| Previous changeset 22:453fbe98925a (2020-11-20) Next changeset 24:d8e2ede293a6 (2022-05-19) |
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Commit message:
Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx |
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modified:
Dockerfile README.md README.txt conf_hmdb.cfg hmdb.tmpl lib/conf.pm lib/csv.pm lib/hmdb.pm static/images/hmdb.png t/hmdb_managerTest.pl t/lib/hmdbTest.pm test-data/input_test01_fake-mzrt-input-with-id.tabular test-data/input_test02_mzrt-input-with-id.tabular test-data/out_test01.html test-data/out_test01.tabular test-data/out_test01.txt test-data/out_test02.html test-data/out_test02.tabular test-data/out_test02.txt test-data/out_test03.html test-data/out_test03.tabular test-data/out_test03.txt test-data/out_test04.html test-data/out_test04.tabular test-data/out_test04.txt wsdl_hmdb.pl wsdl_hmdb.xml |
| b |
| diff -r 453fbe98925a -r 2d8a310e86ce lib/hmdb.pm --- a/lib/hmdb.pm Fri Nov 20 17:29:18 2020 +0000 +++ b/lib/hmdb.pm Thu May 19 13:43:09 2022 +0000 |
| [ |
| b'@@ -21,8 +21,8 @@\n \r\n our $VERSION = "1.0";\r\n our @ISA = qw(Exporter);\r\n-our @EXPORT = qw( map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass );\r\n-our %EXPORT_TAGS = ( ALL => [qw( map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass )] );\r\n+our @EXPORT = qw( parseHmdb5CSVResults getMatchesFromHmdb5WithUA map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass );\r\n+our %EXPORT_TAGS = ( ALL => [qw( parseHmdb5CSVResults getMatchesFromHmdb5WithUA map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass )] );\r\n \r\n =head1 NAME\r\n \r\n@@ -273,7 +273,7 @@\n \r\n =head2 METHOD testMatchesFromHmdbWithUA\r\n \r\n-\t## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra.\r\n+\t## Description : [DEPRECATED] test a single query with tests parameters on hmdb - get the status of the complete server infra.\r\n \t## Input : none\r\n \t## Output : $status_line\r\n \t## Usage : my ( $status_line ) = testMatchesFromHmdbWithUA( ) ;\r\n@@ -288,12 +288,14 @@\n #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and\r\n \r\n \tmy $mech = WWW::Mechanize->new(\r\n-\t\tagent => \'wonderbot for W4M 1.01\',\r\n-\t\tautocheck => 1,\t\r\n+#\t\tagent => \'wonderbot for W4M 1.01\',\r\n+\t\tagent => \'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.14; rv:93.0) Gecko/20100101 Firefox/93.0\' ,\r\n+\t\tautocheck => 0,\r\n \t);\r\n \t\r\n \tmy $statusGetLine = 0 ;\r\n \tmy $statusPostLine = 0 ;\r\n+\tmy $csrftoken = undef ;\r\n \t\r\n \t#receiving cookies and authentication token (CFRS)\r\n \tmy $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");\r\n@@ -302,13 +304,23 @@\n \tif ($statusGetLine == 200 ) {\r\n \t\tdie \'no CSRF_REQUEST_TOKEN_VALUE in page found\'\r\n \t\tunless ($reqInit->decoded_content =~ /\\"csrf-token\\"\\s+content=\\"(.*)\\"/) ;\r\n-\t\tmy $csrftoken = $1;\r\n-#\t\tprint "\\nTOKEN: $csrftoken\\n" ;\r\n+\t\t$csrftoken = $1;\r\n+\t\tprint "\\nTOKEN: $csrftoken\\n" ;\r\n \t\t$mech->add_header("X-CSRFToken", $csrftoken);\r\n+\t\t$mech->add_header(\'Host\', \'specdb.wishartlab.com\');\r\n \t\t$mech->add_header(\'Connection\', \'keep-alive\');\r\n+\t\t$mech->add_header(\'Upgrade-Insecure-Requests\', \'1\');\r\n \t\t$mech->add_header(\'Content-Type\', \'application/x-www-form-urlencoded\');\r\n-\t\t$mech->add_header(\'Referer\', \'http://www.hmdb.ca/spectra/ms/search\');\r\n-\t\t$mech->add_header(\'Accept\', \'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8\');\r\n+\t\t$mech->add_header(\'Accept-Language\', \'en-US,en;q=0.5\');\r\n+\t\t$mech->add_header(\'Accept-Encoding\', \'gzip, deflate\');\r\n+#\t\t$mech->add_header(\'Content-Length\', "300");\r\n+\t\t$mech->add_header(\'Origin\', \'null\');\r\n+\t\t$mech->add_header(\'DNT\', \'1\');\r\n+\t\t$me'..b'## Description : parse the csv results and get data - API 5.0 compliant\r\n+\t## Input : $csv\r\n+\t## Output : $results\r\n+\t## Usage : my ( $results ) = parseHmdb5CSVResults( $csv ) ;\r\n+\t\r\n+=cut\r\n+## START of SUB\r\n+sub parseHmdb5CSVResults {\r\n+\t## Retrieve Values\r\n+ my $self = shift ;\r\n+ my ( $csv, $masses, $max_query ) = @_ ;\r\n+ \r\n+ my $test = 0 ;\r\n+ my ($query_mass,$compound_id,$formula,$compound_mass,$adduct,$adduct_type,$adduct_mass,$delta) = (0, undef, undef, undef, undef, undef, undef, undef) ;\r\n+ \r\n+ my %result_by_entry = () ;\r\n+ my %features = () ;\r\n+ \r\n+# print Dumper $csv ;\r\n+# print Dumper $masses ;\r\n+# print Dumper $max_query ;\r\n+ \r\n+ foreach my $line (@{$csv}) {\r\n+ \t## NEW HMDB format V5.0 - May2022\r\n+\t\tif ($line !~ /query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\\/z,"delta\\(ppm\\),",ccs_value/) {\r\n+\t\t\t#query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value\',\r\n+ \t\t\r\n+ \t\tif ( $line =~ /(\\d+\\.\\d+),(\\w+),(.*),(\\w+),(\\d+\\.\\d+),([\\w|n\\/a|\\s+]+)\\s*,(\\+|\\-),(\\d+\\.\\d+),(\\d+),(\\d*)/ ) {\r\n+ \t\t\tprint "$line\\n" ;\r\n+ \t\t#if ( $line =~ /(\\d+\\.\\d+),(\\w+),(.*),([\\w|n\\/a|\\s+]+)\\s*,(\\w+),(\\d+\\.\\d+),(.*),(\\+|\\-),(\\d+\\.\\d+),(\\d+)/ ) {\r\n+ \t\t\tmy @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;\r\n+\r\n+ \t\t\tif ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }\r\n+ \t\t\t \t\t\r\n+\t \t\t$features{ENTRY_ENTRY_ID} = $entry[1] ;\r\n+\t \t\t$features{ENTRY_ENTRY_NAME} = $entry[2] ;\r\n+\t \t\t$features{ENTRY_FORMULA} = $entry[3] ;\r\n+\t \t\t$features{ENTRY_CPD_MZ} = $entry[4] ;\r\n+\t \t\t$features{ENTRY_ADDUCT} = $entry[5] ;\r\n+\t \t\t$features{ENTRY_ADDUCT_TYPE} = $entry[6] ;\r\n+\t \t\t$features{ENTRY_ADDUCT_MZ} = $entry[7] ;\r\n+\t \t\t$features{ENTRY_DELTA} = $entry[8] ;\r\n+\t \t\t\r\n+\t \t\tmy %temp = %features ;\r\n+\t \t\tpush (@{$result_by_entry{$entry[0]} }, \\%temp) ;\r\n+ \t\t}\r\n+# \t\telsif ($line =~ /(\\d+\\.\\d+)/) { #\r\n+# \t\t\t## 288.082286511284,HMDB0002255,R-Methylmalonyl-CoA, C01213 ,C25H40N7O19P3S,867.131252359,M-3H,-,288.036475,159\r\n+# \t\t\t## 283.108004472276,"Bicyclo_3,1,1heptane-2,3-diol,2,6,6_trimethyl","2,3-Pinanediol",n/a,C10H18O2,170.13067982,M+TFA-H,-,283.116266,29\r\n+# \t\t\t## 174.034120330029,HMDB0011723,2-Methylhippuric acid,\t C01586,C10H11NO3,193.073893223,M-H20-H,-,174.055503,123\r\n+# \t\t\t## 193.139160745841,HMDB0012109,"7-[(1R,2R,3R,5S)-3,5-Dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]cyclopentyl]-5,6-dihydroxyheptanoic acid", C06475,C20H36O7,388.246103506,M-2H,-,193.115776,121\r\n+# \t\t\t## 214.018826827064,HMDB0011723,2-Methylhippuric acid,\t C01586,C10H11NO3,193.073893223,M+Na-2H,-,214.048559,139\r\n+# \t\t}\r\n+# \t\telse {\r\n+# \t\t\t\r\n+# \t\t\twarn "The parsed line ($line) does not match your pattern\\n " ;\r\n+# \t\t}\r\n+ \t}\r\n+ \telse {\r\n+ \t\tprint "Header detected...Parsing is starting...\\n" ;\r\n+ \t\tnext ;\r\n+ \t}\r\n+ } ## end foreach\r\n+ \r\n+ ## manage per query_mzs (keep query masses order by array)\r\n+ my @results = () ;\r\n+ foreach (@{$masses}) {\r\n+ \tif ($result_by_entry{$_}) { \r\n+ \t\r\n+ \t\t## cut all entries > $max_query\t- all entries were already sorted...by hmdb\r\n+ \t\tmy @temp_entries = @{$result_by_entry{$_}} ;\r\n+ \t\tmy @temp_cut = () ;\r\n+ \t\tmy $current_query = 0 ;\r\n+ \t\tforeach (@temp_entries) {\r\n+ \t\t\t$current_query ++ ;\r\n+ \t\t\tif ($current_query > $max_query) {\r\n+ \t\t\t\tlast ;\r\n+ \t\t\t}\r\n+ \t\t\telse {\r\n+ \t\t\t\tpush (@temp_cut, $_) ;\r\n+ \t\t\t}\t\r\n+ \t\t}\r\n+ \t\tpush (@results, \\@temp_cut) ; \r\n+ \t}\r\n+ \telse { push (@results, [] ) ; } ;\r\n+\r\n+ }\r\n+ return(\\@results) ;\r\n+}\r\n+## END of SUB\r\n+\r\n \r\n =head2 METHOD parse_hmdb_csv_results\r\n \r\n-\t## Description : parse the csv results and get data\r\n+\t## Description : [DEPRECATED] parse the csv results and get data\r\n \t## Input : $csv\r\n \t## Output : $results\r\n \t## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ;\r\n' |
| b |
| diff -r 453fbe98925a -r 2d8a310e86ce t/hmdb_managerTest.pl --- a/t/hmdb_managerTest.pl Fri Nov 20 17:29:18 2020 +0000 +++ b/t/hmdb_managerTest.pl Thu May 19 13:43:09 2022 +0000 |
| [ |
| b'@@ -43,68 +43,36 @@\n \t\t[\'175.01\', \'238.19\', \'420.16\', \'780.32\', \'956.25\', \'1100.45\' ] ), \n \t\t\'175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A\', \n \t\t\'Method \\\'prepare_multi_masses_query\\\' works with a list of and return a well formated string for hmdb querying\');\n-\t\t\n+\t\n \tprint "\\n** Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs **\\n" ; $current_test++;\n-\tis_deeply( get_matches_from_hmdb_uaTest(\n+\tis_deeply( getMatchesFromHmdb5WithUATest(\n \t\t\'175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A\', 0.001, \'positive\'),\n \t\t[\n- \'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)\',\n-# \'175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125\',\n-# \'175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676\',\n-# \'175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895\',\n-# \'175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914\',\n-# \'175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914\',\n-# \'420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683\',\n-# \'420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683\'\n-\t\t\t## Update format - 2018-01-19... HMDB V04\n-#\t\t\t\'175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1\',\n-#\t\t\t\'175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4\',\n-#\t\t\t\'175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5\',\n-#\t\t\t\'175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5\',\n-#\t\t\t\'175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5\',\n-#\t\t\t\'420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2\',\n-#\t\t\t\'420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2\',\n-\t\t\t## Update results - 2018-09-20... HMDBv4\n-\t\t\t#\'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)\',\n- \'175.01,HMDB0149376,"2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0\',\n- \'175.01,HMDB0149375,"2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0\',\n- \'175.01,HMDB0149419,"2-{[5,8-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0\',\n- \'175.01,HMDB0149418,"2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0\',\n- \'175.01,HMDB0149392,"2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0\',\n- \'175.01,HMDB0149391,"2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0\',\n- \'175.01,HMDB0000257,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1\',\n- \'175.01,HMDB0060293,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1\',\n- \'175.01,HMDB0141391,{4-[(1E)-3-oxo-3-phenylprop-1-en-1-yl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3\',\n- \'175.01,HMDB0141389,{3-[(1E)-3-oxo-3-phenylprop-1-en-1-yl]phen'..b'\t\t[ [], [], [] ],\n+#\t\t\'Method \\\'parse_hmdb_csv_results\\\' works with a empty csv output and returns an empty but well formatted array\' ) ;\n+#\t\n+#\tprint "\\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list **\\n" ; $current_test++;\n+#\tis_deeply ( parse_hmdb_csv_resultsTest ( [], [] ),\n+#\t\t[],\n+#\t\t\'Method \\\'parse_hmdb_csv_results\\\' works with a empty csv output/mz list and returns an empty but well formatted array\' ) ;\n+#\n+#\t## Other example... from mz 265.0567515\n+#\tprint "\\n** Test $current_test parse_hmdb_csv_results with mz 265.0567515 and the correct inputs for hmdb outputs parsing (csv format) **\\n" ; $current_test++;\n+#\tis_deeply ( parse_hmdb_csv_resultsTest (\n+#\t\t[\n+# \'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)\',\n+#\t\t\'265.0567515,HMDB0059667,3-Methylsulfolene,n/a,C5H8O2S,132.02450019,2M+H,+,265.056276,2\',\n+#\t\t\'265.0567515,HMDB0038767,Camelliaside b,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2\',\n+#\t\t\'265.0567515,HMDB0039759,Kaempferol 3-(2g-apiosylrobinobioside),n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2\',\n+#\t\t\'265.0567515,HMDB0040875,Isoschaftoside 4\\\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2\',\n+#\t\t\'265.0567515,HMDB0040878,Schaftoside 4\\\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2\',\n+#\t\t\'265.0567515,HMDB0059600,erythro-5-Phosphonooxy-L-lysine,C03366,C6H15N2O6P,242.066772734,M+Na,+,265.055991,3\',\n+#\t\t\'265.0567515,HMDB0061174,"2,4-Imidazolidinedione, 3-ethyl-5-(4-hydroxyphenyl)-",n/a,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3\',\n+#\t\t\'265.0567515,HMDB0015571,Oxitriptan,C00643,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3\',\n+#\t\t\'265.0567515,HMDB0000472,5-hydroxy-l-tryptophan,C01017,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3\',\n+#\t\t\'265.0567515,HMDB0030584,Silidianin,n/a,C25H24O10,484.136946988,M+2Na,+,265.057691,4\',\n+# ],\n+# [\'265.0567515\'],\n+# 5\n+#\t),\n+#\t\t[\n+# [\n+# {\n+# \'ENTRY_DELTA\' => \'2\',\n+# \'ENTRY_FORMULA\' => \'C5H8O2S\',\n+# \'ENTRY_ENTRY_ID\' => \'HMDB0059667\',\n+# \'ENTRY_ADDUCT_MZ\' => \'265.056276\',\n+# \'ENTRY_ADDUCT_TYPE\' => \'+\',\n+# \'ENTRY_CPD_MZ\' => \'132.02450019\',\n+# \'ENTRY_ADDUCT\' => \'2M+H\'\n+# },\n+# {\n+# \'ENTRY_ADDUCT_MZ\' => \'265.056128\',\n+# \'ENTRY_ENTRY_ID\' => \'HMDB0038767\',\n+# \'ENTRY_ADDUCT_TYPE\' => \'+\',\n+# \'ENTRY_CPD_MZ\' => \'726.200729034\',\n+# \'ENTRY_ADDUCT\' => \'M+3Na\',\n+# \'ENTRY_DELTA\' => \'2\',\n+# \'ENTRY_FORMULA\' => \'C32H38O19\'\n+# },\n+# {\n+# \'ENTRY_DELTA\' => \'2\',\n+# \'ENTRY_FORMULA\' => \'C32H38O19\',\n+# \'ENTRY_ENTRY_ID\' => \'HMDB0039759\',\n+# \'ENTRY_ADDUCT_MZ\' => \'265.056128\',\n+# \'ENTRY_ADDUCT_TYPE\' => \'+\',\n+# \'ENTRY_CPD_MZ\' => \'726.200729034\',\n+# \'ENTRY_ADDUCT\' => \'M+3Na\'\n+# },\n+# {\n+# \'ENTRY_FORMULA\' => \'C32H38O19\',\n+# \'ENTRY_DELTA\' => \'2\',\n+# \'ENTRY_ADDUCT_TYPE\' => \'+\',\n+# \'ENTRY_ADDUCT_MZ\' => \'265.056128\',\n+# \'ENTRY_ENTRY_ID\' => \'HMDB0040875\',\n+# \'ENTRY_CPD_MZ\' => \'726.200729034\',\n+# \'ENTRY_ADDUCT\' => \'M+3Na\'\n+# },\n+# {\n+# \'ENTRY_ADDUCT_TYPE\' => \'+\',\n+# \'ENTRY_ENTRY_ID\' => \'HMDB0040878\',\n+# \'ENTRY_ADDUCT_MZ\' => \'265.056128\',\n+# \'ENTRY_ADDUCT\' => \'M+3Na\',\n+# \'ENTRY_CPD_MZ\' => \'726.200729034\',\n+# \'ENTRY_FORMULA\' => \'C32H38O19\',\n+# \'ENTRY_DELTA\' => \'2\'\n+# }\n+# ]\n+# ],\n+#\t\t\'Method \\\'parse_hmdb_csv_results\\\' works with a well-formated csv output and returns a a well formated array\' ) ;\t\n+#\t\t\n+#\t\n \n-\n-\n-\n-\n-\n-\n-\n+}\n ## END of the script\n\\ No newline at end of file\n' |
| b |
| diff -r 453fbe98925a -r 2d8a310e86ce t/lib/hmdbTest.pm --- a/t/lib/hmdbTest.pm Fri Nov 20 17:29:18 2020 +0000 +++ b/t/lib/hmdbTest.pm Thu May 19 13:43:09 2022 +0000 |
| [ |
| @@ -8,8 +8,8 @@ our $VERSION = "1.0"; our @ISA = qw(Exporter); -our @EXPORT = qw( parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest); -our %EXPORT_TAGS = ( ALL => [qw( parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest)] ); +our @EXPORT = qw( testMatchesFromHmdb5WithUATest parseHmdb5CSVResultsTest getMatchesFromHmdb5WithUATest parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest); +our %EXPORT_TAGS = ( ALL => [qw( testMatchesFromHmdb5WithUATest parseHmdb5CSVResultsTest getMatchesFromHmdb5WithUATest parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest)] ); use lib '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/hmdb' ; use lib::hmdb qw( :ALL ) ; @@ -49,6 +49,17 @@ return ($hmdb_pages) ; } +## sub +sub getMatchesFromHmdb5WithUATest { + + my ( $hmdb_masses, $delta, $molecular_species ) = @_ ; + + my $oHmdb = lib::hmdb->new() ; + my ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_masses, $delta, $molecular_species) ; + print Dumper $hmdb_pages ; + return ($hmdb_pages) ; +} + ## sub sub test_matches_from_hmdb_uaTest { @@ -58,6 +69,13 @@ return ($status) ; } +## sub +sub testMatchesFromHmdb5WithUATest { + + my $oHmdb = lib::hmdb->new() ; + my $status = $oHmdb->testMatchesFromHmdb5WithUA() ; + return ($status) ; +} ## sub sub check_state_from_hmdb_uaTest { @@ -69,6 +87,15 @@ } +## sub +sub parseHmdb5CSVResultsTest { + my ($hmdb_pages, $mzs, $max ) = @_ ; + + my $oHmdb = lib::hmdb->new() ; + my $result = $oHmdb->parseHmdb5CSVResults($hmdb_pages, $mzs, $max) ; ## hash format result + #print Dumper $result ; + return($result) ; +} ## sub sub parse_hmdb_csv_resultsTest { |
| b |
| diff -r 453fbe98925a -r 2d8a310e86ce wsdl_hmdb.pl --- a/wsdl_hmdb.pl Fri Nov 20 17:29:18 2020 +0000 +++ b/wsdl_hmdb.pl Thu May 19 13:43:09 2022 +0000 |
| b |
| @@ -49,7 +49,7 @@ "output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results ) "output_html|v:s" => \$out_html, ## option : path to the results view (output2) "output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output - "advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only. + #"advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only. "verbose:i" => \$VERBOSE, ## VERBOSE Of the tool ) ; @@ -137,7 +137,7 @@ print "\tand ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ; ## get the hmdb server status by a test query - continuous queries or kill script. - $status = $oHmdb->testMatchesFromHmdbWithUA() ; + $status = $oHmdb->testMatchesFromHmdb5WithUA() ; $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution my $cluster = 1 ; @@ -151,7 +151,7 @@ print "\n\tSubmission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ; - ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdbWithUA($hmdb_masses, $delta, $molecular_species, $hmdb_adducts) ; + ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_masses, $delta, $molecular_species, $hmdb_adducts) ; print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ; # print Dumper $hmdb_pages ; @@ -160,7 +160,7 @@ ## 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, $mzs, 1000) ; ## hash format result + ($result) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_pages, $mzs, 1000) ; ## hash format result ## This previous step return results with cutoff on the number of entries returned ! @@ -215,6 +215,10 @@ my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ; ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ; ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ; + + print Dumper $tbody_object ; + + my $output_html = $oHtml->write_html_skel(\$out_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $CONF->{'HTML_TEMPLATE'}, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ; } ## END IF @@ -305,7 +309,7 @@ =head1 SYNOPSIS -This script manages batch queries on HMDB server. +This script manages batch queries on HMDB server (v5.0). =head1 DESCRIPTION @@ -343,4 +347,6 @@ version 1.6.1 : 30 / 01 / 2019 - Adding adducts and fixxing minors bugs and requirements +version 1.7.0 : 19/ 05 / 2022 - Update HMDB API client - compliant with HMDB 5.0 web portal + =cut \ No newline at end of file |
| b |
| diff -r 453fbe98925a -r 2d8a310e86ce wsdl_hmdb.xml --- a/wsdl_hmdb.xml Fri Nov 20 17:29:18 2020 +0000 +++ b/wsdl_hmdb.xml Thu May 19 13:43:09 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.1"> +<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.0"> <description> search by masses on HMDB online LCMS bank </description> @@ -243,7 +243,7 @@ .. class:: infomark -**Authors** Marion Landi and Franck Giacomoni +**Authors** Marion Landi, Yann Guitton and Franck Giacomoni --------------------------------------------------- @@ -252,6 +252,7 @@ **Please cite** If you use this tool, please add the following reference | Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013. | Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res. 2018. + | Wishart DS et al, HMDB 5.0 - the Human Metabolome Database for 2022, Nucleic Acids Res. 2022. --------------------------------------------------- @@ -376,7 +377,7 @@ .. class:: warningmark -And their "W4M courses 2018": +And their "W4M courses 2021": | Using Galaxy4Metabolomics - W4M table format for Galaxy | Annotation Banks - Annotation @@ -386,5 +387,6 @@ <citations> <citation type="doi">10.1093/nar/gks1065</citation> <citation type="doi">10.1093/nar/gkx1089</citation> + <citation type="doi">10.1093/nar/gkab1062</citation> </citations> </tool> \ No newline at end of file |
