Mercurial > repos > fgiacomoni > hmdb_ms_search

comparison wsdl_hmdb.pl @ 23:2d8a310e86ce draft

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Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx
author fgiacomoni
date Thu, 19 May 2022 13:43:09 +0000
parents 453fbe98925a
children d8e2ede293a6
comparison
equal deleted inserted replaced
22:453fbe98925a 23:2d8a310e86ce
47 "mode:s" => \$molecular_species, ## Molecular species (positive/negative/neutral) 47 "mode:s" => \$molecular_species, ## Molecular species (positive/negative/neutral)
48 "maxquery:i" => \$max_query, ## Maximum query return (default is 20 entries by query // min 1 & max 50 ) 48 "maxquery:i" => \$max_query, ## Maximum query return (default is 20 entries by query // min 1 & max 50 )
49 "output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results ) 49 "output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results )
50 "output_html|v:s" => \$out_html, ## option : path to the results view (output2) 50 "output_html|v:s" => \$out_html, ## option : path to the results view (output2)
51 "output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output 51 "output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output
52 "advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only. 52 #"advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only.
53 "verbose:i" => \$VERBOSE, ## VERBOSE Of the tool 53 "verbose:i" => \$VERBOSE, ## VERBOSE Of the tool
54 ) ; 54 ) ;
55 55
56 #============================================================================= 56 #=============================================================================
57 # EXCEPTIONS 57 # EXCEPTIONS
135 my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ; 135 my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ;
136 136
137 print "\tand ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ; 137 print "\tand ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ;
138 138
139 ## get the hmdb server status by a test query - continuous queries or kill script. 139 ## get the hmdb server status by a test query - continuous queries or kill script.
140 $status = $oHmdb->testMatchesFromHmdbWithUA() ; 140 $status = $oHmdb->testMatchesFromHmdb5WithUA() ;
141 $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution 141 $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution
142 142
143 my $cluster = 1 ; 143 my $cluster = 1 ;
144 foreach my $mzs ( @{$submasses} ) { 144 foreach my $mzs ( @{$submasses} ) {
145 # print Dumper $mzs ; 145 # print Dumper $mzs ;
149 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; 149 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
150 my ($hmdb_adducts, $nb_selected_adducts) = $oHmdb->prepareAdductListFormat($adductType) ; 150 my ($hmdb_adducts, $nb_selected_adducts) = $oHmdb->prepareAdductListFormat($adductType) ;
151 151
152 print "\n\tSubmission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ; 152 print "\n\tSubmission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ;
153 153
154 ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdbWithUA($hmdb_masses, $delta, $molecular_species, $hmdb_adducts) ; 154 ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_masses, $delta, $molecular_species, $hmdb_adducts) ;
155 print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ; 155 print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ;
156 156
157 # print Dumper $hmdb_pages ; 157 # print Dumper $hmdb_pages ;
158 158
159 sleep(1) ; 159 sleep(1) ;
160 160
161 ## hard modification with $max_query fixed at 1000 !!! Need to be refactoring 161 ## hard modification with $max_query fixed at 1000 !!! Need to be refactoring
162 ## Cutof will be done in next method after URI check 162 ## Cutof will be done in next method after URI check
163 ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, 1000) ; ## hash format result 163 ($result) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_pages, $mzs, 1000) ; ## hash format result
164 164
165 ## This previous step return results with cutoff on the number of entries returned ! 165 ## This previous step return results with cutoff on the number of entries returned !
166 166
167 ## clean/max result by testing each HMDB_ID page in HMDB 167 ## clean/max result by testing each HMDB_ID page in HMDB
168 ($cleanedResult) = $oHmdb->checkHmdbUrlEntries($CONF->{'HMDB_METABOCARD_URL'}, $result, $max_query ) ; 168 ($cleanedResult) = $oHmdb->checkHmdbUrlEntries($CONF->{'HMDB_METABOCARD_URL'}, $result, $max_query ) ;
213 if ( ( defined $out_html ) and ( defined $results ) ) { 213 if ( ( defined $out_html ) and ( defined $results ) ) {
214 my $oHtml = lib::hmdb::new() ; 214 my $oHtml = lib::hmdb::new() ;
215 my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ; 215 my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
216 ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ; 216 ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ;
217 ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ; 217 ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ;
218
219 print Dumper $tbody_object ;
220
221
218 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'}) ; 222 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'}) ;
219 223
220 } ## END IF 224 } ## END IF
221 else { 225 else {
222 warn "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ; 226 warn "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ;
303 wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n] 307 wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n]
304 -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] 308 -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file]
305 309
306 =head1 SYNOPSIS 310 =head1 SYNOPSIS
307 311
308 This script manages batch queries on HMDB server. 312 This script manages batch queries on HMDB server (v5.0).
309 313
310 =head1 DESCRIPTION 314 =head1 DESCRIPTION
311 315
312 This main program is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool. 316 This main program is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool.
313 317
341 345
342 version 1.6 : 23 / 01 / 2019 - Manage UA http error and advanced feature from hmdb. 346 version 1.6 : 23 / 01 / 2019 - Manage UA http error and advanced feature from hmdb.
343 347
344 version 1.6.1 : 30 / 01 / 2019 - Adding adducts and fixxing minors bugs and requirements 348 version 1.6.1 : 30 / 01 / 2019 - Adding adducts and fixxing minors bugs and requirements
345 349
350 version 1.7.0 : 19/ 05 / 2022 - Update HMDB API client - compliant with HMDB 5.0 web portal
351
346 =cut 352 =cut