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Merged
xec-cm merged 3 commits into from
May 11, 2026
Merged

Dev #32

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483df38
Revert "Add amd64 platform and build deps to Dockerfile"
xec-cm May 11, 2026
f821245
Revert "Add SEO/meta, sitemap/robots, and UI tweaks"
xec-cm May 11, 2026
778dd1b
update
xec-cm May 11, 2026
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8 changes: 0 additions & 8 deletions Dockerfile
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Expand Up @@ -6,14 +6,6 @@ ADD ./covidapp /srv/shiny-server
RUN chmod -R +r /srv/shiny-server
RUN rm /srv/shiny-server/app_customData.R

RUN apt-get update && apt-get install -y --no-install-recommends \
libuv1 \
libuv1-dev \
cmake \
make \
pkg-config \
&& rm -rf /var/lib/apt/lists/*

# Install deps and package
RUN R -e "devtools::install_deps('/srv/shiny-server')"
RUN R -e "devtools::install('/srv/shiny-server')"
Expand Down
2 changes: 1 addition & 1 deletion Dockerfile_customData
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@@ -1,4 +1,4 @@
FROM microbialgenomics/shiny-geospatial:4.1.2
FROM --platform=linux/amd64 microbialgenomics/shiny-geospatial:4.1.2

# Copy covidseq_dev and set permission
RUN rm -rf /srv/shiny-server/*
Expand Down
83 changes: 16 additions & 67 deletions R/app_funs.R
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@@ -1,54 +1,10 @@
#' SEO metadata shared by CovidTag entry points.
covidtag_seo_head <- function() {
title <- "CovidTag | SARS-CoV-2 variant surveillance in Spain"
description <- paste(
"CovidTag is an interactive dashboard for SARS-CoV-2 genomic",
"surveillance in Spain, tracking variants, mutations and sequencing",
"efforts using GISAID data."
)
url <- "https://covidtag.paseq.org/"
image <- "https://covidtag.paseq.org/images/covidTag.png"

shiny::tags$head(
shiny::includeHTML("google-analytics.html"),
shiny::tags$meta(name = "description", content = description),
shiny::tags$link(rel = "canonical", href = url),
shiny::tags$meta(name = "robots", content = "index, follow"),
shiny::tags$meta(property = "og:type", content = "website"),
shiny::tags$meta(property = "og:title", content = title),
shiny::tags$meta(property = "og:description", content = description),
shiny::tags$meta(property = "og:url", content = url),
shiny::tags$meta(property = "og:image", content = image),
shiny::tags$meta(name = "twitter:card", content = "summary"),
shiny::tags$meta(name = "twitter:title", content = title),
shiny::tags$meta(name = "twitter:description", content = description),
shiny::tags$meta(name = "twitter:image", content = image),
shiny::tags$script(
type = "application/ld+json",
shiny::HTML('{
"@context": "https://schema.org",
"@type": "WebApplication",
"name": "CovidTag",
"url": "https://covidtag.paseq.org/",
"description": "CovidTag is an interactive dashboard for SARS-CoV-2 genomic surveillance in Spain, tracking variants, mutations and sequencing efforts using GISAID data.",
"applicationCategory": "HealthApplication",
"operatingSystem": "Web",
"image": "https://covidtag.paseq.org/images/covidTag.png",
"publisher": {
"@type": "Organization",
"name": "PASEQ"
}
}')
)
)
}

#' Title
#'
#' @export
ui <- function() {
shiny::shinyUI(
shiny::navbarPage(
shiny::tags$head(shiny::includeHTML("google-analytics.html")),
title = shiny::div(
shiny::tags$a(
href = "http://covidtag.paseq.org",
Expand Down Expand Up @@ -104,15 +60,6 @@ ui <- function() {
theme = shinythemes::shinytheme("flatly"),
fluid = TRUE,
collapsible = TRUE,
windowTitle = "CovidTag | SARS-CoV-2 variant surveillance in Spain",
header = shiny::tagList(
covidtag_seo_head(),
shiny::tags$head(shiny::tags$style('
nav .container:first-child {
margin-left:100px; width: 100%;
}')),
shinyjs::useShinyjs()
),

# TAB1: Overview
shiny::tabPanel(
Expand Down Expand Up @@ -149,7 +96,12 @@ ui <- function() {
shiny::br(),
shiny::br(),
footer
)
),
shiny::tags$head(shiny::tags$style('
nav .container:first-child {
margin-left:100px; width: 100%;
}')),
shinyjs::useShinyjs()
)
)
}
Expand All @@ -160,7 +112,7 @@ ui <- function() {
server <- function() {
function(input, output, session) {

shinyjs::runjs('document.title = "CovidTag | SARS-CoV-2 variant surveillance in Spain"')
shinyjs::runjs('document.title = "CovidTag"')
shinylogs::track_usage(storage_mode = shinylogs::store_rds("logs/"))

## Module tab 1
Expand Down Expand Up @@ -223,15 +175,6 @@ ui_2 <- function() {
theme = shinythemes::shinytheme("flatly"),
fluid = TRUE,
collapsible = TRUE,
windowTitle = "CovidTag | SARS-CoV-2 variant surveillance in Spain",
header = shiny::tagList(
covidtag_seo_head(),
shiny::tags$head(shiny::tags$style('
nav .container:first-child {
margin-left:100px; width: 100%;
}')),
shinyjs::useShinyjs()
),

# TAB2: Overview
shiny::tabPanel(
Expand All @@ -241,7 +184,13 @@ ui_2 <- function() {
shiny::br(),
shiny::br(),
footer
)
),

shiny::tags$head(shiny::tags$style('
nav .container:first-child {
margin-left:100px; width: 100%;
}')),
shinyjs::useShinyjs()
)
)
}
Expand All @@ -252,7 +201,7 @@ ui_2 <- function() {
server_2 <- function() {
function(input, output, session) {

shinyjs::runjs('document.title = "CovidTag | SARS-CoV-2 variant surveillance in Spain"')
shinyjs::runjs('document.title = "CovidTag"')
shinylogs::track_usage(storage_mode = shinylogs::store_rds("logs/"))

## Module tab 1
Expand Down
145 changes: 74 additions & 71 deletions R/module_acknowledgements.R
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Expand Up @@ -5,95 +5,97 @@
acknowledgements_module_ui <- function(id) {
ns <- shiny::NS(id)
shiny::pageWithSidebar(
headerPanel = shiny::fluidPage(
shiny::fixedRow(
shiny::h3(
"Notes for a correct interpretation",
align = "center",
style = "font-weight: bold; font-style: italic;"
)
),
shiny::fixedRow(
shiny::h5(
"• Sampling may not be uniform within the different
headerPanel = shiny::headerPanel(
title = shiny::fluidPage(
shiny::fixedRow(
shiny::h3(
"Notes for a correct interpretation",
align = "center",
style = "font-weight: bold; font-style: italic;"
)
),
shiny::fixedRow(
shiny::h5(
"• Sampling may not be uniform within the different
autonomous communities. Therefore, it is important not
to assume that the counts/frequencies shown are
necessarily representative of the region.",
align = "center",
style = "margin-left: 70px; margin-right: 70px; line-height: 25px;"
),
shiny::h5(
"• The charts used are based on the sample collection date,
align = "center",
style = "margin-left: 70px; margin-right: 70px; line-height: 25px;"
),
shiny::h5(
"• The charts used are based on the sample collection date,
and sequencing or GISAID submission date. As a result,
this date may differ from when the sample was processed
and sequenced, and when the data is released to the public.",
align = "center",
style = "margin-left: 70px; margin-right: 70px; line-height: 25px;"
),
shiny::h5(
"• In relation with the last consideration, last data
align = "center",
style = "margin-left: 70px; margin-right: 70px; line-height: 25px;"
),
shiny::h5(
"• In relation with the last consideration, last data
points often has incomplete data and may change as more
sequences come in.",
align = "center",
style = "margin-left: 70px; margin-right: 70px; line-height: 25px;"
),
shiny::h5(
"• The mutations that define SARS-CoV-2 (CoV-19) lineages
align = "center",
style = "margin-left: 70px; margin-right: 70px; line-height: 25px;"
),
shiny::h5(
"• The mutations that define SARS-CoV-2 (CoV-19) lineages
are updated every few days. Therefore, displayed data is
susceptible to change over time.",
align = "center",
style = "margin-left: 70px; margin-right: 70px; line-height: 25px;"
)
),
shiny::br(),
shiny::fixedRow(
shiny::h3("Acknowledgements",
align = "center",
style = "font-weight: bold; font-style: italic;"),
),
shiny::fixedRow(
shiny::h5(
"We are grateful to the data contributors who shared the
align = "center",
style = "margin-left: 70px; margin-right: 70px; line-height: 25px;"
)
),
shiny::br(),
shiny::fixedRow(
shiny::h3("Acknowledgements",
align = "center",
style = "font-weight: bold; font-style: italic;"),
),
shiny::fixedRow(
shiny::h5(
"We are grateful to the data contributors who shared the
data used in this Web Application via the GISAID
Initia-tive*: the Authors, the Originating Laboratories
responsible for obtaining the specimens, and the Submitting
Laboratories that generated the genetic sequences and metadata.",
align = "center",
style = "margin-left: 150px; margin-right: 150px; line-height: 25px;"
)
),
shiny::fixedRow(
shiny::h5(
"* (a) Elbe, S., and Buckland-Merrett, G. (2017) Data,
align = "center",
style = "margin-left: 150px; margin-right: 150px; line-height: 25px;"
)
),
shiny::fixedRow(
shiny::h5(
"* (a) Elbe, S., and Buckland-Merrett, G. (2017) Data,
disease and diplomacy: GISAID’s innovative contribution
to global health. Global Challenges, 1:33-46.
DOI: ",
shiny::a(
" 10.1002/gch2.1018",
href = "https://onlinelibrary.wiley.com/doi/full/10.1002/gch2.1018",
target = "_blank"
),
" PMCID: ",
shiny::a(
" 31565258",
href = "https://pubmed.ncbi.nlm.nih.gov/31565258/",
target = "_blank"
),
" (b) Shu, Y., McCauley, J. (2017) GISAID: From vision
shiny::a(
" 10.1002/gch2.1018",
href = "https://onlinelibrary.wiley.com/doi/full/10.1002/gch2.1018",
target = "_blank"
),
" PMCID: ",
shiny::a(
" 31565258",
href = "https://pubmed.ncbi.nlm.nih.gov/31565258/",
target = "_blank"
),
" (b) Shu, Y., McCauley, J. (2017) GISAID: From vision
to reality. EuroSurveillance, 22(13) DOI: ",
shiny::a(
" 10.2807/1560-7917.ES.2017.22.13.30494",
href = "https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2017.22.13.30494",
target = "_blank"
),
" PMCID: ",
shiny::a(
" PMC5388101",
href = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388101/",
target = "_blank"
),
align = "center",
style = "margin-left: 150px; margin-right: 150px; line-height: 25px;"
shiny::a(
" 10.2807/1560-7917.ES.2017.22.13.30494",
href = "https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2017.22.13.30494",
target = "_blank"
),
" PMCID: ",
shiny::a(
" PMC5388101",
href = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388101/",
target = "_blank"
),
align = "center",
style = "margin-left: 150px; margin-right: 150px; line-height: 25px;"
)
)
)
),
Expand All @@ -112,3 +114,4 @@ acknowledgements_module_server <- function(id) {
# empty
})
}

4 changes: 3 additions & 1 deletion R/module_data_dw.R
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Expand Up @@ -6,7 +6,7 @@
data_dw_module_ui <- function(id) {
ns <- shiny::NS(id)
shiny::pageWithSidebar(
headerPanel = shiny::div(class = "col-sm-12", shiny::h1("")),
headerPanel = shiny::headerPanel(""),

sidebarPanel = NULL,
# main
Expand Down Expand Up @@ -55,3 +55,5 @@ data_dw_module_server <- function(id) {
})
}



3 changes: 2 additions & 1 deletion R/module_per_ca.R
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Expand Up @@ -5,7 +5,7 @@
per_ca_module_ui <- function(id) {
ns <- shiny::NS(id)
shiny::pageWithSidebar(
headerPanel = shiny::div(class = "col-sm-12", shiny::h1("")),
headerPanel = shiny::headerPanel(""),
sidebarPanel = shiny::sidebarPanel(
width = 3,
shiny::h5(
Expand Down Expand Up @@ -114,3 +114,4 @@ per_ca_module_server <- function(id) {
})
})
}

3 changes: 2 additions & 1 deletion R/module_per_variant.R
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Expand Up @@ -8,7 +8,7 @@
per_variant_module_ui <- function(id) {
ns <- shiny::NS(id)
shiny::pageWithSidebar(
headerPanel = shiny::div(class = "col-sm-12", shiny::h1("")),
headerPanel = shiny::headerPanel(""),

# sidebar
sidebarPanel = shiny::sidebarPanel(
Expand Down Expand Up @@ -95,3 +95,4 @@ per_variant_module_server <- function(id) {
shiny::bindCache(input$variant)
})
}

3 changes: 0 additions & 3 deletions www/robots.txt
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6 changes: 0 additions & 6 deletions www/sitemap.xml
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