From: Beck, C. <cb...@em...> - 2010-04-16 12:06:45
|
We are having problems with the export command with our installation. It creates the file but the file is empty. The format for the export does not seem to matter. Does anyone have any suggestions? Thanks, Chris Dr. Christopher Beck Department of Biology Emory University 1510 Clifton Rd. Atlanta, GA 30322 chr...@em... Phone: 404-712-9012 FAX: 404-727-2880 This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). |
From: Matthias S. <mst...@re...> - 2010-04-16 13:45:26
|
Hi Chris, On 16-Apr-10 at 08:06 -0400 Beck, Christopher wrote: > We are having problems with the export command with our > installation. Did the export feature work previously? If so, do you remember what you've changed in the mean time? > It creates the file but the file is empty. This normally indicates that there is an issue with the Bibutils integration. Which version of Bibutils are you using? If you're currently using Bibutils v4.x, please try Bibutils 3.4 which is still available here: <http://bibutils.refbase.org/> Some troubleshooting advice related to Bibutils is given here: <http://www.refbase.net/index.php/Installation-Troubleshooting#Export_of_records_results_in_a_blank_page> You might also want to search the refbase forums for similar topics, e.g. see this thread: <https://sourceforge.net/projects/refbase/forums/forum/218758/topic/3562872> > The format for the export does not seem to matter. Does anyone have > any suggestions? Are you able to export to MODS XML and ODF XML format? Thanks, Matthias |
From: Beck, C. <cb...@em...> - 2010-04-29 19:30:35
|
Matthias, I am still having trouble getting Bibutils to integrate with Refbase properly. I have installed Bibutils 3.4. I have checked the path in the depends table and made sure it was an absolute path. I have made sure that the permissions on the tmp directory and the directory with Bibutils is set to 755. I have also checked the php.ini file and everything is okay. Nothing shows up in the php error log. I have basically followed everything described in the troubleshooting and forum discussion best I can tell, and I still can't get it to work. Any suggestions? Thanks, Chris -- Dr. Christopher Beck Department of Biology Emory University 1510 Clifton Rd. Atlanta, GA 30322 Email: chr...@em... Phone: 404-712-9012 FAX: 404-727-2880 > -----Original Message----- > From: Matthias Steffens [mailto:mst...@re...] > Sent: Friday, April 16, 2010 9:45 AM > To: Beck, Christopher > Cc: ref...@li... > Subject: Re: [refbase-talk] problems with export command > > Hi Chris, > > On 16-Apr-10 at 08:06 -0400 Beck, Christopher wrote: > > > We are having problems with the export command with our > > installation. > > Did the export feature work previously? If so, do you remember what > you've changed in the mean time? > > > It creates the file but the file is empty. > > This normally indicates that there is an issue with the Bibutils > integration. > > Which version of Bibutils are you using? If you're currently using > Bibutils v4.x, please try Bibutils 3.4 which is still available here: > > <http://bibutils.refbase.org/> > > Some troubleshooting advice related to Bibutils is given here: > > <http://www.refbase.net/index.php/Installation- > Troubleshooting#Export_of_records_results_in_a_blank_page> > > You might also want to search the refbase forums for similar topics, > e.g. see this thread: > > > <https://sourceforge.net/projects/refbase/forums/forum/218758/topic/356 > 2872> > > > The format for the export does not seem to matter. Does anyone have > > any suggestions? > > Are you able to export to MODS XML and ODF XML format? > > Thanks, Matthias This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). |
From: Matthias S. <mst...@re...> - 2010-05-03 07:37:02
|
Hi Chris, sorry to hear you're still facing trouble with the Bibutils/refbase integration. Your answers to the below questions might help us to further track down your issue. Just to be sure, may I ask again whether you're to export to MODS XML and ODF XML format? Also, which server platform and server software are you using? What about the PHP 'safe_mode' setting? Is it set to ON? If so, make sure that Bibutils has been installed in the directory specified in the PHP 'safe_mode_exec_dir' directive. And are you running refbase on your own server, or are you using a hosted server account? The latter usually has consequences for the PHP temp/session directory. On a hosted server account, it is often necessary to specify the absolute path to the PHP temp/session directory (that's been given to you by your ISP) in variable '$sessionTempDir' in file 'initialize/ini.inc.php'. If you're running refbase on your own server instead, you could login on the server's shell and try to execute Bibutils manually (on the shell). Does it execute normally? When converting a file, do you get correct output? Also try, reading & writing from the PHP temp/session directory. Does this work as well? Also, may I ask you to post the current contents of your refbase table 'depends', i.e. issue this MySQL command: SELECT * FROM depends; from within your MySQL command line interpreter, or a web-based MySQL tool such as phpMyAdmin. If you don't want to post the actual paths, feel free to send them offline. In addition to the above, it might be worth trying to recompile Bibutils on the server from source (if you've got permission to do so, compilation of Bibutils shouldn't be too hard). There were others who reported that this did solve their problems. To do so, you'd need to download the Bibutils 3.4 source code from: <http://bibutils.refbase.org/bibutils_3.40_src.tgz> upload it to your server, and decompress the archive. Then try to compile it on the server. On a hosted server account, the latter step probably requires help from your hosting provider since regular hosting accounts don't have permission to do so. Thanks, Matthias On 29-Apr-10 at 15:30 -0400 Christopher Beck wrote: > Matthias, > I am still having trouble getting Bibutils to integrate with > Refbase properly. I have installed Bibutils 3.4. I have checked > the path in the depends table and made sure it was an absolute > path. I have made sure that the permissions on the tmp directory > and the directory with Bibutils is set to 755. I have also > checked the php.ini file and everything is okay. Nothing shows up > in the php error log. > > I have basically followed everything described in the > troubleshooting and forum discussion best I can tell, and I still > can't get it to work. Any suggestions? > > -----Original Message----- > > From: Matthias Steffens [mailto:mst...@re...] > > Sent: Friday, April 16, 2010 9:45 AM > > To: Beck, Christopher > > Cc: ref...@li... > > Subject: Re: [refbase-talk] problems with export command > > > > Hi Chris, > > > > On 16-Apr-10 at 08:06 -0400 Beck, Christopher wrote: > > > > > We are having problems with the export command with our > > > installation. > > > > Did the export feature work previously? If so, do you remember > > what you've changed in the mean time? > > > > > It creates the file but the file is empty. > > > > This normally indicates that there is an issue with the Bibutils > > integration. > > > > Which version of Bibutils are you using? If you're currently using > > Bibutils v4.x, please try Bibutils 3.4 which is still available > > here: > > > > <http://bibutils.refbase.org/> > > > > Some troubleshooting advice related to Bibutils is given here: > > > > <http://www.refbase.net/index.php/Installation-Troubleshooting#Export_of_records_results_in_a_blank_page> > > > > You might also want to search the refbase forums for similar > > topics, e.g. see this thread: > > > > <https://sourceforge.net/projects/refbase/forums/forum/218758/topic/3562872> > > > > > The format for the export does not seem to matter. Does anyone have > > > any suggestions? > > > > Are you able to export to MODS XML and ODF XML format? |
From: Beck, C. <cb...@em...> - 2010-05-03 14:11:42
|
Matthias, Thanks for the help with this. See the answers below. Chris > > Just to be sure, may I ask again whether you're to export to MODS XML > and ODF XML format? > Yes, I can export with these formats. > Also, which server platform and server software are you using? Linux x86_64, MySQL 5.1.45-log, PHP 5.2.11 > > What about the PHP 'safe_mode' setting? Is it set to ON? If so, make > sure that Bibutils has been installed in the directory specified in > the PHP 'safe_mode_exec_dir' directive. Safe mode in PHP is off. > > And are you running refbase on your own server, or are you using a > hosted server account? I am using a hosted server account on Bluehost. > > The latter usually has consequences for the PHP temp/session > directory. On a hosted server account, it is often necessary to > specify the absolute path to the PHP temp/session directory (that's > been given to you by your ISP) in variable '$sessionTempDir' in file > 'initialize/ini.inc.php'. I looked up what the session temp directory is in the php.ini and then used the absolute path in ini.inc.php, but that doesn't seem to help. > > If you're running refbase on your own server instead, you could login > on the server's shell and try to execute Bibutils manually (on the > shell). Does it execute normally? When converting a file, do you get > correct output? Also try, reading & writing from the PHP temp/session > directory. Does this work as well? Although I am on a hosted account, I have shell access. When I try to execute from shell, I get the error that "-bash command not found". Reading and writing to the PHP temp/session directory works fine. > > Also, may I ask you to post the current contents of your refbase table > 'depends', i.e. issue this MySQL command: > > SELECT * FROM depends; > > from within your MySQL command line interpreter, or a web-based MySQL > tool such as phpMyAdmin. If you don't want to post the actual paths, > feel free to send them offline. I will send this offline. > > In addition to the above, it might be worth trying to recompile > Bibutils on the server from source (if you've got permission to do so, > compilation of Bibutils shouldn't be too hard). There were others who > reported that this did solve their problems. To do so, you'd need to > download the Bibutils 3.4 source code from: > > <http://bibutils.refbase.org/bibutils_3.40_src.tgz> > > upload it to your server, and decompress the archive. Then try to > compile it on the server. On a hosted server account, the latter step > probably requires help from your hosting provider since regular > hosting accounts don't have permission to do so. I will try this. > > Thanks, > > Matthias > > > On 29-Apr-10 at 15:30 -0400 Christopher Beck wrote: > > > Matthias, > > I am still having trouble getting Bibutils to integrate with > > Refbase properly. I have installed Bibutils 3.4. I have checked > > the path in the depends table and made sure it was an absolute > > path. I have made sure that the permissions on the tmp directory > > and the directory with Bibutils is set to 755. I have also > > checked the php.ini file and everything is okay. Nothing shows up > > in the php error log. > > > > I have basically followed everything described in the > > troubleshooting and forum discussion best I can tell, and I still > > can't get it to work. Any suggestions? > > > > -----Original Message----- > > > From: Matthias Steffens [mailto:mst...@re...] > > > Sent: Friday, April 16, 2010 9:45 AM > > > To: Beck, Christopher > > > Cc: ref...@li... > > > Subject: Re: [refbase-talk] problems with export command > > > > > > Hi Chris, > > > > > > On 16-Apr-10 at 08:06 -0400 Beck, Christopher wrote: > > > > > > > We are having problems with the export command with our > > > > installation. > > > > > > Did the export feature work previously? If so, do you remember > > > what you've changed in the mean time? > > > > > > > It creates the file but the file is empty. > > > > > > This normally indicates that there is an issue with the Bibutils > > > integration. > > > > > > Which version of Bibutils are you using? If you're currently using > > > Bibutils v4.x, please try Bibutils 3.4 which is still available > > > here: > > > > > > <http://bibutils.refbase.org/> > > > > > > Some troubleshooting advice related to Bibutils is given here: > > > > > > <http://www.refbase.net/index.php/Installation- > Troubleshooting#Export_of_records_results_in_a_blank_page> > > > > > > You might also want to search the refbase forums for similar > > > topics, e.g. see this thread: > > > > > > > <https://sourceforge.net/projects/refbase/forums/forum/218758/topic/356 > 2872> > > > > > > > The format for the export does not seem to matter. Does anyone > have > > > > any suggestions? > > > > > > Are you able to export to MODS XML and ODF XML format? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). |
From: Beck, C. <cb...@em...> - 2010-05-03 14:43:42
|
Matthias, Further update. I downloaded the source code, unpacked it, compiled it, and installed it. I still get the "command not found" error. In the bibutils documentation I found that you might need to identify the files as executable. I have tried this with "chmod +x xml2bib", etc and then tried running the command again and I still get the same "command not found error". Chris > -----Original Message----- > From: Matthias Steffens [mailto:mst...@re...] > Sent: Monday, May 03, 2010 3:37 AM > To: refbase-talk Mailing List > Cc: Beck, Christopher > Subject: Re: [refbase-talk] problems with export command > > Hi Chris, > > sorry to hear you're still facing trouble with the Bibutils/refbase > integration. Your answers to the below questions might help us to > further track down your issue. > > Just to be sure, may I ask again whether you're to export to MODS XML > and ODF XML format? > > Also, which server platform and server software are you using? > > What about the PHP 'safe_mode' setting? Is it set to ON? If so, make > sure that Bibutils has been installed in the directory specified in > the PHP 'safe_mode_exec_dir' directive. > > And are you running refbase on your own server, or are you using a > hosted server account? > > The latter usually has consequences for the PHP temp/session > directory. On a hosted server account, it is often necessary to > specify the absolute path to the PHP temp/session directory (that's > been given to you by your ISP) in variable '$sessionTempDir' in file > 'initialize/ini.inc.php'. > > If you're running refbase on your own server instead, you could login > on the server's shell and try to execute Bibutils manually (on the > shell). Does it execute normally? When converting a file, do you get > correct output? Also try, reading & writing from the PHP temp/session > directory. Does this work as well? > > Also, may I ask you to post the current contents of your refbase table > 'depends', i.e. issue this MySQL command: > > SELECT * FROM depends; > > from within your MySQL command line interpreter, or a web-based MySQL > tool such as phpMyAdmin. If you don't want to post the actual paths, > feel free to send them offline. > > In addition to the above, it might be worth trying to recompile > Bibutils on the server from source (if you've got permission to do so, > compilation of Bibutils shouldn't be too hard). There were others who > reported that this did solve their problems. To do so, you'd need to > download the Bibutils 3.4 source code from: > > <http://bibutils.refbase.org/bibutils_3.40_src.tgz> > > upload it to your server, and decompress the archive. Then try to > compile it on the server. On a hosted server account, the latter step > probably requires help from your hosting provider since regular > hosting accounts don't have permission to do so. > > Thanks, > > Matthias > > > On 29-Apr-10 at 15:30 -0400 Christopher Beck wrote: > > > Matthias, > > I am still having trouble getting Bibutils to integrate with > > Refbase properly. I have installed Bibutils 3.4. I have checked > > the path in the depends table and made sure it was an absolute > > path. I have made sure that the permissions on the tmp directory > > and the directory with Bibutils is set to 755. I have also > > checked the php.ini file and everything is okay. Nothing shows up > > in the php error log. > > > > I have basically followed everything described in the > > troubleshooting and forum discussion best I can tell, and I still > > can't get it to work. Any suggestions? > > > > -----Original Message----- > > > From: Matthias Steffens [mailto:mst...@re...] > > > Sent: Friday, April 16, 2010 9:45 AM > > > To: Beck, Christopher > > > Cc: ref...@li... > > > Subject: Re: [refbase-talk] problems with export command > > > > > > Hi Chris, > > > > > > On 16-Apr-10 at 08:06 -0400 Beck, Christopher wrote: > > > > > > > We are having problems with the export command with our > > > > installation. > > > > > > Did the export feature work previously? If so, do you remember > > > what you've changed in the mean time? > > > > > > > It creates the file but the file is empty. > > > > > > This normally indicates that there is an issue with the Bibutils > > > integration. > > > > > > Which version of Bibutils are you using? If you're currently using > > > Bibutils v4.x, please try Bibutils 3.4 which is still available > > > here: > > > > > > <http://bibutils.refbase.org/> > > > > > > Some troubleshooting advice related to Bibutils is given here: > > > > > > <http://www.refbase.net/index.php/Installation- > Troubleshooting#Export_of_records_results_in_a_blank_page> > > > > > > You might also want to search the refbase forums for similar > > > topics, e.g. see this thread: > > > > > > > <https://sourceforge.net/projects/refbase/forums/forum/218758/topic/356 > 2872> > > > > > > > The format for the export does not seem to matter. Does anyone > have > > > > any suggestions? > > > > > > Are you able to export to MODS XML and ODF XML format? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). |
From: Richard K. <kar...@gm...> - 2010-05-03 16:04:58
|
> I still get the same "command not found error". The current working directory is not typically in your path on linux. Are you prefixing the command with the full directory path that it is located in? --Rick |
From: Beck, C. <cb...@em...> - 2010-05-03 16:26:52
|
Thanks Rick. This was the issue that I was having from the command line. When I use the full directory path it works. I had to change all the files that I had compiled on the server to make them executables, but once I did that it also works integrated with refbase. Thanks for all the help. Chris > -----Original Message----- > From: Richard Karnesky [mailto:kar...@gm...] > Sent: Monday, May 03, 2010 12:05 PM > To: Beck, Christopher > Cc: refbase-talk Mailing List > Subject: Re: [refbase-talk] problems with export command > > > I still get the same "command not found error". > > The current working directory is not typically in your path on linux. > Are you prefixing the command with the full directory path that it is > located in? > > --Rick This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). |