Mercurial > repos > fgiacomoni > hmdb_ms_search

comparison wsdl_hmdb.pl @ 8:97788e4bf3fc draft

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planemo upload commit d1a5cd8f1baf00879ffa44649883f91c64f43392-dirty
author fgiacomoni
date Sat, 20 Jan 2018 17:36:51 -0500
parents 6091a80df951
children 4eb2de7c24d1
comparison
equal deleted inserted replaced
7:ecf8e43aceda 8:97788e4bf3fc
121 ## get the hmdb server status by a test query - continuous queries or kill script. 121 ## get the hmdb server status by a test query - continuous queries or kill script.
122 my $status = $oHmdb->test_matches_from_hmdb_ua() ; 122 my $status = $oHmdb->test_matches_from_hmdb_ua() ;
123 $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution 123 $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution
124 124
125 foreach my $mzs ( @{$submasses} ) { 125 foreach my $mzs ( @{$submasses} ) {
126 126 print Dumper $mzs ;
127 my $result = undef ; 127 my $result = undef ;
128 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; 128 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
129 $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ; 129 $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ;
130 ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max_query) ; ## hash format result 130 ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max_query) ; ## hash format result
131 ## This previous step return results with cutoff on the number of entries returned ! 131 ## This previous step return results with cutoff on the number of entries returned !
137 # $hmdb_ids->{'HMDB03125'} = 1 , 137 # $hmdb_ids->{'HMDB03125'} = 1 ,
138 $metabocard_features = $oHmdb->get_hmdb_metabocard_from_id($hmdb_ids, $CONF->{'HMDB_METABOCARD_URL'}) ; ## Try to multithread the querying 138 $metabocard_features = $oHmdb->get_hmdb_metabocard_from_id($hmdb_ids, $CONF->{'HMDB_METABOCARD_URL'}) ; ## Try to multithread the querying
139 139
140 ## Map metabocards with results (add supplementary data) 140 ## Map metabocards with results (add supplementary data)
141 141
142 # print Dumper $results ; 142 print Dumper $results ;
143 # print Dumper $hmdb_ids ; 143 print Dumper $hmdb_ids ;
144 # print Dumper $metabocard_features ; 144 print Dumper $metabocard_features ;
145 145
146 if ( ( defined $results ) and ( defined $metabocard_features ) ) { 146 if ( ( defined $results ) and ( defined $metabocard_features ) ) {
147 $results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ; 147 $results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ;
148 } 148 }
149 149