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

Master branch Updating - - Fxx

13:3587cb923890

    
    if (!defined $$status) {
    	croak "No http status is defined for the distant server" ;
    }
    else {
    	unless ( $$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" ; }
    		else {
    			## None supported http code error ##
    		}
    	}
    }
    
    return (1) ;
}
## END of SUB

	my $req = HTTP::Request->new(
	    POST => 'http://specdb.wishartlab.com/ms/search.csv');
	
	$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');
	 
	my $res = $ua->request($req);
#	print $res->as_string;
	if ($res->is_success) {
	     @page = split ( /\n/, $res->decoded_content ) ;
	 } else {

    
    my %result_by_entry = () ;
    my %features = () ;
    
#    print Dumper $csv ;
    
    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\(ppm\)/) {
    		
    		if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/  ) {
    			my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;

#    		push (@results, $result_by_entry{$_}) ; 
    	}
    	else {push (@results, [] ) ;} ;

    }
    return(\@results) ;
}
## END of SUB

=head2 METHOD parse_hmdb_page_results 

sub write_csv_skel {
	## Retrieve Values
    my $self = shift ;
    my ( $csv_file, $rows ) = @_ ;

    my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
	my $csv = $ocsv->get_csv_object("\t") ;
	$ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
    
    return($csv_file) ;
}

	## Retrieve Values
    my $self = shift ;
    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" ;
    	
    my $i = 0 ;
    	
    foreach my $id (@{$ids}) {
    	my $mass = undef ;

14:625fa968d99a

    
    if (!defined $$status) {
    	croak "No http status is defined for the distant server" ;
    }
    else {
    	unless ( $$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) ;
}
## END of SUB

	my $req = HTTP::Request->new(
	    POST => 'http://specdb.wishartlab.com/ms/search.csv');
	
	$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) {
	     @page = split ( /\n/, $res->decoded_content ) ;
	 } else {

    
    my %result_by_entry = () ;
    my %features = () ;
    
#    print Dumper $csv ;
#    print Dumper $masses ;
#    print Dumper $max_query ;
    
    foreach my $line (@{$csv}) {
    	## 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\(ppm\)/) {
    		
    		if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/  ) {
    			my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;

#    		push (@results, $result_by_entry{$_}) ; 
    	}
    	else {push (@results, [] ) ;} ;

    }
    
    return(\@results) ;
}
## END of SUB

=head2 METHOD parse_hmdb_page_results 

sub write_csv_skel {
	## Retrieve Values
    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() ;
	my $csv = $ocsv->get_csv_object("\t") ;
	$ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
    
    return($csv_file) ;
}

	## Retrieve Values
    my $self = shift ;
    my ( $masses, $ids, $results, $file,  ) = @_ ;

    open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
    print CSV "ID\tQuery(Da)\tDelta(ppm)\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ;
    	
    my $i = 0 ;
    	
    foreach my $id (@{$ids}) {
    	my $mass = undef ;