Adapted `mf_narrow_summ' and `pack_ms2_w_summ' to new data model.

Also adapted metfrag subsystem to new data model.

R/api.R

@@ -783,7 +783,7 @@ metfrag <- function(m) {
                        path = m$run$metfrag$path,
                        subpaths = m$run$metfrag$subpaths,
                        db_file = m$run$metfrag$db_file,
-                       stag_tab = stagtab, ms2 = m$db$extr$cgm$ms2,
+                       stag_tab = stagtab, ms2 = m$db$extr$spectra,
                        runtime=m$run$metfrag$runtime,
                        java_bin=m$run$metfrag$java_bin,
                        nproc = m$conf$metfrag$nproc)

R/metfrag.R

@@ -36,7 +36,7 @@ metfrag_get_stag_tab <- function(summ) {
     ## Argument summ can be a subset of actual `summ' table.
     x = gen_1d_keytab(summ)
     data.table::setnames(x,old="key1d",new="stag")
-    res = x[summ,`:=`(CE=i.CE,ion_mz=mz)]
+    res = x[summ,`:=`(ce=i.ce,ion_mz=mz)]
     res
 }
 
@@ -54,18 +54,21 @@ get_mf_res_ext <- function(fn) {
 
 metfrag_run <- function(param,path,subpaths,db_file,stag_tab,ms2,runtime,java_bin,nproc = 1L) {
     keys = intersect(colnames(stag_tab),colnames(ms2))
+    rms2 = ms2[stag_tab,on=keys,nomatch=NULL]
     message("Generating MetFrag configs.")
-    file_tab = ms2[stag_tab,{
+
+
+    file_tab = rms2[,{
         r = write_metfrag_config(param = ..param,
                                  path = ..path,
                                  subpaths = ..subpaths,
                                  db_file = ..db_file,
-                                 stag = stag,
-                                 adduct = adduct,
-                                 ion_mz = ion_mz,
+                                 stag = first(stag),
+                                 adduct = first(adduct),
+                                 ion_mz = first(ion_mz),
                                  spec = data.table(mz=mz,intensity=intensity))
-        c(r,stag = stag)
-    },by=.EACHI,on=keys]
+        c(r,stag = first(stag))
+    },keyby=keys]
     message("Done generating MetFrag configs.")
 
     withr::with_dir(path,{
@@ -89,21 +92,18 @@ metfrag_run <- function(param,path,subpaths,db_file,stag_tab,ms2,runtime,java_bi
 
 mf_narrow_summ <- function(summ,kv,ms2_rt_i=NA_integer_,ms2_rt_f=NA_integer_) {
     skey = data.table::key(summ)
-    cols = c("adduct","tag","ID","CE","scan","mz","qa_pass","ms2_rt")
-    nsumm = get_rows_from_summ(summ,kv,cols)
+    cols = union(names(skey),c("adduct","tag","ID","ce","precid","scan","mz","qa_pass","ms2_rt"))
+    dtkv = as.data.table(kv)
+    nsumm = summ[dtkv,on=names(kv),.SD,.SDcols=cols]
     nsumm = nsumm[qa_pass==T] # Those that make sense.
-    nsumm_key = union(SUMM_KEY,"ms2_rt")
+    nsumm_key = intersect(union(SUMM_KEY,"ms2_rt"),colnames(nsumm))
     data.table::setkeyv(nsumm,nsumm_key)
     
-    if (!is.na(ms2_rt_i)) {
-        nsumm = nsumm[ms2_rt>(ms2_rt_i)]
-    }
+    ms2_rt_i = if (!is.na(ms2_rt_i)) ms2_rt_i else 0.
+    ms2_rt_f = if (!is.na(ms2_rt_f)) ms2_rt_f else Inf
 
-    if (!is.na(ms2_rt_f)) {
-        nsumm = nsumm[ms2_rt<(ms2_rt_f)]
-    }
+    nsumm[ms2_rt > (ms2_rt_i) & ms2_rt < (ms2_rt_f)]
 
-    nsumm
 }
 
 get_metfrag_targets <- function(stag_tab,ms2) {
@@ -220,7 +220,7 @@ summarise_metfrag_results <- function(param,path,subpaths,cand_parameters,db_sco
     }
 
     .adapt_col_types <- function(x) {
-        x[,(names(db_scores)):=lapply(.SD, as.numeric),.SDcol=names(db_scores)]
+        if (length(db_scores)>0) x[,(names(db_scores)):=lapply(.SD, as.numeric),.SDcol=names(db_scores)] else x
     }
 
     .calc_basic_scores <- function(x) {

R/resources.R

@@ -217,7 +217,7 @@ FIG_DEF_CONF =list(grouping=list(group="adduct",
 SUMM_COLS=c("set",BASE_KEY_MS2,"mz","ms1_rt", "ms1_int", "ms2_rt", "ms2_int",
             "ms1_mean","ms2_sel",QA_FLAGS,"Name", "SMILES", "Formula", "known","Comments","file")
 
-SUMM_KEY = c("set","ID","adduct","tag","scan")
+SUMM_KEY = c("set","ID","adduct","tag","precid","catid","scan")
 
 PLOT_FEATURES = c("adduct",
                    "tag",

R/shiny-ui-base.R

@@ -1372,7 +1372,7 @@ mk_shinyscreen_server <- function(projects,init) {
             fn = file.path(projdir,input$ms2_spectra_tab_name)
             shinymsg(paste0("Saving MS2 spectra table to: ",basename(fn)))
             tab2file(pack_ms2_w_summ(rvs$m$out$tab$summ,
-                                    rvs$m$db$extr$cgm$ms2),
+                                    rvs$m$db$extr$spectra),
                      fn)
             shinymsg("Done saving MS2 spectra table.")
         })
@@ -1634,7 +1634,8 @@ mk_shinyscreen_server <- function(projects,init) {
                                        path = rvs$m$run$metfrag$path,
                                        subpaths = rvs$m$run$metfrag$subpaths,
                                        db_file = rvs$m$run$metfrag$db_file,
-                                       stag_tab = stagtab, ms2 = rvs$m$db$extr$cgm$ms2,
+                                       stag_tab = stagtab,
+                                       ms2 = rvs$m$db$extr$spectra, #rvs$m$db$extr$cgm$ms2,
                                        runtime=rvs$m$run$metfrag$runtime,
                                        java_bin=rvs$m$run$metfrag$java_bin,
                                        nproc = rvs$m$conf$metfrag$nproc)

R/state.R

@@ -408,9 +408,11 @@ pack_ms2_w_summ <- function(summ,ms2) {
     ## Takes summ, finds entries with high quality spectra and subsets ms2 based on that.
 
     ## Take the columns we need from summ.
-    x = summ[ms2_sel==T,.SD,.SDcols=c(key(summ),"mz","SMILES","Formula","Name")]
-    mrg_keys = c(intersect(key(ms2),key(summ)),"scan")
-    ms2[x,.(mz=i.mz,ms2_spectrum=encode_ms2_to_line(.SD[,c("mz","intensity")])),on=mrg_keys,by=.EACHI]
+    x = summ[ms2_sel==T,.SD,.SDcols=c(key(summ),"mz","SMILES","Name")]
+    mrg_keys = intersect(key(ms2),key(summ))
+    mrg_keys = c(mrg_keys,"scan")
+    ## ms2[x,.(mz=i.mz,ms2_spectrum=encode_ms2_to_line(.SD[,c("mz","intensity")])),on=mrg_keys,by=.EACHI]
+    ms2[x,.(ion_mz=i.mz,mz,intensity),on=mrg_keys,by=.EACHI]
 }