Refbase does not show entries

2007-12-07
2013-05-28
  • Hi!

    We have been running refbase for about a year now and it worked all fine. I did not change anything on the server or on the installation, but now I suddenly had the following problem:

    when you do not login, you can search for literature, and you will see the entries. If you click on "show all", you will see that we currently have 495 records, but the literature is not listed.

    If you log in, even searching is not possible - it will show you the right number of results, but not the literature. I have updated to 0.9 right when it came out - and it worked. Is it possible that my database is corrupted in some way? I already replaced all files in the installation folder with the original files - no change.

    has anybody had this problem before?

    thanks for any help!

    Nils

     
    • Hi Nils,

      do I understand you correctly that you've been using refbase-0.9.0 previously and it worked just fine, and that "all of a sudden" it stopped working?

      Are you really sure that nothing was changed on your server? Were Apache, PHP or MySQL updated in the meantime? Did somebody make any changes to the active 'php.ini', 'my.cnf' or 'httpd.conf' files?

      Please take a look at your servers error log, does it say something possibly related to PHP, MySQL or refbase?

      Also, please enable PHP error reporting. To enable error reporting, set the following variables in your php.ini file:

      error_reporting  =  E_ALL
      display_errors = On

      After you've restarted your web server, you should see any PHP error messages printed to your browsers screen.

      Matthias

       
      • Knut Krüger
        Knut Krüger
        2007-12-10

        .. you wrote that you did not change anyting .. but maybe there was an update of your php files, we had also problems with SQL backup and other software because the the memory use of the PHP system increased after the installing a newer version (I do not know which part, but PHP admin f.e is new now) Additionally there was a limit of memory use 24 M for each webspace. Another software (not Refbase) got in trouble with that limitation. I heard that problem a lot of times just in the last couple of weeks.

        Regards Knut

         
    • Nils
      Nils
      2007-12-09

      Thank you for your fast reply.

      I get the following PHP messages:

      Notice: Undefined index: volumeNo in /srv/www/htdocs/refbase/search.php on line 2065

      Notice: Undefined index: pagesNo in /srv/www/htdocs/refbase/search.php on line 2114

      Notice: Undefined index: sortSelector1 in /srv/www/htdocs/refbase/search.php on line 2136

      Notice: Undefined index: sortRadio1 in /srv/www/htdocs/refbase/search.php on line 2140

      Notice: Undefined index: sortSelector2 in /srv/www/htdocs/refbase/search.php on line 2147

      Notice: Undefined index: sortRadio2 in /srv/www/htdocs/refbase/search.php on line 2151

      Notice: Undefined index: sortSelector3 in /srv/www/htdocs/refbase/search.php on line 2158

      Notice: Undefined index: sortRadio3 in /srv/www/htdocs/refbase/search.php on line 2162

      Warning: Cannot modify header information - headers already sent by (output started at /srv/www/htdocs/refbase/search.php:2065) in /srv/www/htdocs/refbase/includes/include.inc.php on line 318

       
    • Nils
      Nils
      2007-12-09

      What I forgot:

      The DB seems to work, we are running a publication list at http://www.spruehkompaktieren.uni-bremen.de/pub-g1.php which extracts our publictions from the refbase database. phpmyadmin also shows me, that there seems to be a lot of data in the db

       
    • Hi Nils,

      Knut makes a good point noting that PHP memory issues could be worth checking. If you have the chance to increase your PHP servers memory limits then please try this to see whether it helps with your problem. See the 'memory_limit' variable in your servers active 'php.ini' file.

      And while you're at it, you might also want to increase values for variable 'max_execution_time' and some other 'php.ini' variables that might affect refbase script execution & performance. More info is available at:

      http://wiki.refbase.net/index.php/Required_PHP-INI_Settings

      Regarding the PHP errors in your server's error log file: I think that these errors are unrelated to your problem. Do you also get any refbase-related errors when clicking the "Show All" link in the refbase header -- or when using the "Quick Search" form on the main page? In other words, do you also get any errors when you're *not* using the "Simple Search" or "Advanced Search" pages for searching?

      Also, could you please clarify again whether this is true: You did run refbase-0.9.0 successfully (i.e. without any problems) before, and all of a sudden you did experience the described display problems? Are you sure that nothing else changed on your server?

      What versions of Apache, PHP and MySQL is your server running at?

      > we are running a publication list at http://www.spruehkompaktieren.uni-bremen.de/pub-g1.php
      > which extracts our publictions from the refbase database.

      Btw, w.r.t. your 'pub-g1.php' script which generates your publication list, it might be interesting for you to hear that, with the upcoming version of refbase, the 'show.php' API allows to include results from a refbase server into foreign web pages. As an example, here are two static sample HTML pages that dynamically include results from a refbase database (in different ways):

      http://beta.refbase.net/include_test.html (uses an <iframe>)
      http://www.refbase.org/javascript/include_test.html (AJAX style)

      A real-world example can be found at:

      http://www.molgeobio.uni-goettingen.de/papers.php

      I've written about this feature (including more examples) and linked to sample code here:

      http://sourceforge.net/forum/message.php?msg_id=4404553

      Matthias

       
    • Nils
      Nils
      2007-12-11

      Thank you for your fast replies.

      I checked the php.ini and increased the memory_limit to 80M and the max execution time to 60000s. This should not be a problem. I also made sure the php settings from the wiki are fine. It seems that the problem is not solved, but got less in some way. Sometimes it works when I search, sometimes not. It seems to be related to the amount of search hits, I hadn't noticed this before. Of course, you can also try on your own:

      http://ameise.iwt.uni-bremen.de/refbase

      do a quick for "ellendt" (when not logged in) and everything works fine. Search for "uhlenwinkel" and it will give you no search results for most if the time, if it gives you results, it will not show page number two of the hits. Again, if you search within the results for "ellendt", it will give you less results and it works again. Seems very weird to me. Same thing when you are logged in. So it does not seem to be a question whether you are logged in or not, but how many search hits you get.

      We had 0.9 running perfectly right after it came out (we used older versions before). I am pretty sure that I did not do any server updates since I used it the last time, especially no changes to the configuration files (php.ini, MySql configuration etc.)

      We are currently using:
      PHP 4.3.4, MySQL 4.1.10, Apache 2.0.49

       
      • Hi Nils, thanks for the detailed response.

        I must admit that I don't have any clue what could cause your problems. I tried searching your refbase database for "ellendt" but this did also return no results. The database appears to be down right now.

        I guess the only thing I could offer you is to try to analyze the SQL dump of your refbase database. However, I don't really think it's related to the refbase MySQL database. Anyways, send me (refbase -at- extracts de) an SQL dump of your database[1] if you like and I'll see if I find anything suspicious.

        It might be also worth to try installing refbase on another machine/server using the generated SQL dump file upon install. This should show you whether the problem lies with your refbase MySQL database, or with your particular server.

        Matthias

        [1]: http://backup.refbase.net/

         
      • Knut Krüger
        Knut Krüger
        2007-12-11

        seems that it is a routing problem
        Try a tracert
        There are appro 700 ms from hop to hop, to our refbase there a apr. 60 ms.
        I am afraid that you will run in timeout errors.

        Regards Knut

         
        • Knut Krüger
          Knut Krüger
          2007-12-11

          Additional info:
          the routing to www.uni-bremen.de is working fine but the routing especially to http://ameise.iwt.uni-bremen.de/refbase is very slow

          Knut

           
          • Nils
            Nils
            2007-12-11

            Would that be rather a problem on our server or (for example) of our subnet router?

             
    • Nils
      Nils
      2007-12-11

      Yes, that is what I also thought. It seems to work partially, but it seems to be a problem of the whole apache/php/mysql environment. I will try it on another server. I do not think the database is corrupted, if it was, searching should not work at all. I will let you know if it works on a different server environment

      Thanks so far for all your help!

      Nils

       
      • I asked in a TCP/IP NG the are suggesting that it is a local problem.

        Maybe it is any hardware problem?
        Is your SQL database at the same server as the PHP scripts or is it on a different server?

        Regards Knut

         
        • Nils
          Nils
          2007-12-12

          In deed it seems to be a local problem. There is a second server connected directly to the same switch and the traceroute to this server is a lot better (20-25ms). The refbase db is also working fine on a different server, so it is not corrupted :-) I will switch to a new network card first (pretty fast - I bought several cards of the same type ;-) ) and see if it changes the traceroute problems. If not, I will stick to the software network configuration. BTW, yes, the apache/php and mysql are running on the same server.

          Thanks for your help again!

          Nils