first commit

Author: glaisney

Diff for: Dockerfile

@@ -0,0 +1,34 @@
+FROM rocker/shiny:4.2.0
+
+RUN apt-get update \
+	&& apt-get install -y \
+	apt-utils \
+	manpages-dev \
+	libnetcdf-dev \
+	libxml2-dev \
+	libglpk-dev \
+	libnode-dev  \
+	libz-dev
+
+RUN R -e "install.packages('BiocManager')"
+# RUN R -e "BiocManager::install('omicsViewer')"
+RUN R -e "BiocManager::install('xcms')"
+RUN R -e "BiocManager::install('MAIT')"
+RUN R -e "install.packages('devtools')"
+RUN R -e 'BiocManager::install(c("survminer", "survival","fastmatch","reshape2","beeswarm","grDevices","shinycssloaders","shinythemes","networkD3","httr","RColorBrewer","psych","stringr","shiny","shinydashboard","shinyWidgets","shinybusy","matrixStats","flatxml","excelR","shinyjs","shinyFiles","DT","plotly","openxlsx","yaml","curl","sortable","BiocManager","password","ggseqlogo","devtools","Matrix","RSQLite"))'
+RUN R -e 'BiocManager::install(c("Biobase", "fgsea", "S4Vectors", "SummarizedExperiment"), update = FALSE)'
+RUN R -e 'devtools::install_github("mengchen18/omicsViewer", dependencies = TRUE)'
+RUN R -e "devtools::install_github('mengchen18/xcmsViewer', upgrade='never')"
+
+
+RUN mkdir /home/shiny/data && \
+	mkdir /home/shiny/app
+
+COPY . /home/shiny/app/
+
+ENV PORT 3838
+
+ENV HOST "0.0.0.0"
+
+CMD ["R", "-e", "shiny::runApp('/home/shiny/app', host = Sys.getenv(\"HOST\"), port = strtoi(Sys.getenv(\"PORT\")))"]
+

Diff for: landingPage.R

@@ -0,0 +1,59 @@
+
+landingPage_ui <- function(id) {
+  ns <- NS(id)
+  tagList(
+    tags$style("#landingpageid{margin: auto;}"),
+    h1("Welcome to BayBioMS xcmsViewer for untargeted metabolomics data!"),
+    absolutePanel(id = "landingpageid", class = "myClass", fixed = TRUE
+                  ,draggable = FALSE, left = 0, right = 0, top = "35%"
+                  ,width = 500, height = "auto", 
+                  wellPanel(
+                    uiOutput(ns("error.ui")),
+                    fluidRow(
+                      column(10, passwordInput(ns("id"), "Your passcode", placeholder = "Enter your passcode here!")),
+                      column(2, actionButton(ns("go"), "Go!"), style = "padding-top:25px")
+                    )
+                  )
+    )
+  )
+}
+
+landingPage_module <- function(input, output, session) {
+  
+  ns <- session$ns
+  
+#  hashTab <- read.delim(
+    # "/dss/ga52cib/xcmsViewer/passcodeList.tsv", header = TRUE,
+#    "/home/shiny/data/xcmsViewer/passcodeList.tsv", header = TRUE, stringsAsFactors = FALSE
+    # "/media/share_LRZCC/xcmsViewer/passcodeList_debug.tsv", header = TRUE, stringsAsFactors = FALSE
+#  )
+  
+   hashTab <- data.frame(
+     code = "metabohub",
+     path = "/home/shiny/data/", #Data will be loaded from here in the Docker container
+     #path = "~/xcmsViewerDBs/",
+     stringsAsFactors = FALSE
+   )
+  
+  m0 <- eventReactive(input$go, {
+    id <- trimws(input$id)
+    i <- which(hashTab[, 1] %in% id)
+    if (length(i) != 1)
+      return(NULL)
+    i
+  })
+  
+  output$error <- renderUI({
+    HTML("There was an error with your passcode, please try again! <br><hr>")
+  })
+  
+  output$error.ui <- renderUI({
+    req(is.null(m0()))
+    uiOutput(ns("error"))
+  })
+  
+  reactive({
+    req(m0())
+    hashTab[m0(), 2]
+  })
+}

Diff for: res.RDS

@@ -0,0 +1,69 @@
+library(xcmsViewer)
+library(omicsViewer)
+source("/home/shiny/app/landingPage.R")
+# source("landingPage.R")
+
+ll <- list(
+  list(
+    tabName = "Annotation",
+    moduleName = "xcmsannot",
+    moduleUi = xcmsViewer:::xcmsAnnotationTab_ui,
+    moduleServer  = xcmsViewer:::xcmsAnnotationTab_module
+  )
+)
+
+returnValueOrNULL <- function(x, v) {
+  r <- x$header[x$axis == v]
+  if (is.na(r))
+    return(NULL)
+  r
+}
+
+server <- function(input, output, session) {
+  
+  ns <- session$ns
+  
+  v <- callModule(landingPage_module, id = "test")
+  showLanding <- reactiveVal(TRUE)
+  
+  observe({
+    showLanding ( length(v()) != 1 )
+  })
+  
+  output$uis <- renderUI({
+    req(showLanding())
+    landingPage_ui("test") 
+  })
+  
+  observe(print(v()))
+  
+  callModule(
+    omicsViewer:::app_module, id = "app", .dir = v,
+    filePattern = ".RDS$|.DB$",
+    esetLoader = function(x) {
+      if (grepl(".db$", x, ignore.case = TRUE)) {        
+        obj <- RSQLite::dbConnect(RSQLite::SQLite(), x)
+        x <- RSQLite::dbGetQuery(obj, 'SELECT * FROM defaultVis;')
+        attr(obj, "fx") <- returnValueOrNULL(x, "fx")
+        attr(obj, "fy") <- returnValueOrNULL(x, "fy")
+        attr(obj, "sx") <- returnValueOrNULL(x, "sx")
+        attr(obj, "sy") <- returnValueOrNULL(x, "sy")
+      } else if (grepl("RDS", x, ignore.case = TRUE)) {
+        obj <- readRDS(x)
+      }
+      obj
+    },
+    exprsGetter = getFeatureExprs,
+    pDataGetter = getPheno,
+    fDataGetter = getFeatureMeta,
+    defaultAxisGetter = function(x, what) attr(x, what),
+    additionalTabs = ll,
+    appName = "XcmsViewer",
+    appVersion = packageVersion("xcmsViewer")
+  )
+
+  output$aout <- renderUI({
+    req(!showLanding())
+    omicsViewer:::app_ui("app")
+  })
+}

Diff for: server.R

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+library(xcmsViewer)
+library(omicsViewer)
+source("/home/shiny/app/landingPage.R")
+# source("landingPage.R")
+
+ui <- fluidPage(
+  uiOutput("uis"),
+  uiOutput("aout")
+)