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 <blond...@googlemail.com> 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 <brian.pr...@insilicos.com> 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 <blond...@googlemail.com> 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 <brian.pr...@insilicos.com> 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 <vishal....@gmail.com> > 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 <blond...@googlemail.com> > 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 <vishal....@gmail.com> 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 > > >> >> > <brian.pr...@insilicos.com>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 < > blond...@googlemail.com> > > >> >> > > 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 <brian.pr...@insilicos.com> > 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 < > blond...@googlemail.com> > > >> >> > > >> 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 > > >> >> > > spctools-disc...@googlegroups.com. > > >> >> > > >> > To unsubscribe from this group, send email to > > > > >> >> > > >> > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@googlegroups.com> > <spctools-discuss%2bunsubscr...@googlegroups.com<spctools-discuss%252bunsubscr...@googlegroups.com> > > > > > > >> >> > > <spctools-discuss%2bunsubscr...@googlegroups.com<spctools-discuss%252bunsubscr...@googlegroups.com> > <spctools-discuss%252bunsubscr...@googlegroups.com<spctools-discuss%25252bunsubscr...@googlegroups.com> > > > > > > >> >> > > >> > . > > >> >> > > >> > 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 > > >> >> > > > spctools-disc...@googlegroups.com. > > >> >> > > > To unsubscribe from this group, send email to > > > > >> >> > > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@googlegroups.com> > <spctools-discuss%2bunsubscr...@googlegroups.com<spctools-discuss%252bunsubscr...@googlegroups.com> > > > > >> >> > > . > > >> >> > > > 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 > > >> >> > > spctools-disc...@googlegroups.com. > > >> >> > > To unsubscribe from this group, send email to > > > > >> >> > > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@googlegroups.com> > <spctools-discuss%2bunsubscr...@googlegroups.com<spctools-discuss%252bunsubscr...@googlegroups.com> > > > > >> >> > > . > > >> >> > > 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 > spctools-disc...@googlegroups.com. > > >> >> > To unsubscribe from this group, send email to > > >> >> > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@googlegroups.com> > . > > >> >> > For more options, visit this group > > >> >> > athttp://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 > spctools-disc...@googlegroups.com. > > >> >> To unsubscribe from this group, send email to > > >> >> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@googlegroups.com> > . > > >> >> 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 > spctools-disc...@googlegroups.com. > > >> > To unsubscribe from this group, send email to > > >> > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@googlegroups.com> > . > > >> > For more options, visit this group at > > > > ... > > > > read more ยป > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@googlegroups.com> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
