api, mix, shiny-ui-base: Introduce the concept of "project" and...

api, mix, shiny-ui-base: Introduce the concept of "project" and "data"directories for script-based workflow.

DESCRIPTION

 Package: shinyscreen
 Title: Pre-screening of Mass Spectrometry Data 
-Version: 1.0.13
+Version: 1.1.0
 Author: Todor Kondić
 Maintainer: Todor Kondić <todor.kondic@uni.lu>
 Authors@R: 

NAMESPACE

@@ -23,15 +23,14 @@ export(merge2rev)
 export(mk_comp_tab)
 export(mk_tol_funcs)
 export(mz_input)
+export(new_project)
 export(new_rv_state)
 export(new_state)
-export(new_state_fn_conf)
 export(plot_struct)
 export(plot_struct_nowrap)
 export(prescreen)
 export(read_rt)
 export(report)
-export(report_old)
 export(rev2list)
 export(rt_input)
 export(run)

R/api.R

@@ -23,14 +23,52 @@ new_state <- function() {
 new_rv_state <- function() react_v(m=list2rev(new_state()))
 
 ##' @export
-new_state_fn_conf <- function(fn_conf) {
+new_project <- function(project) {
     m <- new_state()
+    if (!is.character(project)) stop("Argument `project' must be a character string.")
+    if (!dir.exists(project)) stop('Project directory either does not exist, or is unreadable.')
+    project_path <- normalizePath(project)
+    project <- basename(project)
+    fn_conf <- file.path(project_path,FN_CONF)
     m$conf <- read_conf(fn_conf)
-    init_state(m)
+    m$conf$project <- project
+    m$conf$paths$project <- project_path
+    if (is.null(m$conf$paths$data)) {
+        m$conf$paths$data <- m$conf$paths$project
+    }
+    if (!dir.exists(m$conf$paths$data)) stop("Path to data directory either does not exist, or is inaccesible.")
+    lst_cmpl <- m$conf$compounds$lists
+    lst_fn_cmpl <- lapply(names(lst_cmpl),function (nm) {
+        bfn_cmpl <- lst_cmpl[[nm]]
+        fn <- file.path(m$conf$paths$project,bfn_cmpl)
+        if (!file.exists(fn)) stop("File ", fn, " does not exist in ", m$conf$paths$project," .")
+        fn
+        })
+    names(lst_fn_cmpl) <- names(lst_cmpl)
+    m$conf$paths$compounds$lists <- lst_fn_cmpl
+
+    fn_sets <- m$conf$compounds$sets[[1]] #It's always only one.
+    if (!file.exists(fn_sets)) stop("File ", fn_sets, " does not exist in ", m$conf$paths$project," .")
+    m$conf$paths$compounds$sets <- fn_sets
+
+    tmp <- m$conf$paths$datatab
+    datatab <- if (!is.null(tmp)) {
+                   if (file.exists(tmp)) {
+                       tmp
+                   } else {
+                       file.path(m$conf$paths$project,tmp)
+                   }
+               } else {
+                   file.path(m$conf$paths$project,FN_DATA_TAB)
+               }
+    if (!file.exists(datatab)) stop("A CSV file with data file entries does not exist (`paths$datatab' in config).")
+    datatab <- normalizePath(datatab)
+    m$conf$paths$datatab <-datatab
+    m
 }
 
 ##' @export
-run <- function(fn_conf="",m=NULL,phases=NULL,help=F) {
+run <- function(project="",m=NULL,phases=NULL,help=F) {
     all_phases=list(setup=setup_phase,
                     comptab=mk_comp_tab,
                     extract=extr_data,
@@ -54,14 +92,11 @@ run <- function(fn_conf="",m=NULL,phases=NULL,help=F) {
                                                       all_phases[phases]
                                                   }
     
-    m <- if (nchar(fn_conf)!=0) new_state_fn_conf(fn_conf) else if (!is.null(m)) m else stop("(run): Either the YAML config file (fn_conf),\n or the starting state (m) must be provided\n as the argument to the run function.")
-    
-    dir.create(m$conf$project,
-               showWarnings = F,
-               recursive = T)
-    m <- withr::with_dir(new=m$conf$project,code = Reduce(function (prev,f) f(prev),
-                                                          x = the_phases,
-                                                          init = m))
+    m <- if (nchar(project)!=0) new_project(project) else if (!is.null(m)) m else stop("(run): Either the YAML config file (project),\n or the starting state (m) must be provided\n as the argument to the run function.")
+    ## m$conf$project <- normalizePath(m$conf$project) #FIXME: Test in all workflows!
+    m <- withr::with_dir(new=m$conf$paths$project,code = Reduce(function (prev,f) f(prev),
+                                                            x = the_phases,
+                                                            init = m))
     return(invisible(m))
 }
 
@@ -95,7 +130,7 @@ run_in_dir <- function(m) {
 load_compound_input <- function(m) {
     coll <- list()
     fields <- colnames(EMPTY_CMPD_LIST)
-    fns <- m$conf$compounds$lists
+    fns <- m$conf$paths$compounds$lists
     coltypes <- c(ID="character",
                   SMILES="character",
                   Formula="character",
@@ -138,15 +173,18 @@ load_compound_input <- function(m) {
     
     cmpds[,("known"):=.(the_ifelse(!is.na(SMILES),"structure",the_ifelse(!is.na(Formula),"formula","mz")))]
     m$input$tab$cmpds <- cmpds
-    m$input$tab$setid <- read_setid(m$conf$compounds$sets,
+    m$input$tab$setid <- read_setid(m$conf$paths$compounds$sets,
                                     m$input$tab$cmpds)
     m
 }
 
 ##' @export
 load_data_input <- function(m) {
-    m$input$tab$mzml <- file2tab(m$conf$data)
+    m$input$tab$mzml <- file2tab(m$conf$paths$datatab)
     assert(all(unique(m$input$tab$mzml[,.N,by=c("adduct","tag")]$N)<=1),msg="Some rows in the data table contain multiple entries with same tag and adduct fields.")
+    pref<-m$conf$paths$data
+    m$input$tab$mzml[,file:=fifelse(file.exists(file),file,file.path(..pref,file))]
+    m$input$tab$mzml[,file:=normalizePath(file)]
     m
 
 }
@@ -168,8 +206,9 @@ mk_comp_tab <- function(m) {
     setkey(cmpds,ID)
     ## mzml[,`:=`(wd=sapply(file,add_wd_to_mzml,m$conf$project))]
     assert(nrow(cmpds)>0,msg="No compound lists have been provided.")
+    assert(all(mzml[,unique(set)] %in% setid[,unique(set)]),msg="Not all set names in the `datatab' data file table match those in the provided set list.")
     message("Begin generation of the comprehensive table.")
-    
+
     comp <- cmpds[setid,on="ID"][mzml,.(tag,adduct,ID,RT,set,Name,file,SMILES,Formula,mz,known),on="set",allow.cartesian=T]
     tab2file(tab=comp,file=paste0("setidmerge",".csv"))
     setkey(comp,known,set,ID)
@@ -272,7 +311,7 @@ verify_data_df <- function(mzml,all_sets) {
 
 verify_data <- function(conf,all_sets) {
     ## * Existence of input files
-    fn_data <- conf$data
+    fn_data <- conf$paths$data
     assert(isThingFile(fn_data),msg=paste("Data table does not exist:",fn_data))
     mzml <- file2tab(fn_data)
     verify_data_df(mzml=mzml,all_sets)
@@ -439,7 +478,7 @@ extr_data_future <- function(m) {
 
     fn_ex <- get_fn_extr(m)
     timetag <- format(Sys.time(), "%Y%m%d_%H%M%S")
-    saveRDS(object = m, file = file.path(m$conf$project,
+    saveRDS(object = m, file = file.path(m$conf$paths$project,
                                          paste0(timetag,"_",FN_EXTR_STATE)))
     m
     
@@ -514,7 +553,7 @@ extr_data_serial <- function(m) {
 
     fn_ex <- get_fn_extr(m)
     timetag <- format(Sys.time(), "%Y%m%d_%H%M%S")
-    saveRDS(object = m, file = file.path(m$conf$project,
+    saveRDS(object = m, file = file.path(m$conf$paths$project,
                                          paste0(timetag,"_",FN_EXTR_STATE)))
     m
     
@@ -689,55 +728,6 @@ create_plots <- function(m) {
     m
 }
 
-#' @export
-report_old <- function(m) {
-    figtopdir <- FIG_TOPDIR #file.path(m$conf$project,FIG_TOPDIR)
-    pander::evalsOptions("graph.output","pdf")
-    author <- if (!is.null(m$conf$report$author)) m$conf$report$author else REPORT_AUTHOR
-    title <- if (!is.null(m$conf$report$title)) m$conf$report$title else REPORT_TITLE
-    doc <- pander::Pandoc$new(author,title)
-    doc$add(pander::pandoc.header.return("Plots",level = 1))
-    sets <- m$out$tab$flt_summ[,unique(set)]
-    rep_theme <- ggplot2::labs(title = NULL)
-    for (s in sets) {
-        doc$add(pander::pandoc.header.return(paste('Set', s), level = 2))
-        sdf <- m$out$tab$flt_summ[set==s,]
-        group <- sdf[,unique(adduct)]
-        for (g in group) {
-            asdf <- sdf[adduct==g,] 
-            ids <- asdf[,unique(ID)]
-            for (id in ids) {
-                message("Image ","set: ",s," group: ", g, " id: ",id)
-                doc$add(pander::pandoc.header.return(paste('ID',id),level = 3))
-                tab <- asdf[ID==id,.(tag,ms1_int,ms1_rt,adduct,mz,file)]
-                ms2info <- m$out$tab$ms2_spec[adduct==g & ID==id,.(tag,ID,rt,ms2_max_int,file)]
-                tab2 <- tab[ms2info,on="file"][,.(tag,mz,adduct,"$RT_{ms1}$[min]"=ms1_rt,"$RT_{ms2}$[min]"=rt,"$I{ms1}$"=formatC(ms1_int, format="e",digits = 2), "$I(ms2)$"= formatC(ms2_max_int, format="e",digits = 2))]
-                data.table::setorderv(tab2,c("$I{ms1}$","$I(ms2)$"),c(-1,-1))
-                doc$add.paragraph("")
-                figpath <- fig_path(top=figtopdir,set=s,group=g,id=id,suff="all",ext="pdf")
-                doc$add(pander::pandoc.image.return(img=paste0("file:",figpath)))
-                doc$add.paragraph("")
-                message("Adding table.")
-                doc$add.paragraph(pander::pandoc.table.return(tab2))
-                message("Done adding table.")
-                ## doc$add(print(tab))
-                doc$add.paragraph("")
-                
-            }
-            
-        }
-    }
-    doc$add(pander::pandoc.header.return("Appendix", level = 1))
-    doc$add(pander::pandoc.header.return("Configuration",level = 2))
-    doc$add(m$conf)
-    doc$add(pander::pandoc.header.return("R Session Info",level = 2))
-    doc$add(sessionInfo())
-    m$out$report <- doc
-    m$out$report$export('report.pdf')
-    m
-}
-
-
 #' @export
 #' @title app
 #' @param shiny_args `list`, optional list of arguments conveyed to
@@ -870,12 +860,12 @@ report <- function(m) {
         message("(report) Knitting of chunk ",n," out of ",NROW(keytab)," has been completed.")
         
     }
-    fn_rep <- file.path(m$conf$project,"report.Rmd")
+    fn_rep <- file.path(m$conf$paths$project,"report.Rmd")
     message("(report) Writing Rmd...")
     cat(repdoc,file=fn_rep,sep = "\n")
     message("(report) ...done.")
     message("(report) Render start ...")
-    rmarkdown::render(fn_rep,output_dir = m$conf$project)
+    rmarkdown::render(fn_rep,output_dir = m$conf$paths$project)
     message("(report) ...done.")
     m
 }

R/mix.R

@@ -497,8 +497,8 @@ read_setid <- function(fn,cmpds) {
 
 
 write_conf <- function(m,fn) {
-    m$conf$data <- get_fn_ftab(m)
-    if (NROW(m$input$tab$mzml)>0) tab2file(tab=m$input$tab$mzml,file=file.path(m$conf$project,FN_DATA_TAB))
+    m$conf$paths$data <- get_fn_ftab(m)
+    if (NROW(m$input$tab$mzml)>0) tab2file(tab=m$input$tab$mzml,file=file.path(m$conf$paths$project,FN_DATA_TAB))
     yaml::write_yaml(x=m$conf,file=fn)
     
     
@@ -506,12 +506,12 @@ write_conf <- function(m,fn) {
 }
 write_state <- function(m,fn_conf) {
     write_conf(m,fn_conf)
-    tab2file(tab=m$input$tab$mzml,file=file.path(m$conf$project,FN_DATA_TAB))
+    tab2file(tab=m$input$tab$mzml,file=file.path(m$conf$paths$project,FN_DATA_TAB))
 }
 
 read_conf <- function(fn) {
     cf <- yaml::yaml.load_file(fn)
-    fnl <- cf$compound$lists
+    fnl <- cf$compounds$lists
     if (length(fnl)>0) {
         nms <- character(0)
         for (i in 1:length(fnl)) {
@@ -520,7 +520,7 @@ read_conf <- function(fn) {
         names(fnl) <- nms
         
     }
-    cf$compound$lists <- fnl
+    cf$compounds$lists <- fnl
     ## conf_trans(cf)
     cf
 }
@@ -529,28 +529,28 @@ read_conf <- function(fn) {
 
 ##' @export
 get_fn_comp <- function(m) {
-    file.path(m$conf$project,FN_COMP_TAB)
+    file.path(m$conf$paths$project,FN_COMP_TAB)
 }
 
 ##' @export
 get_fn_summ <- function(m) {
-    file.path(m$conf$project, FN_SUMM)
+    file.path(m$conf$paths$project, FN_SUMM)
 }
 
 ##' @export
 get_fn_extr <- function(m) {
-    file.path(m$conf$project, "extracted.rds")
+    file.path(m$conf$paths$project, "extracted.rds")
 }
 
 ##' @export
 get_fn_conf <- function(m) {
-    file.path(m$conf$project, FN_CONF)
+    file.path(m$conf$paths$project, FN_CONF)
 }
 
 
 ##' @export
 get_fn_ftab <- function(m) {
-    file.path(m$conf$project, FN_DATA_TAB)
+    file.path(m$conf$paths$project, FN_DATA_TAB)
 }
 
 init_state <- function(m) {

R/shiny-ui-base.R

@@ -658,7 +658,7 @@ mk_shinyscreen_server <- function(projects,init) {
 
         isolate({
             rvs$m$conf$project <- in_conf$project
-            rvs$m$conf$data <- in_conf$data
+            rvs$m$conf$paths <- in_conf$paths
             ## Lists
             rvs$m$conf$compounds$lists <- in_conf$compounds$lists
             rvs$m$conf$compounds$sets <- in_conf$compounds$sets
@@ -696,8 +696,8 @@ mk_shinyscreen_server <- function(projects,init) {
                      choices=c("min","s"))
 
             ## Files
-            if (isTruthy(in_conf$data)) {
-                df <- shinyscreen:::file2tab(in_conf$data)
+            if (isTruthy(in_conf$paths$data)) {
+                df <- shinyscreen:::file2tab(in_conf$paths$data)
                 dfile <- data.table::copy(df[,tag:=as.character(tag),with=T])
                 dfile <- dfile[,unique(.SD),.SDcol=c("file","tag")]
                 ## rv_dfile(df[,.(file,tag),by=c("file","tag"),mult="first"][,file:=NULL])
@@ -827,7 +827,7 @@ mk_shinyscreen_server <- function(projects,init) {
         rf_conf_state <- reactive({
             state <- rf_conf_proj()
             ftab <- get_fn_ftab(state)
-            state$conf$data <- ftab
+            state$conf$paths$data <- ftab
             state$conf[["summary table"]]$filter <- rf_get_subset()
             state$conf[["summary table"]]$order <- rf_get_order()
             state
@@ -1170,7 +1170,7 @@ mk_shinyscreen_server <- function(projects,init) {
                 yaml::write_yaml(m$conf,
                                  file = fconf)
                 shinyscreen:::tab2file(tab=m$input$tab$mzml,file=ftab)
-                m$conf$data <- ftab
+                m$conf$paths$data <- ftab
                 saveRDS(object=m,file=fn)
             }
             shinymsg("Saving state completed.")