From 0dae8399f28ca36bc422e90251837cbc5a3fdad5 Mon Sep 17 00:00:00 2001 From: Abdullah Aziz Date: Tue, 20 Aug 2024 17:09:18 +0200 Subject: [PATCH 1/5] Adding serology multidisease data dynamically --- .../dashboards/multidisease_serology.md | 699 ++++-------------- 1 file changed, 127 insertions(+), 572 deletions(-) diff --git a/content/english/dashboards/multidisease_serology.md b/content/english/dashboards/multidisease_serology.md index 74ed37d2..bc947eab 100644 --- a/content/english/dashboards/multidisease_serology.md +++ b/content/english/dashboards/multidisease_serology.md @@ -42,327 +42,20 @@ Proteins designed, expressed, purified, and characterised at the [KTH node of Pr
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Virus TypeVariantProteinDetailsHost
SARS-CoV-2Wildtype virusSpikeSpike, 9 different variantsHEK/CHO
SARS-CoV-2Wildtype virusSpikeSpike RBD, 5 different variantsE. coli/HEK/CHO
SARS-CoV-2Wildtype virusSpikeSpike S1, 14 different variantsE. coli/HEK/CHO
SARS-CoV-2Wildtype virusSpikeSpike S2, 4 different variantsE. coli
SARS-CoV-2Wildtype virusNucleocapsid6 different variantsE. coli/HEK/CHO
SARS-CoV-2Wildtype virusEnvelop2 different variantsE. coli
SARS-CoV-2Wildtype virusMembrane1 variantE. coli
SARS-CoV-2Wildtype virusRNA Polymerase1 variantE. coli
SARS-CoV-2Wildtype virusNon-structural proteins (NSP)24 different variantsE. coli
SARS-CoV-2Wildtype virusORF proteins19 different variantsE. coli
SARS-CoV-2Alpha (B.1.1.7)SpikeMutation only in the RBD-regionHEK
SARS-CoV-2Beta (B.1.351)SpikeMutation only in the RBD-regionHEK
SARS-CoV-2Gamma (P.1)SpikeMutation only in the RBD-regionHEK
SARS-CoV-2Delta (B.1.617.2)SpikeMutation only in the RBD-regionHEK
SARS-CoV-2Delta plus (B.1.617.2.1)SpikeMutation only in the RBD-regionHEK
SARS-CoV-2Eta (B.1.525)SpikeMutation only in the RBD-regionHEK
SARS-CoV-2Kappa (B.1.617.1)SpikeMutation only in the RBD-regionHEK
SARS-CoV-2Omicron BA.1SpikeComplete set of mutationsHEK
SARS-CoV-2Omicron BA.2SpikeComplete set of mutationsHEK
SARS-CoV-2Omicron BA.5SpikeComplete set of mutationsHEK
SARS-CoV-2SpikeHEK
MERS-CoVSpikeHEK
Common human coronaviruses229ESpikeHEK
Common human coronavirusesHKU1SpikeHEK
Common human coronavirusesNL63SpikeHEK
Common human coronavirusesOC43SpikeCHO
Influenza virusA/H1N1/Wisconsin/588/2019HemagglutininHEK
Influenza virusA/H1N1/Wisconsin/588/2019NeuraminidaseCHO
Influenza virusA/H3N2/Cambodia/e0826360/2020HemagglutininHEK
Influenza virusA/H3N2/Cambodia/e0826360/2020NeuraminidaseHEK
Influenza virusB/Victoria/Washington/02/2019HemagglutininHEK
Influenza virusB/Victoria/Washington/02/2019NeuraminidaseHEK
Respiratory Syncytial Virus (RSV)A/A2GlycoproteinHEK
Respiratory Syncytial Virus (RSV)B/18537Fusion proteinCHO
Respiratory Syncytial Virus (RSV)B/18537GlycoproteinCHO
AdenovirusHAdV-B7Fiber proteinHEK
ParainfluenzaHPIV-1 strain C39Fusion Protein
ParainfluenzaHPIV-1 strain Washington/1957Hemagglutinin-neuraminidase
MetapneumovirusHMPV-A strain CAN97-83Fusion Protein
MetapneumovirusHMPV-A strain CAN97-83GlycoproteinHEK
MpoxA29LHEK
MpoxA30LHEK
MpoxE8LHEK
MpoxH3LHEK
+ + + + + + + + + + + + + +
Virus TypeVariantProteinDetailsHost
## Ongoing work and collaborations @@ -376,257 +69,20 @@ The multi-disease serological assay is under constant development and will gradu ### Externally produced antigens
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Virus TypeVariantProteinDetailsHost
Bordetella PertussisFilamentous haemagglutinin
Bordetella PertussisPertussis toxinNative
Bordetella PertussisMembrane protein PertactinE. coli
Bordetella PertussisStrain Tomaha IFilamentous haemagglutininNative
Bordetella PertussisStrain Tomaha INative protein, whole cell
Clostridium TetanisTetanus toxinHeavy chain fragment C
Clostridium TetanisTetanus toxoidNative
Corynebacterium DiphteriaDiphtheria toxinMutated G52E, native full length
Corynebacterium DiphteriaStrain NCTC 10648
CytomegalovirusGlycoprotein BHEK
Epstein Barr VirusGlycoprotein 125HEK
Hepatitis VirusHBVSurface antigen, subtype adwP. pastoris
Human Papillomavirus (HPV)Type 16Capsid protein L1Full lengthYeast
Human Papillomavirus (HPV)Type 18Capsid protein L1Full lengthS. cerevisae
Human Papillomavirus (HPV)Type 6Capsid protein L1E. coli
Human Papillomavirus (HPV)Type 33Capsid protein L1E. coli
Measles VirusNucleoproteinHEK
Measles VirusStrain EdmonstonNativeVero cells
Mumps VirusNucleoproteinE. coli
Mumps VirusStrain Jeryl-LynnNucleoproteinFull lengthHEK
Mumps VirusNucleoprotein
Mumps VirusStrain EndersNativeBSC-1 cells
PoliovirusType 1, Strain SabinCapsid proteinE. coli
PoliovirusType 2Capsid protein VP3-VP1E. coli
PoliovirusType 3Capsid protein VP3-VP1E. coli
Respiratory Syncytial Virus (RSV)RSVAGlycoprotein GHEK
RotavirusStrain Rotavirus A/RVA/Vaccine/USA/Rotarix-AROLA490AB/1988/G1P1AGlycoprotein VP7HEK
RotavirusStrain SA-11MA 104 cells
Rubella VirusGrade 4 antigen
Rubella VirusStrain F-TherienNucleoproteinHEK
Rubella VirusGlycoprotein E1E. coli
Rubella VirusStrain F-TherienSpike glycoprotein E1HEK
Rubella VirusStrain HPV-77Spike glycoprotein E1 & E2Rubella VaccineInsect cells
Streptococcus PneumoniaeCell wall polysaccharide antigenNative
+ + + + + + + + + + + + + +
PathogenVariantProteinDetailsHost
+ + + From 44492eb72e8055af3312eb1bef74a57ce34feb5e Mon Sep 17 00:00:00 2001 From: Abdullah Aziz Date: Wed, 21 Aug 2024 21:45:52 +0200 Subject: [PATCH 2/5] Fixing error messages and keeping consistency --- .../dashboards/multidisease_serology.md | 70 ++++++------------- 1 file changed, 20 insertions(+), 50 deletions(-) diff --git a/content/english/dashboards/multidisease_serology.md b/content/english/dashboards/multidisease_serology.md index bc947eab..9515e07c 100644 --- a/content/english/dashboards/multidisease_serology.md +++ b/content/english/dashboards/multidisease_serology.md @@ -42,7 +42,7 @@ Proteins designed, expressed, purified, and characterised at the [KTH node of Pr
- +
@@ -53,7 +53,7 @@ Proteins designed, expressed, purified, and characterised at the [KTH node of Pr - +
Virus Type
@@ -69,7 +69,7 @@ The multi-disease serological assay is under constant development and will gradu ### Externally produced antigens
- +
@@ -80,42 +80,11 @@ The multi-disease serological assay is under constant development and will gradu - +
Pathogen
- - - - - - + + + + + From c1466bdcea71eb3741ae8689bc5cfc73bd87c290 Mon Sep 17 00:00:00 2001 From: Senthilkumar Panneerselvam Date: Thu, 22 Aug 2024 08:54:33 +0200 Subject: [PATCH 3/5] Fill header dynamically --- .../dashboards/multidisease_serology.md | 29 +++++++++---------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/content/english/dashboards/multidisease_serology.md b/content/english/dashboards/multidisease_serology.md index 9515e07c..fdd48a27 100644 --- a/content/english/dashboards/multidisease_serology.md +++ b/content/english/dashboards/multidisease_serology.md @@ -44,13 +44,7 @@ Proteins designed, expressed, purified, and characterised at the [KTH node of Pr
- - - - - - - + @@ -71,13 +65,7 @@ The multi-disease serological assay is under constant development and will gradu
Virus TypeVariantProteinDetailsHost
- - - - - - - + @@ -172,12 +160,23 @@ The multi-disease serological assay is under constant development and will gradu // Fetch and populate data for both tables when the page loads window.onload = function() { tables.forEach(table => { + // Populate table header + const tableHead = document.getElementById(table.tableId).querySelector('thead'); + tableHead.innerHTML = ''; // Clear any existing content + const tr = document.createElement('tr'); + table.headers.forEach(header => { + const th = document.createElement('th'); + th.textContent = header; + tr.appendChild(th); + }); + tableHead.appendChild(tr); + + // Fetch data and populate table content fetchAndPopulateTable(table.url, table.tableId, table.headers); }); }; - From 966e7571c65b1b16a157dad96d436e2678c399ee Mon Sep 17 00:00:00 2001 From: Abdullah Aziz Date: Fri, 23 Aug 2024 11:45:01 +0200 Subject: [PATCH 5/5] Fixed URLs and improved Date handling --- .../dashboards/multidisease_serology.md | 44 ++++++++++--------- 1 file changed, 24 insertions(+), 20 deletions(-) diff --git a/content/english/dashboards/multidisease_serology.md b/content/english/dashboards/multidisease_serology.md index 58cdbd98..b4545db3 100644 --- a/content/english/dashboards/multidisease_serology.md +++ b/content/english/dashboards/multidisease_serology.md @@ -147,43 +147,47 @@ The multi-disease serological assay is under constant development and will gradu // URLs and headers for the two tables const tables = [ { - url: "https://blobserver.dc.scilifelab.se/blob/KTH-produced-antigens%20240418.xlsx", + url: "https://blobserver.dc.scilifelab.se/blob/KTH-produced-antigens.xlsx", + infoUrl: "https://blobserver.dc.scilifelab.se/blob/KTH-produced-antigens.xlsx/info.json", tableId: "table1", headers: ['Virus type', 'Variant', 'Protein', 'Details', 'Host'] }, { url: "https://blobserver.dc.scilifelab.se/blob/External-PLP-proteinlist.xlsx", + infoUrl: "https://blobserver.dc.scilifelab.se/blob/External-PLP-proteinlist.xlsx/info.json", tableId: "table2", headers: ['Pathogen', 'Variant', 'Protein', 'Details', 'Host'] } ]; - async function fetchLastModifiedDates() { - const jsonUrls = [ - "https://blobserver.dc.scilifelab.se/blob/External-PLP-proteinlist.xlsx/info.json", - "https://blobserver.dc.scilifelab.se/blob/KTH-produced-antigens%20240418.xlsx/info.json" - ]; + async function fetchLastModifiedDates() { - try { - const datePromises = jsonUrls.map(async (url) => { - const response = await fetch(url); + const dates = []; + + for (const {infoUrl} of tables) { + try { + const response = await fetch(infoUrl); if (!response.ok) { - throw new Error("Failed to fetch last modified date."); + console.warn(`Failed to fetch JSON from ${infoUrl}`); + continue; // Skip to the next URL if fetch fails } const data = await response.json(); - return new Date(data.modified); - }); - - const dates = await Promise.all(datePromises); - const latestDate = new Date(Math.max.apply(null, dates)); - + dates.push(new Date(data.modified)); + } catch (error) { + console.warn(`Error fetching or parsing JSON from ${infoUrl}:`, error.message); + continue; // Skip to the next URL on error + } + } + + if (dates.length === 0) { + // If no dates were successfully fetched, show an error message + document.getElementById('last-updated').innerText = 'All data last updated: Unable to retrieve date'; + } else { + // Get the latest date from the successfully fetched dates + const latestDate = new Date(Math.max(...dates)); // Format date as YYYY-MM-DD const formattedDate = latestDate.toISOString().split('T')[0]; - document.getElementById('last-updated').innerText = `All data last updated: ${formattedDate}`; - } catch (error) { - console.error('Error fetching last modified dates:', error.message); - document.getElementById('last-updated').innerText = 'All data last updated: Unable to retrieve date'; } }
PathogenVariantProteinDetailsHost