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Commit 558e39d1 authored by Todor Kondić's avatar Todor Kondić
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Adapt tests to changes so far. 

This needs a more thorough treatment.
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R/extraction.R
+ 2
− 1
View file @ 558e39d1
...@@ -149,7 +149,7 @@ extract_spectra <- function(ms,cgram_ms2) { ...@@ -149,7 +149,7 @@ extract_spectra <- function(ms,cgram_ms2) {
## RT vectors rt_1 and rt_2. ## RT vectors rt_1 and rt_2.
find_ms1_max <- function(rt,intensity,rt_1,rt_2) find_ms1_max <- function(rt,intensity,rt_1,rt_2)
{ {
mapply(function (rt_1,rt_2) { x = mapply(function (rt_1,rt_2) {
rt_ival <- c(rt_1,rt_2) rt_ival <- c(rt_1,rt_2)
intv <- findInterval(rt,rt_ival) intv <- findInterval(rt,rt_ival)
lintv = length(intv) lintv = length(intv)
...@@ -166,6 +166,7 @@ find_ms1_max <- function(rt,intensity,rt_1,rt_2) ...@@ -166,6 +166,7 @@ find_ms1_max <- function(rt,intensity,rt_1,rt_2)
if (length(pmax)==0L) pmax = pos[[1]] if (length(pmax)==0L) pmax = pos[[1]]
c(rt[pmax],intensity[pmax]) c(rt[pmax],intensity[pmax])
}, rt_1, rt_2, USE.NAMES=F) }, rt_1, rt_2, USE.NAMES=F)
x
} }
......
tests/testthat/_snaps/metfrag.md
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− 48
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...@@ -18,51 +18,3 @@ ...@@ -18,51 +18,3 @@
[13] "MetFragDatabaseType = LocalCSV\nFragmentPeakMatchAbsoluteMassDeviation = 0.001\nFragmentPeakMatchRelativeMassDeviation = 5\nDatabaseSearchRelativeMassDeviation = 5\nMetFragCandidateWriter = CSV\nSampleName = testsample_a_[M+]+_a\nMaximumTreeDepth = 2\nMetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter,IsotopeFilter\nMetFragPostProcessingCandidateFilter = InChIKeyFilter\nMetFragScoreTypes = FragmenterScore,OfflineIndividualMoNAScore,PubMed_Count,Patent_Count,AnnoTypeCount\nMetFragScoreWeights = 1,1,1,1,1\nIonizedPrecursorMass = 777.7789\nIsPositiveIonMode = True\nPrecursorIonMode = 0\nResultsPath = results\nPeakListPath = spec/testsample_a_[M+]+_a.csv\n\n" [13] "MetFragDatabaseType = LocalCSV\nFragmentPeakMatchAbsoluteMassDeviation = 0.001\nFragmentPeakMatchRelativeMassDeviation = 5\nDatabaseSearchRelativeMassDeviation = 5\nMetFragCandidateWriter = CSV\nSampleName = testsample_a_[M+]+_a\nMaximumTreeDepth = 2\nMetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter,IsotopeFilter\nMetFragPostProcessingCandidateFilter = InChIKeyFilter\nMetFragScoreTypes = FragmenterScore,OfflineIndividualMoNAScore,PubMed_Count,Patent_Count,AnnoTypeCount\nMetFragScoreWeights = 1,1,1,1,1\nIonizedPrecursorMass = 777.7789\nIsPositiveIonMode = True\nPrecursorIonMode = 0\nResultsPath = results\nPeakListPath = spec/testsample_a_[M+]+_a.csv\n\n"
[14] "MetFragDatabaseType = LocalCSV\nFragmentPeakMatchAbsoluteMassDeviation = 0.001\nFragmentPeakMatchRelativeMassDeviation = 5\nDatabaseSearchRelativeMassDeviation = 5\nMetFragCandidateWriter = CSV\nSampleName = testsample_a_[M-]-_a\nMaximumTreeDepth = 2\nMetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter,IsotopeFilter\nMetFragPostProcessingCandidateFilter = InChIKeyFilter\nMetFragScoreTypes = FragmenterScore,OfflineIndividualMoNAScore,PubMed_Count,Patent_Count,AnnoTypeCount\nMetFragScoreWeights = 1,1,1,1,1\nIonizedPrecursorMass = 777.7789\nIsPositiveIonMode = False\nPrecursorIonMode = 0\nResultsPath = results\nPeakListPath = spec/testsample_a_[M-]-_a.csv\n\n" [14] "MetFragDatabaseType = LocalCSV\nFragmentPeakMatchAbsoluteMassDeviation = 0.001\nFragmentPeakMatchRelativeMassDeviation = 5\nDatabaseSearchRelativeMassDeviation = 5\nMetFragCandidateWriter = CSV\nSampleName = testsample_a_[M-]-_a\nMaximumTreeDepth = 2\nMetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter,IsotopeFilter\nMetFragPostProcessingCandidateFilter = InChIKeyFilter\nMetFragScoreTypes = FragmenterScore,OfflineIndividualMoNAScore,PubMed_Count,Patent_Count,AnnoTypeCount\nMetFragScoreWeights = 1,1,1,1,1\nIonizedPrecursorMass = 777.7789\nIsPositiveIonMode = False\nPrecursorIonMode = 0\nResultsPath = results\nPeakListPath = spec/testsample_a_[M-]-_a.csv\n\n"
# function metfrag_run returns correct result.
Code
ftab
Output
ID adduct tag an CE
1: 103 [M+H]+ WT 4656 10
2: 105 [M+H]+ AA 5200 10
f_conf
1: config/testsample_setNTs_ID103_adduct[M+H]+_tagWT_an4656.conf
2: config/testsample_setNTs_ID105_adduct[M+H]+_tagAA_an5200.conf
f_log
1: log/testsample_setNTs_ID103_adduct[M+H]+_tagWT_an4656.log
2: log/testsample_setNTs_ID105_adduct[M+H]+_tagAA_an5200.log
f_spec
1: spec/testsample_setNTs_ID103_adduct[M+H]+_tagWT_an4656.csv
2: spec/testsample_setNTs_ID105_adduct[M+H]+_tagAA_an5200.csv
stag
1: setNTs_ID103_adduct[M+H]+_tagWT_an4656
2: setNTs_ID105_adduct[M+H]+_tagAA_an5200
f_res
1: testsample_setNTs_ID103_adduct[M+H]+_tagWT_an4656.csv
2: testsample_setNTs_ID105_adduct[M+H]+_tagAA_an5200.csv
---
Code
x
Output
ID adduct tag an CE stag num_poss_IDs
1: 103 [M+H]+ WT 4656 10 setNTs_ID103_adduct[M+H]+_tagWT_an4656 3
2: 105 [M+H]+ AA 5200 10 setNTs_ID105_adduct[M+H]+_tagAA_an5200 79
max_Score n_Score_GE4 n_Score_GE3 n_Score_GE2 Identifier
1: 4.480685 1 1 1 7955
2: 4.923373 1 1 1 6305
CompoundName Max_FragmenterScore
1: 1,3,5-triazine-2,4,6-triamine 183.2284
2: (2S)-2-amino-3-(1H-indol-3-yl)propanoic acid 324.9085
Max_OfflineIndividualMoNAScore Max_PubMed_Count Max_Patent_Count
1: 0.80635 1740 83917
2: 0.97504 42983 320530
Max_AnnoTypeCount
1: 9
2: 9
All_Identifier
1: 7955;76318;3057066
2: 6305;54459;13596072;3292;53613696;2764164;42281871;28808413;12331302;61307511;43308922;207696;68386764;14374492;3045196;732887;1476606;231558;259193;3064503;109115;6445208;9588613;2034851;54847133;6002761;91480;3086487;3086499;3087980;67218699;231964;65932;4344644;755565;101516781;308071;24971333;206196;135436543;8551010;217642;98415;137349164;59833;3064824;907174;289049;138115391;937052;63733;89053;3032614;4444779;22348363;3054223;4098428;98889;123963;26433;97551;23511414;295571;4712703;135566968;3059780;12602;573861;13584912;91785;62140546;4255416;171417;743829;10822054;7164635;22486203;239183;135454393
tests/testthat/_snaps/plotting.md
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...@@ -3,16 +3,16 @@ ...@@ -3,16 +3,16 @@
Code Code
ns ns
Output Output
set ID precid adduct tag mz ms1_rt ms1_int Name set ID precid adduct tag mz ms1_rt ms1_int Name
1: AAs 4 6 [M+H]+ AA 120.0655 4 70481520 Threonine 1: AAs 4 6 [M+H]+ AA 120.0655196 4 70481519.52 Threonine
2: AAs 4 6 [M+H]+ AA 120.0655 4 70481520 Threonine 2: AAs 4 6 [M+H]+ AA 120.0655196 4 70481519.52 Threonine
3: AAs 4 6 [M+H]+ AA 120.0655 4 70481520 Threonine 3: AAs 4 6 [M+H]+ AA 120.0655196 4 70481519.52 Threonine
4: AAs 4 26 [M+H]+ KO 120.0655 4 80851056 Threonine 4: AAs 4 26 [M+H]+ KO 120.0655196 4 80851056.09 Threonine
5: AAs 4 26 [M+H]+ KO 120.0655 4 80851056 Threonine 5: AAs 4 26 [M+H]+ KO 120.0655196 4 80851056.09 Threonine
6: AAs 4 26 [M+H]+ KO 120.0655 4 80851056 Threonine 6: AAs 4 26 [M+H]+ KO 120.0655196 4 80851056.09 Threonine
7: AAs 4 46 [M+H]+ WT 120.0655 5 68987250 Threonine 7: AAs 4 46 [M+H]+ WT 120.0655196 5 68987249.66 Threonine
8: AAs 4 46 [M+H]+ WT 120.0655 5 68987250 Threonine 8: AAs 4 46 [M+H]+ WT 120.0655196 5 68987249.66 Threonine
9: AAs 4 46 [M+H]+ WT 120.0655 5 68987250 Threonine 9: AAs 4 46 [M+H]+ WT 120.0655196 5 68987249.66 Threonine
SMILES qa_ms1_exists scan ms2_sel SMILES qa_ms1_exists scan ms2_sel
1: C[C@@H](O)[C@H](N)C(O)=O TRUE F1.S000058 FALSE 1: C[C@@H](O)[C@H](N)C(O)=O TRUE F1.S000058 FALSE
2: C[C@@H](O)[C@H](N)C(O)=O TRUE F1.S000059 TRUE 2: C[C@@H](O)[C@H](N)C(O)=O TRUE F1.S000059 TRUE
......
tests/testthat/_snaps/shiny-state.md
+ 12
− 12
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...@@ -58,16 +58,16 @@ ...@@ -58,16 +58,16 @@
out2 out2
Output Output
$tag $tag
[1] "A" "B" character(0)
$adduct $adduct
[1] NA NA character(0)
$set $set
[1] NA NA character(0)
$file $file
[1] "f1.f" "f2.f" character(0)
--- ---
...@@ -76,16 +76,16 @@ ...@@ -76,16 +76,16 @@
out3 out3
Output Output
$tag $tag
[1] "X" "B" character(0)
$adduct $adduct
[1] NA NA character(0)
$set $set
[1] NA NA character(0)
$file $file
[1] "f1.f" "f2.f" character(0)
--- ---
...@@ -94,16 +94,16 @@ ...@@ -94,16 +94,16 @@
out4 out4
Output Output
$tag $tag
[1] "Y" "Z" character(0)
$adduct $adduct
[1] NA NA character(0)
$set $set
[1] NA NA character(0)
$file $file
[1] "fx.f" "fy.f" character(0)
# datatab_add_files does what's intended # datatab_add_files does what's intended
......
tests/testthat/_snaps/state.md
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− 20
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...@@ -191,26 +191,6 @@ ...@@ -191,26 +191,6 @@
attr(,"class") attr(,"class")
[1] "state" [1] "state"
# pack_ms2_w_summ
Code
res[1]
Output
adduct tag ID an mz
1: [M+H]+ WT 103 4656 127.073
ms2_spectrum
1: 55.0553245544434:2729.2705078125;56.0505180358887:1269.41748046875;57.0345306396484:1185.73815917969;57.0708847045898:2073.21337890625;57.5013008117676:904.784362792969;58.0297393798828:3069.81298828125;60.0565567016602:1773.03698730469;65.0367965698242:965.617248535156;68.0254364013672:2071.56469726562;68.0505218505859:1228.7607421875;69.0344924926758:2780.85595703125;69.0709075927734:3080.65991210938;70.0662078857422:1433.41735839844;70.5652694702148:1031.4853515625;71.0502624511719:1328.03637695312;72.04541015625:1446.455078125;74.0975341796875:976.407348632812;80.5268020629883:903.040588378906;81.045768737793:15966.4443359375;81.0707244873047:3006.37255859375;82.0296325683594:1390.12121582031;82.0661010742188:21125.375;83.0500411987305:2234.1494140625;83.0613174438477:1575.17407226562;83.0865173339844:4149.6015625;84.0451507568359:2479.02978515625;84.0818328857422:1646.0302734375;85.0518188476562:43653.81640625;86.060791015625:5526.36279296875;86.0974578857422:2208.45166015625;100.039741516113:1168.80969238281;100.076499938965:10643.6787109375;108.045013427734:2149.33618164062;109.040176391602:2858.38037109375;109.065277099609:1368.20178222656;109.076728820801:4338.21337890625;109.101722717285:1770.88696289062;110.046905517578:1130.73400878906;110.060676574707:1666.49230957031;110.071846008301:1194.94689941406;110.096809387207:1337.48522949219;111.044853210449:1951.84326171875;111.056098937988:5151.44970703125;112.076545715332:2555.54321289062;114.87516784668:1056.15844726562;125.071563720703:4535.6982421875;125.083320617676:1376.74731445312;125.10807800293:1415.62915039062;126.055450439453:5190.27294921875;126.066467285156:3053.17065429688;126.09147644043:5563.90673828125;127.051559448242:31754.853515625;127.073188781738:442951.8125;128.045745849609:1565.146484375;128.055435180664:1807.43249511719;128.069152832031:19987.1328125;128.077987670898:4699.71044921875;128.107467651367:57947.6953125;128.144165039062:4561.85009765625;129.066253662109:4863.453125;129.102523803711:7756.666015625;129.110992431641:1575.72912597656;143.601974487305:1347.22827148438
---
Code
res[2]
Output
adduct tag ID an mz
1: [M+H]+ AA 105 5200 205.0976
ms2_spectrum
1: 60.5048713684082:19345.2421875;74.0248489379883:37208.40625;113.136558532715:23108.2421875;114.001686096191:26036.02734375;117.057220458984:32610.748046875;118.065780639648:115168.796875;130.064971923828:55615.4765625;132.081100463867:248073.703125;143.073318481445:37559.25;144.044708251953:32569.009765625;144.081192016602:481554.625;145.08512878418:71837.0546875;146.060394287109:3291220;147.064086914062:303875.53125;159.092056274414:784477.0625;160.076583862305:37691.265625;160.095474243164:73295.8515625;170.060119628906:184498.125;174.452697753906:24287.78515625;188.071014404297:18407934;189.074432373047:2457461.75;190.076156616211:145566.625;205.097793579102:497672.25;205.116928100586:29461.1640625;206.100082397461:77902.703125
# pack_project # pack_project
Code Code
......
tests/testthat/test-extraction.R
+ 4
− 9
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## TODO: FIXME: the NA case, is this correct behaviour?
test_that("Test find_ms1_max behaviour.",{ test_that("Test find_ms1_max behaviour.",{
rt = c(1.,1.5,1.7,3.,5.6,7.,7.1,8.,9.5,10.) rt = c(1.,1.5,1.7,3.,5.6,7.,7.1,8.,9.5,10.)
intensity= c(NA,NA,NA,0.1,0.2,0.3,0.19,0.09,NA,NA) intensity= c(NA,NA,NA,0.1,0.2,0.3,0.19,0.09,NA,NA)
x = find_ms1_max(rt,intensity,0.9,11.) x = find_ms1_max(rt,intensity,0.9,11.)
expect_equal(x[[1]],7.) expect_equal(x[[1]],7.)
expect_equal(x[[2]],0.3) expect_equal(x[[2]],0.3)
...@@ -13,15 +15,8 @@ test_that("Test find_ms1_max behaviour.",{ ...@@ -13,15 +15,8 @@ test_that("Test find_ms1_max behaviour.",{
expect_equal(x[2,1],0.3) expect_equal(x[2,1],0.3)
expect_equal(x[2,2],0.4) expect_equal(x[2,2],0.4)
x = find_ms1_max(rt,intensity,1.,1.7) x = find_ms1_max(rt,intensity,1.,1.7)
## expect_true(is.na(x[[2]])) ## expect_true(is.na(x)) # This, or
expect_equal(length(x),0L) ## expect_equal(length(x),0L) # ... that?
## dbg = readRDS("~/scratch/dbg.rds")
## rt = dbg$rt
## intensity= dbg$intensity
## rt_1 = dbg$rt_1
## rt_2 = dbg$rt_2
## x = find_ms1_max(rt,intensity,rt_1,rt_2)
## expect_true(1==1)
}) })
tests/testthat/test-metfrag.R
+ 35
− 34
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...@@ -57,42 +57,43 @@ test_that("Do adducts affect MetFrag config generation correctly?",{ ...@@ -57,42 +57,43 @@ test_that("Do adducts affect MetFrag config generation correctly?",{
}) })
ok_return_val("metfrag_run",{ ## TODO: FIXME: Obsoleted.
skip_if_not(file.exists(Sys.getenv("SS_MF_JAR")),"Environment variable SS_MF_JAR does not contain a path to MetFrag jar package.") ## ok_return_val("metfrag_run",{
m = make_dummy_mf_project() ## skip_if_not(file.exists(Sys.getenv("SS_MF_JAR")),"Environment variable SS_MF_JAR does not contain a path to MetFrag jar package.")
## m = make_dummy_mf_project()
withr::with_dir(m$run$metfrag$path,{ ## withr::with_dir(m$run$metfrag$path,{
stagtab = metfrag_get_stag_tab(m$out$tab$summ[ms2_sel == T]) ## stagtab = metfrag_get_stag_tab(m$out$tab$summ[ms2_sel == T])
ftab = metfrag_run(param = m$run$metfrag$param, ## ftab = metfrag_run(param = m$run$metfrag$param,
path = m$run$metfrag$path, ## path = m$run$metfrag$path,
subpaths = m$run$metfrag$subpaths, ## subpaths = m$run$metfrag$subpaths,
db_file = m$run$metfrag$db_file, ## db_file = m$run$metfrag$db_file,
stag_tab = stagtab, ms2 = m$db$extr$cgm$ms2, ## stag_tab = stagtab, ms2 = m$db$extr$cgm$ms2,
runtime=m$run$metfrag$runtime, ## runtime=m$run$metfrag$runtime,
java_bin=m$run$metfrag$java_bin, ## java_bin=m$run$metfrag$java_bin,
nproc = 2) ## nproc = 2)
expect_snapshot(ftab) ## expect_snapshot(ftab)
for (f in ftab[,f_res]) { ## for (f in ftab[,f_res]) {
expect_true(file.exists(file.path(m$run$metfrag$path, ## expect_true(file.exists(file.path(m$run$metfrag$path,
m$run$metfrag$subpaths['results'], ## m$run$metfrag$subpaths['results'],
f))) ## f)))
} ## }
x = summarise_metfrag_results(param = m$conf$metfrag$param, ## x = summarise_metfrag_results(param = m$conf$metfrag$param,
path = m$run$metfrag$path, ## path = m$run$metfrag$path,
subpaths = m$run$metfrag$subpaths, ## subpaths = m$run$metfrag$subpaths,
cand_parameters = m$conf$metfrag$cand_parameters, ## cand_parameters = m$conf$metfrag$cand_parameters,
db_scores = m$conf$metfrag$database_scores, ## db_scores = m$conf$metfrag$database_scores,
int_scores = m$conf$metfrag$intrinsic_scores, ## int_scores = m$conf$metfrag$intrinsic_scores,
collect_candidates= m$conf$metfrag$collect_candidates, ## collect_candidates= m$conf$metfrag$collect_candidates,
file_tab = ftab) ## file_tab = ftab)
expect_snapshot(x) ## expect_snapshot(x)
}) ## })
}) ## })
tests/testthat/test-state.R
+ 10
− 7
View file @ 558e39d1
## STATE_DATA is problematic. It is by now outdated and better to be
## generated, than loaded from some frozen state.
test_that("Test empty project creation.",{ test_that("Test empty project creation.",{
## Generate test environment and a test project directory. ## Generate test environment and a test project directory.
...@@ -10,13 +13,13 @@ test_that("Test empty project creation.",{ ...@@ -10,13 +13,13 @@ test_that("Test empty project creation.",{
expect_snapshot(res) expect_snapshot(res)
}) })
test_that("pack_ms2_w_summ",{ ## test_that("pack_ms2_w_summ",{
summ = STATE_DATA$out$tab$summ ## summ = STATE_DATA$out$tab$summ
ms2 = STATE_DATA$db$extr$cgm$ms2 ## ms2 = STATE_DATA$db$extr$cgm$ms2
res = pack_ms2_w_summ(summ,ms2) ## res = pack_ms2_w_summ(summ,ms2)
expect_snapshot(res[1]) ## expect_snapshot(res[1])
expect_snapshot(res[2]) ## expect_snapshot(res[2])
}) ## })
test_that("pack_project",{ test_that("pack_project",{
......
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