diff --git a/R/errors.R b/R/errors.R
index 2859b708ec350770b476c54c324e6f5751c184e5..d6175be288e8afcbae71304653ba8eff6560eebb 100644
--- a/R/errors.R
+++ b/R/errors.R
@@ -39,8 +39,11 @@ check_extension <- function(extfileval,what) {
}
-check_key_absent <- function(key,l,what) {
+check_key_absent <- function(keys,l,what) {
nms = names(l)
- if (! (key %in% nms)) stop(errorCondition(paste0("Key",key, " has not been found for ", what),
- class = paste0(what,'-absent')))
+ keys_in = keys %in% l
+ keys_absent = keys[!keys_in]
+ hv = if (length(keys_absent)>1L) "have" else "has"
+ if (length(keys_absent)>0L) stop(errorCondition(paste0("Keys [",paste0(keys_absent,collapse=', '), "] ",hv," not been found for ", what),
+ class = paste0(what,'-absent')))
}
diff --git a/R/metfrag.R b/R/metfrag.R
index f1f7862e8b93d0515232498cf3af1d20c3d9759c..949fd0190e7e74e0c7d4c0f34efc6589cba928fb 100644
--- a/R/metfrag.R
+++ b/R/metfrag.R
@@ -213,7 +213,7 @@ metfrag_run_many <- function(fn_jar,file_tab, mem = NA_character_, java_bin = "j
}
-summarise_metfrag_results <- function(param,path,subpaths,cand_parameters,scores,collect_candidates,file_tab) {
+summarise_metfrag_results <- function(param,path,subpaths,cand_parameters,db_scores,int_scores,collect_candidates,file_tab) {
## which(max(as.numeric(mf_res$Score))==as.numeric(mf_res$Score))
index_maxScore = 1L
@@ -228,11 +228,13 @@ summarise_metfrag_results <- function(param,path,subpaths,cand_parameters,scores
dt = data.table::rbindlist(lapply(fn,function (ff) as.data.table(readf(ff))))
dt
},
- by = keyz]
+ keyby = keyz]
+
+
}
.adapt_col_types <- function(x) {
- x[,(names(scores)):=lapply(.SD, as.numeric),.SDcol=names(scores)]
+ x[,(names(db_scores)):=lapply(.SD, as.numeric),.SDcol=names(db_scores)]
}
.calc_basic_scores <- function(x) {
@@ -255,33 +257,38 @@ summarise_metfrag_results <- function(param,path,subpaths,cand_parameters,scores
.make_max_cols <- function(x) {
- res = x[,lapply(.SD,function(s) max(s,na.rm=T)),.SDcol=names(scores),keyby=keyz]
- data.table::setnames(res,old = names(res),new = paste0("max_",names(res)))
+ res = x[,{
+ cols = lapply(.SD,function(s) max(s,na.rm=T))
+ names(cols) = lapply(names(.SD),function(nn) paste0("Max_",nn))
+ cols}, .SDcol=c(names(int_scores),names(db_scores)),keyby=keyz]
res
}
.collect_candidates <- function(x) {
- x[,lapply(.SD, function(col) paste(col,collapse=";")),
- .SDcol=collect_candidates,
- keyby=keyz]
+ res = x[,{cols = lapply(.SD, function(col) paste(col,collapse=";"))
+ names(cols) = lapply(names(.SD),function(nn) paste0("All_",nn))
+ cols},
+ .SDcol=collect_candidates,
+ keyby=keyz]
+ res
}
-
+
thetab = .read_results()
.adapt_col_types(thetab)
-
- btab = .calc_basic_scores(thetab)
-
+ btab = .calc_basic_scores(thetab)
cctab = .collect_candidates(thetab)
candtab = .get_candidate_param(thetab)
mxtab = .make_max_cols(thetab)
- res = file_tab
+
+ res = file_tab[,`:=`(f_conf=NULL,f_log=NULL,f_res=NULL,f_spec=NULL)]
+ data.table::setkeyv(res,c(key(res),"stag"))
res = res[btab]
- res = res[cctab]
res = res[candtab]
res = res[mxtab]
+ res = res[cctab]
res
diff --git a/R/state.R b/R/state.R
index fa9f2d854cd126781de5378b8f9a0a76513c7c7d..ace74b402b5a11a72866fac62a8b164292e53095 100644
--- a/R/state.R
+++ b/R/state.R
@@ -121,13 +121,6 @@ new_runtime_state <- function(project,envopts,conf=NULL) {
for (x in subpaths) dir.create(file.path(mfdir,x),showWarnings=F)
metfrag$subpaths = subpaths
- ## Create score and weight entries.
- param = conf$metfrag$param
- param$MetFragScoreTypes = paste0(names(conf$metfrag$scores),collapse = ",")
- param$MetFragScoreWeights = paste0(conf$metfrag$scores,collapse = ",")
-
- ## Fully expanded params end up in run object.
- metfrag$param = param
@@ -142,7 +135,27 @@ new_runtime_state <- function(project,envopts,conf=NULL) {
check_file_absent(fpath,what="metfrag-db-file")
metfrag$cando_local = T
metfrag$db_path = fpath
+
+ # Check if names exist in the database (if local).
+ dbnms = colnames(fread(fpath,nrows=1L))
+ check_key_absent(c(names(conf$metfrag$database_scores),
+ conf$metfrag$cand_parameters,
+ conf$metfrag$collect_candidates),
+ dbnms,what="local-metfrag-database")
+
+
+
}
+
+ ## Create score and weight entries.
+ param = conf$metfrag$param
+
+ scores = c(conf$metfrag$intrinsic_scores,conf$metfrag$database_scores)
+ param$MetFragScoreTypes = paste0(names(scores),collapse = ",")
+ param$MetFragScoreWeights = paste0(scores,collapse = ",")
+ ## Fully expanded params end up in run object.
+ metfrag$param = param
+
}
@@ -350,7 +363,8 @@ metfrag_conf <- function(m) {
metfrag$param = param
- metfrag$scores = METFRAG_DEFAULT_SCORES
+ metfrag$intrinsic_scores = METFRAG_DEFAULT_SCORES
+ metfrag$database_scores = list()
m$conf$metfrag = metfrag
m
diff --git a/tests/testthat/_snaps/metfrag.md b/tests/testthat/_snaps/metfrag.md
index 6fc1013d39d73eb55f0955f533c868f206a64e2b..b6d392e057bd0dd39ff85af8335d474887171b8d 100644
--- a/tests/testthat/_snaps/metfrag.md
+++ b/tests/testthat/_snaps/metfrag.md
@@ -42,3 +42,27 @@
1: testsample_setNTs_ID100_adduct[M+H]+_tagAA_an5413.csv
2: testsample_setNTs_ID100_adduct[M+H]+_tagKO_an5434.csv
+---
+
+ Code
+ x
+ Output
+ ID adduct tag an CE stag num_poss_IDs
+ 1: 100 [M+H]+ AA 5413 10 setNTs_ID100_adduct[M+H]+_tagAA_an5413 86
+ 2: 100 [M+H]+ KO 5434 10 setNTs_ID100_adduct[M+H]+_tagKO_an5434 86
+ max_Score n_Score_GE4 n_Score_GE3 n_Score_GE2 Identifier
+ 1: 4.938569 1 1 1 6057
+ 2: 4.753741 1 1 1 6057
+ CompoundName Max_FragmenterScore
+ 1: (2S)-2-amino-3-(4-hydroxyphenyl)propanoic acid 485.2443
+ 2: (2S)-2-amino-3-(4-hydroxyphenyl)propanoic acid 679.6480
+ Max_OfflineIndividualMoNAScore Max_PubMed_Count Max_Patent_Count
+ 1: 0.99441 107881 76367
+ 2: 0.83380 107881 76367
+ Max_AnnoTypeCount
+ 1: 9
+ 2: 9
+ All_Identifier
+ 1: 6057;6950578;73562;91482;562171;440311;3135546;25418841;17607993;22397448;14451762;72214162;47003404;9442556;447184;602411;45167;20826205;4123006;168705;438;2734814;89843;6422115;12919999;13052275;10678961;7436;201474;223277;73705;220089;72878;113330;7186;175593;18605013;824655;23548;6861469;40148016;2798463;117636;71327507;90407;15480193;89978;67455263;49866537;19756142;81446487;89905;65711231;231242;6871292;10726079;12315638;4105139;3080594;7275229;59323545;18625738;62234616;44600733;21885916;232526;71756776;55266573;139835;122651682;251544;24820110;16218074;59176;21191822;528966;602319;13384341;836717;519003;153707036;602288;81657;597077;197180;13672729
+ 2: 6057;6950578;73562;91482;562171;440311;438;14451762;72214162;22397448;45167;602411;3135546;47003404;17607993;9442556;25418841;7436;10678961;6422115;7186;201474;168705;89843;4123006;447184;13052275;20826205;2734814;220089;12919999;223277;73705;113330;72878;175593;824655;23548;6861469;67455263;18605013;40148016;19756142;89905;81446487;59176;2798463;90407;13384341;15480193;6871292;49866537;71327507;231242;12315638;65711231;117636;71756776;4105139;89978;3080594;59323545;18625738;13672729;251544;55266573;24820110;10726079;232526;16218074;21885916;44600733;7275229;62234616;122651682;139835;528966;836717;602319;153707036;602288;519003;21191822;597077;197180;81657
+
diff --git a/tests/testthat/helper-state.R b/tests/testthat/helper-state.R
index 0e69544cf8350cbc87f8dcf0a20f5b1ac912adf2..d9f526f25a57511c98c4183a8887f119ed0d0960 100644
--- a/tests/testthat/helper-state.R
+++ b/tests/testthat/helper-state.R
@@ -7,7 +7,7 @@ make_dummy_mf_project <- function() {
withr::with_options(list(fn_jar=Sys.getenv("METFRAG_JAR"),
fn_db_dir=Sys.getenv("METFRAG_DB_DIR"),
fn_db = Sys.getenv("METFRAG_DB"),
- p_dir = tempfile(pattern="shinyscreen_dummy_mf_proj")),
+ p_dir = tempfile(pattern="shinyscreen_dummy_mf_proj")),
{
fn_jar = norm_path(getOption("fn_jar"))
if (!file.exists(fn_jar)) fn_jar = ""
@@ -24,11 +24,11 @@ make_dummy_mf_project <- function() {
x$conf$metfrag$param$SampleName = "testsample"
x$conf$metfrag$param$MetFragDatabaseType = "LocalCSV"
x$conf$metfrag$db_file = basename(getOption("fn_db"))
- x$conf$metfrag$scores = list(FragmenterScore=1.0,
- OfflineIndividualMoNAScore=1.0,
- PubMedCount=1.0,
- PatentCount=1.0,
- AnnoTypeCount=1.0)
+ x$conf$metfrag$intrinsic_scores = list(FragmenterScore=1.0,
+ OfflineIndividualMoNAScore=1.0)
+ x$conf$metfrag$database_scores = list(PubMed_Count=1.0,
+ Patent_Count=1.0,
+ AnnoTypeCount=1.0)
x$conf$metfrag$cand_parameters = c("Identifier","CompoundName")
x$conf$metfrag$collect_candidates = c("Identifier")
diff --git a/tests/testthat/test-metfrag.R b/tests/testthat/test-metfrag.R
index 7f3990b2616c8fd3aa39ff91cbcf3f816469d624..40e277bf2290a51f7e8d37a7b3b1ae4beb041572 100644
--- a/tests/testthat/test-metfrag.R
+++ b/tests/testthat/test-metfrag.R
@@ -1,13 +1,14 @@
test_that("Do adducts affect MetFrag config generation correctly?",{
-
+ skip_if_not(file.exists(Sys.getenv("METFRAG_JAR")),"Environment variable METFRAG_JAR does not contain a path to MetFrag jar package.")
withr::with_tempdir({
+ opts = list(fn_jar=Sys.getenv("METFRAG_JAR"),
+ fn_db_dir=Sys.getenv("METFRAG_DB_DIR"),
+ fn_db = Sys.getenv("METFRAG_DB"))
+
o = new_conf()
- dir.create("db_dir")
- saveRDS("","db_dir/dbfile.csv")
- saveRDS("","mf.jar")
- o$conf$metfrag$db_file = "dbfile.csv"
- eo = envopts(metfrag_db_dir="db_dir",
- metfrag_jar="mf.jar")
+ eo = envopts(metfrag_db_dir=opts$fn_db_dir,
+ metfrag_jar=opts$fn_jar)
+ o$conf$metfrag$db_file = basename(opts$fn_db)
yaml::write_yaml(o$conf,file='conf-state.yaml')
pproj = getwd()
m = new_project(pproj,envopts = eo)
@@ -75,9 +76,13 @@ ok_return_val("metfrag_run",{
path = m$run$metfrag$path,
subpaths = m$run$metfrag$subpaths,
cand_parameters = m$conf$metfrag$cand_parameters,
- scores = m$conf$metfrag$scores,
+ db_scores = m$conf$metfrag$database_scores,
+ int_scores = m$conf$metfrag$intrinsic_scores,
collect_candidates= m$conf$metfrag$collect_candidates,
file_tab = ftab)
+
+ expect_snapshot(x)
+
})