mod_fcgi and gbrowse / gbrowse_details error

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mod_fcgi and gbrowse / gbrowse_details error

by Biliards :: Rate this Message:

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Hi all,

I'm using debian lenny system. I install gbrowse v1.994 release and
gbrowse works with (or without) mod_perl method and without apache
error log.

I'm testing gbrowse and mod_fcgi method but I have got some problem. I
install libapache2-mod-fcgid and I tested with and without fcgi
module. My apache gbrowse configuration is:

<IfModule mod_fcgid.c>
Alias /fpublic "/usr/lib/cgi-bin/public"
<Location /fpublic>
SetHandler fcgid-script
Options ExecCGI
SetEnv GBROWSE_CONF "/etc/gbrowse/public"
</Location>
</IfModule>

Results:

* without fcgi module, if I run
http://gbrowse.cribi.unipd.it/fpublic/gbrowse/vitis_vinifera_8x/
I obtain only apache error about page not found
* with fcgi module, if I run
http://gbrowse.cribi.unipd.it/fpublic/gbrowse/vitis_vinifera_8x/
I have got apache error log:

Status: 302 Found
Location: /yeast/

Set-Cookie: gbrowse_sess=b4ee894a1035440c3246d9ac0e4a7559; path=/;
expires=Thu, 09-Jul-2009 21:25:10 GMT
Date: Tue, 09 Jun 2009 21:25:10 GMT
Cache-control: no-cache
Content-Type: text/html; charset=ISO-8859-1

<!DOCTYPE html
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
<head>
<title>Yeast chromosomes 1+2 (basic): 37 kbp from chrI:143,000..180,000</title>
<link type="text/css" media="all" rel="stylesheet"
href="/css/gbrowse_transparent.css" />
...
</body>
</html>[Tue Jun 09 23:25:10 2009] [warn] (104)Connection reset by
peer: mod_fcgid: read data from fastcgi server error.
[Tue Jun 09 23:25:10 2009] [error] [client 147.162.3.222] Premature
end of script headers: gbrowse
[Tue Jun 09 23:25:14 2009] [notice] mod_fcgid: process
/usr/lib/cgi-bin/public/gbrowse(14658) exit(communication error),
terminated by calling exit(), return code: 0

and if I run
http://gbrowse.cribi.unipd.it/fpublic/gbrowse_details/arabidopsis_thaliana?ref=NC_003076;start=425890;end=430028;name=mRNAtigrscan99;class=Sequence;feature_id=6817;db_id=annotations:database
I obtain apache error log:

Invalid source at /usr/lib/cgi-bin/public/gbrowse_details line 89
Content-Type: text/html; charset=ISO-8859-1

<!DOCTYPE html
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
<head>
<title>gbrowse_details error</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
</head>
<body>
<p class="error">This script must be called with one or more of the
parameters name, feature_id or db_id.</p>[Tue Jun 09 23:32:59 2009]
[warn] (104)Connection reset by peer: mod_fcgid: read data from
fastcgi server error.
[Tue Jun 09 23:32:59 2009] [error] [client 147.162.3.222] Premature
end of script headers: gbrowse_details
[Tue Jun 09 23:33:00 2009] [notice] mod_fcgid: process
/usr/lib/cgi-bin/public/gbrowse_details(14672) exit(communication
error), terminated by calling exit(), return code: 0

Any ideas?
Best,
Alessandra.

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Re: mod_fcgi and gbrowse / gbrowse_details error

by zph :: Rate this Message:

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I think that the default GBrowse installation generated wrong
gbrowse2.conf, and developers should correct it. This has been
highlighted by Alessandra's recent questions regarding mod_perl
and mod_fcgid.

The solution is simple (assuming everything else is correct;-) )

ScriptAlias "/fpublic" "/usr/lib/cgi-bin/public"
<IfModule mod_fcgid.c>
<Location /fpublic>
SetHandler fcgid-script
Options ExecCGI
</Location>
DefaultInitEnv GBROWSE_CONF "/etc/gbrowse/public"
</IfModule>

Hope this helps.

Zong-Pei

On Tue, 9 Jun 2009, Alessandra wrote:
Date: Tue, 9 Jun 2009 23:37:50 +0200
From: Alessandra <alessandra.bilardi@...>
To: GMOD GBrowse List <gmod-gbrowse@...>
Subject: [Gmod-gbrowse] mod_fcgi and gbrowse / gbrowse_details error

Hi all,

I'm using debian lenny system. I install gbrowse v1.994 release and
gbrowse works with (or without) mod_perl method and without apache
error log.

I'm testing gbrowse and mod_fcgi method but I have got some problem. I
install libapache2-mod-fcgid and I tested with and without fcgi
module. My apache gbrowse configuration is:

<IfModule mod_fcgid.c>
Alias /fpublic "/usr/lib/cgi-bin/public"
<Location /fpublic>
SetHandler fcgid-script
Options ExecCGI
SetEnv GBROWSE_CONF "/etc/gbrowse/public"
</Location>
</IfModule>

Results:

* without fcgi module, if I run
http://gbrowse.cribi.unipd.it/fpublic/gbrowse/vitis_vinifera_8x/
I obtain only apache error about page not found
* with fcgi module, if I run
http://gbrowse.cribi.unipd.it/fpublic/gbrowse/vitis_vinifera_8x/
I have got apache error log:

Status: 302 Found
Location: /yeast/

Set-Cookie: gbrowse_sess=b4ee894a1035440c3246d9ac0e4a7559; path=/;
expires=Thu, 09-Jul-2009 21:25:10 GMT
Date: Tue, 09 Jun 2009 21:25:10 GMT
Cache-control: no-cache
Content-Type: text/html; charset=ISO-8859-1

<!DOCTYPE html
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
<head>
<title>Yeast chromosomes 1+2 (basic): 37 kbp from chrI:143,000..180,000</title>
<link type="text/css" media="all" rel="stylesheet"
href="/css/gbrowse_transparent.css" />
...
</body>
</html>[Tue Jun 09 23:25:10 2009] [warn] (104)Connection reset by
peer: mod_fcgid: read data from fastcgi server error.
[Tue Jun 09 23:25:10 2009] [error] [client 147.162.3.222] Premature
end of script headers: gbrowse
[Tue Jun 09 23:25:14 2009] [notice] mod_fcgid: process
/usr/lib/cgi-bin/public/gbrowse(14658) exit(communication error),
terminated by calling exit(), return code: 0

and if I run
http://gbrowse.cribi.unipd.it/fpublic/gbrowse_details/arabidopsis_thaliana?ref=NC_003076;start=425890;end=430028;name=mRNAtigrscan99;class=Sequence;feature_id=6817;db_id=annotations:database
I obtain apache error log:

Invalid source at /usr/lib/cgi-bin/public/gbrowse_details line 89
Content-Type: text/html; charset=ISO-8859-1

<!DOCTYPE html
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
<head>
<title>gbrowse_details error</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
</head>
<body>
<p class="error">This script must be called with one or more of the
parameters name, feature_id or db_id.</p>[Tue Jun 09 23:32:59 2009]
[warn] (104)Connection reset by peer: mod_fcgid: read data from
fastcgi server error.
[Tue Jun 09 23:32:59 2009] [error] [client 147.162.3.222] Premature
end of script headers: gbrowse_details
[Tue Jun 09 23:33:00 2009] [notice] mod_fcgid: process
/usr/lib/cgi-bin/public/gbrowse_details(14672) exit(communication
error), terminated by calling exit(), return code: 0

Any ideas?
Best,
Alessandra.

------------------------------------------------------------------------------
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing
server and web deployment.
http://p.sf.net/sfu/businessobjects
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing
server and web deployment.
http://p.sf.net/sfu/businessobjects
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse