Discussion :

[fripette]

Bonjour,
Je souhaiterais exécuter un script CGI en console.
Ce scripts est generalement lancer via l'interface web et se rappelle lui même en version console .

Code :

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my @names = $query->param;
 
if (scalar(@names)>1) { #when add is pressed	
	print "Content-Type: text/html\n\n";
 
	if ($query->param('daily')){ # insert ncbi daily file(s) tblout
		treat_param_daily_case();			
	}else{ # genome part (for run new genome or insertion of genome tblout; one/many file(s) can be launch in the same time )
	    write_param_to_launch_console();
	}		
    print "<META HTTP-EQUIV=\"refresh\" CONTENT=\"0; URL=cazy_views.cgi\">";
}else{
	## batch part 
getopts("ldwm:t:uhs:f:g:");
 
    if ($opt_d){# daily file case
    	my $daily_info_file =$opt_t;
		launch_multiple_daily($daily_info_file);				
    }elsif ($opt_l){# launch multiple file to run new genome (modassign) || to insert tblout (insert_genome)
    	my $authorized = $opt_m;
    	my $no_insert =1 if ($opt_u);
    	my $with_hmm =1 if ($opt_h);
    	my $tblout=1 	if ($opt_t);
		launch_multiple_genomes($authorized,$tblout,$no_insert,$with_hmm);
 
	}elsif ($opt_w){# tblout insertion from command line
    	my $source  = $opt_s;
		my $geno_info  = $opt_g;
		my $fa_file = $opt_f;
		my $authorized = $opt_m;
		my $tblout =$opt_t;	
		process_insert($source,$geno_info,$fa_file,$authorized,$tblout);	
 
	## web part, display form	
	}else{
    	$manage = HTML::Template->new(filename => '../htmltemplate/content_insert_genome.tmpl');
	    $manage->param(TITLE => $title);
	    $manage->param(DESCRIPT => $metadesc);
	    $manage->param(TBLOUT => 1) if ($query->param('tblout'));
	    if ($query->param('daily')){
	    	 $manage->param(DAILY => 1) ;
	    	 $manage->param(TITLE => "Insert Daily Tblout");
	    }
 
	    $manage->param(DIRSERVER => $$global{dirhttp_server});
	    print "Content-Type: text/html\n\n",$manage->output;        
	}   
}

concretement le web va traiter les infos grace a write param_to_launch_console

Code :

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sub write_param_to_launch_console{	
	my $usr = $session->param('usr');
	my $authorized =	check_if_authorized($usr,"Insert Tblout FAILED");	
 
	# read all info from tmpl
	my @all_tax_id=$query->param('tax_id');
    my @organism=$query->param('organism');
    my @strain=$query->param('strain');
    my @source=$query->param('source');
    my @fasta=$query->param('fasta_file');
	my @tblout=$query->param('tblout_file') if ($query->param('tblout'));
	if (!$query->param('tax_id') && !$query->param('organism')){
		my $msg =  "[WebJob] Run Job FAILED<BR> Please provide information<BR>";
		print $msg;
		exit(0);
   	}
 
	# write genome info (tax_id,organism ...) in a file (genome_info_file), will be read by the console version of the script  	
	my $str;
   	for(my $index=0;$index<scalar(@all_tax_id);$index++){   		
   		next if (!$all_tax_id[$index]&& !$organism[$index] && !$strain[$index] && !$source[$index] && !$fasta[$index]);
 
   		if ( !$fasta[$index] ){
   			# if file(s) not found send error msg to user			
		 	my $msg =  "No fasta_file for: ". $organism[$index]. "\n";
			print $msg;
			exit(0);
		}
		# write locally fasta_file passed by User
   		my $fasta_filename= write_file_in_tmp($fasta[$index]);		
   		$str .= $all_tax_id[$index]."\t".$organism[$index]."\t".$strain[$index]."\t".$source[$index]."\t".$fasta_filename;
 
   		 # write locally tblout_file (in case of tblout process/insertion ) passed by User
   		if ($query->param('tblout')){   			
   			if ( !$tblout[$index] ){
   				# if file(s) not found send error msg to user			 		
				my $msg =  "No tblout_file for: ". $organism[$index]. "\n";
   				print $msg;
				exit(0);				
			}
			# write locally fasta_file passed by User
   		  	my $tblout_filename=write_file_in_tmp($tblout[$index]);
   		  	$str.= "\t".$tblout_filename;
   		}   		
   		$str.= "\n";   		
   	}     	
 
   	my $first_name = $1 if($authorized=~/(\w+)\.\w+/);
   	open(LOCAL, ">".$$global{modassign_tmp}."/genome_info_file_".$first_name.".txt") or die $!; 
   	print LOCAL $str;
    close(LOCAL);	   
 
    my $cmd;
    if (param('tblout_file')){ # insert multiple genomes (multiple tblouts will be read and insert)
      	$cmd= "$$global{scripts}/privatesite/insert_genome.cgi -l -m '".$authorized."' -t 1 1>$$global{modassign_tmp}\/modass.log 2>&1&";    
    }else{ # run new genomes (multiple html will be generated )
    	my $no_insert = "-u" if $query->param('no_insert');
    	my $with_hmm = "-h" if $query->param('with_hmm');
    	$cmd= "$$global{scripts}/privatesite/insert_genome.cgi -l -m '".$authorized."' ".$no_insert." ".$with_hmm." 1>$$global{modassign_tmp}\/modass.log 2>&1&";
    }
    print $cmd;
	system ($cmd);
}

La commande lorsque je passe via www-data, pas de soucis ca marche.
Cependant, lorsque j'essaye de le lancer via cron : rien , pas de message d'erreur.

Code :

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#!/bin/bash
 
date=`date +%Y_%m_%d`;
 
daily_info_file="/data/tmp/daily_info_file_$date.txt";
if [ -f $fichier ]
then
	cd /home/fripette/scripts/privatesite/
	perl insert_genome.cgi -d -t '$daily_info_file' >& /data/tmp/tblout_daily.log
fi
 
exit

Rien ne s'ecrit dans le tblout_daily.log.

Merci pour votre aide !
Frip'

[Lolo78]

Je dirais que c'est sans doute plus un problème Unix/Linux que Perl. Sans doute certaine variables d'environnement sont mal définies quand tu exécutes un programme avec cron. Il faut sans doute essayer de sourcer les scripts utilisés quand tu ouvres un terminal.