add code analyzer

tools/utils/code-analyzer.R

@@ -0,0 +1,148 @@
+##
+## This file is part of the Omics Playground project.
+## Copyright (c) 2018-2023 BigOmics Analytics SA. All rights reserved.
+##
+
+
+setwd("~/Playground/omicsplayground")
+rfiles <- dir("components", recursive=TRUE, patter=".*[.][rR]$",full.names=TRUE)
+
+## scan all function declarations
+func.declared <- c()
+f <- rfiles[1]
+for(f in rfiles) {
+  src <- readLines(f)
+  ## detect allw function declaration
+  here.func <- grep("=[ ]*function|<-[ ]*function",src)
+  these.func  <- trimws(sub("<-.*|=.*","",src[here.func]))
+  these.func  <- gsub(".*[ ]|#","",these.func)
+  if(length(these.func)) {
+    ff <- cbind(these.func, f)
+    func.declared <- rbind( func.declared, ff)
+  }
+}
+colnames(func.declared) <- c("function.name","file")
+
+## create regexpression for all functions
+all.func <- func.declared[,"function"]
+func.rexp <- paste0("[\\^ =-\\(]",all.func,"[\\(@,]")  ## NEED RETHINK
+names(func.rexp) <- all.func
+
+## detect which functions are used in each file
+func.used <- c()
+f <- rfiles[10]
+for(f in rfiles) {
+  ## detect functions used
+  src <- readLines(f)
+  using.func <- grep(paste(func.rexp,collapse="|"), src)
+  using.func
+  if(length(using.func)==0) next
+  n=using.func[1]
+  func.calls <- c()
+  for(n in using.func){
+    s <- src[n]
+    f1 <- names(which(sapply(func.rexp, function(f) grepl(f,s))))
+    func.calls <- c(func.calls, f1)
+  }
+  if(length(func.calls)>0) {
+    tt <- table(func.calls)
+    rr <- data.frame(f, "function.called"=names(tt), "nfreq"=as.integer(tt))
+    func.used <- rbind(func.used, rr)
+  }
+}
+colnames(func.used) <- c("file","function.name","nfreq")
+
+head(func.declared,20)
+head(func.used,20)
+
+## detect multiple declared functions
+ndeclared <- table(func.declared[,"function.name"])
+multiple.declared <- names(which(ndeclared > 1))
+ww <- tapply( func.declared[,"file"], func.declared[,"function.name"],
+  function(w) paste(gsub(".*/","",sort(unique(w))),collapse=', '))
+df1 <- data.frame( 'function.name'=names(ndeclared), n.declared=as.integer(ndeclared), where.declared=ww)
+head(df1)
+head(df1[which(df1$n.declared>1),],20)
+
+## detect not used functions
+head(func.declared,20)
+head(func.used,20)
+
+nused <- table(func.used[,"function.name"])
+uu <- tapply( func.used[,"file"], func.used[,"function.name"],
+  function(w) paste(gsub(".*/","",sort(unique(w))),collapse=', '))
+df2 <- data.frame( 'function.name'=names(nused), n.used=as.integer(nused), where.used=uu)
+head(df2)
+
+df2 <- df2[match(df1$function.name, df2$function.name),]
+df2$n.used[is.na(df2$n.used)] <- 0
+df2$function.name <- NULL
+df <- cbind(df1, df2)
+rownames(df) <- NULL
+
+df <- df[,c("function.name","n.declared","n.used","where.declared","where.used")]
+
+## write.csv(df, file="code-analyzer-output.csv")
+
+
+## -----------------------------------------------------------------------------
+## -----------------------------------------------------------------------------
+## -----------------------------------------------------------------------------
+
+library(shiny)
+library(DT)
+
+ui = fluidPage(
+  h2("Code analytics: function declaration and calls"),
+  div( class="row",
+    actionButton("show_all","all"),
+    actionButton("show_multi","multiple-declared"),
+    actionButton("show_notused","not used")
+  ),
+  DT::DTOutput("dt")
+)
+
+server = function(input, output, session) {
+
+  filtered_df <- reactiveVal(df)
+
+  observeEvent( input$show_all, {
+    filtered_df( df )
+  })
+
+  observeEvent( input$show_notused, {
+    df1 <- df[ df$n.used==0,] 
+    df1 <- df1[order(-df1$n.declared),]    
+    filtered_df( df1)
+  })
+
+  observeEvent( input$show_multi, {
+    df1 <- df[ df$n.declared > 1,] 
+    df1 <- df1[order(-df1$n.declared),]    
+    filtered_df(df1)
+  })
+
+  output$dt <- DT::renderDT(
+    DT::datatable( filtered_df(),
+      extensions = 'Scroller',
+      options = list(
+        deferRender = FALSE,
+        dom = 't',
+        ##columnDefs = list(list(className = 'dt-center', targets = 5)),
+        scrollY = 800,
+        scroller = TRUE,
+        scrollX = TRUE,
+        pageLength = 80)
+    ) %>%
+      formatStyle(
+        'n.declared',
+        backgroundColor = styleInterval(1, c('white', 'yellow'))
+      ) %>%
+      formatStyle(
+        'n.used',
+        backgroundColor = styleInterval(0, c('salmon', 'white'))
+      ) 
+  )
+}
+
+shiny::shinyApp(ui, server=server, options=list(launch.browser=TRUE))

tools/utils/init-pgxfolder.R

@@ -1,3 +1,7 @@
+##
+## This file is part of the Omics Playground project.
+## Copyright (c) 2018-2023 BigOmics Analytics SA. All rights reserved.
+##
 
 RDIR="../R"
 FILES="../lib"

tools/utils/testBoard.R

@@ -1,6 +1,6 @@
 ##
 ## This file is part of the Omics Playground project.
-## Copyright (c) 2018-2021 BigOmics Analytics Sagl. All rights reserved.
+## Copyright (c) 2018-2023 BigOmics Analytics SA. All rights reserved.
 ##
 
 library(shiny)

tools/utils/testPlotModule.R

@@ -1,6 +1,6 @@
 ##
 ## This file is part of the Omics Playground project.
-## Copyright (c) 2018-2021 BigOmics Analytics Sagl. All rights reserved.
+## Copyright (c) 2018-2023 BigOmics Analytics SA. All rights reserved.
 ##
 
 if(interactive()) {

tools/utils/update-pgxfolder.R

@@ -1,3 +1,8 @@
+##
+## This file is part of the Omics Playground project.
+## Copyright (c) 2018-2023 BigOmics Analytics SA. All rights reserved.
+##
+
 RDIR = "../R"
 FILES = "../lib"
 FILESX = "../libx"