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Changeset 26:76872ac24fb2 (2023-09-27)

Previous changeset 25:8f7546d0b925 (2022-07-05) Next changeset 27:144e4a8ad000 (2023-11-06)

Commit message:
master branch Updating with tag :CI_COMMIT_TAG - - Fxx

modified:
Dockerfile
lib/hmdb.pm
test-data/out_test04.html
test-data/out_test04.tabular
test-data/out_test04.txt
wsdl_hmdb.xml

diff -r 8f7546d0b925 -r 76872ac24fb2 Dockerfile
--- a/Dockerfile Tue Jul 05 12:39:15 2022 +0000
+++ b/Dockerfile Wed Sep 27 12:21:00 2023 +0000

@@ -1,4 +1,4 @@
-#FROM pfem/perlfull
+#FROM pfem/<
FROM python:3.8-buster

# set author
@@ -28,7 +28,6 @@
     pip install --upgrade pip setuptools && \
     pip install planemo numpy && \
     pip install -U planemo && \
-    #planemo conda_init --conda_prefix "$CONDA" && \
     apt-get autoremove -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*  && \

diff -r 8f7546d0b925 -r 76872ac24fb2 lib/hmdb.pm
--- a/lib/hmdb.pm Tue Jul 05 12:39:15 2022 +0000
+++ b/lib/hmdb.pm Wed Sep 27 12:21:00 2023 +0000

[

@@ -14,6 +14,8 @@
use HTML::Template ;
use XML::Twig ;
use Text::CSV ;
+use URI::Encode ;
+use open qw( :std :encoding(UTF-8) );

use Data::Dumper ;

@@ -169,9 +171,16 @@
$nbAdducts = scalar( my @adducts = ( split (/,/, $adductString) ) ) ;

## Converting string into http post format
- $adductString =~ s/\+/%2B/g ;
- $adductString =~ s/,/%20/g ;
- $formattedAdductString = $adductString ;
+# $adductString =~ s/\+/%2B/g ;
+# $adductString =~ s/,/%20/g ;
+# $formattedAdductString = $adductString ;
+
+ my $uri = URI::Encode->new( { encode_reserved => 1 } );
+ foreach my $adduct (@adducts) {
+ # &results%5Badduct_type%5D%5B%5D=M%2BH&results%5Badduct_type%5D%5B%5D=M%2BNH4-H2O&results%5Badduct_type%5D%5B%5D=M%2BNa
+ my $EncodedAdduct = $uri->encode($adduct);
+ $formattedAdductString .= '&results%5Badduct_type%5D%5B%5D='.$EncodedAdduct ;
+ }
}
else {
warn "\t[WARN]the adduct type is not defined...It will set to 'Unknown'\n" ;
@@ -640,16 +649,19 @@
$mech->add_header('Referer', 'https://www.hmdb.ca/spectra/ms/search');
$mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8');
}
- ## adduct format is adduct_type=M%2BH%202M%2BH
-
if ( (!defined $adducts) or ( $adducts eq '') ) {
$adducts = 'Unknown' ;
}
+ #&results%5Badduct_type%5D%5B%5D=M%2BH&results%5Badduct_type%5D%5B%5D=M%2BNH4-H2O&results%5Badduct_type%5D%5B%5D=M%2BNa
+ # Query
+ #https://hmdb.ca/spectra/ms/generate_csv.csv?results%5Baction%5D=search&results%5Badduct_type%5D%5B%5D=M%2BH&results%5Badduct_type%5D%5B%5D=M%2BNH4-H2O&results%5Badduct_type%5D%5B%5D=M%2BNa&results%5Bauthenticity_token%5D=uN4r4Xme0bl5Lj%2Buv%2BrjebgrdF0oFO7mfxg0T7mHFlHcUSDkVAd%2BRB3qQDzm5fdz3BV4kKX%2F1i2uLOOdvBgK%2FA%3D%3D&results%5Bccs_predictors%5D=&results%5Bccs_tolerance%5D=&results%5Bcommit%5D=Search&results%5Bcontroller%5D=specdb%2Fms&results%5Bms_search_ion_mode%5D=positive&results%5Bquery_masses%5D=175.01&results%5Btolerance%5D=0.05&results%5Btolerance_units%5D=Da&results%5Butf8%5D=%E2%9C%93
+ #&results%5Badduct_type%5D%5B%5D=M%2BH&results%5Badduct_type%5D%5B%5D=M%2BNH4-H2O&results%5Badduct_type%5D%5B%5D=M%2BNa

my $res = $mech->get(
'https://hmdb.ca/spectra/ms/generate_csv.csv?'
.'results%5Baction%5D=search'
- .'&results%5Badduct_type%5D%5B%5D='.$adducts
+ #.'&results%5Badduct_type%5D%5B%5D='.$adducts
+ .$adducts
#.'&results%5Bauthenticity_token%5D='
.'&results%5Bccs_predictors%5D='
.'&results%5Bccs_tolerance%5D='

diff -r 8f7546d0b925 -r 76872ac24fb2 test-data/out_test04.html
--- a/test-data/out_test04.html Tue Jul 05 12:39:15 2022 +0000
+++ b/test-data/out_test04.html Wed Sep 27 12:21:00 2023 +0000

b'@@ -1,1 +1,1 @@\n-<?xml version="1.0" encoding="UTF-8" ?><!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="description" content=""><meta name="author" content="INRA de Clermont-Ferrand"><title>Galaxy HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style/simplePagination.css"/><script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script src="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts/jquery.simplePagination.js"></script><style type="text/css">body {padding-top: 70px}div.lm-table-warning { font-size: 1.4em; font-weight: bold; padding-right: 25px; color: #21536a; margin-left: 3px;}tr.green td {background-color: #eaf2d3; color: black;}tr.blank td {background-color: #9999CC; color: black;}table {font-family:\'Trebuchet MS\',Arial,Helvetica,sans-serif;width:100%;border-collapse:collapse;}table.detail, table.detail tr.parent, table.detail td, table.detail th, table.detail tr.category {border-collapse:collapse;border:1px solid #98bf21;}table.detail th {font-size: 1.2em;text-align: center;padding-top: 5px;padding-bottom: 10px;background-color: #a7c942;color: #ffffff;}td.ca {text-align:center;}footer { margin: 50px 0;}</style><script>function test(pageNumber){ var page="#page-id-"+pageNumber; $(\'.select\').hide() ; $(page).show()}</script></head><body><div class="container"><div class="lm-table-warning">Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05</div><div id="detail_table_source" style="display:none"></div><p><div id="choose"></div><p><div id="ms_search_0" class="ms-search-table"></div><table id="detail_table" class="detail"><col style="width:30px;"><col style="width:30px;"><col style="width:120px;"><col style="width:50px;"><col style="width:40px;"><col style="width:60px;"><col style="width:50px;"><col style="width:20px;"><col style="width:60px;"><col style="width:50px;"><col style="width:120px;"><col style="width:20;"><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct type</th><th>Adduct MW (Da)</th><th>Delta (ppm)</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mz_00001</td><td id="1" class="ca" >175.01</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">4-Hydrazinylpyridine-3-carboxamide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0258083" target="_blank" class="btn">HMDB0258083</a></td><td class="ca">C6H8N4O</td><td class="ca">152.069810894</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">175.059029</td><td class="ca">280</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">9-Sulfanylpurine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0257842" target="_blank" class="btn">HMDB0257842</a></td><td class="ca">C5H4N4S</td><td class="ca">152.015667319</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">175.004885</td><td class="ca">29</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">S-Phenyl thioacetate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0257424" target="_blank" class="btn">HMDB0257424</a></td><td class="ca">C8H8OS</td><td class="ca">152.029586052</td><td class="ca">M+N'..b'lites/HMDB0001196" target="_blank" class="btn">HMDB0001196</a></td><td class="ca">C28H50N2O19P2</td><td class="ca">780.248300452</td><td class="ca">M+NH4-H2O</td><td class="ca">+</td><td class="ca">780.271</td><td class="ca">63</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">3\'-Sialyl-3-fucosyllactose</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0006606" target="_blank" class="btn">HMDB0006606</a></td><td class="ca">C29H49NO23</td><td class="ca">779.269536879</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">780.276813</td><td class="ca">55</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody><tbody class="select" id="page-id-2"><tr class="white"><td class="ca" >mz_00005</td><td id="5" class="ca" >956.25</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">undec-10-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300959" target="_blank" class="btn">HMDB0300959</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Undec-8-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300958" target="_blank" class="btn">HMDB0300958</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Undec-9-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300957" target="_blank" class="btn">HMDB0300957</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Undec-3-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300956" target="_blank" class="btn">HMDB0300956</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">(7E)-Undec-7-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300955" target="_blank" class="btn">HMDB0300955</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >1100.45</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © INRA, N Paulhe, F Giacomoni 2014 </p> </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: 2,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: \'light-theme\',onPageClick: function(pageNumber){test(pageNumber)}}).pagination(\'redraw\');});</script></body></html>\n\\ No newline at end of file\n'

diff -r 8f7546d0b925 -r 76872ac24fb2 test-data/out_test04.tabular
--- a/test-data/out_test04.tabular Tue Jul 05 12:39:15 2022 +0000
+++ b/test-data/out_test04.tabular Wed Sep 27 12:21:00 2023 +0000

[

@@ -1,20 +1,24 @@
ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 175.01 280 [4-Hydrazinylpyridine-3-carboxamide] 152.069810894 C6H8N4O [M+Na] 175.059029 HMDB0258083
-mz_00001 175.01 29 [9-Sulfanylpurine] 152.015667319 C5H4N4S [M+Na] 175.004885 HMDB0257842
-mz_00001 175.01 50 [S-Phenyl thioacetate] 152.029586052 C8H8OS [M+Na] 175.018804 HMDB0257424
-mz_00001 175.01 216 ["n-methyl-6-oxo-1,6-dihydropyridine-3-carboxamide"] 152.058577506 C7H8N2O2 [M+Na] 175.047796 HMDB0255171
-mz_00001 175.01 216 [Methyl pyridone carboxamide] 152.058577506 C7H8N2O2 [M+Na] 175.047796 HMDB0254609
-mz_00002 238.19 204 [Ethyl butylacetylaminopropionate] 215.15214354 C11H21NO3 [M+Na] 238.141362 HMDB0246904
-mz_00002 238.19 204 [Hexaminolevulinate] 215.15214354 C11H21NO3 [M+Na] 238.141362 HMDB0253144
-mz_00002 238.19 149 [œâ-hydroxylaurate] 215.165268181 C12H23O3 [M+Na] 238.154486 HMDB0304547
-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_00001 175.01 78 [DL-Isocitric acid lactone] 174.016437913 C6H6O6 [M+H] 175.023714 HMDB0341313
+mz_00001 175.01 38 [Pyridin-3-yl sulfate] 173.986652367 C5H4NO4S [M+NH4-H2O] 175.016628 HMDB0304907
+mz_00001 175.01 271 [Trinitrosotrimethylenetriamine] 174.050138077 C3H6N6O3 [M+H] 175.057414 HMDB0259249
+mz_00001 175.01 211 [Semidehydroascorbic acid] 175.024262945 C6H7O6 [M+NH4-H2O] 175.046963 HMDB0258226
+mz_00001 175.01 166 ["Naphthalene-1,2,4-trione"] 174.031694053 C10H6O3 [M+H] 175.03897 HMDB0257698
+mz_00002 238.19 41 ["N,N-di-n-propyldopamine"] 237.172878985 C14H23NO2 [M+H] 238.180155 HMDB0255249
+mz_00002 238.19 41 [Deacetylmoxisylyte] 237.172878985 C14H23NO2 [M+H] 238.180155 HMDB0250903
+mz_00002 238.19 109 ["(2E,4E)-pentadeca-2,4-dienoic acid"] 238.193280077 C15H26O2 [M+NH4-H2O] 238.21598 HMDB0340866
+mz_00002 238.19 109 ["(6Z,9Z)-pentadeca-6,9-dienoic acid"] 238.193280077 C15H26O2 [M+NH4-H2O] 238.21598 HMDB0340865
+mz_00002 238.19 109 ["(3Z,5Z)-pentadeca-3,5-dienoic acid"] 238.193280077 C15H26O2 [M+NH4-H2O] 238.21598 HMDB0340864
+mz_00003 420.16 93 [Tapentadol-beta-D-glucuronide] 397.210052342 C20H31NO7 [M+Na] 420.19927 HMDB0341397
+mz_00003 420.16 31 ["10-Chloro-1-[(3S)-3-hydroxypyrrolidine-1-carbonyl]-3-phenyl-6,7-dihydrobenzo[a]quinolizin-4-one"] 420.1240702 C24H21ClN2O3 [M+NH4-H2O] 420.14677 HMDB0259567
mz_00003 420.16 93 ["N-Acetyl-9-aminominocycline, (4R)-"] 397.210052342 C20H31NO7 [M+Na] 420.19927 HMDB0259457
+mz_00003 420.16 91 [Pglu-his-pro-gly; Gly-thyrotropin-releasing hormone] 420.175732517 C18H24N6O6 [M+NH4-H2O] 420.198433 HMDB0259129
mz_00003 420.16 22 [Reduced ketanserin] 397.180169808 C22H24FN3O3 [M+Na] 420.169388 HMDB0257133
-mz_00003 420.16 58 ["1,2,4-Triazolo(4,3-b)pyridazine, 7-cyclobutyl-3-(2,6-difluorophenyl)-6-((1-methyl-1H-1,2,4-triazol-5-yl)methoxy)-"] 397.146264521 C19H17F2N7O [M+Na] 420.135483 HMDB0254773
-mz_00003 420.16 4 [6-[[3-Fluoro-5-(4-methoxyoxan-4-yl)phenoxy]methyl]-1-methylquinolin-2-one] 397.16893642 C23H24FNO4 [M+Na] 420.158154 HMDB0253359
-mz_00003 420.16 40 [CI-1044] 397.153874872 C23H19N5O2 [M+Na] 420.143093 HMDB0250223
mz_00004 780.32 53 [Vaniprevir] 757.372049545 C38H55N5O9S [M+Na] 780.361268 HMDB0259762
+mz_00004 780.32 12 [Ravtansine] 779.3218438 C38H54ClN3O10S [M+H] 780.32912 HMDB0247402
+mz_00004 780.32 37 [2-Hydroxypropyl starch] 780.326323443 C31H56O22 [M+NH4-H2O] 780.349023 HMDB0303342
+mz_00004 780.32 63 ["N,N'-Diacetylchitobiosyldiphosphodolichol"] 780.248300452 C28H50N2O19P2 [M+NH4-H2O] 780.271 HMDB0001196
+mz_00004 780.32 55 [3'-Sialyl-3-fucosyllactose] 779.269536879 C29H49NO23 [M+H] 780.276813 HMDB0006606
mz_00005 956.25 10 [undec-10-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300959
mz_00005 956.25 10 [Undec-8-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300958
mz_00005 956.25 10 [Undec-9-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300957

diff -r 8f7546d0b925 -r 76872ac24fb2 test-data/out_test04.txt
--- a/test-data/out_test04.txt Tue Jul 05 12:39:15 2022 +0000
+++ b/test-data/out_test04.txt Wed Sep 27 12:21:00 2023 +0000

[

diff -r 8f7546d0b925 -r 76872ac24fb2 wsdl_hmdb.xml
--- a/wsdl_hmdb.xml Tue Jul 05 12:39:15 2022 +0000
+++ b/wsdl_hmdb.xml Wed Sep 27 12:21:00 2023 +0000

@@ -1,4 +1,4 @@
-<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.2">
+<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.3">
   <description>
         search by masses on HMDB v5 online LCMS bank
   </description>
@@ -232,7 +232,7 @@
    <param name="delta" value="0.05"/>
    <param name="mode" value="positive"/>
    <param name="maxquery" value="5"/>
-   <param name="adduct_type" value="M+H"/>
+   <param name="data_positive_adducts" value="M+H"/>
    <output name="variableMetadata2" file="out_test03.tabular"/>
    <output name="HmdbOutWeb2" file="out_test03.html"/>
    <output name="HmdbOutXlsx2" file="out_test03.txt"/>