Mercurial > repos > fgiacomoni > hmdb_ms_search
changeset 8:97788e4bf3fc draft
planemo upload commit d1a5cd8f1baf00879ffa44649883f91c64f43392-dirty
| author | fgiacomoni |
|---|---|
| date | Sat, 20 Jan 2018 17:36:51 -0500 |
| parents | ecf8e43aceda |
| children | c32280662103 |
| files | conf_hmdb.cfg lib/hmdb.pm wsdl_hmdb.pl |
| diffstat | 3 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/conf_hmdb.cfg Fri Jan 19 10:27:38 2018 -0500 +++ b/conf_hmdb.cfg Sat Jan 20 17:36:51 2018 -0500 @@ -5,7 +5,7 @@ # ## ARGVT # Hmdb limits per job (max is 700) -HMDB_LIMITS=500 +HMDB_LIMITS=200 ## Maximum query filtered (default is 20 - min : 1 / max 50) HMDB_MAX_QUERY=20 ## Galaxy url for HTML JS and CSS path
--- a/lib/hmdb.pm Fri Jan 19 10:27:38 2018 -0500 +++ b/lib/hmdb.pm Sat Jan 20 17:36:51 2018 -0500 @@ -223,9 +223,9 @@ my @page = () ; - my $ua = new LWP::UserAgent; + my $ua = LWP::UserAgent->new( keep_alive => 10 ); $ua->agent("Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36"); - $ua->timeout(500); + $ua->timeout(240); my $req = HTTP::Request->new( POST => 'http://specdb.wishartlab.com/ms/search.csv');
--- a/wsdl_hmdb.pl Fri Jan 19 10:27:38 2018 -0500 +++ b/wsdl_hmdb.pl Sat Jan 20 17:36:51 2018 -0500 @@ -123,7 +123,7 @@ $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution foreach my $mzs ( @{$submasses} ) { - + print Dumper $mzs ; my $result = undef ; my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ; @@ -139,9 +139,9 @@ ## Map metabocards with results (add supplementary data) -# print Dumper $results ; -# print Dumper $hmdb_ids ; -# print Dumper $metabocard_features ; + print Dumper $results ; + print Dumper $hmdb_ids ; + print Dumper $metabocard_features ; if ( ( defined $results ) and ( defined $metabocard_features ) ) { $results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ;