R/finalize_dependency_si.R

In gelfondjal/IT2: Tracks and manages dependencies for R project

#' Writes dependency data to file in "Dependency" directory
#' @param source_info The source information list that contains dependency object
#' @param write Logical indicated to write the dependency object
#' @param commit Message for git commit
#' @param effort.hours optional hours of work for tracking
#' @details Operates git tracking of program and dependency file. Writes to database when commit message is !=""
#' @return dependency.object 
#' @export

finalize.dependency.si <- function(source_info,write=TRUE,commit="",effort.hours=0){
  
  # read in dependency object from dependency.file in source_info
  # if commit != "", then git commit with db update
  # write to db if database does not already exist
  # return dependency object
  
  current.dir <- getwd()
  
  Write(sessionInfo(),paste0("Session_info_",source_info$file$db.name,".RObj"),paste0("sessionInfo for", source_info$file[["file"]]),save)
  
  if(source_info$pandoc){
  	trier <- "Pandoc not working"
  	try({
  	trier <- ""
    panderOptions("table.split.table",Inf)
    evalsOptions("cache.dir",source_info$tex.dir)
    setwd(source_info$tex.dir)
    source_info$report$format<-'html'
    source_info$report$export(source_info$file$db.name,open=FALSE)
    pandocInfo <- Create.file.info(source_info$tex.dir,paste0(source_info$file$db.name,".html"),"html markdown")
    Write.cap(NULL,pandocInfo,I,source_info)
    })
    
    if(trier!=""){warning(trier)}
    
    setwd(current.dir)
  }
  
  dependency.file <- file.path(source_info$dependency.dir,source_info$dependency.file)
  
  effort.hours <- ifelse(commit=="",0,effort.hours) # Only add hours during commit
  
  dependency.out <- source_info$dependency$data 
  
  dependency.out <- subset(dependency.out,!is.na(dependency))
  
  n.output.files <-	nrow(subset(dependency.out,dependency=="out"))
  print(c("# of output files",n.output.files))
  
  project.path <- dependency.out$project.path[1]
  
  dependency.out$source.git <- NA
  try({
    dependency.out$source.git <- paste(git.info(as.character(dependency.out$path[1]),file.path(dependency.out$source.file.path[1],dependency.out$source.file)[1])[1:5],collapse=" ")
    
  })	
  dependency.out$source.mod.time <- as.character(file.info(file.path(dependency.out$source.file.path[1],dependency.out$source.file[1]))$mtime)
  
  dependency.out$source.hash <-   Digest(file=file.path(dependency.out$source.file.path[1],dependency.out$source.file[1]),serialize=FALSE) 
  
  
  for(dep.row.iter in 1:nrow(dependency.out)){
    
    target.file <- file.path(dependency.out$target.path[dep.row.iter],dependency.out$target.file[dep.row.iter])
    
    #		print(target.file)
    
    dependency.out$target.hash[dep.row.iter] <- Digest(file=as.character(target.file),serialize=FALSE)
    
    dependency.out$target.mod.time[dep.row.iter] <- as.character(file.info(as.character(target.file))$mtime)
    
  }
  
  
  
  
  
  
  
  
  
  dependency.out$commit_message <- commit
  dependency.out$effort_hours <- effort.hours 		
  
  
  committed <- FALSE	
  
  if(commit!=""){
    
    
    
    project.id <- dependency.out$project.id[1]
    
    
    if(gsub("\\.","_",make.names(project.id))!=project.id){
      stop("Project ID is not valid database name")
    }
    
    
    
    
    # Initialize database
    
    
    db.namer <- gsub("\\.","_",paste(paste(names(dependency.out),"TEXT"),collapse=", "))
    db.update.namer <- paste(paste("$",gsub("\\.","_",names(dependency.out)),sep=""),collapse=", ")
    
    drv <- dbDriver("SQLite")
    
    db.path <- file.path(source_info$data.dir,paste0(project.id,".mysql"))
    
    con <- dbConnect(drv, dbname=db.path)
    
    db.name <- project.id
    
    if(!dbExistsTable(con, db.name)){
      
      dbGetQuery(con, paste("CREATE Table",db.name, "(",db.namer,")"))
      
    }
    
    # add 
    
    con <- dbConnect(drv, dbname=db.path)
    res <- dbSendQuery(con, paste("SELECT * FROM",db.name))
    
    prior.commits <- fetch(res,n=-1)$commit_message
    
    if(commit %in% prior.commits){
      warning("commit message non-unique. NO COMMIT made")
    }else{
      
      try({git.commit(dependency.out$project.path[1],commit)})
      
      dependency.out$source.git <- NA		
      
      try({		
        
        dependency.out$source.git <- paste(git.info(as.character(dependency.out$path[1]),file.path(dependency.out$source.file.path[1],dependency.out$source.file)[1])[1:5],collapse=" ")
      })
      
      committed <- TRUE
      
      
      sql <- paste("INSERT INTO",db.name," VALUES (",db.update.namer,")")
      dbBeginTransaction(con)
      
      dependency.out.db <- dependency.out
      names(dependency.out.db) <- gsub("\\.","_",names(dependency.out.db))
      dbGetPreparedQuery(con, sql, bind.data = dependency.out.db)
      
      dbCommit(con)
      
      print(paste("Commit dependencies",commit))
      
    }
    
    dbDisconnect(con)
    
    
  } #if commit != ""
  
  
  setwd(current.dir)
  if(write){
    write.dependency(dependency.out,dependency.file)
    try({	git.add(project.path,file.path(dependency.file))	})
    
    if(committed) {
      
      try({
        
        git.add(dependency.out$project.path[1],file.path(source_info$dependency.dir,source_info$dependency.file))
        git.commit(dependency.out$project.path[1],paste("Track depedency file"))
        
      })
    }
    
    
  }
  
  
  print(paste("Completed",source_info$file[["file"]]))
  
  return(dependency.out)	
  
  
}