Tests: OpenMS DDA (#549)

* fix: prioritized the use of subordinate metadata when choosing between feature level and subordinate level

* tests: updated failing tests with new output

* tests: remaking test data for DDA and updating tests

* tests, examples: updated DDA tests and examples

* tests: removed unneeded DDA test directories and files

* tests: updates to utilities due to additional files

* Updated contrib builds url and use of --user when installing python on MacOS

Co-authored-by: bertrandboudaud <bertrand.boudaud@gmail.com>

Author: dmccloskey

.circleci/config.yml

@@ -113,7 +113,7 @@ jobs:
             brew install cppcheck gnuplot
             brew install libomp
             brew install eigen
-            pip3 install -r tools/smartpeak/requirements.txt
+            pip3 install -r tools/smartpeak/requirements.txt --user
       - run:
           name: "Pull latest (only release)"
           command: |
@@ -130,7 +130,7 @@ jobs:
             git clone --branch develop --depth 1 https://github.com/OpenMS/OpenMS.git &&
             cd OpenMS
             mkdir contrib_build && cd contrib_build
-            curl -C - -O https://abibuilder.informatik.uni-tuebingen.de/archive/openms/contrib/macOS/10.15.4/x64/appleclang-11.0.0/contrib_build.tar.gz
+            curl -C - -O https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/macOS/10.15.4/x64/appleclang-11.0.0/contrib_build.tar.gz
             tar -xzf contrib_build.tar.gz
             sed -i '' 's/std::auto_ptr/std::unique_ptr/g' include/seqan/basic/test_system.h
             rm lib/libz.* && rm -rf lib/pkgconfig
@@ -254,7 +254,7 @@ jobs:
             }
             cd ~/OpenMS
             mkdir contrib_build; cd contrib_build
-            $url_contrib = 'https://abibuilder.informatik.uni-tuebingen.de/archive/openms/contrib/windows/x64/msvc-14.2/contrib_build.tar.gz'
+            $url_contrib = 'https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/windows/x64/msvc-14.2/contrib_build.tar.gz'
             $contrib_tmp = New-TemporaryFile | Rename-Item -NewName { $_ -replace 'contrib_tmp$', 'tar.gz' } –PassThru
             Invoke-WebRequest $url_contrib -OutFile $contrib_tmp
             7z x $contrib_tmp -o'.'

src/examples/data/DDA/features/Germicidin A standard 5e-2_GA1_01_27401_13_BatchName_1900-01-01_000000.csv

@@ -1,11 +1,3 @@
 PrecursorMz	ProductMz	PrecursorCharge	ProductCharge	LibraryIntensity	NormalizedRetentionTime	PeptideSequence	ModifiedPeptideSequence	PeptideGroupLabel	LabelType	CompoundName	SumFormula	SMILES	Adducts	ProteinId	UniprotId	GeneName	FragmentType	FragmentSeriesNumber	Annotation	CollisionEnergy	PrecursorIonMobility	TransitionGroupId	TransitionId	Decoy	DetectingTransition	IdentifyingTransition	QuantifyingTransition	Peptidoforms
-195.101983934443155	111.045648931738441	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_111.046_HMDB:HMDB0000001	0	1	0	1	
-195.101983934443155	121.029828856042727	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_121.03_HMDB:HMDB0000001	0	1	0	1	
-195.101983934443155	122.033189965837721	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_122.033_HMDB:HMDB0000001	0	1	0	1	
-195.101983934443155	128.021266411122014	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_128.021_HMDB:HMDB0000001	0	1	0	1	
-195.101983934443155	148.933888727541955	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_148.934_HMDB:HMDB0000001	0	1	0	1	
-195.101983934443155	149.024935583932148	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_149.025_HMDB:HMDB0000001	0	1	0	1	
-195.101983934443155	150.028105165565989	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_150.028_HMDB:HMDB0000001	0	1	0	1	
-195.101983934443155	151.030013418740566	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_151.03_HMDB:HMDB0000001	0	1	0	1	
-195.101983934443155	167.03554334350784	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_167.036_HMDB:HMDB0000001	0	1	0	1	
-195.101983934443155	93.034766500219604	0	NA	9.078002343750001e04	-1.0			NA								NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	scan=463_93.0348_HMDB:HMDB0000001	0	1	0	1	
+235.07477407390158	134.95685060594775	0	NA	476.0	329.319578751179961			NA						HMDB:HMDB0000001		NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	HMDB:HMDB0000001_scan=440_134.957_370.346	0	1	0	1	
+235.07477407390158	217.105081882742866	0	NA	464.0	329.319578751179961			NA						HMDB:HMDB0000001		NA		-1	NA	-1.0	-1.0	HMDB:HMDB0000001	HMDB:HMDB0000001_scan=440_217.105_370.346	0	1	0	1	

src/examples/data/DDA/features/Germicidin A standard 5e-2_GA1_01_27401_13_BatchName_1900-01-01_000000.featureXML

@@ -1,8 +1,7 @@
 Name: HMDB:HMDB0000001
-Retention Time: 390.259
-base peak intensity: 1.38524e05
-total ion current: 2.10504e05
-Num Peaks: 7
-93.0348:7280 111.046:2760 121.03:41376 122.033:3364 128.021:460 
-148.934:548 149.025:138524 
+Retention Time: 370.346
+base peak intensity: 476.0
+total ion current: 940.0
+Num Peaks: 2
+134.957:476 217.105:464 
 

src/examples/data/DDA/features/Germicidin A standard 5e-2_GA1_01_27401_13_BatchName_1900-01-01_000000.msp

@@ -10,6 +10,8 @@ TargetedSpectraExtractor,AccurateMassSearchEngine:db:struct,['CHEMISTRY/HMDB2Str
 TargetedSpectraExtractor,AccurateMassSearchEngine:positive_adducts,CHEMISTRY/PositiveAdducts.tsv,TRUE,string,,This file contains the list of potential positive adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used.,
 TargetedSpectraExtractor,AccurateMassSearchEngine:negative_adducts,CHEMISTRY/NegativeAdducts.tsv,TRUE,string,,This file contains the list of potential negative adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used.,
 TargetedSpectraExtractor,relative_allowable_product_mass,50,TRUE,float,,Threshold m/z of a product relatively to the precurosor m/z (can be negative),
-TargetedSpectraExtractor,AccurateMassSearchEngine:ionization_mode,negative,TRUE,string,,"Positive or negative ionization mode? If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error.",
+TargetedSpectraExtractor,AccurateMassSearchEngine:ionization_mode,auto,TRUE,string,,"Positive or negative ionization mode? If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error.",
 TargetedSpectraExtractor,AccurateMassSearchEngine:mass_error_value,10,TRUE,float,,Tolerance allowed for accurate mass search.,
-TargetedSpectraExtractor,AccurateMassSearchEngine:keep_unidentified_masses,TRUE,TRUE,bool,,Keep features that did not yield any DB hit.,
+TargetedSpectraExtractor,rt_window,60,TRUE,float,,,
+TargetedSpectraExtractor,mz_tolerance,0.001,TRUE,float,,,
+TargetedSpectraExtractor,AccurateMassSearchEngine:keep_unidentified_masses,TRUE,TRUE,bool,,,