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Develop #1

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1f32b5a
Removed ASReml from side bar
tylerslonecki Jan 12, 2024
40d0b60
Configuration file addition and QBMS DeltaBreed Changes
tylerslonecki Jan 18, 2024
1e1b618
Create icon3.html
tylerslonecki Jan 18, 2024
c9a36c4
Make config import relative, move path to url in QBMS, and and remove…
tylerslonecki Jan 19, 2024
26a561d
Added asreml home page info to config
tylerslonecki Jan 19, 2024
183dc46
Remove .idea directory and add to .gitignore
nickpalladino Jan 19, 2024
b1ad21e
Move .idea to new line
nickpalladino Jan 19, 2024
437bf9a
Bug fix to allow for import of single trials
tylerslonecki Feb 5, 2024
3dbe6b3
Merge branch 'develop' of https://github.com/Breeding-Insight/MrBeanA…
tylerslonecki Feb 5, 2024
8a815bf
Made page size larger
nickpalladino Feb 19, 2025
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,5 @@
.Rhistory
.RData
.Ruserdata
rsconnect/
rsconnect/
.idea
40 changes: 15 additions & 25 deletions R/QBMS.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,52 +10,42 @@
#'
#' @return a list
#' @noRd
qbmsbrapi <- function(url = "https://bms.ciat.cgiar.org/ibpworkbench/controller/auth/login",
engine = c("bms", "breedbase"),
path = ifelse(engine == "bms", "bmsapi", ""),
time_out = ifelse(engine == "bms", 120, 300),
qbmsbrapi <- function(url = "https://qa-test.breedinginsight.net/v1/programs/8397cfd7-7d28-4441-964d-4d5567f67e9e",
engine = '',
path = '',
time_out = 300,
no_auth = FALSE,
brapi_ver = 'v2',
username = NULL,
password = NULL) {
if (is.null(url) | url == "") {
return()
}

bmsbase <- QBMS::set_qbms_config(
url = url,
path = path,
time_out = time_out,
no_auth = no_auth,
engine = engine,
page_size = 5000
page_size = 100000,
brapi_ver = 'v2',
engine = engine
)

if (!no_auth) {
if (is.null(username) | username == "") {
return()
}
if (is.null(password) | password == "") {
return()
}
bmslogin <- QBMS::login_bms(username = username, password = password)
} else {
bmslogin <- NULL
if (is.null(password) | password == "") {
return()
}
QBMS::set_token(password)

crops <- QBMS::list_crops()
return(list(bmsbase = bmsbase, bmslogin = bmslogin, crops = crops))
return(list(bmsbase = bmsbase, crops = crops))
}


#' Get Programs
#'
#' @param crop crop
#'
#' @return a list with programs
#' @noRd
qbmsprograms <- function(crop = NULL) {
if (is.null(crop)) {
return()
}
QBMS::set_crop(crop)
programs <- QBMS::list_programs()
return(programs)
}
Expand Down Expand Up @@ -125,7 +115,7 @@ dataqbms <- function(studies = NULL, dt_studies = NULL) {
) %>%
as.data.frame()
} else {
names(mult_dt) <- dt_studies$trial
names(mult_dt) <- dplyr::filter(dt_studies, trimws(studyName) %in% trimws(studies))$trial
mult_dt <- data.table::rbindlist(
l = mult_dt,
fill = TRUE,
Expand Down
1 change: 1 addition & 0 deletions R/app_server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
#' @import shiny
#' @noRd
app_server <- function(input, output, session) {

sever::sever()
# Home
callModule(mod_home_module1_server, "home_module1_ui_1")
Expand Down
142 changes: 79 additions & 63 deletions R/app_ui.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,12 @@
#' @import shiny
#' @noRd
app_ui <- function(request) {

# Read configuration
app_directory <- system.file("", package = "MrBean")
config_path <- file.path(app_directory, "", "config.yml")
config <- yaml::read_yaml(config_path)

tagList(
# Leave this function for adding external resources
golem_add_external_resources(),
Expand Down Expand Up @@ -125,71 +131,81 @@ app_ui <- function(request) {
icon = shiny::icon("circle", verify_fa = FALSE)
)
),
bs4SidebarHeader("ASReml"),
# Single spatial analysis ASReml
bs4SidebarMenuItem(
text = "Single-Site",
icon = shiny::icon("braille"),
startExpanded = F,
bs4SidebarMenuSubItem(
text = "Model Specs",
tabName = "spats_asreml",
icon = shiny::icon("circle", verify_fa = FALSE)
),
bs4SidebarMenuSubItem(
text = "BLUPs/BLUEs",
tabName = "spats_asreml_effects",
icon = shiny::icon("circle", verify_fa = FALSE)
)
),
# Un-replicated analysis
bs4SidebarMenuItem(
"Unreplicated",
icon = shiny::icon("crosshairs"),
startExpanded = F,
bs4SidebarMenuSubItem(
text = "Model Specs",
tabName = "aug_model",
icon = shiny::icon("circle", verify_fa = FALSE)
),
bs4SidebarMenuSubItem(
text = "BLUPs/BLUEs",
tabName = "aug_result",
icon = shiny::icon("circle", verify_fa = FALSE)
)
),
# Model selector
bs4SidebarMenuItem(
text = "Model Selector",
icon = shiny::icon("hand-pointer"),
startExpanded = F,
bs4SidebarMenuSubItem(
HTML(
paste(
"Model Specs",
bs4Badge("new",
position = "right",
color = "success"
)

# Conditionally include ASReml features
if (config$enable_asreml_features) {
bs4SidebarHeader("ASReml")
},
if (config$enable_asreml_features){
# Single spatial analysis ASReml
bs4SidebarMenuItem(
text = "Single-Site",
icon = shiny::icon("braille"),
startExpanded = F,
bs4SidebarMenuSubItem(
text = "Model Specs",
tabName = "spats_asreml",
icon = shiny::icon("circle", verify_fa = FALSE)
),
bs4SidebarMenuSubItem(
text = "BLUPs/BLUEs",
tabName = "spats_asreml_effects",
icon = shiny::icon("circle", verify_fa = FALSE)
)
),
tabName = "asreml_selector",
icon = shiny::icon("circle", verify_fa = FALSE)
),
bs4SidebarMenuSubItem(
HTML(
paste(
"BLUPs/BLUEs",
bs4Badge("new",
position = "right",
color = "success"
)
)
},
if (config$enable_asreml_features){
# Un-replicated analysis
bs4SidebarMenuItem(
"Unreplicated",
icon = shiny::icon("crosshairs"),
startExpanded = F,
bs4SidebarMenuSubItem(
text = "Model Specs",
tabName = "aug_model",
icon = shiny::icon("circle", verify_fa = FALSE)
),
bs4SidebarMenuSubItem(
text = "BLUPs/BLUEs",
tabName = "aug_result",
icon = shiny::icon("circle", verify_fa = FALSE)
)
),
tabName = "asr_sel_selected",
icon = shiny::icon("circle", verify_fa = FALSE)
)
),
)
},
if (config$enable_asreml_features){
# Model selector
bs4SidebarMenuItem(
text = "Model Selector",
icon = shiny::icon("hand-pointer"),
startExpanded = F,
bs4SidebarMenuSubItem(
HTML(
paste(
"Model Specs",
bs4Badge("new",
position = "right",
color = "success"
)
)
),
tabName = "asreml_selector",
icon = shiny::icon("circle", verify_fa = FALSE)
),
bs4SidebarMenuSubItem(
HTML(
paste(
"BLUPs/BLUEs",
bs4Badge("new",
position = "right",
color = "success"
)
)
),
tabName = "asr_sel_selected",
icon = shiny::icon("circle", verify_fa = FALSE)
)
)
},
bs4SidebarHeader("Two-Stage Analysis"),
# Two-Stage MET
bs4SidebarMenuItem(
Expand Down
81 changes: 45 additions & 36 deletions R/mod_home_module1.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,12 @@
#'
#' @importFrom shiny NS tagList
mod_home_module1_ui <- function(id) {

# Read configuration
app_directory <- system.file("", package = "MrBean")
config_path <- file.path(app_directory, "", "config.yml")
config <- yaml::read_yaml(config_path)

ns <- NS(id)
tagList(
fluidRow(
Expand Down Expand Up @@ -39,15 +45,17 @@ mod_home_module1_ui <- function(id) {
href = "https://cran.r-project.org/web/packages/SpATS/SpATS.pdf",
icon = shiny::icon("braille")
),
bs4Dash::valueBox(
value = "ASReml-R",
subtitle = "AR1xAR1 Correlation",
width = 12,
color = "danger",
elevation = 3,
href = "https://asreml.kb.vsni.co.uk/wp-content/uploads/sites/3/2018/02/ASReml-R-Reference-Manual-4.pdf",
icon = shiny::icon("braille")
),
if (config$enable_asreml_features) {
bs4Dash::valueBox(
value = "ASReml-R",
subtitle = "AR1xAR1 Correlation",
width = 12,
color = "danger",
elevation = 3,
href = "https://asreml.kb.vsni.co.uk/wp-content/uploads/sites/3/2018/02/ASReml-R-Reference-Manual-4.pdf",
icon = shiny::icon("braille")
)
},
bs4Dash::valueBox(
value = "Lme4",
subtitle = "lmer",
Expand All @@ -66,33 +74,34 @@ mod_home_module1_ui <- function(id) {
elevation = 3,
href = "https://www.frontiersin.org/articles/10.3389/fpls.2018.01511/full"
),
bs4Card(
title = "Jump",
status = "danger",
width = 12,
solidHeader = TRUE,
actionLink(
inputId = ns("toAwesome1"),
label = "Data",
icon = icon("database"),
style = "color: #d9534f"
),
br(),
actionLink(
inputId = ns("toAwesome2"),
label = "Spatial",
icon = icon("braille"),
style = "color: #d9534f"
),
br(),
actionLink(
inputId = ns("toAwesome3"),
label = "Lme4",
icon = icon("chart-column", verify_fa = FALSE),
style = "color: #d9534f"
),
br()
)
#remove Jump Card
# bs4Card(
# title = "Jump",
# status = "danger",
# width = 12,
# solidHeader = TRUE,
# actionLink(
# inputId = ns("toAwesome1"),
# label = "Data",
# icon = icon("database"),
# style = "color: #d9534f"
# ),
# br(),
# actionLink(
# inputId = ns("toAwesome2"),
# label = "Spatial",
# icon = icon("braille"),
# style = "color: #d9534f"
# ),
# br(),
# actionLink(
# inputId = ns("toAwesome3"),
# label = "Lme4",
# icon = icon("chart-column", verify_fa = FALSE),
# style = "color: #d9534f"
# ),
# br()
# )
)
)
)
Expand Down
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