.json" height="500px" >}}</div>
-  <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U089.json" height="500px" >}}</div> -->
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U089.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U089.py).
@@ -121,8 +116,7 @@ The maps below show the number of people that received the diagnoses of interest
 The below table displays the most common types of diagnosis (diagnosis groups) that have been reported together with the _U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified_ diagnosis. In particular, the values in the table represent the amount of individuals that received the _U09.9_ diagnosis alongside one of the diagnoses below. The data was recorded between 16th October 2020 and the most recent data update (see above).
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="/img/postcov_plots/accompdiag_table.json" height="527px" >}}</div>
-    <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/accompdiag_table.json" height="527px" >}}</div> -->
+    <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/accompdiag_table.json" height="527px" >}}</div>
 </div>
 
 <span class="text-muted">_Note that an individual may have more than one of the accompanying diagnoses. However, if an individual has the same issue on multiple doctor visits/healthcare contacts, the diagnosis will only be counted once_</span>
@@ -138,8 +132,7 @@ The below plot shows the number of times that patients given the diagnoses of in
 </div>
 
 <div class="d-md-none plot_wrapper">
-  <div class="table-responsive">{{< plotly json="/img/postcov_plots/weeklycontacts_healthcare.json" height="300px" >}}</div>
-    <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="300px" >}}</div> -->
+    <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="300px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare.py).
@@ -155,8 +148,7 @@ The below plots show the number of times that patients given one of the diagnose
 </div>
 
 <div class="plot_wrapper mb-3">
-  <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_healthcare_divsex.json" height="500px" >}}</div> -->
-  <div class="table-responsive">{{< plotly json="/img/postcov_plots/U099_healthcare_divsex.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_healthcare_divsex.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py).
@@ -168,8 +160,7 @@ The below plots show the number of times that patients given one of the diagnose
 </div>
 
 <div class="plot_wrapper mb-3">
-  <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_healthcare_divsex.json" height="500px" >}}</div> -->
-    <div class="table-responsive">{{< plotly json="/img/postcov_plots/U089_healthcare_divsex.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_healthcare_divsex.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py).

content/english/dashboards/variants_region_uppsala.md

@@ -21,7 +21,7 @@ This dashboard includes two visualisations of the data from the section for Clin
 
 ## SARS-CoV-2 Sequence Visualisations
 
-<div class="alert alert-info">Last updated: 2023-11-06 <span id="last_modified_uuclinmicro"></span></div>
+<div class="alert alert-info">Last updated: <span id="last_modified_uuclinmicro"></span></div>
 
 The sequences are presented according to their [World Health Organisation (WHO) label](https://www.who.int/activities/tracking-SARS-CoV-2-variants) (a greek letter) and/or their Pango lineage. The Pango lineage is determined using [Pangolin](https://cov-lineages.org/resources/pangolin.html), [Nextclade](https://clades.nextstrain.org/), and an in-house annotation-based mutation analysis workflow.
 
@@ -36,8 +36,7 @@ Use the **‘Last 16 weeks’ button** to see data only from the last 16 weeks,
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="/img/lineage_four_recent.json" height="600px" >}}</div>
-  <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="600px" >}}</div> -->
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="600px" >}}</div>
 </div>
 
 **Code used to produce plots:** [Graph and data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/ClinMicro/lineage_four_recent.py).
@@ -53,8 +52,7 @@ Use the **’Deselect all lineages’ button** to clear data from all lineages f
 </div>
 
 <div class="plot_wrapper mb-3">
-  <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_one_wholetime.json" height="600px" >}}</div> -->
-    <div class="table-responsive">{{< plotly json="/img/lineage_one_wholetime.json" height="600px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_one_wholetime.json" height="600px" >}}</div>
 </div>
 
 **Code used to produce plots:** [Graph and data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/ClinMicro/lineage_one_plot.py).

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

@@ -22,7 +22,7 @@ Influent wastewater samples were collected from Ryaverket wastewater treatment p
 
 ## Visualisations
 
-<div class="alert alert-info">Last updated: 2023-11-08<span id="last_modified_gu"></span></div>
+<div class="alert alert-info">Last updated: <span id="last_modified_gu"></span></div>
 
 _The blue block on the graph indicates the period where sample collection was not completed (week 45 2022 - week 2 2023)._
 
@@ -60,24 +60,21 @@ _The blue block on the graph indicates the period where sample collection was no
 </div>
 
  <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://raw.githubusercontent.com/ScilifelabDataCentre/covid-portal/develop/static/img/wastewater_gothenburg.json" height="550px" >}}</div>
-  <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_gothenburg.json" height="550px" >}}</div> -->
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_gothenburg.json" height="550px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/gothenburg_covid.py).
 
 ## Commentary from the research group
 
-<div><b>Date: 2023-11-08</b> <br><b>Commentary:</b> There are still low amounts of SARS-CoV-2 in Gothenburg's wastewater. However, there was a small increase in weeks 41, 42, and 43 but there are still low levels. </div>
-<!-- <span id="gu_comment_date"></span>
-<span id="gu_comment"></span> -->
+<div><span id="gu_comment_date"></span>
+<span id="gu_comment"></span></div>
+
 {{< ww_dynamic_content >}}
 
 ## Dataset
 
-**Download the data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://github.com/ScilifelabDataCentre/covid-portal/raw/develop/static/ww_data_temp/wastewater_data_gu_allviruses.xlsx). Results are available for SARS-CoV-2 from week 7 of 2020 (with a small gap over winter 2022-2023), and for enteric viruses from week 2 of 2023. Updated weekly.\
-
-<!-- https://blobserver.dc.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx -->
+**Download the data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dc.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Results are available for SARS-CoV-2 from week 7 of 2020 (with a small gap over winter 2022-2023), and for enteric viruses from week 2 of 2023. Updated weekly.\
 
 **Contact:** <[email protected]>