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Changeset 8:97788e4bf3fc (2018-01-20)

Previous changeset 7:ecf8e43aceda (2018-01-19) Next changeset 9:c32280662103 (2018-09-19)

Commit message:
planemo upload commit d1a5cd8f1baf00879ffa44649883f91c64f43392-dirty

modified:
conf_hmdb.cfg
lib/hmdb.pm
wsdl_hmdb.pl

diff -r ecf8e43aceda -r 97788e4bf3fc conf_hmdb.cfg
--- 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

diff -r ecf8e43aceda -r 97788e4bf3fc lib/hmdb.pm
--- 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');

diff -r ecf8e43aceda -r 97788e4bf3fc wsdl_hmdb.pl
--- 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) ;