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? > > > > >> >> > > >> > -- > > > >> >> > > >> > You received this message because you are subscribed to > > the > > > >> >> > > >> > Google > > > >> >> > > Groups > > > >> >> > > >> > "spctools-discuss" group. > > > >> >> > > >> > To post to this group, send email to > > > >> >> > > [email protected]. > > > >> >> > > >> > To unsubscribe from this group, send email to > > > > >> >> > > >> > [email protected]<spctools-discuss%[email protected]> > > <spctools-discuss%[email protected]<spctools-discuss%[email protected]> > > > > >> >> > > <spctools-discuss%[email protected]<spctools-discuss%[email protected]> > > <spctools-discuss%[email protected]<spctools-discuss%[email protected]> > > > > >> >> > > >> > . > > > >> >> > > >> > For more options, visit this group at > > > >> >> > > >> >http://groups.google.com/group/spctools-discuss?hl=en. > > > > >> >> > > > -- > > > >> >> > > > You received this message because you are subscribed to the > > Google > > > >> >> > > > Groups > > > >> >> > > "spctools-discuss" group. > > > >> >> > > > To post to this group, send email to > > > >> >> > > > [email protected]. > > > >> >> > > > To unsubscribe from this group, send email to > > > > >> >> > > [email protected]<spctools-discuss%[email protected]> > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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