diff --git a/data/services.json b/data/services.json index 56ad183..7b21ac4 100644 --- a/data/services.json +++ b/data/services.json @@ -17,6 +17,64 @@ "maintained_by": "AI4Life BioImage Model Zoo team", "support_website": "https://oeway.typeform.com/to/K3j2tJt7?typeform-source=bioimage.io" }, + { + "target": [ + "researchers" + ], + "type": [ + "portal", + "helpdesk" + ], + "search_tags": [ + "Pathogens portal", + "infectious disease data", + "Swedish Pathogens Portal", + "Pandemic preparedness portal", + "COVID-19", + "SciLifeLab", + "Data Centre", + "Tool" + ], + "name": "Swedish Pathogens Portal", + "description": "Facilitates the sharing and promotion of pandemic preparedness and infectious disease data", + "thumbnail": "/img/service_thumbnails/pathogens.png", + "url": "https://pathogens.se/", + "maintained_by": "SciLifeLab Data Centre", + "maintained_by_url": "https://scilifelab.se/data", + "thumbnail_border": true, + "support_email": "pathogens@scilifelab.se", + "support_github": "https://github.com/ScilifelabDataCentre/covid-portal/tree/develop", + "support_status": "https://status.dc.scilifelab.se/793602036" + }, + { + "target": [ + "researchers" + ], + "type": [ + "portal", + "helpdesk" + ], + "search_tags": [ + "RDM", + "Research data management", + "Guidelines", + "Helpdesk", + "Portal", + "NBIS", + "SciLifeLab", + "Data Centre", + "SciLifeLab RDM Guidelines" + ], + "name": "SciLifeLab RDM Guidelines", + "description": "A portal containing information on research data management in Sweden", + "thumbnail": "/img/service_thumbnails/rdm.jpg", + "url": "https://data-guidelines.scilifelab.se", + "maintained_by": "NBIS, SciLifeLab Data Centre", + "support_email": "data-management@scilifelab.se", + "support_website": "https://data-guidelines.scilifelab.se/contact/", + "support_github": "https://github.com/ScilifelabDataCentre/RDM-guidelines", + "support_status": "https://status.dc.scilifelab.se/793602117" + }, { "target": [ "researchers" @@ -45,7 +103,8 @@ "maintained_by": "SciLifeLab Data Centre", "maintained_by_url": "https://scilifelab.se/data", "support_email": "serve@scilifelab.se", - "support_website": "https://serve.scilifelab.se/user_guide" + "support_website": "https://serve.scilifelab.se/user_guide", + "support_status": "https://status.dc.scilifelab.se/795925203" }, { "target": [ @@ -97,62 +156,6 @@ "support_email": "figshare@scilifelab.se", "support_website": "https://scilifelab.se/data/repository" }, - { - "target": [ - "researchers" - ], - "type": [ - "portal" - ], - "search_tags": [ - "Pathogens portal", - "infectious disease data", - "Swedish Pathogens Portal", - "Pandemic preparedness portal", - "COVID-19", - "SciLifeLab", - "Data Centre", - "Tool" - ], - "name": "Swedish Pathogens Portal", - "description": "Facilitates the sharing and promotion of pandemic preparedness and infectious disease data", - "thumbnail": "/img/service_thumbnails/portal.jpg", - "url": "https://pathogens.se/", - "maintained_by": "SciLifeLab Data Centre", - "maintained_by_url": "https://scilifelab.se/data", - "support_email": "pathogens@scilifelab.se", - "support_github": "https://github.com/ScilifelabDataCentre/covid-portal/tree/develop", - "support_status": "https://status.dc.scilifelab.se/793602036" - }, - { - "target": [ - "researchers" - ], - "type": [ - "portal", - "helpdesk" - ], - "search_tags": [ - "RDM", - "Research data management", - "Guidelines", - "Helpdesk", - "Portal", - "NBIS", - "SciLifeLab", - "Data Centre", - "SciLifeLab RDM Guidelines" - ], - "name": "SciLifeLab RDM Guidelines", - "description": "A portal containing information on research data management in Sweden", - "thumbnail": "/img/service_thumbnails/rdm.jpg", - "url": "https://data-guidelines.scilifelab.se", - "maintained_by": "NBIS, SciLifeLab Data Centre", - "support_email": "data-management@scilifelab.se", - "support_website": "https://data-guidelines.scilifelab.se/contact/", - "support_github": "https://github.com/ScilifelabDataCentre/RDM-guidelines", - "support_status": "https://status.dc.scilifelab.se/793602117" - }, { "target": [ "researchers" @@ -455,7 +458,7 @@ ], "type": [ "tool", - "community" + "Workflow" ], "search_tags": [ "nf-core", @@ -558,7 +561,184 @@ "url": "https://github.com/Clinical-Genomics/chanjo", "maintained_by": "Clinical Genomics Stockholm", "maintained_by_url": "https://www.scilifelab.se/units/clinical-genomics-stockholm/", - "support_github": "https://github.com/Clinical-Genomics/chanjo" + "support_github": "https://github.com/Clinical-Genomics/chanjo", + "support_website": "https://clinical-genomics.github.io/chanjo/" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool" + ], + "search_tags": [ + "Scout", + "clinical genomics", + "patient data", + "variants", + "cases", + "tumour", + "tumor", + "load frequency database", + "gene", + "genes", + "gene pannels", + "VCF files", + "variant call format", + "rare disease", + "aggregate", + "aggregation" + ], + "name": "Scout", + "description": "A visualiser for variant call format (VCF) files. It helps to manage multiple patient cases in an single, user-friendly interface, and enables collaboration between groups.", + "thumbnail": "/img/service_thumbnails/scout.png", + "thumbnail_border": true, + "url": "https://github.com/Clinical-Genomics/scout", + "maintained_by": "Clinical Genomics Stockholm", + "maintained_by_url": "https://www.scilifelab.se/units/clinical-genomics-stockholm/", + "support_github": "https://github.com/Clinical-Genomics/scout?tab=readme-ov-file", + "support_website": "https://clinical-genomics.github.io/scout/" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool" + ], + "search_tags": [ + "LoqusDB", + "variant", + "local variant database", + "genes", + "mongodb", + "variant database", + "VCF file", + "variant call format", + "variant families", + "ped family", + "ped-like family", + "observations database", + "local genomic variation", + "genomic variation", + "variation", + "sequencing", + "clinical genomics" + ], + "name": "LoqusDB", + "description": "A tool to keep track of variant observations from genome sequencing data. Handles a large flow of samples, and samples can be added continuously.", + "thumbnail": "/img/service_thumbnails/clinical_gen_sthlm.png", + "thumbnail_border": true, + "url": "https://github.com/Clinical-Genomics/loqusdb", + "maintained_by": "Clinical Genomics Stockholm", + "maintained_by_url": "https://www.scilifelab.se/units/clinical-genomics-stockholm/", + "support_github": "https://github.com/Clinical-Genomics/loqusdb" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool", + "Workflow" + ], + "search_tags": [ + "nf-core", + "nf-core/rnafusion", + "rnafusion", + "bioinformatic pipeline", + "RNA sequencing", + "detect fusion genes", + "visualise fusion genes", + "fusion genes", + "visualize fusion genes", + "AWS", + "RNA-seq", + "RNA", + "RNA-sequencing", + "gene-fusions" + ], + "name": "nf-core/rnafusion", + "description": "nf-core/rnafusion is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes", + "thumbnail": "/img/service_thumbnails/nf-core-rnafusion.png", + "thumbnail_border": true, + "url": "https://github.com/nf-core/rnafusion", + "maintained_by": "nf-core community", + "maintained_by_url": "https://nf-co.re/contributors", + "support_github": "https://github.com/nf-core/rnafusion", + "support_website": "https://nf-co.re/rnafusion" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool", + "Workflow" + ], + "search_tags": [ + "nf-core", + "nf-core/raredisease", + "rare disease", + "bioinformatic pipelines", + "call variants", + "score variants", + "nextflow", + "WGS", + "whole genome sequencing", + "whole-genome sequencing", + "whole exome sequencing", + "WES", + "whole-exome sequencing", + "raredisease", + "AWS", + "variants" + ], + "name": "nf-core/raredisease", + "description": "nf-core/raredisease is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients.", + "thumbnail": "/img/service_thumbnails/nf-core-raredisease.png", + "thumbnail_border": true, + "url": "https://github.com/nf-core/raredisease", + "maintained_by": "nf-core community", + "maintained_by_url": "https://nf-co.re/contributors", + "support_github": "https://github.com/nf-core/raredisease", + "support_website": "https://nf-co.re/raredisease/" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool", + "Workflow" + ], + "search_tags": [ + "amplicon-multi-cutadapt", + "SBDI", + "gbif", + "preprocessing", + "amplicon sequencing", + "sequencing", + "global biodiversity information facility", + "Swedish biodiversity data infrastructure", + "biodiversity", + "conservation", + "cutadapt", + "snakemake", + "fastq", + "paired-end fastq", + "NBIS", + "National bioinformatics infrastructure sweden", + "Swedish Museum of Natural History" + ], + "name": "Amplicon-multi-cutadapt", + "description": "A snakemake workflow for trimming and quality control of pair-ended FASTQ files", + "thumbnail": "/img/service_thumbnails/sbdi.png", + "thumbnail_border": true, + "url": "https://github.com/biodiversitydata-se/amplicon-multi-cutadapt", + "maintained_by": "Swedish Biodiversity Data Infrastructure", + "maintained_by_url": "https://biodiversitydata.se", + "support_github": "https://github.com/biodiversitydata-se/amplicon-multi-cutadapt" }, { "target": [ @@ -567,6 +747,198 @@ "type": [ "tool" ], + "search_tags": [ + "coidb", + "SBDI", + "gbif", + "metabarcoding", + "sequence", + "downstream metabarcoding", + "global biodiversity information facility", + "Swedish biodiversity data infrastructure", + "biodiversity", + "conservation", + "metadata", + "format sequences", + "NBIS", + "National bioinformatics infrastructure sweden", + "Swedish Museum of Natural History" + ], + "name": "CoiDB", + "description": "A tool that downloads sequences and metadata from GBIF and formats sequences for use with downstream metabarcoding analyses.", + "thumbnail": "/img/service_thumbnails/sbdi.png", + "thumbnail_border": true, + "url": "https://github.com/biodiversitydata-se/coidb", + "maintained_by": "Swedish Biodiversity Data Infrastructure", + "maintained_by_url": "https://biodiversitydata.se", + "support_github": "https://github.com/biodiversitydata-se/coidb" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool", + "Workflow" + ], + "search_tags": [ + "BALSAMIC", + "bioinformatics", + "pipeline", + "bioinformatics pipeline", + "somatic", + "somatic mutations", + "cancer", + "clinical genomics", + "FASTQ", + "VCF file", + "VCF files", + "variant call format", + "variants", + "workflow manager", + "annotated VCF" + ], + "name": "BALSAMIC", + "description": "A bioinformatics analysis pipeline for somatic mutations in cancer.", + "thumbnail": "/img/service_thumbnails/balsamic_logo.png", + "thumbnail_border": true, + "url": "https://github.com/Clinical-Genomics/BALSAMIC", + "maintained_by": "Clinical Genomics Stockholm", + "maintained_by_url": "https://www.scilifelab.se/units/clinical-genomics-stockholm/", + "support_github": "https://github.com/Clinical-Genomics/BALSAMIC", + "support_website": "https://balsamic.readthedocs.io/en/latest/" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool", + "Workflow" + ], + "search_tags": [ + "tomte", + "GMS", + "genomic medicine sweden", + "bioinformatic pipeline", + "RNAseq", + "RNA-seq", + "RNA sequencing", + "rare disease", + "disease", + "nextflow", + "clinical genomics" + ], + "name": "Tomte", + "description": "A bioinformatics best-practice analysis pipeline to analyse RNAseq from rare disease patients.", + "thumbnail": "/img/service_thumbnails/tomte_logo.png", + "thumbnail_border": true, + "url": "https://github.com/genomic-medicine-sweden/tomte", + "maintained_by": "Clinical Genomics Stockholm", + "maintained_by_url": "https://www.scilifelab.se/units/clinical-genomics-stockholm/", + "support_github": "https://github.com/genomic-medicine-sweden/tomte" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool" + ], + "search_tags": [ + "preClinVar", + "clinvar", + "Clinvar submissions", + "genes", + "API", + "clinvar API", + "variation", + "human health", + "health", + "gene", + "genetic", + "genomic", + "genomic variation", + "FastAPI", + "clinical genomics" + ], + "name": "PreClinVar", + "description": "A tool to help to transform files in preparation for submission via the ClinVar API.", + "thumbnail": "/img/service_thumbnails/clinical_gen_sthlm.png", + "thumbnail_border": true, + "url": "https://github.com/Clinical-Genomics/preClinVar", + "maintained_by": "Clinical Genomics Stockholm", + "maintained_by_url": "https://www.scilifelab.se/units/clinical-genomics-stockholm/", + "support_github": "https://github.com/Clinical-Genomics/preClinVar" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool" + ], + "search_tags": [ + "Schug", + "clinical genomics", + "clinical", + "genes", + "transcripts", + "exons", + "REST API", + "ensembl" + ], + "name": "Schug", + "description": "A service that gathers data about genes, transcripts, and exons from multiple sources and merge the information.", + "thumbnail": "/img/service_thumbnails/clinical_gen_sthlm.png", + "thumbnail_border": true, + "url": "https://github.com/Clinical-Genomics/schug", + "maintained_by": "Clinical Genomics Stockholm", + "maintained_by_url": "https://www.scilifelab.se/units/clinical-genomics-stockholm/", + "support_github": "https://github.com/Clinical-Genomics/schug" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool" + ], + "search_tags": [ + "clinical", + "sequencing", + "coverage data", + "chanjo2", + "clinical genomics", + "clinical sequencing", + "Tool", + "d4 format", + "Dense Depth Data Dump format", + "Python", + "genes", + "transcripts", + "exons", + "genomic intervals", + "REST server" + ], + "name": "Chanjo2", + "description": "Chanjo2 is coverage analysis tool for human clinical sequencing data using the d4 (Dense Depth Data Dump) format.", + "thumbnail": "/img/service_thumbnails/clinical_gen_sthlm.png", + "thumbnail_border": true, + "url": "https://github.com/Clinical-Genomics/chanjo2", + "maintained_by": "Clinical Genomics Stockholm", + "maintained_by_url": "https://www.scilifelab.se/units/clinical-genomics-stockholm/", + "support_github": "https://github.com/Clinical-Genomics/chanjo2", + "support_website": "https://clinical-genomics.github.io/chanjo2/" + }, + { + "target": [ + "researchers" + ], + "type": [ + "tool", + "Workflow" + ], "search_tags": [ "pipeline", "germline", diff --git a/layouts/index.html b/layouts/index.html index 8e2c286..7527f19 100644 --- a/layouts/index.html +++ b/layouts/index.html @@ -197,6 +197,39 @@

Apps recently deployed on SciLifeLab Serve

}; req.send(null); } + + // Update banner title for homepage from the blobserver + function updateBanner(data) { + try { + // Get the current language + const lang = document.documentElement.lang; + + // Find the active title for the 'portal' target + const title = data.banner_titles.find(title => title.target === 'data-platform' && 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 + + // Call the function to update banner, if any mentioned in blob server + getDataFromUrl( + decodeURIComponent("https%3A%2F%2Fblobserver.dc.scilifelab.se%2Fblob%2Ffreya-banner.json"), + updateBanner + ) // Creates html entry for latest events function addEvents(data){ diff --git a/layouts/partials/head.html b/layouts/partials/head.html index 8facccd..6c8ef17 100644 --- a/layouts/partials/head.html +++ b/layouts/partials/head.html @@ -22,6 +22,8 @@ + + {{ $recaptcha_pages := slice "contact" "events" "highlights" "jobs" "funding_calls" }} diff --git a/layouts/partials/header.html b/layouts/partials/header.html index 4aac240..fb611de 100644 --- a/layouts/partials/header.html +++ b/layouts/partials/header.html @@ -3,7 +3,9 @@
-

+

+ +

diff --git a/static/img/service_thumbnails/balsamic_logo.png b/static/img/service_thumbnails/balsamic_logo.png new file mode 100644 index 0000000..9e25bf8 Binary files /dev/null and b/static/img/service_thumbnails/balsamic_logo.png differ diff --git a/static/img/service_thumbnails/clinical_gen_sthlm.png b/static/img/service_thumbnails/clinical_gen_sthlm.png new file mode 100644 index 0000000..f20795f Binary files /dev/null and b/static/img/service_thumbnails/clinical_gen_sthlm.png differ diff --git a/static/img/service_thumbnails/nf-core-raredisease.png b/static/img/service_thumbnails/nf-core-raredisease.png new file mode 100644 index 0000000..16b063f Binary files /dev/null and b/static/img/service_thumbnails/nf-core-raredisease.png differ diff --git a/static/img/service_thumbnails/nf-core-rnafusion.png b/static/img/service_thumbnails/nf-core-rnafusion.png new file mode 100644 index 0000000..8283993 Binary files /dev/null and b/static/img/service_thumbnails/nf-core-rnafusion.png differ diff --git a/static/img/service_thumbnails/pathogens.png b/static/img/service_thumbnails/pathogens.png new file mode 100644 index 0000000..4543aed Binary files /dev/null and b/static/img/service_thumbnails/pathogens.png differ diff --git a/static/img/service_thumbnails/portal.jpg b/static/img/service_thumbnails/portal.jpg deleted file mode 100644 index 220615f..0000000 Binary files a/static/img/service_thumbnails/portal.jpg and /dev/null differ diff --git a/static/img/service_thumbnails/sbdi.png b/static/img/service_thumbnails/sbdi.png new file mode 100644 index 0000000..e523391 Binary files /dev/null and b/static/img/service_thumbnails/sbdi.png differ diff --git a/static/img/service_thumbnails/scout.png b/static/img/service_thumbnails/scout.png new file mode 100644 index 0000000..7b53724 Binary files /dev/null and b/static/img/service_thumbnails/scout.png differ diff --git a/static/img/service_thumbnails/tomte_logo.png b/static/img/service_thumbnails/tomte_logo.png new file mode 100644 index 0000000..8389f7f Binary files /dev/null and b/static/img/service_thumbnails/tomte_logo.png differ diff --git a/static/js/notices.js b/static/js/notices.js new file mode 100644 index 0000000..29d8113 --- /dev/null +++ b/static/js/notices.js @@ -0,0 +1,78 @@ +document.addEventListener("DOMContentLoaded", function() { + const noticesUrl = "https://blobserver.dc.scilifelab.se/blob/freya-notices.json"; + const currentSite = "data-platform"; // Change this to dynamically detect the current site if needed. + + fetch(noticesUrl) + .then(response => { + if (!response.ok) { + throw new Error(`HTTP error! status: ${response.status}`); + } + return response.json(); + }) + .then(data => { + const currentDate = new Date(); + if (!data.notices || !Array.isArray(data.notices)) { + throw new Error("Invalid notices data"); + } + + data.notices.forEach(notice => { + try { + let shouldDisplay = false; + + if (!notice.target || !Array.isArray(notice.target) || !notice.target.includes(currentSite)) { + return; // Skip this notice if the target does not include the current site. + } + + if (notice.type === "scheduled") { + const startDate = new Date(notice.start_date); + const endDate = new Date(notice.end_date); + if (currentDate >= startDate && currentDate <= endDate) { + shouldDisplay = true; + } + + // Format dates to a readable format (e.g., '20th December') + const formattedStartDate = startDate.toLocaleDateString('en-US', { day: 'numeric', month: 'long' }); + const formattedEndDate = endDate.toLocaleDateString('en-US', { day: 'numeric', month: 'long' }); + + // Replace placeholders in the messages + notice.message_en = notice.message_en.replace('{{start_date}}', formattedStartDate).replace('{{end_date}}', formattedEndDate); + notice.message_sv = notice.message_sv.replace('{{start_date}}', formattedStartDate).replace('{{end_date}}', formattedEndDate); + } else if (notice.type === "incidental" && notice.active) { + shouldDisplay = true; + } + + if (shouldDisplay) { + const noticeContainer = document.createElement('div'); + noticeContainer.className = 'notice alert d-flex justify-content-center align-items-center rounded-0'; // Use Bootstrap classes + + // Check if style property is provided and not empty, otherwise use default styles + let style = notice.style; + if (!style || style.trim() === "") { + style = notice.type === "scheduled" + ? "background-color: #a7c947; color: #000000;" + : "background-color: #ffc107; color: #000000;"; + } + noticeContainer.style = `${style}; margin-top: 15px; text-align: center;`; // Add top margin and center text + + const siteLanguage = document.documentElement.lang; + let message = notice.message_en; + if (siteLanguage === "sv") { + message = notice.message_sv; + } + + const noticeMessage = document.createElement('div'); + noticeMessage.innerHTML = ` ${notice.title}: ${message}`; + noticeMessage.className = "alert-body"; // Use Bootstrap class for alert body + + noticeContainer.appendChild(noticeMessage); + + // Insert the notice at the top of the body + document.body.insertBefore(noticeContainer, document.body.firstChild); + } + } catch (error) { + console.error('Error processing notice:', error); + } + }); + }) + .catch(error => console.error('Error fetching notices:', error)); +});