# HG changeset patch # User fgiacomoni # Date 1605893358 0 # Node ID 453fbe98925ac2043f50328f6fdef8bfff92d9cd # Parent 63ba1cb240b7d21874cbcaac083adf0ec17a7008 " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" diff -r 63ba1cb240b7 -r 453fbe98925a Dockerfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Dockerfile Fri Nov 20 17:29:18 2020 +0000 @@ -0,0 +1,53 @@ +# ref install: ubuntu 20.04 +FROM ubuntu:20.04 + +# init var +ARG DEBIAN_FRONTEND=noninteractive + +# set author +MAINTAINER Franck Giacomoni + +### +### [CONTAINER CORE FUNCTIONS]: +### xxxx +### xxxx +### [NOTES] +### xxxx + +ENV PATH /opt/conda/bin:$PATH + +RUN apt-get -y update &&\ + apt-get -y install build-essential \ + cpanminus \ + gzip \ + wget \ + bzip2 \ + ca-certificates \ + libglib2.0-0 \ + libxext6 \ + libsm6 \ + libxrender1 \ + libtext-csv-perl \ + libxml-twig-perl \ + libfile-share-perl + +RUN wget --quiet https://repo.anaconda.com/archive/Anaconda3-5.3.0-Linux-x86_64.sh -O ~/anaconda.sh && \ + /bin/bash ~/anaconda.sh -b -p /opt/conda && \ + rm ~/anaconda.sh && \ + ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \ + echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \ + echo "conda activate base" >> ~/.bashrc + +RUN cpan install ExtUtils::MakeMaker && \ + cpan install File::ShareDir::Install && \ + cpan install Module::Release && \ + cpan install Archive::Zip && \ + apt -y install git &&\ + apt -y install python3 python3-pip && \ + apt -y install virtualenv && \ + pip install "pip>=7" && \ + pip install -U git+git://github.com/galaxyproject/planemo.git && \ + apt-get autoremove -y && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + diff -r 63ba1cb240b7 -r 453fbe98925a lib/hmdb.pm --- a/lib/hmdb.pm Thu Feb 14 08:36:52 2019 -0500 +++ b/lib/hmdb.pm Fri Nov 20 17:29:18 2020 +0000 @@ -222,6 +222,55 @@ } ## END of SUB + +=head2 METHOD checkHmdbUrlEntries + + ## Description : check a list of HMDB_IDs by testing what is the status of their uri (HTTP 200 or not) + ## Input : $urlRoot, $entries + ## Output : $validEntries + ## Usage : my ( $validEntries ) = checkHmdbUrlEntries ( $entries ) ; + +=cut +## START of SUB +sub checkHmdbUrlEntries { + ## Retrieve Values + my $self = shift ; + my ( $urlRoot, $clusters, $maxQuery ) = @_; + my ( @ValidResults, @validFeature ) = ( (), () ) ; + + foreach my $resultsByMass (@{$clusters}) { + my $currentQuery = 0 ; + foreach my $feature (@{$resultsByMass}) { + + if ($feature->{ENTRY_ENTRY_ID}) { + + my $url = $urlRoot.$feature->{ENTRY_ENTRY_ID} ; + if ( get($url)) { + $currentQuery ++ ; + if ($currentQuery > $maxQuery) { + last ; + } + else { + push (@validFeature, $feature) ; +# print "Url is valid ($url) - - add to final results\n" ; + } + } + else { +# print "Url is NOT valid ($url) - - Deleting to final results\n" ; + next ; + } + } + } # END FOREACH FEATURE + my @tmp = @validFeature ; + push (@ValidResults, \@tmp) ; + @validFeature = () ; + } # END FOREACH RESULTS + + return (\@ValidResults) ; +} +### END of SUB + + =head2 METHOD testMatchesFromHmdbWithUA ## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra. diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test02.html --- a/test-data/out_test02.html Thu Feb 14 08:36:52 2019 -0500 +++ b/test-data/out_test02.html Fri Nov 20 17:29:18 2020 +0000 @@ -1,1 +1,1 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_000017.02080998
Beryllium(2+)HMDB0002387Be9.012182135M+NH4-H2O+7.0203368NONEDATANONEDATA
mz_0000275.05547146
N-NitrosodimethylamineHMDB0031419C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
AcetohydrazideHMDB0060428C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
GlycinamidHMDB0062472C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
CreatineHMDB0000064C4H9N3O2131.069476547M+H+NH4+75.0552882NONEDATANONEDATA
3-Guanidinopropanoic acidHMDB0013222C4H9N3O2131.069476547M+H+NH4+75.0552882NONEDATANONEDATA
mz_0000375.08059797
PyrophosphateHMDB0000250H4O7P2177.943225506M+H+2Na+75.0805990NONEDATANONEDATA
PyrophosphateHMDB0155221H4O7P2177.943225506M+H+2Na+75.0805990NONEDATANONEDATA
1-ButanolHMDB0004327C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
Tert-butanolHMDB0031456C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
IsobutanolHMDB0006006C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
mz_0000476.03942694
L-Aspartic acidHMDB0000191C4H7NO4133.037507717M+H+NH4+76.0393042NONEDATANONEDATA
GlycinateHMDB0161401C2H4NO274.024751953M+H+76.0393042NONEDATANONEDATA
Ethyl nitriteHMDB0031239C2H5NO275.032028409M+H+76.0393042NONEDATANONEDATA
Aspartic acidHMDB0062186C4H7NO4133.037507709M+H+NH4+76.0393042NONEDATANONEDATA
Aspartic acidHMDB0062501C4H7NO4133.037507709M+H+NH4+76.0393042NONEDATANONEDATA
mz_0000576.07584477
PropanolamineHMDB0140038C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
N-MethylethanolamineHMDB0142449C3H9NO75.068413914M+H+76.075692NONEDATANONEDATA
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
1-amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
2-[ethyl(1-hydroxyethyl)amino]ethan-1-olHMDB0168716C6H15NO2133.110278727M+H+NH4+76.0756892NONEDATANONEDATA
mz_0000676.07593168
PropanolamineHMDB0140038C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
N-MethylethanolamineHMDB0142449C3H9NO75.068413914M+H+76.075693NONEDATANONEDATA
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
1-amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
2-[ethyl(1-hydroxyethyl)amino]ethan-1-olHMDB0168716C6H15NO2133.110278727M+H+NH4+76.0756893NONEDATANONEDATA

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_000017.02080998
BerylliumHMDB0002387Be9.012182135M+NH4-H2O+7.0203368NONEDATANONEDATA
mz_0000275.05547146
glycinamideHMDB0062472C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
N-NitrosodimethylamineHMDB0031419C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
AcetylhydrazineHMDB0060428C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
CreatineHMDB0000064C4H9N3O2131.069476547M+H+NH4+75.0552882NONEDATANONEDATA
Beta-Guanidinopropionic acidHMDB0013222C4H9N3O2131.069476547M+H+NH4+75.0552882NONEDATANONEDATA
mz_0000375.08059797
PyrophosphateHMDB0000250H4O7P2177.943225506M+H+2Na+75.0805990NONEDATANONEDATA
EthanolHMDB0000108C2H6O46.0418648142M+H-H2O+75.080531NONEDATANONEDATA
2-Methylpropan-2-olHMDB0031456C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
1-ButanolHMDB0004327C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
"1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether"HMDB0062326C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
mz_0000476.03942694
L-Aspartic acidHMDB0000191C4H7NO4133.037507717M+H+NH4+76.0393042NONEDATANONEDATA
Ethyl nitriteHMDB0031239C2H5NO275.032028409M+H+76.0393042NONEDATANONEDATA
Iminodiacetic acidHMDB0011753C4H7NO4133.037507717M+H+NH4+76.0393042NONEDATANONEDATA
GlycineHMDB0000123C2H5NO275.032028409M+H+76.0393042NONEDATANONEDATA
Acetohydroxamic AcidHMDB0014691C2H5NO275.032028409M+H+76.0393042NONEDATANONEDATA
mz_0000576.07584477
3-aminopropan-1-olHMDB0140038C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
N-monomethylethanolamineHMDB0142449C3H9NO75.068413914M+H+76.075692NONEDATANONEDATA
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
1-Amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
MethyloxiraneHMDB0031558C3H6O58.041864814M+NH4+76.0756882NONEDATANONEDATA
mz_0000676.07593168
3-aminopropan-1-olHMDB0140038C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
N-monomethylethanolamineHMDB0142449C3H9NO75.068413914M+H+76.075693NONEDATANONEDATA
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
1-Amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
MethyloxiraneHMDB0031558C3H6O58.041864814M+NH4+76.0756883NONEDATANONEDATA

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test02.tabular --- a/test-data/out_test02.tabular Thu Feb 14 08:36:52 2019 -0500 +++ b/test-data/out_test02.tabular Fri Nov 20 17:29:18 2020 +0000 @@ -1,7 +1,7 @@ id mz rt hmdb(delta::name::mz::formula::adduct::id) -1 7.02080998 49.38210915 68::[Beryllium(2+)]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387 -2 75.05547146 0.658528069 "2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetohydrazide]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[Glycinamid]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[3-Guanidinopropanoic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222" -3 75.08059797 1743.94267 "0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[Tert-butanol]::74.073164942::C4H10O::[M+H]::HMDB0031456 | 2::[Isobutanol]::74.073164942::C4H10O::[M+H]::HMDB0006006" -4 76.03942694 51.23158899 "2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[Glycinate]::74.024751953::C2H4NO2::[M+H]::HMDB0161401 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[Aspartic acid]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 2::[Aspartic acid]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062501" -5 76.07584477 50.51249853 "2::[Propanolamine]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[N-Methylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[1-amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716" -6 76.07593168 0.149308136 "3::[Propanolamine]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[N-Methylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[1-amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716" +1 7.02080998 49.38210915 68::[Beryllium]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387 +2 75.05547146 0.658528069 "2::[glycinamide]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[Beta-Guanidinopropionic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222" +3 75.08059797 1743.94267 "0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 1::[Ethanol]::46.041864814::C2H6O::[2M+H-H2O]::HMDB0000108 | 2::[2-Methylpropan-2-ol]::74.073164942::C4H10O::[M+H]::HMDB0031456 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[""1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether""]::74.073164942::C4H10O::[M+H]::HMDB0062326" +4 76.03942694 51.23158899 "2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[Iminodiacetic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0011753 | 2::[Glycine]::75.032028409::C2H5NO2::[M+H]::HMDB0000123 | 2::[Acetohydroxamic Acid]::75.032028409::C2H5NO2::[M+H]::HMDB0014691" +5 76.07584477 50.51249853 "2::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[N-monomethylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB0031558" +6 76.07593168 0.149308136 "3::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[N-monomethylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB0031558" diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test02.txt --- a/test-data/out_test02.txt Thu Feb 14 08:36:52 2019 -0500 +++ b/test-data/out_test02.txt Fri Nov 20 17:29:18 2020 +0000 @@ -1,27 +1,27 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 7.02080998 68 [Beryllium(2+)] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387 +mz_00001 7.02080998 68 [Beryllium] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387 +mz_00002 75.05547146 2 [glycinamide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472 mz_00002 75.05547146 2 [N-Nitrosodimethylamine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0031419 -mz_00002 75.05547146 2 [Acetohydrazide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428 -mz_00002 75.05547146 2 [Glycinamid] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472 +mz_00002 75.05547146 2 [Acetylhydrazine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428 mz_00002 75.05547146 2 [Creatine] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0000064 -mz_00002 75.05547146 2 [3-Guanidinopropanoic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222 +mz_00002 75.05547146 2 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222 mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0000250 -mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0155221 +mz_00003 75.08059797 1 [Ethanol] 46.041864814 C2H6O [2M+H-H2O] 75.08053 HMDB0000108 +mz_00003 75.08059797 2 [2-Methylpropan-2-ol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0031456 mz_00003 75.08059797 2 [1-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0004327 -mz_00003 75.08059797 2 [Tert-butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0031456 -mz_00003 75.08059797 2 [Isobutanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0006006 +mz_00003 75.08059797 2 ["1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether"] 74.073164942 C4H10O [M+H] 75.080441 HMDB0062326 mz_00004 76.03942694 2 [L-Aspartic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0000191 -mz_00004 76.03942694 2 [Glycinate] 74.024751953 C2H4NO2 [M+H] 76.039304 HMDB0161401 mz_00004 76.03942694 2 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0031239 -mz_00004 76.03942694 2 [Aspartic acid] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062186 -mz_00004 76.03942694 2 [Aspartic acid] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062501 -mz_00005 76.07584477 2 [Propanolamine] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 -mz_00005 76.07584477 2 [N-Methylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 +mz_00004 76.03942694 2 [Iminodiacetic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0011753 +mz_00004 76.03942694 2 [Glycine] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0000123 +mz_00004 76.03942694 2 [Acetohydroxamic Acid] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0014691 +mz_00005 76.07584477 2 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 +mz_00005 76.07584477 2 [N-monomethylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 mz_00005 76.07584477 2 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925 -mz_00005 76.07584477 2 [1-amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 -mz_00005 76.07584477 2 [2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716 -mz_00006 76.07593168 3 [Propanolamine] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 -mz_00006 76.07593168 3 [N-Methylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 +mz_00005 76.07584477 2 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 +mz_00005 76.07584477 2 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031558 +mz_00006 76.07593168 3 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 +mz_00006 76.07593168 3 [N-monomethylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 mz_00006 76.07593168 3 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925 -mz_00006 76.07593168 3 [1-amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 -mz_00006 76.07593168 3 [2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716 +mz_00006 76.07593168 3 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 +mz_00006 76.07593168 3 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031558 diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test03.html --- a/test-data/out_test03.html Thu Feb 14 08:36:52 2019 -0500 +++ b/test-data/out_test03.html Fri Nov 20 17:29:18 2020 +0000 @@ -1,1 +1,1 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
"2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"HMDB0149376C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
"2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"HMDB0149375C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
"2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid"HMDB0149391C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
"2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"HMDB0149392C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
"2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"HMDB0149418C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
mz_00002238.19
"(4Z,7Z)-Deca-4,7-dien-1-ol"HMDB0163116C10H18O154.1357652M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
CTK8I1689HMDB0187564C10H18O154.1357652M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
(S)-alpha-TerpineolHMDB0004043C10H18O154.135765198M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
(S)-alpha-TerpineolHMDB0036086C10H18O154.135765198M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
EucalyptolHMDB0004472C10H18O154.1357652M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
mz_00003420.16
N-Desmethyl-O-hydroxy rosiglitazoneHMDB0060836C17H17N3O4S359.093976737M+IsoProp+H+420.1593172NONEDATANONEDATA
N-Desmethyl-p-hydroxyrosiglitazoneHMDB0060838C17H17N3O4S359.093976737M+IsoProp+H+420.1593172NONEDATANONEDATA
"6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0160148C13H20O10336.105646844M+IsoProp+Na+H+420.1607572NONEDATANONEDATA
"6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0160149C13H20O10336.105646844M+IsoProp+Na+H+420.1607572NONEDATANONEDATA
"6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0165020C13H20O10336.105646844M+IsoProp+Na+H+420.1607572NONEDATANONEDATA
mz_00004780.32
"3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-5-yl]oxy}oxane-2-carboxylic acid"HMDB0162081C17H23NO8369.1423667052M+ACN+H+780.3185562NONEDATANONEDATA
"N-[(4-{[5-(acetyloxy)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}phenyl)methyl]methoxycarboximidic acid"HMDB0031947C17H23NO8369.1423667172M+ACN+H+780.3185562NONEDATANONEDATA
"3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-7-yl]oxy}oxane-2-carboxylic acid"HMDB0162078C17H23NO8369.1423667052M+ACN+H+780.3185562NONEDATANONEDATA
"3,4,5-trihydroxy-6-{[4-(methoxymethyl)-5H,6H,7H-cyclopenta[c]pyridin-7-yl]methoxy}oxane-2-carboxylic acid"HMDB0162083C17H23NO8369.1423667052M+ACN+H+780.3185562NONEDATANONEDATA
"3,4,5-trihydroxy-6-[(9-hydroxy-16,17-dimethoxy-15-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tricyclo[12.3.1.1²,⁶]nonadeca-1(17),2,4,6(19),14(18),15-hexaen-3-yl)oxy]oxane-2-carboxylic acid"HMDB0150342C33H44O16696.262935337M+IsoProp+Na+H+780.3180453NONEDATANONEDATA
mz_00005956.25
"2-{2,3,6-trihydroxy-5-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-4-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,5-dien-1-yl}-2-{2,3,4-trihydroxy-5-[3-(4-hydroxyphenyl)prop-2-enoyl]-6-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,4-dien-1-yl}acetic acid"HMDB0041300C44H44O24956.222252336M+NH4-H2O+956.2449525NONEDATANONEDATA
"3,4,5-trihydroxy-6-[2-(2-hydroxy-1-oxo-1H-phenalen-9-yl)phenoxy]oxane-2-carboxylic acid"HMDB0168193C25H20O9464.1107322242M+2H+3H2O+956.2445846NONEDATANONEDATA
"6-[4-(2,3-dioxo-2,3-dihydro-1H-phenalen-4-yl)phenoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0168231C25H20O9464.1107322242M+2H+3H2O+956.2445846NONEDATANONEDATA
"5-(5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl)-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-2,3-dihydro-1-benzofuran-3-carbaldehyde"HMDB0138858C25H20O9464.1107322242M+2H+3H2O+956.2445846NONEDATANONEDATA
"6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0168237C25H20O9464.1107322242M+2H+3H2O+956.2445846NONEDATANONEDATA
mz_000061100.45
NpcHMDB0060499C28H30N4O6518.2165347122M+ACN+Na+1100.4488341NONEDATANONEDATA
"4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"HMDB0158990C24H38O10S518.2185685982M+ACN+Na+1100.4529023NONEDATANONEDATA
"4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"HMDB0158993C24H38O10S518.2185685982M+ACN+Na+1100.4529023NONEDATANONEDATA
"4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"HMDB0157972C24H38O10S518.2185685982M+ACN+Na+1100.4529023NONEDATANONEDATA
"4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"HMDB0158992C24H38O10S518.2185685982M+ACN+Na+1100.4529023NONEDATANONEDATA

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
Phenol sulphateHMDB0060015C6H6O4S173.99867937M+H+175.00595523NONEDATANONEDATA
trans-Aconitic acidHMDB0000958C6H6O6174.016437924M+H+175.02371478NONEDATANONEDATA
cis-Aconitic acidHMDB0000072C6H6O6174.016437924M+H+175.02371478NONEDATANONEDATA
Dehydroascorbic acidHMDB0001264C6H6O6174.016437924M+H+175.02371478NONEDATANONEDATA
dehydroascorbide(1-)HMDB0062706C6H6O6174.016437913M+H+175.02371478NONEDATANONEDATA
mz_00002238.19
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_00003420.16
FenvalerateHMDB0031791C25H22ClNO3419.128821282M+H+420.13609757NONEDATANONEDATA
mz_00004780.32
3'-Sialyl-3-fucosyllactoseHMDB0006606C29H49NO23779.269536879M+H+780.27681355NONEDATANONEDATA
mz_00005956.25
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_000061100.45
UNKNOWNNONEn/an/an/an/an/a0n/an/a

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test03.tabular --- a/test-data/out_test03.tabular Thu Feb 14 08:36:52 2019 -0500 +++ b/test-data/out_test03.tabular Fri Nov 20 17:29:18 2020 +0000 @@ -1,31 +1,11 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 0 ["2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376 -mz_00001 175.01 0 ["2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375 -mz_00001 175.01 0 ["2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391 -mz_00001 175.01 0 ["2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392 -mz_00001 175.01 0 ["2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418 -mz_00002 238.19 4 ["(4Z,7Z)-Deca-4,7-dien-1-ol"] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116 -mz_00002 238.19 4 [CTK8I1689] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564 -mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043 -mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086 -mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472 -mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836 -mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838 -mz_00003 420.16 2 ["6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148 -mz_00003 420.16 2 ["6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149 -mz_00003 420.16 2 ["6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020 -mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-5-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081 -mz_00004 780.32 2 ["N-[(4-{[5-(acetyloxy)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}phenyl)methyl]methoxycarboximidic acid"] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947 -mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-7-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078 -mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-5H,6H,7H-cyclopenta[c]pyridin-7-yl]methoxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083 -mz_00004 780.32 3 ["3,4,5-trihydroxy-6-[(9-hydroxy-16,17-dimethoxy-15-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tricyclo[12.3.1.1²,⁶]nonadeca-1(17),2,4,6(19),14(18),15-hexaen-3-yl)oxy]oxane-2-carboxylic acid"] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342 -mz_00005 956.25 5 ["2-{2,3,6-trihydroxy-5-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-4-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,5-dien-1-yl}-2-{2,3,4-trihydroxy-5-[3-(4-hydroxyphenyl)prop-2-enoyl]-6-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,4-dien-1-yl}acetic acid"] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300 -mz_00005 956.25 6 ["3,4,5-trihydroxy-6-[2-(2-hydroxy-1-oxo-1H-phenalen-9-yl)phenoxy]oxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193 -mz_00005 956.25 6 ["6-[4-(2,3-dioxo-2,3-dihydro-1H-phenalen-4-yl)phenoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231 -mz_00005 956.25 6 ["5-(5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl)-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-2,3-dihydro-1-benzofuran-3-carbaldehyde"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858 -mz_00005 956.25 6 ["6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168237 -mz_00006 1100.45 1 [Npc] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499 -mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990 -mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993 -mz_00006 1100.45 3 ["4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972 -mz_00006 1100.45 3 ["4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992 +mz_00001 175.01 23 [Phenol sulphate] 173.99867937 C6H6O4S [M+H] 175.005955 HMDB0060015 +mz_00001 175.01 78 [trans-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000958 +mz_00001 175.01 78 [cis-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000072 +mz_00001 175.01 78 [Dehydroascorbic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0001264 +mz_00001 175.01 78 [dehydroascorbide(1-)] 174.016437913 C6H6O6 [M+H] 175.023714 HMDB0062706 +mz_00002 238.19 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00003 420.16 57 [Fenvalerate] 419.128821282 C25H22ClNO3 [M+H] 420.136097 HMDB0031791 +mz_00004 780.32 55 [3'-Sialyl-3-fucosyllactose] 779.269536879 C29H49NO23 [M+H] 780.276813 HMDB0006606 +mz_00005 956.25 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test03.txt --- a/test-data/out_test03.txt Thu Feb 14 08:36:52 2019 -0500 +++ b/test-data/out_test03.txt Fri Nov 20 17:29:18 2020 +0000 @@ -1,31 +1,11 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 0 ["2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376 -mz_00001 175.01 0 ["2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375 -mz_00001 175.01 0 ["2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391 -mz_00001 175.01 0 ["2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392 -mz_00001 175.01 0 ["2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418 -mz_00002 238.19 4 ["(4Z,7Z)-Deca-4,7-dien-1-ol"] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116 -mz_00002 238.19 4 [CTK8I1689] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564 -mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043 -mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086 -mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472 -mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836 -mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838 -mz_00003 420.16 2 ["6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148 -mz_00003 420.16 2 ["6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149 -mz_00003 420.16 2 ["6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020 -mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-5-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081 -mz_00004 780.32 2 ["N-[(4-{[5-(acetyloxy)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}phenyl)methyl]methoxycarboximidic acid"] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947 -mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-7-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078 -mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-5H,6H,7H-cyclopenta[c]pyridin-7-yl]methoxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083 -mz_00004 780.32 3 ["3,4,5-trihydroxy-6-[(9-hydroxy-16,17-dimethoxy-15-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tricyclo[12.3.1.1²,⁶]nonadeca-1(17),2,4,6(19),14(18),15-hexaen-3-yl)oxy]oxane-2-carboxylic acid"] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342 -mz_00005 956.25 5 ["2-{2,3,6-trihydroxy-5-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-4-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,5-dien-1-yl}-2-{2,3,4-trihydroxy-5-[3-(4-hydroxyphenyl)prop-2-enoyl]-6-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,4-dien-1-yl}acetic acid"] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300 -mz_00005 956.25 6 ["3,4,5-trihydroxy-6-[2-(2-hydroxy-1-oxo-1H-phenalen-9-yl)phenoxy]oxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193 -mz_00005 956.25 6 ["6-[4-(2,3-dioxo-2,3-dihydro-1H-phenalen-4-yl)phenoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231 -mz_00005 956.25 6 ["5-(5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl)-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-2,3-dihydro-1-benzofuran-3-carbaldehyde"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858 -mz_00005 956.25 6 ["6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168237 -mz_00006 1100.45 1 [Npc] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499 -mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990 -mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993 -mz_00006 1100.45 3 ["4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972 -mz_00006 1100.45 3 ["4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992 +mz_00001 175.01 23 [Phenol sulphate] 173.99867937 C6H6O4S [M+H] 175.005955 HMDB0060015 +mz_00001 175.01 78 [trans-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000958 +mz_00001 175.01 78 [cis-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000072 +mz_00001 175.01 78 [Dehydroascorbic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0001264 +mz_00001 175.01 78 [dehydroascorbide(1-)] 174.016437913 C6H6O6 [M+H] 175.023714 HMDB0062706 +mz_00002 238.19 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00003 420.16 57 [Fenvalerate] 419.128821282 C25H22ClNO3 [M+H] 420.136097 HMDB0031791 +mz_00004 780.32 55 [3'-Sialyl-3-fucosyllactose] 779.269536879 C29H49NO23 [M+H] 780.276813 HMDB0006606 +mz_00005 956.25 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test04.html --- a/test-data/out_test04.html Thu Feb 14 08:36:52 2019 -0500 +++ b/test-data/out_test04.html Fri Nov 20 17:29:18 2020 +0000 @@ -1,1 +1,1 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
MercaptopurineHMDB0015167C5H4N4S152.015666838M+Na+175.00488529NONEDATANONEDATA
SCHEMBL300353HMDB0171211C4H8O4S152.014329912M+Na+175.00354837NONEDATANONEDATA
[(2Z)-but-2-en-1-yloxy]sulfonic acidHMDB0167141C4H8O4S152.014329912M+Na+175.00354837NONEDATANONEDATA
(Methylsulfanyl)(phenyl)methanoneHMDB0029694C8H8OS152.029585568M+Na+175.01880450NONEDATANONEDATA
"9H-Purine-6,8-diol"HMDB0001182C5H4N4O2152.033425392M+Na+175.02264372NONEDATANONEDATA
mz_00002238.19
[2-(Heptanoyloxy)ethyl]trimethylazaniumHMDB0013239C12H26NO2216.196354081M+Na+238.17829649NONEDATANONEDATA
FencamfaminHMDB0015508C15H21N215.167399677M+Na+238.156618140NONEDATANONEDATA
(4-{[4-(dimethylamino)butyl]amino}butyl)dimethylamineHMDB0031202C12H29N3215.236147943M+Na+238.225366148NONEDATANONEDATA
Diethylcarbamazine N-oxideHMDB0060817C10H21N3O2215.163376931M+Na+238.152595157NONEDATANONEDATA
N-NonanoylglycineHMDB0013279C11H21NO3215.152143543M+Na+238.141362204NONEDATANONEDATA
mz_00003420.16
"(2E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-2,8-dienimidic acid"HMDB0161604C19H27NO6S397.155908767M+Na+420.14512735NONEDATANONEDATA
"(4E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-4,8-dienimidic acid"HMDB0161565C19H27NO6S397.155908767M+Na+420.14512735NONEDATANONEDATA
"N-[2-(2-Hydroxy-3,4-dimethoxyphenyl)-6,7-dimethoxynaphthalen-1-yl]-N-methylformamide"HMDB0030435C22H23NO6397.152537473M+Na+420.14175543NONEDATANONEDATA
"6-[(6-carboxy-3,4-dihydroxyoxan-2-yl)oxy]-4-methoxy-6-methyl-2H,5H,6H,7H,8H-[1,3]dioxolo[4,5-g]isoquinolin-6-ium"HMDB0165501C18H24NO9398.144557777M+Na+420.126580NONEDATANONEDATA
"3,4,5-trihydroxy-6-[(4-hydroxy-6-propanoyl-7,8-dihydropteridin-2-yl)amino]oxane-2-carboxylic acid"HMDB0158327C15H19N5O8397.123362592M+Na+420.112581113NONEDATANONEDATA
mz_00004780.32
5-[2-(2-{[1-({1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(4-hydroxyphenyl)ethyl}-C-hydroxycarbonimidoyl)-2-methylpropyl]-C-hydroxycarbonimidoyl}pyrrolidine-1-carbonyl)pyrrolidin-1-yl]-4-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-5-oxopentanoic acidHMDB0164422C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
1-(1-{2-[({1-[2-({2-[(2-amino-1-hydroxy-3-methylbutylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl}(hydroxy)methylidene)amino]-4-carboxybutanoyl}pyrrolidine-2-carbonyl)pyrrolidine-2-carboxylic acidHMDB0164421C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acidHMDB0164418C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acidHMDB0164423C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acidHMDB0164424C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
mz_00005956.25
Α-D-glcnac3S-(1→4)-β-D-glca(1→3)-β-D-gal(1→3)-β-D-gal(1→4)-D-xylHMDB0062476C31H51NO29S933.2267458M+Na+956.21596436NONEDATANONEDATA
(3S)-3-Isopropenyl-6-oxoheptanoyl-CoAHMDB0062370C31H50N7O18P3S933.214589966M+Na+956.20380848NONEDATANONEDATA
mz_000061100.45
UNKNOWNNONEn/an/an/an/an/a0n/an/a

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
MercaptopurineHMDB0015167C5H4N4S152.015666838M+Na+175.00488529NONEDATANONEDATA
S-Methyl benzenecarbothioateHMDB0029694C8H8OS152.029585568M+Na+175.01880450NONEDATANONEDATA
"6,8-Dihydroxypurine"HMDB0001182C5H4N4O2152.033425392M+Na+175.02264372NONEDATANONEDATA
OxypurinolHMDB0000786C5H4N4O2152.033425392M+Na+175.02264372NONEDATANONEDATA
XanthineHMDB0000292C5H4N4O2152.033425392M+Na+175.02264372NONEDATANONEDATA
mz_00002238.19
HeptanoylcholineHMDB0013239C12H26NO2216.196354081M+Na+238.17829649NONEDATANONEDATA
FencamfamineHMDB0015508C15H21N215.167399677M+Na+238.156618140NONEDATANONEDATA
SolamineHMDB0031202C12H29N3215.236147943M+Na+238.225366148NONEDATANONEDATA
Diethylcarbamazine N-oxideHMDB0060817C10H21N3O2215.163376931M+Na+238.152595157NONEDATANONEDATA
N-NonanoylglycineHMDB0013279C11H21NO3215.152143543M+Na+238.141362204NONEDATANONEDATA
mz_00003420.16
SimulansamideHMDB0030435C22H23NO6397.152537473M+Na+420.14175543NONEDATANONEDATA
mz_00004780.32
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_00005956.25
"(2S,3S,4R,5R,6R)-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(3R,4R,5R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxan-4-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4,5-dihydroxy-3-{[(2R,3R,4R,5R,6R)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-4-(sulfooxy)oxan-2-yl]oxy}oxane-2-carboxylic acid"HMDB0062476C31H51NO29S933.2267458M+Na+956.21596436NONEDATANONEDATA
(3S)-3-isopropenyl-6-oxoheptanoyl-CoAHMDB0062370C31H50N7O18P3S933.214589966M+Na+956.20380848NONEDATANONEDATA
mz_000061100.45
UNKNOWNNONEn/an/an/an/an/a0n/an/a

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test04.tabular --- a/test-data/out_test04.tabular Thu Feb 14 08:36:52 2019 -0500 +++ b/test-data/out_test04.tabular Fri Nov 20 17:29:18 2020 +0000 @@ -1,24 +1,16 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID mz_00001 175.01 29 [Mercaptopurine] 152.015666838 C5H4N4S [M+Na] 175.004885 HMDB0015167 -mz_00001 175.01 37 [SCHEMBL300353] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0171211 -mz_00001 175.01 37 [[(2Z)-but-2-en-1-yloxy]sulfonic acid] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0167141 -mz_00001 175.01 50 [(Methylsulfanyl)(phenyl)methanone] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694 -mz_00001 175.01 72 ["9H-Purine-6,8-diol"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182 -mz_00002 238.19 49 [[2-(Heptanoyloxy)ethyl]trimethylazanium] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239 -mz_00002 238.19 140 [Fencamfamin] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508 -mz_00002 238.19 148 [(4-{[4-(dimethylamino)butyl]amino}butyl)dimethylamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202 +mz_00001 175.01 50 [S-Methyl benzenecarbothioate] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694 +mz_00001 175.01 72 ["6,8-Dihydroxypurine"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182 +mz_00001 175.01 72 [Oxypurinol] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000786 +mz_00001 175.01 72 [Xanthine] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000292 +mz_00002 238.19 49 [Heptanoylcholine] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239 +mz_00002 238.19 140 [Fencamfamine] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508 +mz_00002 238.19 148 [Solamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202 mz_00002 238.19 157 [Diethylcarbamazine N-oxide] 215.163376931 C10H21N3O2 [M+Na] 238.152595 HMDB0060817 mz_00002 238.19 204 [N-Nonanoylglycine] 215.152143543 C11H21NO3 [M+Na] 238.141362 HMDB0013279 -mz_00003 420.16 35 ["(2E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-2,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161604 -mz_00003 420.16 35 ["(4E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-4,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161565 -mz_00003 420.16 43 ["N-[2-(2-Hydroxy-3,4-dimethoxyphenyl)-6,7-dimethoxynaphthalen-1-yl]-N-methylformamide"] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435 -mz_00003 420.16 80 ["6-[(6-carboxy-3,4-dihydroxyoxan-2-yl)oxy]-4-methoxy-6-methyl-2H,5H,6H,7H,8H-[1,3]dioxolo[4,5-g]isoquinolin-6-ium"] 398.144557777 C18H24NO9 [M+Na] 420.1265 HMDB0165501 -mz_00003 420.16 113 ["3,4,5-trihydroxy-6-[(4-hydroxy-6-propanoyl-7,8-dihydropteridin-2-yl)amino]oxane-2-carboxylic acid"] 397.123362592 C15H19N5O8 [M+Na] 420.112581 HMDB0158327 -mz_00004 780.32 43 [5-[2-(2-{[1-({1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(4-hydroxyphenyl)ethyl}-C-hydroxycarbonimidoyl)-2-methylpropyl]-C-hydroxycarbonimidoyl}pyrrolidine-1-carbonyl)pyrrolidin-1-yl]-4-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164422 -mz_00004 780.32 43 [1-(1-{2-[({1-[2-({2-[(2-amino-1-hydroxy-3-methylbutylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl}(hydroxy)methylidene)amino]-4-carboxybutanoyl}pyrrolidine-2-carbonyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164421 -mz_00004 780.32 43 [4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164418 -mz_00004 780.32 43 [2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164423 -mz_00004 780.32 43 [1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164424 -mz_00005 956.25 36 [Α-D-glcnac3S-(1→4)-β-D-glca(1→3)-β-D-gal(1→3)-β-D-gal(1→4)-D-xyl] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476 -mz_00005 956.25 48 [(3S)-3-Isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370 +mz_00003 420.16 43 [Simulansamide] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435 +mz_00004 780.32 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00005 956.25 36 ["(2S,3S,4R,5R,6R)-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(3R,4R,5R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxan-4-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4,5-dihydroxy-3-{[(2R,3R,4R,5R,6R)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-4-(sulfooxy)oxan-2-yl]oxy}oxane-2-carboxylic acid"] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476 +mz_00005 956.25 48 [(3S)-3-isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370 mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test04.txt --- a/test-data/out_test04.txt Thu Feb 14 08:36:52 2019 -0500 +++ b/test-data/out_test04.txt Fri Nov 20 17:29:18 2020 +0000 @@ -1,24 +1,16 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID mz_00001 175.01 29 [Mercaptopurine] 152.015666838 C5H4N4S [M+Na] 175.004885 HMDB0015167 -mz_00001 175.01 37 [SCHEMBL300353] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0171211 -mz_00001 175.01 37 [[(2Z)-but-2-en-1-yloxy]sulfonic acid] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0167141 -mz_00001 175.01 50 [(Methylsulfanyl)(phenyl)methanone] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694 -mz_00001 175.01 72 ["9H-Purine-6,8-diol"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182 -mz_00002 238.19 49 [[2-(Heptanoyloxy)ethyl]trimethylazanium] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239 -mz_00002 238.19 140 [Fencamfamin] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508 -mz_00002 238.19 148 [(4-{[4-(dimethylamino)butyl]amino}butyl)dimethylamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202 +mz_00001 175.01 50 [S-Methyl benzenecarbothioate] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694 +mz_00001 175.01 72 ["6,8-Dihydroxypurine"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182 +mz_00001 175.01 72 [Oxypurinol] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000786 +mz_00001 175.01 72 [Xanthine] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000292 +mz_00002 238.19 49 [Heptanoylcholine] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239 +mz_00002 238.19 140 [Fencamfamine] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508 +mz_00002 238.19 148 [Solamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202 mz_00002 238.19 157 [Diethylcarbamazine N-oxide] 215.163376931 C10H21N3O2 [M+Na] 238.152595 HMDB0060817 mz_00002 238.19 204 [N-Nonanoylglycine] 215.152143543 C11H21NO3 [M+Na] 238.141362 HMDB0013279 -mz_00003 420.16 35 ["(2E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-2,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161604 -mz_00003 420.16 35 ["(4E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-4,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161565 -mz_00003 420.16 43 ["N-[2-(2-Hydroxy-3,4-dimethoxyphenyl)-6,7-dimethoxynaphthalen-1-yl]-N-methylformamide"] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435 -mz_00003 420.16 80 ["6-[(6-carboxy-3,4-dihydroxyoxan-2-yl)oxy]-4-methoxy-6-methyl-2H,5H,6H,7H,8H-[1,3]dioxolo[4,5-g]isoquinolin-6-ium"] 398.144557777 C18H24NO9 [M+Na] 420.1265 HMDB0165501 -mz_00003 420.16 113 ["3,4,5-trihydroxy-6-[(4-hydroxy-6-propanoyl-7,8-dihydropteridin-2-yl)amino]oxane-2-carboxylic acid"] 397.123362592 C15H19N5O8 [M+Na] 420.112581 HMDB0158327 -mz_00004 780.32 43 [5-[2-(2-{[1-({1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(4-hydroxyphenyl)ethyl}-C-hydroxycarbonimidoyl)-2-methylpropyl]-C-hydroxycarbonimidoyl}pyrrolidine-1-carbonyl)pyrrolidin-1-yl]-4-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164422 -mz_00004 780.32 43 [1-(1-{2-[({1-[2-({2-[(2-amino-1-hydroxy-3-methylbutylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl}(hydroxy)methylidene)amino]-4-carboxybutanoyl}pyrrolidine-2-carbonyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164421 -mz_00004 780.32 43 [4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164418 -mz_00004 780.32 43 [2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164423 -mz_00004 780.32 43 [1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164424 -mz_00005 956.25 36 [Α-D-glcnac3S-(1→4)-β-D-glca(1→3)-β-D-gal(1→3)-β-D-gal(1→4)-D-xyl] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476 -mz_00005 956.25 48 [(3S)-3-Isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370 +mz_00003 420.16 43 [Simulansamide] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435 +mz_00004 780.32 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00005 956.25 36 ["(2S,3S,4R,5R,6R)-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(3R,4R,5R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxan-4-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4,5-dihydroxy-3-{[(2R,3R,4R,5R,6R)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-4-(sulfooxy)oxan-2-yl]oxy}oxane-2-carboxylic acid"] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476 +mz_00005 956.25 48 [(3S)-3-isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370 mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r 63ba1cb240b7 -r 453fbe98925a wsdl_hmdb.pl --- a/wsdl_hmdb.pl Thu Feb 14 08:36:52 2019 -0500 +++ b/wsdl_hmdb.pl Fri Nov 20 17:29:18 2020 +0000 @@ -144,6 +144,7 @@ foreach my $mzs ( @{$submasses} ) { # print Dumper $mzs ; my $result = undef ; + my $cleanedResult = undef ; my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; my ($hmdb_adducts, $nb_selected_adducts) = $oHmdb->prepareAdductListFormat($adductType) ; @@ -157,9 +158,16 @@ sleep(1) ; - ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max_query) ; ## hash format result - ## This previous step return results with cutoff on the number of entries returned ! - $results = [ @$results, @$result ] ; + ## hard modification with $max_query fixed at 1000 !!! Need to be refactoring + ## Cutof will be done in next method after URI check + ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, 1000) ; ## hash format result + + ## This previous step return results with cutoff on the number of entries returned ! + + ## clean/max result by testing each HMDB_ID page in HMDB + ($cleanedResult) = $oHmdb->checkHmdbUrlEntries($CONF->{'HMDB_METABOCARD_URL'}, $result, $max_query ) ; + + $results = [ @$results, @$cleanedResult ] ; # sleep(1) ; $cluster ++ ; diff -r 63ba1cb240b7 -r 453fbe98925a wsdl_hmdb.xml --- a/wsdl_hmdb.xml Thu Feb 14 08:36:52 2019 -0500 +++ b/wsdl_hmdb.xml Fri Nov 20 17:29:18 2020 +0000 @@ -232,6 +232,7 @@ +