From 82c01822385ff33139b00e9204940aa0cffb2817 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Sun, 17 Apr 2022 06:59:43 -0400 Subject: [PATCH 01/27] create getChartStatus() and add basic tests. #562 --- NAMESPACE | 2 + R/getChartStatus.R | 69 +++++++++++++++++++++ R/mod_safetyGraphicsServer.R | 2 +- R/prepareChart.R | 8 +++ man/getChartStatus.Rd | 47 ++++++++++++++ tests/testthat/test_getChartStatus.R | 92 ++++++++++++++++++++++++++++ 6 files changed, 219 insertions(+), 1 deletion(-) create mode 100644 R/getChartStatus.R create mode 100644 man/getChartStatus.Rd create mode 100644 tests/testthat/test_getChartStatus.R diff --git a/NAMESPACE b/NAMESPACE index 61095cdd..a28e7476 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -59,6 +59,8 @@ importFrom(magrittr,"%>%") importFrom(purrr,keep) importFrom(purrr,map) importFrom(purrr,map2) +importFrom(purrr,map_lgl) +importFrom(purrr,set_names) importFrom(rlang,.data) importFrom(shiny,dataTableOutput) importFrom(shiny,renderDataTable) diff --git a/R/getChartStatus.R b/R/getChartStatus.R new file mode 100644 index 00000000..5890d112 --- /dev/null +++ b/R/getChartStatus.R @@ -0,0 +1,69 @@ +#' Check the status of a chart based on the current mapping +#' +#' Checks a chart's status when column-level chart specifications are provided in chart$dataSpec. Note that safetyGraphicsApp() does not allow a `mapping` value that is not found in `domainData`, so this function only needs to check that an expected parameter exists in `mapping` (not that the specified column is found in the loaded data). +#' +#' Returns a list, with: +#' - `status` (TRUE, FALSE) +#' - `domains` a list specifying wheter all columns are specified in each domain +#' - `columns` a list that matches the structure of chart$dataSpec and indicates which variables are available. +#' +#' @param chart chart object +#' @param mapping the current mapping data.frame +#' +#' @return a list with `status`, `domains` and `columns` properties +#' +#' @examples +#' sample_chart <- list( +#' domains=c("aes","dm"), +#' dataSpec=list( +#' aes=c("id_col","custom_col"), +#' dm=c("id_col","test_col") +#' ) +#' ) +#' +#' sample_mapping <- data.frame( +#' domain=c("aes","aes","dm","dm"), +#' text_key=c("id_col","custom_col","id_col","test_col"), +#' current=c("myID","AEcol","myID","dmCol") +#' ) +#' +#' check <- getChartStatus(chart=ae_chart, mapping=mapping) +#' # check$status=TRUE +#' +#' @importFrom purrr map_lgl set_names +#' @keywords internal + +getChartStatus <- function(chart, mapping){ + stopifnot( + "Can't get status since chart does not have dataSpec associated."=hasName(chart, 'dataSpec') + ) + + # check to see whether each individual column has a mapping defined + colStatus <- names(chart$dataSpec) %>% map(function(domain){ + domainMapping <- generateMappingList(settingsDF=mapping, domain=domain) + requiredCols <- chart$dataSpec[[domain]] + colStatus <- requiredCols %>% map(function(col){ + if(hasName(domainMapping,col)){ + status<-case_when( + domainMapping[[col]]=='' ~ FALSE, + is.na(domainMapping[[col]]) ~ FALSE, + is.character(domainMapping[[col]]) ~ TRUE + ) + } else{ + status<-FALSE + } + return(status) + }) %>% set_names(requiredCols) + return(colStatus) + })%>% set_names(names(chart$dataSpec)) + + # check to see whether all columns in a domain were valid + domainStatus <- colStatus %>% + map(~all(unlist(.x))) %>% + set_names(names(colStatus)) + + # check to see whether all columns in all domains were valid + status <- all(unlist(domainStatus)) + + return(list(columns=colStatus, domains=domainStatus, status=status)) +} \ No newline at end of file diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index 0d7e4b85..c9a76ec2 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -33,7 +33,7 @@ safetyGraphicsServer <- function(input, output, session, meta, mapping, domainDa callModule(homeTab, "home") - #Initialize Chart UI - Adds subtabs to chart menu - this initializes initializes chart UIs + #Initialize Chart UI - Adds subtabs to chart menu - this initializes the chart UIs charts %>% purrr::map(~chartsNav(.x,session$ns)) #Initialize Chart Servers diff --git a/R/prepareChart.R b/R/prepareChart.R index 71ffebc4..cc19aecf 100644 --- a/R/prepareChart.R +++ b/R/prepareChart.R @@ -37,6 +37,14 @@ prepareChart <- function(chart){ tolower(chart$env)=="safetygraphics" ) + # check to see if data specifications are provided in domain + if(typeof(chart$domain)=="list"){ + if(!hasName(chart,"dataSpec")){ + chart$dataSpec <- chart$domain + } + chart$domain <- names(chart$domain) + } + #### Bind Workflow functions to chart object #### if(!hasName(chart,"functions")){ diff --git a/man/getChartStatus.Rd b/man/getChartStatus.Rd new file mode 100644 index 00000000..2ee7d076 --- /dev/null +++ b/man/getChartStatus.Rd @@ -0,0 +1,47 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getChartStatus.R +\name{getChartStatus} +\alias{getChartStatus} +\title{Check the status of a chart based on the current mapping} +\usage{ +getChartStatus(chart, mapping) +} +\arguments{ +\item{chart}{chart object} + +\item{mapping}{the current mapping data.frame} +} +\value{ +a list with \code{status}, \code{domains} and \code{columns} properties +} +\description{ +Checks a chart's status when column-level chart specifications are provided in chart$dataSpec. Note that safetyGraphicsApp() does not allow a \code{mapping} value that is not found in \code{domainData}, so this function only needs to check that an expected parameter exists in \code{mapping} (not that the specified column is found in the loaded data). +} +\details{ +Returns a list, with: +\itemize{ +\item \code{status} (TRUE, FALSE) +\item \code{domains} a list specifying wheter all columns are specified in each domain +\item \code{columns} a list that matches the structure of chart$dataSpec and indicates which variables are available. +} +} +\examples{ +sample_chart <- list( + domains=c("aes","dm"), + dataSpec=list( + aes=c("id_col","custom_col"), + dm=c("id_col","test_col") + ) +) + +sample_mapping <- data.frame( + domain=c("aes","aes","dm","dm"), + text_key=c("id_col","custom_col","id_col","test_col"), + current=c("myID","AEcol","myID","dmCol") +) + +check <- getChartStatus(chart=ae_chart, mapping=mapping) +# check$status=TRUE + +} +\keyword{internal} diff --git a/tests/testthat/test_getChartStatus.R b/tests/testthat/test_getChartStatus.R new file mode 100644 index 00000000..f0586ec4 --- /dev/null +++ b/tests/testthat/test_getChartStatus.R @@ -0,0 +1,92 @@ +context("Tests for the getChartStatus() function") +library(safetyGraphics) +library(safetyCharts) + +# Functional Specification +# [*] chart with no data spec throws error +# [*] status returned correctly for valid chart +# [*] status returned correctly when mapping values for a column are '' and NA +# [*] status returned correctly when dataSpec is not found in mapping + +test_that("chart with no data spec throws error",{ + expect_error(chart=list(domains=c("ae","dm"))) +}) + +test_that("status returned correctly for valid chart",{ + ae_chart <- list( + domains=c("aes","dm"), + dataSpec=list( + aes=c("id_col","custom_col"), + dm=c("id_col","test_col") + ) + ) + + mapping <- data.frame( + domain=c("aes","aes","dm","dm"), + text_key=c("id_col","custom_col","id_col","test_col"), + current=c("myID","AEcol","myID","dmCol") + ) + + status<-getChartStatus(chart=ae_chart, mapping=mapping) + expect_true(status$status) + expect_true(status$domains$aes) + expect_true(status$domains$dm) + expect_true(status$columns$aes$id_col) + expect_true(status$columns$aes$custom_col) + expect_true(status$columns$dm$id_col) + expect_true(status$columns$dm$test_col) +}) + + +test_that("status returned correctly for invalid chart",{ + ae_chart <- list( + domains=c("aes","dm"), + dataSpec=list( + aes=c("id_col","custom_col"), + dm=c("id_col","test_col") + ) + ) + + mapping <- data.frame( + domain=c("aes","aes","dm","dm"), + text_key=c("id_col","custom_col","id_col","test_col"), + current=c(NA,"","myID","dmCol") + ) + + status<-getChartStatus(chart=ae_chart, mapping=mapping) + expect_false(status$status) + expect_false(status$domains$aes) + expect_true(status$domains$dm) + expect_false(status$columns$aes$id_col) + expect_false(status$columns$aes$custom_col) + expect_true(status$columns$dm$id_col) + expect_true(status$columns$dm$test_col) +}) + + +test_that("status returned correctly for invalid chart",{ + ae_chart <- list( + domains=c("aes","dm"), + dataSpec=list( + aes=c("id_col","custom_col","another_col"), + dm=c("id_col","test_col") + ) + ) + + mapping <- data.frame( + domain=c("aes","aes","dm","dm"), + text_key=c("id_col","custom_col","id_col","test_col"), + current=c("myID","aesCol","myID","dmCol") + ) + ml<-generateMappingList(settingsDF=mapping, domain='aes') + expect_false(hasName(ml,"another_col")) + status<-getChartStatus(chart=ae_chart, mapping=mapping) + expect_false(status$status) + expect_false(status$domains$aes) + expect_true(status$domains$dm) + expect_true(status$columns$aes$id_col) + expect_true(status$columns$aes$custom_col) + expect_false(status$columns$aes$another_col) + expect_true(status$columns$dm$id_col) + expect_true(status$columns$dm$test_col) +}) From da59bf3103efd3471dbf4f91ca6e866c9a603fb1 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Mon, 18 Apr 2022 09:55:54 -0400 Subject: [PATCH 02/27] starting on UI updates --- R/getChartStatus.R | 6 +++--- R/makeChartSummary.R | 6 +++--- R/mod_safetyGraphicsServer.R | 42 +++++++++++++++++++++++++++--------- inst/www/index.css | 16 ++++++++++++++ 4 files changed, 54 insertions(+), 16 deletions(-) diff --git a/R/getChartStatus.R b/R/getChartStatus.R index 5890d112..7617c4f9 100644 --- a/R/getChartStatus.R +++ b/R/getChartStatus.R @@ -8,7 +8,7 @@ #' - `columns` a list that matches the structure of chart$dataSpec and indicates which variables are available. #' #' @param chart chart object -#' @param mapping the current mapping data.frame +#' @param mapping the current mapping data.frame #' #' @return a list with `status`, `domains` and `columns` properties #' @@ -63,7 +63,7 @@ getChartStatus <- function(chart, mapping){ set_names(names(colStatus)) # check to see whether all columns in all domains were valid - status <- all(unlist(domainStatus)) + status <- ifelse(all(unlist(domainStatus)),"valid","invalid") - return(list(columns=colStatus, domains=domainStatus, status=status)) + return(list(chart=chart$name, columns=colStatus, domains=domainStatus, status=status)) } \ No newline at end of file diff --git a/R/makeChartSummary.R b/R/makeChartSummary.R index 450b30f9..cfcb7840 100644 --- a/R/makeChartSummary.R +++ b/R/makeChartSummary.R @@ -24,9 +24,9 @@ makeChartSummary<- function(chart, showLinks=TRUE, class="chart-header"){ links<-NULL } - labelDiv<-div(tags$small("Chart"),chart$label) - typeDiv<-div(tags$small("Type"), chart$type) - dataDiv<-div(tags$small("Data Domain"), paste(chart$domain,collapse=" ")) + labelDiv<-div(class="name", tags$small("Chart"),chart$label) + typeDiv<-div(class="type", tags$small("Type"), chart$type) + dataDiv<-div(class="domain", tags$small("Data Domain"), paste(chart$domain,collapse=" ")) if(showLinks){ summary<-div( diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index c9a76ec2..fd0a640f 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -14,15 +14,15 @@ #' @import shiny #' @import dplyr #' @importFrom purrr map -#' @importFrom shinyjs html +#' @importFrom shinyjs html toggleClass #' #' @export safetyGraphicsServer <- function(input, output, session, meta, mapping, domainData, charts, filterDomain){ - #Initialize modules - current_mapping<-callModule(mappingTab, "mapping", meta, domainData) + # Initialize the Home tab + callModule(homeTab, "home") - # Initialize the filter tab + # Initialize the Filter tab - returns list of filtered data as a reactive filtered_data<-callModule( filterTab, "filter", @@ -30,14 +30,15 @@ safetyGraphicsServer <- function(input, output, session, meta, mapping, domainDa filterDomain=filterDomain, current_mapping=current_mapping ) - - callModule(homeTab, "home") - #Initialize Chart UI - Adds subtabs to chart menu - this initializes the chart UIs + # Initialize the Mapping tab - returns the current mapping as a reactive + current_mapping<-callModule(mappingTab, "mapping", meta, domainData) + + # Initialize Charts tab + # Initialize Chart UI - adds subtabs to chart menu and initializes the chart UIs charts %>% purrr::map(~chartsNav(.x,session$ns)) - #Initialize Chart Servers - validDomains <- tolower(names(mapping)) + # Initialize Chart Servers charts %>% purrr::map( ~callModule( module=chartsTab, @@ -48,7 +49,28 @@ safetyGraphicsServer <- function(input, output, session, meta, mapping, domainDa ) ) - #Setting tab + # Keep chart status updated + charts_status <- reactive({ + charts %>% purrr::map(function(chart){ + if(hasName(chart, 'dataSpec')){ + getChartStatus(chart,current_mapping()) + }else{ + list(chart=chart$name,status="missing") + } + }) + }) + + observeEvent(charts_status(),{ + for (check in charts_status()){ + ## code to toggle css for chart-specific tab here + shinyjs::toggleClass(selector= paste0("#sg-safetyGraphicsApp li.dropdown ul li a[data-value='", check$chart, "']"), class="valid", condition=check$status=="valid") + shinyjs::toggleClass(selector= paste0("#sg-safetyGraphicsApp li.dropdown ul li a[data-value='", check$chart, "']"), class="invalid", condition=check$status=="invalid") + shinyjs::toggleClass(selector= paste0("#sg-safetyGraphicsApp li.dropdown ul li a[data-value='", check$chart, "']"), class="missing", condition=check$status=="missing") + + } + }) + + # Initialize the Setting tab callModule(settingsTab, "settings", domains = domainData, metadata=meta, mapping=current_mapping, charts = charts) } diff --git a/inst/www/index.css b/inst/www/index.css index efdc5f3c..bec8866a 100644 --- a/inst/www/index.css +++ b/inst/www/index.css @@ -149,3 +149,19 @@ table.metatable.dataTable tr > td:last-of-type, table.metatable.trdataTable tr > } +/* chart validation formatting */ +#sg-safetyGraphicsApp li.dropdown ul li a.valid div div.name:before { + font-family: "Font Awesome 5 Free"; + font-weight: 900; + content: "\f00c"; + color: green; + padding-left: 0.3em; +} + +#sg-safetyGraphicsApp li.dropdown ul li a.invalid div div.name:before { + font-family: "Font Awesome 5 Free"; + font-weight: 900; + content: "\f00d"; + color: red; + padding-left: 0.3em; +} From 3df73c56ce1ca0023ce7e7b1ca095b268a125ad0 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Mon, 23 May 2022 15:21:16 -0400 Subject: [PATCH 03/27] Update R/getChartStatus.R Co-authored-by: Becca Krouse --- R/getChartStatus.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/getChartStatus.R b/R/getChartStatus.R index 7617c4f9..668e1b4c 100644 --- a/R/getChartStatus.R +++ b/R/getChartStatus.R @@ -63,7 +63,7 @@ getChartStatus <- function(chart, mapping){ set_names(names(colStatus)) # check to see whether all columns in all domains were valid - status <- ifelse(all(unlist(domainStatus)),"valid","invalid") + status <- ifelse(all(unlist(domainStatus)),TRUE, FALSE) return(list(chart=chart$name, columns=colStatus, domains=domainStatus, status=status)) } \ No newline at end of file From 4919803abcadb71b23ca2882766b6ffbb495ffcd Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Tue, 24 May 2022 11:20:55 -0400 Subject: [PATCH 04/27] refactor chart modules to simplify reactive flow --- R/mod_chartsNav.R | 45 ++++++++++++++++++++++++++---------- R/mod_chartsTab.R | 7 +++++- R/mod_safetyGraphicsServer.R | 27 +++------------------- R/mod_safetyGraphicsUI.R | 12 ++++++++-- R/safetyGraphicsApp.R | 9 +++++++- R/safetyGraphicsInit.R | 1 + 6 files changed, 61 insertions(+), 40 deletions(-) diff --git a/R/mod_chartsNav.R b/R/mod_chartsNav.R index 6904a81e..7a1c80d8 100644 --- a/R/mod_chartsNav.R +++ b/R/mod_chartsNav.R @@ -1,22 +1,43 @@ #' Adds a navbar tab that initializes the Chart Module UI #' +#' @param id #' @param chart chart metadata -#' @param ns namespace #' #' @export #' -chartsNav <- function(chart,ns){ - appendTab( - inputId = "safetyGraphicsApp", - menuName = "Charts", - tab = tabPanel( - title = makeChartSummary(chart, showLinks=FALSE, class="chart-nav"), - value = chart$name, - chartsTabUI( - id=ns(chart$name), - chart=chart - ) +chartsNavUI <- function(id, chart){ + ns <- NS(id) + panel<-tabPanel( + title = uiOutput(ns("tabTitle")), + value = chart$name, + chartsTabUI( + id=ns("chart"), + chart=chart ) ) + return(panel) +} + +#' Server for a navbar tab +#' +#' @param chart chart metadata +#' +#' @export +#' + +chartsNav<-function(input, output, session, chart, data, mapping){ + #status <- getChartStatus(chart,current_mapping) + + ns <- session$ns + print(paste("running chartsNav() in:", ns(''))) + output$tabTitle <- renderUI({makeChartSummary(chart, showLinks=FALSE, class="chart-nav")}) + + callModule( + module=chartsTab, + id='chart', + chart=chart, + data=data, + mapping=mapping + ) } \ No newline at end of file diff --git a/R/mod_chartsTab.R b/R/mod_chartsTab.R index 7b274b5f..a4a59f3a 100644 --- a/R/mod_chartsTab.R +++ b/R/mod_chartsTab.R @@ -10,7 +10,7 @@ chartsTabUI <- function(id, chart){ ns <- shiny::NS(id) - header<-div(class=ns("header"), makeChartSummary(chart)) + header<- uiOutput(ns("chart-header")) chartWrap<-chart$functions$ui(ns("chart-wrap")) return(list(header, chartWrap)) @@ -30,6 +30,11 @@ chartsTabUI <- function(id, chart){ chartsTab <- function(input, output, session, chart, data, mapping){ ns <- session$ns + print(paste("running chartsTab in:", ns(''))) + + # Draw the header + output$`chart-header` <- renderUI({makeChartSummary(chart)}) + # Initialize chart-specific parameters params <- reactive({ makeChartParams( diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index fd0a640f..a8b807d4 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -36,40 +36,19 @@ safetyGraphicsServer <- function(input, output, session, meta, mapping, domainDa # Initialize Charts tab # Initialize Chart UI - adds subtabs to chart menu and initializes the chart UIs - charts %>% purrr::map(~chartsNav(.x,session$ns)) + #charts %>% purrr::map(~chartsNavUI(.x$name,.x)) # Initialize Chart Servers charts %>% purrr::map( ~callModule( - module=chartsTab, + module=chartsNav, id=.x$name, chart=.x, data=filtered_data, - mapping=current_mapping + mapping=current_mapping ) ) - # Keep chart status updated - charts_status <- reactive({ - charts %>% purrr::map(function(chart){ - if(hasName(chart, 'dataSpec')){ - getChartStatus(chart,current_mapping()) - }else{ - list(chart=chart$name,status="missing") - } - }) - }) - - observeEvent(charts_status(),{ - for (check in charts_status()){ - ## code to toggle css for chart-specific tab here - shinyjs::toggleClass(selector= paste0("#sg-safetyGraphicsApp li.dropdown ul li a[data-value='", check$chart, "']"), class="valid", condition=check$status=="valid") - shinyjs::toggleClass(selector= paste0("#sg-safetyGraphicsApp li.dropdown ul li a[data-value='", check$chart, "']"), class="invalid", condition=check$status=="invalid") - shinyjs::toggleClass(selector= paste0("#sg-safetyGraphicsApp li.dropdown ul li a[data-value='", check$chart, "']"), class="missing", condition=check$status=="missing") - - } - }) - # Initialize the Setting tab callModule(settingsTab, "settings", domains = domainData, metadata=meta, mapping=current_mapping, charts = charts) } diff --git a/R/mod_safetyGraphicsUI.R b/R/mod_safetyGraphicsUI.R index 523b0a22..03e36288 100644 --- a/R/mod_safetyGraphicsUI.R +++ b/R/mod_safetyGraphicsUI.R @@ -2,6 +2,7 @@ #' #' #' @param id module ID +#' @param charts list of charts in the format produced by safetyGraphics::makeChartConfig() #' @param meta data frame containing the metadata for use in the app. #' @param domainData named list of data.frames to be loaded in to the app. #' @param mapping data.frame specifying the initial values for each data mapping. If no mapping is provided, the app will attempt to generate one via \code{detectStandard()} @@ -11,7 +12,7 @@ #' #' @export -safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){ +safetyGraphicsUI <- function(id, meta, charts, domainData, mapping, standards){ ns<-NS(id) #read css from package @@ -37,6 +38,13 @@ safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){ spinner<-NULL } + #Set up ChartNav + #trick for navbar menu: https://stackoverflow.com/questions/34846469/for-loops-lapply-navbarpage-within-in-ui-r + + chartList <- charts %>% purrr::map(~chartsNavUI(ns(.x$name),.x)) %>% unname + navParams<-c(list(title='Charts', icon=icon("chart-bar")), chartList) + chartNav <- do.call(navbarMenu, navParams) + #app UI using calls to modules ui<-tagList( shinyjs::useShinyjs(), @@ -55,7 +63,7 @@ safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){ tabPanel("Home", icon=icon("home"),homeTabUI(ns("home"))), tabPanel("Mapping", icon=icon("map"), mappingTabUI(ns("mapping"), meta, domainData, mapping, standards)), tabPanel("Filtering", icon=icon("filter"), filterTabUI(ns("filter"))), - navbarMenu('Charts', icon=icon("chart-bar")), + chartNav, tabPanel('',icon=icon("cog"), settingsTabUI(ns("settings"))) ), participant_badge diff --git a/R/safetyGraphicsApp.R b/R/safetyGraphicsApp.R index 9ba1a102..33e2bdb7 100644 --- a/R/safetyGraphicsApp.R +++ b/R/safetyGraphicsApp.R @@ -32,7 +32,14 @@ safetyGraphicsApp <- function( config <- app_startup(domainData, meta, charts, mapping, autoMapping, filterDomain, chartSettingsPaths) app <- shinyApp( - ui = safetyGraphicsUI("sg",config$meta, config$domainData, config$mapping, config$standards), + ui = safetyGraphicsUI( + "sg", + config$meta, + config$charts, + config$domainData, + config$mapping, + config$standards + ), server = function(input,output,session){ callModule( safetyGraphicsServer, diff --git a/R/safetyGraphicsInit.R b/R/safetyGraphicsInit.R index 39762f63..ff7be5ea 100644 --- a/R/safetyGraphicsInit.R +++ b/R/safetyGraphicsInit.R @@ -130,6 +130,7 @@ safetyGraphicsInit <- function(charts=makeChartConfig(), delayTime=1000, maxFile safetyGraphicsUI( "sg", config$meta, + config$charts, config$domainData, config$mapping, config$standards From c68d0be76a1d681041619191a464b77f4f444c04 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Tue, 24 May 2022 12:57:00 -0400 Subject: [PATCH 05/27] add basic UI for chart status --- R/makeChartSummary.R | 17 +++++++++++++++-- R/mod_chartsNav.R | 16 ++++++++++++---- R/mod_chartsTab.R | 4 ++-- inst/www/index.css | 20 +------------------- 4 files changed, 30 insertions(+), 27 deletions(-) diff --git a/R/makeChartSummary.R b/R/makeChartSummary.R index cfcb7840..68c8d290 100644 --- a/R/makeChartSummary.R +++ b/R/makeChartSummary.R @@ -7,7 +7,18 @@ #' #' @export -makeChartSummary<- function(chart, showLinks=TRUE, class="chart-header"){ +makeChartSummary<- function(chart, status=NULL, showLinks=TRUE, class="chart-header"){ + + if(!is.null(status)){ + if(status$status){ + status <- div(class="status", tags$i(class="fa fa-check-circle", style="color: green")) + }else{ + status <- div(class="status", tags$i(class="fa fa-times-circle", style="color: red")) + } + }else{ + status <- NULL + } + if(utils::hasName(chart,"links")){ links<-purrr::map2( chart$links, @@ -23,13 +34,14 @@ makeChartSummary<- function(chart, showLinks=TRUE, class="chart-header"){ }else{ links<-NULL } - + labelDiv<-div(class="name", tags$small("Chart"),chart$label) typeDiv<-div(class="type", tags$small("Type"), chart$type) dataDiv<-div(class="domain", tags$small("Data Domain"), paste(chart$domain,collapse=" ")) if(showLinks){ summary<-div( + status, labelDiv, typeDiv, dataDiv, @@ -38,6 +50,7 @@ makeChartSummary<- function(chart, showLinks=TRUE, class="chart-header"){ ) } else { summary<-div( + status, labelDiv, typeDiv, dataDiv, diff --git a/R/mod_chartsNav.R b/R/mod_chartsNav.R index 7a1c80d8..d01795b0 100644 --- a/R/mod_chartsNav.R +++ b/R/mod_chartsNav.R @@ -21,23 +21,31 @@ chartsNavUI <- function(id, chart){ #' Server for a navbar tab #' -#' @param chart chart metadata +#' @param chart chart metadata #' #' @export #' chartsNav<-function(input, output, session, chart, data, mapping){ - #status <- getChartStatus(chart,current_mapping) + chartStatus <- reactive({ + if(hasName(chart, 'dataSpec')){ + status<-getChartStatus(chart, mapping()) + }else{ + status<-NULL + } + return(status) + }) ns <- session$ns print(paste("running chartsNav() in:", ns(''))) - output$tabTitle <- renderUI({makeChartSummary(chart, showLinks=FALSE, class="chart-nav")}) + output$tabTitle <- renderUI({makeChartSummary(chart, status=chartStatus(), showLinks=FALSE, class="chart-nav")}) callModule( module=chartsTab, id='chart', chart=chart, data=data, - mapping=mapping + mapping=mapping, + status=chartStatus ) } \ No newline at end of file diff --git a/R/mod_chartsTab.R b/R/mod_chartsTab.R index a4a59f3a..ac0cc113 100644 --- a/R/mod_chartsTab.R +++ b/R/mod_chartsTab.R @@ -27,13 +27,13 @@ chartsTabUI <- function(id, chart){ #' #' @export -chartsTab <- function(input, output, session, chart, data, mapping){ +chartsTab <- function(input, output, session, chart, data, mapping, status){ ns <- session$ns print(paste("running chartsTab in:", ns(''))) # Draw the header - output$`chart-header` <- renderUI({makeChartSummary(chart)}) + output$`chart-header` <- renderUI({makeChartSummary(chart, status=status())}) # Initialize chart-specific parameters params <- reactive({ diff --git a/inst/www/index.css b/inst/www/index.css index 8bee564c..f1226335 100644 --- a/inst/www/index.css +++ b/inst/www/index.css @@ -130,7 +130,7 @@ table.metatable.dataTable tr > td:last-of-type, table.metatable.trdataTable tr > display:inline-block; } -.chart-nav div:not(:first-child){ +.chart-nav div:not(.name){ font-size:0.8em; color: #999; } @@ -151,21 +151,3 @@ table.metatable.dataTable tr > td:last-of-type, table.metatable.trdataTable tr > background-color: #d1ecf1; border:1px solid #bee5eb; } - - -/* chart validation formatting */ -#sg-safetyGraphicsApp li.dropdown ul li a.valid div div.name:before { - font-family: "Font Awesome 5 Free"; - font-weight: 900; - content: "\f00c"; - color: green; - padding-left: 0.3em; -} - -#sg-safetyGraphicsApp li.dropdown ul li a.invalid div div.name:before { - font-family: "Font Awesome 5 Free"; - font-weight: 900; - content: "\f00d"; - color: red; - padding-left: 0.3em; -} From 44bf28fee676672ca93240f95a094bacab5825c2 Mon Sep 17 00:00:00 2001 From: jwildfire Date: Tue, 24 May 2022 21:29:51 -0400 Subject: [PATCH 06/27] clear checks --- DESCRIPTION | 2 +- NAMESPACE | 2 ++ R/getChartStatus.R | 2 +- R/makeChartSummary.R | 1 + R/mod_chartsNav.R | 11 ++++++++--- R/mod_chartsTab.R | 1 + R/mod_safetyGraphicsUI.R | 3 +-- man/chartsNav.Rd | 18 +++++++++++++----- man/chartsNavUI.Rd | 16 ++++++++++++++++ man/chartsTab.Rd | 4 +++- man/getChartStatus.Rd | 2 +- man/makeChartSummary.Rd | 9 ++++++++- man/safetyGraphicsUI.Rd | 4 +++- 13 files changed, 59 insertions(+), 16 deletions(-) create mode 100644 man/chartsNavUI.Rd diff --git a/DESCRIPTION b/DESCRIPTION index 34ba1647..3cd5d132 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,7 +16,7 @@ Depends: R (>= 4.0) License: MIT + file LICENSE Encoding: UTF-8 LazyData: true -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.0 Suggests: ggplot2 (>= 3.3.0), knitr (>= 1.34), diff --git a/NAMESPACE b/NAMESPACE index a28e7476..6c11b797 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,6 +3,7 @@ export("%>%") export(app_startup) export(chartsNav) +export(chartsNavUI) export(chartsTab) export(chartsTabUI) export(detectStandard) @@ -74,6 +75,7 @@ importFrom(shinyjs,hide) importFrom(shinyjs,html) importFrom(shinyjs,removeClass) importFrom(shinyjs,show) +importFrom(shinyjs,toggleClass) importFrom(shinyjs,useShinyjs) importFrom(sortable,add_rank_list) importFrom(sortable,bucket_list) diff --git a/R/getChartStatus.R b/R/getChartStatus.R index 668e1b4c..bfceee39 100644 --- a/R/getChartStatus.R +++ b/R/getChartStatus.R @@ -27,7 +27,7 @@ #' current=c("myID","AEcol","myID","dmCol") #' ) #' -#' check <- getChartStatus(chart=ae_chart, mapping=mapping) +#' check <- safetyGraphics:::getChartStatus(chart=sample_chart, mapping=sample_mapping) #' # check$status=TRUE #' #' @importFrom purrr map_lgl set_names diff --git a/R/makeChartSummary.R b/R/makeChartSummary.R index 68c8d290..07b664fe 100644 --- a/R/makeChartSummary.R +++ b/R/makeChartSummary.R @@ -2,6 +2,7 @@ #' @description makes a nicely formatted html summary for a chart object #' #' @param chart list containing chart specifications +#' @param status (optional) chart status from `getChartStatus`. Default is NULL. #' @param showLinks boolean indicating whether to include links #' @param class character to include as class #' diff --git a/R/mod_chartsNav.R b/R/mod_chartsNav.R index d01795b0..c69c257f 100644 --- a/R/mod_chartsNav.R +++ b/R/mod_chartsNav.R @@ -1,7 +1,7 @@ #' Adds a navbar tab that initializes the Chart Module UI #' -#' @param id -#' @param chart chart metadata +#' @param id module id +#' @param chart chart metadata #' #' @export #' @@ -21,7 +21,12 @@ chartsNavUI <- function(id, chart){ #' Server for a navbar tab #' -#' @param chart chart metadata +#' @param input Input objects from module namespace +#' @param output Output objects from module namespace +#' @param session An environment that can be used to access information and functionality relating to the session +#' @param chart list containing a safetyGraphics chart object like those returned by \link{makeChartConfig}. +#' @param data named list of current data sets (Reactive). +#' @param mapping tibble capturing the current data mappings (Reactive). #' #' @export #' diff --git a/R/mod_chartsTab.R b/R/mod_chartsTab.R index ac0cc113..3ba4aa07 100644 --- a/R/mod_chartsTab.R +++ b/R/mod_chartsTab.R @@ -24,6 +24,7 @@ chartsTabUI <- function(id, chart){ #' @param chart list containing a safetyGraphics chart object like those returned by \link{makeChartConfig}. #' @param data named list of current data sets (Reactive). #' @param mapping tibble capturing the current data mappings (Reactive). +#' @param status chart status (Reactive) #' #' @export diff --git a/R/mod_safetyGraphicsUI.R b/R/mod_safetyGraphicsUI.R index 03e36288..e61f677a 100644 --- a/R/mod_safetyGraphicsUI.R +++ b/R/mod_safetyGraphicsUI.R @@ -1,6 +1,5 @@ #' UI for the core safetyGraphics app including Home, Mapping, Filter, Charts and Settings modules. #' -#' #' @param id module ID #' @param charts list of charts in the format produced by safetyGraphics::makeChartConfig() #' @param meta data frame containing the metadata for use in the app. @@ -12,7 +11,7 @@ #' #' @export -safetyGraphicsUI <- function(id, meta, charts, domainData, mapping, standards){ +safetyGraphicsUI <- function(id, charts, meta, domainData, mapping, standards){ ns<-NS(id) #read css from package diff --git a/man/chartsNav.Rd b/man/chartsNav.Rd index d0197e34..b46e9f65 100644 --- a/man/chartsNav.Rd +++ b/man/chartsNav.Rd @@ -2,15 +2,23 @@ % Please edit documentation in R/mod_chartsNav.R \name{chartsNav} \alias{chartsNav} -\title{Adds a navbar tab that initializes the Chart Module UI} +\title{Server for a navbar tab} \usage{ -chartsNav(chart, ns) +chartsNav(input, output, session, chart, data, mapping) } \arguments{ -\item{chart}{chart metadata} +\item{input}{Input objects from module namespace} -\item{ns}{namespace} +\item{output}{Output objects from module namespace} + +\item{session}{An environment that can be used to access information and functionality relating to the session} + +\item{chart}{list containing a safetyGraphics chart object like those returned by \link{makeChartConfig}.} + +\item{data}{named list of current data sets (Reactive).} + +\item{mapping}{tibble capturing the current data mappings (Reactive).} } \description{ -Adds a navbar tab that initializes the Chart Module UI +Server for a navbar tab } diff --git a/man/chartsNavUI.Rd b/man/chartsNavUI.Rd new file mode 100644 index 00000000..bc3cea1f --- /dev/null +++ b/man/chartsNavUI.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mod_chartsNav.R +\name{chartsNavUI} +\alias{chartsNavUI} +\title{Adds a navbar tab that initializes the Chart Module UI} +\usage{ +chartsNavUI(id, chart) +} +\arguments{ +\item{id}{module id} + +\item{chart}{chart metadata} +} +\description{ +Adds a navbar tab that initializes the Chart Module UI +} diff --git a/man/chartsTab.Rd b/man/chartsTab.Rd index 090efb6c..46d4985b 100644 --- a/man/chartsTab.Rd +++ b/man/chartsTab.Rd @@ -4,7 +4,7 @@ \alias{chartsTab} \title{Server for chart module, designed to be re-used for each chart generated.} \usage{ -chartsTab(input, output, session, chart, data, mapping) +chartsTab(input, output, session, chart, data, mapping, status) } \arguments{ \item{input}{Input objects from module namespace} @@ -18,6 +18,8 @@ chartsTab(input, output, session, chart, data, mapping) \item{data}{named list of current data sets (Reactive).} \item{mapping}{tibble capturing the current data mappings (Reactive).} + +\item{status}{chart status (Reactive)} } \description{ Server for chart module, designed to be re-used for each chart generated. diff --git a/man/getChartStatus.Rd b/man/getChartStatus.Rd index 2ee7d076..be1a5a86 100644 --- a/man/getChartStatus.Rd +++ b/man/getChartStatus.Rd @@ -40,7 +40,7 @@ sample_mapping <- data.frame( current=c("myID","AEcol","myID","dmCol") ) -check <- getChartStatus(chart=ae_chart, mapping=mapping) +check <- safetyGraphics:::getChartStatus(chart=sample_chart, mapping=sample_mapping) # check$status=TRUE } diff --git a/man/makeChartSummary.Rd b/man/makeChartSummary.Rd index e5e0ef9e..1bdda058 100644 --- a/man/makeChartSummary.Rd +++ b/man/makeChartSummary.Rd @@ -4,11 +4,18 @@ \alias{makeChartSummary} \title{html chart summary} \usage{ -makeChartSummary(chart, showLinks = TRUE, class = "chart-header") +makeChartSummary( + chart, + status = NULL, + showLinks = TRUE, + class = "chart-header" +) } \arguments{ \item{chart}{list containing chart specifications} +\item{status}{(optional) chart status from \code{getChartStatus}. Default is NULL.} + \item{showLinks}{boolean indicating whether to include links} \item{class}{character to include as class} diff --git a/man/safetyGraphicsUI.Rd b/man/safetyGraphicsUI.Rd index 99b312a5..bba5aeb7 100644 --- a/man/safetyGraphicsUI.Rd +++ b/man/safetyGraphicsUI.Rd @@ -4,11 +4,13 @@ \alias{safetyGraphicsUI} \title{UI for the core safetyGraphics app including Home, Mapping, Filter, Charts and Settings modules.} \usage{ -safetyGraphicsUI(id, meta, domainData, mapping, standards) +safetyGraphicsUI(id, charts, meta, domainData, mapping, standards) } \arguments{ \item{id}{module ID} +\item{charts}{list of charts in the format produced by safetyGraphics::makeChartConfig()} + \item{meta}{data frame containing the metadata for use in the app.} \item{domainData}{named list of data.frames to be loaded in to the app.} From ff390838ffc4211aa894fac76341f813e67f583f Mon Sep 17 00:00:00 2001 From: jwildfire Date: Tue, 24 May 2022 21:39:12 -0400 Subject: [PATCH 07/27] server/ui params --- R/safetyGraphicsApp.R | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/R/safetyGraphicsApp.R b/R/safetyGraphicsApp.R index 33e2bdb7..f2d8dc3f 100644 --- a/R/safetyGraphicsApp.R +++ b/R/safetyGraphicsApp.R @@ -33,22 +33,22 @@ safetyGraphicsApp <- function( app <- shinyApp( ui = safetyGraphicsUI( - "sg", - config$meta, - config$charts, - config$domainData, - config$mapping, - config$standards + id="sg", + meta=config$meta, + charts=config$charts, + domainData=config$domainData, + mapping=config$mapping, + standards=config$standards ), server = function(input,output,session){ callModule( safetyGraphicsServer, - "sg", - config$meta, - config$mapping, - config$domainData, - config$charts, - config$filterDomain + id="sg", + meta=config$meta, + mapping=config$mapping, + domainData=config$domainData, + charts=config$charts, + filterDomain=config$filterDomain ) } ) From caca325c4fd13b09b4f628fb0960e3455034eea7 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 2 Jun 2022 16:09:19 -0400 Subject: [PATCH 08/27] more ui updates --- R/getChartStatus.R | 23 +++++++++++++++++++++-- R/makeChartSummary.R | 11 +++++++---- R/mod_mappingColumn.R | 2 +- inst/www/index.css | 9 ++++++++- 4 files changed, 37 insertions(+), 8 deletions(-) diff --git a/R/getChartStatus.R b/R/getChartStatus.R index bfceee39..8644bec4 100644 --- a/R/getChartStatus.R +++ b/R/getChartStatus.R @@ -39,6 +39,7 @@ getChartStatus <- function(chart, mapping){ ) # check to see whether each individual column has a mapping defined + missingCols<-c() colStatus <- names(chart$dataSpec) %>% map(function(domain){ domainMapping <- generateMappingList(settingsDF=mapping, domain=domain) requiredCols <- chart$dataSpec[[domain]] @@ -51,7 +52,7 @@ getChartStatus <- function(chart, mapping){ ) } else{ status<-FALSE - } + } return(status) }) %>% set_names(requiredCols) return(colStatus) @@ -65,5 +66,23 @@ getChartStatus <- function(chart, mapping){ # check to see whether all columns in all domains were valid status <- ifelse(all(unlist(domainStatus)),TRUE, FALSE) - return(list(chart=chart$name, columns=colStatus, domains=domainStatus, status=status)) + # make a text summary + if(status){ + summary <- "All required mappings found" + }else{ + missingCols <- colStatus %>% imap(function(cols,domain){ + missingDomainCols <- cols %>% imap(function(status, col){ + if(status){ + return(NULL) + }else{ + return(paste0(domain,"$",col)) + } + }) + return(missingDomainCols) + }) + print(missingCols) + summary<- paste0("Missing Mappings: ",paste(unlist(missingCols),collapse=",")) + } + + return(list(chart=chart$name, columns=colStatus, domains=domainStatus, status=status, summary=summary)) } \ No newline at end of file diff --git a/R/makeChartSummary.R b/R/makeChartSummary.R index 07b664fe..2770983b 100644 --- a/R/makeChartSummary.R +++ b/R/makeChartSummary.R @@ -11,10 +11,11 @@ makeChartSummary<- function(chart, status=NULL, showLinks=TRUE, class="chart-header"){ if(!is.null(status)){ + print(status) if(status$status){ - status <- div(class="status", tags$i(class="fa fa-check-circle", style="color: green")) + status <- div(class="status", tags$small("Status"), tags$i(class="fa fa-check-circle", style="color: green"),title=status$summary) }else{ - status <- div(class="status", tags$i(class="fa fa-times-circle", style="color: red")) + status <- div(class="status", tags$small("Status"), tags$i(class="fa fa-times-circle", style="color: red"),title=status$summary) } }else{ status <- NULL @@ -40,21 +41,23 @@ makeChartSummary<- function(chart, status=NULL, showLinks=TRUE, class="chart-hea typeDiv<-div(class="type", tags$small("Type"), chart$type) dataDiv<-div(class="domain", tags$small("Data Domain"), paste(chart$domain,collapse=" ")) + class <- c('chart-summary',class) + if(showLinks){ summary<-div( - status, labelDiv, typeDiv, dataDiv, links, + status, class=class ) } else { summary<-div( - status, labelDiv, typeDiv, dataDiv, + status, class=class ) } diff --git a/R/mod_mappingColumn.R b/R/mod_mappingColumn.R index a08d2f29..b9b7ea25 100644 --- a/R/mod_mappingColumn.R +++ b/R/mod_mappingColumn.R @@ -33,7 +33,7 @@ mappingColumnUI <- function(id, meta, data, mapping=NULL){ col_meta <- meta %>% filter(.data$type=="column") # Exactly one column mapping provided - stopifnot(nrow(col_meta)==1) + stopifnot(msg = nrow(col_meta)==1) col_ui[[1]] <- mappingSelectUI( ns(col_meta$text_key), diff --git a/inst/www/index.css b/inst/www/index.css index f1226335..9dbe0bb9 100644 --- a/inst/www/index.css +++ b/inst/www/index.css @@ -135,7 +135,7 @@ table.metatable.dataTable tr > td:last-of-type, table.metatable.trdataTable tr > color: #999; } -.chart-nav div:last-child::before{ +.chart-nav div.domain::before{ content: "/"; } @@ -151,3 +151,10 @@ table.metatable.dataTable tr > td:last-of-type, table.metatable.trdataTable tr > background-color: #d1ecf1; border:1px solid #bee5eb; } + +/* Right align chart status */ +div.chart-header div.status{ + float:right; + cursor:help +} + From ae5a37dd2c3b3d903033ac6242724d4f876cfdfa Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Fri, 24 Jun 2022 11:07:55 -0400 Subject: [PATCH 09/27] fix #692: add app-level settings --- R/app_startup.R | 3 +- R/mod_homeTab.R | 50 ++++---------- R/mod_safetyGraphicsServer.R | 14 +++- R/mod_safetyGraphicsUI.R | 6 +- R/safetyGraphicsApp.R | 64 ++++++++++++++---- README.md | 2 +- docs/index.html | 2 +- .../noun_heart_rate_210541_ec5d57.png | Bin .../safetyGraphicsHex.png | Bin inst/resources/safetyGraphicsHomeTab.html | 24 +++++++ .../safetyHex.R | 4 +- 11 files changed, 108 insertions(+), 61 deletions(-) rename inst/{safetyGraphicsHex => resources}/noun_heart_rate_210541_ec5d57.png (100%) rename inst/{safetyGraphicsHex => resources}/safetyGraphicsHex.png (100%) create mode 100644 inst/resources/safetyGraphicsHomeTab.html rename inst/{safetyGraphicsHex => resources}/safetyHex.R (65%) diff --git a/R/app_startup.R b/R/app_startup.R index 0f23cc26..aa586860 100644 --- a/R/app_startup.R +++ b/R/app_startup.R @@ -9,7 +9,6 @@ #' @param autoMapping boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the `mapping` parameter overwrite automatically generated mappings when both are found. Defaults to true. #' @param filterDomain domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended. #' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R). All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details. -#' #' #' @return List of elements for used to initialize the shiny app with the following parameters #' \itemize{ @@ -85,4 +84,4 @@ app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, aut ) return(config) -} \ No newline at end of file +} diff --git a/R/mod_homeTab.R b/R/mod_homeTab.R index 06f83ede..d942bd4e 100644 --- a/R/mod_homeTab.R +++ b/R/mod_homeTab.R @@ -4,11 +4,11 @@ #' #' @export -homeTabUI <- function(id){ +homeTabUI <- function(id) { ns <- NS(id) fluidRow( - column(width=8, style='font-size:20px', uiOutput(outputId = ns("about"))), - column(width=4, imageOutput(outputId = ns("hex"))) + column(width=9, style='font-size:20px', uiOutput(outputId = ns("about"))), + column(width=3, imageOutput(outputId = ns("hex"))) ) } @@ -20,40 +20,20 @@ homeTabUI <- function(id){ #' #' @export -homeTab <- function(input, output, session){ +homeTab <- function(input, output, session, config) { ns <- session$ns - output$about <- renderUI({ - HTML(' -

Welcome to the Safety Graphics Shiny App

-

- The Safety Graphics Shiny app is an interactive tool for evaluating clinical trial safety using a flexible data pipeline. - This application and corresponding {safetyGraphics} R package have been developed as part of the Interactive Safety Graphics (ISG) workstream of the ASA Biopharm-DIA Safety Working Group. -

- -

Using the app

-

- Detailed instructions about using the app can be found in our vignette. - In short, the user will initialize the app with their data, adjust settings as needed, and view the interactive charts. - Finally, the user may export a self-contained, fully reproducible snapshot of the charts that can be easily shared with others. -

-

Charts

-

- The app is built to support a wide variety of chart types including static plots (e.g. from {ggplot2}), shiny modules, {htmlwidgets} and even static outputs like RTFs. - Several pre-configured charts are included in the companion {safetyCharts} R Package, and are available by default in the app. - Other charts can be added using the process descibed in this vignette. -

- -

- For more information about {safetyGraphics}, please visit our GitHub repository. - We also welcome your suggestions in our issue tracker. -

- ') + output$about <- renderUI({ + HTML(readLines(config$homeTabPath)) }) - - output$hex <- renderImage({ - list( - src = system.file("safetyGraphicsHex/safetyGraphicsHex.png", package = "safetyGraphics"), width="60%") - }, deleteFile = FALSE + + output$hex <- renderImage( + { + list( + src = config$hexPath, + width = "100%" + ) + }, + deleteFile = FALSE ) } diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index 0d7e4b85..2206fcb1 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -18,7 +18,17 @@ #' #' @export -safetyGraphicsServer <- function(input, output, session, meta, mapping, domainData, charts, filterDomain){ +safetyGraphicsServer <- function( + input, + output, + session, + meta, + mapping, + domainData, + charts, + filterDomain, + config +) { #Initialize modules current_mapping<-callModule(mappingTab, "mapping", meta, domainData) @@ -31,7 +41,7 @@ safetyGraphicsServer <- function(input, output, session, meta, mapping, domainDa current_mapping=current_mapping ) - callModule(homeTab, "home") + callModule(homeTab, "home", config) #Initialize Chart UI - Adds subtabs to chart menu - this initializes initializes chart UIs charts %>% purrr::map(~chartsNav(.x,session$ns)) diff --git a/R/mod_safetyGraphicsUI.R b/R/mod_safetyGraphicsUI.R index 523b0a22..c6f7d510 100644 --- a/R/mod_safetyGraphicsUI.R +++ b/R/mod_safetyGraphicsUI.R @@ -11,7 +11,7 @@ #' #' @export -safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){ +safetyGraphicsUI <- function(id, meta, domainData, mapping, standards, config) { ns<-NS(id) #read css from package @@ -50,9 +50,9 @@ safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){ ) ), navbarPage( - "safetyGraphics", + config$appName, id=ns("safetyGraphicsApp"), - tabPanel("Home", icon=icon("home"),homeTabUI(ns("home"))), + tabPanel("Home", icon=icon("home"), homeTabUI(ns("home"))), tabPanel("Mapping", icon=icon("map"), mappingTabUI(ns("mapping"), meta, domainData, mapping, standards)), tabPanel("Filtering", icon=icon("filter"), filterTabUI(ns("filter"))), navbarMenu('Charts', icon=icon("chart-bar")), diff --git a/R/safetyGraphicsApp.R b/R/safetyGraphicsApp.R index 9ba1a102..723cc7f6 100644 --- a/R/safetyGraphicsApp.R +++ b/R/safetyGraphicsApp.R @@ -15,25 +15,58 @@ #' @export safetyGraphicsApp <- function( - domainData=list( - labs=safetyData::adam_adlbc, - aes=safetyData::adam_adae, - dm=safetyData::adam_adsl + domainData = list( + labs = safetyData::adam_adlbc, + aes = safetyData::adam_adae, + dm = safetyData::adam_adsl ), meta = NULL, - charts=NULL, - mapping=NULL, - autoMapping=TRUE, - filterDomain="dm", + charts = NULL, + mapping = NULL, + autoMapping = TRUE, + filterDomain = "dm", chartSettingsPaths = NULL, - runNow = TRUE + runNow = TRUE, + appName = 'safetyGraphics', + hexPath = system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics"), + homeTabPath = system.file('resources/safetyGraphicsHomeTab.html', package = 'safetyGraphics'), + launchBrowser = NULL ){ message("Initializing safetyGraphicsApp") - config <- app_startup(domainData, meta, charts, mapping, autoMapping, filterDomain, chartSettingsPaths) + + if (!is.character(appName)) + appName <- 'safetyGraphics' + + if (!is.character(hexPath) || !file.exists(hexPath)) + hexPath <- system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics") + + if (!is.character(homeTabPath) || !file.exists(homeTabPath)) + homeTabPath <- system.file('resources/safetyGraphicsHomeTab.html', package = 'safetyGraphics') + + config <- app_startup( + domainData, + meta, + charts, + mapping, + autoMapping, + filterDomain, + chartSettingsPaths + ) + config$appName <- appName + config$hexPath <- hexPath + config$homeTabPath <- homeTabPath + config$launchBrowser <- launchBrowser app <- shinyApp( - ui = safetyGraphicsUI("sg",config$meta, config$domainData, config$mapping, config$standards), - server = function(input,output,session){ + ui = safetyGraphicsUI( + "sg", + config$meta, + config$domainData, + config$mapping, + config$standards, + config + ), + server = function(input, output, session) { callModule( safetyGraphicsServer, "sg", @@ -41,13 +74,14 @@ safetyGraphicsApp <- function( config$mapping, config$domainData, config$charts, - config$filterDomain + config$filterDomain, + config ) } ) - + if(runNow) - runApp(app) + runApp(app, launch.browser = launchBrowser) else app } diff --git a/README.md b/README.md index 0253c04d..fcf7db55 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![R build status](https://www.github.com/safetyGraphics/safetyGraphics/workflows/R-CMD-check-main/badge.svg)](https://github.com/SafetyGraphics/safetyGraphics/actions) -# safetyGraphics: Clinical Trial Monitoring with R +# safetyGraphics: Clinical Trial Monitoring with R The {safetyGraphics} package provides a framework for evaluating of clinical trial safety in R using a flexible data pipeline. The package includes a shiny application that allows users to explore safety data using a series of interactive graphics, including the hepatic safety explorer shown below. The package has been developed as part of the Interactive Safety Graphics (ISG) workstream of the ASA Biopharm-DIA Safety Working Group. diff --git a/docs/index.html b/docs/index.html index 99eb9706..6ca3fb60 100644 --- a/docs/index.html +++ b/docs/index.html @@ -95,7 +95,7 @@

R build status

-

safetyGraphics: Clinical Trial Monitoring with R +

safetyGraphics: Clinical Trial Monitoring with R

The {safetyGraphics} package provides a framework for evaluating of clinical trial safety in R using a flexible data pipeline. The package includes a shiny application that allows users to explore safety data using a series of interactive graphics, including the hepatic safety explorer shown below. The package has been developed as part of the Interactive Safety Graphics (ISG) workstream of the ASA Biopharm-DIA Safety Working Group.

diff --git a/inst/safetyGraphicsHex/noun_heart_rate_210541_ec5d57.png b/inst/resources/noun_heart_rate_210541_ec5d57.png similarity index 100% rename from inst/safetyGraphicsHex/noun_heart_rate_210541_ec5d57.png rename to inst/resources/noun_heart_rate_210541_ec5d57.png diff --git a/inst/safetyGraphicsHex/safetyGraphicsHex.png b/inst/resources/safetyGraphicsHex.png similarity index 100% rename from inst/safetyGraphicsHex/safetyGraphicsHex.png rename to inst/resources/safetyGraphicsHex.png diff --git a/inst/resources/safetyGraphicsHomeTab.html b/inst/resources/safetyGraphicsHomeTab.html new file mode 100644 index 00000000..b796c939 --- /dev/null +++ b/inst/resources/safetyGraphicsHomeTab.html @@ -0,0 +1,24 @@ +

Welcome to the Safety Graphics Shiny App

+

+ The Safety Graphics Shiny app is an interactive tool for evaluating clinical trial safety using a flexible data pipeline. + This application and corresponding {safetyGraphics} R package have been developed as part of the Interactive Safety Graphics (ISG) workstream of the ASA Biopharm-DIA Safety Working Group. +

+ +

Using the app

+

+ Detailed instructions about using the app can be found in our vignette. + In short, the user will initialize the app with their data, adjust settings as needed, and view the interactive charts. + Finally, the user may export a self-contained, fully reproducible snapshot of the charts that can be easily shared with others. +

+ +

Charts

+

+ The app is built to support a wide variety of chart types including static plots (e.g. from {ggplot2}), shiny modules, {htmlwidgets} and even static outputs like RTFs. + Several pre-configured charts are included in the companion {safetyCharts} R Package, and are available by default in the app. + Other charts can be added using the process descibed in this vignette. +

+ +

+ For more information about {safetyGraphics}, please visit our GitHub repository. + We also welcome your suggestions in our issue tracker. +

diff --git a/inst/safetyGraphicsHex/safetyHex.R b/inst/resources/safetyHex.R similarity index 65% rename from inst/safetyGraphicsHex/safetyHex.R rename to inst/resources/safetyHex.R index 716015cc..62102c17 100644 --- a/inst/safetyGraphicsHex/safetyHex.R +++ b/inst/resources/safetyHex.R @@ -1,10 +1,10 @@ #library(hexSticker) #red on white -imgurl <- "./inst/safetyGraphicsHex/noun_heart_rate_210541_ec5d57.png" +imgurl <- "./inst/resources/noun_heart_rate_210541_ec5d57.png" # sticker( # imgurl, -# filename="./inst/safetyGraphicsHex/safetyGraphicsHex.png", +# filename="./inst/resources/safetyGraphicsHex.png", # package = "safetyGraphics", # p_color = "#666666", # p_size = 5, From bc29c840fdb0d2876ed2df86fab1fcaa85c530f3 Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Fri, 24 Jun 2022 11:13:22 -0400 Subject: [PATCH 10/27] handle launchBrowser --- R/safetyGraphicsApp.R | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/R/safetyGraphicsApp.R b/R/safetyGraphicsApp.R index 723cc7f6..ac9877c7 100644 --- a/R/safetyGraphicsApp.R +++ b/R/safetyGraphicsApp.R @@ -30,7 +30,7 @@ safetyGraphicsApp <- function( appName = 'safetyGraphics', hexPath = system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics"), homeTabPath = system.file('resources/safetyGraphicsHomeTab.html', package = 'safetyGraphics'), - launchBrowser = NULL + launchBrowser = FALSE ){ message("Initializing safetyGraphicsApp") @@ -80,8 +80,13 @@ safetyGraphicsApp <- function( } ) - if(runNow) - runApp(app, launch.browser = launchBrowser) - else - app + if (runNow) { + if (launchBrowser == TRUE) { + runApp(app, launch.browser = TRUE) + } else { + runApp(app) + } + } + + app } From 0dd53774492ceecf6ada1b119cfe0175fe650f08 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 2 Feb 2023 11:34:49 -0500 Subject: [PATCH 11/27] basic profile integraion. #701 --- NAMESPACE | 3 +++ R/mod_profileTab.R | 45 ++++++++++++++++++++++++++++++++++++ R/mod_safetyGraphicsServer.R | 27 +++++++++++++++++----- R/mod_safetyGraphicsUI.R | 1 + man/profileTab.Rd | 25 ++++++++++++++++++++ man/profileTabUI.Rd | 14 +++++++++++ 6 files changed, 109 insertions(+), 6 deletions(-) create mode 100644 R/mod_profileTab.R create mode 100644 man/profileTab.Rd create mode 100644 man/profileTabUI.Rd diff --git a/NAMESPACE b/NAMESPACE index 61095cdd..d04f0eb3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -32,6 +32,8 @@ export(mappingSelectUI) export(mappingTab) export(mappingTabUI) export(prepareChart) +export(profileTab) +export(profileTabUI) export(safetyGraphicsApp) export(safetyGraphicsInit) export(safetyGraphicsServer) @@ -52,6 +54,7 @@ import(purrr) import(rclipboard) import(safetyCharts) import(safetyData) +import(safetyProfile) import(shiny) import(yaml) importFrom(DT,renderDT) diff --git a/R/mod_profileTab.R b/R/mod_profileTab.R new file mode 100644 index 00000000..781ac801 --- /dev/null +++ b/R/mod_profileTab.R @@ -0,0 +1,45 @@ +#' @title UI for the profile module in safetyProfile::profile_ui +#' +#' @param id module id +#' +#' @import safetyProfile +#' +#' @export + +profileTabUI <- function(id){ + ns <- NS(id) + + profile_ui<-list( + h1(paste("Participant Profile")), + span("This page shows details for a selected participant."), + profile_ui(ns("profile")) + ) + + return(profile_ui) +} + + +#' @title Server for the filter module in safetyProfile::profile_server +#' +#' @param input Shiny input object +#' @param output Shiny output object +#' @param session Shiny session object +#' @param params reactive containing mapping and data +#' @param current_id reactive containing currently selected participant +#' +#' @return current_id +#' +#' @import datamods +#' @importFrom shinyjs show hide +#' @importFrom shiny renderDataTable +#' +#' @export + +profileTab <- function(input, output, session, params){ + observe({ + print(names(params()$data)) + print(names(params()$settings)) + }) + + callModule(safetyProfile::profile_server, "profile", params) +} diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index 0d7e4b85..83e4a80a 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -19,10 +19,13 @@ #' @export safetyGraphicsServer <- function(input, output, session, meta, mapping, domainData, charts, filterDomain){ - #Initialize modules + #--- Home Tab ---# + callModule(homeTab, "home") + + #--- Mapping Tab ---# current_mapping<-callModule(mappingTab, "mapping", meta, domainData) - # Initialize the filter tab + #--- Filter tab ---# filtered_data<-callModule( filterTab, "filter", @@ -30,10 +33,22 @@ safetyGraphicsServer <- function(input, output, session, meta, mapping, domainDa filterDomain=filterDomain, current_mapping=current_mapping ) - - callModule(homeTab, "home") - #Initialize Chart UI - Adds subtabs to chart menu - this initializes initializes chart UIs + #--- Profile Tab ---# + callModule( + profileTab, + "profile", + params=reactive({ + list( + data=filtered_data(), + settings=safetyGraphics::generateMappingList(current_mapping()) + ) + }) + ) + + + #--- Chart Tab ---# + # Note: Adds subtabs to chart menu - this initializes initializes chart UIs charts %>% purrr::map(~chartsNav(.x,session$ns)) #Initialize Chart Servers @@ -48,7 +63,7 @@ safetyGraphicsServer <- function(input, output, session, meta, mapping, domainDa ) ) - #Setting tab + #--- Setting tab ---# callModule(settingsTab, "settings", domains = domainData, metadata=meta, mapping=current_mapping, charts = charts) } diff --git a/R/mod_safetyGraphicsUI.R b/R/mod_safetyGraphicsUI.R index 523b0a22..5b3a8e2e 100644 --- a/R/mod_safetyGraphicsUI.R +++ b/R/mod_safetyGraphicsUI.R @@ -55,6 +55,7 @@ safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){ tabPanel("Home", icon=icon("home"),homeTabUI(ns("home"))), tabPanel("Mapping", icon=icon("map"), mappingTabUI(ns("mapping"), meta, domainData, mapping, standards)), tabPanel("Filtering", icon=icon("filter"), filterTabUI(ns("filter"))), + tabPanel("Profile", icon=icon("person"), profileTabUI(ns("profile"))), navbarMenu('Charts', icon=icon("chart-bar")), tabPanel('',icon=icon("cog"), settingsTabUI(ns("settings"))) ), diff --git a/man/profileTab.Rd b/man/profileTab.Rd new file mode 100644 index 00000000..e2d43505 --- /dev/null +++ b/man/profileTab.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mod_profileTab.R +\name{profileTab} +\alias{profileTab} +\title{Server for the filter module in safetyProfile::profile_server} +\usage{ +profileTab(input, output, session, params) +} +\arguments{ +\item{input}{Shiny input object} + +\item{output}{Shiny output object} + +\item{session}{Shiny session object} + +\item{params}{reactive containing mapping and data} + +\item{current_id}{reactive containing currently selected participant} +} +\value{ +current_id +} +\description{ +Server for the filter module in safetyProfile::profile_server +} diff --git a/man/profileTabUI.Rd b/man/profileTabUI.Rd new file mode 100644 index 00000000..0db64c61 --- /dev/null +++ b/man/profileTabUI.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mod_profileTab.R +\name{profileTabUI} +\alias{profileTabUI} +\title{UI for the profile module in safetyProfile::profile_ui} +\usage{ +profileTabUI(id) +} +\arguments{ +\item{id}{module id} +} +\description{ +UI for the profile module in safetyProfile::profile_ui +} From c3fd0ff772c0c79d89ccef7f5dbc15faaed42ef9 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Wed, 15 Feb 2023 10:32:19 -0500 Subject: [PATCH 12/27] update module call --- R/mod_profileTab.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/mod_profileTab.R b/R/mod_profileTab.R index 781ac801..495f2768 100644 --- a/R/mod_profileTab.R +++ b/R/mod_profileTab.R @@ -37,9 +37,9 @@ profileTabUI <- function(id){ profileTab <- function(input, output, session, params){ observe({ - print(names(params()$data)) - print(names(params()$settings)) + #print(names(params()$data)) + #print(names(params()$settings)) }) - callModule(safetyProfile::profile_server, "profile", params) + safetyProfile::profile_server("profile", params) } From 3c05b2e0922f21ba24cca9254565ed996bfc10ef Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 16 Feb 2023 12:15:44 -0500 Subject: [PATCH 13/27] add header showing selected participant --- R/mod_profileTab.R | 19 +++++++++++++++++-- R/mod_safetyGraphicsUI.R | 15 ++++++++++++++- inst/www/index.css | 12 +++++++++++- 3 files changed, 42 insertions(+), 4 deletions(-) diff --git a/R/mod_profileTab.R b/R/mod_profileTab.R index 495f2768..5fa4e27b 100644 --- a/R/mod_profileTab.R +++ b/R/mod_profileTab.R @@ -19,7 +19,7 @@ profileTabUI <- function(id){ } -#' @title Server for the filter module in safetyProfile::profile_server +#' @title Server for the patient profile in safetyProfile::profile_server #' #' @param input Shiny input object #' @param output Shiny output object @@ -40,6 +40,21 @@ profileTab <- function(input, output, session, params){ #print(names(params()$data)) #print(names(params()$settings)) }) + + id<-safetyProfile::profile_server("profile", params) + + observe({ + shinyjs::html( + "pt-header", + id(), + asis=TRUE + ) - safetyProfile::profile_server("profile", params) + shinyjs::toggleClass( + selector = "#pt-header", + class = "active", + condition = !is.null(id()) + ) + }) + return(id) } diff --git a/R/mod_safetyGraphicsUI.R b/R/mod_safetyGraphicsUI.R index 5b3a8e2e..5a8fd6a6 100644 --- a/R/mod_safetyGraphicsUI.R +++ b/R/mod_safetyGraphicsUI.R @@ -31,6 +31,18 @@ safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){ "\");" )) ) + + pt_selected<-tags$script( + HTML(paste0( + "var header = $('.navbar > .container-fluid');", + "header.append(\"", + "
", + "None", + "
", + "\");" + )) + ) + if(isNamespaceLoaded("shinybusy")){ spinner<-shinybusy::add_busy_spinner(spin = "atom", position="bottom-right") }else{ @@ -59,7 +71,8 @@ safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){ navbarMenu('Charts', icon=icon("chart-bar")), tabPanel('',icon=icon("cog"), settingsTabUI(ns("settings"))) ), - participant_badge + participant_badge, + pt_selected ) return(ui) } diff --git a/inst/www/index.css b/inst/www/index.css index ded3585c..b264a25b 100644 --- a/inst/www/index.css +++ b/inst/www/index.css @@ -64,8 +64,18 @@ table.metatable.dataTable tr > td:last-of-type, table.metatable.trdataTable tr > margin-top:1em; } +#pt-header.active { + background:#4B9CD3; +} + +#pt-header { + float: right; + margin-top: 1em; + margin-right:1em; +} + #population-header.subset { - background: blue; + background: green; } #dataSettings-previews .nav-tabs{ From 0ba8d123d18558b9999566af1b61c8a05c8fe098 Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Fri, 24 Feb 2023 16:21:29 -0500 Subject: [PATCH 14/27] add chart event listeners and refactor widgets --- R/mod_profileTab.R | 13 ++++++------- R/mod_safetyGraphicsServer.R | 17 +++++++++++++++++ R/mod_safetyGraphicsUI.R | 7 ++++++- 3 files changed, 29 insertions(+), 8 deletions(-) diff --git a/R/mod_profileTab.R b/R/mod_profileTab.R index 5fa4e27b..53eee72a 100644 --- a/R/mod_profileTab.R +++ b/R/mod_profileTab.R @@ -35,13 +35,11 @@ profileTabUI <- function(id){ #' #' @export -profileTab <- function(input, output, session, params){ - observe({ - #print(names(params()$data)) - #print(names(params()$settings)) - }) - - id<-safetyProfile::profile_server("profile", params) +profileTab <- function(input, output, session, params) { + id <- safetyProfile::profile_server( + "profile", + params + ) observe({ shinyjs::html( @@ -56,5 +54,6 @@ profileTab <- function(input, output, session, params){ condition = !is.null(id()) ) }) + return(id) } diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index 83e4a80a..478ca443 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -46,6 +46,23 @@ safetyGraphicsServer <- function(input, output, session, meta, mapping, domainDa }) ) + observeEvent(input$participants_selected, { + cli::cli_alert_info('Selected participant ID: {input$participants_selected}') + + # Navigate to patient profile. + #updateNavbarPage( + # session, + # "safetyGraphicsApp", + # selected = 'profile' + #) + + # Update selected participant. + updateSelectizeInput( + session, + inputId = 'profile-profile-idSelect', + selected = input$participants_selected + ) + }) #--- Chart Tab ---# # Note: Adds subtabs to chart menu - this initializes initializes chart UIs diff --git a/R/mod_safetyGraphicsUI.R b/R/mod_safetyGraphicsUI.R index 5a8fd6a6..ca229469 100644 --- a/R/mod_safetyGraphicsUI.R +++ b/R/mod_safetyGraphicsUI.R @@ -67,7 +67,12 @@ safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){ tabPanel("Home", icon=icon("home"),homeTabUI(ns("home"))), tabPanel("Mapping", icon=icon("map"), mappingTabUI(ns("mapping"), meta, domainData, mapping, standards)), tabPanel("Filtering", icon=icon("filter"), filterTabUI(ns("filter"))), - tabPanel("Profile", icon=icon("person"), profileTabUI(ns("profile"))), + tabPanel( + "Profile", + icon=icon("person"), + value='profile', + profileTabUI(ns("profile")) + ), navbarMenu('Charts', icon=icon("chart-bar")), tabPanel('',icon=icon("cog"), settingsTabUI(ns("settings"))) ), From f5094e3b0746179c3c5b1bdfd46a496c21aea49f Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Fri, 24 Feb 2023 17:18:48 -0500 Subject: [PATCH 15/27] document() --- DESCRIPTION | 2 +- man/profileTab.Rd | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5f73fad9..fb158011 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,7 +16,7 @@ Depends: R (>= 4.0) License: MIT + file LICENSE Encoding: UTF-8 LazyData: true -RoxygenNote: 7.2.1 +RoxygenNote: 7.2.2 Suggests: ggplot2 (>= 3.3.0), knitr (>= 1.34), diff --git a/man/profileTab.Rd b/man/profileTab.Rd index e2d43505..d74e9f09 100644 --- a/man/profileTab.Rd +++ b/man/profileTab.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/mod_profileTab.R \name{profileTab} \alias{profileTab} -\title{Server for the filter module in safetyProfile::profile_server} +\title{Server for the patient profile in safetyProfile::profile_server} \usage{ profileTab(input, output, session, params) } @@ -21,5 +21,5 @@ profileTab(input, output, session, params) current_id } \description{ -Server for the filter module in safetyProfile::profile_server +Server for the patient profile in safetyProfile::profile_server } From dc71c65f308183f0e7237c354c549f8bf66692f6 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Wed, 8 Mar 2023 10:11:48 -0500 Subject: [PATCH 16/27] minor tweaks. re-run docs --- DESCRIPTION | 2 +- R/app_startup.R | 16 ++++++++++++++-- R/safetyGraphicsApp.R | 38 ++++++++++++++++--------------------- man/app_startup.Rd | 11 ++++++++++- man/homeTab.Rd | 2 +- man/safetyGraphicsApp.Rd | 13 +++++++++++++ man/safetyGraphicsServer.Rd | 3 ++- man/safetyGraphicsUI.Rd | 2 +- 8 files changed, 58 insertions(+), 29 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 34ba1647..4f72e9c2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,7 +16,7 @@ Depends: R (>= 4.0) License: MIT + file LICENSE Encoding: UTF-8 LazyData: true -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 Suggests: ggplot2 (>= 3.3.0), knitr (>= 1.34), diff --git a/R/app_startup.R b/R/app_startup.R index aa586860..5d39ca74 100644 --- a/R/app_startup.R +++ b/R/app_startup.R @@ -9,6 +9,9 @@ #' @param autoMapping boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the `mapping` parameter overwrite automatically generated mappings when both are found. Defaults to true. #' @param filterDomain domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended. #' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R). All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details. +#' @param appName character string defining the name of the app (default = "safetyGraphics") +#' @param hexPath path to image file with a hex or other logo. safetyGraphics hex used by default. +#' @param homeTabPath path to html content to be used on the home page. default is a summary of the safetyGraphics framework. #' #' @return List of elements for used to initialize the shiny app with the following parameters #' \itemize{ @@ -20,7 +23,13 @@ #' } #' #' @export -app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, autoMapping=NULL, filterDomain=NULL, chartSettingsPaths=NULL){ +app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, autoMapping=NULL, filterDomain=NULL, chartSettingsPaths=NULL, appName=NULL, hexPath=NULL, homeTabPath=NULL){ + + # Set defaults for app name, hex and home page content. + if (!is.character(appName)) appName <- 'safetyGraphics' + if (!is.character(hexPath) || !file.exists(hexPath)) hexPath <- system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics") + if (!is.character(homeTabPath) || !file.exists(homeTabPath)) homeTabPath <- system.file('resources/safetyGraphicsHomeTab.html', package = 'safetyGraphics') + # If charts are not provided, load them from chartSettingsPath or the safetyCharts package if(is.null(charts)){ if(is.null(chartSettingsPaths)){ @@ -80,7 +89,10 @@ app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, aut domainData=domainData, mapping=mappingObj$mapping, standards=mappingObj$standard, - filterDomain=filterDomain + filterDomain=filterDomain, + appName=appName, + hexPath=hexPath, + homeTabPath = homeTabPath ) return(config) diff --git a/R/safetyGraphicsApp.R b/R/safetyGraphicsApp.R index ac9877c7..493ea701 100644 --- a/R/safetyGraphicsApp.R +++ b/R/safetyGraphicsApp.R @@ -7,6 +7,10 @@ #' @param autoMapping boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the `mapping` parameter overwrite automatically generated mappings when both are found. Defaults to true. #' @param filterDomain domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended. #' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R). All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details. +#' @param appName character string defining the name of the app (default = "safetyGraphics") +#' @param hexPath path to image file with a hex or other logo. safetyGraphics hex used by default. +#' @param homeTabPath path to html content to be used on the home page. default is a summary of the safetyGraphics framework. +#' @param launchBrowser boolean indicating whether to launch the app in a browser. default is false #' @param runNow Should the shiny app object created be run directly? Helpful when writing functions to dispatch to shinyapps, rsconnect, or shinyproxy. #' #' @import shiny @@ -26,36 +30,26 @@ safetyGraphicsApp <- function( autoMapping = TRUE, filterDomain = "dm", chartSettingsPaths = NULL, - runNow = TRUE, appName = 'safetyGraphics', hexPath = system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics"), homeTabPath = system.file('resources/safetyGraphicsHomeTab.html', package = 'safetyGraphics'), - launchBrowser = FALSE + launchBrowser = FALSE, + runNow = TRUE ){ message("Initializing safetyGraphicsApp") - if (!is.character(appName)) - appName <- 'safetyGraphics' - - if (!is.character(hexPath) || !file.exists(hexPath)) - hexPath <- system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics") - - if (!is.character(homeTabPath) || !file.exists(homeTabPath)) - homeTabPath <- system.file('resources/safetyGraphicsHomeTab.html', package = 'safetyGraphics') - config <- app_startup( - domainData, - meta, - charts, - mapping, - autoMapping, - filterDomain, - chartSettingsPaths + domainData=domainData, + meta=meta, + charts=charts, + mapping=mapping, + autoMapping=autoMapping, + filterDomain=filterDomain, + chartSettingsPaths=chartSettingsPaths, + appName=appName, + hexPath=hexPath, + homeTabPath=homeTabPath ) - config$appName <- appName - config$hexPath <- hexPath - config$homeTabPath <- homeTabPath - config$launchBrowser <- launchBrowser app <- shinyApp( ui = safetyGraphicsUI( diff --git a/man/app_startup.Rd b/man/app_startup.Rd index cccaa5ba..258ed325 100644 --- a/man/app_startup.Rd +++ b/man/app_startup.Rd @@ -11,7 +11,10 @@ app_startup( mapping = NULL, autoMapping = NULL, filterDomain = NULL, - chartSettingsPaths = NULL + chartSettingsPaths = NULL, + appName = NULL, + hexPath = NULL, + homeTabPath = NULL ) } \arguments{ @@ -28,6 +31,12 @@ app_startup( \item{filterDomain}{domain used for the data/filter tab. Demographics ("\code{dm}") is used by default. Using a domain that is not one record per participant is not recommended.} \item{chartSettingsPaths}{path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R). All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details.} + +\item{appName}{character string defining the name of the app (default = "safetyGraphics")} + +\item{hexPath}{path to image file with a hex or other logo. safetyGraphics hex used by default.} + +\item{homeTabPath}{path to html content to be used on the home page. default is a summary of the safetyGraphics framework.} } \value{ List of elements for used to initialize the shiny app with the following parameters diff --git a/man/homeTab.Rd b/man/homeTab.Rd index 17447951..08da5ed2 100644 --- a/man/homeTab.Rd +++ b/man/homeTab.Rd @@ -4,7 +4,7 @@ \alias{homeTab} \title{Server for the filter module in datamods::filter_data_ui} \usage{ -homeTab(input, output, session) +homeTab(input, output, session, config) } \arguments{ \item{input}{mod input} diff --git a/man/safetyGraphicsApp.Rd b/man/safetyGraphicsApp.Rd index 5ff05020..4936c37a 100644 --- a/man/safetyGraphicsApp.Rd +++ b/man/safetyGraphicsApp.Rd @@ -13,6 +13,11 @@ safetyGraphicsApp( autoMapping = TRUE, filterDomain = "dm", chartSettingsPaths = NULL, + appName = "safetyGraphics", + hexPath = system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics"), + homeTabPath = system.file("resources/safetyGraphicsHomeTab.html", package = + "safetyGraphics"), + launchBrowser = FALSE, runNow = TRUE ) } @@ -31,6 +36,14 @@ safetyGraphicsApp( \item{chartSettingsPaths}{path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R). All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details.} +\item{appName}{character string defining the name of the app (default = "safetyGraphics")} + +\item{hexPath}{path to image file with a hex or other logo. safetyGraphics hex used by default.} + +\item{homeTabPath}{path to html content to be used on the home page. default is a summary of the safetyGraphics framework.} + +\item{launchBrowser}{boolean indicating whether to launch the app in a browser. default is false} + \item{runNow}{Should the shiny app object created be run directly? Helpful when writing functions to dispatch to shinyapps, rsconnect, or shinyproxy.} } \description{ diff --git a/man/safetyGraphicsServer.Rd b/man/safetyGraphicsServer.Rd index ece88603..8aadddf9 100644 --- a/man/safetyGraphicsServer.Rd +++ b/man/safetyGraphicsServer.Rd @@ -12,7 +12,8 @@ safetyGraphicsServer( mapping, domainData, charts, - filterDomain + filterDomain, + config ) } \arguments{ diff --git a/man/safetyGraphicsUI.Rd b/man/safetyGraphicsUI.Rd index 99b312a5..5dcc2012 100644 --- a/man/safetyGraphicsUI.Rd +++ b/man/safetyGraphicsUI.Rd @@ -4,7 +4,7 @@ \alias{safetyGraphicsUI} \title{UI for the core safetyGraphics app including Home, Mapping, Filter, Charts and Settings modules.} \usage{ -safetyGraphicsUI(id, meta, domainData, mapping, standards) +safetyGraphicsUI(id, meta, domainData, mapping, standards, config) } \arguments{ \item{id}{module ID} From 5cbedc7ce0d5e6ee7500c2e2f6cb5959189512e9 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Wed, 8 Mar 2023 10:43:10 -0500 Subject: [PATCH 17/27] fix merge conflict --- R/mod_safetyGraphicsServer.R | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index effa09ab..9b46d1bf 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -18,13 +18,6 @@ #' #' @export -<<<<<<< HEAD -safetyGraphicsServer <- function(input, output, session, meta, mapping, domainData, charts, filterDomain){ - #--- Home Tab ---# - callModule(homeTab, "home") - - #--- Mapping Tab ---# -======= safetyGraphicsServer <- function( input, output, @@ -37,7 +30,10 @@ safetyGraphicsServer <- function( config ) { #Initialize modules ->>>>>>> dev + #--- Home Tab ---# + callModule(homeTab, "home", config) + + #--- Mapping Tab ---# current_mapping<-callModule(mappingTab, "mapping", meta, domainData) #--- Filter tab ---# @@ -61,7 +57,6 @@ safetyGraphicsServer <- function( }) ) -<<<<<<< HEAD observeEvent(input$participants_selected, { cli::cli_alert_info('Selected participant ID: {input$participants_selected}') @@ -71,9 +66,6 @@ safetyGraphicsServer <- function( # "safetyGraphicsApp", # selected = 'profile' #) -======= - callModule(homeTab, "home", config) ->>>>>>> dev # Update selected participant. updateSelectizeInput( From d38cc0f08aa0ebe3ad17dd005febf79146a3feb6 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Wed, 8 Mar 2023 11:25:50 -0500 Subject: [PATCH 18/27] make patProfile optional --- DESCRIPTION | 1 + NAMESPACE | 1 - R/mod_profileTab.R | 17 +++++------ R/mod_safetyGraphicsServer.R | 56 ++++++++++++++++++++---------------- 4 files changed, 41 insertions(+), 34 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a0df242a..a278bb58 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -21,6 +21,7 @@ Suggests: ggplot2 (>= 3.3.0), knitr (>= 1.34), rmarkdown (>= 2.10), + safetyProfile, shinydashboard (>= 0.7.1), shinytest (>= 1.5.0), testthat (>= 3.0.4), diff --git a/NAMESPACE b/NAMESPACE index d04f0eb3..fe17658c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -54,7 +54,6 @@ import(purrr) import(rclipboard) import(safetyCharts) import(safetyData) -import(safetyProfile) import(shiny) import(yaml) importFrom(DT,renderDT) diff --git a/R/mod_profileTab.R b/R/mod_profileTab.R index 53eee72a..41653241 100644 --- a/R/mod_profileTab.R +++ b/R/mod_profileTab.R @@ -2,19 +2,20 @@ #' #' @param id module id #' -#' @import safetyProfile -#' #' @export profileTabUI <- function(id){ ns <- NS(id) - profile_ui<-list( - h1(paste("Participant Profile")), - span("This page shows details for a selected participant."), - profile_ui(ns("profile")) - ) - + if(isNamespaceLoaded("safetyProfile")){ + profile_ui<-list( + h1(paste("Participant Profile")), + span("This page shows details for a selected participant."), + profile_ui(ns("profile")) + ) + }else{ + profile_ui<-NULL + } return(profile_ui) } diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index 9b46d1bf..c5729b0d 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -46,34 +46,40 @@ safetyGraphicsServer <- function( ) #--- Profile Tab ---# - callModule( - profileTab, - "profile", - params=reactive({ - list( - data=filtered_data(), - settings=safetyGraphics::generateMappingList(current_mapping()) - ) - }) - ) - observeEvent(input$participants_selected, { - cli::cli_alert_info('Selected participant ID: {input$participants_selected}') + if(isNamespaceLoaded("safetyProfile")){ + callModule( + profileTab, + "profile", + params=reactive({ + list( + data=filtered_data(), + settings=safetyGraphics::generateMappingList(current_mapping()) + ) + }) + ) + + observeEvent(input$participants_selected, { + cli::cli_alert_info('Selected participant ID: {input$participants_selected}') - # Navigate to patient profile. - #updateNavbarPage( - # session, - # "safetyGraphicsApp", - # selected = 'profile' - #) + # Navigate to patient profile. + #updateNavbarPage( + # session, + # "safetyGraphicsApp", + # selected = 'profile' + #) - # Update selected participant. - updateSelectizeInput( - session, - inputId = 'profile-profile-idSelect', - selected = input$participants_selected - ) - }) + # Update selected participant. + updateSelectizeInput( + session, + inputId = 'profile-profile-idSelect', + selected = input$participants_selected + ) + }) + } else { + shinyjs::hide(selector = paste0(".navbar li a[data-value='profile']")) + shinyjs::hide(selector = paste0(".navbar #pt-header")) + } #--- Chart Tab ---# # Note: Adds subtabs to chart menu - this initializes initializes chart UIs From 699c7d0ad55a4d85115fb1ed18ca45c1a674a0d7 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 9 Mar 2023 11:30:14 -0500 Subject: [PATCH 19/27] click pt id in header to show profile tab --- R/mod_safetyGraphicsServer.R | 8 ++------ R/mod_safetyGraphicsUI.R | 8 +++++++- inst/www/index.css | 2 ++ 3 files changed, 11 insertions(+), 7 deletions(-) diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index c5729b0d..e6e40321 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -58,16 +58,12 @@ safetyGraphicsServer <- function( ) }) ) - + observeEvent(input$participants_selected, { cli::cli_alert_info('Selected participant ID: {input$participants_selected}') # Navigate to patient profile. - #updateNavbarPage( - # session, - # "safetyGraphicsApp", - # selected = 'profile' - #) + # Update selected participant. updateSelectizeInput( diff --git a/R/mod_safetyGraphicsUI.R b/R/mod_safetyGraphicsUI.R index 09abddb1..ebe19a78 100644 --- a/R/mod_safetyGraphicsUI.R +++ b/R/mod_safetyGraphicsUI.R @@ -39,7 +39,13 @@ safetyGraphicsUI <- function(id, meta, domainData, mapping, standards, config) { "
", "None", "
", - "\");" + "\");", + "var ptheader = $('.navbar > .container-fluid > #pt-header');", + "ptheader.on('click',function(){", + "$('", + '[data-value="profile"]', + "').tab('show');", + "})" )) ) diff --git a/inst/www/index.css b/inst/www/index.css index b264a25b..a09f649c 100644 --- a/inst/www/index.css +++ b/inst/www/index.css @@ -66,6 +66,8 @@ table.metatable.dataTable tr > td:last-of-type, table.metatable.trdataTable tr > #pt-header.active { background:#4B9CD3; + text-decoration:underline; + cursor:pointer; } #pt-header { From 5ee11290928280c430ba9f7784bc2d024409cb56 Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Mon, 13 Mar 2023 12:47:57 -0400 Subject: [PATCH 20/27] charts nav isn't working --- R/mod_safetyGraphicsServer.R | 7 ++++++- R/safetyGraphicsApp.R | 22 +++++++++++----------- 2 files changed, 17 insertions(+), 12 deletions(-) diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index bbdd747c..02178d09 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -43,7 +43,12 @@ safetyGraphicsServer <- function(input, output, session, # Initialize Charts tab # Initialize Chart UI - adds subtabs to chart menu and initializes the chart UIs - #charts %>% purrr::map(~chartsNavUI(.x$name,.x)) + charts %>% purrr::map( + ~chartsNavUI( + .x$name, + .x + ) + ) # Initialize Chart Servers charts %>% purrr::map( diff --git a/R/safetyGraphicsApp.R b/R/safetyGraphicsApp.R index 6820c4ae..faad1804 100644 --- a/R/safetyGraphicsApp.R +++ b/R/safetyGraphicsApp.R @@ -39,16 +39,16 @@ safetyGraphicsApp <- function( message("Initializing safetyGraphicsApp") config <- app_startup( - domainData=domainData, - meta=meta, - charts=charts, - mapping=mapping, - autoMapping=autoMapping, - filterDomain=filterDomain, - chartSettingsPaths=chartSettingsPaths, - appName=appName, - hexPath=hexPath, - homeTabPath=homeTabPath + domainData = domainData, + meta = meta, + charts = charts, + mapping = mapping, + autoMapping = autoMapping, + filterDomain = filterDomain, + chartSettingsPaths = chartSettingsPaths, + appName = appName, + hexPath = hexPath, + homeTabPath = homeTabPath ) app <- shinyApp( @@ -61,7 +61,7 @@ safetyGraphicsApp <- function( config = config ), server = function(input, output, session) { - callModule(safetyGraphicsServer, + callModule(safetyGraphicsServer, id = 'sg', meta = config$meta, mapping = config$mapping, domainData = config$domainData, From 9207f4656138da5cd6f4781be57ff1db9610ec41 Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Mon, 13 Mar 2023 16:35:15 -0400 Subject: [PATCH 21/27] fix bug introduced in merge with dev --- R/app_startup.R | 6 +++--- R/mod_chartsNav.R | 19 ++++++++++++++----- R/mod_safetyGraphicsServer.R | 36 ++++++++++++++++++++++++++---------- R/mod_safetyGraphicsUI.R | 15 +++++++++++++-- R/safetyGraphicsApp.R | 2 +- 5 files changed, 57 insertions(+), 21 deletions(-) diff --git a/R/app_startup.R b/R/app_startup.R index 5d39ca74..1ae9250a 100644 --- a/R/app_startup.R +++ b/R/app_startup.R @@ -55,18 +55,18 @@ app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, aut message("- Dropped ", length(envDrops), " chart(s) with `env` paramter missing or not set to 'safetyGraphics': ",paste(names(envDrops), collapse=", ")) } charts <- charts %>% purrr::keep(~.x$envValid) - + #Drop charts if data for required domain(s) is not found domainDrops <- charts %>% purrr::keep(~(!all(.x$domain %in% names(domainData)))) if(length(domainDrops)>0){ message("- Dropped ", length(domainDrops), " chart(s) with missing data domains: ", paste(names(domainDrops), collapse=", ")) } charts <- charts %>% purrr::keep(~all(.x$domain %in% names(domainData))) - + # sort charts based on order chartOrder <- order(charts %>% map_dbl(~.x$order) %>% unlist()) charts <- charts[chartOrder] - + message("- Initializing app with ",length(charts), " chart(s).") # Set filterDomain to NULL if specified domain doesn't exist diff --git a/R/mod_chartsNav.R b/R/mod_chartsNav.R index c69c257f..d2c3fd76 100644 --- a/R/mod_chartsNav.R +++ b/R/mod_chartsNav.R @@ -6,8 +6,9 @@ #' @export #' -chartsNavUI <- function(id, chart){ +chartsNavUI <- function(id, chart) { ns <- NS(id) + panel<-tabPanel( title = uiOutput(ns("tabTitle")), value = chart$name, @@ -16,6 +17,7 @@ chartsNavUI <- function(id, chart){ chart=chart ) ) + return(panel) } @@ -32,6 +34,8 @@ chartsNavUI <- function(id, chart){ #' chartsNav<-function(input, output, session, chart, data, mapping){ + ns <- session$ns + chartStatus <- reactive({ if(hasName(chart, 'dataSpec')){ status<-getChartStatus(chart, mapping()) @@ -41,9 +45,14 @@ chartsNav<-function(input, output, session, chart, data, mapping){ return(status) }) - ns <- session$ns - print(paste("running chartsNav() in:", ns(''))) - output$tabTitle <- renderUI({makeChartSummary(chart, status=chartStatus(), showLinks=FALSE, class="chart-nav")}) + output$tabTitle <- renderUI({ + makeChartSummary( + chart, + status=chartStatus(), + showLinks=FALSE, + class="chart-nav" + ) + }) callModule( module=chartsTab, @@ -53,4 +62,4 @@ chartsNav<-function(input, output, session, chart, data, mapping){ mapping=mapping, status=chartStatus ) -} \ No newline at end of file +} diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index 02178d09..c7e37d5d 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -27,10 +27,19 @@ safetyGraphicsServer <- function(input, output, session, config ) { # Initialize the Home tab - callModule(homeTab, "home", config) + callModule( + homeTab, + "home", + config + ) # Initialize the Mapping tab - returns the current mapping as a reactive - current_mapping<-callModule(mappingTab, "mapping", meta, domainData) + current_mapping<-callModule( + mappingTab, + "mapping", + meta, + domainData + ) # Initialize the Filter tab - returns list of filtered data as a reactive filtered_data<-callModule( @@ -43,15 +52,15 @@ safetyGraphicsServer <- function(input, output, session, # Initialize Charts tab # Initialize Chart UI - adds subtabs to chart menu and initializes the chart UIs - charts %>% purrr::map( - ~chartsNavUI( - .x$name, - .x - ) - ) + #charts %>% purrr::map( + # ~chartsNav( + # .x, + # session$ns + # ) + #) # Initialize Chart Servers - charts %>% purrr::map( + charts %>% purrr::walk( ~callModule( module=chartsNav, id=.x$name, @@ -62,6 +71,13 @@ safetyGraphicsServer <- function(input, output, session, ) # Initialize the Setting tab - callModule(settingsTab, "settings", domains = domainData, metadata=meta, mapping=current_mapping, charts = charts) + callModule( + settingsTab, + "settings", + domains = domainData, + metadata=meta, + mapping=current_mapping, + charts = charts + ) } diff --git a/R/mod_safetyGraphicsUI.R b/R/mod_safetyGraphicsUI.R index 9aecf633..8a307109 100644 --- a/R/mod_safetyGraphicsUI.R +++ b/R/mod_safetyGraphicsUI.R @@ -46,9 +46,20 @@ safetyGraphicsUI <- function(id, #Set up ChartNav #trick for navbar menu: https://stackoverflow.com/questions/34846469/for-loops-lapply-navbarpage-within-in-ui-r + chartList <- charts %>% + purrr::map(function(chart) { + chartsNavUI(ns(chart$name), chart) + }) %>% + unname + + navParams<-c( + list( + title='Charts', + icon=icon("chart-bar") + ), + chartList + ) - chartList <- charts %>% purrr::map(~chartsNavUI(ns(.x$name),.x)) %>% unname - navParams<-c(list(title='Charts', icon=icon("chart-bar")), chartList) chartNav <- do.call(navbarMenu, navParams) #app UI using calls to modules diff --git a/R/safetyGraphicsApp.R b/R/safetyGraphicsApp.R index faad1804..c2b9b91a 100644 --- a/R/safetyGraphicsApp.R +++ b/R/safetyGraphicsApp.R @@ -56,7 +56,7 @@ safetyGraphicsApp <- function( meta = config$meta, mapping = config$mapping, domainData = config$domainData, - charts = charts, + charts = config$charts, standards = config$standards, config = config ), From 0610e25e03514fdef6994ca160f593de8169c91b Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Tue, 14 Mar 2023 15:38:41 -0400 Subject: [PATCH 22/27] add util- prefix to a few files --- R/getChartStatus.R | 56 +++++++++++++++---- R/mod_chartsTab.R | 6 +- R/{detectStandard.R => util-detectStandard.R} | 0 ...uateStandard.R => util-evaluateStandard.R} | 0 ...ppingList.R => util-generateMappingList.R} | 13 +++-- R/{hasColumn.R => util-hasColumn.R} | 0 R/{hasField.R => util-hasField.R} | 0 ...ListValue.R => util-setMappingListValue.R} | 3 +- R/{textKeysToList.R => util-textKeysToList.R} | 0 9 files changed, 57 insertions(+), 21 deletions(-) rename R/{detectStandard.R => util-detectStandard.R} (100%) rename R/{evaluateStandard.R => util-evaluateStandard.R} (100%) rename R/{generateMappingList.R => util-generateMappingList.R} (85%) rename R/{hasColumn.R => util-hasColumn.R} (100%) rename R/{hasField.R => util-hasField.R} (100%) rename R/{setMappingListValue.R => util-setMappingListValue.R} (99%) rename R/{textKeysToList.R => util-textKeysToList.R} (100%) diff --git a/R/getChartStatus.R b/R/getChartStatus.R index 8644bec4..17f90471 100644 --- a/R/getChartStatus.R +++ b/R/getChartStatus.R @@ -1,16 +1,17 @@ #' Check the status of a chart based on the current mapping #' -#' Checks a chart's status when column-level chart specifications are provided in chart$dataSpec. Note that safetyGraphicsApp() does not allow a `mapping` value that is not found in `domainData`, so this function only needs to check that an expected parameter exists in `mapping` (not that the specified column is found in the loaded data). +#' Checks a chart's status when column-level chart specifications are provided in chart$dataSpec. +#' Note that safetyGraphicsApp() does not allow a `mapping` value that is not found in `domainData`, +#' so this function only needs to check that an expected parameter exists in `mapping` (not that the +#' specified column is found in the loaded data). #' -#' Returns a list, with: -#' - `status` (TRUE, FALSE) -#' - `domains` a list specifying wheter all columns are specified in each domain -#' - `columns` a list that matches the structure of chart$dataSpec and indicates which variables are available. -#' -#' @param chart chart object -#' @param mapping the current mapping data.frame +#' @param chart `list` chart object +#' @param mapping `data.frame` current mapping #' -#' @return a list with `status`, `domains` and `columns` properties +#' @return `list` Named list with properties: +#' - status `logical` +#' - domains `list` list specifying whether all columns are specified in each domain +#' - columns `list` list that matches the structure of chart$dataSpec and indicates which variables are available. #' #' @examples #' sample_chart <- list( @@ -30,9 +31,39 @@ #' check <- safetyGraphics:::getChartStatus(chart=sample_chart, mapping=sample_mapping) #' # check$status=TRUE #' -#' @importFrom purrr map_lgl set_names +#' # Add data spec to +#' charts <- makeChartConfig() %>% +#' map(function(chart) { +#' chart$mapping <- chart$domain %>% +#' map_dfr(function(domain) { +#' do.call( +#' `::`, +#' list( +#' 'safetyCharts', +#' paste0('meta_', domain) +#' ) +#' ) +#' }) %>% +#' distinct(domain, col_key, current = standard_adam) %>% +#' filter(!is.na(current)) %>% +#' select(domain, text_key = col_key, current) +#' +#' chart$dataSpec <- chart$domain %>% +#' map(function(domain) { +#' chart$mapping %>% +#' filter(.data$domain == !!domain) %>% +#' pull(text_key) %>% +#' unique() +#' }) %>% +#' set_names(chart$domain) +#' +#' chart +#' }) +#' +#' @importFrom purrr imap map +#' @importFrom rlang set_names +#' #' @keywords internal - getChartStatus <- function(chart, mapping){ stopifnot( "Can't get status since chart does not have dataSpec associated."=hasName(chart, 'dataSpec') @@ -43,6 +74,7 @@ getChartStatus <- function(chart, mapping){ colStatus <- names(chart$dataSpec) %>% map(function(domain){ domainMapping <- generateMappingList(settingsDF=mapping, domain=domain) requiredCols <- chart$dataSpec[[domain]] + browser() colStatus <- requiredCols %>% map(function(col){ if(hasName(domainMapping,col)){ status<-case_when( @@ -85,4 +117,4 @@ getChartStatus <- function(chart, mapping){ } return(list(chart=chart$name, columns=colStatus, domains=domainStatus, status=status, summary=summary)) -} \ No newline at end of file +} diff --git a/R/mod_chartsTab.R b/R/mod_chartsTab.R index 3ba4aa07..b27c1b63 100644 --- a/R/mod_chartsTab.R +++ b/R/mod_chartsTab.R @@ -30,8 +30,6 @@ chartsTabUI <- function(id, chart){ chartsTab <- function(input, output, session, chart, data, mapping, status){ ns <- session$ns - - print(paste("running chartsTab in:", ns(''))) # Draw the header output$`chart-header` <- renderUI({makeChartSummary(chart, status=status())}) @@ -62,7 +60,7 @@ chartsTab <- function(input, output, session, chart, data, mapping, status){ where="beforeEnd", ui=downloadButton(ns("scriptDL"), "R script", class="pull-right btn-xs dl-btn") ) - + mapping_list<-reactive({ mapping_list <- generateMappingList(mapping() %>% filter(.data$domain %in% chart$domain)) if(length(mapping_list)==1){ @@ -99,7 +97,7 @@ chartsTab <- function(input, output, session, chart, data, mapping, status){ mapping = mapping(), chart = chart ) - + rmarkdown::render( tempReport, output_file = file, diff --git a/R/detectStandard.R b/R/util-detectStandard.R similarity index 100% rename from R/detectStandard.R rename to R/util-detectStandard.R diff --git a/R/evaluateStandard.R b/R/util-evaluateStandard.R similarity index 100% rename from R/evaluateStandard.R rename to R/util-evaluateStandard.R diff --git a/R/generateMappingList.R b/R/util-generateMappingList.R similarity index 85% rename from R/generateMappingList.R rename to R/util-generateMappingList.R index 97c13abe..f1c06f63 100644 --- a/R/generateMappingList.R +++ b/R/util-generateMappingList.R @@ -12,17 +12,22 @@ generateMappingList <- function(settingsDF, domain=NULL, pull=FALSE){ settingsDF$domain_key <- paste0(settingsDF$domain, "--", settingsDF$text_key) domain_keys <- settingsDF$domain_key %>% textKeysToList() - +browser() settingsList<-list() for (i in 1:length(domain_keys) ) { settingsList<-setMappingListValue( key=domain_keys[[i]], - value=ifelse(pull, settingsDF[i,"current"]%>%pull(), settingsDF[i,"current"]), + value=ifelse( + pull, + settingsDF[i,"current"] %>% + pull(), + settingsDF[i,"current"] + ), settings=settingsList, forceCreate=TRUE ) } - +browser() if(is.null(domain)){ return(settingsList) }else if(length(domain)>1){ @@ -30,4 +35,4 @@ generateMappingList <- function(settingsDF, domain=NULL, pull=FALSE){ }else{ return(settingsList[[domain]]) } -} \ No newline at end of file +} diff --git a/R/hasColumn.R b/R/util-hasColumn.R similarity index 100% rename from R/hasColumn.R rename to R/util-hasColumn.R diff --git a/R/hasField.R b/R/util-hasField.R similarity index 100% rename from R/hasField.R rename to R/util-hasField.R diff --git a/R/setMappingListValue.R b/R/util-setMappingListValue.R similarity index 99% rename from R/setMappingListValue.R rename to R/util-setMappingListValue.R index 8debec94..195bfb1c 100644 --- a/R/setMappingListValue.R +++ b/R/util-setMappingListValue.R @@ -27,6 +27,7 @@ setMappingListValue <- function(key, value, settings, forceCreate=FALSE){ } firstKey <- key[[1]] + browser() if(length(key)==1){ if(is.null(value)){ settings[firstKey]<-list(NULL) @@ -38,4 +39,4 @@ setMappingListValue <- function(key, value, settings, forceCreate=FALSE){ settings[[firstKey]]<-setMappingListValue(settings = settings[[firstKey]],key = key[2:length(key)], value=value, forceCreate=forceCreate) return(settings) } -} \ No newline at end of file +} diff --git a/R/textKeysToList.R b/R/util-textKeysToList.R similarity index 100% rename from R/textKeysToList.R rename to R/util-textKeysToList.R From 5accaf9baf3da028730e179ed140e444fab8adbd Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Tue, 14 Mar 2023 15:51:20 -0400 Subject: [PATCH 23/27] update generateMappingList to work with tbl_df-classed data frames --- R/getChartStatus.R | 5 +++-- R/util-generateMappingList.R | 9 ++++++--- R/util-setMappingListValue.R | 1 - 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/R/getChartStatus.R b/R/getChartStatus.R index 17f90471..e033ee7e 100644 --- a/R/getChartStatus.R +++ b/R/getChartStatus.R @@ -31,7 +31,7 @@ #' check <- safetyGraphics:::getChartStatus(chart=sample_chart, mapping=sample_mapping) #' # check$status=TRUE #' -#' # Add data spec to +#' # Add data spec to each chart. #' charts <- makeChartConfig() %>% #' map(function(chart) { #' chart$mapping <- chart$domain %>% @@ -59,6 +59,8 @@ #' #' chart #' }) +#' +#' checks <- map(charts, ~getChartStatus(.x, .x$mapping)) #' #' @importFrom purrr imap map #' @importFrom rlang set_names @@ -74,7 +76,6 @@ getChartStatus <- function(chart, mapping){ colStatus <- names(chart$dataSpec) %>% map(function(domain){ domainMapping <- generateMappingList(settingsDF=mapping, domain=domain) requiredCols <- chart$dataSpec[[domain]] - browser() colStatus <- requiredCols %>% map(function(col){ if(hasName(domainMapping,col)){ status<-case_when( diff --git a/R/util-generateMappingList.R b/R/util-generateMappingList.R index f1c06f63..53d53374 100644 --- a/R/util-generateMappingList.R +++ b/R/util-generateMappingList.R @@ -7,12 +7,15 @@ #' @importFrom stringr str_split #' @export -generateMappingList <- function(settingsDF, domain=NULL, pull=FALSE){ +generateMappingList <- function(settingsDF, domain=NULL, pull=FALSE) { + if ('tbl_df' %in% class(settingsDF)) + pull <- TRUE + settingsList <- list() settingsDF$domain_key <- paste0(settingsDF$domain, "--", settingsDF$text_key) domain_keys <- settingsDF$domain_key %>% textKeysToList() -browser() + settingsList<-list() for (i in 1:length(domain_keys) ) { settingsList<-setMappingListValue( @@ -27,7 +30,7 @@ browser() forceCreate=TRUE ) } -browser() + if(is.null(domain)){ return(settingsList) }else if(length(domain)>1){ diff --git a/R/util-setMappingListValue.R b/R/util-setMappingListValue.R index 195bfb1c..7cea3f80 100644 --- a/R/util-setMappingListValue.R +++ b/R/util-setMappingListValue.R @@ -27,7 +27,6 @@ setMappingListValue <- function(key, value, settings, forceCreate=FALSE){ } firstKey <- key[[1]] - browser() if(length(key)==1){ if(is.null(value)){ settings[firstKey]<-list(NULL) From 9f90959f4c7cbcb03592c25bf2c32d175d06eb93 Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Tue, 14 Mar 2023 16:29:00 -0400 Subject: [PATCH 24/27] remove `print`s --- R/getChartStatus.R | 1 - R/makeChartSummary.R | 1 - R/util-setMappingListValue.R | 1 - 3 files changed, 3 deletions(-) diff --git a/R/getChartStatus.R b/R/getChartStatus.R index e033ee7e..6037729e 100644 --- a/R/getChartStatus.R +++ b/R/getChartStatus.R @@ -113,7 +113,6 @@ getChartStatus <- function(chart, mapping){ }) return(missingDomainCols) }) - print(missingCols) summary<- paste0("Missing Mappings: ",paste(unlist(missingCols),collapse=",")) } diff --git a/R/makeChartSummary.R b/R/makeChartSummary.R index 2770983b..97882fb8 100644 --- a/R/makeChartSummary.R +++ b/R/makeChartSummary.R @@ -11,7 +11,6 @@ makeChartSummary<- function(chart, status=NULL, showLinks=TRUE, class="chart-header"){ if(!is.null(status)){ - print(status) if(status$status){ status <- div(class="status", tags$small("Status"), tags$i(class="fa fa-check-circle", style="color: green"),title=status$summary) }else{ diff --git a/R/util-setMappingListValue.R b/R/util-setMappingListValue.R index 7cea3f80..344b4c69 100644 --- a/R/util-setMappingListValue.R +++ b/R/util-setMappingListValue.R @@ -17,7 +17,6 @@ setMappingListValue <- function(key, value, settings, forceCreate=FALSE){ - if(typeof(settings)!="list"){ if(forceCreate){ settings=list() From 530c54aeab975eaea6549898bc4791c5a971206b Mon Sep 17 00:00:00 2001 From: Spencer Childress Date: Fri, 5 May 2023 11:47:45 -0400 Subject: [PATCH 25/27] fix #716 --- R/safetyGraphicsApp.R | 6 +++--- R/safetyGraphicsInit.R | 41 +++++++++++++++++++++-------------------- 2 files changed, 24 insertions(+), 23 deletions(-) diff --git a/R/safetyGraphicsApp.R b/R/safetyGraphicsApp.R index c2b9b91a..15525ff4 100644 --- a/R/safetyGraphicsApp.R +++ b/R/safetyGraphicsApp.R @@ -39,12 +39,12 @@ safetyGraphicsApp <- function( message("Initializing safetyGraphicsApp") config <- app_startup( - domainData = domainData, meta = meta, - charts = charts, mapping = mapping, - autoMapping = autoMapping, + domainData = domainData, + charts = charts, filterDomain = filterDomain, + autoMapping = autoMapping, chartSettingsPaths = chartSettingsPaths, appName = appName, hexPath = hexPath, diff --git a/R/safetyGraphicsInit.R b/R/safetyGraphicsInit.R index ff7be5ea..bd5dc165 100644 --- a/R/safetyGraphicsInit.R +++ b/R/safetyGraphicsInit.R @@ -116,38 +116,39 @@ safetyGraphicsInit <- function(charts=makeChartConfig(), delayTime=1000, maxFile observeEvent(input$runApp,{ shinyjs::hide(id="init") shinyjs::show(id="sg-app") - config<- app_startup( - domainData = domainData() %>% keep(~!is.null(.x)), + + config <- app_startup( meta = NULL, - charts= charts(), #mapping=NULL, - filterDomain="dm", - autoMapping=TRUE, + domainData = domainData() %>% + keep(~!is.null(.x)), + charts = charts(), + filterDomain = "dm", + autoMapping = TRUE, #chartSettingsPaths = NULL ) output$sg <- renderUI({ - safetyGraphicsUI( - "sg", - config$meta, - config$charts, - config$domainData, - config$mapping, - config$standards + safetyGraphicsUI("sg", + meta = config$meta, + mapping = config$mapping, + domainData = config$domainData, + charts = config$charts, + standards = config$standards, + config = config ) }) # delay is needed to get the appendTab in mod_chartsNav to trigger properly shinyjs::delay( delayTime, - callModule( - safetyGraphicsServer, - "sg", - config$meta, - config$mapping, - config$domainData, - config$charts, - config$filterDomain + callModule(safetyGraphicsServer, "sg", + meta = config$meta, + mapping = config$mapping, + domainData = config$domainData, + charts = config$charts, + filterDomain = config$filterDomain, + config = config ) ) }) From 5c1654c51e8e38b977f977bab48c7b55a4df1bcd Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Fri, 16 Jun 2023 12:58:40 -0400 Subject: [PATCH 26/27] remove header --- R/mod_profileTab.R | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/R/mod_profileTab.R b/R/mod_profileTab.R index 41653241..9c305358 100644 --- a/R/mod_profileTab.R +++ b/R/mod_profileTab.R @@ -8,11 +8,7 @@ profileTabUI <- function(id){ ns <- NS(id) if(isNamespaceLoaded("safetyProfile")){ - profile_ui<-list( - h1(paste("Participant Profile")), - span("This page shows details for a selected participant."), - profile_ui(ns("profile")) - ) + profile_ui<-profile_ui(ns("profile")) }else{ profile_ui<-NULL } From 69ca2fff59dfe787fbd1f38017842e65f4bae437 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Fri, 16 Jun 2023 13:03:47 -0400 Subject: [PATCH 27/27] update id selector css --- R/mod_safetyGraphicsServer.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/mod_safetyGraphicsServer.R b/R/mod_safetyGraphicsServer.R index e4f805e6..dae54fa5 100644 --- a/R/mod_safetyGraphicsServer.R +++ b/R/mod_safetyGraphicsServer.R @@ -69,7 +69,7 @@ safetyGraphicsServer <- function(input, output, session, # Update selected participant. updateSelectizeInput( session, - inputId = 'profile-profile-idSelect', + inputId = 'profile-profile-id-idSelect', selected = input$participants_selected ) })