Various helper functions

* mix.R

** rmbmix.mkdir
   Generates temporary work dir to hold on-the-fly metadata.

** rmbmix.gen_comp_list
   Generate compound list.

** rmbmix.single
   Extend to include the work directory.

mix.R

+## Create a temporary directory to hold the files generated on the
+## fly.
+rmbmix.mkdir<-function() {
+    nm<-tempfile(pattern="rmbmix")
+    dir.create(nm)
+    nm
+}
 
+##
 rmbmix.mk_sett_file<-function(sett_alist,file) {
     require(yaml)
     tmp<-tempfile()
@@ -11,11 +19,47 @@ rmbmix.mk_sett_file<-function(sett_alist,file) {
 }
 
 
+## Generate the RMassBank compound list from the input compound list
+## in CSV file src_fn. The input compound list format is either
+## Chemical Dashboard csv file with, at least, PREFERRED_NAMES and
+## SMILES columns _filled_ out, or just an ordinary csv file with
+## columns SMILES and Names filled. Argument dest_fn is the
+## destination filename.
+rmbmix.gen_comp_list<-function(src_fn,dest_fn) {
+    df<-read.csv(src_fn)
+    ## Names
+    nms<-if ("PREFERRED_NAME" %in% names(df)) df$PREFERRED_NAME else df$Name
+    if (is.null(nms)) stop("Unable to read compound names from the input compound list.")
+    ## SMILES
+    haha<-df$SMILES
+    if (is.null(haha)) stop("Unable to read SMILES from the input compound list.")
+    sz<-length(haha)
+    outdf<-data.frame(Name=nms,SMILES=haha,ID=1:sz,RT=rep("",sz),CAS=rep("",sz))
+    write.csv(outdf,file=dest_fn,row.names=F)
+}
+    
+    
+    
 ## Perform the compound mixture workflow on the data file called
-## fn_data with settings named list called sett_alist.
-rmbmix.single<-function(fn_data,sett_alist) {
+## fn_data with settings named list called sett_alist. Argument
+## fn_cmpd_list is the compound list. Argument wd is the scratch dir
+## to hold generated ini files and the like.
+rmbmix.single<-function(fn_data,sett_alist,fn_cmpd_list,wd) {
     
     require(RMassBank)
-    sfn<-paste(fn_data,".ini",sep='')
+
+
+
+    ## Generate file table.
+    df_table<-data.frame(Files=rep(fn_data,n_cmpd),ID=1:n_cmpd)
+    fn_table<-file.path(wd,paste("fn-table.",fn_data,".csv",sep=''))
+    write.csv(x=df_table,file=fn_table,row.names=F)
+
+    ## Generate settings file and load.
+    sfn<-file.path(wd,paste(fn_data,".ini",sep=''))
     rmbmix.mk_sett_file(sett_alist,sfn)
+    loadRmbSettings(sfn)
+
+    ## Make empty workspace.
+    
 }