Mercurial > repos > fgiacomoni > hmdb_ms_search

comparison wsdl_hmdb.pl @ 20:b5a1d5e43685 draft

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Master branch Updating - - Fxx
author fgiacomoni
date Wed, 23 Jan 2019 07:49:34 -0500
parents f8c8a990688a
children 63ba1cb240b7
comparison
equal deleted inserted replaced
19:f8c8a990688a 20:b5a1d5e43685
128 my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ; 128 my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ;
129 129
130 print "\t and ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ; 130 print "\t and ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ;
131 131
132 ## get the hmdb server status by a test query - continuous queries or kill script. 132 ## get the hmdb server status by a test query - continuous queries or kill script.
133 $status = $oHmdb->test_matches_from_hmdb_ua() ; 133 $status = $oHmdb->testMatchesFromHmdbWithUA() ;
134 $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution 134 $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution
135 135
136 my $cluster = 1 ; 136 my $cluster = 1 ;
137 foreach my $mzs ( @{$submasses} ) { 137 foreach my $mzs ( @{$submasses} ) {
138 # print Dumper $mzs ; 138 # print Dumper $mzs ;
139 my $result = undef ; 139 my $result = undef ;
140 140
141 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; 141 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
142 142
143 print "\t Submission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ; 143 print "\n\tSubmission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ;
144 144
145 ($hmdb_pages, $status) = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ; 145 ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdbWithUA($hmdb_masses, $delta, $molecular_species) ;
146 print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ; 146 print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ;
147 147
148 # print Dumper $hmdb_pages ; 148 # print Dumper $hmdb_pages ;
149 149
150 sleep(1) ; 150 sleep(1) ;