Hi Eliza,
The file being referenced is supposed to be /usr/local/tpp/data
(according to the full filename passed to the pepXML viewer CGI). But
according to your previously-posted check_env results, your webserver's
"document root" is /usr/local/tpp/html/. That typically means that
anything your webserver can display must be under /usr/local/tpp/html/.
That's possibly why the error message says "can't find
/usr/local/tpp/^^^html^^^/data" when the file to display was under
/usr/local/tpp/data.
[And echoing Brian and other's comments about making sure the user which
Apache is running as has full read and write access down through all of
your data directories.]
Hope this helps,
Natalie
On 6/15/10 6:22 AM, Eliza wrote:
Well there does so happen to be an error in the Apache log file...
[Thu Jun 03 11:10:25 2010] [error] [client xxx.xxx.xx.xx] File does
not exist: /usr/local/tpp/html/data, referer:
http://localhost/tpp/cgi-bin/PepXMLViewer.cgi?xmlFileName=/usr/local/tpp/data/Halo11_itraq21_1.xml
but would this be coming from the PepXMLViewer.cgi file which is a bit
difficult to read as it is binary?
On Jun 1, 11:34 pm, Joe Slagel <[email protected]> wrote:
Eliza,
There is a javascript check in the viewer the periodically checks to
see if
the file on the server has changed relative to what is being displayed.
What the message indicates is that it was unable to retrieve the
timestamp
for the file. This shouldn't be too significant of a problem as you
still
should be able to view the file.
There can be a number of different reasons for the file check to fail.
Probably the first place to look at is the apache log files -- your
server
may be blocking HEAD requests, or the URL to the file may be incorrect.
-Joe
On Mon, May 31, 2010 at 4:35 AM, Eliza <[email protected]> wrote:
OK so I was able to figure out how how to set the PATH for the
webserver user and eradicated that error. That still leaves me with
the following error in the browser:
Unable to access xml file via webserver, so cannot check xml file for
changes ()
Check webserver configuration if desired.
(URL: undefined)
Suggestions on what I need to look at to fix this?
On May 24, 7:39 pm, Brian Pratt <[email protected]> wrote:
PATH = /usr/local/bin:/usr/bin:/bin
Doesn't seem to include your TPP executables. You'll need to figure
out how to update that for the Apache process user.
On Mon, May 24, 2010 at 12:39 AM, Eliza <[email protected]>
wrote:
Here is the output (with some details removed)
SCRIPT_NAME = /tpp/cgi-bin/check_env.pl
SERVER_NAME = servername
SERVER_ADMIN = webmas...@localhost
HTTP_ACCEPT_ENCODING = gzip,deflate
HTTP_CONNECTION = keep-alive
REQUEST_METHOD = GET
HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,*/
*;q=0.8
SCRIPT_FILENAME = /usr/local/tpp/cgi-bin/check_env.pl
SERVER_SOFTWARE = Apache/2.2.3 (Debian) PHP/5.2.0-8+etch16
HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7
QUERY_STRING =
REMOTE_PORT = 3975
HTTP_USER_AGENT = Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:
1.9.1.9) Gecko/20100315 Firefox/3.5.9 ( .NET CLR 3.5.30729)
SERVER_PORT = 80
SERVER_SIGNATURE =
Apache/2.2.3 (Debian) PHP/5.2.0-8+etch16 Server at server Port 80
HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5
REMOTE_ADDR = xx.xx.xx.xx
WEBSERVER_ROOT = /usr/local/tpp
HTTP_KEEP_ALIVE = 300
SERVER_PROTOCOL = HTTP/1.1
PATH = /usr/local/bin:/usr/bin:/bin
REQUEST_URI = /tpp/cgi-bin/check_env.pl
GATEWAY_INTERFACE = CGI/1.1
SERVER_ADDR = 130.232.69.141
DOCUMENT_ROOT = /usr/local/tpp/html/
WEBSERVER_TMP = /usr/local/tpp/html/tmp
HTTP_HOST = host
On May 21, 3:15 am, Brian Pratt <[email protected]> wrote:
PATH is of interest as well. Or you could just paste all the results
into a message to this list.
On Thu, May 20, 2010 at 7:38 AM, Vishal Swaroop
<[email protected]>
wrote:
As I have not configured TPP on linux so I am not sure if I will be
of
help.... but check WEBSERVER_ROOT and SCRIPT_FILENAME = <path to
tppbin>/check_env.pl
See, if <path to tppbin> in SCRIPT_FILENAME is set in apache
configuration
file httpd.conf.
As per your post description, does it mean that you are able to
login and
run some of the process from gui, on what event/ click you get this
error,
which browser you are using ?
Thanks
On Thu, May 20, 2010 at 4:42 AM, Eliza <[email protected]>
wrote:
The webserver is working fine, it is used to host a couple other
sites
and they aren't experiencing any issues :-)
I ran check_env.pl but I am not sure what I should which values I
should be verifying, can you provide any advice here?
On May 19, 12:01 am, Vishal Swaroop <[email protected]> wrote:
Hi Eliza,
Brian is right, it is difficult to debug through emails...
Though I have not configured it on linux but your issue seems to
be
related
to environment setting (path for user, etc. as mentioned in 2nd.
post)
- Check your apache httpd.conf file (should be somewhere under
etc/apache...) and check if webserver is working (
http://localhost)
- You should also try checking
http:///localhost/tpp/cgi-bin/check_env.pl ,
to check environment
Not sure if it will help but this is sample httpd.conf entry for
webserver
configured using cygwin...
ServerRoot "/usr"
Listen 81
#
# ISB-Tools Trans Proteomic Pipeline directive
#
ScriptLog /var/logs/apache2/cgi_log
AddType text/html .shtml
AddHandler server-parsed .shtml
SetEnv WEBSERVER_ROOT /cygdrive/c/Inetpub/wwwroot/
SetEnv WEBSERVER_URLhttp://localhost:81/
Alias /ISB/ "/cygdrive/c/Inetpub/wwwroot/ISB/"
<Directory "/cygdrive/c/Inetpub/wwwroot/ISB/">
AllowOverride None
Options Includes Indexes FollowSymLinks MultiViews
Order allow,deny
Allow from all
</Directory>
Alias /tpp-bin/ "/cygdrive/c/Inetpub/tpp-bin/"
<Directory "/cygdrive/c/Inetpub/tpp-bin/">
AllowOverride AuthConfig Limit
Options ExecCGI Includes Indexes MultiViews
AddHandler cgi-script .cgi .pl
Order allow,deny
Allow from all
</Directory>
Thanks
Vishal
On Tue, May 18, 2010 at 4:06 PM, Brian Pratt
<[email protected]>wrote:
I'm sorry you're having a hard time with it, but you just have
to get
in there and mess around with it, or find somebody locally who
will do
so for you. Getting a webserver configured on linux isn't
trivial,
unfortunately, and not really the kind of thing that can be
debugged
by email.
Brian
On Tue, May 18, 2010 at 6:52 AM, Eliza <
[email protected]>
wrote:
OK well this is a shame that no one seems to be able to help
on this
one. It seems to me this is more of a problem with the way
the
application is architected than a problem with the system I
run it
on. It's a bit of a shame that I don't feel I can support
running
TPP
in a Linux environment.
On Mar 23, 6:23 pm, Brian Pratt <[email protected]>
wrote:
Start with the "tpp_hostname: command not found" message.
The
solution
is a
combination of setting the PATH for the webserver user, and
customizing
your
tpp_gui_config.pl file to tell the GUI where you installed
the
various
executables.
Good luck,
Brian
On Tue, Mar 23, 2010 at 6:20 AM, Eliza <
[email protected]>
wrote:
I posted the thread
http://groups.google.com/group/spctools-discuss/browse_thread/thread/.
..
back in January but didn't receive any responses so I am
asking
again
if anybody can assist.
When trying to use the TPP GUI the webserver error log is
filled
with
the following error message:
[Fri Jan 08 14:01:42 2010] [error] [client xxx.xxx.xx.xx]
sh:
tpp_hostname: command not found, referer:
http://localhost/tpp/cgi-bin/tpp_gui.pl?Action=display&page=filebrowser
I am also seeing the same error message in the GUI:
Unable to access xml file via webserver, so cannot check
xml file
for
changes ()
Check webserver configuration if desired.
(URL: undefined)
Debian Etch TPP version 4.3. Suggestions on how to fix
this?
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