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Merged
Cvicnaire merged 1 commit into from
May 5, 2026
Merged

PR to address collection page update. It now reflects the same functi… #22

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248 changes: 155 additions & 93 deletions shiny/modules/collection_module.R
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,13 @@ collection_module_ui <- function(id) {
margin-bottom: 16px;
}

", page_selector, " .collection-toolbar-primary {
display: flex;
align-items: center;
gap: 10px;
flex-wrap: wrap;
}

", page_selector, " .collection-actions {
display: flex;
gap: 10px;
Expand Down Expand Up @@ -124,6 +131,10 @@ collection_module_ui <- function(id) {
margin-bottom: 14px;
color: #597189;
}

", page_selector, " .collection-metadata-table .dataTables_wrapper {
margin-top: 8px;
}
"))),

div(
Expand All @@ -133,22 +144,29 @@ collection_module_ui <- function(id) {
class = "collection-hero",
tags$h2("Browse Collections"),
tags$p(
"Select a collection to review its metadata and included signatures without opening a separate dialog."
"Select a collection from the repository to review metadata, member signatures, and collection-level details in one place."
)
),

div(
class = "collection-card",
div(
class = "collection-toolbar",
actionButton(
ns("open_upload_modal"),
"Upload Collection",
icon = icon("upload"),
class = "btn-primary"
div(
class = "collection-toolbar-primary",
actionButton(
ns("open_upload_modal"),
"Upload Collection",
icon = icon("upload"),
class = "btn-primary"
)
),
uiOutput(ns("collection_actions"))
),
p(
class = "collection-helper",
"Select a collection row to make it active. Use View to load the full collection details when you want to inspect it below."
),
DT::DTOutput(ns("collection_tbl"))
),

Expand All @@ -157,7 +175,7 @@ collection_module_ui <- function(id) {
tags$h3("Selected Collection"),
p(
class = "collection-helper",
"Selecting a row loads the collection details below so you can inspect metadata and member signatures in one place."
"The active collection summary appears immediately. Use View to fetch the collection details and member signatures on demand."
),
uiOutput(ns("collection_detail_panel"))
)
Expand All @@ -167,6 +185,7 @@ collection_module_ui <- function(id) {

collection_module_server <- function(id, collection_db, user_conn_handler, collection_trigger) {
moduleServer(id, function(input, output, session) {
ns <- session$ns
selected_collection <- reactiveVal(NULL)
collection_object <- reactiveVal(NULL)

Expand All @@ -190,12 +209,10 @@ collection_module_server <- function(id, collection_db, user_conn_handler, colle
)
}

df_grouped <- reactive({
grouped_collections <- reactive({
req(user_conn_handler())

df <- collection_db()

df %>%
collection_db() %>%
dplyr::group_by(
collection_id,
collection_name,
Expand All @@ -206,42 +223,41 @@ collection_module_server <- function(id, collection_db, user_conn_handler, colle
) %>%
dplyr::summarise(
signature_count = dplyr::n(),
signatures = paste(signature_name, collapse = ", "),
signature_preview = paste(utils::head(signature_name, 5), collapse = ", "),
.groups = "drop"
)
})

current_collection_signatures <- reactive({
req(selected_collection(), collection_db())

collection_db()[
collection_db()$collection_id == selected_collection()$collection_id[[1]],
,
drop = FALSE
]
})

output$collection_tbl <- renderDT({
DatatableFX(
df = df_grouped(),
df = grouped_collections(),
hidden_columns = c(0, 7),
scrollY = "500px",
row_selection = "single"
)
}, server = TRUE)

observeEvent(input$collection_tbl_rows_selected, {
row <- input$collection_tbl_rows_selected
rows <- input$collection_tbl_rows_selected

if (length(row) == 0) {
if (length(rows) == 0) {
selected_collection(NULL)
collection_object(NULL)
return()
}

df <- df_grouped()
collection_selected <- df[row, , drop = FALSE]
selected_collection(collection_selected)

tryCatch({
collection_object(fetch_selected_collection(collection_selected$collection_id[[1]]))
}, error = function(e) {
collection_object(NULL)
showNotification(
paste("Failed to load collection details:", e$message),
type = "error",
duration = 8
)
})
selected_collection(grouped_collections()[rows, , drop = FALSE])
collection_object(NULL)
})

output$collection_actions <- renderUI({
Expand All @@ -266,6 +282,7 @@ collection_module_server <- function(id, collection_db, user_conn_handler, colle
),
div(
class = "collection-actions",
actionButton(ns("view_btn"), "View", class = "btn-primary"),
actionButton(ns("refresh_btn"), "Refresh"),
actionButton(ns("update_btn"), "Update"),
actionButton(ns("delete_btn"), "Delete"),
Expand All @@ -282,7 +299,41 @@ collection_module_server <- function(id, collection_db, user_conn_handler, colle
return(
div(
class = "collection-empty",
"Choose a collection from the table above to inspect its metadata and included signatures."
"Choose a collection from the table above to inspect it."
)
)
}

if (is.null(collection_object())) {
return(
tagList(
div(
class = "collection-summary-grid",
div(
class = "collection-summary-item",
tags$strong("Collection"),
tags$span(collection_field_value(collection_selected, "collection_name"))
),
div(
class = "collection-summary-item",
tags$strong("Owner"),
tags$span(collection_field_value(collection_selected, "user_name"))
),
div(
class = "collection-summary-item",
tags$strong("Visibility"),
tags$span(collection_field_value(collection_selected, "visibility"))
),
div(
class = "collection-summary-item",
tags$strong("Signatures"),
tags$span(collection_field_value(collection_selected, "signature_count", "0"))
)
),
div(
class = "collection-empty",
"The selected collection has not been loaded yet. Click View to fetch its metadata and member signatures."
)
)
)
}
Expand Down Expand Up @@ -312,38 +363,68 @@ collection_module_server <- function(id, collection_db, user_conn_handler, colle
)
),
tabsetPanel(
tabPanel("Metadata", uiOutput(session$ns("collection_metadata"))),
tabPanel("Signatures", DT::DTOutput(session$ns("collection_sig_tbl")))
tabPanel(
"Metadata",
div(class = "collection-metadata-table", DT::DTOutput(ns("collection_metadata_table")))
),
tabPanel(
"Signatures",
DT::DTOutput(ns("collection_sig_tbl"))
)
)
)
})

output$collection_metadata <- renderUI({
output$collection_metadata_table <- DT::renderDataTable({
req(selected_collection())

tagList(
p(tags$strong("Description:"), collection_field_value(selected_collection(), "description")),
p(tags$strong("Date Created:"), collection_field_value(selected_collection(), "date_created")),
p(tags$strong("User:"), collection_field_value(selected_collection(), "user_name")),
p(tags$strong("Total Signatures:"), collection_field_value(selected_collection(), "signature_count", "0"))
collection_selected <- selected_collection()
metadata_df <- data.frame(
Field = c("collection_id", names(collection_selected)[names(collection_selected) != "collection_id"]),
Value = c(
collection_selected$collection_id[[1]],
vapply(
names(collection_selected)[names(collection_selected) != "collection_id"],
function(field) collection_field_value(collection_selected, field),
character(1)
)
),
stringsAsFactors = FALSE
)
})

output$collection_sig_tbl <- renderDataTable({
req(selected_collection(), collection_db())
DatatableFX(
metadata_df,
hidden_columns = integer(0),
scrollY = "360px"
)
}, server = TRUE)

filtered_collection_tbl <- collection_db()[
collection_db()$collection_name == selected_collection()$collection_name[[1]],
,
drop = FALSE
]
output$collection_sig_tbl <- DT::renderDataTable({
req(selected_collection(), collection_object())

DatatableFX(
filtered_collection_tbl,
hidden_columns = c(3, 4)
current_collection_signatures(),
hidden_columns = c(3, 4),
scrollY = "500px"
)
}, server = TRUE)

observeEvent(input$view_btn, {
req(selected_collection())

tryCatch({
collection_object(fetch_selected_collection(selected_collection()$collection_id[[1]]))
showNotification("Collection details loaded.", type = "message")
}, error = function(e) {
collection_object(NULL)
showNotification(
paste("Failed to load collection details:", e$message),
type = "error",
duration = 8
)
})
})

observeEvent(input$refresh_btn, {
req(selected_collection())

Expand Down Expand Up @@ -374,7 +455,7 @@ collection_module_server <- function(id, collection_db, user_conn_handler, colle
omic_collection = rds_object
)

showNotification("Collection uploaded and added successfully!")
showNotification("Collection uploaded and added successfully!", type = "message")
collection_trigger(isolate(collection_trigger()) + 1)
}, error = function(e) {
showNotification(
Expand All @@ -392,11 +473,11 @@ collection_module_server <- function(id, collection_db, user_conn_handler, colle
showModal(
modalDialog(
title = "Confirm Delete",
paste(
"Are you sure you want to delete collection:",
selected_collection()$collection_name[[1]],
"?"
sprintf(
"Are you sure you want to delete collection %s?",
htmltools::htmlEscape(selected_collection()$collection_name[[1]])
),
easyClose = TRUE,
footer = tagList(
modalButton("Cancel"),
actionButton(ns("confirm_delete_collection"), "Delete", class = "btn-danger")
Expand All @@ -420,9 +501,8 @@ collection_module_server <- function(id, collection_db, user_conn_handler, colle
removeModal()
selected_collection(NULL)
collection_object(NULL)
collection_trigger(collection_trigger() + 1)
collection_trigger(isolate(collection_trigger()) + 1)
}, error = function(e) {
message("Error deleting collection: ", e$message)
showNotification(
paste("Failed to delete collection:", e$message),
type = "error",
Expand All @@ -434,51 +514,33 @@ collection_module_server <- function(id, collection_db, user_conn_handler, colle
observeEvent(input$update_btn, {
req(selected_collection())

collection_name <- selected_collection()$collection_name[[1]]

showModal(modalDialog(
title = "Update collection",
paste("Collection to update:", collection_name),
fileInput(session$ns("update_file_upload"), "Choose an RDS file", accept = ".rds"),
p("The selected collection will be updated with the new collection object you upload."),
footer = tagList(
modalButton("Cancel")
showModal(
modalDialog(
title = "Update Collection",
paste("Collection to update:", selected_collection()$collection_name[[1]]),
fileInput(session$ns("update_file_upload"), "Choose an RDS file", accept = ".rds"),
p("The selected collection will be updated with the new collection object you upload."),
footer = tagList(
modalButton("Cancel")
)
)
))
)
})

observeEvent(input$access_btn, {
req(selected_collection())

user_tbl <- SigRepo::searchUser(conn_handler = user_conn_handler())

showModal(modalDialog(
title = paste("Manage Users for Collection:", selected_collection()$collection_name[[1]]),
tabsetPanel(
tabPanel(
"Add to Collection",
fluidRow(
column(
6,
selectInput(
inputId = "user_selector",
label = "Select users to add:",
choices = user_tbl$user_name,
multiple = TRUE
)
)
),
uiOutput("access_type_ui"),
actionButton("add_users_confirm", "Add Users", class = "btn-primary")
),
tabPanel(
"Delete from Collection",
p("Delete user functionality goes here.")
showModal(
modalDialog(
title = paste("Collection Access:", selected_collection()$collection_name[[1]]),
easyClose = TRUE,
footer = modalButton("Close"),
div(
class = "collection-helper",
"Collection access management is still collection-specific and has not been modernized yet in this refactor."
)
),
easyClose = TRUE,
footer = modalButton("Close")
))
)
)
})

output$download_btn <- downloadHandler(
Expand Down
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