Bibutils installation problems

Help
timt
2010-01-22
2013-05-28
  • timt
    timt
    2010-01-22

    Hello, I have just manually installed refbase-0.9.5 on my university's server  (Apache 1.3.39, MySQL 5.0, PHP 5.2.4) as part of a project for the Latin American Studies collection of our library. Refbase itself is working fine, but I cannot get bibutils to import records (e.g., XML files from EndNote). When I try to import a file, I get a red error message that states, "There were validation errors regarding the data you entered." I tried installing bibutils 3.4 rather than 4.1, but I still get the same error. I have updated the MySQL settings with the bibutils path, etc., but still nothing.

    I am able to import files just fine through the refbase demo site (I am using Windows XP).

    Our webserver allows us to create a custom php.ini file for our account, and I have done so, applying all the settings recommended in the refbase documentation. . . .

    Any help you could provide would be very greatly appreciated. Thanks!

    Tim

     
  • Hi Tim,

    sorry you're facing trouble! I'm assuming you're now using refbase-0.9.5 together with Bibutils 3.4, right?

    Could you list all your changes for all files/tables that you've modified? For example:

    1) What's the result of this MySQL command (executed in your MySQL command line interpreter or phpMyAdmin):

    SELECT * FROM depends WHERE depends_external = "bibutils";
    

    2) What is the current value of variable '$sessionTempDir' in file 'initialize/ini.inc.php'? And have you tried to set its value explicitly? I.e. specify a full path which you know exists and which is accessible & writable by Apache/PHP/Bibutils.

    3) What are the permissions of your Bibutils programs, and where are they located?

    4) Is 'safe_mode' set to On in your active 'php.ini' file? If so, what is the value of 'safe_mode_exec_dir'?

    Thanks,

    Matthias

     
  • timt
    timt
    2010-01-25

    Hi, Matthias,

    Thanks for your quick reply.

    (1) The MySQL command you specified produces the following result:

    depends_id = 2
    depends_external = bibutils
    depends_enabled = true
    depends_path = /ip//bin/bibutils/

    (2) I have set the value of the variable '$sessionTempDir' in my 'php.ini' file. Its path is accessible and writable, and it seems to be working correctly.

    (3) The permissions of my Bibutils programs are all set to 755, as is the directory where they are located.

    (4) 'safe_mode' is set to Off in my active 'php.ini' file.

    Everything appears to be as it should, no? However, there are two other factors I wanted to ask about:

    (1) Our MySQL database is located on a different server from our refbase installation. On which server should I install Bibutils, the MySQL server or the Web server? I initially tried installing and specifying a path on the Web server, and then tried it on the MySQL server. Neither has worked, but I may be missing something. . . .

    (2) Also, and this may be a naive question, but which format of Bibutils should I install? Our server is Apache, but the desktop machine I am using is Windows. So, should I install the Windows binaries of Bibutils?

    Thanks again! We are very exciting about using refbase.

    Tim

     
  • timt
    timt
    2010-01-25

    Oh, and, yes, we are using refbase-0.9.5 with Bibutils 3.4.

     
  • depends_path = /ip//bin/bibutils/

    Does this path actually resolve on your system w/ the webserver?  Open a command prompt on the server & try to 'cd' to this directory.

    On which server should I install Bibutils, the MySQL server or the Web server? I initially tried installing and specifying a path on the Web server

    Yes, this is what you do.  Your depends_path looks a bit suspicious to me, though.

    (2) Also, and this may be a naive question, but which format of Bibutils should I install?

    You install it for the platform the server is running on.  You should test it on the command line of the server.

    Our server is Apache

    Apache runs on multiple platforms

    but the desktop machine I am using is Windows.

    Do you mean you run Apache on Windows?  If so, use the Windows binaries.  Do you mean you run Apache on some sort of *nix & are connecting to it with a client browser running on Windows?  If so, use the binaries for that flavor of *nix.

    -Rick

     
  • timt
    timt
    2010-01-25

    Does this path actually resolve on your system w/ the webserver?

    Yes, I can 'cd' to this directory.

    Do you mean you run Apache on some sort of *nix & are connecting to it with a client browser running on Windows? If so, use the binaries for that flavor of *nix.

    We are running Apache on Linux, so I just tried installing the Bibutils 3.4 Linux binaries on our webserve account. No luck.

    depends_path = /ip//bin/bibutils/

    I tried changing the path to just '/bin/bibutils/', but that didn't seem to help. We are running on a shared server, so each user account is located in the '/ip/' directory, which is directly under 'root'.

    Also, just to clarify, "installing" Bibutils is only a matter of copying the files to a directory, correct? Is there any kind of script or command that I need to run in order to properly install the applications?

    Thanks,

    Tim

     
  • It sounds like your path is correct, then.

    We are running Apache on Linux, so I just tried installing the Bibutils 3.4 Linux binaries on our webserve account. No luck.

    Same error?  Nothing else in the logs when you record all errors/warnings?  Have you tried to run the program from a shell on the server?

    Also, just to clarify, "installing" Bibutils is only a matter of copying the files to a directory, correct?

    Yes.  Assuming you have the correct architecture (e.g. your server can run x86 binaries & you are using statically linked x86 binaries), then that's all you should have to do.  But please try to run the executables so we can differentiate between problems with you running bibutils at all from you being able to run them from refbase.

    Good luck!

    -Rick

     
  • timt
    timt
    2010-01-25

    Nothing else in the logs when you record all errors/warnings?

    I included the following settings in my 'php.ini' file, but do I need to specify a 'log' file? Sorry, I am pretty much a novice.

    error_reporting  =  E_ALL
    display_errors = On

    Have you tried to run the program from a shell on the server?

    What commands would I issue to run Bibutils from a shell? When I try to use 'endx2xml' as a command, for example, I get a 'command not found' message. . . .

    Tim

     
  • timt
    timt
    2010-01-25

    One more question: I believe I set up my MySQL database as UTF-8. Could that interfere with Bibutils?

     
  • Try, for example:

    $ cd /ip/[user id]/bin/bibutils/
    $ ./endx2xml --version
    
     
  • timt
    timt
    2010-01-25

    When I tried to execute

    $ ./endx2xml --version
    

    from the bibutils directory, I got the following error message:

    ./endx2xml: error while loading shared libraries: requires glibc 2.5 or later dynamic linker
    
     
  • Then you must do one of the following (in approximate order of preference):

    * Have your server admin install the binary for you, from the packaging system used in their distribution of linux

    * Obtain binaries that have been compiled for the same glibc version you have on the server

    * Download & compile the source for bibutils on that server

    * Download and compile the source on another machine, but carefully targeting the requirements of the server

    * Have your server admin upgrade glibc

     
  • timt
    timt
    2010-01-25

    Okay, then. I will see what I can do.

    Thanks again for all your help and for the great service you provide!

    Best,

    Tim

     
  • timt
    timt
    2010-01-27

    FYI: Our system administrator was able to compile the Bibutils binaries on our server, and now everything is working smoothly! Within the next few months, we hope to have a new "real-world" refbase installation to share with you.

    Thanks again!

    Tim

     
  • Hi Tim, great to hear it's working for you now, and kudos to your sysadmin!

    Let us know if you run into anything else.

    Matthias