diff --git a/content/english/citation.md b/content/english/citation.md index d762173a3..3c8242de5 100644 --- a/content/english/citation.md +++ b/content/english/citation.md @@ -1,10 +1,9 @@ --- title: How to cite the Portal menu: - top_actions: + navbar_top: name: Cite us - weight: 80 - pre: + weight: 50 footer_about: name: Cite us weight: 30 diff --git a/content/english/contribute.md b/content/english/contribute.md index 7099f2b2d..4d2933984 100644 --- a/content/english/contribute.md +++ b/content/english/contribute.md @@ -1,10 +1,9 @@ --- title: Contribute menu: - top_actions: + navbar_top: name: Contribute - weight: 40 - pre: + weight: 30 --- The _Swedish Pathogens Portal_ was built to serve the community of researchers working on relevant topics and we welcome any contributions from the community or suggestions on how the Portal can help the community. Whenever there is anything that you would like to share with your colleagues, do not hesistate to share it through the Portal. We welcome suggestions for new information or edits in all sections as well as ideas for new sections that could be launched. diff --git a/content/english/dashboards/serology-statistics.md b/content/english/dashboards/serology-statistics.md index b02e9e8f8..1c54cbe35 100644 --- a/content/english/dashboards/serology-statistics.md +++ b/content/english/dashboards/serology-statistics.md @@ -14,6 +14,7 @@ menu: aliases: - /data_types/health_data/serology-statistics/ dashboards_topics: [COVID-19, Infectious diseases] +plotly: true ---
@@ -29,20 +30,6 @@ Serology tests involve testing bodily fluids for the presence of antibodies or o
Data last updated: {{% serology_date_modified %}}.
- - ## Weekly serology tests The number of SARS-CoV-2 serology tests completed by the SciLifeLab Autoimmunity and Serology Profiling unit each week, divided according to whether tests were positive, negative, or research & development (R&D). @@ -51,10 +38,14 @@ The number of SARS-CoV-2 serology tests completed by the SciLifeLab Autoimmunity Scroll the plot sideways to view all of the data.
-
-
+
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weekly_serology_tests.json" height="550px" >}}
+ + +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/weekly-serology-tests.py). + ## Cumulative serology tests The cumulative number of positive, negative, and research & development (R&D) SARS-CoV-2 serology tests completed over time at the SciLifeLab Autoimmunity and Serology Profiling unit. @@ -63,10 +54,14 @@ The cumulative number of positive, negative, and research & development (R&D) SA Scroll the plot sideways to view all of the data.
-
-
+
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/cumulative_serology_tests.json" height="550px" >}}
+ + +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/cumulative-serology-tests.py). + #### About serology testing at the Autoimmunity and Serology Profiling unit Early in the COVID-19 pandemic, work was initiated to [develop a serological assay](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/pandemic-response/other-scilifelab-efforts/serology/) for large scale testing of plasma and serum samples for antibodies against SARS-CoV-2. The work was undertaken by three research groups at [the Department of Protein Science, KTH Royal Institute of Technology (KTH)](https://www.kth.se/pro) and the [Autoimmunity and Serology Profiling unit](https://www.scilifelab.se/facilities/autoimmunity-profiling/) at [SciLifeLab](https://www.scilifelab.se). @@ -74,11 +69,3 @@ Early in the COVID-19 pandemic, work was initiated to [develop a serological ass By comparing and combining a large number of variants of SARS-CoV-2 proteins as antigens, a [highly sensitive and specific multiplex bead-based assay](https://doi.org/10.1002/cti2.1312) was established. The high-throughput assay can be used to process up to 8000 samples per week. The vast majority of samples analysed to date originated from healthcare personnel, population-based studies, personnel in the pharmaceutical and biotechnology industry, and from within multiple research collaborations. Collaborators and sample providers include the community study at Danderyd University Hospital ([see news involving a follow-up study at Danderyd University Hospital](https://www.scilifelab.se/news/four-out-of-five-still-have-antibodies-against-sars-cov-2)), Karolinska University Hospital, Uppsala University Hospital, Skåne University Hospital, Örebro University Hospital, Sophiahemmet Hospital, Public Health Agency of Sweden, RISE (Research Institutes of Sweden), AstraZeneca, Cytiva, SVPH, Karolinska Institutet, KTH, Uppsala University, and Lund University. Check out the [Autoimmunity and Serology Profiling unit page](https://www.scilifelab.se/units/autoimmunity-profiling/) on the SciLifeLab website to find out more about the unit itself. Publications produced by studies making use of the unit are available in the [SciLifeLab Infrastructure Publications database](https://publications.scilifelab.se/label/Autoimmunity%20and%20Serology%20Profiling). - - - - - - - - diff --git a/content/english/dashboards/variants_region_uppsala.md b/content/english/dashboards/variants_region_uppsala.md index 8e5cd63ea..ee7260f40 100644 --- a/content/english/dashboards/variants_region_uppsala.md +++ b/content/english/dashboards/variants_region_uppsala.md @@ -79,6 +79,8 @@ Use the **’Deselect all lineages’ button** to clear data from all lineages f ## Publications +Cumlin, T., Karlsson, I., Haars, J., Rosengren, M., Lennerstrand, J., Pimushyna, M., Feuk, L., Ladenvall, C., Kaden, R. (2024). SARS-CoV-2 to Global Preparedness: A Graphical Interface for Standardised High-Throughput Bioinformatics Analysis in Pandemic Scenarios and Surveillance of Drug Resistance. _Int. J. Mol. Sci._, **25**, 6645. DOI: [10.3390/ijms25126645](https://doi.org/10.3390/ijms25126645). + Haars, J., Palanisamy, N., Wallin, F., Mölling, P., Lindh, J., Sundqvist, M., Ellström, P., Kaden, R., Lennerstrand, J. (2023). Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023. _Microorganisms_, **11**, 2417. DOI: [10.3390/microorganisms11102417](https://doi.org/10.3390/microorganisms11102417). Mannsverk, S., Bergholm, J., Palanisamy, N., Ellström, P., Kaden, R., Lindh, J., Lennerstrand, J. (2022). SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing. _Virology Journal_, **19**, 164. DOI: [10.1186/s12985-022-01896-x](https://doi.org/10.1186/s12985-022-01896-x). diff --git a/content/english/data-sources.md b/content/english/data-sources.md new file mode 100644 index 000000000..410c46423 --- /dev/null +++ b/content/english/data-sources.md @@ -0,0 +1,11 @@ +--- +Title: Data sources & repositories +--- + +This page includes displays **Data Sources** and **Repositories** relevant to the scope of the Swedish Pathogens Portal (i.e. infectious disease and pandemic preparedness in Sweden). **Data sources** are defined as resources where at least some users can access (but not submit) data. **Repositories**, by contrast, are resources in which at least some users can both access and submit data. + +Use the **Search** function to locate data sources/repositries by name/keywords (often more granular than other filters). It is also possible to filter data sources according to **Data Type**. + +[Get in touch](/contact/) about adding further data sources. + +{{< data_sources >}} diff --git a/content/english/events/_index.md b/content/english/events/_index.md index b017f70e1..f9f1e5134 100644 --- a/content/english/events/_index.md +++ b/content/english/events/_index.md @@ -2,6 +2,10 @@ title: Events & Training description: Community-sourced collection of events and training opportunities. recaptcha: true +menu: + navbar_top: + name: Events & Training + weight: 40 --- This section includes a list of upcoming conferences, webinars, workshops, and training opportunities related to pandemic preparedness and infectious disease. This includes events related to the management of data for these topics. We also welcome suggestions for events related to research data management in general. Such events will instead be listed on the [SciLifeLab Data Platform](https://data.scilifelab.se/events/). We highly encourage users to explore those events. diff --git a/content/english/share-data.md b/content/english/share-data.md index 5ce5b8b1b..53466aedf 100644 --- a/content/english/share-data.md +++ b/content/english/share-data.md @@ -1,10 +1,6 @@ --- title: Share data toc: true -menu: - top_actions: - weight: 40 - pre: aliases: - /data_types/genomics_transcriptomics/guidelines/ - /data_types/compound_and_target_data/guidelines/ diff --git a/content/english/support.md b/content/english/support.md index bdcf564aa..7f4d745eb 100644 --- a/content/english/support.md +++ b/content/english/support.md @@ -1,11 +1,6 @@ --- title: Get support toc: false -menu: - top_actions: - name: Get support - weight: 70 - pre: aliases: - /support_services/bioinformatics/ --- diff --git a/content/svenska/citation.md b/content/svenska/citation.md index 085765495..0cfcdc68b 100644 --- a/content/svenska/citation.md +++ b/content/svenska/citation.md @@ -1,10 +1,9 @@ --- title: Citera data, information och resurser från portalen menu: - top_actions: + navbar_top: name: Citera oss - weight: 80 - pre: + weight: 40 footer_about: name: Citera oss weight: 30 diff --git a/content/svenska/contribute.md b/content/svenska/contribute.md index ab31cc735..0eb11a305 100644 --- a/content/svenska/contribute.md +++ b/content/svenska/contribute.md @@ -2,10 +2,9 @@ title: Bidra till Portalen toc: false menu: - top_actions: + navbar_top: name: Bidra till Portalen - weight: 40 - pre: + weight: 30 --- Pathogens Portal Sverige har som syfte att stödja forskare som arbetar inom de forskningsområden som Portalen specifikt är inriktade på. Vi välkomnar både förslag på och bidrag till Portalens innehåll och förslag på hur Portalen kan utvecklas för att bättre stödja forskningen. Som forskare uppmanar vi dig att interagera med Portalen, exempelvis genom att dela data eller information genom Portalen. Vi tar även gärna emot förslag på nytt innehåll, nya sektioner samt förslag på hur nuvarande sektioner kan utvecklas och förnyas. diff --git a/content/svenska/dashboards/post_covid.md b/content/svenska/dashboards/post_covid.md index 9795d4248..7c2f5d7d1 100644 --- a/content/svenska/dashboards/post_covid.md +++ b/content/svenska/dashboards/post_covid.md @@ -205,12 +205,3 @@ I vetenskapliga publikationer och medias rapportering används flera olika begre ### Aktuell forskning Ett stort antal vetenskapliga artiklar, fallrapporter och reviews med fokus på postcovid har publicerats under det senaste året (jmfr. [[Dani _et al._ (2020)](https://doi.org/10.7861/clinmed.2020-0896), [Nabavi (2020)](https://doi.org/10.1136/bmj.m3489), [Sudre _et al._ (2021)](https://doi.org/10.1038/s41591-021-01292-y), [Tarybagil _et al._ (2020)](https://doi.org/10.1136/bcr-2020-241485), [Yelin _et al._ (2020)](https://doi.org/10.1016/j.cmi.2020.12.001)). De flesta vetenskapliga artiklar har haft som syfte att identifiera riskfaktorer och faktorer som kan användas för att prediktera individer som kan utveckla postcovid efter den akuta covid-19 infektionen. En nyligen publicerad studie av [Sudre och kollegor](https://doi.org/10.1038/s41591-021-01292-y) har lagt fram en modell för att prediktera individer som riskerar utveckla postcovid utifrån data från [COVID Symptom Study](/data_types/health_data/symptom_study_sweden/). I denna studie självrapporterar deltagarna sina symtom i en app på sin mobiltelefon. Resultaten indikerade att individer som upplevde fler än fem symtom under den första sjukdomsveckan hade högre risk att utveckla kvarstående symptom efter covid-19 (oddskvot = 3,53 (2,76–4,50)). Dessutom visade studien att postcovid var mer sannolikt hos kvinnor och att risken också ökade med ökande ålder och högre BMI. Forskarna bakom studien föreslår att deras prediktionsmodell kan användas för att identifiera individer som riskerar att utveckla postcovid. Dessa resultat kan användas för förebyggande vård och för att utveckla behandlingsmetoder och stöd vid planering av utbildning och rehabilitering. - - - - - - - - - diff --git a/content/svenska/dashboards/serology-statistics.md b/content/svenska/dashboards/serology-statistics.md index 58bde2dde..43823b487 100644 --- a/content/svenska/dashboards/serology-statistics.md +++ b/content/svenska/dashboards/serology-statistics.md @@ -9,6 +9,7 @@ menu: name: SARS-CoV-2 antikoppstester som utförts av SciLifeLab aliases: - /sv/data_types/health_data/serology-statistics/ +plotly: true ---
@@ -24,20 +25,6 @@ Serologiska tester innebär att kroppsvätskor testas för förekomst av antikro
Senaste uppdatering: {{% serology_date_modified %}}.
- - ## Serologiska tester per vecka Antalet SARS-CoV-2 serologitester som SciLifeLab Autoimmunity and Serology Profiling-enheten genomförde varje vecka, uppdelat efter om testerna var positiva, negativa eller inom forskning och utveckling (R&D). @@ -46,10 +33,14 @@ Antalet SARS-CoV-2 serologitester som SciLifeLab Autoimmunity and Serology Profi Att rotera mobiltelefonen kan förbättra grafens layout
-
-
+
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weekly_serology_tests.json" height="550px" >}}
+ + +**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/weekly-serology-tests.py). + ## Kumulativa serologiska tester Det kumulativa antalet positiva, negativa och forsknings- och utvecklingstester (R&D) av SARS-CoV-2-serologi som slutförts över tid vid SciLifeLab Autoimmunity and Serology Profiling-enheten. @@ -58,10 +49,14 @@ Det kumulativa antalet positiva, negativa och forsknings- och utvecklingstester Att rotera mobiltelefonen kan förbättra grafens layout
-
-
+
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/cumulative_serology_tests.json" height="550px" >}}
+ + +**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/cumulative-serology-tests.py). + #### Om serologisk testning vid enheten för Autoimmunity and Serology Profiling Tidigt under covid-19-pandemin inleddes arbetet med att [utveckla en serologisk analys](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/pandemic-response/other-scilifelab-efforts/serology/) för storskalig testning av plasma- och serumprover för antikroppar mot SARS-CoV-2. Arbetet utfördes av tre forskargrupper vid [institutionen för proteinvetenskap, Kungliga Tekniska Högskolan (KTH)](https://www.kth.se/sv/pro/protein-science-1.784558) och [enheten för autoimmunitet och serologisk profilering](https://www.scilifelab.se/facilities/autoimmunity-profiling/) vid [SciLifeLab](https://www.scilifelab.se). @@ -69,11 +64,3 @@ Tidigt under covid-19-pandemin inleddes arbetet med att [utveckla en serologisk Genom att jämföra och kombinera ett stort antal varianter av SARS-CoV-2-proteiner som antigener etablerades en [mycket känslig och specifik så kallad multiplex bead-based assay](https://doi.org/10.1002/cti2.1312). Assayen med hög kapacitet kan användas för att bearbeta upp till 8000 prover per vecka. De allra flesta prover som hittills har analyserats kommer från vårdpersonal, befolkningsbaserade studier, personal inom läkemedels- och bioteknikindustrin samt från flera olika forskningssamarbeten. Samarbetspartners och provleverantörer inkluderar samhällsstudien vid Danderyds universitetssjukhus ([se nyhet om uppföljningsstudie vid Danderyds universitetssjukhus](https://www.scilifelab.se/news/four-out-of-five-still-have-antibodies-against-sars-cov-2)), Karolinska universitetssjukhuset, Akademiska sjukhuset i Uppsala, Skånes universitetssjukhus, Universitetssjukhuset Örebro, Sophiahemmet, Folkhälsomyndigheten, RISE (Research Institutes of Sweden), AstraZeneca, Cytiva, SVPH, Karolinska Institutet, KTH, Uppsala universitet och Lunds universitet. Kolla in [Autoimmunity and Serology Profiling unit page](https://www.scilifelab.se/units/autoimmunity-profiling/) på SciLifeLabs webbplats för att få reda på mer om själva enheten. Publikationer som producerats av studier som använder enheten finns tillgängliga i databasen [SciLifeLab Infrastructure Publications](https://publications.scilifelab.se/label/Autoimmunity%20and%20Serology%20Profiling). - - - - - - - - diff --git a/content/svenska/dashboards/variants_region_uppsala.md b/content/svenska/dashboards/variants_region_uppsala.md index 920438af2..4bca00adb 100644 --- a/content/svenska/dashboards/variants_region_uppsala.md +++ b/content/svenska/dashboards/variants_region_uppsala.md @@ -79,6 +79,8 @@ Använd knappen **'Deselect all lineages'** för att rensa bort data från alla ## Publikationer +Cumlin, T., Karlsson, I., Haars, J., Rosengren, M., Lennerstrand, J., Pimushyna, M., Feuk, L., Ladenvall, C., Kaden, R. (2024). SARS-CoV-2 to Global Preparedness: A Graphical Interface for Standardised High-Throughput Bioinformatics Analysis in Pandemic Scenarios and Surveillance of Drug Resistance. _Int. J. Mol. Sci._, **25**, 6645. DOI: [10.3390/ijms25126645](https://doi.org/10.3390/ijms25126645). + Haars, J., Palanisamy, N., Wallin, F., Mölling, P., Lindh, J., Sundqvist, M., Ellström, P., Kaden, R., Lennerstrand, J. (2023). Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023. _Microorganisms_, **11**, 2417. DOI: [10.3390/microorganisms11102417](https://doi.org/10.3390/microorganisms11102417). Mannsverk, S., Bergholm, J., Palanisamy, N., Ellström, P., Kaden, R., Lindh, J., Lennerstrand, J. (2022). SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing. _Virology Journal_, **19**, 164. DOI: [10.1186/s12985-022-01896-x](https://doi.org/10.1186/s12985-022-01896-x). diff --git a/content/svenska/share-data.md b/content/svenska/share-data.md index 19e8b62af..be4e22971 100644 --- a/content/svenska/share-data.md +++ b/content/svenska/share-data.md @@ -1,11 +1,6 @@ --- title: Dela data toc: true -menu: - top_actions: - name: Dela data - weight: 40 - pre: aliases: - /sv/data_types/genomics_transcriptomics/guidelines/ - /sv/data_types/compound_and_target_data/guidelines/ diff --git a/content/svenska/support.md b/content/svenska/support.md index 55a91bd1b..f06b60e2b 100644 --- a/content/svenska/support.md +++ b/content/svenska/support.md @@ -1,11 +1,6 @@ --- title: Stödtjänster toc: false -menu: - top_actions: - name: Stödtjänster - weight: 70 - pre: aliases: - /sv/support_services/bioinformatics/ --- diff --git a/devbox.json b/devbox.json new file mode 100644 index 000000000..9f6e950bf --- /dev/null +++ b/devbox.json @@ -0,0 +1,14 @@ +{ + "$schema": "https://raw.githubusercontent.com/jetify-com/devbox/0.11.1/.schema/devbox.schema.json", + "packages": ["hugo@0.123.7"], + "shell": { + "init_hook": [ + "echo 'Welcome to devbox!' > /dev/null" + ], + "scripts": { + "server": [ + "hugo serve" + ] + } + } +} diff --git a/devbox.lock b/devbox.lock new file mode 100644 index 000000000..0a3972e7c --- /dev/null +++ b/devbox.lock @@ -0,0 +1,53 @@ +{ + "lockfile_version": "1", + "packages": { + "hugo@0.123.7": { + "last_modified": "2024-03-08T13:51:52Z", + "resolved": "github:NixOS/nixpkgs/a343533bccc62400e8a9560423486a3b6c11a23b#hugo", + "source": "devbox-search", + "version": "0.123.7", + "systems": { + "aarch64-darwin": { + "outputs": [ + { + "name": "out", + "path": "/nix/store/4sx62xs1vsx1lq0nbzf78q2b45yqvbap-hugo-0.123.7", + "default": true + } + ], + "store_path": "/nix/store/4sx62xs1vsx1lq0nbzf78q2b45yqvbap-hugo-0.123.7" + }, + "aarch64-linux": { + "outputs": [ + { + "name": "out", + "path": "/nix/store/al5gz9r61mlpdw6hb5jz1am4j3bkqkk6-hugo-0.123.7", + "default": true + } + ], + "store_path": "/nix/store/al5gz9r61mlpdw6hb5jz1am4j3bkqkk6-hugo-0.123.7" + }, + "x86_64-darwin": { + "outputs": [ + { + "name": "out", + "path": "/nix/store/xl68hgyc2n83csq8dqf7fzc1cgazikpw-hugo-0.123.7", + "default": true + } + ], + "store_path": "/nix/store/xl68hgyc2n83csq8dqf7fzc1cgazikpw-hugo-0.123.7" + }, + "x86_64-linux": { + "outputs": [ + { + "name": "out", + "path": "/nix/store/hgycj5hqslak89rdhr0q10iwnwdqqi2g-hugo-0.123.7", + "default": true + } + ], + "store_path": "/nix/store/hgycj5hqslak89rdhr0q10iwnwdqqi2g-hugo-0.123.7" + } + } + } + } +} diff --git a/layouts/index.html b/layouts/index.html index 87df43fdf..cfb34d26e 100644 --- a/layouts/index.html +++ b/layouts/index.html @@ -3,30 +3,12 @@
- - - - {{ range .Site.Menus.homepage_dashboards }}
-

{{ .Name }}

+

{{ .Name }}

@@ -48,7 +30,7 @@

{{ .Name }}

{{ range .Site.Menus.homepage_highlights }}
-

{{ .Name }}

+

{{ .Name }}

See all highlights @@ -92,7 +74,7 @@

{{ .Name }}

{{ range .Site.Menus.homepage_available_data }}
-

{{ .Name }}

+

{{ .Name }}

See all datasets @@ -133,7 +115,7 @@

{{ .Name }}

{{ range .Site.Menus.homepage_biobanks }}
-

{{ .Name }}

+

{{ .Name }}

@@ -270,6 +252,34 @@
title.target === 'pathogens-portal' && title.active); + if (title && title[lang]) { + const titleElement = document.querySelector('h2#home-banner'); + titleElement.textContent = title[lang]; + } else { + console.warn('No title found for the language.'); + } + } catch (error) { + console.error('An error occurred while updating banner titles:', error); + } finally { + // Show the hidden banner regardless of whether titles were fetched successfully + const banner1 = document.getElementById("home-banner"); + if (banner1) { + banner1.classList.remove("d-none"); + } else { + console.warn('Banner element with ID "home-banner" not found.'); + } + } + }; // function updateBanner ends here + + // Add the events fetched from blobserver function addEvents(data) { var dataArray = data.items, eventList = []; // Not interested if the deadline has already passed @@ -320,11 +330,18 @@

Events

}; } // function "addEvents" ends here - // Call the function to fetch, parse and display events + // Call the function to update banner, if any mentioned in blob server getDataFromUrl( - decodeURIComponent("https%3A%2F%2Fblobserver.dc.scilifelab.se%2Fblob%2Fpathogens_portal_events.json"), - addEvents - ); + decodeURIComponent("https%3A%2F%2Fblobserver.dc.scilifelab.se%2Fblob%2Ffreya-banner.json"), + updateBanner + ) + // For english site, Call the function to fetch, parse and display events + if (document.documentElement.lang === "en") { + getDataFromUrl( + decodeURIComponent("https%3A%2F%2Fblobserver.dc.scilifelab.se%2Fblob%2Fpathogens_portal_events.json"), + addEvents + ); + }; // Add latest tag to very recent news when content is loaded document.querySelectorAll("#news-items-container .small").forEach( @@ -338,16 +355,4 @@

Events

}); // Document "DOMContentLoaded" trigger ends here - - - - - - - - -{{ end }} \ No newline at end of file +{{ end }} diff --git a/layouts/partials/header.html b/layouts/partials/header.html index e78efc3fd..6da8d71a0 100644 --- a/layouts/partials/header.html +++ b/layouts/partials/header.html @@ -2,7 +2,8 @@ style="background-image: linear-gradient(to bottom, rgba(55, 174, 148, 0.52), rgba(55, 174, 148, 0.73)), url('{{ if .Params.header_illustration }}{{ .Params.header_illustration }}{{ else }}/img/csm_coronavirus_mc.jpg{{ end }}');">
-

{{ if .IsHome }} +

+ {{ if .IsHome }} {{ (index $.Site.Params.lang_strings .Site.Language.Lang).home_title }} {{ else if eq .Parent.Section "highlights_topics" }} {{ with .Site.GetPage "/highlights" }} @@ -18,7 +19,7 @@

{{ if .IsHome }} {{ .Parent.Title }} {{ else }} {{ .Title }} - {{ end }}

+ {{ end }}
{{ if not .IsHome }} diff --git a/layouts/partials/navbar.html b/layouts/partials/navbar.html index 8b9b1d577..678b95715 100644 --- a/layouts/partials/navbar.html +++ b/layouts/partials/navbar.html @@ -1,3 +1,20 @@ + + +{{ $page_lang := dict }} +{{ if .IsTranslated }} + {{ range .AllTranslations }} + {{ $page_lang = merge $page_lang (dict .Language.Lang .RelPermalink) }} + {{ end }} +{{ else if .Parent.IsTranslated }} + {{ $page_lang = merge $page_lang (dict "en" .RelPermalink "sv" (printf "%s%s" "/sv" .Parent.RelPermalink)) }} +{{ else if .Parent.Parent.IsTranslated }} + {{ $page_lang = merge $page_lang (dict "en" .RelPermalink "sv" (printf "%s%s" "/sv" .Parent.Parent.RelPermalink)) }} +{{ else }} + {{ $page_lang = merge $page_lang (dict "en" "/" "sv" "/sv/") }} +{{ end }} + + + -
- -
- Provsamlingsregistret + +
+ +
@@ -229,103 +219,78 @@ {{ if eq $.Site.Language.LanguageName "English" }} -
-
-
-
-
- - -
-
- -
- {{ range .Site.Menus.datasets_menu }} - {{ .Name }} - {{ end }} -
-
- Data Highlights -
-
-
-
-
- - -
- {{ range .Site.Menus.dashboard_menu }} - {{ .Name }} - {{ end }} -
-
-
-
-
- - -
- {{ range .Site.Menus.research_menu }} - {{ .Name }} - {{ end }} -
+
+
+ + +
+ +
+ Data Highlights + Editorials
-
-
-
-
- - -
- Emerging Pathogens - SciLifeLab PLP - Preparedness Resources -
-
-
-
-
- Research Data Management -
+ +
+ +
+ {{ range .Site.Menus.dashboard_menu }} + {{ .Name }} + {{ end }}
-
-
- Sample Collection Database -
+
+ +
+ +
+ Share data + Available datasets + Data dashboards + Data sources & repositories + Sample collection database + Research data management
-
-
-
- - -
- {{ range .Site.Menus.topics_menu }} - {{ .Name }} - {{ end }} -
-
+ +
+ +
+ {{ range .Site.Menus.research_menu }} + {{ .Name }} + {{ end }}
-
-
- Editorials -
+
+ +
+ +
+ Emerging Pathogens + SciLifeLab PLP + PLP Capabilities
-
-
- Events & Training -
+
+ +
+ +
+ {{ range .Site.Menus.topics_menu }} + {{ .Name }} + {{ end }}
+
{{ end }} @@ -335,8 +300,9 @@ {{ if eq $.Site.Language.LanguageName "Svenska" }}
+
- + @@ -346,8 +312,17 @@ {{ end }}
+
- Provsamlingsregistret + + +
+ Dela data + Data dashboards + Provsamlingsregistret +
diff --git a/layouts/shortcodes/data_sources.html b/layouts/shortcodes/data_sources.html new file mode 100644 index 000000000..1f924f28d --- /dev/null +++ b/layouts/shortcodes/data_sources.html @@ -0,0 +1,181 @@ +
+ +
+ + + + + + + + diff --git a/layouts/shortcodes/serology_date_modified.html b/layouts/shortcodes/serology_date_modified.html index a5555b446..921dc761f 100644 --- a/layouts/shortcodes/serology_date_modified.html +++ b/layouts/shortcodes/serology_date_modified.html @@ -6,6 +6,6 @@ document.getElementById("last_modified").innerText = String(dataset_info.modified).substring(0,10); } }; -xmlhttp.open("GET", "https://datagraphics.dc.scilifelab.se/api/dataset/6d6f551abc10413a97a6ab64ebac46bd", true); +xmlhttp.open("GET", "https://blobserver.dc.scilifelab.se/blob/Serology-testing-statistics-dataset-20202021.csv/info.json", true); xmlhttp.send(); diff --git a/static/css/styles.css b/static/css/styles.css index e0985fbaa..494c804dc 100644 --- a/static/css/styles.css +++ b/static/css/styles.css @@ -79,15 +79,21 @@ figure.float-md-end { * Adapt header logo size for smaller mobile devices */ +@media (max-width: 263px) { + .navbar .navbar-brand { + max-width: 65%; + } +} + @media (max-width: 311px) { .navbar .navbar-brand { max-width: 70%; } } -@media (max-width: 263px) { - .navbar .navbar-brand { - max-width: 65%; +@media all and (min-width: 1400px) { + .navbar .navbar-nav a.nav-link { + padding: 0.3em 0.8rem; } } @@ -96,12 +102,6 @@ figure.float-md-end { max-width: 100%; } -@media all and (min-width: 992px) { - .navbar .navbar-nav a.nav-link { - padding: 0.3em 0.8rem; - } -} - a.nav-link:hover, a.nav-link:focus, a.nav-link:active { @@ -110,7 +110,6 @@ a.nav-link:active { .nav-tabs a.nav-link, .nav-list a.nav-link { - /* color: #295986; */ color: #4770b1; font-weight: 500; } @@ -130,91 +129,72 @@ a.nav-link:active { font-weight: 600; } -@media (max-width: 991px) { - .navbar .text-vert { - display: none; - } -} - .navbar .navbar-nav.navbar-top { margin-left: 1rem; } -.navbar .navbar-nav.navbar-top li:not(:first-child) a { - padding-left: 0; +.navbar-nav li.nav-item a.nav-link { + color: rgba(0, 0, 0, 0.75) !important; } -.navbar-top li:not(:last-child) a span { - border-right: 1px solid #ccc; - padding-right: 1rem; +.navbar-nav.navbar-top li.nav-item a.nav-link:hover { + color: rgba(0, 0, 0, 0.85) !important; + text-decoration: underline; + text-decoration-color: rgba(0, 0, 0, 0.85); + text-decoration-thickness: 1px; + text-underline-offset: 6px; } -.navbar-top a img { - width: 1.1rem; - opacity: 0.3; -} -.nav-languages a img { - width: 1.1rem; - opacity: 0.5; - margin-left: 0.1rem; - margin-bottom: 0.1rem; +.navbar-top li.dropdown a.nav-link { + padding-right: 0; } -.nav-languages li:not(:last-child) a span { - border-right: 1px solid #ccc; - padding-right: 1rem; +.nav-languages li a { + text-decoration: none; } -.nav-languages li:not(:first-child) a { - padding-left: 1rem; +.languages-mobile a { + text-decoration: none; + color: rgba(0, 0, 0, 0.75) } -.navbar-top a:hover img, -.navbar-top a:focus img, -.navbar-top a:active img, -.nav-languages a:hover img, -.nav-languages a:focus img, -.nav-languages a:active img { - opacity: 1; +.dropdown-menu.nav-languages { + min-width: 1rem; + border-radius: 2px; + padding: 4px 0px; + margin-top: 0; } -.navbar .navbar-nav a.nav-link.highlight { - border: 1px solid rgba(71, 112, 177, 0.9); - color: rgba(71, 112, 177, 0.9); - padding: 0.3rem 1rem; - margin: 0.5rem 0; - border-radius: 2px; - margin-left: 0.2em; - text-align: center; +.dropdown-menu.nav-languages a.dropdown-item { + padding: 2px 10px; + font-size: 0.9rem; } -.navbar .navbar-nav a.nav-link.highlight:hover, -.navbar .navbar-nav a.nav-link.highlight:focus, -.navbar .navbar-nav a.nav-link.highlight:active { - background-color: #d4de27; - border-color: #d4de27; - color: #1a1c1a; + +.dropdown-menu.nav-languages a.dropdown-item:active { + background-color: rgba(216, 216, 216, 0.5); + color: rgba(0, 0, 0, 0.75); } .main_menu_item { - color: rgba(71, 112, 177, 0.9); + color: rgba(41, 89, 134, 0.85); font-weight: 500; - font-size: 1.25em; + font-size: 1.07em; } .main_menu_item a { - color: rgba(71, 112, 177, 0.9); + color: rgba(41, 89, 134, 0.85); text-decoration: none; } .main_menu_item_sub a { font-weight: 500; - color: rgba(71, 112, 177, 0.9); + color: rgba(41, 89, 134, 0.85); text-align: left; vertical-align: middle; background-color: transparent; border: 1px solid transparent; margin: 0.2rem 0.1rem; - font-size: 1rem; + font-size: 0.95rem; white-space: nowrap; padding-right: 0.5rem; text-decoration: none; @@ -236,8 +216,7 @@ a.nav-link:active { .main_menu_item_sub a:hover, .main_menu_item_sub a:focus, .main_menu_item_sub a:active { - /* color: rgba(41, 89, 134, 1); */ - color: rgba(71, 112, 177, 1); + color: rgba(41, 89, 134, 1); } .main_menu_item_sub_dropdown a { @@ -266,7 +245,7 @@ a.nav-link:active { background-position: center; background-repeat: no-repeat; background-size: cover; - padding: 1.5rem 0; + padding: 1.1rem 0; } .breadcrumbs { @@ -330,27 +309,6 @@ footer img { border: solid 1px #295986; } -/* - -This no longer an issue, commenting out on 2023-01-28, -this commented section can be removed after a month or two - -There is a bug in Safari whereby it stretches an image nested -in a flexbox element to its natural height. I use the class below -for rows with images to fix that. - -.row_cor { - display: -ms-flexbox; - display: flex; - align-items: flex-start !important; - -ms-flex-wrap: wrap; - flex-wrap: wrap; - margin-right: -15px; - margin-left: -15px ; -} - -*/ - #dwbuttons .collapsed { background-color: white !important; color: #5a626a !important;