diff lib/hmdb.pm @ 14:625fa968d99a draft

Master branch Updating - - Fxx

--- a/lib/hmdb.pm	Tue Oct 02 04:59:13 2018 -0400
+++ b/lib/hmdb.pm	Thu Jan 10 09:10:14 2019 -0500
@@ -195,12 +195,15 @@
     	croak "No http status is defined for the distant server" ;
     }
     else {
-    	unless ( $$status == 200 ) { 
+    	unless ( $$status == 200 ) {
     		if  ( $$status == 504 ) { croak "Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server" ; }
+    		if  ( $$status == 500 ) { croak "Internal Server Error: The HMDB server returns an unexpected internal server error" ; }
     		else {
     			## None supported http code error ##
+    			croak "Internal Server Error $$status..." ;
     		}
     	}
+    	if  ( $$status == 200 ) { print "The HMDB server returns that your request was fulfilled" ; }
     }
     
     return (1) ;
@@ -232,7 +235,7 @@
 	
 	$req->content_type('application/x-www-form-urlencoded');
 	$req->content('utf8=TRUE&mode='.$mode.'&query_masses='.$masses.'&tolerance='.$delta.'&database=HMDB&commit=Download Results As CSV');
-	 
+#	print Dumper $req ; 
 	my $res = $ua->request($req);
 #	print $res->as_string;
 	if ($res->is_success) {
@@ -269,26 +272,10 @@
     my %features = () ;
     
 #    print Dumper $csv ;
+#    print Dumper $masses ;
+#    print Dumper $max_query ;
     
     foreach my $line (@{$csv}) {
-    	## HMDB csv output - [DEPRECATED]...
-#    	if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) {
-#    		my @entry = split(/,/, $line) ;
-#    		
-#    		if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
-#    		
-#    		$features{ENTRY_ENTRY_ID} = $entry[1] ;
-#    		$features{ENTRY_FORMULA} = $entry[2] ;
-#    		$features{ENTRY_CPD_MZ} = $entry[3] ;
-#    		$features{ENTRY_ADDUCT} = $entry[4] ;
-#    		$features{ENTRY_ADDUCT_TYPE} = $entry[5] ;
-#    		$features{ENTRY_ADDUCT_MZ} = $entry[6] ;
-#    		$features{ENTRY_DELTA} = $entry[7] ;
-#    		
-#    		my %temp = %features ;
-#    		
-#    		push (@{$result_by_entry{$entry[0]} }, \%temp) ;
-#    	}
     	## NEW HMDB format V4.0 - dec2017
 		if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta\(ppm\)/) {
     		
@@ -341,6 +328,7 @@
     	else {push (@results, [] ) ;} ;
 
     }
+    
     return(\@results) ;
 }
 ## END of SUB
@@ -1030,7 +1018,8 @@
     my $self = shift ;
     my ( $csv_file, $rows ) = @_ ;
 
-    my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
+#    my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
+	my $ocsv = lib::csv::new() ;
 	my $csv = $ocsv->get_csv_object("\t") ;
 	$ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
     
@@ -1053,7 +1042,7 @@
     my ( $masses, $ids, $results, $file,  ) = @_ ;
 
     open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
-    print CSV "ID\tQuery(Da)\tDelta\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ;
+    print CSV "ID\tQuery(Da)\tDelta(ppm)\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ;
     	
     my $i = 0 ;