Thanks again for the wonderfully detailed help yesterday getting RefBase installed:
I deleted everything and started over to avoid any little errors I might have made before. I'm pleased to say that I've now succeeded twice in doing the manual installation but still have some major problems.
The first is that I get an internal server error (500) every time I click login or logout. Pressing the back button after getting the error, sometimes with a reload, gets me to the correct logged in or logged out state, and I've managed to create a new admin user and delete the default one, but obviously it's still a bit worrying.
Also, I haven't managed to import any references. The Upload to Refbase command in Bookends doesn't give any error messages, but after checking in Refbase I can't find any new references (of course I changed the server, username, and password from the default in Bookends preferences). And trying to import by pasting BibTeX* into the import window gives a "There were validation errors regarding the data you entered" message, sometimes with a nasty bunch of PHP errors:
Warning: preg_match() [function.preg-match]: Compilation failed: missing ) at offset 11 in /home/.jong/rickla/rikiwiki/members/bib/refbase/includes/include.inc.php on line 3728
Warning: preg_match() [function.preg-match]: Compilation failed: unmatched parentheses at offset 6 in /home/.jong/rickla/rikiwiki/members/bib/refbase/includes/include.inc.php on line 3728
Warning: preg_match() [function.preg-match]: Compilation failed: missing ) at offset 10 in /home/.jong/rickla/rikiwiki/members/bib/refbase/includes/include.inc.php on line 3728
Warning: preg_match() [function.preg-match]: Compilation failed: unmatched parentheses at offset 5 in /home/.jong/rickla/rikiwiki/members/bib/refbase/includes/include.inc.php on line 3728
Warning: Cannot modify header information - headers already sent by (output started at /home/.jong/rickla/rikiwiki/members/bib/refbase/includes/include.inc.php:3728) in /home/.jong/rickla/rikiwiki/members/bib/refbase/import_modify.php on line 474
The worrying thing is that I don't know what the /.jong/ part of the path is: it's different from the paths shown in the net2ftp web interface I use to manage files, and is not the name of the server where my domain is hosted. I'll probably have to get help on that at DreamHost, since it was similar error messages that made me give up on PmWiki (though DokuWiki works fine). I'm mentioning it here in case anyone happens to understand it.
I know everyone's busy, but in case anyone wants to take a look, the database is at:
I've also taken the liberty of creating a new temporary user, with Matthias's sourceforge email address as login, and refbase as password, just in case you want to try logging in and see for yourself.
Thanks for any additional help you can give.
*Doing the same with RIS additionally gives an "Unrecognized data format" error message.
OK, I've sorted out the path problem: .jong is the dataglob and I don't need to actually use it as DreamHost recommends using symlinks. In any case, this is only really relevant for setting files directories and the like. I haven't yet done any fiddling with files beyond what the instructions told me to do (except for setting the database host in addition to the username and password)
Another thing I've been warned about in the past is that blank lines at the end of PHP scripts can cause errors. I notice that every time I open a file on the server the editor inserts a blank line at the end, but I've been pretty careful to delete those manually before saving.
Any ideas where my problems might be coming from?
Not sure if this adds anything useful, but the latest logout error is:
Parse error: syntax error, unexpected T_STRING, expecting ')' in xxxxxx/refbase/initialize/ini.inc.php on line 260
Sorry I inadvertently put this thread in open discussion rather than the troubleshooting forum.
Please ignore the error on line 260 of ini.inc.php This was caused by a typo. Sorry for the false alarm.
thanks for the pointer to your refbase database and test login, that was helpful.
> Warning: preg_match() [function.preg-match]: Compilation failed: missing ) at offset 11 in
> /home/.jong/rickla/rikiwiki/members/bib/refbase/includes/include.inc.php on line 3728
With regard to your BibTeX import problems, please see this forum post:
Please download the two files linked in that post and replace the corresponding files from refbase-0.9.0 with these updated ones. This should fix your compilation errors when importing BibTeX records into a UTF-8 database.
If you still "There were validation errors regarding the data you entered" message when importing BibTeX records, then Bibutils has not been installed correctly. But judging from one of your other posts it seems as if you've managed to get Bibutils working. Is this correct?
> Doing the same with RIS additionally gives an "Unrecognized data format" error message.
As indicated in another forum thread, it could be that your RIS format is malformed. Please post some sample records so that we can track this down.
> The first is that I get an internal server error (500) every time I click login or logout.
It looks as if the referrer information in function 'showLogin()' (file 'includes/include.inc.php') gets incorrectly assigned. In your case, the login link generated by that function looks like this:
Note the script URL of the referrer parameter ('/cgi-system/php.cgi'), this is not a refbase script. So the refbase login/logout scripts do work but redirect to an incorrect script URL (due to the incorrectly assigned referrer).
In the most recent development version of refbase, the referrer logic in function 'showLogin()' has been rewritten. So you could try to download the updated 'include.inc.php' from:
then copy the updated 'showLogin()' function from that file and replace the old version of this function in your old 'include.inc.php' file (from refbase-0.9.0). In addition, you'll need to copy the newly added function 'scriptURL()' to your old 'include.inc.php' file.
This might help you with your problems. Sorry for the trouble!
Btw, everything would be far easier for you (and us) if we had already released the pending refbase-0.9.1 update which has fixes/solutions for many of the issues you've experienced so far (it's my fault that this newer version has not yet been released so I can't really blame anyone).
> Another thing I've been warned about in the past is that blank lines at the end of PHP scripts can cause errors.
I've never experienced (nor heard of) any problems with blank lines at the end of PHP scripts. So I'd be surprised if this would be the cause of any issues with refbase.
Let us know how it goes,
Thanks as always for the detailed reply, Matthias. I'll try the things you suggest. One thing I just want to confirm, though. The http://wiki.refbase.net/index.php/Installation-Troubleshooting page says:
"You can check that the Bibutils path was correctly configured by viewing the contents of the depends table. The depends_path for the bibutils record should not be NULL as seen below:"
My depends_path is NULL, so I seem to have exactly the problem described here. I can't say that I fully understand the troubleshooting steps (e.g. don't know how to change the path within the table). I guess it's understandable that it wouldn't be installed correctly as I didn't run the install script, just uploaded the bibutils to the server.
Anyway, one thing at a time. I'll run through those steps and get back to you.
> My depends_path is NULL, so I seem to have exactly the problem described here. I can't say that I
> fully understand the troubleshooting steps (e.g. don't know how to change the path within the table).
If you've installed refbase manually, you'll also need to set the path to Bibutils manually. Please see:
For example, if you've installed the Bibutils utilities on your server at 'usr/local/bin/' then you'd issue following SQL command from within your MySQL command line interpreter (or a tool such as phpMyAdmin):
UPDATE depends SET depends_path = '/usr/local/bin/' WHERE depends_external = 'bibutils';
to set the value of the 'depends_path' field in table 'depends' to that path.
Hope this helps, Matthias
I do have a similar problem with exporting from Bookends into our lab's refbase installlation (which works fine otherwise) like in this thread "Also, I haven't managed to import any references. The Upload to Refbase command in Bookends doesn't give any error messages, but after checking in Refbase I can't find any new references (of course I changed the server, username, and password from the default in Bookends preferences)."
has this been solved?
Also, an exported RIS-Format File from Bookends does not import into Refbase
"Unrecognized data format!"
while a RIS-Format file downloaded from ScienceDirect does import.
(The bookends-excported file also does not import into the refbase demo database)
Is this a bookends or refbase issue (I will post to both forums).
Since SD RIS files import fine, I suspect that it might be a BookEnds bug that refbase can work around. Please post or email the minimum failing example from BookEnds. It has been reported elsewhere that some versions of BookEnds produce invalid RIS (as they have too few spaces for tags (two before the hyphen are called for, but some people only get one). I don't know if that is the problem here, though.
which version of refbase are you using? The "Upload to Bookends" feature was added to refbase only recently and requires a refbase version > 0.9.0. Bookends sends records in Endnote XML format, which is currently only supported by the refbase version in the SVN trunk and most recent versions of Bibutils.
I'll have to check again, but I think that a working integration of refbase with Bookends currently requires the refbase version in the bleeding-edge branch of our SVN repository at SourceForge. In other words, only the most recent refbase version (available in the SVN repo) or the next (upcoming) release of refbase does have full support for upload from Bookends. Sorry for the inconvenience!
In order to rule out whether you're seeing a problem with Bookends or with your own refbase installation, please register for a free account at http://www.refbase.org and enter corresponding connection details in your Bookends Internet preferences:
User Name/ID: your email address that you've used upon registration at refbase.org
Password: the password that you've set for your refbase.org account
Now, please try to upload one of your problematic references. Does it work with the refbase database at refbase.org? If so, the record format that Bookends sends should be fine and the issue is with your own/local refbase installation (most probably with the versions of refbase and/or Bibutils you're using).
Hope this helps. Let us know how it goes.
OK, the RIS export problem has been solved:
- need to use the latest version of BE (10.0.3) due to this invalid RIS bug (thanks Rick, was also suggested by Jon from BE), BUT that did not solve it the first way round, I had to additionally set the line breaks of the exported file to UNIX (were Mac), then it worked.
- With regards to the "Upload from Bookends" - I am using the stable version (0.9.0), not the svn one. Might have to better change, this feature is a real killer in our workgroup situation...
tried with the refbase demo - that worked...so better get the SVN version installed ;-)
many thanks for your quick replies - I love an active community like this!
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