R/biolockj_ui.R
In IvoryC/shinyBioLockJ: BioLockJ GUI
Defines functions
biolockj_ui
Documented in
biolockj_ui
#' BioLockJ ui.R
#'
#' @return the shiny ui object
#'
biolockj_ui <- function(){
envType = detect_deployment()
helpMdFile = system.file("md", "HelpPage.md", package = "shinyBioLockJ")
ui <- fluidPage(
shinyFeedback::useShinyFeedback(),
shinyjs::useShinyjs(),
tags$script('
Shiny.addCustomMessageHandler("refocus",
function(e_id) {
document.getElementById(e_id).focus();
});'),
div(style="padding-left: 0px; padding-right: 0px;", navbarPage(id = "topTabs",
position = "fixed-top",
theme = shinythemes::shinytheme("cerulean"),
"BioLockJ",
# Home ####
tabPanel("Home",
tags$style(".shiny-input-container {margin-bottom: 0px} #existingConfig_progress { margin-bottom: 0px } .checkbox { margin-top: 0px}"),
tags$style(".shiny-input-container {margin-bottom: 0px} #defaultPropsFiles_progress { margin-bottom: 0px } .checkbox { margin-top: 0px}"),
tags$style(".shiny-input-container {margin-bottom: 0px} #projectRootDir_progress { margin-bottom: 0px } .checkbox { margin-top: 0px}"),
p("navbar"),p("spacer"),
h1("BioLockJ Pipeline Builder"),
tabsetPanel(id="HomeTabs",
tabPanel("Save to file",
br(),
textInput("projectName", "Project name", value="myPipeline", placeholder = "new project name"),
p(),
checkboxInput("include_standard_defaults", "include values that match defaults"),
checkboxInput("include_biolockj_version", "include BioLockJ version"),
shinyBS::tipify(checkboxInput("gather_shared_props", "gather shared properties"), "reduce dupliated lines when multiple modules use the same property", placement='right'),
shinyBS::tipify(checkboxInput("include_mid_progress", "include work-in-progress"), "include commented list of modules in Trash and their properties, See Modules", placement='right'),
shinyBS::tipify(shinyjs::disabled(checkboxInput("checkRelPaths", "write relative file paths")), "requires project root directory", placement='right'),
#
fluidRow(
column(3, shinyFiles::shinyDirButton("projectRootDir", "Set Project Root Directory", "Select Project Root Directory")),
column(9, verbatimTextOutput("showProjectDir", placeholder=TRUE))
),
fluidRow(
column(3, downloadButton("downloadData", "Download", width='80%')),
column(9, uiOutput("saveButton"))
),
p(),
verbatimTextOutput("configText", placeholder = TRUE)),
tabPanel("Load from file",
br(),
p(em("When you pull values from an existing file, the values from the file will replace anything configured here.")),
h2("Upoad configuration"),
p("This uses the file, but not its location; thus relative file paths are not converted to absolute paths."),
fileInput("uploadExistingConfig", label="Upload an existing config file", accept = c(".properties", ".config")),
shinyjs::disabled(actionButton("populateUploadedConfig", "pull values")),
hr(),
tabsetPanel(
id = "localExistingConfig",
type = "hidden",
tabPanelBody("remote", "When run locally, there is also an option to find local files."),
tabPanelBody("virtual", "When run locally, there is also an option to find local files."),
tabPanelBody("local",
h2("Local configuration"),
p("This will use the file AND its location, allowing for conversion between relative and absolute paths."),
shinyFiles::shinyFilesButton("LocalExistingConfig", "Choose a local config file", "Please select a file", multiple = FALSE, viewtype = "list"),
p(),
verbatimTextOutput("showLocalFile", placeholder=TRUE),
shinyjs::disabled(actionButton("populateFromLocalConfig", "pull values"))
)
),
hr(),
h2("Example configuration"),
p("This will use the read-only example project directory to reference relative files."),
uiOutput("examples"),
actionButton("populateExampleConfig", "pull values")
)
)
),
# Modules ####
tabPanel("Modules",
p("navbar"),p("spacer"),
fluidPage(
h2("BioModule Run Order"),
fluidRow(
column(5, uiOutput("selectModule")),
column(1, "AS", style = "margin-top: 30px;"),
column(4, textInput("newAlias", "",
placeholder = "alternative alias",
width = '100%')),
column(2, actionButton("AddModuleButton", style = "margin-top: 20px;", "add to pipeline", class = "btn-success"))),
uiOutput("manageModules"),
actionButton("emptyModuleTrash", "Empty Trash"),
hr(),
uiOutput("moduleSummary"))),
# Properties ####
tabPanel("Properties",
div(style="", splitLayout(
cellArgs = list(style='white-space: normal; padding-left: 0px; padding-right: 0px;'),
tagList(p("navbar"),p("spacer"),
h2("General Properties"),
checkboxInput("checkLiveFeedback", "show live feedback", value=FALSE),
p("General properties are not specific to any one module."),
tabsetPanel(
tabPanel(
"Backbone Properties",
uiOutput("genProps")),
tabPanel("Custom Properties",
p("Add custom properties here. All property names must be unique."),
p("Any property can reference the exact value of any other property, for example:"),
p("prop2 = build on ${prop1}"),
fluidRow(
column(4, textInput("customPropName","property name")),
column(5, textInput("customPropVal", "= value")),
column(3, actionButton("addCostomPropBtn", "add", style = "margin-top: 25px;"))),
h5("Current custom properties:"),
uiOutput("showCustomProps"),
br(),
h5("Custom values in default properties files:"),
em("These are not included as part of the current config file."),
uiOutput("showDefaultCustomProps"))
)),
tagList(p("navbar"),p("spacer"),
h2("Module Properties"),
textOutput("modulePropsHeader"),
uiOutput("modProps")
)
))),
# Precheck ####
tabPanel("Precheck",
p("navbar"),p("spacer"),
sidebarLayout(
sidebarPanel(
# width=5,
h3("command options"),
checkboxInput("callJavaDirectly", "direct call to java", value=TRUE),
h4("flags"),
checkboxInput("checkPrecheck", "--precheck-only", value=TRUE),
checkboxInput("checkUnused", "--unused-props", value=FALSE),
checkboxInput("checkDocker", "--docker", value=FALSE),
# checkboxInput("checkAws", "--aws", value=FALSE),
checkboxInput("checkForground", "--foreground", value=FALSE),
checkboxInput("checkVerbose", "--verbose", value=FALSE),
checkboxInput("checkMapBlj", "--blj", value=FALSE),
h4("arguments"),
p("When running locally, values for these arguments are set in Settings. Otherwise, these options are unavailable."),
checkboxInput("useExtMods", "--external-modules"),
checkboxInput("useBljProj", "--blj_proj")
),
mainPanel(
# width=7,
h3("Test current configuration"),
p("Pass this config file to BioLockJ to build the pipeline and check dependencies. This does not actually execute the pipeline (because we include the --precheck-only flag), but it rus the initial phases to look for potential problems."),
h4("biolockj command:"),
verbatimTextOutput("precheckCommand"),
actionButton("runPrecheckBtn", "Run Precheck", class = "btn-success"),
h4("command output:"),
uiOutput("precheckOutput")
)
)),
# Defaults ####
tabPanel("Defaults",
p("navbar"),p("spacer"),
fluidPage(
h2("Chain default properties"),
em("(optional)"),
p(em("The property 'pipeline.defaultProps=[file]' allows you to use property values from another file. That file may also include a reference to another file creating a chain. When you run the pipeline, BioLockJ puts all the properties together. Properties defined in multiple files are set according the most recent value in the chain.")),
h4("Locate defaults"),
em("This does not affect your configuration."),
br(),br(),
checkboxInput("ignoreChain", "ignore pipeline.defaultProps in this file", value=FALSE),
tabsetPanel(
id = "localDefaultPropsFinder",
type = "hidden",
tabPanelBody("remote", fileInput("defaultPropsFiles", label="upload default properties files", multiple = TRUE,
accept = c(".properties", ".config"))),
tabPanelBody("virtual", "When run locally, there is also an option to find local files."),
tabPanelBody("local", shinyFiles::shinyFilesButton("findLocalDefaultProps",
"Find properties files",
"Select files...",
multiple = TRUE))
),
br(),
tableOutput("chainableFiles"),
h4("Select defaults"),
em("This is what sets the pipeline.defaultProps for your current pipeline, and the defaults that are reflected throughout this configuration."),
shinyjs::disabled(selectInput("selectDefaultProps", "pipeline.defaultProps", choices = c(none=""), multiple=TRUE)),
tableOutput("chainedFiles"),
shinyjs::disabled(actionButton("loadDefaultProps", "set as defaults")),
h4("Current defaults"),
verbatimTextOutput("currentDefaultProps")
)),
# Settings ####
tabPanel("Settings",
p("navbar"),p("spacer"),
fluidPage(
h2("Settings"),
p("Control aspects of this user interface."),
h4("File access"),
shinyjs::disabled(radioButtons("serverType", "How should this interface access files?",
choiceNames = list("remote server", "local virtual server", "local machine"),
choiceValues = c("remote", "virtual", "local"), inline=TRUE,
selected = envType ) ),
br(),
hr(),
h4("BioLockJ version: "),
textOutput("bljVersion"),
hr(),
uiOutput("coreSettings")
# shinyFiles::shinyFilesButton("biolockjJarFile", "BioLockJ Jar File Location", "Choose jar file", multiple=FALSE, accept=c(".jar"), width='100%'),
# actionButton("updateJar", "update jar location"),
# verbatimTextOutput("showNewJarFile")
)),
# Help ####
tabPanel("Help",
p("navbar"),p("spacer"),
includeMarkdown(helpMdFile))
))
) # end of UI ####
return(ui)
}
IvoryC/shinyBioLockJ documentation built on May 29, 2021, 7:40 a.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions biolockj_ui
Documented in biolockj_ui
#' BioLockJ ui.R
#'
#' @return the shiny ui object
#'
biolockj_ui <- function(){
envType = detect_deployment()
helpMdFile = system.file("md", "HelpPage.md", package = "shinyBioLockJ")
ui <- fluidPage(
shinyFeedback::useShinyFeedback(),
shinyjs::useShinyjs(),
tags$script('
Shiny.addCustomMessageHandler("refocus",
function(e_id) {
document.getElementById(e_id).focus();
});'),
div(style="padding-left: 0px; padding-right: 0px;", navbarPage(id = "topTabs",
position = "fixed-top",
theme = shinythemes::shinytheme("cerulean"),
"BioLockJ",
# Home ####
tabPanel("Home",
tags$style(".shiny-input-container {margin-bottom: 0px} #existingConfig_progress { margin-bottom: 0px } .checkbox { margin-top: 0px}"),
tags$style(".shiny-input-container {margin-bottom: 0px} #defaultPropsFiles_progress { margin-bottom: 0px } .checkbox { margin-top: 0px}"),
tags$style(".shiny-input-container {margin-bottom: 0px} #projectRootDir_progress { margin-bottom: 0px } .checkbox { margin-top: 0px}"),
p("navbar"),p("spacer"),
h1("BioLockJ Pipeline Builder"),
tabsetPanel(id="HomeTabs",
tabPanel("Save to file",
br(),
textInput("projectName", "Project name", value="myPipeline", placeholder = "new project name"),
p(),
checkboxInput("include_standard_defaults", "include values that match defaults"),
checkboxInput("include_biolockj_version", "include BioLockJ version"),
shinyBS::tipify(checkboxInput("gather_shared_props", "gather shared properties"), "reduce dupliated lines when multiple modules use the same property", placement='right'),
shinyBS::tipify(checkboxInput("include_mid_progress", "include work-in-progress"), "include commented list of modules in Trash and their properties, See Modules", placement='right'),
shinyBS::tipify(shinyjs::disabled(checkboxInput("checkRelPaths", "write relative file paths")), "requires project root directory", placement='right'),
#
fluidRow(
column(3, shinyFiles::shinyDirButton("projectRootDir", "Set Project Root Directory", "Select Project Root Directory")),
column(9, verbatimTextOutput("showProjectDir", placeholder=TRUE))
),
fluidRow(
column(3, downloadButton("downloadData", "Download", width='80%')),
column(9, uiOutput("saveButton"))
),
p(),
verbatimTextOutput("configText", placeholder = TRUE)),
tabPanel("Load from file",
br(),
p(em("When you pull values from an existing file, the values from the file will replace anything configured here.")),
h2("Upoad configuration"),
p("This uses the file, but not its location; thus relative file paths are not converted to absolute paths."),
fileInput("uploadExistingConfig", label="Upload an existing config file", accept = c(".properties", ".config")),
shinyjs::disabled(actionButton("populateUploadedConfig", "pull values")),
hr(),
tabsetPanel(
id = "localExistingConfig",
type = "hidden",
tabPanelBody("remote", "When run locally, there is also an option to find local files."),
tabPanelBody("virtual", "When run locally, there is also an option to find local files."),
tabPanelBody("local",
h2("Local configuration"),
p("This will use the file AND its location, allowing for conversion between relative and absolute paths."),
shinyFiles::shinyFilesButton("LocalExistingConfig", "Choose a local config file", "Please select a file", multiple = FALSE, viewtype = "list"),
p(),
verbatimTextOutput("showLocalFile", placeholder=TRUE),
shinyjs::disabled(actionButton("populateFromLocalConfig", "pull values"))
)
),
hr(),
h2("Example configuration"),
p("This will use the read-only example project directory to reference relative files."),
uiOutput("examples"),
actionButton("populateExampleConfig", "pull values")
)
)
),
# Modules ####
tabPanel("Modules",
p("navbar"),p("spacer"),
fluidPage(
h2("BioModule Run Order"),
fluidRow(
column(5, uiOutput("selectModule")),
column(1, "AS", style = "margin-top: 30px;"),
column(4, textInput("newAlias", "",
placeholder = "alternative alias",
width = '100%')),
column(2, actionButton("AddModuleButton", style = "margin-top: 20px;", "add to pipeline", class = "btn-success"))),
uiOutput("manageModules"),
actionButton("emptyModuleTrash", "Empty Trash"),
hr(),
uiOutput("moduleSummary"))),
# Properties ####
tabPanel("Properties",
div(style="", splitLayout(
cellArgs = list(style='white-space: normal; padding-left: 0px; padding-right: 0px;'),
tagList(p("navbar"),p("spacer"),
h2("General Properties"),
checkboxInput("checkLiveFeedback", "show live feedback", value=FALSE),
p("General properties are not specific to any one module."),
tabsetPanel(
tabPanel(
"Backbone Properties",
uiOutput("genProps")),
tabPanel("Custom Properties",
p("Add custom properties here. All property names must be unique."),
p("Any property can reference the exact value of any other property, for example:"),
p("prop2 = build on ${prop1}"),
fluidRow(
column(4, textInput("customPropName","property name")),
column(5, textInput("customPropVal", "= value")),
column(3, actionButton("addCostomPropBtn", "add", style = "margin-top: 25px;"))),
h5("Current custom properties:"),
uiOutput("showCustomProps"),
br(),
h5("Custom values in default properties files:"),
em("These are not included as part of the current config file."),
uiOutput("showDefaultCustomProps"))
)),
tagList(p("navbar"),p("spacer"),
h2("Module Properties"),
textOutput("modulePropsHeader"),
uiOutput("modProps")
)
))),
# Precheck ####
tabPanel("Precheck",
p("navbar"),p("spacer"),
sidebarLayout(
sidebarPanel(
# width=5,
h3("command options"),
checkboxInput("callJavaDirectly", "direct call to java", value=TRUE),
h4("flags"),
checkboxInput("checkPrecheck", "--precheck-only", value=TRUE),
checkboxInput("checkUnused", "--unused-props", value=FALSE),
checkboxInput("checkDocker", "--docker", value=FALSE),
# checkboxInput("checkAws", "--aws", value=FALSE),
checkboxInput("checkForground", "--foreground", value=FALSE),
checkboxInput("checkVerbose", "--verbose", value=FALSE),
checkboxInput("checkMapBlj", "--blj", value=FALSE),
h4("arguments"),
p("When running locally, values for these arguments are set in Settings. Otherwise, these options are unavailable."),
checkboxInput("useExtMods", "--external-modules"),
checkboxInput("useBljProj", "--blj_proj")
),
mainPanel(
# width=7,
h3("Test current configuration"),
p("Pass this config file to BioLockJ to build the pipeline and check dependencies. This does not actually execute the pipeline (because we include the --precheck-only flag), but it rus the initial phases to look for potential problems."),
h4("biolockj command:"),
verbatimTextOutput("precheckCommand"),
actionButton("runPrecheckBtn", "Run Precheck", class = "btn-success"),
h4("command output:"),
uiOutput("precheckOutput")
)
)),
# Defaults ####
tabPanel("Defaults",
p("navbar"),p("spacer"),
fluidPage(
h2("Chain default properties"),
em("(optional)"),
p(em("The property 'pipeline.defaultProps=[file]' allows you to use property values from another file. That file may also include a reference to another file creating a chain. When you run the pipeline, BioLockJ puts all the properties together. Properties defined in multiple files are set according the most recent value in the chain.")),
h4("Locate defaults"),
em("This does not affect your configuration."),
br(),br(),
checkboxInput("ignoreChain", "ignore pipeline.defaultProps in this file", value=FALSE),
tabsetPanel(
id = "localDefaultPropsFinder",
type = "hidden",
tabPanelBody("remote", fileInput("defaultPropsFiles", label="upload default properties files", multiple = TRUE,
accept = c(".properties", ".config"))),
tabPanelBody("virtual", "When run locally, there is also an option to find local files."),
tabPanelBody("local", shinyFiles::shinyFilesButton("findLocalDefaultProps",
"Find properties files",
"Select files...",
multiple = TRUE))
),
br(),
tableOutput("chainableFiles"),
h4("Select defaults"),
em("This is what sets the pipeline.defaultProps for your current pipeline, and the defaults that are reflected throughout this configuration."),
shinyjs::disabled(selectInput("selectDefaultProps", "pipeline.defaultProps", choices = c(none=""), multiple=TRUE)),
tableOutput("chainedFiles"),
shinyjs::disabled(actionButton("loadDefaultProps", "set as defaults")),
h4("Current defaults"),
verbatimTextOutput("currentDefaultProps")
)),
# Settings ####
tabPanel("Settings",
p("navbar"),p("spacer"),
fluidPage(
h2("Settings"),
p("Control aspects of this user interface."),
h4("File access"),
shinyjs::disabled(radioButtons("serverType", "How should this interface access files?",
choiceNames = list("remote server", "local virtual server", "local machine"),
choiceValues = c("remote", "virtual", "local"), inline=TRUE,
selected = envType ) ),
br(),
hr(),
h4("BioLockJ version: "),
textOutput("bljVersion"),
hr(),
uiOutput("coreSettings")
# shinyFiles::shinyFilesButton("biolockjJarFile", "BioLockJ Jar File Location", "Choose jar file", multiple=FALSE, accept=c(".jar"), width='100%'),
# actionButton("updateJar", "update jar location"),
# verbatimTextOutput("showNewJarFile")
)),
# Help ####
tabPanel("Help",
p("navbar"),p("spacer"),
includeMarkdown(helpMdFile))
))
) # end of UI ####
return(ui)
}
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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