OK yeah fixing the document root was all that I needed. I was wondering why I had it set to that but I think it was some configuration settings someone suggested to me when I was having some other probs but all seems fine now. Thanks!
On Jun 15, 7:31 pm, Natalie Tasman <[email protected]> wrote: > 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/... > > > 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]> > > ... > > read more » -- 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]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
