Manual installation

Help
lamjas
2009-07-22
2013-05-28
  • lamjas

    lamjas - 2009-07-22

    I cannot use the install.php to install the refbase, so I need to install it manually. Where should I put the path to bibutils for manual installation?

     
    • Matthias Steffens

      Hi lamjas,

      > Where should I put the path to bibutils for manual installation?

      Yes, good point. Sorry for the trouble. We should really add some infor about this to:

      http://manualinstall.refbase.net/

      Please perform the steps outlined on the "Manual Installation" wiki page, then follow the advice given in the lower part of the following section in our online documentation (starting from "Alternatively, if you'd like to enable Bibutils support for an existing refbase installation, ..."):

      http://www.refbase.net/index.php/Bibutils#Installing_Bibutils_for_use_with_refbase

      Does this help? Let us know if not.

      Matthias

       
    • lamjas

      lamjas - 2009-07-22

      Thanks for your guidelines. I followed them and installed it successfully. However, when I tried to import references (Endnote export, Refer export, BibTex export, etc), I got an error:

      "There were validation errors regarding the data you entered:"

      When I used the same file and imported it on your demo site, it worked perfectly.

      So, what is the common mistake for such error?

       
    • Matthias Steffens

      Hi lamjas,

      good to hear that you're making progress.

      > "There were validation errors regarding the data you entered:"
      > So, what is the common mistake for such error?

      Without more info that's hard to tell. This usually indicates that Bibutils is still not available to refbase. This could be due to an incorrecly given Bibutils path, incorrect permissions for the Bibutils programs and/or incorrect permissions (or path spec) for the temp/session directory, PHP safe_mode, etc.

      Please checkout the points given in this help section:

      http://www.refbase.net/index.php/Installation-Troubleshooting#Export_of_records_results_in_a_blank_page

      and see if that helps. As before, let us know if you still can't get it working.

      Matthias

       
    • lamjas

      lamjas - 2009-07-23

      I installed refbase on a hosted service. I check the following:

      1) Path to bibutils: /home1/xxx/public_html/refbase/bibutils/
      2) depends_enable: true
      3) the permission of directory "bibutlis" is 750, while the permissions of files inside the directory are 755
      4) php.ini:   safe_mode is off
      5) initialize/ini.inc.php:    $sessionTempDir = "/home1/xxx/tmp"; while the permission of tmp is 755

      But, still have errors when I import citation. Any other suggestions?

       
      • Matthias Steffens

        Hi lamjas,

        this looks all good to me. Which server platfrom are you runing on? And which version of Bibutils are you using?

        If you're using Bibutils v4.x, could you try Bibutils v3.40 instead? Just to see whether this makes for any difference. You can get  Bibutils v3.40 here:

        http://bibutils.refbase.org/

        Matthias

         
        • lamjas

          lamjas - 2009-07-23

          My hosting company uses Linux and I used the latest version of bibutils (v4.2). I also tried bibutils v3.4 as you suggested, but still no luck...

           
          • Matthias Steffens

            Hi lamjas,

            > I also tried bibutils v3.4 as you suggested, but still no luck...

            thanks for trying and sorry you're facing trouble.

            Could it be that your hosting company is somehow blocking the PHP 'exec()' function on your account?

            Matthias

             
    • lamjas

      lamjas - 2009-07-24

      I asked my hosting company and they said the server meets all requirement of refbase and they do not block the php exec() function.

      I think the installation of bibutils makes the problem. This is what i did for the bibutils. I downloaded the bibutils package (i386 linux, v4.2). Then, I tried both ways.
      1) Upload the package directly to the server (binary mode). Extract them in shell. Change the permission
      2) Extract the package first and then upload each program to the server (binary mode). Change the permission.
      Import errors occurred anyway... Any solution?

       
    • Reinier Post

      Reinier Post - 2009-09-03

      Just a remark: permission 750 for the bibutils directory should probably be 755.

       
      • Richard Karnesky

        Ideally, the user that apache runs under would belong to the group that owns that directory.

         
    • Reinier Post

      Reinier Post - 2009-09-03

      Just a remark: permission 750 for the bibutils directory should probably be 755.

       
    • Reinier Post

      Reinier Post - 2009-09-03

      I also need to perform the installation manually, because I am not the MySQL database administrator, and I cannot create any databases.  I do have a database I can add tables to.  (It would be nice if install.php would support this use case, by the way.)

      So I needed to prefix the MySQL table names with a refbase-specific prefix in the install.sql file.  This is tedious and error-prone to do by hand, so I wrote a Perl script to it for me.

      Someone else may find this useful, so I posted it here:

        http://www.win.tue.nl/~rp/bin/mysql-rename-tables

      Running it without any arguments will provide a short explanation.

      No guarantees on anything.  Mail me if it doesn't work.

       

       
    • Reinier Post

      Reinier Post - 2009-09-03

      Richard: well, ideally ... you wish.  Meanwhile I also ran intto the problem that I can't edit php.ini on my server, and setting allow_fopen_url in .htaccess has no effect, but Curl is enabled, so I had to use that instead.  Where do I post the patch?

       
      • Richard Karnesky

        If the patch is short, post it here.  If it is longer, use the tracker or the dev list.

        curl is widely available & we can _probably_ default to it.  'fopen' should be left in tact (either as an option or commented out) for those that do not have the extension.

         
        • Reinier Post

          Reinier Post - 2009-09-04

          Posted to the tracker, see

            https://sourceforge.net/tracker/?func=detail&aid=2850969&group_id=64647&atid=508193

          (doesn't this forum software support hyperliking?)

           
          • Richard Karnesky

            As you can see, URLs are autolinked.  You cannot use HTML or other rich markup in the sourceforge forums, though.

             
    • Reinier Post

      Reinier Post - 2009-09-04

      it would be very helpful if the code was instrumented with detailed error messages so these cases could be resolved quicker, e.g. using error_log().  And the text of the error message should change: missing trailing / on the bibutils path is not a validation error!

       

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