[CGI] Résolution de Gateway Incorrecte multi-utilisateur

**Norore** · 01/04/2011, 11h56

Bonjour,

étant actuellement en plein développement d'une interface web mêlant PHP et Perl, les scripts Perl étant appelés par PHP et pouvant afficher les informations relatives aux calculs au format HTML dans la page générée par PHP, je me retrouve à un problème de taille.
Je pense que celui-ci vient du fait que je fais un pré-traitement sur plusieurs fichiers afin de récupérer des tables de hashages pour faire les relations entre les informations qui sont dans les différents fichiers avant l'affichage d'un tableau. Lorsque je lance le script sur une seule session, celui-ci tourne sans problème et m'affiche bien le tableau. Mais lorsque je souhaite faire la même chose en le lançant sous deux sessions, le serveur me renvoit l'erreur suivante :

Gateway incorrecte!

Le serveur proxy a reçu une réponse incorrecte de la part d'un serveur supérieur.

The proxy server could not handle the request <a href="/diyhttp/index.php">GET /diyhttp/index.php</a>. Reason: Error reading from remote server

Si vous pensez qu'il s'agit d'une erreur du serveur, veuillez contacter le gestionnaire du site

Error 502

Etant donné que l'interface que je suis en train de développer a pour objectif d'être un service web, je risque de très rapidement retrouver ce problème si plusieurs utilisateurs souhaitent afficher le tableau généré par le script, ce qui rendra donc mon application totalement inutile. Quelle serait la meilleure solution à utiliser ? Probablement l'utilisation d'une base de données, mais au stade actuel du projet celle-ci n'a pas encore été définie ni construite. Peut-être faudrait-il que je passe par le module FastCGI ou que je procède autrement dans mon cas ?

Si cela peut vous aider, je vous joint le script utilisé actuellement :

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

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#!/usr/bin/perl
 
use CGI;
use strict;
use warnings;
use List::MoreUtils qw(uniq);
 
my $blast = $ARGV[0];
my $genelink = $ARGV[1];
my $organism = $ARGV[2];
my $params = $ARGV[3];
my $cross_check = $ARGV[4];
my $uniprotdbr = "/mnt/Temp2/diyhttp/Databases/DB_relations/unip-id_dbr_".$organism.".dat";
my $gene_info = "/mnt/Temp2/diyhttp/Databases/DB_relations/".$organism."-gene_info.txt";
my $generef = "/mnt/Temp2/diyhttp/Databases/DB_sources/gene2refseq";
my $uniacref = "/mnt/Temp2/diyhttp/Databases/DB_sources/gene_refseq_uniprotkb_collab";
 
# extract some datas from $uniprotdbr :
# - the GeneID for the UniProt-ID;
# - the UniProt-AC for the UniProt-ID.
open (UNIPROT, "<", $uniprotdbr) or ( warn "Can't read file $uniprotdbr\n$!\n" and die );
my (%upid2upac, %upid2geneid);
while(<UNIPROT>){
    chomp;
    my ($upid, $upac, $geneid, $go, $pir, $taxon, $ens) = split(/\t/, $_);
    $upid2geneid{$upid} = $geneid;
    $upid2upac{$upid} = $upac;
}
close UNIPROT;
 
# extract the official symbol for the GeneID
open (GENE, "<", $gene_info) or ( warn "Can't read file $gene_info\n$!\n" and die );
my %geneid2symbol;
my $count = 0;
while(<GENE>){
    chomp;
    my ($taxid, $geneid, $symbol, $update) = split(/\t/, $_);
    $geneid2symbol{$geneid} = $symbol;
}
close GENE;
 
# protgi references for the GeneID
my (%geneid2protgi, %uniac2protacc);
open (GENEREF, "<", $generef) or ( warn "Can't read file $generef\n$!\n" and die );
while(<GENEREF>){
    chomp;
    my ($taxid, $geneid, $status, $rna_acc, $rna_gi, $protacc, $protgi) = split(/\t/, $_);
    if ( ( defined($geneid) and defined($protgi) )
     and ( $geneid !~ "-" and $protgi !~ "-" ) ){
        push(@{$geneid2protgi{$geneid}}, $protgi) ;
    }
}
close GENEREF;
 
open (UNIACREF, "<", $uniacref) or ( warn "Can't read file $uniacref\n$!\n" and die );
while(<UNIACREF>){
    chomp;
    my ($protgi, $uniac) = split(/\t/, $_);
    if ( defined($protgi) and defined($uniac) ){
        $uniac2protacc{$uniac} = $protgi;
    }
}
close UNIACREF;
 
# extract params selected by the user
my @params = split(/-/, $params);
 
# initialise script for writting xml file output
use XML::Writer;
use IO::File;
 
my ($dir, $file_name) = $blast =~ /(.+[\/\\])([^\/\\]+)$/;
 
my $output_file = "tmp/".$file_name.".xml";
my $output = new IO::File("> ".$output_file);
 
my $writer = new XML::Writer(
    OUTPUT      => $output,
    DATA_INDENT => 4,             # indentation, 4 spaces
    DATA_MODE   => 1,             # change line
    ENCODING    => 'utf-8',       # encoding character
);
 
 
$writer->xmlDecl("UTF-8");
$writer->startTag("BlastRead");
# define organism tag
$writer->startTag("Organism");
$writer->characters($organism);
$writer->endTag("Organism");
 
# user could select the GeneID that he evaluates as interesting
print "<table id=\"showlines\">\n";
print "\t<tr id=\"first-line\"><th>#</th><th width=\"10%\">Peptids</th><th>Genes</th><th width=\"10%\">Proteins</th>";
if ( grep(/A|H/, @params) and !grep(/N/, @params) ){
    print "<th>HomoloGene</th>";
}
if ( grep(/A|P/, @params) and !grep(/N/, @params)){
    print "<th>PIRSF</th>"
}
if ( grep(/A|O/, @params) and !grep(/N/, @params)){
    print "<th>OrthoMCL</th>"
}
print "<th>Cross</th>";
print "</tr>\n";
 
open (BLAST, "<", $blast) or ( warn "Can't read $blast file!<br />$!" and die );
my $i = 0;
my $line = 1;
while(<BLAST>){
    chomp;
    my ($nbpept, $peptid, $upid, $homo, $pirsf, $ortho, $cross) = split(/\t/, $_);
    my @crossed = split(/\s/, $cross);
    if ( ( grep(/$cross_check/, @crossed) ) or ( $cross_check =~ /N/ ) )
    {
        # in condition, start Pack tag
        $writer->startTag("Pack", "value"=>$i, "number"=>$nbpept);
        my @peptids = split(/\s/, $peptid);
        my @upids = split(/\s/, $upid);
        my @homos = split(/\s/, $homo);
        my @pirsf_r = split(/\s/, $pirsf);
        my @orthos = split(/\s/, $ortho);
        my @crossed = split(/\s/, $cross);
        print "\t<tr id=\"line$i\">";
 
        print "<td valign=\"top\">";
        print $nbpept;
        print "</td>";
 
        print "<td valign=\"top\">";
        print join(", ", @peptids);
        print "</td>";
 
        $writer->startTag("Peptids");
        $writer->characters( join(", ", @peptids) );
        $writer->endTag("Peptids");
 
        # show list of genes for the peptids pack
        print "<td valign=\"top\">";
        # stat gene tag
        $writer->startTag("Gene");
        my @geneids = map { $upid2geneid{$_} } @upids;
        @geneids = uniq(@geneids);
        my $last_geneid = pop(@geneids);
        foreach my $geneid (@geneids){
            if ( $geneid ){
                if ( $geneid2symbol{$geneid} ){
                    print "<input type=\"checkbox\" name=\"geneid[]\" value=\"".$geneid."+".$geneid2symbol{$geneid}."+".$line."\" />";
                    print "<a href=\"".$genelink."&amp;geneid=".$geneid."&amp;symbol=".$geneid2symbol{$geneid}."&amp;organism=".$organism."\" title=\"".$geneid2symbol{$geneid}."\">".$geneid2symbol{$geneid}."</a>,<br />";
 
                    # input geneid tag
                    $writer->startTag("geneid");
                    $writer->characters($geneid);
                    $writer->endTag("geneid");
 
                    # input gene symbol tag
                    $writer->startTag("genesymbol");
                    $writer->characters($geneid2symbol{$geneid});
                    $writer->endTag("genesymbol");
                }
                else{
                    print "<input type=\"checkbox\" name=\"geneid[]\" value=\"".$geneid."+".$geneid."+".$line."\" />";
                    print "<a href=\"".$genelink."&amp;geneid=".$geneid."&amp;symbol=".$geneid."&amp;organism=".$organism."\" title=\"".$geneid."\">".$geneid."</a>,<br />";
 
                    # input geneid tag
                    $writer->startTag("geneid");
                    $writer->characters($geneid);
                    $writer->endTag("geneid");
 
                    # input gene symbol tag
                    $writer->startTag("genesymbol");
                    $writer->characters("Unknown");
                    $writer->endTag("genesymbol");
                }
            }
            else{
                print "-,<br />";
 
                # input geneid tag
                $writer->startTag("geneid");
                $writer->characters("Unknown");
                $writer->endTag("geneid");
 
                # input gene symbol tag
                $writer->startTag("genesymbol");
                $writer->characters("Unknown");
                $writer->endTag("genesymbol");
                }
            }
            else{
                print "-,<br />";
 
                # input geneid tag
                $writer->startTag("geneid");
                $writer->characters("Unknown");
                $writer->endTag("geneid");
 
                # input gene symbol tag
                $writer->startTag("genesymbol");
                $writer->characters("Unknown");
                $writer->endTag("genesymbol");
            }
        }
 
        if ( $last_geneid ){
            if ( $geneid2symbol{$last_geneid} ){
                print "<input type=\"checkbox\" name=\"geneid[]\" value=\"".$last_geneid."+".$geneid2symbol{$last_geneid}."+".$line."\" />";
                print "<a href=\"".$genelink."&amp;geneid=".$last_geneid."&amp;symbol=".$geneid2symbol{$last_geneid}."&amp;organism=".$organism."\" title=\"".$geneid2symbol{$last_geneid}."\">".$geneid2symbol{$last_geneid}."</a>";
 
                # input geneid tag
                $writer->startTag("geneid");
                $writer->characters($last_geneid);
                $writer->endTag("geneid");
 
                # input gene symbol tag
                $writer->startTag("genesymbol");
                $writer->characters($geneid2symbol{$last_geneid});
                $writer->endTag("genesymbol");
            }
            else{
                print "<input type=\"checkbox\" name=\"geneid[]\" value=\"".$last_geneid."+".$last_geneid."+".$line."\" />";
                print "<a href=\"".$genelink."&amp;geneid=".$last_geneid."&amp;symbol=".$last_geneid."&amp;organism=".$organism."\" title=\"".$last_geneid."\">".$last_geneid."</a>";
 
                # input geneid tag
                $writer->startTag("geneid");
                $writer->characters($last_geneid);
                $writer->endTag("geneid");
 
                # input gene symbol tag
                $writer->startTag("genesymbol");
                $writer->characters("Unknown");
                $writer->endTag("genesymbol");
            }
        }
        else{
            print "-";
 
            # input geneid tag
            $writer->startTag("geneid");
            $writer->characters("Unknown");
            $writer->endTag("geneid");
 
            # input gene symbol tag
            $writer->startTag("genesymbol");
            $writer->characters("Unknown");
            $writer->endTag("genesymbol");
        }
        # end gene tag
        $writer->endTag("Gene");
        print "</td>";
 
        # show proteins with their gi accessor, if exists
        print "<td valign=\"top\">";
        $writer->startTag("Proteins");
        # start tag for listing the Protein gi
        $writer->startTag("ProtGI");
 
        my $last_upid = pop(@upids);
 
        foreach my $upid (@upids){
#       ( $upid2geneid{$upid} ) ? print $geneid2symbol{$upid2geneid{$upid}}.":<br />" : print "Gene not found:<br />";
 
            if ( defined($uniac2protacc{$upid2upac{$upid}}) ){
                print "<a href=\"http://www.ncbi.nlm.nih.gov/protein/".$uniac2protacc{$upid2upac{$upid}}."\">".$upid."</a>,<br />";
 
                # add the protgi
                $writer->startTag("gi");
                $writer->characters($uniac2protacc{$upid2upac{$upid}});
                $writer->endTag("gi");
 
                # add the UniProt-ID which correspond
                $writer->startTag("UniProt-ID");
                $writer->characters($upid);
                $writer->endTag("UniProt-ID");
            }
            else {
                print $upid.",<br />";
                # add the UniProt-ID
                $writer->startTag("UniProt-ID");
                $writer->characters($upid);
                $writer->endTag("UniProt-ID");
            }
        }
 
        if ( defined($uniac2protacc{$upid2upac{$last_upid}}) ){
            print "<a href=\"http://www.ncbi.nlm.nih.gov/protein/".$uniac2protacc{$upid2upac{$last_upid}}."\">".$last_upid."</a><br />";
 
            # add the protgi
            $writer->startTag("gi");
            $writer->characters($uniac2protacc{$upid2upac{$last_upid}});
            $writer->endTag("gi");
 
            # add the UniProt-ID which correspond
            $writer->startTag("UniProt-ID");
            $writer->characters($upid);
            $writer->endTag("UniProt-ID");
        }
 
        else {
            print $last_upid."<br />";
            # add the UniProt-ID
            $writer->startTag("UniProt-ID");
            $writer->characters($last_upid);
            $writer->endTag("UniProt-ID");
        }
 
        # end the protein gi list
        $writer->endTag("ProtGI");
        $writer->endTag("Proteins");
        print "</td>";
 
 
        # user want to see HomoloGene's column
        # show the HomoloGene's list for the peptids pack
        if ( grep(/A|H/, @params) and !grep(/N/, @params) ){
            print "<td valign=\"top\">";
 
            # start homologene tag
            $writer->startTag("HomoloGene");
            if ( scalar(@homos) > 0 ){
#           @homos = uniq(@homos);
                my $last_homo = pop(@homos);
                print map { ( $_ !~ "None" ) ? "<a href=\"http://www.ncbi.nlm.nih.gov/homologene/".$_."\">".$_."</a>,<br />"    : $_.",<br />" ;} @homos;
 
                # input homologeneID tag
                map { $writer->startTag("HomoloGeneID");
                    $writer->characters($_);
                    $writer->endTag("HomoloGeneID");
                } @homos;
 
                ( $last_homo !~ "None" ) ? print "<a href=\"http://www.ncbi.nlm.nih.gov/homologene/".$last_homo."\">".$last_homo."</a>" : print $last_homo;
 
                # input homologeneID tag
                $writer->startTag("HomoloGeneID");
                $writer->characters($last_homo);
                $writer->endTag("HomoloGeneID");
            }
            else{
                print "None";
                # none HomoloGene, input characters
                $writer->characters("None");
            }
 
            # end homologene tag
            $writer->endTag("HomoloGene");
            print "</td>";
        }
 
        # user want to see PIRSF families' column
        # show the PIRSF Families' list for the peptids pack
        if ( grep(/A|P/, @params) and !grep(/N/, @params) ){
            print "<td valign=\"top\">";
 
            # start PIRSF tag
            $writer->startTag("PIRSF");
            if ( scalar(@pirsf_r) > 0){
#           @pirsf_r = uniq(@pirsf_r);
                my $last_pirsf = pop(@pirsf_r);
                print map { ( $_ !~ "None" ) ? $_.",<br />" : $_.",<br />"; } @pirsf_r;
                # input PIRSF Families
                map { $writer->startTag("PIRSF_family");
                      $writer->characters($_);
                      $writer->endTag("PIRSF_family");} @pirsf_r;
                ( $last_pirsf !~ "None" ) ? print $last_pirsf : print $last_pirsf;
                # input last PIRSF Family
                $writer->startTag("PIRSF_family");
                $writer->characters($last_pirsf);
                $writer->endTag("PIRSF_family");
            }
            else{
                print "None";
                # none PIRSF, input characters
                $writer->characters("None");
            }
 
            # end PIRSF tag
            $writer->endTag("PIRSF");
            print  "</td>";
        }
 
        # user want to see OrthoMCL's column
        # show the OrthoMCL's list for the peptids pack
        if ( grep(/A|O/, @params) and !grep(/N/, @params) ){
            print "<td valign=\"top\">";
 
            # start OrthoMCL tag
            $writer->startTag("OrthoMCL");
            if ( scalar(@orthos) > 0 ){
#           @orthos = uniq(@orthos);
                my $last_ortho = pop(@orthos);
                print map { ( $_ !~ "None" ) ? "<a href=\"http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi?rm=sequenceList&groupac=".$_."\">".$_."</a>,<br />" : $_.",<br />"; } @orthos;
 
                # input OrthoMCL access number
                map { $writer->startTag("OrthoMCL_ac");
                      $writer->characters($_);
                      $writer->endTag("OrthoMCL_ac");
                    } @orthos;
                ( $last_ortho !~ "None" ) ? print "<a href=\"http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi?rm=sequenceList&groupac=".$last_ortho."\">".$last_ortho."</a>" : print $last_ortho;
 
                # input OrthoMCL access number
                $writer->startTag("OrthoMCL_ac");
                $writer->characters($last_ortho);
                $writer->endTag("OrthoMCL_ac");
            }
            else{
                print "None";
                # none OrthoMCL, input characters
                $writer->characters("None");
            }
 
            # end OrthoMCL tag
            $writer->endTag("OrthoMCL");
            print "</td>";
        }
 
        print "<td valign=\"top\" align=\"center\">";
        foreach my $pcross (@crossed){
            ( $pcross eq "X" ) ? print "<div class=\"cross\">".$pcross."</div>" : print "<div class=\"differ\">".$pcross."</div>";
 
            # input if datas from HomoloGene, PIRSF and OrthoMCL cross for proteins found or not
            my $pcrossed = ( $pcross eq "X" ) ? "cross" : "uncross";
            $writer->emptyTag("CrossDatas", "value" => $pcrossed );
        }
        print "</td>";
 
        print "</tr>\n";
 
        # end Pack tag
        $writer->endTag("Pack");
        print "\t<script type=\"text/javascript\">\n";
        print "\t\t\$(\"#showlines\").load(\"#line$i\");\n";
        print "\t</script>\n";
        $i++;
        }
    $line++;
}
close BLAST;
 
print "</table>\n";
 
# end writting xml file output
$writer->endTag("BlastRead");
$writer->end();
$output->close();
 
print "<hr /><a href=\"file_downloader.php?file=".$output_file."\">Download table result as XML file output.</a><br />";

Merci d'avance aux personnes qui auront plus d'idées que moi, personnellement je sèche

!
Cordialement, Norore.

**Norore** · 05/04/2011, 12h23

Bonjour,

j'ai résolu le problème à coup de fonctions et de grep afin de ne chercher dans les fichiers que les lignes et valeurs qui m'intéressent. Bon par contre je ne vous cache pas que c'est lent, et même affreusement lent juste pour 2 sessions ! Je préfère ne pas imaginer ce que cela donnera pour plusieurs sessions...

L'un d'entre vous aurait-il une idée pour accélérer les temps de calculs ?

[CGI] Résolution de Gateway Incorrecte multi-utilisateur

Web Perl

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