Mercurial > repos > fgiacomoni > hmdb_ms_search

comparison wsdl_hmdb.pl @ 24:d8e2ede293a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx
author fgiacomoni
date Thu, 19 May 2022 14:41:34 +0000
parents 2d8a310e86ce
children 8f7546d0b925
comparison
equal deleted inserted replaced
23:2d8a310e86ce 24:d8e2ede293a6
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
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) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_pages, $mzs, 1000) ; ## hash format result 163 ($result) = $oHmdb->parseHmdb5CSVResults($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 ) ;
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) ;
218 218
219 print Dumper $tbody_object ; 219 # print Dumper $tbody_object ;
220 220
221 221
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'}) ; 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'}) ;
223 223
224 } ## END IF 224 } ## END IF